cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2lm11b
title: CCDC 2401571: Experimental Crystal Structure Determination

description: Related Article: Dong Li|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2lm1jt
title: CCDC 2401586: Experimental Crystal Structure Determination

description: Related Article: Xiaoxiang Zhang|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.13026/jwdf-q907
title: Dataset for Segmentation and Classification of Cardiac Implantable Electronic Devices in Chest X-Rays

description: This dataset encompasses a comprehensive collection of 2,321 chest radiographs
(originally DICOM, converted to PNG) and 11,072 smartphone images documenting
various cardiac implantable electronic devices (CIEDs) such as implantable
pacemakers, cardioverter defibrillators, cardiac resynchronization therapy
devices, and cardiac monitors, collected from 896 patients at the Charite \-
Universitatsmedizin Berlin over a decade (January 2012 to January 2022). The
dataset's primary objective is to advance the development and validation of
automated techniques for precise segmentation and classification of CIEDs
across both traditional and smartphone-generated imagery. It includes a
diverse array of 27 CIED models from four manufacturers (Medtronic, Biotronic,
Boston Scientific, Abbott Laboratories including St. Jude Medical), captured
in anterior-posterior or posterior-anterior chest radiographs using five
different smartphone brands. This dataset aims to underpin the creation of
deep learning models for accurately identifying CIED types, manufacturers, and
models. Designed to be a robust foundation for research and clinical
applications, it facilitates the exploration of innovative machine learning
solutions for CIED identification leveraging both original radiogrpahs and
smartphone images, thereby addressing a critical need in cardiac care
technology.
DOI: 10.13026/swv0-cd11
title: Dataset for Segmentation and Classification of Cardiac Implantable Electronic Devices in Chest X-Rays

description: This dataset encompasses a comprehensive collection of 2,321 chest radiographs
(originally DICOM, converted to PNG) and 11,072 smartphone images documenting
various cardiac implantable electronic devices (CIEDs) such as implantable
pacemakers, cardioverter defibrillators, cardiac resynchronization therapy
devices, and cardiac monitors, collected from 896 patients at the Charite \-
Universitatsmedizin Berlin over a decade (January 2012 to January 2022). The
dataset's primary objective is to advance the development and validation of
automated techniques for precise segmentation and classification of CIEDs
across both traditional and smartphone-generated imagery. It includes a
diverse array of 27 CIED models from four manufacturers (Medtronic, Biotronic,
Boston Scientific, Abbott Laboratories including St. Jude Medical), captured
in anterior-posterior or posterior-anterior chest radiographs using five
different smartphone brands. This dataset aims to underpin the creation of
deep learning models for accurately identifying CIED types, manufacturers, and
models. Designed to be a robust foundation for research and clinical
applications, it facilitates the exploration of innovative machine learning
solutions for CIED identification leveraging both original radiogrpahs and
smartphone images, thereby addressing a critical need in cardiac care
technology.
DOI: 10.17632/krp65rsddy.1
title: Modulation of Protein Activity by Small RNA Base Pairing Internal to Coding Sequences

description: Most characterized interactions between bacterial small RNAs (sRNAs) and their target mRNAs occur near ribosome binding sites resulting in changes in translation initiation or target mRNA decay. To understand the consequences of sRNA pairing internal to coding sequences detected by global RNA-RNA interactome approaches, we examined the impact of sRNA overexpression on seven target proteins. Overexpression of the sRNA led to decreased target protein levels for two pairs but no differences for the others. By further examining ArcZ-ligA and ArcZ-hemK, we discovered that that ArcZ pairing with the mRNAs leads to translation pausing and increased protein activity. A ligA point mutation that eliminates sRNA pairing resulted in increased sensitivity to DNA damage revealing physiological consequences of the regulation. Thus, regulatory RNA pairing in coding sequences can locally slow translation elongation, likely impacting co-translational protein folding and allowing improved incorporation of co-factors or more optimal folding under specific conditions.
DOI: 10.15468/dl.zwm9cz
title: Occurrence Download

description: A dataset containing 325 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Ammospermophilus harrisii (Audubon & Bachman, 1854)"
 ]
}

 The dataset includes 325 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005415-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3qstdz
title: Occurrence Download

description: A dataset containing 85 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Ammospermophilus interpres (Merriam, 1890)"
 ]
}

 The dataset includes 85 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005417-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r7ajyy
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phaeocollybia oregonensis A.H.Sm. & Trappe"
 ]
}

 The dataset includes 42 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005455-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jmg7q7
title: Occurrence Download

description: A dataset containing 467 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (New Caledonia, Vanuatu, Fiji, Tonga, Samoa, Wallis and Futuna, Solomon Islands, French Polynesia)",
 "TaxonKey is Acacia simplex (Sparrm.) Pedley"
 ]
}

 The dataset includes 467 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005418-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fczj2s
title: Occurrence Download

description: A dataset containing 40977 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((-170 5,-50 5,-50 83,-170 83,-170 5))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Asclepias tuberosa L."
 ]
}

 The dataset includes 40977 records from 178 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005456-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tc53jk
title: Occurrence Download

description: A dataset containing 14837 species occurrences available in GBIF matching the query:
{
 "or" : [
 "Geometry POLYGON((-75.37504 6.15341,-75.37503 6.15348,-75.37502 6.15354,-75.37514 6.15349,-75.37504 6.15341))",
 "Geometry POLYGON((-75.43857 6.245,-75.44247 6.23563,-75.4454 6.23095,-75.44442 6.21925,-75.43896 6.21457,-75.43409 6.19331,-75.43331 6.18551,-75.43565 6.17731,-75.43682 6.1699,-75.43565 6.15527,-75.43506 6.14903,-75.43409 6.14318,-75.42063 6.14806,-75.41204 6.15293,-75.40756 6.15274,-75.39137 6.15118,-75.38474 6.14649,-75.37947 6.14766,-75.38064 6.14123,-75.37596 6.14298,-75.37576 6.1463,-75.37186 6.14649,-75.37089 6.14942,-75.36309 6.15274,-75.36114 6.15566,-75.3584 6.16444,-75.35879 6.16854,-75.35197 6.16873,-75.35158 6.1662,-75.34982 6.16932,-75.34709 6.16971,-75.34573 6.17244,-75.36055 6.17848,-75.36718 6.17946,-75.37732 6.18668,-75.37928 6.19701,-75.38142 6.20228,-75.38396 6.21281,-75.38981 6.22159,-75.39371 6.22569,-75.39546 6.22783,-75.40892 6.22998,-75.41556 6.24188,-75.4218 6.24636,-75.42862 6.25377,-75.43799 6.26041,-75.43721 6.26801,-75.44013 6.26216,-75.43701 6.25807,-75.4376 6.25553,-75.43213 6.24987,-75.43643 6.24792,-75.43857 6.245))"
 ]
}

 The dataset includes 14837 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005416-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.36qwjf
title: Occurrence Download

description: A dataset containing 2333 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Ammospermophilus leucurus (Merriam, 1889)"
 ]
}

 The dataset includes 2333 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005458-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.erds7h
title: Occurrence Download

description: A dataset containing 7016 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((-170 5,-50 5,-50 83,-170 83,-170 5))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Asplenium rhizophyllum L."
 ]
}

 The dataset includes 7016 records from 123 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005419-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14852065
title: Urban-Rural Study Dataset

description: Datasets for "Systems analysis unravels a common rural-urban gradient in immunological profile, function and metabolic dependencies" manuscript.
DOI: 10.5281/zenodo.14967877
title: Urban-Rural Study Dataset

description: Datasets for "Systems analysis unravels a common rural-urban gradient in immunological profile, function and metabolic dependencies" manuscript submitted to Science Advances (adu0419).

Code can also be found in https://github.com/mdmanurung/urban-rural-study
DOI: 10.5281/zenodo.14852064
title: Urban-Rural Study Dataset

description: Datasets for "Systems analysis unravels a common rural-urban gradient in immunological profile, function and metabolic dependencies" manuscript submitted to Science Advances (adu0419).

Code can also be found in https://github.com/mdmanurung/urban-rural-study
DOI: 10.5281/zenodo.14966157
title: Urban-Rural Study Dataset

description: Datasets for "Systems analysis unravels a common rural-urban gradient in immunological profile, function and metabolic dependencies" manuscript submitted to Science Advances (adu0419).

Code can also be found in https://github.com/mdmanurung/urban-rural-study
DOI: 10.5281/zenodo.14968046
title: Dataset for automated milestoning simulations for receptor-ligand complexes with machine-learned force fields

description: Dataset for automated milestoning simulations for receptor-ligand complexes with machine-learned force fields

This dataset was generated to validate the automated milestoning computational pipeline with machine-learned force fields for receptor-ligand complexes. This dataset contains simulation data generated employing the automated multiscale milestoning framework with machine-learned force fields to compute the kinetics and thermodynamics of ligand unbinding for multiple receptor-ligand complexes. The dataset includes per-milestone trajectories, parameter file (model.xml), kinetic rates, and thermodynamic analysis results (images_and_plots) for the following complexes:



Eight Threonine-Tyrosine Kinase (TTK) complexes

Eight Heat Shock Protein 90 (HSP90) complexes

Trypsin-benzamidine Complex 


Each complex directory (TTK_complexes, HSP90_complexes, Trypsin_benzamidine) contains directories labeled 1 through 8 (for TTK and HSP90), corresponding to different inhibitor-ligand pairs studied in the manuscript.

 

data_automated_milestoning

│── TTK_complexes/

│ ├── 1/

│ ├── 2/

│ ├── 3/

│ ├── 4/

│ ├── 5/

│ ├── 6/

│ ├── 7/

│ ├── 8/

│── HSP90_complexes/

│ ├── 1/

│ ├── 2/

│ ├── 3/

│ ├── 4/

│ ├── 5/

│ ├── 6/

│ ├── 7/

│ ├── 8/

│── Trypsin_benzamidine/

 

Each directory within TTK_complexes (1-8), HSP90_complexes (1-8), and Trypsin_benzamidine contains the following structure:

 

│── 1/ (receptor_inhibitor complex)

│ ├── anchor_0/

│ │ ├── building/

│ │ │ ├── Topology PDB file

│ │ │ ├── Restart OpenMM XML file

│ │ ├── prod/

│ │ │ ├── Trajectory DCD file

│ │ │ ├── mmvt1.dcd # Simulation trajectory DCD file

│ │ │ ├── backup.checkpoint # Simulation checkpoint file

│ │ │ ├── mmvt.restart1.out # Transition count file

│ ├── anchor_1/

│ ├── anchor_2/

│ ├── ...

│ ├── ...

│ ├── anchor_15/

│ ├── model.xml # Milestoning simulation XML parameter file

│ ├── images_and_plots/

│ │ ├── free_energy_profile_anchor.png # Free energy plot

│ │ ├── free_energy_profile_milestones.png # Milestone-wise free energy

│ │ ├── milestone_free_energy.txt # Free energy values at each milestone

│ │ ├── rates.out # Computed kinetic rates (koff)

│ │ ├── transition_matrices/ # Transition statistics files

│ │ │ ├── N_ij_alpha

│ │ │ ├── N_alpha_beta

│ │ │ ├── T_alpha

│ │ │ ├── R_i_alpha

│ │ │ ├── pi_alpha.png

│ │ ├── pi_alpha. # Stationary probabilities of milestones

│ │ ├── p_i.png # Probability distribution

│ │ ├── k_alpha_beta # Kinetic transition rates

 

All data has been compressed into a single zip file named data_automated_milestoning.zip for easier storage and transfer.
DOI: 10.5281/zenodo.14968047
title: Dataset for automated milestoning simulations for receptor-ligand complexes with machine-learned force fields

description: Dataset for automated milestoning simulations for receptor-ligand complexes with machine-learned force fields

This dataset was generated to validate the automated milestoning computational pipeline with machine-learned force fields for receptor-ligand complexes. This dataset contains simulation data generated employing the automated multiscale milestoning framework with machine-learned force fields to compute the kinetics and thermodynamics of ligand unbinding for multiple receptor-ligand complexes. The dataset includes per-milestone trajectories, parameter file (model.xml), kinetic rates, and thermodynamic analysis results (images_and_plots) for the following complexes:



Eight Threonine-Tyrosine Kinase (TTK) complexes

Eight Heat Shock Protein 90 (HSP90) complexes

Trypsin-benzamidine Complex 


Each complex directory (TTK_complexes, HSP90_complexes, Trypsin_benzamidine) contains directories labeled 1 through 8 (for TTK and HSP90), corresponding to different inhibitor-ligand pairs studied in the manuscript.

 

data_automated_milestoning

│── TTK_complexes/

│ ├── 1/

│ ├── 2/

│ ├── 3/

│ ├── 4/

│ ├── 5/

│ ├── 6/

│ ├── 7/

│ ├── 8/

│── HSP90_complexes/

│ ├── 1/

│ ├── 2/

│ ├── 3/

│ ├── 4/

│ ├── 5/

│ ├── 6/

│ ├── 7/

│ ├── 8/

│── Trypsin_benzamidine/

 

Each directory within TTK_complexes (1-8), HSP90_complexes (1-8), and Trypsin_benzamidine contains the following structure:

 

│── 1/ (receptor_inhibitor complex)

│ ├── anchor_0/

│ │ ├── building/

│ │ │ ├── Topology PDB file

│ │ │ ├── Restart OpenMM XML file

│ │ ├── prod/

│ │ │ ├── Trajectory DCD file

│ │ │ ├── mmvt1.dcd # Simulation trajectory DCD file

│ │ │ ├── backup.checkpoint # Simulation checkpoint file

│ │ │ ├── mmvt.restart1.out # Transition count file

│ ├── anchor_1/

│ ├── anchor_2/

│ ├── ...

│ ├── ...

│ ├── anchor_15/

│ ├── model.xml # Milestoning simulation XML parameter file

│ ├── images_and_plots/

│ │ ├── free_energy_profile_anchor.png # Free energy plot

│ │ ├── free_energy_profile_milestones.png # Milestone-wise free energy

│ │ ├── milestone_free_energy.txt # Free energy values at each milestone

│ │ ├── rates.out # Computed kinetic rates (koff)

│ │ ├── transition_matrices/ # Transition statistics files

│ │ │ ├── N_ij_alpha

│ │ │ ├── N_alpha_beta

│ │ │ ├── T_alpha

│ │ │ ├── R_i_alpha

│ │ │ ├── pi_alpha.png

│ │ ├── pi_alpha. # Stationary probabilities of milestones

│ │ ├── p_i.png # Probability distribution

│ │ ├── k_alpha_beta # Kinetic transition rates

 

All data has been compressed into a single zip file named data_automated_milestoning.zip for easier storage and transfer.
DOI: 10.15468/dl.nhe7zr
title: Occurrence Download

description: A dataset containing 91040 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is one of (Argentina, Brazil, Paraguay)",
 "TaxonKey is Larus dominicanus M.H.K.Lichtenstein, 1823",
 "Year 1000-2024"
 ]
}

 The dataset includes 91040 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005409-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13380419
title: Establishing Technical Debt Management - A Five-Step Workshop Approach and an Action Research Study

description: The additional material for the paper "Establishing Technical Debt Management - A Five-Step Workshop Approach and an Action Research Study" comprises the following documents:

 

* Guideline_to_Use_TD-SAGAT.docx (.pdf)

  A short guideline on how the use the TD-SAGAT method.

* SAGAT_for_TD_from_Goals_to_Queries.pdf

Determination of survey questions by following the SAGAT approach of following the hierarchy of goals, subgoals, decisions, requirements, queries 

* WIKI page on technical debt.pdf

The teams wiki page on TD management written by the TD manager

 

 

* workshop_slides/TDMGuide_<x>_Workshop.pptx

    Sliedes for each of the six workshops 

* workshop_slides/TDMGuide_0_InitTalk_35Min_EN.pptx

and the initial one-hour introdution into the TD topic

 

 

* evaluations/Backlog_Evaluations_and_Figures.xlsx

- Backlog data from the 5th workshop (for 6th workshop, we used the the PowerBI Visualization instead)

- Evaluation of this data comprising 

- priority calculations based on priority risk and 

- priority calculations based on priority risk based on ROI

 

* evaluations/Meetings_Overview_Observations_Evaluation_Figures.xlsx

- Overview of all meetings plus information on lenght, particpants, whther a visoe exists and was used for evaluation

- Filled-out observation protocols from different meetings

- Summation, evaluations, and resulting figures

 

* evaluations/TD-SAGAT_Survey_and_SurveyResults_Figures.xlsx

- Survey questions for TD-SAGAT plus results

- Evaluation plus figures

 

* evaluations/Workshop_Survey_and_SurveyResults_Figures.xlsx

- Survey questions for Workshops plus results

- Evaluation plus figures

 

* evaluations/Kickoff_Survey_and_SurveyResults.xlsx

- Survey questions for Kickoff Workshops (incl. questions on current TDM process) plus results

- Evaluation in Workshop_Survey_and_SurveyResults_Figures.xslx
DOI: 10.6075/j04x585f
title: A dataset of chronic nicotine-induced genes in HCC38 breast cancer cells

description: For differential gene expression analysis, PyDESeq2 was used to estimate variance-mean dependence in count data from sequencing assays and test for differential expression based on a model using the negative binomial distribution. Velocyto (0.6) was used to estimate the spliced and unspliced counts from the pre-aligned bam files for the dynamic trajectory analysis.
description: PyDESeq2 and Velocyto (0.6) were used to generate differentially expressed genes (DEG) and identify the most dynamic genes in chronic nicotine-treated and control cells.
DOI: 10.15468/dl.nrux4e
title: Occurrence Download

description: A dataset containing 207 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (New Caledonia, Vanuatu, Fiji, Tonga, Samoa, French Polynesia, Wallis and Futuna, Solomon Islands)",
 "Geometry POLYGON((-204.89718 -28.83261,-144.73105 -28.83261,-144.73105 -3.5905,-204.89718 -3.5905,-204.89718 -28.83261))",
 "TaxonKey is Acacia simplex (Sparrm.) Pedley"
 ]
}

 The dataset includes 207 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005420-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ur7jsa
title: Occurrence Download

description: A dataset containing 485 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Leopardus wiedii (Schinz, 1821)",
 "Year 1000-2025"
 ]
}

 The dataset includes 485 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005459-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6073/pasta/03b766cad4ff5257d032b5d3840c8d55
title: Jornada Basin LTER: Wireless substation at NPP G-IBPE site: 30-minute soil volumetric water content data: 2013 - ongoing

description: 30-minute Soil Moisture data is measured at 10cm, 20 cm, and 30 cm soil depths at the NPP G-IBPE substation located in center of 70m x 70m Jornada LTER NPP G-IBPE site. Collection of soil volumetric water content data at Jornada LTER NPP sites, New Mexico, supports the environmental monitoring objectives of the Jornada LTER monitoring program that look at plant-soil water dynamics. Volumetric water content, bulk electrical conductivity, soil temperature, and bulk dielectric permittivity are measured every 30 minutes. This is an ONGOING dataset.
DOI: 10.6084/m9.figshare.28536032
title: Soil moisture data

description: This is the dataset measured over three months from a wheat field and a grass field in Rothamsted Research. This dataset was used to calculate root water uptake from different soil layers in the two plant systemes. The results were published in New Phytologist (2025) - Field plants strategically regulate water uptake from different soil depths by spatiotemporally adjusting their radial root hydraulic conductivity.