cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.dtbjzv
title: Occurrence Download

description: A dataset containing 8045 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Observation, Human Observation, Machine Observation, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Selenia dentaria (Fabricius, 1775)"
 ]
}

 The dataset includes 8045 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009548-250426092105405/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.20926960.v1
title: Supplementary Material for: Comparison of Safety and Outcomes between Endoscopic and Surgical Resections of Intermediate-risk Primary Gastric Gastrointestinal Stromal Tumors

description: The objective of this study was to compare the safety and efficacy of endoscopic resection with surgical resection in the treatment of intermediate-risk gastric GISTs, and to further evaluate whether imatinib adjuvant treatment is necessary for resected intermediate-risk gastric GIST by ER. Methods: We retrospectively studied 128 cases for intermediate-risk gastric GISTs that were distributed in endoscopic (n=33) and surgical groups (n=95) at our center between December 2009 to July 2020. We statistically compared the clinical features, pathological reports, perioperative data, and long-term follow-up outcomes. Results: Compared with the surgery group, the endoscopy group was associated with smaller tumor size (2.4±1.0 vs 6.0±1.7cm, P&lt;0.001), shorter operating time (67.3 ±36.5 vs 145.9±74.8min, P&lt;0.001), fewer incidence of short term post-operative complications (3% vs 32.6%, P=0.002). Shorter post-operative hospital days (4.5±1.4 vs 8.5±2.4d, P&lt;0.001), shorter gastric functional recovery time (P&lt;0.001) and a lower overall medical cost of hospitalization (P&lt;0.001) was detected in the endoscopy group. During the median 44.5 months follow-up period , there were no cases of recurrence, metastasis, and death in the endoscopy group. Among 128 patients, 68 accepted adjuvant therapy with imatinib after resection. It was observed that the OS of the adjuvant treatment group with imatinib was lower than that of the group without imatinib (P=0.033). Conclusions: Endoscopic resection for intermediate-risk gastric GIST is a feasible and safe method. And there is no significant benefit for patients with intermediate-risk gastric GIST to accept imatinib adjuvant treatment after ER.
DOI: 10.6084/m9.figshare.24487111.v1
title: Supplementary Material for: Removal of α1-microglobulin using post-dilution online hemodiafiltration with polymethylmethacrylate membrane: an open-label, single-arm study

description: Introduction: The removal of low and medium-molecular-weight proteins has been improved with online hemodiafiltration (OL-HDF) and hemodialysis using high-flux membranes; however, the outcomes of patients with end-stage kidney disease (ESKD) undergoing dialysis treatment are still worse than in the general population. Alpha-1-microglobulin (α1-m), a molecular weight of 33,000 Da, may contribute to dialysis-related disorders and mortality. However, the removal is insufficient even with current OL-HDF using the polysulfone (PS) membrane, which is common in Japan. Polymethylmethacrylate (PMMA) membranes can remove medium- to high-molecular-weight proteins by adsorption. This study aimed to assess the efficacy of removing medium- to high-molecular-weight proteins, such as α1-m and β2-microglobulin (β2-m), through post-dilution OL-HDF with PMMA (Post-PMMA). The assessment was conducted in comparison to pre-dilution OL-HDF with PS (Pre-PS), using an open-label, single-arm study. Methods: Seven patients with ESKD on Pre-PS underwent Post-PMMA with replacement volume of 30 ml/min (low flow) and 50 ml/min (high flow). Clearance and removal rates of α1-m, β2-m, small molecules, inflammatory cytokines, and albumin were measured at 60 and 240 min of treatment. Results: The clearances of α1-m at 60 min were -2.8 ± 5.2 ml/min with Pre-PS, -0.4 ± 2.6 ml/min with Post-PMMA (low), and 0.6 ± 3.4 ml/min with Post-PMMA (high). The removal rate of α1-m was higher in Post-PMMA than in Pre-HDF-PS [Post-PMMA (high) 17.7 ± 5.9%, Post-PMMA (low) 15.0 ± 5.6%, and Pre-PS 4.1 ± 5.5%]. The adsorption clearance of β2-m was increased with Post-PMMA. Albumin leakage in Post-PMMA was not higher than in Pre-PS. Discussion/Conclusion: The removal rate of α1-m with Post-PMMA was higher than that with Pre-PS. PMMA membrane adsorbed β2-m, suggesting the removal effect of medium- to high-molecular-weight proteins by the adsorption method. Since Post-PMMA effectively removes α1-m without excessive albumin leakage, it will be useful for patients with ESKD, especially those with poor nutritional state.
DOI: 10.6084/m9.figshare.28836359.v1
title: Figure S6 Eye tracking data during two-photon imaging experiments

description: Alignment and position data for tracking the pupils for both eyes for all mice during two-photon imaging.
DOI: 10.6084/m9.figshare.20325195.v5
title: A Representative User-centric GitHub Developers Dataset for Malicious Account Detection

description: Using GitHub APIs, we construct an unbiased dataset of over 10 million GitHub users. The data was collected between Jul. 20 and Aug. 27, 2018, covering 10,000 users. Each data entry is stored in JSON format, representing one GitHub user, and containing the descriptive information in the user’s profile page, the information of her commit activities and created/forked public repositories. <br> Please cite the following paper when using the dataset: Qingyuan Gong, Jiayun Zhang, Yang Chen, Qi Li, Yu Xiao, Xin Wang, Pan Hui. Detecting Malicious Accounts in Online Developer Communities Using Deep Learning. Proc. of the 28th ACM International Conference on Information and Knowledge Management (CIKM'19), Beijing, China, Nov. 2019. <br> Download the file, and decompress the files with the following steps: (1) In MacOSX/Linux systems: (i) open the terminal and switch to the directory where you have downloaded the files (e.g. "cd Downloads/") (ii) run the command: "unzip Github_dataset.zip". (2) In Windows systems: use decompression software (e.g. WinZIP) to decompress the file "Github_dataset.zip". <br>
DOI: 10.6084/m9.figshare.14790516.v1
title: Supplementary Material for: Screening a Prognosis-Related Target Gene in Patients with HER-2-Positive Breast Cancer by Bioinformatics Analysis

description: <b><i>Objective:</i></b> The objective of the present study was to determine a target gene and explore the molecular mechanisms involved in the pathogenesis of HER-2-positive breast cancer. <b><i>Methods:</i></b> Three RNA expression profiles obtained from the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA) were used to identify differentially expressed genes (DEGs) using the R software. A protein-protein interaction network was then constructed, and hub genes were determined. Subsequently, the relationship between clinical parameters and hub genes was examined to screen for target genes. Next, DNA methylation and genomic alterations of the target gene were evaluated. To further explore potential molecular mechanisms, a functional enrichment analysis of genes coexpressed with the target gene was performed. <b><i>Results:</i></b> The differential expression analysis revealed 217 DEGs in HER-2-positive breast cancer samples compared to normal breast tissues. RRM2 was the only hub gene closely associated with lymphatic metastasis and the patients’ prognosis. Additionally, RRM2 was found to be consistently amplified and negatively associated with the level of methylation. Functional enrichment analysis showed that the coexpressed genes were mainly involved in cell cycle regulation. <b><i>Conclusions:</i></b> RRM2 was identified as a target gene associated with the initiation, progression, and prognosis of HER-2-positive breast cancer, which may be considered as a new biomarker and therapeutic target.
DOI: 10.6084/m9.figshare.19686453.v5
title: RNA-seq Titration Results used in plotting for "Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously"

description: This data accompanies the manuscript "Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously" by Foltz, Taroni, and Greene (https://doi.org/10.1038/s42003-023-04588-6). Please refer to our github page. The file contains all data necessary to recreate the main and supplementary figures in our manuscript. Abstract: Large compendia of gene expression data have proven valuable for the discovery of novel biological relationships. Historically, the majority of available RNA assays were run on microarray, while RNA-seq is now the platform of choice for many new experiments. The data structure and distributions between the platforms differ, making it challenging to combine them directly. Here we perform supervised and unsupervised machine learning evaluations to assess which existing normalization methods are best suited for combining microarray and RNA-seq data. We find that quantile and Training Distribution Matching normalization allow for supervised and unsupervised model training on microarray and RNA-seq data simultaneously. Nonparanormal normalization and z-scores are also appropriate for some applications, including pathway analysis with Pathway-Level Information Extractor (PLIER). We demonstrate that it is possible to perform effective cross-platform normalization using existing methods to combine microarray and RNA-seq data for machine learning applications.
DOI: 10.6084/m9.figshare.28057997.v1
title: Observed GEM and DGM data in the Arctic Ocean

description: This dataset includes the observed concentrations of both atmospheric gaseous elemental mercury and marine dissolved gaseous mercury, and the corresponding auxiliary data. This dataset was acquired in the Arctic Ocean in summertime, 2023.
DOI: 10.6084/m9.figshare.14568657.v2
title: trait_anura_cerrado.txt

description: Functional traits from the AmphiBIO dataset (Oliveira et al., 2017): (i) habitat use (fossorial, terrestrial, aquatic, arbreal); (ii) body size (adult snout vent length in mm); (iii) reproductive strategy (presenting larval stage, oviparous with direct development, and viviparous); (iv) geographical range size, extrated from IUCN Red List (https://www.iucnredlist.org/) (IUCN, 2018). <br>
DOI: 10.6084/m9.figshare.28881296.v1
title: DAB images of liver biopsies with GPNMB staining

description: By integrating single-nucleus transcriptomics, spatial multi-omics, and proteomics in human liver samples, we map the evolving landscape of hepatic macrophages across the MASLD spectrum. Attached images include representative immunohistochemistry (DAB) images of liver biopsies from healthy controls, MASL and MASH patients, illustrating the expression of GPNMB, which were used for quantification.<br>
DOI: 10.6084/m9.figshare.28894748.v1
title: Wskaźnikowa analiza rozwoju społeczno-gospodarczego gmin powiatu krośnieńskiego z uwzględnieniem uwarunkowań kulturowych w latach 2018 i 2023

description: Udostępnione dane stanowiły dane wyjściowe dla badania poziomu rozwoju społeczno-gospodarczego gmin powiatu krośnieńskiego w roku 2018 i 2023.
DOI: 10.6084/m9.figshare.8279618.v2
title: Accurate inference of tree topologies from multiple sequence alignments using deep learning

description: Each directory contains Training, Validation and Test datasets in fasta format. Directory names contain the following information about the MSAs: <br>1) Gap (w/ indels) or nogap (w/o indels) MSAs2) Number of MSAs per topology generated for training (i.e. 50k MSA * 3 possible topologies = 150k MSAs in TRAIN.fasta file) Order of topologies: 50k x ((D,A),B,C); 50k x ((D,B),A,C); 50k x ((D,C),A,B);3) MSA length (500, 1000 or 10000)<br>List of all directories:archive1_gap.tar.gz gap50k_1000 gap50k_10000 gap50k_500archive2_nogap.tar.gz nogap150k_1000 nogap300k_1000 nogap50k_1000 nogap50k_10000 nogap50k_500
DOI: 10.6084/m9.figshare.24463669.v1
title: PyGC-MS raw data files

description: PyGC-MS (Agilent) raw data files for all polymers.
DOI: 10.6084/m9.figshare.26288080.v1
title: NatureCommunications_source_data_071224.xlsx

description: Cash transfer policies have been widely discussed as mechanisms to curb intergenerational transmission of socioeconomic disadvantage. In this paper, we take advantage of a large casino-funded family transfer program introduced in an American Indian community to generate difference-in-difference estimates of the link between children’s cash transfer exposure and third grade math and reading test scores of their offspring.
DOI: 10.6084/m9.figshare.26983180.v1
title: Inventory of methane and nitrous oxide emissions from freshwater aquaculture in China

description: Inventory of methane and nitrous oxide emissions from freshwater aquaculture in China
DOI: 10.6084/m9.figshare.28645343.v1
title: Supplementary data.xlsx

description: This study aimed to utilize two publicly available datasets (ProteomeXchange Consortium, Dataset Identifier: PXD043352; Gene Expression Omnibus, GEO: GSE67539) to explore potential age-dependent regulation of presumptive NeuroD2 target genes. Genome-wide NeuroD2 target sequences were filtered and analyzed for potential age-related changes. This approach aimed to shed light on the hypothetical role of NeuroD2 in age-related molecular mechanisms in the hippocampus.
DOI: 10.6084/m9.figshare.20219354.v1
title: Figure 10. Patterns in soil properties under the flatland and hillslope of grassland domains

description: This dataset is to show the influence of hillslope position on soil properties
DOI: 10.6084/m9.figshare.12221711.v1
title: Raw questionnaire data

description: This dataset contains the raw questionnaire data collected from the virtual reality experiment.<br> <br> Each row contains one participant's answers to all questionnaire items for one environment. Given that each participant experienced nine environments, the file contains 9 rows per participant. Environments are represented by a number (1-14), see explanation below. For questions included in the questionnaire, please see the file "Environment questionnaire."<br> <br> <strong>Environments</strong><br> Virtual environments in the experiment varied along 4 dimensions (location, building height, facade quality and number of people present). The following list explains the features of each environment.<br> <br> 1. S-H0-F0-P0<br> 2. S-H2-F0-P0<br> 3. S-H0-F1-P0<br> 4. S-H0-F0-P1<br> 5. S-H0-F1-P1<br> 6. S-H1-F1-P1<br> 7. S-H2-F1-P1<br> 8. B-H0-F0-P0<br> 9. B-H2-F0-P0<br> 10. B-H0-F1-P0<br> 11. B-H0-F0-P1<br> 12. B-H0-F1-P1<br> 13. B-H1-F1-P1<br> 14. B-H2-F1-P1<br> <br> B and S refer to the locations Bedok and Simei respectively.<br> <br> H refers to building height and has three levels:<br> 0 - uniformly tall<br> 1 - tall at the back, low at the front<br> 2 - uniformly low<br> <br> F refers to facade quality and has two levels:<br> 0 - low quality<br> 1- high quality<br> <br> P refers to number of people present and has two levels<br> 0 - few<br> 1- many<br> <br> <strong>Environments experienced by each group</strong><br> Group A (participants 1-25, 51-52): 1, 2, 6, 7, 8, 10, 11, 12, 14<br> Group B (participants 26-50): 1, 3, 4, 5, 7, 8, 9, 13, 14<br> <strong><br> </strong> <strong>Environment quality<br> </strong> The column "Environment quality" refers to hypothesised environment quality. According to our hypothesis, environments with low buildings, high-quality facades and many people present would be the best environments, with each of these features being independently positive. Thus environment quality ranges from 0-3, with a score of 0 being achieved when all these features are at their "worst" (tall buildings, low-quality facades, and few people present), and a score of 1 being achieved when all features have their best possible value.<br> <br> Note that building height has 3 possible values. In this case, tall buildings gain a score of 0, while low buildings gain a score of 1. Buildings that are tall at the back and low at the front gain a score of 0.5. Facade quality and presence of people both have possible values 0 and 1. Thus possible environment scores are 0, 0.5, 1, 1.5, 2, 2.5 and 3.<br> <br> <br> <strong>Missing data</strong> Some participants did not complete the questionnaire fully, and some technical errors also happened. For these reasons, there is some missing data.<br> <br> <br> <br>
DOI: 10.6084/m9.figshare.3544454.v1
title: Appendix D. Density of nematodes in plant community soils and in plant-specific soils.

description: Density of nematodes in plant community soils and in plant-specific soils.
DOI: 10.6084/m9.figshare.4496456.v1
title: pH-taxis by the dispersal stage of choanoflagellates.

description: We used video microscopy to study the response to gradients of pH of choanoflagellate Salpingoeca rosetta. This choanoflagellates presents a life history that includes fast- and slow-swimming unicellular forms and multicellular colonies. In the associated data we show and quantify the presence of both types of unicellular swimmers.The data shows that unicellular fast swimmers exhibited taxis into patches of attractant. When this type of choanoflagellates is exposed to patches with different pH, we observed accumulation of cells in regions where pH is in the range of 6 to 7. In contrast, a repulsive response is observed at lower pH.
DOI: 10.15468/dl.s44yf3
title: Occurrence Download

description: A dataset containing 128 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Observation, Human Observation, Machine Observation, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Cheilosia vulpina (Meigen, 1822)"
 ]
}

 The dataset includes 128 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009549-250426092105405/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.25395640.v1
title: Informed sampling and recommendation of cycling routes: leveraging crowd-sourced trajectories with weighted-latent dirichlet allocation

description: The data and code for the informed sampling and recommendation of cycling routes
DOI: 10.6084/m9.figshare.24495115.v1
title: Supplementary Material for: Prediction of MCI progression to AD based on DTI-derived diffusion parameters: construction and validation of a nomogram

description: Objective: To construct and validate a nomogram that combines diffusion tensor imaging (DTI) parameters and clinically relevant features for predicting the progression of mild cognitive impairment (MCI) to Alzheimer's disease (AD). Method: A retrospective analysis was conducted on the MRI and clinical data of 121 MCI patients, of whom 32 progressed to AD during a four-year follow-up period. The MCI patients were divided into training and validation sets at a ratio of 7:3. DTI features were extracted from MCI patient data in the training set, and their dimensionality was reduced to construct a radiomics signature (RS). Then, combining the RS with independent predictors of MCI disease progression, a joint model was constructed, and a nomogram was generated. Finally, the area under the receiver operating characteristic curve (AUC) and decision curve analysis (DCA) were used to evaluate the diagnostic and clinical efficacy of the nomogram based on the data from the validation set. Result: The AUCs of the RS in the training and validation sets were 0.81 and 0.84, with sensitivities of 0.87 and 0.78 and specificities of 0.71 and 0.81, respectively. Multiple logistic regression analysis showed that the RS, clinical dementia rating scale score, and Alzheimer's disease assessment scale score were the independent predictors of progression and thus used to construct the nomogram. The AUCs of the nomogram in the training and validation sets were 0.89 and 0.91, respectively, with sensitivities of 0.78 and 0.89 and specificities of 0.90 and 0.88, respectively. DCA showed that the nomogram was the most valuable model for predicting the progression of MCI to AD and that it provided greater net benefits than other analysed models. Conclusion: Changes in white matter fibre bundles can serve as predictive imaging markers for MCI disease progression, and the combination of white matter DTI features and relevant clinical features can be used to construct a nomogram with important predictive value for MCI disease progression.
DOI: 10.6084/m9.figshare.14325848.v1
title: Prevalence of musculoskeletal pain in leather products industry workers: cross-sectional study in a city of the state of Minas Gerais

description: ABSTRACT BACKGROUND AND OBJECTIVES: Musculoskeletal injuries induced by labor process and organization are relevant for health/labor relationship. This study aimed at investigating the prevalence of musculoskeletal complaints and associated factors among leather products manufacturers. METHODS: Cross-sectional study where data were obtained by means of self-applied questionnaires to 320 workers distributed among 13 plants of the city of Cristina, MG, between February and March 2011. Nordic questionnaire of musculoskeletal symptoms was applied to measure the prevalence of complaints in different body regions. A descriptive analysis was carried out on the socio-demographic profile of the studied population. Multivariate logistic regression was used to describe the association between dependent variable, musculoskeletal complaint and the set of explanatory variables, with adjusted odds ratio calculation. Logistic regression was used with adjusted odds ratio calculation. RESULTS: The study involved 138 workers. Better adjusted multivariate model after confusion variables control was for knee pain, with prevalence of 40.0% among males and 24.1% among females. Sewing and finishing sectors behaved as "protection", that is, less chance for pain as compared to the cutting sector. Age had negative association, that is, the higher the age the lower the chance of pain. In a different adjusted model for shoulder pain, workers and time working on the job showed higher chance of pain. CONCLUSION: The prevalence of complaints was higher than that found in the literature. Significant variables were identified which may subsidize the prevention of job distress, such as knee pain. Further studies are needed with the inclusion of other variables and other designs to minimize biases.
DOI: 10.6084/m9.figshare.21382131.v1
title: Phylogenomics reveals extensive misidentification of fungal strains from the genus <i>Aspergillus</i>

description: Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. However, the use of one or few molecular markers can lead to inaccurate inferences of species history and errors in classification. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense dataset of 711 fungal genomes from the biomedically and technologically important genus <i>Aspergillus</i>. To do so, we generated a novel set of 1,362 high-quality molecular markers specific for <i>Aspergillus</i> and provide profile Hidden Markov Models for each, facilitating others to use these molecular markers. Examination of the resulting genome-scale phylogeny: (1) helped resolve ongoing taxonomic controversies and identified new ones; (2) revealed extensive strain misidentification, underscoring the importance of population-level sampling in species classification; and (3) identified novel lineages that may shed light on the early evolution of an important genus. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the tree of life.