The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

/pdf/gapped-blast-and-psi-blast-a-new-generation-of-protein-2ybl67x5yx.pdf

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

/pdf/cytoscape-a-software-environment-for-integrated-models-of-2fp1mf0u7b.pdf

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Once foods in the United States were fortified with vitamin D, rickets appeared to have been conquered, and many considered major health problems from vitamin D deficiency resolved. But vitamin D deficiency is common. This review considers the role of vitamin D in skeletal and nonskeletal health and suggests strategies for the prevention and treatment of vitamin D deficiency.

Vitamin D Deficiency

Comparative protein modeling is increasingly gaining interest since it is of great assistance during the rational design of mutagenesis experiments. The availability of this method, and the resulting models, has however been restricted by the availability of expensive computer hardware and software. To overcome these limitations, we have developed an environment for comparative protein modeling that consists of SWISS-MODEL, a server for automated comparative protein modeling and of the SWISS-PdbViewer, a sequence to structure workbench. The Swiss-PdbViewer not only acts as a client for SWISS-MODEL, but also provides a large selection of structure analysis and display tools. In addition, we provide the SWISS-MODEL Repository, a database containing more than 3500 automatically generated protein models. By making such tools freely available to the scientific community, we hope to increase the use of protein structures and models in the process of experiment design.

SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling.

741 742 743 744 745 746 747 748 749 Safety ofDOE Reactors Questioned Document Links NSF Official to Biotech Firm OECD to Set Rules for International Science Doctors Square Off on Employee Drug Testing Yale Takes Action Against Psychiatrists for Financial Improprieties New Look at Health in Developing Nations A Frustrating Glimpse of the True AIDS Epidemic NSF Lends a Hand with DOD Award Why Is Calculus Such a Hurdle? Btefitg: China Renews Pledge to Boost Basic Research * New Vice President and Trustee Named at Hughes

The Evolution of Catalytic Function

This pilot study describes a randomized controlled trial of an audio CD—based interactive guided imagery program for smoking cessation for adults versus a wait-listed control Feasibility, process measures, and biochemically validated abstinence were assessed at end of treatment (6 weeks) and 12 weeks, as well as at 52 weeks for intervention participants Fifty-nine percent of intervention participants attended four of six guided imagery sessions, and 94% found the technique helpful for smoking cessation Intervention participants had greater readiness to quit (Readiness to Quit Ladder, 83 vs 72, p < 05) and lower state anxiety (Spielberger Index, 32 vs 38, p < 05) at end of treatment than the control group Abstinence rates in the intervention versus control groups were 36% versus 18% (p = 43) at 6 weeks and 30% versus 12% (p = 40) at 12 weeks, respectively At 1 year, 24% of intervention participants remained abstinent A guided imagery program for smoking cessation was feasible, perceived to be

https://journals.sagepub.com/doi/pdf/10.1177/1533210106296773

Guided Imagery for Smoking Cessation in Adults: A Randomized Pilot Trial

https://www.onlinelibrary.wiley.com/doi/pdf/10.1002/art.1790090102

Alternative medical therapies for rheumatologic disorders

The science of bioinformatics has developed in the wake of methods to determine the sequences of the informational macromolecules—DNAs, RNAs and proteins. But in a wider sense, the biological world depends in its every process on the transmission of information, and hence bioinformatics is the fundamental core of biology. We here give a consideration of some of the key problems of bioinformatics in the coming decade, and perhaps longer.

/pdf/bioinformatic-challenges-for-the-next-decade-s-1zbjoxzf24.pdf

Bioinformatic challenges for the next decade(s)

https://people.mbi.ucla.edu/david/Reprints/254%20Guo,%20The%20mechanism%20of%20the%20amyloidogenic,%20JBC%202007.pdf

David Eisenberg

Papers

The Evolution of Catalytic Function

Guided Imagery for Smoking Cessation in Adults: A Randomized Pilot Trial

Alternative medical therapies for rheumatologic disorders

Bioinformatic challenges for the next decade(s)

The mechanism of the amyloidogenic conversion of T7 endonuclease I