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1,930 results for “matrix”
Data from: Sorting states of environmental DNA: Effects of isolation method and water matrix on recovery of membrane-bound, dissolved, and adsorbed states of eDNA
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Aligned DNA sequence matrix for phylogenetic analyses in the article "New species of fossorial salamanders of the genus Oedipina (Plethodontidae) from the northwestern Ecuador"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "New species of fossorial salamanders of the genus Oedipina (Plethodontidae) from the northwestern Ecuador". The matrix is in NEXUS format.</p> <p>Gene partitions are arranged as follows (tRNAs are included as part of larger adjacent genes):</p> <p>16S = 4- 789 1761- 1891 ;<br> ND1-codonPos1 = 790-1759\3;<br> ND1-codonPos2 = 791-1760\3;<br> ND1-codonPos3 = 792-1758\3;<br> CytB-codonPos1 = 1893-2274\3;<br> CytB-codonPos2 = 1894-2275\3;<br> CytB-codonPos3 = 1892-2276\3;</p>
Generating an expression matrix for droplet single-cell RNA-seq (dscRNA-seq) data
<p>This tutorial is adapted from the 'Generating an expression matrix' training session at the EBI (https://www.ebi.ac.uk/training/events/2019/single-cell-rna-seq-analysis-questions-clusters).</p>
Video recordings for the female German Matrix Sentence Test (OLSA)
<p>This dataset provides the video recordings for the female German Matrix Sentence Test (OLSA), a speech intelligibility test. The audio recordings are not provided in the dataset, but research licenses are available from Hörzentrum Oldenburg gGmbH. Please refer to Hörzentrum Oldenburg gGmbH for the audio material (<a href="https://www.hz-ol.de/en/matrix.html">https://www.hz-ol.de/en/matrix.html</a>). An example can be seen in "exampleWithAudio.mp4". For testing audiovisual speech perception, the video recordings should be played together with the original speech OLSAf mentioned above. One second of silence at the beginning of each audio file should be added for synchronous playback.</p> <p>Additionally, a web demo is provided to see how the test functions without sound (try it here with Chrome: <a href="http://www.staff.uni-oldenburg.de/gerard.llorach.to/AVOLSA/">http://www.staff.uni-oldenburg.de/gerard.llorach.to/AVOLSA/</a>). In order to make the web demo work, the folders "Video.zip" and "webData.zip" should be unzipped and placed where "A_demo.html" is. The web demo permits to test visual-only, audiovisual, and audio-only modalities. For testing with audio (if acquired), please drag and drop the audio files ("01248.wav", "02064.wav"...) in the web interface. For further information about the web demo, please read the introduction inside the file "A_demo.html". For further information about the material and how it was recorded please refer to the references.</p> <p>Special thanks to Jutta Birkigt, the talker of the audio and video recordings of the female German Matrix Sentence Test.</p> <p>Reference:</p> <p>Llorach, G., Kirschner, F., Grimm, G., Zokoll, M.A., Wagener, K.C. and Hohmann, V., 2021. Development and evaluation of video recordings for the OLSA matrix sentence test. <em>International Journal of Audiology</em>, pp.1-11.</p>
The Ubiquitin Ligase WWP1 Contributes to Shifts in Matrix Proteolytic Profiles and a Myocardial Aging Phenotype with Diastolic Heart Failure
<p><strong><em>Aims</em></strong>. Ubiquitylation is a key event that regulates protein turnover, and induction of the ubiquitin ligase E3 WWP1 has been associated with age. Left ventricular hypertrophy (LVH) commonly occurs as a function of age and can cause heart failure with a preserved ejection fraction (EF; HFpEF). We hypothesized that overexpression (O/E) of WWP1 in the heart would cause LVH as well as functional and structural changes consistent with the aging HFpEF phenotype.</p> <p><strong><em>Methods and Results.</em></strong> Global WWP1 O/E was achieved in mice (n=11) and echocardiography (40 MHz) performed to measure LV mass, EF, Doppler velocities (early-E, late/atrial-A), myocardial relaxation (E’), and isovolumetric relaxation time (IVRT) at 4, 6, and 8 weeks. Age matched wild type animals (n=15) were included as referent controls. LV EF was identical (60+1% vs 60+1%, p>0.90) with no difference in LV mass (67+3 vs 75+5, p>0.25) at 4 weeks. However, at 8 weeks of age, LV mass increased by over two-fold, E/A fell (impaired passive filling), and E/E’ was lower and IVRT prolonged (impaired LV relaxation) - all p<0.05. Collagen percent area increased by over two-fold and fibrillar collagen expression (rtPCR) by over 1.5 fold (p<0.05) with WWP1 O/E. WWP1 with an anti-WWP1 antibody could be identified in isolated cardiac fibroblasts with WWP1 increased by over two-fold in O/E fibroblasts (p<0.05).</p> <p><strong><em>Conclusion.</em></strong> Inducing WWP1 expression caused LVH, preserved systolic function, but impaired diastolic dysfunction, consistent with the HFpEF phenotype. Targeting the WWP1 pathway may be a novel therapeutic target for this intractable form of HF associated with aging.</p>
Landscape heterogeneity shapes bird phylogenetic responses at forest-matrix interfaces in Atlantic Forest, Brazil
<p>Agricultural intensification is one of the major factors driving biodiversity loss. However, most studies in human-dominated landscapes have used taxonomic diversity in their analysis, ignoring evolutionary relationships. Consequently, the relationship between landscape structure and phylogenetic diversity is not well understood. Here, we tested the hypothesis that landscape heterogeneity is positively related to bird phylogenetic indexes of diversity and structure, leading to over-dispersed phylogenies in very heterogeneous landscapes. We analyzed phylogenetic responses in interfaces between forest edges and anthropogenic matrices (forest-pasture and forest-eucalyptus) using generalized linear mixed models. We also compared these indexes between land covers to assess which one best preserves the phylogenetic history of communities. We used both traditional phylogenetic indexes and those corrected for species richness. Our results showed that phylogenetic diversity varied significantly between land cover types, but this did not occur when we removed effects associated with species richness, suggesting that all land covers preserve similar levels of evolutionary history. Additionally, our best models showed a positive relationship between landscape heterogeneity and bird phylogenetic indexes of diversity and structure, but the strength of these relationships may be land-cover dependent. In summary, our work highlights the influence of landscape heterogeneity on the phylogenetic diversity and structure of bird communities, reinforcing the need for its incorporation into conservation-based studies.</p>
the state vectors and transition matrixes of the LULC classification in Nanjing for modified Sankey chart
<p><strong>The original data of the state vectors and transition matrixes of the LULC classification in Nanjing used to create the modified Sankey charts.</strong></p>
Colorectal cancer scRNA-seq 10xG-format data matrix
<p>Metastatic colorectal cancer (CRC) is a major cause of cancer-related death and incidence is rising in the younger population (<50 years). Current chemotherapies can achieve response rates above 50%, but immunotherapies have limited value for patients with microsatellite-stable (MSS) cancers. The present study investigates the impact of chemotherapy on the tumor immune microenvironment. We treat human liver metastases slices with 5-Fluorouracil (5FU) plus either irinotecan or oxaliplatin, then perform single-cell transcriptome analyses. Results from eight cases reveal two cellular subtypes with divergent responses to chemotherapy. Susceptible tumors are characterized by a stemness signature, an activated interferon pathway, and suppression of PD-1 ligands in response to 5FU+irinotecan. Conversely, immune checkpoint TIM-3 ligands are maintained or up-regulated by chemotherapy in CRC with an enterocyte-like signature, and combining chemotherapy with TIM-3 blockade leads to synergistic tumor killing. Together, our analyses highlight chemo-modulation of the immune microenvironment and provide a framework for combined chemo-immunotherapies. </p>
Total Ortholog Median Matrix (TOMM): an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes
<p>The increasing number of available genomic data allowed the development of phylogenomic analytical tools. Current methods compile information from single gene phylogenies, whether based on topologies or multiple sequence alignments. Generally, phylogenomic analyses elect gene families or genomic regions to construct phylogenomic trees. Here, we presented an alternative approach for Phylogenomics, named TOMM (Total Ortholog Median Matrix), to construct a representative phylogram composed by amino acid distance measures of all pairwise ortholog protein sequence pairs from desired species inside a group of organisms. The procedure is divided two main steps, (1) ortholog detection and (2) creation of a matrix with the median amino acid distance measures of all pairwise orthologous sequences. We tested this approach within three different group of organisms: Kinetoplastida protozoa, hematophagous Diptera vectors and Primates. Our approach was robust and efficacious to reconstruct the phylogenetic relationships for the three groups. Moreover, novel branch topologies could be achieved, providing insights about some phylogenetic relationships between some taxa.</p>
Long-Term Stable Metal Organic Framework (MOF) Based Mixed Matrix Membranes for Ultrafiltration
<p><strong>Preprint available here:</strong> Al-shaeli, Muayad; Smith, Stefan J. D.; Jiang, Shanxue; Wang, Huanting; Zhang, Kaisong; Ladewig, Bradley P. (2020): Long-Term Stable Metal Organic Framework (MOF) Based Mixed Matrix Membranes for Ultrafiltration. ChemRxiv. Preprint. <a href="https://doi.org/10.26434/chemrxiv.13399367.v1">https://doi.org/10.26434/chemrxiv.13399367.v1</a></p> <p>Published manuscript: Muayad Al-Shaeli, Stefan J.D. Smith, Shanxue Jiang, Huanting Wang, Kaisong Zhang, Bradley P. Ladewig,<br> Long-term stable metal organic framework (MOF) based mixed matrix membranes for ultrafiltration,<br> Journal of Membrane Science, 2021, 119339, <a href="https://doi.org/10.1016/j.memsci.2021.119339">https://doi.org/10.1016/j.memsci.2021.119339</a></p> <p><strong>Abstract</strong></p> <p>In this study, novel mixed matrix membranes (MMMs) were synthesized by adding metal organic frameworks (MOFs) (UiO-66 and UiO-66-NH<sub>2</sub>) to pristine and sulfonated polyethersulfone (PES). The differing synthetic method resulting in MMM where additives were grafted to the matrix polymer, or formed a natural interface, allowing the impact of these MMM features to be investigated. The composite membranes were characterised by FTIR, PXRD, water contact angle, porosity, pore size, etc. Membrane performance was investigated by water permeation flux, flux recovery ratio, fouling resistance and anti-fouling performance. The stability test was also conducted for all the prepared mixed matrix membranes. A higher reduction in the water contact angle was observed after adding both MOFs to the PES and sulfonated PES membranes compared to pristine PES membranes. An enhancement in membrane performance was observed by embedding the MOFs into PES membrane matrix, with flux increased remarkably (565 LMH for PES+UiO-66-NH<sub>2</sub> at 5% loading and 487.1 LMH for SPES-UiO-66(10% binding) while the BSA rejection was still kept at a high level. By adding the MOFs into PES matrix, the flux recovery ratio was increased greatly (more than 99% for most mixed matrix membranes). The mixed matrix membranes showed higher resistance to protein adsorption compared to pristine PES membranes. After immersing the membranes in water for 3 months, 6 months and 12 months, both MOFs were stable and retained their structure. This study indicates that UiO-66 and UiO-66-NH<sub>2</sub> are great candidates for designing long-term stable mixed matrix membranes (MMMs) for applications in water and wastewater treatment.</p>
Real-time benchmark dynamics of the Ohmic Spin-Boson Model computed with Time-Dependent Variational Matrix Product States. (TDVMPS) coupling strength and temperature parameter space
<p>Data describing the complete propagators (maps) for the evolution of the Ohmic Spin-Boson Model are made available, here. Using a time-dependent variotnal matrix product states (TDVMPS) respresentation of the complete spin-environment wave function, non -perturbative results are presented over a wide range of coupling strengths, temperatures and initial conditions. The results in this repository are associated with the article: </p> <p>https://www.preprints.org/manuscript/202012.0016/v1 </p> <p>A mathematica notebook that allows the data to be visualised and manipulated is also provided. </p>
easyMF: A Web Platform for Matrix Factorization-based Biological Discovery from Large-scale Transcriptome Data
<p>With the development of high-throughput experimental technologies, large-scale RNA sequencing (RNA-Seq) data have been and continue to be produced, but have led to challenges in extracting relevant biological knowledge hidden in the produced high-dimensional gene expression matrices. Here, we present easyMF, a user-friendly web platform that aims to facilitate biological discovery from large-scale transcriptome data through matrix factorization (MF). The easyMF platform enables users with little bioinformatics experience to streamline transcriptome analysis from raw reads to gene expression and to decompose expression matrix from thousands of genes to a handful of metagenes. easyMF also offers a series of functional modules for metagene-based exploratory analysis with an emphasis on functional gene discovery. As a modular, containerized and open-source platform, easyMF can be customized to satisfy users’ specific demands and deployed as a web server for broad applications. easyMF is freely available at https://github.com/cma2015/easyMF. We demonstrated the application of easyMF with four case studies using 940 RNA sequencing datasets from maize (<em>Zea mays </em>L<em>.</em>).</p>
Exact Spin-Boson-Model Tunneling Dynamics with Time Dependent Variation Matrix Product States (TDVMPS). Barrier height and temperature parameter space
<p>Spin-Boson tunnelling data acquired using the T-TEDOA method for Time-Dependent-Variational-Matrix-Product-States (TDVMPS) accompanying the paper <a href="https://doi.org/10.3389/fchem.2020.600731">https://doi.org/10.3389/fchem.2020.600731</a>.</p> <p> </p>
Follow-up: Prospective compound design using the ‘SAR Matrix’ method and matrix-derived conditional probabilities of activity
<p>Details of the conditional probability calculations on exemplary the matrix provided in Figure 3 of the publication (see Gupta-Ostermann, Hirose, Odagami & Bajorath, Follow-up: Prospective compound design using the ‘SAR Matrix’ method and matrix-derived conditional probabilities of activity, F1000Research 2015, 4:75 , DOI: 10.12688/f1000research.6271.1 ) is provided in an excel sheet. </p> <p>Informative SARMs from the PRISM library are included. Due to proprietary issues the structural information of compounds is not included. Key and value fragments of SARMs are provided with an identifier.</p>
The ‘SAR Matrix’ method and its extensions for applications in medicinal chemistry and chemogenomics
<p>SD files of data sets reported in the manuscript that are used to generate the SARMs and CSMs are uploaded. The given data sets are represented by the corresponding figure numbers (as reported in the publication). The file format is provided in the file 'description.txt'.</p>
Multi-entry, matrix-based identification key to Anasillomos as exported from Lucid Builder 3.5 in XML SDD format
Multi-entry, matrix-based identification key to Anasillomos as exported from Lucid Builder 3.5 in XML SDD format
Genus Aconitum in Slovakia: a phenetic approach. S23: Genus Aconitum subgen. Aconitum sect. Cammarum full matrix of morphological traits
<p>This is full dataset of all analyzed morphological traits for genus Aconitum subgen. Aconitum sect. Cammarum in Slovakia coded as 0/1.</p>
Genus Aconitum in Slovakia: a phenetic approach. S24: Genus Aconitum subgen. Aconitum sect. Cammarum matrix of selected morphological traits
<p>This is dataset of analyzed morphological traits, which were specially selected as taxonomically valuable for genus Aconitum subgen Aconitum sect. Cammarum in Slovakia and coded as 0/1.</p>
Genus Aconitum in Slovakia: a phenetic approach. S21: Genus Aconitum subgen. Aconitum sect. Aconitum full matrix of morphological traits
<p>This is full dataset of all analyzed morphological traits for genus Aconitum subgenus Aconitum sect. Aconitum in Slovakia coded as 0/1.</p>
Genus Aconitum in Slovakia: a phenetic approach. S27: Genus Aconitum subgen. Lycoctonum full matrix of morphological traits
<p>This is full dataset of all analyzed morphological traits for genus Aconitum subgen. Lycoctonum in Slovakia coded as 0/1.</p>
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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.