cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11329577
title: MOESM6 of Cytokine production and phenotype of Histomonas meleagridis-specific T cells in the chicken

description: Additional file 6. Frequencies of cytokine-producing lymphocyte subsets for all investigated organs and stimulation variants. Frequencies of cytokine-producing lymphocyte subsets for all investigated organs and stimulation variants are given in this table. In addition, all calculated E. coli corrected values for control and infected birds are listed.
DOI: 10.6084/m9.figshare.11329577.v1
title: MOESM6 of Cytokine production and phenotype of Histomonas meleagridis-specific T cells in the chicken

description: Additional file 6. Frequencies of cytokine-producing lymphocyte subsets for all investigated organs and stimulation variants. Frequencies of cytokine-producing lymphocyte subsets for all investigated organs and stimulation variants are given in this table. In addition, all calculated E. coli corrected values for control and infected birds are listed.
DOI: 10.6084/m9.figshare.11329484
title: MOESM8 of Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas

description: Additional file 8: Table S7. Overrepresented gene sets in the 101 genes correlating with CYTOR.
DOI: 10.6084/m9.figshare.11329484.v1
title: MOESM8 of Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas

description: Additional file 8: Table S7. Overrepresented gene sets in the 101 genes correlating with CYTOR.
DOI: 10.6084/m9.figshare.11329478
title: MOESM7 of Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas

description: Additional file 7: Table S6. Genes correlating with CYTOR in the CGGA cohorts.
DOI: 10.6084/m9.figshare.11329478.v1
title: MOESM7 of Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas

description: Additional file 7: Table S6. Genes correlating with CYTOR in the CGGA cohorts.
DOI: 10.6084/m9.figshare.11329466
title: MOESM6 of Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas

description: Additional file 6: Table S5. Differentially methylated probes between IDH-codel and IDH-intact samples (q-value 0.1).
DOI: 10.6084/m9.figshare.11329466.v1
title: MOESM6 of Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas

description: Additional file 6: Table S5. Differentially methylated probes between IDH-codel and IDH-intact samples (q-value 0.1).
DOI: 10.6084/m9.figshare.11329457
title: MOESM5 of Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas

description: Additional file 5: Table S4. Regions correlating with CYTOR across all samples.
DOI: 10.6084/m9.figshare.11329454
title: MOESM5 of Proteomic analysis of cerebrospinal fluid extracellular vesicles reveals synaptic injury, inflammation, and stress response markers in HIV patients with cognitive impairment

description: Additional file 5: Table S5. EV-depleted CSF proteins from HIV+ subjects (n=20) mapped to cellular components.
DOI: 10.6084/m9.figshare.11329454.v1
title: MOESM5 of Proteomic analysis of cerebrospinal fluid extracellular vesicles reveals synaptic injury, inflammation, and stress response markers in HIV patients with cognitive impairment

description: Additional file 5: Table S5. EV-depleted CSF proteins from HIV+ subjects (n=20) mapped to cellular components.
DOI: 10.6084/m9.figshare.11329445
title: MOESM4 of Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas

description: Additional file 4: Table S3. Genes that correlate with specific open chromatin in IDH mutant LGGs.
DOI: 10.6084/m9.figshare.11329457.v1
title: MOESM5 of Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas

description: Additional file 5: Table S4. Regions correlating with CYTOR across all samples.
DOI: 10.6084/m9.figshare.11329442
title: MOESM4 of Proteomic analysis of cerebrospinal fluid extracellular vesicles reveals synaptic injury, inflammation, and stress response markers in HIV patients with cognitive impairment

description: Additional file 4: Table S4. EV-depleted CSF proteins from HIV+ subjects (n=20) mapped to biological functions.
DOI: 10.6084/m9.figshare.11329445.v1
title: MOESM4 of Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas

description: Additional file 4: Table S3. Genes that correlate with specific open chromatin in IDH mutant LGGs.
DOI: 10.6084/m9.figshare.11329436
title: MOESM3 of Proteomic analysis of cerebrospinal fluid extracellular vesicles reveals synaptic injury, inflammation, and stress response markers in HIV patients with cognitive impairment

description: Additional file 3: Table S3. Mass spectrometry identification of proteins in 20 HIV+ EV-depleted CSF using ABSciex 4800Plus MALDI-TOF/TOF platform.
DOI: 10.6084/m9.figshare.11329439
title: MOESM3 of Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas

description: Additional file 3: Table S2. chromVAR analysis of snATAC-seq data indicates variability scores for 386 transcription factor motifs.
DOI: 10.6084/m9.figshare.11329442.v1
title: MOESM4 of Proteomic analysis of cerebrospinal fluid extracellular vesicles reveals synaptic injury, inflammation, and stress response markers in HIV patients with cognitive impairment

description: Additional file 4: Table S4. EV-depleted CSF proteins from HIV+ subjects (n=20) mapped to biological functions.
DOI: 10.6084/m9.figshare.11329439.v1
title: MOESM3 of Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas

description: Additional file 3: Table S2. chromVAR analysis of snATAC-seq data indicates variability scores for 386 transcription factor motifs.
DOI: 10.6084/m9.figshare.11329424
title: MOESM1 of Proteomic analysis of cerebrospinal fluid extracellular vesicles reveals synaptic injury, inflammation, and stress response markers in HIV patients with cognitive impairment

description: Additional file 1: Table S1. List of abundant proteins.
DOI: 10.6084/m9.figshare.11329427
title: MOESM1 of Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas

description: Additional file 1: Table S1. Statistics on snATAC-seq data.
DOI: 10.6084/m9.figshare.11329430
title: MOESM2 of Proteomic analysis of cerebrospinal fluid extracellular vesicles reveals synaptic injury, inflammation, and stress response markers in HIV patients with cognitive impairment

description: Additional file 2: Table S2. Mass spectrometry identification of proteins in 20 HIV+ CSF EV fractions using ABSciex 4800Plus MALDI-TOF/TOF platform.
DOI: 10.6084/m9.figshare.11329436.v1
title: MOESM3 of Proteomic analysis of cerebrospinal fluid extracellular vesicles reveals synaptic injury, inflammation, and stress response markers in HIV patients with cognitive impairment

description: Additional file 3: Table S3. Mass spectrometry identification of proteins in 20 HIV+ EV-depleted CSF using ABSciex 4800Plus MALDI-TOF/TOF platform.
DOI: 10.6084/m9.figshare.11329427.v1
title: MOESM1 of Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas

description: Additional file 1: Table S1. Statistics on snATAC-seq data.
DOI: 10.6084/m9.figshare.11329430.v1
title: MOESM2 of Proteomic analysis of cerebrospinal fluid extracellular vesicles reveals synaptic injury, inflammation, and stress response markers in HIV patients with cognitive impairment

description: Additional file 2: Table S2. Mass spectrometry identification of proteins in 20 HIV+ CSF EV fractions using ABSciex 4800Plus MALDI-TOF/TOF platform.
DOI: 10.6084/m9.figshare.11329424.v1
title: MOESM1 of Proteomic analysis of cerebrospinal fluid extracellular vesicles reveals synaptic injury, inflammation, and stress response markers in HIV patients with cognitive impairment

description: Additional file 1: Table S1. List of abundant proteins.
DOI: 10.6084/m9.figshare.11329409
title: MOESM2 of The X chromosome of the German cockroach, Blattella germanica, is homologous to a fly X chromosome despite 400 million years divergence

description: Additional file 2 Tables with supporting data showing properties of mixture models fit to log2MF$\log _{2}\frac {M}{F}$ values for cockroach genes with D. melanogaster homologs on element F and elements Aâ€“E.
DOI: 10.6084/m9.figshare.11329400
title: MOESM1 of The X chromosome of the German cockroach, Blattella germanica, is homologous to a fly X chromosome despite 400 million years divergence

description: Additional file 1 Table with supporting data showing read mapping coverage, heterozygosity, and gene expression analysis for each cockroach gene.
DOI: 10.6084/m9.figshare.11329409.v1
title: MOESM2 of The X chromosome of the German cockroach, Blattella germanica, is homologous to a fly X chromosome despite 400 million years divergence

description: Additional file 2 Tables with supporting data showing properties of mixture models fit to log2MF$\log _{2}\frac {M}{F}$ values for cockroach genes with D. melanogaster homologs on element F and elements Aâ€“E.
DOI: 10.6084/m9.figshare.11329400.v1
title: MOESM1 of The X chromosome of the German cockroach, Blattella germanica, is homologous to a fly X chromosome despite 400 million years divergence

description: Additional file 1 Table with supporting data showing read mapping coverage, heterozygosity, and gene expression analysis for each cockroach gene.
DOI: 10.6084/m9.figshare.11329310
title: MOESM3 of Microbial biodiversity as related to crop succession and potato intercropping for management of brown rot disease

description: Additional file 3. Microbial biodiversity.
DOI: 10.6084/m9.figshare.11329310.v1
title: MOESM3 of Microbial biodiversity as related to crop succession and potato intercropping for management of brown rot disease

description: Additional file 3. Microbial biodiversity.
DOI: 10.6084/m9.figshare.11329259
title: MOESM3 of Caste-specific morphological modularity in the ant tribe Camponotini (Hymenoptera, Formicidae)

description: Additional file 3: Table S3. “S3 Character Loadings.xls”. Loadings on principal components (PC) 1–3, for the complete dataset (332 specimens, 7 characters), the minor worker sample (231 specimens, 7 characters), and the sample of gynes and MIC (56 specimens, 8 characters).
DOI: 10.6084/m9.figshare.11329253
title: MOESM2 of Caste-specific morphological modularity in the ant tribe Camponotini (Hymenoptera, Formicidae)

description: Additional file 2: Table S2. “S2 Measurements.xls”. Complete list of specimens examined in this study, measurements (in mm), and measurement error statistics.
DOI: 10.6084/m9.figshare.11329259.v1
title: MOESM3 of Caste-specific morphological modularity in the ant tribe Camponotini (Hymenoptera, Formicidae)

description: Additional file 3: Table S3. “S3 Character Loadings.xls”. Loadings on principal components (PC) 1–3, for the complete dataset (332 specimens, 7 characters), the minor worker sample (231 specimens, 7 characters), and the sample of gynes and MIC (56 specimens, 8 characters).
DOI: 10.6084/m9.figshare.11329244
title: MOESM5 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

description: Additional file 5. Methods: Mesquite file used for parsimony ancestral state reconstruction including RAXML bootstrap trees.
DOI: 10.6084/m9.figshare.11329238
title: MOESM1 of Improvement and use of CRISPR/Cas9 to engineer a sperm-marking strain for the invasive fruit pest Drosophila suzukii

description: Additional file 1: Table S1. List of primers used.
DOI: 10.6084/m9.figshare.11329238.v1
title: MOESM1 of Improvement and use of CRISPR/Cas9 to engineer a sperm-marking strain for the invasive fruit pest Drosophila suzukii

description: Additional file 1: Table S1. List of primers used.
DOI: 10.6084/m9.figshare.11329244.v1
title: MOESM5 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

description: Additional file 5. Methods: Mesquite file used for parsimony ancestral state reconstruction including RAXML bootstrap trees.
DOI: 10.6084/m9.figshare.11329214
title: MOESM1 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

description: Additional file 1. Methods: occurrence data.
DOI: 10.6084/m9.figshare.11329214.v1
title: MOESM1 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

description: Additional file 1. Methods: occurrence data.
DOI: 10.6084/m9.figshare.11329184
title: MOESM2 of What are the impacts of within-field farmland management practices on the flux of greenhouse gases from arable cropland in temperate regions? A systematic map protocol

description: Additional file 2. A List of benchmark articles.
DOI: 10.6084/m9.figshare.11329178
title: MOESM1 of What are the impacts of within-field farmland management practices on the flux of greenhouse gases from arable cropland in temperate regions? A systematic map protocol

description: Additional file 1. ROSES form for systematic map protocols.
DOI: 10.6084/m9.figshare.11329178.v1
title: MOESM1 of What are the impacts of within-field farmland management practices on the flux of greenhouse gases from arable cropland in temperate regions? A systematic map protocol

description: Additional file 1. ROSES form for systematic map protocols.
DOI: 10.6084/m9.figshare.11329184.v1
title: MOESM2 of What are the impacts of within-field farmland management practices on the flux of greenhouse gases from arable cropland in temperate regions? A systematic map protocol

description: Additional file 2. A List of benchmark articles.
DOI: 10.6084/m9.figshare.11329079
title: MOESM4 of HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard

description: Additional file 4. hastaLaVista univariate explorer. R script that illustrates how to use hastaLaVista to explore univariate statistics computed for each variable.
DOI: 10.6084/m9.figshare.11329076
title: MOESM3 of HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard

description: Additional file 3. hastaLaVista scores explorer. R script that illustrates how to use hastaLaVista to explore univariate scores computed by multivariate analysis.
DOI: 10.6084/m9.figshare.11329070
title: MOESM2 of HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard

description: Additional file 2. hastaLaVista metaboscope view. R script that illustrates how to use hastaLaVista to explore results from multivariate analysis including retrieving spectra from reference compounds.
DOI: 10.6084/m9.figshare.11329070.v1
title: MOESM2 of HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard

description: Additional file 2. hastaLaVista metaboscope view. R script that illustrates how to use hastaLaVista to explore results from multivariate analysis including retrieving spectra from reference compounds.
DOI: 10.6084/m9.figshare.11329079.v1
title: MOESM4 of HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard

description: Additional file 4. hastaLaVista univariate explorer. R script that illustrates how to use hastaLaVista to explore univariate statistics computed for each variable.
DOI: 10.6084/m9.figshare.11329076.v1
title: MOESM3 of HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard

description: Additional file 3. hastaLaVista scores explorer. R script that illustrates how to use hastaLaVista to explore univariate scores computed by multivariate analysis.
DOI: 10.6084/m9.figshare.11329064
title: MOESM1 of HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard

description: Additional file 1. hastaLaVista data explorer. R script that illustrates how to use hastaLaVista to explore dataÂ according to metadata.
DOI: 10.6084/m9.figshare.11329064.v1
title: MOESM1 of HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard

description: Additional file 1. hastaLaVista data explorer. R script that illustrates how to use hastaLaVista to explore dataÂ according to metadata.
DOI: 10.6084/m9.figshare.11329022
title: MOESM2 of Stratified reconstruction of ancestral Escherichia coli diversification

description: Additional file 2. E. coli genomes examined. (CSV 1906 kb)
DOI: 10.6084/m9.figshare.11329022.v1
title: MOESM2 of Stratified reconstruction of ancestral Escherichia coli diversification

description: Additional file 2. E. coli genomes examined. (CSV 1906 kb)
DOI: 10.6084/m9.figshare.11328767
title: Acknowledgements sentences dataset

description: Acknowledgements sentences dataset for acknowledgements classification
DOI: 10.6084/m9.figshare.11328767.v2
title: Acknowledgements sentences dataset

description: Acknowledgements sentences dataset for acknowledgements classification
DOI: 10.6084/m9.figshare.11328767.v1
title: Acknowledgements sentences dataset

description: Acknowledgements sentences dataset for acknowledgements classification
DOI: 10.6084/m9.figshare.11328629
title: Dataset for: Novel Methods for the Analysis of Stepped Wedge Cluster Randomized Trials

description: Stepped wedge cluster randomized trials (SW-CRTs) have become increasingly popular and are used for a variety of interventions and outcomes, often chosen for their feasibility advantages. SW-CRTs must account for time trends in the outcome because of the staggered rollout of the intervention. Robust inference procedures and non-parametric analysis methods have recently been proposed to handle such trends without requiring strong parametric modeling assumptions, but these are less powerful than model-based approaches. We propose several novel analysis methods that reduce reliance on modeling assumptions while preserving some of the increased power provided by the use of mixed effects models. In one method, we use the synthetic control approach to find the best matching clusters for a given intervention cluster. Another method makes use of within-cluster crossover information to construct an overall estimator. We also consider methods that combine these approaches to further improve power. We test these methods on simulated SW-CRTs, describing scenarios in which these methods have increased power compared to existing non-parametric methods while preserving nominal validity when mixed effects models are misspecified. We also demonstrate theoretical properties of these estimators with less restrictive assumptions than mixed effects models. Finally, we propose avenues for future research on the use of these methods; motivation for such research arises from their flexibility, which allows the identification of specific causal contrasts of interest, their robustness, and the potential for incorporating covariates to further increase power. Investigators conducting SW-CRTs might well consider such methods when common modeling assumptions may not hold.
DOI: 10.6084/m9.figshare.11328629.v1
title: Dataset for: Novel Methods for the Analysis of Stepped Wedge Cluster Randomized Trials

description: Stepped wedge cluster randomized trials (SW-CRTs) have become increasingly popular and are used for a variety of interventions and outcomes, often chosen for their feasibility advantages. SW-CRTs must account for time trends in the outcome because of the staggered rollout of the intervention. Robust inference procedures and non-parametric analysis methods have recently been proposed to handle such trends without requiring strong parametric modeling assumptions, but these are less powerful than model-based approaches. We propose several novel analysis methods that reduce reliance on modeling assumptions while preserving some of the increased power provided by the use of mixed effects models. In one method, we use the synthetic control approach to find the best matching clusters for a given intervention cluster. Another method makes use of within-cluster crossover information to construct an overall estimator. We also consider methods that combine these approaches to further improve power. We test these methods on simulated SW-CRTs, describing scenarios in which these methods have increased power compared to existing non-parametric methods while preserving nominal validity when mixed effects models are misspecified. We also demonstrate theoretical properties of these estimators with less restrictive assumptions than mixed effects models. Finally, we propose avenues for future research on the use of these methods; motivation for such research arises from their flexibility, which allows the identification of specific causal contrasts of interest, their robustness, and the potential for incorporating covariates to further increase power. Investigators conducting SW-CRTs might well consider such methods when common modeling assumptions may not hold.
DOI: 10.6084/m9.figshare.11328605
title: Development and validation of a prediction model for identifying men with intermediate- or high-risk prostate cancer for whom bone imaging is unnecessary: a nation-wide population-based study

description: <b>Objective:</b> To develop and validate a nomogram that identifies men for whom bone scan is unnecessary. <b>Material and methods:</b> The study datasets were derived from the National Prostate Cancer Register (NPCR) of Sweden. All men in the NPCR ≤80 years of age who were diagnosed with intermediate- or high-risk prostate cancer and who had pretreatment bone imaging (<sup>99m</sup>Tc MDP scintigraphy, plain x-ray, computed tomography, magnetic resonance imaging, and/or positron emission tomography fused with computed tomography) were included. Men diagnosed from 2015–2016 formed a development dataset and men diagnosed in 2017 formed a validation dataset. Outcome was metastasis on bone imaging as registered in NPCR. Multivariable logistic regression was used to develop a nomogram. <b>Results:</b> In the development dataset 482/5084 men (10%) had bone metastasis, the corresponding percentage in the validation dataset was 282/2554 (11%). Gleason grade group, clinical T stage, and prostate-specific antigen were included in the final model. Discrimination and calibration were satisfactory in both the development (AUC 0.80, 95% CI 0.78–0.82) and validation dataset (AUC 0.80, 95% CI, 0.77–0.82). Compared with using the EAU guidelines’ recommendation for selecting men for imaging, using the nomogram with a cut-off at 4% chance of bone metastasis, would have avoided imaging in 519/2068 men (25%) and miss bone metastasis in 10/519 (2%) men in the validation dataset. <b>Conclusion:</b> By use of our nomogram, bone scans of men with prostate cancer can be avoided in a large proportion of men.