SEARCH · PubMed Health

Results for “Programming Languages”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 361 records · Page 20Linked to original sources

PubMed1999

PC controlled toothbrush/dentifrice abrasion machine.

A toothbrush/dentifrice abrasion machine was developed to use in dental research laboratory. The mechanism was designed as a hexagonal block driven by two stepping motors which move the mechanism in four directions. In order to control the stepping motors speed, position and direction commands or signals were generated by a software written in C Programming Language and then these commands were applied the stepping motor drives through parallel port of a personal computer. The toothbrush/dentifrice abrasion machine was finally used to measure different longevity of tooth brush. It was experimentally shown that the mechanism can be used for highly accurate position and speed applications.

Dental Materials↗

PubMed1987

Experimental analysis of syntax training in Broca's aphasia: a generalization and social validation study.

A multiple baseline design across responses was used to examine the effect of syntax training on the sentence production of 4 individuals with chronic Broca's aphasia. Subjects were trained to produce five exemplars of five sentence types from Helm's Elicited Language Program for Syntax Stimulation (Helm-Estabrooks, 1981). Generalization and maintenance of trained sentence types to novel exemplars and novel stimulus conditions served as dependent measures. In addition, five naïve judges rated subjects' responses before and following the treatment in terms of their "adequacy." Generalization to novel exemplars was demonstrated sequentially by 3 subjects (i.e., following the teaching of all five forms), and the remaining subject demonstrated generalization for three of five sentence types trained. Maintenance was variable across subjects and sentence types. Generalization across stimulus conditions was limited for all subjects. Adequacy judgments revealed improved communication skills for wh-questions but limited changes in the perceived adequacy of subjects' declarative responses. These findings indicate that the effects of syntax training procedures are limited to those grammatical constructions taught, that generalization of learned forms to novel stimulus conditions is not an automatic consequence of acquisition, and that the effect of such training on the adequacy of subjects' responses may be limited.

Adult↗

PubMed1998

[Topography-assisted correction of superficial irregularities of the cornea with the excimer laser].

BACKGROUND: A retinal image performance distorted by an asymmetric or irregular corneal surface cannot be compensated for with spherocylindric glasses completely. The best-corrected visual acuity is markedly decreased and contact lens fitting often impossible. The purpose of this study was to calculate the differential height between corneal topography raw data and any regular surface with mathematical methods in order to ablate the differential height with a computer-controlled laser beam, thereafter. METHODS: A Zernike decomposition of radial degree n = 16 was realized within a clinically relevant central corneal area of 8 mm in diameter based on corneal topography raw height data of a commercially available topographer (TMS-1, Tomey, Erlangen). Any target surface could be defined by varying weighting of the Zernike coefficients. The calculated differential height ablation between the raw data and the target surface given in a polar grid was transformed to a Cartesian grid to evaluate the sleeping time at each grid position considering the characteristic ablation curve for the intended ablation of the height difference. Subsequently, differential height ablation was simulated using an automated laser beam control for a modified excimer laser (MEL60, Aesculap-Meditec, Jena). We developed software tools for Zernike decomposition of corneal topography raw height data and time-regulated automatic laser beam control of the grid positions in the higher programming language C (Borland C++ 3.1, Borland Inc., München). RESULTS: Definition of a target surface can be realized alternatively by selecting a set of Zernike coefficients or defining a spherical or spherocylindrical surface by superposition of parabolic terms in a fixed proportion creating a best-fit target surface to the raw data. In originally "relatively flat" areas, the differential height profile indicates a "relatively deep" ablation resulting in relative steepening towards the periphery of the ablation zone. The resolution of the mechanical unit of the laser beam control consisting of two linear stepping motors is 9 microns in the focal plane with a reproducibility of 5 microns. The software unit is guiding the laser beam in a meandering fashion within the ablation area considering the calculated sleeping time for each grid position. Mean overlap of the 1 mm laser spots is 70%. The laser beam diameter of 1 mm effects a peripheral transition zone of 0.5 mm. CONCLUSIONS: Zernike decomposition of corneal topography height data is an efficient tool for localizing and quantifying superficial irregularities and for directly calculating an ablation profile from created differential height data. With an automatic laser beam control a well-defined laser ablation of superficial corneal irregularities is possible, subsequently.

Astigmatism↗

PubMed1987

[Obstetric-perinatologic data collection using a personal computer].

A concept covering the collecting and processing of obstetrical and perinatological data is described. Collecting of patient data is effected on the basis of a case history that has been drawn up in an EDP-adequate manner, which, however, can also be used in the conventional way. This procedure was chosen because for some time to come one cannot do without a document for handwritten notes to avoid duplication of work by "double tracking" and to eliminate transmission errors, and also to continue the present procedure of dealing with the patient. A commercial data base system was chosen for data collection and storage (dBase III by Ashton Tate). This relational data base has its own programming language with very powerful macro calls. Data input is effected by means of programme masks which the user can solicit via menu monitoring. The requisite hardware configuration consists of a computer with a main storage comprising 640 KB, system MS-DOS, and a hard disk of at least 20 MB. This data collection system operates in an obstetric hospital with annually more than 1,600 births and more than 1,200 entries during early pregnancy, to the satisfaction of the users. Besides compiling the usual statistical analyses and formulating research problems, the system automatically prepares the discharge reports. This rationalisation procedure compels the user to collect the data with care and also completely. On the whole, such a data collection system offers to hospitals of any size quick and easy access to data at any time, as well as optimised patient care, without additional effort and at a reasonable cost level.

Computers↗

PubMed2023

Discussion on the mechanism of Lingguizhugan Decoction in treating hypertension based on network pharmacology and molecular simulation technology.

To explore the mechanism of Lingguizhugan Decoction in treating hypertension based on network pharmacology and molecular simulation. The active ingredients and potential targets were screened by the Systematic Pharmacological Analysis Platform of Traditional Chinese Medicine (TCMSP). Hypertension-related targets were obtained from OMIM and GeneCards databases. Common targets between drug and hypertension were screened in the Venny platform. A protein-protein interaction (PPI) network was constructed in the STRING database using intersection targets. Key targets in PPI network were analyzed by Cytoscape. R language program was used for Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Finally, the binding abilities of the main active ingredients to critical targets were verified by molecular simulation. Naringenin, quercetin, kaempferol, and β-sitosterol in Lingguizhugan Decoction, and potential targets such as STAT3, AKT1, TNF, IL6, JUN, PTGS2, MMP9, CASP3, TP53, and MAPK3, were screened out. KEGG Enrichment analysis revealed that the common targets of Lingguizhugan Decoction and hypertension are mainly involved in the lipid and atherosclerosis signaling pathway, AGE-RAGE signaling pathway in diabetic complications, fluid shear stress and atherosclerosis, and IL17 signaling pathway. The molecular simulation results showed that naringenin-MAPK3, quercetin-MMP9, quercetin-PTGS2, and quercetin-TP53 were the top four in the docking scores. Naringenin-MAPK3 and quercetin-MMP9 were stable, with binding free energies of -27.97 ± 1.41 kcal/mol and -21.15 ± 3.17 kcal/mol, respectively. The possible mechanism of Lingguizhugan Decoction in treating hypertension is characterized of multi-component, multi-target, and multi-pathway.Communicated by Ramaswamy H. Sarma.

Network Pharmacology↗

PubMed1995

Using the hypertext software to develop computer-assisted instruction in oncology for medical students.

A new development in computer-assisted medical education has been the introduction of hypertext authoring systems. Authoring systems are computer programs that can allow an instructor to prepare computer-based medical educational materials without the need to know programming languages. Hypertext is a database management system that lets the user connect screens of information using associative links. The authors developed a hypertext authoring system for teaching their medical students the domain of oncology. The features of the system are hierarchical structure, index browsing, and nonsequential browsing. Moreover, the student may become a writer of a hyperdocument by typing a few script commands. In this way the hierarchical structure of a document meets the needs of the reader. Although hypertext brings with it a few difficulties for the student, the authors expect that the system will become a popular mean for organizing textual information for retrieval and browsing in oncology.

Computer-Assisted Instruction↗

PubMed2003

Use of an integrated mercury food web model for ecological risk assessment.

We developed an integrated food web model for mercury, using the CATS (Contaminants in Aquatic and Terrestrial ecoSytems) model developed by Traas and co-workers (Traas, T.P.; Stäb, J.A.; Kramer, P.R.G.; Cofino, W.P.; Aldenberg, T. Modeling and risk assessment of tributyltin accumulation in the food web of a shallow freshwater lake. Environ. Sci. Technol. 1996, 30 (4), 1227-1237). It was translated into the MatLab mathematical programming language and been adapted for the modeling of mercury. Mercury CATS now models four species of mercury (unreactive mercury, zero valent mercury, divalent mercury, and methylmercury) and their environmental and interactions using the mercury speciation kinetics model article by Bale (Bale, A.E. Modeling aquatic mercury fate in Clear Lake, Calif. J. Env. Eng. 2000, 126 (2), 153-163.) as a guideline. The mercury cycling kinetics include methylation of divalent mercury, photo-oxidation of zero valent mercury, reduction of divalent mercury, adsorption and desorption of divalent and methylmercury, volatilization of zero valent mercury, and uptake into the food web. A lake food web consisting of phytoplankton, rooted vegetation, zooplankton, crayfish, freshwater clams, amphipods, chironomids, eels, killifish, bass, and ospreys traces growth of the various compartments, uptake of both divalent and methylmercury, and the movement of both divalent and methylmercury through the food web via feeding relationships. This model design is sufficiently flexible that the incorporation of new scientific information can be easily done as our understanding of both the organisms and mercury's environmental chemistry increases.

Animals↗

PubMed2000

Testing linkage disequilibrium in sibships.

We describe the use of multivariate regression for testing allelic association in the presence of linkage, using marker genotype data from sibships. The test is valid, provided that the correct mean structure is modeled but does not require the correlation structure within families to be specified. The test can be implemented using standard statistical software such as the SAS programming language. In a simulation study, we evaluated this new test in comparison with one from a standard, matched-case-control analysis. First, we noted that the genetic effect needed to be quite extreme before residual familial correlation due to linkage led to false inference using the standard, matched-pair analysis. Second, we showed that under examples of extreme residual familial correlation, the new test had the correct test size. Third, we found that the test was more powerful than the sibship disequilibrium test of Horvath and Laird. Finally, we concluded that although the standard analysis may lead to correct inference for practical purposes, the new test is valid, even under extreme residual familial correlation and with no cost in power at the causal locus.

Alleles↗

PubMed1998

Representing metabolic pathway information: an object-oriented approach.

MOTIVATION: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) is a website providing information and dynamic links for microbial metabolic pathways, enzyme reactions, and their substrates and products. The Compound, Organism, Reaction and Enzyme (CORE) object-oriented database management system was developed to contain and serve this information. RESULTS: CORE was developed using Java, an object-oriented programming language, and PSE persistent object classes from Object Design, Inc. CORE dynamically generates descriptive web pages for reactions, compounds and enzymes, and reconstructs ad hoc pathway maps starting from any UM-BBD reaction. AVAILABILITY: CORE code is available from the authors upon request. CORE is accessible through the UM-BBD at: http://www. labmed.umn.edu/umbbd/index.html.

Databases, Factual↗

PubMed2003

An efficient algorithm for minimal primer set selection.

SUMMARY: We have developed U-PRIMER, a primer design program, to compute a minimal primer set (MPS) for any given set of DNA sequences. The U-PRIMER algorithm, which uses automatic variable fixing and automatic redundant constraint elimination to tackle the binary integer programming problem associated with the MPS selection problem. The program has been tested successfully with 32 adipocyte development-related genes and 9 TB-specific genes to obtain their respective MPSs. AVAILABILITY: A free copy of U-PRIMER implemented in C++ programming language is available from http://www.u-vision-biotech.com

Adipocytes↗

PubMed1988

Biological applications of the SAS system: an overview.

The SAS system provides biologists with a flexible, easy to use software package for data analysis. Through a combination of data management tools, a wide variety of pre-programmed procedures for sorting, graphing, and statistical analysis and a sophisticated programming language, SAS software can perform all analytical needs for most problems. The recent availability of SAS software on mainframes other than IBM, and more recently on the microcomputer, means that most scientists can have access to the software. In this review we discuss the structure of the SAS language and demonstrate its power in the analysis of biological problems. Although to a lesser extent now than originally, the SAS system is statistically oriented and a working knowledge of statistics is recommended before using its statistical capabilities. However, all biologists will find its data management and summarization capabilities very useful.

Biology↗

PubMed2025

Realfreq: real-time base modification analysis for nanopore sequencing.

SUMMARY: Nanopore sequencers allow sequencing data to be accessed in real-time. This allows live analysis to be performed, while the sequencing is running, reducing the turnaround time of the results. We introduce realfreq, a framework for obtaining real-time base modification frequencies while a nanopore sequencer is in operation. Realfreq calculates and allows access to the real-time base modification frequency results while the sequencer is running. We demonstrate that the data analysis rate with realfreq on a laptop computer can keep up with the output data rate of a nanopore MinION sequencer, while a desktop computer can keep up with a single PromethION 2 solo flowcell. AVAILABILITY AND IMPLEMENTATION: Realfreq is a free and open-source application implemented in C programming language and shell scripts. The source code and the documentation for realfreq can be found at https://github.com/imsuneth/realfreq. The version used for the manuscript is also available at https://doi.org/10.5281/zenodo.15128668.

Nanopore Sequencing↗

PubMed2026

A novel method for across-chromosome phasing without relative data.

MOTIVATION: Across-chromosome phasing identifies which haplotypes of different chromosomes come from the same parent. This differs from within-chromosome phasing, which uses linkage disequilibrium patterns to determine which alleles were co-inherited within each chromosome but does not match haplotypes across different chromosomes. While across-chromosome phasing can be conducted using genotypes from parents or close relatives, current methods perform poorly for samples of unrelated individuals. Here, we introduce a novel approach for across-chromosome phasing that employs a window-based SNP-similarity metric, eliminating the need for data from close relatives or detection of identical-by-descent haplotypes. RESULTS: Using UK Biobank offspring with both parents genotyped as a gold standard, we evaluated the performance of our method by phasing the offspring without using parental data. In genomic data with no within-chromosome phase errors, our algorithm achieved a mean across-chromosome phasing accuracy of 95%, with 53% of individuals phased perfectly. When data was pre-phased computationally using a standard within-chromosome phasing algorithm, mean accuracy for across-chromosome phasing dropped to 83.1%. Thus, our method is limited primarily by the accuracy of within-chromosome phasing accuracy and can approach near-perfect across-chromosome phasing accuracy as within-chromosome phasing accuracy improves. AVAILABILITY AND IMPLEMENTATION: The implementation was executed within a multi-node computational environment of University of Colorado Boulder Research Computing (Blanca Cluster: https://www.colorado.edu/rc/resources/blanca), employing parallelization techniques in the C programming language. The source code has been made publicly accessible online at https://github.com/emmanuelsapin/AcrossChromosomesPhasing, thereby facilitating reproducibility of the results for researchers with authorized access to the UK Biobank dataset.

Algorithms↗

PubMed2026

An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.

MOTIVATION: CRISPR-Cas9 genome-editing efficiency is strongly influenced by the sequence composition and positional context of single-guide RNAs (sgRNAs). Although numerous deep learning-based models have been developed to predict Cas9 efficiency from sgRNA sequences, most operate as black boxes, offering limited insight into the sequence determinants underlying Cas9 activity. In addition, previous studies often overlook how the positional context of sequence motifs within sgRNAs influences their effects on Cas9 binding or cleavage. RESULTS: We introduce DeepCC9, an interpretable machine learning framework that combines explicit sequence feature extraction with a residual block-based deep architecture to improve interpretability and identify composition- and position-based motifs governing Cas9 genome-editing efficiency. We applied this method to multiple Cas9 variant datasets, achieving superior predictive performance compared with existing methods while enabling direct interpretation of sequence motifs and their positional effects. Our analysis uncovered 74 sequence motifs enriched or depleted at specific positions within sgRNAs and strongly associated with Cas9 efficiency, providing mechanistic insight into sequence features that influence guide performance. Together, these results establish DeepCC9 as a generalizable and interpretable framework for modeling sequence-function relationships and advancing the understanding of the sequence determinants underlying CRISPR-Cas9 genome editing. AVAILABILITY AND IMPLEMENTATION: The authors have implemented their algorithm in the Python programming language (version 3.X), which is accessible using (https://zenodo.org/records/20073890).

Deep Learning↗

PubMed2026

SNPannotator: automated functional annotation of genetic variants and linked proxies.

SUMMARY: Genome-wide association studies (GWASs) have identified thousands of genetic variants associated with complex traits and diseases. However, explaining the mechanisms underlying phenotypic variation remains challenging. Here, we introduce SNPannotator, an automated post-GWAS analysis software package designed to streamline the interpretation of GWAS findings. Our pipeline implements a multi-step process that identifies proxy variants in high linkage disequilibrium (LD) with associated lead variants, then queries comprehensive resources (including Ensembl, the GTEx Portal, the eQTL Catalog, and STRING DB) for genomic position, deleteriousness, regulatory annotations, clinical significance, trait associations, expression (eQTLs) and splicing quantitative trait loci (sQTLs), and functional enrichment analyses and compiles the results into user-friendly reports. This package is implemented in the R programming language and includes auxiliary functions for variant lookup and LD exploration. SNPannotator provides a practical framework for efficiently deriving biologically meaningful insights from GWAS data and for assisting researchers in prioritizing candidate variants for functional validation. AVAILABILITY AND IMPLEMENTATION: The SNPannotator package is available from the Comprehensive R Archive Network (CRAN) at https://cran.r-project.org/web/packages/SNPannotator. The development version and tutorial is available on GitHub (https://github.com/omicslaboratory/SNPannotator). The online version of the package is available at https://omicslab.org/snpannotator.

Software↗

PubMed2003

Reconstructing the temporal ordering of biological samples using microarray data.

MOTIVATION: Accurate time series for biological processes are difficult to estimate due to problems of synchronization, temporal sampling and rate heterogeneity. Methods are needed that can utilize multi-dimensional data, such as those resulting from DNA microarray experiments, in order to reconstruct time series from unordered or poorly ordered sets of observations. RESULTS: We present a set of algorithms for estimating temporal orderings from unordered sets of sample elements. The techniques we describe are based on modifications of a minimum-spanning tree calculated from a weighted, undirected graph. We demonstrate the efficacy of our approach by applying these techniques to an artificial data set as well as several gene expression data sets derived from DNA microarray experiments. In addition to estimating orderings, the techniques we describe also provide useful heuristics for assessing relevant properties of sample datasets such as noise and sampling intensity, and we show how a data structure called a PQ-tree can be used to represent uncertainty in a reconstructed ordering. AVAILABILITY: Academic implementations of the ordering algorithms are available as source code (in the programming language Python) on our web site, along with documentation on their use. The artificial 'jelly roll' data set upon which the algorithm was tested is also available from this web site. The publicly available gene expression data may be found at http://genome-www.stanford.edu/cellcycle/ and http://caulobacter.stanford.edu/CellCycle/.

Algorithms↗

PubMed1984

Microcomputer programs for back translation of protein to DNA sequences and analysis of ambiguous DNA sequences.

Three computer programs are described which may be used to translate a DNA sequence into a protein sequence, back translate the protein sequence into an ambiguous DNA sequence, and then do pattern searching in the ambiguous sequence. The programs are written in the C programming language, have been compiled to run on a microcomputer under the CP/M 80 operating system, and may be copied in binary format through a modem. They are also to become available for the IBM/PC.

Amino Acid Sequence↗

PubMed1988

Apple Macintosh programs for nucleic and protein sequence analyses.

This paper describes a package of programs for handling and analyzing nucleic acid and protein sequences using the Apple Macintosh microcomputer. There are three important features of these programs: first, because of the now classical Macintosh interface the programs can be easily used by persons with little or no computer experience. Second, it is possible to save all the data, written in an editable scrolling text window or drawn in a graphic window, as files that can be directly used either as word processing documents or as picture documents. Third, sequences can be easily exchanged with any other computer. The package is composed of thirteen programs, written in Pascal programming language.

Amino Acid Sequence↗