SEARCH · PubMed Health

Results for “Python”

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 91 records · Page 5Linked to original sources

PubMed2026

Plotgardener App: a graphical interface for publication-ready genomic visualization.

SUMMARY: Plotgardener is an R package used for generating high-quality genomic visualizations. Despite its broad range of functions and versatility, its reliance on code presents a barrier for many potential users. To address this, we developed a macOS desktop application version of Plotgardener that enables users to create publication-ready genomic plots with no programming experience. The application employs a modular architecture comprising an Electron.js backend, a React frontend, and a Python parser that dynamically analyzes the Plotgardener package to ensure interface fields remain synchronized with package updates. By lowering the technical barrier to advanced genomic visualization, the Plotgardener desktop application broadens access to powerful visualization workflows for researchers and clinicians. AVAILABILITY: The current release of the Plotgardener App is an open source macOS desktop application built with Electron (Node.js), featuring a React frontend and a Python-based parser. The download link is available at https://phanstiellab.github.io/plotgardener/articles/guides/plotgardenerApp.html and on Zenodo (doi: https://doi.org/10.5281/zenodo.21684228). The source code is hosted on GitHub at https://github.com/rishabhsvemuri/ThePlotgardenerApp.

Genomics↗

PubMed2025

MyESL: A Software for Evolutionary Sparse Learning in Molecular Phylogenetics and Genomics.

Evolutionary sparse learning uses supervised machine learning to build evolutionary models where genomic sites loci are parameters. It uses the Least Absolute Shrinkage and Selection Operator with bi-level sparsity to connect a specific phylogenetic hypothesis with sequence variation across genomic loci. The MyESL software addresses the need for open-source tools to perform evolutionary sparse learning analyses, offering features to preprocess input phylogenomic alignments, post-process output models to generate molecular evolutionary metrics, and make Least Absolute Shrinkage and Selection Operator regression adaptable and efficient for phylogenetic trees and alignments. The core of MyESL, which constructs models with logistic regressions using bi-level sparsity, is written in C++. Its input data preprocessing and result post-processing tools are developed in Python. Compared to other tools, MyESL is more computationally efficient and provides evolution-friendly inputs and outputs. These features have already enabled the use of MyESL in two phylogenomic applications, one to identify outlier sequences and fragile clades in inferred phylogenies and another to build genetic models of convergent traits. In addition to the use in a Python environment, MyESL is available as a standalone executable compatible across multiple platforms, which can be directly integrated into scripts and third-party software. The source code, executable, and documentation for MyESL are openly accessible at https://github.com/kumarlabgit/MyESL.

Phylogeny↗

PubMed1989

[A histological study of striated muscle and nerve fiber in the human caused by a high voltage electric current].

A case of an electrocution is reported, involving a 37-year-old man who while engaged in an electrical work, received an electric shock by touching an electric wire of 11,000 volts. Both of his arms had to be amputated. A piece of muscle tissue was removed from the amputated arm to be examined by light and electron microscopy. Under light microscopy, the muscle tissue, after myoglobin staining, showed a particular pattern that closely resembled the pattern on the skin of a python. Thus the author has named the pattern seen in this case as the "Python-pattern". The electron microscopy inspection revealed on myoglobin staining excessive stretching and fragmentation of the myofibrils where the myoglobin staining was negative in the slide.

Adult↗

PubMed1989

Death caused by a constricting snake--an infant death.

A 21-month-old male was found dead in his crib. An escaped pet python snake (Python reticulatus) was found near the child on a cribside shelf. Autopsy findings included petechiae associated with asphyxial death plus puncture wounds consistent with the reptile's teeth. This report details this 1982 death of a child in Reno, Nevada, and includes illustration of the reptile's bite marks plus description of snake jaw mechanics in swallowing.

Animals↗

PubMed1985

Disease patterns in the Detroit Zoo: a study of reptilian and amphibian populations from 1973 through 1983.

A retrospective study was conducted to determine disease patterns in reptilian and amphibian populations at the Detroit Zoo from 1973 through 1983. In the reptilian population (mean +/- SD = 285.2 +/- 28), overall annual mortality rates were 1% to 40%. Mortality rates were highest in the fall months (20%) and lowest in the winter months (6%). The most frequently affected reptiles were iguana (Iguana iguana), reticulated python (Python reticulatus), rattlesnakes (Crotalus spp), common boa (Constrictor constrictor), and lizards (various genera of suborder Lacertilia). Of the 1,300 reptilian deaths from 1973 through 1983, 36.6% were caused by microbial agents, 12% by parasites, 11.6% by trauma, and 9.3% by nutritional deficiencies. The main microbial organisms that caused death were Aeromonas spp, Salmonella spp, Pseudomonas spp, Proteus spp, and Edwardsiella spp. The main parasites that caused death were Entamoeba spp and lungworms. Among amphibians, frogs and toads were the most frequently affected, and starvation and trauma were the most frequent causes of death.

Amphibians↗

PubMed1985

Plasma concentrations of chloramphenicol in snakes.

Plasma chloramphenicol concentrations after a subcutaneous injection were studied in 87 snakes of 16 different species. The biological half-life of chloramphenicol varied from 3.3 hours in the indigo snake (Drymarchon corais couperi) to 22.1 hours in the midland water snake (Nerodia sipedon). A single dosage of 50 mg of chloramphenicol/kg of body weight produced plasma concentrations greater than 5 micrograms/ml for nearly 72 hours in 2 species of water snakes (Nerodia erythrogaster, Nerodia sipedon), for 24 hours in the Burmese python (Python molurus bivittatus), and for less than 12 hours in the gray rat snake, Indigo snake, and eastern king snake (Elaphe obsoleta spiloides, Drymarchon coraise couperi, and Lampropeltis getulus getulus). A dosage of 50 mg/kg administered to water snakes every 72 hours for 18 days maintained a minimum plasma concentration of chloramphenicol between 2 and 5 micrograms/ml.

Animals↗

PubMed2025

Using Prime Editing Guide Generator (PEGG) for high-throughput generation of prime editing sensor libraries.

Prime editing enables the generation of nearly any small genetic variant. However, the process of prime editing guide RNA (pegRNA) design is challenging and requires automated computational design tools. We developed Prime Editing Guide Generator (PEGG), a fast, flexible, and user-friendly Python package that enables the rapid generation of pegRNA and pegRNA-sensor libraries. Here, we describe the installation and use of PEGG (https://pegg.readthedocs.io) to rapidly generate custom pegRNA-sensor libraries for use in high-throughput prime editing screens.

Gene Editing↗

PubMed1991

Comparative aspects of the basal ganglia-tectal pathways in reptiles.

To determine how the basal ganglia in reptiles may influence visuomotor behavior, the connections from the basal ganglia to the tectum of the midbrain were studied in several species of reptiles. Immunohistochemical studies by means of antibodies against Leu-enkephalin (LENK) as well as experimental hodological studies with anterograde (PHA-L) and retrograde (HRP, Fluorogold, Cholera toxin) tracers were carried out. The results indicate that within the class of Reptilia, two different patterns occur: one in which information from the basal ganglia is relayed to the tectum via the substantia nigra as well as via a pretectal, enkephalinergic cell group, and another one in which only the ventral route, via the substantia nigra, is present. The former pattern is found in turtles, crocodiles, and the lacertid lizards Podarcis and Gallotia, and the latter pattern in the gekkonid lizards Gekko and Eublepharis, in Varanus, and in the snakes Python and Thamnophis. The presence or absence of the pretectal relay center is reflected in the laminar distribution of LENK immunoreactivity in the tectum. The apparent lack of a pretectal relay in nocturnal gekkonids and in snakes underlines the hypothesis (Reiner et al., '84: T.I.N.S. 7:320-325) that a de-emphasis of visual-basal ganglia mechanisms has occurred during the evolution of ancestral reptiles to modern mammals.

Animals↗

PubMed1986

Plasma levels and renal handling of endogenous amino acids in snakes: a comparative study.

Plasma levels of 22 endogenous amino acids were measured by ion-exchange chromatography in four species of snakes: Thamnophis sirtalis, T. radix, Aipysurus laevis, and Python molurus. Despite considerable interspecific variation in the amino acid composition, all species showed relatively high plasma concentrations of histidine, a feature apparently unique to reptiles. The renal handling of these amino acids was studied by renal clearance methods. As in other vertebrates, net tubular absorption of filtered amino acids predominated. However, net tubular secretion of taurine, cysteic acid and/or phosphoserine and beta-alanine was observed, with taurine being the predominant amino acid secreted. The percentage reabsorption of the total amino acids filtered by the snake kidneys ranged from 79 to 95%. Evidence for the postrenal absorption of amino acids in these reptiles is presented. In species that normally undergo hibernation (Thamnophis spp.), the ability of the kidney to reabsorb amino acids was depressed by cold acclimation. Cold acclimation significantly decreased plasma levels of all amino acids except taurine, whose concentration increased. The increase in plasma taurine level may have resulted from cellular osmoregulation. Under these conditions, renal excretion of taurine increased concomitantly with the increase in plasma taurine concentration.

Amino Acids↗

PubMed1979

Contrasting DNA sequence organisation patterns in sauropsidian genomes.

The genomic DNA organisation patterns of four sauropsidian species, namely Python reticularis, Caiman crocodilus, Terrapene carolina triungius and Columba livia domestica were investigated by reassociation of short and long DNA fragments, by hyperchromicity measurements of reannealed fragments and by length estimations of S1-nuclease resistant repetitive duplexes. While the genomic DNA of the three reptilian species shows a short period interspersion pattern, the genome of the avian species is organised in a long period interspersion pattern apparently typical for birds. These findings are discussed in view of the close phylogenetic relationships of birds and reptiles, and also with regard to a possible relationship between the extent of sequence interspersion and genome size.

Alligators and Crocodiles↗

PubMed1987

Resting metabolic rates in boid snakes: allometric relationships and temperature effects.

Resting metabolic rates (RMR) of 34 species from 18 genera of boas and pythons (Serpentes: Boidae), with body masses ranging from 2 to 67,800 g, were determined as oxygen consumption (VO2) and carbon dioxide production (VCO2) at three ambient temperatures (Ta). The temperature coefficient of metabolism (Q10) averaged 2.61 between Ta of 20-30 degrees C and 2.65 between 30 and 34 degrees C. The respiratory exchange ratio RE (= VCO2/VO2) increased slightly with increasing Ta (0.795 at 20 degrees C, 0.819 at 30 degrees C, and 0.834 at 34 degrees C). Interspecific differences in Q10 and RE were slight or insignificant. A multiple regression relating metabolism (VO2) to mass and Ta explained 97% of the variance in the pooled interspecific data. The mass exponent was 0.806, which is approximately the same as reported for squamates and for all reptilian taxa combined. The mean within-species slope (0.732) was significantly less than the slope for pooled data, but did not differ significantly from 0.75. In 40 of 42 cases (14 species at 3 Ta), within-species slopes did not differ from each other. Values of the adjusted mean Y, from covariance analysis, were significantly and positively correlated with mass, indicating that the mass coefficient increases with increasing mass. Considerable variation in metabolic rate is apparent both within and between ecological and taxonomic categories.

Acclimatization↗

PubMed1992

A survey of Blastocystis in reptiles.

A total of 28 species of reptiles were investigated for Blastocystis using light microscopy and in vitro culture in biphasic egg slant medium. Blastocystis species were detected in 8 (28.6%) of these 28 species in 3 tortoises (Geochelone elephantopus, G. elegans and G. carbonaria), 3 snakes (Boiga dendrophilla, Python reticulatus and Elaphe radiata), 1 crocodile (Crocodylus porosus) and 1 iguana lizard (Cyclura cornuta). The reptilian Blastocystis appeared to be morphologically similar to B. hominis.

Alligators and Crocodiles↗

PubMed2026

Network-based integration of metabolomics data from large-scale repositories.

INTRODUCTION: Public metabolomics data repositories such as MetaboLights and Metabolomics Workbench host rapidly growing volumes of raw data, processed results, and metadata. As data deposition becomes a prerequisite for funding and publication, there is an increasing need for tools that enable integration and joint reanalysis of datasets across studies to maximise reuse and reproducibility. OBJECTIVES: This study aims to enable large-scale integrative meta-analysis of public metabolomics data, exploiting harmonised metabolite annotations to identify robust multi-study metabolite and pathway signatures and to provide global visual overviews of repository content. METHODS: We developed a network-based integration framework operating at both the study (dataset) level and the metabolite or pathway level. Metabolite-level meta-networks integrate studies with shared biological context using co-occurrences of differential metabolites represented as bipartite graphs. Study-level networks compare observed metabolites for overall repository exploration. Networks can be explored interactively using a dedicated Python Dash app available at https://github.com/EloisaRL/Metabolomic-data-analysis-app/tree/main . RESULTS: As an example, the approach was applied to six COVID-19 plasma datasets from MetaboLights generated using LC-MS and NMR. Ten metabolites were identified as differential in at least three studies, including consistently up-regulated pyroglutamic acid, in agreement with the literature. Pathway-level networks provided an overview of shared biological processes across studies. A global network of 1,181 studies in Metabolomics Workbench demonstrated clustering by assay coverage and associated metadata, as expected. CONCLUSION: Network-based integration of harmonised metabolomics data enables robust cross-study analyses and highlights the critical importance of standardised annotation pipelines. Such approaches enhance the reuse, reproducibility, and impact of public metabolomics datasets, accelerating biological discovery.

Metabolomics↗

PubMed1992

Animal phobias versus claustrophobias: exteroceptive versus interoceptive cues.

The overall purpose of this investigation was to examine heterogeneity among specific phobias. In particular, the goals were to compare features of fear responding between individuals fearful of claustrophobic situations and individuals fearful of spiders/snakes, and to compare their response to hyperventilation challenges. By so doing, specific predictions were tested in relation to a conceptual model of exteroceptive and interoceptive fear cues. Using a nonclinical sample, 19 subjects with spider/snake phobias, 18 nonphobics, and 9 subjects with claustrophobias were exposed on two separate occasions to a live tarantula or python, a small closet, and a hyperventilation challenge. Dependent measures included subjective anxiety, panic attacks, physical symptoms, cognitive symptoms (or, fear of symptoms) and heart rate. In addition, subjects completed a standardized self-report scale that measures fear of bodily symptoms of arousal. It was found that subjects with claustrophobia reported more physical symptoms and cognitive symptoms than did subjects with snake/spider phobias, in response to their fear-relevant stimulus. In addition, claustrophobic subjects were more fearful of hyperventilation challenges and reported more fear of bodily symptoms, than did snake/spider phobic subjects. Finally, subjects with claustrophobia were as fearful of hyperventilation as they were of their fear-relevant stimulus. Theoretical and empirical implications of these findings are discussed.

Adult↗

PubMed1978

Air flow in snake ventilation.

Ventilation in resting, unrestrained Boa constrictor, Python regius and Thanmophis s. sirtalis was monitored using various combinations of a closed Kopfkappe (head chamber), intratracheal pressure catheters, strain gauges around the trunk, and a flow meter connected to one of the nostrils. Records of intratracheal pressure with and without closing the Kopfkappe show that the latter device induces artifacts in the normal ventilatory pattern. Flow meter readings from quiescent snakes indicate that ventilation is biphasic (outflow-inflow-pause) rather than triphasic (outflow-inflow-outflow-pause), while simultaneous pressure and strain gauge records are variably tri- or quadriphasic.

Animals↗

PubMed2026

A genome-wide coverage-based pipeline for the identification of host-derived candidate DNA biomarkers from cell-free blood.

We have created a new data-analysis pipeline for the discovery of host-specific candidate DNA biomarkers derived from sequencing data of cell-free blood. Unlike approaches that rely on specific molecular or genetic signatures, our method leverages the coverage distribution of cell-free DNA sequences mapped to a reference genome, applying statistical analyses to identify informative short genomic regions for biomarker discovery. The pipeline is applicable to diverse diseases and can be used to analyze cell-free DNA sequences from plasma or serum to identify candidate biomarkers that are characteristic of disease states in mammals. Core functionalities were developed in Java and integrated with open-source software tools for the preprocessing of raw sequencing data, complemented by Python scripts for the machine-learning analysis and statistical validation. The pipeline is designed for HPC use and users can access the pipeline through a Galaxy workflow, which offers a user-friendly web interface for input selection prior to execution and analysis progress monitoring. Performance tests, carried out using duplicate sets of COVID-19 samples and controls, showed linear scalability of execution time with an increasing dataset size, as well as a substantial reduction in execution time through parallelized computation, whereby each HPC node is used to process the data of one chromosome. Further statistical tests confirmed the quality of the pipeline's results by showing that the set of identified candidate biomarkers remained stable across varying dataset sizes.

Biomarkers↗

PubMed2026

Community-driven advances in computational mass spectrometry: The perspective of EuBIC-MS members.

Advances in data acquisition, artificial intelligence, and integrative bioinformatics are driving the rapid evolution of computational mass spectrometry, and in turn, transforming modern proteomics, metabolomics, and lipidomics. These developments have greatly increased the scale and complexity of mass spectrometry data, underscoring the importance of evolving accurate, transparent, efficient and reproducible data processing workflows. Addressing these challenges requires collaborative innovation that brings together expertise in software engineering, statistics, and biology. The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS), an initiative of the European Proteomics Association (EuPA), fosters a culture of open, community-driven development through its biennial Developers Meetings and Winter Schools. This commentary summarizes the scientific background and outcomes of the EuBIC-MS Developers Meeting 2025, which took place in Novacella, Italy. Three keynote presentations highlighted major frontiers in the field: deep proteome and phosphoproteome profiling, text mining for protein-protein interaction extraction, and scalable proteomics for AI-driven drug discovery. Seven community-selected hackathons addressed emerging challenges such as single-cell proteomics data analysis, FAIR metadata extraction, deep learning frameworks, R-Python interoperability, and DIA validation. Together, these efforts demonstrate the potential for scientific and technical innovation to arise from open collaboration, and highlight how community-driven initiatives can accelerate progress in computational mass spectrometry. SIGNIFICANCE: Modern proteomics increasingly depends on computational advances to translate complex, high-dimensional data into biological knowledge. The EuBIC-MS Developers Meeting 2025 exemplifies how community-driven collaboration can directly accelerate this process by bringing together experts from bioinformatics, statistics, and experimental proteomics to co-develop open, interoperable, and reproducible analytical tools. By fostering shared software frameworks, transparent benchmarking, and collaborative problem solving, the EuBIC-MS community helps ensure that technological innovation translates into reliable biological insights. This collaborative model strengthens the foundation for quantitative, system-level understanding of proteomes and establishes a sustainable path for integrating artificial intelligence and next-generation data acquisition into routine biological discovery. This commentary shows some current highlights in the field of computational mass spectrometry and community-based approaches undertaken during the most recent Developers Meeting to solve these challenges. The approaches discussed and initiated during the meeting - ranging from deep proteome profiling and phosphosite mapping to text mining, single-cell data analysis, and FAIR metadata extraction - address key bottlenecks that currently limit the biological interpretability and comparability of proteomics data.

Mass Spectrometry↗

PubMed2026

pmultiqc: An Open-Source, Lightweight, and Metadata-Oriented QC Reporting Library for MS Proteomics.

The increasing scale and complexity of proteomics data demand robust, scalable, and interpretable quality control (QC) frameworks to ensure data reliability and reproducibility. Here, we present pmultiqc, an open-source Python package that standardizes and generates web-based QC reports across multiple proteomics data analysis platforms. Built on top of the widely adopted MultiQC framework, pmultiqc offers specialized modules tailored to mass spectrometry workflows, with full initial support for quantms, DIA-NN, MaxQuant/MaxDIA, FragPipe, and mzIdentML/mzML-based pipelines. The package computes a wide range of QC metrics, including raw intensity distributions, identification rates, retention time consistency, and missing value patterns, and presents them in interactive, publication-ready reports. By leveraging sample metadata in the Sample and Data Relationship Format format, pmultiqc enables metadata-aware QC and introduces, for the first time in proteomics, QC reports and metrics guided by standardized sample metadata. Its modular architecture allows easy extension to new workflows and formats. Alongside comprehensive documentation and examples for running pmultiqc locally or integrated into existing workflows, we offer a cloud-based service that enables users to generate QC reports from their own data or public PRIDE datasets.

Proteomics↗