cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4542418
title: Datasets of search_TPS - A Bioinformatics Tool for Efficient Retrieval of High-Confidence Terpene Synthases (TPS) and Application to the Identification of TPS in Coffea and Quillaja

description: Here we have support data for the chapter "A Bioinformatics Tool for Efficient Retrieval of High-Confidence Terpene Synthases (TPS) and Application to the Identification of TPS in Coffea and Quillaja". We include here the guide tree that was used for the development of TPS specific HMM profiles (PB_all.pdf). We detail here the datasets of cured TPS genes we used for tool validation (from<em> Arabidopsis thaliana</em>, <em>Solanum lycopersicum</em> and <em>Setaria italica</em>), in CaseStudy1.xlsx file. We also describe the TPS genes identified in <em>Coffea canephora</em>, <em>Coffea eugenioides</em>, <em>Coffea arabica </em>and <em>Quillaja saponaria (</em>ValidatioTablev1.xlsx). In the case of <em>Q. saponaria</em>, we reassembled the transcriptome based on public RNA-seq data (Bioproject PRJEB8056). We followed the protocol "Best Practices for De Novo Transcriptome Assembly with Trinity" (Published on Tue 29 September 2020 By Adam Freedman, Nathan Weeks [https://informatics.fas.harvard.edu/best-practices-for-de-novo- transcriptome-assembly-with-trinity.html]) and obtained a transcriptome assembly with the following statistics: Total trinity 'genes': 36582 Total trinity transcripts: 47608 Median contig length: 547 Average contig: 787.36 The transcripts were annotated using the Trinotate v3.2.1 pipeline (http://trinotate.github.io). All of the annotated peptide sequences (Trinity_Qsap_pep.fasta) were used as input for search_TPS. search_TPS (search_TPS_Tutorialvf.pdf) is freely available at https://github.com/liliane-sntn/TPS. To report bugs, to ask for help and to give any feedback, please contact Liliane S. Oliveira (liliane.sntn@gmail.com) or Douglas S. Domingues (douglas.domingues@unesp.br).
description: This work was partially financed by the São Paulo State Research Foundation (FAPESP) (grants number 2016/10896-0; 2017/01455-2, 2019/15477-3). SMCL receives a CAPES fellowship (Finance Code - 001). DSD is a CNPq research productivity fellow (#312823/2019-3). Douglas S. Domingues, Liliane S. Oliveira and Suzana T. Ivamoto-Suzuki contributed equally to this work.
DOI: 10.5517/ccdc.csd.cc21clyz
title: CCDC 1887991: Experimental Crystal Structure Determination

description: Related Article: Hiba Souidi, Hamza Triki, Slaheddine Kamoun|2021|J.Mol.Struct.|1232|129994|doi:10.1016/j.molstruc.2021.129994
DOI: 10.6084/m9.figshare.14036585.v1
title: Illumina, pacbio and ont sequencing reads

description: This is the example 30X dataset of Illumina, pacbio and ONT sequencing data of the CFT073 E. coli strain (BioSample: SAMN10819847).<br><br>Data was produced by researchers from the University of Oxford, UK.<br>
DOI: 10.5281/zenodo.4542431
title: Fitofaladoiro IES Castro da Uz. As Pontes de García Rodríguez (A Coruña)

description: Datos recollidos nos cursos 2017-2018 e 2018-2019
DOI: 10.6084/m9.figshare.13728220
title: Annual rasters of estimated Tasmanian devil density from 1985-2035

description: Maps of estimated of Tasmanian devil density from 1985-2035, as estimated by the joint-likelihood model from Cunningham et al (2021) Ecology Letters. Each layer of the raster "predictionStack_devils_1985to2035.tif" corresponds to a map of estimated devil densities in a given year, with the first layer corresponding to 1985 and increasing by one year for each subequent raster layer. In the same way, we also present the raster "SD_stack_devils_1985to2035.tif", with each layer corresponding to the estimated standard deviations in a given year.<br>The easiest way to use this data would be to read the rasters into R using the 'brick' function of the 'raster' package. If you use this data, please cite Cunningham et al (2021) Ecology Letters.
DOI: 10.5281/zenodo.4542459
title: Fitofaladoiro do IES San Rosendo. Mondoñedo (Lugo)

description: Datos recollidos nos cursos 2015-2016 e 2016-2017
DOI: 10.13023/kgs.data.2021.03
title: Landslide Soil Hydrology Data for Three Landslides in Kentucky

description: This data is from three landslides monitored in Kentucky between October 2015 and September 2020. The purpose was to capture and analyze subsurface hydrologic conditions within the landslides at different slope positions over time. The site descriptions, field methodology, data-acquisition techniques, and observations provide a general picture of soil moisture in hillslope soils. Data collected includes volumetric water content, soil water potential, bulk electrical conductivity, bulk dielectric permittivity, temperature. Water potential is the energy state of water in the soil, a determination of stress in the soil based on how water moves. Water potential can be described as the negative pore pressures exerted by the soil matrix that determine water flow in unsaturated soil. Rainfall was measured at each landslide with a tipping-bucket gage and a data logger. Rainfall collection was standalone, and not connected to the system collecting the soil-moisture data. Rainfall data provided here is in inches. The field instrumentation and implementation are cost-effective techniques that can be used for subsequent projects such as slope-stability assessment and landslide-susceptibility modeling.
description: © 2021 University of Kentucky
DOI: 10.26186/144568
title: Australian Petroleum Blocks 2020 - Geodatabase

description: The dataset was created by Geoscience Australia using the framework described in Section 33 of the Offshore Petroleum and Greenhouse Gas Storage Act 2006 (OPGGS Act) and previous Acts.
The international, scheduled areas and coastal waters used in this dataset are those found in the current Australian Maritime Boundary Dataset 2020 (AMB2020).  The 2020 release has been updated to reflect the 2018 Timor Sea Treaty. 

Available for download in GDA94 or GDA2020.

The dataset is comprised of both polygons and points created to very high precision, accurate to within millimetres.

The blocks have been cut by Australia's international boundaries, the scheduled areas and the coastal waters. Each block is assigned a polygon, including partial blocks. All blocks are titled with their block ID, and a list of vertices that make up the blocks. Each vertex of the dataset is also replicated as a discrete point in the points dataset.
The design of the dataset allows for the exact location of every vertex to be known to millimetre precision. The corner coordinates of blocks are now defined to a high precision, and can be found by querying the appropriate point.

The blocks are attributed with fields containing information on:
- Block ID
- Parent 1 Million Mapsheet
- Offshore Area
- Epoch of the boundaries used to cut the data  AMB2014
- Datum
- Origin of the mapsheet in AGD66
- The position of all vertices in the block
- The number of vertices in the block
- The area of the block in acres
- The area of the block in hectares
The calculation used to find the area of the blocks is estimated to be precise to better than 1%. This is considered to be sufficient as under the permit and licensing arrangements in the OPGGS Act, the area of a block has no relevance. Therefore the area figure is provided solely for reference.
DOI: 10.5281/zenodo.4542454
title: Dataset for "A cross–nearest neighbor/Monte Carlo algorithm for single molecule localization microscopy defines interactions between p53, Mdm2, and MEG3"

description: Dataset for "A cross–nearest neighbor/Monte Carlo algorithm for single molecule localization microscopy defines interactions between p53, Mdm2, and MEG3" p53-Mdm2 Well A: +Dox -Nut Well B: -Dox -Nut Well C: +Dox +Nut Well D: -Dox +Nut p53-MEG3 Well A: MEG3 +Dox Well B: MEG3 -Dox Well C: GAPDH +Dox Well D: GAPDH -Dox FKBP12-mTOR First alphabetic well: -Rap Second alphabetic well: +Rap
DOI: 10.5281/zenodo.3892994
title: Dataset for "A cross–nearest neighbor/Monte Carlo algorithm for single molecule localization microscopy defines interactions between p53, Mdm2, and MEG3"

description: Dataset for "A cross–nearest neighbor/Monte Carlo algorithm for single molecule localization microscopy defines interactions between p53, Mdm2, and MEG3" p53-Mdm2 Well A: +Dox -Nut Well B: -Dox -Nut Well C: +Dox +Nut Well D: -Dox +Nut p53-MEG3 Well A: MEG3 +Dox Well B: MEG3 -Dox Well C: GAPDH +Dox Well D: GAPDH -Dox FKBP12-mTOR First alphabetic well: -Rap Second alphabetic well: +Rap
DOI: 10.26186/144570
title: Australian Mineral Blocks 2020 - Geodatabase

description: Australian Mineral Blocks (2020) - Aligned with the current Australian Maritime Boundary Dataset (AMB2020).

ESRI Geodatabase. 

Available for download as GDA94 or GDA2020.

The dataset was created by Geoscience Australia using the framework described in Section 17 of the Offshore Minerals Act 1994.

The international, scheduled areas and coastal waters used in this dataset are those found in the current Australian Maritime Boundary Dataset 2020 (AMB2020).  The 2020 release has been updated to reflect the 2018 Timor Sea Treaty.

The dataset is comprised of both polygons and points created to very high precision, accurate to within millimetres.

The blocks have been cut by Australia's international boundaries, the scheduled areas and the coastal waters. Each block is assigned a polygon, including partial blocks. All blocks are titled with their block ID, and a list of vertices that make up the blocks. Each vertex of the dataset is also replicated as a discrete point in the points dataset.

The design of the dataset allows for the exact location of every vertex to be known to millimetre precision. The corner coordinates of blocks are now defined to a high precision, and can be found by querying the appropriate point.
DOI: 10.5519/qd.6hx1c99m
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (4 records)
DOI: 10.3886/e120685v1
title: Black Racial Ideologies and Help-Seeking

description: Black people underutilize mental health services compared to White people, and the current study sought to examine if racial identity might explain why. Specifically, this studyinvestigated how differences in racial ideology influenced help-seeking behavior in Blackcollege students. A total of 326 Black college students completed online measures assessing racial identity and help-seeking. Oppressed Minority ideology was linked to increased mental health help-seeking. When ideologies were modeled as latent classes, the Integrationist class (e.g., high Assimilation, high Humanist, high Oppressed Minority, low Nationalism) had greater help-seeking than the Nationalist class (i.e., high Nationalism, low in all other ideologies). Results suggest that Black students high in Nationalism and low in other ideologies may underutilize mental health services. Limitations and future directions are provided.
description: Response Rates: The initial sample consisted of 394 individuals. Data from 67 individuals were deletedbecause of failure of at least one of four attention checks (e.g., please pick “strongly disagree” to show you are paying attention). Outlier data from one individual was identified during latent class analysis, as this individual comprised their own class, and this data was excluded. The final participant number was 326.
description: Presence of Common Scales: The ideology subscales of the Multidimensional Inventory of Black Identity (MIBI) wereused to measure racial identity (Sellers et al., 1997). Respondents reported the extent to which they agreed with each statement using a 7-point Likert scale (1 = strongly disagree; 7 = strongly agree), with higher scores indicating higher levels of each respective construct. Four subscales are included: Nationalist, Oppressed Minority, Assimilationist, and Humanist.<br><br>The 24-item Inventory of Attitudes toward Seeking Professional Psychological Services(IASMHS) contains three subscales: psychological openness, help-seeking propensity, and indifference to stigma. Items were rated using a 5-point Likert type scale ranging from 0 (disagree) to 4 (agree).
description: Black college students from a large Southeastern minority-serving university..
description: Black participants were recruited via an online SONA system at a Southeastern university.
DOI: 10.3886/e131561
title: Community Response to Solar

description: In order to learn what the most common community reactions were to utility-scale solar energy projects in Michigan, Wisconsin, Minnesota, and Indiana, this study conducts a content analysis of locally-based newspaper articles. The data collection of articles was generated through a keyword search of all local newspaper articles in each targeted state from 1 January 2019 [M1] to 12 May 2020, a time period intended to capture the most recent experiences with solar at the genesis of this research project in Summer of 2020. In order to ensure that this study captured all of the newspaper mentions of utility-scale solar developments within these dates, a variety of terms for solar projects were tested. Ultimately, the terms “solar farm,” “solar development” and “solar project”—each in both the singular and plural form—provided the most full and focused sample. The data sample, as of 1/1/2019 to 5/12/2020, resulted in 153 articles for Michigan, 246 articles for Wisconsin, 149 articles for Minnesota, and 244 articles for Indiana.
DOI: 10.3886/e131561v2
title: Community Response to Solar

description: In order to learn what the most common community reactions were to utility-scale solar energy projects in Michigan, Wisconsin, Minnesota, and Indiana, this study conducts a content analysis of locally-based newspaper articles. The data collection of articles was generated through a keyword search of all local newspaper articles in each targeted state from 1 January 2019 [M1] to 12 May 2020, a time period intended to capture the most recent experiences with solar at the genesis of this research project in Summer of 2020. In order to ensure that this study captured all of the newspaper mentions of utility-scale solar developments within these dates, a variety of terms for solar projects were tested. Ultimately, the terms “solar farm,” “solar development” and “solar project”—each in both the singular and plural form—provided the most full and focused sample. The data sample, as of 1/1/2019 to 5/12/2020, resulted in 153 articles for Michigan, 246 articles for Wisconsin, 149 articles for Minnesota, and 244 articles for Indiana.
DOI: 10.5281/zenodo.4542491
title: Tables of Occupations by Race/Ethnicity of Parents of School Age Children, 2019 & 2020

description: These files contain occupational codes for those parents of school age children who are actively working. Actively working is defined as has a job and is not on leave.
DOI: 10.5281/zenodo.4542494
title: Tables of Occupations by Race/Ethnicity of Parents of School Age Children, 2019 & 2020

description: These files contain occupational codes for those parents of school age children who are actively working. Actively working is defined as has a job and is not on leave.
DOI: 10.5281/zenodo.4542490
title: Tables of Occupations by Race/Ethnicity of Parents of School Age Children, 2019 & 2020

description: These files contain occupational codes for those parents of school age children who are actively working. Actively working is defined as has a job and is not on leave.
DOI: 10.5523/bris.1271fsyng8y2z2cjyvlss1i8d2
title: Supporting data for "Insights from CPTu and seismic cone testing in the Kathmandu Valley, Nepal"

description: CPTu and seismic cone test data collected during a ground investigation in the Kathmandu Valley, Nepal - April 2019.
DOI: 10.6084/m9.figshare.14036696
title: Ribosomal protein database of Morganella morganii

description: This work presents the ribosomal protein database of <i>Morganella morganii. </i>Original data for the work came from the annotated proteome data of the bacterium downloaded from UniProt. Using an in-house MATLAB ribosomal protein database analysis software, the original proteome data file was parsed to extract protein name and amino acid sequence of all ribosomal proteins in the species. The database also includes calculated variables such as number of residues, molecular weight, and nucleotide sequence. Overall, the presented database could serve as a ribosomal protein mass fingerprint for use in microbial identification, or it could be used in fundamental studies seeking to uncover new insights into ribosomal protein biology.
DOI: 10.6084/m9.figshare.14036696.v1
title: Ribosomal protein database of Morganella morganii

description: This work presents the ribosomal protein database of <i>Morganella morganii. </i>Original data for the work came from the annotated proteome data of the bacterium downloaded from UniProt. Using an in-house MATLAB ribosomal protein database analysis software, the original proteome data file was parsed to extract protein name and amino acid sequence of all ribosomal proteins in the species. The database also includes calculated variables such as number of residues, molecular weight, and nucleotide sequence. Overall, the presented database could serve as a ribosomal protein mass fingerprint for use in microbial identification, or it could be used in fundamental studies seeking to uncover new insights into ribosomal protein biology.
DOI: 10.5281/zenodo.4542495
title: CoVaxxy Tweet IDs data set

description: A collection of Tweet IDs related to Covid-19 Vaccines, gathered from Twitter since Jan 4, 2021. Please see https://arxiv.org/abs/2101.07694 for more information.
DOI: 10.25345/c5dr4b
title: MassIVE MSV000086873 - Metabolomics Workbench ST001378 - GNPS Global metabolomics of COPD2020
title: b'To discover distinctive endogenous metabotype of patients with COPD associated with TB from those originated from Tabaco smoking. Cross-sectional metabolomic analyses of serum samples were performed for subjects including TB-associated COPD (T-COPD), smoking-associated COPD (S-COPD) and healthy subjects. To retain a broad spectrum of metabolites, technically distinct analyses (global metabolomic profiling using liquid chromatography quadrupole time-of-flight mass spectrometry) were employed. Frozen samples were diluted with either an acetonitrile:methanol:water (3:3:4) mixture. Each sample (5 L) was loaded onto an C18 column and was analyzed using an Agilent 6530 QTOF mass spectrometer (Agilent Technologies). Detailed protocol is obtained in this project'
DOI: 10.25345/c58z2d
title: MassIVE MSV000086874 - Diacetyl vapor exposure promotes ubiquitin proteasome stress and precedes bronchiolitis obliterans
title: Proteomic data from human airway epithelial cells treated with PBS and diacetyl vapor for two consecutive days. Samples were digested with trypsin, then analyzed by LC-MS/MS. Data was searched with MaxQuant.
DOI: 10.6073/pasta/9a4877016583357cf04b8f68eb53b648
title: Time series of high-frequency sensor data measuring water temperature, dissolved oxygen, pressure, conductivity, specific conductance, total dissolved solids, chlorophyll a, phycocyanin, and fluorescent dissolved organic matter at discrete depths in Beaverdam Reservoir, Virginia, USA in 2020

description: We monitored water quality in Beaverdam Reservoir (Vinton, Virginia, USA) with high-frequency (10-minute) sensors in 2020. Beaverdam Reservoir is owned and managed by the Western Virginia Water Authority as a secondary drinking water source for Roanoke, Virginia. Depth profiles of water temperature were measured on ~1-meter intervals from above the surface of the reservoir to 0.5 m above the sediments on an anchored thermistor chain to account for water level fluctuations. Dissolved oxygen was monitored at 1.5 m, in the mid-water column at 3.33-4.65 m depth, and bottom waters at 0.5 m above the sediments, which corresponded to 10.65-11.98 m depth. A YSI EXO2 sonde measured temperature, conductivity, specific conductance, chlorophyll a, phycocyanin, total dissolved solids, dissolved oxygen, and fluorescent dissolved organic matter at ~1.5 m depth. Due to variable water levels in the reservoir, the position of some sensors were held stationary to the sediments and presented as positions (thermistor temperature, dissolved oxygen, and pressure sensor), whereas the EXO sonde variables (temperature, dissolved oxygen, pressure, conductivity, specific conductance, chlorophyll a, phycocyanin, total dissolved solids, and fluorescent dissolved organic matter) were deployed with a buoy to remain fixed at 1.5 m depth from the water's surface. All variables were measured at the deepest site of the reservoir adjacent to the dam.
DOI: 10.25345/c5579w
title: MassIVE MSV000086875 - Metabolomics Workbench ST001514 - GNPS Community metabolomes reflect taxon-specific fingerprints of phytoplankton in the ocean
title: b'Phytoplankton transform inorganic carbon into thousands of biomolecules, including polar metabolites that represent an important pool of labile fixed carbon, nitrogen, and sulfur. Metabolite production is not identical among phytoplankton, and the flux of these molecules through the microbial loop depends on compound-specific bioavailability to a wider microbial community. Yet relatively little is known about the diversity or concentration of polar metabolites within marine plankton. Here we evaluate 313 metabolites in 21 phytoplankton species and in natural marine particles across environmental gradients to show that bulk community metabolomes reflect the phytoplankton community on a chemical level.'
DOI: 10.25345/c51j57
title: MassIVE MSV000086876 - GNPS - Metabolomics data complemented drug use information in epidemiological databases: pilot study of potential kidney donors
title: Import from https://yareta.unige.ch/#/home/detail/1671012c-e04b-46cd-9628-45e264b49759 Objective : The objective of this study was to investigate whether clinical metabolomics, which is increasingly applied in population-based and epidemiological studies, can be used to provide analytical evidence of exposures, and whether such information can be useful to strengthen and/or complement corresponding clinical database entries, taking drug use as an example. Study design and setting : Liquid chromatography-mass spectrometry (LC-MS) metabolomics analyses were performed on urine from 100 randomly-selected control subjects (50% females) from the TransplantLines Food and Nutrition Biobank and Cohort Study (NCT identifier NCT02811835), and drugs were identified through spectral library searching and targeted signal extraction. Results : In 83 subjects for whom drug use information was available, 22 expected and 26 unexpected prescription-only drugs were identified, while 28 expected prescription-only drugs remained undetected. In addition, 7 prescription-only drugs were found in 17 subjects for whom drug use information was unavailable, and 58 over-the-counter drugs were identified in all 100 subjects. Conclusion : Molecular evidence for many drugs could be retrieved from LC-MS metabolomics data, which could be useful to complement and strengthen epidemiological databases given that considerable discrepancies were found between analytically-identified drugs and drugs listed in the available clinical database.
DOI: 10.6084/m9.figshare.14036585.v2
title: Illumina, pacbio and ont sequencing reads

description: Data has been temporarily removed!<br>
DOI: 10.18112/openneuro.ds003518.v1.0.0
title: SimonConflict
DOI: 10.25345/c5wr39
title: MassIVE MSV000086877 - Metabolomics Workbench ST001290 - GNPS Lipidome Signatures of Metastasis in a Transgenic Mouse Model of Sonic Hedgehog Medulloblastoma.
title: b'Metabolic alternations were investigated by applying Ultra Performance Liquid Chromatography Mass Spectrometry (UPLC-MS) to mice brain tissue samples collected from SmoA1-Math-GFP mice with (n=18) and without (n=7) metastasis. All samples were analyzed using reverse phase (RP) UPLC-MS analysis in positive and negative ion modes.'