cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh3358096.08fu
title: SH3358096.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3358097.08fu
title: SH3358097.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3358098.08fu
title: SH3358098.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.5066/p9mt4fvl
title: Digital terrain model of upper North Fork Toutle River valley, Washington, derived from historical topographic maps

description: This digital terrain model represents historical elevations along the valley of the North Fork Toutle River upstream of its confluence with the Green River in Cowlitz and Skamania Counties, Washington. Most elevations were derived from U.S. Geological Survey 1:62,500 scale topographic quadrangle maps published from 1953 to 1958 that were derived from aerial photographs taken in 1951 and 1952. Elevations representing the bed of Spirit Lake, at the head of the valley, were derived from a bathymetric map based on survey data from 1974. Elevations are in units of meters and have been adjusted to the North American Vertical Datum of 1988.
DOI: 10.6084/m9.figshare.21950474
title: Effectiveness of the Deterministic and Stochastic Bivariate Latent Change Score Models for Longitudinal Research

description: The Bivariate Latent Change Score (BLCS) model is a popular framework for the study of dynamics in longitudinal research. Despite its popularity, there is little evidence of the ability of this model to recover latent dynamics when the latent trajectories are affected by stochastic innovations (i.e., dynamic error). The deterministic specification of the BLCS model does not account for the effect of these innovations in the system. In contrast, the stochastic specification of the BLCS model includes parameters that capture the effect of such innovations at the latent level. Through Monte Carlo simulation, we generated two developmental processes and examined the recovery of the parameters in the deterministic and stochastic BLCS models under a broad range of empirically relevant conditions. Based on our findings, we provide specific guidelines and recommendations for the application of BLCS models in developmental research.
DOI: 10.6084/m9.figshare.21950474.v1
title: Effectiveness of the Deterministic and Stochastic Bivariate Latent Change Score Models for Longitudinal Research

description: The Bivariate Latent Change Score (BLCS) model is a popular framework for the study of dynamics in longitudinal research. Despite its popularity, there is little evidence of the ability of this model to recover latent dynamics when the latent trajectories are affected by stochastic innovations (i.e., dynamic error). The deterministic specification of the BLCS model does not account for the effect of these innovations in the system. In contrast, the stochastic specification of the BLCS model includes parameters that capture the effect of such innovations at the latent level. Through Monte Carlo simulation, we generated two developmental processes and examined the recovery of the parameters in the deterministic and stochastic BLCS models under a broad range of empirically relevant conditions. Based on our findings, we provide specific guidelines and recommendations for the application of BLCS models in developmental research.
DOI: 10.5281/zenodo.8039850
title: Amphisbaena anomala distribution extention

description: Supplementary table for the article: Revising the distribution map of <em>Amphisbaena anomala</em> (Squamata: Amphisbaenidae) utilizing data sourced from citizen science
DOI: 10.5281/zenodo.8039849
title: Amphisbaena anomala distribution extention

description: Supplementary table for the article: New southernmost record of <em>Amphisbaena anomala</em> (Squamata: Amphisbaenidae) based on citizen science, with an updated distribution map
DOI: 10.5281/zenodo.8048455
title: Amphisbaena anomala distribution extention

description: Supplementary table for the article: New southernmost record of <em>Amphisbaena anomala</em> (Squamata: Amphisbaenidae) based on citizen science, with an updated distribution map
DOI: 10.5281/zenodo.8040416
title: Amphisbaena anomala distribution extention

description: Supplementary table for the article: New southernmost record of <em>Amphisbaena anomala</em> (Squamata: Amphisbaenidae) based on citizen science, with an updated distribution map
DOI: 10.5519/qd.b49gvmr5
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (134 records)
DOI: 10.5281/zenodo.8048437
title: Lavakas of Madagascar

description: This GIS database (created with ArcMap v. 10.8) contains location, elevation, and slope aspect data for 61,223 lavakas throughout Madagascar. These data underpin the analysis presented in Cox et al. (2010) "<em>Shakedown in Madagascar: Occurrence of lavakas (erosional gullies) associated with seismic activity</em>". The image base for counting these lavakas was created from orthorectified Landsat ETM+ images, sharpened to 15 m/pixel resolution. We selected images taken in April or May where possible, because vegetation cover differences are most marked at the end of the rainy season in Madagascar, providing maximum colour contrast between active gullies and non-lavaka'd terrain. We used 7-4-2 band composites, imported into ENVI for image processing. The band composites were first linearly enhanced, and then run through Gram-Spectral sharpening using the panchromatic band 8 (to which a median pass filter had first been applied). The sharpened images were projected in ArcMap 9.2, and further enhanced: first by applying a second pan-sharpening (simple mean) using the panchromatic band 8 image, and finally by increasing image brightness by 8-12% and increasing contrast by 45-55% (both adjustments via the “properties” function of the projected image layer). Lavakas were counted by systematic east-west lawnmowing on 33-km2 panels (5 km x 6.5 km) at a scale of 1:25,000. Exposed laterite or saprolite—indicating active erosion—showed as dramatic pink in the enhanced images. Only active lavakas (those clearly showing exposed earth in their interiors) were included. Lavakas were distinguished from other gully or ravine types by their characteristic tadpole or inverted-teardrop shapes; and from non-gullied areas of bare ground by the combination of shape and shadowing indicating steep amphitheatre walls. Comparing the data with ≈2 m/pixel imagery indicates that the database is complete for the largest 50% of lavakas, and close to complete for the largest two-thirds. Lavakas &lt;900 m2 (4 pixels), representing about a third of lavakas (based on field measurements of 433 lavakas: Wells et al., 1991, and unpublished data), are underrepresented in the database because of resolution issues. Works cited: Cox, Rónadh, et al. "Shakedown in Madagascar: Occurrence of lavakas (erosional gullies) associated with seismic activity." <em>Geology</em> v. 38 (2010): p. 179-182. Wells, Neil A., Benjamin Andriamihaja, and HF Solo Rakotovololona. "Patterns of development of lavaka, Madagascar's unusual gullies." <em>Earth Surface Processes and Landforms</em> v. 16 (1991): p. 189-206.
DOI: 10.5281/zenodo.8048436
title: Lavakas of Madagascar

description: This GIS database (created with ArcMap v. 10.8) contains location, elevation, and slope aspect data for 61,223 lavakas throughout Madagascar. These data underpin the analysis presented in Cox et al. (2010) "<em>Shakedown in Madagascar: Occurrence of lavakas (erosional gullies) associated with seismic activity</em>". The image base for counting these lavakas was created from orthorectified Landsat ETM+ images, sharpened to 15 m/pixel resolution. We selected images taken in April or May where possible, because vegetation cover differences are most marked at the end of the rainy season in Madagascar, providing maximum colour contrast between active gullies and non-lavaka'd terrain. We used 7-4-2 band composites, imported into ENVI for image processing. The band composites were first linearly enhanced, and then run through Gram-Spectral sharpening using the panchromatic band 8 (to which a median pass filter had first been applied). The sharpened images were projected in ArcMap 9.2, and further enhanced: first by applying a second pan-sharpening (simple mean) using the panchromatic band 8 image, and finally by increasing image brightness by 8-12% and increasing contrast by 45-55% (both adjustments via the “properties” function of the projected image layer). Lavakas were counted by systematic east-west lawnmowing on 33-km2 panels (5 km x 6.5 km) at a scale of 1:25,000. Exposed laterite or saprolite—indicating active erosion—showed as dramatic pink in the enhanced images. Only active lavakas (those clearly showing exposed earth in their interiors) were included. Lavakas were distinguished from other gully or ravine types by their characteristic tadpole or inverted-teardrop shapes; and from non-gullied areas of bare ground by the combination of shape and shadowing indicating steep amphitheatre walls. Comparing the data with ≈2 m/pixel imagery indicates that the database is complete for the largest 50% of lavakas, and close to complete for the largest two-thirds. Lavakas &lt;900 m2 (4 pixels), representing about a third of lavakas (based on field measurements of 433 lavakas: Wells et al., 1991, and unpublished data), are underrepresented in the database because of resolution issues. Works cited: Cox, Rónadh, et al. "Shakedown in Madagascar: Occurrence of lavakas (erosional gullies) associated with seismic activity." <em>Geology</em> v. 38 (2010): p. 179-182. Wells, Neil A., Benjamin Andriamihaja, and HF Solo Rakotovololona. "Patterns of development of lavaka, Madagascar's unusual gullies." <em>Earth Surface Processes and Landforms</em> v. 16 (1991): p. 189-206.
DOI: 10.5281/zenodo.8048473
title: aglantha_digitale_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8048472
title: aglantha_digitale_zanfona_1.fasta.gz

description: .
DOI: 10.34740/kaggle/dsv/5826112
title: Nigerian Presidential Election 2023 Tweets
DOI: 10.5519/qd.xn28b8xz
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (5 records)
DOI: 10.6084/m9.figshare.21295352.v1
title: Curated and harmonized gut microbiome 16S rRNA amplicon sequences, metadata, and OTU tables from dietary fiber intervention studies in humans

description: Data associated with the <em>Scientific Data </em>Data Descriptor " Curated and harmonized gut microbiome 16S rRNA amplicon data from dietary fiber intervention studies in humans". Please see the Data Descriptor for an detailed description.
DOI: 10.6084/m9.figshare.23277437.v1
title: Magmatic arc evolution during the tectonic closure of the Rocas Verdes basin: insights from Cretaceous-earliest Paleocene intrusive rocks of Navarino Island (55°S), Fuegian Andes

description: U-Pb_INS-45d
DOI: 10.5519/qd.lmloxdhb
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (3 records)
DOI: 10.13140/rg.2.2.35156.17288
title: Codes for examining mammal communities‘ nocturnality in Southwest China
DOI: 10.5519/qd.oeefhhms
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (152 records)
DOI: 10.34740/kaggle/dsv/5826226
title: Mahanagar Yatayat Dataset
DOI: 10.57745/xwbxjd
title: Plan_de_Gestion_de_Données_de_Structure_de_l'unité_ETTIS.pdf

description: Fichier généré à partir du modèle DMP Structure de INRAE, à partir de l'outil DMP OPIDoR
DOI: 10.6084/m9.figshare.22352920
title: Supplementary Material for: Molecular genetic analysis and growth hormone treatment in a three-generation Chinese family with Tricho-rhino-phalangeal syndrome I

description: Background: Tricho-rhino-phalangeal syndrome (TRPS) is a rare genetic disorder characterized by craniofacial and skeletal abnormalities, which is caused by variations in the TRPS1 gene. Methods: Clinical information and follow-up data were collected. Whole-exome sequencing (WES) was performed for variations and validated by Sanger sequencing. Bioinformatic analysis was performed to predict the pathogenicity of the identified variation. Moreover, wild-type and mutated TRPS1 vectors were constructed and transfected into human embryonic kidney (HEK) 293T cells. Immunofluorescence experiments were performed to assess the localization and expression of the mutated protein. Western blot analysis and RT-qPCR were used to detect the expression of downstream genes. Results: The affected family members had typical craniofacial phenotype including sparse lateral eyebrows, pear-shaped nasal tip, and large prominent ears, plus skeletal abnormalities including short stature and brachydactyly. WES and Sanger sequencing identified the TRPS1 c.880_882delAAG variation in affected family members. In vitro functional studies showed that the TRPS1 variation did not affect the cellular localization and the expression of TRPS1, but the transcriptional repression effect of the TRPS1 on the RUNX2 and STAT3 was disturbed. The proband and his brother have been treated with growth hormone (GH) for two years until now, and we observed the improvement of the linear growth in both. Conclusions: The variation of c.880_882delAAG in TRPS1 was responsible for the pathogenesis of the Chinese family with TRPS I. The treatment of GH could be beneficial for the height outcome in TRPS I patients, and earlier initiation and longer duration of the therapy in prepubertal or early pubertal stage could be associated with better height outcomes.
DOI: 10.25345/c51z4237j
title: MassIVE MSV000092077 - A network medicine approach to elucidate mechanisms underlying menopause-induced knee osteoarthritis
title: This study was aimed at understanding the effects of menopause on knee osteoarthritis, specifically the cartilage proteome. Middle-aged female mice were randomized to receive intraperitoneal injections of either 4-vinylcyclohexene diepoxide (VCD) or sesame oil for 10 consecutive days. Through a serious of validation experiments, we and others have shown that VCD induces a menopausal phenotype, as evidenced by loss of estrus cyclicity and modification to sex hormone profiles. We also showed in our work that VCD injected mice present with more severe cartilage degeneration than sesame oil injected mice. Knee cartilage from the tibial plateau and femoral condyles were microdissected at mid-perimenopause (75 days after the first injection), start of menopause (115 days after the first injection), and late menopause (195 days after the first injection). These times points were chosen since cartilage pathology first presented in the VCD group, but not the sesame oil group, at the start of menopause. Cartilage samples were lyophilized and mass spectrometry proteomics were performed.
DOI: 10.22002/chp24-jzk61
title: S. aureus

description: Raw data files of S. aureus
description: <strong>Tilt Series Date:</strong> 2017-11-06</p>
<strong>Data Taken By:</strong> Georges Chreifi</p>
<strong>Species / Specimen:</strong> Staphylococcus aureus</p>
<strong>Strain:</strong> subsp. aureus str. Newman</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-51.0°, 50.0°), step: 1.5°, constant angular increment, dosage: 280.0 eV/Å²,  defocus: -7.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
description: Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/gca2017-11-06-41</p>Sa_rpsF0041.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.9 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Sa_rpsF0041_full.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
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DOI: 10.22002/mzfmg-h5869
title: JV5460

description: JV5460 Legionella (Superdeletion+CDH)
description: <strong>Tilt Series Date:</strong> 2016-08-13</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.50°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal at Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate and cysteine hydrochloride (no thymidine). Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0.</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the JV5460 strain at OD~2.9. Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-13-69</p>atlas7a0022.mrc,  Tilt Series (Pixel Size 0.42 nm), 1.2 GB  
        
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DOI: 10.6084/m9.figshare.19793701
title: Supplemental Table S3

description: Dynamics of oxygen balance characteristics during hypoxic-hyperoxic preconditioning
DOI: 10.6084/m9.figshare.19799008.v1
title: Supplemental Table S3

description: Dynamics of oxygen balance characteristics during hypoxic-hyperoxic preconditioning.
DOI: 10.6084/m9.figshare.19761808.v1
title: Supplemental Table S1

description: Dynamics of perioperative parameters.
DOI: 10.6084/m9.figshare.19793701.v1
title: Supplemental Table S3

description: Dynamics of oxygen balance characteristics during hypoxic-hyperoxic preconditioning
DOI: 10.6084/m9.figshare.19799008
title: Supplemental Table S3

description: Dynamics of oxygen balance characteristics during hypoxic-hyperoxic preconditioning.
DOI: 10.6084/m9.figshare.19761817
title: Supplemental Table S2

description: Correlation between the intragastric pH level and surgery parameters.
DOI: 10.6084/m9.figshare.19761808
title: Supplemental Table S1

description: Dynamics of perioperative parameters.
DOI: 10.6084/m9.figshare.19761817.v1
title: Supplemental Table S2

description: Correlation between the intragastric pH level and surgery parameters.
DOI: 10.22002/y3vcc-89292
title: WT LP01 from Liu lab, Yale

description: Type four secretion system, T4SS
description: <strong>Tilt Series Date:</strong> 2016-11-28</p>
<strong>Data Taken By:</strong> Yuxi Liu</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-51.0°, 51.0°), step: 3°, constant angular increment, dosage: 50.0 eV/Å²,  defocus: -5.0 μm,  magnification: 15500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> None</p>
<strong>Collaborators and Roles:</strong> Data collected by Bo Hu in Jun Liu lab at Yale from their Polara. Partial WT strain data set. Primary literature:  doi: 10.1038/s41564-018-0165-z</p>
description: Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2016-11-28-320</p>T4SSWTNov26A027_driftcorr.mrc,  Tilt Series (Pixel Size 0.25 nm), 2.0 GB  
        
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