cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13720693
title: Supplementary Material for: Visual Analysis of Biomarkers Reveals Differences in Lipid Profiles and Liver Enzymes before and after Gastric Sleeve and Bypass

description: <b><i>Introduction:</i></b> Bariatric surgery results in both intentional and unintentional metabolic changes. In a high-volume bariatric center, extensive laboratory panels are used to monitor these changes pre- and postoperatively. Consecutive measurements of relevant biochemical markers allow exploration of the health state of bariatric patients and comparison of different patient groups. <b><i>Objective:</i></b> The objective of this study is to compare biomarker distributions over time between 2 common bariatric procedures, i.e., sleeve gastrectomy (SG) and gastric bypass (RYGB), using visual analytics. <b><i>Methods:</i></b> Both pre- and postsurgical (6, 12, and 24 months) data of all patients who underwent primary bariatric surgery were collected retrospectively. The distribution and evolution of different biochemical markers were compared before and after surgery using asymmetric beanplots in order to evaluate the effect of primary SG and RYGB. A beanplot is an alternative to the boxplot that allows an easy and thorough visual comparison of univariate data. <b><i>Results:</i></b> In total, 1,237 patients (659 SG and 578 RYGB) were included. The sleeve and bypass groups were comparable in terms of age and the prevalence of comorbidities. The mean presurgical BMI and the percentage of males were higher in the sleeve group. The effect of surgery on lowering of glycated hemoglobin was similar for both surgery types. After RYGB surgery, the decrease in the cholesterol concentration was larger than after SG. The enzymatic activity of aspartate aminotransferase, alanine aminotransferase, and alkaline phosphate in sleeve patients was higher presurgically but lower postsurgically compared to bypass values. <b><i>Conclusions:</i></b> Beanplots allow intuitive visualization of population distributions. Analysis of this large population-based data set using beanplots suggests comparable efficacies of both types of surgery in reducing diabetes. RYGB surgery reduced dyslipidemia more effectively than SG. The trend toward a larger decrease in liver enzyme activities following SG is a subject for further investigation.
DOI: 10.5281/zenodo.4506354
title: Sample data for the paper: Extending the CMDI Universe: Metadata for Bioinformatics Data by Olaf Brandt, Holger Gauza, Steve Kaminski, Mario Trojan, Thorsten Trippel and Johannes Werner submitted to CLARIN2020 Post-Conference Proceedings

description: This data set contains the sample data referenced in the paper: Extending the CMDI Universe: Metadata for Bioinformatics Data by Olaf Brandt, Holger Gauza, Steve Kaminski, Mario Trojan, Thorsten Trippel and Johannes Werner submitted to CLARIN2020 Post-Conference Proceedings. It contains the two XSchemas mentioned and one sample data set.
DOI: 10.5281/zenodo.4506353
title: Sample data for the paper: Extending the CMDI Universe: Metadata for Bioinformatics Data by Olaf Brandt, Holger Gauza, Steve Kaminski, Mario Trojan, Thorsten Trippel and Johannes Werner submitted to CLARIN2020 Post-Conference Proceedings

description: This data set contains the sample data referenced in the paper: Extending the CMDI Universe: Metadata for Bioinformatics Data by Olaf Brandt, Holger Gauza, Steve Kaminski, Mario Trojan, Thorsten Trippel and Johannes Werner submitted to CLARIN2020 Post-Conference Proceedings. It contains the two XSchemas mentioned and one sample data set.
DOI: 10.6084/m9.figshare.13720690
title: treat_pile_compare.bw

description: Comparison of two analysis
DOI: 10.6084/m9.figshare.13720690.v1
title: treat_pile_compare.bw

description: Comparison of two analysis
DOI: 10.5519/qd.57tm4crt
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (89687 records)
DOI: 10.5281/zenodo.4506404
title: Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions

description: This data set contains i. input topologies and coordinates for 179 non-modified and post-translationally modified (174 in normal and 87 in stress conditions) yeast protein complexes, ii. scripts and parameters for performing molecular dynamics simulations and binding energy calculation with per-residue decomposition, iii. trajectory snapshots of solvent stripped protein complexes, which can be visualized using the corresponding topology files, iv. RMSD calculations (backbone and entire protein) from the production phase of the MD, and v. pdb of the representative structure of the largest cluster from 100 snapshots of the last 10 ns in each simulation.
DOI: 10.6084/m9.figshare.13720528
title: Observations of hydrodynamic processes and implications for sediment transport on the deep reef flats of atolls in the Nansha Islands, South China Sea

description: Hydrodynamic observations at 10-20 m deep flats of four atolls in the South China Sea demonstrate strong nonbreaking waves with moderate tidal currents.
DOI: 10.6084/m9.figshare.13720528.v2
title: Observations of hydrodynamic processes and implications for sediment transport on the deep reef flats of atolls in the Nansha Islands, South China Sea

description: Hydrodynamic observations at 10-20 m deep flats of four atolls in the South China Sea demonstrate strong nonbreaking waves with moderate tidal currents.
DOI: 10.6084/m9.figshare.13720528.v1
title: Observations of hydrodynamic processes and implications for sediment transport on the deep reef flats of atolls in the Nansha Islands, South China Sea

description: Hydrodynamic observations at 10-20 m deep flats of four atolls in the South China Sea demonstrate strong nonbreaking waves with moderate tidal currents.
DOI: 10.6084/m9.figshare.13720573
title: GRL_Tornado_Data

description: Data for GRL Tornado paper.
DOI: 10.6084/m9.figshare.13720573.v1
title: GRL_Tornado_Data

description: Data for GRL Tornado paper.
DOI: 10.22024/unikent/01.01.140
title: The Lady's Magazine Index

description: A fully annotated index to the just over 15000 text items in the Lady’s Magazine; or, Entertaining Companion for the Fair Sex from its first series (1770 to 1818).
DOI: 10.5281/zenodo.4506257
title: MODIS LST monthly daytime and nighttime low (0.05), median (0.50) and high (0.95) temperatures for year 2003 at 1-km

description: Layers include: Land Surface Temperature daytime low (0.05), median (0.50) and high (0.95) temperatures for the year 2003. Derived using the data.table package and quantile function in R. For more info about the MODIS LST product see: https://lpdaac.usgs.gov/dataset_discovery/modis/modis_products_table/mod11a2_v006. Antarctica is not included. To access and visualize maps use: OpenLandMap.org To download and compute with maps using Cloud-Optimized-GeoTIFF see <strong>this tutorial</strong>. If you discover a bug, artifact or inconsistency in the OpenLandMap maps, or if you have a question please use some of the following channels: Technical issues and questions about the code: https://gitlab.com/openlandmap/global-layers/-/issues General questions and comments: https://disqus.com/home/forums/landgis/ All files internally compressed using "COMPRESS=DEFLATE" creation option in GDAL. File naming convention: clm = theme: climate, lst = variable: land surface temperature, mod11a2.daytime = determination method: MOD11A2 product, day time values, d = median value / sd = standard deviation / u.95 = aggregation/statistics method: 95% probability upper quantile, 1km = spatial resolution / block support: 1 km, s0..0cm = vertical reference: land surface, 2000..2020 = time reference: from 2000 to 2020, v1.1 = version number: 1.1,
description: This work has received funding from the European Union's the Innovation and Networks Executive Agency (INEA) under Grant Agreement Connecting Europe Facility (CEF) Telecom project 2018-EU-IA-0095 (https://ec.europa.eu/inea/en/connecting-europe-facility/cef-telecom/2018-eu-ia-0095).
DOI: 10.5281/zenodo.4506256
title: MODIS LST monthly daytime and nighttime low (0.05), median (0.50) and high (0.95) temperatures for year 2003 at 1-km

description: Layers include: Land Surface Temperature daytime low (0.05), median (0.50) and high (0.95) temperatures for the year 2003. Derived using the data.table package and quantile function in R. For more info about the MODIS LST product see: https://lpdaac.usgs.gov/dataset_discovery/modis/modis_products_table/mod11a2_v006. Antarctica is not included. To access and visualize maps use: OpenLandMap.org To download and compute with maps using Cloud-Optimized-GeoTIFF see <strong>this tutorial</strong>. If you discover a bug, artifact or inconsistency in the OpenLandMap maps, or if you have a question please use some of the following channels: Technical issues and questions about the code: https://gitlab.com/openlandmap/global-layers/-/issues General questions and comments: https://disqus.com/home/forums/landgis/ All files internally compressed using "COMPRESS=DEFLATE" creation option in GDAL. File naming convention: clm = theme: climate, lst = variable: land surface temperature, mod11a2.daytime = determination method: MOD11A2 product, day time values, d = median value / sd = standard deviation / u.95 = aggregation/statistics method: 95% probability upper quantile, 1km = spatial resolution / block support: 1 km, s0..0cm = vertical reference: land surface, 2000..2020 = time reference: from 2000 to 2020, v1.1 = version number: 1.1,
description: This work has received funding from the European Union's the Innovation and Networks Executive Agency (INEA) under Grant Agreement Connecting Europe Facility (CEF) Telecom project 2018-EU-IA-0095 (https://ec.europa.eu/inea/en/connecting-europe-facility/cef-telecom/2018-eu-ia-0095).
DOI: 10.5281/zenodo.4506428
title: An African leaf-cutting, fungus-growing ant: a case of convergent evolution

description: This repository includes two Tables and five files presenting the details of metabarcoding analysis, as well as ITS1 sequences and OTUs for fungi recorded during this study 1- Tables SA and SB Table SA. Taxonomic assignment to OTU and number of reads recorded for the three nest samples analyzed (CN1, CN2 and CN3) and for the control (CT) (see Fig. S3). OTUs are sorted by total reads in decreasing order of abundance. OTUs belonging to Capnodiales<em> s.l.</em> and to Chaetothyriales are in bold. Table SB. List of sequences included in phylogenetic trees. Accessions are included for the Capnodiales <em>s.l.</em> tree (underlined; corresponds to Fig. S4) and the Chaetothyriales tree (double underlined, corresponds to Fig. S5). Grey shaded lines indicate ant associated fungi. Fungi belonging to Capnodiales <em>s.l.</em> and to Chaetothyriales recorded in this study are in bold. 2- Capno-ITS-ML-Tree (ITS of the Capnodiales). Alignment of sequences and maximum likehood phylogenetic tree for Capnodiales <em>s.l.</em> showing the phylogenic position of the recorded OTUs belonging to Capnodiales <em>s.l.</em> 3- Chaeto-ITS-ML-Tree (ITS of Chaetothyriales). Alignment of sequences and maximum likehood phylogenetic tree for Chaetothyriales showing the phylogenic position of the recorded OTUs belonging to Chaetothyriales. 4- Tab_Data_All_Sequences_OTU. Datamatrix of sequences (reads) across samples 5- Blast_Results-First-50_Hits-Table-72_OTU. Dataset of BLAST results. List of the 50 first BLAST hits obtained with ITS1 sequences for each of the 72 OTUs recorded in <em>Crematogaster</em> nests. Best hits are in bold. 6- Tab-OTU-Seqs. List of recorded OTUs and their ITS1 sequences. OTUs belonging to Capnodiales <em>s.l.</em> and Chaetothyriales are in bold
DOI: 10.5281/zenodo.4506427
title: An African leaf-cutting, fungus-growing ant: a case of convergent evolution

description: This repository includes two Tables and five files presenting the details of metabarcoding analysis, as well as ITS1 sequences and OTUs for fungi recorded during this study 1- Tables SA and SB Table SA. Taxonomic assignment to OTU and number of reads recorded for the three nest samples analyzed (CN1, CN2 and CN3) and for the control (CT) (see Fig. S3). OTUs are sorted by total reads in decreasing order of abundance. OTUs belonging to Capnodiales<em> s.l.</em> and to Chaetothyriales are in bold. Table SB. List of sequences included in phylogenetic trees. Accessions are included for the Capnodiales <em>s.l.</em> tree (underlined; corresponds to Fig. S4) and the Chaetothyriales tree (double underlined, corresponds to Fig. S5). Grey shaded lines indicate ant associated fungi. Fungi belonging to Capnodiales <em>s.l.</em> and to Chaetothyriales recorded in this study are in bold. 2- Capno-ITS-ML-Tree (ITS of the Capnodiales). Alignment of sequences and maximum likehood phylogenetic tree for Capnodiales <em>s.l.</em> showing the phylogenic position of the recorded OTUs belonging to Capnodiales <em>s.l.</em> 3- Chaeto-ITS-ML-Tree (ITS of Chaetothyriales). Alignment of sequences and maximum likehood phylogenetic tree for Chaetothyriales showing the phylogenic position of the recorded OTUs belonging to Chaetothyriales. 4- Tab_Data_All_Sequences_OTU. Datamatrix of sequences (reads) across samples 5- Blast_Results-First-50_Hits-Table-72_OTU. Dataset of BLAST results. List of the 50 first BLAST hits obtained with ITS1 sequences for each of the 72 OTUs recorded in <em>Crematogaster</em> nests. Best hits are in bold. 6- Tab-OTU-Seqs. List of recorded OTUs and their ITS1 sequences. OTUs belonging to Capnodiales <em>s.l.</em> and Chaetothyriales are in bold
DOI: 10.6084/m9.figshare.13686835
title: Supplemtal DataFile 2 from Chiral triclinic metamaterial crystals supporting isotropic acoustical activity and isotropic chiral phonons

description: COMSOL model for calculating band structure of the chiral unit cell in Fig.1(c).
DOI: 10.6084/m9.figshare.13686835.v1
title: Supplemtal DataFile 2 from Chiral triclinic metamaterial crystals supporting isotropic acoustical activity and isotropic chiral phonons

description: COMSOL model for calculating band structure of the chiral unit cell in Fig.1(c).
DOI: 10.6084/m9.figshare.13686847
title: Supplemtal DataFile 1 from Chiral triclinic metamaterial crystals supporting isotropic acoustical activity and isotropic chiral phonons

description: Geomtry of the chiral unit cell as shown in Fig.1(c).
DOI: 10.6084/m9.figshare.13686847.v1
title: Supplemtal DataFile 1 from Chiral triclinic metamaterial crystals supporting isotropic acoustical activity and isotropic chiral phonons

description: Geomtry of the chiral unit cell as shown in Fig.1(c).
DOI: 10.15161/oar.it/73467
title: CovidStat project data

description: This record contains the daily updated data of the CovidStat project. CovidStat is a project carried out by the CovidStat Working Group at INFN, whose creation was promoted within the Italian National Institute of Nuclear Physics with the aim of making a statistical analysis of the data provided daily by the Civil Protection on the spread of the pandemic in Italy. CovidStat data can interactively be browsed at https://covid19.infn.it.
description: The software to process this Root TTree is in the related identifier. Be sure to use the right corresponding version, based on the data in which Root TTree was generated.
DOI: 10.6084/m9.figshare.13720708
title: Supplementary Material for: The Diagnostic Yield of Prenatal Genetic Technologies in Congenital Heart Disease: A Prospective Cohort Study

description: <b><i>Introduction:</i></b> The objective was to evaluate: (i) the proportion of prenatally diagnosed congenital heart disease (CHD) associated with an abnormal quantitative fluorescence-PCR (QF-PCR), chromosome microarray (CMA), and exome sequencing (ES) result; and (ii) the diagnostic yield of these technologies based on CHD category and presence of extra-cardiac anomalies (ECAs). <b><i>Methods:</i></b> This prospective cohort study was set across 12 UK foetal medicine centres. All cases underwent QF-PCR, CMA, and ES, and the diagnostic yield in <i>n</i> = 147 cases of prenatally diagnosed CHD was assessed. <b><i>Results:</i></b> In 34.7% (<i>n</i> = 51/147), a genetic diagnosis was obtained. Using a stepwise testing strategy, the diagnostic yield for QF-PCR, CMA, and ES was 15.6% (<i>n</i> = 23/147), 13.7% (<i>n</i> = 17/124), and 10.2% (<i>n</i> = 11/107), respectively. Abnormal QF-PCR/shunt (septal) defects 31.4% (<i>n</i> = 11/35), <i>p</i> = 0.046, and abnormal CMA/conotruncal anomalies 22.7% (<i>n</i> = 10/44), <i>p</i> = 0.04, had significant associations. Monogenic variants were commonest in complex CHD 36.4% (<i>n</i> = 4/11). Multisystem CHD had a greater diagnostic yield overall compared to isolated OR 2.41 (95% CI, 1.1–5.1), particularly in association with brain and gastrointestinal tract anomalies. The proportion of variants of uncertain significance was 4.7% (<i>n</i> = 5/107) with ES, with none in the CMA group. <b><i>Conclusion:</i></b> In the era of prenatal ES, there remains an important role for QF-PCR and CMA. Identification of monogenic pathologic variants further allows delineation of prognosis in CHD.
DOI: 10.6084/m9.figshare.13710001.v1
title: Projecting 1 km-grid population distributions from 2020 to 2100 globally under shared socioeconomic pathways

description: Spatially explicit population datasets can play an important role in climate change, urban planning, resource management and other fields. Several gridded datasets already exist, but global data, especially high-resolution data on future population are largely lacking. Based on the open-accessed LandScan datasets from 2010 to 2018 and linear extrapolation model, we present a population dataset covering 233 countries or areas at an approximately 1 km (30 arc-seconds) spatial resolution with 10-year intervals for the period 2020–2100 by implementing two steps: land-use dependence and total constraint. These data are quantitatively consistent with the Shared Socioeconomic Pathways’ (SSPs) national population and urbanization projections. Considering the outbreak of COVID-19, we add SSP3-COV scenario to describe the global population distribution affected by the pandemic. The global gridded population projection data are validated by comparing 2010 and 2015 population projection data with the LandScan population data at the sub-national level. The verification results show that our dataset can serve as an input for predictive research in various fields.<br>
DOI: 10.25345/c59794
title: MassIVE MSV000086811 - AFFF 3M Light Water Non-Targeted PFAS Analysis for FluoroMatch 2.0 Manuscript - Agilent Q-TOF
title: Because of the pervasiveness, persistence, and toxicity of per- and polyfluoroalkyl substances (PFAS), there is growing concern over PFAS contamination, exposures, and health effects. The diversity of potential PFAS is astounding, with nearly 10,000 catalogued in databases to date (and growing). The ability to detect the thousands of known PFAS, and discover previously uncatalogued PFAS, is necessary to understand the scope of PFAS contamination and to identify appropriate remediation and regulatory solutions. Current non-targeted methods for PFAS analysis require manual curation and are time-consuming, prone to error, and not comprehensive. FluoroMatch Flow 2.0 is the first software to cover all steps of data processing for PFAS discovery in liquid chromatography high resolution tandem mass spectrometry samples. These steps include feature detection, feature blank filtering, exact mass matching to catalogued PFAS, mass defect filtering, homologous series detection, retention time pattern analysis, class-based MS/MS screening, fragment screening, and predicted MS/MS from SMILES structures. In addition, a comprehensive confidence level criterion is implemented to help users understand annotation certainty and integrate various layers of evidence to reduce overreporting. Applying the software to aqueous film forming foam analysis, we discovered over one thousand likely PFAS including previously unreported species. Furthermore, we were able to filter out 96 percent of features which were likely not PFAS. FluoroMatch Flow 2 increased coverage of likely PFAS by over tenfold compared to the previous release. This software will enable researchers to better characterize PFAS in the environment and in biological systems. An aliquot of a mixed AFFF product collected from a holding tank at a field site in 1999 was prepared by 100,000x dilution in 70:30 water:methanol (Fisher Scientific Optima LCMS-grade). Blanks consisting of 70:30 water:methanol were run before and after AFFF injections. The AFFF sample was characterized previously and is known to contain primarily electrochemically-fluorinated 3M Light Water AFFF mixed with some fluorotelomer-based AFFF. This AFFF sample is representative of mixtures that are widespread at historical AFFF-contaminated sites. The diluted sample was injected four times for iterative exclusion information-dependent analysis (Iterative MS/MS) at 50 uL onto an Agilent 1290 Infinity II ultra-high performance liquid chromatography (UHPLC) system connected to an Agilent 6545 quadrupole time-of-flight mass spectrometer (Q-TOF MS).
DOI: 10.5281/zenodo.4309853
title: Unraveling a black box: An open-source methodology for the field calibration of small air quality sensors

description: This repository contains data for the manuscript: "Unraveling a black box: An open-source methodology for the field calibration of small air quality sensors." This includes: Raw data from the low-cost prototype EarthSense Zephyrs, as well as raw data from reference instrumentation. SC stands for "Summer Campaign" and WC stands for "Winter Campaign", denoting the two different campaigns assessed in this study. <strong>Abstract</strong> The last two decades have seen substantial technological advances in the development of low-cost air pollution instruments using small sensors. While their use continues to spread across the field of atmospheric chemistry, challenges remain in ensuring data quality and comparability of calibration methods. This study introduces a seven-step methodology for the field calibration of low-cost sensors using reference instrumentation with user-friendly guidelines, open access code, and a discussion of common barriers to such an approach. The methodology has been developed and is applicable for gas-phase pollutants, such as for the measurement of nitrogen dioxide (NO<sub>2</sub>) or ozone (O<sub>3</sub>). A full example of the application of this methodology to a case study in an urban environment using both Multiple Linear Regression (MLR) and the Random Forest (RF) machine-learning technique is presented with relevant R code provided, including error estimation. In this case, we have applied it to the calibration of metal oxide gas-phase sensors (MOS). Results reiterate previous findings that MLR and RF are similarly accurate, though with differing limitations. The methodology presented here goes a step further than most studies by including explicit, transparent steps for addressing model selection, validation, and tuning, as well as addressing the common issues of autocorrelation and multicollinearity. We also highlight the need for standardized reporting of methods for data cleaning and flagging, model selection and tuning, and model metrics. In the absence of a standardized methodology for the calibration of low-cost sensors, we suggest a number of best practices for future studies using low-cost sensors to ensure greater comparability of research.