cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7093013
title: Multi-method gene clusters at species-level resolution for 125 prokaryotic pangenomes

description: This dataset contains 9 sets of species-level gene clusters and high-resolution species trees for 125 representative bacterial and archaeal species, encompassing a total of 6,851 nearly complete genomes. Each set represents a different approach to homology-, orthology-, and synteny-based gene clustering as implemented by 6 popular tools for comparative genomics and pangenome analysis (Roary, panX, OrthoFinder, MMseqs2/PanACoTa, CD-HIT, and eggNOG-mapper). For <em>Escherichia coli</em>, <em>Cutibacterium acnes</em>, <em>Bacteroides uniformis</em>, and <em>Staphylococcus epidermidis</em>, we provide additional sets that combine high-quality genomes with different proportions of medium- and low-quality metagenome-assembled genomes (MAGs). This dataset is a helpful resource for benchmarking gene clustering tools and pangenome analysis workflows, as well as for testing their robustness with respect to the presence of incomplete or contaminated genomic assemblies. <strong>Reference:</strong> Manzano-Morales S, Liu Y, González-Bodí S, Huerta-Cepas J, Iranzo J. 2022. Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses. <em>bioRxiv</em> doi: 10.1101/2022.09.25.509376
description: Changes with respect to previous version: addition of gene clusters for medium- and low-quality MAGs.
description: {"references": ["https://www.biorxiv.org/content/10.1101/2022.09.25.509376"]}
DOI: 10.5285/14fb1745-00ed-4a0d-922b-d2c94157d17f
title: Age model tie points and micropalaeontological data for International Ocean Discovery Program Hole U1488A, southern part of the Eauripik Rise, Pacific Ocean

description: Age model tie points and micropalaeontological data for International Ocean Discovery Program Hole U1488A. Relative abundances of Neogloboquadrina acostaensis and six morphospecies of Pulleniatina (planktonic foraminifera) from the hole. Coiling ratios (% dextral) specimens for lineages of Pulleniatina with 95% confidence intervals.
Supplementary data table to Pearson, Young, King and Wade (submitted), Biochronology and evolution of Pulleniatina. Table includes data relating to the Pulleniatina lineage from International Ocean Discovery Program Hole U1488A.
DOI: 10.60635/c35p4w
title: rGrapCor: a tool for Graphic Correlation Supplementary Dataset

description: It contains the supplementary files associated with a manuscript that describes rGraphCor, a R application to perform Graphic Correlationit containsSupplementary File 1 Testing Data.txt - Contains the code (R) used to generate simulation of data to test the rGraphCor Supplementary File 2 Formating Files.docx - Extensive description of the files required to run rGraphCorSupplementary File 3 rGRAPHCOR_APP_V23.R - rGraphCor, the complete set of functions in R to run the app Supplementary File 4 rGraphCor Manual.docx - User Manual of the rGraphCor AppSupplementary File 5 Project Data - Table with the counts from the fifteen hypotetical species in four sitesSupplementary File 6 Site Metadata. Table with the site name and type of site (core, outcrop, ditch-cutting)Supplementary File 7 Composite section. It contains the correlation session and it is produced by rGraphCor during the correlation session.
DOI: 10.6084/m9.figshare.24939264.v1
title: Data for "the retrieval of neutral and positive autobiographical memories: a pilot study".xlsx

description: <b>Background:</b> Several studies have shown that the retrieval of positive memories may play a role in emotional regulation. However, it is unclear whether the effects of neutral and positive autobiographical memories differ. There is a need to confirm that genuinely neutral autobiographical memories can be retrieved without bias in response to a prompt to recall neutral memories. <b>Methods:</b> In this pilot study, using “home” and “study” as cue words, we investigated whether participants were able to retrieve appropriate autobiographical memories when asked to recall a limited number of neutral or positive memories.
DOI: 10.6084/m9.figshare.25347538
title: Dataset for "Generation and Impacts of Whistler-mode Waves during Energetic Electron Injections in Jupiter’s Outer Radiation Belt"

description: This is the dataset for.the paper "Generation and Impacts of Whistler-mode Waves during Energetic Electron Injections in Jupiter’s Outer Radiation Belt" submitted to Journal of Geophysical Research: Space Physics.Energetic particle injections are commonly observed in Jupiter’s magnetosphere and have important impacts on the radiation belts. We evaluate the roles of electron injections in the dynamics of whistler-mode waves and relativistic electrons using Juno measurements and wave-particle interaction modeling. The Juno spacecraft observed injected electron flux bursts at energies up to 300 keV at M shell ~11 near the magnetic equator during perijove-31. The electron injections are correlated with chorus wave bursts at 0.05-0.5 fce frequencies, where fce is the electron gyrofrequency. The electron pitch angle distributions are anisotropic, peaking near 90° pitch angle, and the fluxes are high during injections. We calculate the whistler-mode wave growth rates using the observed electron distributions and linear theory. The frequency spectrum of the wave growth rate is consistent with that of the observed chorus magnetic intensity, suggesting that the observed electron injections provide free energy to generate whistler-mode chorus waves. We further use quasilinear theory to model the impacts of chorus waves on 0.1-10 MeV electrons. Our modeling shows that the chorus waves could cause the pitch angle scattering loss of electrons at &lt;1 MeV energies and accelerate relativistic electrons at multiple MeV energies in Jupiter’s outer radiation belt. The electron injections also provide an important seed population at several hundred keV energies to support the acceleration to higher energies. Our wave-particle interaction modeling demonstrates the energy flow from the electron injections to the relativistic electron population through the medium of whistler-mode waves in Jupiter's outer radiation belt.
DOI: 10.6084/m9.figshare.27045172
title: A global dataset of salmonid biomass in streams

description: A global dataset of estimated salmonid biomass using published material of over 1000 rivers, covering 27 countries and 11 salmonid species. The data spans 84 years and is the largest known compilation of published studies on salmonid biomass in streams, allowing detailed analyses of differences in biomass by species, period, and sampling techniques.
DOI: 10.6084/m9.figshare.27222609
title: Supplementary Material for: SARS-CoV-2-induced remission of chemotherapy resistance B-cell non-Hodgkin lymphoma: A case report

description: Introduction: Investigation on virus-host interaction may provide new clues for anti-tumor immunotherapy. Case presentation:In this case report we describe an unusual case of B-cell non-Hodgkin lymphoma in an aged woman who recovered following SARS-COV-2 infection. We discuss the case and suggest that virus induced cross-reactivity against tumor account for the remission. Conclusion: Mapping epitope characteristics on B cell non-Hodgkin lymphoma antigen and on SARS-COV-2 antigen may provide much needed information for antigen based anti-tumor immune therapy in the future.
DOI: 10.6084/m9.figshare.27239742
title: Supplementary Material for: Evaluation of physiological variables determining time to mortality after stroke-associated pneumonia

description: Introduction
Stroke-associated pneumonia (SAP) frequently complicates stroke and is associated with significant mortality. Clinicians often use physiological variables within the National Early Warning Score (NEWS) when diagnosing and prescribing antibiotics for SAP, but little is known of its association with mortality. We investigated the relationship of the NEWS 2 score and its components (respiratory rate, heart rate, temperature, oxygen requirement, oxygen saturation and alertness level) prior to antibiotic initiation, with time-to-mortality in SAP. 
Methods
We included patients with SAP (n=389) from a single hyperacute stroke unit. Diagnosis of SAP was made if pneumonia occurred within 7 days of hospital admission. Kaplan-Meier survival curves were generated to assess NEWS 2 parameters influencing survival at pre-defined time periods (1 year and 5 years). The association of these parameters on time-to-mortality were analysed using multivariable Cox regression models to account for a set of pre-specified potential confounders. 
Results
The median age was 80y (71y-87y) and median NIHSS was 7 (IQR 4-17). Mortality within 1 year was 52.4% and 65.8% within 5 years. In the multivariable analyses, time-to-mortality was independently associated with respiratory rate (HR 1.04, 95% CI 1.01 to1.08, p=0.009) and total NEWS 2 score (HR 1.13, 95% CI 1.06 to 1.21, p=&lt;0.001).
Conclusions
In patients with SAP, higher respiratory rate and total NEWS 2 score prior to antibiotic initiation were independently associated with time-to-mortality. Further studies are warranted to identify potential opportunities for intervention and ultimately guide treatment to improve outcomes in SAP patients.
DOI: 10.6084/m9.figshare.27618960
title: Supplementary Material for: A NOVEL NOTCH3 VARIANT LEADING TO LATERAL MENINGOCELE SYNDROME: PRENATAL DIAGNOSIS AND POSSIBLE EXPANSION OF THE PHENOTYPE

description: Introduction: NOTCH3, one of the four mammalian Notch receptors, acts as a transcriptional activator in a variety of tissues. Variants in NOTCH3 lead to distinct phenotypes, depending on variant type and location. Truncating variants in the last exon generate a protein lacking the PEST domain, responsible for degradation, leading to a gain-of-function effect and causing Lateral Meningoceles syndrome (LMS), characterized by dysmorphisms and variable cardiac, skeletal, and connective tissue abnormalities; motor delay may occur, but the cognitive function is usually normal. Case presentation: We report the first case of prenatal molecular diagnosis of LMS, which was made using prenatal exome sequencing after an ultrasound with findings of fetal cystic hygroma, mild bilateral ventriculomegaly, and facial dysmorphisms. After birth, magnetic resonance imaging (MRI) confirmed the presence of lateral meningoceles. A complete clinical evaluation was performed and unexpected biliary anomalies were found. Conclusion: The occurrence of biliary anomalies has not been previously reported in LMS, but may have biological plausibility. Expression of NOTCH3 has been demonstrated in biliary development and is thought to play a role in the differentiation of hepatoblasts into biliary epithelial cells, and also in liver regeneration and repair. We hypothesize that the findings reported here might expand the phenotype of LMS.
DOI: 10.6084/m9.figshare.7145825.v2
title: Hierarchies of evolutionary radiation in the world’s most species rich vertebrate group, the Neotropical <i>Pristimantis</i> leaf litter frogs

description: The Neotropical leaf litter frog genus <i>Pristimantis</i> is very species-rich, with 526 species described to date, but the full extent of its diversity is much higher and remains unknown. This study explores the phylogenetic processes and resulting evolutionary patterns of diversification in <i>Pristimantis</i>. Given the well-recognised failure of morphology- and community-based species groups to describe diversity within the genus, we apply a new test for the presence and phylogenetic distribution of higher evolutionary units. We developed a phylogeny based on 260 individuals encompassing 149 <i>Pristimantis</i> presumed species, sampled at mitochondrial and nuclear genes (3718 base pair alignment), combining new and available sequence data. Our phylogeny broadly agrees with previous studies, both in topology and age estimates, with the origin of <i>Pristimantis</i> at 28.97 (95% HDP =21.59 – 37.33) million years ago (MYA). New taxa that we add to the genus, which had not previously been included in <i>Pristimantis</i> phylogenies, suggest considerable diversity remains to be described. We assessed patterns of lineage origin and recovered 14 most likely (95% CI: 13–19) phylogenetic clusters or higher evolutionary significant units (hESUs) within <i>Pristimantis</i>. Diversification rates decrease towards the present following a density-dependent pattern for <i>Pristimantis</i> overall and for most hESU clusters, reflecting historical evolutionary radiation. The timing of diversification suggests that geological events in the Miocene, such as Andes orogenesis and Pebas system formation and drainage, may have had a direct or indirect impact on the evolution of <i>Pristimantis</i> and thus contributed to the origins of evolutionary independent phylogenetic clusters.
DOI: 10.7267/j9602723w
title: Land Cover Classification (5-meter) - Kings River Fisher Project 2014 - 2018 
title: Tree Mortality Dataset - Kings River Fisher Project 2014 - 2018

description: These high resolution (5x5-meter pixel) categorical models of land cover were created by training random forest classification models on RapidEye (Planet Labs Inc.) satellite spectral data for each year and then predicting those models across the landscape. Training data were created by visually interpreting random plots over high resolution NAIP aerial imagery. Land cover classes include bare ground, live forest, shrub, herbaceous, and tree mortality. Class definitions generally follow California Wildlife Habitat Relationships (CWHR) categories. CWHR tree dominated habitats were combined to represent a single “live forest” category where trees were alive and “tree mortality” where dead. Shrub dominated habitats, namely Mixed and Montane Chaparral, were included in the “shrub” class. Perennial grasslands and wet meadow habitats were included in the “herbaceous” class, and non-vegetated habitats along with annual grasslands made up the “bare ground” class. We interpreted 75-125 samples per land cover class, per year. Model accuracy was evaluated using a 30% holdout of training data per class. A set of conditional rules were applied to the predictions to limit the occurrence of illogical land cover transitions through time (e.g., bare ground to tree mortality).
DOI: 10.12751/g-node.qj5hs7
title: Developing Human Connectome Project spatio-temporal surface atlas of the fetal brain

description: This repository contains spatio-temporal surface atlas, spanning 21-36 weeks of gestation, generated by adapting the procedure developed for the neonatal surface atlas in Bozek et al., 2018, which iteratively refines templates through a repeated alignment of individuals to a common space using MSM algorithm to the fetal data. At each iteration, the age-specific templates are obtained through weighted averaging of co-registered surfaces, whereby weights are defined by the Gaussians centred on the gestational weeks for which templates are calculated, and are subsequently used as a target space for the following iteration. Adaptive kernel regression, compensating for a difference in the number of scans available for different ages, was used to parameterise the width of the Gaussians. The atlas was generated in three stages: first, a common reference space was initialised via affine sulcal-depth-based registration to the dHCP neonatal GW36 template. At the next iteration, the template was refined using sulcal-depth-based nonlinear alignment, followed by 4 iterations of curvature-based alignment (a more fine-grained feature than the sulcal depth).
description: IsSupplementTo: J. Bozek, A. Makropoulos, A. Schuh, S. Fitzgibbon, R. Wright, M. F. Glasser, T. S. Coalson, J. O’Muircheartaigh, J. Hutter, A. N. Price, L. Cordero-Grande, R. P. A. G. Teixeira, E. Hughes, N. Tusor, K. P. Baruteau, M. A. Rutherford, A. D. Edwards, J. V. Hajnal, S. M. Smith, D. Rueckert, M. Jenkinson, E. C. Robinson. (2018). Construction of a neonatal cortical surface atlas using Multimodal Surface Matching in the Developing Human Connectome Project. NeuroImage. 179, 11–29. (https://doi.org/10.1016/j.neuroimage.2018.06.018)
DOI: 10.13026/kg8b-1t49
title: Kinematic dataset of actors expressing emotions

description: We produced a kinematic dataset to assist in recognizing cues from all parts
of the body that indicate human emotions (happy, sad, angry, fearful, ,
disgust, surprise) and neutral. The present dataset was created using a
portable wireless motion capture system. Twenty-two semi-professional actors
(50% female) completed performances. A total of 1402 recordings at 125 Hz were
collected, consisting of the position and rotation data of 72 anatomical
nodes. We hope this dataset will contribute to multiple fields of research and
practice, including social neuroscience, psychiatry, computer vision, and
biometric and information forensics.
DOI: 10.1594/pangaea.972530
title: Lowered ADCP current measurements during RV MARIA S. MERIAN cruise MSM107

description: Ocean velocity profiles were collected using an ADCP (300 kHz Teledyne RD Instruments Workhorse Sentinel ADCP) mounted on the CTD-Rosette during the Maria S. Merian cruise MSM107. During CTD-Rosette casts, the Lowered Acoustic Doppler Current Profiler (LADCP) collected full-depth profiles of velocities and echo intensity under the CTD frame over a 110.17 m profile with 27 bins of 4 m. The short profiles were combined into a record of full-depth absolute (i.e. in the Earth's frame of reference) velocities using the LDEO Software provided by A.M. Thurnherr (https://www.ldeo.columbia.edu/~ant/LADCP.html) and the CTD data (to know the vertical velocity of the LADCP frame and accurately calculate sound velocity throughout the water column), the ship position (to correct for horizontal movements) and the data from a ship mounted ADCP (to better constrain LADCP data close to the surface). A total of 16 profiles were collected. The processed ADCP data show the water velocity magnitude and direction over the whole water column every 4 m.
description: Elevation of event: full water depth at the station position
DOI: 10.23636/1135
title: Ground Truth transcriptions for training OCR of historical Arabic handwritten texts

description: This dataset comprises 120 digitised images (TIFF files) drawn from a selection of historical Arabic scientific manuscripts (10th-19th century) digitised through the British Library Qatar Foundation Partnership. Also contained are ground truth transcriptions (XML) for each page that can be used for training optical character recognition (OCR) or handwritten text recognition (HTR) software on historical Arabic handwritten texts. The folder contains the images and ground truth used for the RASM2018 and RASM2019 competitions, part of ICFHR 2018 and ICDAR 2019. The images are out of copyright and the transcriptions are also public domain.
DOI: 10.25928/gwr-ecowas.1
title: Ressources en eaux souterraines dans la région de la CEDEAO
title: Groundwater resources in the ECOWAS region
title: GWR ECOWAS

description: La carte « Ressources en eaux souterraines dans la région de la CEDEAO » saisit et normalise les données existantes sur les eaux souterraines de l'Afrique de l'Ouest et donne un aperçu régional cohérent sur les ressources en eaux souterraines. Elle fournit une évaluation quantitative de la productivité de l'aquifère en utilisant une combinaison du type d'écoulement de l'aquifère et du rendement attendu du forage. La carte met en évidence l’aptitude des aquifères pour l'approvisionnement en eau à différentes échelles tout en montrant les limites physiques du développement des eaux souterraines. L'élaboration de la carte comprenait l'harmonisation des cartes géologiques continentales et régionales existantes et l'attribution des unités hydrogéologiques avec les données de rendement attendu compilées à partir d'une méta-enquête bibliographique. Les cartes en encart mettent en évidence la structure géologique, les niveaux de fond géogéniques d'arsenic et de fluorure et la recharge des eaux souterraines.
description: The map “Groundwater resources in the ECOWAS region” captures and standardises existing groundwater data of West Africa and gives a consistent regional overview on the groundwater resources. It provides a quantitative assessment of aquifer productivity using a combination of aquifer flow type and expected borehole yield. The map highlights the suitability of aquifers for water supply on different scales while at the same time showing the physical limits of groundwater development. Map elaboration comprised the harmonisation of existing continental and regional geological maps and the attribution of hydrogeological units with expected yield data compiled from a literature meta-survey. Insert maps highlight the geological structure, geogenic background levels of arsenic and fluoride, and groundwater recharge.
DOI: 10.25984/1873866
title: U.S. Wind Siting Regulation and Zoning Ordinances

description: A machine readable collection of documented wind siting ordinances at the state and local (e.g., county, township) level throughout the United States. The data were compiled from several sources including, DOE's Wind Exchange Ordinance Database (Linked in the submission), National Conference of State and Legislatures Wind Energy Siting (also linked in the submission), and scholarly legal articles. The citations for each ordinance are included in the spreadsheet. This data is an updated to a previously developed database of wind ordinances found in OEDI Submission 1932: "U.S. Wind Siting Regulation and Zoning Ordinances"
DOI: 10.25984/1873867
title: U.S. Solar Siting Regulation and Zoning Ordinances

description: A machine readable collection of documented solar siting ordinances at the state and local (e.g., county, township) level throughout the United States. The data were compiled based on a locality-by-locality review zoning ordinances after completing an initial review of scholarly legal articles. The citations for each ordinance are included in the spreadsheet.
DOI: 10.34740/kaggle/ds/3505991
title: Crystal Clean: Brain Tumors MRI Dataset
DOI: 10.34740/kaggle/dsv/7135047
title: Malaysian Sign Language (MSL) Image Dataset
DOI: 10.5066/p9jn6h0n
title: A High-Resolution Seismic Catalog for the Initial 2019 Ridgecrest Earthquake Sequence

description: I use template matching and precise relative relocation techniques to develop a high-resolution earthquake catalog for the initial portion of the 2019 Ridgecrest earthquake sequence, from July 4-16, encompassing the foreshock sequence and the first 10+ days of aftershocks following the Mw 7.1 mainshock. Using 13,525 routinely cataloged events as waveform templates, I detect and precisely locate a total of 34,091 events. Precisely located earthquakes reveal numerous cross-cutting fault structures with dominantly perpendicular SW- and NW-strikes. Foreshocks of the Mw 6.4 event appear to align on a NW-striking fault. Aftershocks of the Mw 6.4 event suggest that it further ruptured this NW-striking fault, as well as the SW-striking fault where surface rupture was observed. Finally, aftershocks of the Mw 7.1 show a highly complex distribution, illuminating a primary NW-striking fault zone consistent with surface rupture, but also numerous cross-cutting SW-striking faults. Aftershock relocations suggest that the Mw 7.1 event ruptured adjacent to the previous NW-striking rupture of the Mw 6.4, perhaps activating a subparallel structure southwest of the earlier rupture. Both the NW and SE rupture termini of the Mw 7.1 rupture exhibited multiple-fault branching, with particularly high rates of aftershocks and multiple fault orientations in the dilatational quadrant NE of the NW rupture terminus.
DOI: 10.5067/terra/misr/mil3daen_l3.004
title: MISR Level 3 Component Global Aerosol product in netCDF format covering a day - Version 4