cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10775518
title: Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD

description: Set of data and scripts for the analysis of RAMD dissociation trajectories generated for BN-NS and BT/BCT-BPTI mutants, reported in the manuscript:

"Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD"

by Giulia D'Arrigo, Daria B. Kokh, Ariane Nunes-Alves and Rebecca C. Wade

 



RAMD movies of WT Bn-Bs and D35Abn mutant dissociation pathway (WT-diss.mp4 and D35Abn-diss.mp4)

Protein-Protein.zip contains:




README - set of instructions to go through files and for the use of the scripts

Jupyter notebooks: tauRAMD_PP_Residence_time.ipynb and tauRAMD_PP_Unbinding_pathways.ipynb

Scripts used for analysis and postprocessing RAMD simulations - for the correct usage of the scripts check the corresponding file header

System input files in BN-BS/ and BT_BCT-BPTI/

Experimental data used

2 RAMD movies (.mp4) showing dissociation of WT Bn-Bs and D35Abn mutant
DOI: 10.5281/zenodo.10728327
title: Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD

description: Set of data and scripts for the analysis of RAMD dissociation trajectories generated for BN-NS and BT/BCT-BPTI mutants, reported in the manuscript:

"Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD"

by Giulia D'Arrigo, Daria B. Kokh, Ariane Nunes-Alves and Rebecca C. Wade

 

Protein-Protein.zip contains:

 



README - set of instructions to go through files and for the use of the scripts

Jupyter notebooks: tauRAMD_PP_Residence_time.ipynb and tauRAMD_PP_Unbinding_pathways.ipynb

Scripts used for analysis and postprocessing RAMD simulations - for the correct usage of the scripts check the corresponding file header

System input files in BN-BS/ and BT_BCT-BPTI/

Experimental data used

2 RAMD movies (.mp4) showing dissociation of WT Bn-Bs and D35Abn mutant
DOI: 10.15468/dl.wwrdm3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.605311 -33.972733, 148.605311 -33.977225, 148.612048 -33.977225, 148.612048 -33.983962, 148.618785 -33.983962, 148.618785 -33.977225, 148.614294 -33.977225, 148.614294 -33.972733, 148.605311 -33.972733))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070106-240626123714530/datasets/export for details.
DOI: 10.15468/dl.td4mqz
title: Occurrence Download

description: A dataset containing 349531 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Herbario Nacional Colombiano (COL)"
 ]
}

 The dataset includes 349531 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070089-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.acazfa
title: Occurrence Download

description: A dataset containing 425 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cuscuta monogyna Vahl"
 ]
}

 The dataset includes 425 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070107-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4bcqwp
title: Occurrence Download

description: A dataset containing 23413 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is Norway",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "TaxonKey is Tetrao urogallus Linnaeus, 1758",
 "Year 1970-2024"
 ]
}

 The dataset includes 23413 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070108-240626123714530/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.24416171.v1
title: Additional file 1 of Prescription pattern analysis of Type 2 Diabetes Mellitus: a cross-sectional study in Isfahan, Iran

description: Additional file 1.
DOI: 10.6084/m9.figshare.24416171
title: Additional file 1 of Prescription pattern analysis of Type 2 Diabetes Mellitus: a cross-sectional study in Isfahan, Iran

description: Additional file 1.
DOI: 10.15468/dl.8hrtr9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.630014 -33.972733, 148.630014 -33.977225, 148.634506 -33.977225, 148.634506 -33.979471, 148.636752 -33.979471, 148.636752 -33.977225, 148.643489 -33.977225, 148.643489 -33.972733, 148.630014 -33.972733))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070109-240626123714530/datasets/export for details.
DOI: 10.15468/dl.enrraf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((147.125329 -33.977225, 147.125329 -33.979471, 147.132067 -33.979471, 147.132067 -33.977225, 147.125329 -33.977225))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070110-240626123714530/datasets/export for details.
DOI: 10.6084/m9.figshare.24416217
title: Additional file 2 of Efficacy and safety of mesenchymal stem cell therapy in liver cirrhosis: a systematic review and meta-analysis

description: Additional file 2. Detailed search strategy.
DOI: 10.6084/m9.figshare.24419024.v1
title: Additional file 2 of Association between fibrosis-related gene polymorphism and long-term allograft outcome in renal transplant recipients

description: Additional file 2: Table S1. The genes related to fibrosis.
DOI: 10.6084/m9.figshare.26735539.v1
title: Code

description: The full code of the manuscript "<b>Impact of first primary lung cancer chemoradiotherapy on second primary lung cancer prognosis</b>".
DOI: 10.6084/m9.figshare.26630404
title: Additional file 6 of Association between fibrosis-related gene polymorphism and long-term allograft outcome in renal transplant recipients

description: Additional file 6: Table S5. The risk score of high-risk group and low-risk group.
DOI: 10.15468/dl.2nhezq
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.430138 -33.977225, 148.430138 -33.979471, 148.432384 -33.979471, 148.432384 -33.977225, 148.430138 -33.977225))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070112-240626123714530/datasets/export for details.
DOI: 10.5255/ukda-sn-857297
title: Centre for Climate Change and Social Transformations: Cardiff Travel Survey, Wave 4, 2024

description: The Cardiff Travel Survey is a longitudinal survey that aims to (a) establish current and previous (before the coronavirus outbreak) travel habits; (b) explore how travel-related attitudes, social norms and perceptions change over time; and (c) examine the interplay between individual (perceptual) and environmental (infrastructural) factors in travel mode choice, in particular in relation to the uptake of active travel such as walking and cycling in the City of Cardiff, Wales. The Cardiff Travel Survey 2024 (Wave 4) is an opportunity sample that was collected in 2024 (n=2,427) by the Centre for Climate Change and Social Transformations (CAST), and is the fourth of a longitudinal series of surveys to be held annually for the duration of the centre. Data for the Cardiff Travel Survey 2024 were collected between 11 April 2023 and 05 June 2024. Participants of the Cardiff Travel Survey 2023 who consented (n=1,324) were recontacted via email to invite them to take part in the 2024 survey. Furthermore, participants were recruited through posts on social media, such as Facebook® and Twitter®. Invitations were posted on CAST and investigator accounts. The survey was hosted on the Qualtrics online survey platform and available in both English and Welsh. Inclusion criteria were that participants had to be at least 18 years of age and live in or travel regularly to Cardiff. The English version of the survey was completed by 2,628 respondents and the Welsh version by 9 respondents. There was evidence of bot activity in the English survey. This led to 1,630 responses to be removed. Incomplete responses (n=129), defined as those without any answers beyond socio-demographic, were removed from the dataset. A further 81 respondents did not complete the first section on current travel behaviours and were also removed. This left a final sample of n=797 adults. Participants were asked to create a unique code that can be used match this survey to the previous and next surveys without knowing their identity. Main topic areas of the questionnaire were: Demographics, Travel behaviours, Physical activity, Physical health and mental wellbeing, Perceptions of infrastructure and environmental quality, Travel-related social identity, Attitudes to active travel, Active travel related social norms, Support for active travel policies, and Unique ID.
DOI: 10.15468/dl.chv2nf
title: Occurrence Download

description: A dataset containing 2201 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cebus capucinus (Linnaeus, 1758)"
 ]
}

 The dataset includes 2201 records from 116 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070113-240626123714530/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.26735539
title: Code and Supplementary Tables S1-S40

description: The full code and Supplementary Tables S1-S40 of the manuscript "<b>Impact of first primary lung cancer chemoradiotherapy on second primary lung cancer prognosis</b>".
DOI: 10.6084/m9.figshare.26735539.v3
title: Code and Supplementary Tables S1-S40

description: The full code and Supplementary Tables S1-S40 of the manuscript "<b>Impact of first primary lung cancer chemoradiotherapy on second primary lung cancer prognosis</b>".
DOI: 10.6084/m9.figshare.26735539.v2
title: Code

description: The full code of the manuscript "<b>Impact of first primary lung cancer chemoradiotherapy on second primary lung cancer prognosis</b>".
DOI: 10.15468/dl.nzpjuz
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.796204 -33.977225, 148.796204 -33.983962, 148.802941 -33.983962, 148.802941 -33.979471, 148.798449 -33.979471, 148.798449 -33.977225, 148.796204 -33.977225))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070115-240626123714530/datasets/export for details.
DOI: 10.6084/m9.figshare.26742776
title: Additional file 2 of Tissue of origin detection for cancer tumor using low-depth cfDNA samples through combination of tumor-specific methylation atlas and genome-wide methylation density in graph convolutional neural networks

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.26742779
title: Additional file 3 of Tissue of origin detection for cancer tumor using low-depth cfDNA samples through combination of tumor-specific methylation atlas and genome-wide methylation density in graph convolutional neural networks

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.26742785
title: Additional file 5 of Tissue of origin detection for cancer tumor using low-depth cfDNA samples through combination of tumor-specific methylation atlas and genome-wide methylation density in graph convolutional neural networks

description: Supplementary Material 5
DOI: 10.1594/pangaea.821115
title: Downwelling spectral irradiance as measured in different depths at radiometer station PS75/285-4
DOI: 10.1594/pangaea.821139
title: Downwelling spectral solar irradiance as measured above water surface at radiometer station PS75/285-4
DOI: 10.1594/pangaea.400845
title: Hydrochemistry measured on water bottle samples at station B8/89_565 during the MRI-LDEO cooperative study

description: For pCO2 measurements were about 0.5 liter of air equilibrated with sample. Sample volume 4. Nutrient samples are collected in 250 ml soft low density polyethylene acid washed bottles. They are kept refrigerated until analysis if it was not carried out soon after sampling. Otherwisee samples are stored at -20°C.
DOI: 10.1594/pangaea.323222
title: Water temperature and salinity real-time profiles from cruise 4900699 (DCQC)

description: For definition of quality flags see hdl:10013/epic.31518.d001
DOI: 10.1594/pangaea.821138
title: Downwelling spectral solar irradiance as measured above water surface at radiometer station PS75/283-4
DOI: 10.6084/m9.figshare.26629783
title: Additional file 1 of Transcriptome and metabolome analyses revealed the response mechanism of pepper roots to Phytophthora capsici infection

description: Supplementary Material 1
DOI: 10.1594/pangaea.890704
title: Physical oceanography during KOMMANDOR JACK cruise 02+03 (KJACK2001)

description: Hydrographic observations on the Iceland-Faeroe Ridge and Wyville-Thomson Ridge, as well as in the Faeroe-Bank Channel and Faeroe-Shetland Channel during 12.-19. July 2001 from Kommandor Jack cruise 2 and 3.
DOI: 10.1594/pangaea.821114
title: Downwelling spectral irradiance as measured in different depths at radiometer station PS75/283-4
DOI: 10.1594/pangaea.821116
title: Downwelling spectral irradiance as measured in different depths at radiometer station PS75/286-5
DOI: 10.1594/pangaea.399555
title: Current veolcity from SOFAR float RI2

description: Processing method: splined, velocity algorithm: splined. Data have been checked by the WOCE Subsurface Float Data Assembly Center. See hdl:10013/epic.32931.d001 for further information.
DOI: 10.1594/pangaea.787725
title: (Table T1) Radioelement concentration and radiogenic heat production of ODP Holes 173-1067A and 173-1068A

description: Mean values of radiogenic heat production are derived from measurements of radioelements on the following rock types: amphibolite (0.358 ± 0.118 µW/m**3) and tonalite gneiss (0.802 ± 0.039 µW/m**3) at Site 1067 and serpentinized peridotite (0.0108 ± 0.0003 µW/m**3) at Site 1068. The results for serpentinized peridotite and amphibolite are consistent with previous measurements on samples from Sites 897 and 900. These results suggest that the thin continental crust in this region would contribute very little to the conductive heat flow.
description: Supplement to: Louden, Keith E; Whitmarsh, Robert B; Mareschal, Jean-Claude (2000): Data report: Measurements of radiogenic heat production on basement samples from Sites 1067 and 1068. In: Beslier, M-O; Whitmarsh, RB; Wallace, PJ; Girardeau, J (eds.) Proceedings of the Ocean Drilling Program, Scientific Results, College Station, TX (Ocean Drilling Program), 173, 1-4
DOI: 10.1594/pangaea.322130
title: Water temperature real-time profiles from cruise 4154498 (DCQC)

description: For definition of quality flags see hdl:10013/epic.31518.d001
DOI: 10.1594/pangaea.856632
title: Physical oceanography during METEOR cruise M84/3
DOI: 10.1594/pangaea.112396
title: Endeavor shipboard meteorology of cruise EN198
DOI: 10.1594/pangaea.810503
title: (Table 4) Geochemistry at DSDP Hole 74-527
DOI: 10.1594/pangaea.112397
title: Near surface oceanography using SIAL-loop system of cruise EN198
DOI: 10.1594/pangaea.854151
title: (Table S1, Figure 2) Sedimentation rates for 108 sediment core sites during the LGM and HS1

description: The SR errors in Fig.2 are given by the averaged values of 'Error [+, 97.5%]' and 'Error [-, 2.5%]'.The calculation focused on 19-21 ka since the age model did not cover the whole LGM period.
DOI: 10.1594/pangaea.860938
title: Compilation of planktonic foraminiferal census counts from the Southern Hemisphere Oceans

description: We present an improved database of planktonic foraminiferal census counts from the Southern Hemisphere Oceans (SHO) from 15°S to 64°S. The SHO database combines 3 existing databases. Using this SHO database, we investigated dissolution biases that might affect faunal census counts. We suggest a depth/[DCO3]2- threshold of ~3800 m/[DCO3]2- = ~-10 to -5 µmol/kg for the Pacific and Indian Oceans, and ~4000 m/[DCO3]2- = ~0 to 10 µmol/kg for the Atlantic Ocean, under which core-top assemblages can be affected by dissolution and are less reliable for paleo-sea surface temperature (SST) reconstructions. We removed all core-tops beyond these thresholds from the SHO database. This database has 598 core-tops and is able to reconstruct past SST variations from 2° to 25.5°C, with a root mean square error of 1.00°C, for annual temperatures. To inspect dissolution affects SST reconstruction quality, we tested the data base with two "leave-one-out" tests, with and without the deep core-tops.We used this database to reconstruct Summer SST (SSST) over the last 20 ka, using the Modern Analog Technique method, on the Southeast Pacific core MD07-3100. This was compared to the SSST reconstructed using the 3 databases used to compile the SHO database. Thus showing that the reconstruction using the SHO database is more reliable, as its dissimilarity values are the lowest. The most important aspect here is the importance of a bias-free, geographic-rich, database. We leave this dataset open-ended to future additions; the new core-tops must be carefully selected, with their chronological frameworks, and evidence of dissolution assessed.
description: Supplement to: Haddam, Naoufel; Michel, Elisabeth; Siani, Giuseppe; Cortese, Giuseppe; Bostock, Helen C; Duprat, Josette M; Isguder, Gulay (2016): Improving past sea surface temperature reconstructions from the Southern Hemisphere oceans using planktonic foraminiferal census data. Paleoceanography, 31(6), 822-837
DOI: 10.1594/pangaea.793119
title: Hydrochemistry during L'Atalante cruise ATA_IFMGEOMAR-4

description: # 51 CTD station.Region: Tropical Atlantic. # Chief Scientist - P. Brandt # Hydro (G. Krahmann). Status-final. # Nutrients (F. Malien). Status - final. # Precision for nutrient analysis determined from 75 double samples from 37 stations. # Precision for: Nitrite: 0.006 umol/kg. Nitrate: 0.13 umol/kg. Phosphate: 0.008 umol/kg. Silicate: 0.18 umol/kg. # O2 (F. Malien). Status - final. Winkler titration. # Precision for O2: 0.3 umol/kg (from 2 duplicate samples taken and analyzed at all 51 stations). # Salinity samples analyzed with a Guildline Autosal salinometer (Kiel AS7).
DOI: 10.1594/pangaea.892825
title: North Atlantic EM-122 multibeam swath bathymetry collected during RRS Discovery cruise DY081 (links to raw files and gridded data)

description: This data release includes 56,432 square kilometers of multibeam swath bathymetry collected during a 2017 (June - August) research expedition onboard the RRS Discovery, DY081, in the North Atlantic Ocean. DY081 was the first fieldwork component of a European Research Council funded project, ICY-LAB, led by Dr. K. Hendry from the University of Bristol to study nutrient cycling in the North Atlantic. Four sites of interest were surveyed with an EM-122 echosounder prior to scientific operations, such as CTD deployment, sediment coring, and/or ROV dives. The four sites were Orphan Knoll off the coast of Newfoundland, and Nuuk, Nasrsaq, and Cape Farewell off southwest Greenland. Multibeam data was also recorded and processed during transit between locations. Data from the study sites and transits (EM-122 raw .all files and 25-meter resolution grids) are provided.
DOI: 10.1594/pangaea.861842
title: Surfactants during upwelling events in the sea-surface microlayer and 1 m depth during METEOR cruise M117, Baltic Sea

description: Results from a study of surfactants (SAS) in the sea surface microlayer (SML) and underlying water (ULW) at different locations in the Baltic Sea. The total SAS concentrations were measured using phase-sensitive alternative current voltammetry with hanging mercury drop electrode (HMDE) in unfiltered samples. The concentrations of SAS were expressed as the equivalent concentration of nonanionic surfactants Triton-X-100. The enrichment factors (EF) of SAS were calculated as the ratio of concentration in SML to the corresponding ULW samples.
DOI: 10.1594/pangaea.770378
title: (Table 1) Initial depth tie points between ODP Site 162-983 and IODP Site 306-U1314

description: Sediment depth is given in mcd.
DOI: 10.1594/pangaea.861762
title: Extracellular carbonic anhydrase concentration at the sea-surface microlayer and 1 m depth during METEOR cruise M117, Baltic Sea

description: We developed an effective fluorometric technique to quantify extracellular carbonic anhydrase (eCA) present in natural seawater samples. The technique includes the separation of eCA from cells to achieve low detection limits through high signal : noise ratios. eCA was efficiently extracted from cell membranes by treatment with 0.1 M phosphate buffer containing 2.5 M NaCl. The free eCA specifically forms a fluorescent complex with dansylamide, and the detection limit of the complex is below 0.1 nM. We applied the technique to samples from different culture solutions and natural seawater collected from the Baltic Sea. We observed eCA concentrations to be in the range of 0.10-0.67 nM in natural seawater. The data indicated that this technique is very sensitive, accurate, and feasible for routine and shipboard measurement of eCA from natural seawater. It is therefore an effective and rapid tool to investigate the carbon acquisition of phytoplankton both in mono culture as well natural communities.
description: Supplement to: Mustaffa, Nur Ili Hamizah (2017): Extracellular carbonic anhydrase: Method development and its application to natural seawater. Limnology and Oceanography-Methods, 15(5), 503-517
DOI: 10.1594/pangaea.763280
title: (Table 1) Age model tie-points from IODP Site 306-U1314

description: Sediment depth is given in mcd.
DOI: 10.1594/pangaea.770380
title: (Table 2) Astronomical age constraints for magnetic polarity reversals in IODP Site 306-U1314

description: Sediment depth is given in mcd.
DOI: 10.1594/pangaea.763282
title: (Appendix A) Ostracod taxa from IODP Site 306-U1314

description: Sediment depth is given in mcd.
DOI: 10.1594/pangaea.770381
title: Element intensities and concentrations of K, Ti and Ca, true molar ratios of these elements and derived CaCO3 at IODP Site 306-U1314

description: Sediment depth is given in mbsf. Element intensities were measured with X-ray fluorescence core scanning in Bremen (core scanner XRF2) at 10 kV. True molar ratios and concentrations were derived from a log ratio calibration with 54 quantitative XRF measurements on discrete samples.
DOI: 10.1594/pangaea.770379
title: (Table 1) Age model of IODP Site 306-U1314

description: Sediment depth is given in mcd.
DOI: 10.1594/pangaea.770383
title: Geochemistry of the solid phase of IODP Site 306-U1314
DOI: 10.1594/pangaea.830904
title: (Table 1) Final age model of IODP Site 306-U1314

description: DEPTH, sediment/rock [m] is given in mcd.
DOI: 10.1594/pangaea.830905
title: (Table 2) Astronomical age constraints for magnetic polarity reversals of IODP Site 306-U1314
DOI: 10.1594/pangaea.708065
title: (Appendix A2) Trace element concentrations for DSDP Site 91-596 sediments
DOI: 10.1594/pangaea.708064
title: (Appendix A2) Trace element concentrations for DSDP Hole 91-595A sediments
DOI: 10.1594/pangaea.830903
title: (Table 1) Initial depth tie points between ODP Site 162-983 and IODP Site 306-U1314

description: DEPTH, sediment/rock [m] is given in mcd.