cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.35092/yhjc.12459545.v1
title: Dataset from Mouse 1 for Sit & Goard: Distributed and Retinotopically Asymmetric Processing of Coherent Motion in Mouse Visual Cortex

description: Accompanying dataset for Sit KK, Goard MJ. Distributed and Retinotopically Asymmetric Processing of Coherent Motion in Mouse Visual Cortex.<br>This dataset contains the data for mouse 1 / 10<br>Mouse SKKS057<br>See all data in collection here: https://doi.org/10.35092/yhjc.c.5018363<br>These datasets contain calcium imaging data taken from L2/3 of the primary visual cortex in mice. Mice were head fixed and passively watching a random dot kinematogram stimulus. The stimulus data vector for processing these data are also included. The accompanying code to analyze these data can be found at: https://github.com/kevinksit/CoherentMotionProject<br>Data are either in preprocessed DFF matrices, which represent the change in neural activity compared to a baseline or raw images from the microscope. All data are processed with MATLAB 2018b.<br>The purpose of these data is to understand the organization of neural activity in response to coherent motion in the murine visual cortex.<br>The manuscript associated with these data is Sit KK, Goard MJ. Distributed and Retinotopically Asymmetric Processing of Coherent Motion in Mouse Visual Cortex.<br>ABSTRACTPerception of visual motion is important for a range of ethological behaviors in mammals. In primates, specific visual cortical regions are specialized for processing of coherent visual motion. However, whether mouse visual cortex has a similar organization remains unclear, despite powerful genetic tools available for measuring population neural activity. Here, we use widefield and 2-photon calcium imaging of transgenic mice to measure mesoscale and cellular responses to coherent motion. Imaging of primary visual cortex (V1) and higher visual areas (HVAs) during presentation of natural movies and random dot kinematograms (RDKs) reveals varied responsiveness to coherent motion, with stronger responses in dorsal stream areas compared to ventral stream areas. Moreover, there is considerable anisotropy within visual areas, such that neurons representing the lower visual field are more responsive to coherent motion. These results indicate that processing of visual motion in mouse cortex is distributed heterogeneously both across and within visual areas.
DOI: 10.35092/yhjc.12459554.v1
title: Dataset from Mouse 2 for Sit & Goard: Distributed and Retinotopically Asymmetric Processing of Coherent Motion in Mouse Visual Cortex

description: Accompanying dataset for Sit KK, Goard MJ. Distributed and Retinotopically Asymmetric Processing of Coherent Motion in Mouse Visual Cortex.<br><br>This dataset contains the data for mouse 2 / 10<br>Mouse SKKS058<br>See all data in collection here: https://doi.org/10.35092/yhjc.c.5018363<br>These datasets contain calcium imaging data taken from L2/3 of the primary visual cortex in mice. Mice were head fixed and passively watching a random dot kinematogram stimulus. The stimulus data vector for processing these data are also included. The accompanying code to analyze these data can be found at: https://github.com/kevinksit/CoherentMotionProject<br>Data are either in preprocessed DFF matrices, which represent the change in neural activity compared to a baseline or raw images from the microscope. All data are processed with MATLAB 2018b.<br>The purpose of these data is to understand the organization of neural activity in response to coherent motion in the murine visual cortex.<br>The manuscript associated with these data is Sit KK, Goard MJ. Distributed and Retinotopically Asymmetric Processing of Coherent Motion in Mouse Visual Cortex.<br>ABSTRACTPerception of visual motion is important for a range of ethological behaviors in mammals. In primates, specific visual cortical regions are specialized for processing of coherent visual motion. However, whether mouse visual cortex has a similar organization remains unclear, despite powerful genetic tools available for measuring population neural activity. Here, we use widefield and 2-photon calcium imaging of transgenic mice to measure mesoscale and cellular responses to coherent motion. Imaging of primary visual cortex (V1) and higher visual areas (HVAs) during presentation of natural movies and random dot kinematograms (RDKs) reveals varied responsiveness to coherent motion, with stronger responses in dorsal stream areas compared to ventral stream areas. Moreover, there is considerable anisotropy within visual areas, such that neurons representing the lower visual field are more responsive to coherent motion. These results indicate that processing of visual motion in mouse cortex is distributed heterogeneously both across and within visual areas.
DOI: 10.35092/yhjc.12461714
title: Sequences of Homologs to the Bacterial Coat Protein CexE and Model for Secetion of CexE to the Outer Membrane

description: Fasta formatted protein sequences of CexE variants from several pathogenic species of bacteria. These proteins have been shown to be outer membrane coat proteins in enterotoxigenic (ETEC) and enteroaggregative (EAEC) <i>Escherichia coli,</i> and <i>C. rodentium</i>. Additionally, CexE has been shown to enhance the pathogenicity of<i> C. rodentium</i> in murine infection studies. The CexE polypeptide is transported from the cytoplasm to the periplasm by the SecYEG complex. Secretion across the outer membrane requires five additional genes named <i>cexPABCD</i> or <i>aatPABCD</i> depending on the species. CexC is predicted to be a cytosolic ATPase. Mutations in cexC abolish secretion of CexC to the outer membrane and attenuate <i>C. rodentium</i> virulence in murine infection models. CexP and CexD are predicted to be inner membrane proteins with several transmembrane helices each. CexA is likely an outer membrane beta-barrel protein as it has homology to TolC. The majority of CexB likely resides in the periplamsic where it may function in a manner analogous to membrane fusion proteins of Type I secretion systems.<br>Supports publication: "CexE is a Coat Protein and Virulence Factor of Diarrheagenic Pathogens" Rivas et al. Frontiers in Microbiology, 2020. doi: 10.3389/fmicb.2020.01374.<br>
DOI: 10.35092/yhjc.12461714.v1
title: Sequences of Homologs to the Bacterial Coat Protein CexE and Model for Secetion of CexE to the Outer Membrane

description: Fasta formatted protein sequences of CexE variants from several pathogenic species of bacteria. These proteins have been shown to be outer membrane coat proteins in enterotoxigenic (ETEC) and enteroaggregative (EAEC) <i>Escherichia coli,</i> and <i>C. rodentium</i>. Additionally, CexE has been shown to enhance the pathogenicity of<i> C. rodentium</i> in murine infection studies. The CexE polypeptide is transported from the cytoplasm to the periplasm by the SecYEG complex. Secretion across the outer membrane requires five additional genes named <i>cexPABCD</i> or <i>aatPABCD</i> depending on the species. CexC is predicted to be a cytosolic ATPase. Mutations in cexC abolish secretion of CexC to the outer membrane and attenuate <i>C. rodentium</i> virulence in murine infection models. CexP and CexD are predicted to be inner membrane proteins with several transmembrane helices each. CexA is likely an outer membrane beta-barrel protein as it has homology to TolC. The majority of CexB likely resides in the periplamsic where it may function in a manner analogous to membrane fusion proteins of Type I secretion systems.<br>Supports publication: "CexE is a Coat Protein and Virulence Factor of Diarrheagenic Pathogens" Rivas et al. Frontiers in Microbiology, 2020. doi: 10.3389/fmicb.2020.01374.<br>
DOI: 10.35092/yhjc.12462332
title: Two-photon Dataset from All Mice for Sit & Goard: Distributed and Retinotopically Asymmetric Processing of Coherent Motion in Mouse Visual Cortex

description: Accompanying dataset for Sit KK, Goard MJ. Distributed and Retinotopically Asymmetric Processing of Coherent Motion in Mouse Visual Cortex.<br><br>This dataset contains all the two-photon recordings in L2/3 V1 for all mice used.<br><br> See related data in collection here: https://doi.org/10.35092/yhjc.c.5018363<br><br> The purpose of these data is to understand the organization of neural activity in response to coherent motion in the murine visual cortex. <br>The manuscript associated with these data is Sit KK, Goard MJ. Distributed and Retinotopically Asymmetric Processing of Coherent Motion in Mouse Visual Cortex. <br>ABSTRACT Perception of visual motion is important for a range of ethological behaviors in mammals. In primates, specific visual cortical regions are specialized for processing of coherent visual motion. However, whether mouse visual cortex has a similar organization remains unclear, despite powerful genetic tools available for measuring population neural activity. Here, we use widefield and 2-photon calcium imaging of transgenic mice to measure mesoscale and cellular responses to coherent motion. Imaging of primary visual cortex (V1) and higher visual areas (HVAs) during presentation of natural movies and random dot kinematograms (RDKs) reveals varied responsiveness to coherent motion, with stronger responses in dorsal stream areas compared to ventral stream areas. Moreover, there is considerable anisotropy within visual areas, such that neurons representing the lower visual field are more responsive to coherent motion. These results indicate that processing of visual motion in mouse cortex is distributed heterogeneously both across and within visual areas.
DOI: 10.35092/yhjc.12521222
title: Supplementary Table 1 for Mueller et al "Sex Hormone Relations to Histologic Severity of Pediatric Nonalcoholic Fatty Liver Disease"

description: Supplementary table 1. P values for interaction by sex in the association of SHBG and sex hormones with features of NAFLD.<br><br>Supports manuscript: Mueller et al "Sex Hormone Relations to Histologic Severity of Pediatric Nonalcoholic Fatty Liver Disease"<br><br> Appendix lists the 12 pediatric clinical centers across the United States participating in Nonalcoholic Steatohepatitis Clinical Research Network (NASH-CRN) database.<br><br>This study aimed to examine associations of circulating sex hormone binding globulin (SHBG), estrogens, and androgens with key histologic features of pediatric, biopsy-confirmed nonalcoholic fatty liver disease (NAFLD).<br><br>We used linear regressions treating log-transformed SHBG and sex hormones as dependent variables and histologic features as independent features. We tested effect measure modification by sex on the multiplicative scale, P values obtained were shown in this table. Model adjusted for age, race/ethnicity, BMI z score, and Tanner stage.
DOI: 10.35092/yhjc.12521237
title: Supplementary Table 2 for Mueller et al "Sex Hormone Relations to Histologic Severity of Pediatric Nonalcoholic Fatty Liver Disease"

description: Supplementary Table 2. Multivariable adjusted geometric means (95% CI) of SHBG and sex hormones by features of NAFLD in boys from the NASH CRN.<br><br>Supports manuscript: Mueller et al "Sex Hormone Relations to Histologic Severity of Pediatric Nonalcoholic Fatty Liver Disease"<br><br>Appendix lists the 12 pediatric clinical centers across the United States participating in Nonalcoholic Steatohepatitis Clinical Research Network (NASH-CRN) database.<br><br>This study aimed to examine association of circulating sex hormone binding globulin (SHBG), estrogens, and androgens with key histologic features of pediatric, biopsy-confirmed nonalcoholic fatty liver disease (NAFLD).<br><br>We reported the estimated geometric mean and 95% confidence interval of each hormone across levels of each histologic feature in boys in NASH CRN in this table. Model adjusted for age, race/ethnicity, BMI z score, and Tanner stage.
DOI: 10.15156/bio/sh1229251.08fu
title: SH1229251.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1229252.08fu
title: SH1229252.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/th028947
title: TH028947
title: Agfidae

description: Here we present the novel 'taxon hypothesis' (TH) concept to accommodate fungal 'species hypothesis' (SH) into existing classification frameworks for taxonomic communication. As supplied with Digital Object Identifiers (DOIs), THs are flexible in time and enable direct cross-communication of higher level taxa along with evolving classification schemes. Every TH includes given number of SHs and consequently fixed number of fungal rDNA ITS sequences. DNA sequences generated by High-throughput or Sanger sequencing studies and identified against UNITE SHs will be automatically assigned to THs as well.
DOI: 10.15156/bio/th028948
title: TH028948
title: Angiostomatidae

description: Here we present the novel 'taxon hypothesis' (TH) concept to accommodate fungal 'species hypothesis' (SH) into existing classification frameworks for taxonomic communication. As supplied with Digital Object Identifiers (DOIs), THs are flexible in time and enable direct cross-communication of higher level taxa along with evolving classification schemes. Every TH includes given number of SHs and consequently fixed number of fungal rDNA ITS sequences. DNA sequences generated by High-throughput or Sanger sequencing studies and identified against UNITE SHs will be automatically assigned to THs as well.
DOI: 10.35092/yhjc.11872434.v1
title: Supplemental Tables A to F for "Cord blood DNA methylation reflects cord blood C-reactive protein levels..."

description: Results using EPIC microarray to investigate maternal CRP in the pregnancy and delivery with cord blood DNA methylation. Results from model 1 adjusting for maternal age, smoking, income, pre-pregnancy BMI, and plate. Model 2 additionally adjusts for cell type distribution using the cord blood reference as published by Bakulski et al. 2016. Model 3 adjusts for model 1 covariates and cell type distribution using the cord blood reference published by Gervin, Salas et al. 2019. Results are from first trimester (week 8), second trimester (week 20), third trimester (week 36), cord blood, cumulative (AUC) or persistent (extreme tertiles) CRP.<br>Supports the publication:<br>Yeung, E.H., Guan, W., Zeng, X. et al. Cord blood DNA methylation reflects cord blood C-reactive protein levels but not maternal levels: a longitudinal study and meta-analysis. Clin Epigenet 12, 60 (2020). https://doi.org/10.1186/s13148-020-00852-2<br>
DOI: 10.35092/yhjc.12386102.v2
title: MRI dataset supporting "Comparison of T1-Post and FLAIR-Post MRI for identification of traumatic meningeal enhancement in traumatic brain injury patients"

description: This dataset supports the publication: <br>Davis TS, Nathan JE, Tinoco Martinez AS, De Vis JB, Turtzo LC, Latour LL (2020) ­­­­­Comparison of T1-Post and FLAIR-Post MRI for identification of traumatic meningeal enhancement in traumatic brain injury patients. PLoS ONE 15(7): e0234881. https://doi.org/10.1371/journal.pone.0234881<b><br></b><br>This zip archive contains the dataset of deidentified brain MRI (T1 and FLAIR pre- and post-contrast sequences in dicom format) that were analyzed by blinded readers for the T1 FLAIR manuscript. The folder numbers/subject numbers on the images correspond to the subject numbers listed in the manuscript's Table 2. That table shows how each blinded reader scored the images.
DOI: 10.35092/yhjc.12521222.v1
title: Supplementary Table 1 for Mueller et al "Sex Hormone Relations to Histologic Severity of Pediatric Nonalcoholic Fatty Liver Disease"

description: Supplementary table 1. P values for interaction by sex in the association of SHBG and sex hormones with features of NAFLD.<br><br>Supports manuscript: Mueller et al "Sex Hormone Relations to Histologic Severity of Pediatric Nonalcoholic Fatty Liver Disease"<br><br> Appendix lists the 12 pediatric clinical centers across the United States participating in Nonalcoholic Steatohepatitis Clinical Research Network (NASH-CRN) database.<br><br>This study aimed to examine associations of circulating sex hormone binding globulin (SHBG), estrogens, and androgens with key histologic features of pediatric, biopsy-confirmed nonalcoholic fatty liver disease (NAFLD).<br><br>We used linear regressions treating log-transformed SHBG and sex hormones as dependent variables and histologic features as independent features. We tested effect measure modification by sex on the multiplicative scale, P values obtained were shown in this table. Model adjusted for age, race/ethnicity, BMI z score, and Tanner stage.
DOI: 10.35092/yhjc.12521237.v1
title: Supplementary Table 2 for Mueller et al "Sex Hormone Relations to Histologic Severity of Pediatric Nonalcoholic Fatty Liver Disease"

description: Supplementary Table 2. Multivariable adjusted geometric means (95% CI) of SHBG and sex hormones by features of NAFLD in boys from the NASH CRN.<br><br>Supports manuscript: Mueller et al "Sex Hormone Relations to Histologic Severity of Pediatric Nonalcoholic Fatty Liver Disease"<br><br>Appendix lists the 12 pediatric clinical centers across the United States participating in Nonalcoholic Steatohepatitis Clinical Research Network (NASH-CRN) database.<br><br>This study aimed to examine association of circulating sex hormone binding globulin (SHBG), estrogens, and androgens with key histologic features of pediatric, biopsy-confirmed nonalcoholic fatty liver disease (NAFLD).<br><br>We reported the estimated geometric mean and 95% confidence interval of each hormone across levels of each histologic feature in boys in NASH CRN in this table. Model adjusted for age, race/ethnicity, BMI z score, and Tanner stage.
DOI: 10.35092/yhjc.12521285
title: Supplementary Table 3 for Mueller et al "Sex Hormone Relations to Histologic Severity of Pediatric Nonalcoholic Fatty Liver Disease"

description: Supplementary Table 3. Multivariable adjusted geometric means (95% CI) of SHBG and sex hormones by features of NAFLD in girls from the NASH CRN<br><br>Supports manuscript: Mueller et al "Sex Hormone Relations to Histologic Severity of Pediatric Nonalcoholic Fatty Liver Disease".<br><br>Appendix lists the 12 pediatric clinical centers across the United States participating in Nonalcoholic Steatohepatitis Clinical Research Network (NASH-CRN) database.<br><br>This study aimed to examine association of circulating sex hormone binding globulin (SHBG), estrogens, and androgens with key histologic features of pediatric, biopsy-confirmed nonalcoholic fatty liver disease (NAFLD).<br><br>We reported the estimated geometric mean and 95% confidence interval of each hormone across levels of each histologic feature in girls in NASH CRN in this table. Model adjusted for age, race/ethnicity, BMI z score, and Tanner stage.
DOI: 10.35092/yhjc.12521285.v1
title: Supplementary Table 3 for Mueller et al "Sex Hormone Relations to Histologic Severity of Pediatric Nonalcoholic Fatty Liver Disease"

description: Supplementary Table 3. Multivariable adjusted geometric means (95% CI) of SHBG and sex hormones by features of NAFLD in girls from the NASH CRN<br><br>Supports manuscript: Mueller et al "Sex Hormone Relations to Histologic Severity of Pediatric Nonalcoholic Fatty Liver Disease".<br><br>Appendix lists the 12 pediatric clinical centers across the United States participating in Nonalcoholic Steatohepatitis Clinical Research Network (NASH-CRN) database.<br><br>This study aimed to examine association of circulating sex hormone binding globulin (SHBG), estrogens, and androgens with key histologic features of pediatric, biopsy-confirmed nonalcoholic fatty liver disease (NAFLD).<br><br>We reported the estimated geometric mean and 95% confidence interval of each hormone across levels of each histologic feature in girls in NASH CRN in this table. Model adjusted for age, race/ethnicity, BMI z score, and Tanner stage.
DOI: 10.35092/yhjc.12536015
title: Data tables and analysis scripts supporting "Kinetics of fast tetramerization of the huntington exon 1 protein probed by concentration-dependent on-resonance R1rho measurements" A. Ceccon, V. Tugarinov and G.M. Clore, J. Phys. Chem. Lett.

description: Experimental data (15N/13Calpha exchange induced shifts and R1rho data at 3 RF field strengths) and MATLAB analysis scripts for the paper entitled "Kinetics of fast tetramerization of the huntington exon 1 protein probed by concentration-dependent on-resonance R1rho measurements" by A. Ceccon, V. Tugarinov and G.M. Clore. J. Phys. Chem. Lett. jz-2020-016369 http://dx.doi.org/10.1021/acs.jpclett.0c01636<br><br>Abstract: An approach for the quantitative description of the kinetics of very fast exchange processes (t<sub>ex</sub> &lt; 50-100 microseconds) associated with transient, reversible protein oligomerization, is presented. We show that on-resonance <sup>15</sup>N-<i>R1rho</i> measurements conducted as a function of protein concentration at several spin-lock radio-frequency field strengths are indispensable for unambiguous determination of the rate constants for interconversion between monomeric and higher order oligomeric species. The approach is experimentally demonstrated on the study of fast, reversible tetramerization of full-length huntingtin exon 1 protein, htt<sup>ex1</sup>, responsible for Huntington’s disease. Incorporation of concentration-dependent <sup>15</sup>N-<i>R</i><sub>2,eff</sub> data, obtained from on-resonance <i>R1rho</i> measurements performed at three spin-lock field strengths, into analysis of the kinetic scheme describing reversible tetramerization of htt<sup>ex1</sup>, allowed us to uniquely determine the rate constants of interconversion between the various species. This approach serves as a valuable complement to the existing array of NMR techniques for studying early, transient oligomerization events in protein aggregation pathways.