cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/pp3ymvhvcp
title: Fluid flow, mineralization and deformation in an oceanic detachment fault: Microtextural, geochemical and isotopic evidence from pyrite at 13°30’N on the Mid-Atlantic Ridge

description: Fluid flow, mineralization and deformation in an oceanic detachment fault: Microtextural, geochemical and isotopic evidence from pyrite at 13°30’N on the Mid-Atlantic Ridge Andrew J. Martin1*, John W. Jamieson2, Sven Petersen3, Mostafa Fayek4, Javier Escartin5 1 Geoscience, University of Nevada, Las Vegas, 89154, USA 2 Department of Earth Sciences, Memorial University of Newfoundland, A1B 1L9, Canada 3 GEOMAR, Helmholtz Centre for Ocean Research Keil, 24128, Germany 4Department of Earth Sciences, University of Manitoba, R3T 2N2, Canada 5Laboratoire de Géologie (CNRS UMR8538), Ecole Normale Supérieure de Paris, PSL University, Paris, France * Corresponding author: Andrew.martin@unlv.edu Geochemical and isotopic dataset for the above manuscript.
DOI: 10.6084/m9.figshare.1211906.v1
title: Vignette Mask

description: Vignette data applied by the filter multiplicatively
DOI: 10.6084/m9.figshare.29137106.v1
title: Rainy spring delayed the late Neogene expansion of C4 biomass over East Asia

description: The clumped isotope and triple oxygen isotope compositions of calcite nodules from three Red Clay sections on the Chinese Loess Plateau
DOI: 10.17632/bcytth299t
title: Data and stata code article

description: Data and stata code for a research article .
DOI: 10.6084/m9.figshare.13614083.v7
title: Soluble alpha klotho in acromegaly: Comparison to traditional markers of disease activity_Supplemental material

description: Soluble alpha klotho in acromegaly: Comparison to traditional markers of disease activity_Supplemental material
DOI: 10.6084/m9.figshare.4144881.v1
title: Supplementary Material for: Association of Dystrobrevin-Binding Protein 1 Polymorphisms with Sustained Attention and Set-Shifting in Schizophrenia Patients

description: <i>Background:</i> Despite extensive research in the past decades, the influence of genetics on cognitive functions in schizophrenia remains unclear. Dystrobrevin-binding protein 1 <i>(DTNBP1)</i> is one of the most promising candidate genes in schizophrenia. An association of <i>DTNBP1</i> with cognitive dysfunction, particularly memory impairment, has been reported in a number of studies. However, the results remain inconsistent. The aim of this study was to measure the association between <i>DTNBP1</i> polymorphisms and cognitive domains in a well-characterized sample. <i>Methods:</i> Ninety-one clinically stable schizophrenia outpatients underwent a battery of cognitive tests. Six single nucleotide polymorphisms (SNPs) of <i>DTNBP1</i> were genotyped in all participants. Statistical and multivariate analyses were performed. <i>Results:</i> Factor analysis revealed 4 factors corresponding to distinct cognitive domains, namely sustained attention, set-shifting, executive functioning, and memory. We found a significant association of the rs909706 polymorphism with attention (p = 0.030) and a nonsignificant trend for set-shifting (p = 0.060). The other SNPs and haplotypes were not associated with cognitive function. <i>Discussion:</i>Replication of this finding in a larger sample is needed in order to confirm the importance of this particular polymorphism in the genetics of schizophrenia, particularly the distinct cognitive domains. In conclusion, the present study supports the involvement of <i>DTNBP1 </i>in the regulation of cognitive processes and demonstrates association in particular with sustained attention and set-shifting in schizophrenia patients.
DOI: 10.6084/m9.figshare.5123491.v1
title: Supplementary Material for: Activation of Transforming Growth Factor-β/Smad Signaling Reduces Aggregate Formation of Mislocalized TAR DNA-Binding Protein-43

description: <b><i>Background:</i></b> TAR DNA-binding protein of 43 kDa (TDP-43) is naturally located in the nucleus and has been identified as the major component of cytoplasmic ubiquitinated inclusions in patients with amyotrophic lateral sclerosis (ALS). We have reported that TDP-43 and phosphorylated Smad2 (pSmad2), an intracellular mediator protein of transforming growth factor-β (TGFβ) signaling, are co-localized within cytoplasmic inclusions in the anterior horn cells of sporadic ALS patients. <b><i>Objective:</i></b> To investigate the possible pathophysiological linkage between pathologic cytoplasmic inclusions containing TDP-43 and TGFβ/Smad signaling. <b><i>Methods:</i></b> We replicated cytoplasmic aggregates of TDP-43 in HEK293T cells by transfecting the cells with a nuclear localization signal deletion mutant of TDP-43 and inhibiting proteasome activity, and assessed the effect of TGFβ/Smad signaling on the cytoplasmic aggregate formation. <b><i>Results:</i></b> The aggregates contained ubiquitinated, phosphorylated, and fragmented TDP-43, consistent with the essential features of the human pathology. Moreover, the aggregates were co-localized with pSmad2 under continuous TGFβ stimulation. Overexpression of Smad2 reduced the amount of cytoplasmic aggregates in HEK293T cells, and TGFβ stimulation augmented this reduction effect in a dose-dependent manner. <b><i>Conclusion:</i></b> Activation of the TGFβ/Smad signaling system is protective against aggregate formation of cytoplasmically mislocalized TDP-43 and may be a potential therapeutic approach to delay progression of ALS.
DOI: 10.6084/m9.figshare.7924337.v2
title: Predicting session-by-session outcomes with the Consultation Interaction Coding Scheme in Cognitive Behaviour Therapy for Severe Health Anxiety

description: This is the SPSS 24 dataset and the SPSS syntax used for the analysis. The syntax files provides guidance notes for each stage of analysis.<br>In a secondary analysis of trial data, two trained raters blind to outcome used audio-visual recordings and transcripts to rate each interaction in the first and second session of cognitive behaviour therapy amongst 50 high service utilisers with severe health anxiety. The Consultation Interaction Coding Scheme (CICS) was used to rate each interaction on the basis of patient activation – a person’s confidence and perceived ability to manage their own health. Sessions were also assessed using the observer-rated working alliance inventory (WAI-O). Multilevel modelling was used to estimate the predictive validity of CICS and WAI-O scores on wellbeing assessed session-by-session using the Outcome Rating Scale.<br>
DOI: 10.17632/v3kbj24jzc
title: Surface Wettability Measurement Instrument

description: This include CAD design part, assembly part, a real time demonstration video file, MATLAB code for determining contact angle, and Arduino code to run the Surface Wettability Measurement Instrument.
DOI: 10.17632/zp9gskrbvg
title: GPU accelerated simulation of channeling radiation of relativistic particles

description: In this paper we describe and demonstrate a C++ code written to determine the trajectory of particles traversing oriented single crystals and a CUDA code written to evaluate the radiation spectra from charged particles with arbitrary trajectories. The CUDA/C++ code can evaluate both classical and quantum mechanical radiation spectra for spin 0 and 1/2 particles. We include multiple Coulomb scattering and energy loss due to radiation emission which produces radiation spectra in agreement with experimental spectra for both positrons and electrons. We also demonstrate how GPUs can be used to speed up calculations by several orders of magnitude. This will allow research groups with limited funding or sparse access to super computers to do numerical calculations as if it were a super computer. We show that one Titan V GPU can replace up to 100 Xeon 36 core CPUs running in parallel. We also show that choosing a GPU for a specific job will have great impact on the performance, as some GPUs have better double precision performance than others.
DOI: 10.6084/m9.figshare.1039393.v1
title: Introduction to Professional Networking for Career Development in Bioinformatics

description: Slides and a handout to introduce and lead an activity aimed at introducing scientists (it was delivered to a group of people interested in bioinformatics) to ways of thinking about professional networking, focused on helping them use it in their career development. The activity focuses on initiating contact with people you don't know at scientific meetings. The material was delivered at the 11th Heidelberg Unseminar in Bioinformatics Meeting in May 2014.
DOI: 10.6084/m9.figshare.12826412.v1
title: Supplementary Material for: Multinational Survey of Treatment Practices of Clinicians Managing Subclinical Hypothyroidism in Older People in 2019

description: <b><i>Background:</i></b> International societies have recommended that levothyroxine should not routinely be prescribed in older individuals for the management of mild subclinical hypothyroidism (SCH). However, it is unknown whether clinicians managing people with SCH are either aware of or adhere to these guidelines. <b><i>Methods:</i></b> A web-based survey of members of several international thyroid associations and general practitioners in North-East England was conducted. Respondents were presented with a vignette of an 80-year-old gentleman with mild persistent SCH experiencing tiredness. Multivariable logistic regression analyses were performed to evaluate predictors of awareness of guidelines and responses to treatment. <b><i>Results:</i></b> The survey response rate was 21.9% (565/2,583). Only 7.6% of clinicians were unaware of guidelines regarding management of SCH in older people. Twenty percent of clinicians stated that they would treat the older patient with mild SCH, whereas 13% were unsure. Clinicians from North America were more likely to treat the older person with mild SCH than clinicians from elsewhere (OR 2.24 [1.25–3.98]). Likewise, non-endocrinologists were also more likely than endocrinologists to treat the older person with mild SCH (OR 3.26 [1.45–6.47]). <b><i>Conclusion:</i></b> The majority of clinicians are aware of guidelines regarding management of SCH in older individuals. However, a considerable proportion of clinicians would still treat an older person with non-specific symptoms and mild SCH. These guidelines need to be disseminated more widely and more research is required to understand barriers to adherence to international recommendations.
DOI: 10.6084/m9.figshare.22109117.v1
title: ESD-1

description: Event-based Segmentation Dataset (ESD), a high-quality 3D spatial and temporal dataset for object segmentation in an indoor cluttered environment. 

MATLAB source code repository:
 yellow07200/ESD_labeling_tool (github.com)
DOI: 10.17632/mkhngj5b27
title: Tokenomics model simulations for bachelor thesis

description: The data is saved in an Excel file, which contains three pages. Page "Attributes" shows the data sets of project community members and their attributes, that are used for the 12 main simulations. Page "DEX simulations" calculations of 12 main simulations. Page "Bonus DEX simulations" shows calculations and data sets of project community members of six bonus DEX simulations.
DOI: 10.6084/m9.figshare.12044307.v1
title: RDF Outputs

description: RML+FnO and GTFS@RDf RDF datasets
DOI: 10.6084/m9.figshare.27273297.v1
title: Supplementary materials for research article titled "Modeling and interpreting the probability of soil heavy metal contamination in China"

description: This zip includes the Supplementary materials mentioned in the paper.
DOI: 10.6084/m9.figshare.12116457.v1
title: Database Oenanthe moult Ibis

description: Raw data employed for data analyses<br>
DOI: 10.25452/figshare.plus.28633379.v1
title: Dataset for "<i>In Vivo</i> Delineation of a Body-Part-Specific Topography in Mouse Secondary Motor Cortex"

description: ̄This dataset accompanies the manuscript: <i>In Vivo</i> Delineation of a Body-Part-Specific Topography in Mouse Secondary Motor Cortex. It includes simultaneous neuronal, hemodynamic, and behavioral recordings, collected using wide-field optical mapping (WFOM).The dataset is organized into the following key components:<b>steps_data</b>: Raw and processed neuronal and hemodynamic signals acquired via WFOM.<b>webcams_data</b>: Synchronized mouse behavioral data captured through video recordings.<b>prepares_data</b>: Processed data used for analysis.<b>figures_data</b>: Supporting data for figures and movies included in the manuscript.All files are systematically structured within clearly labeled folders, corresponding to specific analyses or figure generation.For a detailed description of the repository structure, please visit: GitHub Repository.
DOI: 10.4121/15074172.v2
title: Intracavity time-domain characterisation of a high-power hybrid integrated laser in mode-locked operation

description: This dataset includes raw measurement data and scripts used to process and plot the data used in the resource article.<br>The purpose of the measured data was to observe phase locking of the hybrid laser in multimode operation and reconstruct the time domain both at the outputs and intravacity.<br>The raw measurement data is obtained by a 20 GSa/s real time oscilloscope measuring the beating between a tuneable laser source acting as local oscillator and the hybrid integrated laser where the local oscillator is stepped between each pair of lines of the hybrid laser.<br>Details of the measurement can be found in the resource article, where the measurement followed the procedure described in: "Stepped-heterodyne optical complex spectrum analyzer" by Reid et al. (see reference link)<br><br>
DOI: 10.6084/m9.figshare.14268392.v1
title: Hydrogeochemical characterization of groundwater for public supply in the Northeastern portion of the Guarani Aquifer System

description: ABSTRACT The Guarani Aquifer System (GAS) comprises one of the most important aquifers in the world due to its large water reserve and its groundwater quality. However, some regions that comprise the GAS groundwater for human supply are not thoroughly characterized on water chemistry and its relation with the local geology. This work presents the hydrogeochemical characterization of groundwater from the northeast region of the GAS used for human public supply in São Carlos (São Paulo, Brazil) based on samples from 27 deep boreholes. The groundwater exploration occurs mainly from GAS. However, it is also possible to verify the presence of the Botucatu, Piramboia, Serra Geral, Itaqueri, Adamantina, and Cenozoic sediments. Although little mineralized, there is a large ionic variability in the groundwater composition, also evidenced by spatial distribution of the electrical conductivity in the research area. These results explain four hydrochemical water types: mixed bicarbonate; calcium bicarbonate; sodium bicarbonate; and sodium fluoride, in decreasing order of representativeness. The concentration of ions in groundwater reflects the geological heterogeneity, through mineral dissolution and possible groundwater mixing. A Principal Component Analysis demonstrated that 62.7% of the total sample set variability is explained by two main factors. The first one represents 38.7% of the variability; mainly attributed to ions from minerals dissolution (HCO3−, Ca2+, Na+, Mg2+) and parameters related to this process (pH and electrical conductivity). The second group showed 24.0% of the total variability, which may be associated with anthropic activities origins, such as the presence of Cl−, N-NO3−, SO42-, F−, and K+.
DOI: 10.6084/m9.figshare.21378330.v1
title: iTOL input files for Mtb L4 in southeast asia

description: The data files needed to make the iTOL figures.
DOI: 10.6084/m9.figshare.29146886.v1
title: Pretrained Models

description: A foundation model for scRNA analysis.
DOI: 10.6084/m9.figshare.8131949.v3
title: Chapter 4

description: Data and R code associated with the chapter 4 of the PhD thesis entitled "Vertebrate community disassembly in human-induced Amazonian forest islands".<br>
DOI: 10.17632/zmkc9db4zj
title: QMMM 2023: A program for combined quantum mechanical and molecular mechanical modeling and simulations

description: Combined quantum mechanical and molecular mechanical (QM/MM) methods play an important role in multiscale modeling and simulations. QMMM 2023 is a general-purpose program for single-point calculations, geometry optimizations, transition-state optimizations, and molecular dynamics (MD) at the QM/MM level. It calls a QM package and an MM package to perform the required single-level calculations and combines them into a QM/MM energy by a variety of schemes. QMMM 2023 supports GAMESS-US, Gaussian, and ORCA as QM packages and Tinker as the MM package. Four types of treatments are available for embedding the QM subsystem in the MM environment: mechanical embedding with gas-phase calculations of the QM region, electronic embedding that allows polarization of the QM region by the MM environment, polarizable embedding for mutual polarization of the QM and MM regions, and flexible embedding for both mutual polarization and partial charge transfer between the QM and MM regions. Boundaries between QM and MM regions that pass through covalent bonds can be treated by several methods, including the redistributed charge (RC) scheme, redistributed charge and dipole (RCD) scheme, balanced-RC scheme, balanced-RCD scheme, screened charge scheme that takes account of charge penetration effects, and smeared charge scheme that delocalizes the MM charges near the QM–MM boundary. Geometry optimization can be done using the optimizer implemented in QMMM 2023 or the Berny optimizer in Gaussian through external calls to Gaussian. Molecular dynamics simulations can be performed at the pure-MM level, pure-QM level, fixed-partitioning QM/MM level, and adaptive-partitioning QM/MM level. The adaptive-partitioning treatments permit on-the-fly relocation of the QM–MM boundary by dynamically reclassifying atoms or groups into the QM or MM subsystems.
DOI: 10.15468/dl.nftekv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sagamichthys schnakenbecki (Krefft, 1953)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((7.9186 1.8496,7.918 1.8981,7.6701 2.1458,7.2444 2.1771,6.9224 1.8988,6.9096 1.8496,7.9186 1.8496))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013105-250525065834625/datasets/export for details.
DOI: 10.6084/m9.figshare.10653830.v1
title: Supplementary Material for: Development of a Novel Inflammation-Based Index for Hepatocellular Carcinoma

description: <b><i>Background:</i></b> The aim of current study was to (1) construct and validate a novel hepatocellular carcinoma (HCC)-specific inflammatory index; (2) compare the performances of the Integrated Liver Inflammatory Score (ILIS) to existing 4 inflammatory indices in HCC; (3) explore the association between the inflammatory indices and systemic/intratumoral inflammatory markers. <b><i>Methods:</i></b> Two cohorts from Hong Kong (HK; <i>n</i> = 1,315) and Newcastle (<i>n</i> = 574) were studied. A novel index was constructed from the HK training set (<i>n</i> = 627). The index was constructed from the training set by combing independent prognostic circulating parameters, followed by validating in the validation set of HK cohort (<i>n</i> = 688) and the Newcastle cohort. Its prognostic performance was compared to 4 inflammatory indices, namely, the neutrophil to lymphocyte ratio, platelet-to-lymphocyte ratio, prognostic nutrition index, and systemic immune-inflammation index, were compared in the HK cohort. Circulating cytokines and intratumoral gene expression were analyzed in a subset of patients with available samples and correlated with the inflammatory indices. <b><i>Results:</i></b> In the training set of the HK cohort, the ILIS, was generated: –0.057 × albumin (g/L) + 0.978 × log (Bilirubin, µmol/L) + 1.341 × log (alkaline phosphatase, IU/L) + 0.086 × Neutrophil (10<sup>9</sup>/L) + 0.301 × log (alpha-fetoprotein, µg/L). With cutoff of 2.60 and 3.87, the ILIS could categorize patients into 3 risk groups in the both validation cohorts. ILIS outperforms other inflammatory indices and remains an independent prognosticator for overall survival after adjustment with Barcelona Clinic Liver Cancer (hazard ratio 31.90, <i>p</i> &lt; 0.001). The ILIS had the best prognostic performances as compared to other inflammatory indices. In exploratory analyses, the ILIS correlated with circulating inflammatory cytokines (e.g., IL-8) but not with any intratumoral inflammatory gene expression. <b><i>Conclusions:</i></b> ILIS is an HCC-specific prognostic index built on 5 readily available blood parameters. Its versatility is validated both Eastern and Western population of HCC. The score is correlated with levels of circulating cytokines.
DOI: 10.6084/m9.figshare.26543653.v1
title: Structure, thermodynamics, and viscosity of MgSiO<sub>3</sub> liquid in super-Earths and sub-Neptunes

description: Data used in the figures and examples of outputs from molecular dynamics simulations
DOI: 10.6084/m9.figshare.28369787.v1
title: Data for Elsden et al., 2025 submitted to JGR Space Physics: Theory and Modelling of Large Scale Plasmapause Surface Waves

description: Data files for reproducing figures in the manuscript.