cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5sn01f4c
title: MassIVE MSV000092810 - Simultaneous xylose and glucose utilization by an E. coli crp mutant
title: As advances are made toward the industrial feasibility of mass-producing biofuels and commodity chemicals with sugar-fermenting microbes, high feedstock costs continue to inhibit commercial application. Hydrolyzed lignocellulosic biomass represents an ideal feedstock for these purposes as it is cheap and prevalent. However, many microbes, including Escherichia coli, struggle to efficiently utilize this mixture of hexose and pentose sugars due to the regulation by the carbon catabolite repression (CCR) system. CCR causes a sequential utilization of sugars, rather than simultaneous utilization, resulting in reduced carbon yield and complex process implications in fed-batch fermentation. A mutation in the gene encoding the cyclic AMP receptor protein, Crp*, has been shown to disable CCR and improve co-utilization of mixed sugar substrates. Here, we present the strain construction and characterization of a site specific crp* chromosomal mutant in E. coli BL21 starTM (DE3). The crp* mutant strain demonstrates simultaneous consumption of glucose and xylose, suggesting a deregulated CCR system. The proteomic analysis further showed that cells link xylose consumption to energy production through the de novo nucleotide synthesis pathway, explaining the relatively slower growth of the crp* mutant strain. This highly characterized strain can be particularly beneficial for chemical production by simultaneously utilizing both C5 and C6 substrates from lignocellulosic biomass.
DOI: 10.6084/m9.figshare.24076704
title: <b>Research ethics review during the COVID-19 pandemic: An international study</b><b>Raw data from Qualtrics survey</b>

description: This document contains the raw data from an anonymous, cross-sectional, global online survey that aimed to identify the experiences and operation of research ethics review committees (ERCs) during the COVID-19 pandemic. Respondents were chairs (or their delegates) of ERCs who were involved in the review of COVID-19-related research protocols after March 2020. The 203 participants [130 from high-income countries (HICs) and 73 from low- and middle-income countries (LMICs)] came from diverse entities and organizations from 48 countries (19 HICs and 29 LMICs) in all World Health Organization regions.The survey questionnaire, administered through the Qualtrics Experience Management (XM) online platform, consisted of 50 items, with opportunities for open text responses. This document includes two Excel spreadsheets with the original data from Qualtrics, one for participants from HICs and the other for participants from LMICs.The study received approval from Western University’s Non-Medical Research Ethics Board (Protocol ID 120455). Additionally, it was evaluated by the World Health Organization Research Ethics Review Committee (Protocol ID CERC.0181) and was exempted from further review.
DOI: 10.6084/m9.figshare.24076704.v1
title: <b>Research ethics review during the COVID-19 pandemic: An international study</b><b>Raw data from Qualtrics survey</b>

description: This document contains the raw data from an anonymous, cross-sectional, global online survey that aimed to identify the experiences and operation of research ethics review committees (ERCs) during the COVID-19 pandemic. Respondents were chairs (or their delegates) of ERCs who were involved in the review of COVID-19-related research protocols after March 2020. The 203 participants [130 from high-income countries (HICs) and 73 from low- and middle-income countries (LMICs)] came from diverse entities and organizations from 48 countries (19 HICs and 29 LMICs) in all World Health Organization regions.The survey questionnaire, administered through the Qualtrics Experience Management (XM) online platform, consisted of 50 items, with opportunities for open text responses. This document includes two Excel spreadsheets with the original data from Qualtrics, one for participants from HICs and the other for participants from LMICs.The study received approval from Western University’s Non-Medical Research Ethics Board (Protocol ID 120455). Additionally, it was evaluated by the World Health Organization Research Ethics Review Committee (Protocol ID CERC.0181) and was exempted from further review.
DOI: 10.5281/zenodo.8311805
title: Comparison of Maximal End Component Decomposition Algorithms: Data and Code

description: Code and Data used for the Bachelor Thesis "Comparison of Maximal End Component Decomposition Algorithms"
DOI: 10.5281/zenodo.8311804
title: Comparison of Maximal End Component Decomposition Algorithms: Data and Code

description: Code and Data used for the Bachelor Thesis "Comparison of Maximal End Component Decomposition Algorithms"
DOI: 10.6084/m9.figshare.24078027
title: Permuted Datasets

description: Permuted Relational-Event Model datasets. Hybrid datasets containing observed events and corresponding 'non-events' generated by the permutation procedure. <b>ptests_perm1</b>: Permuted Relational-Event Model datasets. Hybrid datasets containing observed events and corresponding 'non-events' generated by the permutation procedure. Output of procudure 1 in MK_permutations.R (available from https://github.com/mkings-220920/Cornish-Jackdaws/tree/main/Code/Main scripts). Non-independent permutation of Source and Target labels (see Supplementary Fig. 3a).<b>ptests_perm2_CS</b>: The permutation procedure (see procedure 2 in MK_permutations.R) randomizes sets of 'Target' labels (i.e. datasets are 'conditioned' on "SOURCE" - see Supplementary Table 10 for glossary of REM terminology) within subsets of the dataset (see Supplementary Fig. 3b). 10,000 datasets.<b>ptests_perm4_Duration</b>: Output of procedure four in MK_permutations.R (available from https://github.com/mkings-220920/Cornish-Jackdaws/tree/main/Code/Main scripts). Permutation of edge weights (See Supplementary Fig. 3d), in this case association event duration.<b>ptests_perm4_Latency</b>: Output of procedure four in MK_permutations.R (available from https://github.com/mkings-220920/Cornish-Jackdaws/tree/main/Code/Main scripts). Permutation of edge weights (see Supplementary Fig. 3d), in this case association event arrival latencies.
DOI: 10.6084/m9.figshare.24078027.v1
title: Permuted Datasets

description: Permuted Relational-Event Model datasets. Hybrid datasets containing observed events and corresponding 'non-events' generated by the permutation procedure. <b>ptests_perm1</b>: Permuted Relational-Event Model datasets. Hybrid datasets containing observed events and corresponding 'non-events' generated by the permutation procedure. Output of procudure 1 in MK_permutations.R (available from https://github.com/mkings-220920/Cornish-Jackdaws/tree/main/Code/Main scripts). Non-independent permutation of Source and Target labels (see Supplementary Fig. 3a).<b>ptests_perm2_CS</b>: The permutation procedure (see procedure 2 in MK_permutations.R) randomizes sets of 'Target' labels (i.e. datasets are 'conditioned' on "SOURCE" - see Supplementary Table 10 for glossary of REM terminology) within subsets of the dataset (see Supplementary Fig. 3b). 10,000 datasets.<b>ptests_perm4_Duration</b>: Output of procedure four in MK_permutations.R (available from https://github.com/mkings-220920/Cornish-Jackdaws/tree/main/Code/Main scripts). Permutation of edge weights (See Supplementary Fig. 3d), in this case association event duration.<b>ptests_perm4_Latency</b>: Output of procedure four in MK_permutations.R (available from https://github.com/mkings-220920/Cornish-Jackdaws/tree/main/Code/Main scripts). Permutation of edge weights (see Supplementary Fig. 3d), in this case association event arrival latencies.
DOI: 10.6084/m9.figshare.24077829.v1
title: Eventnet Output

description: Output of Eventnet processing of permuted REM datasets (see 'Permuted Datasets' in Figshare collection). Eventnet configuration file provided in Figshare collection.
DOI: 10.6084/m9.figshare.24077829
title: Eventnet Output

description: Output of Eventnet processing of permuted REM datasets (see 'Permuted Datasets' in Figshare collection). Eventnet configuration file provided in Figshare collection.
DOI: 10.6084/m9.figshare.24078087
title: sample_metadata.xlsx

description: The file contains sample information for 10x based sequencing.
DOI: 10.6084/m9.figshare.24078087.v1
title: sample_metadata.xlsx

description: The file contains sample information for 10x based sequencing.
DOI: 10.6084/m9.figshare.23615436
title: Data for reproducing Figures

description: Relational Event-Model (REM) predicted values used in the production of figures, given as .RData files, along with other files used for plotting ('coop_only.RData', 'Fig3__perc_store_list.RData'). Figures can be produced by loading the data files in R and running the relevant section of the MK_REMs.R script (available from https://github.com/mkings-220920/Cornish-Jackdaws).- Figure 2 = 'model2__pred_list2.RData', see code section beginning line 473 in MK_REMs.R- Figure 3 = 'Fig3__perc_store_list.RData', see code section beginning line 501 in MK_REMs.R- Figure 4 = 'model4__pred_list4.RData' and 'model5__pred_list5.RData', see code section beginning line 555 in MK_REMs.R- Figure 5 = 'coop_only.RData', see code section beginning line 611 in MK_REMs.R- Figure 6 = 'model8_pred_list8.RData', see code section beginning line 712 in MK_REMs.R- Supplementary Fig. 1 = 'coop_only.RData', see code section beginning line 743 in MK_REMs.R<br>'model2__pred_list2.RData', 'model4__pred_list4.RData', 'model5__pred_list5.RData', and 'model8_pred_list8.RData' contain model predictions used in figures. Median predicted values and prediction intervals were calculated from these distributions of predicted values.'coop_only.RData' is a dataset that contains all of the time-varying covariates (as calculated in Eventnet), but without 'non-events' (i.e. hypothetical/expected events as generated by the permutation procedure). As it only contains the observed events, this dataframe is used at points in the 'MK_REMs' script for plotting. 'Fig3__perc_store_list.RData' is a dataset containing cumulative success/fail differential (across the duration of the experiment) for the 'non-events' in permuted datasets. See 'permuted' in Fig. 3
DOI: 10.6084/m9.figshare.23615436.v2
title: Data for reproducing Figures

description: Relational Event-Model (REM) predicted values used in the production of figures, given as .RData files, along with other files used for plotting ('coop_only.RData', 'Fig3__perc_store_list.RData'). Figures can be produced by loading the data files in R and running the relevant section of the MK_REMs.R script (available from https://github.com/mkings-220920/Cornish-Jackdaws).- Figure 2 = 'model2__pred_list2.RData', see code section beginning line 473 in MK_REMs.R- Figure 3 = 'Fig3__perc_store_list.RData', see code section beginning line 501 in MK_REMs.R- Figure 4 = 'model4__pred_list4.RData' and 'model5__pred_list5.RData', see code section beginning line 555 in MK_REMs.R- Figure 5 = 'coop_only.RData', see code section beginning line 611 in MK_REMs.R- Figure 6 = 'model8_pred_list8.RData', see code section beginning line 712 in MK_REMs.R- Supplementary Fig. 1 = 'coop_only.RData', see code section beginning line 743 in MK_REMs.R<br>'model2__pred_list2.RData', 'model4__pred_list4.RData', 'model5__pred_list5.RData', and 'model8_pred_list8.RData' contain model predictions used in figures. Median predicted values and prediction intervals were calculated from these distributions of predicted values.'coop_only.RData' is a dataset that contains all of the time-varying covariates (as calculated in Eventnet), but without 'non-events' (i.e. hypothetical/expected events as generated by the permutation procedure). As it only contains the observed events, this dataframe is used at points in the 'MK_REMs' script for plotting. 'Fig3__perc_store_list.RData' is a dataset containing cumulative success/fail differential (across the duration of the experiment) for the 'non-events' in permuted datasets. See 'permuted' in Fig. 3
DOI: 10.6084/m9.figshare.23615436.v1
title: Data for reproducing Figures

description: Relational Event-Model (REM) predicted values used in the production of figures, given as .RData files. Figures can be produced by loading the data files in R and running the relevant section of the MK_REMs.R script (available from ) <br> - Figure 2 = 'model1b__pred_list1b.RData', see code section beginning line 465 in MK_REMs.R - Figure 3 = 'Fig3__perc_store_list.RData', see code section beginning line 494 in MK_REMs.R - Figure 4 = 'model3a__pred_list_3a.RData' and 'model3b__pred_list_3b.RData', see code section beginning line 551 in MK_REMs.R - Figure 5 = 'coop_only.RData', see code section beginning line 677 in MK_REMs.R - Figure 6 = 'model6_pred_list_6.RData', see code section beginning line 774 in MK_REMs.R - Supplementary Fig. 1 = 'coop_only.RData', see code section beginning line 620 in MK_REMs.R
DOI: 10.5281/zenodo.8311856
title: daptrius_ater_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8311855
title: daptrius_ater_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8311865
title: falco_ardosiaceus_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8311864
title: falco_ardosiaceus_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8311873
title: falco_biarmicus_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8311872
title: falco_biarmicus_zanfona_1.fasta.gz

description: .
DOI: 10.6084/m9.figshare.24078123
title: REM coefficients

description: Coefficients for each term in each REM. 10,000 sets of coefficients per model type. Coefficient distributions were used to calculate median coefficient values and confidence intervals. For details of the different models and the terms in each model see 'REM specifications' in Supplementary Methods.
DOI: 10.6084/m9.figshare.24078123.v1
title: REM coefficients

description: Coefficients for each term in each REM. 10,000 sets of coefficients per model type. Coefficient distributions were used to calculate median coefficient values and confidence intervals. For details of the different models and the terms in each model see 'REM specifications' in Supplementary Methods.
DOI: 10.21227/btfq-t298
title: Abaqus user-defined elements subroutine for cohesive zone model of hydrofracturing of surface crevasses in ice shelves

description: We present a finite-element-based cohesive zone model for simulating the nonlinear fracture process driving the propagation of water-filled surface crevasses in floating ice tongues. The fracture process is captured using an interface element whose constitutive behavior is described by a bilinear cohesive law, and the bulk rheology of ice is described by a nonlinear elasto-viscoplastic model. The additional loading due to meltwater pressure within the crevasse is incorporated by combining the ideas of poromechanics and damage mechanics. We performed several numerical studies to explore the parametric sensitivity of surface crevasse depth to ice rheology, cohesive strength, density, and temperature, for different levels of meltwater depth. We find that viscous (creep) strain accumulation promotes crevasse propagation and that surface crevasses propagate deeper in ice shelves/tongues if we consider depth-varying ice density and temperature profiles. Therefore, ice flow models must account for depth-varying density and temperature-dependent viscosity to describe calving outcomes appropriately.This dataset contains the ABAQUS input files for simulating floating ice shelves with constant density assuming linear elastic rheology or elasto-visco-plastic rheology and ABAQUS user-defined elements subroutine for water-filled cohesive zone elements. Jupyter notebooks for generating the figures in the paper are also included in this dataset.
DOI: 10.5281/zenodo.8311883
title: falco_concolor_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8311882
title: falco_concolor_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8311895
title: phalcoboenus_megalopterus_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8311894
title: phalcoboenus_megalopterus_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8311900
title: microhierax_latifrons_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8311899
title: microhierax_latifrons_zanfona_1.fasta.gz

description: .
DOI: 10.6084/m9.figshare.3761562.v2696
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.5281/zenodo.8311943
title: microhierax_caerulescens_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8311942
title: microhierax_caerulescens_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8200781
title: Dataset for "A high-performance neuroprosthesis for speech decoding and avatar control"

description: The dataset associated with the publication: "A high-performance neuroprosthesis for speech decoding and avatar control"
DOI: 10.5281/zenodo.8311905
title: Dataset for "A high-performance neuroprosthesis for speech decoding and avatar control"

description: The dataset associated with the publication: "A high-performance neuroprosthesis for speech decoding and avatar control"
DOI: 10.5281/zenodo.8311947
title: falco_dickinsoni_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8311946
title: falco_dickinsoni_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8285002
title: Dataset for "A high-performance neuroprosthesis for speech decoding and avatar control"

description: The dataset associated with the publication: "A high-performance neuroprosthesis for speech decoding and avatar control". Please use the most recently available version of the deposition instead of this version. Please note that the LICENSE file from version 1.1.0 of this deposition applies to all of the contents of this version as well. By accessing and downloading files from this version of the deposition, you are agreeing to the terms of the LICENSE file in version 1.1.0.
DOI: 10.5281/zenodo.8200782
title: Dataset for "A high-performance neuroprosthesis for speech decoding and avatar control"

description: The dataset associated with the publication: "A high-performance neuroprosthesis for speech decoding and avatar control" . Please use the most recently available version of the deposition instead of this version. Please note that the LICENSE file from version 1.1.0 of this deposition applies to all of the contents of this version as well. By accessing and downloading files from this version of the deposition, you are agreeing to the terms of the LICENSE file in version 1.1.0.
DOI: 10.5281/zenodo.8311964
title: falco_jugger_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8311963
title: falco_jugger_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8309975
title: Genomic Answers for Kids pangenome graph and allele definitions

description: This publication contains the Genomic Answer for Kids genome graph, the observes alleles and their frequencies. Included is a short document describing how to generate the graph, genotype samples, merge genotypes and identify singleton SVs. Related information such as assembly contig sizes, assembly intervals validated with Flagger, sequencing depth and repeat masking results are also included. Miscellaneous scripts that process and generate some of this data is also included. However, the assemblies and the genotypes, of each assembly, or any combination of identifying information cannot be included.
DOI: 10.5281/zenodo.8309976
title: Genomic Answers for Kids pangenome graph and allele definitions

description: This publication contains the Genomic Answer for Kids genome graph, the observes alleles and their frequencies. Included is a short document describing how to generate the graph, genotype samples, merge genotypes and identify singleton SVs. Related information such as assembly contig sizes, assembly intervals validated with Flagger, sequencing depth and repeat masking results are also included. Miscellaneous scripts that process and generate some of this data is also included. However, the assemblies and the genotypes, of each assembly, or any combination of identifying information cannot be included.
DOI: 10.5281/zenodo.8311983
title: falco_rupicolus_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8311982
title: falco_rupicolus_zanfona_1.fasta.gz

description: .
DOI: 10.5517/ccdc.csd.cc288st5
title: CCDC 2093827: Experimental Crystal Structure Determination

description: Related Article: Yu Kawamata, Keun Ah Ryu, Gary N. Hermann, Alexander Sandahl, Julien C. Vantourout, Aleksandra K. Olow, La-Tonya A. Adams, Eva Rivera-Chao, Lee R. Roberts, Samer Gnaim, Molhm Nassir, Rob C. Oslund, Olugbeminiyi O. Fadeyi, Phil S. Baran|2023|Nature Chemistry|15|1267|doi:10.1038/s41557-023-01240-y
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.cc2ddbdk
title: CCDC 2216388: Experimental Crystal Structure Determination

description: Related Article: Abigail Cousino, Lanka D. Wickramasinghe, Widana Kaushalya, S. Sameera Perera, Habib Baydoun, Alice R. Walker, Cláudio N. Verani|2023|J.Phys.Chem.C|127|16654|doi:10.1021/acs.jpcc.3c03616
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.cc2dftth
title: CCDC 2217827: Experimental Crystal Structure Determination

description: Related Article: Abigail Cousino, Lanka D. Wickramasinghe, Widana Kaushalya, S. Sameera Perera, Habib Baydoun, Alice R. Walker, Cláudio N. Verani|2023|J.Phys.Chem.C|127|16654|doi:10.1021/acs.jpcc.3c03616
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: 10.5281/zenodo.8311993
title: falco_sparverius_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8311992
title: falco_sparverius_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8312001
title: falco_subbuteo_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8312000
title: falco_subbuteo_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8312013
title: ibycter_americanus_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8312012
title: ibycter_americanus_zanfona_1.fasta.gz

description: .
DOI: 10.17909/2mqc-ff85
title: GJ3470b FUV Transit

description: FUV transit spectra of exoplanet GJ 3470b using HST/STIS and HST/COS instruments.
DOI: 10.5281/zenodo.8312020
title: micrastur_ruficollis_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8312019
title: micrastur_ruficollis_zanfona_1.fasta.gz

description: .
DOI: 10.17909/cd9k-xv08
title: HAT-P-11b FUV Transit

description: FUV spectra of HAT-P-11b transit using HST/STIS and HST/COS instruments
DOI: 10.5281/zenodo.8312029
title: falco_zoniventris_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8312028
title: falco_zoniventris_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8312045
title: Original dataset of the study entitled Effects of trabectedin on the hepatic metabolism of adult zebrafish Danio rerio

description: Original chromatograms (.qgd files) and normalized peak areas of the annotaded metabolites (.csv file)