cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7450803
title: KMCP Manuscript Data

description: # KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping ## 1.code-and-documents This directory contains the source code, executable binaries, and documents of KMCP,<br> which are also hosted at Github: https://github.com/shenwei356/kmcp . Databases, usage, and tutorials of KMCP are also available at https://bioinf.shenwei.me/kmcp/. - [Installation](https://bioinf.shenwei.me/kmcp/download)<br> - [Databases](https://bioinf.shenwei.me/kmcp/database)<br> - Tutorials<br> - [Taxonomic profiling](https://bioinf.shenwei.me/kmcp/tutorial/profiling)<br> - [Sequence and genome searching](https://bioinf.shenwei.me/kmcp/tutorial/searching)<br> - [Usage](https://bioinf.shenwei.me/kmcp/usage)<br> - [Benchmarks](https://bioinf.shenwei.me/kmcp/benchmark)<br> - [FAQs](https://bioinf.shenwei.me/kmcp/faq) ## 2.databases This directory contains the building steps and reference genome accessions for<br> KMCP databases used in the manuscript. cami2 Databases used in benchmarks on CAMI2 mouse gut datasets<br> kmcp Databases used in other benchmarks<br> <br> ## 3.figures Each subdirectory contains steps to run the benchmark (`README.md`), steps for plotting (`README-plot.md`),<br> benchmark results, and figures.<br>
description: This work was supported by the National Natural Science Foundation of China [32000474 to W.S.]; by the China Postdoctoral Science Foundation [2021M700640 to W.S.]; and by the Chongqing Talents Project [cstc2021ycjh-bgzxm0150 to P.H.].
DOI: 10.5281/zenodo.7811871
title: Parameters of 220 million stars from Gaia BP/RP spectra

description: We present parameters of 220 million stars, based on Gaia XP spectra and near-infrared photometry from 2MASS and WISE. Instead of using ab initio stellar models, we develop a data-driven model of Gaia XP spectra as a function of the stellar parameters, with a few straightforward built-in physical assumptions. Here, we provide the resulting catalog of stellar parameters, our trained stellar model, and a few Python scripts that demonstrate how to interact with the catalog and model. See the README.md for more information.
DOI: 10.5518/290
title: Influence of conformity on the wear of total knee replacement: An experimental study - dataset

description: Wear of total knee replacement continues to be a significant factor influencing the clinical longevity of implants. The aim of this study was to investigate the effect of insert conformity on the wear performance of a fixed bearing total knee replacement through experimental simulation. Two geometries of insert were studied under standard gait conditions. This dataset contains the images and wear data relating to the study understanding conformity influence on wear of a fixed bearing total knee replacement.
DOI: 10.6084/m9.figshare.22224742.v1
title: miRNA profiling of MSC secretome

description: miRNA profiling data from MSC secretome using NanoString Technology
DOI: 10.6084/m9.figshare.5044804
title: The Kalochori Accelerometric Network (KAN), database and Web-GIS portal

description: The Kalochori Accelerometric Network (KAN) operates since 2014 in the urban area of Kalochori, 7 km west of Thessaloniki in Northern Greece, as part of a multi-sensor monitoring scheme developed during the INDES-MUSA project (http://www.indes-musa.gr/en/). KAN is composed of seven accelerometric stations; three ground stations installed in distinct urban zones (i.e. residential, industrial and tanks zone), three stations on top of a selected structure within each urban zone and one free-field station away from the built environment. All the stations are documented with installation and operating features, available characteristics of the housing structures and geotechnical data at the stations sites. The data linked to this DOI refer to seventy eight (78) earthquakes that have been recorded by KAN between 01/16/2014 and 12/31/2016. More specifically, the uploaded dataset includes KAN stations monographs, filtered and unfiltered acceleration recordings and metadata of the recorded earthquakes. An online demonstration of the Kalochori Accelerometric Network and dissemination of the above data is provided through the INDES-MUSA Web-GIS platform http://apollo.itsak.gr/apollo-portal/ApolloPro.aspx.
DOI: 10.17632/ggty3v22cx.1
title: TCBO CAD and measured IRs

description: The dataset contains the CAD and the material properties of the TCBO (Teatro Comunale Bologna) Measured IRs are available too.
DOI: 10.21335/nmdc-1821375519
title: Seabed sediment data (upper 6 cm) on water content, total nitrogen, total carbon, total organic carbon, total inorganic carbon, carbon and nitrogen isotopic composition from the Nansen Legacy seasonal cruise 2021703 (Q1).

description: This dataset includes contents of water content, total nitrogen (TN), total carbon (TC), total organic carbon (TOC), total inorganic carbon (TIC), and carbon and nitrogen isotopic composition (d13C, d15N) in marine sediments. Samples were collected during the Nansen Legacy cruises in March as part of cruise 2021703 (Q1) in the northern Barents Sea. Sediment material was subsampled from three replicate deployments of a giant box corer at four stations (P1 to P6). At P7, only two deployments were completed. The samples were immediately sliced into 1 cm layers (0 - 6 cm) and placed into plastic jars, and frozen on board. Two replicates at P1 were sliced down to 3 cm. All samples were freeze-dried under vacuum in the laboratory and homogenized. Elemental analysis of carbon and nitrogen concentrations was undertaken with an Elemental Analyser - Isotope Ratio Mass Spectrometry (EA-IRMS; Iso - Analytical Ltd., UK). Before d13C analysis, samples were acidified with 1M HCl and left overnight to allow the inorganic carbon to be liberated as CO2. The samples were then neutralized by repetitively washing with distilled water and oven drying at 60 degrees Celsius. The standards d13CV-PDB (Vienna PeeDee Belemnite) and d15NAIR (atmospheric N2) were used as references for the carbon and nitrogen isotope values, respectively. The measured TOC content was corrected for weight loss upon acid washing, TIC content was calculated by subtracting TOC from TC.
DOI: 10.21335/nmdc-490057692
title: Seabed sediment data (upper 6 cm) on grain size, water content, total nitrogen, total carbon, total organic carbon, total inorganic carbon, carbon and nitrogen isotopic composition from the Nansen Legacy seasonal cruise 2019706 (Q3).

description: This dataset includes contents of water content, total nitrogen (TN), total carbon (TC), total organic carbon (TOC), total inorganic carbon (TIC), and carbon and nitrogen isotopic composition (d13C, d15N) in marine sediments. Samples were collected during the Nansen Legacy cruises in March as part of cruise 2019706 (Q3) in the northern Barents Sea. Sediment material was subsampled from three replicate deployments of a giant box corer at six stations (P1 to SICE4). The samples were immediately sliced into 1 cm layers (0 - 6 cm) and placed into plastic jars, and frozen on board. All samples were freeze-dried under vacuum in the laboratory and homogenized. Elemental analysis of carbon and nitrogen concentrations was undertaken with an Elemental Analyser - Isotope Ratio Mass Spectrometry (EA - IRMS; Iso-Analytical Ltd., UK). Before d13C analysis, samples were acidified with 1M HCl and left overnight to allow the inorganic carbon to be liberated as CO2. The samples were then neutralized by repetitively washing with distilled water and oven drying at 60 degrees Celsius. The standards d13CV-PDB (Vienna PeeDee Belemnite) and d15NAIR (atmospheric N2) were used as references for the carbon and nitrogen isotope values, respectively. The measured TOC content was corrected for weight loss upon acid washing, TIC content was calculated by subtracting TOC from TC. Grain size distribution of non-acidified samples was assessed with a Beckman Coulter LS 13 320 Particle Size Analyser. The organic matter was removed with 10 % H2O2, and deflocculated with a 5 % Calgon solution (sodium hexametaphosphate and sodium carbonate) in an ultrasonic bath prior to analysis. The particle diameter within the 0.04–2000 μm range was measured at 0.004 μm resolution.
DOI: 10.25716/gude.1vjx-3key
title: Ab initio study of highly tunable charge transfer in β-RuCl3/graphene heterostructures

description: Heterostructures of graphene in proximity to magnetic insulators open the possibility to investigate exotic states emerging from the interplay of magnetism, strain and charge transfer between the layers. Recent reports on the growth of self-integrated atomic wires of $\beta$-RuCl$_3$ on graphite suggest these materials as versatile candidates to investigate these effects. Here we present detailed first principles calculations on the charge transfer and electronic structure of $\beta$-RuCl$_3$/graphene heterostructures and provide a comparison with the work function analysis of the related honeycomb family members $\alpha$-RuX$_3$ (X = Cl,Br,I). We find that proximity of the two layers leads to a hole-doped graphene and electron-doped RuX$_3$ in all cases, which is sensitively dependent on the distance between the two layers. Furthermore, strain effects due to lattice mismatch control the magnetization which itself has a strong effect on the charge transfer. Charge accumulation in $\beta$-RuCl$_3$ strongly drops away from the chain making such heterostructures suitable candidates for sharp interfacial junctions in graphene-based devices.
description: All input files required to run the calculations are included. Some of the small size output files are also included. For detailed information check the README.
DOI: 10.26030/qasa-rr29
title: miRNA signature detection and countermeasures against HZE radiation exposure for tissue degeneration-Plasma

description: Biological risks associated with space radiation and microgravity are major concerns for long-term space travel. Through a Systems Biology approach, our previous NASA work has shown both TGFβ signaling pathways and miRNAs have a critical impact on defining health risks with and without space irradiation. We hypothesize that circulating microRNA (miRNA) signatures are driving microvascular disease and muscle degeneration associated with accelerating aging and will be enhanced by exposure to the space environment (radiation and microgravity). We investigated this hypothesis both in vivo and in vitro and test novel antagonist therapies to these miRNA signatures as countermeasures to reduce space radiation-induced health risks. A comprehensive Systems Biology approach was used to examine the influence by high atomic number by high (H) atomic number (Z) and energy (E) (HZE) irradiation. To simulate low-dose exposure due to galactic cosmic rays (GCR), we used the ions, energy, and doses determined by a NASA consensus formula of 7 different ions to represent GCR (referred to as GCR sim model). To simulate high-dose radiation exposure due to solar particle events (SPE), we used an acute dose of SPE simulated beam at 1Gy which has energies ranging from 50MeV to 150MeV. C57BL/6 wild-type mice were utilized for irradiation with our established simulated microgravity model (hindlimb suspension model) and an in vitro 3D microvasculature tissue model under simulated microgravity (clinostat) conditions will also be irradiated. To expand on the circulating miRNA signature determined from our preliminary data, we determined a group of conserved miRNAs which are commonly being regulated in the majority of the organs and tissues throughout the host using our established techniques. MiRNA-sequencing on serum (before IR and at time of sacrifice), liver, heart, and muscle tissue for all radiation groups revealed the key circulating miRNA signature (consisting of multiple miRNAs) impacting disease risk. Collectively, understanding of how whole body space radiation impacts microvascular and tissue degeneration through circulating miRNAs will greatly enhance health risk prognostication and provide possible new mechanisms for protection against space radiation.
DOI: 10.4225/87/lcveu3
title: Young Minds Matter: The second Australian Child and Adolescent Survey of Mental Health and Wellbeing, 2013-14

description: The objective of the Young Minds Matter survey was to estimate the prevalence, severity, and impact of mental disorders in children and adolescents in Australia. Seven mental disorders were assessed using the parent or carer completed version of the Diagnostic Interview Schedule for Children Version IV (DISC-IV), and major depressive disorder was also assessed using the youth self-report version of the DISC-IV. Severity and impact were assessed using an extended version of the DISC-IV impact on functioning questions, and days absent from school due to symptoms of mental disorders. Data were collected in a national face-to-face survey of 6,310 parents or carers of children and adolescents aged 4-17 years, accompanied by self-report surveys of 2,969 young people aged 11-17 years. The 12-month prevalence of mental disorders was 13.9%. The most common class of disorders was ADHD followed by anxiety disorders. Mental disorders were more common in step-, blended- or one parent families, in families living in rented accommodation and families where one or both carers were not in employment. Some 2.1% of children and adolescents had severe disorders, 3.5% had moderate disorders and 8.3% had mild disorders. Mental disorders were associated with a substantial number of days absent from school, particularly in adolescents.
DOI: 10.5063/f1x065hw
title: r-values of D. mawii individuals for three UMAs in south Mexico.

description: The database shows the kinship relationship values ​​of the founders individuals in 3 UMAs in Tabasco, Mexico
DOI: 10.5281/zenodo.4780815
title: Audio Spatialisation for Headphones - Impulse Response Dataset

description: The Audio Spatialisation for Headphones Impulse Response Dataset (ASH IR Dataset) is a set of impulse responses that can be used for binaural synthesis of spatial audio systems on headphones. It includes binaural room impulse responses (BRIRs), headphone compensation filters (HpCFs) and configuration files for Equalizer APO. The dataset can be used to create spatial surround sound on headphones by convolving an audio stream with a set of BRIRs and a HpCF. The dataset contains: A set of equalised binaural room impulse responses that can be used to simulate a variety of rooms including control rooms, listening rooms, seminar rooms, studios, and more A set of compensation filters that can be used to equalise a wide range of headphones to the diffuse-field target frequency response A set of configuration files for Equalizer APO that can be used to simulate common speaker configurations (Stereo, 5.1 surround, 7.1 surround) within the rooms More information can be found at the github repository: https://github.com/ShanonPearce/ASH-IR-Dataset
DOI: 10.6084/m9.figshare.20182859
title: Strains of Bradyrhizobium barranii sp. nov. associated with legumes native to Canada are symbionts of soybeans and belong to different subspecies (subsp. barranii subsp. nov. and subsp. apii subsp. nov.) and symbiovars (sv. glycinearum and sv. septentrionale)

description: <strong>Supplementary Data</strong> <br> Supplementary files for 'Strains of <em>Bradyrhizobium barranii</em> sp. nov. associated with legumes native to Canada are symbionts of soybeans and belong to different subspecies (subsp. <em>barranii </em>subsp. nov.and subsp. <em>apii </em>subsp. nov.) and symbiovars (sv. glycinearum and sv. septentrionale)', as described in <em>International Journal of Systematic and Evolutionary Microbiology</em>
DOI: 10.6084/m9.figshare.21445617
title: Teste de Fidedignidade

description: Teste de Fidedignidade das categorias criadas na Dissertação.
DOI: 10.6084/m9.figshare.26411008
title: Efficacy of China's clean air actions to tackle PM2.5 pollution between 2013 and 2020

description: Beginning in 2013, China launched two phases (2013–2017 and 2017–2020) of clean air actions that have led to substantial reductions in PM<sub>2.5</sub> concentrations. However, improvement in PM<sub>2.5</sub> pollution was notably slowing down during Phase II. Here, we quantified the efficacy and drivers of PM<sub>2.5</sub> improvement and evaluated the associated cost during 2013–2020 using an integrated framework that combines an emission inventory model, a chemical transport model, and detailed cost information.
DOI: 10.6084/m9.figshare.26977141
title: Supplementary Material for: Virulence-related genes expression in planktonic mixed cultures of Candida albicans and non-albicans Candida species

description: Introduction. Candida albicans is the most common opportunistic pathogen causing fungal infections worldwide, especially in high-risk patients. Its pathogenicity is related to virulence factors gene expression, such as hyphal growth (HWP1), cell adhesion (ALS3), and protease secretion (SAP1) during infection spreading mechanisms. In recent years, an increase in non-albicans Candida infections has been reported, which may present co-infection or competitive interactions with C. albicans, potentially aggravating the patient's condition. This study aims to evaluate the expression of genes related to virulence factors of C. albicans and non-albicans Candida during planktonic stage. 
Methods. Candida albicans (ATCC MYA-3573) as well as with three clinical strains (C. albicans DCA53, C. tropicalis DCT6, and C. parapsilosis DCP1) isolated from blood samples, were grown in 24-well plates at 37°C for 20 hours, either in monocultures or mixed cultures. RT-qPCR was used to evaluate the expression levels of the genes HWP1, ALS3, and SAP1 in cells collected during the planktonic stage. In addition, hyphal filamentation was observed using a Scanning Electron Microscope
Results. The overexpression of HWP1 and ASL3 genes in mixed growth conditions between C. albicans and non-albicans Candida species suggests a synergistic relationship as well as an increased capacity for hyphal growth and adhesion. In contrast, C. parapsilosis vs C. tropicalis interaction shows an antagonistic relationship during mixed culture, suggesting a decreased virulence profile of C. parapsilosis during initial co-infection with C. tropicalis. 
Conclusion. The expression of HWP1, ALS3 and SAP1 genes associated with virulence factors varies under competitive conditions among species of the genus Candida during planktonic stage.
DOI: 10.6084/m9.figshare.27191838
title: Supplementary Material for: Prevalence, incidence, and mortality of Myasthenia Gravis and myasthenic syndromes: a systematic review

description: Introduction: No systematic reviews were published in the last years investigating epidemiological data, involving Myasthenia Gravis (MG) and related myasthenic syndromes. The aim of this systematic review was to estimate the prevalence, incidence, and mortality of all MG types and myasthenic syndromes worldwide.
Methods: All literature published up to February 2024 was retrieved by searching the databases “Medline”, “Embase”, “ISI Web of Science” and “CINAHL” using the following search terms: (epidemiolog* OR frequency OR prevalence OR incidence OR mortality) AND (myasth* OR “anti-acetylcholine receptor antibody” OR “AChR” OR “MuSK” OR “anti-muscle specific kinase antibody” OR “LRP4” OR “seronegative MG”).
Results: A total of 94 studies, performed between 1952 and 2022, were included. Prevalence of MG ranged from 20 to 475 cases per million, with a mean prevalence of 173.3 (95% CI: 129.7-215.5) cases per million and a median prevalence of 129.6 cases per million. Incidence rates ranged from 2.3 to 61.3 cases per million person-years, with a mean incidence of 15.7 (95% CI: 11.5-19.9) and a median of 13.3 cases. Mortality rates showed a mean of 1.4 (95% CI: 0.8-2.1) cases per million person-years. AChR-MG was the clinical subtype more frequent in terms of prevalence and incidence.
Discussion: The prevalence and incidence of MG have significantly increased over the last years worldwide, probably due to the improvement of epidemiological methodologies and current advances in diagnosis. However, we observed a significant variation in frequencies of MG between and within countries because of methodological biases and complex heterogeneity of the disease characterized by several phenotypes and different clinical responses.
DOI: 10.7910/dvn/drsaca/hjfg1k
title: 102slersuoacontest20181024-1.tab

description: THIS IS PROBABLY THE FILE YOU WANT: Stata file with SLERs restructured so that the contest is the unit of analysis.
DOI: 10.15468/dl.8nuq8d
title: Occurrence Download

description: A dataset containing 151 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Viet Nam",
 "Geometry POLYGON((464.68605 8.54721,464.95987 8.54721,464.95987 8.82935,464.68605 8.82935,464.68605 8.54721))",
 "HasCoordinate is true",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 151 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048354-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dch2ab
title: Occurrence Download

description: A dataset containing 424 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Barathronus Goode & Bean, 1886"
 ]
}

 The dataset includes 424 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025621-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tm9epn
title: Occurrence Download

description: A dataset containing 2382 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acridotheres tristis (Linnaeus, 1766)",
 "Country is French Polynesia",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 2382 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033965-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w8gnuh
title: Occurrence Download

description: A dataset containing 9040550 species occurrences available in GBIF matching the query:
{
 "BasisOfRecord" : [
 "is Fossil"
 ]
}

 The dataset includes 9040550 records from 508 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021129-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.738766
title: Pollen profile CZE1, Marais de Charauze, France

description: The EPD (http://www.europeanpollendatabase.net) accepted species name is given in the parameter comment. This dataset was archived on 2010-05-11 from the EPD database.
DOI: 10.1594/pangaea.739484
title: Pollen profile LORAS84, Loras, France

description: The EPD (http://www.europeanpollendatabase.net) accepted species name is given in the parameter comment. This dataset was archived on 2010-05-11 from the EPD database.