cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13521521.v1
title: Supplementary Material for: Comparative Genome-Wide Characterization of Microsatellites in <b><i>Candida albicans</i></b> and <b><i>Candida dubliniensis</i></b> Leading to the Development of Species-Specific Marker

description: <b><i>Background:</i></b> Microsatellites or simple sequence repeats (SSR) are related to genomic structure, function, and certain diseases of taxonomically different organisms. <b><i>Objective:</i></b> To characterize microsatellites in two closely related <i>Candida</i> species by searching and comparing 1–6 bp nucleotide motifs and utilizing them to develop species-specific markers. <b><i>Methods:</i></b> Whole-genome sequence was downloaded from the public domain, microsatellites were mined and analyzed, and primers were synthesized. <b><i>Results:</i></b> A total of 15,821 and 7,868 microsatellites, with mono-nucleotides (8,679) and trinucleotides (3,156) as most frequent microsatellites, were mined in <i>Candida dubliniensis</i> and <i>Candida albicans</i>, respectively. Chromosome size was found positively correlated with microsatellite number in both the species, whereas it was negatively correlated with the relative abundance and density of microsatellites. A number of unique motifs were also found in both the species. Overall, microsatellite frequencies of each chromosome in <i>C. dubliniensis</i> were higher than in <i>C. albicans</i>. <b><i>Conclusion:</i></b> The features of microsatellite distribution in the two species’ genomes revealed that it is probably not conserved in the genus <i>Candida</i>. Data generated in this article could be used for comparative genome mapping and understanding the distribution of microsatellites and genome structure between these closely related and phenotypically misidentified species and may provide a foundation for the development of a new set of species-specific microsatellite markers. Here, we also report a novel microsatellite-based marker for <i>C. dubliniensis</i>-specific identification.
DOI: 10.6084/m9.figshare.14990430.v1
title: Examining climate change and fast fashion.pdf

description: In this research project, we interrogate fast fashion in the 21st century in the context of a changing climate, by assessing emergent trends in sustainable fashion as an alternative consumption pathway through the annual ‘Trash the Runway’ event in Boulder, Colorado. We interviewed and surveyed designers and analyzed workshops and activities that led up to their annual fashion show. We also surveyed and interviewed students at the University of Colorado Boulder who worked with designers to produce short films about them and their work. The project provides youth – who are often marginalized in decision-making processes – a literal stage to suggest policy and behavior changes to address climate change and sustainability. We found that designers expressed reticence before the workshops and events to speak about climate change in everyday life, yet their design work creatively spoke powerfully for them, and they expressed less discomfort after the experience while they advanced their skillset as climate communicators. Moreover, we found that both designers and student partners reported that they think climate change will impact people greatly in the future, yet fewer respondents reported that climate change impacts them personally. While engagement with sustainable fashion helps to de-fetishize production processes and link consumption habits with awareness of climate and environmental change, more creative work should be done through fast- and sustainable-fashion to draw out temporal considerations of climate change threats here and now.This poster was presented at the 2021 Earth Science Information Partners (ESIP) Summer Meeting held virtually in July 2021.
DOI: 10.6084/m9.figshare.23415371.v1
title: TCGA SL LASSO coefficients

description: TCGADEPMAP synthetic lethality
DOI: 10.6084/m9.figshare.16413255.v1
title: ds_10000000_100000000.hdf5

description: A synthetic dataset generated to demonstrate the merge performance of ExeTera (https://github.com/KCL-BMEIS/ExeTera.git). It contains two tables, one with 10 million rows and one with 100 million rows. The primary key of the smaller table is a foreign key of the large table<br>Please see the wikis hosted at https://github.com/KCL-BMEIS/ExeTeraEval/wiki and https://github.com/KCL-BMEIS/ExeTera/wiki for details of how to use ExeTera to load and view this data. Please see ExeTeraEval for details of how to regenerate this and similar datasets.
DOI: 10.6084/m9.figshare.20282097.v1
title: Supplementary Material for: Are There Racial Differences in Inpatient Outcomes and Treatment Utilization Following Hospitalization for Myasthenia Gravis Exacerbation?

description: Introduction Racial differences in healthcare utilization and outcomes in the United remain an important issue. Little is known about racial differences in inpatient outcomes following hospitalizations for myasthenia gravis (MG). In this study, we used a claim-based database to assess racial differences in outcomes in hospitalized myasthenics. Methods The 2006 to 2014 National Inpatient Sample (NIS) database was queried using the International Classification of Diseases 9th Edition (ICD-9) diagnosis code (358.01) to identify adult patients (age &gt;17 years) undergoing hospitalization for MG. Race was categorized into – White, Black/African American, Asian or Pacific Islander, Hispanic, Native American, and other. Complications assessed included urinary tract infections, acute renal failure, cardiac complications, systemic infection, deep venous thrombosis, and pulmonary embolism. Multivariate logistic regression analyses were used to assess whether race was associated with a difference in outcomes, after controlling for baseline demographics, hospital characteristics and treatment factors. For regression purposes, White race was used as the reference. Results A total of 56,189 patient admissions, using a weighted sample, underwent hospitalization for MG between 2006 to 2014. Black/ African American patients had significantly higher odds of experiencing systemic infections (OR 1.35 [95% CI 1.16-1.58]; p&lt;0.001), deep venous thrombosis (OR 2.11 [95% CI 1.36-3.27]; p=0.001) and renal failure (OR 1.19 [95% CI 1.05-1.35]; p=0.005). Black/African American patients were more likely to be intubated (OR 1.09 [95% CI 1.01-1.19]; p=0.028) and receive non-invasive mechanical ventilation (OR 1.62 [95% CI 1.46-1.79]; p&lt;0.001), however, were less likely to receive IVIG (OR 0.77 [95% CI 0.73-0.82]; p&lt;0.001) and plasmapheresis (OR 0.77 [95% CI 0.72-0.82]; p&lt;0.001). Black/African American and Hispanic patients had lower mortality (OR 0.74 [95% CI 0.59-0.94; p=0.012]. Conclusions Significant racial differences exist in both treatment utilization and inpatient outcomes for patients hospitalized for MG.
DOI: 10.6084/m9.figshare.21720389.v3
title: Sex and timing of gonadectomy relative to puberty interact to influence weight, body composition, and feeding behaviors in mice

description: Supplementary statistics file related to Klappenbach et al. 2022.
DOI: 10.6084/m9.figshare.6304400.v1
title: EtNAM data

description: This object includes original files and scripts for the EtNAM population paper by Kidane et al. published on the Plant Biotechnology Journal and available open acces at doi:10.1111/pbi.13062Included, you will find:-genotypic data developed on EtNAM RILs using the Illumina Infinium 15k wheat array at TraitGenetics GmbH (in hmp and vcf format). SNP positions are derived from the wild emmer wheat genome (see paper for details).-phenotypic data for phenology and plant height.-R scripts used to generate the analyses featured in the paper.<br><br>
DOI: 10.48420/28270223.v1
title: Galen: Simple Drugs in Syriac Book 9 [pdf]

description: The Graeco-Arabic translation movement has been well studied, but Syriac, the vital connection between these two languages, is often ignored. This is partly the result of a lack of surviving Syriac texts. One such text, a sixth-century translation of Galen's On Simple Drugs by Sergius of Rēš ʿAynā, exists in the undertext of an eleventh-century liturgical work, known as the Syriac Galen Palimpsest. This palimpsest contains part of this translation. By using pioneering philological and imaging techniques, the team deciphered most of the undertext of books 6–9 and collated it with other direct and indirect witnesses. We present our digital critical edition here for the first time.
DOI: 10.6084/m9.figshare.22258975.v1
title: Diversity and Teamwork in Student Software Teams

description: Diversity is becoming an increasingly relevant topic in computer science, especially software development. Since software develop- ment is concerned with human and social processes, there is an agreement that a higher diversity rate in professional software teams positively influences communication, innovation, and per- formance. However, there is a lack of understanding of the impact of diversity in software development teams at an educational level to identify potential challenges and opportunities that might affect later professional stages. In this paper, we investigate the impact of diversity on key teamwork skills such as communication, collab- oration, and productivity in student software development teams. Therefore, we conducted several surveys on project work progress in an introductory software engineering course with students and their tutors regarding these teamwork metrics. We link these self- assessments and the project outcome to seven aspects of diversity. Our results show correlations between teamwork satisfaction and team diversity. Considering the changes in teamwork over the project timeline, we identified deteriorations in certain teamwork metrics—independent of the team diversity. These findings serve to enhance understanding and improvement of students’ team- work for students and educators. In particular, it is essential in software development courses at an undergraduate level to support our future software engineers to keep them motivated and decrease possible frustrations regarding teamwork.
DOI: 10.6084/m9.figshare.27300960.v1
title: Open Pit Mine Object Detection Dataset

description: The Open-Pit-Mine-Object-Detection-Dataset is a remarkable and specialized collection. It consists solely of remote sensing images of open-pit mines and their corresponding object detection bounding boxes. These bounding boxes are painstakingly hand-annotated using labelme, and the dataset provides annotations in JSON format. The remote sensing images offer a detailed and comprehensive view of the mine landscapes, presenting a wealth of visual information. With the precisely hand-annotated JSON format bounding boxes, researchers and developers have a valuable resource at their disposal. They can utilize this dataset with confidence to train and enhance object detection algorithms that are specifically designed for open-pit mines. This, in turn, holds great potential for improving safety and efficiency in mining operations, as accurate object detection can lead to better monitoring, management, and decision-making in the complex environment of open-pit mines.<br>
DOI: 10.6084/m9.figshare.5120575.v1
title: Supplementary Material for: Acute Treatment Costs of Stroke in Brazil

description: <i>Background and Purpose:</i> Although stroke is the leading cause of death in Brazil, little information exist on the acute treatment provided for stroke and its associated costs. This study addresses this gap by both clinically and economically characterizing the acute treatment of first-ever intracerebral hemorrhage (ICH) and ischemic stroke (IS) in Brazil. <i>Methods:</i> Retrospective medical chart review using data from two high-volume stroke centers in São Paulo, Brazil. Clinical and resource utilization data for all patients admitted to the stroke centers with a first-ever stroke between January 1, 2006 and May 31, 2007 were collected and the mean acute treatment costs per person were calculated by assigning appropriate unit cost data to all resource use. Cost estimates in Brazilian reals (BRL) were converted to US dollars (USD) using the 2005 purchasing power parity index. National costs of acute treatment for incident strokes were estimated by extrapolation of mean cost estimate per person to national incidence data for the two types of stroke. The mean costs of acute treatment on a national scale were examined in sensitivity analysis. <i>Results:</i> A total of 316 stroke patients were identified and their demographic and clinical characteristics, patterns of care, and outcomes were examined. Mean length of hospital stay was 12.0 ± 8.8 days for ICH and 13.3 ±23.4 days for IS. Ninety-one percent of the ICH patients and 68% of the IS patients were admitted to an intensive care unit (ICU). Mean total costs of initial hospitalization were USD 4,101 (SD ±4,254) for ICH and USD 1,902 (SD ±1,426) for IS. In multivariate analysis, hemorrhagic stroke, development of pneumonia, neurosurgical intervention, stay in ICU, and physical therapy were all significant independent predictors of acute treatment costs. Aggregate national health care expenditures for acute treatment of incident ICH were USD 122.4 million (range 30.8–274.2) and USD 326.9 million for IS (range 82.4–732.2). <i>Conclusion:</i> Acute treatment costs of incident ICH and IS in Brazil are substantial and primarily driven by the intensity of hospital treatment and in-hospital complications. With the expected increase in the incidence of stroke in Brazil over the coming decades, these results emphasize the need for effective preventive and acute medical care.
DOI: 10.6084/m9.figshare.9955001.v2
title: A Likelihood Ratio Approach to Sequential Change Point Detection for a General Class of Parameters

description: In this article, we propose a new approach for sequential monitoring of a general class of parameters of a <i>d</i>-dimensional time series, which can be estimated by approximately linear functionals of the empirical distribution function. We consider a closed-end method, which is motivated by the likelihood ratio test principle and compare the new method with two alternative procedures. We also incorporate self-normalization such that estimation of the long-run variance is not necessary. We prove that for a large class of testing problems the new detection scheme has asymptotic level <i>α</i> and is consistent. The asymptotic theory is illustrated for the important cases of monitoring a change in the mean, variance, and correlation. By means of a simulation study it is demonstrated that the new test performs better than the currently available procedures for these problems. Finally, the methodology is illustrated by a small data example investigating index prices from the dot-com bubble. Supplementary materials for this article are available online.
DOI: 10.17632/8nkv6ctcjv
title: Data for: JABBA-Select: Incorporating life history and fisheries' selectivity into surplus production models

description: The example and source code are intended to be accessible to the editor and reviewers during the review process and will uploaded on the open access online platform GitHub (https://github.com/jabbamodel/JABBA-Select) - pending publication.
DOI: 10.6084/m9.figshare.1430526.v1
title: Weekly data for 2008

description: Weekly data for 2008
DOI: 10.6084/m9.figshare.25223990.v1
title: DocuQA

description: DocuQA - Document Question Answering Dataset
DOI: 10.6084/m9.figshare.c.3832354_d1.v1
title: Additional file 1: of The Dark Proteome Database

description: An image file showing the validation tests used to check overall features and a range of individual proteins. (ZIP 1123 kb)
DOI: 10.6084/m9.figshare.13070672.v1
title: Proteome database of Klebsiella pneumoniae

description: <i>Klebsiella pneumoniae</i> is a facultative anaerobic, lactose-fermenting, enterococci bacterium whose natural habitat is the soil environment. Able to fix nitrogen, and thus a diazotroph, the bacterium is also a natural commensal in the gastrointestinal tract of humans. However, when displaced to the lungs, <i>K. pneumoniae</i> could cause serious lung infections with characteristic sputum. This work sought to provide the proteome information of <i>K. pneumoniae</i> by parsing the annotated proteome file of the bacterium downloaded from UniProt. Comprising protein name and amino acid sequence, the database was further refined by calculating associated number of residues, molecular weight, and nucleotide sequence of each protein in the proteome of the bacterium. Altogether, the resource should be useful as starter kit for investigating the varied roles of <i>K. pneumoniae</i> in the environment and in pathogenesis, which may help provide an overarching theme for the metabolic processes and their regulation in this bacterium.
DOI: 10.6084/m9.figshare.14877162.v1
title: NGS-2020-10-02584-T_S3.xlsx

description: Data S3 from the manuscript "Global chemical weathering dominated by continental arcs since the mid-Paleozoic"<br>Gernon et al. 2021. Nature Geoscience.<br><br>Filename:NGS-2020-10-02584-T_S3.xlsx<br><br>S3 tabulates the empirical rank correlations (CEmp) and BN correlations (CBN) for all individual input parameters and lagged parameters (the predictor nodes) with (87Sr/86Sr)sw (the node of interest). These were calculated by generating a saturated Bayesian Network with all 254 nodes (including lags), and computing CEmp and CBN for all predictor nodes with (87Sr/86Sr)sw . Correlations have been calculated using both the original (‘best estimate’) input data set and also the simulated data set, to evaluate the effect of input uncertainty (see Methods and Extended Data Fig. 2 in manuscript).
DOI: 10.6084/m9.figshare.17118740.v1
title: Sperm VS CO2.xlsx

description: Post-euthanasia cryopreservation of epididymal sperm is a common method to preserve and distribute valuable mouse models worldwide. However, the euthanasia method used prior to sperm collection must not adversely affect sperm quality. The most common method of euthanasia in mice is CO<sub>2</sub> asphyxiation, but its effect on sperm quality is largely unknown. The objective of this study was to determine the effects of CO<sub>2</sub> euthanasia on C57BL/6 mouse sperm post-recoveries and following freezing and thawing. First, post-mortem sperm concentration, progressive motility, curvilineal velocity (VCL), average path velocity (VAP), and progressive velocity (VSL) were analyzed for mice euthanized via either CD, high flow CO<sub>2</sub> (100%), or low flow CO<sub>2</sub> (30%) displacement/minute, respectively. Then, i<i>n-vitro</i> fertilization and embryonic development rates were determined using frozen-thawed sperm from each euthanasia method. There were no differences in sperm concentrations, progressive motility, VAP or VCL for fresh or frozen-thawed sperm. Frozen-thawed sperm collected from the CD group had higher VCL values compared to sperm collected from the low flow group (<i>P</i>=0.039). There were no differences in fresh sperm, or between sperm collected from the CD vs high flow CO<sub>2 </sub>or high flow vs low flow CO<sub>2</sub>. There were no differences between groups for fertilization (<i>P</i>=0.452) and blastocyst development rates (<i>P</i>=0.298) from using frozen-thawed sperm collected between the groups. The results suggest that CO<sub>2 </sub>euthanasia method can serve as an alternative to CD in the case of technical or personal reasons to obtain optimal quality mouse sperm for cryopreservation and comply with the animal and human welfare.
DOI: 10.6084/m9.figshare.22688191.v1
title: Prairie et al_data.xlsx

description: Sustainability of agricultural production and mitigation of global warming rely on the regeneration of soil organic carbon (SOC), in particulate organic carbon (POC) and mineral-associated organic carbon (MAOC) forms. We conducted a global systematic meta-analysis of the effects of regenerative management practices on SOC, POC, and MAOC in cropland, finding: 1) no-till (NT) and cropping system intensification increase SOC (11.3% and 12.4%, respectively), MAOC (8.5% and 7.1%, respectively), and POC (19.7% and 33.3%, respectively) in topsoil (0 to 20 cm), but not in subsoil (&gt;20 cm); 2) experimental duration, tillage frequency, the intensification type, and rotation diversity moderate the effects of regenerative management; and 3) NT synergized with crop–livestock systems to greatly increase POC (38.1%) and cropping intensification synergized with crop–livestock systems to greatly increase MAOC (33.1 to 53.6%). This analysis shows that regenerative agriculture is a key strategy to reduce the soil C deficit inherent to agriculture to promote both soil health and long-term C stabilization.
DOI: 10.6084/m9.figshare.24236311.v1
title: The transcriptome assembly of the annelid worm <i>Hediste diversicolor</i>

description: Hediste_diversicolor_transcriptome_V1.fa.gz - version 1 of the transcriptome assembly of Hediste divesicolorHediste_diversicolor_transcriptome_V2.fa.gz - version 2 of the transcriptome assembly of Hediste divesicolorHediste_diversicolor_proteins.fa.gz - Protein sequences of transcriptome of Hediste divesicolorHediste_diversicolor_mrna.fa.gz - mrna sequences of transcriptome of Hediste divesicolorHediste_diversicolor_genes.fa.gz - Genes sequences of transcriptome of Hediste divesicolorHediste_diversicolor_cds.fa.gz - Cds sequences of transcriptome of Hediste divesicolorHediste_diversicolor_annotation.gff3.gz - Annotation file of transcriptome of Hediste divesicolor
DOI: 10.6084/m9.figshare.26089299.v1
title: HiGTS_2016s4

description: HiGTS is a high temporal resolution global gridded dataset of human thermal stress metrics. Derived using climate variables from ERA5-Land and ERA5, the HiGTS consists of hourly gridded maps of Universal Thermal Climate Index (UTCI), Universal Thermal Stress (UTS), and daily Thermal Stress Duration (TSD) at 0.1° × 0.1° spatial resolution over the global land surface.HiGTS_2016s4 contains the data from October 1, 2016 to December 31, 2016.
DOI: 10.17632/dtykpv66wh
title: Povidone iodine gel use as a conductive and antiseptic in ultrasound-guided invasive procedures.

description: The uses of ultrasound continue to grow. Thanks to the correct delimitation and localization of subcutaneous lesions, more and more invasive ultrasound-guided procedures are being performed. Proof of this would be the ultrasound-guided infiltration of Triamcinolone in subcutaneous tunnels in Hidradenitis Suppurativa or ultrasound-guided treatments in Aesthetic Dermatology that are catching on.
DOI: 10.6084/m9.figshare.29123420.v2
title: all_genes_expression_of_diapause_silkworm

description: These tables show the gene expression patterns (fpkm)of diapause silkworm embryos and larvae that were congenitally infected with N. bombycis, and the gene expression patterns of N. bombycis in diapause silkworm embryos and larvae.
DOI: 10.6084/m9.figshare.7812044.v2
title: SREP-18-40084A Data 2 sorption kinetics

description: Effects of contact time on adsorption capacity of Cu(II) onto different adsorbents (adsorbent dosage= 0.5 g, contact time = 5, 10, 15, 25, 35, 50, 65 h, initial Cu(II) concentration = 300 mg L<sup>-1</sup>, initial solution pH = 5.0 ± 0.1, temperature = 25°C).<br>Plots for the intra-particle diffusion, Pseudo-first-order and Pseudo-second-order sorption kinetics of Cu(II) onto different adsorbents.
DOI: 10.60893/figshare.adv.28320239.v1
title: Supplement Number 1

description: elastic stiffness coefficients of SGMZ and Pr:SA
DOI: 10.17632/sg7267bcs6
title: Data for GIS-based spatial vulnerability analysis in the area of Alessandria in Italy in case of road network disruption

description: The input file contains supply data (based on data from geoportal of piedmont and OSM data) and flood map (based on data from geoportal of piedmont) for the Alessandria area in Italy, detailing both basic and disrupted flood scenarios to be analyzed in GIS software. It includes information on closed bridges during flood events. The output file presents the analysis results for both the basic and disrupted scenarios.