cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7953551
title: Unprecedented recent regional increase in Organic Carbon and Lithogenic fluxes in high altitude Pyrenean lakes (Dataset)

description: The datasets generated during and/or analysed in the article "Unprecedented recent regional increase in Organic Carbon and Lithogenic fluxes in high altitude Pyrenean lakes" (Scientific reports)
DOI: 10.34740/kaggle/dsv/5731081
title: Dota 2 Pro League Matches 2023
DOI: 10.6084/m9.figshare.19808841
title: Digitization of three-dimensional spine curvature profile in adolescent idiopathic scoliosis using anatomical palpation

description: The need for spaced radiological follow-up of adolescents with idiopathic scoliosis (AIS) stimulates the development of radiation-free methodologies to document spinal curvature parameters. The aim of the study was to develop a methodology, referred to as A-Palp, using index finger pulp palpation to assess 3D spinal curvature in the standing position in patients and control group. To estimate repeatability for 2D/3D curvature angles, three manual palpations of spinal curvature were performed by one examiner using an index finger pulp calibrated in an optoelectronic system to acquire these curvature angles in the sagittal and frontal planes and in the 3D plane of maximum curvature. The intrarater repeatability was analysed by generalisability theory and the dependability index <i>ϕ</i> combined with a decision D-study to judge the number of desirable repetitions. The A-Palp/radiograph concurrent validity of 2D/3D apex angles was studied by linear regression and Bland–Altman plot. For the scoliosis angle in AIS patients, the <i>ϕ</i> index was excellent, above 0.9, with a standard error of measurement and minimal detectable change below 3° and 9°, respectively. For A-Palp/radiograph comparison, 95% of 2D and 3D measurement results were between 8° and 11° below and 12° and 5° above the radiographic apex angle, respectively, with a bias below 3°. The good repeatability and concurrent validity show that this innovative radiation-free 3D methodology seems suitable for the assessment of AIS patients when the same examiner repeats the measurement two or three times according to the D-study.
DOI: 10.6084/m9.figshare.19808841.v1
title: Digitization of three-dimensional spine curvature profile in adolescent idiopathic scoliosis using anatomical palpation

description: The need for spaced radiological follow-up of adolescents with idiopathic scoliosis (AIS) stimulates the development of radiation-free methodologies to document spinal curvature parameters. The aim of the study was to develop a methodology, referred to as A-Palp, using index finger pulp palpation to assess 3D spinal curvature in the standing position in patients and control group. To estimate repeatability for 2D/3D curvature angles, three manual palpations of spinal curvature were performed by one examiner using an index finger pulp calibrated in an optoelectronic system to acquire these curvature angles in the sagittal and frontal planes and in the 3D plane of maximum curvature. The intrarater repeatability was analysed by generalisability theory and the dependability index <i>ϕ</i> combined with a decision D-study to judge the number of desirable repetitions. The A-Palp/radiograph concurrent validity of 2D/3D apex angles was studied by linear regression and Bland–Altman plot. For the scoliosis angle in AIS patients, the <i>ϕ</i> index was excellent, above 0.9, with a standard error of measurement and minimal detectable change below 3° and 9°, respectively. For A-Palp/radiograph comparison, 95% of 2D and 3D measurement results were between 8° and 11° below and 12° and 5° above the radiographic apex angle, respectively, with a bias below 3°. The good repeatability and concurrent validity show that this innovative radiation-free 3D methodology seems suitable for the assessment of AIS patients when the same examiner repeats the measurement two or three times according to the D-study.
DOI: 10.6084/m9.figshare.21080638
title: Development of a model to predict 3D femur morphology in infants and young children

description: The purpose of this study was to develop a predictive model to generate representative 3D paediatric femur models for age 0–3 years based on child characteristics. Computed tomography (CT) images of 79 decedent (age 0–3 years) femurs were used to develop a statistical shape model characterising femur shape. A regression model predicted shape parameters from child characteristics (age, height, and weight). The predictive model demonstrated good fit (R<sup>2</sup> = 0.976) in predicting femur shape (surface coordinates) in the test set (n = 17) and thus, can be used to generate representative 3D paediatric femur models in the absence of CT imaging.
DOI: 10.6084/m9.figshare.21080638.v1
title: Development of a model to predict 3D femur morphology in infants and young children

description: The purpose of this study was to develop a predictive model to generate representative 3D paediatric femur models for age 0–3 years based on child characteristics. Computed tomography (CT) images of 79 decedent (age 0–3 years) femurs were used to develop a statistical shape model characterising femur shape. A regression model predicted shape parameters from child characteristics (age, height, and weight). The predictive model demonstrated good fit (R<sup>2</sup> = 0.976) in predicting femur shape (surface coordinates) in the test set (n = 17) and thus, can be used to generate representative 3D paediatric femur models in the absence of CT imaging.
DOI: 10.6084/m9.figshare.20373826
title: Robust whole-tumour 3D volumetric CT-based radiomics approach for predicting the WHO/ISUP grade of a ccRCC tumour

description: Clear Cell Renal Cell Carcinoma (ccRCC) is a common and major type of cancer. It is clinically vital to know the nuclear grade of a ccRCC tumour pre-surgically and non-invasively as this may impact therapeutic actions. We hypothesise that using three-dimensional (3D) radiomic features and ensemble learning models can increase the discrimination power between grades. The hybrid feature selection method was used to reduce the number of features. Besides the actual tumour volume, five additional volumes of interests (VOIs) were created to consider peritumour regions and test the robustness of the model against variations in segmentation. The best result was acquired when Synthetic Minority Oversampling Technique (SMOTE) was used in combination with Light Gradient Boosting Machine (LightGBM). The area under the curve (AUC) for this model was 0.89 ± 0.02. The results were 0.86 and 0.83 when the contour was made smaller and larger by 2 mm. We conclude that a ccRCC tumour grade can be predicted from 3D CT images with a high reliability, despite the inadequacy of a dataset. The algorithm is moderately robust against deviations in segmentation by observers. The features from the peritumour area did not result in any significant improvement.
DOI: 10.6084/m9.figshare.20373826.v1
title: Robust whole-tumour 3D volumetric CT-based radiomics approach for predicting the WHO/ISUP grade of a ccRCC tumour

description: Clear Cell Renal Cell Carcinoma (ccRCC) is a common and major type of cancer. It is clinically vital to know the nuclear grade of a ccRCC tumour pre-surgically and non-invasively as this may impact therapeutic actions. We hypothesise that using three-dimensional (3D) radiomic features and ensemble learning models can increase the discrimination power between grades. The hybrid feature selection method was used to reduce the number of features. Besides the actual tumour volume, five additional volumes of interests (VOIs) were created to consider peritumour regions and test the robustness of the model against variations in segmentation. The best result was acquired when Synthetic Minority Oversampling Technique (SMOTE) was used in combination with Light Gradient Boosting Machine (LightGBM). The area under the curve (AUC) for this model was 0.89 ± 0.02. The results were 0.86 and 0.83 when the contour was made smaller and larger by 2 mm. We conclude that a ccRCC tumour grade can be predicted from 3D CT images with a high reliability, despite the inadequacy of a dataset. The algorithm is moderately robust against deviations in segmentation by observers. The features from the peritumour area did not result in any significant improvement.
DOI: 10.23728/b2share.ae08189026c44147bf747701fe97b1e0
title: Monte Carlo Simulations for the ACCESS white paper

description: The ACCESS (Array of Cryogenic Calorimeters to Evaluate Spectral Shapes) project aims to establish a novel technique to perform precision measurements of forbidden β-decays, which can serve as an important benchmark for nuclear physics calculations and represent a significant background in astroparticle physics experiments. ACCESS will operate a pilot array of cryogenic calorimeters based on natural and doped crystals containing β-emitting radionuclides. In this way, natural (e.g. Cd-113 and In-115) and synthetic isotopes (e.g. Tc-99) will be simultaneously measured with a common experimental technique. The array will also include further crystals optimized to disentangle the different background sources, thus reducing the systematic uncertainty. In this dataset, we collect the Monte Carlo simulations (based on GEANT 4 and stored as ROOT files) that we developed for the design study of an indium iodine based detector to measure the In-115 decay.
DOI: 10.34740/kaggle/dsv/5731172
title: Dota 2 Pro League Matches 2023
DOI: 10.5281/zenodo.6645475
title: Is brain-derived neurotropic factor methylation involved in the association between prenatal stress and maternal postnatal anxiety during the covid-19 pandemic?

description: This database includes the raw data linked with the paper “IIs brain-derived neurotropic factor methylation involved in the association between prenatal stress and maternal postnatal anxiety during the covid-19 pandemic?”. This publication is part of the longitudinal and multi-centric “Measuring the outcomes of maternal COVID-19-related prenatal exposure (MOM-COPE)” research project. In this paper, we report data on the association among pandemic-related stress during pregnancy, maternal BDNF methylation, and postnatal anxiety symptoms.<br> <strong>Procedures. </strong>At birth, the mothers filled in the ad-hoc questionnaire attached about the pandemic related stress (file name: 22-06-14_momcope_bdnf_adhoc.pdf) and the State-Trait Anxiety Inventory (Spielberger, 1983). The maternal BDNF methylation was estimated in 11 CpG sites in DNA from mothers’ buccal cells by PCR amplification of bisulfite-treated DNA followed by Next Generation Sequencing (NGS) on a NEXTSeq-500 (Illumina, San Diego, California, USA).<br> <strong>Analytical plan. </strong>Separate Pearson’s bivariate correlations were used to assess the presence of significant associations among pandemic-related stress during pregnancy, maternal anxious symptoms after delivery, and CpG-specific BDNF % methylation. CpG-specific BDNF % methylation values for which a significant association emerged with both pandemic-related stress and anxious symptoms were subsequently tested in a mediation model to assess their role as significant mediators of the relationship between pandemic-related stress and maternal anxious symptoms.<br> <strong>Findings in brief. </strong>Results showed that pandemic-related stress was associated with an increased risk of postnatal anxiety (r = .20, p &lt;.05). CpG-specific BDNF methylation was significantly associated with both prenatal pandemic-related stress (r = .21, p &lt; .05) and postnatal maternal anxious symptoms (r = .25, p = .01). Moreover, a complete mediation by the BDNF CpG6 methylation emerged between pandemic-related stress during pregnancy and postnatal maternal anxiety (ACME = .66, p &lt; .05).
description: Funding: 5 x 1000 (2017); Fondazione Roche "Per la Ricerca Indipendente" 2020
DOI: 10.5281/zenodo.6645474
title: Is brain-derived neurotropic factor methylation involved in the association between prenatal stress and maternal postnatal anxiety during the covid-19 pandemic?

description: This database includes the raw data linked with the paper “IIs brain-derived neurotropic factor methylation involved in the association between prenatal stress and maternal postnatal anxiety during the covid-19 pandemic?”. This publication is part of the longitudinal and multi-centric “Measuring the outcomes of maternal COVID-19-related prenatal exposure (MOM-COPE)” research project. In this paper, we report data on the association among pandemic-related stress during pregnancy, maternal BDNF methylation, and postnatal anxiety symptoms.<br> <strong>Procedures. </strong>At birth, the mothers filled in the ad-hoc questionnaire attached about the pandemic related stress (file name: 22-06-14_momcope_bdnf_adhoc.pdf) and the State-Trait Anxiety Inventory (Spielberger, 1983). The maternal BDNF methylation was estimated in 11 CpG sites in DNA from mothers’ buccal cells by PCR amplification of bisulfite-treated DNA followed by Next Generation Sequencing (NGS) on a NEXTSeq-500 (Illumina, San Diego, California, USA).<br> <strong>Analytical plan. </strong>Separate Pearson’s bivariate correlations were used to assess the presence of significant associations among pandemic-related stress during pregnancy, maternal anxious symptoms after delivery, and CpG-specific BDNF % methylation. CpG-specific BDNF % methylation values for which a significant association emerged with both pandemic-related stress and anxious symptoms were subsequently tested in a mediation model to assess their role as significant mediators of the relationship between pandemic-related stress and maternal anxious symptoms.<br> <strong>Findings in brief. </strong>Results showed that pandemic-related stress was associated with an increased risk of postnatal anxiety (r = .20, p &lt;.05). CpG-specific BDNF methylation was significantly associated with both prenatal pandemic-related stress (r = .21, p &lt; .05) and postnatal maternal anxious symptoms (r = .25, p = .01). Moreover, a complete mediation by the BDNF CpG6 methylation emerged between pandemic-related stress during pregnancy and postnatal maternal anxiety (ACME = .66, p &lt; .05).
description: Funding: 5 x 1000 (2017); Fondazione Roche "Per la Ricerca Indipendente" 2020
DOI: 10.5281/zenodo.4620851
title: Data for "Artificial out-of-plane Ising antiferromagnet on the kagome lattice with very small further neighbour couplings"

description: Open access data and small scripts for the Figures of Colbois, Hofhuis, Luo, Wang, Hrabec, Heyderman and Mila, PRB 2021 (please cite upon using this data). Each folder contains a specific README file regarding its content. Here is only a short summary of the various folders contents: Colbois_Hofhuis_Micromagnetics_FurtherNeighbourInteractions_DATA : raw data from the micromagnetic simulations with MuMax Colbois_Micromagnetics_FurtherNeighbourInteractions_Analysis : Mathematica and Jupyter notebooks for the analysis of the micromagnetic simulations results and the creation of the corresponding Figures. Hofhuis_MFMandTIF_DATA : raw images and data for the spin configurations for the various samples of the experiment. Luo_Wang_Hofhuis_Protocols : text files describing the protocols for the sample fabrication and for the demagnetization process. Colbois_ExperimentalConfigurations_ANALYSIS : results and figures of the analysis of the data in Hofhuis_MFMandTIF_DATA. Colbois_MCandTNdata_J1 : data and analysis for the nearest neighbour model in zero field. Colbois_TNdata_J1-h : data and analysis for the nearest neighbour model in a field Colbois_J1J2_Data : MC data for all the plots related to the J1-J2 model Colbois_J1J2J3ph_Data : MC correlations data for the 1/3 magnetisation plateau, and magnetisation data for all fields.
DOI: 10.5281/zenodo.4620850
title: Data for "Artificial out-of-plane Ising antiferromagnet on the kagome lattice with very small further neighbour couplings"

description: Open access data and small scripts for the Figures of Colbois, Hofhuis, Luo, Wang, Hrabec, Heyderman and Mila, PRB 2021 (please cite upon using this data). Each folder contains a specific README file regarding its content. Here is only a short summary of the various folders contents: Colbois_Hofhuis_Micromagnetics_FurtherNeighbourInteractions_DATA : raw data from the micromagnetic simulations with MuMax Colbois_Micromagnetics_FurtherNeighbourInteractions_Analysis : Mathematica and Jupyter notebooks for the analysis of the micromagnetic simulations results and the creation of the corresponding Figures. Hofhuis_MFMandTIF_DATA : raw images and data for the spin configurations for the various samples of the experiment. Luo_Wang_Hofhuis_Protocols : text files describing the protocols for the sample fabrication and for the demagnetization process. Colbois_ExperimentalConfigurations_ANALYSIS : results and figures of the analysis of the data in Hofhuis_MFMandTIF_DATA. Colbois_MCandTNdata_J1 : data and analysis for the nearest neighbour model in zero field. Colbois_TNdata_J1-h : data and analysis for the nearest neighbour model in a field Colbois_J1J2_Data : MC data for all the plots related to the J1-J2 model Colbois_J1J2J3ph_Data : MC correlations data for the 1/3 magnetisation plateau, and magnetisation data for all fields.
DOI: 10.6084/m9.figshare.15020579
title: Additional file 4 of Application of CRISPR/Cas9 technology in wild apple (Malus sieverii) for paired sites gene editing

description: Additional file 4. Off target site Sanger sequencing.
DOI: 10.6084/m9.figshare.15020573
title: Additional file 2 of Application of CRISPR/Cas9 technology in wild apple (Malus sieverii) for paired sites gene editing

description: Additional file 2. Primer used in this study.
DOI: 10.6084/m9.figshare.12399236.v1
title: Additional file 1 of Psychological status and behavior changes of the public during the COVID-19 epidemic in China

description: Additional file 1.
DOI: 10.6084/m9.figshare.8207501
title: MOESM2 of LncRNA H19 regulates PI3Kâ Akt signal pathway by functioning as a ceRNA and predicts poor prognosis in colorectal cancer: integrative analysis of dysregulated ncRNA-associated ceRNA network

description: Additional file 2. The miRNAs and their target mRNAs in the ceRNA network.
DOI: 10.6084/m9.figshare.12399257.v1
title: Additional file 2 of Ancestry-specific predisposing germline variants in cancer

description: Additional file 2: Table S1. The demographic information of TCGA PanCanAtlas cohort with separate admixture populations. Table S2a. Ancestry-specific cancer-gene associations discovered from multivariate regression analyses. Table S2b. Ancestry-specific cancer-gene associations discovered from rare variant burden testing (Total Frequency Test- TFT). Table S3. Frequency of predisposing variants in TCGA PanCanAtlas and gnomAD-non-cancer subset across all ancestries. Table S4a. Ancestry-Specific Predisposing Variants as identified from Supp. Table.2. Table S4b. Summary of somatic second hit mutations in carriers of germline predisposing variants. Table S5a. Statistical analysis of gene expression in tumor samples of the variant carriers vs. non-carriers within each ancestry-cancer combination. Table S5b. Tumor RNAseq variant allele fractions and the somatic second hit events in germline predisposing variants with extreme expression within that cancer type. Table S6a. Post hoc power analyses to detect rare-variant associations in an aggregation test using SKAT. Table S6a. Down-sampling analysis for PCGP and SARC (cancers with at least 5 significantly associated germline genes in the European ancestry). Table S7. Prior studies that report ancestry-specific germline predisposition.
DOI: 10.6084/m9.figshare.12923411
title: Additional file 3 of Chloride intracellular channel 4 participate in the protective effect of Ginkgolide B in MPP+ injured MN9D cells: insight from proteomic analysis

description: Additional file 3: Differential expressed proteins (DEPs)in GB group compared with MPP+ group.
DOI: 10.6084/m9.figshare.15020573.v1
title: Additional file 2 of Application of CRISPR/Cas9 technology in wild apple (Malus sieverii) for paired sites gene editing

description: Additional file 2. Primer used in this study.
DOI: 10.6084/m9.figshare.12399383
title: Additional file 1 of Seasonal variability of stable isotopes in the Changjiang (Yangtze) river water and its implications for natural climate and anthropogenic impacts

description: Additional file 1. A summary of sample information and their δD and δ18O.
DOI: 10.6084/m9.figshare.15020624
title: Additional file 1 of Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica

description: Additional file 1: Table S1. Anther and hull color in Yugu18, Jigu19 and RILs. Table S2. Number of SNPs, indels and effective SNPs on nine chromosomes in two parents by aligning against reference genome. Table S3. Heterozygosity of each sample in the final variations set. Table S4. Detailed bin information. Table S5. The gene list and functional annotation of QTL related to anther color and hull color in millet. Table S6. The annovar annotation result of the SNPs and indels in QTL IRA1AC of Jigu19. Table S7. The annovar annotation result of the SNPs and indels in QTL IRA1AC of Yugu18. Table S8. The annovar annotation result of the SNPs and indels in QTL IRA2HC of Jigu19. Table S9. The annovar annotation result of the SNPs and indels in QTL IRA2HC of Yugu18. Table S10. The annovar annotation result of the SNPs and indels in QTL IRA3HC of Jigu19. Table S11. the annovar annotation result of the SNPs and indels in QTL IRA3HC of Yugu18. Table S12. The SNPs and indels located in the QTL of IRA1AC in vcf format. Table S13. The SNPs and indels located in the QTL of IRA2HC in vcf format. Table S14. The SNPs and indels located in the QTL of IRA3HC in vcf format.
DOI: 10.6084/m9.figshare.7156547
title: Latitudinal variation in reproductive performance of <i>Leymus chinensis</i>: implications for its response to future climate warming

description: <i><b>Background</b></i>: Sexual reproduction of plants is likely to be related to climate in their distribution range. Therefore, the investigation of spatial pattern of reproductive traits might provide valuable insights into the potential responses of a plant species to climate change. <i><b>Aims</b></i>: We studied the latitudinal pattern of sexual reproduction in Leymus chinensis to uncover the underlying ecological factors and their roles. <i><b>Methods</b></i>: We established a latitude transect in the Inner Mongolian steppe and investigated reproductive performance of L. chinensis, followed by modelling the relationship between traits and ecological factors. <i><b>Results</b></i>: Stalk height, spike length and spikelet number were non-linearly related to latitude. The spike-stalk ratio, seed viability and shoot density displayed significantly negative response to increasing latitude. Overall, increased latitude posed adverse impacts on sexual reproduction of L. chinensis. Annual mean temperature was positively correlated with the traits relevant to fitness, such as floret number and seed viability and annual mean precipitation to the development and growth of shoots. <i><b>Conclusions</b></i>: Under climate change scenarios, the shift of reproductive pattern in L. chinensis, i.e. likely more successful sexual reproduction, will have considerable contribution to its potential of adaptation to changing environment, and to its capacity of migration towards more suitable habitats.