cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13017812.v1
title: All_SNPs.vcf

description: Salinity is a major abiotic constraint for rice farming. Although rice is sensitive to salt stress, tremendous natural variability in world germplasm provides opportunity for both basic and applied research to improve its adaptation under saline environment. The whole genome sequences of two salt tolerant (Pokkali and Nona Bokra) and three salt susceptible (Bengal, Cocodrie, and IR64) rice genotypes were analyzed to provide genetic insights into salt tolerance mechanisms through discovery of DNA polymorphisms and their consequences. The frequency and density of SNPs and InDels was highest in pairs involving Bengal followed by Cocodrie and IR64. Analysis of DNA polymorphisms between salt tolerant and salt susceptible genotypes revealed 2347 nonsynonymous SNPs and 51 frameshift mutations. The integrated analysis of genome-wide polymorphism data with QTL mapping and expression profiling resulted in identification of 396 and 573 differentially expressed genes with large effect variants, which were involved in ion transport, oxidative stress tolerance, signal transduction, stress response, and transcriptional regulation. Overall, the complexity in salt tolerance was clearly apparent due to involvement of genes associated with multiple salt tolerance mechanisms. This study, however, provided a useful genomic resource on salt stress related genes and their variants to design salt tolerant rice varieties.
DOI: 10.6084/m9.figshare.7940990.v1
title: gVCF_NA20544

description: 1000 Genomes gVCF mapped to hs37d5 for NA20544. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.20317179.v1
title: Supplementary Material for: Transfusion-Transmitted Malaria and Mitigation Strategies in Nonendemic Regions

description: <b><i>Background:</i></b> Malaria is a mosquito-borne infectious disease caused by protozoan parasites of the genus <i>Plasmodium</i>. These parasites can be transmitted by blood transfusion especially through Red Cell Blood Concentrates collected from asymptomatic and parasitemic donors. As migration of populations from endemic areas to Europe and overseas recreational travel to endemic regions increase, there is growing risk of transfusion-transmitted malaria (TTM) in nonendemic regions of the world. The present work provides an overview of the mitigation strategies in nonendemic countries and their effectiveness and discusses possible approaches to evolve the strategies in order to maintain both a safe and adequate blood supply. <b><i>Summary:</i></b> The historical and current situation of malaria and TTM in Europe and on the North American continent are described. The infectivity of <i>Plasmodium</i> in blood components and the consequences of TTM are presented, along with the regulations and guidelines for TTM mitigation in Europe, USA, and Canada. The regulations/guidelines currently in place in Europe allow a certain amount of leeway for local policies. A questionnaire was used to survey European countries regarding their current strategies and recent TTM cases. From the questionnaire and published cases, approximately 20 cases of TTM were identified in the past 20 years in the USA and Europe. The vast majority of implicated donors have been former residents of malaria-endemic areas, particularly former residents of hyperendemic areas in Africa. The most recent TTM cases are discussed in detail to provide insight into the gaps in current strategies. The utility and uncertainties of pathogen reduction and serological and molecular testing methods are discussed. <b><i>Key Messages:</i></b> Overall, the risk of transfusion-associated malaria in nonendemic countries is considered to be low and very few TTM cases occurred in these regions in the last 20 years. The questionnaire-based strategy with questions about risk in relation to malaria exposure with or without selective testing based on questioning seems to be relatively effective, although rare and sometimes fatal transmissions still occur. An outstanding question is whether in the future molecular methods may further improve the safety of blood products and help constrain the loss of donors.
DOI: 10.6084/m9.figshare.5127238.v1
title: Supplementary Material for: Crocetin, a Carotenoid Derived from Saffron (<b><i>Crocus sativus</i></b> L.), Improves Acetylcholine-Induced Vascular Relaxation in Hypertension

description: <b><i>Background:</i></b> Hypertension is associated with endothelial dysfunction characterized by decreased vasorelaxation. Crocetin, a bioactive compound of saffron, exhibits favorable cardiovascular properties. We analyze the vasomodulatory effects of crocetin in hypertension. <b><i>Methods:</i></b> Myographical experiments were performed to compare the relaxation induced by acetylcholine (ACH) on aortic rings from normotensive (Wistar) and hypertensive (SHR) rats, incubated with or without crocetin or saffron extract and L-NAME or indomethacin. Extracts were also assayed in deendothelialized rings. UV-vis spectrophotometry and HPLC-DAD were used to characterize and quantify the saffron used. <b><i>Results: </i></b>Crocetin enhanced the ACH relaxations in aorta from hypertensive (strongly) and normotensive rats (weakly). Saffron extract did not modify this. Crocetin plus L-NAME abolished the relaxant response in SHR but not in Wistar aorta. Crocetin plus indomethacin did not modify the indomethacin response in either SHR or Wistar aorta. Crocetin in rubbed segments did not modify the ACH responses. In contrast, saffron increased this response in rubbed segments from SHR but not Wistar rats. <b><i>Conclusion:</i></b> Crocetin exerts healthy vasomodulatory effects in hypertension, strongly improving endothelium-dependent ACH relaxations via endothelial nitric oxide but not the cyclooxygenase pathway. This work proposes that crocetin supplements are a possible complement in the therapy of hypertension.
DOI: 10.25452/figshare.plus.23284622.v1
title: THINGS-data: fMRI Single Trial Responses to Test Stimuli in IT

description: fMRI voxel responses in IT (inferior temporal cortex) to the repeatedly presented test stimuli as part of the THINGS-data collection. `sub-{subject}_TestResponsesIT.npy` contains voxel-wise responses to each presented image. `sub-{subject}_StimulusMetadataTestset.csv` contains additional data about each stimulus, e.g. which session or run it was presented in, or which THINGS category it belongs to. <br> Part of THINGS-data: A multimodal collection of large-scale datasets for investigating object representations in brain and behavior. <br> See related materials in Collection at: https://doi.org/10.25452/figshare.plus.c.6161151
DOI: 10.6084/m9.figshare.17090834.v1
title: Supplementary Material for: Cognitive Predictors of Delirium on Long-Term Follow-Up after TIA and Stroke: Population-Based Cohort Study

description: <b><i>Introduction:</i></b> TIA and stroke cause cognitive impairment with a typical “vascular” pattern, including prominent frontal/executive deficits. Cognitive impairment is associated with increased delirium risk and the few available data suggest that executive dysfunction is important. We therefore determined the predictive value of both severity and pattern of cognitive deficits for delirium on long-term follow-up after TIA/stroke. <b><i>Methods:</i></b> Surviving TIA/stroke participants on October 1, 2013, in the Oxford Vascular Study (OXVASC) were assessed prospectively for delirium during all hospitalizations over the subsequent 6 months. Associations between OXVASC pre-admission mini-mental state examination (MMSE) and Montreal Cognitive Assessment (MoCA) scores, and delirium during hospitalizations on follow-up were determined using logistic regression adjusted for covariates, including demographic factors, history of depression, baseline stroke severity, and admission illness severity. <b><i>Results:</i></b> Among 1,565 TIA/stroke survivors, 158 patients (mean/SD age = 79.2/11.5 years) had ≥1 admission and 59 (37%) had ≥1 delirium episode. Mean/SD time between baseline TIA/stroke and admission was 4.7/3.6 years and between most recent OXVASC cognitive testing and admission was 1.7/1.8 years. MMSE and MoCA scores were associated with delirium: odds ratio (OR) = 1.16 (95% CI 1.07–1.27, <i>p</i> &lt; 0.0001 per point decrease in MMSE) and OR = 1.20 (1.11–1.30, <i>p</i> &lt; 0.0001 MoCA) and associations were robust to adjustment for all covariates, including stroke severity: OR = 1.11 (1.01–1.22, <i>p</i> = 0.03, MMSE) and OR = 1.15 (1.05–1.25, <i>p</i> = 0.003, MoCA). All 10 subtests on the MoCA and 4/11 on the MMSE were significantly associated with delirium with highest predictive value for frontal/executive and recall domains. <b><i>Conclusions:</i></b> Cognitive impairment of increasing severity after TIA/stroke predisposed to delirium particularly deficits in frontal/executive domains and recall. Long-term risk of delirium should be considered as part of the overall cerebrovascular disease burden.
DOI: 10.6084/m9.figshare.12423776.v3
title: Autoantibodies measured in plasma samples from the TACERA Study

description: A Luminex bead-based antigen array (Protagen-AG) was used to measure the autoantibody response against 192 human protein antigens at baseline and 6 months in plasma samples in early Rheumatoid Arthritis (RA) patients and healthy controls. <br>RA Patients recieved methotrexate at baseline.
DOI: 10.6084/m9.figshare.24578740.v2
title: CI/CD repos with tools

description: CI/CD repositories with tools used
DOI: 10.6084/m9.figshare.25105901.v1
title: Chibatamoto FBC Data Set.xlsx

description: <b>Background:</b> Breast cancer continues to be a public health issue in Botswana. However, there is limited evidence on the association of risk factors with the stages at which diagnosis is done. This study provides evidence on association between risk factors and the stages at which breast cancer is diagnosed among adult females in Botswana.<b>Methods</b>: A cross‐sectional study of 211 Botswana adult women with confirmed breast cancer at public oncology centers was conducted over 10 months in 2022. Data on known risk factors was collected, and statistical tests performed using STATA.<b>Results:</b><b> </b>The median age of participants at the time of first diagnosis was 50 years. Forty-six percent (46%) of the diagnosed women had advanced stages of breast cancer. Univariate analysis showed significant association of the following four factors with late breast cancer diagnosis; single and never married (OR 0.18, 95% CI: 0.036-0.932), history of iregular menses (OR 1.63, 95% CI: 1.013-2.627), breast cup size (OR 0.57, 0.336-0.968), and age at first full-time pregnancy (OR 0.86, 0.606-1.209). In a bivariate analysis, occupation (p = 0.029), age at first full-term pregnancy (p = 0.042) and type of current breast cancer (p = 0.002) were observed to be associated with late breast cancer diagnosis among women in Botswana. In a multivariate analysis, known second degree family history (OR 0.34, 95% CI: 0.129-0.893) and ductal carcinoma (OR 2.56, 95% CI: 1.083-6.071) were significant predictors of late breast cancer diagnosis among women in four cancer designated catchment centres in Botswana.<b>Conclusion:</b> Women in Botswana present with advanced stages of breast cancer at time of first diagnosis. The risk factors associated with this delayed diagnosis have been identified. We recommend upscaled campaigns targeting women to raise awareness of risk factors and the importance of early detection and access to care.
DOI: 10.6084/m9.figshare.842633.v1
title: HitCompanies Dataset

description: Worldwide Companies Dataset contains information on random 10,000 worldwide companies, including name, registration number, website url, addresses, phone numbers, industry codes, aliases, associated domain names and key changes such as people changes, contact changes, etc.<br><br>Original data available at http://endb-consolidated.aihit.com/datasets.htm
DOI: 10.6084/m9.figshare.21707129.v12
title: Effects of Epidural Analgesia at 1 cm Cervical Dilatation on Labor Interventions in Full-term Primigravida: A Retrospective Cohort Study

description: <strong>Effects of Epidural Analgesia at 1 cm Cervical Dilatation on Labor Interventions in Full-term Primigravida: A Retrospective Cohort Study</strong>
DOI: 10.6084/m9.figshare.24012786.v1
title: 城市水体高光谱图像

description: 用于监测城市地表水质的城市水体高光谱图像。
DOI: 10.6084/m9.figshare.22188802.v4
title: Test Cases for A Smart Switch Configuration and Reliability Assessment Method for Offshore Wind Farm Electrical Collector System

description: This is the dataset for paper: A Smart Switch Configuration and Reliability Assessment Method for Offshore Wind Farm Electrical Collector System
DOI: 10.6084/m9.figshare.14346959.v1
title: Data from: A farewell to EQ: A new brain size measure for comparative primate cognition

description: Both absolute and relative brain size vary greatly among and within the major vertebrate lineages. Scientists have long debated how larger brains in primates and hominins translate into greater cognitive performance, and in particular how to control for the relationship between the non-cognitive functions of the brain and body size. One solution to this problem is to establish the slope of cognitive equivalence, that is the line connecting organisms with an identical bauplan but different body sizes. The original approach to estimate this slope through intraspecific regressions was abandoned after it became clear that it generated slopes that were too low by an unknown margin due to estimation error. Here, we revisit this method. We control for the error problem by focusing on highly dimorphic primate species with large sample sizes and fitting a line through the mean values for adult females and males. We obtain the best estimate for the slope of ca 0.27, a value much lower than those constructed using all mammal species, and close to the value expected based on the genetic correlation between brain size and body size. We also find that the estimate of cognitive brain size based on cognitive equivalence fits empirical cognitive studies better than the encephalization quotient (EQ), which should therefore be avoided in future studies on primates, and presumably mammals and birds in general. The use of residuals from the line of cognitive equivalence may change conclusions concerning the cognitive abilities of extant and extinct primate species, including hominins.
DOI: 10.6084/m9.figshare.28692515.v3
title: <b>Molecular mechanism of phenol 2-monooxygenase (FgPhm)</b><b>in regulating virulence and DON biosynthesis in </b><b><i>Fusarium graminearum</i></b>

description: this study has demonstrated that FgPhm1 is crucial for the growth and development of F. graminearum and the production of Deoxynivalenol (DON), and plays an important role in the pathogenicity and stress response processes of F. graminearum. Through depth research on phenol2-monooxygenase, it lays a foundation for fundamentally revealing the mechanism of action of phenol2-monooxygenase during the growth and development process of F. graminearum, and reveals the relationship between phenol metabolism and the pathogenic mechanism in F. graminearum. Thiswill provides a theoretical basis for the development of new pesticides and the prevention and control of Fusarium head blight of wheat.
DOI: 10.6084/m9.figshare.14336609.v1
title: What happens when individuals answer questionnaires in two different languages

description: This is the data used in the article: "What happens when individual answer questionnaires in two different languages". The aim of the study was to compare scores from the English and the Spanish versions of two well-known measures of psychological distress using a within-subject approach. This method involved bilingual participants completing both measures in four conditions. For two groups of people, measures were offered in the same language both times and for the other two groups, each language version was offered, the order differing between the groups. The measures were the Clinical Outcomes in Routine Evaluation-Outcome Measure (CORE-OM; Evans et al., 2000, 2002)(CORE-OM; Evans et al., 2000, 2002)(CORE-OM; Evans et al., 2000, 2002)and the Schwartz Outcome Scale-10, both originally created in English and then translated to Spanish. The responses of 167 participants are included for the first occasion, of those 109 participants responded also to the second occasion. Participants are divided in four groups:) English on both occasions (EE), 2) English the first occasion and Spanish on the second occasion (ES), 3) Spanish the first occasion and English on the second occasion (SE), and 4) Spanish on both occasions (SS)
DOI: 10.6084/m9.figshare.26832475.v1
title: images_part_2

description: Camera trap imagery has become an invaluable asset in contemporary wildlife surveillance, enabling researchers to observe and investigate the behaviors of wild animals. While existing methods rely solely on image data for classification, this may not suffice in cases of suboptimal animal angles, lighting, or image quality. We approach this problem by integrating metadata with images.
DOI: 10.6084/m9.figshare.27906315.v1
title: Data and R code needed to perform species interaction occupancy analyses for Spatio-temporal Interactions Facilitate Sympatry in a Diverse Mammalian Community

description: Understanding mechanisms underlying coexistence among potential competitors, and between predators and prey, is a persistent challenge in community ecology. Using 6-yrs (2013–2018) of camera-trapping data and species interaction models, we investigated spatio-temporal pattern of inter- and intra-guild interspecific interactions in a diverse terrestrial mammalian community in Pakke Tiger Reserve (PTR), Northeast India. We found no evidence of spatial interaction among apex predators (tiger <i>Panthera tigris,</i> leopard <i>Panthera pardus </i>and dhole <i>Cuon alpinus</i>). However, dholes temporally separated themselves from tigers and leopards. Among small carnivores, marbled cat (<i>Pardofelis marmorata</i>) and leopard cat (<i>Prionailurus bengalensis</i>) exhibited temporal separation, whereas leopard cat overlapped spatially and temporally with other small carnivores. Herbivores exhibited neither spatial nor temporal separation with each other. All apex predators exhibited diel activity and space use patterns to overlap with their preferred prey. Our results suggest that the assembly of the diverse mammalian community of PTR is a complex process, and coexistence among potential competitors, and predators and prey is likely facilitated by several mechanisms including spatial and temporal segregation, and potentially dietary separation.<br><br>
DOI: 10.6084/m9.figshare.15167061.v4
title: Global Asymmetry of Hot Flow Anomaly

description: Partial data and figures for paper " Global Asymmetry of Hot Flow Anomaly<br>" by Yu Lin et al.(2021). You could contact @ ylin01@auburn.edu and/or wangxue@auburn.edu to get more data.<br>
DOI: 10.6084/m9.figshare.20491026.v1
title: Data from "Burrowing depth mediates the extent of metabolic suppression in a soil-overwintering insect"

description: <em>Metadata are provided in each data sheet. Links to a Shiny app of an interactive simulation, and the underlying R script (on GitHub) are provided below. Refer to manuscript for full details.</em> <br> <strong>Abstract</strong> 1. Conserving energy through winter is important for the fitness of temperate insects. While insects can use buffered microhabitats, metabolic suppression, or decreases in the thermal sensitivity of metabolic rate to override seasonal-scale thermal trends, the relative importance of these strategies for limiting energy use by insects overwintering in soil remains largely underexplored. 2. We used a combined laboratory, field, and simulation approach to investigate the overwintering energetics of the western bean cutworm (<em>Striacosta albicosta</em>), a univoltine lepidopteran pest of dry beans and corn that overwinters underground as a dormant prepupa. 3. We hypothesized that (1) the selection of thermally-buffered microhabitats (<em>i.e.</em> deeper soil sites) reduces energy use in early autumn and late spring, and that (2) changes in the metabolic rate-temperature relationship reduce the impact of elevated temperatures on overwintering energy use. 4. We provide evidence that during the warmest parts of winter, dormant <em>S. albicosta</em> prepupae that had burrowed deep benefited from a cool, stable microclimate, whereas those near the soil surface appeared to rely on deeper metabolic suppression to maintain their energy stores. 5. Although elevated temperatures in the laboratory depleted their energy reserves, these strategies appear sufficient to limit energy drain under natural conditions in the field. 6. We suggest that small-scale variation in the depth of soil refuges may mediate the interaction between the risk of energy drain and changes in the metabolic rate-temperature relationship in soil-overwintering insects. <br> <br>
DOI: 10.6084/m9.figshare.28573908.v1
title: Partially Linear Single-Index Models and Functional Principal Component Analysis of Spatially and Temporally Indexed Point Processes

description: We model spatially and temporally indexed point process data as a multi-level log-Gaussian Cox process where the log intensity function depends on a partially linear single-index structure of spatio-temporal covariates and three latent functional random effects representing the spatial and temporal random effects as well as their interactions. We assume that the latent functional effects are Gaussian processes with Karhunen-Loève representations, and model the unknown link function of the single-index as well as the covariance functions of the latent functional effects as splines. We propose to estimate the partially linear coefficients and the single-index link function using a Poisson maximum likelihood method, and the covariance functions of the latent processes using maximum composite likelihood methods. We also propose approaches to predict the functional principal component scores. Under the multi-level dependence structure and allowing the spatio-temporal covariates to be non-stationary, the proposed estimators follow rather unconventional convergence rates which depend on both the number of locations and the number of repeated measures in time. We illustrate the proposed methods through simulation studies and a real-data application in modeling bike-sharing events.
DOI: 10.6084/m9.figshare.3465356.v1
title: Supplementary Material for: Effects of Lithium Monotherapy for Bipolar Disorder on Gene Expression in Peripheral Lymphocytes

description: <b><i>Background:</i></b> This study investigated the effect of lithium monotherapy on peripheral lymphocyte gene expression in bipolar disorder (BD). <b><i>Method:</i></b> Twenty-two medication-free bipolar subjects (11 hypomanic, 11 depressed) were started on lithium monotherapy. Closely matched healthy subjects (n = 15) were included as controls but did not receive treatment. Blood RNA samples were collected at baseline and after 2 and 8 weeks of treatment. RNA expression was measured using the Affymetrix GeneChip® Human Gene 1.0 ST Array followed by Ingenuity pathways analysis. The results for the contrast of weeks 2 and 8 were not significantly different and were combined. <b><i>Results:</i></b> In BD subjects, 56 genes showed significant (false discovery rate &lt;0.1) expression changes from baseline; the effect sizes and directions for all of these were similar at weeks 2 and 8. Among these were immune-related genes (IL5RA, MOK, IFI6, and RFX2), purinergic receptors (P2RY14, P2RY2, and ADORA3) and signal transduction-related genes (CAMK1 and PIK3R6). Pathway and upstream regulator analysis also revealed that lithium altered several immune- and signal transduction-related functions. Differentially expressed genes did not correlate with week 8 clinical response, but other genes involved in protein synthesis and degradation did. <b><i>Conclusion:</i></b> Peripheral gene expression may serve as a biomarker of lithium effect.