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At least 685 records · Page 38Linked to original sources
PubMed1983

Basolateral potassium channel in turtle colon. Evidence for single-file ion flow.

Treatment of the apical surface of the isolated, ouabain-inhibited turtle colon with the polyene antibiotic amphotericin B permitted the properties of a barium-sensitive potassium conductance in the basolateral membrane to be discerned from the measurements of transepithelial fluxes and electrical currents. Simultaneous measurements of potassium currents and 42K fluxes showed that the movement of potassium was not in accord with simple diffusion. Two other cations, thallium and rubidium, were also permeable and, in addition, exhibited strong interactions with the potassium tracer fluxes. The results indicate that permeant cations exhibit positive coupling, which is consistent with a single-file mechanism of ion translocation through a membrane channel.

Animals↗
PubMed2003

Using hospital discharge files to enhance cancer surveillance.

Use of the traditional mechanism for cancer surveillance, hospital-based registries, may limit ascertainment of incident cases. In this study, the authors evaluated the ability of a statewide hospital discharge file (HDF) to enhance central cancer registry reporting. Incident cancers from a Virginia cancer registry were linked with an HDF for 1995. Medical record abstractions for over 2,000 cancers verified HDF and registry data. There were 19,740 unique cases ascertained from the two combined data sources. The registry captured approximately 83% of cases, while the HDF captured 62%. Although the HDF missed a substantial number of registry cases, the HDF positive predictive value for identifying the correct cancer site was 94%. Logistic regression was used to identify significant characteristics of cases likely to be captured only by the HDF; these characteristics included hospital cancer program certification, the position of the cancer diagnosis on the claim, and cancer surgery. This study represents the evaluation of a novel approach to enhancing registry completeness and accuracy using statewide HDFs. The results strongly suggest that neither a central cancer registry nor an HDF is a sufficient source for complete capture of cases. Using HDFs to supplement a central cancer registry may be a valuable and efficient method for improving registry completeness of reporting.

Aged↗
PubMed1997

Two applications to facilitate the viewing of database search result files on the Macintosh.

MOTIVATION: MacBOB (Macintosh BLAST Output Browser) and MacBOB Filter are two Macintosh-based applications that greatly simplify the viewing of BLAST and FASTA search results files. AVAILABILITY: The programs can be obtained via anonymous ftp from ftp.ri.bbsrc.ac.uk from the directory/pub/software/MacBOB, or via WWW from the Roslin Institute Home Page (http://www.ri.bbsrc.ac.uk/).

Base Sequence↗
PubMed2001

SIR: a simple indexing and retrieval system for biological flat file databases.

SUMMARY: SIR is a Simple Indexing and Retrieval tool for indexing and searching biological flat file databases. SIR is a cross-platform solution entirely written in Python. Since the package is very small and installation is trivial, this would be an ideal solution for database providers to provide a custom retrieval tool to access them. AVAILABILITY: The modules will be made available at http://www.EMBLHeidelberg.de/~chenna/PySAT/sir.html

Abstracting and Indexing↗
PubMed1992

REF-LIST: program to list references found in DOS text files of scientific manuscripts.

A computer program, coded in QuickBASIC language, is used to make a non-redundant list of references, in alphabetical order, that are found in a scientific manuscript (formatted as a DOS text file). The program can extract either direct or indirect citations as in the following: Byers (1983a, b, 1984) and Miller and Keen, 1960; Byers et al., 1984; Byers 1984) An IBM-compatible personal computer is required to run the executable program.

Algorithms↗
PubMed1993

SRS--an indexing and retrieval tool for flat file data libraries.

SRS (Sequence Retrieval System) is an information indexing and retrieval system designed for libraries with a flat file format such as the EMBL nucleotide sequence databank, the SwissProt protein sequence databank or the Prosite library of protein subsequence consensus patterns. SRS supports the data structure of these libraries by providing special indices for implementing lists of subentities (e.g. feature tables) or hierarchically structured data-fields (e.g. taxonomic classification). A language (ODD) has been designed for the convenient specification of library format and organization, representation of individual data-fields within the system (design of indices) and structuring other data needed during retrieval. This ensures flexibility required for coping with different library formats, which are subject to continuous change. Queries and inspection of retrieved entries can be performed from a user interface with pull-down menus and windows. SRS supports various input and output formats but is particularly well adapted to the GCG programs.

Abstracting and Indexing↗
PubMed1993

Transforming a set of biological flat file libraries to a fast access network.

SRS (Sequence Retrieval System), an indexing system for flat file libraries, provides fast access to individual library entries via retrieval by keywords from various data fields. SRS is now also able to build indices using cross-references that most libraries provide. Fifteen libraries of DNA and protein sequences and structures have been selected. These libraries interact with at least one other by means of cross-references. Indexing these cross-references allows a complete network of libraries to be built. In the network an entry from one library can be linked in principle to every other library. If two libraries are not directly cross-referenced, the linkage can be made with a succession of single links between neighbouring, cross-referenced libraries. A new operator has been added to the query language of SRS for convenient specification of links amongst complete libraries or entry sets generated by previous queries on particular libraries. All the information in the network can now be used to retrieve an entry in a specific library, e.g. the full information given in amino acid sequence entries from SwissProt can now be used to retrieve related tertiary structure entries from PDB. Furthermore, a search in a single library can be extended to a search in the complete library network, e.g. all entries in all databases pertaining to elastase can be found.

Algorithms↗
PubMed2025

vcfgl: a flexible genotype likelihood simulator for VCF/BCF files.

MOTIVATION: Accurate quantification of genotype uncertainty is pivotal in ensuring the reliability of genetic inferences drawn from NGS data. Genotype uncertainty is typically modeled using Genotype Likelihoods (GLs), which can help propagate measures of statistical uncertainty in base calls to downstream analyses. However, the effects of errors and biases in the estimation of GLs, introduced by biases in the original base call quality scores or the discretization of quality scores, as well as the choice of the GL model, remain under-explored. RESULTS: We present vcfgl, a versatile tool for simulating genotype likelihoods associated with simulated read data. It offers a framework for researchers to simulate and investigate the uncertainties and biases associated with the quantification of uncertainty, thereby facilitating a deeper understanding of their impacts on downstream analytical methods. Through simulations, we demonstrate the utility of vcfgl in benchmarking GL-based methods. The program can calculate GLs using various widely used genotype likelihood models and can simulate the errors in quality scores using a Beta distribution. It is compatible with modern simulators such as msprime and SLiM, and can output data in pileup, Variant Call Format (VCF)/BCF, and genomic VCF file formats, supporting a wide range of applications. The vcfgl program is freely available as an efficient and user-friendly software written in C/C++. AVAILABILITY AND IMPLEMENTATION: vcfgl is freely available at https://github.com/isinaltinkaya/vcfgl.

Software↗
PubMed2025

DeNoFo: a file format and toolkit for standardized, comparable de novo gene annotation.

MOTIVATION: De novo genes emerge from previously non-coding regions of the genome, challenging the traditional view that new genes primarily arise through duplication and adaptation of existing ones. Characterized by their rapid evolution and their novel structural properties or functional roles, de novo genes represent a young area of research. Therefore, the field currently lacks established standards and methodologies, leading to inconsistent terminology and challenges in comparing and reproducing results. RESULTS: This work presents a standardized annotation format to document the methodology of de novo gene datasets in a reproducible way. We developed DeNoFo, a toolkit to provide easy access to this format that simplifies annotation of datasets and facilitates comparison across studies. Unifying the different protocols and methods in one standardized format, while providing integration into established file formats, such as fasta or gff, ensures comparability of studies and advances new insights in this rapidly evolving field. AVAILABILITY AND IMPLEMENTATION: DeNoFo is available through the official Python Package Index (PyPI) and at https://github.com/EDohmen/denofo. All tools have a graphical user interface and a command line interface. The toolkit is implemented in Python3, available for all major platforms and installable with pip and uv.

Software↗
PubMed2003

PDB file parser and structure class implemented in Python.

UNLABELLED: The biopython project provides a set of bioinformatics tools implemented in Python. Recently, biopython was extended with a set of modules that deal with macromolecular structure. Biopython now contains a parser for PDB files that makes the atomic information available in an easy-to-use but powerful data structure. The parser and data structure deal with features that are often left out or handled inadequately by other packages, e.g. atom and residue disorder (if point mutants are present in the crystal), anisotropic B factors, multiple models and insertion codes. In addition, the parser performs some sanity checking to detect obvious errors. AVAILABILITY: The Biopython distribution (including source code and documentation) is freely available (under the Biopython license) from http://www.biopython.org

Computer Simulation↗
PubMed2004

GeneRecords: a relational database for GenBank flat file parsing and data manipulation in personal computers.

UNLABELLED: Extracting the desired data from a database entry for later analysis is a constant need in the biological sequence analysis community; GeneRecords 1.0 is a solution for GenBank biological flat file parsing, as it implements a structured representation of each feature and feature qualifier in GenBank following import in a common database managing system usable in a personal computer (Macintosh and Windows environments). This collection of related databases enables the local management of GenBank records, allowing indexing, retrieval and analysis of both information and sequences on a personal computer. AVAILABILITY: The current release, including the FileMaker Pro runtime application (built for Windows and Macintosh environments), is freely available at http://apollo11.isto.unibo.it/software/

Database Management Systems↗
PubMed1993

A novel use of the link-file system for longitudinal studies of HIV infection: a practical solution to an ethical dilemma.

BACKGROUND: Longitudinal studies that collect sensitive data, such as test results for HIV antibodies, present difficult ethical problems for investigators. Personal identifiers are needed for longitudinal follow-up, but current regulations in the United States require that all subjects be informed of their HIV test results when identifiers are retained. Therefore, subjects who do not wish to learn their HIV status must be excluded from prospective research. Because these subjects may be at particularly high risk for HIV infection, this situation may lead to substantial bias. METHODS: We describe a new application of a methodology for blinding such studies, based on the link-file system used for protecting subjects' sensitive research data. This design enables investigators to hold each subject's HIV test result and survey data for multiple ascertainments over time while effectively severing any link between this information and the subject's identity. This objective is achieved by a process of sequential coding, using at least two coders who are not associated with the study. CONCLUSIONS: The method described in this paper permits investigators in the United States to perform important prospective epidemiologic studies while adhering to current regulations for the conduct of such investigations.

Anonymous Testing↗
PubMed2025

DeNoFo: a file format and toolkit for standardised, comparable de novo gene annotation.

MOTIVATION: De novo genes emerge from previously non-coding regions of the genome, challenging the traditional view that new genes primarily arise through duplication and adaptation of existing ones. Characterised by their rapid evolution and their novel structural properties or functional roles, de novo genes represent a young area of research. Therefore, the field currently lacks established standards and methodologies, leading to inconsistent terminology and challenges in comparing and reproducing results. RESULTS: This work presents a standardised annotation format to document the methodology of de novo gene datasets in a reproducible way. We developed DeNoFo, a toolkit to provide easy access to this format that simplifies annotation of datasets and facilitates comparison across studies. Unifying the different protocols and methods in one standardised format, while providing integration into established file formats, such as fasta or gff, ensures comparability of studies and advances new insights in this rapidly evolving field. AVAILABILITY AND IMPLEMENTATION: DeNoFo is available through the official Python Package Index (PyPI) and at https://github.com/EDohmen/denofo . All tools have a graphical user interface and a command line interface. The toolkit is implemented in Python3, available for all major platforms and installable with pip and uv.

Journal Article↗
PubMed2002

Transient behavior in single-file systems.

We have used Monte Carlo methods and analytical techniques to investigate the influence of the characteristics, such as pipe length, diffusion, adsorption, desorption, and reaction rates on the transient properties of single-file systems. The transient or the relaxation regime is the period in which the system is evolving to equilibrium. We have studied the system when all the sites are reactive and also when only some of them are reactive. Comparisons between mean-field predictions, cluster approximation predictions, and Monte Carlo simulations for the relaxation time of the system are shown. We outline the cases where the mean-field analysis gives good results compared to dynamic Monte Carlo results. For some specific cases we can analytically derive the relaxation time. Occupancy profiles for different distributions of the sites both for the mean field and simulations are compared. Different results for slow and fast reaction systems and different distributions of reactive sites are discussed.

Journal Article↗
PubMed2002

From gene families and genera to incomes and internet file sizes: why power laws are so common in nature.

We present a simple explanation for the occurrence of power-law tails in statistical distributions by showing that if stochastic processes with exponential growth in expectation are killed (or observed) randomly, the distribution of the killed or observed state exhibits power-law behavior in one or both tails. This simple mechanism can explain power-law tails in the distributions of the sizes of incomes, cities, internet files, biological taxa, and in gene family and protein family frequencies.

Journal Article↗
PubMed2003

Analytical results for the reactivity of a single-file system.

We derive analytical expressions for the reactivity of a single-file system with fast diffusion and particles entering and leaving the system at one end. If the conversion reaction is fast, then the reactivity depends only very weakly on the system size, and the conversion is about 100%. If the reaction is slow, then the reactivity becomes proportional to the system size, the loading, and the reaction rate constant. If the system size increases the reactivity goes to the geometric mean of the reaction rate constant and the rate of particles entering and leaving the system. For large systems, the number of unconverted particles decreases exponentially with distance from the open end.

Journal Article↗
PubMed2006

Single file diffusion in macroscopic Wigner rings.

The single file diffusion in a circular channel of millimetric charged balls is studied. The evolution in time of the mean square displacement is shown to be subdiffusive, but slower than the powerlike t1/2 behavior observed in circular colloidal systems or predicted in one-dimensional infinite systems.

Journal Article↗
PubMed2004

Single-file diffusion of colloids in one-dimensional channels.

We study the diffusive behavior of colloidal particles which are confined to one-dimensional channels generated by scanning optical tweezers. At long times t, the mean-square displacement is found to scale as t(1/2), which is expected for systems where single-file diffusion occurs. In addition, we experimentally obtain the long-time, self-diffusive behavior from the short-time collective density fluctuations of the system as suggested by a recent analytical approach [Phys. Rev. Lett. 90, 180602 (2003)].

Journal Article↗