cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17155227
title: Osmolyte structural and thermodynamic effects across the protein folding landscape

description:  

Supplementary data files for the article

 

"Osmolyte structural and thermodynamic effects across the protein folding landscape"

Ander Francisco Pereira and Leandro Martínez

Institute of Chemistry and Center for Computing in Engineering & Sciences - Universidade Estadual de Campinas (UNICAMP)

https://doi.org/10.1021/jacsau.5c00813

 

Contains:

 

1. PULCHRA generated structures, equilibrated structures, and resulting solvation analyses performed with ComplexMixtures.jl for all 5000 models of each protein/cosolvent system.

These files contain, for each protein (`SH3` or `BdpA`), and for each cosolvent `Urea` or `TMAO`: a) the reconstruction of the SBM model by Pulchra. b) The equilibrated structure model, used to initiate production runs for the simulations of solvation. c) The final solvation analyzes of solvation, performed with ComplexMixtures.jl, including two files: `results_water.json` and `results_urea.json` or `results_tmao.json`, which contain the analyzes of distributions of each solvent component, performed over the trajectories.

Files:

SH3_TMAO.zip

SH3_Urea.zip

BdpA_TMAO.zip

BdpA_Urea.zip

 

2. Resulting solvation analsyses with ComplexMixtures.jl for all simulations performed for the determination of the transfer free energies:

The files contain, for each concentration, the output of the ComplexMixtures.jl calculation that appends the distribution functions and results of all simulation replicas for that concentration. The files are in the ".json" format, and must be read with `ComplexMixtures.load("file.json")`. Files with `Water` identifiers correspond to the calculations for the water as the solvent. The files without `Water` correspond to computing the distributions considering the cosolute (`Urea` or `TMAO`) as the solvents. `SH3` and `BdpA` indicate which protein is analyzed.

Files:

SH3_ComplexMixtures-Transfer-WaterUrea.zip    SH3_ComplexMixtures-Transfer-WaterTMAO.zipSH3_ComplexMixtures-Transfer-Urea.zipSH3_ComplexMixtures-Transfer-TMAO.zip

BdpA_ComplexMixtures-Transfer-WaterUrea.zip    BdpA_ComplexMixtures-Transfer-WaterTMAO.zipBdpA_ComplexMixtures-Transfer-Urea.zipBdpA_ComplexMixtures-Transfer-TMAO.zip

 

3. CSV data tables with the m-values and zeta-angle analyses for all 5000 models of each protein/cosolvent system, with:

3.1. mvalue-estimates and contributions of the side-chains and backbones for the estimates.

3.2. Exposed surface area for every type of residue, in each of the models.

3.4. fraction of zeta angles within 2 standard deviations of expected values, computed for the PULCHRA and equlibrated models.

Files:

SH3_mvalues_zeta.zip

BdpA_mvalues_zeta.zip

 

Additional files, simulation trajectories, and analysis scripts may be obtained upon request to authors.
DOI: 10.5281/zenodo.17349019
title: Total metal concentrations of Na, Al, non-sea salt Ca, and Fe in the SE-Dome ice core, southeastern Greenland
DOI: 10.5281/zenodo.17349283
title: PHONO-ML Database

description: This database provides Middle Chinese phonetic transcriptions (Baxter-Sagart notation) for a set of 26 224 character/transcription pairs, or 20 276 characters.

In this repository, you will find the following files:



phonoML_matches.csv, with one line representing only one character/transcription match.

phonoML_characters.csv, with one line representing one character and all of its matching transcriptions.

phonoML_transcriptions.csv, with one line representing one transcription and all of its matching characters.
DOI: 10.5281/zenodo.17349353
title: Daten der Notaufnahmesurveillance

description: Der Datensatz "Daten der Notaufnahmesurveillance" wird durch das Robert Koch-Institut und das AKTIN-Notaufnahmeregister bei Krankenhausaufnahmen bereitgestellt. Der Datensatz beinhaltet aggregierte Routinedaten aus deutschen Notaufnahmen zur syndromischen Überwachung von akuten Erkrankungen. Dazu zählen grippeähnliche Erkrankungen (ILI), Coronavirus-Erkrankungen (COVID-19), akute respiratorische Erkrankungen (ARE), gastrointestinale Infektionen (GI) und schwere akute respiratorische Infektionen (SARI). Dabei wird der relative Anteil dieser Erkrankungen an der Gesamtzahl der Notaufnahmevorstellungen sowie die berechneten Erwartungswerte und Prädiktionsintervalle ausgewiesen. Die Daten sind nach Notaufnahmetypen und Altersgruppen aggregiert. Damit bietet der Datensatz eine wertvolle Ressource für die Forschung im Bereich der Notfallmedizin und der Überwachung akuter Gesundheitsereignisse in Deutschland.
DOI: 10.17632/xpzsw566z3
title: Tail_Kinematic_Project_JEB

description: These are the dictionaries that should be loaded in the scripts available at the GitHub page scripts_Tail_Kinematic_Project_JEB_sub
DOI: 10.17632/xpzsw566z3.2
title: Tail_Kinematic_Project_JEB

description: These are the dictionaries that should be loaded in the scripts available at the GitHub page scripts_Tail_Kinematic_Project_JEB_sub
DOI: 10.17632/33fts3g7mt
title: Impact of slope on soil water availability and crop yield in fruit tree-based agroforestry systems on sloping land

description: These data sets present data of soil water availability and tree/crop performance in different slope positions (zones) in a longan-mango-maize-grass agroforestry experiment on sloping land in Northwest Vietnam. For further information, please refer to the material and methods section of the study: DOI: https://doi.org/10.1016/j.jafr.2025.102045.
DOI: 10.17632/33fts3g7mt.1
title: Impact of slope on soil water availability and crop yield in fruit tree-based agroforestry systems on sloping land

description: These data sets present data of soil water availability and tree/crop performance in different slope positions (zones) in a longan-mango-maize-grass agroforestry experiment on sloping land in Northwest Vietnam. For further information, please refer to the material and methods section of the study: DOI: https://doi.org/10.1016/j.jafr.2025.102045.
DOI: 10.17632/pb69jyn924.2
title: High-resolution stalagmite δ13C and δ18O records during 146-136.6 ka BP, central China.

description: High-resolution stalagmite (LS12) δ13C and δ18O records during 146-136.6 ka BP from Luoshui Cave, central China.
DOI: 10.17632/gb3gs84zjf.1
title: Evaluation of Post-Extraction Wound Healing in Patients Taking Zoledronic Acid Medication: A Prospective Study

description: raw data
DOI: 10.17632/j33g3nsm9k.2
title: Vegetables Image Dataset for Machine Applications

description: We developed the Vegetable Image Dataset to offer a collection of high-quality images featuring some of the most widely consumed and traded vegetables around the Pune. The dataset includes six types of vegetables: potato, chili, tomato, cucumber, beans, and okra. Each vegetable is further categorized into subclasses — potatoes are divided into three size-based classes (large, medium, and small) , while the other vegetables have two distinct varieties each (e.g., Chilies: Sitara, Jipoor, and Jwala; Tomatoes: Regular and Gaavran; Cucumbers: Regular and Gaavran; Beans: Long and Short; Okra: Long and Short) . This results in a total of 13 unique classes within the dataset . The images were taken under various lighting conditions — both natural and artificial — and against White backgrounds, including white, to ensure diversity and realism in the visual context. Given that the visual appearance of vegetables plays a significant role in their market value, this dataset supports research that evaluates vegetable quality through visual inspection . Although there are numerous datasets available for fruits and vegetables, many machine learning projects and applications still require a vegetable-specific dataset due to the unique nutritional importance and visual characteristics of vegetables . A robust dataset like this one enables machine learning models to achieve high accuracy in tasks such as classification and recognition . It's particularly useful for applications in research, education, and agriculture, including areas like detecting pest damage or monitoring quality degradation .
DOI: 10.3535/4nx-qlg-p11
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wyb-rrx-0fb
title: Cnidaria

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2j9-rwz-hyr
title: Diploastrea Matthai, 1914

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/361-cdg-bvm
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2vd-wt1-j72
title: Pseudosaynella

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6mv-2hw-s4s
title: Astartidae A. d'Orbigny, 1844 (1840)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lch-xnn-l80
title: Ostracoda Latreille, 1802

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qdj-lrr-bcy
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vqy-nnd-tr3
title: Cidaris Leske, 1778

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qrb-j6e-k8e
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/sne-p9r-qfe
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/f9z-4h8-pfj
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rdz-dc5-kqc
title: Chordata

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/bhg-97a-0jy
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xzj-mkz-hzh
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5jf-375-6bj
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5r3-3c5-3tq
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/b40-vvy-x48
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4gm-cf4-bt1
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7pf-dan-1tb
title: Hibolithes

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dmj-56c-4k5
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q00-nq8-xn8
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q2j-f2v-v0a
title: †Belemnitida

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/shh-fyz-y6m
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wjz-x06-2q9
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.adxa23
title: Occurrence Download

description: A dataset containing 10138 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ribes petraeum)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 10138 records from 261 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019939-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/a74-vzp-q9f
title: Bovidae Gray, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vrq-261-85d
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/779-xyr-ww8
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lpt-byz-9p8
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/50b-1np-rkn
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/66p-qtg-hpe
title: Diploastrea Matthai, 1914

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mh1-qhh-6qp
title: Hibolithes

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/spq-a74-p8n
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/czh-mfh-8s8
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4d6-5fl-gd3
title: Lamna

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wrw-d2h-c98
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/06m-dfg-v1g
title: Belemnites

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/prh-e91-0yw
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9x6-pk4-7g9
title: Hexanchidae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wrj-yyy-c65
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1sj-wr1-db1
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zwk-0xw-9sa
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ck5-art-ygz
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fgg-vj7-etk
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/05e-7n9-fee
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/70e-fzl-nnp
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hks-vcg-j6k
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/x7f-yva-55s
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z7d-thp-rtq
title: †Punctospirifer North, 1920

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6v6-ap3-hgp
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lse-yr2-kw0
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/p6j-2yw-ft6
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0vm-c93-fxq
title: Cervus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4b6-nkb-plp
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25921/4dt8-3581
title: NOAA/WDS Paleoclimatology - Howard and Prell 1994 Late Quaternary Southern Ocean Carbon Cycling Data

description: Recent geochemical models invoke ocean alkalinity changes, particularly in the surface Southern Ocean, to explain glacial age pCO2 reduction. In such models, alkalinity increases in glacial periods are driven by reductions in North Atlantic Deep Water (NADW) supply, which lead to increases in deep-water nutrients and dissolution of carbonate sediments, and to increased alkalinity of Circumpolar Deep Water upwelling in the surface Southern Ocean. We use cores from the Southeast Indian Ridge and from the deep Cape Basin in the South Atlantic to show that carbonate dissolution was enhanced during glacial stages in areas now bathed by Circumpolar Deep Water. This suggests that deep Southern Ocean carbonate ion concentrations were lower in glacial stages than in interglacials, rather than higher as suggested by the polar alkalinity model [Broecker and Peng, 1989]. Our observations show that changes in Southern Ocean CaCO3 preservation are coherent with changes in the relative flux of NADW, suggesting that Southern Ocean carbonate chemistry is closely linked to changes in deepwater circulation. The pattern of enhanced dissolution in glacials is consistent with a reduction in the supply of nutrient-depleted water (NADW) to the Southern Ocean and with an increase of nutrients in deep water masses. Carbonate mass accumulation rates on the Southeast Indian Ridge (3200–3800 m), and in relatively shallow cores (<3000 m) from the Kerguelen Plateau and the South Pacific were significantly reduced during glacial stages, by about 50%. The reduced carbonate mass accumulation rates and enhanced dissolution during glacials may be partly due to decreases in CaCO3:Corg flux ratios, acting as another mechanism which would raise the alkalinity of Southern Ocean surface waters. The polar alkalinity model assumes that the ratio of organic carbon to carbonate production on surface alkalinity is constant. Even if overall productivity in the Southern Ocean were held constant, a decrease in the CaCO3:Corg ratio would result in increased alkalinity and reduced pCO2 in Southern Ocean surface waters during glacials. This ecologically driven surface alkalinity change may enhance deepwater-mediated changes in alkalinity, and amplify rapid changes in pCO2.
DOI: 10.5517/cc82qlm
title: CCDC 240950: Experimental Crystal Structure Determination

description: Related Article: Xian-He Bu, Ming-Liang Tong, Ya-Bo Xie, Jian-Rong Li, Ho-Chol Chang, S.Kitagawa, J.Ribas|2005|Inorg.Chem.|44|9837|doi:10.1021/ic050886d
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/cc82qmn
title: CCDC 240951: Experimental Crystal Structure Determination

description: Related Article: Xian-He Bu, Ming-Liang Tong, Ya-Bo Xie, Jian-Rong Li, Ho-Chol Chang, S.Kitagawa, J.Ribas|2005|Inorg.Chem.|44|9837|doi:10.1021/ic050886d
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: 10.25921/464d-k762
title: NOAA/WDS Paleoclimatology - Schweingruber - Col D'Allos - ABAL - ITRDB FRAN015

description: Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives.  Most data sets include raw treering measurements (most are annual ring width, with some collections of earlywood or latewood width or wood density), plus chronologies (standardized growth indices for a site compiled from multiple treering samples). Reconstructions of climate variables are included with some of these data sets.  Each data type is stored in a separate data file; the data type is coded into the file name. For details please see: http://www.ncdc.noaa.gov/paleo/treeinfo.htmll
description:  NOAA Template Chronology file added 2019-01-08. NOAA Template Raw Measurements file added 2019-02-05.
DOI: 10.5517/cc92q57
title: CCDC 270728: Experimental Crystal Structure Determination

description: Related Article: Y.Garcia, G.Bravic, C.Gieck, D.Chasseau, W.Tremel, P.Gutlich|2005|Inorg.Chem.|44|9723|doi:10.1021/ic050971l
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/cc92q68
title: CCDC 270729: Experimental Crystal Structure Determination

description: Related Article: Y.Garcia, G.Bravic, C.Gieck, D.Chasseau, W.Tremel, P.Gutlich|2005|Inorg.Chem.|44|9723|doi:10.1021/ic050971l
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/cc8wtfc
title: CCDC 265063: Experimental Crystal Structure Determination

description: Related Article: C.Platas-Iglesias, L.Vaiana, D.Esteban-Gomez, F.Avecilla, J.A.Real, A.de Blas, T.Rodriguez-Blas|2005|Inorg.Chem.|44|9704|doi:10.1021/ic051119h
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: 10.15468/dl.sc6czw
title: Occurrence Download

description: A dataset containing 20435 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carpinus cordata"
 ]
}

 The dataset includes 20435 records from 213 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025005-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.