biology

..For the thousand abstracts, 53 relationships were extracted of which 43 were correct, giving a specificity of 81 percent. These results are promising for multi-object identification and relationship finding from biological documents...

..However, before stepping into the limelight, next-generation sequencing had to overcome the inertia of a field that relied on Sanger-sequencing for 30 years...

Synthetic biology is a research field that combines the investigative nature of biology with the constructive nature of engineering...

..the automated detection and quantitative analysis of particle trajectories as recorded by video imaging in cell biology. The tracking process requires no a priori mathematical modeling of the motion, it is self-initializing, it ..

DNA Data Bank of Japan (DDBJ) provides Web-based systems for biological analysis, called Web APIs for biology (WABI). So far, we have developed over 20 SOAP services and several workflows that consist of a series of method invocations...

A survey of the use of graph theoretical techniques in Biology is presented...

..experimentally validated on a large scale, leaving many bioinformatic methods unproven and underutilized in the biology community...

..Self-organization concepts that were first developed in chemistry and physics and then applied to various morphogenetic problems in biology over the past century are now beginning to be applied to the organization of the living cell.

..We introduce, in particular, a mechanism based on a phosphorylation-dephosphorylation cycle. This mechanism enjoys a remarkable insulation property, due to the fast timescales of the phosphorylation and dephosphorylation reactions...

..The single-molecule approach to biology offers distinct advantages over the conventional approach of taking bulk measurements; this additional ..

..As the population ages and prostate cancer prevalence increases, challenges remain in the diagnosis of clinically relevant prostate cancer as well as the management of the metastatic and androgen-independent metastatic disease states...

..of process, there are a number of equally curious parallels and connections between the development of methods in biology and historical linguistics...

..This focus on the logic of organelles defined a crucial turning point in biomedical science. The following article sketches Palade's research, as part of a larger community that flourished after the Second World War...

Many areas of biology are open to mathematical and computational modelling. The application of discrete, logical formalisms defines the field of biomedical ontologies. Ontologies have been put to many uses in bioinformatics...

..Textpresso can be accessed at http://www.textpresso.org or via WormBase at http://www.wormbase.org...

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..In this review we focus on the role of circulating endothelial progenitor cells in endothelial cell repair mechanisms at the vascular wall and their potentially protective and therapeutic role in atherosclerotic disease...

..In this report, we will review these clinical implications of transforming growth factor-beta ...

A key component of any synthetic biology effort is the use of quantitative models. These models and their corresponding simulations allow optimization of a system design, as well as guiding their subsequent analysis...

New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully...

..The present review gives an update on the biochemistry, biology and clinical aspects of hepoxilin-based drug development...

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..development of robust extraction and quantification protocols for circulating RNA, new information regarding its biology and characteristics has been obtained...

..The prospects of plant proteomics are discussed...

The osmotic virial equation was used to predict osmolalities of solutions of interest in biology. The second osmotic virial coefficients, Bi, account for the interactions between identical solute molecules...

..In all these applications, the predictive model yields correct classification rates ranging from 80 to 100%. This provides motivation for pursuing its use as a medical diagnostic, monitoring and decision-making tool...

..It is then argued that biology arguably has no genuine laws of its own...

..Finally, applications for FHV as an epitopepresenting system are described with particular reference to its recent use for the development of a novel anthrax antitoxin and vaccine...

..Here we examine the recent literature looking at how structural biology has been used in a variety of successful fragment-screening applications...

..These findings reveal collective human behaviors in scientific research and help design better strategies in future knowledge exploration...

..Their widespread adoption could have a major impact on the introductory training of biology students.

..progresses faster when researchers operate within an explicit framework of concepts and theories, but currently biology has no explicit, overarching conceptual framework and few general theories...

..and the life sciences offers a broad palette of opportunities for researchers with interests ranging from coordination chemistry and spectroscopy to supramolecular chemistry and molecular recognition to metals in biology and medicine.

..and the goal of predictively and quantitatively understanding its function is one of the next great challenges in biology. Much of what we know about the cell concerns its constituent parts, but to a great extent we have yet to decode ..

The categorical data set is an important data class in experimental biology and contains data separable into several mutually exclusive categories...

..numbers of open reading frames into expression vectors are of critical importance for challenging structural biology projects...

..Symmetry breaking is essential for cell movement, polarity, and developmental patterning. Amplification of initial asymmetry is key to the conserved mechanisms involved...

..become widely recognized that in vitro culture systems must become three dimensional to correctly model in vivo biology. Attempts to modify conventional 2-D culture technology to accommodate 3-D cell growth such as embedding cells in ..

..In this respect biology resembles alternative model-rich frameworks, such as economics and engineering...

..Due to their versatility and vast body of known properties liposome-based formulations will continue to occupy a leading role among the large selection of emerging DDS...

Small-molecule fluorescent probes embody an essential facet of chemical biology. Although numerous compounds are known, the ensemble of fluorescent probes is based on a modest collection of modular "core" dyes...

..Several applications have been developed at PDBj for structural biology and biomedical studies: (i) a Java-based molecular graphics viewer, jV; (ii) display of electron density maps for ..

..This spatial control of bacterial gene expression could be used to 'print' complex biological materials, for example, and to investigate signalling pathways through precise spatial and temporal control of their phosphorylation steps...

..Different types of error bars give quite different information, and so figure legends must make clear what error bars represent. We suggest eight simple rules to assist with effective use and interpretation of error bars...

..Planarians are therefore an excellent model system for studying many aspects of stem cell biology. Here we report the cloning and initial characterization of 71 miRNAs from the planarian Schmidtea mediterranea...

..If allostatic load is chronically high, then pathologies develop. Type 2 allostatic overload does not trigger an escape response, and can only be counteracted through learning and changes in the social structure...

..This transformation requires a significant shift in the approach and attitude of the instructors and students, as well as in the procedures and techniques that are required to teach cell biology.

..This paper reviews the available information on the biology of DG, the abnormalities found in human cancers, and the implications of these findings with respect to our ..

..of novel biological systems by combining basic building blocks represents a dominant paradigm in synthetic biology. Creating and maintaining a database of these building blocks is a way to streamline the fabrication of complex ..

..e. pathway names, medical subject heading (MeSH) terms, etc)...

..These techniques will be useful for answering important biological questions in the future...

..The failure of many bio-ontologies to follow international standards for ontology design and description is hampering their application and threatens to restrict their future use...

..Biologists often feel overwhelmed by the huge amount of and the great diversity of distributed heterogeneous biological information...

..Although the current project requires this function only for plant taxa, the principle is extensible to the entire taxonomy. AVAILABILITY: www.plantgenomics.iastate.edu/PathBinderH. Source code and databases on request...

Laboratory classes are commonplace and essential in biology departments but can sometimes be cumbersome, unreliable, and a drain on time and resources...

..To our best knowledge, our system is the first one that copes with the cascaded phenomena...

The immense volume of data which is now available from experiments in molecular biology has led to an explosion in reported results most of which are available only in unstructured text format...

b>Biology has now become an information science, and researchers are increasingly dependent on expert-curated biological databases to organize the findings from the published literature...

..AVAILABILITY: The software is available at http://www.tm4.org. SUPPLEMENTARY INFORMATION: Results from the analysis of significant genes from the published Ang II study...

..jax.org/) resource provides the research community with access to information on the genetics, genomics, and biology of the laboratory mouse...

For most systems in biology, a large body of literature exists that describes the complexity of the system based on experimental results...

..ihop-net.org/UniPub/iHOP/info/logs/). Here we describe a public programmatic API that enables the integration of main iHOP functionalities in bioinformatic programs and workflows...

..The tool is designed to be used by experimental biologists with no training in bioinformatics. In the current state, the system presents a list of human cancer genes. Available at http://cargo.bioinfo.cnio.es...

High-throughput molecular biology provides new data at an incredible rate, so that the increase in the size of biological databanks is enormous and very rapid...

..g. micro-array analysis tools), often associated with steep learning curves and requiring expert knowledge...

Integration of heterogeneous data types is a challenging problem, especially in biology, where the number of databases and data types increase rapidly...

b>Biology can be regarded as a science of networks: interactions between various biological entities (eg genes, proteins, metabolites) on different levels (eg gene regulation, cell signalling) can be represented as graphs and, thus, ..

..The server and the underlying software are available to the public...

..The system is developed under the GPL license and can be downloaded from http://sourceforge.net/projects/ondex/..

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Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined...

..We conclude by outlining a research agenda to raise performance of named entity tagging to a level where it can be used to perform tasks of biological importance...

We review recent results in literature data mining for biology and discuss the need and the steps for a challenge evaluation for this field...

..In other domains, the technology plateaued at about 60% recall and precision. Even if applications to biomedical text do no better than this, they could still prove to be of immense help to curatorial activities...

..RESULTS: GENIA corpus version 3.0 consisting of 2000 MEDLINE abstracts has been released with more than 400,000 words and almost 100,000 annotations for biological terms...

..We report on the evaluation results and describe the techniques used by the top performing groups...

..Our evaluation shows that our extraction techniques could be a valuable supplement to resources such as SWISSPROT, as our systems were able to capture gene and protein synonyms not listed in the SWISSPROT database...

Recent advances in genomics and structural biology have resulted in an unprecedented increase in biological data available from Internet-accessible databases...

..Overall, BioRAT recalled 20.31% of the target facts from the abstracts with 55.07% precision, and achieved 43.6% recall with 51.25% precision on full-length papers...

Diffusion and osmosis are central concepts in biology, both at the cellular and organ levels. They are presented several times throughout most introductory biology textbooks (e.g...

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While researching student assumptions for the development of the Biology Concept Inventory (BCI; http://bioliteracy...

..Less well known is that he once made greater contributions to Biology and has been misunderstood in some aspects...

..sexual selection and altruism, endosymbiosis and eukaryotic cell evolution, evolutionary developmental biology, phenotypic plasticity, epigenetic inheritance and molecular evolution, experimental bacterial evolution, and ..

..Reviews of Steven Rose's The richness of life: the essential Stephen Jay Gould and Stephen Jay Gould's Punctuated equilibrium...

..We analyze these ambiguities and make suggestions for a standardization of mereological relations in biomedical ontologies...

..Hence, there is much interest in text mining, the use of computational tools to enhance the human ability to parse and understand complex text...

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How new morphologies evolve is a fundamental question in biology. Most morphological evolution involves changes in the size of organs, which is basically achieved in two ways, by changes in cell size and cell number...

The Science Education Partnership and Assessment Laboratory (SEPAL) in the Department of Biology at San Francisco State University (SFSU) - in strong collaboration with the San Francisco Unified School District (SFUSD), the ..

..From these studies we anticipate that we will develop a predictive understanding of how the cannabinoid and Galphao regulated signaling network triggers neurite extension. ..

..We will use the filtration barrier of the kidney cortex as our model system. We will use a combination of mathematical models and engineering approaches to develop a 3D tissue assembly. ..

..We anticipate that the proposed studies should provide new insights into how G protein coupling to other signal pathways can be used to evoke biological effects. ..

..It is anticipated that these studies will lead to the identification of key intracellular sites that are potential targets for therapeutic agents that have their effects by modulation of G protein signaling pathways. ..

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..We plan to use a systems biology approach to study how subunits of heterotrimeric Gi/o trigger neurite outgrowth in the Neuro-2A cell line and ..

..From such analysis we hope to define the key criteria involved in determining the characteristics of microdomains of signaling molecules within the cell. ..

..Such understanding could lead to new long acting therapeutic agents for many diseases. ..

..These core software enhancements will contribute to the longevity of MEGA for use in molecular evolution, bioinformatics, functional genomics, computational biology, and basic biomedicine applications.

..used to separate, characterize, and manipulate proteins is broadly important in biochemistry and molecular biology: areas of application include proteomics and systems biology, purification of protein therapeutics, use in lab-on-..

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..This research will be multidisciplinary, involving synthetic organic chemistry, molecular biology, structural biology, NMR spectroscopy, and computer calculations...

..Insights into the conditions under which children can succeed may yield procedures that might prove helpful to those afflicted with disorders affecting these critical functions. ..

..The proposed research program plans to develop greater program expertise in molecular biology. Additionally, it proposes to add a new faculty with NIDA interests...

..This has commercial application to orthopedic and periodontal surgical treatments of joint replacement, fracture repair, and bone resorption secondary to tooth decay...

..The peptide sequences under investigation extend the biological of the research to AIDS, malaria, influenza, and neurochemistry. ..

..In addition, how cells break symmetry and establish a polarity is a profound problem in cell biology. Understanding cell's intrinsic ability to polarize may lead to fundamental insights into the physical principles ..

..This approach could be used to select patients for individualized therapy using targeted sensitizing agents based on the proposed preclinical studies. ..

..Our preliminary results and the further work proposed will provide high-resolution structural information on AMPK, and should directly enable the rational design of AMPK-directed therapeutics. ..

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..will fulfill the day-to-day needs of basic and applied researchers as well as students in many areas of molecular biology crucial in human health research, including computational genomics, molecular genetics, developmental biology, ..

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..Together these observation should have important implications for understanding the behavior of molecular and inductive networks in general and the prevention and/or amelioration of neural crest defects in particular. ..

Nucleic acid transfection is one of the most important tools in modern biology, and an emerging tool for biomedical applications. In our proposed research, we will use gold nanoparticles as transfection vectors...

..FlyExpress informatics system will directly facilitate basic and applied research in many areas of molecular biology crucial in human health research, including computational genomics, molecular genetics, developmental biology, ..