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13,621 results for “Biologics”
ktest_data_genome_biology_2024
<p>This repository contains the reversion dataset and the scChIP-Seq dataset analysed in Ozier-Lafontaine et. al 2024. </p> <p>Files associated to reversion dataset : </p> <ul> <li>reversion_SCT_residuals.csv : Pearson residuals of the scRNAseq dataset based on the R package sctransform </li> <li>reversion_SCT_residuals_batch_corrected.csv : Batch-centered Pearson residuals of the scRNAseq dataset based on the R package sctransform </li> <li>RTqPCR_reversion_logx.csv : log(X+1) normalization of the RTqPCR dataset </li> <li>RTqPCR_reversion_logcentered.csv Batch-centered log(X+1) normalization of the RTqPCR dataset </li> </ul> <p>Files associated to the scChIP-Seq dataset : </p> <ul> <li>human_epdnew_qoQwV.bed </li> <li>MM468_H3K27me3_peaks_3000_10000_95_uncorrected_correlation_filtered.qs </li> </ul> <p> </p> <p>The scripts to perform the data analysis are on the github repository https://github.com/AnthoOzier/ktest_experiment_genome_biology_2024 </p> <p>The reversion dataset comes from Zreika, S., Fourneaux, C., Vallin, E. <em>et al.</em> Evidence for close molecular proximity between reverting and undifferentiated cells. <em>BMC Biol</em> <strong>20</strong>, 155 (2022). https://doi.org/10.1186/s12915-022-01363-7</p> <p> </p>
Biological Samples Inventory from the "Exercise, Nutrition, and Healthy Lifestyle Research Group" (INCLIVA)
<h4><strong>Title: </strong>Biological Matrices Inventory from the Exercise, Nutrition, and Healthy Lifestyle Research Group (INCLIVA)</h4> <h4><strong>Author: </strong>Exercise, Nutrition, and Healthy Lifestyle Research Group, INCLIVA</h4> <p><strong>Abstract:</strong><br>This dataset contains detailed information about the biological matrices available in the Exercise, Nutrition, and Healthy Lifestyle Research Group at INCLIVA. The dataset is in Excel format and is organized into three sheets:</p> <ol> <li><strong>Read-me:</strong> Explains how the data is organized and the conventions used.</li> <li><strong>Mouse Samples Inventory:</strong> Details the mouse-derived samples, including their origin and characteristics.</li> <li><strong>Human Samples Inventory:</strong> Provides information on the human-derived samples available, including their origin and characteristics.</li> </ol> <p>This resource is intended for researchers seeking collaborations.</p> <h4><strong>Keywords: </strong>Biological matrices, Nutrition, Healthy lifestyle, Physical exercise, Biobanks, INCLIVA, Public health</h4>
Fig. 2 in SYNOPSIS OF THE BIOLOGICAL DATA ON THE LOGGERHEAD SEA TURTLE CARETTA CARETTA (LINNAEUS 1758)
Fig. 2. Ventral view of plastron of adult loggerhead (Pritchard and Trebbau 1984).
Fig. 4 in SYNOPSIS OF THE BIOLOGICAL DATA ON THE LOGGERHEAD SEA TURTLE CARETTA CARETTA (LINNAEUS 1758)
Fig. 4. Forearm of adult loggerhead (Romer 1956).
Fig. 1 in SYNOPSIS OF THE BIOLOGICAL DATA ON THE LOGGERHEAD SEA TURTLE CARETTA CARETTA (LINNAEUS 1758)
Fig. 1. Dorsal view of carapace of adult loggerhead (Deraniyagala 1939).
Data for: Exposure and sensitivity of terrestrial vertebrates to biological invasions worldwide
<div> <p><em><strong>All details on the dataset are provided in the README. Details on the methods are in the Supplementary Material of the associated paper.</strong></em></p> <p>This dataset is the product of data complilation for the article <strong>Exposure and sensitivity of terrestrial vertebrates to biological invasions worldwide</strong>. It comprises, at a global scale for 110km grid cells:</p> <ul> <li>the exposure to the threat of biological invasions for 304 invasive alien species (3 exposure metrics with 3 alternative normalization methods)</li> <li>the sensitivity of birds, mammals, and reptiles to this threat (1 sensitivity metric with 3 alternative normalization methods)</li> <li>the data completeness associated with exposure and sensitivity, calculated with 2 components for each metric</li> </ul> <p>All the column details are provided in the "Metadata" sheet of each excel file. We also provide the shapefile of land cell units to allow for a full reproduction of the analyses and the maps.</p> <p>Additionally, we provide the sources to access the raw data used to derive the metrics for invasive alien species. </p> </div>
Semantic audio-visual congruence modulates visual sensitivity to biological motion across awareness levels
<p>This repository contains all experimental scripts, analysis and data files for the manuscript "Semantic audio-visual congruence modulates visual sensitivity to biological motion across awareness levels".</p>
Subterranean Biology (832)
Subterranean Biology is an international journal published by Pensoft on behalf of the International Society for Subterranean Biology [SIBIOS] for the publication of original and significant contributions on all aspects of subterranean life. All published papers can be freely copied, downloaded, printed and distributed at no charge for the reader. Authors are thus encouraged to post the pdf files of published papers on their homepages or elsewhere to expedite distribution. There is no charge for color.<p></p>Subterranean Biology is an international journal published by Pensoft on behalf of the International Society for Subterranean Biology [SIBIOS] for the publication of original and significant contributions on all aspects of subterranean life. All published papers can be freely copied, downloaded, printed and distributed at no charge for the reader. Authors are thus encouraged to post the pdf files of published papers on their homepages or elsewhere to expedite distribution. There is no charge for color.
Selected biological journal names and sample bibliography databases
<p>This 3rd version contains a full backup of X Dong's bibliographic files entered in BiBTeX format; it also includes an update of the three journal name database files (with over 4800 multidisciplinary journal names). Each of the bibliographic files is a collection of references under a certain topic, but sometimes the references were gathered in a specific file just for convenience of writing a specific manuscript. One may combine all the bibliographic files (with about 4000 references) into one .bib file, but beware that sometimes there are duplications, which can lead to LaTeX to complain during compilation. To prevent that from happening again, one may go back to remove the duplicated entries. Like the previous versions, for journal articles, only the nicknames of the respective journals are used in all of the bibliographic files. This assumes the bibliographic files will be used along with one of the three journal name database files (always list the journal name database file first; see description of Version 1).</p> <p>### <br>compens -- references related to root water uptake compensation<br>cotton_drought -- related to plant drought tolerance, in particular of cotton <br>cover -- related to cover crops<br>Ghg -- related to greenhouse gas flux/management/measurement etc., from natural or managed ecosystems<br>Ghg_Ai -- additional references related to greenhouse gas<br>gpr -- related to ground penetrating radar application to agriculture<br>guayule -- related to the study of guayule, a natural rubber plant native to the Chihuahuan desert<br>hemp -- related to industrial hemp, esp. physiology and agronomy<br>JLong -- the journal name database with full journal names <br>Jshort -- the journal name database with abbreviated journal names <br>Jshort_dod -- the journal name database with abbreviated journal names and a period<br>leaf_wax -- related to leaf wax<br>Mycorr -- related to mycorrhizae<br>onion_water -- related to water stress and irrigation scheduling of onion<br>opt1 -- related to optimization, esp. mathematical modeling applications in biology and agriculture<br>pv -- related to pressure-volume curves for studying plant water relations<br>RainPulse -- related to variations of rainfall in natural ecosystems<br>Root-dist -- related to plant root distribution<br>Stat_Mod -- related to statistical modeling and its applications in biology and agriculture<br>XDref -- a collection of miscellaneous references </p> <p> </p> <p> </p> <p> </p> <p> </p>
Unified Understanding of Biological Effects Caused by Radiation: Overcoming LQM Difficulties
<p>We propose the Sea Saw (SS) model, which provides a unified description of the biological effect caused by radiation. This can be directly applied to clinic plans in radiotherapy and the basic formula for radioprotection. This can be replaced by the so-called LNT or LQM bases to describe the effects caused by radiation exposure and we can estimate exactly the effects of fractionation cases or we can directly take account of dose rate effect without any additional DDREF. This can be done by introducing the cell exclusion effect. The model is very simple and intuitively acceptable by expressing the dose-rate effect and can be easily extended to the radiation clinic cases and overcomes the difficulties of the standard method using LQM based BED. The calculated result of our model reproduces the existing data of the time dependence of the cancer volume during the cancer treatment measurement. We demonstrate that different initial volumes, namely for the cases where irradiation starts with a smaller initial volume is more effective than a larger volume. Especially if the cancer volume is almost full in the tissue, the radiation effect of the cancer treatment is very small. On the other hand, for the smaller initial volume, the cancer treatment is found to work more effectively to reduce the cancer volume. Using this model we can predict the time dependence of the cancer volume, and clarify how the effect of radiation therapy depends on the cancer stage on the starting time of the radiation treatment.</p> <p>After explaining the essential difference between our SS model and traditional LQ treatment with BED index, we would like to report the results of SS model by displaying the comparison of our prediction of the estimated results with the relevant new data from the radiation therapy sectional group of Osaka International and will report the comparison those with our prediction. We can also consider continuous but time-dependent irradiation cases and got interesting outcomes on the time dependence of the tumor volume for various clinic plans. Especially by choosing the value of the dose rate to be balanced with the total growth rate, the tumor volume is kept constant.</p> <p>Finally, I would like to emphasize that our SS model leads us not only with a unified description of radiation therapy but also indicates the misleading principle based on LNT or LQM hypothesis which is still adopted in the society of radiation protection.</p>
Biologically informed machine learning for identifying human placental cellular heterogeneity and preeclampsia discovery
<p>Single-cell transcripts of 20,518 placental cells and identified 12 major placental cell clusters were collected from the European Bioinformatics Institute (EBI; accession no. EGAS00001002449) (29). Based on the same parameters, we clustered and visualized highly similar cells using t-distribution random neighbourhood embedding (T-SNE) to identify 17 cell subpopulations. we selected nine placental cell clusters that have received more attention from biologists for our study according to the literature survey (Table 1). Considering the sample balance, 7178 single-cell transcriptome data were used to identify human placental cell subpopulations. The samples were randomly divided into a 4809-sample training set and a 2369-sample testing set. The same strategy was applied to split single-cell transcriptomic datasets from healthy and preeclampsia patients (EBI; accession no. EGAS00001002449), with 9852 samples (healthy 4705, preeclampsia 5147) in the training set and 5305 samples (healthy 2473, preeclampsia 2832) in the independent test set</p>
Fig. 16 in Taxonomic Review Of Euphydryas Maturna (Linnaeus, 1758) (Lepidoptera, Nymphalidae) With Description Of A New Subspecies From Dobrogea (Romania) And Notes On Conservation Biology
Fig. 16. Distribution of Euphydryas maturna in Eurasia and in SE Europe
FIGURE 17 in Collohmannia Johnstoni N. Sp. (Acari, Oribatida) From West Virginia (U.S.A.), Including Description Of Ontogeny, Setal Variation, Notes On Biology And Systematics Of Collohmanniidae
FIGURE 17: Collohmannia johnstoni n. sp. immatures, light micrographs, DIC (A, B, E) and incident (C, D) illumination: A – protonymph, separated prodorsal shield, ventral view; B – larva, anterior part of prodorsum, lateral view; C-E – tritonymph: C – ventral view, D – lateral view, E – anterior part of separated prodorsum, lateral optical section. Abbreviations: AD – adanal segment, AG – aggenital region, AN – anal segment (paraproctal valves), c.fr – cheliceral frame (line bt of Grandjean 1966), GE – genital valves, gla – orifice of opisthonotal gland, pK – prodorsal condyle, nl – lateral rib (nervure), po – porose area, pa.a – postanal apodeme, pr.a – preanal apodeme, rb – rostral bulge, sa – sagittal apodeme; bo, in, le, ro, xa – prodorsal setae or their alveoli; e, h – gastronotic setae. Each image layered and color- and sharpness-enhanced (see Material and Methods).
FIGURE 12 in Collohmannia Johnstoni N. Sp. (Acari, Oribatida) From West Virginia (U.S.A.), Including Description Of Ontogeny, Setal Variation, Notes On Biology And Systematics Of Collohmanniidae
FIGURE 12: Collohmannia johnstoni n. sp. adult, details of gnathosoma, separated structures. Transmitted light micrographs, with brightfield (A), DIC (B-I) or polarized (J-L) illumination: A – chelicera overview, showing positions of B-D; B – optical section of cheliceral trochanter and vicinity; C – Trägårdh's organ and hyaline margin of trochanteral tectum; D – detail of surface around lamellated organ (left), with successive optical sections (right, deepest at bottom); E – movable digit of chelicera, ventral view, distal to right; F – cheliceral chela; G – posterior region of subcapitulum, ventral view; H – posterior half of subcapitulum, dorsal view; I – cross-section of subcapitulum at level of (*) in H, posterior view; J – posterolateral corner of subcapitulum, lateral view; K – dorsal face of rutellum, distal to lower left, with rare single spine; L – same view of rutellum with typical two spines. Abbreviations: c.ap – capitular apodema, car – carinae, cp – podocephalic canal, pha – pharynx, sr – supporting rib of labrum, te – tendons of muscles; others given in Fig. 11. Each image layered and color- and sharpness-enhanced (see Material and Methods).
FIGURE 8 in Collohmannia Johnstoni N. Sp. (Acari, Oribatida) From West Virginia (U.S.A.), Including Description Of Ontogeny, Setal Variation, Notes On Biology And Systematics Of Collohmanniidae
FIGURE 8: Collohmannia johnstoni n. sp. adult, bothridium and bothridial seta, transmitted light micrographs, DIC: A – shallow optical section from external view (arrow points to bothridial opening); B – same, slightly deeper; C – internal view, showing locules of region 3; D – optical section, showing all regions in cross-section; E – distal region of bothridial seta. Abbreviations: iso – isotropic tip of seta bo, lo – locules, br.1- br.3 – bothridial regions (see text), * – insertion of seta bo. Each image color- and sharpness-enhanced; C, D layered (see Material and Methods).
FIGURE 5 in Collohmannia Johnstoni N. Sp. (Acari, Oribatida) From West Virginia (U.S.A.), Including Description Of Ontogeny, Setal Variation, Notes On Biology And Systematics Of Collohmanniidae
FIGURE 5: Collohmannia johnstoni n. sp. adults, brightfield transmitted light micrographs of notogastral fragments from dissected specimens: A-C – humeral region. A – anterolateral view, showing posterior extension of transitional cuticle; B – internal view showing gland-like cells of porose area near seta c3; C – external view of same cuticle; D – vicinity of opisthonotal gland opening; E – region of setae p1 and p2 showing fragmented porose area; note ring of pores around alveolus p1 and shape of setal insertion in alveolar membrane; F – vicinity of setae h2 and h3 with porose area and group of larger pores (see note to E); G – vicinity of seta p3 with lyrifissure ips in transitional cuticle along ventral margin of notogaster. Abbreviations: col – notogastral 'collar', gl – gland associated with porose area; mu – muscle, nod – nodule, po – porose area, por – separate pore, prod – prodorsum, t.cu – transitional cuticle. Each image layered and color- and sharpness-enhanced (see Material and Methods).
FIGURE 2 in Collohmannia Johnstoni N. Sp. (Acari, Oribatida) From West Virginia (U.S.A.), Including Description Of Ontogeny, Setal Variation, Notes On Biology And Systematics Of Collohmanniidae
FIGURE 2: Collohmannia johnstoni n. sp. adults, light micrographs, incident illumination: A, B – female and male (respectively) in ventral view; arrows indicate the reach of femur IV. C – male leg IV, note seta v" and the broad articulation (arrow) allowing dorsal flexing of tibia. D – male with aberrant cuticle coloration, dorsal view; superimposed angle is indicative of gender (see explanation in text). Abbreviations: pr.a – preanal apodeme, cp – position of notogastral seta. Each image layered and color- and sharpness-enhanced (see Material and Methods).
FIGURE 1 in Collohmannia Johnstoni N. Sp. (Acari, Oribatida) From West Virginia (U.S.A.), Including Description Of Ontogeny, Setal Variation, Notes On Biology And Systematics Of Collohmanniidae
FIGURE 1: Collohmannia johnstoni n. sp. adults, scanning electron micrographs: A – male, dorsal view; B – female, ventral view; C – male, lateral view; D – male, frontal view. Abbreviations: col – notogastral collar, ex.l – exobothridial lobe; rb – rostral bulge, sej – sejugal articulation, sz – linear groove, vsj.f – ventrosejugal furrow.
FIGURE 11 in Collohmannia Johnstoni N. Sp. (Acari, Oribatida) From West Virginia (U.S.A.), Including Description Of Ontogeny, Setal Variation, Notes On Biology And Systematics Of Collohmanniidae
FIGURE 11: Collohmannia johnstoni n. sp. adult, details of gnathosoma: A – left chelicera, adaxial view, with sheath removed except to show attachment line; B – same, but cheliceral sheath shown; C – right palp, posterior (abaxial) view, slightly flattened in preparation; D – subcapitulum, ventral view, palps omitted, setae on left side of image represented only by alveoli. Abbreviations: a, m – genal setae, art – part of articulation with trochanter, cha, chb – cheliceral setae, cK – cheliceral condyle, c.sh – cheliceral sheath, en – line of attachment of cheliceral sheath, ep – post-palpal seta, f – dorsolateral fissure at the base of rutellum, l.br – proximal limit of birefringence, l.or – lamellated organ, ls – labrum, md.s – abaxial scale of movable digit, men – mentum, mu – muscle, op', op.v – adaxial and ventral oncophyses, ph.s – pharyngeal sclerite, r.ap – retractor apophysis, r.sp – rutellar spine, Tg – Trägårdh's organ, T.sc – scale at base of Trägårdh's organ, tr – thickest part of ventral cuticle of trochanter. tr.m – fringed distal margin of trochanteral tectum, gen - gena, h – hypostomal seta, rut – rutellum.
FIGURE 6 in Collohmannia Johnstoni N. Sp. (Acari, Oribatida) From West Virginia (U.S.A.), Including Description Of Ontogeny, Setal Variation, Notes On Biology And Systematics Of Collohmanniidae
FIGURE 6: Collohmannia johnstoni n. sp. adults, scanning electron micrographs: A, B – male; C, D – female. A – partly extended spermatopositor, posteroventral view; B – genital region, sagittal view, venter to top, anterior to right, showing partly extended spermatopositor and part of leg IV showing modified genual seta v" (heavy black arrow indicates meeting of anterior lobe pair); C – hysterosoma, ventral view; D – subcapitulum and rostrum, ventral view. Abbreviations: cl – posterior cleft, sf – secondary fold; SP – spermatopositor, Τd – distal eupathidia.
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.