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1,930 results for “matrix”
Effect of older age and/or ACL injury on the dose–response relationship between ambulatory load magnitude and immediate load-induced change in serum cartilage oligomeric matrix protein
<p>The data presented here was used in the models in the pulication doi <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.jshs.2024.100993" target="_blank" rel="noreferrer noopener"><span><span>https://doi.org/10.1016/j.jshs.2024.100993</span></span></a>.</p> <p>The purpose of this study was to assess the influence of age, anterior cruciate ligament (ACL) injury, and sex on resting sCOMP concentration, on the immediate load-induced sCOMP kinetics after a 30-minute treadmill walking stress, and on the dose-response relationship between ambulatory load magnitude and the load-induced sCOMP change.</p> <p>Overall, data of 85 participants in four groups (20–30 years healthy, HEA<sub>20–30</sub>, n=24; 20–30 years ACL-injured, ACL<sub>20–30</sub>, n=23; 40–60 years healthy, HEA<sub>40–60</sub>, n=23; 40–60 years ACL-injured, ACL<sub>40–60</sub>, n=15) were included in this dataset. ACL injured participants suffered from an ACL injury 2-10 years prior to inclusion. The dateaset includes, patient data and serum cartilage oligomeric matrix protein (sCOMP) concentration measured on three testdays (m1, m2, m3) immediately before (t0) and immediately after 30 minutes of treadmill walking (t1) where the ambulatory loads were 80% bodyweight (BW), 100% BW or 120% BW (block randomized order). This dateset represents a subset of data collected in the parent study.</p> <p>The detailed experimental protocol of the parent study has been described in Herger, S., Vach, W., Nüesch, C., Liphardt, A. M., Egloff, C., & Mündermann, A. (2022). Dose-response relationship of in vivo ambulatory load and mechanosensitive cartilage biomarkers—The role of age, tissue health and inflammation: A study protocol. <em>PLoS One, 17</em>(8), e0272694. <a href="https://doi.org/10.1371/journal.pone.0272694">https://doi.org/10.1371/journal.pone.0272694</a></p>
Figure 1 in Construction of a phylogenetic matrix: Scripts and guidelines for phylogenomics
Figure 1. Flowchart of constructing a phylogenetic matrix for phylogenomics. The custom scripts used in each step are marked as italic. Dashed boxes indicate that these strategies of each step choose only one or more suitable strategies.
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
<p>Environmental DNA (eDNA) once shed can exist in numerous states with varying behaviors including degradation rates and transport potential. In this study we consider three states of eDNA: 1) a membrane-bound state referring to DNA enveloped in a cellular or organellar membrane, 2) a dissolved state defined as the extracellular DNA molecule in the environment without any interaction with other particles, and 3) an adsorbed state defined as extracellular DNA adsorbed to a particle surface in the environment. Capturing, isolating, and analyzing a target state of eDNA provides utility for better interpretation of eDNA degradation rates and transport potential. While methods for separating different states of DNA have been developed, they remain poorly evaluated due to the lack of state-controlled experimentation. We evaluated the methods for separating states of eDNA from a single sample by spiking DNA from three different species to represent the three states of eDNA as state-specific controls. We used chicken DNA to represent the dissolved state, cultured mouse cells for the membrane-bound state, and salmon DNA adsorbed to clay particles as the adsorbed state. We performed the separation in three water matrices, two environmental and one synthetic, spiked with the three eDNA states. The membrane-bound state was the only state that was isolated with minimal contamination from non-target states. The membrane-bound state also had the highest recovery (54.11 ± 19.24 %), followed by the adsorbed state (5.08 ± 2.28 %), and the dissolved state had the lowest total recovery (2.21 ± 2.36 %). This study highlights the potential to sort the states of eDNA from a single sample and independently analyze them for more informed biodiversity assessments. However, further method development is needed to improve recovery and reduce cross-contamination.</p>
Table S1. Uncorrected p distance matrix
<p>Uncorrected p distance values for combined COI and 16S sequences from phylogenetic analysis of <em>Helminthoglypta</em> land snails (Mollusca: Gastropoda: Helminthoglyptidae) from northern California and southern Oregon, USA.</p> <p>Note: Specimen numbers marked with * were missing COI sequences.</p> <p>Table in both Excel (*.xlsx) and comma-separated value (*.csv) formats.</p> <p> </p>
New and modified scores in the phylogenetic matrix from Schoch (2013)
<p>Temnospondyl amphibians are a common component of non-marine Triassic assemblages, including in the Fremouw Formation (Lower to Middle Triassic) of Antarctica. Temnospondyls were among the first tetrapods to be collected from Antarctica, but their record from the lower Fremouw Formation has long been tenuous. One taxon, '<i>Austrobrachyops jenseni</i>,' is represented by a type specimen comprising only a partial pterygoid, which is now thought to belong to a dicynodont. A second taxon, '<i>Cryobatrachus kitchingi</i>,' is represented by a type specimen comprising a nearly complete skull, but the specimen is only exposed ventrally, and uncertainty over its ontogenetic maturity and some aspects of its anatomy has led it to be designated as a nomen dubium by previous workers. Here we redescribe the holotype of '<i>C. kitchingi</i>,' an undertaking that is augmented by tomographic analysis. Most of the original interpretations and reconstructions cannot be substantiated, and some are clearly erroneous. Although originally classified as a lydekkerinid, the purported lydekkerinid characteristics are shown to be unfounded or no longer diagnostic for the family. We instead identify numerous features shared with highly immature capitosaurs, a large-bodied clade documented in the upper Fremouw Formation of Antarctica and elsewhere in the Lower Triassic. Additionally, we describe a newly collected partial skull from the lower Fremouw Formation that represents a relatively mature, small-bodied individual and that we provisionally refer to Lydekkerinidae; this specimen represents the most confident identification of a lydekkerinid from Antarctica to date.</p>
MPIData: Optimized System Matrix Sampling
<p>This data repository contains magnetic particle imaging data. The files are stored in the <a href="https://arxiv.org/pdf/1602.06072.pdf">MDF file format</a> and the folder structure is organized as an <a href="https://github.com/MagneticParticleImaging/MPIFiles.jl">MDF store</a>. The data is used in this code example: <a href="https://github.com/IBIResearch/IncreasedDynamicRange">https://github.com/IBIResearch/IncreasedDynamicRange</a></p>
Data from: Context matters: the landscape matrix determines the population genetic structure of temperate forest herbs across Europe
<p>Context. Plant populations in agricultural landscapes are mostly fragmented and their functional connectivity often depends on seed and pollen dispersal by animals. However, little is known about how the interactions of seed and pollen dispersers with the agricultural matrix translate into gene flow among plant populations.</p> <p>Objectives. We aimed to identify effects of the landscape structure on the genetic diversity within, and the genetic differentiation among, spatially isolated populations of three temperate forest herbs. We asked, whether different arable crops have different effects, and whether the orientation of linear landscape elements relative to the gene dispersal direction matters.</p> <p>Methods. We analysed the species' population genetic structures in seven agricultural landscapes across temperate Europe using microsatellite markers. These were modelled as a function of landscape composition and configuration, which we quantified in buffer zones around, and in rectangular landscape strips between, plant populations.</p> <p>Results. Landscape effects were diverse and often contrasting between species, reflecting their association with different pollen- or seed dispersal vectors. Differentiating crop types rather than lumping them together yielded higher proportions of explained variation. Some linear landscape elements had both a channelling and hampering effect on gene flow, depending on their orientation.</p> <p>Conclusions. Landscape structure is a more important determinant of the species' population genetic structure than habitat loss and fragmentation <i>per se</i>. Landscape planning with the aim to enhance the functional connectivity among spatially isolated plant populations should consider that even species of the same ecological guild might show distinct responses to the landscape structure.</p>
A semi-analytical solution for heat transport in rock with parallel fractures and a heat source in both fracture and matrix
<p>In this study, we propose a two-dimensional semi-analytical solution framework based on a Green’s function approach for a flexible heat source definition, including source dimensions, energy delivery strength and duration, and the presence of a heat source in the matrix and/or fracture. The solution fully accounts for heat conduction, advection, dispersion and transient heat exchange between the mobile and immobile phases in a system of parallel fractures. The solution having a strip heat source extending from a fracture into the matrix indicates that one-dimensional heat conduction in the matrix underestimates and overestimates temperature responses at early and later times, respectively.</p> <p>The dataset is for the figures 2-7 in the journal paper. </p>
Data for the "Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1"
<p>Bottom-up mass spectrometry-based proteomic analysis (trypsin) was performed on four biological replicates of HIV-1 virions. These virions were isolated from HEK293T cells transfected with a HIV-1 proviral plasmid derived from the pNL4-3 molecular clone, rendered biosafe due to inactivating point mutations in both the env and vpr reading frames. There are 8 total spectra, 4 are from unlabeled aliquots of sample, and 4 are from aliquots of sample treated with glutathione to label dehydroamino acids (Spectra can be accessed on MassIVE (MSV000088220). All data was analyzed using MetaMorpheus version 0.0.319 (https://github.com/smith-chem-wisc/MetaMorpheus). Provided here are the results of this analysis.</p>
Application of multi-analyte / multi-matrix screening method for pesticide residues in fruits and vegetables to Interaboratory Comparison Study on Pesticide Residues in Food (ILC)
<p>The suitability of multi-analyte / multi-matrix screening method for pesticide residues in fruits and vegetables and related products, developed within activities of task (Multi-analyte / multi-matrix screening method for pesticide residues in fruits and vegetables (including tea) and fruit juices), was evaluated by the Interaboratory Comparison Study on Pesticide Residues in Food (ILC). Test material (“Pesticide Residues in green tea”), prepared from the batch used for another proficiency test (PT), was provided by Fapas (Fera Science Ltd, York, UK).</p> <p>Data set obtains (i) information about performance characteristics of the analytical method and (ii) compilation of results of interlaboratory study.</p>
The Surface Biology and Geology Architecture Study Science and Applications Traceability Matrix (SATM)
<p>This dataset provides a synthesis of the National Academies of Sciences 2017 Earth Science Decadal Survey mission most and very important objectives for the Surface Biology and Geology Earth Observing system consisting of a global visible to shortwave infrared imaging spectrometer and a multi-spectral thermal infrared radiometer. These objectives are traced to performance criteria used for assessing hundreds of potential architecture variants in an architecture study outlined in a paper titled: "Designing an Observing System to Study the Surface Biology and Geology (SBG) of the Earth in the 2020s".</p>
Data for Corre et al., Bacterial matrix metalloproteases and serine proteases contribute to the extra-host inactivation of enterovirus in lake water, ISMEJ 2022
<p>Data for Corre et al., <em>Bacterial matrix metalloproteases and serine proteases contribute to the extra-host inactivation of enterovirus in lake water</em>, ISMEJ 2022</p> <p>The first file contains all data pertaining to experiments with isolates: collection date, isolation temperature, protease activity measured by 4 different approaches, antiviral effect on E11 and CVA9 (three replicates each); this table corresponds to the data shown in Supplementary Table 2.</p> <p>The second file contains the raw data for all lake water experiments (Figures 1 and 6): information on sample type, antiviral effect (measured in triplicate), presence of a protease inhibitor.</p>
Small extracellular vesicles from malignant ascites of patients with advanced ovarian cancer provide insights into the dynamics of the extracellular matrix
<p>Representative Atomic Force Microscope images collected in liquid on Extracellular Vesicles from Ascite and Cell cultures. Data were collected by Broker Multimode VIII. Images like these were used in the paper to measure the contact angle and size distribution.</p>
Data Matrix Landmarks in Cluttered Indoor Environments
<p>We used the <a href="https://labelbox.com/">LabelBox</a> online toolbox to create this data set.</p> <p>It consists of 6 different cluttered environments:</p> <ol> <li>a laboratory </li> <li>3 different industrial-like environments </li> <li>a corridor</li> <li>hall</li> </ol> <p>We proposed to split the data set into three sets - training, validation, and test sets - as follows: (1) the training set has 156 frames equally distributed by the laboratory and 1 workshop; (2) the validation set is also divided into two environments - the corridor (158 frames) and a different workshop (66 frames); (3) the test set consists of 145 frames collected on a neat hall with overshadowed and over-lightened landmarks in different planes; a classroom laboratory with various electronic equipment arranged in an orderly manner; and a very challenging scenario with multiple pieces of machinery spread out all over the place.</p> <p>One should filter out images with no markers.</p>
Trained Models from "General Cross-Architecture Distillation of Pretrained Language Models into Matrix Embeddings"
<p>Trained models from the paper:</p> <p>Lukas Galke, Isabell Cuber, Christoph Meyer, Henrik Ferdinand Noelscher, Angelina Sonderecker, and Ansgar Scherp: <strong>General Cross-Architecture Distillation of Pretrained Language Models into Matrix Embeddings</strong>, in: <em>International Joint Conference on Neural Networks (IJCNN), </em>2022.</p> <ul> <li>File seq2mat_hybrid_bidirectional_sbertlike-100p-bsz512 holds the model from pretraining</li> <li>File ws2020_transformer_final_models holds the fine-tuned models for each task of the GLUE benchmark</li> </ul>
Dataset for Effect of matrix solidification on the structure formation in electromagnetic suspensions
<p><strong>Introduction:</strong> Dataset from numerical simulations describing the structure formation in suspensions with electromagnetically active particles in an external field, as described in detail in the paper</p> <ul> <li>Konstantinos Manikas, Markus Hütter, Patrick D. Anderson: Effect of matrix solidification on the structure formation in electromagnetic suspensions. Appl. Phys. A, 128: 709 (11 pages), 2022. DOI: 10.1007/s00339-022-05844-y WWW: https://doi.org/10.1007/s00339-022-05844-y</li> </ul> <p>which should be cited whenever this dataset is used. The data compiled here is the basis for figures 4, 5, and 6 in that paper.</p> <p> </p> <p><strong>Format:</strong> The files are provided in plain-text format (ascii).</p> <p> </p> <p><strong>Filenames:</strong> The nomenclature for the filenames follows the following scheme:</p> <ul> <li>data_fig{number}_{param}_{value}.txt</li> </ul> <p>where {number} specifies the number of the figure in the paper, {param} is the parameter that is studied and {value} denotes its numerical value (see the paper for details).</p> <p> </p> <p><strong>File content:</strong> Each datafile contains 1 header line, in which the meaning of the data-columns are explained (time, S2, N*, lambda* -- see paper for details), and the studied parameter and its value are listed. After this header line, the data is presented in tab-delimited columns.</p> <p> </p> <p>For further details, the reader is referred to the paper mentioned above.</p>
Mandarin matrix sentence test recordings: Lombard and plain speech with different speakers
<p>This dataset was recorded within the Deutsche Forschungsgemeinschaft (DFG) project: Experiments and models of speech recognition across tonal and non-tonal language systems (EMSATON, Projektnummer 415895050).</p> <p>The Lombard effect or Lombard reflex is the involuntary tendency of speakers to increase their vocal effort when speaking in loud noise to enhance the audibility of their voice. Up to date, the phenomena of Lombard effects were observed in different languages. The present database aimed at providing recordings for studying the Lombard effect with Mandarin speech.</p> <p>Eleven native-Mandarin talkers (6 female and 5 male) were recruited, both Lombard/plain speech were recorded from the same talker in the same day. </p> <p>All speakers produced fluent standard Mandarin speech (North China). All listeners were normal-hearing with pure tone thresholds of 20 dB hearing level or better at audiometric octave frequencies between 125 and 8000 Hz. All listeners provided written informed consent, approved by the Ethics Committee of Carl von Ossietzky University of Oldenburg. Listeners received an hourly compensation for their participation.</p> <p>The recording sentences were same as the official Mandarin Chinese matrix sentence test (<a href="#_ENREF_2">CMNmatrix, Hu et al. 2018</a>). </p> <p> One hundred sentences (ten base lists of ten sentences) of the CMNmatrix were recorded from each speaker in both plain and Lombard speaking styles (each base list containing all 50 words). The 100 sentences were divided into 10 blocks of 10 sentences each, and the plain and Lombard blocks were presented in an alternating order. The recording took place in a double-walled, sound-attenuated booth fulfilling ISO 8253-3 (ISO 8253-3, 2012), using a Neumann 184 microphone with a cardioid characteristic (Georg Neumann GmbH, Berlin, Germany) and a Fireface UC soundcard (with a sampling rate of 44100 Hz and resolution of 16 bits). The recording procedure generally followed the procedures of Alghamdi et al. (2018). A Mandarin-native speaker and a phonetician participated in the recording session and listened to the sentences to control the pronunciations, intonation, and speaking rate. During the recording, the speaker was instructed to read the sentence presented on a frontal screen. In case of any mispronunciation or change in the intonation, the speaker was asked via the screen to repeat the sentence again, and on average, each sentence was recorded twice. In Lombard conditions the speaker was regularly asked via a prompt to repeat a sentence, to keep the speaker in the Lombard communication situation. For the plain-speech recording blocks, the speakers were asked to pronounce the sentences with natural intonation and accentuation, and at an intermediate speaking rate, which was facilitated by a progress bar on the screen. Furthermore, the speakers were asked to keep the speaking effort constant and to avoid any exaggerated pronunciations that could lead to unnatural speech cues. For the Lombard speech recording blocks, speakers were instructed to imagine a conversation to another person in a pub-like situation. During the whole recording session, speakers wore headphones (Sennheiser HDA200) that provided the audio signal of the speaker.. In the Lombard condition, the stationary speech-shaped noise ICRA1 (Dreschler et al., 2001) was mixed with the speaker’s audio signal at a level of 80 dB SPL (calibrated with a Brüel & Kjær (B&K) 4153 artificial ear, a B&K 4134 0.5-inch inch microphone, a B&K 2669 preamplifier, and a B&K 2610). Previous studies showed that this level induced a robust Lombard speech without the danger of inducing hearing damage (Alghamdi et al., 2018).</p> <p>The sentences were cut from the recording, high-pass filtered (60 Hz cut-off frequency) and set to the average root-mean-square level of the original speech material of the Mandarin Matrix test (Hu et al., 2018). Then the best version of each sentence was chosen by native-Mandarin speakers regarding pronunciation, tempo, and intonation.</p> <p>For more detailed information, please contact hongmei.hu@uni-oldenburg, sabine.hochmuth@uni-oldenburg.de. </p> <p><em>Hu H, Xi X, Wong LLN, Hochmuth S, Warzybok A, Kollmeier B (2018) Construction and evaluation of the mandarin chinese matrix (cmnmatrix) sentence test for the assessment of speech recognition in noise. International Journal of Audiology 57:838-850. https://doi.org/10.1080/14992027.2018.1483083</em></p> <p> </p>
Text-fig. 2. CT slices on Block 2. Details of other skeletal parts (a). The familiar shape of an ammonite (a, c). Holes, cracks and empty cavities in both the limestone matrix and within the vertebrate fossil (b, c). Heterogeneity of the 'tuffeau' limestone, the more porous areas of the matrix clearly distinguishable from the more compact ones (c). Ferric nodules (c). in Hidden Treasures Uncovered: Successful Detection Of Fossils Below The Surface In Large Limestone Blocks Using A Standard Medical X-Ray Ct Scanner
Text-fig. 2. CT slices on Block 2. Details of other skeletal parts (a). The familiar shape of an ammonite (a, c). Holes, cracks and empty cavities in both the limestone matrix and within the vertebrate fossil (b, c). Heterogeneity of the 'tuffeau' limestone, the more porous areas of the matrix clearly distinguishable from the more compact ones (c). Ferric nodules (c).
Text-fig. 1. CT slices on Block 1. Details of the internal bone structure (a, b), teeth (b, c). Invertebrate imprints (a, c). Holes, cracks and empty cavities in both the limestone matrix and within the vertebrate fossil (b). in Hidden Treasures Uncovered: Successful Detection Of Fossils Below The Surface In Large Limestone Blocks Using A Standard Medical X-Ray Ct Scanner
Text-fig. 1. CT slices on Block 1. Details of the internal bone structure (a, b), teeth (b, c). Invertebrate imprints (a, c). Holes, cracks and empty cavities in both the limestone matrix and within the vertebrate fossil (b).
Text-fig. 3. CT slices on Block 3. Invertebrate moulds (a, c) and remains of their hard skeletons (a, b). Large areas of limestone matrix hold either only a few scattered invertebrates or no fossil at all (b, c). Ring artefacts seen close to the isocentre of the scan (b, c) are a well-known phenomenon caused by the X-ray beams traversing the block at an insufficient radiation dose (as expected in such a large block of dense material), and are not part of any physical structure present therein (Triche et al. 2019). in Hidden Treasures Uncovered: Successful Detection Of Fossils Below The Surface In Large Limestone Blocks Using A Standard Medical X-Ray Ct Scanner
Text-fig. 3. CT slices on Block 3. Invertebrate moulds (a, c) and remains of their hard skeletons (a, b). Large areas of limestone matrix hold either only a few scattered invertebrates or no fossil at all (b, c). Ring artefacts seen close to the isocentre of the scan (b, c) are a well-known phenomenon caused by the X-ray beams traversing the block at an insufficient radiation dose (as expected in such a large block of dense material), and are not part of any physical structure present therein (Triche et al. 2019).
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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.