cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21493617
title: Supplementary Material for: A Diagnostic Predictive Model of Bronchoscopy with Radial Endobronchial Ultrasound for Peripheral Pulmonary Lesions

description: <b><i>Background:</i></b> Several factors have been reported to affect the diagnostic yield of bronchoscopy with radial endobronchial ultrasound (R-EBUS) for peripheral pulmonary lesions (PPLs). However, it is difficult to accurately predict the diagnostic potential of bronchoscopy for each PPL in advance. <b><i>Objectives:</i></b> Our objective was to establish a predictive model to evaluate the diagnostic yield before the procedure. <b><i>Method:</i></b> We retrospectively analysed consecutive patients who underwent diagnostic bronchoscopy with R-EBUS between April 2012 and October 2015. We assessed the factors that were predictive of successful bronchoscopic diagnosis of PPLs with R-EBUS using a multivariable logistic regression model. The accuracy of the predictive model was evaluated using the receiver operator characteristic area under the curve (ROC AUC). Internal validation was analysed using 10-fold stratified cross-validation. <b><i>Results:</i></b> We analysed a total of 1,634 lesions; the median lesion size was 25.0 mm. Of these, 1,138 lesions (69.6%) were successfully diagnosed. In the predictive logistic model, significant factors affecting the diagnostic yield were lesion size, lesion structure, bronchus sign, and visible on chest X-ray. The predictive model consisted of seven factors: lesion size, lesion lobe, lesion location from the hilum, lesion structure, bronchus sign, visibility on chest X-ray, and background lung. The ROC AUC of the predictive model was 0.742 (95% confidence interval: 0.715–0.769). Internal validation using 10-fold stratified cross-validation revealed a mean ROC AUC of 0.734. <b><i>Conclusions:</i></b> The predictive model using the seven factors revealed a good performance in estimating the diagnostic yield.
DOI: 10.18112/openneuro.ds004197.v1.0.2
title: FMRI-EEG Prestudy
DOI: 10.5281/zenodo.3952159
title: High-resolution gridded climate data for Europe based on bias-corrected EURO-CORDEX: the ECLIPS-2.0 dataset

description: We developed a new climate dataset for Europe referred to as ECLIPS (European CLimate Index ProjectionS), which contains gridded data for 80 annual, seasonal, and monthly climate variables for two past (1961-1990, 1991-2010) and five future periods (2011-2020, 2021-2140, 2041-2060, 2061-2080, 2081-2100). The future data are based on five Regional Climate Models (RCMs)driven by two greenhouse gas concentration scenarios, RCP 4.5 and 8.5. The ECLIPS dataset has two versions; ECLIPS 1.1 contains data with spatial resolution of 0.11° × 0.11°, which is the resolution of underlying RCMs. ECLIPS1.1 is available at https://doi.org/10.5281/zenodo.1181780. The ECLIPS 2.0 presented here contains a subset of climate indices of ECLIPS 1.1, downscaled to the resolution of 30 arcsec by means of the delta correction approach. Both ECLIPS versions were evaluated by testing their relationship with independent station data from the European Climate Assessment (ECA) dataset. Correlations of the empirical testing data to ECLIPS 1.1 ranged from 0.63 to 0.78,and to ECLIPS 2.0 from 0.78 to 0.93. suggesting substantial improvement due to downscaling. A large number of climate projections, time periods and indices as well as the availability of these data at two different spatial resolutions can support diverse studies across a range of disciplines and thus extend our understanding of climate-sensitive dynamics of many social-ecological systems The zipfile ECLIPS2.0 contains 5 folders with subfolders File naming system for the subfolders / folder are as follows ECLIPS2.0_196191: past climate 1961-1990: &lt; climate index&gt;&lt;period&gt; ECLIPS2.0_199110: past climate 1991-2010 &lt; climate index&gt;&lt;period&gt; ECLIPS2.0_45 : future climate RCP4.5 &lt;subfolder-Model name&gt; &lt; climate index&gt;&lt;period&gt; ECLIPS2.0_85 : future climate RCP8.5 &lt;subfolder-Model name&gt; &lt; climate index&gt;&lt;period&gt; Incase zpfile reader 7zip is not available, please install from here: https://www.7-zip.org/
description: File naming system is as follows ECLIPS2.0_196191: past climate 1961-1990: &lt; climate index&gt; ECLIPS2.0_199110: past climate 1991-2010 &lt; climate index&gt; ECLIPS2.0_45 : future climate RCP4.5 &lt; climate index&gt; ECLIPS2.0_85 : future climate RCP8.5 &lt; climate index&gt;
DOI: 10.5281/zenodo.4751241
title: X-ray diffraction tomography dataset of archaeological ceramic

description: <br> This dataset contains a subset of processed data that was acquired using X-ray diffraction tomography (XRD-CT) at the ID15A beamline at the European Synchrotron (ESRF), Grenoble, France. The imaged object is an archaeological ceramic, whose fragments are kept at the University of Milan. High-energy X-ray diffraction measurements were taken at the ID15A beamline using a monochromatic pencil beam (90 keV energy). Data was collected of 3 horizontal slices, spaced 7 mm apart, and acquisition of each slice took 20 minutes. Acquisition was performed in 273 translation steps over a scan range of 12 mm and in 225 rotational steps over an angular range of 180 degrees. Sinograms were computed from the acquired images using the pyFAI library. A subset of the sinograms was selected, containing 3 horizontal slices with 11 channels each. The provided HDF5 file contains two subdatasets: - omega: 225 elements<br> - rotation angle in degrees<br> - sinograms: 11 x 3 x 225 x 273 elements<br> - 11 channels (corresponding to diffraction angle)<br> - 3 horizontal slices<br> - 225 rotation angles<br> - 273 horizontal pixels
DOI: 10.6084/m9.figshare.12317591
title: Coral species richness, coral hue, and reef fish richness across 74 ecoregions within four oceanic basins.

description: Data supporting Cox et al. 2021 'Regional heterogeneity in coral species richness and hue reveals novel global predictors of reef fish intra‐family diversity' <br>https://doi.org/10.1038/s41598-021-97862-8
DOI: 10.6084/m9.figshare.21509889
title: Supplementary Material for: Dietary Protein and Fiber Affect Gut Microbiome and Treg/Th17 Commitment in Chronic Kidney Disease Mice

description: <b><i>Background:</i></b> Patients with chronic kidney disease (CKD) have dysbiosis, dysmetabolism, and immune dysregulation. Gut microbiome plays an important role shaping the immune system which is an important modulator of CKD progression. <b><i>Methods:</i></b> We compared the effect of a diet low in protein and high in fiber (LP-HF; <i>n</i> = 7) to that of diet rich in protein, but low in fiber (HP-LF; <i>n</i> = 7) on gut microbiome and T-cell commitment in male CKD (Alb/TGF-β1) mice. The gut microbiomes of these mice were subjected to 16S rRNA taxonomic profiling at baseline, 6 weeks and 12 weeks of the study. <b><i>Results:</i></b> The LP-HF diet was associated with an increase in <i>Butyricicoccus pullicaecorum</i> BT, a taxon whose functions include those closely related to butyric acid synthesis (Kendall’s W statistic = 180 in analysis of microbiome composition). HP-LF diet was associated with increased abundance of two predominantly proteolytic bacterial strains related to <i>Parabacteroides distasonis</i> (W statistic = 173), <i>Mucispirillum schaedleri</i>, and <i>Bacteroides dorei</i> (W statistic = 192). Pathway analysis suggested that the LP-HF diet induced carbohydrate, lipid, and butyrate metabolism. As compared with HP-LF mice, LP-HF mice had 1.7-fold increase in CD4+Foxp3+Treg cells in spleen and 2.4-fold increase of these cells in peripheral blood. There was an 87% decrease in percentage of CD4+ Th17 + cells in spleen and an 85% decrease in peripheral blood, respectively, in LP-HF mice compared to the HP-LF mice. <b><i>Conclusion:</i></b> The LP-HF diet promotes the proliferation of saccharolytic bacteria and favors T-cell commitment toward Treg cells in a CKD mouse of model. Clinical significance of the finding needs to be further investigated.
DOI: 10.6084/m9.figshare.21510975
title: Supplementary Material for: Trends in Adherence to Recommended Physical Activity and Its Association with Mortality and Disease Progression among US Adults with Chronic Kidney Disease

description: <b><i>Introduction:</i></b> This study aimed to examine the trends in adherence to the Physical Activity Guidelines (PAG) for aerobic activity and sedentary time and their effects on mortality and disease progression among US adults with chronic kidney disease (CKD). <b><i>Methods:</i></b> We studied individuals from the National Health and Nutrition Examination Survey 2007–08 to 2017–18 with a mortality file in 2015. Multivariate regression models were used to evaluate the association between adherence to PAG and sedentary time with mortality, estimated glomerular filtration rate (eGFR), and urine albumin-to-creatinine ratio. <b><i>Results:</i></b> For the CKD population, adherence rate increased from 48.2% in 2007–08 to 55.0% in 2017–18, and sedentary time peaked in 2013–14 (7.5 h/day) and then decreased afterward. There was no difference in the trends across the non-CKD and CKD population. For the CKD population, adherence to the PAG was significantly associated with all-cause mortality (HR, 0.49; 95% CI: 0.38–0.63), malignant neoplasm mortality (HR, 0.30; 95% CI: 0.17–0.52), and albumin-creatinine ratio (OR, −0.27; 95% CI: −0.39 to −0.15). Sedentary time was significantly associated with all-cause mortality (HR, 1.12; 95% CI: 1.08–1.15), heart disease mortality (HR, 1.13; 95% CI: 1.08–1.19), and eGFR (OR, −0.49; 95% CI: −0.72 to −0.26). <b><i>Conclusions:</i></b> Favorable trends were observed in adherence to the PAG and sedentary time. Adherence to the PAG and reduction in sedentary time reduced all-cause and cause-specific mortality and prevented disease progression differently. Efforts are needed to decrease sedentary time rather than adhering to the PAG for aerobic activity alone.
DOI: 10.18112/openneuro.ds003382.v1.3.1
title: Monash vis-fPET-fMRI
DOI: 10.23636/1209
title: DUKweb (Diachronic UK web)

description: We present DUKweb, a set of large-scale resources useful for the diachronic analysis of contemporary English. The dataset is derived from JISC UK Web Domain Dataset (1996-2013), which collects resources from the Internet Archive that were hosted on domains ending in ‘.uk’. The dataset includes co-occurrences matrices for each year and two types of word vectors by year, Temporal Random Indexing vectors and word2vec embeddings.
DOI: 10.5281/zenodo.3527983
title: Monthly word embeddings for Twitter random sample (English, 2012-2018)

description: This dataset contains monthly word embeddings created from the tweets available via the statuses/sample endpoint of the Twitter Streaming API from 2012 to 2018. Full details of the creation of the dataset are given in Room to Glo: A Systematic Comparison of Semantic Change Detection Approaches with Word Embeddings. The md5sum of the gzipped tarball file is a76888ffec8cc7aebba09d365ca55ace .
DOI: 10.5281/zenodo.3537579
title: CLDF dataset derived from Haspelmath and Tadmor's "World Loanword Database" from 2009

description: Cite the source dataset as Haspelmath, Martin & Tadmor, Uri (eds.) 2009. World Loanword Database. Leipzig: Max Planck Institute for Evolutionary Anthropology. (Available online at https://wold.clld.org)
DOI: 10.5281/zenodo.3939133
title: Annotation and analysis of the secondary structure elements in the Cytochrome P450 protein family

description: We collected all currently available structures for proteins in the Cytochrome P450 family and annotated their secondary structure elements using SecStrAnnotator software (https://webchem.ncbr.muni.cz/Wiki/SecStrAnnotator). We used 2nnjA as the template domain for the annotation. Based on these annotations, we analysed the occurrence, length distribution, amino acid sequence, and presence of structural irregularities (β-bulges, 3<sub>10</sub>-helices, π-helices) of each secondary structure element class. We also statistically compared the bacterial vs eukaryotic structures. For the secondary structure element classes with sufficient sequence conservation, the most conserved residue is annotated as the reference residue. Main files: <strong>set_ALL.json</strong> - Set-ALL: list of 1012 protein domains belonging to the Cytochrome P450 family (CATH accession 1.10.630.10 + Pfam accession PF00067, accessed on 7 July 2020, one domain per PDB entry) <strong>set_NR.json</strong> - Set-NR: non-redundant list of 183 domains (one domain per UniProt ID) <strong>domain_lists_table.tsv</strong> - Overview of Set-ALL and Set-NR and separation into subsets Set-NR-Bact (bacterial), Set-NR-Euka (eukaryotic), Set-NR-Arch (archaeal), Set-NR-Viru (viral) <strong>structures/template_2NNJ-template.sses.json</strong> - Manually prepared annotation template (domain 2nnjA) <strong>structures/template_2NNJ.cif</strong> - Structure of the template domain (2nnjA) <strong>annotations_with_reference_residues_ALL.json, annotations_with_reference_residues_ALL.tsv</strong> - Annotation of secondary structure elements for Set-ALL <strong>annotations_with_reference_residues_NR.json, annotations_with_reference_residues_NR.tsv</strong> - Annotation of secondary structure elements for Set-NR <strong>aligments_NR</strong> - Multiple sequence alignments for each SSE class (Set-NR) <strong>logos_NR</strong> - Sequence logos for each SSE class (Set-NR) <strong>plots</strong> - Plots of SSE occurrence, length distribution, contained helix types and beta-bulge occurrence (Set-NR), some plots show the comparison between Set-NR-Bact and Set-NR-Euka <strong>statistical_tests.ods</strong> - Comparison of SSE occurrence between Set-NR-Bact and Set-NR-Euka by the test of equal proportions and the Fisher test, comparision of the SSE length by the Kolmogorov-Smirnov test and the two-sample Wilcoxon test
description: {"references": ["Midlik A, Navr\u00e1tilov\u00e1 V, Moturu TR, Ko\u010da J, Svobodov\u00e1 R, Berka K. Uncovering of Cytochrome P450 Anatomy by SecStrAnnotator. bioRxiv 2020.04.15.042531. doi: 10.1101/2020.04.15.042531"]}
DOI: 10.5281/zenodo.3998873
title: Source data for PointNovo

description: Source data used to generate the analysis in PointNovo paper
DOI: 10.5281/zenodo.4548793
title: Chinese Environmentally Extended Input-Output (CEEIO) Database for 2017 and 2018

description: The 2017 and 2018 Chinese Environmentally Extended Input-Output (CEEIO) databases contain 44 and 28 types of environmental pressures, respectively. To be consistent with previous CEEIO databases (www.ceeio.com), we present the 2017 and 2018 databases in 45- and 91-sector classifications. In addition, we provide the databases in 149 and 153 sectors as the 2017 and 2018 benchmark EIO tables, respectively. Another two sector classifications, 49 and 96 sectors, are also provided for flexible applications. All economic transactions in various sector classifications are in both Chinese yuan and US dollar based on the average exchange rates of the RMB against the US dollar in 2017 and 2018.
DOI: 10.5281/zenodo.4997453
title: SOIL-WATERGRIDS v1, mapping dynamic changes in soil moisture and depth of water table from 1970 to 2014, dataset and modelling

description: SOIL-WATERGRIDS is a comprehensive data product of the monthly estimates of volumetric soil water content at three depths within the root zone and the depth of the water table globally gridded at a resolution of 0.25x025 degree per grid cell from 1970 to 2014. The SOIL-WATERGRIDS data product also provides the full-scale global model (BRTSim, https://sites.google.com/site/thebrtsimproject/home) that allows third party users to assess the entire volumetric soil water content and water table dynamics from land surface to 50 m depth. This package includes a Technical Documentation with the details about the use of the data product.
DOI: 10.5525/gla.researchdata.1133
title: Single-pixel imaging and compressed sensing in the far-field of the spatial light modulator

description: The dataset contains the raw data collected; signals from the photomultiplier tube, corresponding idealised Hadamard patterns and iterative reconstruction results. The data used for the images in the publication are the photomultiplier tube signals and the idealised Hadamard patterns. The iterative reconstruction results are for reference/comparison/visualisation.
DOI: 10.6073/pasta/dcbc5a5649c12cfc28af9554d4c7089b
title: Bonanza Creek LTER: Hourly Evaporation measurements at Core Sites from 1988 to Present in the Bonanza Creek Experimental Forest near Fairbanks, Alaska

description: This study is a survey of the vegetation of the 35 control sites in Bonanza Creek LTER. The 35 sites represent replicates each of six successional stages of primary succession on the floodplain of the Tanana River and four stages of succession uplandsas well as a few recently burned sites. Data include percent cover of all species and count based on twenty 1 m2 or 4 m2 plots. Plots in young stages of succession were remeasured every 1 to 2 years; those in older stages every 3 to 5 years. Some information on biomass in these stages is available. Although most sites were established in 1988 some sites have vegetation plots that have been sampled periodically since 1965. 2009 was the last year of sampling using visual estimates of percent cover. In 2007 a new point framing system was developed and is now used for collecting vegetation data from these sites.
DOI: 10.6084/m9.figshare.11328152
title: Genomic annotation of the yellow drum

description: Structural and functional gene annotation of the assembled genome was predicted using de novo, homolog-based, and PacBio full-length transcriptome-based strategies. The repetitive sequences detected above were masked before de novo prediction annotation. We used both Augustus (augustus-3.2.1) 26 and Genscan 27 to formulate de novo predictions, yielding 38,857 and 38,807 protein-coding genes, respectively. The protein sequences of closely related fish species, including <i>D. rerio</i>, <i>G. morhua</i>, <i>G. aculeatus</i>, <i>O. niloticus</i>, <i>O. latipes</i>, <i>T. rubripes</i>, <i>T. nigroviridis</i>, and <i>X. maculatus</i>, were downloaded from Ensembl 28 to facilitate homolog-based gene prediction. All of the protein sequences were mapped to the yellow drum genome using the Basic Local Alignment Search Tool All (BLASTALL). We predicted 23,119 genes based on the PacBio full-length transcriptomic data, which were then used in transcriptome-based annotation. We then integrated the results of the de novo predictions, homolog-based annotations, and transcriptome-based annotations using GLEAN 29, finally obtaining a dataset containing 27,069 protein-coding genes
DOI: 10.6084/m9.figshare.12209672
title: Comparative genomic analyses of the Yellow drum

description: We provide orignal outputs of the phylogenic tree, divergence time, expanded and contracted gene families, synteny analysis of the Yellow drum and other 11 bony fish species.
DOI: 10.6084/m9.figshare.12250910
title: High-density genetic map of the yellow drum (Nibea albiflora)

description: We have built a full-sib F<sub>1</sub> family consisting 200 individuals of the yellow drum. We sequenced the whole genomes of the parents and the F<sub>1</sub> offspring applying Illumina HiSeq X TEN platform. The raw reads were filtered by removing low quality reads and adapters by using Trimmomatic (v0.36) <sup>41</sup>. An average of 9.8 Gb data was obtained for each individual. The clean reads were mapped to the reference assembly using “BWA-MEM” in BWA (v0.7.10-r78) <sup>42</sup>. Genomic alignments showed that the average sequence depth of the parents and the F1 individuals was 45.9× and 15.54×, respectively.For SNP calling, the high-quality mapped reads of the 202 individuals were analyzed in GATK (v 3.3-0) <sup>43</sup>. A number of 3.36 million raw SNPs were called for subsequent filtering: 1) only bi-allele SNPs were retained in all individuals. 2) genotype depth of SNPs of parents and offspring were between 10-30 and 5-20, respectively. 3) genotype quality of all variants &gt; 10. 4) all SNPs in the parents should not be missing and at least one of the parents should be heterozygous. 5) missing rate of each SNP should be &lt; 15%. Then filtered SNPs were obtained and transmitted into JoinMap4.1 <sup>44</sup> for Chi-squared test (<i>P</i> &lt;0.05). Finally, 6,219 SNPs were used for constructing linkage map by Joinmap4.1. Twenty-four linkage groups were clustered using 6,219 SNP markers across the yellow drum genome, with the number of SNPs on each chromosome ranging from 179 to 359. Each linkage group contained an average of 260 SNP markers. The maximum likelihood method was used to sort the markers on each linkage group and estimate the genetic distances between markers. The consensus map spanned 4,300.2 cM and covered nearly the whole genome with a resolution of 0.69 cM. Compared to the previous linkage map constructed by Qiu <i>et al</i>. <sup>5</sup>, we have used more individuals with more genetic markers and produced a genetic linkage map with higher resolution. This high-density linkage map will facilitate the ongoing marker-assisted selection and genomic study of the yellow drum.
DOI: 10.6084/m9.figshare.12317489
title: Phenotypic descriptive of 202 yellow drum individuals

description: Detailed sequencing statistics and phenotypes of 202 individuals in this project.
DOI: 10.6084/m9.figshare.12563192.v2
title: CovMulNet19.zip

description: CovMulNet19 is a comprehensive network containing all available known interactions involving SARS-CoV-2 proteins, interacting-human proteins, diseases and symptoms that are related to these human proteins, and compounds that can potentially target them. Extensive network analysis methods, based on a bootstrap approach, allow us to prioritise a list of diseases that display a high similarity to \covid and a list of drugs that could potentially be beneficial to treat patients. As a key feature of CovMulNet19, the inclusion of symptoms allows a deeper characterization of the disease pathology, representing a useful proxy for CoVid19-related molecular processes. We recapitulate many of the known symptoms of the disease and we find the most similar diseases to COVID-19 reflect conditions that are risk factors in patients. <br>
DOI: 10.6084/m9.figshare.13258640
title: Experimental datasets

description: Experimental datasets (MCBJ, IVs, Raman) accompanying the manuscript 'Benchmark and application of unsupervised classification approaches for univariate data'.<br>
DOI: 10.6084/m9.figshare.14955189
title: Frontoparietal network resilience is associated with protection against cognitive decline in Parkinson’s disease

description: Please see manuscript for details.
DOI: 10.17632/cc95xkyp3j.1
title: Data for "Evaluation of the airport runway flexible pavement macro-texture using digital image processing Technique (DIPT)"

description: Data including: animation of detection by each digital image processing method for sample pavement texture images (rough and smooth(Figure 3 a, b)), raw images and processed images of 33 stations of runways pavement (132 images) by each digital image processing method (1-Butterworth Band-pass Filter Method, 2- Edge Pixels Count Method and 3- Fuzzy Logic Edge Detection Method). Validation of Counting Algorithm (for Fuzzy Logic Edge Detection Method). Derived parameter by three methods (BPF, EPP and FCN parameters) and MTD data for 132 processed Image in (Data.xlsx) file. For details of each method please visit the published paper at: https://doi.org/10.1080/10298436.2021.1968393