cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25853371.v1
title: Supplementary Material for: Interaction of statherin derived peptide with the surface of hydroxyapatite: perspectives based on molecular dynamics simulations

description: Introduction: Statherin-derived peptide (StatpSpS) has shown promise against erosive tooth wear. To elucidate its interaction with the hydroxyapatite (HAP) surface, the mechanism related to adsorption of this peptide with HAP was investigated through nanosecond long all atom molecular dynamics simulations. Methods: StatpSpS was positioned parallel to the HAP surface in 2 orientations: 1 - neutral and negative residues facing the surface; 2 - positive residues facing the surface. A system containing StatpSpS without HAP was also simulated as control. In the case of systems with HAP, both partially restrained surface and unrestrained surface were constructed. Structural analysis, interaction pattern and binding free energy were calculated. Results: In the peptide system without the HAP there were some conformational changes during the simulation. In the presence of the surface, only moderate changes were observed. Many residues exhibited short and stable distances to the surface, indicating strong interaction. Specially, the residues ASP1 and SER2 have an important role to anchor the peptide to the surface, with positively charged residues, mainly arginine, playing a major role in the further stabilization of the peptide in an extended conformation, with close contacts to the HAP surface. Conclusion: The interaction between StatpSpS and HAP is strong, and the negative charged residues are important to the anchoring of the peptide in the surface, but after the initial placement the peptide rearranges itself to maximize the interactions between positive charged residues.
DOI: 10.17632/v26fwnttz2.1
title: LINF_170009200

description: Zinc finger (RING-type)-containing protein; Leishmania infantum (strain JPCM5)
DOI: 10.6084/m9.figshare.22082330.v1
title: DataSet.xlsx

description: Sociodemographic factors, comorbidities, in-hospital complications, and outcomes of ischaemic stroke patients in the context of the COVID-19 pandemic in Lithuania: a retrospective record-based observational study.
DOI: 10.6084/m9.figshare.24003654.v1
title: Supplementary Material for: Recurrent Acute on Chronic Respiratory Failure in Stiff Person Syndrome

description: Abstract: Stiff person syndrome (SPS) is an extremely rare disease that presents with episodic painful muscle spasms and progressive muscle rigidity. Recent evidence suggests that SPS can rarely manifest with life threatening respiratory complications. However, the pathophysiology behind respiratory failure in SPS is still not clearly understood. Here we explored an extremely rare case of a 36-year-old African-American female with SPS presenting with multiple episodes of respiratory failure events for the past 9 years. She had an in-situ tracheostomy and was admitted to the hospital for tracheostomy evaluation and decannulation. She initially presented 11 years ago with gait abnormalities, stiffness and spastic episodes. She was diagnosed one year later with SPS after detecting elevated anti-glutamic acid decarboxylase antibody levels in her blood. Through this report we were able to follow a very rare case of SPS that presented with multiple episodes of respiratory failure. We pointed out the importance of early start and regular administration of diazepam, baclofen and IVIg in not only controlling the symptoms and progression of the disease but also in preventing further respiratory failure and possible sudden death.
DOI: 10.6084/m9.figshare.28705895.v2
title: Analysis of the distribution of CpG sites across the genomes of two Bat SARS-like coronaviruses, ZXC21 and ZC45 (2015-2017), using a sliding window approach.

description: This project analyzes the distribution of CpG sites across the genomes of two Bat SARS-like coronaviruses, ZXC21 and ZC45 (2015-2017), using a sliding window approach. Key findings include:<br>- CpG Counts : Both viruses exhibit regions with elevated CpG densities, suggesting potential functional significance.- Observed/Expected Ratios : Most regions show CpG depletion (O/E ratio &lt; 1), consistent with evolutionary pressures observed in coronaviruses.- Comparison : The results for ZXC21 and ZC45 are nearly identical, indicating similar CpG dynamics and evolutionary strategies.<br> Dataset Includes:- Tab-delimited files (`ZXC21_sliding_window_cpg_analysis.txt`, `ZC45_sliding_window_cpg_analysis.txt`) containing CpG counts and O/E ratios for each sliding window.- Visualizations: - Bar charts showing CpG counts across sliding windows for both viruses. - Line plots illustrating observed/expected (O/E) ratios for both viruses.- Python scripts used for performing the sliding window analysis and generating plots.- Input genome files (`MG772933.gb`, `MG772934.gb`).<br> Methods:The analysis was performed using the following steps:1. Divided the genomes into fixed-size windows (100 bp) with a step size of 50 bp.2. Calculated CpG counts and observed/expected (O/E) ratios for each window.3. Generated visualizations using Python libraries like Pandas and Matplotlib.<br> Implications:This work contributes to understanding the genomic architecture of Bat SARS-like coronaviruses and their evolutionary strategies. The findings align with broader trends observed in coronaviruses, highlighting shared mechanisms of CpG dynamics.<br>Published on Figshare: 10.6084/m9.figshare.28705895
DOI: 10.6084/m9.figshare.8396873.v1
title: Data for The importance of preferential associations and group cohesion: Constraint or optimality

description: Data for The importance of preferential associations and group cohesion: Constraint or optimality<br>Contents: <br>Social networksDominance hierarchies<br>
DOI: 10.6084/m9.figshare.16936906.v1
title: Experimental data(Main, SI)

description: All experimental data
DOI: 10.6084/m9.figshare.23798379.v1
title: Neurips_randomoversampling.h5ad

description: Neurips random oversampling dataset.
DOI: 10.6084/m9.figshare.24144246.v1
title: <b>A comprehensive analysis of the causal relationship between homocysteine and diabetic nephropathy: Mendelian randomization and mediator analysis</b>

description: the supplyment data for A comprehensive analysis of the causal relationship between homocysteine and diabetic nephropathy: Mendelian randomization and mediator analysis
DOI: 10.17632/rkmf4gxdwb.1
title: LINF_170009400

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.6084/m9.figshare.28669043.v1
title: Data Source for Day-Ahead Dispatch with Feature Decomposition and Built-in Modeling of Intra-Interval Power Balance

description: We use IEEE 30-bus system and practical 661-bus utility system to verify the effectiveness of the proposed day-ahead dispatch method. The parameters of generators in the IEEE 30-bus system and the practical 661-bus utility system have been uploaded.
DOI: 10.6084/m9.figshare.28869017.v1
title: Microstructure & physicochemical properties dataset of NaCl-based salt mixtures for concentrating solar power

description: We create two Excel files in our dataset. The details of the thermal expansion coefficient, thermal conductivity, specific enthalpy of fusion, specific capacity, density, and viscosity for 21 NaCl-based molten salt mixtures in different temperature ranges are recorded in an Excel file named <i>physicochemical properties dataset</i>. And another Excel file named <i>microstructure dataset </i>contains the details of the ionic self-diffusion coefficient, coordination bond angle, coordination bond length, and coordination number of different ion pairs for the mixtures in different temperature ranges.
DOI: 10.6084/m9.figshare.12681824.v1
title: Gabay & Weinstein - Spirituality, Emotional Labor, productivity [312 subjets].csv

description: Gabay & Weinstein: Spirituality, Emotional Labor, productivity [312 subjects]
DOI: 10.6084/m9.figshare.21313233.v1
title: 2022_Jayakumar_CurrentBiology_rawdata

description: This project contains all the raw data used in Jayakumar P, Thomas S. A., Brown S. P. and Kümmerli R (2022) Collective decision-making in <em>Pseudomonas aeruginosa </em>involves transient segregation of quorum sensing activities across cells (Current Biology)
DOI: 10.6084/m9.figshare.21620856.v1
title: Genotype_file

description: Chicken ped and map files
DOI: 10.6084/m9.figshare.18551078.v1
title: Spreadsheet data for LIMS Paper 2022

description: results of survey and ESS pre & post COVID delay to treatment
DOI: 10.6084/m9.figshare.25857631.v1
title: Codes and data for "Climate regulates the effects of abrupt vegetation shifts on soil moisture on the Loess Plateau, China"

description: The codes and dataset were used in article "Climate regulates the effects of abrupt vegetation shifts on soil moisture on the Loess Plateau, China"
DOI: 10.6084/m9.figshare.28013798.v1
title: Supplementary Material for: Regional deprivation and diabetic ketoacidosis at type 1 diabetes diagnosis in children and adolescents: International comparison among 6 countries

description: Introduction: The incidence of diabetic ketoacidosis (DKA) at the time of diagnosis of type 1 diabetes in youth varies between countries and is influenced by socioeconomic factors. We investigated the relationship between regional deprivation indices and DKA at diagnosis of type 1 diabetes in six countries.

Methods: We analyzed children 0.5 to 17.0 years old diagnosed with type 1 diabetes between 2019-2022 across six diabetes registries. Regional deprivation index within each country was standardized to compare each individual’s socioeconomic status internationally. Log-binomial regression models assessed the association between the standardized deprivation index and DKA, with sex, age group, and year as covariates.

Results: Among 21,020 children (mean age 9.08 [SD 4.19] years) the DKA rate of 36.5%. Cohorts were: Germany (n=13,561, DKA 32.5%), Italy (4,659, 42.5%), Colorado USA (1,318, 54.9%), Wales (769, 35.2%), New Zealand (407, 43.7%), and Slovenia (306, 37.6%). Deprivation was associated with increased risk of DKA in children 0.5-&lt; 6 (OR 1.16 [95% CI 1.10 - 1.23], p &lt; 0.0001) and 6-&lt;12 years of age (1.05 [1.05 – 1.11], p = 0.02). Female sex increased risk of DKA (1.06, [1.00 - 1.13], p = 0.04). The proportion of DKA was lower in 2019 than in 2020, 2021, and 2022 (each p &lt; 0.0001).

Conclusion: Deprivation was significantly associated with the risk of DKA at the diagnosis of type 1 diabetes, and DKA was more common during the pandemic years 2020-2022 than in 2019. Younger children appear to be more vulnerable to deprivation than older patients. Understanding and reducing local and demographic-specific disparities is essential for effective intervention.
DOI: 10.6084/m9.figshare.5418907.v2
title: Table S1. Protein sequence accession numbers from Novel and divergent genes in the evolution of placental mammals.

description: List of NCBI and Ensembl protein IDs used to generate the combined data set, numerical identifiers for the Homology Group each protein was placed into, and indication of whether genes/HG were assigned to Novel Ancestral Placental and Novel Core Placental HG. Excel file.
DOI: 10.23645/epacomptox.16744162.v4
title: Development of a Flame Retardant and an Organohalogen Flame Retardant Chemical Inventory

description: Katherine Phillips dataset for journal article "The US CPSC/EPA Flame Retardant and Organohalogen Flame Retardant Inventory" for Scientific Data<br>Science Inventory, CCTE products: https://cfpub.epa.gov/si/si_public_search_results.cfm?advSearch=true&showCriteria=2&keyword=CCTE&TIMSType=&TIMSSubTypeID=&epaNumber=&ombCat=Any&dateBeginPublishedPresented=07/01/2017&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&DEID=&personName=&personID=&role=Any&journalName=&journalID=&publisherName=&publisherID=&sortBy=pubDate&count=25
DOI: 10.6084/m9.figshare.20977168.v1
title: Immunostaing HCV protocol

description: Immunostaining HCV on Huh7 cells
DOI: 10.17632/bh576fdcbm.1
title: LINF_170010000

description: EF-hand calcium-binding domain-containing protein; Leishmania infantum (strain JPCM5)
DOI: 10.6084/m9.figshare.13317686.v1
title: Interactive effects of temperature, water, and nitrogen availability on the growth, floral traits, and pollination of white mustard, Sinapis alba

description: Data accompanying the following manuscript:Akter A. & Klečka J. (2020) Interactive effects of temperature, water, and nitrogen availability on the growth, floral traits, and pollination of white mustard, <i>Sinapis alba</i>.<br>
DOI: 10.17632/vnn22jdmjn.1
title: LINF_170010100

description: Qa-SNARE protein; Leishmania infantum (strain JPCM5)
DOI: 10.6084/m9.figshare.21176449.v1
title: Data study metaphors of time

description: TIME is a highly abstract concept and prevalent in languages worldwide. Cross-cultural and cross-linguistic research suggests that TIME is embodied dissimilarly in different languages. Still the literature has not received sufficient attention in examining the differences. This study aimed to identify and compare how TIME is metaphorically represented and embodied worldwide. We investigated 14 languages; Arabic, Assamese, Chinese, English, Finnish, French, German, Japanese, Kikuyu, Persian, Polish, Russian, Spanish, and Swedish, which represent nine language families. The metaphors were categorized conceptually as TIME IS AN ORGANISM, TIME IS MOTION, TIME IS SPACE, and TIME IS VALUABLE to see how universally these concepts were embodied. We employed a two-part paper-based task. The first part consisted of generation of metaphor items and the second part consisted of a valence rating task. 'The key variables considered were 'metaphor category' and 'language family' while controlling for demographic variables such as gender, age and handedness. Data from 513 participants were collected. Results showed a significant association between language categories and the valences of time metaphors. The data of this study suggest that within the languages of a certain category, there might be some similarity between the valences of words that are used to realize a given conceptual metaphor.
DOI: 10.6084/m9.figshare.19425515.v1
title: TRECCOVID-RF-Aspire

description: This is a copy of the TRECCOVID-RF dataset used in the paper "Multi-Vector Models with Textual Guidance for Fine-Grained Scientific Document Similarity" by Sheshera Mysore, Arman Cohan, Tom Hope. The TRECCOVID dataset presents an ad-hoc search dataset. The versions of the original dataset used may be accessed here: query topics, relevance annotations, and the metadata for papers is obtained from the CORD-19 dataset in the 2021-06-21 release. The dataset released here converts the original TRECCOVID dataset into a reformulated form, TRECCOVID-RF which is used in the paper. <br><br>See further details of the paper, how this dataset was compiled, and how it was used: https://github.com/allenai/aspire<br>The contents of the dataset are as follows: <br><code>abstracts-treccovid.jsonl</code>: <code>jsonl</code> file containing the paper-id, abstracts, and titles for the queries and candidates which are part of the dataset.<br> <code><code>treccovid</code>-queries-release.csv</code>: Metadata associated with every query.<code>test-pid2anns-</code><code><code>treccovid</code>.json</code>: JSON file with the query paper-id, candidate paper-ids for every query paper in the dataset. Use these files in conjunction with <code>abstracts-</code><code><code>treccovid</code>.jsonl</code> to generate files for use in model evaluation. <br><code><code>treccovid</code>-evaluation_splits.json</code>: Paper-ids for the splits to use in reporting evaluation numbers. <code>aspire/src/evaluation/ranking_eval.py</code> included in the github repo accompanying this dataset implements the evaluation protocol and computes evaluation metrics. Please see the paper for descriptions of the experimental protocol we recommend to report evaluation metrics.<br>
DOI: 10.6084/m9.figshare.21836586.v1
title: Total-data.xlsx

description: The study covers a large area of natural forests in Northeastern China. The latitudinal and longitudinal ranges of the study region extend from 39–54°N (across 15 degree range) and 119–134°E (15 degree range), respectively. The climate varies from a middle temperate zone to a cool temperate zone. All these zones are characterized by strong seasonality with four distinctly different seasons. The main precipitation period is between July and September, and there is a harsh dry spring season. The database includes 262 plots, each containing four 100 m<sup>2</sup> circular subplots. The distance between any two adjacent subplots is 15 m. The latitudinal range of these plots extends from 39 to 54° N (a range of 15°). The total land area of the investigated region is approximately 700 000 km<sup>2</sup>, of which more than one-third is covered by temperate broadleaf and mixed coniferous forests (FAO & UN, 2020; Olson et al., 2001).
DOI: 10.6084/m9.figshare.25416583.v3
title: ner dataset and code of paper "Accelerating the Exploration of Information in Chinese Geological Texts Using Pretrained Model and Self Attention"

description: The datasets and code used in this study are publicly available.Datasets:The datasets used in this study have been divided into training, testing, and validation sets.Code:This code repository includes Python scripts that replicate the experimental setup described in the paper. The code is organized into the following modules:Data Preprocessing: This module contains code for loading, cleaning, and transforming the datasets.Model Training: This module includes code for training various named entity recognition models using pre-trained language models. The code also includes implementations of the ablation experiments and data augmentation techniques described in the paper.Evaluation: This module contains code for evaluating the performance of the trained models on the held-out data sets.The data and code are provided to facilitate reproducibility and further research on named entity recognition in the Chinese language.<br><b>Clarification: None of the authors are affiliated with Tsinghua University.</b>
DOI: 10.6084/m9.figshare.27106726.v1
title: <b>Tabela 1. </b>Caracterização dos serviços de saúde participantes da pesquisa nos estados do Rio Grande do Norte e Rio de Janeiro

description: <b>Tabela 1. </b>Caracterização dos serviços de saúde participantes da pesquisa nos estados do Rio Grande do Norte e Rio de Janeiro
DOI: 10.6084/m9.figshare.26520031.v1
title: Supplementary Material for: Coagulation risk predicting in anticoagulant-free CRRT

description: Introduction: Continuous Renal Replacement Therapy (CRRT) is a prolonged continuous extracorporeal blood purification therapy to replace impaired renal function. Typically, CRRT therapy requires routine anticoagulation, but for patients at risk of bleeding and with contraindications to sodium citrate, anticoagulant-free dialysis therapy is necessary. However, this approach increases the risk of CRRT circuit coagulation, leading to treatment interruption and increased resource consumption. In this study, we utilized artificial intelligence machine learning methods to predict the risk of CRRT circuit coagulation based on pre-CRRT treatment metrics.
Methods: We retrospectively analyzed 212 patients who underwent anticoagulant-free CRRT from October 2022 to October 2023. Patients were categorized into high-risk and low-risk groups based on CRRT circuit coagulation within 24 hours. We employed eight machine learning methods to predict the risk of circuit coagulation. The performance of the model was evaluated using the area under the curve (AUC) of the receiver operating characteristic (ROC). 5-fold cross-validation was used to validate the machine learning models. Feature importance and SHAP plots were used to interpret the model's performance and key drivers.
Results: We identified 88 patients (41.51%) at high risk of circuit coagulation within 24 hours of CRRT. Our machine learning models showed excellent predictive performance, with ensemble learning (EL) achieving an AUC of 0.863 (95% CI 0.860 - 0.868), outperforming individual algorithms. Random forest (RF) was the best single-algorithm model, with an AUC of 0.819(95% CI 0.814 - 0.823). The top three features identified as most important by the SHAP summary plot and feature importance graph are platelet, FF, and triglycerides. 
Conclusion: We created a model using machine learning to predict the risk of circuit coagulation during anticoagulant-free CRRT therapy. Our model performs well (AUC 0.863) and identifies key factors like platelets, filtration fraction, and triglycerides. This facilitates the development of personalized treatment strategies by clinicians, aimed at reducing circuit coagulation risk, thereby enhancing patient outcomes and reducing healthcare expenses.
DOI: 10.6084/m9.figshare.8230517.v1
title: Supplementary Material for: Age-Related Oxidative Changes in Primary Porcine Fibroblasts Expressing Mutated Huntingtin

description: <b><i>Background:</i></b> Huntington’s disease (HD) is a devastating neurodegenerative disorder caused by CAG triplet expansions in the huntingtin gene. Oxidative stress is linked to HD pathology, although it is not clear whether this is an effect or a mediator of disease. The transgenic (TgHD) minipig expresses the N-terminal part of human-mutated huntingtin and represents a unique model to investigate therapeutic strategies towards HD. A more detailed characterization of this model is needed to fully utilize its potential. <b><i>Methods:</i></b> In this study, we focused on the molecular and cellular features of fibroblasts isolated from TgHD minipigs and the wild-type (WT) siblings at different ages, pre-symptomatic at the age of 24–36 months and with the onset of behavioural symptoms at the age of 48 months. We measured oxidative stress, the expression of oxidative stress-related genes, proliferation capacity along with the expression of cyclin B1 and D1 proteins, cellular permeability, and the integrity of the nuclear DNA (nDNA) and mitochondrial DNA in these cells. <b><i>Results:</i></b> TgHD fibroblasts isolated from 48-month-old animals showed increased oxidative stress, which correlated with the overexpression of <i>SOD2</i> encoding mitochondrial superoxide dismutase 2, and the <i>NEIL3</i> gene encoding DNA glycosylase involved in replication-associated repair of oxidized DNA. TgHD cells displayed an abnormal proliferation capacity and permeability. We further demonstrated increased nDNA damage in pre-symptomatic TgHD fibroblasts (isolated from animals aged 24–36 months). <b><i>Conclusions:</i></b> Our results unravel phenotypic alterations in primary fibroblasts isolated from the TgHD minipig model at the age of 48 months. Importantly, nDNA damage appears to precede these phenotypic alterations. Our results highlight the impact of fibroblasts from TgHD minipigs in studying the molecular mechanisms of HD pathophysiology that gradually occur with age.
DOI: 10.6084/m9.figshare.7270868.v4
title: Supplemental Table 1. Pubertal stage and ovarian function of patients with nonclassic LCAH

description: Supplemental Table 1 (J Clin Endocrinol Metab. 2018 Nov 23. doi: 10.1210/jc.2018-01752.)
DOI: 10.17632/vkrknvvcgz
title: LINF_170010300

description: RING-type zinc finger domain-containing protein; Leishmania infantum (strain JPCM5)
DOI: 10.17632/vkrknvvcgz.1
title: LINF_170010300

description: RING-type zinc finger domain-containing protein; Leishmania infantum (strain JPCM5)