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Data from the behavioural and Magnetic resonance imaging of the Ts66Yah and Ts65Dn male model of Down syndrome
<p>Please find enclosed the behavioural and Magnetic Resonnance Imaging (MRI) variables used for comparing the Ts66Yah DS models with the parental line Ts65Dn. The raw data are found as two CVS files</p> <p>- Behavioural phenoParameters_Ts65Dn_Ts66Yah.csv</p> <p>- MRI phenoParameters_Ts65Dn_Ts66Yah.csv</p> <p>while the processed data used for the GDAPHEN analysis (https://github.com/YaH44/GDAPHEN/releases/tag/Public) are available as Excel docs.</p> <p> </p> <p>The processing has been done with a low level of imputation for missing data detailed in the Formating_decision_phenoParameters_Ts65Dn_Ts66Yah. ...</p>
DataSet of "No renal dysfunction or salt and water retention in acute mountain sickness at 4,559 m among young resting males after passive ascent"
<p><strong>Abstract</strong></p> <p><strong>Purpose</strong>: This study examined the role and function of the kidney at high altitude in relation to fluid balance and the development of acute mountain sickness (AMS), avoiding confounders that have contributed to conflicting results in previous studies.</p> <p><strong>Methods</strong>: We examined 18 healthy male volunteers (18 - 40 years) not acclimatized to high altitude while on a controlled diet and resting recumbently for 24 h at Lausanne (altitude: 560 m) followed by a period of 44 hours after reaching the Regina Margherita hut (4,559 m) by helicopter.</p> <p><strong>Results</strong>: AMS scores peaked after 20 h at 4,559 m. AMS was defined as functional Lake Louise score <span class="math-tex">\({\ge}\)</span> 2.There were no significant differences between 10 subjects with and 8 subjects without AMS for urinary flow, fluid balance and weight change. Sodium excretion rate was lower in those with AMS after 24 h at altitude. Microalbuminuria increased at altitude but not differently between the groups. Creatinine clearance was not affected by altitude or AMS, while sinistrin and PAH clearances decreased slightly, more markedly in those without AMS. Plasma concentrations of epinephrine, norepinephrine, atrial natriuretic factor and vasopressin increased while renin activity, angiotensin and aldosterone decreased at altitude. Hormones levels did not differ between those with and without AMS.</p> <p><strong>Conclusions</strong>: 1) Renal function is not affected by hypoxia at 4,559 m in resting subjects except for minor microalbuminuria, 2) high altitude diuresis does not occur and 3) AMS is not associated with salt and water retention or renal dysfunction.</p>
Data and script for: "Increased birth rank of homosexual males: disentangling the older brother effect and sexual antagonism hypothesis"
<p>Data and script for Tables 2, 3, S2, S3, S4, and S5, and Figures 1, 3, 4, and S1.</p> <p>Individual dataset:</p> <p>France: <a href="https://zenodo.org/api/files/acdb78f8-397c-4bc3-8f68-ec048edbc5f5/France_data_df12.csv">France_data_df12.csv </a><br> Indonesia: <a href="https://zenodo.org/api/files/acdb78f8-397c-4bc3-8f68-ec048edbc5f5/Indonesia_data.csv">Indonesia_data.csv </a><br> Greece: <a href="https://zenodo.org/api/files/acdb78f8-397c-4bc3-8f68-ec048edbc5f5/Greek_data.csv">Greek_data.csv </a></p> <p>The file <a href="https://zenodo.org/api/files/acdb78f8-397c-4bc3-8f68-ec048edbc5f5/France_script.Rmd">France_script.Rmd </a>contains all the analyses of the french data set, including values presented Tables 2, 3, S3, S4, S5, Figures 3, 4 (output in file <a href="https://zenodo.org/api/files/acdb78f8-397c-4bc3-8f68-ec048edbc5f5/France_script.html">France_script.html</a>). Same thing for files <a href="https://zenodo.org/api/files/acdb78f8-397c-4bc3-8f68-ec048edbc5f5/Indonesia_script.Rmd">Indonesia_script.Rmd </a> and <a href="https://zenodo.org/api/files/acdb78f8-397c-4bc3-8f68-ec048edbc5f5/Greek_script.Rmd">Greek_script.Rmd</a>.</p> <p>For figure 1: <a href="https://zenodo.org/api/files/acdb78f8-397c-4bc3-8f68-ec048edbc5f5/Fig1.html">Fig1.html </a><br> For Figure S1: <a href="https://zenodo.org/api/files/acdb78f8-397c-4bc3-8f68-ec048edbc5f5/Fig_S1.html">Fig_S1.html </a><br> For Table S2: <a href="https://zenodo.org/api/files/acdb78f8-397c-4bc3-8f68-ec048edbc5f5/Table_S2_script.html">Table_S2_script.html </a><br> </p> <p> </p> <p><br> </p> <p> </p> <p> </p> <p> </p>
Backpain exercise therapy remodels human epigenetic profiles in buccal and human peripheral blood mononuclear cells: An exploratory study in young male participants
<pre><strong>###### Files description #####</strong><br> <strong>Notes</strong>. 1) "BT" refers to before therapy and "AT" to after therapy. 2) 0 refers to FALSE and 1 to TRUE for binary variables. The provided files have tab-separated columns except the .RDS which is and R output of the mixOmics DIABLO integration analysis. <strong># Questionnaire</strong> > participants_categories.tsv: per participant (rows), output of the clustering with the participant ("ID") category ("category") per class<br> ("class") > questionnaire_agility_metrics.tsv: questionnaire and agility metrics per participant (rows) for the participants ("ID") with at least one paired AT+BT data in one type of biological sample (indicated in the columns "swab", "PBMC", and "plasma") <strong># PTMs</strong> Samples´ names are encoded as PBMC_AT_8_batch1, i.e. cells origin_time upon therapy_ID_batch (we removed _batch column suffix for the <br>processed files). NA indicates an undetected intensity. > raw_PBMC_light_labelled_intensities.tsv: raw intensity of light/endogenous peptides (row) by precursor per sample (column) from PBMC > raw_swab_light_labelled_intensities.tsv: idem from buccal cells > raw_PBMC_heavy_labelled_intensities.tsv: raw intensity of light/endogenous peptides (row) by precursor per sample (column) from PBMC > raw_swab_heavy_labelled_intensities.tsv: idem from buccal cells > raw_PBMC_heavynormalized_intensities.tsv: raw intensity of light peptides normalized by heavy peptides intensity (row) by precursor per <br>sample (column) > raw_swab_heavynormalized_labelled_intensities.tsv: idem from buccal cells > processed_cleaned_PBMC_log2intensities.tsv: processed (heavy normalized, imputed, batch-corrected) intensity of peptides aggregated by modification (PTM, row) by precursor per sample (column) after log2-transformation. The relative abundances are computed from this file. Rows without me/ac suffix represents the amount of unmodified peptide for the considered site. > processed_cleaned_swab_log2intensities.tsv: idem from buccal cells > rel_abundance_PTM_PBMC.tsv: relative abundance computed per precursor, e.g. for a given sample, the H3_K4+H3_K4me1+H3_K4me2+H3_K4me3 <br>relative abundance values must sum to 100, with the relative abundance of H3_K4 representing the absence of modified K4. > rel_abundance_PTM_swab.tsv: idem from buccal cells > tests_from_rel_abundance_PTM_swab_PBMC.tsv: per type of samples ("Sample.origin", i.e.swab of PBMC) and per PTM (rows, "PTM"), report <br>the output of classic (p-values, adjusted with Benjamini-Hochberg (BH), or Benjamini-Yekutieli procedure (BY), from raw and arcsin square <br>root transformed percentage) and PLS-DA tests (VIP - Variable Importance score - and its 95% confidence interval). The percentage of change<br>of each PTM after therapy relative tobefore therapy is reported in "perc_change.AT.over.BT" column. The "is_candidate" indicates if the PTM has been considered as a hit in the swab or PBMC. <strong># Plasma</strong> Samples´ names are encoded as PLASMA_AT_8_batch1, i.e. cells origin_time upon therapy_ID_batch. NA indicates an undetected intensity. > raw_plasma_maxquant_log2ibaq_intensities.tsv: raw data from protein group MaxQuant file. The iBAQ columns are used in later steps. > processed_cleaned_plasma_log2intensities.tsv: processed (imputed, batch-corrected) intensity of protein groups after log2-transformation. > tests_from_intens_plasma.tsv: per protein group ("Proteins.ID"), report the output of classic (p-values, adjusted Benjamini-Hochberg (BH),<br>or Benjamini-Yekutieli procedure (BY), from log2-transformed intensities) and PLS-DA tests (VIP and its 95% confidence interval). The log2 <br>fold change after therapy relative to before therapy is reported in "log2FC.AT.over.BT" column. The "is_candidate" indicates if the protein group has been considered as a hit. <strong># Integration</strong> > circos_input: output of DIABLO analysis with correlation threshold set to 0.7. Use the readRDS R function to open.</pre> <p> </p>
Differences in Chemo-signaling Compound-Evoked Brain Activity in Male and Female Young Adults: A Pilot Study in the Role of Sexual Dimorphism in Olfactory Chemo-Signaling
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Raw male and female fitness data
<p>Raw male and female fitness data for 223 hemiclonal genotypes sampled from the LH<sub>M</sub> laboratory adapted population. See Gilks et al (2017; https://f1000research.com/articles/5-2644/v3) for full details on how these lines were established. Assays were designed to measure total adult lifetime fitness for both males and females from each line, under conditions that match as close as possible those experienced by adults in the base population (Chippindale <em>et al.</em>, 2001; Rice, 2005; Rice <em>et al.</em>, 2006).</p> <p><em>Male fitness assay</em><br> 5 hemiclonal males per line were combined in adult competition vials with 10 competitor <em>bw</em><sup>-</sup> males and 15 virgin <em>bw</em><sup>-</sup> females. After 2 days, each <em>bw</em><sup>- </sup>female was isolated into individual oviposition test-tubes (containing the cornmeal-molasses-agar media but with no additional dried yeast) and left to oviposit for 18 hours. On Day 12, progeny were scored for eye-colour, in two observation rounds to allow ensure that as many eclosing offspring were included. Hemiclonal males were assigned paternity to progeny with wild-type red eyes (progeny of competitors are homozygous for the <em>bw</em><sup>-</sup> allele and therefore have brown eyes), giving an average fitness score (number of offspring sired) for the 5 hemiclonal males that were assayed per line. This assay was independently replicated 5 times, representing data from a total of 25 hemiclonal males per line. Male fitness was calculated as the proportion of offspring sired per assayed male, which accounts for instances where less than 5 hemiclonal males were included (6 out of 1105 assays).</p> <p><em>Female fitness assays</em><br> Assays of female fitness followed a similar protocol to the male assays, again to match as close as possible the timing and conditions experienced by individuals in the base population. In this case, 5 virgin hemiclonal females were combined in adult competition vials with 10 competitor <em>bw</em><sup>- </sup>females and 15 <em>bw</em><sup>- </sup>males for 2 days. After 2 days, the 5 hemiclonal females were isolated into individual test-tubes and left to oviposit for 18hrs. The tubes were immediately chilled (4°C) to halt embryo development and the number of eggs per female was counted to provide a measure of fecundity. Data was excluded for tubes in which the female was either dead or not present. Since unmated females are known to produce eggs at a low rate, we also excluded data from females where egg counts were 0 or 1 as these are likely to represent output from unmated females (see Supplementary figure 1). By averaging fecundity across all 5 females this provided an average female fitness score for that line. This assay was independently replicated 5 times, representing a total of 25 hemiclonal females per line.</p> <p><strong>Dataset Column headings:</strong></p> <p><strong><em>Male</em></strong><br> sex - all male (value = 1)<br> rep - replicate (values from 1 to 5)<br> line - hemiclonal line (223 different lines, values from 1 to 230 with 7 lines missing)<br> red_1 - number of wild-type red-eyed offspring in first round of counting<br> red_2 - number of wild-type red-eyed offspring in second round of counting<br> brown_1 - number of brown-eyed offspring in first round of counting<br> brown_2 - number of brown-eyed offspring in second round of counting<br> total_red - number of offspring counted with wild-type red eyes (genotype bw<sup>+</sup>/bw<sup>-</sup>)<br> total_brown - number of offspring counted with brown eyes (genotype bw<sup>-</sup>/bw<sup>-</sup>)<br> male_density - number of hemiclonal males per vial (value usually 5, but may be less due to missing males)</p> <p>note: NA - missing value</p> <p><em><strong>Female</strong></em><br> sex - all female (value = 2)<br> rep - replicate (values from 1 to 5)<br> line - hemiclonal line (223 different lines, values from 1 to 230 with 7 lines missing)<br> f1 - fecundity of female 1<br> f2 - fecundity of female 2<br> f3 - fecundity of female 3<br> f4 - fecundity of female 4<br> f5 - fecundity of female 5</p> <p>note: NA - missing value</p> <p><strong>References</strong></p> <p>Chippindale, A.K., Gibson, J.R. & Rice, W.R. 2001. Negative genetic correlation for adult fitness between sexes reveals ontogenetic conflict in Drosophila. <em>Proc. Natl. Acad. Sci.</em> <strong>98</strong>: 1671–1675.</p> <p>Gilks WP, Pennell TM, Flis I et al. Whole genome resequencing of a laboratory-adapted <em>Drosophila melanogaster</em> population sample [version 3; referees: 2 approved]. F1000Research 2016, 5:2644 (doi: 10.12688/f1000research.9912.3)</p> <p>Rice, W.R. 2005. Inter-locus antagonistic coevolution as an engine of speciation: Assessment with hemiclonal analysis. <em>Proc. Natl. Acad. Sci.</em> <strong>102</strong>: 6527–6534.</p> <p>Rice, W.R., Stewart, A.D., Morrow, E.H., Linder, J.E., Orteiza, N. & Byrne, P.G. 2006. Assessing sexual conflict in the Drosophila melanogaster laboratory model system. <em>Philos. Trans. R. Soc. B Biol. Sci.</em> <strong>361</strong>: 287–299.</p>
Bivariate GWAS for female and male fitness in Drosophila melanogaster (Sussex, LHm)
<p>Code, logs, results and graphs for genome-wide association study of reproductive fitness in D.melanogaster hemiclone lines, using the R package 'Mulitphen'.</p>
An assessment of the (anti)androgenic properties of hexachloronaphthalene (HxCN) using a model of immature male rats (Hershberger Bioassay)
<p>The persistent organic pollutants (POPs) include polychlorinated naphthalenes (PCNs); of these, the most toxic, abundant and found in human tissues are the hexachloronaphthalenes (HxCNs). The aim of this study was to evaluate the (anti)androgenic action of HxCN using the Hershberger Bioassay (OECD 441). Castrated male Wistar rats were exposed per os to HxCN at daily doses ranging from 0.3-3.0 mg*kg b.w.-1 for 10 days. Testosterone propionate (TP) was used as the reference androgen, and flutamide (FLU) as the reference antiandrogen. Five assessor sex tissues (ASTs) were weighed: ventral prostate, seminal vesicles, levator ani-bulbocavernosus muscle (LABC), glans penis and Cowper gland. In addition to determining the absolute weight of the ASTs, a number of other tests were performed on serum hormone levels (testosterone [T], triiodothyronine 99 [T3], thyroxine [T4], LH and FSH) and the histopathology of the ASTs. </p>
Vibrational signals produced by wing buzzing in Cacopsylla pyrisuga males (Hemiptera: Psyllidae)
<p>High-speed camera (video files) and laser vibrometer (audio files) recordings of Cacopsylla pyrisuga males producing vibrational signals - a dataset accompanying the publication</p> <p>Polajnar J., Kvinikadze E., Harley A.W., Malenovský I. (2024) Wing buzzing as a mechanism for generating vibrational signals in psyllids (Hemiptera: Psylloidea). Insect Science. See the publication for details about the methodology used.</p> <p>The dataset additionaly includes tracked points at wing and abdomen tips from two videos, and an R script with instructions to read this data.</p>
A diet containing mango peel silage impacts upon feed intake, energy supply and growth performances of dairy male calves
<p>The major challenges for disposal of waste from fruit processing factories are high transportation costs, limited landfill availability and environmental pollution. Therefore, developing efficient waste management techniques to reduce transportation costs and environment pollution is important. Mango peels (MP) are abundant during the mango season and high in fermentable carbohydrate, which can easily breakdown and pollute the environment if a proper waste management method is not implemented. Thus, in this study, fresh MP were ensiled after sun-dried for one day and then fed to dairy male calves as the roughage source to evaluate its effect on feed intake, digestibility, energy balance, body weight gain, feed efficiency and blood metabolites. Eight growing crossbred dairy male calves (Holstein Friesians × Zebu) were allocated into two groups [Control (n = 4) and mango peel silage (MPS, n = 4)]. This experiment lasted for 12 weeks and daily feed offered and refusal were recorded to determine the daily feed intake. Digestion trial was performed at the last five days of experiment. Body weight and measurement were recorded every two weeks interval to determine the weight gain and body physical improvement. Blood was collected at the end of experiment to analyze the serum biochemical parameters. Ensiling improved the energy and protein contents and decreased fibre content of MP, thereby improving the forage quality. Feeding MPS to calves increased (<i>P</i> < 0.05) feed intake, energy supply and energy balance, changes in body measurements, weight gain, feed efficiency, and glucose concentration, as well as lowered (<i>P</i> < 0.05) the urea nitrogen concentration. Ensiling fresh MP after sun-drying for one day improved silage quality, and feeding MPS to dairy male calves as a roughage source improved feed intake, energy supply and growth performances. Therefore, ensiling fresh MP could improve the feed supply for ruminant production and be an effective waste management strategy for fruit processing businesses. </p>
Male biased sex ratio in the offspring of roe deer
<p>The file "metafor_roe_sex.csv" was used for the meta-analysis regarding the sex ratio of roe deer juveniles. It contains the columns: </p> <p>Author (author(s) of the publication, Country (country were the study was publised), Location (specific location, in case that the data set contains several different locations the term "divers" is used), Year (year(s) were the sex of roe deer offspring were documented), Pub-Year (Year of publication) , N (number of offspring), N_female (number of female offspring), Sex ratio (primary - P or secondary - S sex ratio), Habitat conditions (F - free ranging, I - Island conditions, C - captive), Proportion female (proportion of female juveniles), Low_95 (lower boundary for the proportion of females using an exact binomial test with a 95% confidence interval), High_95 (upper boundary for the proportion of females using an exact binomial test with a 95% confidence interval), d (effect size), d_se (standard error of the effect size), North (Latitude), East (Longitude)</p> <p>The file "sex_bw.csv" contains information about roe deer juveniles tacked in Baden-Württemberg. The columns read as: Year (year were the juvenile was tacked), sex (the sex of the juvenile, m- male; f- female), and Hasl (elevation in m)</p> <p>The file "temp_data_comma_sep.csv" contains the montly mean values for temperature (Temp) and precipitation (NDS) for the months January, February, March, ..., December for the German federal state Baden-Württemberg (Source German Weather Service).</p> <p>All data sets were used for analysis presented in: Evidence for a male-biased sex ratio in the offspring of a large herbivore: the role of environmental conditions in the sex ratio variation.</p> <p> </p> <p> </p>
Schistosoma mansoni ATAC-seq results for IGV (female and male worms with and without LSD1 inhibitor)
<p>In this study, the anti-schistosomal activity of 39 <em>Homo sapiens</em> Lysine Specific Demethylase 1 (HsLSD1) inhibitors was investigated on parasitic life cycle stages associated with both definitive and intermediate host infection. Amongst this collection of small molecules, compound <strong>33</strong> was the most potent and reduced <em>ex vivo</em> viabilities of schistosomula, juveniles, miracidia and adults. At its sub-lethal concentration to adults (3.13 µM), compound <strong>33 </strong>also significantly impacted oviposition, ovarian as well as vitellarian architecture and gonadal/neoblast stem cell proliferation. ATAC-seq analysis of adults demonstrated that compound <strong>33</strong> significantly affected chromatin structure (intragenic regions > intergenic regions), especially in genes differentially expressed in cell populations (e.g., germinal stem cells, hes2<em><sup>+</sup></em>stem cell progeny, S1 cells and late female germinal cells) linked to these <em>ex vivo</em> phenotypes.</p> <p>The data presented here allow for visualisation in IGV https://igv.org/app/</p> <p>Produced in collaboration with IHPE. </p>
Data from: Male long-distance migrant turned sedentary; The West European pond bat (Myotis dasycneme) alters their migration and hibernation behaviour
<p>Winter survey data, temperature data and mark recapture data of <em>Myotis dasycneme</em>. This study aimed to better understand the migration, mating and hibernation choices of the pond bat.</p> <p> </p> <p>The study area covered the whole of the Netherlands, Belgium and East Frisia (northwest Germany). We defined two study periods, data collected between 1930 and 1980 (Sluiter and van Heerdt) and data between 1980 and 2015 (Haarsma). All available mark and recovery data (ringing) of both the historical and recent migration research were digitized. Observations include location and date of capture, species, sex and ring number. The latest observations in the recent dataset (Haarsma) also include biometric measurements (forearm length, body mass) and information about age and reproductive status. These biometric measurements show that male pond bats are on average smaller and lighter than females (body mass (g)/ forearm length (mm) females: 18.9/47.1, males: 16.4/46.4). The dataset shows changes in the fat mass of both sexes during a year.</p> <p>This study also compares migration data with winter monitoring survey data. We selected winter roosts with three or more records of three or more pond bats in one or both of the study periods. Only data from sites with long-term data series (from the hibernacula in the Dutch provinces of Zuid-Holland, Gelderland and Limburg) were used to analyse trends and annual abundance. Our selection included 59 limestone mines in the province of Limburg and 16 WOII bunkers in Gelderland and 38 in Zuid-Holland. We divided the sites into 'core' and 'satellite' sites depending on the timing of first colonization.</p> <p> </p> <p><strong>Bunker limestone mine microclimate</strong></p> <p> </p> <p>Radiation temperature: radiation temperature of the wall, measured with a non-contact infrared thermometer</p> <p>How many bats: the group size of each bat/ group of bats observed, categorized as alone and group.</p> <p>Where: the hanging location of the observed bat, categorized as hidden (in crevice) or free (free on ceiling or wall)</p> <p>Date: date of the observation</p> <p>Xy-coord: The coordinates of the entrance of the bunker or limestone mine. The RD (Rijks-Driehoek) system is the coordinate system used by the Dutch geographical service.</p> <p>Type: Bunker or limestone</p> <p>Location description: description of the name of the site</p> <p> </p> <p><strong>Bunker monitoring core and satellite</strong></p> <p> </p> <p>Date: date</p> <p>Winter: the period between September and April is defined as the winter of the year starting in January.</p> <p>Location description: description of the name of the site</p> <p>N of pond bats: total number of observed pond bats</p> <p>Province: the province</p> <p>Type: hibernacula categorized as a core or satellite site, sites occupied by pond bats since 1977 and 1997 respectively.</p> <p>XY-coord: The coordinates of the entrance of the bunker or limestone mine. The RD (Rijks-Driehoek) system is the coordinate system used by the Dutch geographical service.</p> <p> </p> <p> </p> <p><strong>Supporting information (as referenced in the published paper, hence also available with plos one)</strong></p> <p><br> <strong>S1 Fig. The range of the West European pond bat population (TIF).</strong> The shaded areas indicate the<br> areas where the bulk of the surveys were carried out.</p> <p><br> <strong>S2 Fig. The distribution of the pond bat in Europe (country boundaries are only indicative) (JPG).</strong> Within the whole range of the species distribution seven groups can be separated.<br> A The Netherlands, Belgium and Northwest Germany (~the West European population),<br> B Jutland Peninsula,<br> C Central European lakelands,<br> D The Baltic States,<br> E Ural Mountains (hibernacula),<br> F Volga Valley (summer nurseries),<br> G Hungary and Romania.<br> <br> <strong>S3 Fig. The distribution of hibernacula used by the western pond bat population (TIF). </strong>These are<br> sites with three or more records of pond bats in one or both study periods. We identified four<br> roost categories: Roosts which have been used ever since 1900 (= green squares), roosts used<br> only between 1900–1980 (= open black squares), roosts occupied after 1980 (= purple circles),<br> roosts occupied after 1997 (= blue asterisks). Detailed maps, all with the same enlargement, of<br> the clusters in the provinces of Zuid-Holland (1), Gelderland (1) and Limburg (3) are provided.<br> <br> </p> <p><strong>S1 Table. Summary of the average weight of pond bats over the study period.</strong> The weight is averaged per week. The table gives average weight of females, males both adults and juveniles.</p> <p> </p> <p>Avg weight: average weight of pond bats of each sex, in a certain week</p> <p>Sex: male of female</p> <p>Week number: number of the week</p> <p>Age: juvenile (or young of the year). Defined as the from birth until the onset of first hibernation. Subadult or sexual immature, defined as individuals with no signs of (past) reproductive activity. Adult or sexual mature, defined as all individuals with signs of (previous) reproductive activity.</p> <p>N observations: number of observations within each subset.<br> </p> <p><strong>S2 Table. Mark and recapture data from the historical dataset.</strong><br> </p> <p>Ringnumber: the label of the ring</p> <p> Sex: male or female</p> <p>capture date: date of capture</p> <p>capture location: description of capture location</p> <p>x y coordinate: The coordinates of the capture location in RD. The RD (Rijks-Driehoek) system is the coordinate system used by the Dutch geographical service.</p> <p>recapture date: date of recapture</p> <p>recapture location: description of recapture location</p> <p>x y coordinate: The coordinates of the recapture location in RD. The RD (Rijks-Driehoek) system is the coordinate system used by the Dutch geographical service.</p> <p> </p> <p><strong>S3 Table. Mark and recapture data from the recent dataset.</strong></p> <p> </p> <p>Same dataset as the historical set, but now including age (see definition used in S1)<br> <br> </p>
Chacma baboon male-male greeting dataset, Gorongosa National Park, Mozambique
<p><em><strong>See README file for more complete information</strong></em></p> <p><strong>Overview: </strong>This dataset provides presence/absence data for each of 55 observations from Gorongosa National Park. Each observation is one male-male greeting. Data was first collected using BORIS (Friard and Gamba, 2016) following an ethogram (DOI:10.5281/zenodo.7314291), then cleaned using Python version 3.8.5 and R version 4.3.1 to format as a presence/absence matrix. Some of these observations (with observation IDs ending in "_greet[xx]" also appear in the more general approach dataset found under the following DOI 10.5281/zenodo.10339023. These observations are part of both datasets as they qualify both as male-male greetings and also as approaches from outside 5 m to within 2 m. </p> <p><strong>Study species: </strong><em>Papio ursinus griseipes</em> (chacma baboon)</p> <p><strong>Dates of data collection:</strong> Videos in Gorongosa National Park were filmed 2018-10 to 2018-11 and 2019-07 to 2019-11. </p> <p><strong>Geographic location of data collection:</strong> Gorongosa National Park, Mozambique<br><br><strong>Video coding software: </strong>BORIS (Friard and Gamba, 2016)</p> <p><strong>Recommended citation in BibTex form:</strong></p> <p>@ELECTRONIC{Muschinski2024,<br> author = {Muschinski, Jana and Carvalho, Susana},<br> year = {2024},<br> title = {Chacma baboon male-male greeting dataset, {G}orongosa {N}ational {P}ark, {M}ozambique},<br> doi = {10.5281/zenodo.11097938},<br> owner = {Paleo-Primate Project, Gorongosa National Park},<br> organization = {Paleo-Primate Project, Gorongosa National Park}<br>}</p>
Prefrontal cortex activation and functional connectivity during human male orgasm measured with fNIRS
<p>A portable fNIRS system Brite MKII (Artinis, NE) was placed on the PFC of the self-experimenting participant (Male, 43 years). Ten sources and eight detectors are combined into 22 long separation channels (30mm) and two short-separation channels (SSC) to cover the PFC (Figure 1A). The experiment lasted 392s where the participant was subject to pornographic video clips (V) and performed genital self-stimulation (M) until orgasm was reached (O).<br>Citation of the article related to this dataset:</p> <div> <div><strong>Guevara, E.</strong> (2024). <em>Prefrontal cortex activation and functional connectivity during human male orgasm measured with fNIRS</em> [Preprint]. OSF. <a href="https://doi.org/10.31219/osf.io/6y2ze">https://doi.org/10.31219/osf.io/6y2ze</a></div> </div>
Lukas, D. and Clutton-Brock, T. 2014: Male Tenure Length
Lukas, D. and Clutton-Brock, T. 2014. Costs of mating competition limit male lifetime breeding success in polygynous mammals. Proceedings of the Royal Society B, 281 20140418 doi:10.1098/rspb.2014.0418<p></p>Lukas, D. and Clutton-Brock, T. 2014. Costs of mating competition limit male lifetime breeding success in polygynous mammals. Proceedings of the Royal Society B, 281 20140418 doi:10.1098/rspb.2014.0418
Cuckoo male bumblebees perform slower and longer flower visits than free-living male and worker bumblebees
<p>These .txt files include the dataset (tab-separated) and the annotated R-scripts (R-scripts_R1 is the final version) used in the analyses reported in the preprint "Cuckoo male bumblebees perform slower and longer flower visits than free-living male and worker bumblebees".</p> <p>The preprint is available on Zenodo (<a href="https://doi.org/10.5281/zenodo.4489066">https://doi.org/10.5281/zenodo.4489066</a>) and has been recommended by PCI Zoology (<a href="http://zool.peercommunityin.org/articles/rec?id=44">https://zool.peercommunityin.org/articles/rec?id=44</a>). The article has then been published in the Belgian Journal of Zoology (2021, 151:193:203, <a href="https://belgianjournalofzoology.eu/index.php/BJZ/article/view/93">https://doi.org/10.26496/bjz.2021.93</a>)</p> <p> </p>
Assembled transcriptomes of ovary, testis, and brain (male and female) of Amphibolurus muricatus (jacky dragon) generated using Trinity v2.11.0
<p><strong><em>A. muricatus</em> transcriptome assemblies generated using Trinity v2.11.0 (Haas et al. 2013; Grabherr et al. 2011; Henschel et al. 2012)</strong><br> • Amphibolurus-muricatus_brain.fa.tar.gz: Combined Trinity assembly of <em>A. muricatus</em> brain (male and female).<br> • Amphibolurus-muricatus_combined.fa.tar.gz: Combined Trinity assembly of <em>A. muricatus</em> ovary, testis, and brain (male and female).<br> • Amphibolurus-muricatus_female_brain.fa.tar.gz: Trinity assembly of female <em>A. muricatus</em> brain.<br> • Amphibolurus-muricatus_male_brain.fa.tar.gz: Trinity assembly of male <em>A. muricatus</em> brain.<br> • Amphibolurus-muricatus_ovary.fa.tar.gz: Trinity assembly of <em>A. muricatus</em> ovary.<br> • Amphibolurus-muricatus_testis.fa.tar.gz: Trinity assembly of <em>A. muricatus</em> testis.</p> <p> </p> <p><strong>References</strong></p> <ul> <li>Grabherr, M.G., B.J. Haas, M. Yassour, J.Z. Levin, D.A. Thompson et al., 2011 Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29 (7):644-652.</li> <li>Haas, B.J., A. Papanicolaou, M. Yassour, M. Grabherr, P.D. Blood et al., 2013 De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8 (8):1494-1512.</li> <li>Henschel, R., M. Lieber, L.-S. Wu, P.M. Nista, B.J. Haas et al., 2012 Trinity RNA-Seq assembler performance optimization, pp. 45 in Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond. Association for Computing Machinery, Chicag, IL, USA.</li> </ul> <p> </p>
Quartet of familiar males – 16p11.2 Del mouse strain – 2 WT + 2 Del/+ - M1
<p>We monitored the individual and social behaviours of each quartet of mice over three days and nights in the Live Mouse Tracker system (LMT, plugin 931; de Chaumont et al. 2019 Nat. Biomed. Engin.). This system tracks individually mice living in a group over several days and nights and extracts automatically the number, total duration and mean duration of more than thirty behavioural events describing the posture of the mouse, the types of social contacts, the dynamic social approach and escapes and complex social groupings (see de Chaumont et al. 2019 Nat. Biomed. Engin.). In this system, the four mice (10-14 weeks of age; 2 WT mice and 2 Del/+ mice) from the same housing cage (housed together from weaning on) were left undisturbed for 71 hours in a large transparent Plexiglas cage (50 x 50 x 40 cm), with fresh bedding, a house (width: 100 mm, depth: 75 mm, height: 40 mm) in red Plexiglas, 6 dental cotton rolls as well as food and water ad libitum. Light/dark cycle and temperature conditions were similar to those of the housing room (12/12h light/dark, lights on at 07:00 AM, 100 lux when the lights were on). Each recording session started between 03:00 and 04:00 PM. At the end of the session, mice were placed back in their home cage and the LMT setup was cleaned with soap water and dried with paper towels. The upload includes the sqlite database from LMT (processed).</p>
Quartet of familiar males – 16p11.2 Del mouse strain – 2 WT + 2 Del/+ - M3
<p>We monitored the individual and social behaviours of each quartet of mice over three days and nights in the Live Mouse Tracker system (LMT, plugin 931; de Chaumont et al. 2019 Nat. Biomed. Engin.). This system tracks individually mice living in a group over several days and nights and extracts automatically the number, total duration and mean duration of more than thirty behavioural events describing the posture of the mouse, the types of social contacts, the dynamic social approach and escapes and complex social groupings (see de Chaumont et al. 2019 Nat. Biomed. Engin.). In this system, the four mice (10-14 weeks of age; 2 WT mice and 2 Del/+ mice) from the same housing cage (housed together from weaning on) were left undisturbed for 71 hours in a large transparent Plexiglas cage (50 x 50 x 40 cm), with fresh bedding, a house (width: 100 mm, depth: 75 mm, height: 40 mm) in red Plexiglas, 6 dental cotton rolls as well as food and water ad libitum. Light/dark cycle and temperature conditions were similar to those of the housing room (12/12h light/dark, lights on at 07:00 AM, 100 lux when the lights were on). Each recording session started between 03:00 and 04:00 PM. At the end of the session, mice were placed back in their home cage and the LMT setup was cleaned with soap water and dried with paper towels. The upload includes the sqlite database from LMT (processed).</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.