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6,234 results for “phenotypes”
Lethal phenotypes in Mendelian disorders - Supplementary Files
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Analysis of maize growth under drought in an automated plant phenotyping platform
<p>Supplemental data accompanying the PhD thesis of Lennart Verbraeken.</p>
GBS and phenotype data for MASPOT population, a panel of tetraploid potato clones
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Fig. 4. A in Ontogenetic modifications produce similar phenotypes in distantly related click beetles (Coleoptera: Elateridae)
Fig. 4. A—Cebrio (Tibesia) igelmimen Rattu et François, 2021 from Morocco, female, general appearance. Cebriorhipis sp. from Bali. B—head, ventral view; C, D—pronotum, lateral and ventral view; F—elytron; G–I male genitalia, ventral, dorsal, and lateral view; J—abdomen, ventral view; K—terminal abdominal segments; L—mesoscutellum; M—metathoracic leg. Scales 1.0 mm. Figure 4A was published by Rattu and François (2021) and is here reprinted with permission of the authors who retain the copyright of this photo.
Fig. 1 in Ontogenetic modifications produce similar phenotypes in distantly related click beetles (Coleoptera: Elateridae)
Fig. 1. The mitogenomic relationships of soft-bodied and/or non-clicking genera Paulusiella, Cebrio, Scaptolenus, Analestesa, Plastocerus, Drilus, and their clicking relatives.The numbers at branches designate ultrafast bootstrap values and posterior probabilities. (A)The maximum likelihood analysis of the mt/nDNA dataset with single partition, non-focal clades are collapsed, Lissominae and Pityobiinae omitted. (B)The maximum likelihood analysis of thirteen protein-coding mitochondrial genes at the nucleotide level with coding masked by the degen software and partitioned by genes. (C)The Bayesian analysis using PhyloBayes at the nucleotide level.The trees with full-length branches and the results of additional analyses are shown in Supplementary Figs. S2–S14. Paulisiella, Cebrio, and Cebriorrhipis (red or grey colored)—the taxa earlier placed in Cebrionini; Plastocerus, Selasia, Drilus, and Malacogaster (magenta or grey colored)—non-clicking elaterids earlier placed in families Drilidae and Plastoceridae.
Fig. 3 in Ontogenetic modifications produce similar phenotypes in distantly related click beetles (Coleoptera: Elateridae)
Fig. 3. Analestesa arabica (Paulus, 1981) from Saudi Arabia (except for Fig. 3I). A—general appearance, dorsal view; B–D—frontal part of the body, dorsally (B, C) and ventrally); E—head in lateral view; F–H—pronotum, lateral, dorsolateral, and posterior view; I—antenna; J—elytron; K, M—male genitalia, ventrally, dorsally, laterally; l—Male genitalia of Dicronychus cinereus (Herbst, 1784); N—hind tarsus and apical part of tibia; O—abdomen, ventral view; P—terminal abdominal segments. Scales 0.5 mm.
Fig. 2 in Ontogenetic modifications produce similar phenotypes in distantly related click beetles (Coleoptera: Elateridae)
Fig. 2. Paulusiella sp. from Iran. A—general appearance, dorsal view; B, C—frontal part of the body, dorsally and ventrally; D—antenna; E—head and pronotum in lateral view; F, G—head, ventral and dorsal view; H—mesonotum; I—elytron; J–L—pronotum, dorsally, laterally, posterior view, M prosternal process, and mesosternal pit; N–P male genitalia, ventrally, dorsally, laterally; Q—terminal abdominal segments. Scales 0.5 mm.
Fig. 5 in Ontogenetic modifications produce similar phenotypes in distantly related click beetles (Coleoptera: Elateridae)
Fig. 5. Hemiops sp. from Laos. A–C general appearance, dorsal, ventral, and lateral aspects; D—pronotum; E—basal antennomeres; F—pronotum and head, ventrolateral view; G—head, dorsally; H—prosternal process and mesosternal pit; I, J—male genitalia; K—metathoracic leg; L—head ventrally; M—mesonotum; N, O º pronotum, dorsal, and posterior view; P—terminal abdominal segments. Scales 1.0 mm.
Fig. 5 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)
Fig. 5. Color phenotypes and phyloheatmap of the morphological characters of E. meriana and E. atleticana, visualized using the (A) mtDNA and (B) UCE phylogenies. Circles at the end of individual names indicate the color phenotype of that individual. Names above the phyloheatmaps indicate the character that was measured. BL, Body length; HW, Head width; ID, Intertegular distance;WTII,Width of colored bands on tergum II; WTIII,Width of colored bands on tergum III. In this phyloheatmap, each column of the measured characters was standardized to have the same variance prior to analysis.The scale below indicates how much each value deviates from the mean.The colors of the clades correspond to geographic regions outlined in Fig. 1. Green: Central America, Orange: Choco region, Blue: Amazon Forest, and Pink: Atlantic Forest.
Fig. 4 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)
Fig. 4. Chronogram of the phylogenetic relationships in the E. meriana and E. bombiformis species complexes estimated using BEAST2 and 500 UCE loci. All nodes had a posterior probability of 1. The arrow indicates the node used for calibration of the tree and acronyms correspond to geographic regions outlined in Fig. 1. CA, Central America; CR, Choco Region; AM, Amazon Forest; AF, Atlantic Forest. In the calibration point, M = mean age, and S = confidence interval.
Fig. 2 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)
Fig. 2. Phylogenetic relationships of the E. meriana and E. bombiformis species complexes based on (A) mitochondrial data (mtDNA; CO1 and Cytb) and (B) ultraconserved elements (UCE; 2022 loci). The mtDNA phylogeny was estimated using Bayesian inference in BEAST2, posterior probabilities on nodes were all above 0.9 except for nodes with asterisks (*). The UCE phylogeny was estimated with maximum likelihood using IQ-TREE and a concatenated 100% completeness matrix. Support values on nodes indicate ultrafast bootstrap (UFB) and SH-like (SH) approximate likelihood ratio test scores (SH-aLRT). All support values were above 95/95 except for nodes indicated with asterisks (* or **). One of the E. cingulata individuals (TA12) was pruned to improve the cophylogenetic visualization.The colors of the clades correspond to geographic regions outlined in Fig. 1. Green: Central America, Orange: Choco region, Blue: Amazon Forest, and Pink: Atlantic Forest.
Fig. 1 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)
Fig. 1. Geographic distribution of the different color phenotypes in the E. meriana and E. bombiformis species complexes. (A) Colored areas in the map indicate approximate distribution for both species complexes as well as the different areas that correspond to lineages recovered in López-Uribe et al. (2014), including Central America (green), Choco region (orange), Amazon Forest (blue), and Brazilian Atlantic Forest (pink). (B) Photos of color phenotypes are shown for each species and the geographic region in which that phenotype is present. Photos of E. meriana and E. bombiformis by NashTurley, photos of E. niveofasciata and E. atleticana by Marcelo de Oliveira Gonzaga.
Fig. 3 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)
Fig. 3. Maximum clade credibility (MCC) species tree of the phylogenetic relationships in the E. meriana and E. bombiformis species complexes estimated under the multi-species coalescent model (MSC) using *BEAST in BEAST2.The species tree was estimated using the 50 most informative UCE loci from the 100% completeness dataset. Nodes without labels had posterior probabilities <0.5.The colors of the clades correspond to geographic regions outlined in Fig. 1. Green: Central America, Orange: Choco region, Blue: Amazon Forest, and Pink: Atlantic Forest.
Fig. 6 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)
Fig. 6. Scatterplots of first against second principal component of the morphological measurements of the (A) E. bombiformis and (B) E. meriana complexes. Insets display boxplots of the first principal component between groups outlined by geographic regions: CA, Central America (Green); CR, Choco Region (Orange); AM, Amazon Forest (Blue); AF, Atlantic Forest (Pink). The letters above boxplots represent groups that are statistically differentiated after a Tukey′s honest significant test. Colors represent individuals grouped by geographic regions.
Phenotypically active ORF and CRISPR consensus profiles
This hosts the files on phenotypically active genes for JUMP, derived from https://zenodo.org/records/14025602 after filtering samples with no matches above a given threshold (see filenames for thresholds).
A digital phenotyping dataset for impending panic symptoms: a prospective longitudinal study
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Supplementary data for: Identification of genes, cell types, and phenotypes under selective pressure across primate evolution
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A digital phenotyping dataset for impending panic symptoms: a prospective longitudinal study
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Blood memory CD8 T cell phenotypes in lung cancer patients predict immune checkpoint treatment responses
<p>Rscript for figure generation and data analysis:</p> <p>GenerateFigures.R</p> <p> </p> <p>Seurat objects containing processed data after quality control:</p> <p><a href="../api/records/10867209/draft/files/NCCS_For_Zenodo.RDS/content" target="_blank" rel="noopener noreferrer">NCCS_For_Zenodo.RDS</a> - NCCS discovery cohort.</p> <p><a href="../api/records/10867209/draft/files/Pavia_For_Zenodo.RDS/content" target="_blank" rel="noopener noreferrer">Pavia_For_Zenodo.RDS</a> - Pavia validation cohort.</p> <p> </p> <p>RDS files containing DEGs or differentially abundant surface markers:</p> <p>TestResults2Groups.rds - Cell type specific LTR vs Non Responder DEG </p> <p>TestResults2GroupsADT.rds - Cell type specific LTR vs Non Responder differential surface markers</p> <p>TestResults2GroupsLungOnly.rds - Cell type specific LTR vs Non Responder DEG on lung samples only</p> <p>TestResults2GroupsLungOnlyADT.rds - Cell type specific LTR vs Non Responder differential surface markers on lung samples only</p> <p>TestResults3Groups.rds - Cell type specific LTR vs R vs Non Responder differential DEG</p> <p>TestResults3GroupsGeneralADT.rds - Across cell type LTR vs R vs Non Responder differential surface markers</p> <p>TestResults2GroupsGeneralRNA.rds - Across cell type LTR vs Non Responder DEG </p> <p>TestResults2GroupsGeneralADT.rds - Across cell type LTR vs Non Responder differential surface markers</p> <p>TestResults2GroupsLungOnlyGeneralRNA.rds - Across cell type LTR vs Non Responder DEG on lung samples only</p> <p>TestResults2GroupsLungOnlyGeneralADT.rds - Across cell type LTR vs Non Responder differential surface markers on lung samples only</p> <p>TestResults3GroupsGeneralRNA.rds - Across cell type LTR vs R vs Non Responder differential DEG</p> <p>TestResults3GroupsGeneralADT.rds - Across cell type LTR vs R vs Non Responder differential surface markers</p> <p> </p> <p>Logistic regression models trained on the NCCS discovery cohort:</p> <p>PerCellPredictions <CellType> * - Celltype specific models predicting either LTR, R or control group trained on all NCCS samples</p> <p>PerCellPredictions_2Groups_LungOnly <CellType> * - Celltype specific models predicting either LTR or NonResponder group, trained on lung samples only.</p> <p>PerCellPredictions_2Groups_<CellType> * - Celltype specific models predicting either LTR or NonResponder trained on all NCCS samples</p>
DeepCanola: Phenotyping Brassica Pods Using Semi-Synthetic Data and Active Learning
<p>Dataset accomapnying the publication: <em>DeepCanola: Phenotyping Brassica Pods Using Semi-Synthetic Data and Active Learning </em>by Van Vliet, Atkins et al.</p> <p>We provide model weights, training and vlidation datasets, as well as phenotype outputs. Each file/folder is outlined below:</p> <ul> <li><em>deepcanola.pth - </em>Model weights for the final Model 4, named DeepCanola</li> <li><em>generated_datasets</em> - Datasets generated at each stage of the active learning process, datasets 1-4 <ul> <li>Each folder is an iteration of the active learning process, inside each folder are the generated images and associated annotations stored in the COCO format.</li> </ul> </li> <li><em>real_world_datasets - </em>Real-world datasets used for either creation of the pod pools or validation. Datasets include: <ul> <li><em>br9</em> - Ordered and disordered dataset of images with generated pod length data of the ordered images stored in the `br9_gt_lengths.csv` file</li> <li><em>br11</em> - Ordered and disordered dataset of images only</li> <li><em>br17</em> - Ordered dataset with ground-truth of images with length annotations collected in ImageJ and stored in the `BR017 POD SCAN DATA.csv` file.</li> <li><em>misc</em> - Dataset of m<span>iscellaneous images including Brassica napus from Rothamstead and brassica relatives</span></li> </ul> </li> <li><em>data_generation_pools</em> - Pools used to generate semi-synthetic data at each step of the active learning process. Pools include: <ul> <li><em>background_pool</em> - Created background images to be selected at random by the semi-synthetic data generation script</li> <li><em>pod_pools - </em>Pools of pods used in the semi-synthetic data generation process. Pod pools include: <ul> <li><em>br9 - </em>673 pods with associated masks</li> <li><em>br9 and br17 - </em>673 + 332 pods with associated masks</li> </ul> </li> </ul> </li> <li><em>deepcanola_outputs - </em>Phenotype data outputs generated by DeepCanola. Each output is stored as a .csv file of both length measurements of each pod (with <em>_objects.csv</em> suffix), and average length measurements per image (with <em>_averages.csv</em> suffix). Outputs include: <ul> <li><em>br9_ordered</em></li> <li><em>br9_disordered</em></li> <li><em>br17</em></li> </ul> </li> </ul>
ScienceDex guides
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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.