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At least 1,117 records · Page 62Linked to original sources

PubMed2006

MHC-BPS: MHC-binder prediction server for identifying peptides of flexible lengths from sequence-derived physicochemical properties.

Major histocompatibility complex (MHC)-binding peptides are essential for antigen recognition by T-cell receptors and are being explored for vaccine design. Computational methods have been developed for predicting MHC-binding peptides of fixed lengths, based on the training of relatively few non-binders. It is desirable to introduce methods applicable for peptides of flexible lengths and trained by using more diverse sets of non-binders. MHC-BPS is a web-based MHC-binder prediction server that uses support vector machines for predicting peptide binders of flexible lengths for 18 MHC class I and 12 class II alleles from sequence-derived physicochemical properties, which were trained by using 4,208 approximately 3,252 binders and 234,333 approximately 168,793 non-binders, and evaluated by an independent set of 545 approximately 476 binders and 110,564 approximately 84,430 non-binders. The binder prediction accuracies are 86 approximately 99% for 25 and 70 approximately 80% for five alleles, and the non-binder accuracies are 96 approximately 99% for 30 alleles. A screening of HIV-1 genome identifies 0.01 approximately 5% and 5 approximately 8% of the constituent peptides as binders for 24 and 6 alleles, respectively, including 75 approximately 100% of the known epitopes. This method correctly predicts 73.3% of the 15 newly published epitopes in the last 4 months of 2005. MHC-BPS is available at http://bidd.cz3.nus.edu.sg/mhc/ .

Algorithms↗

PubMed1997

HOSEpipe--a WWW-hosted data management and analysis system for STS content mapping projects.

We have developed a data management system, 'HOSEpipe' (High Output STS Evaluation pipeline) to aid sample tracking and data analysis in STS content mapping projects. The system is based around a World Wide Web (WWW) server that provides a number of pages including forms for sample processing and data entry accessible via a standard WWW browser application. The system is split into two main modules: firstly, a sequence evaluation and annotation module that takes de novo sequence for a potential STS, screens it against existing STSs and DNA sequence databases, followed by appropriate primer sequence design; secondly, a module that handles YAC library STS screening and includes facilities for both sample tracking and experimental data analysis. We present the design and rationale of the HOSEpipe system and its development to support a whole chromosomal physical mapping project. This software and design approach is potentially applicable to physical mapping projects of varying sizes and resolution and to similar projects, such as sample sequencing and the construction of sequence-ready maps.

Animals↗

PubMed1989

Platelet activating factor is a potent colonic secretagogue with actions independent of specific PAF receptors.

Several candidate mediators of acute inflammation such as E-type prostaglandins, histamine and bradykinin are potent pro-diarrhoeal colonic secretagogues. They act to increase serosal to mucosal transport of chloride and passive water efflux. We investigated the effects of platelet activating factor (PAF) on muscle-stripped rat colon, measuring transepithelial potential difference (p.d.) and, under voltage clamp conditions, short circuit current (Isc). PAF induced dose-dependent increases in p.d. and Isc, with an approximate EC50 of 1.5 X 10(-10) M; similar concentrations of lyso-PAF had a much smaller but discernible effect. PAF and lyso-PAF both displayed 'sidedness' with serosal application effective and mucosal application ineffective. Inhibitor studies suggest that chloride is the principal ion carrier, but the specific PAF receptor antagonists kadsurenone, L652731, CV 3988 and WEB 2086 did not block the response. Unlike bradykinin, PAF did not cause the release of PGE2 into the serosal bathing fluid, and its action was not attenuated by the cyclo-oxygenase inhibitors piroxicam, mefenamic acid or flurbiprofen. We conclude that PAF has a powerful pro-diarrhoeal secretory action on colonic epithelium which is not mediated by the previously defined PAF receptor(s) and is independent of prostanoid generation.

Animals↗

PubMed2026

DeepMASS v.2: An enhanced deep learning platform for large-scale discovery and structural annotation of unknown plant metabolites.

Determining the structures of unknown metabolites remains a fundamental bottleneck in plant metabolomics, as the vast chemical diversity of plant secondary metabolites far exceeds the coverage of existing spectral libraries. Here, we present DeepMASS v.2, a substantially enhanced platform for annotating unknown metabolites from liquid chromatography-tandem mass spectrometry data, designed to address this challenge at scale. DeepMASS v.2 leverages a semantic spectral representation model trained on millions of spectra from GNPS, NIST, and in-house resources. By integrating Spec2Vec-based embeddings with HNSW (hierarchical navigable small world) graph retrieval and a unified chemical space defined by molecular fingerprints, DeepMASS v.2 identifies structurally related neighbors of unknown spectra and ranks candidate structures according to their proximity to the predicted structural neighborhoods within chemical space. Benchmarking against Critical Assessment of Small Molecule Identification datasets and a curated natural product collection demonstrated that DeepMASS v.2 outperforms state-of-the-art in silico annotation tools, including SIRIUS, CFM-ID, MetFrag, and MS-Finder. Importantly, DeepMASS v.2 maintains strong performance for metabolites absent from spectral libraries, highlighting its capacity to annotate genuinely unknown compounds. Application of DeepMASS v.2 to large-scale plant metabolomics datasets demonstrated its ability to expand accessible metabolome coverage. Implemented as an intuitive web platform, DeepMASS v.2 provides the community with a scalable, interpretable, and high-throughput solution for structural annotation, enabling more comprehensive characterization of plant chemical diversity and accelerating natural product discovery in molecular plant science. The DeepMASS v.2 web server is publicly available at http://deepmass.cn.

Metabolomics↗

PubMed2003

A human tissue and data resource: an overview of opportunities, challenges, and development of a provider/researcher partnership model.

As we continue to strive to apply the findings of in vitro and animal studies to human disease and transition from genomics to proteomics, we will experience an ever-increasing need for human tissues. A web based system that provides access to tissues repositories and associated data will best facilitate the access to these vital resources and the application of research information to human disease treatment. There are organizational and design requirements that must be addressed in the implementation of the infrastructures that are needed to implement such a system, with special attention paid to the protection of patient anonymity. This report describes the implementation of a prototype human tissue network in the hope of encouraging implementation of similar systems among other consortia of providers and researchers.

Animals↗

PubMed2004

A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins.

MOTIVATION: The dearth of structural data on alpha-helical membrane proteins (MPs) has hampered thus far the development of reliable knowledge-based potentials that can be used for automatic prediction of transmembrane (TM) protein structure. While algorithms for identifying TM segments are available, modeling of the TM domains of alpha-helical MPs involves assembling the segments into a bundle. This requires the correct assignment of the buried and lipid-exposed faces of the TM domains. RESULTS: A recent increase in the number of crystal structures of alpha-helical MPs has enabled an analysis of the lipid-exposed surfaces and the interiors of such molecules on the basis of structure, rather than sequence alone. Together with a conservation criterion that is based on previous observations that conserved residues are mostly found in the interior of MPs, the bias of certain residue types to be preferably buried or exposed is proposed as a criterion for predicting the lipid-exposed and interior faces of TMs. Applications to known structures demonstrates 80% accuracy of this prediction algorithm. AVAILABILITY: The algorithm used for the predictions is implemented in the ProperTM Web server (http://icb.med.cornell.edu/services/propertm/start).

Algorithms↗

PubMed1998

The PIR-International Protein Sequence Database.

From its origin the Protein Information Resource (http://www-nbrf. georgetown.edu/pir/) has supported research on evolution and computational biology by designing and compiling a comprehensive, quality controlled, and well-organized protein sequence database. The database has been produced and updated on a regular schedule since 1984. Since 1988 it has been maintained collaboratively by the PIR-International, an association of data collection centers engaged in international cooperation for the development of this research resource during a period of explosive acquisition of new data. As of June 1997, essentially all sequence entries have been classified into families, allowing the efficient application of methods to propagate and standardize annotation among related sequences. The databases are available through the Internet by the World-Wide Web and FTP, or on CD-ROM and magnetic media.

Amino Acid Sequence↗

PubMed1999

DBcat: a catalog of biological databases.

The DBcat (http://www.infobiogen.fr/services/dbcat) is a comprehensive catalog of biological databases, maintained and curated on a daily basis at GIS Infobiogen. It contains more than 400 databases classified by application domains. The DBcat is a structured flat file library, that can be searched by means of an SRS server or a dedicated Web interface. The files are available for downloading from Infobiogen anonymous ftp server.

Biology↗

PubMed2004

LINKER: a web server to generate peptide sequences with extended conformation.

LINKER was developed as an online server to assist biomedical researchers to design linker sequences for constructing functional fusion proteins. The program automatically generates a set of peptide sequences that are known to adopt extended conformations as determined by X-ray crystallography and NMR. In addition to the desired linker sequence length, the web interface provides a number of optional input parameters so that the users may enhance sequence selection based on the requirements of specific applications. The output of LINKER includes a list of peptide sequences with specified length and sequence characteristics. A graphical subroutine was implemented to highlight the chemical features of every linker sequence by hydrophobicity plots. LINKER can be accessed at http://astro.temple.edu/~feng/Servers/BioinformaticServers.htm.

Amino Acid Sequence↗

PubMed2006

QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences.

The quadruplex structures formed by guanine-rich nucleic acid sequences have received significant attention recently because of growing evidence for their role in important biological processes and as therapeutic targets. G-quadruplex DNA has been suggested to regulate DNA replication and may control cellular proliferation. Sequences capable of forming G-quadruplexes in the RNA have been shown to play significant roles in regulation of polyadenylation and splicing events in mammalian transcripts. Whether quadruplex structure directly plays a role in regulating RNA processing requires investigation. Computational approaches to study G-quadruplexes allow detailed analysis of mammalian genomes. There are no known easily accessible user-friendly tools that can compute G-quadruplexes in the nucleotide sequences. We have developed a web-based server, QGRS Mapper, that predicts quadruplex forming G-rich sequences (QGRS) in nucleotide sequences. It is a user-friendly application that provides many options for defining and studying G-quadruplexes. It performs analysis of the user provided genomic sequences, e.g. promoter and telomeric regions, as well as RNA sequences. It is also useful for predicting G-quadruplex structures in oligonucleotides. The program provides options to search and retrieve desired gene/nucleotide sequence entries from NCBI databases for mapping G-quadruplexes in the context of RNA processing sites. This feature is very useful for investigating the functional relevance of G-quadruplex structure, in particular its role in regulating the gene expression by alternative processing. In addition to providing data on composition and locations of QGRS relative to the processing sites in the pre-mRNA sequence, QGRS Mapper features interactive graphic representation of the data. The user can also use the graphics module to visualize QGRS distribution patterns among all the alternative RNA products of a gene simultaneously on a single screen. QGRS Mapper can be accessed at http://bioinformatics.ramapo.edu/QGRS/.

Computer Graphics↗

PubMed2002

Identity and search in social networks.

Social networks have the surprising property of being "searchable": Ordinary people are capable of directing messages through their network of acquaintances to reach a specific but distant target person in only a few steps. We present a model that offers an explanation of social network searchability in terms of recognizable personal identities: sets of characteristics measured along a number of social dimensions. Our model defines a class of searchable networks and a method for searching them that may be applicable to many network search problems, including the location of data files in peer-to-peer networks, pages on the World Wide Web, and information in distributed databases.

Algorithms↗

PubMed2004

Database for the collection and analysis of clinical data and images of neoplasms of the sinonasal tract.

The Neoplasms of the Sinonasal Tract software package (NSNT v 1.0) implements a complete visual database for patients with sinonasal neoplasia, facilitating standardization of data and statistical analysis. The software, which is compatible with the Macintosh and Windows platforms, provides multiuser application with a dedicated server (on Windows NT or 2000 or Macintosh OS 9 or X and a network of clients) together with web access, if required. The system hardware consists of an Apple Power Macintosh G4500 MHz computer with PCI bus, 256 Mb of RAM plus 60 Gb hard disk, or any IBM-compatible computer with a Pentium 2 processor. Image acquisition may be performed with different frame-grabber cards for analog or digital video input of different standards (PAL, SECAM, or NTSC) and levels of quality (VHS, S-VHS, Betacam, Mini DV, DV). The visual database is based on 4th Dimension by 4D Inc, and video compression is made in real-time MPEG format. Six sections have been developed: demographics, symptoms, extent of disease, radiology, treatment, and follow-up. Acquisition of data includes computed tomography and magnetic resonance imaging, histology, and endoscopy images, allowing sequential comparison. Statistical analysis integral to the program provides Kaplan-Meier survival curves. The development of a dedicated, user-friendly database for sinonasal neoplasia facilitates a multicenter network and has obvious clinical and research benefits.

Computers↗

PubMed2006

The Australian experiment: the use of evidence based medicine for the reimbursement of surgical and diagnostic procedures (1998-2004).

BACKGROUND: In 1998 a formal process using the criteria of safety, effectiveness and cost-effectiveness (evidence based medicine) on the introduction and use of new medical procedures was implemented in Australia. As part of this process an expert panel, the Medical Services Advisory Committee (MSAC) was set up. This paper examines the effectiveness of this process based on the original criteria, that is, evidence based medicine. METHOD: The data for this analysis was sourced primarily from that made available in the public domain. The MSAC web site provided Minutes from MSAC meetings; Annual Reports; Assessment and Review reports; Progress status; and Archived material. RESULTS: The total number of applications submitted to the MSAC has been relatively low averaging approximately only fourteen per year. Additionally, the source of applications has quickly shifted to the medical devices, equipment and diagnostic industry as being the major source of applications. An overall average time for the processing of an application is eighteen months. Negative recommendations were in most cases based on insufficient clinical evidence rather than clinical evidence that clearly demonstrated a lack of clinical effectiveness. It was rare for a recommendation, either positive or negative, to be based on cost-effectiveness. CONCLUSION: New medical procedures are often the result of a process of experimentation rather than formally conducted research. Affordability and the question of who should pay for the generation, collection and analysis of the clinical evidence is perhaps the most difficult to answer. This is especially the case where the new procedure is the result of a process of experimentation with an old procedure. A cost-effective way needs to be found to collect acceptable levels of evidence proving the clinical effectiveness of these new procedures, otherwise the formal processes of evaluation such as that used by the Australian MSAC since 1998 will continue to run the risk of committing Type II errors, that is, denying access to medical procedures that are beneficial and efficient.

Journal Article↗

PubMed2005

SOP3: a web-based tool for selection of oligonucleotide primers for single nucleotide polymorphism analysis by Pyrosequencing.

SOP3 is a web-based software tool for designing oligonucleotide primers for use in the analysis of single nucleotide polymorphisms (SNPs). Accessible via the Internet, the application is optimized for developing the PCR and sequencing primers that are necessary for Pyrosequencing. The application accepts as input gene name, SNP reference sequence number, or chromosomal nucleotide location. Output can be parsed by gene name, SNP reference number, heterozygosity value, location, chromosome, or function. The location of an individual polymorphism, such as an intron, exon, or 5' or 3' untranslated region is indicated, as are whether nucleotide changes in an exon are associated with a change in an amino acid sequence. SOP3 presents for each entry a set of forward and biotinylated reverse PCR primers as well as a sequencing primer for use during the analysis of SNPs by Pyrosequencing. Theoretical pyrograms for each allele are calculated and presented graphically. The method has been tested in the development of Pyrosequencing assays for determining SNPs and for deletion/insertion polymorphisms in the human genome. Of the SOP3-designed primer sets that were tested, a large majority of the primer sets have successfully produced PCR products and Pyrosequencing data.

Algorithms↗

PubMed2000

PACS and RIS: approaches to integration.

PACS and RIS have traditionally been discrete information systems with separate databases. Maintaining more than one database containing identical data sets creates the potential for outdated information being used in parallel with accurate information. Today, because of increased implementation of PACS and improved Web technology, this problem must be solved. Furthermore, as PACS technology is applied to areas outside radiology such database issues become more critical. Application of XML offers a cost-effective and workable solution to many of the thorniest problems that will likely become more prevalent in the post-Y2K era.

Database Management Systems↗

PubMed2001

What is bioinformatics? A proposed definition and overview of the field.

BACKGROUND: The recent flood of data from genome sequences and functional genomics has given rise to new field, bioinformatics, which combines elements of biology and computer science. OBJECTIVES: Here we propose a definition for this new field and review some of the research that is being pursued, particularly in relation to transcriptional regulatory systems. METHODS: Our definition is as follows: Bioinformatics is conceptualizing biology in terms of macromolecules (in the sense of physical-chemistry) and then applying "informatics" techniques (derived from disciplines such as applied maths, computer science, and statistics) to understand and organize the information associated with these molecules, on a large-scale. RESULTS AND CONCLUSIONS: Analyses in bioinformatics predominantly focus on three types of large datasets available in molecular biology: macromolecular structures, genome sequences, and the results of functional genomics experiments (e.g. expression data). Additional information includes the text of scientific papers and "relationship data" from metabolic pathways, taxonomy trees, and protein-protein interaction networks. Bioinformatics employs a wide range of computational techniques including sequence and structural alignment, database design and data mining, macromolecular geometry, phylogenetic tree construction, prediction of protein structure and function, gene finding, and expression data clustering. The emphasis is on approaches integrating a variety of computational methods and heterogeneous data sources. Finally, bioinformatics is a practical discipline. We survey some representative applications, such as finding homologues, designing drugs, and performing large-scale censuses. Additional information pertinent to the review is available over the web at http://bioinfo.mbb.yale.edu/what-is-it.

Computational Biology↗

PubMedDate not supplied

From idea to market: the drug approval process.

BACKGROUND: Each year many new prescription drugs are approved by the Food and Drug Administration (FDA). The process of developing and bringing new drugs to market is important for primary care physicians to understand. METHODS: We describe the drug development process based on a review of the literature and Web sites addressing FDA processes and policies. RESULTS: The process starts with preclinical testing. For drugs that appear safe, an investigational new drug application is filed with the FDA. If approved, clinical trials begin with phase 1 studies that focus on safety and pharmacology. Phase 2 studies examine the effectiveness of the compound. Phase 3 is the final step before submitting a new drug application (NDA) to the FDA. An NDA contains all the information obtained during all phases of testing. Phase 4 studies, or postmarketing studies, are conducted after a product is approved. Recent changes in legislation have streamlined the approval process. Critics contend that these changes have compromised public safety, resulting in the need to recall several products from the market. Proponents claim that changes in the approval process help patients with debilitating diseases, such as acquired immunodeficiency syndrome, that were previously denied critical medication because of bureaucratic regulations.

Drug Approval↗

PubMedDate not supplied

Supporting families' savvy use of the Internet for health research.

An increasing number of health care consumers are using the Internet for health-related research through Web sites, newsgroups, chat rooms, and listserves. This use of the Internet can be empowering for consumers. It encourages both collaboration and a family-centered approach to care and could contribute to improved outcomes and cost savings. At the same time, care and caution are needed regarding interpretation of health-related information obtained on the Internet. Nurses can help consumers become Internet savvy and learn ways to evaluate the likelihood that information they find on the Internet is from a reputable site. First, health care consumers using the Web should be encouraged to be skeptical and to approach Internet health research with a clear list of questions that can be used to evaluate Internet sites. Second, several on-line "site-checkers" can be applied to achieve a similar evaluation. A third approach is to look for the emblem of the Health on the Net Foundation's voluntary Code of Conduct (HONCode) for medical and health Web sites. Finally, open, collaborative relationships among health care consumers, families, and health care providers will encourage a discussion of the relevance and applicability of an individual's Internet research findings to the medical or nursing care plan.

Caregivers↗