cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8343473
title: Pangenome gene alignments of 571 Rhizobiaceae

description: All predicted protein sequence were extracted from the 571Rhizob dataset and clustered into homologous gene families (with possibly multiple copies per genome) using MMSeqs2 release 2 (commit e5d64b2) (Steinegger & Söding 2017).Protein sequences from each gene family were aligned using ClustalOmega (Sievers et al. 2011) and reverse-translated into coding sequence (CDS) alignments using PAL2NAL (Suyama et al. 2006). This resulted in a set of 50,791 final non-ORFan CDS families, including 9,589 homogeneous (derived from identical protein sequences) families.<br>
DOI: 10.6084/m9.figshare.8343473.v1
title: Pangenome gene alignments of 571 Rhizobiaceae

description: All predicted protein sequence were extracted from the 571Rhizob dataset and clustered into homologous gene families (with possibly multiple copies per genome) using MMSeqs2 release 2 (commit e5d64b2) (Steinegger & Söding 2017).Protein sequences from each gene family were aligned using ClustalOmega (Sievers et al. 2011) and reverse-translated into coding sequence (CDS) alignments using PAL2NAL (Suyama et al. 2006). This resulted in a set of 50,791 final non-ORFan CDS families, including 9,589 homogeneous (derived from identical protein sequences) families.<br>
DOI: 10.6084/m9.figshare.8343542.v1
title: Čerňansky and Syromyatnikova Lacerta trilineata NHMW 27665

description: The CT data of Lacerta trilineata NHMW 27665 rom Čerňanský and syromyatnikova Plos One. It can be open via winrar and volume graphics. <br>
DOI: 10.6084/m9.figshare.8343449
title: Čerňansky and Syromyatnikova PLOS one, Lacerta strigata NHMW 39765

description: The CT data of Lacerta strigata NHMW 39765 from Čerňanský and Syromyatnikova PLOS One. They can be open by winrar and volume graphics.<br>
DOI: 10.6084/m9.figshare.8343449.v1
title: Čerňansky and Syromyatnikova PLOS one, Lacerta strigata NHMW 39765

description: The CT data of Lacerta strigata NHMW 39765 from Čerňanský and Syromyatnikova PLOS One. They can be open by winrar and volume graphics.<br>
DOI: 10.6084/m9.figshare.8343413
title: Čerňansky and Syromyatnikova, Plos One, Lacerta pamphylica NHMW 35861

description: The CT data of <i>Lacerta pamphylica</i> NHMW 35861 from Čerňanský and syromyatnikova, Plos one. Can be open by winrar and Volume Graphics.<br>
DOI: 10.6084/m9.figshare.8343413.v1
title: Čerňansky and Syromyatnikova, Plos One, Lacerta pamphylica NHMW 35861

description: The CT data of <i>Lacerta pamphylica</i> NHMW 35861 from Čerňanský and syromyatnikova, Plos one. Can be open by winrar and Volume Graphics.<br>
DOI: 10.17028/rd.lboro.8343308
title: Supplementary analyses

description: Supplementary analyses: analyses conducted in response to peer review
DOI: 10.17028/rd.lboro.8343308.v1
title: Supplementary analyses

description: Supplementary analyses: analyses conducted in response to peer review
DOI: 10.6084/m9.figshare.8343257
title: Čerňanský and Syromyatnikova, Lacerta media SNMW 38408

description: CT data of <i>Lacerta media </i>SNMW 38408 from Čerňanský and syromyatnikova Plos One. DICOM files, can be open by AVIZO<br>
DOI: 10.6084/m9.figshare.8343263
title: Genetic diversity, linkage disequilibrium, and population structure analysis of the tea plant (Camellia sinensis) from an origin center, Guizhou plateau, using genome-wide SNPs developed by genotyping-by-sequencing

description: Genotyping of 79016 SNPs based on GBS in 415 tea accessions.
DOI: 10.6084/m9.figshare.8343263.v1
title: Genetic diversity, linkage disequilibrium, and population structure analysis of the tea plant (Camellia sinensis) from an origin center, Guizhou plateau, using genome-wide SNPs developed by genotyping-by-sequencing

description: Genotyping of 79016 SNPs based on GBS in 415 tea accessions.
DOI: 10.6084/m9.figshare.8343257.v1
title: Čerňanský and Syromyatnikova, Lacerta media SNMW 38408

description: CT data of <i>Lacerta media </i>SNMW 38408 from Čerňanský and syromyatnikova Plos One. DICOM files, can be open by AVIZO<br>
DOI: 10.6084/m9.figshare.8343113
title: Simulation code from Epidemic growth rates and host movement patterns shape management performance for pathogen spillover at the wildlife-livestock interface

description: Managing pathogen spillover at the wildlife-livestock interface is a key step towards improving global animal health, food security and wildlife conservation. However, predicting the effectiveness of management actions across host–pathogen systems with different life histories is an on-going challenge since data on intervention effectiveness are expensive to collect and results are system-specific. We developed a simulation model to explore how the efficacies of different management strategies vary according to host movement patterns and epidemic growth rates. The model suggested that fast-growing, fast-moving epidemics like avian influenza were best-managed with actions like biosecurity or containment, which limited and localized overall spillover risk. For fast-growing, slower-moving diseases like foot-and-mouth disease, depopulation or prophylactic vaccination were competitive management options. Many actions performed competitively when epidemics grew slowly and host movements were limited, and how management efficacy related to epidemic growth rate or host movement propensity depended on what objective was used to evaluate management performance. This framework may be a useful step in advancing how we classify and prioritise responses to novel pathogen spillover threats, and evaluate current management actions for pathogens emerging at the wildlife-livestock interface.This article is part of the theme issue ‘Dynamic and integrative approaches to understanding pathogen spillover’.
DOI: 10.6084/m9.figshare.8343110
title: Fischer_phosphoTRAP-code_ESM from The neural basis of tadpole transport in poison frogs

description: R code for PhosophoTRAP analysis.
DOI: 10.6084/m9.figshare.8343113.v1
title: Simulation code from Epidemic growth rates and host movement patterns shape management performance for pathogen spillover at the wildlife-livestock interface

description: Managing pathogen spillover at the wildlife-livestock interface is a key step towards improving global animal health, food security and wildlife conservation. However, predicting the effectiveness of management actions across host–pathogen systems with different life histories is an on-going challenge since data on intervention effectiveness are expensive to collect and results are system-specific. We developed a simulation model to explore how the efficacies of different management strategies vary according to host movement patterns and epidemic growth rates. The model suggested that fast-growing, fast-moving epidemics like avian influenza were best-managed with actions like biosecurity or containment, which limited and localized overall spillover risk. For fast-growing, slower-moving diseases like foot-and-mouth disease, depopulation or prophylactic vaccination were competitive management options. Many actions performed competitively when epidemics grew slowly and host movements were limited, and how management efficacy related to epidemic growth rate or host movement propensity depended on what objective was used to evaluate management performance. This framework may be a useful step in advancing how we classify and prioritise responses to novel pathogen spillover threats, and evaluate current management actions for pathogens emerging at the wildlife-livestock interface.This article is part of the theme issue ‘Dynamic and integrative approaches to understanding pathogen spillover’.
DOI: 10.6084/m9.figshare.8343101
title: Fischer_SAS-code_ESM from The neural basis of tadpole transport in poison frogs

description: Representative SAS statistical code.
DOI: 10.6084/m9.figshare.8343098
title: Fischer_Dtinctorius-brain-atlas_ESM from The neural basis of tadpole transport in poison frogs

description: Dendrobates tinctorius brain atlas
DOI: 10.6084/m9.figshare.8343110.v1
title: Fischer_phosphoTRAP-code_ESM from The neural basis of tadpole transport in poison frogs

description: R code for PhosophoTRAP analysis.
DOI: 10.6084/m9.figshare.8343101.v1
title: Fischer_SAS-code_ESM from The neural basis of tadpole transport in poison frogs

description: Representative SAS statistical code.
DOI: 10.6084/m9.figshare.8342978
title: Table PD-L1 and CD47 scoring

description: Table scoring PD-L1 and CD47 intensity and %TC expression
DOI: 10.6084/m9.figshare.8342807
title: Replication Package

description: This package contains all the documents required to replicate the studies reported in Paper II, III, IV and V.
DOI: 10.6084/m9.figshare.8342759
title: Results Package

description: This package contains the results from all five publications (Paper I - Paper V)
DOI: 10.6084/m9.figshare.8342729
title: Automated global delineation of human settlements from 40 years of Landsat satellite data archives

description: This paper presents the analysis of Earth Observation data records collected between 1975 and 2014 for assessing the extent and temporal evolution of the built-up surface in the frame of the Global Human Settlement Layer project. The scale of the information produced by the study enables the assessment of the whole continuum of human settlements from rural hamlets to megacities. The study applies enhanced processing methods as compared to the first production of the GHSL baseline data. The major improvements include the use of a more refined learning set on built-up areas derived from Sentinel-1 data which allowed testing the added-value of incremental learning in big data analytics. Herein, the new features of the GHSL built-up grids and the methods are described and compared with the previous ones using a reference set of building footprints for 277 areas of interest. The results show a gradual improvement in the accuracy measures with a gain of 3.6% in the balanced accuracy, between the first production of the GHSL baseline and the latest GHSL multitemporal built-up grids. A validation of the multitemporal component is also conducted at the global scale establishing the reliability of the built-up layer across time.
DOI: 10.6084/m9.figshare.8342759.v1
title: Results Package

description: This package contains the results from all five publications (Paper I - Paper V)
DOI: 10.6084/m9.figshare.8342720
title: Dataset 3

description: This is data of cortisol and testosterone concentrations in serum aceh cattle after exposure repeated freeze-thaw cycles 0-8 times.
DOI: 10.6084/m9.figshare.8342729.v1
title: Automated global delineation of human settlements from 40 years of Landsat satellite data archives

description: This paper presents the analysis of Earth Observation data records collected between 1975 and 2014 for assessing the extent and temporal evolution of the built-up surface in the frame of the Global Human Settlement Layer project. The scale of the information produced by the study enables the assessment of the whole continuum of human settlements from rural hamlets to megacities. The study applies enhanced processing methods as compared to the first production of the GHSL baseline data. The major improvements include the use of a more refined learning set on built-up areas derived from Sentinel-1 data which allowed testing the added-value of incremental learning in big data analytics. Herein, the new features of the GHSL built-up grids and the methods are described and compared with the previous ones using a reference set of building footprints for 277 areas of interest. The results show a gradual improvement in the accuracy measures with a gain of 3.6% in the balanced accuracy, between the first production of the GHSL baseline and the latest GHSL multitemporal built-up grids. A validation of the multitemporal component is also conducted at the global scale establishing the reliability of the built-up layer across time.
DOI: 10.6084/m9.figshare.8342720.v1
title: Dataset 3

description: This is data of cortisol and testosterone concentrations in serum aceh cattle after exposure repeated freeze-thaw cycles 0-8 times.
DOI: 10.6084/m9.figshare.8342702
title: Čerňanský and Syromyatnikova PLOS one, Lacerta bilineata 18599 hlava.vgl

description: <i>Lacerta bililineata </i>NHMV 18599 from Čerňanský and Syromyatnikova Plos One. The files can be open by Volume Graphics.<br>
DOI: 10.6084/m9.figshare.8342675
title: Supplementary Material for: Epigenetic Modification of Enhancer of Zeste Homolog 2 Modulates the Activation of Dendritic Cells in Allergen Immunotherapy

description: <b><i>Background:</i></b> Allergen immunotherapy (AIT) is the only etiological and potentially curative therapy for allergic rhinitis (AR). <b><i>Objectives:</i></b> We sought to investigate the role of epigenetic regulator enhancer of zeste homolog 2 (EZH2) in the activation of dendritic cells (DCs) in AIT. <b><i>Method:</i></b> In this study, EZH2 expression in circulating myeloid DCs (mDCs) and plasmacytoid DCs (pDCs) were evaluated using flow cytometry. Clinical information from 56 AR patients receiving AIT was collected, including 30 subjects with subcutaneous immunotherapy (SCIT) and 26 subjects with sublingual immunotherapy (SLIT). In vitro, the effect of EZH2 inhibitor, 3 Deazaneplanocin A (DZNep), on the phenotypic and functional activation of monocyte-derived DCs (moDCs) was evaluated. <b><i>Results:</i></b> EZH2 expression in circulating mDCs and pDCs were both negatively correlated to treatment time of AIT (<i>r</i> = –0.39, <i>p</i> = 0.003 and <i>r</i> = –0.47, <i>p</i> = 0.0002, respectively). Furthermore, there was a higher correlation between EZH2 expression and AIT treatment time in the SCIT group compared to that of the SLIT group in mDCs (<i>r</i> = –0.42, <i>p</i> = 0.02 vs. <i>r</i> = –0.23, <i>p</i> = 0.26)and pDCs (<i>r</i> = –0.52, <i>p</i> = 0.003 vs. <i>r</i> = –0.33, <i>p</i> = 0.10). In vitro, the co-stimulatory molecules on moDCs, such as CD80, CD86, and CD83, were significantly inhibited by DZNep in a dose-dependent manner. The ­DC-driven T-cell proliferation was suppressed by DZNep (MD = 22.88, 95% CI 7.809–37.96, <i>p</i> &lt; 0.05). <b><i>Conclusions:</i></b> Our study shows that EZH2, which is required in the activation of DCs, mediates the epigenetic modification in AIT and stresses the importance of patient adherence during AIT.
DOI: 10.6084/m9.figshare.8342702.v1
title: Čerňanský and Syromyatnikova PLOS one, Lacerta bilineata 18599 hlava.vgl

description: <i>Lacerta bililineata </i>NHMV 18599 from Čerňanský and Syromyatnikova Plos One. The files can be open by Volume Graphics.<br>
DOI: 10.6084/m9.figshare.8342651
title: Dataset 2

description: This is data of cortisol concentrations in aceh cattle before and after transportation and data of testosterone concentrations in bulls and cows measured using a commercial enzyme-linked immunosorbent assay kits (DRG Instrument GmbH, Germany)
DOI: 10.6084/m9.figshare.8342651.v1
title: Dataset 2

description: This is data of cortisol concentrations in aceh cattle before and after transportation and data of testosterone concentrations in bulls and cows measured using a commercial enzyme-linked immunosorbent assay kits (DRG Instrument GmbH, Germany)
DOI: 10.6084/m9.figshare.8342591
title: Comparison of Illumina 450K and EPIC arrays in placental DNA methylation

description: Illumina HumanMethylation450 BeadChip (450K) has been commonly used to investigate DNA methylation in human tissues. Recently, it has been replaced by Illumina HumanMethylationEPIC BeadChip (EPIC) covering over 850,000 CpGs distributed genome-wide. Many consortia have now datasets coming from both arrays and aspire to analyze the two together. The placenta shows a high number of intermediate methylation levels and is often investigated for obstetric/birth outcomes, and potentially for long-term programming in offspring. We performed a systematic comparison between the two arrays using 108 duplicate placental samples from Gen3G birth cohort. We find that placenta shows a high per-sample correlation between the arrays, and higher median correlations at individual CpGs than those reported for blood. We identify 26,340 probes with absolute difference in per cent methylation &gt;10%. We conclude that EPIC and 450K placental data can be combined, and we provide two lists of CpGs that should be excluded to avoid misleading results.
DOI: 10.6084/m9.figshare.8342591.v2
title: Comparison of Illumina 450K and EPIC arrays in placental DNA methylation

description: Illumina HumanMethylation450 BeadChip (450K) has been commonly used to investigate DNA methylation in human tissues. Recently, it has been replaced by Illumina HumanMethylationEPIC BeadChip (EPIC) covering over 850,000 CpGs distributed genome-wide. Many consortia have now datasets coming from both arrays and aspire to analyze the two together. The placenta shows a high number of intermediate methylation levels and is often investigated for obstetric/birth outcomes, and potentially for long-term programming in offspring. We performed a systematic comparison between the two arrays using 108 duplicate placental samples from Gen3G birth cohort. We find that placenta shows a high per-sample correlation between the arrays, and higher median correlations at individual CpGs than those reported for blood. We identify 26,340 probes with absolute difference in per cent methylation &gt;10%. We conclude that EPIC and 450K placental data can be combined, and we provide two lists of CpGs that should be excluded to avoid misleading results.
DOI: 10.6084/m9.figshare.8342558
title: Supplementary Material for: Diagnostic Performance of Retinopathy in the Detection of Diabetic Nephropathy in Type 2 Diabetes: A Systematic Review and Meta-Analysis of 45 Studies

description: <b><i>Aims:</i></b> To conduct an evidence-based evaluation of diabetic retinopathy (DR) for the diagnosis of diabetic nephropathy (DN) in type 2 diabetics with kidney disease. <b><i>Methods:</i></b> We systematically searched PubMed, EMBASE, and the Cochrane Library from inception to June 27, 2018, including the reference lists of identified primary studies. A study was included if it (1) used DR as a diagnostic test for DN; and (2) used histological evaluation of renal tissues as the reference standard. <b><i>Results:</i></b> The analysis included 45 studies (4,561 patients). A bivariate analysis yielded a sensitivity of 0.67 (95% CI 0.61–0.74) and a specificity of 0.78 (95% CI 0.73–0.82). The summary receiver operating characteristic curve analysis provided an area under the curve (AUC) of 0.79 (95% CI 0.76–0.83). In a setting of 41% prevalence of DN, the probability of DN would be 68% if the test of DR was positive, and the probability of DN would be 23% if it was negative. In addition, although the mean specificity of proliferative DR for the detection of DN was 0.99 (95% CI 0.45–1.00), the mean sensitivity was 0.34 (95% CI 0.24–0.44), and the AUC was 0.58 (95% CI 0.53–0.62). <b><i>Conclusions:</i></b> DR is helpful in diagnosing DN in persons with type 2 diabetes and kidney disease, but the severity of DR may not parallel the presence of DN.
DOI: 10.6084/m9.figshare.8342591.v1
title: Comparison of Illumina 450K and EPIC arrays in placental DNA methylation

description: Illumina HumanMethylation450 BeadChip (450K) has been commonly used to investigate DNA methylation in human tissues. Recently, it has been replaced by Illumina HumanMethylationEPIC BeadChip (EPIC) covering over 850,000 CpGs distributed genome-wide. Many consortia have now datasets coming from both arrays and aspire to analyze the two together. The placenta shows a high number of intermediate methylation levels and is often investigated for obstetric/birth outcomes, and potentially for long-term programming in offspring. We performed a systematic comparison between the two arrays using 108 duplicate placental samples from Gen3G birth cohort. We find that placenta shows a high per-sample correlation between the arrays, and higher median correlations at individual CpGs than those reported for blood. We identify 26,340 probes with absolute difference in per cent methylation &gt;10%. We conclude that EPIC and 450K placental data can be combined, and we provide two lists of CpGs that should be excluded to avoid misleading results.
DOI: 10.6084/m9.figshare.8342558.v1
title: Supplementary Material for: Diagnostic Performance of Retinopathy in the Detection of Diabetic Nephropathy in Type 2 Diabetes: A Systematic Review and Meta-Analysis of 45 Studies

description: <b><i>Aims:</i></b> To conduct an evidence-based evaluation of diabetic retinopathy (DR) for the diagnosis of diabetic nephropathy (DN) in type 2 diabetics with kidney disease. <b><i>Methods:</i></b> We systematically searched PubMed, EMBASE, and the Cochrane Library from inception to June 27, 2018, including the reference lists of identified primary studies. A study was included if it (1) used DR as a diagnostic test for DN; and (2) used histological evaluation of renal tissues as the reference standard. <b><i>Results:</i></b> The analysis included 45 studies (4,561 patients). A bivariate analysis yielded a sensitivity of 0.67 (95% CI 0.61–0.74) and a specificity of 0.78 (95% CI 0.73–0.82). The summary receiver operating characteristic curve analysis provided an area under the curve (AUC) of 0.79 (95% CI 0.76–0.83). In a setting of 41% prevalence of DN, the probability of DN would be 68% if the test of DR was positive, and the probability of DN would be 23% if it was negative. In addition, although the mean specificity of proliferative DR for the detection of DN was 0.99 (95% CI 0.45–1.00), the mean sensitivity was 0.34 (95% CI 0.24–0.44), and the AUC was 0.58 (95% CI 0.53–0.62). <b><i>Conclusions:</i></b> DR is helpful in diagnosing DN in persons with type 2 diabetes and kidney disease, but the severity of DR may not parallel the presence of DN.
DOI: 10.6084/m9.figshare.8342552
title: Supplementary_Table_9_Correlated_bacteria_public_annotations.xlsx

description: Supplementary Table 9. List of Disbiome database annotations related to CRC concerning bacterial species characterized by a significant correlation between metagenomic and sRNA-Seq relative abundances.
DOI: 10.6084/m9.figshare.8342552.v1
title: Supplementary_Table_9_Correlated_bacteria_public_annotations.xlsx

description: Supplementary Table 9. List of Disbiome database annotations related to CRC concerning bacterial species characterized by a significant correlation between metagenomic and sRNA-Seq relative abundances.