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4,566 results for “marker”
Walter Cooper Grave Marker
Walter Cooper is buried in the same plot as Alice Maria Paxton Cooper (https://sketchfab.com/models/5a98051aae9740828a5fe967418a9b7a). The Sacramento County Archives list him as being 31 at the time of his death, but a record in the New England Historical and Genealogical Register of 1896 indicates that his tombstone said "32". Either way, since he died in 1870, that would put his birth year at roughly 1838-1839. It seems, based on accounts of his having built a saloon in Felton and leased a property in Felton to one Mr. McCoy, as though Mr. Cooper was involved in real estate. His business partner was J. M. Merrill. http://www.feltonfire.com/pictures/feltonhistory.html https://books.google.com/books?id=FA8ALY0ZtYYC&pg=PA440&lpg=PA440&dq=walter+cooper+santa+cruz+1870&source=bl&ots=buEsM3UM1u&sig=FZKU-7kKaAjcoU9dQYUMwkpoI3k&hl=en&sa=X&ei=aI1oVf6ICcGtogTat4KgDg&ved=0CCsQ6AEwAg#v=onepage&q=walter%20cooper%20santa%20cruz%201870&f=false http://files.usgwarchives.net/ca/sacramento/newspapers/sacramen19nw.txt Source: Objaverse 1.0 / Sketchfab
Ferns Cemetery Grave Marker 3
A grave marker in Ferns Cemetery, St. Edan's Church, Ireland. The headstone marks the resting place of two people. Source: Objaverse 1.0 / Sketchfab
Grave marker for Pompeia Margaris
https://data.fitzmuseum.cam.ac.uk/id/object/65525 Pediment, with woman reclining on a sofa and her dog trying to wake her, inscribed for Pompeia Margaris Source: Objaverse 1.0 / Sketchfab
Data from: Quantitative PCR as a marker for preemptive therapy and its role in therapeutic control in Trypanosoma cruzi/HIV coinfection
<p><strong>Background: </strong><em>Trypanosoma cruzi</em> and HIV coinfection can evolve with depression of cellular immunity and increased parasitemia. We applied quantitative PCR (qPCR) as a marker for preemptive antiparasitic treatment to avoid fatal Chagas disease reactivation and analyzed the outcome of treated cases.</p> <p><strong>Methodology:</strong> This mixed cross-sectional and longitudinal study included 171 Chagas disease patients, 60 coinfected with HIV. Of these 60 patients, ten showed Chagas disease reactivation, confirmed by parasites identified in the blood, cerebrospinal fluid, or tissues, 12 exhibited high parasitemia but no reactivation, and 38 had low parasitemia and no reactivation.</p> <p><strong>Results</strong>: We showed, for the first time, the success of the timely introduction of benznidazole in the non-reactivated group with high levels of parasitemia detected by qPCR and the absence of parasites in reactivated cases with at least 58 days of benznidazole. HIV+ and HIV+ without reactivation had a 4.0 – 5.1 higher chance of having parasitemia than HIV seronegative cases. A positive correlation was found between parasite and viral loads. Remarkably, treated <em>T. cruzi/</em>HIV-coinfected patients had 77.3% conversion from positive to negative parasitemia compared to 19.1% of untreated patients. Additionally, untreated patients showed ~13.6 times higher odds of having positive parasitemia in the follow-up period compared with treated patients. Treated and untreated patients showed no differences regarding the evolution of Chagas disease. The main factors associated with all-cause mortality were higher parasitemia, lower CD4 counts/µL, higher viral load, and absence of antiretroviral therapy.</p> <p><strong>Conclusion</strong>: We recommend qPCR prospective monitoring of <em>T. cruzi</em> parasitemia in HIV+ patients and point out the value of pre-emptive therapy for patients with temporary high parasitemia. In parallel, an early antiretroviral therapy introduction is advisable, aiming at viral load control, immune response restoration, and major survival. We also suggest an earlier antiparasitic treatment for all coinfected patients, followed by effectiveness analysis alongside antiretroviral therapy.</p>
Mapping of the QTLs governing grain micronutrients and thousand kernel weight in wheat (Triticum aestivum L.) using high density SNP markers
<p>The mapping population consists of 166 recombinant inbred lines (RILs) derived from a cross between HD3086 and HI1500.</p> <p><strong>Phenotypic data</strong><br>The RILs population along with parents were evaluated under four conditions namely timely sown irrigation (TSIR) taken as control, timely sown restricted irrigation (TSRI), late sown irrigation (LSIR), and late sown restricted irrigation (LSRI) conditions at Delhi, and under restricted irrigation condition at Indore. From each plot, 20 random spikes were harvested and spikes from each plot were threshed separately. While cleaning, care was taken to prevent metal and dust contamination. The grain iron concentration (GFeC) and grain zinc concentration (GZnC) were measured using Energy Dispersive X-ray Fluorescence (ED-XRF) machine (model X-Supreme 8000 M/s Oxford Inc, USA). The thousand kernel weight (TKW) was recorded by counting 1000 grains manually and weighted with an electronic balance.</p> <p><strong>Genotypic data</strong><br>DNA was extracted from 21 days old seedlings using CTAB method (Murray and Thompson, 1980). Genomic DNA quality was determined using 0.8% agarose gel electrophoresis with λ DNA as the standard and quantified using nanodrop. The 35K SNP Axiom breeders' array was used for genotyping of parents and the RILs population.</p>
Development of twenty-four microsatellite markers for Afrotropical Ornithodoros ticks
<p><strong>Background: </strong>Soft ticks of the genus <em>Ornithodoros</em> are responsible for the maintenance and transmission of the <em>African swine fever </em>(ASF)<em> virus</em> in the sylvatic and domestic viral cycles in Southern Africa. They are also the main vectors of <em>Borrelia</em> species causing relapsing fevers. Currently, no genetic markers are available for Afrotropical <em>Ornithodoros </em>ticks. As ASF spreads globally, such markers are needed to assess the role of ticks in the emergence of new outbreaks. The aim of this study was to design microsatellite markers that could be used for ticks of the <em>Ornithodoros moubata</em> complex, particularly <em>Ornithodoros phacochoerus</em>, to assess population structure and tick movements in ASF endemic areas.</p> <p><strong>Methods: </strong>One hundred and fifty-one markers were designed using the <em>O. moubata </em>and <em>O. porcinus</em> genomes after elimination of repeated sequences in the genomes. All designed markers were tested on <em>O. phacochoerus </em>and <em>O. porcinus </em>DNA to select the best markers.</p> <p><strong>Results:</strong> Twenty-four microsatellite markers were genotyped on two populations of <em>O. phacochoerus</em> and on few individuals from four other <em>Ornithodoros</em> species. Nineteen markers were selected to be as robust as possible for population genetic studies on <em>O. phacochoerus</em>.</p> <p><strong>Conclusions:</strong> The microsatellite markers developed here represent the first genetic tool to study nidicolous populations of Afrotropical <em>Ornithodoros</em>. This dataset contains the genotyping results obtained for all twenty-four markers tested.</p>
SNP markers used for QTL mapping in the inbred lines
<p><span>Young leaves of the 175 inbred lines and their seven parents were collected from seedlings grown in a greenhouse. </span><span>About 200 mg bulk leaf sample from three plants of a line was placed in 2 ml safe-lock </span><span>Eppendorf tube and stored at ‒80 </span><span>˚C for one night prior to crushing using a Mixer Mill (TissueLyser II, Qiagen, Germany). Genomic DNA was extracted using SIGMA DNA extraction kit (Sigma-Aldrich, St. Louis, MO, USA) following the manufacturer's instruction. DNA concentration and purity of the samples were assessed using a NanoDrop 2000c spectrophotometer (Thermo Scientific, Wilmington, DE, USA). The samples were processed and sequenced using tunable genotyping-by-sequencing (tGBS®) method by Data2Bio (Ames, IW, USA). Genomic DNA was digested using two restriction enzymes NSpI (5′-RCATG^Y-3′) and BfuCI/Sau3AI (5′-^GATC-3′) which created 3´and 5´overhangs, respectively. Two single-stranded oligos, one containing a sample-specific internal barcode and the other a universal oligo, were ligated to the complementary 3´ and 5´ overhangs, respectively. </span>All 175 inbred lines' and seven parents' treated DNA was pooled for construction of the tGBS library and sequencing. The raw sequence data were demultiplexed by barcode, which was subsequently removed bioinformatically from each sequence. The barcode-trimmed sequence reads of genotype were further trimmed using the trimming software, Lucy (Chou & Holmes, 2001; Li & Chou 2004) to remove low-quality reads based on Phred quality scores of Q15.</p>
Database of giant viruses, Mirusviruses genomes, and marker genes
<p>Nucleotide sequences of 1,629 viral genomes (1,518 <em>Nucleoviricota</em> and 111 <em>Mirusviricota</em>), and marker genes found in these genomes.</p>
NASTRA: Accurate analysis of short tandem repeat markers by nanopore sequencing with repeat-structure-aware algorithm
<p><span>Forensic short-tandem repeats (STR) genetic markers are multi-allelic and widely utilized for individual identification, kinship testing, and cell-line authentication. Nanopore sequencing, known for its portability, is emerging as a promising approach for STR typing, facilitating real-time and in-field testing. However, its efficacy is often hampered by sequencing noise. Previous methods rely on alignment-based genotyping, necessitating known alleles, which limits their applicability to unknown alleles. Here, we introduced NASTRA, an innovative allele reference-free tool for precise germline analysis of STR genetic markers. NASTRA incorporates a recursive algorithm to infer repeat structures of allele sequences using only known repeat motifs. Our tests, conducted on 80 individual samples and 8 DNA standards, have demonstrated NASTRA's exceptional 100% accuracy in genotyping nearly all diploid STRs across various multiplex kits and flow cells. It surpasses alignment-based methods in accuracy and speed. In a paternity testing case study, NASTRA accurately identified three relationships among six individuals within an 18-minute sequencing duration. These results underscore NASTRA's ability to perform STR analysis on both NGS and nanopore sequencing platforms, significantly enhancing the utility of nanopore sequencing in relevant applications.</span></p>
Heart rate variability: Can it serve as a marker of mental health resilience?
<p>Heart rate variability: Can it serve as a marker of mental health resilience?</p> <p>Background: Stress resilience influences mental well-being and vulnerability to psychiatric disorders. Usually, measurement of resilience is based on subjective<br> reports, susceptible to biases. It justifies the need for objective biological/physiological biomarkers of resilience. One promising candidate as biomarker of mental<br> health resilience (MHR) is heart rate variability (HRV). The evidence for its use was reviewed in this study.<br> Methods: We focused on the relationship between HRV (as measured through decomposition of RR intervals from electrocardiogram) and responses to laboratory<br> stressors in individuals without medical and psychiatric diseases. We conducted a bibliographic search of publications in the PubMed for January 2010–September<br> 2018.<br> Results: Eight studies were included. High vagally mediated HRV before and/or during stressful laboratory tasks was associated with enhanced cognitive resilience to<br> competitive/self-control challenges, appropriate emotional regulation during emotional tasks, and better modulation of cortisol, cardiovascular and inflammatory<br> responses during psychosocial/mental tasks.<br> Limitations: All studies were cross-sectional, restricting conclusions that can be made. Most studies included only young participants, with some samples of only<br> males or females, and a limited array of HRV indexes. Ecological validity of stressful laboratory tasks remains unclear.<br> Conclusions: Vagally mediated HRV may serve as a global index of an individual's flexibility and adaptability to stressors. This supports the idea of HRV as a plausible,<br> noninvasive, and easily applicable biomarker of MHR. In future longitudinal studies, the implementation of wearable health devices, able to record HRV in naturalistic<br> contexts of real-life, may be a valuable strategy to gain more reliable insight into this topic.</p>
Data for article on "Selectives ("topic markers") on subordinate clauses", published in Linguistics
<p>Dataset for study on "Selectives (“topic markers”) on subordinate clauses" (Appendix F)</p>
Data from: Diversity of land snail tribe Helicini (Gastropoda: Stylommatophora: Helicidae): where do we stand after 20 years of sequencing mitochondrial markers?
<p>Sequences of mitochondrial genes revolutionized the understanding of animal diversity and continue to be an important tool in biodiversity research. In the tribe Helicini, a prominent group of the western Palaearctic land snail fauna, mitochondrial data accumulating since the 2000s helped to newly delimit genera, inform species-level taxonomy, and reconstruct past range dynamics. We combined the published data with own unpublished sequences and provide a detailed overview of what they revealed about the diversity of the group. The delimitation of <i>Helix</i> is revised by placing <i>Helix godetiana</i> back in the genus and new synonymies are suggested within the genera <i>Codringtonia</i> and<i> Helix</i>. The spatial distribution of intraspecific mitochondrial lineages of several species is shown for the first time. Comparisons between species reveal considerable variation in distribution patterns of intraspecific lineages, from broad postglacial distributions to regions with a fine-scale pattern of allopatric lineage replacement. To provide a baseline for further research and information for anyone re-using the data, we thoroughly discuss the gaps in the current dataset, focusing on both taxonomic and geographic coverage. Thanks to the wealth of data already amassed and the relative ease with which they can be obtained, mitochondrial sequences remain an important source of information on intraspecific diversity over large areas and taxa.</p>
Panmixia and active colonisation of the invasive palm Trachycarpus fortunei (Arecaceae) in Southern Switzerland and Northern Italy as inferred by microsatellites and SNP markers
<p>Dataset for the paper named "Panmixia and active colonisation of the invasive palm Trachycarpus fortunei (Arecaceae) in Southern Switzerland and Northern Italy as inferred by microsatellites and SNP markers"</p> <p>GBS analysis:</p> <p>- variants.vcf.gz : compressed non filtered VCF file with 208 samples and 73685 markers on 36195 loci</p> <p>- variants.filt.vcf.gz: Filtered Variant call file (compressed) - Samples with > 50% missing genotypes, and variants with genotype calls in less than 80% of samples are removed; variants with maf < 1% are removed -207 samples and 31312 markers on 19301 loci - 1 samples removed 6CL</p> <p>Microsatellites:</p> <p>TFT.fortunei_Microsatellites_FSTATFINAL_Pop.dat</p> <p>Samples file</p> <p>-Trachycarpus_Samples_sheet.xlsx : list of samples used (lab extractions) </p> <p> </p> <p> </p>
Raw STED Images of MRG markers
<p>Raw image data acquired with STED SP8 Leica microscope.</p> <p>All granule markers were acquired with 55% power of the depletion laser, in U2OS cells. </p> <p>Each file contains a combination of a confocal image of multiple cells and the STED image of zoomed-in fractions of mitochondria in individual cells. </p>
Reduced genetic diversity associated with the northern expansion of an amphibian species with high habitat-specialization, Ascaphus truei, resolved using two types of genetic markers
<p>Reconstruction of historical relationships between geographic regions within a species' range can indicate dispersal patterns and help predict future responses to shifts in climate. <em>Ascaphus truei </em>(coastal tailed frog) is an indicator species of the health of forests and perennial streams in the Coastal and Cascade Mountains of the Pacific Northwest of North America. We used two genetic techniques — microsatellite and genotype-by-sequencing (GBS) — to compare the within region genetic diversity of populations near the northern extent of the species' range (British Columbia, Canada) to two geographic regions in British Columbia and two in Washington, USA, moving towards the core of the range. Allelic richness and heterozygosity declined substantially as latitude increased. The northernmost region had the lowest mean expected heterozygosities for both techniques (microsatellite, M = 0.20, SE = 0.080; GBS, M = 0.025, SE = 0.0010) and the southernmost region had the highest (microsatellite, M = 0.88, SE = 0.054; GBS, M = 0.20, SE = 0.0029). The northernmost regions (NC and MC) clustered together in population structure models for both genetic techniques. Our discovery of reduced diversity may have important conservation and management implications for population connectivity and the response of <em>A. truei</em> to climate change.</p>
T a b l e 4 in Molecular Characterization Of Lates Niloticus (Perciformes, Latidae) Populations From Three Nigerian Waterbodies Using Random Amplified Polymorphic Dna And Microsatellite Markers
T a b l e 4. Microsatellites results
Proteomic analysis of serum markers in patients maintained on Antipsychotics
<p><strong>Background:</strong> Schizophrenia (SZ) and bipolar disorder (BD) share many features: overlap in mood and psychotic symptoms, common genetic predisposition, treatment with antipsychotics (APs), and similar metabolic comorbidities. The pathophysiology of both is still not well defined, and no biomarkers can be used clinically for diagnosis and management. This study aimed to assess the plasma proteomics profile of patients with SZ and BD maintained on APs compared to those who had been off APs for six months and to healthy controls (HCs).</p> <p><strong>Methods:</strong> We analyzed the data using functional enrichment, random forest modeling to identify potential biomarkers, and multivariate regression for the associations with metabolic abnormalities. </p> <p><strong>Results:</strong> We identified several proteins known to play roles in the differentiation of the nervous system like NTRK2, CNTN1, ROBO2, and PLXNC1, which were downregulated in AP-free SZ and BD patients but were "normalized" in those on APs. Other proteins (like NCAM1 and TNFRSF17) were "normal" in AP-free patients but downregulated in patients on APs, suggesting that these changes are related to medications' effects. We found significant enrichment of proteins involved in neuronal plasticity, mainly in SZ patients on APs. Most of the proteins associated with metabolic abnormalities were more related to APs use than having SZ or BD. The biomarkers identification showed specific and sensitive results for schizophrenia, where two proteins (PRL and MRC2) produced adequate results. </p> <p><strong>Conclusions:</strong> Our results confirmed the utility of blood samples to identify protein signatures and mechanisms involved in the pathophysiology and treatment of SZ and BD.</p>
Profiling, monitoring and conserving caterpillar fungus in the Himalayan region using anchored hybrid enrichment markers
<p>The collection of caterpillar fungus accounts for 50-70% of the household income of thousands of Himalayan communities and has an estimated market value of $5-11 billion across Asia. However, Himalayan collectors are at multiple economic disadvantages compared with collectors on the Tibetan plateau because their product is not legally recognized. Using a customized hybrid-enrichment probe set and market-grade caterpillar fungus (with samples up to 30 years old) from 94 production zones across Asia, we uncovered clear geography-based signatures of historical dispersal and significant isolation-by-distance among caterpillar fungus hosts. This high-throughput approach can readily distinguish samples from major production zones with definitive geographical resolution, especially for samples from the Himalayan region that form monophyletic clades in our analysis. Based on these results, we propose a two-step procedure to help local communities authenticate their produce and improve this multi-national trade route without creating opportunities for illegal exports and other forms of economic exploitation. We argue that policy makers and conservation practitioners must encourage the fair trade of caterpillar fungus in addition to sustainable harvesting to support a transboundary conservation effort that is much needed for this natural commodity in the Himalayan region.</p>
Characterization and microsatellite marker development for Geosmithia obscura, a common bark and ambrosia beetle associate
<p class="MsoNormal"><strong><span>Background. </span></strong><span>S</span><span>ymbioses between <em>Geosmithia</em> fungi and </span><span>wood-boring and bark beetles</span><span> seldom result in disease induction within the plant host. Yet exceptions exist such as <em>Geosmithia</em> <em>morbida</em>, the causal agent of Thousand Cankers Disease (TCD) of walnuts and wingnuts and <em>Geosmithia</em> sp. 41, the causal agent of Foamy Bark Canker disease of oaks. Isolates of<em> G. obscura </em>were recovered from black walnut trees in eastern Tennessee and<em> </em>at least one isolate induced cankers following artificial inoculation. Due to the putative pathogenicity and lack of recovery of <em>G. obscura </em>from natural lesions, a molecular diagnostic screening tool was developed using microsatellite markers mined from the <em>G. obscura </em>genome.</span></p> <p class="MsoNormal"><strong><span>Results. </span></strong><span>A total of 3,256 candidate microsatellite markers were identified (2236, 789, 137 di-, tri-, and tetra- motifs were identified, respectively), with 2011, 703, 101 di-, tri-, and tetra- motifs containing markers with primers. From these, 75 microsatellite markers were randomly selected, screened, and optimized, resulting in 28 polymorphic markers that yielded single, consistently recovered bands which were used in downstream analyses. Five of these microsatellite markers were found to be specific to <em>G. obscura </em>and did not cross-amplify into other, closely related species. Although the remaining tested markers could be useful, they cross-amplified within different <em>Geosmithia</em> species, making them not reliable for <em>G. obscura </em>detection.</span></p> <p class="MsoNormal"><strong><span>Conclusion.</span></strong><span> Five novel microsatellite markers (GOBS9, GOBS10, GOBS41, GOBS43, GOBS50) were developed based on <em>G. obscura</em> genome. These species-specific microsatellite markers are available as a tool for use in molecular diagnostics and can assist future surveillance studies.</span></p>
FIG. 8 in Gaming and divination pieces, markers of ownership, or all three? Zooarchaeology and the interpretation of knuckle bones found in tombs of the Iberian necropolis of El Poblado (Coimbra del Barranco Ancho, Murcia, Spain)
FIG. 8. — Knuckle bones found in Tomb 116. Scale bar: 2 cm. Photo credit: J. Gómez Carrasco.
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.