This is page is maintained by Sabine
Jacques, Xiaodong Yan, Suchart Chansawatkit
RULES FOR PUBLISHING A SUBMISSION (as per Dr. K)
There has been a lot of confusion regarding my evolving policy towards the links and their reviews.
Effective TODAY (March 2, 2001) these are the new rules for writing links. Please read this before you submit your links. Please ask a question before submitting. Failure to adhere to the formatting conventions means your review will be bounced back to you for more work.
Your published links will be used for your final grade. You must have a
minimum of 20 links published, with at least five in each category. You
may not submit your 20 links at the end of the semester. Failure to keep
current will means you may fail this course. If you have problems with
English,
Ask your classmates to read it before you submit. Dr. K will stop correcting
English and will return links without comment for revision. USE A SPELLING
CHECKER. USE A GRAMMAR CHECKER. There is no reason/excuse for egregious (look
it up) misspellings. Your links should NOT be on straight medicine without any
computer science content. Your links should not be on classical computer
science unless there is some medical/biological tie in. Links on biological
topics without computer science or engineering content are also unacceptable.
Remember, both topics (Biology / Medicine and Computer Science) should be in
the link.
READ YOUR LINK THOROUGHLY. UNDERSTAND IT. If it appears you cut and paste from your link it will be returned. Don't pick links you don't understand. Don't pick links that are impossible to understand (like the NIH web site in its totality). Do not pick links to entire universities, departments, companies, or planets without there being some specific item you are reviewing in that site. Do not review software without explaining what it does and how it does it.
YOU MAY WORK IN GROUPS. DISCUSS THE LINKS BEFORE YOU SUBMIT. GROUP MEMBERS SHOULD NOT SUBMIT IDENTICAL LINKS. E-mail links between yourselves before submitting.
In order to make it clear what the topic of your e-mail is about, you MUST HAVE YOUR SUBJECT LINE FORMATTED precisely as follows:
If one link is in the e-mail message:
HOT_LINK: <CATAGORY>
If two or more links are in the e-mail message:
HOT_LINKS: <CATAGORY>
Where <CATAGORY> is one of the categories below.
Instructions for submitting a hot link:
1) e-mail your link(s) to Dr. Karron
2) The subject line should be precisely as follow:
HOT_LINK (S): <topic or subject area>
or
LINK: <topic or subject area>
This is so that I know that you want to submit this for the class links page.
3) I will review your review for English, for Content, and for Subject
Suitability.
Please make certain you read link. Do not submit entire web site. Review single
articles.
Articles can be tutorial, research reports, newspaper articles, professional
journal articles (no pay-per read please!).
4) If your review needs further editing, if it reads badly, or if the topic is inappropriate (i.e., the topic is medicine, computer science without any biology), Dr. K will return it to you for more work. You MUST the link and review it, and cite at least one or two important points from the piece. Your goal is to motivate others to read the link because there was something interesting to you in the piece. That is the purpose of these reviews, to find useful and interesting links on BioInformatics on the web, and make them available to others in this class and on the web.
Click here to go to any of the categories below:
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http://arrakis.bic.nus.edu.sg/Kleisli-CPL-tutorial/
Reviewed by Aamir Babar
This is an interesting site, which gives a deep introduction of a high-level query language known as CPL. CPL is an abbreviated word of "THE COLLECTION OF PROGRAMMING LANGUAGE" and it is used to transform biological data into a unified form and can map them according to your need. The site contains an introduction to CPL, then object orientation, some basic operation, function definition etc. which are I think enough to get some know how about a new language.
http://csm.jmu.edu/biology/courses/bio220/aotw7.html
Reviewed by Aamir Babar
This site contains a tutorial about gene structure. The goal of this
tutorial is to strengthen your understanding of gene structure, genome
organization, and how molecular biologists use computers. The site contains
some questions. The students have to answer these questions by searching Internet
databases containing sequence information and answer a series of questions. By
completing tutorial you will have been exposed to databases used by researchers
that use the tool of molecular biology, and will gain a better understanding of
nucleotide and amino acid sequence information.
http://bio.com/articles/bioinformatics.html
Reviewed by Danian Cao
This article is an excellent tutorial on bioinformatics. It provides basic information about bioinformatics, which is a scientific discipline that encompasses all aspects of biological information. It combines the tools of mathematics, computer science and biology with the aim of understanding the biological significance of a variety of data. The science of bioinformatics is created by the combination of powerful innovative software with sophisticated database systems and automated biological research methods. This site also gives background knowledge about human genome project, protein sequence, genome analysis, and comparative genomic and expressed sequences tag. Sequence data from entire organism provides a database to determine the functions of each gene. The interactivity of databases creates another level of genome analysis. There are variety useful links about DNA, protein, gene, database and a list of bioinformatics companies, which are devoted to the development of software, database and consulting services. Main technologies of those companies are also introduced on the list
http://www.hgmp.mrc.ac.uk/CCP11/
Reviewed by Ruiwen Jiang
This site provides basic information about Bioinformatics and a variety of informatics resources about genes, protein, and computing. That's the most useful site I found for beginner and experienced. It also provides research newsletter, sources of funding, training courses, Bioinformatics tutorials and Journals related to Bioinformatics. It provides the subjects (information & tutorials) including Molecular sequence analysis, structure prediction, algorithms and representation for bioinformatics and methods of biocomputing, methods of genome analysis and programming for bioinformatics and Internet. Some interesting links are available. It is good for experienced and experts.
http://www.bioinformatics.ucla.edu/help/about.htm
Reviewed by Ruiwen Jiang
This site is designed for researchers not familiar with Genomics and Bioinformatics. The page describes: the concept of Bioinformatics which requires a strong connection to Biology and to the basic issues of how and where biological data can be made systemic, through the development of high – throughput experimental methods. An introduction to the field in which it describes the history, development in particular in genomics technologies and the future of Bioinformatics, methods of analysis, synthesis of Bioinformatics, advantages of Bioinformatics. It also provides some useful links and researches at UCLA (University of California, Los Angles). It is also good for beginner and students.
http://www.ipam.ucla.edu/programs/fg/tutorials.html
Reviewed by Ruiwen Jiang
It provides the Tutorials for Functional Genomics /Expression Array. They explain why biologists need mathematicians, how to collect biological data, experimental design and data analysis, Genome analysis, graph models, network analysis, image analysis of cDNA microarray, classification of cell line using cDNA microarray. It's good for experienced and experts.
http://www.cpb.uokhsc.edu/ojvr/xmlpaper.html
Reviewed by Ruiwen Jiang
The article describes how to evaluate the current genetic terms, XML, DTD genomic files and genetic databases for the purpose of developing a wider electronic access platform. The authors found that many of the current genomic DTDs consisted of general access, formatting, reference and genetic elements in one XML file. So it solves the problem on the restriction of only presently using multiple sequence databases analysis, comparing of algorithms, computing and analyzing alignments or linkage results at databases level. It also provides related links and resources. It is worth to read for experienced. It is Online Journal of Bioinformatics; you can find and read other interesting articles from this site.
http://bioinformer.ebi.ac.uk/newsletter/archives/5/armchair.html
Reviewed by Peng Qu
This is an article about the theory of evolution using bioinformation. Traditional researchers study the species evolution from fossil or from behavior of living species. The discovery in DNA put the problem into the hands of molecular biologists. This new technology might solve many of the problems from DNA. Bioinformatics promise to be the driving force in the developing field of "molecular archaeology".
http://www.techfak.uni-bielefeld.de/bcd/ForAll/Ethics/welcome.html
Reviewed by Peeyush Rathkanthiwar
The author of this article Peter Hjelmstrom tells us about the ethical
issues in biocomputing and basically tells what biocomputing is? Biocomputing
could be defined as the construction and use of computers which function like
living organisms or contain biological components, so-called biocomputers. This
essay is going to address issues in the intersection between biology, computing
and ethics in the framework of a society. Ethics in biocomputing is the
systematic study of human moral conduct in use of computers in the life
sciences. There are basically two ethical issues discussed in this article,
first is the interesting question for most biocomputists is, however, not
whether information about genetic diversity among populations and groups should
be stored in freezers, but if the information should be publicly accessible in
computer databases and second is who should maintain the biological databases.
http://www.nap.edu/html/transgenic/examples.html
Reviewed by Aamir Babar
This site contains information about the usage GM technology in the field of agriculture. The term GM technology stands for genetic modification technology. Today there some 800 million people in the developing world that do not have access to sufficient food. Malnutrition plays an important role in half of the nearly 12 million deaths each year of children under five in developing countries. In addition to lack of food, deficiencies in micronutrient are wide spread. Furthermore changes in the pattern of global climate and alteration in the use of land will exacerbate the problem of regional production and demand for food. Increasing the amount of land available to cultivate crops without having a serious impact on the environment and natural resources is a limited option. GM technology has shown its potential to address micronutrient deficiencies, low per acre production without having any serious impact on the environment.
http://www.boston.com/dailyglobe2/045/business/Biology_by_computer+.shtml
Reviewed by Aamir Babar
The above site is about the use of computer technology in the field of biology. The column illustrate that it is the computer science working quietly behind the scenes of genomic revolution, helping to generate, manage, and analyze the flood of data spewing from the worlds laboratories on life's innermost workings. Instead of discovering a drug by the trial and error fashion in the past, now the scientist will design a new drug entirely on computer, piecing together models of protein with their chemical structures of potential drug. Drug companies are already using computers to rapidly screen thousand of chemical compounds to help select those that might be used as drugs. They are using software to scan world 's vast collection of public databases for genetic and other information. There are pharmaceutical and biotech companies developing a variety bioinformatics tools for their own use to speed and streamline the drug discovery process. The column also describes the fact that the field of bioinformatics is kind of new but it is emerging rapidly, and big companies are now entering in this field.
http://www.nytimes.com/2001/02/13/health/13MOUS.html
Reviewed by D. Chen
Dr. Mark D. Adams of Celera hold a news conference currently to present the first analysis of human genome and announced the genome sequence of mouse had been assembled. It is important to study the genetic sequence, because "It's a narrative of the journey of species through time, an incredibly detailed blueprint for building every human cell, the new immense power to treat, prevent and cure disease" said by Dr. Eric S. Collins. The DNA in mouse and human has been changed constantly, even they had the same ancestor about 100 million years ago, but not both genes and control regions. These facts lead to scientists to research the gene of mouse. Also these results unveil some unknown regions of conserved sequence may help genomes diverged completely. This unknown region would be a new category in research of genomes.
http://washingtonpost.com/wp-dyn/health/chronicdiseases/news/A1853-2001Apr10.html
Reviewed by Hanjie Huang
This article reports a female teacher with early Alzheimer's disease receipt gene therapy in an effort to slow her mental decline; Alzheimer’s is a progressive brain disorder. It gradually damages and destroys cells in many regions of the brain, initially causing loss of recent memory and eventually rendering its victims helpless and often unable to recognize loved ones Doctors used brain-imaging tests and special equipment to pinpoint the target of the treatment, an area at the base of the brain's frontal lobe called the nucleus basalis of Meynert. It contains nerve cells, called cholinergic cells. Then they injected half a million genetically modified cells into each of five sites on the right side of her brain. In most gene therapy, virus is as a gene carrier. In this case doctors used a modified virus, with its disease-causing genes removed. Swedish researchers previously treated patients with nerve growth factor by pumping it into the fluid surrounding their brains, but that treatment produced severe side effects. It stimulated cells, causing pain. The gene cannot be taken orally because digestive enzymes break it down. So doctors chose patient's cell called fibroblasts from her skin. Fibroblasts implanted in the brain have been shown to live and produce nerve growth factor for at animal test. Because Dr. Tuszynski is a co-founder of Ceregene Inc., a San Diego company that owns the product rights to the technology used to make the modified cells. The patient was released from the hospital. It could take several weeks before researchers can detect any impact on the woman's brain function, and several years before they know whether the treatment is effective.
http://www.nih.gov/news/stemcell/primer.htm
Reviewed by Sabine Jacques
This is a well-written article that provides detail background information about stem cells. This link provides information about the scientific, medical, and ethical issues involved in stem cell research. In addition to addressing these issues, it also provides definitions of scientific terms, well illustrated figures, and presents the paragraphs in questions and answer format. The question and answer format helps guides those unfamiliar to biomedical terminology. This article defines stem cells as cells that have the ability to divide for indefinite periods in culture and to give rise to specialized cells. The argument presented is that the cell is totipotent; meaning all of its potential is stored. If placed in a woman's womb, it can give rise to a fetus. This then presents an ethical dilemma. Even though there are many ethical dilemmas involved in this type of research, the fact is stem cell research has great potential for use in both research and in the development of cell therapies.
http://www.nih.gov/news/stemcell/stemfactsheet.htm
Reviewed by Sabine Jacques
This article is a guideline/fact sheet provided by the NIH with regards to
stem cell research. It addresses the promises that stem cell research holds,
the potential of adult stem cell research, the need for guidelines to govern
research using pluripotent stem cells, the requirements for investigators
applying for funds, and provides compliance guidelines. In addition to
providing this information, it also explains the importance of stem cell
work. These include: 1) Generating cells and tissue for transplantation.
2) Culturing pluripotent stem cells that have the potential to develop into
specialized cells that could be used as replacement cells and tissues to treat
many diseases and conditions, including Parkinson's disease, spinal cord injury,
stroke, burns, heart disease, diabetes, osteoarthritis, and rheumatoid
arthritis 3) Helping to improve our understanding of the complex events that
occur during normal human development and also help us understand what causes
birth defects and cancer 4) Helping to change the way we develop drugs and test
them for safety. Furthermore, testing of drugs on cells developed from
pluripotent stem cells would reduce the number of animal models used for drug
testing. Only when sufficient testing has been done on the cells could the drug
testing proceed to animal models.
http://www.nih.gov/news/stemcell/achieve.htm
Reviewed by Sabine Jacques
This article addresses a question asked by the NIH: "What would you
hope to achieve from human pluripotent stem cell research?" The
"you" in this question refers to all the institutes funded by the
NIH. Some of these include: National Cancer Institute, National Heart,
Lung, and Blood Institute, and the National Human Genome Research
Institute. In the case of National Cancer Institute, they state that one
of the advantages of doing stem cell research is that "pluripotent stem
cells may be used to treat the tissue toxicity brought on by cancer therapy".
This would also help to further advance gene therapy. This article
offers each institute an opportunity to justify why the NIH should fund stem
cell research. It is a thorough and well-organized article presented in
question and answer format.
http://cancernet.nci.nih.gov/clinpdq/therapy/Questions_and_Answers_About_Gene_Therapy.html
Reviewed by Ying Jiang
This article defines gene therapy, and explains how gene therapy could be
used to treat diseases such as cancer. Provided by the National Cancer
Institute. Gene Therapy is to alter patients' genetic material to fight or
prevent disease. One major goal of gene therapy is to supply cells with healthy
copies of missing or flawed genes. Instead of giving a patient a drug to treat
or control the symptoms of a genetic disorder, physicians attempt to correct
the basic problem by altering the genetic makeup of some of the patient's
cells.
Gene therapy could be used to alter germ cells (egg or sperm) in order to
prevent a genetic defect from being transmitted to future generations. It could
also be used as a drug delivery system. To accomplish this, a gene that
produces a useful product would be inserted into the DNA of the patient's
cells. For example, during blood vessel surgery, a gene that makes an anti
clotting factor could be inserted into the DNA of cells lining blood vessels to
help prevent dangerous blood clots from forming.
http://news.bbc.co.uk/hi/english/health/newsid_1191000/1191334.stm
Reviewed by Ying Jiang
A gene therapy technique has successfully prevented cancer in mice for what the researchers claim is the first time. The researchers targeted a gene called FHIT, which is damaged in many common forms of cancer, such as those affecting the breast and colon. FHIT causes damaged cells to commit suicide before they can start the out-of-control growth of cancer. The researchers provided mice with a working copy of the FHIT gene, and let them expose to a chemical known to cause esophageal cancer. The mice appeared to be protected from developing cancer.
http://www.thirteen.org/innovation/show1/html/2sb-therapy.html
Reviewed by Ying Jiang
This article explains what gene therapy is. Gene therapy, which was first conceived in the mid-1970s, aims to insert working copies of genes into cells containing dysfunctional ones. The DNA that genes are made of usually won't penetrate into cells, so it must be somehow transported in. Viruses are the most widely used carriers because they are little more than genes wrapped in a protein coat. It provides a conceptual illustration of the gene therapy process. It is good for the beginner.
http://unisci.com/stories/20012/0409012.htm
Reviewed by Ying Jiang
In an era of heightened concern about gene therapy safety, a new University of Florida study provides reassurance that corrective DNA can be administered without simultaneously causing harmful genetic changes. Scientists had worried that if the genetic material did integrate into the cell's own genetic wiring by becoming part of a chromosome, it potentially could disrupt the function of a healthy gene or lead to tumor development. The new research shows that in mice, new genes delivered inside a modified adeno-associated virus dwell independently in cells, reducing the risk of such problems. In the absence of this protein, over time, much of newly inserted DNA integrates into the host cell's chromosome. Theoretically, that's the kind of event that in some small percentage of cases would be harmful. But in the presence of this protein, the new DNA stayed in this independent string form. There are no detectable integrations. These experiments were conducted in mice, rather than people, but from these mouse models we've been able to get a very good understanding of cellular mechanisms of gene therapy.
http://www.pitt.edu/~rsup/phgt/corelabs.html
Reviewed by Naveen Menezes
This article contains valuable research on Gene Therapy conducted at the Pittsburgh Human Gene Therapy Center. The strategy of transferring genes to the human body to alter the course of a disease is referred to as Gene Therapy. The purpose of Gene Therapy is to express therapeutic proteins or genes in a manner that is most natural to the body. The core research being conducted here includes Automatic DNA Sequencing which consists of labeling DNA fragments with fluorescent dyes that emit light at different wavelengths so as to identify the A,G,C & T extension reactions. This site also contains Research documentation on Disease Gene Mapping, Peptide Synthesis and cell & tissue imaging.
http://www.loci.wisc.edu/4d/native/4d.html
Reviewed by Naveen Menezes
The Laboratory for optical & computational instrumentation (LOCI), Wisconsin-Madison is currently undertaking extensive research in the area of biomedical imaging & 4D Optical instrumentation. 4D microscopy is the study of three-dimensional specimens as they grow or change over time. The 4D software being developed at LOCI include a 4D Viewer developed in C, which is compatible for both PPC as well as Macintosh computers. This viewer allows the user to roam through the 4D data set divided into frames, backward and forward in time while also allowing him to move up or down in focus through the sample. This can be accomplished either by mouse or keyboard commands and can be done by allowing the movie to play at its full frame rate, or by analyzing the data set in a frame-by-frame fashion. This site also contains images, links, QuickTime movies and some interesting articles written by Charles Thomas, 4d co-coordinator & Senior Programmer at Loci.
http://www.pitt.edu/~rsup/phgt/corelabs.html
Reviewed by Naveen Menezes
This article contains valuable research on Gene Therapy conducted at the Pittsburgh Human Gene Therapy Center. The strategy of transferring genes to the human body to alter the course of a disease is referred to as Gene Therapy. The purpose of Gene Therapy is to express therapeutic proteins or genes in a manner that is most natural to the body. The core research being conducted here includes Automatic DNA Sequencing which consists of labeling DNA fragments with fluorescent dyes that emit light at different wavelengths so as to identify the A,G,C & T extension reactions. This site also contains Research documentation on Disease Gene Mapping, Peptide Synthesis and cell & tissue imaging.
http://www.thirteen.org/innovation/show1/html/story2.html
Reviewed by Naveen Menezes
This article talks about how gene therapy is used to cure a fatal disease called Severe Combined Immunodeficiency (SCID). This virus is known to destroy much of the immune system particularly the white blood cells called T cells, which leaves patients mainly newborn infants defenseless against many life-threatening infections. This article cites the case of Andrew Gobea born in 1993 with SCID. In Andrew's case, he had two defective copies of the gene that codes for a critical enzyme, adenosine deaminase (ADA). Dr. Donald Kohn successfully performed the gene therapy on Andrew at the Children's Hospital in Los Angeles. In babies the approach is to take the 100 mL of blood left behind in the umbilical cord or placenta and blood from the bone marrow in adults. This blood is rich in blood-forming stem cells that give rise to a host of blood cells. The problem is that the cells lack a functioning ADA gene. The next task is to insert DNA containing a working ADA gene into the stem cells. Packaging the gene into a virus that would ferry the new message into the cells does this. These viruses invade the cells and deposit the genes into enough cells to give the patient a working immune system.
http://www.ornl.gov/hgmis/publicat/hgn/v10n1/15wilson.html
Reviewed by Yu Shi
Human Gene Therapy: Present and Future
Human gene therapy is in its experimental stage and its purpose is to modify
the format or structure of some human genes to treat, cure, and finally prevent
diseases. Dr. James M. Wilson presents this article from Institute of Human
Gene Therapy, U of Pennsylvania. In the mid-1980s, the focus of gene
therapy was entirely on treating diseases caused by such single-gene defects as
hemophilia. In 1995, a public debate led to the consensus that gene
therapy has value although many unanswered questions require continued basic
research. As the field has matured over the last decade, it has caught the
attention of the biopharmaceutical industry, which has begun to sort out its
own role in gene therapy.
This is critical because ultimately this industry will bring gene therapies to
large patient populations. Wilson concluded his presentation by outlining
future milestones in the field: proof of concept in the next few years in model
inherited diseases, followed by cancer and cardiovascular diseases; continued
explosive activity in technological development; development of regulatory
policy (with the Food and Drug Administration); and commercial development.
http://www.nytimes.com/2001/05/06/magazine/06HOWTO.html
Reviewed by Jianxin Wang
This article talks about that "The Genomic Revolution", an
exhibition will be held at the American Museum of Natural History later this
month. The article describes how to sequence your own genome and what it means
to people. The following is how to write your own “DNA book”: 1. Provide a pure
specimen of DNA-2 cc's of blood or sperm or ova. 2. Separate the DNA in to even
smaller pieces for study by different techniques (sound baths and nebulizers).
They will use some detergent, salt and ethanol to fragment the DNA at the
exhibition. 3. Attract the tiny strands of DNA by a glass stirring rod and Put
the machines to work. Different DNA analyzer machines are available to do the
work and a PC crunches the results to solve like a jigsaw puzzle for each gene.
4. It will take 10 years to finish the sequencing of your genome with one Prism
DNA analyzer and a PC system, but the Museum lab technicians will take 5 hrs to
sequence a single gene. It really means that they will express variation among
people and make comparisons with other species possible from them genetically.
http://www.nih.gov/news/pr/feb2001/nhgri-21.htm
Reviewed by Min Wang
This is an informative article about a new genetic test to distinguish
between hereditary and sporadic types of breast cancer. Dr. Jeffrey Trent
of the National Human Genome Research Institute and his assistants applied a
method known as gene-expression profiling to differentiate between these two
categories of tumors. Using a DNA chip called a microarray, the Trent
team analyzed over 6000 genes in breast cancer cell samples and observed that
different patterns in gene activity revealed whether the cancer was hereditary
or sporadic. Their findings could be an important step in improving the
diagnosis and treatment of breast cancer according to its type. The test
involved a glass slide (a microarray) on which dots of DNA from different genes
were arranged in a grid pattern. The scientists’ isolated samples of DNA
from breast tumor cells and, using a robot, deposited them onto the glass
slide. If any DNA from the samples matched a gene on the microarray, it
would attach itself. Any non-matching DNA would be washed away.
Computerized detectors then measured the amount of DNA attached to the dots on
the microarray to determine how active the genes were in the tissue
sample. Computer-based statistical analysis of these genes showed that
they differed in relation to the type of cancer cell. In the beginning,
the research team tested thousands of genes to determine the category of a
breast cancer, but with computerized techniques they succeeded in reducing this
number to approximately 50. Their work could be the basis for future
research as well as the starting point for the development of new drugs.
This article is highly recommended for scientifically oriented readers with an
interest in computer technology and medicine.
http://library.northernlight.com/FC20010503320000219.html?cb=0&dx=1006&sc=0
Reviewed by Min Wang
This article is about a project to develop an information system to make it possible for doctors to design individualized cancer treatments according to a patient's unique genetic "fingerprint." The project is a collaboration between researchers at the Winship Cancer Institute of Emory University, NuTec Sciences, Inc., and IBM. The information system will detect genes that cause cancer as well as genetic risk factors that suggest a predisposition for the disease. In addition, it will give pharmaceutical companies the opportunity to invite patients to participate in clinical trials to test new drugs.
The first step in the system is to analyze blood and tissue samples from a patient, using microarray chips. NuTec Sciences' supercomputer will record how the genes on the chip are expressed as a result of coming into contact with the patient's tissues. The computer will run algorithms to pinpoint the cancer-causing gene combinations and to select the most effective treatments. The NuTec hardware will be used with IBM storage systems, which will enable physicians to get the analysis results quickly and contact their patients using PCs or wireless computers. Dr. Michael S. Keehan, Chairman of NuTec Sciences, notes that the integrated information system will have the power to scan thousands of genetic profiles at a time to identify differences in expression between diseased and normal cells.
http://www.unisci.com/stories/20002/0601003.htm
Reviewed by Min Wang
This article reports on a genetic study of heart tissue from mice, using robotic microarray techniques. The study was done at the Lawrence Berkeley National Laboratory of the Department of Energy. Its findings showed that 55 genes were associated with cardiac hypertrophy, a condition in which the heart is stressed – such as by high blood pressure. Another finding was that 8 genes were involved with regression, which is the condition of recovery from cardiac hypertrophy.
The researchers began the study by inducing cardiac hypertrophy in male mice through drugs (angiotensin II or isoproteronol), then withdrawing the drugs to allow for recovery. A saline solution was administered to mice in the control group. The researchers tested every stage of hypertrophy and recovery by extracting messenger RNA (mRNA) from heart tissue samples. These extracts were placed on glass microarray slides dotted with gene fragments deposited by a robotic microarrayer. The scientists used red-fluorescing dye to label the mRNA from the hypertrophied hearts and green-fluorescing dye for the mRNA from the normal hearts. As the mRNA reacted with the gene fragments on the glass slide, a computer compared the expressions and identified the various genes: spots on the microarray that glowed red indicated a gene active in hypertrophy or recovery; spots that glowed green signaled a gene expressed by a normal heart.
James Bristow, a staff scientist at the Lawrence Berkeley Laboratory,
Believes that the gene profiling accomplished in this study could be used to
improve treatments for patients suffering from hypertrophy.
http://www.bioresearchonline.com/content/news/article.asp?DocID={6E4BC8AA-F166-11D4-A770-00D0B7694F32}&Bucket=Guest+Columnists
Reviewed by Suchart C.
Peter C. Johnson, the founder and president of Tissue informatics, Inc., had discovered a new technique that can automate quality control of the engineered skin tissue products. The quality control must be accurate, fast, and also must prior detect changes in product quality. The software uses microscope-mounted robotics to capture the images of engineered skin attached on microscope slides and afterwards, analyze cell numbers and distribution, cell density and organization, cell shape and thickness of layers. And finally tells whether the skin structure is normal or abnormal. By quantifying the locations of cells and cellular components, tissue structure is analyzed. Tissue informatics has flexibility with their software imaging analysis. It can recognize cell structures such as nuclei, capable of working with lighting technique such as fluorescence, and expression technique like in situ hybridization. Basically, the company provides image processing and data management tools for tissue-derived information.
http://www.hunger.brown.edu/Research/TB-HIV_Lab/epimatrix/epimatrix.html
Reviewed by Danian Cao
This site introduced a new algorithm----Epimatrix, which was designed by the TB/HIV Research Laboratory at Brow University. Epimatrix is a computer-driven prediction algorithm for compiling information on peptides that have been demonstrated to bind to MHC molecules into an epitope matrix. MHC molecules are host-cell glycoproteins that can combine antigen peptides and deliver them to the cell surface. That T can recognize MHC-peptide complex cells and arouse T cell immune response. Epimatrix can step through the sequence of protein we are interested, scoring peptides in 10-mer frame, and intelligently direct subsequent in vitro testing by eliminating peptides that are unlikely to be MHC binders, reduce the total number of region to be evaluated, permitting more rapid resolution of pressing research questions. It is very useful for researchers working on vaccines and therapeutics for HIV and other pathogens.
http://www.paproc.de/
Reviewed by Danian Cao
This is a well-designed web site that provides an automated prediction device for a proteasomal cleavage. It also presents readers background information about proteasome which including: what proteasomes are, why proteasomal cleavage is specificity important for immune responses. Proteasomes are cryptozoic multisubunit proteases that are involved in cell cycle control, transcription factor activation and the generation of peptide ligands for MHC I molecules. They are very important parts of immune system. The more we study and understand them, the more benefit we will get. It is a good site with excellent images and links for both beginner and experts.
http://www.mpiib-berlin.mpg.de/MAPPP/
Reviewed by Danian Cao
This link tells about the development of a computer algorithm called MAPPP
for predicting possible antigenic peptides to be processed and finally
presented on the cell surfaces. Cytoplasmic proteins are transported to the ER
after being fragmented into peptides. The correct sized peptides bind to MHC
class I molecules and move to the cell surface. That T can recognize
MHC-peptide complex cells and arouse T cell immune response. MAPPP first
generates a probability for the cleavage of each possible peptide from a protein
by the proteasome in the cell. This probability is based on a
statistic-empirical method developed by H. -G.Holzhutter. Peptides with the
highest probabilities are then given a score reflecting their ability of
binding to MHC molecules. This binding score employs coefficient table deduced
from the literature by Kenneth Parker.
http://bimas.dcrt.nih.gov/molbio/hla_bind/
Reviewed by Danian Cao
Ronald Taylor at National Institutes of Health created this web site, in collaboration with Dr. Kenneth Parker. It is another prediction site which allows users to locate and rank 8-mer, 9-mer, or 10-mer peptides that contain peptide-binding motif for HLA class I molecules. The human MHC was studied first using antibody reactions with white blood cells and is now called the human leukocyte antigen, or HLA, system. This site introduces the basic algorithm for the analysis and gives detail instructions about how to use it. It is another useful tool for immunoinformatics research.
http://www.scripps.edu/newsandviews/e_20010326/torbett1.html
Reviewed by Zhuo Chen
Bruce Torbett, an associate professor of molecular medicine, is developing
and testing a gene delivery technique that may be used to deliver genes into
cells, providing a high level of protection against HIV or cancer in the
future. This technique involves treating hematopoietic stem cells (HSC). The
idea is to give these cells genes that will allow them to resist an HIV
infection, and then implant them into tissue where they can freely grow,
develop, and resist HIV infection. The same approach can be used to inhibit
cells from becoming cancerous. This gene delivery technique is achieved
by following processes. First, the patient' bone marrow are taken out. Then,
the stem cells are removed and infected with the intrabody gene using the HIV
vector. Finally, these cells are returned to the patient. The stem cells would then
develop into dendritic cells and blood cells, including cells that HIV infects,
such as macrophages and T-cells. These new cells would be phenotypically
equivalent to CCR5 negative cells since the intrabody would prevent the
coreceptors from reaching the cellular surfaces. These progeny cells would be
effectively resistant to HIV. Another application of Torbett's work to control
cellular function is the treatment of a certain type of cancer called acute
myeloid leukemia (AML). Torbett is looking at ways of controlling AML by
controlling PU.1 transcription. PU.1 plays an important role in normal or
abnormal myeloid development because it regulates transcription of those genes
that control the lineage and differentiation of myeloid cells. He uses in vivo
models that mimic what happens in normal myeloid development in humans and he
manipulates PU.1 to gain insight into normal and pathological states and to
understand gene regulation.
http://www.hunger.brown.edu/Research/TB-HIV_Lab/epimatrix/TIGR/epimer1.htm
Reviewed by Naveen Menezes
This article talks about the development of a computer algorithm called Epimer for analyzing protein sequences to identify which regions of these proteins have a high density of MHC-binding motifs. The MHC molecule-binding predictions are useful to build a combination of peptides & proteins called an Epitope Matrix which are useful to researchers & therapeutics involved in the development of vaccines for diseases like cancer & HIV. The binding depends on the prevalence of MHC Class I or Class II alleles in the geographic region of interest. These MHC molecules-binding dense regions may permit binding to and presentation of the peptide by more than one MHC molecule and such regions may be useful for inclusion in subunit vaccines destined for use in humans. Epimer utilizes a library of published MHC-binding motifs to identify regions within proteins that are likely to be T cell epitopes. According to an analysis done by Epimer, Peptides that contain more than three to four MHC binding motifs are generally two fold more likely to stimulate stronger immune responses to viral cells.
http://www.epimmune.com/tpipeline.htm
Reviewed by Naveen Menezes
This article describes the Epitope Identification System (EIS) developed by Epimmune, which identifies DNA fragments with a strong cellular immune response. These fragments are called antigen-specific epitopes and are used for the treatment and prevention of certain infectious diseases and tumors. The idea is to rationally create a multi-specific cellular response, causing the immune system to be specifically stimulated against multiple select epitopes that meet stringent criteria. The genetic sequence of a tumor-associated antigen, virus or bacteria is taken as input. This system performs the following analysis to rapidly identify fragments that meet pre-determined criteria. In this system, Computer algorithms analyze the sequence of all known antigens for the presence of peptides that contain the epitope motifs. The epitopes from variable regions of the antigen are avoided to meet sequence conservancy requirements. Peptides meeting these requirements are synthesized and their ability to bind broadly within a family of HLA molecules is determined. Later the peptides are tested for immunogenicity, both in vivo in mice that express human MHC and in vitro against infected or transfected cells. Using EIS, Epimmune has already identified epitopes for a number of indications, including breast, lung and colon cancers, as well hepatitis C, hepatitis B, HIV and malaria.
http://www.paproc.de/expl1.html
Reviewed by Naveen Menezes
This article talks about a prediction algorithm for proteasomal cleavages developed at the Institute for Cell Biology Department of Immunology, University of Tubingenfor, Germany. Proteasomes are proteolytic sites in eukaryotic cells that play an important part in the regulation of specific immune responses. PAProC (Prediction Algorithm for Proteasomal Cleavages) is a prediction tool for proteasomal cleavages, which has been developed from an experimental basis into the ready-to-use public tool. This algorithm is a freeware provided on this website which takes the amino acid sequence code as input. With this algorithm, the effect of amino acid mutations in viral or tumor-specific proteins on antigen presentation can be assessed. Thus, proteasomal cleavage prediction would lend a hand in rational vaccine design. The basic assumptions for this model is to determine whether to cut or not, the proteasome inspects only a small neighborhood of the prospective cleavage site. The affinity parameters of the model, which decide for or against cleavage, correspond with the cleavage motifs determined experimentally. PAProC offers information on both the general cleavability of amino acid sequences and individual cleavages.
http://unisci.com/stories/19994/1101992.htm
Reviewed by Danian Cao
Brain tumor operations are currently guided by preoperative imaging techniques such as MRI and CT. Two major disadvantages are that the brain, as well as the tumor, can shift during open operations. A CT-or MRI-guided biopsy can inadvertently tear a blood vessel traversing the brain on the way to the tumor. Dr. Robert Mah and his colleagues at NASA Ames Research center are developing a "smart probe" which can detect blood vessels on the path to the tumor, allowing the surgeon to redirect the biopsy needle to avoid causing hemorrhage. By using multiple microsensors, the NASA Smart Probe can instantaneously gather a large amount of information about the tissue at the Probe's tip. Neural net algorithms analyze the information and provide real-time interpretations. The neural net software is taught to distinguish tumors from normal brain tissue by remembering the unique signatures for each kind of tissue. This new technique has the potential for applications not only in neurosurgery, but also in the treatment of breast or prostate cancer.
http://unisci.com/stories/20003/0927003.htm
Reviewed by Danian Cao
Dr. William Dooley at Johns Hopkins Breast Center has developed a new technique to find breast cancers that currently undetectable by mammography and MRI. The technique uses a novel endoscope that is less than 1 millimeter in diameter. It allows surgeons to visualize breast tissue magnified up to 60 times normal size. With the advantage of tiny scope, the endoscope can be easily inserted through the nipple into the ducts that line the breast, examine the breast tissue, identifying breast lesions up to 1/100 of the size of those seen with mammography and MRI. This new method also improves women's chances for breast conserving surgery.
http://unisci.com/stories/19993/0728994.htm
Reviewed by Ruiwen Jiang
A Whitaker Foundation Fellow Jonathan S. Thierman developed a new medical
probe that can feel, see and hear. This device is capable of
"feeling" for lumps under tissue inside the body without requiring
actual penetration to "see" the suspected tumor, and of
"hearing" blood vessels in order to avoid or reduce bleeding. The
device produces computer-generated images of lumps or other hard structures
lying under softer surfaces by mathematically mapping the distortion of the
surface of a small latex bubble with a fiber optic camera as the probe is
dragged over the upper tissue surfaces, much as a finger outside the body would
feel for a lump under the skin. Small microphones also sense the
"swish" of blood around the probe to alert surgeons to the presence
of blood vessels in the area and to clearly distinguish blood vessels from
ducts and similar tissue structures. Currently, surgeons rely on purely visual
feedback from the endoscope in minimally invasive surgery, remaining
"numb" and "deaf" at the point of contact
within the body.
http://unisci.com/stories/19994/1101992.htm
Reviewed by Ruiwen Jiang
A "smart probe" intended by the NASA Ames Research Center can detect blood vessels on the path to the tumor, allowing the surgeon to redirect the biopsy needle to avoid causing a hemorrhage, can determine the nature of the tissue at the probe's tip in real-time, so that additional samples may be taken immediately if, for example, a highly malignant tumor is suspected. The NASA Smart Probe uses multiple microsensors, such as optical spectroscopy, micro-ultrasound, micro blood flow monitor, micro-endoscopy and microelectrode recording to instantaneously gather a large amount of information about the tissue at the Probe's tip. The neural net software helps focus camcorders, learns to distinguish tumors from normal brain tissue by remembering the unique signatures for each kind of tissue and then making a model and analyzes the information and provides real-time interpretations. The Smart Probe can be used not only in neurosurgery, but also in the treatment of breast or prostate cancer.
http://unisci.com/stories/19993/0728994.htm
Reviewed by Ying Jiang
Title: New Medical Probe Feels, Sees And Hears
A new device is capable of "feeling" for lumps under tissue inside the body without requiring actual penetration to "see" the suspected tumor, and of "hearing" blood vessels in order to avoid or reduce bleeding. This new medical device produces computer-generated images of lumps or other hard structures lying under softer surfaces. It does this by mathematically mapping the distortion of the surface of a small latex bubble with a fiber optic camera as the probe is dragged over the upper tissue surfaces, much as a finger outside the body would feel for a lump under the skin.
http://www.scoliosisrx.com/ndominus.htm
Reviewed by Naveen Menezes
This is about a field in endoscopic surgery that involves Minimally Invasive surgery Correction of Scoliosis that is a condition of the diaphragm. This article last revised on Jan 2nd 2001 may still be revised as I hope enhancements will be made in this direction. At present surgery is only being done till the 2nd or maybe the 3rd Lumbar Vertebra under the diaphragm. This is a good article with excellent images and links.
http://toffelcenter.com/procedure.html
Reviewed by Naveen Menezes
This article talks about the Endoscopic Laser-Assisted & Stereo computer-guided Sinus Surgery being done at the Southern California Nasal & Sinus center. To perform this procedure surgeons insert an endoscope, which are a small cutting or biting instrument and/or a laser through the nose into the sinuses. A fiber optic headlight supplements the endoscopic view for three-dimensional control and accuracy. The endoscopic technique allows surgeons to clear the sinus passages at the narrow areas where mucous drains into the nose. Steriotactic computer-guided sinus surgery adds another level of safety to this surgery. A personal satellite is placed on the patient's head while steriotactic computer x-ray scans are taken pre-operatively. Then at surgery, the satellite headset is plugged into a computer workstation which demonstrates by 3-D computer x-rays, the location of the working surgical instruments in real time while the surgeon is operating.
http://www.parsec.it/summit/sympat1e.htm
Reviewed by Naveen Menezes
Hyperhidrosis is a genetic condition in which the patient suffers from excessive sweating of the hands, face, scalp and underarms beyond the emotional and physiological need. This article written by Dr. Ivo Tarfusser, MD talks about a cure for this condition by a method called as Endoscopic thoracic sympathectomy. This operation consists in making a tiny incision behind the pectoralis-fold in the armpit thru which a small amount of CO2 is insufflated into the thoracic cavity to allow access with an endoscopic instrument. This device has a diameter of 7.3 mm (0.3") and makes it possible for the surgeon to identify and severe the sympathetic nerve-nodes where the nervous signals to the sweat glands in the upper limb and the face start. In facial hyperhidrosis, it is sufficient to sharply divide the fibers running from the 2nd thoracic ganglion upward, leaving the 2nd ganglion almost intact. This procedure is also repeated on the other side. This technique is very safe and it definitely supersedes the conventional technique of Open sympathectomy, which consists of long hospitalization periods and recovery.
http://www.sls.org/patientinfo/colon.html
Reviewed by Naveen Menezes
This article discusses the treatment of colon cancer using minimally invasive surgery. In conventional open dissection surgery, operations are done my making large incisions running the length of the abdomen. In Laproscopic surgery, three to five small puncture wounds are made in which insufflation ports are inserted. Through these ports, a gas mixture is used to distend the abdomen providing room inside for the surgeon’s instruments to move about. Through these incisions, a video camera and miniature versions of the usual surgical instruments are inserted. The surgical team then performs the same operation without having to dissect the abdomen. The portion of the bowel is removed by enlarging one of the port sites enough to pull the bowel portion out. Typically three or four incisions of 10 mm or less and possibly one larger incision of several inches are made. The malignant section of the colon is removed and the two ends of the bowel are joined back together to complete the surgery.
http://www.nwinspine.com/current.htm#intradiscal
Reviewed by Naveen Menezes
This article discusses how endoscopic surgery can be used to treat spinal
deformity and back pain. This surgery known as Kyphoplasty in medical terms is
used to correct vertebral fracture and deformity. Inserting a small
device like an endoscope inside the fractured vertebra performs it. The device
is then pulled out and the void left behind is filled with material to enforce
the bone and stabilize the fracture. Intradiscal Electrothermal Therapy (IDET)
is a minimally invasive outpatient procedure for osteoporotic patients. This
operation is performed to treat back pain caused by an injury to the spine that
produces cracks and ruptures in the spinal disc's outer ring. In this
procedure, a controlled level of heat energy is applied to the spine. The heat
contracts and thickens the collagen of the disc wall and results in closure and
repair of the disc rupture.
http://www.sls.org/patientinfo/kidneystones.html
Reviewed by Naveen Menezes
This article discusses the treatment and removal of kidney stones using minimally invasive surgery. Small kidney stones that do not pass out through the urine on their own can be treated with no incision and very little anesthetic. This treatment called Extracorporeal Shock Wave Lithotripsy (ESWL) uses shockwaves from outside the body. These waves are focused on the stone, to break up the stone into sand and gravel, which is then passed out in the urine. For larger stones, a surgery called as Ureteroscopy is used. This operation uses a small telescopic instrument, which is passed through the urethra (the tube from the bladder to the outside of the body), through the bladder and up the ureter (the tube that drains urine from the kidney to the bladder) into the kidney. A laser is then inserted through this instrument to break up stones in the kidney or the urethra. Samples of tissue are taken to rule out cancer and to burn areas of bleeding in the kidney. An ultrasound probe is then inserted through the endoscope to pulverize the stone and suck it out of the kidney.
http://www.
endosymposium. com/facial/index.htm
Reviewed by Naveen Menezes
This article provides detailed information on the pros and cons of
Endoscopic Facial surgery. World-renowned endoscopic plastic surgeon Dr Nicanor
G. Isse, M. D., discusses how facial remodeling can be done with minimal
incisions and scars. In this surgery only a few incisions, each less than one
inch long are needed to insert the endoscope and other surgical instruments as
opposed to longer incisions made in an open facial surgery. Using Endoscopic
Plastic surgery, post-surgery effects like bleeding, swelling & recovery
time can also be minimized.
http://www.spineuniverse.com/technology/tk_091700_robotics.html?lsm01
Reviewed By Peeyush Rathkanthiwar
This article consists of advance use of endoscope in spine surgery, improvements in camera equipment and advances in medical robotics. John J Regan Medical Director of Research and Education talks how Surgeons are implementing Robotics and computers and are able to remove a ruptured discussing a small endoscope. This can be achieved by repairing a painful discussing electro thermal energy and fuse a painful degenerated disc with the aid of a miniature camera. One of the best examples now being performed is fallopian tube repair in women, microsurgery on the fetus, and minimally invasive coronary bypass surgery. The major role of computers in this field is image guidance systems to give the surgeon real time images and allow them to navigate to the specific location on the spine. The surgeon can use digital information obtained before surgery such as MRI or CAT scans or use real time fluoroscopic x-rays to develop a three dimensional image of the spine with the exact location of a probe placed on the spine.
http://www.sls.org/patientinfo/aboutlap.html
Reviewed by Peilin Zhang
This article is about laproscopic surgery. The surgeons first make a small cut in the skin and then introduce a harmless gas into the body cavity to expand it and create a large working space. Through additional small cuts, a rod shaped telescope, attached to a camera, and other long and narrow surgical instruments are placed into the newly formed space. By this means, under high magnification diseased organs can be examined with minimal trauma to the patient. It's amazing that almost every part of the human body has become accessible to the surgeon's camera and scalpel now. For example, gallstones can now be removed with the gallbladder by laproscopic surgery. Instead of months of bed rest and limited activities, which was associated with the old method of removing the gallbladder, patients can now usually resume their normal activities in several weeks. Many other organs can now also be approached in a similar manner. These include the stomach, intestines, pancreas and spleen, kidneys and all the females’ organs. It's for sure this modern surgery has two advantages. First, since the overall trauma to the skin and muscles is reduced, postoperative pain is less, allowing patients recover sooner. The second advantage is a reduced infection rate. This is because delicate tissues are not exposed to the air of the operating room over long periods of time.
http://www.nhs.uk/nhsmagazine/story51.htm
Reviewed by Peillin Zhang
Patients currently take three months to recover fully from traditional heart surgery and are left with a neck to navel scar. But this will soon be the history. Doctors in the UK are to be the first to perform a heart by-pass operation using robot surgery. The pioneering technique, called the da Vinci Surgical System, is expected to slash the amount of time heart patients spend in hospital and drastically cut waiting times. The system features a robotic unit with three mechanical arms and tiny metallic fingers, which mimic the action of a human hand and wrist. A surgeon, who sits at a control station a few feet from the operating table, carries out the procedure by moving the robotic arms with a series of joysticks. A medical team has already carried out six bowel and stomach procedures using the system. With da Vinci, the patient has a heart by-pass operation will be at work within a fortnight - with a tiny centimeter-wide scar the only evidence of the procedure. It is hoped this incredible procedure will eventually become commonplace for the 25,000 people a year who undergo heart by-pass surgery in the UK in the near future.
http://www.hsforum.com/stories/articleReader$49
Reviewed by Shiqiang Wang
The web page discusses the essential steps toward image-guided completely endoscopic coronary bypass surgery with robot assistance. The researchers present their preliminary efforts toward the development of a three-dimensional (3-D) virtual cardiac surgical planning platform (VCSP) for endoscopic coronary artery bypass grafting (ECABG). The key methods are utilized: Preoperative 3-D images of the thorax acquired with computed tomography and electrocardiogram-gated magnetic resonance imaging are imported into VCSP. Using VCSP, a user may interactively visualize and manipulate the simulated thoracic ports in 3-D within the reconstructed thoracic region. They have also implemented a virtual endoscope to simulate the endoscopic view observed by the surgeon during the operation. Once the port placements for optimal access to the target vessels are determined, the positions of the simulated tools can be recorded and marked on the patient to specify the positions for port incisions. The VCSP image-guided surgical system allows a surgeon to visualize a patient's thorax in a 3-D interactive environment for planning surgical procedures, and to determine the optimum port placement based on preoperative 3-D images.
http://www.plasticsurgery.org/surgery/endoscop.htm
Reviewed by Shiqiang Wang
The web page introduces the formal concept of the Endoscopic Plastic Surgery (EPS). It seeks to give a basic understanding of endoscopy (a form of internal surgery) in plastic surgery: how it's performed, what risks are involved. The following areas are covered: advantages of endoscopy, uses in plastic surgery, special consideration and risks for (EPS), cosmetic surgery, reconstructive surgery, finding a well-trained surgeon and deciding if endoscopic surgery is right for you. Medical professionals and FAQ are also included. This site is ideal for those who have no knowledge about Endoscopic Plastic Surgery.
http://www.hsforum.com/stories/articleReader$359
Reviewed by Shiqiang Wang
The web page presents a training program and technology for cardiac surgeons
with special focus on 2D- and 3D-visualization operation before they are able
to complete endoscopic coronary artery bypass grafting. The program is prepared
to make cardiac surgeons become familiar with this technology and endoscopic
viewing. The following steps are crucial: A thoracic skeleton, covered with a
neoprene suit, served as model for the chest wall. Either a glove, fixed on a
metal plate, or a pig heart were placed inside for training. On the glove, a
suture line consisting of some lines with proper points. On the pig heart, the LAD
is prepared and incised; subsequently an anastomosis is done using the
dissected right coronary artery as a graft. The time required is measured for
both models. For suturing, the Zeus¢â System (Computer Motion, Goleta, CA) is
used and the third robotic arm positioned the endoscopic camera. The scopes are
connected to a 3D-camera and the picture is displayed on a headset with two
integrated monitors. Visualization is set to either 2D or 3D. Three surgeons
could be involved in the study. 3D-visualization facilitated quick and precise
movements result in shorter anastomosis times. The surgical training program is
mandatory for the trainee to become familiar with these new technologies.
http://www.patent-roboticlaserbrainsurgery.com/
Reviewed by Ying Bao
This website introduced Robotic Laser Brain Surgery based on Patent Number
5,823,941, invented by Jerome Shaunnessey, presents an innovative robotic
system and apparatus for ablating deep seated brain tumors with a laser beam
from inside the brain tumor without performing a conventional craniotomy.
The brain operation is planed by a image processing computer which converts
into the optimum trajectory line to the patient's brain tumor by the
'Endoscopic Surgical Laser and performed entirely by a computer controlled
robotic system that positions and inserts an 'Endoscopic Surgical Laser' thru a
minimally invasive incision in the patient's brain, and into the brain tumor,
which is then directed by the computer to robotically ablate the brain tumor.
Small blood vessels existing within the brain tumor are detected by the image processing
computer when analyzing each MRI brain scan, and incorporated into each scan
plane computer program to regulate the laser beam power for cauterizing the
blood vessel in each scan plane to prevent bleeding.
The 'Image Processing Computer' is the main workstation for gathering
information, processing MRI images, displaying graphics, monitoring the
operation, and producing the computer programs for planning and
directing the brain operation.
A square laser beam is ideal for this application, since it is vitally
important that the entire brain tumor be ablated and it operates in a pulsed
mode, and rotates at discrete angles to ablate successive squares of tumor
tissue along each layer. A special optics delivery system is employed for this
purpose, which is comprised of a variable width aperture for shaping the square
laser beam, and a special homogenizer for producing a flat top hat energy
distribution. Additional diffractive optic devices are also employed to produce
a wedge shaped top hat energy distribution, which enables the square laser beam
to also ablate the curved portions of the tumor contour.
http://www.howstuffworks.com/robotic-surgery1.htm
Reviewed by Ying Bao
This article introduced that robotics are being introduced to medicine
because they allow for unprecedented control and precision of surgical
instruments in minimally invasive procedures. Here are three surgical robots
that have been recently developed: 1) da Vinci Surgical System 2) ZEUS
Robotic Surgical System 3) AESOP Robotic System. . The da Vinci
system consists of two primary components: 1) A viewing and control console 2)
A surgical arm unit. In using da Vinci for gallbladder surgery, three incisions
-- no larger than the diameter of a pencil -- are made in the patient's
abdomen, which allows for three stainless-steel rods to be inserted. The rods
are held in place by three robotic arms. One of the rods is equipped with a
camera, while the other two are fitted with surgical instruments that are able
to dissect and suture the tissue of the gallbladder.
Another robotic system that is close to being cleared by the FDA is the ZEUS
System, made by Computer Motion. The ZEUS system employs the assistance
of the Automated Endoscopic System for Optimal Positioning (AESOP) Robotic
System.
Robotic surgery has several advantages over conventional surgery, including
enhanced precision and reduced trauma to the patient. In essence, as with all
automation, surgical robots will eventually eliminate the need for some of that
personnel and the use of a computer console to perform operations from a
distance opens up the idea of tele-surgery, which would involve a doctor
performing delicate surgery miles away from the patient.
http://www.bbc.co.uk/hi/english/health/newsid_503000/503521.stm
Reviewed by Suchart C.
This article discusses about a new technique for surgery using computer equipment that operated by voice commands. The Californian Medical Equipment Company Stryker Corporation developed the system, called Hermes. It can be used for many types of surgery, form simple operations to complex heart bypasses. The system can change lighting, apply suction, cut and slice tissue by speaking through a headset. This technology is expected to reduce tissue damage and time of operation. Hermes is voice-sensitive which only allow specific surgeon's voice that programmed into the computer to activate the system. This new technique is being tested for the first time in England and certified to be completely reliable.
http://news.bbc.co.uk/hi/english/health/newsid_672000/672815.stm
Reviewed by Suchart C.
Scientists are developing a robot that can perform a surgery. The spine of human body needs an extra delicate and rigorous surgery, and the surgical robot, supposedly, will have a more steadier and more accurate operation. The robot is capable of inserting screws very precisely into vertebrae by using ultrasound measurements. This links the robot to a navigation system. At the same time, surgeon will have all the information on the screen to make sure he or she can interfere at any time during the operation.
http://www.wired.com/news/technology/0,1282,38250,00.html
Reviewed by Suchart C.
Dr. Donald Galen, a surgical director of the Reproductive Science Center of
the San Francisco Bay Area, has performed a first infertility surgery called
microsurgical tubal reanastomosis or MTR, by using a robotic system, which
allows surgeons to operate through tiny incisions. The da Vinci surgery
system, designed by Intuitive Surgical, which was first used to perform heart
surgery, uses the technique of robotics and computer imaging. The system
consists of surgeon's console, a patient-side cart, and a high performance
vision system. Surgeons can operate with joysticks that gives flexibility
of movements at the wrists while sitting at a console viewing a result from a
tiny cameras attached to the probe in a 3-D image of the surgical field.
This technology provides the precision of the surgeon's movements in real-time
together with the movements of the surgical instruments inside the
patient. The patient will benefit from this procedure because of smaller
incisions and will have less time for recovery. The da Vinci surgery
system cost about one million dollars and is approved by the Food and Drug
Administration to perform all laproscopic procedures.
http://www.stn2.com/articles/view.php3?language=english&type=article&article_id=218391387
Reviewed by Suchart C.
This article explains us about the new technique for hip surgery.
Robodoc was invented with the collaborative effort of Dr. Russell H. Taylor at
Johns Hopkins University, Thomas J. Watson of IBM, and researchers at
University of California, Davis. Robodoc, a robotic surgical systems are
designed to assist the operation of the hip. In traditional hip surgery, a
procedure is done by hands and is never precise enough. It's extremely
important to have hip implants correctly. No perfect fit creates movement
and movement creates pain. With the new method, Robodoc operates by
using computed tomography (CT) scans precisely to measure the
patient's femur for putting titanium pin which will hold the hip
implants. All the information is kept in the memory section of the
robotic surgeon. Before performing a surgery, human doctors have to
figure out the correct size and shape of the hip implant. This new method
has not yet in the US, but it's already out in the European hospitals.
To learn more about the products, please visit www.robodoc.com
http://lims.mech.northwestern.edu/publications/jlea/RegImo.text
Reviewed by Liang Cai
This article discusses about registration and immobilization, two key problems in robotic systems for computer-assisted surgery. Jon T. Lea, Dane Watkins, Aaron Mills, Michael A. Peshkin, Thomas C. Kienzle III and David S. Stulberg from Northwestern University discuss the following approaches to these two problems and solutions. For Registration, they discussed: 1) Artificial vs. anatomic fiducials Most surgical robot systems to date use artificial fiducials. But anatomic fiducials are preferable to artificial fiducials since they do not require an invasive implant procedure. 2) Point and spatial fiducials can also be categorized by their geometry, which determines the number of degrees of freedom that the fiducial identifies. Point fiducials and spatial fiducials are the most common, although linear and planar fiducials are theoretically possible. For Immobilization, they discussed: 1) Accuracy requirements Immobilization is most critical to maintain the desired accuracies. 2) Partially constraining vs. fully constraining immobilization. They also give us some materials and methods to solve these two problems: Computer Assisted Total Knee Replacement Surgery (TKR).
http://www.technocopia.com/robots-19991124-roboheart.html
Reviewed by Liang Cai
This article describes Robotic Heart Surgery. Robot-assisted laproscopic surgery, first introduced in the 1970s, is routine for gall bladder, gynecological, and many chest, abdomen, and vascular operations. But it's only the first step in what promises to be a radical revolution in health care. The AESOP 3000 endoscopic positioning system, developed by Computer Motion, Inc. Goleta, Calif., is a commonly used laproscopic system. Its robot arms can hold the scope steadier and longer than a person, and uses voice commands (thus, keeping the surgeon's hands free) to position the scope. The surgeon still does the cutting and sewing. The ultimate goal of robotic surgery is to have robots do all the manipulation if not the thinking in an operation. Dr. Ralph Damiano, Jr., chief of cardiothorcic surgery at Pennsylvania State University's College of Medicine, has been one of the pioneers of robotic-assisted heart bypass surgery. He uses Computer Motion's next generation ZEUS Robotic Surgical System. With ZEUS, three pencil-sized holes are punctured in the chest. Through one hole a fiber-optic video camera is placed. Through the others go tiny (3 mm to 5 mm) versions of common surgical implements such as scalpels, forceps or needles. Tiny robotic arms hold the instruments. Surgery is about to become cheaper, more convenient, and less traumatic as using robots.
http://www.beyond2000.com/news/Nov_99/story_314.html
Reviewed by Wenguang Han
This article introduces a new robot operating system that is robotically
assisted coronary bypasses system. It is developed by a team including Dr Ralph
J. Damiano Jr., professor of surgery and chief of cardiothorcic and vascular
surgery at Hershey Medical Center, Penn State University and manufactured by
Computer Motion Inc. of California.
It comprises robotic, force feedback and speech recognition technologies to
embellish the surgeon's human skills and knowledge. There are three robotic
arms, all attached to the operating table. One positions the light/camera
assembly of the endoscope. This arm is voice-controlled by the surgeon, who
wears a headset microphone. It responds to simple, spoken commands (back.
forward etc.). The other two arms manipulate the surgical instruments and are
under the direct control of the surgeon.
The doctor isn't even by the patient's side. He performs the operation seated
in front of a monitor and holding the ends of the other two robot arms, which
end in controls based on traditional surgical instruments. Movement of the
tools is scaled as needed. They could be set so that if the surgeon's hand
moves one centimeter, the cutting tool moves half a millimeter. Hand tremors
below a certain minimum are ignored.
The robotic bypass surgery needs only three, pencil-sized holes in the
patient's chest, leaving just tiny scars and a much faster and less painful
recovery time.
http://www.osu.edu/units/research/archive/surgpics.htm
Reviewed by Ruiwen Jiang
The Ohio State University Medical Center has developed a new
minimally invasive heart surgery technique utilizing robotic technology. This
da Vinci Computer-Enhanced Surgical System uses sensitive remote-controlled
surgical instruments guided by a surgeon at a computer keyboard. The
system involves using a tiny camera with multiple lenses inserted
into the patient's chest, providing a three-dimensional image of the
heart. The surgeon, at a nearby computer workstation, watches through a
viewport to see inside the chest as a pair of joysticks is manipulated to
control two precisely engineered robotic arms. The arms hold specially designed
surgical instruments that mimic the actual movement of the surgeon's hands on
the joysticks. Using the robotic technology, only three holes - each about the
diameter of a pencil - are needed to complete the surgery.
http://www.cnn.com/HEALTH/9805/28/germany.robot.surgery/index.html
Reviewed by Naveen Menezes
Robotic surgery is being used at the Heart center in Leipzig, Germany to perform heart bypass surgery. This system called Intuitive uses three surgical arms that are inserted into the chest cavity through small incisions that are less than a centimeter wide. The surgeon watches the magnified image of the heart in a monitor and manipulates the robotic arms with two handles. One of the arms holds a miniature camera; the other two hold standard surgical instruments. When the surgeon grasps the handles, Intuitive's "motion-scaling" software translates large natural movements into precise micro-movements in the surgical instruments. This system gives surgeons a clear, magnified, stable and easily controlled view of the surgical site and eliminates awkward operating techniques.
http://health.phillynews.com/encyclopedia/KRTinteractive/packages/robot/html/robot4.htm
Reviewed by Naveen Menezes
A robotic device has been developed by the Engineers at the California Institute of Technology that could help people who suffer from small bowel diseases like ulcerative colitis and intestinal blockage. With this device called the gastrointestinal robot, minimally invasive surgery would be required. During surgery this device is attached to an air hose and fed into the body through a small hole in the stomach or colon. Some segments expand in width with air-filled balloons to grip the intestinal wall, while others expand in length with springs. This robotic device is battery-operated and remote-controlled with a computer. As the gastrointestinal robot moves through the 22-foot-long small intestine, it helps doctors detect abnormalities. This device also assists in the removal of blockages or to deliver drugs accurately to a particular part of the body in the treatment of diseases.
http://webmd.lycos.com/content/article/1728.50631
Reviewed by Naveen Menezes
Heart surgeons at Ohio State University (OSU) in Columbus have recently
performed a coronary artery bypass surgery on a 73-year-old man using a
computer-enhanced, completely robotic system. This new robotic technology
actually enhances surgeons' visualization and precision while operating. The
cardiac surgeon sits at a computer console, which does not even have to be in
the operating room and places each of his hands in holders that he can
manipulate. These movements, in turn, are transmitted to a computer and finally
to the tiny robotic hands that are in contact with the patient. The surgeon
watches a three-dimensional magnified image of his progress through a
viewfinder similar to that found in microscopes. In such type of surgery, a
surgeon is involved but his hands belong to the new robotic surgery device. The
only problem associated with this type of operation is to train endoscopic and
cardiac surgeons in this technology. The robotic approach is more intuitive
than endoscopic surgery, because the robot exactly replicates the surgeons'
movements to the left and right. The surgeons' intended
movements must be made in the opposite directions which means that surgeons new
to the technique must unlearn their former, hands-on methods of performing
procedures.
http://health.phillynews.com/encyclopedia/KRTinteractive/packages/robot/html/robot3.htm
Reviewed by Naveen Menezes
This article discusses how Remote Robotic Surgery can be used to operate on patients who are miles away, located in remote areas or even hostile environments. Despite the distance the doctor has a better sense of touch even though he may not directly use his or her hands to manipulate the instruments and tubes inside the patient's body. Robotic arms would perform the actual operation wherein the doctor would control the instrument tip with hand controls. The hand instruments guide robotic arms that perform the actual operation while providing real feedback to the doctor. In such systems a surgeon uses a video display with hand controls. The robotic arms are inserted manually into the patient using tubes. A computer system links the doctor's hand motions to the robotic arms, and a camera allows the doctor to see what he or she is doing. This technique is being designed for minimally invasive surgery that uses small incisions to access the body. Unfortunately, there are disadvantages due to the reduced dexterity, workspace, and sensory input to the surgeon, which is only available through a single video image.
http://www.journalstar.com/features?story%20id=2325
Reviewed by Xin Li
Computer Motion Corp. in California, has developed a very good robotic
surgical system, which includes three parts: 1) Aesop - a robotic device that
holds a tiny camera that peers into the body and projects what it sees onto a
monitor. 2) Hermes - a voice control system that allows the surgeon to direct
Aesop. 3) Zeus - the composite of all three parts including robotic arms that
allow the surgeon to operate sitting down at a console instead of standing over
the patient.
This system is a voice-controlled surgical instrument. Using it, surgeons can
do whole operation on the computer screen without even look into the patient.
They can just tell the computer to move the robotic arm and see this whole
operation basically on the TV screen. It can also help surgeons to do cases,
which may not be done with standard laparoscopy.
Another definite advantage for this system is that, it is a step-graded system;
hospitals can purchase each piece separately as they need. The first two parts
of the system - Aesop and Hermes - cost a total of $100,000, comparably less
than the full system price of $1 million.
http://www.lapsurgery.com/robotics.htm
Reviewed by Xin Li
Robots gain growing role in general surgery, in open-heart surgery and even
in laproscopic inguinal hernia repair. Dr. Ralph J. Damiano Jr., chief of heart
surgery at the Medical Center of Hershey, are using robots which can grasp the
handle of an 18-inch instrument probe without causing and can adjust its own
degree of movement to a millionth of an inch. The robotic camera can magnify
the stitches by a power of 16. There is no doubt that these medical devices are
about to revolutionize the treatment of patients.
In New Jersey, the Hackensack University Medical Center has been using a
simpler Computer Motion robot system, known as AESOP, for four years. You can
find a picture of AESOP 2000, if you are as curious as I do about what a
robotic surgical system looks like.
In Hackensack, Fan has done an operation on Howard Walker, a Rutherford
sanitation worker who had an inguinal hernia. In the operating room, fan just
give vocal orders to a battalion of voice-activated medical devices, called AESOP,
and the repair surgery was done beautifully. To make AESOP recognize commands,
each surgeon has a voice card that is inserted into the robot whenever that
surgeon operates. As Damiano said, " In five to 10 years, robots will
change the face of surgery". Robots may be expected to make surgery
safer and cheaper, and recovery much faster.
http://www.beyond2000.com/news/mar_01/story_1064.html
Reviewed by Peng Qu
This article introduces a Robot Assisted Microsurgery System (RAMS). RAMS is
developed by National Aeronautics and Space Administration (NASA)'s Jet
Propulsion Laboratory, as a means of conducting emergency surgery via remote
control.
RAMS serves as an intermediary between the surgeon's hands and the surgical
instruments. The system consists of a set of robotic arms and an operating arm
that actually performs the surgery. During operation, the surgeon manipulates
the controls. Hand motions are transferred in real time through a computer
system, where they are processed to automate the robot. The advantage of the
robotic system is that it could remove some of the random factors that affect
surgery. It allows the surgeon to filter out the slight tremors that are
present in even the most skilled human hands. The problem of long-range
telerobotics is time. It takes too long for the robot to return haptic/video
information, and for the user to move and wait for the robot to catch up. The
speed of light means there is a hard limit for how far the user can operate a
robot remotely.
http://www.robotbooks.com/robot-surgeon.htm
Reviewed by Peng Qu
This article describes a robotic probe that uses neural net software to
"learn" the brain's physical characteristics. The software learns to
distinguish tumors from normal brain tissue by remembering the pressure
signatures or profiles for each kind of tissue, and then making a model. A
“smart” computer program that continues to learn as it gains more experience
controls the speed and maximum pressure in the brain it is operating on.
By using pressure sensor, this system is able to 'feel' brain structures. The
probe, equipped with a tiny pressure sensor, will enter the brain, gently
locating the edges of tumors while preventing damage to critical arteries. If
it hits an artery, the probe will stop before it penetrates. If the computer
stops the probe, the surgeon can decide what to do next.
This new procedure could further reduce potential brain damage. A modified form of the brain surgery robot could be used for other kinds of surgery. Principal investigators Dr. Robert W. Mah of the NeuroEngineering Group at the National Aeronautics and Space Administration (NASA)'s Ames Research Center and Dr. Russell J. Andrews of the Veterans Affairs Palo Alto Health Care System and clinical associate professor of neurosurgery at Stanford university have worked together since 1994 to develop the smart robot.
http://ed.tsud.edu/tcubed/cool_tech/robotic_surgery.htm
Reviewed By Peeyush Rathkanthiwar
This interesting site tells how robotic surgery is getting useful to the doctors. Dr. Ralph Damiano performed the first coronary bypass surgery in a human patient using robotic arms manipulated by the surgeon. The bypass surgery was performed on a 70-year-old woman and the device used called the Zeus Robotic Surgical System, consists of three robotic arms that are used to manipulate instruments inserted into the chest through pencil-sized incisions. It consists of voice-controlled robotic arm that controls the endoscope, the camera used to visualize the surgery, and two arms are attached to surgical instruments that are manipulated by the surgeon with handles similar to those seen on conventional instruments.
http://www.acs.ohio-state.edu/units/research/archive/1stsurg.htm
Reviewed By Peeyush Rathkanthiwar
This article tells about the new minimally invasive heart surgery technique utilizing robotic technology performed at the Ohio State University Medical Center in which, daVinci Computer-Enhanced Surgical System uses sensitive remote-controlled surgical instruments guided by a surgeon at a computer keyboard. Michler performed this, with his surgical team members Drs. David Brown and Randall Wolf. Basic attraction of this operation is, it allows surgeons to perform operations using incisions in the chest wall that are much smaller than those normally required. The da Vinci system involves using a tiny camera with multiple lenses inserted into the patient's chest, providing a three-dimensional image of the heart. The surgeon, at a nearby computer workstation, can watch through a viewport to see inside the chest as a pair of joysticks is manipulated to control two precisely engineered robotic arms. The arms hold specially designed surgical instruments that mimic the actual movement of the surgeon's hands on the joysticks.
http://www.patent-roboticlaserbrainsurgery.com/
Reviewed by Hongying Ruan
This paper is about an innovative robotic system and apparatus for ablating
deep-seated brain tumors with a laser beam. The system can right position to
the patient's brain tumor, opens a small hole in the patient's skull, a surgical
knife is advanced through the patient's brain up to the tumor in question. A
small diameter 'Guide Tube' is advanced through the incision, and securely
fastened to the patient's skull with small screws. A round laser beam is then
activated to fire a number of pulses to core out a hole through the center of
the tumor that will allow the 'Endoscopic Surgical Laser' to enter the tumor.
The brain operation is planed by an image-processing computer and performed
entirely by a computer controlled robotic system.
http://www.technocopia.com/robots-19991124-roboheart.html
Reviewed by Tony Song
Dr. Ralph Damiano, Jr., chief of cardiothorcic surgery at Pennsylvania State University's College of Medicine, does a robotic-assisted heart bypass surgery with the equipment called ZEUS, which is Computer Motion's next generation ZEUS Robotic Surgical System. During the surgery, three pencil-sized holes are punctured in the patient chest, one hole is for a fiber-optic video camera, the others go tiny (3mm to 5mm) versions of common surgical implements, tiny robotic arms hold the instruments. With the robot assistants, patient needs not be touched by human hand except for the initial punctures. The robot's movements entirely are guided by the surgeon's voice commands. The robotic arms position the instruments and scope, and then move to cut or stitch according to instructions conveyed via a joystick-like input device. A computer translates all movements. This article also discusses the advantages of robotic-assisted heart bypass surgery procedure and patient recovery over the traditional heart bypass surgery.
http://www.findarticles.com/cf_0/m0EIN/2000_March_30/60946852/p1/article.jhtml?term=robotic+surgery
Reviewed by Tony Song
This article is about the most used medical robotic technologies developed by Computer Motion Inc. Three major systems developed by Computer Motion have been effectively used across a broad range of surgical disciplines around world. They are the voice-controlled AESOP(R) Robotic Endoscopic Positioning System, the HERMES(tm) Control Center and the ZEUS(tm) Robotic Surgical System. Freidrich Mohr, M.D., Ph.D., Chief of Cardiac Surgery at University Leipzig, Leipzig, Germany, leads a cardiac surgery team that has performed more than 200 AESOP-assisted minimally invasive heart valve surgeries through a 4-6 cm incision in the patients’ chest. Dr. Mohr stated that with AESOP, their team could expect safe, reliable and repeatable operative results with less patient pain, trauma and recovery time. A global pioneer in Minimally Invasive Surgery (MIS) with vast experience in beating heart procedures, London Health Sciences Center in Ontario Canada, rapidly and successfully integrated the AESOP and ZEUS technology into their MIS program, completed both the world’s first completely closed-chest, beating hart bypass surgery and the world’s first completely closed-chest, beating heart hybrid revascularization procedure. Dr. Alan Menkis of London Health Sciences Center commented that the patients were the real beneficiaries because of the significantly reduced pain and trauma, shorter convalescent periods and the expectation for excellent long-term results. The HERMES (tm) Control Center is a centralized system that enables the surgeon to voice control a network of “smart” medical devices. Computer Motion Inc. announced the completion of more than 100,000 computer and robotically assisted MIS procedures with their robotic technology by March 30, 2000. According to U.S. News and World Report, four of the top ten best heart centers are using ZEUS technology and nine of the top ten are avid AESOP users.
http://www.cs.jhu.edu/~rht/Papers/Miccai99/YaoPaper.pdf
Reviewed by Jianxin Wang
This article described that a research group of John Hopkins University develop a computer integrated system to assist surgeons in revision total hip replacement surgery (RTHR). The new method of the research is to direct the robot to cut a precise cavity using intra-operative portable C-arm fluoroscopy as guidance. Their new method provides a couple of new functions. (a) A checkerboard plate was designed to correct the geometric distortion within fluoroscopic images. The distortion correction approach works very well and the accuracy of the distortion correction verified by experiments; (b) A corkscrew (a single X-ray image of a know 3D arrangement of fiducials and computing the appropriate transformation) attached to the robot was designed, and based in the 2D projection of the corkscrew a 6D pose C-arm estimation method is developed and used in robot-imager registration and imager co-registration; (c) They are investigating a progressive cutting scheme and develop an iterative cut cavity location algorithm which utilizes image subtraction and 2D anatomy contour techniques to measure the errors after each cut using the fluoroscopic C-arm. The preliminary results indicate that a fluoroscopy based registration method and progressive cutting is a promising alternative for RTHR surgery based on several experiments.
http://www.patent-roboticlaserbrainsurgery.com/
Reviewed by Jianxin Wang
This website described that Mr. Jerome Shaunnessey has applied patent for an apparatus for directing the movement of an endoscopic surgical laser especially for use in vaporizing brain tumors. Based on his invention, the mechanism is simple, it is comprised of essentially two elements; an endoscope for probing into the brain, and a slim guide tube that the endoscope fits inside of. I don't think that the inventor, Mr. Jerome Shaunnessey has built the machine. The laser beam makes a cored hole through the tumor, and an endoscope is inserted through the cored hole, which has a mirror mounted at a 45-degree angle near the end of it and mounted with in it, that is capable of reflecting the laser beam at a 90 degree angle. Destruction of the tumor is accomplished by taking CAT or MRI scans of the tumor in plans perpendicular to the endoscope, and positioning the 45-degree corner reflector in one of the CAT or MRI scan plans, then rotating the reflected Laser beam to destroy the tumor tissue in that particular plane. The reflected Laser beam can be rotated continually or be instructed to only oscillate between some angle. Complete destruction of the tumor is accomplished by moving the corner reflector to successive plans. The entire process is accomplished by digital computer analysis the profile of each individual CAT or MRI scan, then using this information to guide the positioning and rotation or oscillation of the 90 degree reflected Laser beam to destroy the tumor tissue in that particular scan plane. As an inventor, He does not have a right to block research in this area and he might block surgery using this technique. A lot of scientists are doing the research right now. I think they should share the information to develop the technique together. I really hope that it will work. This invention could provide a method for reaching brain tumors that were previously un-reachable. It could provide a method for removing brain tumors without actually performing a craniotomy. It also could reduce the risk of brain surgery and the neurological damage it can cause to patients and reduce the brain operation time. It sounds great. I think that it will work in the near future.
http://www.cs.jhu.edu/~rht/Papers/Miccai99/SteadyHandFinal.pdf
Reviewed by Jianxin Wang.
This article described that a research group of John Hopkins develop a robotic system for microsurgery. This paper reports the new robotic system developed to extend a human's ability to perform small-scale (sub-millimeter) manipulation tasks requiring human judgments, sensory integration and hand-eye coordination. Usually tasks that require very precise, controlled motion are difficult or impossible for most people. For these tasks, They rely on machines. Their approach that is called "steady hand" micromanipulation is for tools to be held simultaneously both by a specially designed robot arm and the operator's hand. The robot hardware control runs on a Pentium-II 450MHz PC with the Windows NT operating system. An 8-axis DSP controller card is used to control the robot. The robot’s controller sense force exerted by the operator on the tool and by the tool on the environment, and uses this information in different control modes to provide smooth, tremor-free precise positional control and force scaling. Initial indications of experiments for the steady hand manipulation system are that the basic design assumptions of a stiff robot with force control are valid for surgical manipulations at a micro-scale. Their goal is to develop a manipulation robotic system with the precision and sensitivity of a machine, but with the manipulative transparency and immediacy of hand-held tools for tasks characterized by compliant or semi-rigid contacts with the environment.
http://my.webmd.com/content/article/1728.50450
Reviewed by Min Wang
This article discusses the use of robots to assist in cardiac surgery, based
on a series of clinical trials. The results of these trials, conducted in
the United States and Germany, were reported at the 1999 Annual Conference of
the American Heart Association. Commenting on these developments, Dr. Ralph J.
Damiano, Chief of Cardiothorcic and Vascular Surgery at the Hershey,
Pennsylvania Medical Center, stated that the ultimate goal of such technology
would be to minimize invasiveness while improving surgical precision. When
open-heart surgery is performed conventionally, a large incision is made in the
patient's chest and the ribs are spread apart to expose the heart. The
surgeon takes a blood vessel from the chest or leg and grafts it to the heart,
where it bypasses the blood around blocked arteries. By contrast, when robots
are put to use, three small incisions are made and there is no need to spread
the ribs apart. The surgeon sits at a console near the operating table
and directs the robots by remote control. Each robot has three mechanical
arms: two arms hold the surgical instruments and the third arm holds a camera.
From the console, the surgeon manipulates handles which send digitized messages
to the robot, telling it what to do with the instruments and where to move and
point the camera. The camera enables the surgeon to track and plan every
movement of the robot. Making use of robotics enhances the surgeon's technique
and removes the problem of natural hand tremor.
Dr. Damiano believes that robotic surgery will someday be a routine procedure,
but cautions that it will be very expensive. This is an appropriate article for
general readers with an interest in the applications of computers to medicine.
http://robotics.eecs.berkeley.edu/~mcenk/medical/
Reviewed by Shiqiang Wang
This web page presents the projects relevant to medical robotics. The University of California at Berkeley, Endorobotics Corporation and the University of California at San Francisco host it. They are developing improved tools for endoscopic manipulation, sensing, and human interfaces for a teleoperative surgical workstation. These tools could be used within the operating room or remotely for procedures in hazardous environments such as the battlefield. Surgeons may employ these tools to minimize surgical trauma and damage to healthy tissue, resulting in shorter patient recovery time. This web page introduces their collaborative above tools, projects and applications: Virtual Reality Training Simulator for Minimally Invasive Surgery, Toward a Telesurgical Workstation with Force Feedback and Stereo Teletaction, Endo-Platform, Laproscopic Manipulators, Surgical Master, Glove, Visual Display, Bilateral Teleoperation System Design, Tactile Sensing Display. If you are still thirsty for further detail research paper after your reading them, you can check the papers attached to it.
http://www.hsforum.com/stories/articleReader$690
Reviewed by Shiqiang Wang
The web page presents a technique on animal experience determining the
feasibility of using a robotically assisted microsurgical system to perform ECABG
(Endoscopic coronary artery bypass grafting). The researcher utilized a
cadaveric pig heart model after following preliminary work, thus acute and
chronic animal studies were performed. Calves were placed on cardiopulmonary
bypass after the left internal mammary artery (LIMA) was harvested. Subxiphoid
endoscopic ports (2 instrument, 1 camera) were placed and a robotic system was
used to perform ECABG between the LIMA and left anterior descending coronary
artery. LIMA graft flow (LIMAQ) was measured,
and excised hearts underwent angiographic and histological analyses. All
anastomoses were successfully completed in both the acute and chronic studies.
This research shows that ECABG is feasible in an animal model with excellent
results. The FDA has given approval for clinical trials of this new technology.
http://www.beyond2000.com/news/Sep_00/story_790.html
Reviewed by Suchart C.
Marc Madou, a professor of materials science and engineering, and his colleague, L. James Lee, a chemical engineer at Ohio State University are developing a new technique using compact disc player that could help doctors to conduct blood tests and other diagnostics. The tiny reservoirs and channels etched to the surface of a CD would allow medical samples to mix with diagnostic chemicals while the disc spins. With this new technology, a patient would only have to put a drop of blood or urine on a CD, and a computer system would do the rest. As the CD spins in the system, the forces form center pushes the liquid medical samples from the inner channels out to the edge. All tests are taken at this time, which will force equally to the perimeter. The CD player is also can connect to the Internet directly to the doctor's office for consultation and record any personal unique data of patients.
http://unisci.com/stories/20004/1023004.htm
Reviewed by Danian Cao
Dr. Yun Xu together with Dr. Simon Thom and Professor Alan Hughes at Imperial College London has developed a unique computer model of how blood flows in human arteries. The way blood flows through vessels has a role in the progress that causes heart attacks and strokes. Understanding the mechanisms of how blood flows can lead to greater understanding of those diseases. With the data provided by ultrasound and MR scans, the researchers built a computer model, which could take account of complex interaction between the blood and elastic wall of the vessel. Linking together two standard computer programs created this model, one is a computational fluid dynamics program; the other is a "solid mechanics" program that can deliver information about how a solid surface will deform depending on its "dynamic loading". By using this model, the researchers should be able to provide reliable prediction about the stresses on the vessel wall at a given point with the data from the clinic.
http://www.mrcas.ri.cmu.edu/papers/caos97_sense.pdf
Reviewed by Dongyang Chen
This article describes the intra-operative position sensing and tracking devices, which are integral components in computer-assisted orthopedic surgical system (CAOS). The sensors can be divided into two groups. One is position sensor and another is surface sensor whether or not the sensor comes into physical contact with the object being measured. These devices are used during surgery to precisely localize conventional surgical tools, rigid anatomical structures, other medical imaging equipment (e.g., X-Ray or ultrasound scanners), surgical implants, etc. The interventional magnetic resonance imaging (IMRI) is a new type of intra-operative sensor that is currently being used in several research hospitals. In this article, it presents sensor characteristics, comparisons of sensing modalities and examples. It is a very useful reference to these people who would like to build (CAOS) system.
http://www.nytimes.com/2001/04/26/technology/26NEXT.html
Reviewed by Dongyang Chen
This article briefly discussed the new development of Accelerometer sensor industry. Accelerometers were very expensive devices, which were used in aircrafts and other engineering devices to measure stress, strain and vibration. Piezoelectric crystals with a mass, which likes a mass connected on a spring, make traditional accelerometers. When an accelerometer is starting or stopping to move, the mass in the sensor will move back or forward because of inertia. The spring will change the length, which means the force on spring changed. It likes you push the spring by hand, you will feel the force changed on your hand. The piezoelectric crystals can produce electricity when they are pressed or bent. The devices detect the change of electrical current to determine the acceleration or deceleration. Because of development of the microchips industry, this kind of devices becomes more and more inexpensive now. Analog Devices, a company based in Norwood, Mass, makes about 700,000 low-cost accelerometers a week. They use the same photo-etching technology to build sensor chips. This chip contains two tiny weights and computing circuits to translate signals or send the information out instead of piezoelectric crystal sensor that has separate circuits to support its work. Mr. Lemarie, an engineer of the company, said these sensors are used in the airbag system now, as long as the price goes down, they will be used in washing machines. In other development, Dr. Gaitan's lab at NIST is taking a different approach, which is using heat change to measure motion. Dr Gaitan said to make a chip with a microheater than one with microscopic weight to implement and this kind of sensor will be inexpensive enough to be place inside box to measure the abuse of parcel delivery.
http://www.computermotion.com/pressr146.html
Reviewed by Dongyang Chen
This page reported the development of a new telesurgery system – SOCRATE,
which is invented by Computer Motion, Inc. The system combines computer-aided
surgical robotics and video telecommunication via networking technology to
enable a new way of remote surgical training and education. The SOCRATES system
cooperated with HERMES and AESOP produced by same company provides a surgeon to
directly access the operation environment and key patient information and even
check the status and/or control of a number of peripheral medical device
through HERMES. The remote surgeon even can remotely control the position of
the endoscope visually via AESOP. SOCRATES moves Telesurgery forward a huge
step from only sharing audio and video information to a real interactive
cooperation. With this system, a surgeon could do operation by a new technique
with an expert “hands-on” manner. It will extremely short the learning curve
for surgeons mastering a new operation technique.
http://fuzzy.fzk.de/mammography/mammography.html
Reviewed by Zhuo Chen
This project describes computer assisted diagnosis method that replaces
conventional X-ray mammography to determine breast cancer. A computer assisted
diagnosis station applied in mammography implements following steps: 1.
Digitization of X-ray mammograms 2. Segmentation of mamma tissue 3. Discovery
of regions, which may contain microcalcifications 4. Segmentation of
microcalcifications 5. 3-dimensional visualization of clusters of
microcalcifications 6. Detection of visible tissue changes 7. Automatic
suggestion of diagnosis. Computer assisted diagnosis of digitized mammograms
improve detection and interpretation of microcalcifications and other
structural changes within breast tissue. The accuracy of diagnosis is increased
and costs of breast cancer precaution checkups are strongly reduced. The goal
of the project is the implementation of computer aided diagnosis station for
X-ray mammogram evaluation that gives radiologists a "second
diagnosis" in clinical use. Radiologists must keep their decision
capability; they only need some support by the computer. Fast response times
are as important as results that confirm the radiologist’s diagnosis.
http://www.boston.com/dailynews/123/ascribe/_Emory_University_NuTec_SciencP.shtml
Reviewed by Zhuo Chen
Scientists at the Winship Cancer Institute of Emory University are grouping
with NuTec Sciences, Inc. and IBM to develop an integrated information system
that will enable physicians to trim cancer treatments based on a patient's
genetic makeup. In other words, the system will eliminate much of the work
involved with prescribing cancer treatments that today are often ineffective or
lead to harmful side effects. And determining the genetic information of a
patient will allow physicians to choose the specific treatment. NuTec and IBM
have integrated disparate technologies for storing, retrieving, processing, and
analyzing patient genetic data. The new system will combine NuTec Sciences
software for searching and analyzing gene expression and the gene combinations
with the processing power of the world's fastest commercial supercomputer. IBM
software for Web application serving and data integration will enlarge the
system, enabling doctors to access updated results and consult with their
patients using their desktop and handheld computers. GenesysSI will work by
comparing a patient's genetic fingerprint to thousands of different genetic
profiles from public and private databases. The results will be returned within
hours and will be sent via the Internet to Emory, where doctors can review the
reports with their patients and make treatment recommendations.
http://unisci.com/stories/20002/0420006.htm
Reviewed by Lei Dong
This article talks about a novel way to diagnose sleep apnea. Sleep apnea is
a very common disease among Americans. It is dangerous because it causes people
to stop breathing during sleep and may cause other diseases. However, sleep
apnea is usually untreated because people don't realize they have
it. Researchers at Polytechnic Institute developed a computer system that
can record a person's breathing sounds and recognize any irregularity so that
sleep apnea can be identified. With the help of this system, the testing
can be done in the comfort of the patient's home.
http://www.caesar.de/english/download/C96-2.html
Reviewed by Wenguang Han
This article discusses interactive surgical simulation system. This system is using computer-based three-dimensional visualization techniques to model a precise preoperative visualization of the patient's appearance after craniofacial surgery. In the data acquisition phase, the skull is reconstructed by computer tomography; a Cyberware scanner obtains the geometry of patient’s skin surface. Then an adaptive reduction technique is used to reduce the size of both datasets up to 80% without sacrificing the visible detail of the objects. The researchers use two different physical-based tissue models, a MASS SPRING and a FINITE ELEMENT, which are applied to individual anatomical structures. Both models are integrated into surgical simulation system. So the postoperative appearance of a patient after craniofacial surgery can be predicted.
http://www.mayo.edu/bir/reprints/CAS.html
Reviewed by Wenguang Han
This article talk about a comprehensive software system called ANALYZE and its new specifically program Virtual Reality Assisted Surgery Program (VRASP). This system has provided surgeons and physician with interactive visualization, manipulation and measurement of multi-modality 3-D medical image support. Surgeons can use it for pre-operative surgical and treatment planning and for post-operative evaluation. Surgeons can visualize 3-D renderings of CT and MRI data with hands-free manipulation of the virtual display. The surgeon will be able to scale, orient and position prescanned body imagery on-line in real time from any desired perspective. This system has been applied to (1) craniofacial surgery planning, (2) neurosurgery planning for brain tumors and epilepsy, (3) radiation treatment planning of brain tumors, and evaluation of tumor response to treatment, (4) orthopedic surgery planning, including trauma evaluation and physical bar removal, (5) assessment of extent and severity of prostate cancer, (6) and special surgical applications, including lung transplant analysis and surgical separation of conjoined ("Siamese") twins. This system has been used and evaluated at the Mayo Clinic for Computer Aided Surgery (CAS) and Radiation Treatment Planning (RTP) for more than a decade. This article uses ANALYZE to illustrate all application.
http://www.mrcas.ri.cmu.edu/projects/hipnav/paper.html
Reviewed by Wenguang Han
This article talks about The Hip Navigation or HipNav system. This system has
been developed to permit accurate placement of the acetabular component during
total hip replacement (THR) surgery. The system consists of three components: a
preoperative planner, a range of motion simulator, and an intraoperative
tracking and guidance system. The preoperative planner allows the surgeon to
specify the alignment of the acetabular component within the pelvis, based upon
preoperative computed tomography (CT) images. A kinematic range of motion
(ROM) simulator determines range of joint motion based upon the specific bone
and implant geometry and alignment. The feedback provided by the simulator
permits the surgeon to determine the optimal, patient-specific acetabular
implant alignment for any implant system and determines an "envelope"
of safe range of motion. Several devices are used during surgery to allow
the surgeon to accurately achieve the implant alignment specified in the
preoperative plan. An intraoperative computer displays to the surgeon the
position and orientation of the implant with respect to the patient at the time
of implant placement.
The goals of the HipNav system are to:
1.Reduce dislocations following total hip replacement due to acetabular
malposition. 2.Determine and potentially increase the "safe"
range of motion.
3.Reduce wear debris resulting from impingement of the implant's femoral neck
with the acetabular rim. 4.Track in real time the position of the pelvis
and acetabulum during surgery.
http://www.darpa.mil/dso/ or http://vishwa.tfe.gatech.edu/gtwm/gtwm.html
Reviewed by Wenguang Han
DARPA Research Helps Advance Medical Diagnostics
This article talks about Smart Shirts that is a new diagnostic tool for remote
patient monitoring. This program is researched at the Georgia Institute of
Technology and is one of Defense Sciences Office's Advanced BioMedical
Technologies Program. "Smart Shirt," a garment made of a special
lightweight fabric integrated with non-invasive sensory equipment capable
of monitoring heart rate, respiration, EKG, temperature and other important
vital signs. Termed the "Georgia Tech Wearable Motherboard"
(GTWM), the Smart Shirt serves as a mobile information infrastructure that
collects, processes, and transmits real-time data about the wearer from a
remote location. At the same time, this unobtrusive garment allows for
patient mobility and flexibility. This design was woven into a single-piece
garment (an undershirt) on a weaving machine to fit a 38-40" chest. The
plastic optical fiber (POF) is spirally integrated into the structure during
the fabric production process without any discontinuities at the armhole or the
seams using a novel modification in the weaving process. An interconnection
technology was developed to transmit information from (and to) sensors mounted
at any location on the body thus creating a flexible "bus" structure.
T-Connectors -- similar to "button clips" used in clothing -- are
attached to the fibers that serve as a data bus to carry the information from
the sensors (e.g., EKG sensors) on the body. The sensors will plug into these
connectors and at the other end similar T-Connectors will be used to transmit
the information to monitoring equipment or DARPA's (Defense Advanced Research
Projects Agency) personal status monitor.
"Smart Shirts" will have a significant impact on these key facets of
human endeavor and will lead to the following:
1. Personalized Information Processing 2. Healthcare and Telemedicine
3. Space Exploration and Specialized Monitoring Applications 4. Spawning of a
New Industry
http://www.intuitivesurgical.com/html/davinci.html
Reviewed by Ruiwen Jiang
Intuitive Surgical, Inc. has developed an advanced surgical system - microsurgery robot, daVinci Surgical System. By placing computer-enhanced technology between the surgeon and patient, the daVinci Surgical System enables surgeons to perform better surgery in a manner never before experienced. It can seamlessly translate the surgeon's natural hand movements at a console into corresponding micro-movements of the instruments positioned inside the patient through small puncture incisions, or ports. Surgeon operates while seated comfortably at a console viewing a 3-D image of the surgical field when is using this system. The surgeon's fingers grasp the instrument controls below the display with wrists naturally positioned relative to his or her eyes. Intuitive Surgical, Inc. has received FDA approval in June 1999 and over 250 operations has been done successfully using this system, mainly in cardiac procedures.
http://unisci.com/stories/19994/1011993.htm
Reviewed by Ruiwen Jiang
The U.S. Collaborative OralCDx (the Computer-Assisted Brush Biopsy Test for
the Detection of Oral Cancer) study group, composed of researchers from
throughout the nation, found a computer-assisted method of analysis of oral
brush biopsies. They undertook the
study to evaluate the sensitivity and specificity of OralCDx detection by using
computer-image analysis optimized to detect tissue abnormalities unique to
brush biopsy samples. The brush biopsy is performed with a micro stiff brush to
obtain a specimen containing cells from all three layers (basal, intermediate,
and superficial layers) of the epithelium from all regions of the oral cavity,
this resulted in minimal or no bleeding and required no topical or local
anesthetic. Then a computer programmed to read the slide identified the most
suspicious cells to be evaluated by a pathologist. This nationwide study
compared results of the computer-assisted image analysis with those of scalpel
biopsy of suspicious oral lesions, as well as using the computer-assisted
analysis on oral lesions that appeared benign clinically. In 945 patients,
computer-assisted analysis independently detected every case of histologically
confirmed oral dysplasia and carcinoma. Every 'positive' result from the
computerized analysis was subsequently confirmed by histology as abnormal or
carcinoma. 4.5% of clinically benign-appearing lesions would not have received
additional testing or attention other than clinical follow-up were identified
through computer-assisted analysis as dysplasia or carcinoma. “The results
demonstrate the potential value of computer-assisted image analysis as an
adjunct to the oral cavity examination in identifying pre-cancerous and
cancerous lesions at early stages, when curative therapies are most effective,”
Dr. Sciubba said.
http://www.biocomputer.com/ias.html
Reviewed by Xin Li
This article introduces a new Ultrasound Based Analysis System, which may improve the ability of ultrasound to detect prostate cancer. The BCR neural network and fuzzy logic analysis techniques, called the Image Analysis System (IAS) were tested to determine whether it was possible to extract tissue temperature and injury information - - fundamentally new information - - from standard ultrasound images as an aid in guiding minimally invasive surgery. Their research shows excellent correlation between the end-point processed ultrasound image, which demonstrated permanent tissue injury, and the gross pathology of the excised glands.
http://www.biocomputer.com/prostate.html
Reviewed by Xin Li
This article is about computer aided prostate cancer detection. Three
diagnostic modalities (DRE, TRUS, and the Prostate Specific Antigen (PSA) test)
were compared by Cooner. The low biopsy hit rate (29%) with TRUS implies the
need for a more sensitive and specific computer aided method for evaluation of
the ultrasound image. A computer method, "image metamorphosis", is
proposed which preliminarily has demonstrated an ability to detect small foci
of carcinoma based upon pathological studies of excised prostates. Their
results show that the Image Metamorphosis Computer System greatly improved the
sensitivity of TRUS and provided an improvement in the biopsy-hit rate by
locating tiny foci, which would never be seen without the aid of the computer
system.
The term "Image metamorphosis", has recently been trademarked
and applied to the process of image valuation by machine intelligent algorithms
It encompasses the extraction and encoding of backscatter patterns which
implement determinants that actually change the form and content of the image.
Thus the much used term "image processing is avoided because the type of
information gained is virtually changed in form and content by morphosing the
image. The morphosing process, remapping of each pixel based on the FUZZ-I-NET
evaluation of the imaged tissue radial determinant patterns and their deviation
from normal tissue determinant patterns, is based on a color scale of green for
least deviation to red for greatest deviation.
http://www.cnn.com/2000/HEALTH/10/02/inet2.demo.story/index.html
Reviewed by Peng Qu
Tele-medicine is one of the practical examples of technology entering the
doctor's office. Tele-medicine technology allows doctors to witness surgeries
from remote locations. This article introduces a tele-medicine system called
Internet2. Internet2 makes remote diagnosis a step closer to reality.
The benefits of tele-medicine are far-reaching. A specialist could give advice
to a doctor remotely for on-site medical care, or even guide that doctor during
a surgery. A medical student could watch a rare procedure that would otherwise
be unavailable. Researchers could readily swap and exchange information.
Currently, the problems of tele-medicine are: (1) system hardware problems.
Developers of Internet2 are working to make fully redundant systems to help
with the technical kinks. If part of the system crashes, it should be able to
switch over to a backup without any noticeable downtime. (2) There also needs
to be a way to set priorities on who get access to the system.
Unlike the Internet, access to Internet2 is more discriminating: First, it's a
collaborative effort led by United States research universities wanting to
create more dynamic tools for advanced research and education. Second,
Internet2 costs big bucks to join and the annual fees are also expensive. But
the cost is worthwhile compared to what the technology offers.
http://www2.crl.go.jp/jt/jt221/jiang/lsct.html
Reviewed by Peeyush Rathkanthiwar
This article by Senior Researcher Hao JIANG describes Computer-Aided Diagnosis for lung cancer screening. Basic understanding here is Computer-aided diagnosis by CT has made the life easier for the doctors than the diagnosis by radiography using the X-ray film one by one. Computer-aided diagnosis by CT can increase the correctness and efficiency by providing the support information, which is obtained from automatic detection of candidates, and 2D, 3D display and animation of original images. The CAD system consists of two parts 1.Automatic processing and 2.Image based diagnosis. Computers to detect the regions of lung cancer do automatic processing and this information for diagnosis is passed to the image based diagnosis part for the doctor's to support information for increasing the performance of screening.
http://www.hoise.com/vmw/00/articles/vmw/LV-VM-01-00-18.html
Reviewed By Peeyush Rathkanthiwar
Dr. Nicholas Ayache and his colleagues found the objective of Epidaure (Project Images, Diagnostic Automatique, Robotique) to modify the trend of X-ray imaging technique. The article represents the development in the design tools for the computer analysis of multidimensional, multimodal medical images. The main issue discussed here is the user interaction with medical images, particularly in the context of surgical simulation. It focuses to refine both diagnosis and therapy, especially when the therapy can be guided by computed images in video-surgery, interventional radiology, and radiotherapy. To understand the development in this field senior research scientist, Dr. Herve Delingette, offers an example of the new imaging potential in an anatomical liver segmentation. The image of the patient's liver is partitioned into a number of image point subsets that correspond to meaningful objects. The liver image consists of eight separate functional segments, which have to be identified correctly before moving on to actual surgery. The surgeon can remove about half of the organ and still, it will regenerate itself very quickly, growing back to its original size, but only if the physician is able to strategically target the segments through the use of separate colors in the image. Dr. Delingette uses mathematical morphology that tells how imaging helps the liver surgery. In this technique Differential operators are applied in 3D images to characterize points, lines or singular surfaces. The INRIA software generates 3D shapes at those points where lesions appeared on the initial CT scan and the segments can be identified in the diseased area, to have the computer automatically create a safety zone, indicating the region where the surgeon has to cut. This 3D model imaging gives the way for liver surgery.
http://iregt1.iai.fzk.de/KISMET/kis_apps_med.html
Reviewed By Peeyush Rathkanthiwar
This article consists of realistic modeling and simulation techniques for deformable objects in a virtual reality based minimal invasive surgery. Dr. Cakmak in his PhD thesis has invented this technique and made possible to perform surgical tasks on all elastodynamic objects in the virtual surgery scene in real time such as grasping, cutting and setting of clips. New research results include the simulation of pulse, pulsatile bleeding after arterial injuries, irrigation, suction, visualization and animation of coagulation smoke, which causes steaming up of the endoscopic lenses. A spline-based modeler for elastodynamic objects known as KisMo describes the 3d geometry and elastodynamical parameters of organ models, which are connected with each other to complete surgery scenes. Using KisMo a new virtual surgery-training environment has been created for the minimally invasive surgery in gynecology. Basic principle for Minimally Invasive Surgery is implemented with a phantom box, which is called a 'man-in-the-loop'-simulation. This realistic user-interface allows the trainee surgeon to manipulate the instruments in the usual way. Graphical workstation known as Central unit with the simulation system 'KISMET' is used as core software. KISMET does all the necessary calculations and generates the virtual endoscopic view in real-time.
http://www.cs.huji.ac.il/~josko/papers/cas98.pdf
Reviewed by Jianxin Wang
This article described that the research group from Israel has developed a
computer-integrated orthopedic system, called FRACAS (Fracture Computer-Aided
Surgery), for assisting surgeons in performing closed medullar nailing of long
bone fractures.
The FRACAS’ goals are listed bellow: 1.Reduction of the surgeon’s cumulative
exposure to radiation. 2.Reduction of surgical complications associated with
alignment and positioning errors of bone fragments, distal screws locking and
nail insertion. 3.To improve the positioning and navigation accuracy by
replacing uncorrelated static fluoroscopic images with a virtual reality
display of 3-D bone models created from preoperative CT and tracked in
real-time. 4.Fluoroscopic images are used for registration-establishing a
common reference link – between the bone models and the intraoperative
situation, and to examine that the registration is maintained.
This article also described that the system comprises four unites: (1) a
standard fluoroscopic C-arm, (2) a real-time optical position tracking system,
(3) a computer workstation with data processing and
visualization software, and (4) an adjustable drill guide device for assisting
the surgeon in distal locking. The article explained very detail about the
system concept, the preoperative modules (modeling and validation, nail
selection module and visualization module), the fluoroscopic image acquisition,
processing and tracking, and a series of experimental results to date. They
have satisfactorily tested the modeling preoperative planning, and
visualization modules on six clinical cases. For fluoroscopic image processing,
their experiments suggest that the sub-millimetric spatial positioning accuracy
is achievable.
http://www.nt.e-technik.uni-erlangen.de/~wsoergel/publications/aachen98.pdf
reviewed by Jianxin Wang
This article described a system for computer-aided diagnosis of bone lesions in the facial skeleton. Actually bone lesions in the jaws are different and can be based on the radiologic findings. Their system can really helps to do the differential diagnosis of these.
The following are how the system works: A new image is digitized orthopantomograph. This work is still done by the user. They rely on the user to find the lesion with a single mouse click. The boundaries of a present lesion must be outlined. Based on input the contour boundaries are outlined using active contour model. They usually use three regions for image analysis: rectangular regions and bounding the contour and the polygonal bounded region.
Image gray-level histograms, texture features and Gabor filter features are
computed for the lesion region. Each of these features is compared to the
corresponding feature for each case in the database and is saved to the
database. They also use the age and the sex of a patient to find similar images
in a query. The database contains 236 cases from 20 different disease classes.
The finally results are presented to the user with tumors location marked and
with all available annotations, a number of similar cases is shown to the user
also. They show good matches between their results from the system and
differential diagnosis given by humans.
http://www.hoise.com/vmw/articles/LV-VM-08-98-14.html
Reviewed by Min Wang
This article concerns a surgical technology called the Hip Navigational System (HipNav), which was designed by researchers at the Harvard Medical School and the Centre for Medical Robotics and Computer Assisted Surgery. HipNav was developed to help surgeons perform total hip replacement operations. It enables surgeons to more accurately position the implant in the patient's pelvis, minimizing the danger of impingement of the surrounding joints. The HipNav system has three components: a pre-operative planner, a range of motion simulator, and an intra-operative tracking and guidance system. Rather than traditional X-rays, surgeons take computed tomography (CT) images and feed them into the pre-operative planner. This gives them orthogonal views of the pelvis, allowing them to determine the size and position of the implant. The range of motion simulator helps predict the femoral positions before surgery begins. During the actual operation, doctors use the intra-operative tracking and guidance system to adjust the surgery to the individual patient. An optical tracking camera known as the "Optotrak" pinpoints the positions of light emitting diodes (LEDs), which are attached to both pelvis and the surgical instruments. This allows physicians to know the exact locations of the pelvis and socket joint while doing the implant. A digitizing probe analyzes the surfaces of the pelvis and the socket and compares these data with the CT images previously taken. While surgeons perform the operation, a television monitor provides navigational feedback. The article demonstrates how computer technology can be applied to improve the efficiency of surgery.
http://www.hoise.com/vmw/00/articles/vmw/LV-VM-03-00-10.html
Reviewed by Min Wang
This article focuses on an endoscopic sinus simulator, which has been
developed by the Lockheed Martin Corporation for the purpose of training
surgeons for sinus operations. MedOps LCC markets this tabletop device,
and Montefiore Medical Center in the Bronx; New York was the first institution
to purchase one. The simulator, which has been named "Martin,"
is a computer that provides virtual reality training to medical students and
experienced surgeons alike, h1/0elping them perfect their skills and prepare
for actual surgery.
Otolaryngology residents at Montefiore Medical Center who train with Martin do
their practice on a software-driven mannequin that enables them to move an
endoscope, scalpels and other surgical tools through a virtual nose. The
anatomy simulated by Martin is very lifelike, giving trainees the feel of
cutting into real nasal tissue. Traditionally, physicians have trained
for surgery using cadavers. However, the sinus surgery simulator has an
advantage over cadavers, because it allows trainees to correct their mistakes
by practicing operations over and over again. Since nasal surgery is
classified as high risk, training involving much repetition can improve the
chances for success.
The sinus surgery simulator uses equipment like that found in most operating
rooms, such as monitors for viewing procedures, endoscopes, and scalpels.
Martin the computer is activated by voice commands. For example, when a
student gives the command, "Wake up, Martin. Scissors,” an animated
image of a pair of scissors appears in the virtual naval cavity being displayed
on the monitor. By using a hand-held device, the student maneuvers the
scissors through the simulated three-dimensional space and removes any abnormal
tissue. Martin can give commands, too, such as when a scalpel gets
dangerously close to the eye: "Warning. You have cut the lamina
papyracea." The main advantages of the simulator are that it can
virtually replicate many surgical tools, has tactile feedback and enables
students to learn to operate on various ailments: it can be commanded to create
a tumor or a polyp, for example.
http://www.hoise.com/vmw/articles/LV-VM-02-98-16.html
Reviewed by Min Wang
This article concerns a device called the Virtual Brain Bench (VBB), which
was designed to facilitate the planning and execution of brain surgery.
Developed at the National University of Singapore by Luis Serra and a team of
researchers, it offers for the first time software to assist doctors in the
virtual and actual placement of fixation devices to patients' heads. The
VBB has two essential components: the first is the Electronic Brain Atlas,
which takes data from printed brain atlases and digitizes, enhances, labels,
and converts these data into 3D extensions; the second component is the Virtual
Workbench, a tool that controls 3D data and makes it convenient for the
physician to interact with the patient's data throughout the surgery.
To prepare for an operation, the surgeon uses the VBB to create virtual
versions of the steriotactic frame and the fixation device, which are standard
pieces of equipment in brain surgery. These are placed over a 3D computer
image of the patient's head, enabling the surgeon to plan the location of the
screws needed for attachment. The actual frame and fixation device are then
attached to the patient's head and a scan of the brain is taken. The data
from the scan are linked with the brain atlas, while a 3D grid system allows
the atlas to conform to the patient's brain scan. When the surgery
begins, a probe guide assists the surgeon in selecting a path for incision that
minimizes damage to brain tissue. More detailed assistance is provided by
the Vessel Editor, which makes it possible for the surgeon to sketch edges,
points, and polylines on volume data so as to display blood vessels, cranial
nerves, and other brain structures. Serra and his team are considering building
networking technology into the Virtual Brain Bench, so that distant users could
view data sets simultaneously.
http://www.hoise.com/vmw/articles/LV-VM-08-97-7.html
Reviewed by Min Wang
In this article a computer-guided surgical technique for the treatment of
hip and pelvic fractures is discussed. Dr. David Kahler, a surgeon and
professor at the University of Virginia Health Sciences Center, demonstrated
the technique at the Second Annual Meeting of Computer Assisted Orthopaedic
Surgery. This method offers the advantages of more precise surgical
incisions and minimal invasion of body tissues. Kahler has used his
computer-assisted method on twenty patients to date. These patients'
injuries were difficult to treat due to the high probability of infection,
potentially heavy blood loss, and risk of nerve damage. The integrated
system of hardware used by Kahler, known as StealthStation, has a UNIX-based
workstation with an optical digitizer attached to it. To prepare for an
operation, Kahler loads his system with a computed tomography (CT) scan of a
patient's pelvis. This produces a three-dimensional visual model, which
he examines from different angles to determine the best location for inserting
screws. When the operation begins, a computer display shows Kahler the
patient's pelvis, as a precision camera scans the anatomy. With his
surgical instruments - which are fitted with LEDs - he makes an incision and
installs the screws. During the surgery he is careful to follow the
guidelines provided by the computer model. The article is recommended for
general readers with an interest in medical technology.
http://www.hoise.com/vmw/99/articles/vmw/LV-VM-08-99-4.html
Reviewed by Min Wang
The topic of this article is the Computer Assisted Orthopaedic System, known as CAOS, which was developed by the Muller Institute at the University of Bern in Switzerland. It is currently being used at the University Hospital of Antwerp in Belgium to improve the precision of bone, head and spinal surgery, as well as hip prostheses implants. Since being introduced in 1997, the CAOS system has helped surgeons at the University Hospital reduce the inaccurate placement of screws in spinal surgery from 25% of cases to 2%.
To use the CAOS system, the surgeon first does Computed Tomography (CT) scans of the patient's lesion. These scans are then run through a computer to produce a 3-D reconstruction of the affected area. In the case of spinal surgery, the surgeon studies the 3-D reconstruction to plan the operation on the computer. When the operation begins, the computer screen shows the doctor the virtual spinal column, the trajectory of the surgery, and the exact location of the surgical instruments. Light emitting diodes (LEDs) attached to the instruments are tracked by infrared cameras. The LEDs signal the locations of anatomic landmarks that were established in the pre-operative CT scans, enabling the CAOS computer to determine the exact position of the patient's spinal column. The accurate matching between real and virtual body parts is essential to the effectiveness of the CAOS system. Using the computer screen as a reference, the surgeon can quickly determine, in millimeters, the maximum possible deviation permitted in the trajectory of the surgical instruments.
http://www.vr.clemson.edu/vr/bioe/bioe.html
Reviewed by Peilin Zhang
Just like we need a draft before we write our journal, it will be a nice
thing if a "virtual" surgery can be performed before any type of
physical surgery takes place. And now, we can do this. This article introduced a
pre-operative planning using virtual reality that allows the doctor and surgeons
to not only visually see the patient’s data in three dimensions, it also allows
them to visually manipulate the data. This planning actually involves 3 steps.
First the doctor need obtain patient's CT slice files for the bone data they
want, then they reconstruct these data to get a three dimensional
representation of the original slice data, after that, the surgeon uses a head
mounted display and a data glove to view and manipulate the patients
reconstructed data. If you have time, the link also provide an animation of a
virtual bone fracture, you can dig a little deeper.
http://www.iop.org/Physics/News/0290j
Reviewed by Aamir Babar
This site is contains some interesting material about the use of optical computing in determining the quality of wood. The quality of wood is of great importance for all aspects of the forestry industry. Wood quality is related to its density, which in turn directly related to how easily it shrinks or swells, how it reacts to heat or sound. By using optical methods, the researchers have found a correlation between signals and properties of wood such as density simple measurement of the transmission and the absorption of infrared light in wood can be used to infer the bulk density of the wood. Developing these compact and robust optical measuring instruments will be use both in laboratory and for industrial application.
http://www.bu.edu/bioinformatics/research/Computational/SmithC.htm
Reviewed by Aamir Babar:
This site describes a project that focuses on the field of molecular
biotechnology. The project involves the development and application of
comparative methods for understanding the effect of DNA stability on
development, aging and disease processes. The goal is to understand how DNA changes
contribute to complex phenotypes like schizophrenia or hypertension. These
studies are carried out by new system called targeted genomic differential
display (TGDD). This system targets analysis to difference gene families and
classes of DNA sequence. TGDD is being enhanced as it is reformatted for DNA
chips.
http://panizzi.shef.ac.uk/msdn/avis/avisi.html
Reviewed by Aamir Babar
This site contains some interesting material about AVIS, which stands for animal virus information system. It contains the data on animal viruses. AVIS was created as a tool for virologists, molecular biologists, clinical personnel, epidemiologists, and industrial users. Information is coded into two different formats, as) dBASE III plus format and ii) an extended RKC format by developing numerical codes for virus characteristics. The information is also coded for oracle 6.The data allows analysis of various properties of viruses and numerical taxonomy pictorial information, such as electron micrographs, are provided in computer reachable form. The site also provides description on animal viruses that are isolated from an animal or infecting an animal.
http://www.kbasecorp.com/product/fuzzy/fuzzydecision.htm
Reviewed by Aamir Babar
The above site describes about fuzzy logic decision. It shows that how fuzzy
logic system (in the form fuzzy decision) can be used to manage the business. Fuzzy
decison can make human like decisions in all those business matters, which
involves some sort of if, or then in real quick time. It has been found of
great usefulness in the finance and decision making process. Since this topic
is related to our everyday life therefore it is pretty much interesting to
read.
http://unisci.com/stories/19994/1209994.htm
Reviewed by Suchart C.
This article talks about a new technique that uses a mathematical concept known as chaos theory for predicting some types of epileptic seizures. Developed by the researchers at the University of Florida Brain Institute and the Malcom Randall Veterans Affairs Medical Center in Gainesville. This technique uses a sophisticated mathematical formula to sort through the brain's complex electrical signals, which recorded by electroencephalograms, or EEGs. If electrode pairs begin to move around during an EEG, that's the signal of seizure. This method might not be able to point out the exact time of occurrence, but it can determine whether a patient is in danger or not.
http://www.abc.net.au/science/news/health/HealthRepublish_249667.htm
Reviewed by Suchart C.
Peter Liddle has developed a new way, which is based on a learning system
called neural network, to diagnose schizophrenia. Dr. Liddle is a
psychiatrist specializing in brain imaging at the University of British Columbia
in Vancouver. His neural network was trained to use positron emission
tomography to scan patient's brain, analyzing characteristics in ceberal blood
flow, and able to tell whether a patient has schizophrenia. This method
has been proven to be 100% accurate.
http://www.sciencedaily.com/releases/2001/02/010223081414.htm
Reviewed by Suchart C.
Michael Ferris, a computer scientist at the University of Wisconsin, Madison and medical physicists at the University of Maryland Medical School are developing a computer program that will reduce the threat of human error in setting radiation treatment plans. They are improving the precision of a unique technology called the gamma knife, which was exclusively designed for treating brain tumors. The computer-based optimization takes a non-linear approach to the problem for better reflection on how radiation dosage behaves within a tumor. By using the bell-shaped design, the computer model will be able to get the different radiation shots to kill tumor cells. And the speed of this method is amazing, it can map out a treatment plan is 20 minutes or less, so the neurosurgeons can work out with several setups and find the best one.
http://splweb.bwh.harvard.edu:8000/pages/papers/warfield/sc2000/brainmatch.pdf
Reviewed by Liang Cai
This paper talks about intraoperative nonrigid registration algorithm, which
accurately simulates the biomechanical properties of the brain and its
deformations during surgery. The algorithm was designed to allow for improved
surgical navigation and quantitative monitoring of treatment progress in order
to improve the surgical outcome and to reduce the time required in the
operating room. This algorithm has been applied to two neurosurgery cases with
promising results. High performance computing is a key enabling technology that
allows the biomechanical simulation to be executed quickly enough for the
algorithm to be practical. This parallel implementation was evaluated on a
symmetric multi-processor and two clusters and exhibited similar performance
characteristics on each. The implementation was sufficiently fast to be used in
the operating room during a neurosurgery procedure. It allowed a
three-dimensional volumetric deformation to be simulated in less than ten
seconds.
http://unisci.com/stories/20001/0114005.htm
Reviewed by Danian Cao
Professor Lloyd Smith, Robert Corn and their research team from the University of Wisconsin-Madison reported in the journal Nature that the vast potential of DNA can perform the same tasks that now require silicon and miniature electronic circuits. The idea of DNA computing is that a binary string can be represented by a unique sequence of nucleotides in single-stranded DNA, such as, TGCGG might stand for 001. For n variables, there are 2 raised to the nth power unique solution strands. For each strand, there is also a complementary antisense strand created by the base-pairing rule: A bonds to T, and C bonds to G. In the Wisconsin experiments, a set of DNA molecules encoding all the candidate solutions to the computational problem of interest are synthesized and attached to the solid surface. Successive cycles of hybridization operations and exonuclease digestion are used to identify and eliminate those members of the set that are not solutions. The wrong answers are weeded out, leaving only the DNA molecules with the right answers.
http://unisci.com/stories/20001/0315006.htm
Reviewed by Danian Cao
Professor Henry Gray at Southern Methodist University has developed the first computer software program that can convert voice commands into mathematical expressions. The software can recognize all mathematical symbols and equations. For example, if you want to write 1+2+3...+n=n (n+1)/2, you can just tell the computer that "The sum of a series of (n) integers is equal to one-half of the product of (n) times (n+1)". If you say, "A times x plus B times y plus C equals to zero", an equation, Ax+By+C=0, will appear on the computer screen. It is a great help for those paralyzed students. He has also developed a version of software that can be used by visually impaired students. This version can translate the mathematical formulas into Braille, which can then be output using an embosser. It is a remarkable work, which gives those people with disabilities more confidence in their life.
http://unisci.com/stories/20004/1109004.htm
Reviewed by Danian Cao
This site talks about a new computer algorithm for x-ray crystallography that is being developed by Professor Veit Elser at Cornell University. To determine protein structure, experts use a beam of x-rays to fire through a crystallized protein sample. By studying the pattern of the scattered beam, experts can find out the arrangement of the atoms and the shape of the protein molecule. But the process is not easy; it may take weeks or even months to find the structure of a large protein. Crystallographers measure the amplitude of the x-ray emerging from a sample by scanning across a plane on the output side. To speed up the process of find the structure, Elser is using a computer to try combining the measured amplitudes with random patterns of phase. When the computer tries a random pattern of phases, it looks at the total charge of the electrons in the structure that results and decides whether or not it is going in the right direction. Otherwise, it discards the group of related patterns it was trying and starts at a different place. The aim of this project is "Feeding the data into the computer will give you the protein structure in a matter of minutes."
http://unisci.com/stories/20003/0925002.htm
Reviewed by Danian Cao
Professor Nicholas Peppas, Rashid Bashir and their graduate student Jennifer Ward at Purdue University have developed a new technique that could be used to glue cells or DNA to the surfaces of computer "biochips". The idea of this technique involved using a material made primarily from a polymer, or plastic, called polyethylene glycol. The unusual optical properties of the polymer make it easy to be formed into patterns by using ultraviolet lights. The polymer with precise patterns that certain regions attract water and others repel water is applied to the surface of silicon chips as a film. Then the glued biological materials on a biochip's surface would precisely fit specific cells, molecules and strands of DNA in a sample being analyzed. When a targeted substance passed by the chip, it would become attached the surface and the chip would signal that the substance had been detected. It is an amazing technology that might be used to make diagnostic devices to be implanted in the body or quickly analyze food and laboratory samples.
http://unisci.com/stories/20011/0314015.htm
Reviewed by Danian Cao
A computational program for predicting the number and likely location of
crossovers may soon be finished by Penn State research team. DNA shuffling uses
related genes from different species or genes with related function fragments
them and reassembles them through recombination. Researchers then place
recombined genes into E. coli to identify which new genes produce usable or
potentially interesting products. By using thermodynamics and reaction
engineering to evaluate and model this complex reaction network, scientists now
can predict where the DNA from different parents gene will recombine, how
fragment length, annealing temperature, sequence identity and the number of
shuffled parent sequences affect the number, type and distribution of
crossovers along the length of reassembled sequences.
http://www-dept.cs.ucl.ac.uk/research/genprog
Reviewed by Dongyang Chen
This site introduces the detailed description on the genetic programming (actually we should call it Genetic Algorithm). The Genetic Algorithm is a model of machine learning that derives its behavior from a metaphor of the processes of evolution in nature. This is done by the creation within a machine of a population of individuals represented by chromosomes, in essence a set of character strings that are analogous to the base-4 chromosomes that we see in our own DNA. In nature, the encoding for genetic information (genome) is done in a way that admits sexual reproduction. At the molecular level what occurs (wild oversimplification alert) is that a pair of chromosomes bump into one another, exchange chunks of genetic information and drift apart. When the genetic algorithm is implemented it is usually done in a manner that involves the following cycle: Evaluate the fitness of all of the individuals in the population. Create a new population by performing operations such as crossover, fitness-proportionate reproduction and mutation on the individuals whose fitness has just been measured. Discard the old population and iterate using the new population. This site provides a working sample, which was written in C++ to simulate evolution. This program will run on Linux and Unix systems. From this site, we can found other information and developments about Genetic Programming. This site is very suitable to students who study in computer science and other people who are interested in Genetic Programming field.
http://www.unisci.com/stories/20001/0114005.htm
Reviewed by Xi Chen
The researchers from the university of Wisconsin-Madison have taken an
important step in realizing DNA computing by experiments other than theoretical
work. DNA computing is the technology that seeks to capitalize on the enormous
informational capacity of DNA. It represents information as a pattern of
molecules arranged on a strand of DNA. Certain enzymes are capable of reading
that code, copying and manipulating it in predictable ways. In the Wisconsin
experiments, a set of DNA molecules were applied to a small glass plate
overlaid with gold. In each experiment, the DNA was tailored so that all
possible answers to a computational problem were included. By exposing the
molecules to certain enzymes, the molecules with the wrong answers were weeded
out, leaving only the DNA molecules with the right answers. DNA computing is
known to be one potential way for future computational need while the
conventional computing is approaching its limitation. The work of the
researchers has been published in 'Nature', and it is clearly a big step
forward in this area.
http://www.scripps.edu/newsandviews/e_20010319/abagyan1.html
Reviewed by Zhuo Chen
This news reports professor Ruben Abagyan and his colleagues at Scripps Research Institute (TSRI) Department of Molecular Biology use Computational Biology to interpret the Human Genome. They create an environment where all genomic information can be sorted and the redundancies can be removed. The individual databases can be consumed, combined, digested, and displayed in a standardized form. A functional map of the human genome will be produced. In this map, all the genes are identified and understood. A protein catalog of clustered genes is represented by a hierarchical folders, using a standardized annotations and conventions. Abagyan and his colleagues are also working ways to organize the annotated human genome by using homology modeling and docking. Homology modeling is a traditional tool for determining which functional family a gene or a protein belongs to by comparing a sequence from an unknown protein or gene to a database of known entities, but Abagyan works on new procedures to align sequences involving large gaps, dissimilar fragments in the middle of an alignment, and iterative chains of sequence comparisons. Docking is another tool to annotate the genome. The basis for docking ligands to certain receptors comes from knowledge of the atomic structures of the receptors themselves. Abagyan subjects target receptors to hundreds of thousands of available compounds. The flexible docking procedure samples hundreds of possible conformations of the ligands in the surface pockets of the receptor and assigns a score to the ligands. The score is used to rank and order the entire chemical collection. The end result will be many of virtual inhibitors, lead compounds that can then be taken into the laboratory used as inhibitors.
http://miralabwww.unige.ch/ARTICLES/cas2000.pdf
Reviewed by Zhuo Chen
This paper reviews the approaches employed in computer animation for skin modeling, wrinkle formation and aging process. Two methods have been presented: image based and model based. Image based method employs eight generic mask as templates, which characterize wrinkles. The image based method enables display of simulation results. In the model-based method, skin is considered as elastic membrane that has layers of different materials. The ultimate goal is to devise a practical system, which can enable modeling of skin of an individual person using biomechanical parameters. The system is capable to simulate the visual effect of external treatment on the skin.
http://unisci.com/stories/20001/0321005.htm
Reviewed Lei Dong
The long-standing myth that "bumblebees cannot fly, according to conventional aerodynamics" was dispelled recently by a computer simulation by Cornell University physicist Z. Wang. Her programs simulate rapidly oscillating wings and the complex motions of fluids, which have proved that insect flight conforms to the physical principles of aerodynamics. Unlike fixed-wing aircraft with their steady, almost inviscid flow dynamics, insects fly in a sea of vortices and they depend on vortices to keep them aloft, especially when they are hovering. The unsteady effects play a significant role in insect flight, however, they are the most difficult to deal with because the unsteady flows are coupled to moving boundaries. The simulation required the development by Wang of some new computational tools -- "tricks," to resolve unsteady flows and forces, which are governed by a mathematical calculation called the Navier-Stokes Equation -- and hundreds of hours of number-crunching by a supercomputer. Her simulation result was the first ever proof that dragonflies produce sufficient lift to stay above the ground -- at least in a two-dimensional simulation. The same simulation in three dimensions will require more computational "tricks" and computer time, and Wang currently is working on that. Looking ahead to the construction of tiny flying machines for aerial surveillance and other purposes, Wang says the designs need not resemble fixed-wing airplanes or helicopters. Now that the rules for insect flight are quantified, designs for bug-like devices of almost any size can be tested in the computer. Various designs can virtually hover, fly backward and perform acrobatic maneuvers in full accordance with the principles of unsteady viscous fluid dynamics. Or crash virtually if they don't.
http://www.news.cornell.edu/releases/Dec00/genemaps.ws.html
Reviewed by Ming Feng
Cornell University researchers have come up with a way to do comparing the
genomes of two related species in a few hours on a computer. By comparing
genomes, scientists can trace the evolutionary paths, and there are immediate
practical applications. The idea of comparative mapping is to align genes in
the order they are found along the chromosomes of the first or "base"
species with those found in the same order on a single chromosome of the second
or "target" species. The raw data consists of ordered lists of the
genes and gene markers of both species that have been identified in "wet
lab" experiments. In early stages of the work, they called
"penalties," the computer was directed to minimize both the number of
segments it created and the number of out-of-place genes in each segment. While
promising, when applied to a comparison between rice and maize this approach
still didn't produce a map close enough to one made by hand, Goldberg says.
Among other things, the computer often introduced too few breaks where a small
part of one sequence appeared in the middle of another. The researchers tested
their computer method by comparing a computer-generated comparative map of rice
and maize with a handmade map prepared in 1999 by William A. Wilson and several
colleagues at Cornell and Iowa State University. The results were remarkably
similar, although in their paper they note some minor differences. They also
point out that handmade maps usually are made with reference to additional
information that biologists hold in their memories, such as the order of genes along
the chromosomes of other related species.
http://americanscientist.org/issues/Comsci01/compsci2001-05.html
Reviewed by Ming Feng
This article talks about digital logic units based on the metabolism of living cells, with the aim of building a computer out of colonies of Escherichia coli or some other single-celled organism. In principle, computing machines can be made out of almost anything, and there is no reason that lipid sacs of proteins and nucleic acids should not also qualify as computer building blocks. From perspective of computer science, an agar plate coated with microscopic bacteria is not much different from a silicon wafer etched with microscopic transistors.
A digital technology usually starts with Boolean logic gates—devices that
operate on signals with two possible values, such as true and false. In
electronic circuits, a not gate can be made from a single
transistor, wired so that a high voltage at the input produces a low voltage at
the output, and vice versa. When the gate switches between its two states, it
does so abruptly.
Researchers at MIT are developing such computer. The first step of the MIT group is to develop design rules and a parts catalogue for biological computers. The elements of the MIT biocomputing design library will be repressor proteins. In this way gates can be linked together in a chain or cascade. Biomolecular computer is very different from an electronic one, where all signals are carried by the same medium—an electric current. The reason for the difference is that electronic signals are steered by the pattern of conductors on the surface of the chip, so that they reach only their intended target. The biological computer is a wireless device, where signals are broadcast throughout the cell. On electronic chips, communication pathways claim a major share of the real estate. In a biochemical computer, communication comes for free.
Another important design tool is a simulator. The MIT group is building a
BioSpice simulator. It will be developed into a crop of programmable biological
sensors, actuators and messengers.
http://www.sciencedaily.com/releases/2001/04/010406074517.htm
Reviewed by Ying Jiang
A newly developed computer program predicts the chances of brain cells dying as the result of a stroke and may refine the use of brain saving stroke drugs. The computer software, which uses artificial intelligence techniques, very rapidly combines several new types of images obtained by magnetic resonance imaging (MRI) into a map of the brain allowing physicians to assess the risk of brain damage with high specificity and sensitivity. The computer breaks the advanced MRI brain scan into tiny, distinct cubes about one-tenth of an inch in diameter. Two key pieces of information are measured for each cube. One tells whether blood flow through vessels in the area is blocked. The other indicates whether the brain tissue is living or dying. Currently, the program focuses on middle cerebral artery strokes. The researchers plan to expand it to encompass all strokes caused by blocked arteries.
http://www.krasnow.gmu.edu/ascoli/CNG/TNA/index.htm
Reviewed by Xin Li
This article introduces the progress in COMPUTATIONAL NEUROANATOMY. Different kinds of modeling algorithm are discussed, which will give you a really good picture of the development in this area. For example, Giorgio Ascol et al developed modified L-systems, called L-Neuron algorithm. When modeled neurons are distributed in 3D and biologically plausible rules governing axonal navigation and connectivity are added to the simulations, entire portions of the nervous system can be grown as anatomically realistic neural networks. These computational constructs are useful to determine the influence of local geometry on system neuroanatomy, and to investigate systematically the mutual interactions between anatomical parameters and electrophysiological activity at the network level. A detailed computer model of a virtual brain that was truly equivalent to the biological structure could in principle allow scientists to carry out experiments that could not be performed on real nervous systems because of physical constraints.
http://www.voicenet.com/~rybak/iod.html
Reviewed by Naveen Menezes
This project is based on another interesting field of Bioinformatics called Neural Networks that finds interesting applications in areas like Image Processing. This project is based in the Research on the Experimental Study & Computational Modeling of Orientation Selectivity in the Visual Cortex. Orientation selectivity is a remarkable property of neurons in the visual cortex that is supposed to provide the detection of local bars and edges in the processed visual images and encoding of their orientations.
http://www.ebi.ac.uk/proteome
Reviewed by Naveen Menezes
A nice article on Genome sequencing aimed to exploit the areas of research done on the Genome domain structure and function, gene duplication and protein families in different groups. The genome sequencing projects are providing a vast amount of sequence data, which remain largely unexploited. With access to whole genome sequences from various organisms and with the imminent completion of many more, the SWISS-PROT group at the European Bioinformatics Institute EBI) has developed the Proteome Analysis Database; a research oriented initiative in order to utilize all the existing resources and provide comparative analysis of the predicted protein coding sequences of all complete genomes. Research is also being done on preliminary proteome analysis for the human genome.
http://ncmir.ucsd.edu/NCDB/
Reviewed by Naveen Menezes
This is a very well written article, which represents the research being done in the field of neurobiology for modeling the molecular complexity of the nervous system. This project is a study of the techniques representation of what they call immunocytochemical data on the 3-D distribution of cellular constituents within models based on the structures based on the neuronal model. Macromolecules involved in inter-cellular and intra-cellular signaling such as ion channels and neurotransmitter receptors will be localized using light and electron microscopic immunocytochemistry. Basically what I understood from this article is that research is being done on the realistic morphological representations of the neurons and neuronal compartments in which these proteins will be obtained from intracellularly injected neurons. Higher resolution data will be obtained using high voltage electron microscopy combined with electron tomography
http://www.ai.univie.ac.at/oefai/nn/siesta/
Reviewed by Naveen Menezes
An interesting project on Polygraphic Sleep Recordings in the study of sleep
disorders. This project involves extensive research on sleep analysis
with the help of advanced methods like electroencephalography (EEG) based on
polygraphic
measurements. The project (SIESTA) aims at a computerized system for
analyzing Nocturnal Human Sleep, which would help in the research of sleep
disorders.
http://www-fp.mcs.anl.gov/~gaasterland/sg-review-slides.html
Reviewed By Peeyush Rathkanthiwar
This article briefly describes the outcome of the recent Workshop on Structural Genomics held at Argonne National Laboratory organized by Paul Bash, Andrzej Joachimiak, Andrei Mirzabekov, and Terry Gaasterland of Argonne National Laboratory and by Joel Berendzin and Tom Terwilliger of Los Alamos National Laboratory. Different sets has been discussed as follows: 1.The first set of images illustrates how methods from computational biology will facilitate structural genomics by helping to select targets (before), helping to solve and store structures (during), and helping to understand the resulting structures (after). 2.The second set of images show examples of protein domains, folds, biochemical surfaces, and whole predicted structures. The broad coverage of "structure space" in the context of genomic "sequence space" that can result from a high-throughput structure determination initiative will yield a rich field of data for computational biology. The main task of protein expression, purification and crystallization, data collection on high-flux synchrotron beams lines, and a computational analysis of the resulting data are clear and focus a potential impact on computational biology and bioinformatics.
http://opus.ncifcrf.gov/MAExplorer/
Reviewed By Peeyush Rathkanthiwar
This article describes a Java-based program 'MAExplorer' which is a bioinformatics
exploratory data-analysis and data-mining facility for analyzing sets of
quantitative cDNA microarray data. Initially this was designed for the analysis
of the array data from the mouse mammary tissue from Mammary Genome Anatomy
Project (MGAP), after that it was extended to work with other types of arrays
and cDNA labeling methods [LemP00]. These include 33P labeled membranes,
Cy3/Cy5 glass slides, non-geometric chip data, and other chip supports with
different geometries and numbers of duplicate spots/gene. This document
describes the MAExplorer's functionality, which also provides tutorials and
contains documentation for using it with other arrays. The three main
advantages of this program are as follows:
1) analyze expression of individual genes;
2) analyze expression of gene families and clusters;
3) compare expression patterns for multiple hybridization samples.
MAExplorer is written in Java and runs as a stand-alone Java application. There
are some bugs in this program right now. Some are explained below. This
standalone application can be run in limited web browsers and requires faster
computers with good memory since lot of computation is required. MAExplorer is
difficult to use with a system with a small screen because of the size and
number of multiple graphic images and plots.
http://www-scf.usc.edu/~pwkr/des.pdf
Reviewed by Yu Shi
This article introduces the method of molecular computation in attacking the United States Date Encryption Standards (DES). DES is one of the most widely used cryptographic systems. It produces a 64-bit ciphertext from a 64-bit plaintext under the control of a 56-bit key. The research team presents a description of the attack using sticker model of molecular computation. The attack uses approximately 2^56 identical ssDNA memory strands (each of them contains a key and the memory for the computation) and a sticker machine (a three-steps algorithm) to try all the possible keys. The result of the computation will be on the memory strands and by special procedures, the correct key is selected. The whole process may take 9 month. An analysis of error rate and possibility to pick up the correct key is also given. This is the first time of using DNA computing on practical problems.
http://bioinformer.ebi.ac.uk/newsletter/archives/5/gene_prediction.html
Reviewed by Peng Qu
This article discusses the standards to create clean data sets for Gene Prediction. It provides the steps and criteria involved for approaching high quality data sets and the computational gene prediction tools to annotation of sequenced DNA regions. Several graphs also illustrate the main points in this article, such as the decision tree for human acceptor sites. It is good for the researchers who work in gene prediction field and other advanced learners.
http://industry.ebi.ac.uk/~alan/Papers/ISMB97/ISMB97.html
Reviewed by Peng Qu
This article discusses the development of techniques that allow researchers to extract new and useful information from the continuing increase biological databases. It includes: 1) Widgets. 2) Information murals. 3) Semantic lenses and filters tools. A more interesting idea is to combine these techniques together. Thus semantic lenses and filters could be used on information murals. The information mural approach could be used within the hyperbolic projection viewer. By using these tools, we can see they are designed not to be dependent upon the semantic nature of the data. The information mural widget can be used to display the feature maps of long DNA sequences as well as to show average base composition. The applications have also included zoomable information murals that allow users to magnify and examine interesting regions in more details. This paper also uses interesting graphs to illustrate the results of these techniques.
http://www.cs.unm.edu/~immsec/
Reviewed by Yu Shi
Today's computer security research can learn from how natural immune systems
protect animals from dangerous pathogens. This article tries to build the
computer security system as much more sophisticated notions of identity and
protectin than current operation systems can supply. Four examples of their
work have been presented separately: a host based intrusion-detection method, a
network based intrusion-detection system, a distributable change-detection
algorithm, and a diversity to reduce vulnerability method. The important point
here is a computer security system should be able to act as the immune system
by identifying "self" and "nonself" and proceed to eliminate
the dangerous nonself. Noself might be malicious intrusions like unauthorized
user, foreign code as virus or even Trojan horse.
From the left "Papers" link, several papers are categorized by: The
Big Picture, Automated Response, Security Through Diversity, Intrusion Detection,
and Distributed Change Detection. All come with either Postscript or PDF format
or both. Among them, Immunology as information processing by S. Forrest
and S.A. Hofmeyr, is trying to give a brief and clear introduction for this
topic.
http://www.minimed.com/patientfam/pf_products_cgms_ov_completepic.shtml
Reviewed by Abdul Sikder
The Continuous Glucose Monitoring System (CGMS) by The MiniMed Inc. is a device, which continuously monitors a patient's glucose levels. It consists of a sensor, a monitor, and special CGMS software. A doctor inserts The CGMS sensor beneath the skin of a patient's abdomen and secures the monitor, which is connected to the sensor by a short wire, to the patient's body or clothing. The device then stores glucose measurements as often as every five minutes for a period up to three days in length. While wearing the device, the patient can use the monitor to mark the time of meals, exercise, and other events. After the monitoring period, the sensor is removed and the data is downloaded to a computer, which provides an overview of the patient's glucose levels throughout the period of use. Along with the periodic measurements, the CGMS software graph displays all marked events and their corresponding glucose levels. CGMS provides a wealth of continuous data that is not available in current testing methods such as the finger stick test.
http://www.diabetesnet.com/sit.html#Cygnus
Reviewed by Abdul Sikder
Cygnus Inc. of California developed a device the size and shape of a GlucoWatch, which is little bigger than a regular wristwatch. This device provides diabetics with information needed to manage their disease. The Food and Drug Administration (FDA) approved the GlocoWatch on March 22, 2001. This device is very convenient to use, and diabetics can wear it daily, just like a wristwatch. The GlucoWatch is projected to one day eliminate painful daily finger-pricking blood glucose tests. The GlucoWatch uses a consumable transdermal pad called an AutoSensor, which adheres to the skin and contains a biosensor, connected it. Fluids are extracted from the skin through the transmission of an extremely low electrical current. These fluids are drawn every 20 minutes for a 12-hour sleeping period to monitor glucose levels. The GlucoWatch sounds an alarm if the diabetic's glucose amount reaches dangerous levels. At this time, the Cygnus GlucoWatch is available through a prescription for diabetic adults aged 18 and older. The retail price for this device is around $250.00 to $300.00, and the 12-hour AutoSensor retails around $4.00.
http://wings.buffalo.edu/computing/publications/interface/vol-29/iss-1/html/art24.html
Reviewed by Abdul Sikder
Diabetes is a complex condition that can cause many other related illnesses. Diabetics need to pay special attention to their diets and their lifestyle in order to prevent further complications. Self-blood glucose monitoring (SBGM) is a simple device for blood test. You can use this portable device at home that indicates what a diabetic's glucose level is. This SBGM use sensor technology, it measure small electrical currents produced by the chemical interaction between the glucose in the blood and the chemicals on the test strip. This tiny computerized device that stores 250 tests into its memory, it takes 45 seconds to get a reading, and is programmable. This device can be connected to a computer to transfer data from the device to the computer; the collected data can then be print as reports in various forms. This recorded data is for both treatment and research activities.
http://www.darpa.mil/DARPATech2000/Speeches/MTOSpeeches/Lee.pdf
Reviewed by Aamir Babar
This site contains some interesting information about the objectives and application of Bio-fluidic chips program or Bioflips. This program is going on under the auspices of DARPA. The state of the art biochips primarily aimed at high throughput screening and combinatorial chemistry for drug discovery and other genomic applications. The bioflips program will target sample preparation of complex fluids on a chip scale .To achieve this, the briefly program will focus on a new micro fabrication platforms that integrate multiple fluidic components onto single chips. These components can be microstructures, micro pumps, micro valves, and various other micro sensors. Total chip-scale integration is the ultimate goal of this program. A second goal of the program is to develop active fluidic chips. This will be achieved by integrating fluidic transport components with in situ sensors that enable local feedback control in the micro channels. With active chips, reconfiguration and self-calibration of the sensing parameters will be made possible. This is very difficult with the passive Micro fluidic chips available today. For MEM-based sensors, the self-calibration was the reason it could compete and replace more conventional sensors. To conclude, Bioflips program will focus on the total integration of on-chip functionality. This program is truly at the intersection of the Biotechnology and micro technology.
http://www.bu.edu/bioinformatics/research/Computational/Collins.htm
Reviewed by Aamir Babar
This site describes the use of biomedical engineering. Research
is already in progress to construct and design a genetic applet. A genetic
applet is an artificial virus that once delivered into a cell would coordinate
the sequential expression of multiple genes. These genes could be used to
execute a series of specific tasks that would repair, enhance or modify cell
function. Genetic applet would be programmed into DNA and delivered into cell
as cellular software.
http://news.bbc.co.uk/hi/english/health/newsid_131000/131697.stm
Reviewed by Suchart C.
The British scientists had developed a computer program for robot doctor that can diagnose cancer. This program is a brain-like function, and uses the technique of magnetic resonance spectroscopy or MRS to scan the pattern of chemicals in tumors and calculate whether there's cancer. It has proven to be 80% accurate. The scientists predicted that there would be a high rate of success for the robot doctor and can make it even more accurate in the future.
http://www.stn2.com/articles/view.php3?language=english&type=article&article_id=218391176
Reviewed by Suchart C.
Scientists at Sandia National Laboratories of the US Department of Energy had developed a new technique called smart scalpel for detecting the presence of cancer cells, which are usually obscured, by blood and tissue. The device has a size of a dime, which is called biological microcavity laser, should help surgeons cut away malignant growths more accurately while trying to minimize the amount of tissue removed. It could also tell surgeons when to stop cutting as removing too much tissue can cause major damage. This device works by incorporating blood cells into the lasing process, analyzing individual cells back and forth through the tiny channels of the device. The speed of laser light changes if cancerous cells contain more protein than normal cells. Finally, algorithm translates data into a graph that provides surgeons to know when blood pumped from the incision has been cleared out of cancerous cells. This device is very useful for brain surgery.
http://www.jpost.com/Editions/2001/02/26/Health/Health.22023.html
Reviewed by Suchart C.
This article discusses about how aerodynamics could help whether a woman with fertility problems can become pregnant. The work was taken a look by Prof. David Elad of biomedical engineering department at Tel Aviv University and Dr. Ariel Yaffo and Dr. Osnat Eitan, gynecologists at Lis Hospital in Tel Aviv. They claim that a woman's uterus is like an airplane wing because the same mathematical and physics equations used to calculate air movements around the wing can also be applied for describing the movement of body fluids in the womb. Elad developed a computerized model of uterine contractions on movement of sperm and ova in fertile women based on his knowledge of liquid flow, frequencies, pressures, and speeds. The examination was taken between the 10th and 16th day of menstrual cycle. The new information about uterine-wall movement will have a better understanding of fertilization and also will improve the rate of the implantation of embryo.
http://www.unisci.com/stories/20003/0925002.htm
Reviewed by Suchart C.
Scientists at Purdue University led by Rashid Bashir, an assistant professor of electrical and computer engineering, have created the first protein biochips, in which a biological protein mated to a silicon computer chip, might be able to detect specific microbes, disease, and harmful chemicals quickly and cheaply. The procedure involves attaching two proteins to the chip by applying an overlay onto the chips first by using a process called photolithography, which helps defining the channels and metal surface regions on the chip. The proteins then attached by using the electrical charges naturally occurred in the proteins. The biochips are expected to get an approval form the Food and Drug Administration because it could be very useful for food production too.
http://www.technologyreview.com/magazine/mar00/chase.asp
Reviewed by Suchart C.
This article talks about a new technique that could help paralyzed people to move their limbs just by thinking about it. The invention, called Freehand, took more than a decade of experiment and developed by P. Hunter Peckham, a biomedical engineer at Case Western Reserve University. The strategy combines two technologies into a system, functional electrical stimulation (FES), in which electrodes are implanted under the skin are used to capture movement in the muscles of paralysis victims. And combined with a newer technology known as computer-brain interface (BCI), the Freehand could use the brain waves alone to move paralyzed parts. The Freehand's neuroprosthetic enables paralyzed people to open and close hands and to do a lot of things that normal people can do.
http://www.e4engineering.com/item.asp?ch=e4e_chem_process&type=News&id=34207
Reviewed by Suchart C.
Scientists at the Northwestern University Medical School led by Karen Fleming, are using the brain of a lamprey to control a robot's movement. Lamprey controls balance while swimming by using the nervous system called vestibular system. The vestibular system is a feedback circuit, which can detect drift and order muscles to compensate, and this feedback circuit is able to translate into robotic commands. In the process, lamprey's brain and spinal cord are cut off and connected with Khepera, which is a lab robot equipped with sensors and wheels. The mobile robot acts as an artificial body, which delivers sensory information to the brain through its light sensors, and is controlled by command signals generated by the brain itself. Signals then patched from sensors into brainstem of the lamprey and then directed nerve impulses from the spinal cord, which transmits signals from the brain to muscles, and to the robot's wheels. The lamprey brain learned to send signal by a light source, which controlled robot's motion. This research, supposedly, will help in the development of robotic prostheses for humans.
http://www.e4engineering.com/item.asp?ch=e4e_chem_process&type=News&id=29115
Reviewed by Suchart C.
A recent research shows that microfluidic network on a chip could sort, detect, and identify individual chemicals or proteins. Developed by Sandia National Laboratories of the Department of Energy, a new microchip processing technique that creates microscopic canals on chips which liquids or gases can flow from one chip feature to another. These canals are called microfluidic devices that make use of chemical and electrical properties of semiconductors on a single chip. Researchers made the canals by patterning a thin layer of photoresist on the wafer's surface by using conventional photo mask and light. Then develop areas away of the photoresist exposed to the light, leaving network of photoresist ridges on the wafer's surface that finally becomes canals' interiors. The wafer is heated to create square-edged a hemispherical shape. Using new-patented technique on silicon, glass, or quartz surfaces that are 8 to 100 microns in diameter creates hemispherical canals. The canals should be small enough that liquids or gases can pass through them easily. This technique could be used to detect air pollution; DNA analyzers for crime scenes, and for pharmaceutical companies, these devices could help find new ways for drug development.
http://news.bbc.co.uk/hi/english/health/newsid_307000/307919.stm
Reviewed by Suchart C.
This article discusses about new gene techniques uses to develop a treatment for the most common and dangerous type of brain cancer called glioma. The British scientists led by Dr. Saghir Akhtar at Aston University, Birmingham, developed the new technique called DNA chip technology. Dr. Akhtar pays attention on a cancer gene called c-erbBI that triggers the growth of cancer cells. By using this new technique, the mechanism can be targeted in which genetic instructions leading to the growth of cancer cells are read. The templates of molecules called RNA are only copies that sent out into the cells to be read. Dr. Akhtar is using an approach known as anti-sense for developing a means of destroying RNA copies of c-erbBI before their harmful instructions are read. Using chips of DNA, which closely mirror part of RNA structure, can do this. Cells will be damaged if not stick with the copies c-erbBI while leaving RNA. The computer examines the results once the chips are washed in the special solution. This latest technology has advantage that hundred of pieces of DNA can be tested to find out gene's instructions.
http://www.bio.com/os/htmlos/p.a.g.e/news/research/view_research.html/356.1.10540345469
Reviewed by Liang Cai
This article talks about the news that human fat can be transformed into
bone, muscle, and cartilage. Fat has been isolated as source of stem cells
used to grow a variety of human tissues in the laboratory. In the past, people
can only harvest stem cells from bone marrow, brain and fetal tissue, limited
sources that pose a variety of logistical and ethical challenges. The
availability of the plentiful source of stem cells will accelerate development
of new procedures for repairing and replacing damaged, dead or missing tissue
in people. With fat as a plentiful source of stem cells, researchers may be
able to accelerate the pace of overcoming obstacles that prevent broader
applications. These challenges include finding ways to supply blood to larger
tissues, control growth and maturation, and eliminate scarring.
http://unisci.com/stories/19993/0902995.htm
Reviewed by Danian Cao
The link describes the efforts of Xie George Xu, assistant professor of nuclear engineering and engineering physics at Rensselaer Polytechnic Institute, in his development of a 3-D virtual model of the effects of radiation on the human body; specifically the skin, lens of the eye, optic nerve, GI-tract, and bone marrow. This model, which he calls "Visible Photographic Man" (VIP-Man), is generated from CT scans, MRIs, and photos provided by the Visible Human Project form the National Library of Medicine. When developed into a computer simulation program for medical diagnosis, VIP-Man will be able to assess the level of tissue damage in relation to the dose of radiation administered. This is particularly beneficial for planning treatment for patients requiring radiation therapy. Xu's work will also benefit industries and government programs such as NASA that have an interest in radiation risk assessment.
http://unisci.com/stories/20011/0315013.htm
Reviewed by Danian Cao
The link tells about the work of a team of researchers at UC Santa Cruz under the direction of David Deamer, professor of chemistry and biochemistry, on analyzing single-stranded DNA molecules. Deamer's team utilized the toxin alpha-hemolysin ion channel, which is produced by Staphylococcus bacteria to create holes in a host animal's cells, as a sieve to isolate and identify single-stranded DNA. In the experimental setup, different DNA molecules passing through the channel will generate different electrical signatures, which can be recognized and collected by a computer program. The program is sensitive enough to tell apart two DNA molecules that differ by only one base. The technology may have important clinical applications in the future in being able to detect single nucleotide polymorphisms (SNPs), which may account for genetic differences between individuals. Before that, Deamer's team hopes to increase the sensitivity to the level of being able to distinguish individual DNA bases.
http://www.nytimes.com/2001/04/17/health/17NERV.html?searchpv=site01
Reviewed by Danian Cao
This article describes the effort of Dr. Douglas H. Smith; a neurosurgeon of University of Pennsylvania Medical School, in his development of a way of stretching nerves to bridge damaged spinal cords. He starts to grow human nerve cells and make mutual connections on two plastic slabs, when he slowly pulls the slabs apart, the connections between cells, which called axons, begin to stretch. He succeeds to create thick, half-inch-long bundles of healthy, living axons. Dr. Smith and his colleagues are trying to implant the axons into animals with severed spinal cords, with promising results. After birth, human's axons stop grow via chemical signals but from mechanical tension applied by the growing brain. Therefore, those approaches have not been very successful when people have tried to bridge injured spinal cords by using chemical signals that fool axons into growing the way they do in the embryonic brain. The stretching idea is a fundamentally novel and very elegant approach. Although there is no evidence that the method will work in human, it is regarded as promising. Smith's team hopes to implant those living axons into damaged or severed spinal cords, bridging the gap left by the injury and restoring two-way communication up and down the spine.
http://unisci.com/stories/19993/0813994.htm
Reviewed by Danian Cao
MSU University Professor Richard Lenski and his colleagues have created an artificial world inside a computer to mimic the evolution of life. The program, called Avida, made two kinds of digital organisms, which are cousins: simple and complex. The simple ones' only task is to reproduce, while the complex one not only reproduce but also perform mathematical calculations. Avida randomly adds mutations to the programs, thus spurring natural selection and evolution. The scientists then program changes in the environment to see how the bugs adapt. With the enormous advantage offered by digital organisms, scientists have been able to scrutinize more than a billion genotypes in a similar experiment run on Avida. The research is exciting since the approach demonstrates researchers to answer important biological questions can use that digital organism.
http://www.stanford.edu/dept/news/report/news/may2/living_cell.html
Reviewed By Dongyang Chen
The challenge of simulating a living cell is that reassembling millions of bits of experimental data into a cohesive model system. But alternative splicing and multifunctional proteins could inflate the effective number of components beyond the 35,000 genes that have been identified. And identifying interactions between the components is extremely complicated. So it's not clear whether the computational power exists to crunch the numbers of the billions of interactions that occur in a cell, and whether enough experimental data exists to support this goal.
http://purduenews.uns.purdue.edu/UNS/htmlarchive/html4ever/00Q3/0009.Peppas.micropatterns.html
Reviewed By Dongyang Chen
This article reported engineers in WEST LAFAYETTE, Inc have developed a
technique that might be used to make "biochips” for computer, a technology
aimed at making diagnostic devices to be implanted in the body or used to
quickly analyze food and laboratory samples. Unlike normal micro fabrication
used for etching electronic circuits, the technique used to fashion “micro
patterns" out of a material made primarily from a polymer, or plastic
called polyethylene glycol. “The patterns” smallest features were 5
micrometers, which makes them as small as some cells. Engineers at Purdue
University previously had announced that they had made the first protein
biochips, in which a protein mated to a silicon computer chip might be used to
detect chemicals, microbes and disease. To use this material can attach to
attach many other types of biological entities to “chips” that are capable of
quickly detecting a wider range of substances, either in the body or in
laboratory samples. Using this material, the glued biological materials on a
biochip's surface would precisely fit specific cells, molecules and strands of
DNA, enabling a lock-and-key sort of attachment. When a targeted substance
passed by the chip, it would become attached to the surface and the chip would
signal that the substance had been detected. In another hand, this material,
unlike many synthetic materials, is not attacked by the body's immune system.
It will be acceptable for implantation to human body.
http://www-dept.cs.ucl.ac.uk/research/genprog
Reviewed by Dongyang Chen
This site introduces the detailed description on the genetic programming
(actually we should call it Genetic Algorithm). The Genetic Algorithm is a
model of machine learning that derives its behavior from a metaphor of the
processes of evolution in nature. This is done by the creation within a machine
of a population of individuals represented by chromosomes, in essence a set of
character strings that are analogous to the base-4 chromosomes that we see in
our own DNA. In nature, the encoding for genetic information (genome) is
done in a way that admits sexual reproduction. At the molecular level what
occurs (wild oversimplification alert) is that a pair of chromosomes bump into
one another, exchange chunks of genetic information and drift apart. When
the genetic algorithm is implemented it is usually done in a manner that
involves the following cycle: Evaluate the fitness of all of the individuals in
the population. Create a new population by performing operations such as
crossover, fitness-proportionate reproduction and mutation on the individuals
whose fitness has just been measured. Discard the old population and iterate
using the new population. This site provides a working sample, which was
written in C++ to simulate evolution. This program will run on Linux and Unix
systems. From this site, we can found other information and developments about
Genetic Programming. This site is very suitable to students who study in
computer science and other people who are interested in Genetic Programming
field.
http://www.techfak.uni-bielefeld.de/bcd/ForAll/Introd/drugdesign.html
Reviewed by Lei Dong
In order to be effective, protein drugs (key) must have the ability to bind
(attach) specific molecules (Receptors, lock), which are located on/in cells.
After the drugs-receptors attachment, a chain reaction will be initiated, and
then either stimulatory or inhibitory functions will be delivered. Therefore,
the specificity of the drugs must be identified to limit all those other side
effects (accidentally open other "Locks"), and select more potent
drugs that bind to Receptor better. It has been very difficult to screen a
promising new Drug for the final clinical tests from usually tens of thousands
of compounds.
But now, with helping Powerful computers, it seems very straightforward. The
input of biocomputing in drug discovery is Twofold: firstly the by creating the
databases of the Pharmacological profile of excising drugs, computer may help
to guide the synthesis of new and "better" compounds. Secondly, as
more and more structural Information on possible protein targets and their
biochemical role in the cell becomes available, completely new therapeutic
concepts can be developed. The most techniques applied in using the computer
for Drug design is to analyze the interactions between the drug (key) and its
receptor site (lock) and to "Design" molecules that give an optimal
fit. The Techniques Provided by computational methods include computer Graphics
for visualization and the methodology of theoretical chemistry If the specific
receptor structure is already known, one can apply docking algorithms that
simulate the binding of drugs to the respective receptor site. One could create
a negative image of the target site first, and place the putative ligands into
the site, and finally they evaluate the quality of the fit. If we don't know
the structure of the receptor, the so called "homology modeling"
could be used. It basically uses information of existing molecules that have
similar sequences (backbones) to keep the general structure of the protein and
to evaluate the specific properties of the unknown protein with respect to
key-lock interaction. A prominent example is the design of potent HIV protease
inhibitors (Science, 263, 1994, 380).
http://recomb2000.
ims. u-tokyo. ac. jp/Posters/list-posters.html
Reviewed by Lei Dong
Bio-calculus: Its Concept, and an Application for Molecular Interaction There is a big gap between biology and computer science when they communicate to investigate biological phenomena. One of the problems is the difference between their expression systems. The expressions of biology clarify the components (e. g. gene, protein, and cells). Their transition and interaction are diagramed. Computer science expression systems have been proposed for expressing biological phenomena, but the transition and interaction of the components are far less visualized than in the diagramed expressions of biology. To bridge the gap between biology and computer science, the paper introduces bio-calculus. Bio-calculus fulfills the following four requirements: 1) the description of bio-calculus clarifies the components of biological systems. 2) The description diagrams transition and communication of the components. 3) The description includes information essential for simulation analysis. 4) The description possesses background of mathematics.
http://unisci.com/stories/20002/0605003.htm
Reviewed by Lei Dong
Physicians have been relying on their hands to do important diagnoses such as detecting subtle signs of disease or injury just by touching a patient. However, this is just about to change. Researchers at University at Buffalo are developing a system called physically based VR, which will provide physicians with a customized virtual-reality glove during the patient examination. This glove will collect data on what the physician is feeling through sensors located in the glove's fingertips and save them. Those data then will be accessible to the examining physician at a later time or to consulting physicians at another location. The VR system will enhance the current method of clinical palpation by transforming it from a qualitative to a quantitative examination. UB researchers are also trying to create a database of information that accurately describes the biotechnical properties of soft tissue under various conditions. Using a very powerful graphics computer, the researchers "supersample" smaller and smaller sections of the data set for a given body part or organ, enabling them to get more and more detailed pictures of each one and develop increasingly complex equations about how each tiny section will respond to applied forces. If a patient is injured, just by comparing the database information and what the physician is feeling, the surgeons will be able to go right into the operating room without having to obtain a CAT scan. UB's Virtual Human Model also could enhance the training of new physicians in one of the most formidable medical procedures they have to learn -- incubation.
http://www.unisci.com/stories/20004/1023004.htm
Reviewed by Lei Dong
As we know, it has been known for a long time that the way blood flows through vessels has a role in the process that causes heart attacks and stroke, known as arteriosclerosis. To predict accurately how blood flows is not simple. The geometry of the arterial system is complex, with branches and bends. In addition, the flow of blood is not steady, since a pulsating pump, the heart, drives it. In addition, the force of the blood, which in turn affects the flow inside the vessel, deforms the walls of arteries. The story told us excited researchers in the UK have developed news that a unique computer model of how blood flows in human arteries. The model could help doctors understand the stresses that blood places on the walls of vessels and provide new insights into vascular disease. Dr. Yun Xu together with Dr. Simon Thom and Professor Alan Hughes at Imperial College London carried out this work. To construct the mode, the researchers used information obtained from patients attending a clinic at St. Mary's Hospital in London, where their blood flow was monitored by ultrasound and images of their blood vellums were taken by magnetic resonance scans. The ultrasound data can tell you about bulk flow rate, but not about the complex flow patterns within the vessel. Ultrasound also shows how the diameter of the blood vessel changes during the cardiac cycle, giving a measure of the elastic properties of the vessel wall. The MR. scans provide information about the three dimensional geometry of the vessels. The researchers built a computer model that could take account of the complex interaction between the blood and the elastic wall of the vessel. They did this by linking together two standard computer programs. One is a computational fluid dynamics program widely used in industry. It can predict factors such as the three-dimensional pattern of flow and the rate of "shear stress" at a given point. But it doesn't predict the movement of the wall of the vessel. The second program deals with this aspect. It is a "solid mechanics" program that can deliver information about how a solid surface will deform depending on its "dynamic loading" -the changing forces it experiences. One of the innovative aspects of this research was to link these two programs together; using data from the scans we can reconstruct a 3D image of the vessel on the computer. We then feed in the information about the pressure, the elasticity of the walls, the flow rate and so on. The computer models the effect of the pulsating flow on the vessel wall. Information about the new shape of the wall is fed back to the fluid part of the program, which modifies its predictions about the flow according to the new geometry of the vessel. In this way, information between the two parts of the model-the solid mechanics aspect and the fluid mechanics aspect-is updated and exchanged until there is agreement between the two. Using data from the clinic we should be able to provide reliable predictions about the stresses on the vessel awl at a given point. Once the program has been refined and validated it might be possible to correlate these with the patient's pathology.
http://www.darpa.mil/MTO/bioflips/presentations/2001-1/index.html?1
Reviewed by Ming Feng
This is the DARPA Bioflips program. The goal is to demonstrate technologies for integrated biofluidic microprocessors capable of on-chip reconfiguration and self-calibration via feedback control. The applications are high-throughput screening and combinatorial chemistry for drug discovery and pharmacogenomics. These biochips focus mainly on the back-end analytical processes and require extensive front-end sample preparation. The BioFlips projects are organized into four categories according to their deliverables: (1) total integrated BioFlips, (2) on-chip transport/control of biofluids, (3) integrated on-chip detection on plastic substrates, and (4) novel integration-enabling component and subsystem technologies. These projects are aimed at developing platforms to tackle critical technical barriers of total integration. The BioFlips program provides the technological foundation to directly assess the vitality of defense personnel, both individually and collectively. BioFlips technology can be extended to improve national healthcare by the unobtrusive and continuous monitoring of high-risk patients.
http://news.uns.purdue.edu/html4ever/0007.Ladisch.biochips.html
Reviewed by Ming Feng
Professor Michael Ladish, Rashid Bashir, and their groups at Purdue
University have created the first protein "biochips," mating silicon computer
chips with biological proteins. Chips containing thousands of proteins could be
organized into a device about the size of a handheld computer that could
quickly and cheaply detect specific microbes, disease cells and harmful or
therapeutic chemicals. If the first real-world tests of the biochips are
successful, the protein-encrusted silicon chips could appear in dozens of
applications in a few years.
Although biochips containing DNA already are used to automate the sequencing of
genes, many scientists have been interested in mating proteins with computer
chips because proteins are very specific about which other proteins or
biochemicals they will interact with. They believe they will be able to detect
specific microbes, disease cells and harmful or therapeutic chemicals quickly
and cheaply.
Their research successfully attached the protein avidin to the chip. A key
element of this research was verifying that the chips actually held the
proteins. They used advanced microscopic techniques to detect interactions at
the surface of these chips and verify the attachment of the proteins.
Researchers from several schools and disciplines at Purdue played key roles in
the development of the biochip.
http://www.rpi.edu/web/Campus.News/oct00/oct_16/home.html#2
Reviewed by Wenguang Han
This article talks about a new technology that will diagnose lung disease
using signal processing. This is developed by Michael Savic, professor of
electrical, computer, and systems engineering, and his graduate student, Thrasos
Axiotis in Rensselaer Polytechnic Institute.
Researchers have programmed software to use features of lung sounds to identify
lung diseases, such as pneumonia, asthma, and bronchitis. Lung sounds come from
a professionally made database, which have about 50 lung diseases sounds. Lung
sounds are transformed into electronic signals and brought into a computer.
Then computer analyzes the signal and determines if the lungs are healthy or not.
If the lungs are not healthy, a graphical display on the computer screen
indicates the nature of the disease with a specific color, called a cluster.
There are presently a few clusters that overlap, indicating that those diseases
share some of the same features.
http://www.sciam.com/1998/1298issue/1298wilmut.html
Reviewed by Ruiwen Jiang
This article describes the biologists how to clone the Lamb Dolly in Rosli Institute in Scotland, which is the famous institute on cloning; it describes the cloning method – Nuclear Transfer in detail. It also describes how to clone with a difference from cultured cells, and the biologists used genetic modified technique to produce a transgenic sheep – Polly who contains the gene for human factor IX, a blood – clotting protein used to treat hemophilia B. This is the revolution in biology and medicine that can produce the generation of genetically modified animal organs that are suitable for transplantation into human, produce the disease – free such as prion – free animals, produce animals with a precisely engineered genetic constitution could be employed more directly in cell – based therapies for important illnesses. This article also describes how to make human stem cells and provides some related links and further reading references.
http://unisci.com/stories/20003/0821001.htm
Reviewed by Ruiwen Jiang
The researchers at Rensselaer Polytechnic Institute has developed a robotic
system - RPI SHE Machine that rapidly scans cell cultures to detect if
potential new products could be harmful, linked to cancer and other diseases
and is faster than animal testing (days instead of months), requires far fewer
animals, and correlates strongly with animal tests. The system performs
automatic scoring of the SHE (Syrian Hamster Embryo) Cell Transformation Assay.
In this procedure, cells of a hamster embryo are exposed to the substance and
cultured in 250 petri dishes. The petri dishes are attached to each of 21 trays
in an elevator mechanism. An automatic feeder brings one tray at a time to a
scanning mechanism, and a motion stage follows a computer-controlled pattern
that places each dish under the scanner. A computer algorithm analyzes the
images and uses objective standards to classify and label colonies as normal or
abnormal.
http://unisci.com/stories/20004/1117001.htm
Reviewed by Ruiwen Jiang
The ABI (Adaptive Brain Interfaces) project of European Commission's Joint Research Center (JRC) has developed a portable brain-computer interface based on the analysis of electroencephalogram (EEG) signals. A cap with a few integrated electrodes acquires brain signals that are pre-processed and sent to a notebook for further analysis, biofeedback and completion of the task required. The portable brain interface has an embedded neural network classifier that recognizes what mental task the wearer is concentrating on. It analyzes continuous variations of EEG rhythms over several cortical areas of the brain.
Each mental task is associated with a simple command such as "select right item." This enables people to communicate using their brain activity, as the interface only requires users to be conscious of their thoughts and to concentrate sufficiently on the mental expression of the commands required to carry out the desired task. By composing command sequences (thoughts), the user can read a web page, interact with games, turn on appliances, or even guide a wheelchair. For example, the interface can be used to select letters from a virtual keyboard on a computer screen and write a message. As the user concentrates on different mental tasks, the keyboard is successively split in smaller parts until a letter is selected.
An individual brain interface will be much helpful when it is adapted to its owner since no two people are identical, either physically or psychologically. The approach is based on a mutual learning process in which the user and the ABI interface are coupled together and adapt to each other. The neural network learns user-specific EEG patterns that describe the mental tasks desired, while the user learns to think in a manner that enables the personal interface to better understand them. Every single user chooses his/her most natural mental tasks to concentrate on (e.g. arithmetic, preparation of movements) and also the preferred strategies to undertake those tasks. Also, since the user and his/her personal ABI learn simultaneously from each other, people with no previous experience with brain interfaces can master use of the system quite rapidly. This application of ABI can help physically disabled or impaired people by increasing their independence and facilitating access to the Information Society, anyone can use it for a myriad of purposes, e.g. health and safety concerns (e.g. monitoring a person's level of alertness).
http://unisci.com/stories/19993/0813994.htm
Reviewed by Ruiwen Jiang
Scientists at Michigan State University, Caltech and UCLA have created an artificial world of living organisms inside a computer. They go forth and multiply, they mutate, and they adapt by natural selection. Studying these digital organisms offers a chance to test generalizations about how life has evolved. The program, called Avida, is basically an artificial petri dish. Two kinds of digital organisms are created: simple and complex, the simple ones' only task is to reproduce, the complex not only reproduces but also perform mathematical calculations. Avida randomly adds mutations to the programs, thus spurring natural selection and evolution. The team programs changes in the environment to see how the bugs adapt. The digital organisms offer an enormous advantage over the speedy evolution; the team has been able to scrutinize more than a billion genotypes.
http://trc.telemed.org/telemedicine/primer.asp
Reviewed by Ying Jiang
Telemedicine has been defined as the use of telecommunications to provide medical information and services. It may be as simple as two health professionals discussing a case over the telephone, or as sophisticated as using satellite technology to broadcast a consultation between providers at facilities in two countries, using video conferencing equipment. There are two different kinds of technology: first, called store and forward, is used for transferring digital images from one location to another. A digital image is taken using a digital camera, ('stored') and then sent ('forwarded') to another location. This is typically used for non-emergent situations, when a diagnosis or consultation may be made in the next 24 - 48 hours and sent back. The image may be transferred within a building, between two buildings in the same city, or from one location to another anywhere in the world. Teleradiology, the sending of x-rays, CT scans, or MRIs (store-and-forward images) is the most common application of telemedicine in use today. Telepathology is another common use of this technology. Images of pathology slides may be sent from one location to another for diagnostic consultation. Dermatology is also a natural for store and forward technology, (although practitioners are increasingly using interactive technology for dermatological exams). Digital images may be taken of skin conditions, and sent to a dermatologist for diagnosis. The other widely used technology, two-way interactive television (IATV), is used when a 'face-to-face' consultation is necessary. It is usually between the patient, their provider and a specialist, but may be any combination of the three. Video conferencing equipment at both locations allows a 'real-time' consultation to take place. The technology has decreased in price and complexity over the past five years, and many programs now use desktop video conferencing systems. There are many configurations of an interactive consultation, but most typically it is from an urban-to-rural location.
http://news.lycos.com/headlines/Science/article.asp?docid=RTSCIENCE-CANCER-FLUORESCENT-DC&date=20010314
Reviewed by Peng Qu
This article introduces a new technology that tracks and illuminates breast cancerous cells. The method relies on a substance called tricarbo-cyanine, which is often used for testing liver function. The tricarbo-cyanine is administered into the bloodstream and accumulates in the breast tissue. It is imaged by sending very short pulses of red light through tumors inside the breast tissue. A sensitive optical sensor will capture the signal and produce the breast tissue image. This method has the ability to detect very small cancers at early cancer stage.
http://bioinformatics.oupjournals.org/cgi/screenpdf/16/5/451.pdf
Reviewed by Peng Qu
This paper presents a method for sequence clustering and domain detection. It detects homologous groups of proteins by comparing every sequence in the database. Clusters are built by associating each protein sequence with a list of detected neighboring sequences. Once multi-domain proteins are detected, clusters can be broken into separate ones. Clusters that contain two separate families are split into their constituent families. Hence Multi-domain proteins can be members of more than one cluster. After separation, all clustering information (including multi-domain information) will be represented in a cluster table.
http://www.the-scientist.com/yr2001/mar/hollon_p1_010305.html
Reviewed by Peng Qu
This article introduces a web-based software to assist the treatment of HIV. It combines BioInformatics with artificial intelligence to evaluate HIV drugs. The software will trace and compare the patients' responses. Based on the feedback information, it can look at all the possible ways of treating a patient and conduct a comprehensive genotype analysis. This process may create a better way to cure HIV.
http://www.the-scientist.com/yr2000/jul/russo_p8_000724.htmly
Reviewed by Peng Qu
This article talks about the potential to multiple interpret the humane genome. Automatic annotation uses computers to sift through the huge amount of Human Genome Project sequence information and predict biological features. Investigators also rely on manual annotation. Annotation projects could present geneticists with significantly different genome schematics. It is difficult to filter out the gnomic noise and find the meaningful bits of the human genome figures. We need find a way to avoid multiple interpret to the same genomes.
http://bioinformatics.oupjournals.org/cgi/screenpdf/16/5/484.pdf
Reviewed by Peng Qu
This paper introduces the Viral Genome DataBase (VGDB) at the University of Victoria, Canada. The VGDB contains detailed information of the genes. It predicts protein sequences from 15 completely sequenced genomes of large viruses. Results of queries can be easily sorted by any of the individual parameters. This paper also tells us how to use VGDB query to request information. VGDB is a useful tool for researchers. It can save significant amounts of time in the analysis of genomes.
http://www.sciencemag.org/cgi/content/full/291/5507/1260
Reviewed by Peng Qu
This article talks about how to integrate computer science with molecular
biology applications. Genomic research has generated massive quantities of
data. This article identifies two major challenges to the advancement of
bioinformatics research:
(1) how to define permissible use of data released to the community before
publication. In order to recognize the value of early data release, the
solution is to adopt a policy of prepublication data release. Many genome
projects will adhere to similar rules. (2) Restrictions on the further analysis
and reposting of published data available on proprietary Web sites. This second
challenge derives not from restrictions on data access but from restrictions on
downstream use, such as incorporation into new or existing databases. To solve
this challenge, we should consider carefully what precedent to establish for
the near future, as considerations of data-release and data-use policy are
likely to have far-reaching implications for all of biomedical research.
http://unisci.com/stories/20004/1011005.htm
Reviewed by Peng Qu
This article talks about how to use secure medical website to improve medical data interchange. Security advances such as data encryption and computer certification make it safe to use the vast Internet resources. Dr. Wesley Marshall, clinical instructor of internal medicine, and Dr. Robert Haley, chief of epidemiology at UT Southwestern, outline how physicians could gather research data more quickly, efficiently and easily by using a secure website. The data collection through the Internet must be continuously monitored, information must be encrypted and communication between server and client computers carefully controlled. Entering data into a secure Internet site allows researchers anywhere to use data through identical computer screens. The cost for such a website is less than older methods.
http://www.darpa.mil/dso/thrust/bwd/advdiag/programs/ambri.html
or http://www.ambri.com/
Reviewed by Peng Qu
This link introduces Biosensor Technology from the Australian Membrane and Biotechnology Research Institute (AMBRI). The AMBRI biosensor emulates natural sensory systems to achieve high sensitivity with rapid response times. It is a synthetic lipid bilayer membrane containing ion channels which can be switched on and off in response to the presence of an analyte. The key elements of biosensor are: (1) membrane-forming molecules chemically tethered to a surface. (2) Simple ion channels within the membrane that facilitate the transport of ions like sodium. (3)a reservoir space between the surface and the membrane to store ions. (4) Receptors attached to the membrane to recognize target molecules. Biosensor is very useful in both medical and non-medical applications. In medical field, it can be used in Near Patient Testing or in the traditional critical care environments of surgery, emergency or intensive care. In non-medical field, it can be used in the testing of food contamination, individual components of wines and drinks, veterinary diagnostics, etc.
http://www.artificialbrains.com/neuroscience/pottergroup.html
Reviewed by Peeyush Rathkanthiwar
This article is about the neural cell culture, which has been developed by Dr Steve Potter, at the California Institute of Technology. This consists of technologies for the electrical linking of neurons in a petri dish to a computer. The computer is able to electrically stimulate the cells and to record their responses. The basic idea of potter's work is to culture dishes fitted with an array of microelectrodes. At the top of these electrodes thin layer of hundreds, or thousands, of dissociated neurons are grown. By analyzing the reactions of cells to specific stimuli, Potter is trying to understand the language used in neural communication. Also, by studying morphological changes in the neurons they understand how these are related to learning and memory.
http://www.mrcas.ri.cmu.edu/projects/overlay.html
Reviewed by Peeyush Rathkanthiwar
This article talks about the application of robotic and computer technologies within medicine. The important topic here is Image overlay, which is a visualization method, combines 3D computer generated images with the user's view of the real world. Image overlay systems are useful in at least two distinct medical applications: enhancement of surgical environments and telemedicine. Image overlay is being widely used in neurosurgery, orthopedics, microsurgery, obstetrics, plastic surgery and other specialties. In these applications, the physician can view medical images or computer-generated graphics overlaid on and registered with the patient. Telemedicine is the application of Image overlay in which physician can experience what is occurring at a remote site.
http://www.darpa.mil/mto/simbiosys/
Reviewed By Peeyush Rathkanthiwar
This article by the DARPA program manager Dr. Anantha Krishnan describes about the Simulation of Bio-Molecular Microsystems. Broad vision of DARPA is the use of integrated microsystems for the sensing and detection of chemical/biological agents requires that these sensors be designed with a good understanding of the interface between the biology and the engineering in these systems. This Simulation of Bio-Molecular Microsystems program will focus on the development of advanced computational design tools that enable the efficient integration of bio-molecular phenomena with electronic, MEMS and photonic technologies. Simbiosys program will develop data, models and algorithms that can be used for the following purposes: Analysis of 1.Molecular recognition processes, 2. Transduction of molecular recognition signals into measurable optical, electrical and mechanical signals, and 3.On-chip fluidic/molecular transport phenomena. To conclude Simbiosys will produce advanced computer aided design (CAD) tools for routine analysis and design of integrated bio-molecular microsystems.
http://www.esc.auckland.ac.nz/Groups/Bioengineering/Movies/
Reviewed by Abdul Sikder
This link was taken from University of Auckland department of Engineering
science. In this link you will find a collection of Bioengineering animations.
In the middle of the page you will find Heart surgery robot movie. In this case
little robot is fixed in the heart, it moves with the heart. So surgeon can see
fixed image for an operating section without any interruption. Using robot
surgery and bypass surgery is possible without stopping the
heart.
http://cbsnews.com/now/story/0,1597,239748-412,00.shtml
Reviewed by Abdul Sikder
Genetically engineered plants will work as vaccines in the future. By gene splicing viruses and genetically altering fruit, plants may produce characteristics that provide medical benefits. There are many benefits of using engineered plants to cure common ailments. For example, diarrhea is a disease that kills 2.5 million people in a year. In the near future, children may not need to rely on shots to prevent and treat this illness, which may be costly and unavailable to certain groups in the population. Instead, the food they eat every day, such as tomatoes or bananas, which have been enhanced by biotechnology, may prevent frequent onset of this condition, providing an efficient way to resolve a potentially massive problem. Golden rice is another example. This biotech invention of Switzerland is full of vitamin A, and can be used to cure vitamin A deficiency in millions of people.
http://www.napa.ufl.edu/2001news/facial.htm
Reviewed by: Abdul Sikder
Didem Gökçay of University of Florida doctoral candidate in computer and information sciences wrote the facial analysis software program CHEES (for Computerized Human Expression Evaluation System). University of Florida researchers turned to computer technology to quantify gender differences in one component of emotional expression and how the face reveals it. They discovered that although men and women are equally expressive, men display most of their joy, disgust or other sentiments in the lower left quadrant of their face. Women, on the other hand, show their emotions across their entire countenance. The computer program sums up differences in gray-scale intensity of the pixels that constitute each frame. The resulting scores showed that men and women moved their faces a similar amount to reveal an emotion. But when facial regions broke down the scores, it became clear that men's expressions were asymmetrical, with the bulk of the movement confined to the lower left quadrant. The University of Florida developed computer methodology for "digitizing the moving face" holds potential for assessing pain in patients who cannot speak. It also could be refined to enable computers to recognize and respond to human emotions.
http://unisci.com/stories/20012/0412016.htm
Reviewed by Abdul Sikder
Badri Roysam and Chuck Stewart of Researchers at Rensselaer Polytechnic Institute are developing a preliminary design for a laser surgery instrument that uses computer vision technology. The new system developed at Rensselaer will allow surgeons to work from a three-dimensional image of the retina rather than a flat surface representation, and will precisely pinpoint locations on the image in real time. Their research could benefit the nearly 20 million individuals in the U.S. alone who suffer from age-related macular degeneration, diabetic. They hope to have a prototype in the next two years.
http://www.darpa.mil/DARPATech2000/Speeches/ITOSpeeches/ITOSensIT(Kumar).doc
Reviewed by: Abdul Sikder
Above Sensor Information Technology link was presented by Sri Kumar of ITO office of DARPA. Networked micro sensors technology, is a key technology for the future. ITO of DARPA is developing micro-sensor hardware a new networking techniques. Cheap, smart devices with multiple on-board sensors, networked through wireless links and the Internet, deployable in large numbers, provide unprecedented opportunities for instrument and controlling to our advantage homes, cities, the environment, and indeed, the battlefield. There are two major goals for those sensor devices or nodes that should be ready for rapid deployment, in an ad-hoc fashion, and in highly dynamic environments. Second one is information processing-how to extract useful, reliable, and timely information from the deployed sensor network.
http://www.sandia.gov/media/NewsRel/NR2000/canals.htm
Reviewed by Min Wang
This article is about a technique for processing microchips that constructs
microscopic canals on the chips. Scientists at the Department of Energy’s
Sandia National Laboratories developed the technique, and the resulting canals
allow liquids and gases to flow freely from one feature of a chip to another.
Canals of this type are compatible with microfluidic devices that utilize the
chemical properties of gases and liquids as well as the electrical properties
of semiconductors. Such devices could contribute to the improvement of
informatics in the future: for better detection of air and water pollutants;
for the processing of DNA in forensic crime work; for the study of proteins to
further both biomedical research on toxins and diseases and the development of
pharmaceutical drugs.
The canals created by the Sandia researchers are raised, hemispherical, and 8
to 10 microns in diameter. The chip surfaces are made of silicon, glass and
quartz. The researchers begin the manufacturing process by coating the surface
of a wafer with a thin layer of photoresist, using a photo mask and light.
Then, areas of the photoresist exposed to the light are developed, creating a
network of ridges, which will become the interiors of the canals. The next step
in the process is to heat the wafer to 100 degrees C for approximately 20
seconds, which results in the ridges assuming a hemispheric shape. The final
step is to deposit a thin film of silicon oxynitride over the photoresist on
the ridges and to soak the wafer in acetone. This dissolves the photoresist and
leaves hollow tunnels, which become the canals. The Sandia technique for
creating canals is much faster than the traditional "trench and seal"
method, which required intense heat of up to 1,000 degrees C. With the new
technique, the canals are nearly indestructible.
http://www.ahsc.arizona.edu/bmeidp/News/Desert_Leaf.htm
Reviewed by Peilin Zhang
"From head to toe, inside and out, bioengineering is already changing patient's lives,” says Dr. Williams, director of the Division of Biomedical Engineering and chairman of the new Graduate Interdisciplinary Program in Biomedical Engineering. His introduction of some areas of bioengineering is very interesting to me. I feel very excited when I read this article, cause this give me hope to have human being a better life. He talked about the most exciting biomedical research projects involve getting the body itself to grow spare parts. For example, in the next few decades, it is being able to take tissue from a patient and grow a brand-new heart, outside of the body, that can be implanted to replace the failing heart. As we know, many patients die on the way waiting their donative heart. Another aspect of bioengineering is to take materials that were not intended to reside in the body, modify those materials and trick the body in accepting them. For example, people undergoing surgical procedures often require the insertion of catheters, some for many weeks. One of the biggest problems with indwelling catheters is infection; another problem with surgically implanted devices up to now has been fibrosis. And more discuss about the material for implanted in people such as artificial joints, production of artificial bone. Dr. William focuses on improving this material by engineering.
http://www.vr.clemson.edu/vr/bioe/bioe.html
Reviewed by Peilin Zhang
Just like we need a draft before we write our journal, it will be a nice
thing if a "virtual" surgery can be performed before any type of
physical surgery takes place. And now, we can do this. This article introduced a
pre-operative planning using virtual reality that allows the doctor and surgeons
to not only visually see the patient’s data in three dimensions, it also allows
them to visually manipulate the data. This planning actually involves 3 steps.
First the doctor need obtain patient's CT slice files for the bone data they
want, then they reconstruct these data to get a three dimensional representation
of the original slice data, after that, the surgeon uses a head mounted display
and a data glove to view and manipulate the patients reconstructed data. If you
have time, the link also provide an animation of a virtual bone fracture, you
can dig a little deeper.
http://www.unisci.com/stories/20003/0804004.htm
Reviewed by Lei Dong
This article talk about the news that scientists challenged to predict disease from Database sponsored by the National Center for Research Resources at the National Institutes of Health, Principal investigator Aryl Gold Berger, M.D., Director of the Margaret and H.A. Rey Laboratory and his colleagues have Established a new website to store, analyze, discuss and understand data of Hidden clinical information in heartbeats, brain waves and other Physiological signals. The PhysioNet offers a large and growing archive of data form anonymous Patients who may have life-threatening arrhythmia's, congestive heart failure, Sleep apnea, neurological disorders and aging-related conditions. PhysioNet can do for biomedical research what Greenback's public gene sequence database has done for deciphering the human genome. PhysioNet evolved from collaborations between Gold Berger and his colleagues at Boston University. The website, which is free, recently helped an intrepid Canadian high school student win a national science fair with his analysis Of heart rate variability. PhysioNet is demonstrating its potential to accelerate clinical research by Challenging physicists, mathematicians and bioengineers to predict sleep Apnea (intermittent cessation of breathing) in people using only a database of electrocardiograms.
http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v409/n6822/full/409824a0_fs.html
Reviewed by Peng Qu
This article provides us an overview of different sources about the human genome. The modern information technology, in particular the Internet, can allow us to link these sources together. This paper talks about the methods to investigate the human genome. Genes can be found through an implied relationship to other genes in another species. Genes can also be searched through their position. Another way to find a gene is by looking for paralogues-family members derived by gene duplication. The draft gene sequence provides us with the first comprehensive integration of diverse genomic resources.
http://www.oncolink.upenn.edu/pdq_html/4/engl/400325.html
Reviewed by Min Wang
This article covers a study by a group of scientists who used DNA microarray
technology to show that the type of cancer known as large B-cell lymphoma is in
fact two distinct diseases. In DNA microarray technology, scientists use
small glass slides on which they assemble tiny quantities of genes in a grid
pattern. Tissue samples can then be placed on these genes. As the
tissues and genes interact, scientists record the way the genes express
themselves. Louis Staudt of the National Cancer Institute (NCI), one of the
lead scientists in this study, said that the study's findings explained why
only about 40% of lymphoma patients can be cured with standard chemotherapy --
the remaining 60% appear to have a different strain of lymphoma.
Staudt and his colleagues first took data from the NCI Tumor Gene Index
Database, which is a catalog of genes expressed in normal and cancerous
cells. The scientists arrayed some 15,000 of these genes, along with
about 3,000 other genes associated with various cancers, on a penny-sized glass-slide
chip called a "lymphochip." Using fluorescent dye, they
collected and tagged gene transcripts to determine which of the arrayed genes
were active in normal cells or cancerous B-cells. The color and intensity
of the fluorescent glow on the individual genes revealed this information.
The researchers were focusing on the genetic makeup of diffuse large B-cell
lymphoma (DLBCL). As their study proceeded, they observed that the genes
in their DLBCL samples showed distinct differences in expression. This
suggested to them that more than one cancer might be present. Further
analyses confirmed that the arrayed genes belonged to two biologically separate
forms of DLBCL.
This study demonstrated that DNA microtechnology is vital to both research and
medical practice in that it has the potential for identifying previously
unknown diseases, in addition to making possible less invasive biopsies.
Moreover, it provides hope that the medical community will be able to design better-targeted
treatments for lymphatic cancer patients, according to the type of lymphoma
they have. This is a fascinating article, ideal for readers with an
interest in biotechnology.
http://www.nhgri.nih.gov/NEWS/media.htm
Reviewed by Min Wang
A study of the genetic makeup of melanoma -- a type of skin cancer -- is the
topic of this informative article. Conducted by scientists from the National
Human Genome Research Institute (NHGRI) and the National Institutes of Health
(NIH), this study used a technology for genetic analysis known as gene
expression profiling to detect a genetic signature in a sample of genes from
tumor tissue. This allowed the scientists to distinguish among different forms
of melanoma, which could lead to more accurate diagnosis and treatment of this
disease.
The researchers used small glass slides called DNA microarrays (gene chips),
which were dotted with minute amounts of thousands of known genes. When samples
of cancer tissue were placed on the microarrays, the gene chips detected which
of the known genes were expressed, or turned on. Computers equipped with
statistical software to locate patterns in gene expression from the tumor
samples then analyzed the data from the gene chips.
The NHGRI / NIH study analyzed about 7000 different genes from 40 patients. The
scientists found that nineteen cancers were similar in gene expression,
differing significantly from the other tumors. The patients' histories showed
that these tumors were less aggressive than most cases of melanoma. The
findings from this study could enable doctors in the future to tailor
treatments for their patients according to the type of melanoma they have, as
revealed by gene expression profiling.
Scientifically oriented readers should enjoy this clearly written article.
http://www.bio.com/os/htmlos/p.a.g.e/news/research/view_research.html/4024.2.5448771629
Reviewed by Min Wang
This article is concerned with protein microarrays, which were developed and tested by Stuart Schreiber and Gavin MacBeath at Harvard University. The two researchers used computerized robots and standard laboratory equipment to produce their protein microarrays - also called "protein chips." These were similar to the DNA microarrays ("gene chips") that have been featured in medical news publications recently. Their goal in developing this technique was to profile the variety of proteins and enzymes in cells. Schreiber and MacBeath started with a common glass microscope slide, onto which they deposited over 10,000 dots of protein. They used a contact-printing robot, which placed 1,600 protein samples per square centimeter on the slide, thus forming a microarray (a chip). To ensure that the samples adhered to the slide, the scientists coated the surface with an aldehyde-based reagent, which attaches to primary amines -- chemicals common to proteins. To study the functionality of proteins, Schreiber and MacBeath devised three types of experiments. In the first one, they placed proteins with fluorescent labels on the microarrays to detect protein-protein interactions. The second experiment involved treating the protein chips with radiolabeled kinase substrates and developing them in a photographic emulsion. The researchers could then detect the radiolabels as spots on the microarrays, which showed the interactions between enzymes and their substrates. In the third experiment, they revealed molecule-protein interactions by creating arrays of small molecules. When these were treated with proteins coated with fluorescent material, spots developed on the arrays, which demonstrated that there was normal binding. The article shows an interesting example of how computer robotics can be applied to medical research.
http://www.bio.com/os/htmlos/p.a.g.e/news/research_body.html/2949.5.3789989928
Reviewed by Min Wang
This article is about the application of DNA microarray technology to research being done on multiple sclerosis (MS), and a technique for interpreting the huge amount of data resulting from this research. Aidong Zhang and Murali Ramanathan, professors at the University of Buffalo, were the lead researchers of this multidisciplinary study, which could lead to improved treatments for people with MS.
For their study Zhang and Ramanathan used DNA microarrays, which are glass laboratory slides dotted with thousands of gene samples arranged in a grid pattern. When they applied blood samples from MS patients to the microarrays, they were able to measure how gene expression was affected by the disease itself and by the drug used for treatment - interferon-B. The two scientists realized that, of the thousands of genes being profiled, only a small number of them would yield useful information. Therefore, they turned to computer scientists to perform an operation known as data mining.
In data mining, previously unknown
information is extracted from large databases and is used to make important
decisions. Cluster analysis was one of the techniques used by Zhang and
Ramanathan to interpret the data they extracted. This technique involved
devising a clustering algorithm to group the patients in their study as either
control (untreated) patients or those being treated with interferon-B.
The clustering algorithm was made possible by converting the data obtained from
a gene expression profile into a model that revealed a pattern. This article
illustrates an example of an effective partnership between computer science,
pharmaceutical science, and medicine.
http://www.cellsalive.com/
Reviewed by Aamir Babar
This site describes the electronic enhancement of the images. Even poorly lit image with very low contrast can be drastically enhanced by adjustments in the video brightness and contrast. Some video cameras used for research also have the capability of stepwise adjustment of sharpen filter in programs like Photoshop. The site also contains some images that have been enhanced after image enhancement techniques.
http://www.findarticles.com/cf_0/m1272/2661_128/62685275/p1/article.jhtml?term=biomedical+engineering
Reviewed by Suchart C.
Dobelle Eye is new equipment invented for artificial vision system. Developed by the Dobelle Institute in New York. It gives an opportunity for blind people to achieve the visual acuity of about 20/400. The equipment consists of a mini television camera and an ultrasonic distance sensor that mounted on eyeglasses with the use of complex computer-imaging technology and edge detection algorithms to capture and simplify the image. The second microcomputer then activated allowing pulses to transmit to an array of 68 electrodes that are inserted on the surface of the visual cortex of the brain. Dobelle Eye weighs about 10 pounds and has a size of a dictionary.
http://www.lbl.gov/Science-Articles/Archive/anatomical-imaging.html
Reviewed by Suchart C.
Ravi Malladi and James Sethian at Lawrence Berkeley National Laboratory of Department of Energy had developed a fast new way to compute three-dimensional models of internal organs and other anatomical features. The intention of this method is to make an easier visualization and reconstruction of medical shapes for doctors. It uses a mathematical approach called an implicit representation of curves. Level Sets and Fast Marching are two methods in recovering medical shapes. Level Sets is a method of modeling curves and solids by joining an extra dimension. Fast Marching is a procedure of approximating the position of curve and surfaces moving under a speed law. By using these two methods, a computer algorithm can determine the boundaries information, both internal and external of anatomical solids faster and clearer than traditional ways.
http://news.bbc.co.uk/hi/english/health/newsid_760000/760240.stm
Reviewed by Suchart C.
This is a new method that uses computer to analyze the eye diseases. This procedure took
about ten years of study and was developed at University of Aberdeen, England.
The new technique simply scans through a patient's eyes, take pictures of the
retina, and analyze to check for abnormalities. What the new software
does is after scanning through all images, the system will simply tells
yes or no, whether or not there is retinopathy.
http://www.unisci.com/stories/19993/0902995.htm
Reviewed by Suchart C.
This article talks about an evolution on radiation dosimeter. Xie George Xu, an assistant professor of nuclear engineering and engineering physics at Rensselaer Polytechnic Institute, has created a 3-D virtual man called Visible Photographic Man or VIP-Man. It is so complex that it's capable of modeling the effects of radiation on the skin, lens of the eye, optic nerve, GI-tract mucous membranes, and bone marrow. Primarily, areas those are susceptible to radiation. These models are generated by Computed Tomography (CT), Magnetic Resonance Images (MRI), and photo images; it will allow patient CAT scans and MRI images to be paired directly with a computer simulation program for more accurate planning of treatment for diseases that require radiation therapy such as cancer. Xu's VIP-Man received a 1999 Faculty Early Career Development (CAREER) award from the National Science Foundation.
http://www.wired.com/news/topstories/0,1287,20273,00.html
Reviewed by Suchart C.
This article talks about a new technique developed for brain surgery. This technique uses magnetic resonance image, or MRI, to capture the images of the patient's brain, and then transfer the images to the hospital to a planning workstation, so scientists can work out the procedure for surgeons. This procedure seeks to come up with coordinates by using computational intensive math for surgeons to target. Then surgeons perform surgery by using gamma knife, which is fast and pain-free method.
http://www.spl.harvard.edu:8000/pages/papers/neurosurgery/neuro.html
Reviewed by Liang Cai
This article talks about computer assisted interactive three-dimensional planning for neurosurgical procedures. In this research, scientists have used three-dimensional (3D) reconstruction MRI techniques to understand the anatomic complexity of operative brain lesions and improve preoperative surgical planning. Experience with 14 cases including intra- and extra-axial tumors and a vascular malformation are reported. In each case preoperative planning was performed using MRI based 3D renderings of surgically critical structures such as eloquent cortex, gray matter nuclei, white matter tracts, and blood vessels.
Simulations using interactive manipulation of 3D data provided an efficient and
comprehensive way to appreciate the anatomic relationships. Interactive 3D
computer assisted preoperative simulations provided otherwise inaccessible
information useful for the surgical removal of brain lesions.
http://www.dai.ed.ac.uk/CVonline/LOCAL_COPIES/GILLES1/mutual_info.html
Reviewed by Liang Cai
This article is taking about imaging matching. It introduces a computer
vision method, originally for finding the pose of an object in an image, has
been extended to the case of 2D image matching. The method designed by Paul
Viola is a subtle refinement of
weighted neighbors in the sense that once the formulas for the derivative of
these criteria have been calculated, they bear a striking resemblance. It tries
to find the transformation that best matches two images, in optimizing the
mutual information between the two images. Intuitively, if the two images are
correctly matched, knowing one image gives information about the other.
Therefore their mutual information is high. Conversely, two independent signals
or images will have very low mutual information.
http://www.mssm.edu/cnic/research.html
Reviewed by Danian Cao
The Computational Neurobiology and Imaging Center in Mount Sinai School of Medicine is currently undertaking extensive research in relationships between neural function and structure in two kinds of neurons with recognized roles in neural activity underlying working memory. One goal the research is to understand how age-related variations in dendritic branching topology and spine morphology relate to decrements in cognitive abilities and working memory during normal aging in primates. A second goal is to determine the structural and biophysical correlates of observed variations in integrative behavior in brainstem neurons that comprise the velocity storage neural integrator (VSNI neurons) in goldfish. The research center also aims to develop computational tools to allow high-resolution imaging and 3-dimensional reconstruction of dendritic branching structure and spine morphology in these two neural types. In future, the research center hopes to investigate age-related changes in spine morphology and geometry, as well as dendritic complexity using automated 3-dimensional reconstructions of dendritic arbors at high magnification on a laser scanning confocal microscope.
http://unisci.com/stories/19994/1012993.htm
Reviewed by Danian Cao
This link describes the work of a group of researchers at Wake Forest University Baptist Medical Center under the direction of Greg Hundley, assistant professor of cardiology and radiology, on success using MRI to view the heart during vigorous beating. Aiming to use MRI as a screening and diagnostic tool for heart disease, Craig Hamilton, assistant professor of radiology, developed the software that allowed the researchers to see the heart's action almost immediately; previously, it took an average of five minutes before the images could be seen. The most promising use of the new technique will be in visualizing blockages and measuring blood flow in vessels leading to the heart. It is particularly beneficial for patient with multiple symptoms.
http://unisci.com/stories/19993/0708994.htm
Reviewed By Dongyang Chen
The researchers at the University of Illinois have created an optical system that produce 3-D image without a lens. This system is similar to holography but not require using laser. The camera uses numbers of beam splitters and folding mirrors to capture a sequence of “snapshots” and CCD (charge-coupled device) to detect the images. The same way as does a radio telescope, the camera collects data on interference patterns. These two-dimensional data frames are then processed to form a 3-D representation of the object, which can be displayed on a computer screen or in a virtual reality environment. To generate 3-D images, the researchers use a reconstruction algorithm that is not based on conventional computer vision and image-processing techniques. An algorithm has been used in cone–bean tomography – a new medical X-ray photograph technique other than the more popular cross-sectional slices. Comparing with conventional 3-D devices, a lens less camera has an infinite depth of field. The object is always in the focus, which will reduce the amount of data processing. The lens less camera could be used to microscope and machine vision etc. Also it could help these people who need a quick and reliable way to capture 3-D information about the optical world to put into their database, because this system produces a numerical 3-D representation of the object.
http://miralabwww.unige.ch/ARTICLES/VHP-paper.pdf
Reviewed by Zhuo Chen
This paper presents two techniques for the organ reconstruction from the Visible Human Dataset. The first technique describes a method that is a semi-automatic reconstruction by defining organ configurations on each slice. The user defines the organ configuration with the snake technique. The reconstruction process is defined in two steps.1.The user defines the organ configuration on each slice. The researcher has to put a set of points around the organ on the slice. The snake technique allows the polygon to fit to the configuration one the slice. 2.The organs have been interpreted and labeled on the different cross-sections as configurations. Joining the configurations of all the pertinent slices performs the 3D reconstruction. The second technique in this paper uses Shape Constrained Deformable Model. The reconstruction process is also defined in two steps. First, the researcher has to place an initial shape of the organ to the position of the organ to be reconstructed. Then, using the image information and the shape memory deforms this initial shape. The shape memory of a model can be able to come back to its original form. The image information is used to move points of the model to image configurations. This paper also provides examples of three anatomical organs that can be reconstructed. They are bones, muscles and skin.
http://unisci.com/stories/20002/0419006.htm
Reviewed by Lei Dong
Mr. Badri Roysam and Mr. Chuck Stewart are teaching at Rensselaer Polytechnic Institute. This link introduces this two associate professor's research to provide a three-dimensional image of the retina that could markedly improve results of retinal surgery. One of the reasons why the current success rate for retinal laser surgery is below 50 percent is because the combination of the image of the retina in the visible spectrum and the image of the layer beneath the retina in the near-infrared spectrum is often inaccurate by using a fluorescent dye that reveals blocked blood vessels. 3-D image system will allow surgeons to see both views simultaneously while simulating curves of the retina. The Rensselaer researchers think of this system as a sort of GPS (global positioning satellite system) that is much like military personnel use GPS to target missiles accurately. They also think this 3-D modeling can be used for diagnosis and treatment procedures prior to surgery, which will much improve the methods already in use.
http://www.nytimes.com/2001/04/26/technology/26HOWW.html?searchpv=site04
Reviewed by Ming Feng
It's a new technique that can project images directly onto the viewer's
retina superimposes data on what is viewed without hampering the person's
vision. Therefore a computer-generated image could be seen on top of a
real-life background. The invention of Microvision Inc., called Nomad, expects
to market by fall. The strategy of this invention works somewhat like a
television set. Just as a cathode-ray tube in a television or monitor scans a
beam of electrons onto the front face of the tube, the tiny projector inside a
head-mounted display beams light through the pupil and onto the nerve cells in
the retina. On the surface, Nomad is mounted at the front of a molded plastic
headpiece; its box of optical, electrical and mechanical components has a
single window that can slide over either eye. The components are linked to a
computer that can be worn on a belt. The technology may have important clinical
application in the future in superimposing information about a patient,
including vital signs and medical images. It can also be used for the control
of industrial machines, aviation and military.
http://www.nytimes.com/2001/03/15/technology/15NEXT-CIR.html
Reviewed by Hanjie Huang
Scientists at M.I.T. have developed a miniature microscope. Dr. Xingde Li, Dr. James G. Fujimoto and their colleagues at the Research Laboratory of Electronics and the department of electrical engineering and computer science at the Massachusetts Institute of Technology developed this needle type microscope. The needle is a stainless steel tube, which is less than a half- millimeter in diameter. It is inserted directly into tissue or organs. Inside the needle, like a ship in a bottle, is the optics. An optical fiber runs through the center of the tube, and at the end of the tube is a lens, a microprism and a tiny window through which pulses of infrared light travel. The area can be scanned as the needle is rotated. Pulses of infrared light leave the needle and bounce off nearby tissue, then travel back through the fiber for computerized image analyses. The needle is an application of an imaging technology called optical coherence tomography. The technique make higher magnification and resolution 100 ~ 10 times than ultrasound. Scanning the light beam across the tissue generates the cross-sectional images and measuring the time it takes for the light to echo back for each position of the scan. Instruments based on optical coherence tomography are manufactured by Zeiss Humphrey Systems of Dublin, Calif. It is already available for getting images of the retina. Tools using needle type microscope are also being developed to detect the plaque that can block coronary arteries and to find signs of gastrointestinal cancer. Optical coherence tomography might one day improve the early detection of some cancers, and reduces the damage of the tissue.
http://www.sciencedaily.com/releases/1999/11/991123080107.htm
Reviewed by Hanjie Huang
Researchers have been able to produce three-dimensional images of plaque, the blobs of "garbage" that clog the brains of Alzheimer's disease patients. This milestone, made possible by marrying high-resolution magnetic resonance microscopy (MRM) with powerful computers, is the first step toward non-invasive detection of plaques in Alzheimer's MRM technology was designed by Duke researchers in order to create highly detailed images of tiny structures and specimens. The technique is a refined version of magnetic resonance imaging (MRI) used in hospitals, but is much more powerful, using higher magnetic fields to create superb resolution. To make their three-dimensional images, the researcher removed tiny "plugs" of brain tissue from patients. To image plaque inside the centimeter-wide brain samples, a specially-engineered magnetic coil was developed by Johnson so that it could come as close to the tissue as possible. They then took hundreds of individual images while rotating the sample, so that when a computer blended all the images together, a high-resolution three-dimensional portrait of brain plaques was created.
http://www.sciencedaily.com/releases/1997/10/971017065158.htm
Review by Haung jie Huang
A 3D program is bringing a new level of accuracy; consistency and
standardization to the evaluation of burn patients. It has developed by a team
of researchers at the University of Chicago Hospitals' Burn Center.
The burn centers have long had to rely on the doctor's pencil drawings 2 D
charts on paper charts, known as Lund-Browder diagrams. Reliance on these
two-dimensional charts results in wide variation in assessment of identical
injuries.
The computer, using software, allows the burn team to begin assessment on a
frame; assembled from 10,000 tiny triangles that closely resemble the patient.
After keying in sex, height and weight, the physician can manually adjust the
resulting image to pull out a bigger abdomen, for example, or shrink the
shoulders to match the burned patient's physique.
The burns are drawn directly onto the rotatable 3-D computer diagram with a
resolution of 0.01%. On the display, different colors indicate different wound
depths: yellow for superficial, red for deep-partial thickness or brown for
full-thickness burns. Then the program computes the percentage of body surface
area affected as well as fluid and nutritional requirements.
Users can factor in other injuries or treatments that affect the patient's
metabolism. The computer program automatically adjusts for these variables and
then calculates nutritional requirements. The computer is also able to zoom.
Body parts can be displayed separately or magnified for accuracy. Wound
diagrams can be updated and compared as treatment progresses. Skin grafts,
biological dressings and donor sites (which become partial-thickness wounds)
can be included in the diagram.
The program is easy to use; it requires few keyboard commands. A mouse and
simple pull-down menus control most functions.
http://www.cs.unc.edu/Research/nano/index.html
Reviewed by Ruiwen Jiang
The University of North Carolina developed the nanoManipulator (nM) system, which provides an improved, natural interface to Scanning-probe microscopes (SPMs), including Scanning Tunneling Microscopes (STMs) and Atomic Force Microscopes (AFMs). The nM couples the microscope to a virtual-reality interface providing virtual telepresence on the surface. SPMs allow the investigation and manipulation of surfaces down to the atomic scale by rastering a tip across a surface, sampling its height at locations on a regular grid. The data is typically viewed in real time as a grayscale map viewed from above. The nM interface tiles the surface with triangles and uses a highly parallel graphics supercomputer to render the image as a shaded surface. Specular highlights bring out features in the data that are missed in the grayscale image. SPMs can modify the surface without feedback under program control by using a force-feedback probe to allow the user to directly control tip motion. SPMs can acquire multiple data sets and display several side-by-side grayscale images, one per data set. The nM is investigating the use of color and programmable shading to display these data sets overlaid on the topography, allowing user to view correlation between topography and other data. This tool has led to new results in the study of biology, in particular in gene therapy, materials science, carbon nanotubes, and electrical engineering.
http://unisci.com/stories/19993/0902995.htm
Reviewed by Ruiwen Jiang
Xie George Xu, assistant professor of nuclear engineering and engineering physics at Rensselaer Polytechnic Institute, has created a 3-D virtual man called "Visible Photographic Man" (VIP-Man) that is so sophisticated it can model the effects of radiation on the skin, lens of the eye, optic nerve, GI-tract mucous membranes, and bone marrow--areas previously too minute to accurately model, but which are highly susceptible to radiation. These models are generated from CT, MRI, and photo images and data provided by The Visible Human Project from the National Library of Medicine. It allows patient CAT scans and MRI images to be coupled directly with a computer simulation program for more accurate treatment planning for diseases that require radiation therapy -- such as cancer. That coupled with the latest computer technologies is of importance to radiation safety in the nuclear industry, medical treatment planning, and space radiation risk assessment for NASA.
http://unisci.com/stories/sparchives_misc6.htm
Reviewed by Ruiwen Jiang
Researchers at University of California San Francisco (UCSF) developed a High-Dose 3D Conformal Radiation that allows multiple x-ray beams of radiation to be designed with the use of computer software to pinpoint the exact shape of the prostate. Only the prostate receives the maximum dose of radiation, while minimal doses are delivered to adjacent tissues and organs. It was proved more favorable for patients with high-grade prostate tumors (high PSA) and is far more effective than standard low-dose radiation. In addition, radiation may be used on some tumors that are inoperable. More than half of the patients in the study weren't considered surgical candidates.
\
Reviewed by Xin Li
In this paper, William M. Wells describes a new method called adaptive segmentation
that uses knowledge of tissue properties and intensity inhomogenities to
correct and segment MR images. Using the expectation-maximization algorithm,
this method allows for more accurate segmentation of tissue types as well as
better visualization of MRI data.
Using this method, they model intra- and inter-scan MRI intensity inhomogenities
with a spatially varying factor called the gain field that multiplies the
intensity data. The application of a logarithmic
transformation to the intensities allows the artifact to be modeled as an
additive bias field. Then they use a Bayesian approach to estimating the bias
field that represents the gain artifact in log-transformed MR intensity
data. Their result shows that the adaptive segmentation is consistent
with the manual segmentations in the sense that it does not have big average
difference. Comparing with Supervised Segmentation, the adaptive segmentation
shows better agreement with Manual Segmentation.
This method has also been found to be substantially insensitive to parameter
settings. For a given type of acquisition, intensity variations across
patients, scans, and equipment changes have been accommodated in the estimated
bias fields without the need for manual intervention. In this sense, the method
is fully automatic for segmenting healthy brain tissue.
http://www.ai.mit.edu/projects/medical-vision/surgery/surgical_navigation.html
Reviewed by Xin Li
The Computer Vision Group of the MIT Artificial Intelligence Lab has
developed a system to support image guided surgery, which will enable surgeons
to visualize internal structures through an automated overlay of 3D
reconstructions of internal anatomy on top of live video views of a patient.
The system consists of a portable cart containing a Sun UltraSPARC workstation
and the hardware to drive the laser scanner and Flashpoint tracking system.
In order to register the patient to the segmented MRI skin, they use a laser
scanner to collect 3D data of the patient's scalp surface as positioned on the
operating table. The surface rendering techniques are then used to display the
segmented MRI structures. This procedure consists of first extracting bounding
surfaces from the segmented MRI volume using the marching cubes algorithm. This
algorithm generates a set of connected triangles to represent the 3D surface
for each segmented structure. These surfaces are then displayed by selecting a
virtual viewing eZulacamera location and orientation in the MRI coordinates
frame and using standard computer graphics techniques to project the surface
onto the viewing camera.
Using this system, surgeon can peel back the MRI skin and see where the
internal structures are located relative to the viewpoint of the camera. Thus
the surgeon has x-ray vision, a capability that will be needed more and more as
we continue moving towards minimally invasive surgeries. In addition, a bipolar
simulator to the trackable probe is attached, which is used to determine the
location of vital regions of the brain, including motor and sensory cortex and
language area. When the probe is attached to the stimulator, surgeons can
obtain the position of the tip during stimulations and immediately produce a
color-coded visualization highlighting these important areas.
http://ditzel.rad.jhu.edu/projects/neurosurg/html/neurosurg.html
Reviewed by Naveen Menezes
An algorithm has been developed at the Center for Biomedical Image Computing that will calculate the risk associated with every possible surgical trajectory before conducting brain surgery. Using this algorithm an interactive tool has been developed to find the optimal surgical plan in the steriotactic surgery of the brain to treat conditions like brain tumors. This digital imaging software written in the C Language and built for UNIX systems, computes the cost path associated with each point on the outer brain boundary, which comprises of about 5,000 candidate entry points to a prespecified target point. The various structures such as thalamic nuclei, optic nerve radiations and individual Brodman's areas can be defined on the atlas and transferred onto the patient's brain image through the spatial transformation. The cost of a particular path associated with each structure and the total cost of each path are computed and displayed allows the surgeon to visualize an arbitrary cross-section through the patient's brain that contains this path and to examine all the cross-sectional images orthogonal to that path. From this data the surgeon can determine the lowest cost path, which is the safest, and the least invasive trajectory path to perform the surgery.
http://www.loni.ucla.edu/~thompson/IEEE_abs.html
Reviewed by Peng Qu
This research paper presents an automatic, accurate technique for calculating the high-dimensional deformation brain anatomies. It introduces a surface-based approach for the elastic warping of anatomical images. Applying vector and tensor matrix operators to the transformation field required to locally deform one brain volume into another can assess differences in regional shape. These invoke deformation fields, which match one brain with a large number of others. Accurate matching of brain data requires the individual matching of entire systems of anatomic surface boundaries and relevant curved and point landmarks. Structures can be extracted automatically in parametric form. It can automatically produce parameterized models without manual initialization.
http://www.unesco.org/webworld/public_domain/tunis97/com_35/com_35.html
Reviewed by Peng Qu
This report studies the current status and future perspectives of medical imaging. While the final images of many medical techniques have many similarities to each other, the technologies involved are completely different. And the parameters represented in the images are also different. In each case, different mathematical or statistical models are used with different equations. This report emphasizes the methodologies for visualizing internal body anatomy and function. It also introduces the future developments of morphological imaging, functional imaging and volume visualization. With the rapid development of digital imaging modalities in medicine, there is also an increasing need for an efficient management and archival of digital medical images. Furthermore, it is even more useful if the Internet can be used to provide resources to the medical imaging community. The World Wide Web might also provide additional functionality such as online medical imaging analysis.
http://cfi.lbl.gov/~budinger/medTechdocs/Xray.html#x-rayCT
Reviewed by Peng Qu
This site provides basic information about X-ray transmission imaging. It explains how x-ray imaging is generated. Based on the theory of X-ray, Computed Tomography (CT) is then invented. CT is considered one of the major technological advances of medical science. This article also illustrates the first, fourth generation CT and spiral X-ray CT using graphs. In its mother site, 9 other medical imaging techniques are introduced. It is good for beginners and students.
http://bioinformer.ebi.ac.uk/newsletter/archives/5/armchair.html
Reviewed by Peng Qu
This is an article about the theory of evolution using bioinformation. Traditional researchers study the species evolution from fossil or from behaviour of living species. The discovery in DNA put the problem into the hands of molecular biologists. This new technology might solve many of the problems from DNA. Bioinformatics promise to be the driving force in the developing field of "molecular archaeology".
http://bioinformer.ebi.ac.uk/newsletter/archives/5/gene_prediction.html
Reviewed by Peng Qu
This article discusses the standards to create clean data sets for Gene
Prediction. It provides the steps and criteria involved for approaching high
quality data sets and the computational gene prediction tools to annotation of
sequenced DNA regions. Several graphs also illustrate the main points in this
article, such as the decision tree for human acceptor sites. It is good for the
researchers who work in gene prediction field and other advanced learners.
http://www.oandp.org/jpo/13/13182.asp
Reviewed By Peeyush Rathkanthiwar
This article says about the development and application of computer-aided-design and computer-aided-manufacturing (CAD-CAM) technology to foot orthotics for replacing most of the normal manufacturing stages. The finished cast impression of the foot is digitized using a wand digitizer. This digitizer, signals to the computer its position in space as it touches the inner surface of the cast impression. The location in space of the surface of the cast impression is transmitted to a computer file assigned to each patient. The computer using a special computer program can correct the digital data. The main advantage of the software or computer program is, it allows over 35 different modifications in contour of the actual foot, and over 40 different modifications in the actual orthotic design. The completed orthosis can be viewed from a cross-sectional perspective or in a three-dimensional perspective. When the computer corrected orthosis is confirmed to be acceptable in the order review process, the completed digital data file is sent to a numerically controlled (computer driven) milling machine. The milling machine cuts out the completed orthosis from a solid block of material according to the information received from the computer. The advantage in this technique is the reduced cost of orthotic devices. This has increased the number of users and due to increase in profitability it has created a demand for the computerized production systems. Low-cost optic scanning device that will be used in-office by practitioners to obtain optical "castings" (impressions) of patient’s feet. These optical casts will be transmitted via computer modem to facilities using the Ortho-Cam production system, completely eliminating the need for traditional cast impression techniques.
http://www.nytimes.com/library/tech/00/08/biztech/articles/28gene.html
Reviewed by Peeyush Rathkanthiwar
This article has been published in New York Times informs "Supercomputers Track Human Genome". The power in the technology is that it is good for breaking the code the genetic one. The machines are being snapped up to sift the blizzard of data being generated by the Human Genome Project and various private genomics efforts. The need for machines stems from biology's shift from a "wet" science performed in test tubes to at least partly a "dry" one, in which much of the crucial analysis is done on computers. This has given rise to a field called bioinformatics, the use of computer science in life science.
http://www.zurichmednet.com/development/InaHealthRevolution.htm
Reviewed By Peeyush Rathkanthiwar
This article is telling us about how computers are useful for doctors from their home or office. Explaining how doctor's can key any of their patients into computer and instantly spy almost every piece of information they need results from a blood test and X-rays, the operating room's report from recent surgery and the patient's next appointment. Showing the pictures outside the emergency rooms, surgeon examining X-rays. Nurses and doctors on the labor and delivery floor of hospital can monitor patients labor from their computer screens. Doctors can plug drug orders into a computer program that will check the drug against a patient's other medications and immediately warn of possible dangers or unexpected interactions.
http://www.cad.ornl.gov/cad_cp/text/med-imaging.html
Reviewed By Peeyush Rathkanthiwar
This article is about the visible human project. The objective of the Visible Human Project is to create complete, anatomically detailed, three-dimensional representations of the male and female human bodies. The Visible Human Project data sets are designed to serve as a common reference point for the study of human anatomy, as a set of common public domain data for testing medical imaging algorithms, and as a test bed and model for the construction of image libraries that can be accessed through networks. Image overlay is basically used in neurosurgery, orthopedics, microsurgery, obstetrics, plastic surgery and other specialties. In these applications, the physician can view medical images or computer-generated graphics overlaid on and registered with the patient. The perfect example for this is, in neurosurgery a rendering of a brain tumor can be displayed inside the patient's head during surgery, providing localization and guidance to a surgeon.
http://ltswww.epfl.ch/research/medim.html
Reviewed By Peeyush Rathkanthiwar
As importance of medical imaging acquisition and tele-medicine is rapidly increasing one of the current developments in medical imaging is processing of skin cancer images. There are many people affected by the disease called malignant melanoma a kind of skin cancer. The basic interest is that Image processing which can provide important information such as color extraction, texture, size, shape and symmetry. The imaging technique used, called dermatoscopy or dermoscopy, was based on epiluminescence microscopy (ELM). This technique uses an oil immersion that renders the skin translucent. Pigmented structures located in the lower layers of the epidermis become visible, improving thus the lesion analysis. The three slides shown illustrate respectively the concept of computer-aided diagnosis, the different processing steps, and finally the design of a medical network for medical diagnosis applications.
http://www.automaatioseura.fi/jaostot/mvn/mvn4/medicine.html
Reviewed By Peeyush Rathkanthiwar
This article describes about the Real-time image processing and visualization in medicine and their advantages over the X-rays and Medical Resonance Imaging. This Intra-operative Real-time Visualization and Instrument Tracking (IRVIT) is being studied currently at Oulu University Hospital. IRVIT covers two major things: 1.Accurate instrument tracking 2.Real-time image processing and visualization. Surgeon moves an instrument according to the visual feedback he gets for which moving the instrument triggers an image update, which shows the instruments new position with respect to the anatomy. In order to be able to control the image acquisition and thereby provide visual feedback, it is necessary to be able to assess the location of the instrument accurately for which IRVIT technology is used. A new technological device, the ESR marker, has been developed and this can be used to measure the location of the surgical instrument. The marker is a very small crystal that can be integrated into the tip of an instrument 1.2mm in diameter. By measuring the electron spin resonance (ESR) signal from the crystal, the location of the instrument can be determined. As the MRI scanner is used to measure both the ESR marker location and the anatomical images, most of the sources of error will be the same, and thus their net effect is cancelled out. As a result excellent relative localization accuracy can be achieved. The images obtained by the scanner itself are insufficient for the efficient performance of a surgical intervention and various image-processing techniques are necessary in order to make the most important features more easily visible. In addition, real-time volume rendering techniques can provide essential added value to the visual feedback.
http://www.nature.com/genomics/human/papers/409860a0_fs_1.html
Reviewed By Peeyush Rathkanthiwar
This article discusses about the initial sequencing and analysis of the human genome from the genome-sequencing consortium. The ultimate goal is to compile a complete list of all human genes and their encoded proteins, to serve as a 'periodic table' for biomedical research. Since human genes tend to have small exons (encoding an average of only 50 codons) separated by long introns (some exceeding 10 kb) this is a difficult task than organisms with small genomes. This article describes there way to recognize both the RNA genes and protein-coding genes in the human genome and also study the properties of the predicted human protein set, attempting to discern how the human proteome differs from those of invertebrates such as worm and fly.
http://splweb.bwh.harvard.edu:8000/pages/ppl/mark/ms/ms.html
Reviewed by Yu Shi
Charles R.G. Guttmann heads the Multiple Sclerosis (MS) Project in the MRI
Division of the Department of Radiology at Brigham and Women’s Hospital. The
purpose of this project is to quantify and categorize the MS tumors or lesions
to understand this disease, by monitoring the progression of MS tumors or
lesions over a time period of several years.
Fifty patients are required to be scanned in the Brigham and Women's Magnetic
Resonance Imaging (MRI) scanner twenty four times each. The scans were done
over time intervals of from one week to two months in between scans.
The important part of this project is that the approach to understanding our
data was an elaborate one that evolved over time and was primarily developed by
Dr. Kikinis and Dr. Guttmann, with many novel image processing algorithms
supporting the project developed by numerous computer scientists and
programmers at MIT Artificial Intelligence Laboratory, and GE Corporate R&D
as well as in the SPL (Surgical Planning Lab).
At each patient visit, an Image Processing Pipeline (IPP) was applied to the
datasets generated. The major components of the pipeline are described and
illustrated in the link. The IPP begins with Intracranial Cavity Generation.
http://www.sciam.com/1999/0399issue/0399smith.html#links
Reviewed by Tony Song
Bradley R. Smith, Director, Biomedical Illustration School of Art and Design, University of Michigan wrote this article. Mr. Smith was an assistant research professor in the department of radiology at Duke University Medical Center. He and his colleagues of Duke University Medical Center had developed the Multidimensional Human Embryo project using the magnetic resonance microscopy (MRM) techniques and computer software. The Multidimensional Human Embryo is an on-line database of virtual human embryos based on the Carnegie Collection of Human Embryos, which housed at the National Museum of Health and Medicine of the Armed Forces Institute of Pathology in Washington, D.C., consists of preserved human embryos from each stage of embryonic development. The MRM technique developed at Duke University by G. Allan Johnson and his colleagues is founded on the same physical principles as its clinical cousin, magnetic resonance imaging (MRI). MRM can record voxels (volume elements) that are a million times smaller. By using MRM, researchers can generate no distorted, detailed three-dimensional virtual embryo (data set) from an embryo specimen in less than two hours. Then, researchers use volume-rendering software to display results. The multidimensional human embryo will make the precious resource of Carnegie Collection available to the researchers around the world.
http://splweb.bwh.harvard.edu:8000/pages/papers/mamata/JMRI2001/MRT-JMRI.pdf
Reviewed by Jianxin Wang
This article described that line scan diffusion-weighted images (LSDI) were
obtained in three brain tumor cases during neurosurgical procedures in a
vertical gap open-configuration 0.5 Tesla MRI system. Diffusion trace images
were received in acute alchemic stroke cases. It takes 46secons and 94 seconds
per slice scan time for diffusion-tensor images. Diagnosis of acutely developed
vascular occlusion was confirmed with follow-up scans. Diffusion tensor imaging
was used to display the displaced white matter tracts around the tumor and to
detect alchemic complications. The feasibility and potential of this technique
in MRI-guided neurosurgery has been demonstrated. The diagnostic utility of
line scan diffusion imaging was established.
http://www.newswise.com/articles/2001/2/NEURO.MCW.html
Reviewed by Min Wang
This article is about the work of researchers at the medical College of Wisconsin and the Veterans Medical Center in Albuquerque. Using medical imaging, they located the parts of the brain, which control the time needed to do everyday functions, such as catching a ball. In other words, their research was on the areas of the brain responsible for hand-eye coordination. The researchers found that the basal ganglia and the parietal lobe are the areas for this timekeeping system. They used the functional magnetic resonance imaging technique (fMRI) to measure changes in brain activity. This article was written for general readers. It is interesting because it explains how this research can be used to treat Parkinson's disease, Huntington's disease, Attention-Deficit Hyperactivity Disorder, and strokes.
http://www.nytimes.com/2001/03/15/technology/15NEXT-CIR.html?searchpv=nyToday
Reviewed by Min Wang
This article describes a miniature, fiber-optic microscope developed at M.I.T. that combines electrical engineering and computer science with medical technology. This tiny microscope is installed at the end of a tube the size of a needle. The tube is equipped with a lens, a microprism and an optical fiber running through the center. Doctors will be able to insert the needle-sized microscope directly into an organ, such as the prostrate or the pancreas, and scan the organ tissue by rotating the needle. Infrared light pulses through the imaging needle, then travels back through the optical fiber for computerized analysis. The imaging needle uses optical coherence tomography, which is an application of imaging technology. This technique is similar to ultrasound, except that it uses light to produce images. The new method offers doctors much higher resolution than ultrasound. The imaging needle collects cross-sectional images by scanning light beams across tissue, then measuring the time required for the light to bounce back to the position of the scan. This article gives a fascinating look at a new development, which allows physicians to detect cancerous cells with minimal invasion.
http://www.berkeley.edu/news/media/releases/2000/11/20_mri.html
Reviewed by Min Wang
This article discusses the functions and operation of a powerful magnetic
resonance imaging (MRI) scanner recently unveiled at the University of
California at Berkeley. The MRI scanner brings about a convergence of
computer science, physics, chemistry, biology, and psychology to benefit and
advance medical research. This instrument, designed by Varian, Inc. of
Palo Alto, California, is being operated through Berkeley's Brain Imaging
Center. It will be used in studies of individuals with neurological
impairments. These studies could lead to a better understanding of the
effects of aging on memory, and to new treatments for Parkinson's disease,
Alzheimer's disease, and attention deficit disorder.
The MRI scanner is capable of visualizing details of the anatomy, which are
less than a millimeter in size. In addition, its speed allows advanced
work with functional MRI (fMRI), by which neuroscientists study brain activity,
which is less than a second in length. Individuals undergoing a scan with
this equipment face no risk, as the procedure is non-invasive.
The Berkeley MRI scanner detects brain activity according to the blood flow
throughout the brain. As neurons in the brain draw oxygen from the blood,
this produces changes in the hemoglobin, which the scanner detects as radio
signals. Neuroscientists then use a computer to analyze these signals to
construct a visual image of the brain activity. Research at Berkeley
involving the scanner includes studies of aging and memory as well as studies
of subjects who have experienced neurological damage.
This article reports on an excellent example of a successful partnership
between private enterprise, higher education and medicine.
http://oncolink.upenn.edu/pdq_html/6/engl/600514.html
Reviewed by Min Wang
This article discusses several research projects that the National Cancer Institute (NCI) is funding in order to develop imaging technologies for the diagnosis and treatment of breast cancer. One of these is digital mammography, which is a computerized method of displaying images using an infinite number of gray tones. Digital images show promise of improving the quality of X-rays and enhancing the sensitivity of mammography. In addition, they use less radiation and allow for computer-aided diagnosis.
Magnetic resonance imaging (MRI) and ultrasound are part of another project supported by the NCI. Both of these have proven to be effective in distinguishing between benign and malignant cancers and in locating tumors in dense breast tissue. Moreover, MRI has the ability to reveal the extent (staging) of local anatomic tumors, a quality that can be crucial for doctors planning treatments.
A third research area receiving NCI funding involves image-guided needle biopsies. Using this technology, physicians can perform biopsies with the removal of surgical tissue and with minimal invasion. This method reduces waiting time until diagnosis and results in cost savings.
http://stanford.edu/dept/news/report/news/february9/brain-29.html
Reviewed by Min Wang
This article covers a study conducted by a group of neurosurgeons at
Stanford University led by Dr. Gary Steinberg. For the study, Steinberg
and his colleagues operated on 56 patients who had vascular malformations in
the brain. The surgeons were able to remove deep brain lesions with
minimal damage to surrounding tissues by mapping out the anatomical geography
of each patient's brain and adjusting the surgical entry site according to the
exact location of the lesions. Steinberg's team used magnetic resonance
imaging (MRI) before surgery to obtain a three-dimensional location of each
vascular malformation. During the operations a laser pointer calibrated
to an image that was computer-generated in three planes guided their scalpels.
Digital equipment monitored sensory signals from the patients' muscles and
alerted the doctors if they came too close to sensitive brain structures. The
computer-assisted surgical techniques in the Stanford study have resulted in a
ninety percent success rate for the operations. This article is
recommended for lay readers with an interest in biotechnical applications in
medicine.
http://www.newswise.com/articles/2001/2/NEURO.MCW.html
Reviewed by Min Wang
This article is about the work of researchers at the medical College of
Wisconsin and the Veterans Medical Center in Albuquerque. Using medical
imaging, they located the parts of the brain, which control the time needed to
do everyday functions, such as catching a ball. In other words, their
research was on the areas of the brain responsible for hand-eye
coordination. The researchers found that the basal ganglia and the
parietal lobe are the areas for this timekeeping system. They used the
functional magnetic resonance imaging technique (fMRI) to measure changes in
brain activity. This article was written for general readers. It is
interesting because it explains how this research can be used to treat
Parkinson's disease, Huntington's disease, Attention-Deficit Hyperactivity
Disorder, and strokes.
http://vsd.pennnet.com/Articles/Article_Display.cfm?Section=Archives&Subsection=Display&ARTICLE_ID=52214&KEYWORD=medical%20image
Reviewed by Peilin Zhang
ISCAN Inc. developed a vision-system prototype that incorporate eye-tracking
technology into a wearable system that enables impaired children to structure
messages and initiate commands. A specialized word-processing program, called
Look and Select model, is used in one version of the prototype. A patient who
is paralytic can type; dial a telephone, watch television, and control simple
electrical appliances by eye fixating on PC-monitor icons for a prescribed
time. This Head-Mounted Eye-Imaging system comprises a miniature video camera,
an optical assembly that includes a micro liquid-crystal display (LCD), and an
infrared illuminator designed to capture high-contrast eye-initiated images
suitable for processing by a custom image-processing chip. The ISCAN
eye-tracking technology is based on the automatic recognition and tracking of
the eye`s dark pupil. When the patient wearing the head-mounted system stares
at an icon within the micro display. The corresponding icon on the PC screen
immediately changes color, which indicates to the patient or system operator
that the icon has been initially selected. After the patient’s adjustable
fixation time has elapsed, the icon`s color changes again, indicating that the
selection of that icon has been entered into the PC. The patient can also focus
on an icon of a speech synthesizer, which then sounds an assembled message. The
future work for this system will focus on writing the software for a simpler
mouse-driven model and reducing the cost.
http://www.ncgr.org/research/genex/
Reviewed by Aamir Babar
This site describes the GeneX project that provide an internet-available
repository of gene expression with an integrated toolset that will enable researchers
to analyze their data and compare their result with other such data. The GeneX
project plans to make the greatest use of gene expression data by
creating an Internet available relational database of public data derived from
these multiple technologies, as well as making the same database technology
available for local installation. It is expected that the GeneX project will
eventually allow results from different technologies to be directly compared,
and will encourage better noise reduction, equalization, analytical
algorithms to be developed.
http://www.cnn.com/2000/TECH/computing/09/07/smell.digiscents.reut/index.html
Reviewed by Aamir Babar
This site contains some useful information about the sense IT. Dehiscent Inc, a highly touted US start up seeking to give computers a sense of smell. Sense IT was founded by Eli fisch. The idea is that as few primary colors can be used to create thousands of shades, so too essential oils can be blended to create widely recognizable scents. The scientist are basically striving to create the RGB of scents, using the analogy of red green standards used to define the television and computer monitors. This new technology would be a hardware device that connects to personal computers. It can be used to blend 128 basic scents in a theoretically unlimited number of scents.
http://www.nytimes.com/2001/05/03/technology/03FACE.html
Reviewed by Ying Bao
This article introduced one kind of the bioinformatics software--face
recognition software, which works by converting video images, photos or even
police composites of faces into strings of numbers, then
comparing them with other strings of numbers that stand for known faces — is
very much in its infancy.
Face recognition is one of several types of biometric systems, which use physical measurements to identify people. It works by describing faces in terms of how much they resemble each of 128 archetypal faces. Combining hundreds of real faces in a databank and then using mathematical formulas to analyze similarities and differences have created the archetypes.
There also has another system which is called local feature analysis, it
involves plotting out the relative positions of a dozen or more points at
places where the curvature of the face changes — the features that make a face
unique — and trying to find other faces with similar constellations of critical
points.
http://www.sciencedaily.com/releases/2000/02/000225080127.htm
Reviewed by Suchart C.
The study of the activity of genes in living cells and the Human Genome
Project's gene sequencing efforts are creating huge amounts of raw data.
And these data are rapidly increasing in many types of public computer
databases. The idea behind bioinformatics is to come up with the complex
computer models for pulling out useful information from them, as computer
analysis will be an important part of identifying and understanding genes'
functions.
Bioinformatics plays a significant role in the Human Genome Project, roughly
about 100,000 human genes are being comprehended and identified. David
Haussler, professor of computer science, is working with the researchers at
Massachusetts Institute of Technology's Whitehead Institute for analyzing the
rough draft of the human genome sequence that is difficult because the rough
draft does not provide a continuous DNA sequence across each chromosome.
They used a computer program called Genie which employed by the statically
method known as Hidden Markov Modeling (HMM) to locate genes within the genome
sequence. Haussler’s team and researchers at the Lawrence Berkeley
National Laboratory first developed genie. Like gene chips or DNA
microarrays give detail information about gene expression also produce enormous
amounts of raw data and can be understood only by using the complex
computational method. Genome sequencing technology and gene chips are powerful
techniques for understanding molecular biology.
http://www.sciencedaily.com/releases/1988/12/981202075222.htm
Reviewed by Suchart C.
Dr. Mark Borodovsky, a professor of biology at Georgia Tech, had developed a software program that uses mathematical model called Hidden Markov Models or HMM, to predict the locations of genes on a strand of DNA. This method has been proven to be 98% accurate and been used by all over the world.
http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/
Reviewed by Danian Cao
This site briefly summarizes five ongoing software projects that are developed for analysis of genetic data. They are: 1) FASTLINK, a kind of software which is designed for genetic linkage analysis. Genetic linkage analysis is a statistical technique used to map genes and find the approximate locations of disease genes. 2) MSA, multiple sequence alignment software. 3) CASPAR, the software to do conditional linkage analysis of polygenic diseases such as diabetes, asthma and glaucoma. 4) PedNunter is currently being used at NCBI to query the Amish Genealogy database, a database of over 85,000 members of the Amish and Mennonite religious groups, and their relatives. 5) CGH, the software to analyze data on tumors and study models of oncogenesis. This site also provides hyperlinks to a more detailed page about each project, download software, and reference for paper. It is a very useful site for genetic experts.
http://www.eragen.com/TechnologyToolbox/TechnologyToolbox.html
Reviewed by Dongyang Chen
This site introduces a software tool “MasterCatalog”, a web-based tool that
combines genomic database organization and search capabilities with
evolutionary biological information.
Unlike many bioinformatics tools, MasterCatalog goes beyond the conventional
“homology equals function” paradigm and provides the researcher with additional
evidence that allows better prediction of function. It allows the researcher to
easily find and understand the relation of a gene to all other known
genes. It can help researchers with novel target elucidation, cloning of
functional domains, homology modeling, and species selection for candidate
testing.
http://genome.nhgri.nih.gov/arraydb/
Reviewed by D. Chen
This page provides an interactive user interface tool suite <ArrayDB> to analysis of microarray gene statement data. It can be used in the fields in studying the molecular basis of human genetic disease; developing technologies to accelerate genetic research and resolve multi-gene diseases (DNA microarray, spectral karyotyping, high throughput genotyping). All of the analyzed statement data from a microarray experiment, as well as information about the clones used in the experiment, are stored in a relational database that could be either Sybase or Oracle. The upload tools allow individual investigators to directly populate the database through a Web front-end, which is build by CGI script and Java applets. The CGI scripts provide connections to the relational database, and the applets provide a graphical representation of the experimental data. The two main applets currently available are the Experiment Viewer and the Multi-Experiment Viewer. The Experiment Viewer presents the statement data for a single experiment in histogram form, allowing specific areas of the histogram to be selected. Once a selection is made, the actual microarray slide image is displayed, as well as detailed information about each of the clones in the selected range. Each clone is also linked to a variety of external databases. The Multi-Experiment Viewer allows the user to query a range of related experiments at one time in order to see changes in the pattern of statement of the same gene over different experiments.
http://www.techfak.uni-bielefeld.de/bcd/ForAll/Introd/eduneed.html
Reviewer by Xi Chen
Because RNA and DNA sequence data has been flooding out in the past 10 years, biologists are facing the problem of storing and analyzing so much data. Thus computer technologies can be of great help in computational biology. Today, user friendly and powerful software for sequence analysis is available. Hence, biologists do not necessarily need to be expert in mathematics and computer science. But they should not treat software as a black box; they need to understand the assumptions and the principles on which they rely. The article uses an example, sequence database searching, to explain the point. During the process, we must pay attention to: 1) Importance of Knowing the Assumptions when a researcher has obtained the DNA sequence of a new gene, he/she still knows nothing about it, either 3-D structure or function. Thus, if a query sequence is highly similar to a protein whose 3-D structure and function are known, one can build a model for the new sequence. 2) Importance of Knowing the Principles a. sensitivity versus specificity there are different ways to estimate similarity between two sequences. We must modify the sensitivity and specificity of the results. (This is one additional reason explaining why biologists should not treat software as a black box) Efficient Use of the Program: if a researcher knows the principles, he will be able to increase the sensitivity. This will improve the ability of the program to recognize distantly related sequences. From above, we can understand that, when we use program for sequence analysis, the researcher must have the relevant knowledge of biocomputing. Knowing the capabilities and the drawbacks of the programs will help to use them in a more accurate and efficient way.
http://www.techfak.uni-bielefeld.de/bcd/ForAll/Introd/drugdesign.html
Reviewer by Xi Chen
On the molecular level, drug specificity includes two independent
mechanisms. Both mechanisms are mediated by a variety of interactions
between the drug and its receptor site. Usually tens of thousands of compounds
have to be screened to find a promising new drug. Looking for help from
powerful computational techniques, such as commercial available software, seems
straightforward.
The input of biocomputing in drug discovery is twofold: 1) the software may
help to optimize the pharmacological profile of existing drugs by guiding the
synthesis of new and "better" compounds. 2) The software can
help developing new therapeutic concepts by finding out about possible
biological functions of a protein and understanding the molecular workings of a
given protein structure. Thus, using the computer for drug design is very
useful in analysis the interactions between the drug and its receptor site. Besides,
even if the researcher doesn't know the structure of the receptor site, the
software may help to figure out how it might look by comparing the chemical and
physical properties of drugs that are known to act at a specific site. During
the past ten years, the field has undergone a tremendous progress. More
and more new drugs have been developed with the help of computer techniques.
Despite that computational power is yet insufficient to simulate complex
biochemical reactions, we still can say, the field will be continuing to grow.
http://www.unisci.com/stories/19993/0806995.htm
Reviewed by Xi Chen
The article is about the success in simulating a protein solely from the physical laws. Cells make proteins by stringing together long chains of amino acids. The chain quickly folds into a compact shape to form the final shape. On the average, the shape can get the protein molecule has the lowest possible potential energy. Thus, computer software could calculate all the possible shapes for a given chain of amino acids and choose the one with the lowest potential energy. However, there are so many possibilities of the shapes, so, many researchers to shorten the computation by starting out with a simplified version of the chain. Harold Scheraga's group at Cornell University have developed a computer algorithm, which ignores the nitrogen at first and carbon atoms at end and work with a simplified version of the central carbon and its side chains to generate several rough structures, to calculate how the forces between atoms affect their arrangement. Using this algorithm, the researchers produced the best match to the actual structure of any simulation based solely on physical laws.
http://www.unisci.com/stories/19993/0805991.htm
Reviewed by Xi Chen
The Alternative Splicing Data Base, or ASDB, was created by several research
Center for Bioinformatics and Computational Genomics. The new database can
identify clusters of proteins arising from alternative
gene splicing.
That "one gene, one protein" was considered a basic tenet of biology.
But now, we found that genes can be spliced alternately to produce different
proteins and that alternative splicing plays a crucial role in the development
and health of many organisms.
Here are several steps lie between a gene and protein. 1) Messenger RNA copies
the gene, then carries he information to a ribosome. 2) The ribosome reads the
RNA and cranks out an amino-acid string, which folds into the functional
protein.
In 1977, researchers found that large chunks of some genes are edited out,
after the RNA leaves the DNA strand and before it is processed by a ribosome.
We call these genes "split" genes.
Spli genes have a remarkable property: their exons (discarded pieces of the gene)
can be added or deleted. They play a vital role in higher organisms and are
also important in generating antibodies.
The ASDB currently contains some 1,700-protein sequences. It can be searched to
find out how many known proteins can be derived from a single gene sequence or
to find all known products of alternative splicing in a given organism. Thus,
in its first half year of operation, it has received more than 35,000 requests
from researchers in genetics and cell and developmental biology around the
world.
http://www.perzoholik.miesto.sk/meteory/protokoly/interval_analysis.htm
Reviewed by Ming Feng
Gene sequencing efforts such as the Human Genome Project, combined with new
techniques for studying the activity of genes in living cells, are generating
enormous amounts of raw data. These data are accumulating at a rapidly
accelerating pace in a variety of public computer databases. Bioinformatics is
playing an increasingly important role in the project. Locating genes within
genomic DNA sequences is one of the first tasks for which scientists have
turned to bioinformatics. Less than 10 percent of the human genome is thought
to comprise protein-coding gene sequences. Interspersed with the genes are
control sequences, which regulate gene activity, and other "noncoding
regions" whose functions are obscure. They introduced a now widely used
statistical method called hidden Markov modeling to attack this problem. The
first task Haussler and the Whitehead group are tackling is to line up all of
the segments of the human genome sequenced so far in their proper order and
orientations along the chromosomes. The next step will be to locate genes
within the genome sequence. According to Haussler, the role for bioinformatics
in this type of research is steadily increasing as the experimental methods
become more sophisticated and complex. DNA microarrays or "gene chips,"
provide valuable information about gene expression -- when, where, and to what
extent specific genes are active. This information is critical to understanding
a gene's biological function. But gene chips, like genomic sequencing
technology, produce enormous amounts of data that can only be analyzed and
understood using sophisticated computational approaches. To analyze these
complex datasets, Haussler is pioneering the use of a new statistical method
based on the theory of support vector machines (SVMs). SVMs are a new
generation learning system based on recent advances in statistical learning
theory. SVMs deliver state-of-the-art performance in real-world applications
such as text categorization. The foundations of SVMs are gaining popularity due
to many attractive features, and promising empirical performance. SVMs are able
to handle high-dimensional datasets in which each data point has many features
or attributes.
http://www.nytimes.com/2001/05/03/technology/03FACE.html
Reviewed by Ming Feng
Face recognition is one of several types of biometric systems, which use
physical measurements to identify people. It works by converting video images,
photos or even police composites of faces into strings of numbers, then
comparing them with other strings of numbers that stand for known faces - is
very much in its infancy.
It works reasonably well at confirming the identity of someone who wants to log
on to a computer or pass through a security checkpoint. A couple of dozen
police departments in the United States and Canada use it to help figure out
who their suspects really are. Election officials in Mexico and Uganda are
using it to prevent double voting.
But it has yet to yield consistent results in-law-enforcement and surveillance
settings. The technology burst into the public consciousness, and caused dismay
among many privacy advocates when it was revealed that the faces of everyone
entering the stadium had been compared against a mug shot file of criminals and
terrorists.
Face recognition works by describing faces in terms of how much they resemble
each of 128 archetypal faces. Combining hundreds of real faces in a data bank
and then using mathematical formulas to analyze similarities and differences
have created the archetypes.
There also has another system which is called local feature analysis, it
involves plotting out the relative positions of a dozen or more points at
places where the curvature of the face changes - the features that make a face
unique - and trying to find other faces with similar constellations of critical
points.
Facial recognition was developed at universities over the past decade at the
request of the Defense Department, which thought that it could be used to
tighten security at border crossings and fight drug smuggling.
http://www.rad.unc.edu/CADDLab/projects/Liver
Transplant/main.html
Reviewed by Naveen Menezes
The specific goal of this project is to develop and evaluate a software package that facilitates three partial-liver transplant image analysis tasks:(1) Understanding the donor's and the recipient's anatomy and vascular network for surgical path planning, (2) Specifying a surgical path and predicting both donor and recipient outcome based on the surgical path complexity, graft volume, and the path's effect on the liver's vascular network, and (3) Assessing liver regeneration in the donor and the recipient by quantifying volume and vessel network change by registering the donor's pre-operative liver vessel network with the donor's and the recipient's post-operative liver vascular networks six weeks following the operation. This method accomplishes these tasks by integrating three methods into a software package that runs on standard PCs for the analysis of MR and CT images: (1) Automated vessel and organ segmentation for interactive 3D visualization and volume estimation, (2) Automated vessel branch point identification, vessel/path crossing detection, and anatomical landmark identification for automated path planning and patient outcome prediction, and (3) Automated registration of the vascular networks of pre and post-operative images to detect changes in vascular networks.
http://www.techfak.uni-bielefeld.de/bcd/ForAll/Introd/drugdesign.html
Reviewed by Peeyush Rathkanthiwar
This article gives the understanding of how computers are useful for drug
design. The basic principle is to analyze the interactions between the drug and
its receptor site (protein) and to "design" molecules that give an
optimal fit. The techniques provided by computational methods include computer
graphics for visualization and the methodology of their chemistry. An important
criterion to determine the medical value of a drug is specificity: the
physiological effect of the drug should be as clearly defined as possible. How
biocomputing is useful is explained firstly the computer may help to optimize
the pharmacological profile of existing drugs by guiding the synthesis of new
and "better" compounds. Secondly, as more and more structural
information on possible protein targets and their biochemical role in the cell
becomes available, completely new therapeutic concepts can be developed.
http://www.halls.md/body-mass-index/av.htm
Reviewed by Abdul Sikder
Here is a simple tool to calculate your BMI. From the above BMI (Body Mass Index) link you can tell if you are overweight of underweight. According to a definition of obesity was issued by the National Heart, Lung, and Blood Institute, "overweight" is as a BMI value between 25 and 29.9 and "obesity" is a BMI value greater than or equal to 30. If your BMI is between 17 to 22, your life expectancy is longer than average. You have no need to lose weight. Men are usually satisfied with a BMI of 23 to 25 and women tend to believe they look their best at values between 20 to 22. If your BMI is between 23 and 25, most people does not consider you overweight, but your life expectancy isn't increased. If your BMI is 26 or more, you are considered overweight and statistically likely to have a lower life expectancy.
http://www.nytimes.com/1999/12/21/technology/21gene.html?searchpv=tech
Reviewed by Ying Bao
This article described that the biotechnology industry is now tapping into that same technology in a bid to speed up its own growth significantly.
These biochips look like the integrated circuits in a personal computer, but instead of containing tiny semiconductors, they are loaded with bits of actual DNA that make up genes or fragments of genes. Inserted in a PC-sized analytical instrument, the chips allow scientists to perform thousands of biochemical experiments at a fraction of the cost and time required for traditional tests.
Biochips, or microarrays will bring genomics, the study of all the genes in a living organism, out of the research laboratory and into the daily practice of medicine.
The initial market for biochips has been in drug discovery, and the major customers have been the large drug companies. By analyzing the subtle changes in genes when a cell becomes cancerous or is infiltrated by a virus, scientists search for new molecular targets for drugs.
The biochip makers are now chasing a bigger opportunity personal genomics. Even as the public and private efforts to spell out the three-billion biochemical letters that make up the human genetic code race to a conclusion.
Sophisticated genetic analysis could be performed at the individual level,
making possible early prediction or detection of disease, more accurate
diagnosis and customized therapy. The biochip space lies at the intersection
between high-technology chip manufacturing, signal processing software skills
and more traditional molecular biology and genomics.
http://bio.com/articles/dnachip/dnachip.html
Reviewed by Danian Cao
This article introduces a new technology designed to quickly analyze large amount of genomic information--DNA chip. DNA chip assays are also referred to as biochips, which require hybridization of an unknown nucleotide sequence to an ordered array of known DNA immobilized onto a glass slide or silicon chip. The hybridization results are detected by fluorescence and analyzed by pattern recognition; DNA chips are manufactured using one of two available basic technologies. One method begins by synthesizing oligonucleotide; the other format begins with complementary DNA (cDNA). This new technology has an advantage over gel-based assays because the nucleic acids are bound to a reusable solid support allowing biomedical researchers to study entire genes and gather information about expression and gene mutation patterns. DNA chip array assay has been wildly used to detect changes in patterns of gene expression, gene mutations, sequencing and human diagnostics. It has become an affordable and versatile instrument for drug discovery and basic science research.
http://www.sciencedaily.com/releases/2000/01/000126080913.htm
Reviewed by Danian Cao
Dr. Laura Landweber, assistant professor at Princeton University and her research team have developed a kind of computer that uses the biological molecular RNA to solve complex problems. The research team used a test tube containing 1,024 different strands of RNA to solve a simple version of the "knight problem", a chess puzzle that is representative of a class of problems that requires brute-force computing. The test-tube computer will probably never completely replace silicon technology, but it does have attractive aspects. One advantage is that the genetic molecules DNA and RNA, which encode all the instructions for creating and running life, can store much more data in a give space than conventional memory chips. Another benefit is that, a biomolecular computer could perform thousands or millions of calculation at the same time. There is more flexibility to use RNA instead of DNA in developing a computing system. There is a limited set of restriction enzymes for DNA, so scientists may not be able to cut the molecule where they want. With RNA, one universal enzyme will target any part of the molecule. This achievement marks a significant advance in molecular computing.
http://www.newswise.com/articles/2000/1/RNACOMP.PTU.html
Reviewed by Zhuo Chen
Researchers at Princeton University have developed a kind of computer that uses the biological molecule RNA to solve complex problems. Laura Landweber, the leader of this research project, an assistant professor of ecology and evolutionary biology. Other people who work on this project are Richard Lipton, professor of computer science, and Dirk Faulhammer, and Anthony Cukras, a student. The achievement advances an emerging field in which scientists use molecules such as DNA and RNA to solve certain problems more efficiently than conventional computing. They use a test tube containing 1,024 different strands of RNA to solve a chess puzzle. That is representative of a class of problems that requires computing. The chess puzzle asks how many and where can one place knights on a chessboard so they cannot attack each other. In a series of five steps, a targeted enzyme cut away all the strands that did not match the requirements of a correct solution. For the purposes of their experiment, the researchers restricted the board to just nine squares, so there were 512 possible combinations. This RNA computer has two advantages. One is that the genetic molecules DNA and RNA can store much more data in a given space than conventional memory chips. Another advantage is that, with vast numbers of genetic fragments floating in a test tube, a biomolecular computer could perform thousands or millions of calculations at the same time. It is an extreme example of parallel computing, which is a rapidly growing area of computer technology.
http://americanscientist.org/issues/Comsci01/compsci2001-05.html
Reviewed by Peng Qu
This article introduces the basic concepts of biological computer-- digital logic units based on the metabolism of living cells, with the aim of building a computer out of colonies of Escherichia coli or some other single-celled organism. In the expression of any genes, synthesis of the lac enzymes is a two-stage process. First the DNA is transcribed into messenger RNA by the enzyme RNA polymerase; then the messenger RNA is translated into protein by ribosomes. The process is controlled at the transcription stage. The researchers at MIT are developing such computer. The first step is to develop design rules and a parts catalogue for biological computers. The elements of the MIT biocomputing design library will be repressor proteins. The biological computer is a wireless device, where signals are broadcast throughout the cell. In such a device, communication will be at no cost. Biochemical computer will be developed into a crop of programmable biological sensors, actuators and messengers.
http://unisci.com/stories/20001/0119006.htm
Reviewed by Peng Qu
This article introduces the molecular computer that uses RNA. The molecular computing is an emerging field to solve complex problems. One advantage is that the genetic molecules can store much more data in a given space than conventional memory chips can. Another benefit is that a biomolecular computer can perform millions of calculations simultaneously. It is an extreme example of parallel computing. Compare with DNA, RNA is more flexible in developing a computing system. Because DNA has a limited set of restriction enzymes, scientists may not be able to cut the molecule where they want. RNA uses just one universal enzyme that targets any part of the molecule. This aspect makes RNA easy to use and makes it inherently scalable to larger problems. RNA can reduce the complexity of big systems.
http://www.englib.cornell.edu/scitech/w96/DNA.html
Reviewed by Shiqiang Wang
This web page introduces how the Dr. Leonard Adleman solved the Hamiltonian path problem with the DNA computing. Dr. Adleman found a way to exploit the speed and efficiency the biological reactions to solve the problem .It was the first time using the DNA computing to have the issue solved in the world. The following steps were crucial in the experiment: the firs one was to synthesize DNA strands of known sequences, each strand 20 nucleotides long. Dr. Adleman represented each of the six vertices of the path by a separate strand, and further represented each edge between two consecutive vertices. Then, through the sheer amount of DNA molecules joining together in all possible combinations, many random paths were generated. The power of molecular computers is still worth comparing to today's systems. In speed, the DNA computing performing 1,000 operations per second more than the fastest supercomputers. This web page is also illustrated to make it more readable and understandable.
http://www.jsonline.com/alive/news/0607dna.stm
Reviewed by Peilin Zhang
This article introduces DNA computers that are faster and more efficient because of their two chief attributes. One is its microscopic size, and the other is the powerful search function that can explore all possible answers simultaneously.
DNA represents information as a pattern of molecules on a strand, each strand represents one possible answer, and trillions of strands of DNA can be embedded on a small plate of glass. So the DNA computers can store much more data in a give space than conventional memory chips.
The DNA computers are built with a molecular computer chip made of a small glass plate covered with a thin layer of gold. DNA is tailored so that all conceivable answers are included. The researchers then subject all the molecules to precise chemical reactions that imitate the computation abilities of a traditional computer. With its search function, it can go through all the possible answers simultaneously. Enzymes are applied to strip out the entire DNA with incorrect ones, leaving one molecule with the right answer to solve the calculation.
The experts think with these two advantages of the DNA computers, they will complement today's computers in the future, and will specialize in solving large computational problems in which the number of possible answer is enormous.
http://www.englib.cornell.edu/scitech/w96/DNA.html
Reviewed by Peilin Zhang
Dr. Leonard Adleman use DNA computing
exploiting the speed and efficiency the biological reactions to solve the
"traveling salesman problem." The "traveling salesman
problem" basically involves finding all the possible paths between a
certain number of vertices. Adleman used DNA to solve a system of six vertices,
which is not difficult for modern computers, but as the number of cities grows
so does the number of paths between them, making a 1,000-city path impossible
to solve for even the best supercomputers. Adleman's first step was to
synthesize DNA strands of known sequences, each strand 20 nucleotides long. He
represented each of the six vertices of the path by a separate strand, and
further represented each edge between two consecutive vertices. After
generating the numerous random paths in the first step, he used polymerase
chain reaction (PCR) to amplify and keep only the paths that began on vertex 1
and ended at vertex 6. The next two steps kept only those strands that passed
through six vertices, entering each vertex at least once. At this point, any
paths that remained would code for a Hamiltonian path, thus solving the
problem. The power of molecular computers is worth comparing to today's
systems. In speed, the DNA clearly wins the race, performing 1,000 operations
per second more than the fastest supercomputers .In energy efficiency, a
biological system such as a cell can perform 2x1019 power operations using one
joule of energy, while a supercomputer only manages 1010 operations, making it
1010 less energy efficient! Even though Adleman's molecular computer would have
a hard time solving an easy task compare to one of today's electronic
computers, its capability to solve complex problems is unparalleled. The
computers of tomorrow are on the threshold.
http://www.nytimes.com/2001/02/20/science/20WEEK.html
Reviewed by Prof. Karron
In his weekly review of the week in science, New York Times staff science writer Nicholas Wade cites (with links) the week’s turmoil in the genome. The surprising finding of the relative few genes that make the human proteome may be due to a systematic error in the genome decoding algorithms. Despite the confirmation by Celera (headed by J. Craig Ventner) and a consortium of academic research centers funded by NIH (headed by Dr. Francis Collins), both teams used much the same set of tools they may both have got the same wrong answer. Some alternate theories are that human's use their genes in more and different ways than a mouse. So while we may have more in common with a mouse configuration wise, metaprograms control the different circumstances that the same genes produce differing transcriptions into proteins. One of the most intriguing hints that new biology may be discovered in the genome comes from an initial survey of the mouse genome, which Celera said this week it had assembled. Laying the mouse genome sequence over the human sequence is extremely revealing because most of the DNA has diverged in the 100 million years since mouse and man last shared a common ancestor. The DNA regions that are similar between the two species are those important enough to have been conserved. Dr. Craig Venter has now stated that there is a third category of similar DNA regions, which are not genes but are too extensive to be control regions. No one yet knows what the mystery regions are doing.
http://www.nytimes.com/2001/02/26/business/26DRUG.html
Reviewed by Prof. Karron
William Haseltine, Chief executive of Human Genome Sciences and Glaxo SmithKline announced that they have developed a small protein drug directly from Genome database information. Big drug companies tend to favor small-molecule drugs, which can be taken as pills, whereas larger proteins must be injected because the digestive system would digest them. Drug companies view the gene and its associated protein as targets, and try to synthesize a short chain polypeptide chemical that can be taken as a pill and will interact with a protein that occurs naturally in the body. GlaxoSmithKline used the Human Genome Database to find the gene for an enzyme that studies have shown is associated with a higher risk of coronary heart disease. Clinical Trials are underway where the new drug reduced the level of the enzyme, known as Lp-PLA2, in patients.
http://www.post-gazette.com/healthscience/20010226digitalhuman3.asp
Review by Prof. Karron
This popular newspaper piece takes a light look at the visible human project. With the recent spate of anatomic effects movies (Hollow Man, The Invisible Man) interest focuses on the Digital Human, or attempts to capture anatomy digitally.
Last Modified: May 20, 2001 SCJ, XY, SC, Dr. K.