cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22059481.v1
title: Transcriptome profiling of bovine endometrial epithelial cells induced by lipopolysaccharides <i>in vitro</i>

description: Endometritis is an inflammation of the surface of the endometrium that does not penetrate the submucosa and can cause infertility and increase the elimination rate in cows. Endometrial epithelial cells are the first barrier of the endometrium against foreign stimuli and bacterial infection. Understanding the genetic changes in stimulated endometrial epithelial cells will help in the efforts to prevent and treat endometritis. This study investigated changes in bovine endometrial epithelial (BEEC) gene expression induced by lipopolysaccharide (LPS)-induced inflammation and compared transcriptome-wide gene changes between LPS- and phosphate-buffered saline (PBS)- treated BEECs by RNA sequencing. Compared with the PBS group, the LPS group showed 60 differentially expressed genes (DEGs) (36 upregulated, 24 downregulated). Gene Ontology enrichment analysis revealed that most enrichment occurred during CXCR chemokine receptor binding, inflammatory response, and neutrophil migration. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed DEGs mainly concentrated in cytokine–cytokine receptor interactions; IL-17, tumor necrosis factor, NOD-like receptor, chemokine, Toll-like receptor, and nuclear factor-κB signaling pathways; and the cytoplasmic DNA sensing pathway. Moreover, results revealed that cytokines <i>SAA3</i> and <i>HP</i> increased significantly after LPS treatment. These effects of LPS on BEECs transcriptome and the molecular mechanism of endometritis provide a basis for improved clinical treatment and novel drug development.
DOI: 10.6084/m9.figshare.24324668
title: Tracing the genetic footprints: India’s role as a gateway for pig migration and domestication across continents

description: This study explored the maternal genetic diversity in the pig genetic resources of India by analyzing a mitochondrial D-loop fragment and comparing it with the corresponding sequences of previously published studies involving domestic pigs and wild boars. Sequencing of 103 samples representing different domestic pig populations revealed existence of 32 maternal haplotypes. The indices of haplotype and nucleotide diversity in Indian domestic pigs were 0.9421 and 0.015, respectively. Median-Joining network revealed that Indian pigs belong to Clade A and show conformity to 6 haplogroups reported worldwide (D1a, D1a1, D1a2, D1e, D1h and D3a). Among these, D1e and D1a2 were shared with Asian wild boars too. Interestingly, haplotype sharing was evident between Indian pigs and samples from other countries representing Africa, Asia, Europe and Oceania. This study substantiates India’s contribution as a possible pig domestication center and highlights the importance of the Indian subcontinent in dispersal of the species to other continents. Additionally, genetic evidence suggested the influence of trading routes and historical interactions in shaping pig genetic exchange. Overall, this investigation provides valuable insights into the genetic diversity, historical migration, and domestication of Indian domestic pigs, contributing to the broader understanding of global pig genetic resources and their evolutionary history.
DOI: 10.6084/m9.figshare.24324668.v1
title: Tracing the genetic footprints: India’s role as a gateway for pig migration and domestication across continents

description: This study explored the maternal genetic diversity in the pig genetic resources of India by analyzing a mitochondrial D-loop fragment and comparing it with the corresponding sequences of previously published studies involving domestic pigs and wild boars. Sequencing of 103 samples representing different domestic pig populations revealed existence of 32 maternal haplotypes. The indices of haplotype and nucleotide diversity in Indian domestic pigs were 0.9421 and 0.015, respectively. Median-Joining network revealed that Indian pigs belong to Clade A and show conformity to 6 haplogroups reported worldwide (D1a, D1a1, D1a2, D1e, D1h and D3a). Among these, D1e and D1a2 were shared with Asian wild boars too. Interestingly, haplotype sharing was evident between Indian pigs and samples from other countries representing Africa, Asia, Europe and Oceania. This study substantiates India’s contribution as a possible pig domestication center and highlights the importance of the Indian subcontinent in dispersal of the species to other continents. Additionally, genetic evidence suggested the influence of trading routes and historical interactions in shaping pig genetic exchange. Overall, this investigation provides valuable insights into the genetic diversity, historical migration, and domestication of Indian domestic pigs, contributing to the broader understanding of global pig genetic resources and their evolutionary history.
DOI: 10.6084/m9.figshare.23144100.v1
title: Development and evaluation of gold nanoprobe based lateral flow device for rapid and sensitive serodetection of Bluetongue in sheep

description: Bluetongue (BT) disease is a viral, insect borne, noncontagious illness of small ruminants caused by <i>Orbivirus</i>, impacting huge economic loss worldwide. The existing BT diagnostic techniques are costly, time-consuming and require both specialized equipment and also skilled personnel. So there is need to develop a rapid, sensitive, on site detection assay for diagnosis of BT. This study utilized secondary antibody derivatized Gold nanoprobes for rapid and sensitive detection of BT over lateral flow device (LFD). The detection limit for this assay was found 1.875 µg of BT IgG/ml and a comparison between LFD and indirect ELISA was performed and the sensitivity and specificity was found at 96% and 99.23%, respectively, with observed kappa value of 0.952. This developed LFD may therefore offer a quick, affordable and accurate diagnosis of BT disease at the field level.
DOI: 10.6084/m9.figshare.22109066
title: Screening of lncRNA profiles during intramuscular adipogenic differentiation in <i>longissimus dorsi</i> and <i>semitendinosus</i> muscles in pigs

description: Intramuscular fat content is an important factor that determines meat quality in pigs. In recent years, epigenetic regulation has increasingly studied the physiological model of intramuscular fat. Although long noncoding RNAs (lncRNAs) play essential roles in various biological processes, their role in intramuscular fat deposition in pigs remains largely unknown. In this study, intramuscular preadipocytes in the <i>longissimus dorsi</i> and <i>semitendinosus</i> of Large White pigs were isolated and induced into adipogenic differentiation in vitro. High-throughput RNA-seq was carried out to estimate the expression of lncRNAs at 0, 2 and 8 days post-differentiation. At this stage, 2135 lncRNAs were identified. KEGG analysis showed that the differentially expressed lncRNAs were common in pathways involved with adipogenesis and lipid metabolism. lnc_000368 was found to gradually increase during the adipogenic process. Reverse-transcription quantitative polymerase chain reaction and a western blot revealed that the knockdown of lnc_000368 significantly repressed the expression of adipogenic genes and lipolytic genes. As a result, lipid accumulation in porcine intramuscular adipocytes was impaired by the silencing of lnc_000368. Overall, our study identified a genome-wide lncRNA profile related to porcine intramuscular fat deposition, and the results suggest that lnc_000368 is a potential target gene that might be targeted in pig breeding in the future.
DOI: 10.6084/m9.figshare.19611342
title: Transcriptomic analysis to elucidate the response of <i>Apis mellifera</i> ligustica brain tissue to fluvalinate exposure

description: As a commonly used acaricide in apiculture, fluvalinate is used to kill Varroa mites, while it also damages the nervous system of honeybees. To date, the transcriptomic characteristics associated with fluvalinate-induced neuronal injury in the bee brain have not been reported. Here, we performed transcriptome sequencing on <i>Apis mellifera</i> ligustica (<i>A. mellifera</i> ligustica) brain tissues collected before and after fluvalinate treatment. A total of 546 differentially expressed genes (DEGs) were detected, and these DEGs mainly showed 4 different expression patterns. Further analysis revealed that DEGs with different expression patterns were mainly involved in lipid metabolism, amino acid metabolism, visual transduction, and neural response-related GO terms and KEGG pathways. Moreover, protein–protein interaction network analysis revealed five protein-coding DEGs as key genes, which may play important roles in the resistance to fluvalinate-induced honeybee brain nerve tissue damage. In summary, this study is the first to perform a detailed characterization and functional analysis of genes related to fluvalinate stimulation in honeybee brains.
DOI: 10.6084/m9.figshare.22059478.v1
title: Association of single nucleotide polymorphisms in heat stress protein 70 (<i>HSP70</i>) and 90 (<i>HSP90</i>) with the susceptibility of Pakistani sheep breeds to hemoparasitic infections

description: The present study was designed to report the genotypic and allelic frequency of single nucleotide polymorphism (SNP) at 222 G &gt; A in <i>HSP70</i> and at ex6-7390T22G in the <i>HSP90</i> gene of 204 sheep (Baluchi = 11, Kajli = 29, Latti = 06 and Mundri = 158) enrolled from District Rajanpur in Punjab and to report the susceptibility of these sheep to the blood-borne parasitic infection. The tetra-primer amplification refractory mutation system–polymerase chain reaction (T-ARMS–PCR) approach revealed a significant variation (<i>p</i> &lt; 0.001) in the genotype frequency of four enrolled sheep breeds at SNP 222 G &gt; A in the <i>HSP70</i> gene while the allelic frequency remained unaffected (<i>p</i> = 0.08). In all sheep breeds, GG (wild) genotype was most common. T-ARMS–PCR analysis revealed a similar trend for ex6-7390T22G in the <i>HSP90</i> gene and it was observed that sheep had significantly higher wild-type (GG) (<i>p</i> &lt; 0.05) at the studied SNPs. Studied epidemiological factors (sex and sampling sites) were not found associated with both SNPs. Chi-square test revealed that no specific genotype and allelic frequency at 222 G &gt; A in <i>HSP70</i> and at ex6-7390T22G in the <i>HSP90</i> gene of the enrolled sheep breed was associated with the susceptibility to blood-borne parasitic infection (<i>p</i> &gt; 0.05). In conclusion, we are reporting that Pakistan is blessed to have majority of sheep, from all breeds, having wild genotype at analyzed SNPs in heat stress genes. We highly recommend the genotypic screening of sheep before their selection as breeders to reduce the possibility of having sheep with polymorphic genotypes at 222 G &gt; A in <i>HSP70</i> and at 7390T22G in <i>HSP90</i> genes that will improve the profitability and sustainability of animal production systems in Pakistan.
DOI: 10.6084/m9.figshare.23634376.v1
title: Allele mining in prolactin receptor gene and its association with some economic traits in Egyptian goat breeds

description: The objectives of the current study were to identify polymorphism in the prolactin receptor (PRLR) gene among three Egyptian goat breeds (Zaraibi, Damascus, and Barki) and to investigate the association between PRLR genotype, parity, season of kidding, and litter size factors with milk yield and reproductive traits of Zaraibi goats. One hundred and ninety blood samples were collected for DNA extraction, with 110 from Zaraibi, 40 from Barki, and 40 from Damascus breeds. Three genotypes, CC, CT and TT, for the prolactin receptor gene were identified in the 190 DNA samples using restriction fragment length polymorphism and were confirmed by direct sequencing technique. Milk yield during suckling and lactation periods in addition to age at first conception, gestation length, and litter size were determined in 110 Zaraibi goats. The Zaraibi goats recorded the highest heterozygosity (0.495) and the effective number of alleles (1.972). The g.62130C &gt; T SNP showed a significant association (<i>p</i> &lt; 0.01) with suckling, lactation, and total milk yield of Zaraibi goats with the highest values recorded at the third parity. Age at the first conception and gestation length traits were significantly influenced by the kidding season (<i>p</i> &lt; 0.05) with younger age in autumn and shorter length in spring seasons. Milk yield during the suckling period was significantly (<i>p</i> &lt; 0.01) higher in the case of triplets’ litter size. The current study showed that litter size and parity played an important role in the amount of Zaraibi goats’ milk yield. The g.62130C &gt; T SNP of the PRLR gene may be a useful marker for assisted selection programs to improve goat milk yield during suckling and lactation periods with the heterozygous genotype CT recording the highest values.
DOI: 10.6084/m9.figshare.22059478
title: Association of single nucleotide polymorphisms in heat stress protein 70 (<i>HSP70</i>) and 90 (<i>HSP90</i>) with the susceptibility of Pakistani sheep breeds to hemoparasitic infections

description: The present study was designed to report the genotypic and allelic frequency of single nucleotide polymorphism (SNP) at 222 G &gt; A in <i>HSP70</i> and at ex6-7390T22G in the <i>HSP90</i> gene of 204 sheep (Baluchi = 11, Kajli = 29, Latti = 06 and Mundri = 158) enrolled from District Rajanpur in Punjab and to report the susceptibility of these sheep to the blood-borne parasitic infection. The tetra-primer amplification refractory mutation system–polymerase chain reaction (T-ARMS–PCR) approach revealed a significant variation (<i>p</i> &lt; 0.001) in the genotype frequency of four enrolled sheep breeds at SNP 222 G &gt; A in the <i>HSP70</i> gene while the allelic frequency remained unaffected (<i>p</i> = 0.08). In all sheep breeds, GG (wild) genotype was most common. T-ARMS–PCR analysis revealed a similar trend for ex6-7390T22G in the <i>HSP90</i> gene and it was observed that sheep had significantly higher wild-type (GG) (<i>p</i> &lt; 0.05) at the studied SNPs. Studied epidemiological factors (sex and sampling sites) were not found associated with both SNPs. Chi-square test revealed that no specific genotype and allelic frequency at 222 G &gt; A in <i>HSP70</i> and at ex6-7390T22G in the <i>HSP90</i> gene of the enrolled sheep breed was associated with the susceptibility to blood-borne parasitic infection (<i>p</i> &gt; 0.05). In conclusion, we are reporting that Pakistan is blessed to have majority of sheep, from all breeds, having wild genotype at analyzed SNPs in heat stress genes. We highly recommend the genotypic screening of sheep before their selection as breeders to reduce the possibility of having sheep with polymorphic genotypes at 222 G &gt; A in <i>HSP70</i> and at 7390T22G in <i>HSP90</i> genes that will improve the profitability and sustainability of animal production systems in Pakistan.
DOI: 10.6084/m9.figshare.23634376
title: Allele mining in prolactin receptor gene and its association with some economic traits in Egyptian goat breeds

description: The objectives of the current study were to identify polymorphism in the prolactin receptor (PRLR) gene among three Egyptian goat breeds (Zaraibi, Damascus, and Barki) and to investigate the association between PRLR genotype, parity, season of kidding, and litter size factors with milk yield and reproductive traits of Zaraibi goats. One hundred and ninety blood samples were collected for DNA extraction, with 110 from Zaraibi, 40 from Barki, and 40 from Damascus breeds. Three genotypes, CC, CT and TT, for the prolactin receptor gene were identified in the 190 DNA samples using restriction fragment length polymorphism and were confirmed by direct sequencing technique. Milk yield during suckling and lactation periods in addition to age at first conception, gestation length, and litter size were determined in 110 Zaraibi goats. The Zaraibi goats recorded the highest heterozygosity (0.495) and the effective number of alleles (1.972). The g.62130C &gt; T SNP showed a significant association (<i>p</i> &lt; 0.01) with suckling, lactation, and total milk yield of Zaraibi goats with the highest values recorded at the third parity. Age at the first conception and gestation length traits were significantly influenced by the kidding season (<i>p</i> &lt; 0.05) with younger age in autumn and shorter length in spring seasons. Milk yield during the suckling period was significantly (<i>p</i> &lt; 0.01) higher in the case of triplets’ litter size. The current study showed that litter size and parity played an important role in the amount of Zaraibi goats’ milk yield. The g.62130C &gt; T SNP of the PRLR gene may be a useful marker for assisted selection programs to improve goat milk yield during suckling and lactation periods with the heterozygous genotype CT recording the highest values.
DOI: 10.22003/xfel.eu-data-007036-00
title: SXP optimization for 2024-I
DOI: 10.5281/zenodo.10371450
title: Data for:  Electroluminescence as a probe of strong exciton-plasmon coupling in few-layer WSe2
DOI: 10.5281/zenodo.10371451
title: Data for:  Electroluminescence as a probe of strong exciton-plasmon coupling in few-layer WSe2
DOI: 10.15468/dl.99mr7w
title: Occurrence Download

description: A dataset containing 128364 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Xerces Society - Bumble Bee Watch"
 ]
}

 The dataset includes 128364 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021651-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7kyq7k
title: Occurrence Download

description: A dataset containing 1193 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "DatasetKey is one of (HBRG Insects Dataset Vol 1, HBRG Insects Dataset Vol 2, BeeWalk bumblebee distributions for Great Britain 2008-2022)",
 "GadmGid is one of (GBR.3_1, GBR.3.13_1)",
 "OccurrenceStatus is Present",
 "TaxonKey is Bombus distinguendus Morawitz, 1869",
 "Year 1970-2025"
 ]
}

 The dataset includes 1193 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021659-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.13221821
title: The Comics Grid: Journal of Comics Scholarship: Number of Published Articles per Volume 2013-2020

description: Data collated and shared by Ernesto Priego, November 2020.<br>Source: https://www.comicsgrid.com/issue/archive/.<br>Data includes one extra article not yet published in 2020- this has been deposited here so that it can be cited in that article.<br>Once the final article is published the data here will match that on the archive linked above and in the references. <br>
DOI: 10.6084/m9.figshare.13221821.v1
title: The Comics Grid: Journal of Comics Scholarship: Number of Published Articles per Volume 2013-2020

description: Data collated and shared by Ernesto Priego, November 2020.<br>Source: https://www.comicsgrid.com/issue/archive/.<br>Data includes one extra article not yet published in 2020- this has been deposited here so that it can be cited in that article.<br>Once the final article is published the data here will match that on the archive linked above and in the references. <br>
DOI: 10.21227/359t-0665
title: DIABETIC RETINOPATHY- FUNDUS IMAGE DATASET(AGAR300)

description: Diabetic Retinopathy is the second largest cause of blindness in diabetic patients. Early diagnosis or screening can prevent the visual loss. Nowadays , several computer aided algorithms have been developed to detect the early signs of Diabetic Retinopathy ie., Microaneurysms. The AGAR300 dataset presented here facilitate the researchers for benchmarking MA detection algorithms using digital fundus images. Currently, we have released the first set of database which consists of 28 color fundus images, shows the signs of Microaneurysm. The images were captured in 45-degree field-of-view with resolution of 2448x3264. An article describing the results using AGAR300 was published in Biomedical Signal Processing and Control, Elsevier. This database images can be freely downloaded and used for research purposes with proper citation. The AGAR300 Microaneurysms dataset will be available online and more images can be submitted via this IEEE DataPort in future.
DOI: 10.21227/qpwg-kc04
title: Effect of Paddy Rice vegetation on path-loss between CC2650 SoC based sensor nodes operating at 2.4 GHz Radio Frequency (RF)

description: Here we introduce so-far the largest subject-rated database of its kind, namely, "Effect ofPaddy Ricevegetation on path-loss betweenCC2650 SoC 32-bit Arm Cortex-M3based sensor nodes operating at2.4 GHzRadio Frequency (RF)".This database contains received signal strengthmeasurementscollected through campaigns in theIEEE 802.15.4standard precision agricultural monitoring infrastructure developed for Paddy rice crop monitoring from period03/07/2019 to 18/11/2019.
DOI: 10.5281/zenodo.4268408
title: Brittle faulting of ductile rock induced by pore fluid pressure build-up

description: his is the ReadMe file corresponding to the study entitled: "Brittle faulting of ductile rock induced by pore fluid pressure build-up" By Noël C., Passelègue X. F., Violay M. This study is under review at JGR: Solid Earth This Read-Me file has been last edited in November 2020 This readme file describes the data repository and supplementary files accompanying the above publication. <br> For any further queries please contact corentin.noel@epfl.ch
DOI: 10.6073/pasta/2ebb7f5e89391d3caada53acd8c9a5d7
title: North Temperate Lakes LTER: Pelagic Macroinvertebrate Summary 1983 - current

description: This is a summary of dataset NTL 13. Derived data include the mean and standard deviation of the number of each species captured as well as the mean and standard deviation of the density of individuals on both an areal and volumetric basis. Five vertical tows are done at the deepest point of each of the seven primary lakes in the Trout Lake area (Allequash, Big Muskellunge, Crystal, Sparkling, and Trout lakes and bog lakes 27-02 [Crystal Bog], and 12-15 [Trout Bog]) using a 1-mm mesh net with a 1-m wide mouth. On Trout Lake four additional sites are sampled, where depths are approximately at 10 m, 15 m, 20 m, and 25 m respectively, with three tows done at each site. Trout Lake was the only lake sampled in 2020. All samples are taken in darkness. Samples are preserved and counted, yielding numbers caught. These night tows target the large invertebrate planktivore component of the pelagic zooplankton community. Sampling Frequency: annually Number of sites: 11
DOI: 10.6084/m9.figshare.13222070
title: Structural determination of fasamycin and formicamycin congeners isolated from regulator mutants of S. formicae

description: Structural determination of fasamycin and formicamycin congeners isolated from regulator mutants of S. formicae. See manuscript for details including methodology.