cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11574900
title: Supplementary Tables for the paper 'Causal relationships between blood lipids and depression phenotypes: A Mendelian randomization analysis'

description: Supplementary Tables for the paper <b>'Causal relationships between blood lipids and depression phenotypes: A Mendelian randomization analysis'</b>
DOI: 10.6084/m9.figshare.11574900.v1
title: Supplementary Tables for the paper 'Causal relationships between blood lipids and depression phenotypes: A Mendelian randomization analysis'

description: Supplementary Tables for the paper <b>'Causal relationships between blood lipids and depression phenotypes: A Mendelian randomization analysis'</b>
DOI: 10.6084/m9.figshare.11574726
title: Molecular characterization of a large unselected cohort of metastatic colorectal cancers in relation to primary tumor location, rare metastatic sites and prognosis

description: <b>Background:</b> We have reported that <i>BRAF</i> V600E mutations and microsatellite instability-high (MSI-H) are more prevalent in a population-based cohort of metastatic colorectal cancer (mCRC) patients than has been reported from clinical trials or hospital-based patient groups. The aim was to explore if other mutations in mCRC differ in prevalence between these cohorts in relation to mismatch repair status and primary tumor location and if presence of bone or brain metastases is associated with any mutations. <b>Material and methods:</b> A population-based cohort of 798 mCRC patients from three regions in Scandinavia was used. Forty-four cancer related genes were investigated in a custom designed Ampliseq hotspot panel. Differences in survival were analyzed using the Kaplan–Meier estimator and the Cox regression analysis. <b>Results:</b> Determination of mutations was possible in 449/501 patients for 40/44 genes. Besides <i>BRAF</i> V600E, seen in 19% of the tumors, none of the other mutations appeared more prevalent than in trial cohorts. <i>BRAF</i> V600E and MSI-H, seen in 8%, were associated with poor prognosis as was right-sided primary tumor location (39%) when compared to left-sided and rectum together; however, in a multivariable regression, only the <i>BRAF</i> mutation retained its statistical significance. No other mutations were associated with poor prognosis. ERBB2 alterations were more common if bone metastases were present at diagnosis (17% vs. 4%, <i>p</i> = .011). No association was found for brain metastases. Fifty-two percent had an alteration that is treatable with an FDA-approved targeted therapy, chiefly by EGFR-inhibitor for RAS wild-type and a check-point inhibitor for MSI-H tumors. <b>Conclusions:</b> Right-sided tumor location, <i>BRAF</i> V600E mutations, but no other investigated mutation, and MSI-H are more commonly seen in an unselected cohort than is reported from clinical patient cohorts, likely because they indicate poor prognosis. Half of the patients have a tumor that is treatable with an already FDA-approved targeted drug for mCRC.
DOI: 10.6084/m9.figshare.11574726.v2
title: Molecular characterization of a large unselected cohort of metastatic colorectal cancers in relation to primary tumor location, rare metastatic sites and prognosis

description: <b>Background:</b> We have reported that <i>BRAF</i> V600E mutations and microsatellite instability-high (MSI-H) are more prevalent in a population-based cohort of metastatic colorectal cancer (mCRC) patients than has been reported from clinical trials or hospital-based patient groups. The aim was to explore if other mutations in mCRC differ in prevalence between these cohorts in relation to mismatch repair status and primary tumor location and if presence of bone or brain metastases is associated with any mutations. <b>Material and methods:</b> A population-based cohort of 798 mCRC patients from three regions in Scandinavia was used. Forty-four cancer related genes were investigated in a custom designed Ampliseq hotspot panel. Differences in survival were analyzed using the Kaplan–Meier estimator and the Cox regression analysis. <b>Results:</b> Determination of mutations was possible in 449/501 patients for 40/44 genes. Besides <i>BRAF</i> V600E, seen in 19% of the tumors, none of the other mutations appeared more prevalent than in trial cohorts. <i>BRAF</i> V600E and MSI-H, seen in 8%, were associated with poor prognosis as was right-sided primary tumor location (39%) when compared to left-sided and rectum together; however, in a multivariable regression, only the <i>BRAF</i> mutation retained its statistical significance. No other mutations were associated with poor prognosis. ERBB2 alterations were more common if bone metastases were present at diagnosis (17% vs. 4%, <i>p</i> = .011). No association was found for brain metastases. Fifty-two percent had an alteration that is treatable with an FDA-approved targeted therapy, chiefly by EGFR-inhibitor for RAS wild-type and a check-point inhibitor for MSI-H tumors. <b>Conclusions:</b> Right-sided tumor location, <i>BRAF</i> V600E mutations, but no other investigated mutation, and MSI-H are more commonly seen in an unselected cohort than is reported from clinical patient cohorts, likely because they indicate poor prognosis. Half of the patients have a tumor that is treatable with an already FDA-approved targeted drug for mCRC.
DOI: 10.6084/m9.figshare.11574615
title: MOESM2 of Custom selected reference genes outperform pre-defined reference genes in transcriptomic analysis

description: Additional file 2: Table S1. TAIR IDs of custom selected references for each transcriptome permutation. Table S2. DESeq2 results summary of analysis without reference genes or with different reference sets (Custom selected, from T Czechowski, M Stitt, T Altmann, MK Udvardi and W-R Scheible [26], from B Zhuo, S Emerson, JH Chang and Y Di [11] or Commonly used references). Table presents the number of genes found up- and down-regulated in Table S3 to S5. Summary of the results of several analyses for all the genes evaluated in this article: Column A: TAIR ID; Column B: ranking calculated with geNorm with the function “selectHKs” from the R package “NormqPCR”; Column C: average TPM value; Column D: covariance of the TPM values; Column E: the difference of expression of a gene between two samples calculated with NormFinder; Column F: the common standard deviation of the expression of a gene between two samples calculated with NormFinder; Column G: stability measure from NormFinder; Column H: log2-transformed fold change of each gene calculated with DESeq2 without using reference genes; Column I: adjusted p value of the gene deregulation calculated with DESeq2 without using reference genes; Column J: sources that identified the gene as a reference, when more than one source selected the gene as reference they are separated by a “;”. Table S3. Permutation Mlp37347 vs Control; Table S4. Permutation Mlp124499 vs Control; Table S5. Permutation Mlp124499 vs Mlp37347. Table S6. Metadata of samples used; replicate identification, number of sequenced reads, average length of the separation between two paired reads, number of reads after trimming and filtering and number of aligned reads for each of the 4 replicates of the three samples used in this study.
DOI: 10.6084/m9.figshare.11574543
title: MOESM4 of Compensating for over-production inhibition of the Hsmar1 transposon in Escherichia coli using a series of constitutive promoters

description: Additional file 4: Table S3. Number of GFP positive cells in the flow cytometry experiments.
DOI: 10.6084/m9.figshare.11574543.v1
title: MOESM4 of Compensating for over-production inhibition of the Hsmar1 transposon in Escherichia coli using a series of constitutive promoters

description: Additional file 4: Table S3. Number of GFP positive cells in the flow cytometry experiments.
DOI: 10.6084/m9.figshare.11574513
title: MOESM1 of Molecular diversity of Bulinus species in Madziwa area, Shamva district in Zimbabwe: implications for urogenital schistosomiasis transmission

description: Additional file 1: Table S1. List of sequences drawn from the Genbank incorporated for phylogenetic analysis. Table S2. Fst values for B. globosus populations. Table S3. Accession numbers of individual sequences for the haplotypes recorded in Madziwa, Zimbabwe.
DOI: 10.6084/m9.figshare.11574513.v1
title: MOESM1 of Molecular diversity of Bulinus species in Madziwa area, Shamva district in Zimbabwe: implications for urogenital schistosomiasis transmission

description: Additional file 1: Table S1. List of sequences drawn from the Genbank incorporated for phylogenetic analysis. Table S2. Fst values for B. globosus populations. Table S3. Accession numbers of individual sequences for the haplotypes recorded in Madziwa, Zimbabwe.
DOI: 10.6084/m9.figshare.11574444
title: MOESM1 of A microRNA signature of toxic extrasynaptic N-methyl-D-aspartate (NMDA) receptor signaling

description: Additional file 1. miRNA microArray results.
DOI: 10.6084/m9.figshare.11574444.v1
title: MOESM1 of A microRNA signature of toxic extrasynaptic N-methyl-D-aspartate (NMDA) receptor signaling

description: Additional file 1. miRNA microArray results.
DOI: 10.6084/m9.figshare.11574267
title: MOESM2 of VGF-derived peptide TLQP-21 modulates microglial function through C3aR1 signaling pathways and reduces neuropathology in 5xFAD mice

description: Additional file 2: Table S2. Canonical Pathways and other analyses generated by the Ingenuity Pathway Analysis (IPA) software for the C3aR1 vs WT comparison.
DOI: 10.6084/m9.figshare.11574267.v1
title: MOESM2 of VGF-derived peptide TLQP-21 modulates microglial function through C3aR1 signaling pathways and reduces neuropathology in 5xFAD mice

description: Additional file 2: Table S2. Canonical Pathways and other analyses generated by the Ingenuity Pathway Analysis (IPA) software for the C3aR1 vs WT comparison.
DOI: 10.6084/m9.figshare.11574258
title: MOESM1 of VGF-derived peptide TLQP-21 modulates microglial function through C3aR1 signaling pathways and reduces neuropathology in 5xFAD mice

description: Additional file 1: Table S1. List of Differential Expressed Genes (DEGs) for the following comparisons: C3aR1 vs WT, C3aR1+TLQP-21 vs WT and C3aR1+C3aSA vs WT. DEGs have been sorted depending on whether they are down- or up-regulated.
DOI: 10.6084/m9.figshare.11574258.v1
title: MOESM1 of VGF-derived peptide TLQP-21 modulates microglial function through C3aR1 signaling pathways and reduces neuropathology in 5xFAD mice

description: Additional file 1: Table S1. List of Differential Expressed Genes (DEGs) for the following comparisons: C3aR1 vs WT, C3aR1+TLQP-21 vs WT and C3aR1+C3aSA vs WT. DEGs have been sorted depending on whether they are down- or up-regulated.
DOI: 10.6084/m9.figshare.11574249
title: MOESM4 of Transcriptome analysis defines myocardium gene signatures in children with ToF and ASD and reveals disease-specific molecular reprogramming in response to surgery with cardiopulmonary bypass

description: Additional file 4: Table S3. Differentially expressed probe sets in Post-CPB vs Pre-CPB right atrial samples from ASD patients.
DOI: 10.6084/m9.figshare.11574246
title: MOESM3 of Transcriptome analysis defines myocardium gene signatures in children with ToF and ASD and reveals disease-specific molecular reprogramming in response to surgery with cardiopulmonary bypass

description: Additional file 3: Table S2. Differentially expressed probe sets in Post-CPB vs Pre-CPB right atrial samples from ToF patients.
DOI: 10.6084/m9.figshare.11574249.v1
title: MOESM4 of Transcriptome analysis defines myocardium gene signatures in children with ToF and ASD and reveals disease-specific molecular reprogramming in response to surgery with cardiopulmonary bypass

description: Additional file 4: Table S3. Differentially expressed probe sets in Post-CPB vs Pre-CPB right atrial samples from ASD patients.
DOI: 10.6084/m9.figshare.11574246.v1
title: MOESM3 of Transcriptome analysis defines myocardium gene signatures in children with ToF and ASD and reveals disease-specific molecular reprogramming in response to surgery with cardiopulmonary bypass

description: Additional file 3: Table S2. Differentially expressed probe sets in Post-CPB vs Pre-CPB right atrial samples from ToF patients.
DOI: 10.6084/m9.figshare.11574234
title: MOESM1 of Transcriptome analysis defines myocardium gene signatures in children with ToF and ASD and reveals disease-specific molecular reprogramming in response to surgery with cardiopulmonary bypass

description: Additional file 1: Table S1. Differentially expressed probe sets in TOF vs ASD right atrial samples.
DOI: 10.6084/m9.figshare.11574234.v1
title: MOESM1 of Transcriptome analysis defines myocardium gene signatures in children with ToF and ASD and reveals disease-specific molecular reprogramming in response to surgery with cardiopulmonary bypass

description: Additional file 1: Table S1. Differentially expressed probe sets in TOF vs ASD right atrial samples.
DOI: 10.6084/m9.figshare.11574210
title: MOESM4 of Expanding our view of Bartonella and its hosts: Bartonella in nest ectoparasites and their migratory avian hosts

description: Additional file 4: Table S4. BICc ranking of nucleotide substitution models for the gltA tree.
DOI: 10.6084/m9.figshare.11574210.v1
title: MOESM4 of Expanding our view of Bartonella and its hosts: Bartonella in nest ectoparasites and their migratory avian hosts

description: Additional file 4: Table S4. BICc ranking of nucleotide substitution models for the gltA tree.
DOI: 10.6084/m9.figshare.11574201
title: MOESM3 of Expanding our view of Bartonella and its hosts: Bartonella in nest ectoparasites and their migratory avian hosts

description: Additional file 3: Table S3. BICc ranking of nucleotide substitution models for the 16S rRNA tree.
DOI: 10.6084/m9.figshare.11574201.v1
title: MOESM3 of Expanding our view of Bartonella and its hosts: Bartonella in nest ectoparasites and their migratory avian hosts

description: Additional file 3: Table S3. BICc ranking of nucleotide substitution models for the 16S rRNA tree.
DOI: 10.6084/m9.figshare.11574192
title: MOESM1 of Expanding our view of Bartonella and its hosts: Bartonella in nest ectoparasites and their migratory avian hosts

description: Additional file 1: Table S1. BLASTn analysis of ASVs identified as Bartonella spp. in this study.
DOI: 10.6084/m9.figshare.11574195
title: MOESM2 of Expanding our view of Bartonella and its hosts: Bartonella in nest ectoparasites and their migratory avian hosts

description: Additional file 2: Table S2. Sequences obtained from GenBank and used in phylogenetic trees.
DOI: 10.6084/m9.figshare.11574195.v1
title: MOESM2 of Expanding our view of Bartonella and its hosts: Bartonella in nest ectoparasites and their migratory avian hosts

description: Additional file 2: Table S2. Sequences obtained from GenBank and used in phylogenetic trees.
DOI: 10.6084/m9.figshare.11574192.v1
title: MOESM1 of Expanding our view of Bartonella and its hosts: Bartonella in nest ectoparasites and their migratory avian hosts

description: Additional file 1: Table S1. BLASTn analysis of ASVs identified as Bartonella spp. in this study.
DOI: 10.6084/m9.figshare.11574150
title: MOESM1 of Highly specific PCR-RFLP assays for karyotyping the widespread 2Rb inversion in malaria vectors of the Anopheles gambiae complex

description: Additional file 1: Table S1. Detailed genotypic concordance between cytological karyotype and individual PCR-RFLP genotyping assay.
DOI: 10.6084/m9.figshare.11573880
title: Lehallier-AgingProteome-SupplementaryTables-Proteomicsdata011020.xlsx

description: Human and mouse aging plasma proteome
DOI: 10.6084/m9.figshare.11573499
title: Prisoner's Dilemma data

description: This fileset contains data from the study entitled, "Effects of episodic simulation and gender on cooperative behaviour in the Prisoner’s Dilemma" and submitted to the Journal of Experimental Social Psychology for publication. The study involves an experiment in which 120 undergraduates played the Prisoner's Dilemma game after either imagining helping their game partner in a situation of need (imagine condition) or performing a filler task (words/baseline condition). The gender of participants' game partner (a computer algorithm disguised as a human) was also manipulated. Details about each variable can be found in the pd_vars.txt file.<br>
DOI: 10.6084/m9.figshare.11573403
title: CEAP-Stack gas concentrations, 2014-2017

description: This dataset provides plant-level information on absolute emissions, fuel uses, generating capacities, geographic locations, etc. <br>
DOI: 10.6084/m9.figshare.11573412
title: CEAP-Absolute emissions, 2014-2017

description: This dataset provides plant-level information on absolute emissions, fuel uses, generating capacities, geographic locations, etc. <br>
DOI: 10.6084/m9.figshare.11573412.v1
title: CEAP-Absolute Emissions, 2014-2017

description: This dataset provides plant-level information on absolute emissions, fuel uses, generating capacities, geographic locations, etc. <br>
DOI: 10.6084/m9.figshare.11573403.v1
title: CEAP-Pollution concentrations, 2014-2017

description: This dataset provides plant-level information on absolute emissions, fuel uses, generating capacities, geographic locations, etc. <br>
DOI: 10.6084/m9.figshare.11573412.v2
title: CEAP-Absolute emissions, 2014-2017

description: This dataset provides plant-level information on absolute emissions, fuel uses, generating capacities, geographic locations, etc. <br>
DOI: 10.6084/m9.figshare.11573403.v2
title: CEAP-Stack gas concentrations, 2014-2017

description: This dataset provides plant-level information on absolute emissions, fuel uses, generating capacities, geographic locations, etc. <br>
DOI: 10.6084/m9.figshare.11573397
title: CEAP-Summary descriptions, 2014–2017

description: This dataset provides plant-level information on absolute emissions, fuel uses, generating capacities, geographic locations, etc.
DOI: 10.6084/m9.figshare.11573397.v1
title: CEAP-Summary descriptions, 2014–2017

description: This dataset provides plant-level information on absolute emissions, fuel uses, generating capacities, geographic locations, etc.
DOI: 10.6084/m9.figshare.11573397.v2
title: CEAP-Summary descriptions, 2014–2017

description: This dataset provides plant-level information on absolute emissions, fuel uses, generating capacities, geographic locations, etc.
DOI: 10.6084/m9.figshare.11569533
title: Consensus of best practice in intrauterine contraception in France

description: <b>Objective:</b> Our aim was to provide a consensus of best practice in intrauterine contraception (IUC) for French practitioners. <b>Methods:</b> A meeting of 38 gynaecologists was held to establish a consensus of best practice in IUC, using the validated nominal group (NG) method to reach consensus. Seventy questions were posed covering insertion, monitoring and removal of IUC devices. Two working groups were formed and all proposals were voted on, discussed and approved by the NG. <b>Results:</b> Of the 70 questions asked, answers to only four failed to reach NG consensus. While, in general, the IUC practices of French gynaecologists are in line with international guidelines, some notable differences were identified: for example, when to use the levonorgestrel-releasing intrauterine system versus the copper intrauterine device; practice recommendations in the event of upper genital tract infections; and immediate postpartum insertion. Clinicians are encouraged to inform women about IUC, irrespective of their age or parity. In general, the wishes and characteristics of the woman must be the main criteria informing the choice of IUC, once all potential contraindications have been excluded and information about IUC shared. <b>Conclusions:</b> This consensus paper is intended to update and standardise knowledge about IUC for health care professionals, to address any reticence about use of this contraceptive method.
DOI: 10.6084/m9.figshare.11569533.v1
title: Consensus of best practice in intrauterine contraception in France

description: <b>Objective:</b> Our aim was to provide a consensus of best practice in intrauterine contraception (IUC) for French practitioners. <b>Methods:</b> A meeting of 38 gynaecologists was held to establish a consensus of best practice in IUC, using the validated nominal group (NG) method to reach consensus. Seventy questions were posed covering insertion, monitoring and removal of IUC devices. Two working groups were formed and all proposals were voted on, discussed and approved by the NG. <b>Results:</b> Of the 70 questions asked, answers to only four failed to reach NG consensus. While, in general, the IUC practices of French gynaecologists are in line with international guidelines, some notable differences were identified: for example, when to use the levonorgestrel-releasing intrauterine system versus the copper intrauterine device; practice recommendations in the event of upper genital tract infections; and immediate postpartum insertion. Clinicians are encouraged to inform women about IUC, irrespective of their age or parity. In general, the wishes and characteristics of the woman must be the main criteria informing the choice of IUC, once all potential contraindications have been excluded and information about IUC shared. <b>Conclusions:</b> This consensus paper is intended to update and standardise knowledge about IUC for health care professionals, to address any reticence about use of this contraceptive method.
DOI: 10.6084/m9.figshare.11569461
title: Image_Data

description: H&E images
DOI: 10.6084/m9.figshare.11569437
title: Zebrafish data from alternative models

description: We provide comparative model simulations of wild-type zebrafish patterns generated using two alternative models based off of the agent-based model from "Volkening A and Sandstede B (2018) Iridophores as a source of robustness in zebrafish stripes and variability in Danio patterns. Nat. Commun. 9(3231)." <br>Aternative model I has the following parameter values: B90(Id) = 115 um, B75(Id) = 25 um, Omega-long(Id) = 230 um, B90(Il) = 130 um, B75(ll) = 10 um, and Omega-long(Il) = 190 um, with all other parameters set to the default values in Volkening and Sandstede (2018). Alternative model II was simulated by removing the weak attraction of Xd cells to Id cells from the agent-based model of Volkening and Sandstede (2018). Patterns generated from alternative model II resemble the idefix mutation. All simulations were run in MATLAB, and we run 1000 model simulations per model.<br>Each simulation output contains data in the form of .mat files. Within each .mat file are the cell locations of all cells across the simulation, an array that tracks the distances that the cells moved throughout the simulation, vectors containing the number of cells born/dead/present at each day of the simulation, and the x- and y-boundaries of the domain for each day of the simulations. The cell locations are stored in N X 2 X T arrays, where N is an upper bound on the total number of cells in the simulation, and T is the number of days that the simulation was run for. For example, cellsM(:,:,T) contains the x- and y-coordinates of the melanophore cells on the last day of the simulation. Similarly, cellsIl contains the cell coordinates of the loose iridophores, cellsId contains the cell coordinates of the dense iridophores, cellsXc contains the cell coordinates of the dense xanthophores, and cellsXsn contains the cell coordinates of the loose xanthophores.
DOI: 10.6084/m9.figshare.11569434
title: Appendices

description: This appendix relates to the research paper "How Software Practitioners Use Informal Local Meetups to Share Software Engineering Knowledge"
DOI: 10.6084/m9.figshare.11569434.v1
title: Appendices

description: This appendix relates to the research paper "How Software Practitioners Use Informal Local Meetups to Share Software Engineering Knowledge"
DOI: 10.6084/m9.figshare.11569407
title: Processed_Data

description: Processed data of CyCIF
DOI: 10.6084/m9.figshare.11569407.v1
title: Processed_Data

description: Processed data of CyCIF
DOI: 10.6084/m9.figshare.11569392
title: Processed_Data

description: Processed data of MALDI-TOF