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At least 73 records · Page 4Linked to original sources
PubMed2026

scSNViz: visualization and analysis of cell-specific expressed SNVs.

MOTIVATION: Accurately characterizing expressed genetic variation at the single-cell level is essential for understanding transcriptional heterogeneity, allelic regulation, and mutational dynamics within complex tissues. However, few tools enable comprehensive visualization and quantitative analysis of expressed variants across individual cells. RESULTS: scSNViz is an R package for the exploration, quantification, and visualization of expressed single-nucleotide variants (SNVs) from cell-barcoded single-cell RNA sequencing (scRNA-seq) data. The software supports estimation of variant allele fractions, clustering of SNV expression profiles, and 2D and 3D visualization of individual SNVs or user-defined SNV groups. Beyond visualization, scSNViz facilitates investigation of cell-, cluster-, or lineage-specific variant expression patterns, as well as allelic dynamics including imprinting, random allele inactivation, and transcriptional bursting. It interoperates seamlessly with established single-cell frameworks-Seurat for clustering, Slingshot for trajectory inference, scType for cell-type annotation, and CopyKat for copy-number profiling-enabling integrative multi-omic analyses of expressed variation. AVAILABILITY AND IMPLEMENTATION: scSNViz is implemented in R and freely available at https://github.com/HorvathLab/scSNViz (DOI: 10.5281/zenodo.17307516). The package includes comprehensive documentation and example workflows designed for users with limited bioinformatics experience.

Software↗
PubMed1991

[Quantified EEG in the diagnosis of Alzheimer's type dementia].

79 subjects (mean age 70.2 ans, 31 males, 48 females) selected as probable dementia of the Alzheimer type, at the early stage of the disease and 17 normal aged people (mean age: 72.2, 5 males, 12 females) were recorded with a 16 channel computerized-EEG (C-EEG) with topographical analysis of the observed changes and with classical visual analysis of the EEG. Quite simple C-EEG parameters as mean dominant frequency (MF) and alpha to theta ratio are able to discriminate patients from normal with a greater accuracy than visual analysis. The values of 8.6 for the MF and 1.3 for the alpha/theta ratio are proposed as cut off values between normal and DAT patients. The topographical analysis appear to be of no additional usefulness in the discrimination of the two groups.

Aged↗
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↗
PubMed1990

Correlative velocity estimation: visual motion analysis, independent of object form, in arrays of velocity-tuned bilocal detectors.

The visual estimation of object velocity in systems of tuned bilocal detector units (simplified Hassenstein-Reichardt detectors) is investigated. The units contain delay filters of an arbitrary low-pass characteristic. Arrays of such detector units with identical delay filters are assumed to cover the plane of analysis. The global evaluation of the output signals of suitably arranged detector units is exemplified by the analysis of frontoparallel translations of rigid objects. The correlative method permits the estimation of the instantaneous object velocity, independently of object form. The time course of the resulting estimate is shown to be the convolution of the true velocity profile with a time-invariant kernel that depends solely on the impulse response of the delay filters and thus characterizes the analyzer system. The mathematical analysis of the processing principle is illustrated by considering idealized detector systems. The response of correlative motion analyzers to compound motion and to motion of nonrigid objects is discussed.

Models, Psychological↗
PubMed1988

White-noise analysis in visual neuroscience.

In 1827, plant biologist Robert Brown discovered what is known as Brownian motion, a class of chaos. Formal derivative of Brownian motion is Gaussian white-noise. In 1938, Norbert Wiener proposed to use the Gaussian white-noise as an input probe to identify a system by a series of orthogonal functionals known as the Wiener G-functionals. White-noise analysis is uniquely suited for studying the response dynamics of retinal neurons because (1) white-noise light stimulus is a modulation around a mean luminance, as are the natural photic inputs, and it is a highly efficient input; and (2) the analysis defines the response dynamics and can be extended to spike trains, the final output of the retina. Demonstrated here are typical examples and results from applications of white-noise analysis to a visual system.

Action Potentials↗
PubMed1989

Sequential ideal-observer analysis of visual discriminations.

Visual stimuli contain a limited amount of information that could potentially be used to perform a given visual task. At successive stages of visual processing, some of this information is lost and some is transmitted to higher stages. This article describes a new analysis, based on the concept of the ideal observer in signal detection theory, that allows one to trace the flow of discrimination information through the initial physiological stages of visual processing, for arbitrary spatio-chromatic stimuli. This ideal-observer analysis provides a rigorous means of measuring the information content of visual stimuli and of assessing the contribution of specific physiological mechanisms to discrimination performance. Here, the analysis is developed for the physiological mechanisms up to the level of the photoreceptor. It is shown that many psychophysical phenomena previously attributed to neural mechanisms may be explained by variations in the information content of the stimuli and by preneural mechanisms.

Attention↗
PubMed1985

Spatio-temporal EEG measures and their application to human intracranially recorded epileptic seizures.

We describe analysis methods which involve the computation of band-integrated, intrachannel spectral measures from the EEG. These measures require only very general assumptions, have a simple interpretation and achieve significant data reduction, while providing a quantitative assessment of significant EEG modification at seizure or onset or in the course of seizure evolution. In developing these measures, we experimented with various measures derived from spatio-temporal power spectra. Bandpass (8-30 Hz) integrated relative energy measures appear to be the most useful since they objectively measure paroxysmal modification. Two such measures are illustrated in this report: the band-integrated power z-score (BIPZ), which is a quantitative measure designed to allow significance testing, and the band-integrated power ratio (BIPR), which is a simply calculated qualitative measure that behaves very similarly to the BIPZ measure and may be useful for real-time data screening. In addition to developing these intrachannel measures, we have also developed methods of displaying these measures in a format appropriate to the analysis of interchannel relationships. In a general sense, the displays provide objective information regarding the spatio-temporal dynamics of the EEG in a condensed format which is still readily understandable to the electroencephalographer. This analysis was applied to 29 spontaneous, depth-recorded seizures in 14 patients with the aim of identifying the initial locus of seizure activity in each seizure episode. The initial locus was defined as that location (or set of locations) to first exhibit statistically significant values of the BIPZ measure. The method was very effective in this regard, as shown by correspondence between the conclusions of this automated analysis and conventional visual analysis.

Brain↗
PubMed1989

The implementation of an autoregressive model with exogenous input in a single sweep visual evoked potential analysis.

Based on a model of signal-noise interaction, we present a method for single-sweep analysis of Visual Evoked Potentials. The EEG is represented as an autoregressive process and the single-sweep VEP as a filtered version of a reference signal taken as the running average of 20 consecutive sweeps. The algorithm for model identification and filtering is an ARX (AutoRegressive with eXogenous input) which provides a fast and efficient solution by means of a least squares approach. The choice of reference signal, as well as the complexity of the model, is also discussed. A further advantage of this approach is parameter reduction: all the single-sweep information is contained in 18 model coefficients and the reference signal.

Evoked Potentials, Visual↗
PubMed1990

Detection of mild coronary stenoses using the Dynamic Spatial Reconstructor.

The accuracy of the Dynamic Spatial Reconstructor (DSR) in the detection of moderate coronary artery stenoses was examined in 20 closed-chest dogs. Twenty-eight hollow plastic cylinders were embolized into the left coronary arteries and produced 25% to 56% reductions in arterial lumina diameter. For each dog, one three-dimensional (3-D) image of the heart was reconstructed from each DSR scan recorded during injection of contrast into the aortic root. Analysis involved blinded visual analysis by four independent observers of multiview projection images computed from the single 3-D image. Postmortem coronary angiograms of the isolated heart were considered definitive for location of the stenoses. Overall sensitivity of detection by DSR was 89% and specificity 81%. Sensitivity of detecting stenoses greater than or equal to 50% was 98%. Receiver operating characteristics (ROC) analysis showed that detection of stenoses in the left coronary arteries is of equal sensitivity and specificity.

Animals↗
PubMed1992

Postictal switch in blood flow distribution and temporal lobe seizures.

The ictal increase of regional cerebral blood flow has yet to be fully utilised in the investigation of focal seizures. Although single photon emission tomography (SPECT) is being increasingly used in the localisation of epileptic foci, the evolution and time courses of the peri-ictal perfusion changes have yet to be clarified. We performed serial SPECT studies in the interictal, ictal and immediate postictal states in 12 patients with refractory temporal lobe epilepsy to define the patterns and duration of peri-ictal cerebral blood flow changes. Visual analysis showed a constant pattern of unilateral global increases in temporal lobe perfusion during seizures which suddenly switched to a pattern of relative mesial temporal (hippocampal) hyperperfusion and lateral temporal hypoperfusion in the immediate postictal period. Quantitative analysis confirmed the visual assessment. Lateral temporal cortex ictal/normal side to side ratios were increased by mean 35.1% (95% confidence interval 21.8% to 48.4%) more in the ictal studies than in the interictal studies and mesial temporal cortex ratios increased by mean 30.8% (22.4% to 39.2%). In the postictal state, however, lateral temporal ratios were reduced by mean 7.7% (-15.8% to 0.4%) compared with interictal values, whereas mesial temporal perfusion was maintained compared with the interictal studies. These observations provide critical information for interpreting scans which can be used in the localisation of epileptic foci. This postictal switch in blood flow patterns may reflect the underlying metabolic processes of neuronal activation and recovery and have implications for understanding the neurobiology of human epileptic seizures.

Basal Ganglia↗
PubMed1989

[Visual EEG analysis in controlling intravenous anesthesia using propofol].

Since the discovery of brain waves by Berger, repeated efforts have been made to use the electroencephalogram EEG for monitoring and controlling anesthesia. Owing to its susceptibility to failure and the high expenditure regarding technology and personnel, the technique has not yet been adopted in routine anesthesia, however. In the study now reported an attempt was made to apply the positive experience with the recording and interpretation of EEG in the development of new anesthetic agents in the experimental laboratory, during routine clinical operations. The anesthetic used in the study was Propofol, an induction hypnotic that has only recently been introduced, together with nitrous oxide and repeated doses of fentanyl. Propofol is distinguished by its fast onset of action and short inactivation time; it is therefore suitable for induction and maintenance of anesthesia. The aim of the study was to maintain predetermined stages of sleep during anesthesia with the aid of visual on-line analysis of the EEG and to establish the dose of Propofol required for this purpose. The operations-general and orthopedic surgery-lasted 70-190 min (average duration: 120 min). In accordance with the randomization plan, the maintenance dose of Propofol was controlled in such a way that in ten patients light sleep levels (C0 to D1) and in the other ten deep sleep levels were maintained. The EEG was recorded via five active scalp electrodes (FP2, F4, C4, P4, O2) with reference to a joint electrode (A2). The stages of sleep were classified according to Kugler.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed1991

A comparison of the sensitivities of adaptive tracking, eye movement analysis and visual analog lines to the effects of incremental doses of temazepam in healthy volunteers.

The effects of single oral doses of 5, 10, and 20 mg temazepam were evaluated with the adaptive tracking test, analysis of smooth-pursuit and saccadic eye movements, and visual analog lines in a placebo-controlled, double-blind, crossover experiment with 12 healthy volunteers. Pharmacodynamic testing was performed until 10 hours and pharmacokinetics were evaluated until 24 hours. Temazepam, 20 mg, caused effects in all tests, with peak effects occurring at 30 minutes. The 10 mg dose caused effects on saccadic eye movements and subjective scores of alertness, whereas 5 mg temazepam was detected only by analysis of saccadic eye movements. Linear relationships between plasma concentrations and effects were found in nine subjects for saccadic peak velocity and eight subjects for subjective scores of alertness. The results of this study demonstrate manifest differences in the sensitivities of performance tests and stress the importance of validation of methods when effects of drugs on human performance are studied.

Adult↗
PubMed1988

Visualization and analysis techniques for three dimensional information acquired by confocal microscopy.

Confocal Scanning Laser Microscopy (CSLM) is particularly well suited for the acquisition of 3-dimensional data of microscopic objects. In the CSLM a specific volume in the object is sampled during the imaging process and the result is stored in a digital computer as a three-dimensional memory array. Optimal use of these data requires both the development of effective visual representations as well as analysis methods. In addition to the well known stereoscopic representation method a number of alternatives for various purposes are presented. When rendering in terms of solid-looking or semitransparent objects is required, an algorithm based on a simulated process of excitation and fluorescence is very suitable. Graphic techniques can be used to examine the 3-dimensional shape of surfaces. For (near-)real time applications a representation method should not require extensive previous data-processing or analysis. From the very extensive field of 3-D image analysis two examples are given.

Cell Nucleus↗
PubMed1989

[Assessment of myocardial viability by quantitative analysis of stress Tl-SPECT--comparison with FDG-PET].

Stress Tl-201 tomography (SPECT) is widely used for evaluating myocardial viability. To assess its value, redistribution (RD) on SPECT was compared with metabolic imaging using FDG. Thirty patients with coronary artery disease underwent stress-3 hour Tl-201 SPECT and PET using N-13 ammonia and FDG. RD was classified into 4 grading, including complete RD (CR), incomplete RD (IR), persistent defect (PD) and additional minimal RD (MR) defined as no definite RD on visual analysis but faint RD with Bull's eye quantitative analysis (QNT). All but one segment with CR or IR were viable regions (normal or ischemic regions) by PET. Of 74 segments without RD on visual analysis, 31 segments (42%) had RD by QNT (MR). All of them were viable regions by PET. Thus, QNT identified 31 segments (63%) of the metabolically viable segments which the visual Tl-201 analysis did not show RD and classified as myocardial scar. However, even such QNT cannot detect ischemic myocardium in 18 segments (42%) containing metabolic activity on PET. These data indicate that QNT of RD on Tl-201 SPECT is considered as a valuable means for assessing myocardial ischemia.

Aged↗
PubMed1991

Regression analysis of visual field progression in low tension glaucoma.

Eighty four patients (168 eyes) with low tension glaucoma were retrospectively reviewed (mean follow-up was 28 months). The mean age was 66 years, and 69% were females. Regression analysis of their automated Humphrey fields (a mean of eight fields per eye) showed progression in 50% of patients and in 37% of eyes. There was no statistically significant difference between patients with progression and non-progression with respect to age (p less than 0.05) or intraocular pressure (p less than 0.5). Visual field defects were located most frequently in the superior hemifield in both groups of patients. A considerable proportion of patients had advanced field loss at the time of diagnosis.

Adult↗
PubMed1991

Can transcutaneous recordings detect gastric electrical abnormalities?

The ability of transcutaneous recordings of gastric electrical activity to detect gastric electrical abnormalities was determined by simultaneous measurements of gastric electrical activity with surgically implanted serosal electrodes and cutaneous electrodes in six patients undergoing abdominal operations. Transient abnormalities in gastric electrical activity were seen in five of the six patients during the postoperative period. Recognition of normal gastric electrical activity by visual analysis was possible 67% of the time and with computer analysis 95% of the time. Ninety four per cent of abnormalities in frequency were detected by visual analysis and 93.7% by computer analysis. Abnormalities involving a loss of coupling, however, were not recognised by transcutaneous recordings. Transcutaneous recordings of gastric electrical activity assessed by computer analysis can usually recognise normal gastric electrical activity and tachygastria. Current techniques, however, are unable to detect abnormalities in electrical coupling.

Diagnosis, Computer-Assisted↗
PubMed1985

Correlation functions in the analysis of visual evoked potentials.

Our "vision" laboratory has been working for several years on stimulation methods and data processing. We present here the results of an analysis of correlation functions between VEPs obtained by flashes and patterned stimulations. This study provides additional information about possible interpretations.

Evoked Potentials, Visual↗