cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19367186.v1
title: Supplementary Material for: Nephrotoxin Exposure in the 3 Years following Hospital Discharge Predicts Development or Worsening of Chronic Kidney Disease among Acute Kidney Injury Survivors

description: <b><i>Introduction:</i></b> Survivors of acute kidney injury (AKI) are at high risk of progression to chronic kidney disease (CKD), for which drugs may be a modifiable risk factor. <b><i>Methods:</i></b> We conducted a population-based cohort study of Olmsted County, MN residents who developed AKI while hospitalized between January 1, 2006, and December 31, 2014, using Rochester Epidemiology Project data. Adults with a hospitalization complicated by AKI who survived at least 90 days after AKI development were included. Medical records were queried for prescription of potentially nephrotoxic medications over the 3 years after discharge. The primary outcome was de novo or progressive CKD defined by either a new diagnosis code for CKD or ≥30% decline in estimated glomerular filtration rate from baseline. The composite of CKD, AKI readmission, or death was also evaluated. <b><i>Results:</i></b> Among 2,461 AKI survivors, 2,140 (87%) received a potentially nephrotoxic medication during the 3 years following discharge. When nephrotoxic medication use was analyzed in a time-dependent fashion, those actively prescribed at least one of these drugs experienced a significantly higher risk of de novo or progressive CKD (HR 1.38: 95% CI: 1.24, 1.54). Similarly, active potentially nephrotoxic medication use predicted a greater risk of the composite endpoint of CKD, AKI readmission, or death within 3 years of discharge (HR 1.41: 95% CI: 1.28, 1.56). <b><i>Conclusion:</i></b> In this population-based cohort study, AKI survivors actively prescribed one or more potentially nephrotoxic medications were at significantly greater risk for de novo or progressive CKD. An opportunity exists to reassess nephrotoxin appropriateness following an AKI episode to improve patient outcomes.
DOI: 10.6084/m9.figshare.5123011.v1
title: Supplementary Material for: Towards Understanding the Cause of Stroke in Young Adults Utilising a New Stroke Classification System (A-S-C-O)

description: <i>Background:</i> Stroke in younger people is relatively common and frequently unexplained. While understanding of the causes of young stroke has improved, there remains uncertainty over the role of low-risk lesions such as a patent foramen ovale (PFO). The TOAST criteria are often used to describe stroke aetiology, but in younger people in whom PFOs are frequent, there is a very high proportion of cases attributed to cardiac embolism. The impact of using the newer A-S-C-O criteria on stroke aetiology was investigated. <i>Methods:</i> Consecutive patients with ischaemic stroke were investigated and categorised by the TOAST and ASCO1 criteria. Stroke aetiology was presented and compared by the different classification systems. <i>Results:</i> Of the 106 ischaemic stroke cases, by TOAST 6% were ‘large artery atheroma’, 11% ‘small vessel occlusion’, 28% ‘cardioembolic’, 22% ‘other determined cause’ and 33% ‘undetermined cause’. The vascular territory and associated causes are presented. With the ASCO1 criteria, there were more cases of unclassified stroke (51.9 vs. 34.0%; p &lt; 0.001) and fewer cases of cardiac embolism. Kappa ranged from 0.5 for ‘undetermined aetiology’ to 1.0 for both ‘large artery atheroma’ and ‘other determined aetiology’. Younger cases (&lt;45 years) were less likely to be either ‘large artery atheroma’ or ‘small vessel occlusion’. <i>Conclusion:</i> Using the ASCO criteria, more patients fall into the undetermined group which more accurately reflects our current uncertainty regarding the pathogenic relevance of PFOs in this age group.
DOI: 10.6084/m9.figshare.5977840.v1
title: Assessing sources of uncertainty in length-based estimates of body growth in populations of fishes and macroinvertebrates with bootstrapped ELEFAN

description: <b>Supplementary material for the paper</b>:<br>Schwamborn, R, Mildenberger, T.K., Taylor, M.H., submitted. Assessing sources of uncertainty in length-based estimates of body growth in populations of fishes and macroinvertebrates with bootstrapped ELEFAN.<br><br><b>Description</b>:<br>The fileset provides R scripts and results presented in the paper by Schwamborn et al (submitted). The analyses uses functions available in the new R package "fishboot" (Schwamborn et al. 2018), which builds on ELEFAN functions available in the TropFishR package (Mildenberger et al. 2017, 2018, Taylor et al. 2017), to provide confidence intervals of growth parameter estimates using a bootstrapping procedure applied to length frequency data. <br><br><b>Contents</b>:<br><b>Supplement_Schwamborn_etal.Rproj</b> - RStudio project file. When opened in RStudio, script file paths should remain compatible across platforms.<br><b>/results</b> - results of bootstrapping experiments provided as .Rdata and graphical files. <br><b>/scripts</b> - scripts for running bootstrapping analyses on "alba" and "synLFQb" datasets. A basic bootstrapping demonstration using the "alba" dataset is also provided.<br><br><b>References</b>:<br>- Mildenberger, T.K., Taylor, M.H., Wolff, M., 2017. TropFishR: an R package for fisheries analysis with length-frequency data. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210X.12791<br>- Mildenberger, T.K., Taylor, M.H., and Wolff, M., 2018. TropFishR: Tropical Fisheries Analysis with R. R package version 1.2.1. https://CRAN.R-project.org/package=TropFishR<br>- Schwamborn, R, Mildenberger, TK, Taylor, MH, 2018. fishboot: Bootstrap-based methods for the study of fish stocks and aquatic populations. R package version 0.1. https://github.com/rschwamborn/fishboot<br>- Taylor, M.H, Mildenberger, T.K., 2017. Extending electronic length frequency analysis in R. Fisheries Management and Ecology. 24:330-338. https://doi.org/10.1111/fme.12232
DOI: 10.6084/m9.figshare.22301020.v4
title: The high-resolution (1km) groundwater storage and depletion maps across Irrigated Indus Basin (IIB) during 2002-2019

description: We provided high-resolution (1km) groundwater storage (GWS) and depletion (DEPgw) maps across Irrigated Indus Basin (IIB) for 2002-2019. We applied two independent methodologies (1) spatial downscaling for improving GRACE-based GWS data, and (2) SWAT (Soil Water Assessment Tool) and pixel-based water balance approach for DEPgw estimates. GWS were estimated from the GRACE data, then downscaled to 1 km × 1 km using data-driven spatial downscaling models. We combined the downscaled GRACE-based GWS estimates with results from a calibrated SWAT hydrological model to estimate the DEPgw. The resultant maps delineate the groundwater depletion hotspots of cropping systems in the 55 canal command areas of IIB and could contribute to sustainable water use and agricultural development in the region. <br> <br> Readers can refer to the following publication for more details on the methods. <br> Arshad, A., Mirchi, A., Samimi, M. and Ahmad, B., 2022. Combining downscaled-GRACE data with SWAT to improve the estimation of groundwater storage and depletion variations in the Irrigated Indus Basin (IIB). <em>Science of the Total Environment</em>, <em>838</em>, p.156044.
DOI: 10.6084/m9.figshare.28436330.v1
title: Dataset: Precise and accurate Ga isotopic analysis of solution standards and geological reference materials by MC-ICP-MS

description: <b>Table 1 </b>Elution scheme for separation of Ga from matrices in geologic samples.<b>Table 2 </b>Operating parameters of the MC-ICP-MS (Neptune plus) during Ga isotope measurements.<b>Table 3 </b>Test of influences of matrix elements, acid molarity and concentration mismatch on Ga isotopic analysis.<b>Table 4 </b>Gallium isotopic compositions of geological reference materials in this study and literature.
DOI: 10.6084/m9.figshare.25845664.v1
title: MainDatasetKAP_V1.xlsx

description: This is a excel data of study titled "<b>Knowledge, Attitude, and Practice towards Hepatitis B and Vaccination Status of Pre-clinical Medical Students at Sylhet Women’s Medical College, Bangladesh</b>".
DOI: 10.17632/wz9bdfm9y7
title: References pertaining to the potential impact of Paxlovid on PASC.

description: A compilation of references pertaining to the potential impact of Paxlovid on post-acute sequelae of SARS-CoV-2 infection (PASC).
DOI: 10.6084/m9.figshare.11296118.v1
title: OligoMM12_early_life_16S_rRNA_Illumina.csv16s rRNA sequencing data Gnotobiotic mice

description: 14 samples from C1 and C2 colonized mice were sequenced for the V5-V6 region of 16S rRNA genes. 56 samples from C3, C4, C5, C6, OligoMM12, KB1+YL58, YL44+YL58 and YL44+KB1+YL58 colonized mice and 91 samples from young OligoMM12 colonized mice were sequenced for V4 region of 16S rRNA genes. Sequencing was performed using Ion PGMTM platform (V5-V6) and Illumina (V4) platform.14 samples from C1 and C2 colonized mice were sequenced for the V5-V6 region of 16S rRNA genes. 56 samples from C3, C4, C5, C6, OligoMM12, KB1+YL58, YL44+YL58 and YL44+KB1+YL58 colonized mice and 91 samples from young OligoMM12 colonized mice were sequenced for V4 region of 16S rRNA genes. Sequencing was performed using Ion PGMTM platform (V5-V6) and Illumina (V4) platform.
DOI: 10.6084/m9.figshare.11402166.v1
title: Proteome database of Proteus vulgaris ATCC 49132

description: Known for its swarming motility, <i>Proteus vulgaris</i> is a Gram-negative, rod-shaped bacterium that inhabits a variety of environments ranging from the human gastrointestinal tract to soil and water. Ability to thrive in a variety of environmental and nutritional environments may partially explain why <i>P. vulgaris </i>is also an opportunistic human pathogen causing, for example, wound infections. But, the defining feature of this bacterium remains its coordinate movement across surfaces known as swarming motility, which endows it with model organism status in this field of research. This work sought to provide some fundamental information of <i>P. vulgaris</i> ATCC 49132 through parsing the organism’s UniProt proteome file through an in-house MATLAB software. Altogether, a proteome database comprising protein name, amino acid sequence, number of residues, molecular weight and nucleotide sequence was constructed that, in addition to providing key features of each protein in <i>P. vulgaris </i>ATCC 49132, also informs researchers of the metabolic and signalling pathways present in the species. Such information should find use in a variety of basic microbiological investigations seeking to decipher the question: why and how <i>P. vulgaris</i> moves on surfaces in coordinated fashion? <br><br>
DOI: 10.6084/m9.figshare.23498667.v1
title: SNP Wheat

description: The sequencing data of 126 accessions
DOI: 10.17632/xpf3s2xcrb
title: Dataset: Simulations of Flettner rotors across fourteen global shipping routes

description: Dataset for manuscript titled: Quantifying voyage optimisation with wind propulsion for short-term CO2 mitigation in shipping.

Authors: James Mason, Alice Larkin, Simon Bullock, Nico van der Kolk, John F. Broderick

This dataset contains data from over 200,000 simulated departures across fourteen global shipping routes, providing fuel savings estimations of Flettner rotors on a Panamax bulk carrier ship. Both great circle route and weather routing simulation results are provided.
DOI: 10.6084/m9.figshare.25471207.v1
title: Supplementary Material for: PAX1 and SOX1 gene methylation as a detection and triage method for cervical intraepithelial neoplasia diagnosis

description: Introduction: Methylation assays have demonstrated potential as dependable and high-precision approaches for identifying or triaging individuals with cervical cancer (CA) or cervical intraepithelial neoplasia (CIN). Our investigation aimed to assess the efficacy of diagnosis and triage of the PAX1/SOX1 methylation panel in detecting CIN or CA.
Methods: A total of 461 patients with abnormal high-risk human papillomavirus (hrHPV) or cytology test results were recruited for this study. Each patient underwent an assortment of assessments comprising cytology test, hrHPV test, colposcopy examination, and PAX1 and SOX1 methylation test. 
Results: The extent of methylation of both genes demonstrates a positive correlation with the severity of CIN lesions and CA. To determine the correlation for patients with CIN2 or worse (CIN2+), the area under curve (AUC) was 0.821 (95%CI 0.782-0.853) for PAX1 and 0.800 (95%CI 0.766-0.838) for SOX1, while for CIN3 or worse (CIN3+),0.881 (95%CI 0.839-0.908) for PAX1 and 0.867 (95% 0.830-0.901) for SOX1. The PAX1/SOX1 methylation marker panel performed sensitivity and specificity of 77.16% and 91.67% for CIN2+, 84.76% and 90.50% for CIN3+, respectively. Regarding triaging hrHPV+ patients, the PAX1/SOX1 methylation test only referred 11.83% of the patients who are unnecessary for coloscopy examination, which is comparatively lower than cytology， thereby signifying a promising triage strategy for hr-HPV positive women. Furthermore, we observed that the positive PAX1/SOX1 methylation test result for untreated CIN1 or less patients would result in a higher likelihood of progression upon a 24-month follow-up visit. 
Conclusion: The present investigation demonstrates that the PAX1/SOX1 methylation marker panel exhibits a favorable diagnostic performance in CIN detection and holds the potential to be employed for individual CIN tests or hrHPV-positive triage.
DOI: 10.6084/m9.figshare.28255133.v1
title: Training matrices

description: Training matrices containing RPM of 12 high throughput sequencing datasets scored within experimental R-loop peaks and random regions in HEK293, K562 and HeLa cell lines.
DOI: 10.17632/x3kxjddv9d
title: The influence of parasite load on transcriptional activity and morphology of a cestode and its ant intermediate host

description: Parasites with complex life cycles are known to induce phenotypic changes in their intermediate hosts to increase transmission to the final host. The magnitude of these changes could increase with the number of parasites, which would be beneficial to co-infecting parasites. Yet, adverse effects of high parasite load (i.e., many parasites in a single host) might stress both hosts and parasites (e.g., through an increased immune response). We investigated the consequences of parasite load on the transcriptional activity and morphology of the cestode Anomotaenia brevis and its intermediate host, the ant Temnothorax nylanderi. We demonstrated that many differentially expressed host genes shifted with parasite load, and their functions indicate a stronger immune response and fight against oxidative stress in heavily infected hosts. The expression of other host genes responded to infection in an all-or-nothing manner, as did the morphology of the host workers. However, the cestodes became smaller when they competed with other parasites for resources from a single host. Their expression profile further indicated shifts in host immune avoidance, starvation resistance and vesicle-mediated transport. In summary, our study reveals clear consequences of parasite load and highlights specific processes and traits affected by this.
DOI: 10.6084/m9.figshare.24750402.v2
title: <b>Efficacy and Safety of Levetiracetam for Epilepsy in Children: A Systematic Review and Meta-Analysis</b>

description: <b>Objective</b>To investigate and validate the clinical efficacy and safety of levetiracetam intervention drug administered as a monotherapy or adjunctive therapy in treating children below 18 years of age diagnosed with epilepsy.<br><b>Methods</b>Online databases (PubMed (Medline), Web of Science, Cochrane Library, and EMBASE) were electronically searched with Keywords and MeSH terms including pediatric, child, neonate, seizure, epilepsy, anticonvulsive, levetiracetam, and Keppra from inception to September 2022 to establish high-quality studies for inclusion in this study. The data were extracted, and outcomes were measured on seizure-free rates, a seizure-frequency reduction from baseline (≥50% reduction rates), and the adverse effects. The meta-analysis was performed using the RevMan version 5.4 software.<br><b>Results</b>After being ascertained based on the predetermined eligibility criteria, a total of 14 articles were finally included in this meta-analysis. Based on the pooled meta-analysis results of different outcomes, the study suggested a superior efficacy and safety profile of levetiracetam over placebo or other AEDs. Some forms of minor adverse events were also associated with AED drug administration. Compared with others, such as PHB and COX, the incidences of adverse events were substantially lower in levetiracetam, making it safe for children.<br><b>Conclusion</b>The meta-analysis concluded that levetiracetam was clinically effective and safe in treating epilepsy in children.
DOI: 10.17632/9m3vtnbyrs
title: Database of research papers on PLA degradation: 1973-2023

description: Data generated on the list of research articles dealing with Poly Lactic Acid degradation from 1972-2023 assorted through a systematic review approach using the PRISMA framework. All the articles have been annotated with 11 parameters describing the scope and extent of the study.
DOI: 10.17632/xgxz6t93xp
title: Mathematical Modelling data
DOI: 10.6084/m9.figshare.5104402.v1
title: Supplementary Material for: Generation of a 5.5-Mb BAC/PAC contig of pig chromosome 6q1.2 and its integration with existing RH, genetic and comparative maps

description: We generated a sequence-ready BAC/PAC contig spanning approximately 5.5 Mb on porcine chromosome 6q1.2, which represents a very gene-rich genome region. STS content mapping was used as the main strategy for the assembly of the contig and a total of 6 microsatellite markers, 53 gene-related STS and 116 STS corresponding to BAC and PAC end sequences were analyzed. The contig comprises 316 BAC and PAC clones covering the region between the genes GPI and LIPE. The correct contig assembly was verified by RH-mapping of STS markers and comparative mapping of BAC/PAC end sequences using BLAST searches. The use of microsatellite primer pairs allowed the integration of the physical maps with the genetic map of this region. Comparative mapping of the porcine BAC/PAC contig with respect to the gene-rich region on the human chromosome 19q13.1 map revealed a completely conserved gene order of this segment, however, physical distances differ somewhat between HSA19q13.1 and SSC6q1.2. Three major differences in DNA content between human and pig are found in two large intergenic regions and in one region of a clustered gene family, respectively. While there is a complete conservation of gene order between pig and human, the comparative analysis with respect to the rodent species mouse and rat shows one breakpoint where a genome segment is inverted.
DOI: 10.6084/m9.figshare.25738086.v1
title: Transcription files

description: This dataset holds the AI-generated interview transcripts of the 15 interviews done for the study titled:<br>"Evaluation Of Multi-Stream Levels On The Engagement Of Participants In mHealth Applications"
DOI: 10.6084/m9.figshare.7033577.v16
title: Deep image reconstruction from human brain activity

description: Shen, Horikawa, Majima, and Kamitani (2019) Deep image reconstruction from human brain activity. PLos Comput Biol. (bioRxiv preprint)
Here we provide DNN features decoded from human brain activity (decodedfeatures-*.mat files) as well as preprocessed fMRI data used for the decoding (sub-*.h5 files).<br>
Raw fMRI data are available at OpenNeuro.
Demo code is available at GitHub.
History
2022-10-14: Add fMRI data (sub-03) preprocessed by fmriprep (*_fmriprep_volume_native.h5)
2022-10-13: Add fMRI data (sub-01, sub-02) preprocessed by fmriprep (*_fmriprep_volume_native.h5)<br>
2022-01-27: Minor update on fMRI data (v2; "stimulus_name" was added).<br>
2020-09-09: True DNN features (unit activations) of VGG19 for natural image training and test images were added.
2020-09-08: True DNN features (unit activations) of VGG19 (except conv1) for natural image training images were added.
2020-08-05: fMRI data version 2, which applied slightly different preprocessng and ROIs from the original study, were added (for the natural image experiment only; *_perceptionNaturalImageTraining/Test_VC_v2.h5).
2020-05-18: The following fMRI data files of artificial images, letters, and imagery experiments contained incorrect samples and were fixed.

 sub-01_perceptionLetterImage_original_VC.h5
 sub-02_perceptionArtificialImage_original_VC.h5
 sub-02_perceptionLetterImage_original_VC.h5
 sub-02_imagery_original_VC.h5
 sub-03_perceptionArtificialImage_original_VC.h5
 sub-03_perceptionLetterImage_original_VC.h5
 sub-03_imagery_original_VC.h5

<br>
DOI: 10.6084/m9.figshare.22068863.v1
title: 01.sav

description: happiness color metaphor
DOI: 10.6084/m9.figshare.7346750.v2
title: TrakEm2 project files and corresponding electron microscopy files for "The architecture of cell differentiation in choanoflagellates and sponge choanocytes"

description: TrakEM2 project files and corresponding electron microscopy files<br>Transmission elelectron microscopy serial sections were imported as z-stacks into the Fiji plugin TrakEM2 and automatically aligned using default parameters, except for increasing steps per octave scale to 5 and reducing maximal alignment error to 50 px. Alignments were manually curated and adjusted if deemed unsatisfactory. Organelles and subcellular compartments were manually segmented and 3D reconstructed by automatically merging traced features along the z-axis. Meshes were then preliminarily smoothed in TrakEM2.
DOI: 10.17632/2tttgmhbng
title: Data for A Study of Implicit Speech-Act Recognition by Chinese Speakers

description: The original data for the paper A Study of Implicit Speech-Act Recognition by Chinese Speakers, including the data for the test materials and results of the three pre-test questionnaires and three online experiments (data input and results in the form of SPSS tables).
DOI: 10.17632/f7y9s3cpt3
title: Effects of Student Self-Assessment on Knowledge Achievement and Academic Thinking

description: This study investigated the effects of student self-assessment on English-as-a-Foreign-Language (EFL) students' knowledge achievement and academic thinking.
DOI: 10.17632/z8xwsxc5jd
title: Fingerprinting Asian-derived sand in the deep central South China Sea since the Late Miocene

description: These supplementary files (Figure S1 and Tables S1-S7) are associated with the paper entitled "Fingerprinting Asian-derived sand in the deep central South China Sea since the Late Miocene" by Cao et al. and contain additional information on samples, data acquired during the heavy mineral analysis and zircon U-Pb dating, data compilation, as well as statistical results.
DOI: 10.6084/m9.figshare.26056726.v7
title: test

description: It includes the data, the Python project, the SPSS project, and the project tutorial that support the findings of the study (Assessing the coordination of the transportation service network and the population mobility network in mega-urban agglomerations: A deviation-based framework).
DOI: 10.6084/m9.figshare.1583226.v1
title: A Brief Introduction of Immunoprecipitation

description: Protein is always the focus of research for global scientists for it is the most important molecule in living forms. Immunoprecipitation is a classical method to researching interaction different proteins on the basis of specificity between antibody and antigen and it is also regarded as an effective way to recognize the mutual physiological action between two kinds of proteins in cells.
DOI: 10.6084/m9.figshare.21510831.v1
title: Multidimensional Social Cognitive Decision-Making

description: Behavioural data for the fMRI experiment. There is a commented script to run the main analyses.