cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6695369.v4
title: Poliovirus induces autophagic signaling independent of the ULK1 complex

description: Poliovirus (PV), like many positive-strand RNA viruses, subverts the macroautophagy/autophagy pathway to promote its own replication. Here, we investigate whether the virus uses the canonical autophagic signaling complex, consisting of the ULK1/2 kinases, ATG13, RB1CC1, and ATG101, to activate autophagy. We find that the virus sends autophagic signals independent of the ULK1 complex, and that the members of the autophagic complex are not required for normal levels of viral replication. We also show that the SQSTM1/p62 receptor protein is not degraded in a conventional manner during infection, but is likely cleaved in a manner similar to that shown for coxsackievirus B3. This means that SQSTM1, normally used to monitor autophagic degradation, cannot be used to accurately monitor degradation during poliovirus infection. In fact, autophagic degradation may be affected by the loss of SQSTM1 at the same time as autophagic signals are being sent. Finally, we demonstrate that ULK1 and ULK2 protein levels are greatly reduced during PV infection, and ATG13, RB1CC1, and ATG101 protein levels are reduced as well. Surprisingly, autophagic signaling appears to increase as ULK1 levels decrease. Overexpression of wild-type or dominant-negative ULK1 constructs does not affect virus replication, indicating that ULK1 degradation may be a side effect of the ULK1-independent signaling mechanism used by PV, inducing complex instability. This demonstration of ULK1-independent autophagic signaling is novel and leads to a model by which the virus is signaling to generate autophagosomes downstream of ULK1, while at the same time, cleaving cargo receptors, which may affect cargo loading and autophagic degradative flux. Our data suggest that PV has a finely-tuned relationship with the autophagic machinery, generating autophagosomes without using the primary autophagy signaling pathway. <b>Abbreviations:</b> ACTB - actin beta; ATG13 - autophagy related 13; ATG14 - autophagy related 14; ATG101 - autophagy related 101; BECN1 - beclin 1; CVB3 - coxsackievirus B3; DMV - double-membraned vesicles; EM - electron microscopy; EMCV - encephalomyocarditis virus; EV-71 - enterovirus 71; FMDV - foot and mouth disease virus; GFP - green fluorescent protein; MAP1LC3B/LC3B - microtubule associated protein 1 light chain 3 beta; MOI - multiplicity of infection; MTOR - mechanistic target of rapamycin kinase; PIK3C3 - phosphatidylinositol 3-kinase catalytic subunit type 3; PRKAA2 - protein kinase AMP-activated catalytic subunit alpha 2; PSMG1 - proteasome assembly chaperone 1; PSMG2 - proteasome assembly chaperone 2PV - poliovirus; RB1CC1 - RB1 inducible coiled-coil 1; SQSTM1 - sequestosome 1; ULK1 - unc-51 like autophagy activating kinase 1; ULK2 - unc-51 like autophagy activating kinase 2; WIPI1 - WD repeat domain, phosphoinositide interacting 1
DOI: 10.6084/m9.figshare.6695369.v3
title: Poliovirus induces autophagic signaling independent of the ULK1 complex

description: Poliovirus (PV), like many positive-strand RNA viruses, subverts the macroautophagy/autophagy pathway to promote its own replication. Here, we investigate whether the virus uses the canonical autophagic signaling complex, consisting of the ULK1/2 kinases, ATG13, RB1CC1, and ATG101, to activate autophagy. We find that the virus sends autophagic signals independent of the ULK1 complex, and that the members of the autophagic complex are not required for normal levels of viral replication. We also show that the SQSTM1/p62 receptor protein is not degraded in a conventional manner during infection, but is likely cleaved in a manner similar to that shown for coxsackievirus B3. This means that SQSTM1, normally used to monitor autophagic degradation, cannot be used to accurately monitor degradation during poliovirus infection. In fact, autophagic degradation may be affected by the loss of SQSTM1 at the same time as autophagic signals are being sent. Finally, we demonstrate that ULK1 and ULK2 protein levels are greatly reduced during PV infection, and ATG13, RB1CC1, and ATG101 protein levels are reduced as well. Surprisingly, autophagic signaling appears to increase as ULK1 levels decrease. Overexpression of wild-type or dominant-negative ULK1 constructs does not affect virus replication, indicating that ULK1 degradation may be a side effect of the ULK1-independent signaling mechanism used by PV, inducing complex instability. This demonstration of ULK1-independent autophagic signaling is novel and leads to a model by which the virus is signaling to generate autophagosomes downstream of ULK1, while at the same time, cleaving cargo receptors, which may affect cargo loading and autophagic degradative flux. Our data suggest that PV has a finely-tuned relationship with the autophagic machinery, generating autophagosomes without using the primary autophagy signaling pathway. <b>Abbreviations:</b> ACTB - actin beta; ATG13 - autophagy related 13; ATG14 - autophagy related 14; ATG101 - autophagy related 101; BECN1 - beclin 1; CVB3 - coxsackievirus B3; DMV - double-membraned vesicles; EM - electron microscopy; EMCV - encephalomyocarditis virus; EV-71 - enterovirus 71; FMDV - foot and mouth disease virus; GFP - green fluorescent protein; MAP1LC3B/LC3B - microtubule associated protein 1 light chain 3 beta; MOI - multiplicity of infection; MTOR - mechanistic target of rapamycin kinase; PIK3C3 - phosphatidylinositol 3-kinase catalytic subunit type 3; PRKAA2 - protein kinase AMP-activated catalytic subunit alpha 2; PSMG1 - proteasome assembly chaperone 1; PSMG2 - proteasome assembly chaperone 2PV - poliovirus; RB1CC1 - RB1 inducible coiled-coil 1; SQSTM1 - sequestosome 1; ULK1 - unc-51 like autophagy activating kinase 1; ULK2 - unc-51 like autophagy activating kinase 2; WIPI1 - WD repeat domain, phosphoinositide interacting 1
DOI: 10.6084/m9.figshare.6695357
title: Additional file 5 of Estimation of delay to diagnosis and incidence in HIV using indirect evidence of infection dates

description: Stan model template file (which is annotated and can be viewed as plain text) to fit the â incidence and delay-to-diagnosisâ model with change in incidence prior to and during observation window. (STAN 17 kb)
DOI: 10.6084/m9.figshare.6695351
title: Additional file 4 of Estimation of delay to diagnosis and incidence in HIV using indirect evidence of infection dates

description: Comma-separated value file containing posterior covariance matrix for parameters of model fitted to the calibration dataset (without accounting for inter-lab variation in nucleotide ambiguity proportions). (CSV 52 kb)
DOI: 10.6084/m9.figshare.6695351.v1
title: Additional file 4 of Estimation of delay to diagnosis and incidence in HIV using indirect evidence of infection dates

description: Comma-separated value file containing posterior covariance matrix for parameters of model fitted to the calibration dataset (without accounting for inter-lab variation in nucleotide ambiguity proportions). (CSV 52 kb)
DOI: 10.6084/m9.figshare.6695345
title: Additional file 3 of Estimation of delay to diagnosis and incidence in HIV using indirect evidence of infection dates

description: Comma-separated value file containing posterior mean values for parameters of model fitted to the calibration dataset (without accounting for inter-lab variation in nucleotide ambiguity proportions). (CSV 4 kb)
DOI: 10.6084/m9.figshare.6695345.v1
title: Additional file 3 of Estimation of delay to diagnosis and incidence in HIV using indirect evidence of infection dates

description: Comma-separated value file containing posterior mean values for parameters of model fitted to the calibration dataset (without accounting for inter-lab variation in nucleotide ambiguity proportions). (CSV 4 kb)
DOI: 10.6084/m9.figshare.6695339
title: Additional file 2 of Estimation of delay to diagnosis and incidence in HIV using indirect evidence of infection dates

description: R script (viewable as plain text) to read in parameter estimates for the calibration dataset and to then simulate a cohort of patients with increasing incidence of HIV and a limited observation window for diagnoses. The same R script fits an â incidence and delay-to-diagnosisâ model to the generated data using a Stan model template file provided. (R 17 kb)
DOI: 10.6084/m9.figshare.6695339.v1
title: Additional file 2 of Estimation of delay to diagnosis and incidence in HIV using indirect evidence of infection dates

description: R script (viewable as plain text) to read in parameter estimates for the calibration dataset and to then simulate a cohort of patients with increasing incidence of HIV and a limited observation window for diagnoses. The same R script fits an â incidence and delay-to-diagnosisâ model to the generated data using a Stan model template file provided. (R 17 kb)
DOI: 10.6084/m9.figshare.6695312
title: Additional file 8: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: eQTL regions that overlap with QTLdb regions identified from the same dataset. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.6695312.v1
title: Additional file 8: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: eQTL regions that overlap with QTLdb regions identified from the same dataset. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.6695276
title: Additional file 6: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: Variant effect annotation of trans-eQTLs by VEP tool. (XLSX 262 kb)
DOI: 10.6084/m9.figshare.6695276.v1
title: Additional file 6: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: Variant effect annotation of trans-eQTLs by VEP tool. (XLSX 262 kb)
DOI: 10.6084/m9.figshare.6695255
title: Additional file 5: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: Variant effect annotation of cis-eQTLs by VEP tool. (XLSX 212 kb)
DOI: 10.6084/m9.figshare.6695255.v1
title: Additional file 5: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: Variant effect annotation of cis-eQTLs by VEP tool. (XLSX 212 kb)
DOI: 10.6084/m9.figshare.6695210
title: Additional file 3: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: All information about the cis and trans-eQTLs identified from RNA-Seq and genotyping data of Nellore steers population. (XLSX 2154 kb)
DOI: 10.6084/m9.figshare.6695210.v1
title: Additional file 3: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: All information about the cis and trans-eQTLs identified from RNA-Seq and genotyping data of Nellore steers population. (XLSX 2154 kb)
DOI: 10.6084/m9.figshare.6695207
title: Additional file 2: of Comparing tariff and medical assistant assigned causes of death from verbal autopsy interviews in Matlab, Bangladesh: implications for a health and demographic surveillance system

description: Cause-specific mortality fractions for medical assistants, Tariff, and reallocated Tariff by age group. Three separate tables that provide cause-specific mortality fractions for medical assistants, Tariff, and reallocated Tariff for adults, children, and neonates. These tables differ from Tables 1, 2, and 3 because these include Tariff cause-specific mortality fractions prior to reallocation of the undetermined cause of death. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.6695207.v1
title: Additional file 2: of Comparing tariff and medical assistant assigned causes of death from verbal autopsy interviews in Matlab, Bangladesh: implications for a health and demographic surveillance system

description: Cause-specific mortality fractions for medical assistants, Tariff, and reallocated Tariff by age group. Three separate tables that provide cause-specific mortality fractions for medical assistants, Tariff, and reallocated Tariff for adults, children, and neonates. These tables differ from Tables 1, 2, and 3 because these include Tariff cause-specific mortality fractions prior to reallocation of the undetermined cause of death. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.6695192.v1
title: MOESM1 of Genome-scale metabolic model analysis indicates low energy production efficiency in marine ammonia-oxidizing archaea

description: Additional file 1: Table S1. Transport reactions in the model for the exchange of metabolites between the cell and the environment. Table S2. Biomass components and their coefficients.
DOI: 10.6084/m9.figshare.6695150
title: Additional file 1: of Individual differences in face identity processing

description: Participant-level data for studies 1 and 2. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.6695150.v1
title: Additional file 1: of Individual differences in face identity processing

description: Participant-level data for studies 1 and 2. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.6695135
title: Additional file 17: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: Co-expression network results and functional enrichment. (XLSX 21960 kb)
DOI: 10.6084/m9.figshare.6695135.v1
title: Additional file 17: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: Co-expression network results and functional enrichment. (XLSX 21960 kb)
DOI: 10.6084/m9.figshare.6695090
title: Additional file 1: of Altering cortical input unmasks synaptic phenotypes in the YAC128 cortico-striatal co-culture model of Huntington disease

description: Individual data values. Individual values for data with nÂ
DOI: 10.6084/m9.figshare.6695090.v1
title: Additional file 1: of Altering cortical input unmasks synaptic phenotypes in the YAC128 cortico-striatal co-culture model of Huntington disease

description: Individual data values. Individual values for data with nÂ
DOI: 10.6084/m9.figshare.6695084
title: Additional file 15: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: Top ten transcription factor binding sites (TFBSs) over-represented in promoter sequence of genes that were associated with USF1. (XLSX 91 kb)
DOI: 10.6084/m9.figshare.6695084.v1
title: Additional file 15: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: Top ten transcription factor binding sites (TFBSs) over-represented in promoter sequence of genes that were associated with USF1. (XLSX 91 kb)
DOI: 10.6084/m9.figshare.6695081
title: Additional file 3: of Migration motives and integration of international human resources of health in the United Kingdom: systematic review and meta-synthesis of qualitative studies using framework analysis

description: Quality scoring summary. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.6695081.v1
title: Additional file 3: of Migration motives and integration of international human resources of health in the United Kingdom: systematic review and meta-synthesis of qualitative studies using framework analysis

description: Quality scoring summary. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.6695078
title: Additional file 8: of Identification of sonic hedgehog-regulated genes and biological processes in the cranial neural crest mesenchyme by comparative transcriptomics

description: Table of enriched biological categories for concordant genes. (XLS 80 kb)
DOI: 10.6084/m9.figshare.6695078.v1
title: Additional file 8: of Identification of sonic hedgehog-regulated genes and biological processes in the cranial neural crest mesenchyme by comparative transcriptomics

description: Table of enriched biological categories for concordant genes. (XLS 80 kb)
DOI: 10.6084/m9.figshare.6695066
title: Additional file 14: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: Top ten transcription factor binding sites (TFBSs) over-represented in promoter sequence of genes that were associated with RUNX1T1. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.6695066.v1
title: Additional file 14: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: Top ten transcription factor binding sites (TFBSs) over-represented in promoter sequence of genes that were associated with RUNX1T1. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.6695051
title: Additional file 13: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: Top ten transcription factor binding sites (TFBSs) over-represented in promoter sequence of genes that were associated with EGR4. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.6695051.v1
title: Additional file 13: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: Top ten transcription factor binding sites (TFBSs) over-represented in promoter sequence of genes that were associated with EGR4. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.6695039
title: Additional file 6: of Identification of sonic hedgehog-regulated genes and biological processes in the cranial neural crest mesenchyme by comparative transcriptomics

description: Ranking of negatively regulated concordant genes for Fig. 4e. (XLS 46 kb)
DOI: 10.6084/m9.figshare.6695030
title: Additional file 5: of Identification of sonic hedgehog-regulated genes and biological processes in the cranial neural crest mesenchyme by comparative transcriptomics

description: Ranking of positively regulated concordant genes for Fig. 4e. (XLS 44 kb)
DOI: 10.6084/m9.figshare.6695030.v1
title: Additional file 5: of Identification of sonic hedgehog-regulated genes and biological processes in the cranial neural crest mesenchyme by comparative transcriptomics

description: Ranking of positively regulated concordant genes for Fig. 4e. (XLS 44 kb)
DOI: 10.6084/m9.figshare.6695021
title: Additional file 11: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: Association test between hotspot eQTLs and IMF content-traits. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.6695021.v1
title: Additional file 11: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: Association test between hotspot eQTLs and IMF content-traits. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.6695009
title: Additional file 4: of Identification of sonic hedgehog-regulated genes and biological processes in the cranial neural crest mesenchyme by comparative transcriptomics

description: Table of common genes dysregulated in both in vivo and in vitro microarrays with respective expression data. Concordant genes are marked in the last column. (XLS 93 kb)
DOI: 10.6084/m9.figshare.6695009.v1
title: Additional file 4: of Identification of sonic hedgehog-regulated genes and biological processes in the cranial neural crest mesenchyme by comparative transcriptomics

description: Table of common genes dysregulated in both in vivo and in vitro microarrays with respective expression data. Concordant genes are marked in the last column. (XLS 93 kb)
DOI: 10.6084/m9.figshare.6695003
title: Additional file 4 of CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness

description: Supplementary Table 3. CSV file of time-series gene expression data sets and CpG island size enrichment testing results. (CSV 1 kb)
DOI: 10.6084/m9.figshare.6695003.v1
title: Additional file 4 of CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness

description: Supplementary Table 3. CSV file of time-series gene expression data sets and CpG island size enrichment testing results. (CSV 1 kb)
DOI: 10.6084/m9.figshare.6694994
title: Additional file 10: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: R-squared values of linkage disequilibrium between each pair of hotspot eQTLs. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.6694994.v1
title: Additional file 10: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits

description: R-squared values of linkage disequilibrium between each pair of hotspot eQTLs. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.6694991
title: Additional file 3: of Identification of sonic hedgehog-regulated genes and biological processes in the cranial neural crest mesenchyme by comparative transcriptomics

description: Table of all genes with respective expression data for in vivo microarray analysis. (XLS 6587 kb)
DOI: 10.5281/zenodo.4007068
title: SAR Stack of Pichincha volcano in Ecuador, from Sentinel-1

description: A stack of Coregistered SLCs on Pichincha volcano, Ecuador Sensor: Sentinel-1 Ascending track 18 Time: 2019.01.01 - 2019.06.12, 23 acquisitions Processor: ISCE/topsStack Tropospheric delay estimated from ERA-5 using PyAPS is attached. This is an input dataset for the time series analysis with MiNoPy.
DOI: 10.6084/m9.figshare.6694991.v1
title: Additional file 3: of Identification of sonic hedgehog-regulated genes and biological processes in the cranial neural crest mesenchyme by comparative transcriptomics

description: Table of all genes with respective expression data for in vivo microarray analysis. (XLS 6587 kb)
DOI: 10.6084/m9.figshare.6694982
title: Additional file 3 of CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness

description: Supplementary Table 2. CSV file describing single cell RNA-sequencing data sets used in this study, with cell numbers and accession numbers to publicly available data. (CSV 1 kb)
DOI: 10.6084/m9.figshare.6694982.v1
title: Additional file 3 of CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness

description: Supplementary Table 2. CSV file describing single cell RNA-sequencing data sets used in this study, with cell numbers and accession numbers to publicly available data. (CSV 1 kb)
DOI: 10.6084/m9.figshare.6694976
title: Additional file 2: of Identification of sonic hedgehog-regulated genes and biological processes in the cranial neural crest mesenchyme by comparative transcriptomics

description: Table of enriched biological categories for in vitro analysis. (XLS 36 kb)
DOI: 10.6084/m9.figshare.6694976.v1
title: Additional file 2: of Identification of sonic hedgehog-regulated genes and biological processes in the cranial neural crest mesenchyme by comparative transcriptomics

description: Table of enriched biological categories for in vitro analysis. (XLS 36 kb)
DOI: 10.6084/m9.figshare.6694946
title: Additional file 1: of Identification of sonic hedgehog-regulated genes and biological processes in the cranial neural crest mesenchyme by comparative transcriptomics

description: Table of all genes with respective expression data for in vitro microarray analysis. (XLS 36513 kb)
DOI: 10.6084/m9.figshare.6694946.v1
title: Additional file 1: of Identification of sonic hedgehog-regulated genes and biological processes in the cranial neural crest mesenchyme by comparative transcriptomics

description: Table of all genes with respective expression data for in vitro microarray analysis. (XLS 36513 kb)