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19,342 results for “Sequence”
Enumeration of Williamson Sequences of Even Order
<p>These files contain an enumeration of all inequivalent Williamson sequences of even orders n < 65 as defined in the paper "A SAT+CAS Method for Enumerating Williamson Matrices of Even Order" by Bright, Kotsireas, and Ganesh. This paper has been accepted to appear at AAAI-18, the thirty-second AAAI conference on artificial intelligence.</p> <p>Every line in each file contains exactly one Williamson sequence, with spaces separating the members A, B, C, and D of the Williamson sequences. The sequence entries are encoded using the characters + for 1 and - for −1.</p>
Data and code for "Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR"
<p>This data set provides data files and R code to accompany the article <em>Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR</em> published by F1000Research.</p> <p>The data consists of Reduced Representation BS-seq methylation profiles of epithelial populations from the mouse mammary gland, with n=2 biological replicates for each of three cell populations.</p> <p>RNA-seq expression profiles of luminal and basal mammary epithelial populations are also provided.</p> <p>The R code undertakes an differential methylation analysis of the BS-seq profiles and demonstrates a strong negative correlation between the differential methylation and differential expression results.</p>
Figure 5. Forward walking image sequence-Design and Implementation of an Autonomous Humanoid Robot Based on Fuzzy Rule-Based Motion Controller
<p>The behavior module determines the target position and orientation according to the results<br> of localization and the sensor measurements, and then constructs an action series which consists of<br> the elementary gaits to realize omni directional walking. The implementation of forward walking is<br> applying Virtual Slope Walking in the sagittal plane with the Lateral Swing Movement for lateral<br> stability. The sideward walking and turning is realized by carefully designing the key frames. All of<br> above gait is generated by connecting the key frames with smooth sinusoids. The forward walking<br> speed of PERSIA Humanoid Robot is 25cm/s. The image sequences of forward walking are shown<br> in Figure 5.</p>
Assessment of microphytobenthos communities in the Kinzig catchment using photosynthesis-related traits, digital light microscopy and 18S-V9 amplicon sequencing
<p>This folder contains the datasets used in the article submitted to Frontiers in Ecology and Evolution in which we investigated the functional and compositional responses of microphytobenthos communities to surrounding land uses in the Kinzig River catchment, central Germany. We measured photosynthetic biomass using a Benthotorch, and analysed the diatom community using a newly developed digital light microscopy approach and 18S-V9 amplicon sequencing to characterise the whole protistan assemblages at sampling sites located in rural vs. urban areas.</p> <p>The folder contain the following datasets:</p> <p>kinzig2021_18SV9_filtered.csv # microphytobenthos 18SV9 amplicon sequencing data</p> <p>kinzig_paper.csv # OMNIDIA output of diatom data from microscopy and diatom subset from 18SV9 amplicon sequencing (including 4 letters OMINIDIA taxa codes for diatoms)</p> <p>kinzig2021_benthotorch.csv # Photosynthetic biomass (BenthoTorch data)</p> <p>Kinzig2021_fieldData.csv # environmental data</p> <p>env_dataKinz2021.csv # environment dataset</p> <p>Kinzig2021_diatDM&18S.R # Rscript used for analysis</p>
Structures extracted from the AlphaFold database for the set of sequences used in Rosenberg et al. Nat. Comm. 2022.
<p>Structures extracted from the AlphaFold database for the set of sequences used in Rosenberg, A.A., Marx, A. & Bronstein, A.M. Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon. Nat Commum 13, 2815 (2022) <a href="https://doi.org/10.1038/s41467-022-30390-9">https://doi.org/10.1038/s41467-022-30390-9</a>.</p>
Figures 31–35 in DNA sequencing reveals three new species of Chamberlainium (Corallinales, Rhodophyta) from South Africa, all formerly passing under Spongites yendoi
Figures 31–35: Chamberlainium occidentale habit and vegetative anatomy. (31) Rock fragment with holotype specimen showing the region (white arrow) of the holotype from which all analyses were done (L 3986120, gametangial and tetrasporangial). Scale bar = 10 mm. (32) Vertical section through the margin (black arrow) showing the monomerous thallus construction with plumose medulla (M) giving rise to cortical filaments (C) that terminate in a single layer of epithallial cells (black arrowhead) (UWC 15/59). Scale bar = 50 μm. (33) Vertical section of the inner thallus showing cell fusions (f) between adjacent medullary filaments (UWC 15/56). Scale bar = 20 μm. (34) Vertical section of the outer thallus showing a single layer of epithallial cells (e) subtended by a layer of subepithallial initials (i). Note the cell fusions (f) between adjacent cortical filaments (UWC 15/59). Scale bar = 20 μm. (35) Vertical section of the outer thallus showing a single layer of epithallial cells (e) subtended by a layer of subepithallial initials (i). Note a cluster of bottle-shaped trichocytes (t) each separated by vegetative filaments (UWC 15/59). Scale bar = 20 μm.
Single-cell and single-nucleus RNA-sequencing from paired normal-adenocarcinoma lung samples provides both common and discordant biological insights
<p>The datasets generated by <em>Cellranger </em>for all 24 samples (.h5 format).<br><br></p>
Targeted Gene Panel Sequencing Data of RELN paper - Meyer Children's Hospital IRCCS
<h3>Dataset description</h3> <p> </p> <p>The dataset has been prepared according the Minimal Information about a high throughput SEQuencing Experiment (MINSEQE) as reported in: <a href="https://doi.org/10.5281/zenodo.5706412">https://doi.org/10.5281/zenodo.5706412</a></p> <p>This dataset includes:</p> <ul> <li>The Targeted Gene Panel Sequencing Raw Data (FASTQ files) from two individuals harbouring RELN variants</li> <li>The ‘final’ processed data, submitted both as VCF and TXT files, and obtained from the ANNOVAR annotations of the two patients</li> </ul> <p>The gene panel list used in the targeted capture and the essential experimental and data processing protocols has been reported in the RELN paper.</p> <h3>Identifiers</h3> <p>The 444D indentifier correspond to <strong>DN1 patient</strong> in the RELN paper.</p> <p>Tissue: peripheral blood sample</p> <p>Sex: female</p> <p>Age at sequencing: 21 years</p> <p>The 528T indentifier correspond to <strong>DN2 patient </strong>in the RELN paper.</p> <p>Tissue: peripheral blood sample</p> <p>Sex: female</p> <p>Age at sequencing: 1.5 years</p>
FedscGen: privacy-aware federated batch effect correction of single-cell RNA sequencing data -- Preprocessed datasets
<div> <div> <div> <div> <p>This dataset accompanies the publication "FedscGen: Privacy-Aware Federated Batch Effect Correction of Single-Cell RNA Sequencing Data" and includes eight single-cell RNA sequencing (scRNA-seq) datasets used to benchmark the FedscGen and scGen methods. The datasets are provided in <code>.h5ad</code> format and include comprehensive metadata necessary for replication and further analysis.</p> <h3>Datasets</h3> <p>We analyze various datasets to compare FedscGen against scGen (centralized) in terms of batch correction. For simplicity, we refer to the dataset by abbreviations:</p> <ol> <li> <p><strong>Cell Line (CL)</strong>:</p> <ul> <li>Derived from the 293t_jurkat experiment with three batches: Zheng et al., 2017.</li> </ul> </li> <li> <p><strong>Human Dendritic Cells (HDC)</strong>:</p> <ul> <li>scRNA-seq data of human dendritic cells across two batches: Villani et al., 2017.</li> </ul> </li> <li> <p><strong>Human Pancreas (HP)</strong>:</p> <ul> <li>Consolidated data from five sources with 14,767 cells each: Baron et al., 2016; Muraro et al., 2016; Segerstolpe et al., 2016; Wang et al., 2016; Xin et al., 2016.</li> </ul> </li> <li> <p><strong>Mouse Brain (MB)</strong>:</p> <ul> <li>Merged datasets with 691,600 and 141,606 cells: Saunders et al., 2018; Rosenberg et al., 2018.</li> </ul> </li> <li> <p><strong>Mouse Cell Atlas (MCA)</strong>:</p> <ul> <li>Data focusing on 11 cell types from various organs: Han et al., 2018; The Tabula Muris Consortium, 2018.</li> </ul> </li> <li> <p><strong>Mouse Hematopoietic Stem and Progenitor Cells (MHSPC)</strong>:</p> <ul> <li>Data from SMART-seq2 and MARS-seq protocols: Nestorowa et al., 2016; Paul et al., 2015.</li> </ul> </li> <li> <p><strong>Mouse Retina (MR)</strong>:</p> <ul> <li>Data from two unassociated laboratories with 26,830 and 44,808 cells: Macosko et al., 2015; Shekhar et al., 2016.</li> </ul> </li> <li> <p><strong>PBMC (human Peripheral Blood Mononuclear Cell)</strong>:</p> <ul> <li>scRNA-seq data with two batches: Zheng et al., 2017.</li> </ul> </li> </ol> <p><strong>Usage Notes</strong>: Each dataset is provided in <code>.h5ad</code> format, compatible with common single-cell analysis tools such as Scanpy. Detailed metadata is included within each file.</p> <p><strong>Keywords</strong>: Single-cell RNA sequencing, scRNA-seq, Batch effect correction, Privacy-aware, Federated learning, scGen, FedscGen, Clinical multi-center studies, Genomics, Bioinformatics</p> <p><strong>Contact</strong>: For questions or further information, please contact Mohammad Bakhtiari at <a href="mailto:mohammad.bakhtiari@uni-hamburg.de.">mohammad.bakhtiari@uni-hamburg.de.</a></p> <p><strong>License</strong>: Creative Commons Attribution 4.0 International (CC BY 4.0)</p> </div> </div> </div> </div> <div> <div> <div> </div> </div> </div>
Fig. 1 in Extensive testing of a multi-locus sequence typing scheme for Giardia dUodenaliS assemblage A confirms its good discriminatory power
Fig. 1 DCC outbreak in Sweden, described by Ankarklev et al. [13]; GVB outbreak in Italy, described by Resi et al. [14]; and several longitudinal samples of different patients showing similar genotypes, described by Woschke et al. [15]
Paired-end sequencing data toy example (measles)
<p>700,000 paired-end reads essentially Morbillivirus hominis to be used for testing purpose in the Sequana project</p>
Fig. 8 in Comparative cranial osteology of subadult eucentrosauran ceratopsid dinosaurs from the Two Medicine Formation, Montana, indicates sequence of ornamentation development and complex supraorbital ontogenetic change
Fig. 8. Size comparison of squamosal versus face in Einiosaurus procurvicornis Sampson, 1995, subadult MOR 456 8-8-87-1 (A) and MOR 456 8-9-6-1, holotype (B, mirrored); squamosal superimposed in B. C. Outline of MOR 456 8-8-87-1 (red) superimposed over outline of MOR 456 8-9-6-1 (grey). D. Outline of MOR 591 (blue) superimposed over outline of MOR 456 8-9-6-1 (grey). Outlines aligned by otic notch.
Fig. 5 in Comparative cranial osteology of subadult eucentrosauran ceratopsid dinosaurs from the Two Medicine Formation, Montana, indicates sequence of ornamentation development and complex supraorbital ontogenetic change
Fig. 5. Lateral views of jugals of Einiosaurus procurvicornis Sampson, 1995, MOR 456 8-8-87-1 (A) and eucentrosauran (Einiosaurus procurvicornis or Achelousaurus horneri Sampson, 1995), MOR 591 (B, mirrored), from the Campanian Two Medicine Formation, Montana, USA. Arrow indicates epijugal.
Fig. 6 in Comparative cranial osteology of subadult eucentrosauran ceratopsid dinosaurs from the Two Medicine Formation, Montana, indicates sequence of ornamentation development and complex supraorbital ontogenetic change
Fig. 6. Ontogenetic series of supraorbital ornamentation of Einiosaurus procurvicornis Sampson, 1995 from the Campanian Canyon Bonebed, Two Medicine Formation (TM-046), Montana, USA. A, B. Juvenile, MOR 456 8-10-87-20 (A) and MOR 456 8-8-87-19 (B). C, D. Early subadult, MOR 456 8-9-7-3 (C) and MOR 456 2020-C-1 (D). E, F. Late subadult, MOR 456 8-8-87-1 (E) and MOR 456 8-23-87 (F). G, H. Young adult, MOR 456 2020-C-2 (G) and MOR 456 8-9-6-1 (H). B and D are mirrored. All specimens in anterior view, lateral is to the right in A–D, G, H; E, entire skull width; F, lateral is to the left.
Fig. 4 in Comparative cranial osteology of subadult eucentrosauran ceratopsid dinosaurs from the Two Medicine Formation, Montana, indicates sequence of ornamentation development and complex supraorbital ontogenetic change
Fig. 4. Anterior views of supraorbital ornamentation of Einiosaurus procurvicornis Sampson, 1995, MOR 456 8-8-87-1 (A) and eucentrosauran Einiosaurus procurvicornis or Achelousaurus horneri Sampson, 1995), MOR 591 (B), from the Campanian Two Medicine Formation, Montana, USA.
Fig. 7 in Comparative cranial osteology of subadult eucentrosauran ceratopsid dinosaurs from the Two Medicine Formation, Montana, indicates sequence of ornamentation development and complex supraorbital ontogenetic change
Fig. 7. Ontogenetic series of supraorbital ornamentation of Einiosaurus procurvicornis Sampson, 1995 from the Campanian Canyon Bonebed (TM-046), Montana, USA. A, B. Juvenile, MOR 456 8-10-87-20 (A) and MOR 456 8-8-87-19 (B). C, D. Early subadult, MOR 456 8-9-7-3 (C) and MOR 456 2020- C-1 (D). E, F. Late subadult, MOR 456 8-8-87-1 (E) and MOR 456 8-23-87 (F). G, H. Young adult, MOR 456 2020-C-2 (G) and MOR 456 8-9-6-1 (H). B, D–G are mirrored. All specimens in lateral view, anterior is to the left in all images.
Fig. 3 in Comparative cranial osteology of subadult eucentrosauran ceratopsid dinosaurs from the Two Medicine Formation, Montana, indicates sequence of ornamentation development and complex supraorbital ontogenetic change
Fig. 3. Right lateral views of supraorbital ornamentation of Einiosaurus procurvicornis Sampson, 1995, MOR 456 8-8-87-1 (A) and eucentrosauran (Einiosaurus procurvicornis or Achelousaurus horneri Sampson, 1995), MOR 591 (B) from the Campanian Two Medicine Formation, Montana, USA.
Fig. 2 in Comparative cranial osteology of subadult eucentrosauran ceratopsid dinosaurs from the Two Medicine Formation, Montana, indicates sequence of ornamentation development and complex supraorbital ontogenetic change
Fig. 2. Right lateral views of nasal horncores of Einiosaurus procurvicornis Sampson, 1995, MOR 456 8-8-87-1 (A) and eucentrosauran (Einiosaurus procurvicornis or Achelousaurus horneri Sampson, 1995), MOR 591 (B, mirrored), from the Campanian Two Medicine Formation, Montana, USA.
Fig. 1 in Comparative cranial osteology of subadult eucentrosauran ceratopsid dinosaurs from the Two Medicine Formation, Montana, indicates sequence of ornamentation development and complex supraorbital ontogenetic change
Fig. 1. Lateral views of articulated crania of subadult eucentrosaurans from the Campanian Two Medicine Formation, Montana, USA. A. Einiosaurus procurvicornis Sampson, 1995, MOR 456 8-8-87-1. B. Eucentrosauran (Einiosaurus procurvicornis or Achelousaurus horneri Sampson, 1995), MOR 591. Photographs (A1 and B1), osteological line drawings (A2, B2). Face of MOR 591 mirrored, with parietosquamosal frill superimposed. The contact outlines between the postorbital, jugal, and squamosal in A2 are estimated due to lack of externally visible sutures and may appear different from MOR 591 due to some breaks and gaps. P4–P7, parietal processes.
Figure 5 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES
Figure 5. Ancestral area reconstruction produced by means of the RASP–Bayesian binary Markov Chain Monte Carlo method and based on the occurrence of Verbesina L. (Heliantheae–Asteraceae) species. Nodes with a predicted dispersal component are circled in blue, and those with a significant vicariance component are circled in green. The green bar indicates the consensus age of the closure of the Panama Isthmus (age based on Leigh et al., 2013; O'Dea et al., 2016). BOL, Bolivia; BRA, Brazil; CAR, Caribbean; COL, Colombia; CRC, Costa Rica; ECU, Ecuador; MEX, Mexico; NIC, Nicaragua; PER, Peru; USA, United States of America; VEN, Venezuela.
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.