cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6078278
title: Distinct mechanistic responses to replication fork stalling induced by either nucleotide or protein deprivation

description: Incidents that slow or stall replication fork progression, collectively known as replication stress, represent a major source of spontaneous genomic instability. Here, we determine the requirement for global protein biosynthesis on DNA replication and associated downstream signaling. We study this response side by side with dNTP deprivation; one of the most commonly used means to investigate replication arrest and replicative stress. Our <i>in vitro</i> interrogations reveal that inhibition of translation by cycloheximide (CHX) rapidly impairs replication fork progression without decoupling helicase and polymerase activities or inducing DNA damage. In line with this, protein deprivation stress does not activate checkpoint signaling. In contrast to the direct link between insufficient dNTP pools and genome instability, our findings suggest that replication forks remain stable during short-term protein deficiency. We find that replication forks initially endure fluctuations in protein supply in order to efficiently resume DNA synthesis upon reversal of the induced protein deprivation stress. These results reveal distinct cellular responses to replication arrest induced by deprivation of either nucleotides or proteins.
DOI: 10.6084/m9.figshare.6078278.v1
title: Distinct mechanistic responses to replication fork stalling induced by either nucleotide or protein deprivation

description: Incidents that slow or stall replication fork progression, collectively known as replication stress, represent a major source of spontaneous genomic instability. Here, we determine the requirement for global protein biosynthesis on DNA replication and associated downstream signaling. We study this response side by side with dNTP deprivation; one of the most commonly used means to investigate replication arrest and replicative stress. Our <i>in vitro</i> interrogations reveal that inhibition of translation by cycloheximide (CHX) rapidly impairs replication fork progression without decoupling helicase and polymerase activities or inducing DNA damage. In line with this, protein deprivation stress does not activate checkpoint signaling. In contrast to the direct link between insufficient dNTP pools and genome instability, our findings suggest that replication forks remain stable during short-term protein deficiency. We find that replication forks initially endure fluctuations in protein supply in order to efficiently resume DNA synthesis upon reversal of the induced protein deprivation stress. These results reveal distinct cellular responses to replication arrest induced by deprivation of either nucleotides or proteins.
DOI: 10.6084/m9.figshare.6078008
title: A Distributed Estimation Method over Network Based on Compressed Sensing

description: A Distributed Estimation Method over Network Based on Compressed Sensing <br>
DOI: 10.6084/m9.figshare.6078008.v1
title: A Distributed Estimation Method over Network Based on Compressed Sensing

description: A Distributed Estimation Method over Network Based on Compressed Sensing <br>
DOI: 10.6084/m9.figshare.6077801
title: Additional file 4: of The integrated stress response regulates BMP signalling through effects on translation

description: Tables S1â S15. Analysis of transcriptional data. Table S1. mRNAs induced in S2 cells expressing HA-crc for 3 h. Table S2. mRNAs induced in S2 cells expressing HA-crc for 6 h. Table S3. mRNAs repressed in S2 cells expressing HA-crc for 3 h. Table S4. mRNAs repressed in S2 cells expressing HA-crc for 6 h. Table S5. Gene Ontology (GO) term enrichment of mRNAs induced in S2 cells expressing HA-crc for 3 h. Table S6. GO term enrichment of mRNAs induced in S2 cells expressing HA-crc for 6 h. Table S7. GO term enrichment of mRNAs repressed in S2 cells expressing HA-crc for 3 h. Table S8. GO term enrichment of mRNAs repressed in S2 cells expressing HA-crc for 6 h. Table S9. mRNAs induced in S2 cells expressing dGCN2-CA-V5 for 6 h. Table S10. mRNAs induced in S2 cells expressing dGCN2-CA-V5 for 12 h. Table S11. mRNAs repressed in S2 cells expressing dGCN2-CA-V5 for 12 h. Table S12. mRNAs repressed in S2 cells expressing dGCN2-CA-V5 for 12 h. Table S13. GO term enrichment of mRNAs induced in S2 cells expressing dGCN2-CA-V5 for 6 h. Table S14. GO term enrichment of mRNAs induced in S2 cells expressing dGCN2-CA-V5 for 12 h. Table S15. GO term enrichment of mRNAs repressed in S2 cells expressing dGCN2-CA-V5 for 12 h. (XLSX 284 kb)
DOI: 10.6084/m9.figshare.6077801.v1
title: Additional file 4: of The integrated stress response regulates BMP signalling through effects on translation

description: Tables S1â S15. Analysis of transcriptional data. Table S1. mRNAs induced in S2 cells expressing HA-crc for 3 h. Table S2. mRNAs induced in S2 cells expressing HA-crc for 6 h. Table S3. mRNAs repressed in S2 cells expressing HA-crc for 3 h. Table S4. mRNAs repressed in S2 cells expressing HA-crc for 6 h. Table S5. Gene Ontology (GO) term enrichment of mRNAs induced in S2 cells expressing HA-crc for 3 h. Table S6. GO term enrichment of mRNAs induced in S2 cells expressing HA-crc for 6 h. Table S7. GO term enrichment of mRNAs repressed in S2 cells expressing HA-crc for 3 h. Table S8. GO term enrichment of mRNAs repressed in S2 cells expressing HA-crc for 6 h. Table S9. mRNAs induced in S2 cells expressing dGCN2-CA-V5 for 6 h. Table S10. mRNAs induced in S2 cells expressing dGCN2-CA-V5 for 12 h. Table S11. mRNAs repressed in S2 cells expressing dGCN2-CA-V5 for 12 h. Table S12. mRNAs repressed in S2 cells expressing dGCN2-CA-V5 for 12 h. Table S13. GO term enrichment of mRNAs induced in S2 cells expressing dGCN2-CA-V5 for 6 h. Table S14. GO term enrichment of mRNAs induced in S2 cells expressing dGCN2-CA-V5 for 12 h. Table S15. GO term enrichment of mRNAs repressed in S2 cells expressing dGCN2-CA-V5 for 12 h. (XLSX 284 kb)
DOI: 10.6084/m9.figshare.6077780
title: Additional file 4: of Proteomic analysis of adipose tissue during the last weeks of gestation in pure and crossbred Large White or Meishan fetuses gestated by sows of either breed

description: Mass parameters for protein identities. (XLS 474 kb)
DOI: 10.6084/m9.figshare.6077780.v1
title: Additional file 4: of Proteomic analysis of adipose tissue during the last weeks of gestation in pure and crossbred Large White or Meishan fetuses gestated by sows of either breed

description: Mass parameters for protein identities. (XLS 474 kb)
DOI: 10.6084/m9.figshare.6077648
title: MOESM7 of Genome-wide analysis of gene regulation mechanisms during Drosophila spermatogenesis

description: Additional file 7: Table 2. Direct and indirect gene targets of the proteins studied. Direct gene targets are defined as the genes that have a significant peak of a given protein within 1Â kb of their TSSs and showing at least eightfold down-regulation in the corresponding mutant. Genes showing reduced expression but lacking detectable protein factor binding within such distance are referred to as indirect targets. Primary data on protein binding and expression are shown in the worksheets.
DOI: 10.6084/m9.figshare.6077648.v1
title: MOESM7 of Genome-wide analysis of gene regulation mechanisms during Drosophila spermatogenesis

description: Additional file 7: Table 2. Direct and indirect gene targets of the proteins studied. Direct gene targets are defined as the genes that have a significant peak of a given protein within 1Â kb of their TSSs and showing at least eightfold down-regulation in the corresponding mutant. Genes showing reduced expression but lacking detectable protein factor binding within such distance are referred to as indirect targets. Primary data on protein binding and expression are shown in the worksheets.
DOI: 10.6084/m9.figshare.6077618
title: MOESM5 of Genome-wide analysis of gene regulation mechanisms during Drosophila spermatogenesis

description: Additional file 5: Table 1. The lists of testis- and ovary-specifically expressed genes used in this study.
DOI: 10.6084/m9.figshare.6077618.v1
title: MOESM5 of Genome-wide analysis of gene regulation mechanisms during Drosophila spermatogenesis

description: Additional file 5: Table 1. The lists of testis- and ovary-specifically expressed genes used in this study.
DOI: 10.6084/m9.figshare.6077600
title: Additional file 2: of The association between circulating adiponectin levels, lung function and adiposity in subjects from the general population; data from the Akershus Sleep Apnea Project

description: Dataset. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.6077600.v1
title: Additional file 2: of The association between circulating adiponectin levels, lung function and adiposity in subjects from the general population; data from the Akershus Sleep Apnea Project

description: Dataset. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.6077588
title: MOESM7 of Engineering of E. coli inherent fatty acid biosynthesis capacity to increase octanoic acid production

description: Additional file 7. GAMS compatible files for the iAF1260 model and the OptForce code.
DOI: 10.6084/m9.figshare.6077588.v1
title: MOESM7 of Engineering of E. coli inherent fatty acid biosynthesis capacity to increase octanoic acid production

description: Additional file 7. GAMS compatible files for the iAF1260 model and the OptForce code.
DOI: 10.6084/m9.figshare.6077555
title: MOESM5 of Engineering of E. coli inherent fatty acid biosynthesis capacity to increase octanoic acid production

description: Additional file 5: Table S2. Primers and sequence used in this study.
DOI: 10.6084/m9.figshare.6077555.v1
title: MOESM5 of Engineering of E. coli inherent fatty acid biosynthesis capacity to increase octanoic acid production

description: Additional file 5: Table S2. Primers and sequence used in this study.
DOI: 10.6084/m9.figshare.6077489
title: MOESM1 of Engineering of E. coli inherent fatty acid biosynthesis capacity to increase octanoic acid production

description: Additional file 1: Table S1. The simulations predicted by the iAF1260 genome-scale metabolic model of E. coli.
DOI: 10.6084/m9.figshare.6077489.v1
title: MOESM1 of Engineering of E. coli inherent fatty acid biosynthesis capacity to increase octanoic acid production

description: Additional file 1: Table S1. The simulations predicted by the iAF1260 genome-scale metabolic model of E. coli.
DOI: 10.6084/m9.figshare.6077468
title: MOESM2 of Streamlined, PCR-based testing for pfhrp2- and pfhrp3-negative Plasmodium falciparum

description: Additional file 2. FASTA file containing Sanger sequences of amplicons produced by pfhrp2/3 exon 1/2 assays when applied to Dd2 (pfhrp2-negative), HB3 (pfhrp3-negative), and 3D7 (pfhrp2/3-positive) DNA
DOI: 10.6084/m9.figshare.6077468.v1
title: MOESM2 of Streamlined, PCR-based testing for pfhrp2- and pfhrp3-negative Plasmodium falciparum

description: Additional file 2. FASTA file containing Sanger sequences of amplicons produced by pfhrp2/3 exon 1/2 assays when applied to Dd2 (pfhrp2-negative), HB3 (pfhrp3-negative), and 3D7 (pfhrp2/3-positive) DNA
DOI: 10.6084/m9.figshare.6077450
title: Additional file 5: of A statistical approach to identify, monitor, and manage incomplete curated data sets

description: The Excel file which includes model results and data analysis results. (XLSX 8346 kb)
DOI: 10.6084/m9.figshare.6077450.v1
title: Additional file 5: of A statistical approach to identify, monitor, and manage incomplete curated data sets

description: The Excel file which includes model results and data analysis results. (XLSX 8346 kb)
DOI: 10.6084/m9.figshare.6077438
title: Additional file 4: of A statistical approach to identify, monitor, and manage incomplete curated data sets

description: The ConstructComponents.txt file. (TXT 1807 kb)
DOI: 10.6084/m9.figshare.6077438.v1
title: Additional file 4: of A statistical approach to identify, monitor, and manage incomplete curated data sets

description: The ConstructComponents.txt file. (TXT 1807 kb)
DOI: 10.6084/m9.figshare.6077429
title: MOESM15 of Genome-wide analysis of gene regulation mechanisms during Drosophila spermatogenesis

description: Additional file 15: Table 4. The list of 28 genes that display substantially reduced expression in testes of CG9879-null males.
DOI: 10.6084/m9.figshare.6077429.v1
title: MOESM15 of Genome-wide analysis of gene regulation mechanisms during Drosophila spermatogenesis

description: Additional file 15: Table 4. The list of 28 genes that display substantially reduced expression in testes of CG9879-null males.
DOI: 10.6084/m9.figshare.6077426
title: Additional file 3: of A statistical approach to identify, monitor, and manage incomplete curated data sets

description: The GenePublication.txt file. (TXT 22006 kb)
DOI: 10.6084/m9.figshare.6077426.v1
title: Additional file 3: of A statistical approach to identify, monitor, and manage incomplete curated data sets

description: The GenePublication.txt file. (TXT 22006 kb)
DOI: 10.6084/m9.figshare.6077414
title: Additional file 2: of A statistical approach to identify, monitor, and manage incomplete curated data sets

description: The MachineLearningReport.txt file. (TXT 2317 kb)
DOI: 10.6084/m9.figshare.6077414.v1
title: Additional file 2: of A statistical approach to identify, monitor, and manage incomplete curated data sets

description: The MachineLearningReport.txt file. (TXT 2317 kb)
DOI: 10.6084/m9.figshare.6077390
title: Additional file 9: of Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil

description: Table S8. Library sizes. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.6077390.v1
title: Additional file 9: of Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil

description: Table S8. Library sizes. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.6077369
title: Additional file 8: of Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil

description: Table S7. Result of PERMANOVA analysis. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.6077369.v1
title: Additional file 8: of Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil

description: Table S7. Result of PERMANOVA analysis. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.6077351
title: Additional file 7: of Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil

description: Table S6. Level of polycyclic aromatic hydrocarbon (PAH) metabolites in fish bile samples measured by gas chromatography mass spectrometry (GC-MS). (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.6077351.v1
title: Additional file 7: of Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil

description: Table S6. Level of polycyclic aromatic hydrocarbon (PAH) metabolites in fish bile samples measured by gas chromatography mass spectrometry (GC-MS). (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.6077345
title: MOESM11 of Genome-wide analysis of gene regulation mechanisms during Drosophila spermatogenesis

description: Additional file 11: Table 3. Interplay between meiosis arrest genes. tMAC does not affect the expression of genes encoding tTAFs. Can mutation results in reduced expression of topi, achi, and vis. Additionally, Can peaks are detectable in the immediate vicinity of TSSs of these genes.
DOI: 10.6084/m9.figshare.6077345.v1
title: MOESM11 of Genome-wide analysis of gene regulation mechanisms during Drosophila spermatogenesis

description: Additional file 11: Table 3. Interplay between meiosis arrest genes. tMAC does not affect the expression of genes encoding tTAFs. Can mutation results in reduced expression of topi, achi, and vis. Additionally, Can peaks are detectable in the immediate vicinity of TSSs of these genes.
DOI: 10.6084/m9.figshare.6077339
title: Additional file 6: of Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil

description: Table S5. Level of polycyclic aromatic hydrocarbon (PAH) metabolites in fish bile samples measured by fixed fluorescence (FF). (XLSX 8Â kb)
DOI: 10.6084/m9.figshare.6077339.v1
title: Additional file 6: of Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil

description: Table S5. Level of polycyclic aromatic hydrocarbon (PAH) metabolites in fish bile samples measured by fixed fluorescence (FF). (XLSX 8Â kb)
DOI: 10.6084/m9.figshare.6077324
title: Additional file 5: of Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil

description: Table S4. Condition indices (CI) and hepatosomatic indices (HSI) of oil exposed Atlantic cod specimens. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.6077324.v1
title: Additional file 5: of Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil

description: Table S4. Condition indices (CI) and hepatosomatic indices (HSI) of oil exposed Atlantic cod specimens. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.6077303
title: Additional file 4: of Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil

description: Table S3. Polycyclic aromatic hydrocarbon (PAH) content of oil dispersion in header tank. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6077303.v1
title: Additional file 4: of Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil

description: Table S3. Polycyclic aromatic hydrocarbon (PAH) content of oil dispersion in header tank. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6077294
title: Additional file 3: of Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil

description: Table S2. Composition of Troll C crude oil. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6077294.v1
title: Additional file 3: of Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil

description: Table S2. Composition of Troll C crude oil. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6077291
title: MOESM8 of Characterization of a novel sugar transporter involved in sugarcane bagasse degradation in Trichoderma reesei

description: Additional file 8. INTERACTION PROFILE: the detailed amount of energy required for each atom in the protein to interact with each one of the ligands, through hydrogen bonding (H) and Van der Waals contact (V).
DOI: 10.6084/m9.figshare.6077291.v1
title: MOESM8 of Characterization of a novel sugar transporter involved in sugarcane bagasse degradation in Trichoderma reesei

description: Additional file 8. INTERACTION PROFILE: the detailed amount of energy required for each atom in the protein to interact with each one of the ligands, through hydrogen bonding (H) and Van der Waals contact (V).
DOI: 10.6084/m9.figshare.6077279
title: Additional file 2: of Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil

description: Table S1. Primer and barcode sequences. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.6077279.v1
title: Additional file 2: of Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil

description: Table S1. Primer and barcode sequences. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.6077276
title: MOESM7 of Characterization of a novel sugar transporter involved in sugarcane bagasse degradation in Trichoderma reesei

description: Additional file 7. LOCAL ACCURACY: the divergence of the modeling represented by the distance (Å) between the protein designed and the template used for the construction of it. RES: residue number; SS: predicted secondary structure (C: random coil, H: alpha-helix, S: beta-strand; SA: predicted solvent accessibility at 25% cutoff (E: exposed, B: buried); COV: alignment coverage; BFP: predicted normalized B-factor; RSQ_1: Residue-Specific Quality of the template (the estimated deviation of the residue on the template from the built protein)).
DOI: 10.6084/m9.figshare.6077276.v1
title: MOESM7 of Characterization of a novel sugar transporter involved in sugarcane bagasse degradation in Trichoderma reesei

description: Additional file 7. LOCAL ACCURACY: the divergence of the modeling represented by the distance (Å) between the protein designed and the template used for the construction of it. RES: residue number; SS: predicted secondary structure (C: random coil, H: alpha-helix, S: beta-strand; SA: predicted solvent accessibility at 25% cutoff (E: exposed, B: buried); COV: alignment coverage; BFP: predicted normalized B-factor; RSQ_1: Residue-Specific Quality of the template (the estimated deviation of the residue on the template from the built protein)).
DOI: 10.6084/m9.figshare.6077273
title: Additional file 3: of The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool

description: OTU table bacteria. This file contains the OTU table of the bacterial community that was generated as described in the â Methodsâ section and that was used for further analyses and creation of some of the figures. This file is to be published online as Supporting Information. (CSV 568Â kb)
DOI: 10.6084/m9.figshare.6077273.v1
title: Additional file 3: of The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool

description: OTU table bacteria. This file contains the OTU table of the bacterial community that was generated as described in the â Methodsâ section and that was used for further analyses and creation of some of the figures. This file is to be published online as Supporting Information. (CSV 568Â kb)
DOI: 10.6084/m9.figshare.6077255
title: MOESM6 of Characterization of a novel sugar transporter involved in sugarcane bagasse degradation in Trichoderma reesei

description: Additional file 6. SCORING FUNCTIONS: the global accuracy for the five designed candidates. The chosen structure was the Model 1, which was predicted based on the 4ZWB.A (human GLUT3 glucose transporter (N45T mutant) with bound d-glucose, outward-occluded conformation), determined by Deng et al. [39], since it presents not only the highest value for C-score, but also satisfactory values for the TM-score and the RMSD, also being the largest cluster. C-score: the confidence of the construction essentially based on the template alignments and the parameters for assembling the structure, whereas the higher the value, the higher the confidence and quality. TM-Score and RMSD: the similarity between the designed model and the template used, being less and more sensitive to local error, respectively. TM-score &gt; 0.5 indicates a correct topology. Number of decoys: the amount of conformations generated by the software. Cluster density: the size of the clusters formed for each model, whereas the larger the cluster, the lowest the free energy of the model.
DOI: 10.6084/m9.figshare.6077255.v1
title: MOESM6 of Characterization of a novel sugar transporter involved in sugarcane bagasse degradation in Trichoderma reesei

description: Additional file 6. SCORING FUNCTIONS: the global accuracy for the five designed candidates. The chosen structure was the Model 1, which was predicted based on the 4ZWB.A (human GLUT3 glucose transporter (N45T mutant) with bound d-glucose, outward-occluded conformation), determined by Deng et al. [39], since it presents not only the highest value for C-score, but also satisfactory values for the TM-score and the RMSD, also being the largest cluster. C-score: the confidence of the construction essentially based on the template alignments and the parameters for assembling the structure, whereas the higher the value, the higher the confidence and quality. TM-Score and RMSD: the similarity between the designed model and the template used, being less and more sensitive to local error, respectively. TM-score &gt; 0.5 indicates a correct topology. Number of decoys: the amount of conformations generated by the software. Cluster density: the size of the clusters formed for each model, whereas the larger the cluster, the lowest the free energy of the model.