cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14013284
title: Folding@Home simulations of RS-Peptide using Amber03ws force field and Tip4p/2005 water model

description: This dataset contains simulation trajectory for 24-residue RS-Peptide. The RS-peptide is a highly charged intrinsically disordered region (IDR) found in serine/arginine-rich proteins, such as the serine/arginine-rich splicing factor 1 (SRSF1), known to play a crucial role in RNA metabolism. These trajectories were created as a part of the publication "ExEnDiff: An Experiment-guided Diffusion model for protein conformational Ensemble generation", that introduces a deep-learning-based method that enables the rapid generation of diverse protein conformations while ensuring they adhere to key physical principles through guidance from experiments.

METHODOLOGY

We ran long unbiased simulations of up to 2 milliseconds of simulation time, with 20 unique starting structures, each run with 100 clones of ~1 micro-second each using Amber03ws force field and Tip4p/2005 water model. 

The system was initially solvated, and neutralizing ions were added. Energy minimization was performed using the steepest descent algorithm to remove steric clashes, with a maximum force tolerance of 1000 kJ/mol/nm. The system underwent equilibration in two stages: first, a 100 ps NVT equilibration at 300K, with temperature kept constant using the v-rescale thermostat (with a time constant of 0.1 ps), followed by a 1 ns NPT equilibration at 1 bar with the Parrinello-Rahman barostat (with a time constant of 2.0 ps). The production simulation was run with a 2 fs time step. Electrostatic interactions were treated using Particle Mesh Ewald (PME) with a cutoff of 1.0 nm, and other non-bonded interactions were modified with the Potential-shift-Verlet scheme with a cutoff of 1.2 nm. Constraints on bonds involving hydrogen were applied using the LINCS algorithm. The simulations were performed in the Folding@Home distributed computing environment.

ACKNOWLDEGEMENT

We would also like to thank the Folding@home community and Géraud Krawezik (software engineer at Flatiron Institute) for helping us set up Folding@home simulations.
DOI: 10.5281/zenodo.14013285
title: Folding@Home simulations of RS-Peptide using Amber03ws force field and Tip4p/2005 water model

description: This dataset contains simulation trajectory for 24-residue RS-Peptide. The RS-peptide is a highly charged intrinsically disordered region (IDR) found in serine/arginine-rich proteins, such as the serine/arginine-rich splicing factor 1 (SRSF1), known to play a crucial role in RNA metabolism. These trajectories were created as a part of the publication "ExEnDiff: An Experiment-guided Diffusion model for protein conformational Ensemble generation", that introduces a deep-learning-based method that enables the rapid generation of diverse protein conformations while ensuring they adhere to key physical principles through guidance from experiments.

METHODOLOGY

We ran long unbiased simulations of up to 2 milliseconds of simulation time, with 20 unique starting structures, each run with 100 clones of ~1 micro-second each using Amber03ws force field and Tip4p/2005 water model. 

The system was initially solvated, and neutralizing ions were added. Energy minimization was performed using the steepest descent algorithm to remove steric clashes, with a maximum force tolerance of 1000 kJ/mol/nm. The system underwent equilibration in two stages: first, a 100 ps NVT equilibration at 300K, with temperature kept constant using the v-rescale thermostat (with a time constant of 0.1 ps), followed by a 1 ns NPT equilibration at 1 bar with the Parrinello-Rahman barostat (with a time constant of 2.0 ps). The production simulation was run with a 2 fs time step. Electrostatic interactions were treated using Particle Mesh Ewald (PME) with a cutoff of 1.0 nm, and other non-bonded interactions were modified with the Potential-shift-Verlet scheme with a cutoff of 1.2 nm. Constraints on bonds involving hydrogen were applied using the LINCS algorithm. The simulations were performed in the Folding@Home distributed computing environment.

ACKNOWLDEGEMENT

We would also like to thank the Folding@home community and Géraud Krawezik (software engineer at Flatiron Institute) for helping us set up Folding@home simulations.
DOI: 10.5281/zenodo.14013778
title: Investigating the Casual Associations among the Gut Microbiota, Metabolites, and Bladder Cancer: A Mediation Mendelian Randomization Study
DOI: 10.5281/zenodo.14013779
title: Investigating the Casual Associations among the Gut Microbiota, Metabolites, and Bladder Cancer: A Mediation Mendelian Randomization Study
DOI: 10.5281/zenodo.13357912
title: WildDESED: An LLM-Powered Dataset for Wild Domestic Environment Sound Event Detection System

description: A new large language model (LLM)-powered dataset namely wild domestic environment sound event detection (WildDESED). It is crafted as an extension to the original DESED dataset to reflect diverse acoustic variability and complex noises in home settings. We leveraged LLMs to generate eight different domestic scenarios based on target sound categories of the DESED dataset. Then we enriched the scenarios with a carefully tailored mixture of noises selected from AudioSet and ensured no overlap with target sound. We consider widely popular convolutional neural recurrent network to study WildDESED dataset, which depicts its challenging nature. We then apply curriculum learning by gradually increasing noise complexity to enhance the model's generalization capabilities across various noise levels.
DOI: 10.5281/zenodo.13910598
title: WildDESED: An LLM-Powered Dataset for Wild Domestic Environment Sound Event Detection System

description: A new large language model (LLM)-powered dataset namely wild domestic environment sound event detection (WildDESED). It is crafted as an extension to the original DESED dataset to reflect diverse acoustic variability and complex noises in home settings. We leveraged LLMs to generate eight different domestic scenarios based on target sound categories of the DESED dataset. Then we enriched the scenarios with a carefully tailored mixture of noises selected from AudioSet and ensured no overlap with target sound. We consider widely popular convolutional neural recurrent network to study WildDESED dataset, which depicts its challenging nature. We then apply curriculum learning by gradually increasing noise complexity to enhance the model's generalization capabilities across various noise levels.
DOI: 10.15468/dl.33547c
title: Occurrence Download

description: A dataset containing 62846 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Country is Netherlands",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Anguilla anguilla (Linnaeus, 1758)"
 ]
}

 The dataset includes 62846 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012310-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5518/783
title: Dataset associated with ‘Development of robust finite element models of porcine tibiofemoral joints loaded under varied flexion angles and tibial freedoms’

description: This dataset contains an excel sheet with the raw results data from models found in the associated study: " Development of robust finite element models of porcine tibiofemoral joints loaded under varied flexion angles and tibial freedoms". Python scripts used to generate the models with Abaqus are also included, as well as some example Abaqus files.
DOI: 10.17632/v3k8psx895.2
title: IMI configuration files and TROPOMI data

description: This repository contains configuration files for running the Integrated Methane Inversion (IMI) model for a domain focused on Denmark. 
- config_JulAug2019.yml: IMI configuration file for a two-month inversion covering July and August 2019.
- DNK_adm2.shp and DNK_adm2.shx: Shapefile components for Denmark. These files can be used to delimit emissions and other model outputs to Denmark's boundaries.
- IMI_xch4_prior_posterior_comparison.ipynb: Jupyter notebook to evaluate the prior and posterior XCH4 concentrations throughout the study period.
- StateVectorJulAug2019.nc: State vector file. This file is automatically generated based on the lat/lon bounds of the region of interest.
TROPOMI data (in pickle format) for all bi-monthly periods from May-June 2018 to May-June 2022, where sufficient data is available for the inversions, is also provided in the TROPOMI_data.tar.gz file.
DOI: 10.17632/chrzcxtfbb.1
title: Expansion Potential Metrics Correlation Heatmap

description: General Description of the Dataset
The dataset data_expansion is designed to simulate key metrics that are essential for evaluating a company's potential for expansion. It consists of four primary variables, each representing a different dimension of expansion strategy and operational capacity:
Adoption Rate: This variable quantifies the percentage of customers or users who adopt a new product or service. It is generated using a normal distribution with a mean of 40 and a standard deviation of 12. This indicates that while many observations will cluster around the average adoption rate, there is variability reflecting differences in market acceptance and consumer willingness to engage with new offerings.
Adaptability: This metric assesses how well a company can adjust to changes in the market or its operational environment. Simulated using a uniform distribution ranging from 1 to 5, where higher values indicate greater adaptability, this score helps evaluate a company's responsiveness to evolving consumer needs and market dynamics.
Expansion Cost: This variable represents the financial investment required for expansion efforts, generated from a normal distribution with a mean of $100,000 and a standard deviation of $20,000. This reflects the typical costs associated with scaling operations, including expenses related to marketing, infrastructure development, and workforce expansion.
Scalability: This metric evaluates how easily a business can grow its operations without being hindered by its existing structure or resource limitations. Like adaptability, scalability is generated using a uniform distribution from 1 to 5, where higher scores indicate better potential for scaling operations effectively.
The dataset contains 100 observations for each variable, providing a robust foundation for analysis.
DOI: 10.15468/dl.mskcnq
title: Occurrence Download

description: A dataset containing 2256 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Vaccinium ovalifolium Sm."
 ]
}

 The dataset includes 2256 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012311-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/v3k8psx895.1
title: IMI configuration files and TROPOMI data

description: This repository contains configuration files for running the Integrated Methane Inversion (IMI) model for a domain focused on Denmark. 
- config_JulAug2019.yml: IMI configuration file for a two-month inversion covering July and August 2019.
- DNK_adm2.shp and DNK_adm2.shx: Shapefile components for Denmark. These files can be used to delimit emissions and other model outputs to Denmark's boundaries.
- StateVectorJulAug2019.nc: State vector file. This file is automatically generated based on the lat/lon bounds of the region of interest.
TROPOMI data (in pickle format) for all bi-monthly periods from May-June 2018 to May-June 2022, where sufficient data is available for the inversions, is also provided in the TROPOMI_data.tar.gz file.
DOI: 10.15468/dl.976nwd
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Hypselotriton orientalis David, 1873"
 ]
}

 The dataset includes 8 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012312-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eppe7z
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (Computarización de las colecciones de vertebrados terrestres de la Escuela Nacional de Ciencias Biológicas, IPN Fase 4 (Mamíferos), Digitalización y Sistematización de las Colecciones Biológicas Nacionales del Instituto de Biología, UNAM (vertebrados), Actualización de la base de datos de la Colección de mamíferos del Museo de Zoología 'Alfonso L. Herrera', Código de barras de ejemplares de la Colección Nacional de Mamíferos del Instituto de Biología, UNAM, Fortalecimiento de la Colección de fotocolectas biológicas (CFB): una propuesta del uso de la imagen digital al servicio del conocimiento de la biodiversidad, Análisis de la heterogeneidad ambiental y conectividad de las áreas naturales del sur del Valle de México, CNMA/Colección Nacional de mamíferos, Biodiversidad mastozoológica del Eje Volcánico Transversal, Importancia del Parque Estatal Cerro de la Tortuga para la conservación de los mamíferos del estado de Morelos, México)",
 "Geometry POLYGON((-109.75286 14.11348,-95.78787 14.11348,-95.78787 25.94603,-109.75286 25.94603,-109.75286 14.11348))",
 "HasCoordinate is true",
 "TaxonKey is Sylvilagus cunicularius (Waterhouse, 1848)",
 "Year 1982-2024"
 ]
}

 The dataset includes 59 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012313-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pbuj9k
title: Occurrence Download

description: A dataset containing 2334330 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is South Africa",
 "DatasetKey is iNaturalist Research-grade Observations"
 ]
}

 The dataset includes 2334330 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012307-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.27338955
title: Supplementary Material for: A Rare Case of Uterine Serous Carcinoma: Importance of Early Detection and Comprehensive Treatment in Postmenopausal Women

description: Background: Uterine serous carcinoma (USC) is an uncommon but highly aggressive subtype of endometrial cancer, constituting approximately 10% of all endometrial carcinoma cases. Due to its aggressive nature, it is often diagnosed at an advanced stage, with a significant proportion of patients presenting with metastasis.
Case Presentation: This report deals with a case of a 75-year-old postmenopausal female with a history of obesity and hypertension, presenting with abnormal vaginal bleeding over two years. Her obstetric history included three cesarean sections, and she had not undergone a speculum examination for 35 years. Transvaginal ultrasound revealed a heterogeneous structure with cystic changes nearly filling the uterine cavity, suggestive of an intrauterine polyp. Dilation and curettage (D&C) under general anesthesia disclosed. The uterine cavity is filled with gray, soft endometrial material. Histopathological examination confirmed the diagnosis of serous papillary carcinoma of the endometrium. Subsequent imaging was unremarkable for distal metastasis. The patient underwent an abdominal total hysterectomy with bilateral adnexectomy and pelvic lymphonodectomy. Histopathology indicated high-grade papillary serous adenocarcinoma (GIII) with minimal myometrial invasion and metastasis in 3 out of 10 regional lymph nodes. Postoperatively, she received 25 sessions of radiotherapy and four doses of chemotherapy with paclitaxel and carboplatin.
Outcome and Follow-Up: Nine months post-surgery, the patient remains in good health and adheres to a strict monitoring protocol. This case emphasizes the necessity of comprehensive diagnostic evaluations and aggressive treatment in postmenopausal women presenting with vaginal bleeding.
Conclusion: Despite its typically poor prognosis, early diagnosis and treatment of USC can lead to favorable outcomes. This case underscores the importance of timely intervention in managing postmenopausal vaginal bleeding, particularly in the context of potential malignancies.
DOI: 10.6084/m9.figshare.27338955.v1
title: Supplementary Material for: A Rare Case of Uterine Serous Carcinoma: Importance of Early Detection and Comprehensive Treatment in Postmenopausal Women

description: Background: Uterine serous carcinoma (USC) is an uncommon but highly aggressive subtype of endometrial cancer, constituting approximately 10% of all endometrial carcinoma cases. Due to its aggressive nature, it is often diagnosed at an advanced stage, with a significant proportion of patients presenting with metastasis.
Case Presentation: This report deals with a case of a 75-year-old postmenopausal female with a history of obesity and hypertension, presenting with abnormal vaginal bleeding over two years. Her obstetric history included three cesarean sections, and she had not undergone a speculum examination for 35 years. Transvaginal ultrasound revealed a heterogeneous structure with cystic changes nearly filling the uterine cavity, suggestive of an intrauterine polyp. Dilation and curettage (D&C) under general anesthesia disclosed. The uterine cavity is filled with gray, soft endometrial material. Histopathological examination confirmed the diagnosis of serous papillary carcinoma of the endometrium. Subsequent imaging was unremarkable for distal metastasis. The patient underwent an abdominal total hysterectomy with bilateral adnexectomy and pelvic lymphonodectomy. Histopathology indicated high-grade papillary serous adenocarcinoma (GIII) with minimal myometrial invasion and metastasis in 3 out of 10 regional lymph nodes. Postoperatively, she received 25 sessions of radiotherapy and four doses of chemotherapy with paclitaxel and carboplatin.
Outcome and Follow-Up: Nine months post-surgery, the patient remains in good health and adheres to a strict monitoring protocol. This case emphasizes the necessity of comprehensive diagnostic evaluations and aggressive treatment in postmenopausal women presenting with vaginal bleeding.
Conclusion: Despite its typically poor prognosis, early diagnosis and treatment of USC can lead to favorable outcomes. This case underscores the importance of timely intervention in managing postmenopausal vaginal bleeding, particularly in the context of potential malignancies.
DOI: 10.17632/yhsbfxdkdr.1
title: Supplemental Materials 24.10.30

description: Supplemental materials for JDS
DOI: 10.15468/dl.y27r9v
title: Occurrence Download

description: A dataset containing 352 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-77.02814 2.0719,-77.09232 2.00173,-77.04324 1.87419,-76.80539 1.884,-76.82804 2.06662,-77.02814 2.0719))",
 "HasGeospatialIssue is false",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 352 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012315-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12210876
title: OSIRIS-REx re-entry seismic data - Johns Hopkins

description: Data from the Johns Hopkins seismic deployment under the OSIRIS-REx trajectory at Bean Flats, Nevada.
DOI: 10.5281/zenodo.12210877
title: OSIRIS-REx re-entry seismic data - Johns Hopkins

description: Data from the Johns Hopkins seismic deployment under the OSIRIS-REx trajectory at Bean Flats, Nevada.
DOI: 10.5281/zenodo.14013835
title: Dataset_The impact of large aneurysm diameter on the outcomes of thoracoabdominal aneurysm repair by fenestrated and branched endografts
DOI: 10.5281/zenodo.14013836
title: Dataset_The impact of large aneurysm diameter on the outcomes of thoracoabdominal aneurysm repair by fenestrated and branched endografts
DOI: 10.15468/dl.6jcnps
title: Occurrence Download

description: A dataset containing 2334330 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is South Africa",
 "DatasetKey is iNaturalist Research-grade Observations"
 ]
}

 The dataset includes 2334330 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012309-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.27338583
title: GEAR

description: GEAR is an automated approach to construct consistent GC workloads for different managed language runtimes, which can be further used to fairly evaluate GC algorithms across runtimes. More information can be found in the README.md.
DOI: 10.6084/m9.figshare.27338583.v1
title: GEAR

description: GEAR is an automated approach to construct consistent GC workloads for different managed language runtimes, which can be further used to fairly evaluate GC algorithms across runtimes. More information can be found in the README.md.
DOI: 10.15468/dl.46za7v
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Living Specimen, Occurrence evidence)",
 "Country is Costa Rica",
 "OccurrenceStatus is Present",
 "TaxonKey is Periplaneta australasiae (Fabricius, 1775)",
 "Year 2021-2024"
 ]
}

 The dataset includes 35 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003642-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rynn2p
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence, Living Specimen)",
 "Country is Costa Rica",
 "OccurrenceStatus is Present",
 "TaxonKey is Nasutitermes corniger (Motschulsky, 1855)",
 "Year 2021-2024"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003151-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v4c9g9
title: Occurrence Download

description: A dataset containing 65 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Living Specimen, Occurrence evidence)",
 "Country is Costa Rica",
 "OccurrenceStatus is Present",
 "TaxonKey is Rhinostomus barbirostris (J.C.Fabricius, 1775)",
 "Year 2021-2024"
 ]
}

 The dataset includes 65 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003636-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.