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4,153 results for “survival”
Defining the genes required for survival of Mycobacterium bovis in the bovine host offers novel insights into the genetic basis of survival of pathogenic mycobacteria
<p>Supplementary dataset from "<strong><em>Defining the genes required for survival of Mycobacterium bovis in the bovine host offers novel insights into the genetic basis of survival of pathogenic mycobacteria</em></strong>"</p> <p> </p> <p><strong>Supplementary Figure legends</strong></p> <p><strong>Figure S1. Illustration of the transposon insertions around the <em>M. bovis </em>genome. </strong>Sequencing of the input library showed that transposon insertions were evenly distributed around the genome and 27,419 of the permissible 66,931 thymine–adenine dinucleotide (TA) sites contained an insertion representing an insertion density of ~41%. The outer ring are the genomic coordinates, the blue lines represent transposon insertions and the gray boxes indicate regions of that did not have any insertions. Plot made with Circlize (Gu et al, 2014).</p> <p> </p> <p><strong>Figure S2. Diversity of the output library isolated from lung and thoracic lymph node lesions compared to the input library. </strong>On average, libraries recovered from lung lesions contained 14,456 unique mutants and those recovered from the lymph nodes contained an average of 16,210 unique mutants. Insertion density is represented as a proportion of the TA sites that contained insertions. The numbers on the x-axis refer to the sequencing file from that sample and come from individual animals (Bioproject ID: PRJNA816175, Submission ID: SUB11067380).</p> <p> </p> <p><strong>Figure S3. Volcano plots showing the distribution of log<sub>2</sub> fold-changes and -log<sub>10</sub> of adjusted p-values for representative lung (A) and lymph node (B) samples. </strong>Adjusted p-values (BH-fdr correction) < 0.000001 cluster at the limits of the plot and precision reflects the number of resampling iterations (10,000).</p> <p> </p> <p><strong>Figure S4. Scatterplot of mean log<sub>2</sub> fold change per gene for all lung samples against all thoracic lymph node samples</strong>. Correlation between mean log<sub>2</sub> fold change among genes between the tissues was calculated with Spearman's ranked correlation, = 0.878, p-value < 2.2e-16.</p> <p> </p> <p><strong>Figure S5. Fold-changes caused by transposon insertions in <em>RD1<sup>BCG</sup></em> and <em>RD1<sup>MIC</sup> </em>in the lungs and lymph nodes of infected cattle. </strong>Boxplot for log<sub>2 </sub>fold-changes in genes of the RD1<sup>BCG</sup> region. Samples with adjusted p-values (BH-fdr corrected) <0.05 are indicated with purple points. Gene names highlighted in magenta have fewer than 5 TA sites located in the gene; too few to determine the statistical significance of changes in insertion levels with this method.</p> <p> </p> <p><strong>Supplementary Tables </strong></p> <p><strong>Table S1. Sequencing statistics of the input and output transposon libraries. </strong>The numbers in the column labelled “filename” refers to the sequencing file from that sample and come from individual animals (Bioproject ID: PRJNA816175, Submission ID: SUB11067380).</p> <p> </p> <p><strong>Table S2. Tissues collected and scored for gross pathology. </strong>Tissues from head and neck lymph nodes (from the right and left sub-mandibular lymph nodes, the right and left medial retropharyngeal lymph nodes), thoracic lymph nodes (the right and left bronchial lymph nodes, the cranial tracheobronchial lymph nodes, the cranial and caudal mediastinal lymph nodes) and from lung lesions, were collected and scored.</p> <p> </p> <p><strong>Table S3. Log<sub>2</sub> fold-changes for insertions across the entire genome of <em>M. bovis</em> AF2122/97. </strong>Cells are coloured according to log<sub>2</sub> fold-change. Refer to the text for the gene groups in individual tabs.</p> <p> </p> <p><strong>Table S4. </strong>Custom transposon sequencing primers and adaptors used in sequencing of the transposon libraries.</p> <p> </p>
Investigating Types and Survivability of Performance Bugs in Mobile Apps
<p>Replication package of the paper entitled "Investigating Types and Survivability of Performance Bugs in Mobile Apps" published in The Empirical Software Engineering Journal</p>
Supplementary material for "Dynamics of a goshawk population across half a century is driven by the variation of first-year survival"
<p><strong><span>Abstract</span></strong></p> <p><span>Population dynamics are driven by stochastic and density-dependent processes acting on demographic rates. Individuals differ demographically, and to capture these differences, models of population dynamics are usually structured by age and stage, rarely by sex. An effect of sex on population dynamics is expected if the dynamics of males and females differ, requiring an unequal sex ratio at birth and/or sex-specific survival probabilities. Goshawks (<em>Accipiter gentilis</em>) show large sexual size dimorphism and differential survival, but it is unknown whether males and females contribute differently to population dynamics. We studied a goshawk population in northern Germany over 47 years using brood monitoring data, collected feathers and nestling ringing data. We jointly analyzed the data using a two-sex integrated population model and performed retrospective and prospective population analyses to understand whether the demographic drivers of population change differ between the sexes. The population showed large fluctuations, during which the number of breeding pairs doubled, but the long-term trend of the population was slightly negative. Female survival exceeded male survival during the first year of life. Females started to reproduce at a younger age than males, productivity increased with female age, the sex ratio of nestlings was male biased and there was moderate male immigration. Despite these differences, temporal variation in sex ratio did not contribute to population dynamics and the contribution of temporal variation in survival was similar for both sexes. Variation in first-year survival was the strongest driver in this population, regulated by a weak density-dependent feedback acting through female first-year survival. Overall, the contributions of the two sexes to population dynamics were similar in this monogamous species with strong sexual size dimorphism.</span></p> <p><strong><span>Read me</span></strong></p> <p><span>Data files and code for carrying out all analyses and generating all figures presented in the paper. The six data files are provided in csv format. There are five code files written for R, but some of the main analyses require the NIMBLE software. The main code (IPM_Code.txt) contains a description of the data, code for loading and managing the data, and for fitting the integrated population models. The other files contain custom written functions (Functions.txt), code for performing posterior predictive tests (PPT_Code.txt), code for reporting results and performing various other analyses (Output_analyses_Code.txt), and code for generating figures (Figures_Code.txt).</span></p>
Metadata for RadPhysBio: A Radiobiological Database for the Prediction of Cell Survival upon Exposure to Ionizing Radiation
<p>This is the Metadata of our recent publication https://doi.org/10.3390/ijms25094729 </p> <p>Based on the need for radiobiological databases, in this work, we mined experimental ionizing radiation data of human cells treated with X-rays, γ-rays, carbon ions, protons and α-particles, by manually searching the relevant literature in PubMed from 1980 until 2024. In order to calculate normal and tumor cell survival α and β coefficients of the linear quadratic (LQ) established model, as well as the initial values of the double-strand breaks (DSBs) in DNA, we used WebPlotDigitizer and Python programming language. We also produced complex DNA damage results through the fast Monte Carlo code MCDS in order to complete any missing data. In the attached files you will find</p> <ol> <li>Current database for photons</li> <li>Current database for particle radiation</li> <li>Helping supplementary information</li> <li>Tips for help with our Database</li> </ol>
Structured Power Grid Simulation Dataset for Machine Learning: Failure and Survival Events in Grid2Op's L2RPN WCCI 2022 Environment
<p>This dataset was developed for and used in the paper titled <em>"Fault Detection for Agents in Power Grid Topology Optimization: A Comprehensive Analysis"</em> by Malte Lehna, Mohamed Hassouna, Dmitry Degtyar, Sven Tomforde, and Christoph Scholz, presented at the <em>Workshop on Machine Learning for Sustainable Power Systems (ML4SPS)</em>, part of <em>ECML PKDD 2024</em>. While the paper is pending formal publication, a preprint version is available on arXiv.</p> <p>The dataset contains structured training, validation, and test data comprising failure and survival events observed in transmission power grid simulations. These were generated using Grid2Op with the WCCI 2022 L2RPN environment. Each data instance is labeled with one of four classes, representing survival or impending failure in 1, 3, and 5 timesteps. This dataset was used to train, validate and test machine learning models that predict grid agent failures in topology optimization tasks. </p>
Data and code for: Growth, development and survival in the brown widow spider, Latrodectus geometricus under different feeding regimes.
<p><span>Here, we compared mortality, growth and development of the brown widow spider, <em>Latrodectus geometricus</em>, from neonate to adult under two different prey availability regimes. </span></p>
Mammary single-cell RNA-seq analysis and prostate cancer survival as a function of H2AFJ expression for the paper entitled: The histone variant H2A.J is enriched in luminal epithelial cells
<p>H2A.J is a poorly studied mammalian-specific variant of histone H2A. We used immunohistochemistry to study its localization in various human and mouse tissues. H2A.J showed cell-type specific expression with a striking enrichment in luminal epithelial cells of multiple glands including those of breast, prostate, pancreas, thyroid, stomach, and salivary glands. H2A.J was also highly expressed in many carcinoma cell lines and in particular, those derived from luminal breast and prostate cancer. H2A.J thus appears to be a novel marker for luminal epithelial cancers. Knocking-out the H2AFJ gene in T47D luminal breast cancer cells reduced the expression of several estrogen-responsive genes which may explain its putative tumorigenic role in luminal-B breast cancer.</p>
Pathobionts in the tumour microbiota predict survival following resection for colorectal cancer - pre-processed data
<p>A multicentre, prospective observational study was conducted of colorectal cancer (CRC) patients undergoing primary surgical resection in the United Kingdom and Czech Republic. Analysis was performed using metataxonomics (microbiome) and ultra-performance liquid chromatography mass spectrometry (UPLC-MS, metabolomics). Both datasets were pre-processed as described in the methods section of the main article. The data here were used as the input to the data analysis workflows available from <a href="https://github.com/jmp111/CRC">Github</a>.</p>
Predicting Survival of Tongue Cancer Patients by Machine Learning Models
<p>This repository contains the dataset used in the paper "Predicting Survival of Tongue Cancer Patients by Machine Learning Models." The dataset contains information on 1712 tongue cancer curative surgery recipients. Each row represents one patient. The meaning of each variable is summarized here:</p> <ul> <li>id: patient identifier</li> <li>gender: patient sex</li> <li>survival: patient survival status at follow-up; 0: survival, 1: death</li> <li>follow_time: length of follow-up period in days</li> <li>part: site of operation</li> <li>stage: tumor stage; 0: very small, no spreading, 1: small, no spreading, 2: some growth, spreading, 3: large, spreading to surrounding tissue or lymph nodes, 4A/4B/4C: larger, metastasis to at least one other organ</li> <li>op: operation status; 1: complete</li> <li>rt: radiation therapy status; 0: not received, 1: received</li> <li>ct: chemotherapy status; 0: not received, 1: received</li> <li>t_stage: tumor size; 1 (small) to 4 (large)</li> <li>n_stage: metastasis to lymph nodes; 0 (no metastasis) to 3 (metastasis to multiple lymph nodes)</li> <li>grade: tumor grade; 1 (no proliferation) to 3 (aggressive proliferation)</li> </ul>
Nest survival data of Anthus hellmayri
<p><strong>File 1: a_hellmayri_survival.csv</strong></p> <p>Nest survival data of <em>Anthus hellmayri </em>collected during 2017-2018, 2018-2019, and 2019-2020 breeding seasons in Punta Indio, Buenos Aires, Argentina. Used to estimate daily nest survival rates and include covariates in the models.</p> <p><strong>File 2: Readme_a_hellmayri_survival.docx</strong></p> <p>File conainting information about the columns and data</p> <p><strong>File 3: script_ah.R</strong></p> <p>Example code to be used in R software. This code leads to the main result of the paper.</p>
ArrayCGH microarray images for 'Autoencoder and NCA based neural network model to estimate survival prognosis in multiple myeloma using arrayCGH data'
<p>ArrayCGH microarray images for 'Autoencoder and NCA based neural network model to estimate survival prognosis in multiple myeloma using arrayCGH data'</p>
Dataset for Bayesian parametric models for survival prediction in medical applications
<p><strong>Data Source</strong></p> <p>The data for these experiments were derived from these sources:</p> <p>* Hosmer Jr DW, Lemeshow S, May S. Applied Survival Analysis: Regression Modeling of Time-to-Event Data. 2nd ed: John Wiley & Sons; 2008.</p> <p>* Jd K, Prentice R. The statistical analysis of failure time data. New York: John Wiley and Sons; 1980.</p> <p>* Fleming T, Harrington D. Counting Processes and Survival Analysis: John Wiley & Sons; 1991.</p> <p> </p> <p>The raw data was downloaded from web archive.</p> <p>https://web.archive.org/web/20170114043458/http://www.umass.edu/statdata/statdata/data/</p> <p><strong>Contents</strong></p> <p>Each folder contains the original data, a textfile with a description of the data, and the pre-processed version with one-hot encoded variables. An additional YAML file is included with the list of included variables, name of the time and censor variable, name of continuous variables and splitting and partitioning information.</p>
Growth, development, activity, and survival of wood frog tadpoles from different populations in eastern NY in 2022.
These data were collected as two lab experiments that examined larval (i.e., tadpole) wood frog populations. The first was a time-to-death experiment in which we exposed individuals tadpoles to either a control or lethal concentrations of NaCl. The second was a growth and development experiment in which we raised tadpoles from the same populations in a sublethal concentration of NaCl for several weeks to examine their growth and development (i.e. Gosner developmental stage).
Transplanted Sapling Long-term Survivability with Experimental Fungicide and Fencing at Multiple Michigan Sites (2009-2023)
Long-term transplant sapling recruitment (2009-2023) in Michigan, seeking to understand the effects of transplanting northern, southern, and locally sourced tree seeds. Regional sapling transplants simulate the effects of climate change as well as different tree species' ability to survive human-assisted northward migration. This dataset includes >25 species of trees and woody plants with approximately 500 surviving saplings out of ~24,000 transplanted throughout 2009-2017. Saplings are also experimentally treated with fungicide, some fenced to prevent deer browse, and planted under differing levels of canopy cover. Saplings are censused yearly, most recently 2023, recording survival and height.
Tussock survival from 1980 through 2010 for the 1980-82 Eriophorum vaginatum reciprocal transplant experiment
These data were collected in July 2010 for tussocks transplanted in 1980-82 in a reciprocal transplant experiment and harvested in 2011. Important variables are garden name, source population, and whether the tussocks were alive in 1983,1993,2009, and 2010.
Lapland longspur and Gambel's white crowned sparrow egg and nestling survival near Toolik Field Station, Alaska, summers 2012-2016
This data set contains information about the daily status (alive/ dead) of Lapland longspur and Gambel's white-crowned sparrow eggs and nestlings studied near Toolik Field Station from 2012 to 2016 under National Science Foundation (NSF) Office of Polar Programs ARC 0908444 (to Laura Gough), ARC 0908602 (to Natalie Boelman), and ARC 0909133 (to John Wingfield). It is associated with publication DOI: 10.1111/jav.01712.
Known-fate survival information for radio-tagged snowshoe hares captured in Bonanza Creek Experimental Forest from June 2008 to November 2012
This dataset contains known-fate survival information for radio-tagged snowshoe hares captured in two 200 x 450 m live-trapping grids in Bonanza Creek Experimental Forest from June 2008 to November 2012. The data can be sorted and viewed by year, site, number at risk, and number of mortalities.
Salamander survival and growth cage experiment at the Coweeta Hydrologic Laboratory, Otto, NC
Climate change is predicted to alter biotic communities and, as a result, cause changes in ecosystem processes. Such predictions assume that future communities will lack species capable of compensating for the loss of other species. In southern Appalachian headwater streams, abundant larval Black-bellied Salamanders (Desmognathus quadramaculatus) represent a significant standing crop of nitrogen (N) and phosphorus (P). Desmognathus quadramaculatus are projected to be extirpated from the southern Appalachian highlands under most climate change scenarios, which would result in the loss of most salamander standing crop of limiting nutrients unless other species compensate for the loss of D. quadramaculatus biomass. Eurycea cirrigera, which has an abundant congener Eurycea wilderae already in the headwaters, and Gyrinophilus porphyriticus, which currently occurs in low densities in the headwaters, are projected to remain within southern Appalachian highlands. We used field cages to measure (1) the amount of compensatory survival and growth Eurycea would show in the absence of the larger, predatory D. quadramaculatus, and (2) whether replacement of D. quadramaculatus by G. porphyriticus, which is known to be a more efficient predator, would reduce Eurycea and total salamander biomass.
Figure 1 in Does the river blenny Salaria fluviatilis (Asso, 1801) (Actinopterygii: Perciformes) still survive on the Mediterranean island of Cyprus?
Figure 1. Map of all sampled sites (n = 170); black dots represent sites with fish present; white dot sites had no fish present during the survey. Grey areas show the river basins (n = 31) that were explored. The outline shows the legislative boundaries of the District of Limassol (were the presence of the S. fluviatilis was confirmed in 1909).
Digitized patient level time to event data of overall survival
<p>This dataset contains digitized patient level time to event data for overall survival of patients with locally advanced and metastatic (stage IIIB/IV) Non-small cell lung cancer (NSCLC). The data can be used to recreate the original Kaplan-Meier survival curves that were published in randomized controlled trials, in order to perform secondary analysis on the survival data. In order to recreate a survival curve, you need two csv.files per trial arm that are in this <br> database: (1) starting with 'surv_', containing the individual patient level time to event data, and (2) starting with 'natrisk_', containing the corresponding numbers at risk table. For the methodology and r-code that can be used for this purpose we refer to article that is linked to this dataset. </p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.