42 results match your criteria Journal of Biomedical Discovery and Collaboration [Journal]

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Two Similarity Metrics for Medical Subject Headings (MeSH): An Aid to Biomedical Text Mining and Author Name Disambiguation.

J Biomed Discov Collab 2016 Apr 6;7:e1. Epub 2016 Apr 6.

University of Illinois at Chicago.

In the present paper, we have created and characterized several similarity metrics for relating any two Medical Subject Headings (MeSH terms) to each other. The article-based metric measures the tendency of two MeSH terms to appear in the MEDLINE record of the same article. The author-based metric measures the tendency of two MeSH terms to appear in the body of articles written by the same individual (using the 2009 Author-ity author name disambiguation dataset as a gold standard). Read More

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http://journals.uic.edu/ojs/index.php/jbdc/article/view/e1
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http://dx.doi.org/10.5210/disco.v7i0.6654DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4845330PMC
April 2016
5 Reads

The language of discovery.

Authors:
Wiley Souba

J Biomed Discov Collab 2011 Jun 17;6:53-69. Epub 2011 Jun 17.

Dartmouth.

Discovery, as a public attribution, and discovering, the act of conducting research, are experiences that entail "languaging" the unknown. This distinguishing property of language - its ability to bring forth, out of the unspoken realm, new knowledge, original ideas, and novel thinking - is essential to the discovery process. In sharing their ideas and views, scientists create co-negotiated linguistic distinctions that prompt the revision of established mental maps and the adoption of new ones. Read More

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http://dx.doi.org/10.5210/disco.v6i0.3634DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3139986PMC
June 2011
3 Reads

Bias associated with mining electronic health records.

J Biomed Discov Collab 2011 Jun 6;6:48-52. Epub 2011 Jun 6.

Columbia University.

Large-scale electronic health record research introduces biases compared to traditional manually curated retrospective research. We used data from a community-acquired pneumonia study for which we had a gold standard to illustrate such biases. The challenges include data inaccuracy, incompleteness, and complexity, and they can produce in distorted results. Read More

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http://dx.doi.org/10.5210/disco.v6i0.3581DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149555PMC
June 2011
3 Reads

Literature-based Resurrection of Neglected Medical Discoveries.

Authors:
Don R Swanson

J Biomed Discov Collab 2011 Apr 20;6:34-47. Epub 2011 Apr 20.

University of Chicago.

It is possible to find in the medical literature many articles that have been neglected or ignored, in some cases for many years, but which are worth bringing to light because they report unusual findings that may be of current scientific interest. Resurrecting previously published but neglected hypotheses that have merit might be overlooked because it would seem to lack the novelty of "discovery" -- but the potential value of so doing is hardly arguable. Finding neglected hypotheses may be not only of great practical value, but also affords the opportunity to study the structure of such hypotheses in the hope of illuminating the more general problem of hypothesis generation. Read More

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http://dx.doi.org/10.5210/disco.v6i0.3515DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3097086PMC
April 2011
3 Reads

A cognitive task analysis of a visual analytic workflow: Exploring molecular interaction networks in systems biology.

J Biomed Discov Collab 2011 Mar 21;6:1-33. Epub 2011 Mar 21.

.

Background: Bioinformatics visualization tools are often not robust enough to support biomedical specialists’ complex exploratory analyses. Tools need to accommodate the workflows that scientists actually perform for specific translational research questions. To understand and model one of these workflows, we conducted a case-based, cognitive task analysis of a biomedical specialist’s exploratory workflow for the question: What functional interactions among gene products of high throughput expression data suggest previously unknown mechanisms of a disease?

Results: From our cognitive task analysis four complementary representations of the targeted workflow were developed. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090070PMC
http://dx.doi.org/10.5210/disco.v6i0.3410DOI Listing
March 2011
6 Reads

NEMO: Extraction and normalization of organization names from PubMed affiliations.

J Biomed Discov Collab 2010 Oct 4;5:50-75. Epub 2010 Oct 4.

Lnx Research LLC, 750 The City Drive Suite 490, Orange, CA 92868, USA.

Background: Today, there are more than 18 million articles related to biomedical research indexed in MEDLINE, and information derived from them could be used effectively to save the great amount of time and resources spent by government agencies in understanding the scientific landscape, including key opinion leaders and centers of excellence. Associating biomedical articles with organization names could significantly benefit the pharmaceutical marketing industry, health care funding agencies and public health officials and be useful for other scientists in normalizing author names, automatically creating citations, indexing articles and identifying potential resources or collaborators. Large amount of extracted information helps in disambiguating organization names using machine-learning algorithms. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990275PMC
October 2010
3 Reads

EpiphaNet: An Interactive Tool to Support Biomedical Discoveries.

J Biomed Discov Collab 2010 Sep 21;5:21-49. Epub 2010 Sep 21.

University of Texas Health Science Center.

Unlabelled: Background. EpiphaNet is an interactive knowledge discovery system which enables researchers to explore visually sets of relations extracted from MEDLINE using a combination of language processing techniques. In this paper, we discuss the theoretical and methodological foundations of the system, and evaluate the utility of the models that underlie it for literature-based discovery. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990276PMC
September 2010
4 Reads

Recall and bias of retrieving gene expression microarray datasets through PubMed identifiers.

J Biomed Discov Collab 2010 Mar 28;5:7-20. Epub 2010 Mar 28.

University of Pittsburgh.

Background: The ability to locate publicly available gene expression microarray datasets effectively and efficiently facilitates the reuse of these potentially valuable resources. Centralized biomedical databases allow users to query dataset metadata descriptions, but these annotations are often too sparse and diverse to allow complex and accurate queries. In this study we examined the ability of PubMed article identifiers to locate publicly available gene expression microarray datasets, and investigated whether the retrieved datasets were representative of publicly available datasets found through statements of data sharing in the associated research articles. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990274PMC
March 2010
2 Reads

MLTrends: Graphing MEDLINE term usage over time.

J Biomed Discov Collab 2010 Jan 25;5:1-6. Epub 2010 Jan 25.

Ottawa Hospital Research Institute.

The MEDLINE database of medical literature is routinely used by researchers and doctors to find articles pertaining to their area of interest. Insight into historical changes in research areas may be gained by chronological analysis of the 18 million records currently in the database, however such analysis is generally complex and time consuming. The authors' MLTrends web application graphs term usage in MEDLINE over time, allowing the determination of emergence dates for biomedical terms and historical variations in term usage intensity. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990277PMC
January 2010
12 Reads
3 Citations

Tracking the current rise of chinese pharmaceutical bionanotechnology.

J Biomed Discov Collab 2009 Oct 14;4. Epub 2009 Oct 14.

Jenkins Collaboratory, Duke University, Durham, NC 27708, USA.

Background: THE CONTEXT AND PURPOSE OF THE STUDY: Over the last decade China has emerged as a major producer of scientific publications, currently ranking second behind the US. During that time Chinese strategic policy initiatives have placed indigenous innovation at the heart of its economy while focusing internal R&D investments and the attraction of foreign investment in nanotechnology as one of their four top areas. China's scientific research publication and nanotechnology research publication production has reached a rank of second in the world, behind only the US. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850247PMC
October 2009
3 Reads

Concepts and synonymy in the UMLS Metathesaurus.

Authors:
Gary H Merrill

J Biomed Discov Collab 2009 Oct 14;4. Epub 2009 Oct 14.

GlaxoSmithKline, Research Triangle Park, NC 27709, USA.

This paper advances a detailed exploration of the complex relationships among terms, concepts, and synonymy in the UMLS Metathesaurus, and proposes the study and understanding of the Metathesaurus from a model-theoretic perspective. Initial sections provide the background and motivation for such an approach, and a careful informal treatment of these notions is offered as a context and basis for the formal analysis. What emerges from this is a set of puzzles and confusions in the Metathesaurus and its literature pertaining to synonymy and its relation to terms and concepts. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850250PMC
October 2009
6 Reads

Open-access publishing - a new path.

J Biomed Discov Collab 2009 Jun 16;4. Epub 2009 Jun 16.

UIC Psychiatric Institute, University of Illinois at Chicago, Chicago, IL 60612, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850248PMC
June 2009
4 Reads

Life science research and drug discovery at the turn of the 21st century: the experience of SwissBioGrid.

J Biomed Discov Collab 2009 Apr 22;4. Epub 2009 Apr 22.

Oxford e-Research Centre, Oxford University, St Giles, Oxford, UK.

Background: It is often said that the life sciences are transforming into an information science. As laboratory experiments are starting to yield ever increasing amounts of data and the capacity to deal with those data is catching up, an increasing share of scientific activity is seen to be taking place outside the laboratories, sifting through the data and modelling "in silico" the processes observed "in vitro." The transformation of the life sciences and similar developments in other disciplines have inspired a variety of initiatives around the world to create technical infrastructure to support the new scientific practices that are emerging. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850249PMC
April 2009
3 Reads

3D medical collaboration technology to enhance emergency healthcare.

J Biomed Discov Collab 2009 Apr 19;4. Epub 2009 Apr 19.

Department of Computer Science, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3175, USA.

Two-dimensional (2D) videoconferencing has been explored widely in the past 15-20 years to support collaboration in healthcare. Two issues that arise in most evaluations of 2D videoconferencing in telemedicine are the difficulty obtaining optimal camera views and poor depth perception. To address these problems, we are exploring the use of a small array of cameras to reconstruct dynamic three-dimensional (3D) views of a remote environment and of events taking place within. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850251PMC
April 2009
12 Reads

The continuity of scientific discovery and its communication: the example of Michael Faraday.

Authors:
Alan G Gross

J Biomed Discov Collab 2009 Feb 25;4. Epub 2009 Feb 25.

University of Minnesota-Twin Cities, Minneapolis, MN, USA.

This paper documents the cognitive strategies that led to Faraday's first significant scientific discovery. For Faraday, discovery is essentially a matter seeing as, of substituting for the eye all possess the eye of analysis all scientists must develop. In the process of making his first significant discovery, Faraday learns to dismiss the magnetic attractions and repulsions he and others had observed; by means of systematic variations in his experimental set-up, he learns to see these motions as circular: it is the first indication that an electro-magnetic field exists. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850252PMC
February 2009
2 Reads

Supporting cognition in systems biology analysis: findings on users' processes and design implications.

Authors:
Barbara Mirel

J Biomed Discov Collab 2009 Feb 13;4. Epub 2009 Feb 13.

School of Education, University of Michigan, Ann Arbor, Michigan, USA.

Background: Current usability studies of bioinformatics tools suggest that tools for exploratory analysis support some tasks related to finding relationships of interest but not the deep causal insights necessary for formulating plausible and credible hypotheses. To better understand design requirements for gaining these causal insights in systems biology analyses a longitudinal field study of 15 biomedical researchers was conducted. Researchers interacted with the same protein-protein interaction tools to discover possible disease mechanisms for further experimentation. Read More

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http://dx.doi.org/10.1186/1747-5333-4-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2649900PMC
February 2009
2 Reads

Are figure legends sufficient? Evaluating the contribution of associated text to biomedical figure comprehension.

J Biomed Discov Collab 2009 Jan 6;4. Epub 2009 Jan 6.

Department of Health Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201-0413, USA.

Background: Biomedical scientists need to access figures to validate research facts and to formulate or to test novel research hypotheses. However, figures are difficult to comprehend without associated text (e.g. Read More

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http://dx.doi.org/10.1186/1747-5333-4-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631451PMC
January 2009
3 Reads

Basic Blue Skies Research in the UK: Are we losing out?

Authors:
Belinda Linden

J Biomed Discov Collab 2008 Feb 29;3. Epub 2008 Feb 29.

12 Balcaskie Road, Eltham, London SE9 1HQ, UK.

Background: The term blue skies research implies a freedom to carry out flexible, curiosity-driven research that leads to outcomes not envisaged at the outset. This research often challenges accepted thinking and introduces new fields of study. Science policy in the UK has given growing support for short-term goal-oriented scientific research projects, with pressure being applied on researchers to demonstrate the future application of their work. Read More

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http://dx.doi.org/10.1186/1747-5333-3-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2292148PMC
February 2008
3 Reads

Anne O'Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results.

J Biomed Discov Collab 2008 Feb 15;3. Epub 2008 Feb 15.

Department of Psychiatry and Psychiatric Institute, MC912, University of Illinois at Chicago, Chicago, IL 60612, USA.

Background: PubMed is designed to provide rapid, comprehensive retrieval of papers that discuss a given topic. However, because PubMed does not organize the search output further, it is difficult for users to grasp an overview of the retrieved literature according to non-topical dimensions, to drill-down to find individual articles relevant to a particular individual's need, or to browse the collection.

Results: In this paper, we present Anne O'Tate, a web-based tool that processes articles retrieved from PubMed and displays multiple aspects of the articles to the user, according to pre-defined categories such as the "most important" words found in titles or abstracts; topics; journals; authors; publication years; and affiliations. Read More

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http://dx.doi.org/10.1186/1747-5333-3-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2276193PMC
February 2008
2 Reads

An open-source framework for large-scale, flexible evaluation of biomedical text mining systems.

J Biomed Discov Collab 2008 Jan 29;3. Epub 2008 Jan 29.

Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA.

Background: Improved evaluation methodologies have been identified as a necessary prerequisite to the improvement of text mining theory and practice. This paper presents a publicly available framework that facilitates thorough, structured, and large-scale evaluations of text mining technologies. The extensibility of this framework and its ability to uncover system-wide characteristics by analyzing component parts as well as its usefulness for facilitating third-party application integration are demonstrated through examples in the biomedical domain. Read More

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http://j-biomed-discovery.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/1747-5333-3-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2276192PMC
January 2008
2 Reads

Generalization through similarity: motif discourse in the discovery and elaboration of zinc finger proteins.

J Biomed Discov Collab 2007 Oct 3;2. Epub 2007 Oct 3.

Department of Speech Communication, 110 Terrell Hall, University of Georgia, Athens, GA, USA.

Background: Biological organisms and their components are better conceived within categories based on similarity rather than on identity. Biologists routinely operate with similarity-based concepts such as "model organism" and "motif." There has been little exploration of the characteristics of the similarity-based categories that exist in biology. Read More

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http://dx.doi.org/10.1186/1747-5333-2-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2225388PMC
October 2007
2 Reads

Corpus refactoring: a feasibility study.

J Biomed Discov Collab 2007 Sep 13;2. Epub 2007 Sep 13.

Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA.

Background: Most biomedical corpora have not been used outside of the lab that created them, despite the fact that the availability of the gold-standard evaluation data that they provide is one of the rate-limiting factors for the progress of biomedical text mining. Data suggest that one major factor affecting the use of a corpus outside of its home laboratory is the format in which it is distributed. This paper tests the hypothesis that corpus refactoring - changing the format of a corpus without altering its semantics - is a feasible goal, namely that it can be accomplished with a semi-automatable process and in a time-effcient way. Read More

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http://dx.doi.org/10.1186/1747-5333-2-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2072937PMC
September 2007
12 Reads

Nano-Bio-Genesis: tracing the rise of nanotechnology and nanobiotechnology as 'big science'.

Authors:
Rajan P Kulkarni

J Biomed Discov Collab 2007 Jul 14;2. Epub 2007 Jul 14.

Centre for Economics & Policy, Institute for Manufacturing, Department of Engineering Cambridge University, Cambridge CB2 1RX, UK.

Nanotechnology research has lately been of intense interest because of its perceived potential for many diverse fields of science. Nanotechnology's tools have found application in diverse fields, from biology to device physics. By the 1990s, there was a concerted effort in the United States to develop a national initiative to promote such research. Read More

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http://dx.doi.org/10.1186/1747-5333-2-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1976605PMC
July 2007
3 Reads

Applied information retrieval and multidisciplinary research: new mechanistic hypotheses in complex regional pain syndrome.

J Biomed Discov Collab 2007 May 4;2. Epub 2007 May 4.

Safety Assessment, AstraZeneca R&D Mölndal, Sweden.

Background: Collaborative efforts of physicians and basic scientists are often necessary in the investigation of complex disorders. Difficulties can arise, however, when large amounts of information need to reviewed. Advanced information retrieval can be beneficial in combining and reviewing data obtained from the various scientific fields. Read More

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http://dx.doi.org/10.1186/1747-5333-2-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1871567PMC
May 2007
6 Reads

Biological information specialists for biological informatics.

J Biomed Discov Collab 2007 Feb 12;2. Epub 2007 Feb 12.

Graduate School of Library and Information Science, University of Illinois at Urbana-Champaign, USA.

Data management and integration are complicated and ongoing problems that will require commitment of resources and expertise from the various biological science communities. Primary components of successful cross-scale integration are smooth information management and migration from one context to another. We call for a broadening of the definition of bioinformatics and bioinformatics training to span biological disciplines and biological scales. Read More

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http://dx.doi.org/10.1186/1747-5333-2-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1802079PMC
February 2007
3 Reads

GOAnnotator: linking protein GO annotations to evidence text.

J Biomed Discov Collab 2006 Dec 20;1:19. Epub 2006 Dec 20.

Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, Portugal.

Background: Annotation of proteins with gene ontology (GO) terms is ongoing work and a complex task. Manual GO annotation is precise and precious, but it is time-consuming. Therefore, instead of curated annotations most of the proteins come with uncurated annotations, which have been generated automatically. Read More

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http://dx.doi.org/10.1186/1747-5333-1-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1769513PMC
December 2006
5 Reads

What makes us human: revisiting an age-old question in the genomic era.

J Biomed Discov Collab 2006 Nov 29;1:18. Epub 2006 Nov 29.

Howard Hughes Medical Institute, Department of Human Genetics and Committee on Genetics, University of Chicago, Chicago, IL 60637, USA.

In 1970, Karl Pribram took on the immense challenge of asking the question, what makes us human? Nearly four decades later, the most significant finding has been the undeniable realization of how incredibly subtle and fine-scaled the unique biological features of our species must be. The recent explosion in the availability of large-scale sequence data, however, and the consequent emergence of comparative genomics, are rapidly transforming the study of human evolution. The field of comparative genomics is allowing us to reach unparalleled resolution, reframing our questions in reference to DNA sequence--the very unit that evolution operates on. Read More

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http://dx.doi.org/10.1186/1747-5333-1-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716182PMC
November 2006
9 Reads

Who's afraid of Homo sapiens?

Authors:
Todd M Preuss

J Biomed Discov Collab 2006 Nov 29;1:17. Epub 2006 Nov 29.

Division of Neuroscience, and Center for Behavioral Neuroscience, Yerkes National Primate Research Center, Emory University, 954 Gatewood Road, Atlanta, GA 30329, USA.

Understanding how humans differ from other animals, as well as how we are like them, requires comparative investigations. For the purpose of documenting the distinctive features of humans, the most informative research involves comparing humans to our closest relatives-the chimpanzees and other great apes. Psychology and anthropology have maintained a tradition of empirical comparative research on human specializations of cognition. Read More

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http://dx.doi.org/10.1186/1747-5333-1-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764430PMC
November 2006
4 Reads

Karl Pribram, The James Arthur lectures, and what makes us human.

Authors:
Ian Tattersall

J Biomed Discov Collab 2006 Nov 29;1:15. Epub 2006 Nov 29.

Division of Anthropology, American Museum of Natural History, New York NY 10024, USA.

Background: The annual James Arthur lecture series on the Evolution of the Human Brain was inaugurated at the American Museum of Natural History in 1932, through a bequest from a successful manufacturer with a particular interest in mechanisms. Karl Pribram's thirty-ninth lecture of the series, delivered in 1970, was a seminal event that heralded much of the research agenda, since pursued by representatives of diverse disciplines, that touches on the evolution of human uniqueness.

Discussion: In his James Arthur lecture Pribram raised questions about the coding of information in the brain and about the complex association between language, symbol, and the unique human cognitive system. Read More

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http://dx.doi.org/10.1186/1747-5333-1-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1698933PMC
November 2006
4 Reads

What makes humanity humane.

Authors:
Karl H Pribram

J Biomed Discov Collab 2006 Nov 29;1:14. Epub 2006 Nov 29.

Cognitive Neuroscience, Department of Psychology Georgetown University, 37th and O Streets, Washington, DC 20057-1001, USA.

Scientific and popular lore have promulgated a connection between emotion and the limbic forebrain. However, there are a variety of structures that are considered limbic, and disagreement as to what is meant by "emotion". This essay traces the initial studies upon which the connection between emotion and the limbic forebrain was based and how subsequent experimental evidence led to confusion both with regard to brain systems and to the behaviors examined. Read More

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http://dx.doi.org/10.1186/1747-5333-1-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1693914PMC
November 2006
3 Reads

What makes man human: thirty-ninth James Arthur lecture on the evolution of the human brain, 1970.

Authors:
Karl H Pribram

J Biomed Discov Collab 2006 Nov 29;1:13. Epub 2006 Nov 29.

Neuropsychology laboratories, Stanford University, USA.

What makes man human is his brain. This brain is obviously different from those of nonhuman primates. It is larger, shows hemispheric dominance and specialization, and is cytoarchitecturally somewhat more generalized. Read More

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http://dx.doi.org/10.1186/1747-5333-1-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1702366PMC
November 2006
3 Reads

What makes us human? A biased view from the perspective of comparative embryology and mouse genetics.

J Biomed Discov Collab 2006 Nov 29;1:16. Epub 2006 Nov 29.

Developmental Neurobiology Unit, University of Louvain Medical School, 73, Avenue Mounier, Box 7382, B1200 Brussels, Belgium.

For a neurobiologist, the core of human nature is the human cerebral cortex, especially the prefrontal areas, and the question "what makes us human?" translates into studies of the development and evolution of the human cerebral cortex, a clear oversimplification. In this comment, after pointing out this oversimplification, I would like to show that it is impossible to understand our cerebral cortex if we focus too narrowly on it. Like other organs, our cortex evolved from that in stem amniotes, and it still bears marks of that ancestry. Read More

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http://dx.doi.org/10.1186/1747-5333-1-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1769396PMC
November 2006
2 Reads

The emergence and diffusion of DNA microarray technology.

J Biomed Discov Collab 2006 Aug 22;1:11. Epub 2006 Aug 22.

Jenkins Collaboratory for New Technologies in Society, Duke University, John Hope Franklin Center, 2204 Erwin Road, Durham, North Carolina 27708-0402, USA.

Unlabelled: The network model of innovation widely adopted among researchers in the economics of science and technology posits relatively porous boundaries between firms and academic research programs and a bi-directional flow of inventions, personnel, and tacit knowledge between sites of university and industry innovation. Moreover, the model suggests that these bi-directional flows should be considered as mutual stimulation of research and invention in both industry and academe, operating as a positive feedback loop. One side of this bi-directional flow--namely; the flow of inventions into industry through the licensing of university-based technologies--has been well studied; but the reverse phenomenon of the stimulation of university research through the absorption of new directions emanating from industry has yet to be investigated in much detail. Read More

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http://dx.doi.org/10.1186/1747-5333-1-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1590052PMC
August 2006
11 Reads

Tools for knowledge acquisition within the NeuroScholar system and their application to anatomical tract-tracing data.

J Biomed Discov Collab 2006 Aug 8;1:10. Epub 2006 Aug 8.

Information Sciences Institute, 4676 Admiralty Way, Marina Del Rey, CA 90292, USA.

Background: Knowledge bases that summarize the published literature provide useful online references for specific areas of systems-level biology that are not otherwise supported by large-scale databases. In the field of neuroanatomy, groups of small focused teams have constructed medium size knowledge bases to summarize the literature describing tract-tracing experiments in several species. Despite years of collation and curation, these databases only provide partial coverage of the available published literature. Read More

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http://dx.doi.org/10.1186/1747-5333-1-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1564149PMC
August 2006
3 Reads

Center for Behavioral Neuroscience: a prototype multi-institutional collaborative research center.

J Biomed Discov Collab 2006 Jul 17;1. Epub 2006 Jul 17.

Center for Behavioral Neuroscience, Georgia State University, P,O, Box 3966, Atlanta, Georgia 30302-3966, USA.

The Center for Behavioral Neuroscience was launched in the fall of 1999 with support from the National Science Foundation, the Georgia Research Alliance, and our eight participating institutions (Georgia State University, Emory University, Georgia Institute of Technology, Morehouse School of Medicine, Clark-Atlanta University, Spelman College, Morehouse College, Morris Brown College). The CBN provides the resources to foster innovative research in behavioral neuroscience, with a specific focus on the neurobiology of social behavior. Center faculty working in collaboratories use diverse model systems from invertebrates to humans to investigate fear, aggression, affiliation, and reproductive behaviors. Read More

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http://dx.doi.org/10.1186/1747-5333-1-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557540PMC
July 2006
2 Reads

Collaborative development of the Arrowsmith two node search interface designed for laboratory investigators.

J Biomed Discov Collab 2006 Jul 3;1. Epub 2006 Jul 3.

Department of Psychiatry and Psychiatric Institute, University of Illinois, MC912, 1601 W, Taylor Street, Chicago, IL 60612, USA.

Arrowsmith is a unique computer-assisted strategy designed to assist investigators in detecting biologically-relevant connections between two disparate sets of articles in Medline. This paper describes how an inter-institutional consortium of neuroscientists used the UIC Arrowsmith web interface http://arrowsmith.psych. Read More

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http://j-biomed-discovery.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/1747-5333-1-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1559644PMC
July 2006
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The effects of business practices, licensing, and intellectual property on development and dissemination of the polymerase chain reaction: case study.

J Biomed Discov Collab 2006 Jul 3;1. Epub 2006 Jul 3.

Center for Genome Ethics, Law & Policy, Institute for Genome Sciences & Policy, Duke University, Box 90141, Durham, NC 27708, USA.

Introduction: Polymerase chain reaction (PCR) was a seminal genomic technology discovered, developed, and patented in an industry setting. Since the first of its core patents expired in March, 2005, we are in a position to view the entire lifespan of the patent, examining how the intellectual property rights have impacted its use in the biomedical community. Given its essential role in the world of molecular biology and its commercial success, the technology can serve as a case study for evaluating the effects of patenting biological research tools on biomedical research. Read More

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http://dx.doi.org/10.1186/1747-5333-1-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1523369PMC
July 2006
21 Reads

Collaboration and distances between German immunological institutes--a trend analysis.

J Biomed Discov Collab 2006 Jun 14;1. Epub 2006 Jun 14.

Department of Library and Information Science, Humboldt University Berlin, Dorotheenstr, 26, D-10099 Berlin, Germany.

Background: The hypothesis that distance matters but that in recent years geographical proximity has become less important for research collaboration was tested. We have chosen a sample--authors at German immunological institutes--that is relatively homogeneous with regard to research field, language and culture, which beside distance are other possible factors influencing the willingness to co-operate. We analyse yearly distributions of co-authorship links between institutes and compare them with the yearly distributions of distances of all institutes producing papers in journals indexed in the Science Citation Index, editions 1992 till 2002. Read More

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http://dx.doi.org/10.1186/1747-5333-1-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1533863PMC
June 2006
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A tutorial on information retrieval: basic terms and concepts.

J Biomed Discov Collab 2006 Mar 13;1. Epub 2006 Mar 13.

Department of Computer Science, University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607, USA.

This informal tutorial is intended for investigators and students who would like to understand the workings of information retrieval systems, including the most frequently used search engines: PubMed and Google. Having a basic knowledge of the terms and concepts of information retrieval should improve the efficiency and productivity of searches. As well, this knowledge is needed in order to follow current research efforts in biomedical information retrieval and text mining that are developing new systems not only for finding documents on a given topic, but extracting and integrating knowledge across documents. Read More

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http://dx.doi.org/10.1186/1747-5333-1-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1459215PMC
March 2006
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The TREC 2004 genomics track categorization task: classifying full text biomedical documents.

J Biomed Discov Collab 2006 Mar 14;1. Epub 2006 Mar 14.

Department of Medical Informatics and Clinical Epidemiology, School of Medicine, Oregon Health & Science University, 3181 S,W, Sam Jackson Park Road, Mail Code: BICC, Portland, Oregon, 97239-3098, USA.

Background: The TREC 2004 Genomics Track focused on applying information retrieval and text mining techniques to improve the use of genomic information in biomedicine. The Genomics Track consisted of two main tasks, ad hoc retrieval and document categorization. In this paper, we describe the categorization task, which focused on the classification of full-text documents, simulating the task of curators of the Mouse Genome Informatics (MGI) system and consisting of three subtasks. Read More

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http://dx.doi.org/10.1186/1747-5333-1-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1440303PMC
March 2006
5 Reads

Enhancing access to the Bibliome: the TREC 2004 Genomics Track.

J Biomed Discov Collab 2006 Mar 13;1. Epub 2006 Mar 13.

Oregon Health & Science University, Portland, OR, USA.

Background: The goal of the TREC Genomics Track is to improve information retrieval in the area of genomics by creating test collections that will allow researchers to improve and better understand failures of their systems. The 2004 track included an ad hoc retrieval task, simulating use of a search engine to obtain documents about biomedical topics. This paper describes the Genomics Track of the Text Retrieval Conference (TREC) 2004, a forum for evaluation of IR research systems, where retrieval in the genomics domain has recently begun to be assessed. Read More

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http://dx.doi.org/10.1186/1747-5333-1-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1440302PMC
March 2006
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Nomen est Omen: do antidepressants increase p11 or S100A10?

J Biomed Discov Collab 2006 Apr 13;1. Epub 2006 Apr 13.

The Psychiatric Institute, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois 60612, USA.

Occasionally, multiple names are given to the same gene/protein. When this happens, different names can be used in subsequent publications, for example in different research areas, sometimes with little or no awareness that the same entity known under a different name may have a major role in another field of science. Recent reports about the protein p11 presented findings that this protein, commonly known as S100A10, may play a crucial role in depression and antidepressant treatment mechanisms. Read More

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http://dx.doi.org/10.1186/1747-5333-1-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1481606PMC
April 2006
2 Reads
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