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30,947 results for “Profile”
Data from: Combining RNA-seq and proteomic profiling to identify seminal fluid proteins in the migratory grasshopper Melanoplus sanguinipes (F)
Background: Seminal fluid proteins control many aspects of fertilization and in turn, they play a key role in post-mating sexual selection and possibly reproductive isolation. Because effective proteome profiling relies on the availability of high-quality DNA reference databases, our knowledge of these proteins is still largely limited to model organisms with ample genetic resources. New advances in sequencing technology allow for the rapid characterization of transcriptomes at low cost. By combining high throughput RNA-seq and shotgun proteomic profiling, we have characterized the seminal fluid proteins secreted by the primary male accessory gland of the migratory grasshopper (Melanoplus sanguinipes), one of the main agricultural pests in central North America. Results: Using RNA sequencing, we characterized the transcripts of ~ 8,100 genes expressed in the long hyaline tubules (LHT) of the accessory glands. Proteomic profiling identified 353 proteins expressed in the long hyaline tubules (LHT). Of special interest are seminal fluid proteins (SFPs), such as EJAC-SP, ACE and prostaglandin synthetases, which are known to regulate female oviposition in insects. Conclusions: Our study provides new insights into the proteomic components of male ejaculate in Orthopterans, and highlights several important patterns. First, the presence of proteins that lack predicted classical secretory tags in accessory gland proteomes is common in male accessory glands. Second, the products of a few highly expressed genes dominate the accessory gland secretions. Third, accessory gland transcriptomes are enriched for novel transcripts. Fourth, there is conservation of SFPs' functional classes across distantly related taxonomic groups with very different life histories, mating systems and sperm transferring mechanisms. The identified SFPs may serve as targets of future efforts to develop species- specific genetic control strategies.
Data from: PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment
Modeling across site variation of the substitution process is increasingly recognized as important for obtaining more accurate phylogenetic reconstructions. Both finite and infinite mixture models have been proposed, and have been shown to significantly improve on classical single-matrix models. Compared to their finite counterparts, infinite mixtures have a greater expressivity. However, they are computationally more challenging. This has resulted in practical compromises in the design of infinite mixture models. In particular, a fast but simplified version of a Dirichlet process model over equilibirum frequency profiles implemented in PhyloBayes (Lartillot et al, 2007) has often been used in recent phylogenomics studies, while more refined model structures, more realistic and empirically more fit, have been practically out of reach. We introduce an Message Passing Interface (MPI) version of PhyloBayes, implementing the Dirichlet process mixture models as well as more classical empirical matrices and finite mixtures. The parallelization is made efficient thanks to the combination of two algorithmic strategies: a partial Gibbs sampling update of the tree topology, and the use of a truncated stick-breaking representation for the Dirichlet process prior. The implementation shows close to linear gains in computational speed for up to 64 cores, thus allowing faster phylogenetic reconstruction under complex mixture models. PhyloBayes MPI is freely available from our website www.phylobayes.org.
Data from: An improved hypergeometric probability method for identification of functionally linked proteins using phylogenetic profiles
Predicting functions of proteins and alternatively spliced isoforms encoded in a genome is one of the important applications of bioinformatics in the post-genome era. Due to the practical limitation of experimental characterization of all proteins encoded in a genome using biochemical studies, bioinformatics methods provide powerful tools for function annotation and prediction. These methods also help minimize the growing sequence-to-function gap. Phylogenetic profiling is a bioinformatics approach to identify the influence of a trait across species and can be employed to infer the evolutionary history of proteins encoded in genomes. Here we propose an improved phylogenetic profile-based method which considers the co-evolution of the reference genome to derive the basic similarity measure, the background phylogeny of target genomes for profile generation and assigning weights to target genomes. The ordering of genomes and the runs of consecutive matches between the proteins were used to define phylogenetic relationships in the approach. We used Escherichia coli K12 genome as the reference genome and its 4195 proteins were used in the current analysis. We compared our approach with two existing methods and our initial results show that the predictions have outperformed two of the existing approaches. In addition, we have validated our method using a targeted protein-protein interaction network derived from protein-protein interaction database STRING. Our preliminary results indicates that improvement in function prediction can be attained by using coevolution-based similarity measures and the runs on to the same scale instead of computing them in different scales. Our method can be applied at the whole-genome level for annotating hypothetical proteins from prokaryotic genomes.
Data from: Profiling the immunome of little brown myotis provides a yardstick for measuring the genetic response to white-nose syndrome
White-nose syndrome (WNS) has devastated populations of hibernating bats in eastern North America, leading to emergency conservation listings for several species including the previously ubiquitous little brown myotis (Myotis lucifugus). However, some bat populations near the epicenter of the white-nose syndrome panzootic appear to be stabilizing after initial precipitous declines, which could reflect a selective immunogenetic sweep. To investigate the hypothesis that WNS exerts significant selection on the immunome of affected bat populations, we developed a novel, high-throughput sequence capture assay targeting 138 adaptive, intrinsic, and innate immunity genes of putative adaptive significance, as well as their respective regulatory regions (~370-kbp of genomic sequence/individual). We used the assay to explore baseline immunogenetic variation in M. lucifugus and to investigate whether particular immune genes/variants are associated with WNS susceptibility. We also used our assay to detect 1,038 putatively neutral single-nucleotide polymorphisms and characterize contemporary population structure, providing context for the identification of local immunogenetic adaptation. Sequence capture provided a cost-effective, 'all-in-one' assay to test for neutral genetic and immunogenetic structure and revealed fine-scale, baseline immunogenetic differentiation between sampling sites < 600 kilometers apart. We identified functional immunogenetic variants in M. lucifugus associated with WNS susceptibility. This study lays the foundations for future investigations of range-wide immunogenetic adaptation to white-nose syndrome in M. lucifugus, and provides a blueprint for studies of evolutionary rescue in other host-pathogen systems.
Data from: Metabolite profile of a mouse model of Charcot-Marie-Tooth type 2D neuropathy: implications for disease mechanisms and interventions
Charcot-Marie-Tooth disease encompasses a genetically heterogeneous class of heritable polyneuropathies that result in axonal degeneration in the peripheral nervous system. Charcot-Marie-Tooth type 2D neuropathy (CMT2D) is caused by dominant mutations in glycyl tRNA synthetase (GARS). Mutations in the mouse Gars gene result in a genetically and phenotypically valid animal model of CMT2D. How mutations in GARS lead to peripheral neuropathy remains controversial. To identify putative disease mechanisms, we compared metabolites isolated from the spinal cord of Gars mutant mice and their littermate controls. A profile of altered metabolites that distinguish the affected and unaffected tissue was determined. Ascorbic acid was decreased fourfold in the spinal cord of CMT2D mice, but was not altered in serum. Carnitine and its derivatives were also significantly reduced in spinal cord tissue of mutant mice, whereas glycine was elevated. Dietary supplementation with acetyl-L-carnitine improved gross motor performance of CMT2D mice, but neither acetyl-L-carnitine nor glycine supplementation altered the parameters directly assessing neuropathy. Other metabolite changes suggestive of liver and kidney dysfunction in the CMT2D mice were validated using clinical blood chemistry. These effects were not secondary to the neuromuscular phenotype, as determined by comparison with another, genetically unrelated mouse strain with similar neuromuscular dysfunction. However, these changes do not seem to be causative or consistent metabolites of CMT2D, because they were not observed in a second mouse Gars allele or in serum samples from CMT2D patients. Therefore, the metabolite 'fingerprint' we have identified for CMT2D improves our understanding of cellular biochemical changes associated with GARS mutations, but identification of efficacious treatment strategies and elucidation of the disease mechanism will require additional studies.
[Dataset] 1H‑NMR based‑metabolomics reveals alterations in the metabolite profiles of chickens infected with ascarids and concurrent histomonosis infection
<p>The dataset associated with the publication "1H‑NMR based‑metabolomics reveals alterations in the metabolite profiles of chickens infected with ascarids and concurrent histomonosis infection" in <i>Gut Pathogens</i> (DOI: 10.1186/s13099-023-00584-7) comprises NMR measurements of plasma and liver samples. This dataset stems from a controlled study involving laying hens subject to mixed infections of <i>Ascaridia galli</i> and<i> Heterakis gallinarum</i>. Monitoring 108 individual hens over weeks 2 to 18 post-infection, samples of plasma and liver were collected at specific intervals. The dataset encompasses measurements of antibodies against histomonas, alpha 1 acid glycoprotein, and worm burdens, providing essential information for understanding the metabolic alterations induced by these infections in chickens.</p>
Pulse Profile Modelling of Thermonuclear Burst Oscillations II: Handling variability
<p>Pulse Profile Modelling of Thermonuclear Burst Oscillations II: Handling variability</p>
Single cell RNA-seq transcriptomic profile of circulating immune and progenitor cells in a mouse model of neonatal hypoxic/ischemic (HI) brain damage.
<p>Hematopoietic cells play a pivotal role in regulating the inflammatory and reparative immune responses triggered after ischemic tissue damage. The response initiated within the injured tissue leads to compositional and transcriptional changes in circulating hematopoietic and progenitor cells, which have been utilized as biomarkers. While the importance of different immune and progenitor cell subtypes in the development of ischemic damage has been extensively researched in adult tissue injuries, there has been limited investigation in neonates. This is a critical developmental stage where ischemic damage can result in severe and irreversible health consequences if not promptly treated. To determine how ischemic damage could affect circulating cells in neonates, we have induced hypoxic-ischemic (HI) brain damage in seven-day-old mice, characterized by focal white and gray-matter injury (Rice-Vannucci model). Brain damage and circulating cells were analyzed at 48h post-HI, the intermediate reparative/inflammatory response phase post-injury. We applied scRNAseq to dissect the transcriptional and cellular composition changes in the peripheral blood of HI-treated and SHAM control neonates. This study provides the first scRNAseq dataset for immune and progenitor circulating cells in newborns with cerebral HI damage. It may help to identify biomarkers and selective therapeutic approaches aimed at modulating inflammatory and reparative pathways. </p><p>CD1 postnatal day 7 (P7) mice were subjected to hypoxic/ischemic (HI) brain injury by permanent ligation of the left common carotid artery followed, after 2h recover, by relocation to a hypoxia chamber for 90 minutes. Sham control mice (SHAM) underwent a skin incision and wound closure followed by hypoxia exposure. Circulating blood cells were collected from SHAM and HI mice at P9. After red blood cells (RBC) lysis, 7AAD-Ter119- cells were FACS sorted and analysed using sc RNAseq. Other samples were FACS sorted for CD45+CD11+ and CD45-CD31+ cells and mixed.</p>
Tracking Decomposition Layer Formation in Thin-Film Si Electrodes via Thermogalvanic Profiles
<p>This dataset contains the raw data for the publication "Tracking Decomposition Layer Formation in Thin-Film Si Electrodes via Thermogalvanic Profiles" by Hubrechtsen et al, published in Small Methods. The upload includes all data for the original figures presented in the main paper and the supporting information, organized in labelled folders containing raw data and the corresponding figure. </p>
Cultivar and harvest time of almonds modify the antioxidant and nutritional profile of almonds through gut microbiota modifications (Supplementary materials)
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Immuno-transcriptomic profiling of blood and tumor tissue identifies gene signatures associated with immunotherapy response in metastatic bladder cancer
<p>The dataset contains RNA-sequencing data (raw fastq files, not trimmed) of whole blood and whole bladder tissue samples and metadata file with sample annotation. The samples have been collected in the context of the study "Immuno-transcriptomic profiling of blood and tumor tissue identifies gene signatures associated with immunotherapy response in metastatic bladder cancer". In this study, we investigated which are the local and systemic immune changes in an experimental model of muscle-invasive bladder cancer upon immunotherapy. The RNA-sequencing data have been used to produce the results presented in the study. Please refer to the study publication material and methods and the metadata file for details.</p>
500 Hourly Synthetic Single-Family Household Heat Pump Load Profiles for Karlsruhe, Germany (2021)
<p>We created a synthetic dataset of 500 hourly single-family household water-to-water heat pump load profiles based on the weather profile of Karlsruhe, Germany in 2021. We have applied the open-source methodology published in [1], which applies a k-means clustering process to match daily weather profiles with randomly drawn empirical observations from the high-quality heat pump load profile dataset published in [2]. We have selected a number of 5 clusters, for a good balance between variance of profiles and accuracy, as discussed in [1]. The dataset can be used for modeling large numbers of heat pumps in grid sections or energy communities. </p> <p>The unit of the measurement is Wh. Through the "SFH" identifier, the underlying, randomly drawn households from [2] can be identified. </p> <p>[1] Semmelmann, L., Jaquart, P., & Weinhardt, C. (2023). Generating synthetic load profiles of residential heat pumps: a k-means clustering approach. <em>Energy Informatics</em>, <em>6</em>(Suppl 1), 37.</p> <p>[2] Schlemminger, M., Ohrdes, T., Schneider, E., & Knoop, M. (2022). Dataset on electrical single-family house and heat pump load profiles in Germany. <em>Scientific data</em>, <em>9</em>(1), 56.</p>
Dynamic profiling and binding affinity prediction of NBTI antibacte-rials against DNA gyrase enzyme by multidimensional machine learning and molecular dynamics simulations
<p>The chemical libraries used in this study comprised of 199 and 133 structurally diverse novel bacterial topoisomerase inhibitors (<em>alias</em> NBTIs), with experimentally determined <em>in vitro</em> antibacterial potencies against <em>Staphylococcus aureus</em> DNA gyrase (IC<sub>50</sub>=0.007-50 µM) and <em>Escherichia coli</em> DNA gyrase (IC<sub>50</sub>=0.020-100 µM), respectively (named as NBTI<em><sub>SA</sub></em> and NBTI<em><sub>EC</sub></em>), were compiled from the literature as *.sdf file format. The chemical structures comprising both NBTI libraries were initially sketched by using ChemDraw Professional 20.1.1 suite and subsequently energetically minimized utilizing Discovery Studio’s integrated Merck Molecular Force Field (MMFF) module. Moreover 4D ligands ensembles of both libraries ready to be used for multidimensional QSAR modeling are available, as well.</p>
MITO END-3: efficacy of Avelumab immunotherapy according to molecular profiling in first line endometrial cancer therapy
<p>Immunotherapy combined to chemotherapy significantly improves progression free survival compared to first line chemotherapy alone in advanced endometrial cancer, with a much larger effect size in microsatellite-instability high (MSI-H) cases. New biomarkers might help to select patients that may have benefit among those with a microsatellite-stable (MSS) tumor.</p> <p>Methods.</p> <p>In a pre-planned translational analysis of the MITO END-3 trial we assessed the significance of genomic abnormalities in patients randomized to standard carboplatin/paclitaxel without or with avelumab.</p> <p>Results.</p> <p>Out of 125 randomized patients, 109 had samples eligible for Next Generation Sequencing (NGS) analysis and 102 had MSI tested. According to The Cancer Genome Atlas (TCGA) there were 29 cases MSI-H, 26 MSS TP53 wild type (wt), 47 MSS TP53 mutated (mut), and one case with <em>POLE</em> mutation. Four mutated genes were present in more than 30 % of cases: <em>TP53</em>,<em> PIK3CA</em>,<em> ARID1A</em>,<em> PTEN</em>. Eleven patients (10 %) had a BRCA 1/2 mutation (5 in MSI-H and 6 in MSS). High TMB (≥ 10Muts/Mb) was observed in all MSI-H patients, in 4 out of 47 MSS/<em>TP53</em>mut, and in no case in the MSS/<em>TP53</em>wt category. The effect of avelumab on progression-free survival (PFS) significantly varied according to TCGA categories, being favorable in MSI-H and worst in MSS/TP53mut (P interaction=0.003); a similar non-significant trend was seen in survival analysis. <em>ARID1A</em> and <em>PTEN</em> also showed a statistically significant interaction with treatment effect, that was better in presence of the mutation (<em>ARID1A</em> P interaction=0.01; <em>PTEN</em> P interaction=0.002).</p> <p>Conclusion</p> <p>The MITO END-3 trial results suggest that <em>TP53 </em>mutation is associated with poor effect of avelumab, while mutations of <em>PTEN</em> and <em>ARID1A</em> are related to a positive effect of the drug in patients with advanced endometrial cancer.</p>
Lemur Database for Taxonomic Profiling (bacteria, archaea, fungi)
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Datasets: Integrative Multi-omics Profiling in Human Decedents Receiving Pig Heart Xenografts
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Supplementary data for "Profiling the peripheral immune landscape of metastatic HER2+ breast cancer"
<p>Supplementary data (Supplementary Table III.1) and high-resolution versions of figures III.3 - III.9 for Chapter III of the PhD thesis "The effect of dual HER2 blockade on anti-tumor immune cells" (ITQB-NOVA, Oeiras, Portugal).</p>
Figure 1 from: Marinov T, Kokanova-Nedialkova Z, Nedialkov P (2024) UHPLC-HRMS-based profiling and simultaneous quantification of the hydrophilic phenolic compounds from the aerial parts of Hypericum aucheri Jaub. & Spach (Hypericaceae). Pharmacia 71: 1-11. https://doi.org/10.3897/pharmacia.71.e122436
Figure 1 Chromatographic separation of the standards chlorogenic acid, mangiferin, and hyperoside under the optimized conditions.
US soil profile EW code
<p>README file, Matlab code, datasets for modelling ERW across the US </p>
Smart and sustainable tourism: profile and behavior of the argentine tourist
<p>Ponencia - IV Congreso Latinoamericano de Marketing Social</p>
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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.