cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20145425.v1
title: Methanobacteriaceae

description: <strong>Data for the Methanobacetriaceae analysis.</strong> <br> Metagenomes and associated sample metadata from a globally distributed set of studies were gathered from the curatedMetagenomicData (Pasolli et al. 2017) by Youngblut et al. (2020). Briefly, (i) metagenome were profiled with the HUMAnN2 pipeline to obtain metabolic pathways profiles based on the MetaCyc database and with Kraken2 and Bracken v2.2 based on a customized Genome Taxonomy Database (GTDB), Release 89.0 created with Struo v0.1.6 (available athttp://ftp.tue.mpg.de/ebio/projects/struo/) for the taxonomic profiles; (ii) rare taxa were filtered out and taxonomic ranks from family to species were included (n = 2190 taxa; 181 families, 562 genera and 1447 species); (iii) relative abundances of MetaCyc metabolic pathways at the community level with complete coverage and a prevalence greater than 25 % were included (n = 117 pathways). <br> ---------------------------------------------- <br> Metadata: information on samples <br> Taxa relative abundances - no methanogens: relative abundances of at the family, genus, and species levels; all Methanobacteriaceae were removed. <br> MetaCyc pathways - no methanogens: relative abundances at the community level of MetaCyc pathways; all pathways to which Methanobacteriaceae participate were removed. <br> Methanogens-targets: predicted target = presence/absence of Methanobacteriaceae (Mtbc). The Msmi column corresponds to the presence/absence of the species Methanobrevibacter smithii. <br> <br>
DOI: 10.5066/p9ghpds1
title: Water-level and well-discharge data related to aquifer testing in Fountain Creek alluvial aquifer, El Paso County, Colorado, 2019

description: U.S. Geological Survey (USGS) in cooperation with the U.S. Air Force Civil Engineering Center conducted short-term aquifer tests at 11 wells to estimate hydraulic properties in the Fountain Creek alluvial aquifer, in El Paso County, Colorado. Data were collected in July 2019 over three days. Single-hole pumping and recovery tests were completed at five wells, and multiple single-hole displacement (solid slug) tests were conducted at all 11 wells. This data release contains water-level data collected at various time intervals (0.25 seconds, 0.5 seconds, and variable during a manual test with a stopwatch) and well-discharge rates for the aquifer tests in comma separated value (CSV) files for the 34 tests analyzed. All water-level displacement data for a given well are provided in a single CSV file for the well. Data are further categorized by the type of aquifer test used for data collection (slug or pumping). Well logs, graphs of the test data, and plots of analytical solutions are included in file, "FCAA_aquifer_testing_description_plots_vFINAL.pdf."
DOI: 10.7916/d8-0kap-h241
title:  GRID3 Cabo Verde Settlement Extents, Version 01.01
DOI: 10.21227/v185-3158
title: Analysis and Preliminary Design of a Passive Upper Limb Exoskeleton - MATLAB code

description: A folder that contains the Matlab code for the proposed design tool of the paper "Analysis and Preliminary Design of a Passive Upper Limb Exoskeleton" can be freely downloaded.A detailed analytical model is developed to support the designer in the preliminary design stage, investigating the exoskeleton kinetic-static behaviour and deriving optimal design parameters for the springs over the human arm workspace. By defining specific functional requirements (i.e., the user’s features and simulated movements), computationally efficient optimization studies may be carried out to determine the optimal coefficients and positions of the springs, thus, maximizing the accuracy of the gravity balancing.
DOI: 10.6084/m9.figshare.20145209
title: Cirrhosis data

description: Data were originally published by Qin et al., 2014 (DOI: 10.1038/nature13568) and were downloaded from the ML repo (https://github.com/knights-lab/MLRepo, accessed on 27/01/2021). <br> The data set consists of 130 stool samples from cirrhotic and healthy individuals, from which Qin et al. extracted gDNA and sequenced it via an Illumina HiSeq sequencer. They profiled metagenomes with BURST and Prokaryotic RefSeq Genomes. The downloaded taxonomic profiles consisted of read counts for taxonomic levels not collapsed at coarser level (i.e., if a read count had been assigned to the species level, the number of count of the genus was not indicated). Consequently, we calculated the read counts for each taxonomic level by summing read counts of all species in the clade. Relative abundances were then normalized per the total number of reads to obtain relative abundances. Taxa were filtered using a progressive threshold as described in our paper (https://www.biorxiv.org/content/10.1101/2022.01.03.474763v1). <br> ------------------------------------------------------ <br> Cirrhosis_X: relative abundances of human gut microbiome of individuals with/without cirrhosis <br> Cirrhosis_y: labeling of healthy and cirrhosis individuals <br>
DOI: 10.15151/esrf-es-811755321
title: Experimental determination of Iodine partitioning between hydrous fluids and silicate melts at HP-HT conditions

description: To better understand and quantify the Iodine contribution of volcanic systems to the atmosphere, we propose to study Iodine partitioning in almost-natural subduction related systems using natural basalt and synthetic trondhjemite both coexisting with a I-enriched hydrous fluid. We will determine the Iodine content for all phases in situ during successive decompression of the system. It will allow us to calculate partition coefficients and to estimate magmatic Iodine fluxes. we will better understand the process of Iodine-release from the melt during its ascent and magmatic degassing. Furthermore, the results can give insight to the Iodine content in magmatic systems. For the first time, we will use a natural basaltic rock for these types of experiments on Iodine. To reach the solidus of the basalt we will also for the first time combine a modified Bassett type hydrothermal diamond anvil cell with a laser heating system.
DOI: 10.6084/m9.figshare.19649766
title: chemical data of female Japanese macaques, Rigaill et al. 2022 AJP doi/10.1002/ajp.23411

description: These files contain the data analyzed in Rigaill et al. 2022.Chemical cues of identity and reproductive status in Japanese macaques (currently ms AJP-22-0014). In this study, we analyzed 67 urine samples from 5 captive female Japanese macaques (<em>Macaca fuscata</em>) and 30 vaginal swabs from 3 of these females using gas chromatography–mass spectrometry and examined the relationship between odor (compounds identified, richness, intensity, and diversity) and female identity as well as cycle phase. The files contain the following information for each sample: the name of the female (female-id), whether we sampled the first or second cycle of the mating season (cyle), the date of sampling (date), the cycle phase (cycle-phase) which was determined a posteriori from hormonal analyses, and the different compounds identified (UC1 to UC36 for urine samples, and VC1 to VC68 for vaginal samples). The file presents the abundance of each compound detected for each sample. For the analyses of similarity, we excluded compounds that co-eluted from our dataset (urine: exclusion of UC13, vaginal secretion: exclusion of VC16, VC27, VC33, VC34, VC39, VC44, VC45, VC46, VC48, VC50, VC52).
DOI: 10.6084/m9.figshare.19649766.v1
title: chemical data of female Japanese macaques, Rigaill et al. 2022 AJP doi/10.1002/ajp.23411

description: These files contain the data analyzed in Rigaill et al. 2022.Chemical cues of identity and reproductive status in Japanese macaques (currently ms AJP-22-0014). In this study, we analyzed 67 urine samples from 5 captive female Japanese macaques (<em>Macaca fuscata</em>) and 30 vaginal swabs from 3 of these females using gas chromatography–mass spectrometry and examined the relationship between odor (compounds identified, richness, intensity, and diversity) and female identity as well as cycle phase. The files contain the following information for each sample: the name of the female (female-id), whether we sampled the first or second cycle of the mating season (cyle), the date of sampling (date), the cycle phase (cycle-phase) which was determined a posteriori from hormonal analyses, and the different compounds identified (UC1 to UC36 for urine samples, and VC1 to VC68 for vaginal samples). The file presents the abundance of each compound detected for each sample. For the analyses of similarity, we excluded compounds that co-eluted from our dataset (urine: exclusion of UC13, vaginal secretion: exclusion of VC16, VC27, VC33, VC34, VC39, VC44, VC45, VC46, VC48, VC50, VC52).
DOI: 10.7916/d8-v430-5w77
title:  GRID3 Cabo Verde Settlement Extents Version 01, Alpha

description: NOTE: This initial version of the Cabo Verde settlement extents has been superseded by the final version, "GRID3 Cabo Verde Settlement Extents, Version 01", now available here: https://doi.org/10.7916/d8-8dny-v772 The database constitutes a comprehensive set of settlement polygons nationwide. It is in geodatabase format and consists of three feature classes for built up areas (BUA), small settlement areas (SSA), and hamlets (hamlets). This work has been undertaken as part of the Geo-referenced Infrastructure and Demographic Data for Development (GRID3) initiative in Cabo Verde. GRID3 works with countries to generate, validate and use geospatial data on population, settlements, infrastructure, and subnational boundaries. For more information, see https://grid3.org/ Keywords: built up areas, BUA, small settlement areas, SSA, hamlets, settlement aggregation, settlement extent, CIESIN, GRID3, Novel-T
DOI: 10.5281/zenodo.6515018
title: Astra Memory Error and System Monitoring Data Sets

description: Memory error events and system monitoring information gathered on Astra while it was operating from January 20, 2019 to September 14, 2019. See the dataset description files in the archive for additional details.
DOI: 10.18430/m37v0h
title: X-ray diffraction data for the crystal Structure of Putative glucose 1-dehydrogenase from Burkholderia cenocepacia in complex with NADP and a potential reaction product (7V0H)
DOI: 10.18430/m38cso
title: X-ray diffraction data for the crystal Structure of Orotidine 5'-phosphate decarboxylase from Klebsiella pneumoniae in complex with Uridine-5'-monophosphate (8CSO)
DOI: 10.18430/m38d1x
title: X-ray diffraction data for the crystal Structure of aminopeptidase A from Neisseria gonorrhoeae (8D1X)
DOI: 10.5285/5af9e5cf-657d-4640-8ff3-dd3ec2f43367
title: Observational data and model output for sediment nutrient cycling at Patagonian fjords

description: Glacier meltwater supplies a significant amount of silicon (Si) and iron (Fe) sourced from weathered bedrock to downstream ecosystems. However, the extent to which these essential nutrients reach the ocean is regulated by the nature of the benthic cycling of dissolved Si and Fe within fjord systems, given the rapid deposition of reactive particulate fractions at fjord heads. The dataset is used to examine the benthic cycling of the two nutrients at Patagonian fjord heads through geochemical analyses of sediment pore waters and reaction-transport modeling for Si. The dataset contains: (i) pore water redox-sensitive nitrate (NO3-) and dissolved manganese (dMn) concentration data, nutrient dissolved silicon (DSi) and iron (dFe) concentration and isotope data (delta30 Si, delta56 Fe); (ii) mild alkaline leachable (Si-Alk) and acid leachable (Si-HCl) sediment silica content and isotope data; and (iii) reaction transport model output for the benthic cycling of Si. The pore water and sediment samples were collected from four sites: SJ (48.228o S, 73.502o W, 106 m depth), SH (47.679 S, 73.715 W, 203 m depth), SP (48.179 S, 73.347 W, 248 m depth) and SB (47.787 S, 73.610 W, 151 m depth) in the Baker-Martinez Fjord Complex on the research vessel Sur-Austral in February 2017. Funded by NERC-CONICYT grant NE/P003133/1-PII20150106.
description: Silicon and nitrate concentrations were measured with spectrophotometry. Dissolved iron concentration, manganese concentration, iron isotopes and silicon isotopes were measured with inductively coupled plasma-mass spectrometry. The reaction transport model employed is the Biogeochemical Reaction Network Simulator. The model was run under steady state assumption. Pore water data depth resolution: 5 cm - 15 cm Sediment data depth resolution: 10 cm - 50 cm Model data depth resolution: 0.1 cm - 1 cm
description: (1) Thermo Scientific X-Series 2 quadrupole inductively coupled plasma-mass spectrometer (dissolved iron and manganese concentration measurements) (2) Thermo-Finnigan Neptune multicollector-inductively coupled plasma-mass spectrometer (silicon and iron isotope measurements) (3) Maple computing environment version 2016.0 (compile inputs for reaction transport modeling)
description: The accuracies of the pore water elemental concentration and isotope analyses were assessed with measurements of standard solutions. Errors associated with sediment and pore water analyses were assessed with replicate measurements of samples and standards. Analytical errors for: (i) NO3- concentration is about 0.5% (ii) dMn concentration and dFe concentration are 0.7% - 8.9%; (iii) DSi concentration is about 2.5%; (iv) Si-Alk content is 25%; (v) Si-HCl content is 15%; (vi) delta30 Si is 0.08‰ - 0.34‰, and (vii) delta56 Fe is 0.04‰ - 0.08‰. Model's best fit with observational data was determined by minimizing the root-mean-square error.
DOI: 10.34740/kaggle/dsv/3870318
title: The state of hiring discrimination
DOI: 10.25919/mfzz-kx24
title: Parkes observations for project P1054 semester 2022APRS_11

description: With this proposal we ask time to continue our timing follow-up campaign of pulsars discovered with the MeerKAT telescope. Fourteen sources have been discovered in targeted observations of Fermi unidentified point sources, three in the Small Magellanic Cloud, 37 in Globular Clusters and 34 in a survey of the Galactic plane. A large fraction of the new discoveries are recycled pulsars (including at least one double neutron star system and several 'spider' binaries), or young pulsars. Timing observations have an essential role in exploiting the full potential of any pulsar discovery, allowing the precise measurement of rotational, astrometric and orbital parameters which, in turn, give us powerful tools to improve our understanding of the physics in extreme environments as well as of the population of neutron stars as a whole. The UWL receiver of the Parkes telescope is a sensitive, versatile instrument that is allowing us to successfully time these new sources, in the bright-end of TRAPUM discoveries. The UWL has also the unique advantage of allowing detailed studies of the eclipses of the so-called 'spider' pulsars, which make up about 1/3rd of the sources we aim at following-up with this project.
DOI: 10.17861/b6bc020c-1eea-43b3-866c-5b4960a3d715
title: Data supporting paper: High resolution TCSPC imaging of diffuse light with a one-dimensional SPAD array scanning system

description: Data and code supporting the publication, to appear shortly in Optics Express. Arxiv version available: https://arxiv.org/abs/2204.07582 Data describes light scattering through phantoms, as recorded by a single photon imaging system, described in detail in the publication.
DOI: 10.7916/d8-n8bx-0v66
title:  GRID3 Seychelles Settlement Extents, Version 01.01
DOI: 10.6084/m9.figshare.20130794.v2
title: Dataset: An IoT-Enriched Event Log for Process Mining in Smart Factories

description: Modern technologies such as the Internet of Things (IoT) are becoming increasingly important in various domains, including Business Process Management (BPM) research. One main research area in BPM is process mining, which can be used to analyze event logs, e.g., for checking the conformance of running processes. However, there are only a few IoT-based event logs available for research purposes. Some of them are artificially generated and the problem occurs that they do not always completely reflect the actual physical properties of smart environments. In this paper, we present an IoT-enriched XES event log that is generated by a physical smart factory. For this purpose, we create the SensorStream XES extension for representing IoT-data in event logs. Finally, we present some preliminary analysis and properties of the log.
DOI: 10.5281/zenodo.6760409
title: OTU level 16s sequence data for "Algae drive convergent bacterial community assembly when nutrients are scarce"

description: 16s sequence data at the OTU level for the experiments conducted in "Algae drive convergent bacterial community assembly when nutrients are scarce" The file is in fasta format, which can be read by many software packages including biopython, R, and SILVA's alignment, classification and tree service. The sequence ids can be used to find the phylogeny and OTU ID of the sequences from Supplementary dataset 4.
DOI: 10.5281/zenodo.6760408
title: OTU level 16s sequence data for "Algae drive convergent bacterial community assembly when nutrients are scarce"

description: 16s sequence data at the OTU level for the experiments conducted in "Algae drive convergent bacterial community assembly when nutrients are scarce" The file is in fasta format, which can be read by many software packages including biopython, R, and SILVA's alignment, classification and tree service. The sequence ids can be used to find the phylogeny and OTU ID of the sequences from Supplementary dataset 4.
DOI: 10.5281/zenodo.6759156
title: Polifonia_Corpus_Wikipedia_Annotation_EN

description: Polifonia_Corpus_Wikipedia_Annotation_EN
DOI: 10.5281/zenodo.6701773
title: Polifonia_Corpus_Wikipedia_Annotation_EN

description: Polifonia_Corpus_Wikipedia_Annotation_EN
DOI: 10.7916/d8-83eq-cj87
title:  GRID3 Seychelles Settlement Extents, Version 01

description: The dataset consists of settlement extents across Seychelles, as well as accompanying population estimates for each settlement extent. This data product contains all information contained in the previous GRID3 Seychelles Settlement Extents, Version 01 Alpha product, with updates. Updates in this version include: a single settlement extent feature class (Alpha contained the same data in three (3) separate feature class layers: BUAs, SSAs & Hamlets), and new population estimate fields ("Population" and "Pop_UN_adj") for each settlement extent . This work has been undertaken as part of the Geo-Referenced Infrastructure and Demographic Data for Development (GRID3) programme. GRID3 works with countries to generate, validate and use geospatial data on population, settlements, infrastructure, and subnational boundaries. For more information, see https://grid3.org/ Keywords: Settlements, Hamlets, Built-up Areas (BUA), Small Settlement Areas (SSA) The programme is funded by the Bill & Melinda Gates Foundation and United Kingdom's Foreign, Commonwealth, Development Office. It is implemented by Flowminder Foundation, WorldPop at the University of Southampton, the United Nations Population Fund (UNFPA), and the Center for International Earth Science Information Network (CIESIN) at Columbia University.
DOI: 10.5281/zenodo.6760585
title: CFT trial dataset

description: Background One-size-fits-all interventions reduce chronic low back pain (CLBP) a small amount. An individualised intervention called cognitive functional therapy (CFT) was superior for CLBP compared with manual therapy and exercise in one randomised controlled trial (RCT). However, systematic reviews show group interventions are as effective as one-to-one interventions for musculoskeletal pain. This RCT investigated whether a physiotherapist-delivered individualised intervention (CFT) was more effective than physiotherapist-delivered group-based exercise and education for individuals with CLBP. Methods 206 adults with CLBP were randomised to either CFT (n=106) or group-based exercise and education (n=100). The length of the CFT intervention varied according to the clinical progression of participants (mean=5 treatments). The group intervention consisted of up to 6 classes (mean=4 classes) over 6–8 weeks. Primary outcomes were disability and pain intensity in the past week at 6 months and 12months postrandomisation. Analysis was by intention-to-treat using linear mixed models. Results CFT reduced disability more than the group intervention at 6 months (mean difference, 8.65; 95% CI 3.66 to 13.64; p=0.001), and at 12 months (mean difference, 7.02; 95% CI 2.24 to 11.80; p=0.004). There were no between-group differences observed in pain intensity at 6 months (mean difference, 0.76; 95% CI -0.02 to 1.54; p=0.056) or 12 months (mean difference, 0.65; 95% CI -0.20 to 1.50; p=0.134). Conclusion CFT reduced disability, but not pain, at 6 and 12 months compared with the group-based exercise and education intervention. Future research should examine whether the greater reduction in disability achieved by CFT renders worthwhile differences for health systems and patients.
description: Dr Mary O'Keeffe is supported by funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 750492
DOI: 10.5281/zenodo.6760584
title: CFT trial dataset

description: Background One-size-fits-all interventions reduce chronic low back pain (CLBP) a small amount. An individualised intervention called cognitive functional therapy (CFT) was superior for CLBP compared with manual therapy and exercise in one randomised controlled trial (RCT). However, systematic reviews show group interventions are as effective as one-to-one interventions for musculoskeletal pain. This RCT investigated whether a physiotherapist-delivered individualised intervention (CFT) was more effective than physiotherapist-delivered group-based exercise and education for individuals with CLBP. Methods 206 adults with CLBP were randomised to either CFT (n=106) or group-based exercise and education (n=100). The length of the CFT intervention varied according to the clinical progression of participants (mean=5 treatments). The group intervention consisted of up to 6 classes (mean=4 classes) over 6–8 weeks. Primary outcomes were disability and pain intensity in the past week at 6 months and 12months postrandomisation. Analysis was by intention-to-treat using linear mixed models. Results CFT reduced disability more than the group intervention at 6 months (mean difference, 8.65; 95% CI 3.66 to 13.64; p=0.001), and at 12 months (mean difference, 7.02; 95% CI 2.24 to 11.80; p=0.004). There were no between-group differences observed in pain intensity at 6 months (mean difference, 0.76; 95% CI -0.02 to 1.54; p=0.056) or 12 months (mean difference, 0.65; 95% CI -0.20 to 1.50; p=0.134). Conclusion CFT reduced disability, but not pain, at 6 and 12 months compared with the group-based exercise and education intervention. Future research should examine whether the greater reduction in disability achieved by CFT renders worthwhile differences for health systems and patients.
description: Dr Mary O'Keeffe is supported by funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 750492