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220 results for “sequence age”
Data from: A cost-effective blood DNA methylation-based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus), and Panthera species, using targeted bisulfite sequencing and machine learning models
<p><span>Knowledge of individual age can help both in-situ and ex-situ conservation programs to design more efficient and suitable management plans for targeted wildlife species. DNA methylation is one of the epigenetic aging markers that has emerged as a promising tool that can estimate age with high accuracy using only a tiny amount of biological material, which can be collected in a minimally invasive way. Here, we sequenced five targeted genetic regions and used </span><span>8–23</span><span> selected CpG sites to build age estimation models with machine learning methods </span><span>with about only $3–7 per sample</span><span>, using blood samples of seven Felidae species—ranging from small to big, and domestic to endangered species: domestic cats (<em>Felis catus</em>, 139 samples), Tsushima leopard cats (<em>Prionailurus bengalensis euptilurus</em>, 84 samples), and five<em> Panthera </em>species (96 samples). </span><span>The models built achieved satisfactory accuracy—the mean absolute error of the best models was 1.966, 1.348, and 1.552 years in domestic cats, Tsushima leopard cats, and <em>Panthera</em> spp., respectively.</span><span> Our models in domestic cats and Tsushima leopard cats were applicable to individuals regardless of health conditions, indicating the high applicability of our models to samples collected from diverse situations, e.g., rescued individuals in the context of conservation. We also showed the possibility of developing universal age estimation models for the five<em> Panthera</em> spp. using two of the five genetic regions, suggesting an even lower cost to use our models for future applications.</span></p>
Combined Effects of Rotation and Age Spreads on Extended Main-Sequence Turn Offs - Isochrones and Stellar Tracks
<p>Theoretical isochrones and EEP stellar tracks featured in <a href="https://ui.adsabs.harvard.edu/abs/2019ApJ...887..199G/abstract">Gossage et al. 2019</a> (Combined Effects of Rotation and Age Spreads on Extended Main-Sequence Turn Offs). These 1D stellar evolution models are based on <a href="https://docs.mesastar.org/en/release-r22.11.1/">MESA</a> r7503, and utilize the same physical assumptions as in MIST v1.0 (<a href="https://ui.adsabs.harvard.edu/abs/2016ApJ...823..102C/abstract">Choi et al. 2016</a>).</p> <p>The models are described in <a href="https://ui.adsabs.harvard.edu/abs/2018ApJ...863...67G/abstract">Gossage et al. 2018</a> and <a href="https://ui.adsabs.harvard.edu/abs/2019ApJ...887..199G/abstract">Gossage et al. 2019</a>\(^1\), but salient features include:</p> <ul> <li>Metallicities [Fe/H] = -0.45, -0.30, -0.15, 0.0, 0.15, 0.30, 0.45 (assuming <a href="https://ui.adsabs.harvard.edu/abs/2009ARA%26A..47..481A/abstract">Asplund et al. 2009</a> protosolar abundances \(\rm Z_{\odot}\) = 0.0142).</li> <li>Rotation rates from v/v<sub>crit </sub>= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9 (initiated at ZAMS)</li> <li>Masses from 0.1 to 8 solar masses with spacings of: <ul> <li>\(\rm \Delta M = 0.05 M_{\odot}\) for \(\rm M < 1 M_{\odot}\)</li> <li>\(\rm \Delta M = 0.04 M_{\odot}\) for \(\rm 1 M_{\odot} \leq M < 2 M_{\odot}\)</li> <li>\(\rm \Delta M = 0.2 M_{\odot}\) for \(\rm 2 M_{\odot} \leq M \leq 8 M_{\odot}\)</li> </ul> </li> <li>Models are evolved up to the first thermal pulse.</li> </ul> <p><strong>File name convention:</strong> zip files, e.g., \(\texttt{MIST_v1.0_feh_p0.15_rotating_tracks.zip}\), contain theoretical models at a particular metallcity ([Fe/H] = 0.15 in this case), at all rotation rates and masses. The file \(\texttt{MIST_v1.0_feh_m0.15_rotating_tracks.zip}\) contains models at [Fe/H] = -0.15, and so on. \(\texttt{*_tracks.zip}\) contain EEP stellar track files and \(\texttt{*_isochrones.zip}\) files contain theoretical isochrone files, both in the same format as EEP track and theoretical isochrones found on the <a href="https://waps.cfa.harvard.edu/MIST/index.html">MIST website</a>. Zip files labeled, e.g.,\(\texttt{*_isochrones_FILTERSET.zip}\) contain observable isochrones, with synthetic photometry produced for a particular filter set (as on the <a href="https://waps.cfa.harvard.edu/MIST/model_grids.html">MIST packaged grids</a> site, which contains more information on the filter sets), computed without extinction (\(A_V=0\)). At the moment, filter sets for \(\texttt{UBVRIplus}\) (containing Gaia filters), \(\texttt{HST_WFC3}\), \(\texttt{HST_ACSWF}\), \(\texttt{HST_WFPC2}\), and \(\texttt{CFHTugriz}\) are included, but more can be added upon request\(^2\). </p> <p><strong>Notes:</strong></p> <p>\(^1\) These are the same models as featured in <a href="https://ui.adsabs.harvard.edu/abs/2018ApJ...863...67G/abstract">Gossage et al. 2018</a>, but in that work, [Fe/H] = -0.60 and -0.75 were featured as well and only included models up to v/v<sub>crit </sub>= 0.6. We include these models from <a href="https://ui.adsabs.harvard.edu/abs/2018ApJ...863...67G/abstract">Gossage et al. 2018</a> here as well. Models at [Fe/H] = -0.60 have been extended to v/v<sub>crit </sub>= 0.9, while [Fe/H] = -0.75 only includes up to the original v/v<sub>crit </sub>= 0.6.</p> <p>\(^2\) These tracks and isochrones may be converted into observable tracks and isochrones (w/ gravity darkening effects if desired) via Aaron Dotter's <a href="https://github.com/aarondotter/iso">iso code</a>.</p> <p>\(^3\) Although astroseismic \(\nu_{max}\) and \(\Delta \nu\) are included in the included history files, be aware that these are based on scaling relations reliant on solar values, assuming the Coriolis and centrifugal forces do not play a role. While an OK assumption for the Sun, this is less applicable models with rapid rotation and their values should not be trusted in such regimes.</p>
Data from: A cost-effective blood DNA methylation-based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus), and Panthera species, using targeted bisulfite sequencing and machine learning models
Open the record for dataset details and reuse information.
Single-cell repertoire and transcriptome sequencing reveals clonally expanded and transcriptionally distinct lymphocytes in aged CNS
<p>Single-cell repertoire and transcriptome sequencing reveals clonally expanded and transcriptionally distinct lymphocytes in aged CNS. Gene expression and immune receptor repertoire sequencing was performing for both B and T cells. This dataset contains the VDJ sequencing information for the four samples. Each B cell and T cell library was sequenced across four lanes. </p> <p> </p> <p>Files with _WT_ in their name correspond to the young (4-6 week B6 mice) </p> <p>Files with _12_ in their name before the BDJ or VDJ text correspond to the 12-month-old cohort.</p> <p>Files with _18_ in their name before the BDJ or VDJ text correspond to the 18-month-old cohort in which four brains were pooled.</p> <p>Files with 4_18_ in their name before the BDJ or VDJ text correspond to the 18-month-old mouse that was processed and sequenced alone. </p> <p> </p> <p>The L001 - L004 in the file names indicates the sequencing lane. Samples with BDJ correspond to the B cell repertoire library (B cell VDJ). Samples with TDJ correspond to the T cell repertoire library (T cell VDJ). </p>
Whole-transcriptome sequencing identifies neuroinflammation, metabolism and blood-brain barrier related processes in the hippocampus of aged mice during perioperative period
<p><span><strong>Aim</strong>:</span><span> Perioperative neurocognitive disorders (PND) occur frequently after surgery and anesthesia, especially in aged patients. Previous studies have shown multiple PND related mechanisms in the hippocampus, however, their relationships remain unclear. Meanwhile, the perioperative neuropathological processes are sophisticated and changeable, single period study could not reveal the accurate mechanisms. Thus, multiperiod whole-transcriptome study is necessary to elucidate the gene expression patterns during perioperative period.</span></p> <p><span><strong>Methods</strong>: </span><span>Aged</span><span> C57BL/6 mice were subjected to exploratory laparotomy under sevoflurane anesthesia. Whole-transcriptome sequencing (RNA-seq analysis) was performed on the hippocampi from control condition (Con), 30 minutes (Day0), 2 days (Day2) and 7 days (Day7) after surgery. Gene Ontology</span><span>/Kyoto Encyclopedia of Genes and Genomes analyses,</span><span> quantitative Real-Time PCR, immunofluorescence and fear conditioning test were also performed to elucidate the pathological processes and modulation networks during the period.</span></p> <p><span><strong>Results</strong>: </span><span>Through RNA-seq analysis, 328, 3597 and 4179 differentially expressed genes (DEGs) were screened out in intraoperative period (Day0 vs Con), early postoperative period (Day2 vs Day0) and late postoperative period (Day7 vs Day2). The involved GO biological processes were divided into 9 categories, and positive-regulated processes were more than negative-regulated ones. Seventy-four transcription factors were highlighted. The potential synaptic and neuroinflammatory pathways were constructed for Neurotransmitter, Synapse and Neuronal alteration categories with 9 DEGs (<em>Htr1a, Rims1, Ezh2,</em> etc.). The metabolic and mitochondrial pathways were constructed for Metabolism, Oxidative stress and Biological rhythm categories with 9 DEGs (<em>Gpld1, Sirt1, Cry2, </em>etc.). The blood-brain barrier and neurotoxicity related pathways were constructed for Blood-brain barrier, Neurotoxicity and Cognitive function categories with 10 DEGs (<em>Mmp2, Itpr1, Nrf1, </em>etc.).</span></p> <p><span><strong>Conclusion</strong>:</span><span> The results revealed gene expression patterns and modulation networks in the aged hippocampus during perioperative period, which provide insights into overall mechanisms and potential therapeutic targets for prevention and treatment of perioperative central nervous system diseases, such as PND, from the genetic level.</span></p>
Discovering molecular regulators of ageing using mixture models with RNA-sequencing data
<p>Identifying the molecular regulators that control ageing is challenging because the ageing process is influenced by a combination of genetic and environmental factors which makes it difficult to source the contribution of a single gene. Multiple studies have demonstrated that as humans age, increased gene expression heterogeneity results in the dysregulation of key regulators and pathways. Given the dynamic nature of gene expression, it is vital that this data be modelled by statistical approaches that can appropriately account for changes in variability to understand the contribution of heterogeneity during the aging process and properly identify its regulators. This study demonstrates the utility of using mixture models to model biological variability of gene expression occurring during ageing and how novel potential regulators of ageing can be identified.</p> <p>Our mixture modelling approach was applied to gene expression data from the Genotype-Tissue Expression (GTEx) cohort. For every gene, the expression profile was modelled using a mixture model across the cohort where the subset of donors corresponding to each mode was tested for a significant change in age group. The multi-tissue aspect of GTEx was leveraged to find ageing regulators based on this mixture model approach genes that were common across multiple tissues, suggesting that the regulation of ageing may also be controlled through a set of genes that have non-tissue-specific activity.</p> <p>Our approach identified well-documented ageing regulators <em>mTOR </em>and <em>RICTOR</em> and other potential ageing regulators such as <em>IL4</em> and <em>GPR4</em> which were detected only by our approach. Genes identified by edgeR, DESeq2 and the mixture model-based approach were enriched for similar biological pathways. This suggests that while the specific ageing regulators identified from our approach may be distinct, they generally belong in the same pathways as the genes identified by standard approaches. Overall, these results indicate that modelling gene expression variability using mixture models in conjunction with standard differential gene expression can help uncover new regulators that have a potential role for understanding human ageing.</p> <p>I</p>
Data from: Palynology of a short sequence of the Lower Devonian Beartooth Butte Formation at Cottonwood Canyon (Wyoming): Age, depositional environments and plant diversity
<p>The Beartooth Butte Formation hosts the most extensive Early Devonian macroflora of western North America. The age of the flora at Cottonwood Canyon (Wyoming) has been constrained to the Lochkovian-Pragian interval, based on fish biostratigraphy and unpublished palynological data. We present a detailed palynological analysis of the plant-bearing layers at Cottonwood Canyon. The palynomorphs comprise 32 spore, five cryptospore, two prasinophycean algae and an acritarch species. The stratigraphic ranges of these palynomorphs indicate a late Lochkovian - Pragian age, confirming previous age assignments. Analyses on samples from three different depositional environments of the plant-bearing sequence – layers with in situ lycophyte populations, flood layers that buried those populations and an organic matter accumulation zone within a flood layer – demonstrate distinct palynofacies. Comparisons between palynomorph and plant macrofossil diversity reveal some discrepancies. Whereas zosterophylls and lycophytes, most diverse and abundant among the macrofossils, have only one known corresponding spore type (assignable to zosterophylls) in the palynomorph assemblage, the trimerophytes, rare in the macrofossil assemblage, are represented by three spore types. Some of these discrepancies reflect taphonomic differences between macrofossils and palynomorphs, others could be due to the fact that the parent plants of most palynomorph types in the Cottonwood Canyon assemblage are unknown. These observations emphasize the need for concerted efforts to bring together the knowledge of macro- and microfloras within Early Devonian localities. Nevertheless, given the palaeophytogeographic significance of the Beartooth Butte Formation flora, its palyno- and macrofossil assemblages, taken together, provide new data relevant to future discussions of Early Devonian biogeography.</p>
454-sequence data of Iron Age cattle from Althiburos – Tunisia
<p>The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on mitochondrial <em>D-loop</em> sequences obtained for 12 archaeological specimens of Iron Age (~2,800 cal BP–2,000 cal BP) domestic cattle from the Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althiburos specimens, respectively. Our results corroborate the introgression of aurochs females into the domestic stock of cattle from Althiburos. </p>
Whole-transcriptome sequencing identifies neuroinflammation, metabolism and blood-brain barrier related processes in the hippocampus of aged mice during perioperative period
Open the record for dataset details and reuse information.
454-sequence data of Iron Age cattle from Althiburos – Tunisia
Open the record for dataset details and reuse information.
Data from: Palynology of a short sequence of the Lower Devonian Beartooth Butte Formation at Cottonwood Canyon (Wyoming): Age, depositional environments and plant diversity
Open the record for dataset details and reuse information.
Data from: Estimating bloodstain age in the short term based on DNA fragment length using nanopore sequencer
<p>We used a nanopore sequencer to quantify DNA fragments > 10,000 bp in size and then evaluated their relationship with short-term bloodstain age. Moreover, DNA degradation was investigated after bloodstains were wetted once with water. Bloodstain samples on cotton gauze were stored at room temperature and low humidity for up to 6 months. Bloodstains stored for 1 day were wetted with nuclease-free water, allowed to dry, and stored at room temperature and low humidity for up to 1 week. The proportion of fragments > 20,000 bp in dry bloodstains tended to decrease over time, particularly for fragments > 50,000 bp in size. This trend was modeled using a power approximation curve, with the highest R2 value (0.6475) noted for fragments > 50,000 bp in size; lower values were recorded for shorter fragments. The proportion of longer fragments was significantly reduced in bloodstains that were dried after being wetted once, and there was significant difference in fragments > 50,000 bp between dry conditions and once-wetted. This result suggests that even temporary exposure to water causes significant DNA fragmentation, but not extensive degradation. Thus, bloodstains that appear fresh but have a low proportion of long DNA fragments may have been wetted previously. Our results indicate that evaluating the proportion of long DNA fragments yields information on both bloodstain age and the environment in which they were stored.</p>
Data from: Demographic inference from whole-genome and RAD sequencing data suggests alternating human impacts on goose populations since the last ice age
We investigated how population changes and fluctuations in the pink-footed goose might have been affected by climatic and anthropogenic factors. First, genomic data confirmed the existence of two separate populations: western (Iceland) and eastern (Svalbard/Denmark). Second, emographic inference suggests that the species survived the last glacial period as a single ancestral population with a low population size (100-1,000 individuals) that split into the current populations at the end of the Last Glacial Maximum with Iceland being the most plausible glacial refuge. While population changes during the last glaciation were clearly environmental, we hypothesize that more recent demographic changes are human-related: (1) the inferred population increase in the Neolithic is due to deforestation to establish new lands for agriculture, increasing available habitat for pink-footed geese (2) the decline inferred during the Middle Ages is due to human persecution and (3) improved protection explains the increasing demographic trends during the 20th century. Our results suggest both environmental (during glacial cycles) and anthropogenic effects (more recent) can be a threat to species survival.
Supplementary material 3 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265
Common OTU lists and Statistical analysis : Explanation note: This file contains detected OTUs in both methods and biodiversity analysis (GLM and t-test)
Supplementary material 2 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265
Biodiversity workflow in R : Explanation note: Bundle of files for biodiversity analysis in R. All necessary input files and a commented script of R-commands are provided.
Supplementary material 4 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265
Master data sheet : Explanation note: Spreadsheet file containing information about read abundances of operational taxonomic units (OTUs) and sample metadata. Here, data were prepared for subsequent biodiversity analysis in R.
Supplementary material 1 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265
Bioinformatics pipeline : Explanation note: This file provides all steps and commands necessary for quality filtering and demultiplexing of raw paired fastq sequences.
Properties of intermediate- to high-mass stars in the young cluster M17 Characterizing the (pre-)Zero Age Main Sequence
<p>Data and extra figures of the paper "Properties of intermediate- to high-mass stars in the young cluster M17 -- Characterizing the (pre-)Zero Age Main Sequence" by Frank Backs. Published in Astronomy and Astrophysics.</p> <p>The observed data and the fitted models are included. The fitting algorithm Kiwi-GA is available on Github: https://github.com/sarahbrands/Kiwi-GA</p> <p>Additional figures are available. These figures give an overview of the best fit models for each line like Fig. 1 in the paper. </p>
SQL database with detailed characteristic measurement results of photovoltaic modules that were subjected to accelerated aging sequences
<p>All measurement results are organized in an optimized database, which forms the information base for setting up models for climate sensitive ageing and degradation processes/mechanisms. The database is structured around the modules (module = device under test), see general scheme given in <a href="https://doi.org/10.1002/pip.3090">https://doi.org/10.1002/pip.3090</a>. Modules are logically connected via their specific ageing module groups with strictly associated ageing actions and instances. As stated above, a set of three identical modules is stored together in each specific ageing action (= accelerated ageing test as described in detail in Table <a title="Link to table" href="https://onlinelibrary.wiley.com/doi/10.1002/pip.3090#pip3090-tbl-0001">1</a> of <a href="https://doi.org/10.1002/pip.3090">https://doi.org/10.1002/pip.3090</a>) in order to increase the statistical reliability. Those triples are logically grouped in the database with the corresponding acquired measurement results being canonicalized and stored in the database as well. For future applications (modelling), all measurement information is kept as complete as possible; aggregation is avoided.</p> <a href="https://onlinelibrary.wiley.com/cms/asset/d5235350-b448-4094-b022-3b572d4c9317/pip3090-fig-0001-m.jpg" target="_blank" rel="noopener"></a>
Comparative Analysis of Filmed Sequences for the Assessment of Discomfort in Atopic Dermatitis of Infants Under 6 Months of Age
ClinicalTrials.gov study NCT03684343. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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.