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At least 199 records · Page 11Linked to original sources
PubMed1994

Convolution: a method for data analysis in perifusion systems.

Considerable interest has developed in defining how imposed stimuli effect dynamic changes in cellular metabolism. We have developed a miniature perifusion system that can reveal alterations in extracellular protons within seconds after application of metabolic perturbants. This perifusion system contains two pH sensors: one before the cells records changes between medium and test solutions, and one, located just past the cells, records these alterations plus cellular modifications. Because distortion occurs as chemicals pass through perifusion systems, the shape of pH changes induced by switching from medium to test solutions is different at each electrode. This study describes and validates convolution to correct this distortion. Data from HeLa cells exposed to the metabolic uncoupler of oxidative phosphorylation carbonyl cyanide m-chlorophenyl hydrazone have been analyzed with convolution. Cellular response to oxidative phosphorylation removal is comprised of multiple components, is consistent with a rapid uncoupling, and is followed by cellular adaptation. Therefore convolutional analysis can provide an important adjunct to the analysis of data acquired by perifusion and can provide new insights into cellular responsiveness and metabolism.

Carbonyl Cyanide m-Chlorophenyl Hydrazone↗
PubMed2026

SimpleMicrobiome: An integrated web-based platform for streamlined microbiome data analysis and visualization.

Microbiome studies require multiple analytical steps after initial sequence processing. These steps commonly include data harmonization, preprocessing, taxonomic profiling, diversity analysis, differential abundance testing, predictive modeling, network inference, and preparation of publication-ready outputs. Although robust packages are available for many of these tasks, routine use often depends on command-line workflows, repeated data reformatting, and method-specific scripting. These requirements can limit accessibility for experimental researchers and complicate consistent analysis across interdisciplinary teams. We developed SimpleMicrobiome, a web-based R Shiny platform that integrates established microbiome analysis methods into a single interactive downstream workflow. The application accepts standard abundance, taxonomy, and metadata tables, supports interactive preprocessing and sample filtering, and provides modules for taxa profile visualization, alpha and beta diversity analysis, ANCOM-BC2 and MaAsLin2 differential abundance testing, Random Forest modeling with SHAP-based interpretation, microbial association network inference using SparCC and SPIEC-EASI through NetCoMi, correlation heatmaps, and dbRDA/CAP-style association biplots. The platform is implemented as a modular Shiny application so that preprocessing choices are propagated across downstream analyses, results can be exported as figures and tables, and the same application can be run through the public server, source-code installation, or a Docker image. SimpleMicrobiome consolidates major downstream microbiome analysis tasks in an accessible browser-based environment while retaining links to established analytical frameworks. The platform may reduce technical barriers for non-programming users, improve consistency across exploratory and reporting-oriented analyses, and support collaborative microbiome research. The public application is available at https://simplemicrobiome.mglab.org, the source code is available at https://github.com/yjcho2252/SimpleMicrobiome, and a Docker image for local deployment is available at https://hub.docker.com/r/mglab2252/simplemicrobiome.

differential abundance↗
PubMed1975

Multivariate data analysis based on a computerized patient monitoring system.

Multivariate time series data in post-operative patients (respiratory and cardiovascular) are compared to reference groups. Using this technique under the program control of a computerized patient monitoring system (IBM 1800) various classes in the respiratory and cardiovascular spectrum can define the co-ordinate system in hyperspace. The patient in crisis is recognised by his deviation from normal rates of change of the variable set, as well as by the time trajectories of recovery in the hyperspace.

Computers↗
PubMed1991

Experiences in data analysis and modelling with a multichannel biomagnetic system.

Evaluation of MEG/MCG data, measured with the Siemens biomagnetic multichannel system KRENIKON, in patients with epilepsy, infarction, Wolff-Parkinson-White (WPW) syndrome or extra systoles are in good agreement with the results of different investigation techniques. The evaluations have been performed using an equivalent current dipole model within a sphere or a half-space with homogeneous conductivity. In cases where the current dipole model is not adequate, multiple dipoles or complete distributions of current sources have to be considered. Results from simulations and applications to in vivo data and the influence of geometries better adjusted to realistic geometries are discussed.

Brain↗
PubMed1995

[Strategies for data analysis of brain activation studies with functional MR tomography].

The sensitivity of gradient-echo magnetic resonance imaging (MRI) to changes in cerebral blood oxygenation has been introduced for mapping functional brain activation. To benefit from the high spatial and temporal resolution of the respective dynamic MRI data sets, their analysis requires algorithms that are capable of both precisely delineating task-related activation patterns and demonstrating functional connectivity of interacting areas. Here, we present various strategies for data evaluation by means of correlational analyses that surpass the quality of subtraction-based activation maps by improving both sensitivity and robustness. On a pixel-by-pixel basis the approach correlates signal time courses with a reference function, reflecting the temporal sequence of activated and control states. Extended versions employ the calculation of auto- or cross-correlation functions that increase sensitivity, but require periodic stimulations. Following individual correction for non-specific but correlated signal fluctuations, mapping of task-related coherent activation can be improved using neighborhood principles. Such refined strategies are expected to enhance the usefulness of oxygenation-sensitive MRI for studying the functional anatomy of the human brain under both physiological and pathological conditions.

Algorithms↗
PubMed1983

A computer-based data analysis system for enzyme-linked immunosorbent assays.

A computerized system is presented for automating the data collection, processing, and displaying tasks involved in enzyme-linked immunosorbent assays. This system uses a through-the-well absorbance reader of microtiter plates interfaced to a minicomputer running the UNIX operating system. Optical density in each well of a 96-well microtiter plate is recorded as a function of time for up to 10 time points. These data are automatically transmitted to the remote computer. The rate of product formation is then calculated for each well, and a battery of analysis, display, and comparison programs can then be used by the researcher for data presentation. Using the initial rate of reaction as the basis for quantifying enzyme-linked immunosorbent assays focuses on the catalytic property of the enzyme and allows a large dynamic range of the assay on any plate. These programs can be adapted to virtually any mini- or microcomputer with a graphics display or a plotting device. Assuming moderately powerful computing hardware, throughputs of 50 plates per day are easily achieved. The programs work equally well with peroxidase, beta-galactosidase, or alkaline phosphatase conjugated second antibodies, and with whole cell or soluble antigens.

Antibodies, Monoclonal↗
PubMed1994

Data analysis.

Explore the source record for details and available documents.

Data Interpretation, Statistical↗
PubMed1993

Exploratory data analysis of three sexual behaviour surveys: implications for HIV-1 transmission in the U.K.

Recently, the number of European and North American heterosexually transmitted AIDS cases has begun to increase. It appears that injecting drug users may be acting as an important infection source for heterosexual transmission, and that the HIV-1 epidemic may be slowly diffusing out into the general population. Therefore, the question arises, as to whether there will be an extensive heterosexually transmitted epidemic in Europe or North America. The possibility of such an epidemic occurring depends upon three factors: sexual mixing patterns, the prevalence and the distribution of specific risk factors, and changes in risk behaviours. To assess the potential for an extensive sustained heterosexually transmitted epidemic it is necessary to estimate these three factors by conducting large-scale linked behavioural and seroprevalence surveys. Unfortunately, such surveys have yet to be conducted in any country. However, a limited amount of sexual behaviour data are available from three small studies that have been conducted in the U.K. Although each of the studies suffers from methodological imperfections, together they may be used as the basis for a preliminary assessment of the potential effects of heterosexual transmission in the U.K. In this paper I discuss the results from an exploratory analysis of these data; the results are organized into five sections: (i) assessment of the prevalence and distribution of specific risk behaviours; (ii) determination of covariates of risk behaviours (and hence characterization of the subgroups that may be at risk); (iii) assessment of age-dependent sexual mixing patterns; (iv) assessment of sexual behaviour changes; and (v) calculation of epidemiological parameters. The validity and the reliability of the data from the three studies are assessed. The analysis suggests that it is possible that a heterosexually transmitted HIV-1 epidemic could occur in the U.K. Hence, it is essential to conduct longitudinal surveys that collect linked seroprevalence and behavioural data.

Adolescent↗
PubMed2026

Identification of Critical Genes for Recurrent Aphthous Ulcer by Transcriptome Data Analysis and Mendelian Randomization.

PURPOSE: Recurrent aphthous ulcer (RAU) is a common oral mucosal disorder with a poorly understood etiology, significantly affecting patients' quality of life. This study aims to investigate critical genes linked to RAU and explore their biological mechanisms using transcriptomic data and Mendelian randomization (MR) analysis. MATERIALS AND METHODS: RAU-related gene expression data from the GEO database (GSE37265) were analyzed to identify differentially expressed genes (DEGs). A two-sample MR approach was used to assess the causal impact of expression quantitative trait loci (eQTL) on RAU. Critical genes were identified by intersecting DEGs with significant MR findings. GO and KEGG pathway enrichment analyses were performed, along with GSEA and immune cell infiltration analysis, to investigate the functions and mechanisms of these genes in RAU. RESULTS: A total of 184 differentially expressed genes (DEGs) were identified, while 339 RAU-associated genes were screened through MR analysis. Cross-validation further identified 7 critical genes. Among these, CCR1, ERP27, HCK, MICB, and SLC2A3 showed protective associations with RAU risk, whereas CD177 and IFITM1 were positively associated with increased risk. Enrichment analysis revealed that these genes are involved in specific biological processes, including cell migration, immune response, and metabolic regulation, which are closely linked to RAU pathogenesis. CONCLUSION: This systematic study comprehensively investigates the critical causative genes underlying RAU, emphasizing the intricate relationships between immune regulation and metabolic disturbances in its pathology. These findings lay a solid foundation for the development of novel biomarkers and may inform future research on targeted therapeutic strategies for RAU.

Stomatitis, Aphthous↗