cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.35092/yhjc.12133545
title: ChR2 induced Fos protein expression counts among distant brain sites

description: This dataset shows quantifications of Fos protein expression in sites distal to CeA after optogenetic stimulation of CeA (ChR2) during certain behavioral conditions. Specifically, rats were either earning sucrose or cocaine rewards, or interacting with a shock rod, brains were extracted 90 min later and Fos protein expression was measured in various brain sites (see document). Atlas pages with which Fos protein was measured are listed in the first sheet.<br><br>Dataset supporting: Warlow, S.M., Naffziger, E.E. & Berridge, K.C. The central amygdala recruits mesocorticolimbic circuitry for pursuit of reward or pain. <i>Nat Commun</i> <b>11</b>, 2716 (2020). https:/doi.org/10.1038/241467-020-16407-1<br><br>Abstract: How do brain mechanisms create maladaptive attractions? Here intense maladaptive attractions were created in laboratory rats by pairing optogenetic channelrhodopsin (ChR2) stimulation of central nucleus of amygdala (CeA) in rats with encountering either sucrose, cocaine, or a painful shock-delivering object. Pairings made the respective rats pursue either sucrose exclusively, or cocaine exclusively, or repeatedly self-inflict shocks. CeA-induced maladaptive attractions, even to the painful shock-rod, recruited mesocorticolimbic incentive-related circuitry. Shock-associated cues also gained positive incentive value and were pursued. Yet the motivational effects of paired CeA stimulation could be reversed to negative valence in a Pavlovian fear learning situation, where CeA ChR2 pairing increased defensive reactions. Finally, CeA ChR2 valence could be switched to neutral by pairing with innocuous stimuli. These results reveal valence plasticity and multiple modes for motivation via mesocorticolimbic circuitry under the control of CeA activation.<br><br>Find other related resources in the collection here: https://doi.org/10.35092/yhjc.c.4939542<br>
DOI: 10.35092/yhjc.12133545.v1
title: ChR2 induced Fos protein expression counts among distant brain sites

description: This dataset shows quantifications of Fos protein expression in sites distal to CeA after optogenetic stimulation of CeA (ChR2) during certain behavioral conditions. Specifically, rats were either earning sucrose or cocaine rewards, or interacting with a shock rod, brains were extracted 90 min later and Fos protein expression was measured in various brain sites (see document). Atlas pages with which Fos protein was measured are listed in the first sheet.<br><br>Dataset supporting: Warlow, S.M., Naffziger, E.E. & Berridge, K.C. The central amygdala recruits mesocorticolimbic circuitry for pursuit of reward or pain. <i>Nat Commun</i> <b>11</b>, 2716 (2020). https:/doi.org/10.1038/241467-020-16407-1<br><br>Abstract: How do brain mechanisms create maladaptive attractions? Here intense maladaptive attractions were created in laboratory rats by pairing optogenetic channelrhodopsin (ChR2) stimulation of central nucleus of amygdala (CeA) in rats with encountering either sucrose, cocaine, or a painful shock-delivering object. Pairings made the respective rats pursue either sucrose exclusively, or cocaine exclusively, or repeatedly self-inflict shocks. CeA-induced maladaptive attractions, even to the painful shock-rod, recruited mesocorticolimbic incentive-related circuitry. Shock-associated cues also gained positive incentive value and were pursued. Yet the motivational effects of paired CeA stimulation could be reversed to negative valence in a Pavlovian fear learning situation, where CeA ChR2 pairing increased defensive reactions. Finally, CeA ChR2 valence could be switched to neutral by pairing with innocuous stimuli. These results reveal valence plasticity and multiple modes for motivation via mesocorticolimbic circuitry under the control of CeA activation.<br><br>Find other related resources in the collection here: https://doi.org/10.35092/yhjc.c.4939542<br>
DOI: 10.35092/yhjc.12148428
title: Supplementary Table 2 RNAseq read count file for "RNA-seq reveals sub-zones in mouse adrenal zona fasciculata and the sexually dimorphic responses to thyroid hormone"

description: Supplementary Table 2 for the paper "RNA-seq reveals sub-zones in mouse adrenal zona fasciculata and the sexually dimorphic responses to thyroid hormone":<br>This is the RNAseq read count file which aims to study the effect of thyroid hormone treatment on the mouse adrenal gland. <br>Tab1: Sexual Dimorphic T3-responsive Genes (total 104 genes)Tab2: Male-biased genes (344 genes)<br>Tab3: Female-biased genes (555 genes)Tab4: T3-responsive genes in males (512 genes)Tab5: T3-responsive genes in females (1162 genes)
DOI: 10.15156/bio/sh1229245.08fu
title: SH1229245.08FU

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/sh1229246.08fu
title: SH1229246.08FU

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/th028941
title: TH028941
title: Tylenchidae

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/th028942
title: TH028942
title: Tylenchulidae

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.11991336
title: Dataset for "Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade"

description: Dataset<b> </b>supporting publication: Le, D. T., Durham, J. N., Smith, K. N., Wang, H., Bartlett, B. R., Aulakh, L. K., ... & Wong, F. (2017). Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade. <i>Science</i>, 357(6349), 409-413.<br><br><b>Abstract: </b>The genomes of cancers deficient in mismatch repair contain exceptionally high numbers of somatic mutations. In a proof-of-concept study, we previously showed that colorectal cancers with mismatch repair deficiency were sensitive to immune checkpoint blockade with antibodies to programmed death receptor-1 (PD-1). We have now expanded this study to evaluate the efficacy of PD-1 blockade in patients with advanced mismatch repair-deficient cancers across 12 different tumor types. Objective radiographic responses were observed in 53% of patients, and complete responses were achieved in 21% of patients. Responses were durable, with median progression-free survival and overall survival still not reached. Functional analysis in a responding patient demonstrated rapid in vivo expansion of neoantigen-specific T cell clones that were reactive to mutant neopeptides found in the tumor. These data support the hypothesis that the large proportion of mutant neoantigens in mismatch repair-deficient cancers make them sensitive to immune checkpoint blockade, regardless of the cancers' tissue of origin.<br><br><b>Supplemental Tables included here</b>: Baseline characteristics, response to treatment, and somatic mutations of subjects enrolled in the trial. The data cutoff was 19 December 2016.
DOI: 10.35092/yhjc.11991336.v1
title: Dataset for "Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade"

description: Dataset<b> </b>supporting publication: Le, D. T., Durham, J. N., Smith, K. N., Wang, H., Bartlett, B. R., Aulakh, L. K., ... & Wong, F. (2017). Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade. <i>Science</i>, 357(6349), 409-413.<br><br><b>Abstract: </b>The genomes of cancers deficient in mismatch repair contain exceptionally high numbers of somatic mutations. In a proof-of-concept study, we previously showed that colorectal cancers with mismatch repair deficiency were sensitive to immune checkpoint blockade with antibodies to programmed death receptor-1 (PD-1). We have now expanded this study to evaluate the efficacy of PD-1 blockade in patients with advanced mismatch repair-deficient cancers across 12 different tumor types. Objective radiographic responses were observed in 53% of patients, and complete responses were achieved in 21% of patients. Responses were durable, with median progression-free survival and overall survival still not reached. Functional analysis in a responding patient demonstrated rapid in vivo expansion of neoantigen-specific T cell clones that were reactive to mutant neopeptides found in the tumor. These data support the hypothesis that the large proportion of mutant neoantigens in mismatch repair-deficient cancers make them sensitive to immune checkpoint blockade, regardless of the cancers' tissue of origin.<br><br><b>Supplemental Tables included here</b>: Baseline characteristics, response to treatment, and somatic mutations of subjects enrolled in the trial. The data cutoff was 19 December 2016.
DOI: 10.35092/yhjc.11991546.v2
title: Data for comparison of automated and manual co-registration for magnetoencephalography

description: De-identified, de-faced structural MRI files for 90 participants, as well as co-registration error data used in the computation of intra-class correlations.<br><br>Dataset supporting publication: Houck JM, Claus ED (2020) A comparison of automated and manual co-registration for magnetoencephalography. PLoS ONE 15(4): e0232100. https://doi.org/10.1371/journal.pone.0232100<br><br>Abstract: Magnetoencephalography (MEG) is a neuroimaging technique that accurately captures the rapid (sub-millisecond) activity of neuronal populations. Interpretation of functional data from MEG relies upon registration to the participant’s anatomical MRI. The key remaining step is to transform the participant’s MRI into the MEG head coordinate space. Although both automated and manual approaches to co-registration are available, the relative accuracy of two approaches has not been systematically evaluated. The goal of the present study was to compare the accuracy of manual and automated co-registration. Resting MEG and T1-weighted MRI data were collected from 90 participants. Automated and manual co-registration were performed on the same subjects, and the inter-method reliability of the two methods assessed using the intra-class correlation. Median co-registration error for both methods was within acceptable limits. Inter-method reliability was in the “good” range for co-registration error, and the “good” to “excellent” range for translation and rotation. These results suggest that the output of the automated co-registration procedure is comparable to that achieved using manual co-registration.
DOI: 10.35092/yhjc.11996931.v2
title: Data from: Noninvasive Electromagnetic Source Imaging of Spatio-temporally Distributed Epileptogenic Brain Sources

description: This database includes the de-identified interictal spike information in 9 focal epilepsy patients who became seizure-free after surgery. All underwent intra-cranial EEG (iEEG) monitoring prior to surgery and information about seizure onset zone (SOZ) based on iEEG study was available in these patients. <br> This dataset was collected under support from the National Institutes of Health via grants<b> </b>R01NS096761 and R01EB021027, to Dr. Bin He and Dr. Greg Worrell. The human data were collected and deidentified as part of NIH funded research at Mayo Clinic, Rochester, overseen by Dr. Greg Worrell, and processed and organized at Dr. Bin He’s lab at Carnegie Mellon University.<br> This dataset has been used and analyzed to study epilepsy networks and the results are reported in: Sohrabpour et al, “Noninvasive Electromagnetic Source Imaging of Spatio-temporally Distributed Epileptogenic Brain Sources,” Nature Communications, 2020 (https://doi.org/10.1038/s41467-020-15781-0). Please cite this paper if you use any data included in this dataset. Codes related to this study are also available from https://github.com/bfinl/FAST-IRES.
DOI: 10.35092/yhjc.12111570.v2
title: Clinical benefit of remdesivir in rhesus macaques infected with SARS-CoV-2

description: <b>Background:</b> Effective therapeutics to treat COVID-19 are urgently needed. Remdesivir is a nucleotide prodrug with in vitro and in vivo efficacy against coronaviruses. Here, we tested the efficacy of remdesivir treatment in a rhesus macaque model of SARS-CoV-2 infection. <b>Methods:</b> To evaluate the effect of remdesivir treatment on SARS-CoV-2 disease outcome, we used the recently established rhesus macaque model of SARS-CoV-2 infection that results in transient lower respiratory tract disease. Two groups of six rhesus macaques were infected with SARS-CoV-2 and treated with intravenous remdesivir or an equal volume of vehicle solution once daily. Clinical, virological and histological parameters were assessed regularly during the study and at necropsy to determine treatment efficacy. <b>Results:</b> In contrast to vehicle-treated animals, animals treated with remdesivir did not show signs of respiratory disease and had reduced pulmonary infiltrates on radiographs. Virus titers in bronchoalveolar lavages were significantly reduced as early as 12hrs after the first treatment was administered. At necropsy on day 7 after inoculation, lung viral loads of remdesivir-treated animals were significantly lower and there was a clear reduction in damage to the lung tissue. <b>Conclusions:</b> Therapeutic remdesivir treatment initiated early during infection has a clear clinical benefit in SARS-CoV-2-infected rhesus macaques. These data support early remdesivir treatment initiation in COVID-19 patients to prevent progression to severe pneumonia.
DOI: 10.35092/yhjc.12111570.v3
title: Clinical benefit of remdesivir in rhesus macaques infected with SARS-CoV-2

description: <b>Background:</b> Effective therapeutics to treat COVID-19 are urgently needed. Remdesivir is a nucleotide prodrug with in vitro and in vivo efficacy against coronaviruses. Here, we tested the efficacy of remdesivir treatment in a rhesus macaque model of SARS-CoV-2 infection. <b>Methods:</b> To evaluate the effect of remdesivir treatment on SARS-CoV-2 disease outcome, we used the recently established rhesus macaque model of SARS-CoV-2 infection that results in transient lower respiratory tract disease. Two groups of six rhesus macaques were infected with SARS-CoV-2 and treated with intravenous remdesivir or an equal volume of vehicle solution once daily. Clinical, virological and histological parameters were assessed regularly during the study and at necropsy to determine treatment efficacy. <b>Results:</b> In contrast to vehicle-treated animals, animals treated with remdesivir did not show signs of respiratory disease and had reduced pulmonary infiltrates on radiographs. Virus titers in bronchoalveolar lavages were significantly reduced as early as 12hrs after the first treatment was administered. At necropsy on day 7 after inoculation, lung viral loads of remdesivir-treated animals were significantly lower and there was a clear reduction in damage to the lung tissue. <b>Conclusions: </b>Therapeutic remdesivir treatment initiated early during infection has a clear clinical benefit in SARS-CoV-2-infected rhesus macaques. These data support early remdesivir treatment initiation in COVID-19 patients to prevent progression to severe pneumonia.<br><br>Dataset supports publication:Williamson, B.N., Feldmann, F., Schwarz, B. et al. Clinical benefit of remdesivir in rhesus macaques infected with SARS-CoV-2. Nature (2020). https://doi.org/10.1038/s41586-020-2423-5<br><br>Also previously shared on bioRxiv: https://doi.org/10.1101/2020.04.15.043166
DOI: 10.35092/yhjc.12145626
title: Source Data for Wang et al. 2021: Budding Epithelial Morphogenesis Driven by Cell-Matrix vs. Cell-Cell Adhesion

description: This dataset can be used to reproduce all plots in Wang et al., 2021 titled: "Budding Epithelial Morphogenesis Driven by Cell-Matrix vs. Cell-Cell Adhesion" in combination with the Jupyter notebook scripts available from this Github repository: https://github.com/snownontrace/public-scripts-Wang2020-branching-morphogenesis.git<br><br>1. Download and decompress the dataset zip file.<br>2. Place the "data" folder and the "scripts" folder (from GitHub) in the same folder.<br> Note: This folder organization is necessary because relative path is used to read in data in all scripts (e.g., '../data/specific_data_folder/data_table').<br>3. Run scripts to reproduce plots of interest. Refer to the table in the README file of the Github repository to find out which scripts were used to generate which figures.<br>Abstract:Many embryonic organs undergo epithelial morphogenesis to form tree-like hierarchical structures. However, it remains unclear what drives the budding and branching of stratified epithelia, such as in embryonic salivary gland and pancreas. Here, we performed live-organ imaging of mouse embryonic salivary glands at single-cell resolution to reveal that budding morphogenesis is driven by expansion and folding of a distinct epithelial surface cell sheet characterized by strong cell-matrix adhesions and weak cell-cell adhesions. Profiling of single-cell transcriptomes of this epithelium revealed spatial patterns of transcription underlying these cell adhesion differences. We then synthetically reconstituted budding morphogenesis by experimentally suppressing E-cadherin expression and inducing basement membrane formation in 3D spheroid cultures of engineered cells, which required β1 integrin-mediated cell-matrix adhesion for successful budding. Thus, stratified epithelial budding, the key first step of branching morphogenesis, is driven by an overall combination of strong cell-matrix adhesion and weak cell-cell adhesion by peripheral epithelial cells.<br>
DOI: 10.35092/yhjc.12148467
title: Supplementary Table 1 RNAseq read count file for "RNA-seq reveals sub-zones in mouse adrenal zona fasciculata and the sexually dimorphic responses to thyroid hormone"

description: Original read count file for the paper "RNA-seq reveals sub-zones in mouse adrenal zona fasciculata and the sexually dimorphic responses to thyroid hormone".<br>This is the RNAseq read count file which aims to study the effect of thyroid hormone treatment on the mouse adrenal gland.
DOI: 10.35092/yhjc.12198225
title: Live-cell imaging data for DASC (disassembly asymmetry score classification) analysis of calthrin-mediated endocytosis

description: This dataset is for sharing all of the raw images analyzed in the paper, “<b><i>DASC, a sensitive classifier for measuring discrete early stages in clathrin-mediated endocytosis</i></b>”, https://doi.org/10.7554/eLife.53686. In the paper, we proposed a new method that can unbiasedly classify two populations of clathrin structures during endocytosis, clathrin coated pits and abortive coats. Based on this new classification, we measured phenotypes of siRNA knockdown of 11 endocytic accessory protein (EAP), analyzed clathrin-AP2 dual channel images and measured curvature formation during endocytosis.<br><br>Images in all four experiments are included in this data set, ‘EAP knockdown’, ‘alphaPIP2-’ as a positive control experiment, ‘CLC_AP2_dual’ as another control experiment, and ‘EpiTIRF’ for curvature measurement. Each experiment has various conditions, see the metadata file for details.<br><br>Readers can follow this README to obtain the entire data and then apply DASC, one experiment by one experiment, to reproduce the results in the associated paper. The software of DASC is available on GitHub: https://github.com/DanuserLab/cmeAnalysis. See the instruction on the GitHub page for how to use DASC to analyze the images.<br><br>Files in this data are compressed. Each ‘.tif.bz’ file is a compressed tif image sequence of fluorescently labeled cells. The names of these compressed files include descriptive information of ‘experiment’, ‘condition’, ‘date’, ‘cell name’ and ‘channel name’ (optional). These descriptors are separated by ‘#’.<br><br>The compressed files can be automatically decompressed by running the Matlab script ('Decompression.m') in a Linux system.