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4,566 results for “marker”
Data from: Novel microsatellite markers for epiphytic bromeliad Tillandsia recurvata L., in an urban landscape in South-eastern Brazil
<p><span>The authors present seven novel microsatellite markers for </span><em>Tillandsia recurvata</em> L. The genome assemble sequences of <em>T. recurvata</em> were obtained from NCBI (7.2Gb) (Sayers <em>et al</em>. 2022). The BioProject Accession and accession numbers are PRJNA701548 and SRX10089449, respectively. The microsatellite identification software Krait (0.5.2) (Du <em>et al</em>. 2018) was used to detect suitable microsatellites, both genome-wide and in the noncoding regions of <em>T. recurvata</em>. The single sequence repeats (SSRs) were refined to a minimum number of seven repeats of di-, tri-, or tetra-nucleotide repeat motifs. These sequences were further limited to SSRs of more than 100bp in length and low GC content (<50%). Krait (0.5.2) (Du <em>et al</em>. 2018) was also used to design the primers for the selected SSR sequences, in conjunction with the integrated Primer3 software. The criteria for primer selection included: a primer length of 18-26bp, an optimal melting temperature (Tm) of 54-59°C and GC content of <50%. These designed primers were single-plexed and amplified using the following PCR cycle: initial denaturation (95°C for 3 min), 34 cycles of 95°C for 30s, annealing for 30s (JP01-JP12: 54°C, 4873TD + 35251TD: 56°C, 19286TD: 53°C, 5044TD + 186664TD + 214633TD: 58°C), 72°C for 1 min and a final extension of 72°C for 5 mins. The authors make this information available to other researchers, to continue the investigation of epiphyte genetics.</p>
Inferring phenotypes of single cells based on the expression profiles of phenotype-associated marker genes in bulks and single cells
<p>The datasets analysed in the manuscript "Inferring phenotypes of single cells based on the expression profiles of phenotype-associated marker genes in bulks and single cells".</p>
Evaluation of oxidative stress markers in Rwanda during the SARS-CoV-2 pandemic: a cross-sectional study
<p>SARS-CoV-2 is mainly described as endothelial dysfunction, and due to the bidirectional link between oxidative stress and endothelial dysfunction, we initiated a program directed to the evaluation of the oxidative status of the population of Rwanda by measuring spectrophotometrically their plasma Reactive Oxygen Metabolites (dROMs) and Plasma Antioxidant Potential (PAT). The reference population was chosen to reflect the absence of actual or past SARS-CoV-2 infections as well as other clinically established infective status and reference intervals for d-ROM and PAT were identified.</p> <p>The average d-ROM was 378.6 UCARR with a standard deviation of 105.2. The average PAT value was 2853.6, with a standard deviation of 635.7 UCOR. On the basis of the published values for the Caucasian and East Asian populations, the average value of d-ROM obtained in Rwanda was significantly higher than expected. Conversely, the average PAT value was at the upper limit according to the averaged values for healthy Caucasian populations. The results of this study, the first so far reported on a sub-Saharan population, can effectively be used as a baseline value for clinical management of inflammatory conditions, for the stratification of at-risk individuals and to inform recommendations for effective use of public health resources.</p>
Sample extraction and SNP sequencing data for: Identification of sex-linked SNP markers in wild populations of monomorphic birds
<p><span>Single-nucleotide polymorphism (SNP) analyses are a powerful tool for population genetics, pedigree reconstruction and phenotypic trait mapping. However, the untapped potential of SNP markers to discriminate the sex of individuals in species with reduced sexual dimorphism or of individuals during immature stages remains a largely unexplored avenue. Here, we develop a novel protocol for molecular sexing of birds based on the detection of unique Z- and W-linked SNP markers. Our method is based on the identification of two unique loci, one in each sexual chromosome. Individuals are considered males when they show no calls for the W-linked SNP and are heterozygotic or homozygotic for the Z-linked SNP, while females show both Z- and W-linked SNP calls. We validated the method in the Jackdaw (<em>Corvus</em> <em>monedula</em>). The reduced sexual dimorphism in this species makes it difficult to sex individuals in the wild. We assessed the reliability of the method using 36 individuals of known sex and found that their sex was correctly assigned in 100% of cases. The sex-linked markers also proved to be widely applicable to discriminate males and females from a sample of 927 genotyped individuals of different maturity stages with an accuracy of 99.5%. Given that SNP markers are increasingly used in quantitative genetic analyses of wild populations, the approach we propose has a great potential to be integrated into broader genetic research programmes without the need for additional sexing techniques.</span></p>
Data for: Russian honey bee genotype identification through enhanced marker panel set
<p>Russian honey bees (RHB) are a breeding population developed by USDA-ARS as an effort to provide Varroa-resistant honey bees to beekeepers. The selection strategy for this breeding population was the first in honey bees to incorporate genetic stock identification (GSI). The original GSI approach has been in use for over a decade, and though effective, novel technologies and analytical approaches recently developed provide an opportunity for improvement. Here we outline a novel genotyping assay that capitalizes on the markers used in the GSI as well as novel loci recently identified in a whole genome pooled study of commercial honey bee stocks. Our approach utilizes a microfluidic platform and machine learning analyses to arrive at an accurate, high throughput assay. This novel approach provides an improved tool that can be readily incorporated into breeding decisions towards healthier more productive bees.</p>
Defining and identifying Discourse Markers in spontaneous speech. A corpus-based and experimental proposal
<p>The paper has a twofold goal: (i) to identify the cathegory of Discourse Markers (DM) and their different specific functions; (ii) to validate the proposal with a perceptual experiment. First, we propose how to identify DM and their different functions in spontaneous speech. Both the identification of the categorycategory of DM and that of specific DM functions are based on prosodic criteria. In order to identify a DM, speech segmentation is crucial, since DMs necessarily appear isolated in a prosodic unit. Besides prosodic isolation, DMs do not feature pragmatic and prosodic autonomy, but depend on the illocutionary unit of the utterance. Than we show that a same lexical item can fulfill more functions, while the formal cues that convey the function are prosodic ones. The last part of the chapter is devoted to presenting the methodology and the results of a perceptual experiment that tests the theoretical hypothesis by asking the listeners to recognize three different functions by means of prosodic cues only.</p>
Defining and identifying Discourse Markers in spontaneous speech: a corpus-based and experimental proposal
<p>Audio files used as examples in the paper.</p>
Dataset for: Utilizing high-resolution genetic markers to track population-level exposure of migratory birds to renewable energy development
<p class="MsoNormal"><span>With new motivation to increase the proportion of energy demands met by zero-carbon sources, there is a greater focus on efforts to assess and mitigate the impacts of renewable energy development on sensitive ecosystems and wildlife, of which birds are of particular interest. One challenge for researchers, due in part to a lack of appropriate tools, has been estimating the effects from such development on individual breeding populations of migratory birds. To help address this, we utilize a newly developed, high-resolution genetic tagging method to rapidly identify the breeding population of origin of carcasses recovered from renewable energy facilities and combine them with maps of genetic variation across geographic space (called 'genoscapes') for five species of migratory birds known to be exposed to energy development, to assess the extent of population-level effects on migratory birds. We demonstrate that most avian remains collected were from the largest populations of a given species. In contrast, those remains from smaller, declining populations made up a smaller percentage of the total number of birds assayed. Results suggest that application of this genetic tagging method can successfully define population-level exposure to renewable energy development and may be a powerful tool to inform future siting and mitigation activities associated with renewable energy programs.</span></p>
Marker-MAGu Marker Gene DB
<p>This contains a tarball of the Marker-MAGu Marker Gene Database. It is a single file in multi-fasta format. It contains species/SGB-specific marker genes for viruses (Trove of Gut Virus Genomes, v1.1) and bacteria, archaea (metaphlan4, vOct22).</p> <p>The header is formatted as such with ";" as field separators.</p> <p>><strong>unique_gene_name</strong>;<em><strong>hierarchical_lineage</strong></em>;<strong>genome_name</strong></p> <p> </p> <p>You should follow instructions on the Marker-MAGu <a href="https://github.com/cmmr/Marker-MAGu">GitHub</a>.</p> <p>Marker-MAGu/DBs/v1.0/Marker-MAGu_markerDB.fna</p> <p> </p>
Data from: genetic resources of macroalgae: development of an efficient method using microsatellite markers in non-model organisms
<p><span>Red and brown seaweeds are species with high ecological and economic importance. Here we report the feasibility of cost-effective molecular marker development in 6 species from different clades. Microsatellites markers of two brown seaweed species <em>Alaria esculenta</em>, <em>Pylaiella littoralis</em>, and of four red seaweed species <em>Calliblepharis jubata</em>, <em>Gracilaria gracilis</em>, <em>Gracilaria dura </em>and <em>Palmaria palmata</em> were identified and characterized using genomic sequences of Double-Digest Restriction site Associated DNA (ddRAD). A total of 64,623,186 reads were generated from two runs of multiplexed Illumina Miseq sequencing for which 30,636 reads containing microsatellites and 15,443 microsatellite loci with primers pairs were found. Five hundred seventy-six primers pairs were selected for amplification trials and levels of polymorphism. From the 338 that gave a positive amplification, 142 primers pairs were polymorphic. For genetic analyses two or three populations per species from 13 different geographic locations were used. A total of 28 usable polymorphic markers for <em>A. esculenta</em>, 18 for <em>P. littoralis</em>, 11 for <em>C. jubata</em>, 14 for <em>G. gracilis</em>, 21 for <em>G. dura </em>and 13 for <em>P. palmata </em>were developed. The overall number of alleles per locus ranged from 2 to 22. These 105 new microsatellite markers will be useful for further studies of population genetics, breeding programs and conservation genetics of these species. Compared with traditional approaches, our study yielded thousands of microsatellite loci in a short tim</span><span>e with affordable costs in six different species. This study based on ddRAD-sequencing for the development of microsatellite markers provides preliminary data u</span><span>sing a few individuals from two distinct populations on the genetic structure and reproduction mode of a non-model species as shown </span>with the detection of clonality for the two red algae, <em>C. jubata </em>and <em>G. dura</em> and the detection of highly genetically divergent populations corresponding probably to different cryptic species under the name of<em> P. littoralis</em>.</p>
Genotype data of Philippine native pigs, Duroc, Landrace, Large White and Berkshire, using 20 ISAG-FAO recommended microsatellite markers
<p>Microsatellite genotyping is a cost-effective method for the genetic diversity analysis of under-studied populations, such as the Philippine native pigs. We genotyped <em>n</em> = 196 pigs representing 7 Philippine native pig populations (<em>n </em>= 20 to 27 for each population) and 4 commercial transboundary breeds (<em>n</em> = 9 to 11 for each population). Twenty microsatellite markers, recommended by the International Society of Animal Genetics (ISAG)-FAO, were used to generate the dataset for population analysis (S0005, S0155, S0026, S0355, Sw830, Sw2410, Swr1941, Sw632, Sw24, S0228, Sw936, S0097, Sw857, Sw122, Sw2406, IGF1, Sw240, S0090, S0226, Sw72). S0218 was used as a sex marker (data not shown). All loci, except Sw24, did not deviate from Hardy Weinberg equilibrium. Each marker showed an average <em>PIC </em>of 0.779. A total of 260 alleles of length 86 to 272 bp were obtained. Using this dataset, we determined population structure and conservation priorities in the Philippine native pigs. This dataset contains both the raw files (.fsa) and the processed file (.txt). This dataset can be used by colleagues to increase their research coverage and achieve multi-population and multi-country comparisons, especially among Asian indigenous pigs.</p>
Big stone grave marker
Big stone grave maker photoscanned at Hollybrook Cemetery, Southampton Source: Objaverse 1.0 / Sketchfab
Edmund J. Cox Grave Marker
This stone belongs to Edmund Cox, who was originally from Australia, but died in Santa Cruz in 1895. He was christened in Sydney in December 1837, the son of Jane and John Cox. I was unable to figure out how he ended up in America or when specifically he arrived, but some archives from New Zealand indicate that he left Sydney on the ship Shamrock in June 1841, was "captured" in March 1867, was a solicitor (?), and was a "respectable citizen" in San Jose, CA by January 1875. He became a U.S. citizen in the county and district courts on April 14, 1880, according to the Santa Cruz Sentinel. http://www.newspapers.com/newspage/50297408/ Source: Objaverse 1.0 / Sketchfab
St Magnus the Martyr Parish Boundary Marker
A parish boundary marker located at St Magnus the Martyr Church, Lower Thames Street, London. Date: 1836 Photos taken in February 2019 with a Sony a6000 and processed in Agisoft Metashape. Source: Objaverse 1.0 / Sketchfab
Multi OIT to Test Immune Markers After Minimum Maintenance Dose
ClinicalTrials.gov study NCT03181009. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Serum Markers in Gluten Challenge
ClinicalTrials.gov study NCT00931892. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Markers of Alzheimers Disease and Cognitive Outcomes After Perioperative Care
ClinicalTrials.gov study NCT01993836. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Michigan Medicine COVID-19 Cohort: Clinical Characteristics, Inflammatory Markers and Outcomes of Patients Hospitalized for COVID-19
ClinicalTrials.gov study NCT04706533. IPD Sharing: NO. Countries: 1. Publications: 19.
Impact of INsulin Sensitivity on Cardiovascular Risk Markers During 10-20 Years of FOllow up
ClinicalTrials.gov study NCT01412554. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Effects of β-alanine and Sodium Bicarbonate Supplementation on Physical Capacity and Biochemical Markers Concentrations
ClinicalTrials.gov study NCT07092930. IPD Sharing: YES. Countries: 1. Publications: 2.
ScienceDex guides
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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.