cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5400739.v1
title: OPEN RESEARCH: Keio University - September 12, 2017

description: Event poster, information and photos of speakers from the Keio University event about Open Research: The Future of Scholarly Communication.September 12, 2017Tokyo, Japan<br>Speakers:- Jiro Kokuryo - Vice President for International Collaboration and Information Infrastructure; Professor of Policy Management, Keio University- Ed Gerstner - Regional Scientific Director, Greater China, SpringerNature- Nobuko Miyairi - Regional Director, Asia Pacific, ORCiD- Mark Hahnel - Founder and CEO, figshare (part of the Digital Science portfolio)- Yasuhiro Murayama - Research Executive Director of the Strategic Program Office, National Institute of Information and Communications Technology (NICT)
DOI: 10.6084/m9.figshare.5400769.v1
title: conformational dynamics of the transcription bubble in RNAP-promoter open complex - usALEX-smFRET raw data for figure 2

description: The dataset includes the raw data of usALEX-smFRET measurements (stored in photon-HDF5 file format) of 3 different doubly-labeled lacCONS promoter dsDNA constructs. This raw data is the basis for figure 2.
DOI: 10.6084/m9.figshare.5400667
title: Qom puberty database for sitar models

description: Pre-processed dataset used for SITAR growth velocity models
DOI: 10.6084/m9.figshare.5400661
title: Qom Puberty R code

description: R code for suvival analysis (time to menarche) and sitar growth velocity curves for Qom (Toba) girls.
DOI: 10.6084/m9.figshare.5400664
title: Qom puberty shared database

description: Database used for descriptive statistics and survival analysis of time to menarche in Qom (Toba) girls.
DOI: 10.6084/m9.figshare.5400667.v1
title: Qom puberty database for sitar models

description: Pre-processed dataset used for SITAR growth velocity models
DOI: 10.6084/m9.figshare.5400628
title: Widefield GCaMP6 Imaging in Awake and Anesthetized Mice

description: Representative evoked and spontaneous GCaMP6 and HbO2 imaging data in awake and anesthetized mice associated with the manuscript "Functional Connectivity of Calcium Dynamics in Anesthetized and Awake Mice" by Wright et al., 2017 (PLOS ONE). Please see PLOS_DataSharing_Key for descriptions of individual items within this fileset.
DOI: 10.6084/m9.figshare.5400649
title: Dataset for: Inflammation alters AMPA-stimulated calcium responses in dorsal striatal D2 but not D1 spiny projection neurons

description: Neuroinflammation precedes neuronal loss in striatal neurodegenerative diseases and can be exacerbated by the release of proinflammatory molecules by microglia. These molecules can affect trafficking of AMPARs. The preferential trafficking of calcium-permeable versus impermeable AMPARs can result in disruptions of [Ca<sup>2+</sup>]<sub>i</sub> and alter cellular functions. In striatal neurodegenerative diseases, changes in [Ca<sup>2+</sup>]<sub>i</sub> and L-type voltage-gated calcium channels (VGCCs) have been reported. Therefore, the present study sought to determine whether a proinflammatory environment alters AMPA-stimulated [Ca<sup>2+</sup>]<sub>i</sub> through calcium-permeable AMPARs and/or L-type VGCCs in dopamine-2 and dopamine-1 expressing striatal spiny projection neurons (D2 and D1 SPNs) in the dorsal striatum. Mice expressing the calcium indicator protein, GCaMP in D2 or D1 SPNs, were utilized for calcium imaging. Microglial activation was assessed by morphology analyses. To induce inflammation, acute mouse striatal slices were incubated with lipopolysaccharide (LPS). Here we report that LPS treatment potentiated AMPA responses only in D2 SPNs. When a nonspecific VGCC blocker was included, we observed a decrease of AMPA-stimulated calcium fluorescence in D2 but not D1 SPNs. The remaining agonist induced [Ca<sup>2+</sup>]<sub>i</sub> was mediated by calcium-permeable AMPARs because the responses were completely blocked by a selective calcium-permeable AMPAR antagonist. We used isradipine, the highly selective L-type VGCC antagonist to determine the role of L-type VGCCs in SPNs treated with LPS. Isradipine decreased AMPA-stimulated responses selectively in D2 SPNs after LPS treatment. Our findings suggest that dorsal striatal D2 SPNs are specifically targeted in proinflammatory conditions and that L-type VGCCs and calcium-permeable AMPARs are important mediators of this effect.
DOI: 10.6084/m9.figshare.5400661.v1
title: Qom Puberty R code

description: R code for suvival analysis (time to menarche) and sitar growth velocity curves for Qom (Toba) girls.
DOI: 10.6084/m9.figshare.5400664.v1
title: Qom puberty shared database

description: Database used for descriptive statistics and survival analysis of time to menarche in Qom (Toba) girls.
DOI: 10.6084/m9.figshare.5400649.v1
title: Dataset for: Inflammation alters AMPA-stimulated calcium responses in dorsal striatal D2 but not D1 spiny projection neurons

description: Neuroinflammation precedes neuronal loss in striatal neurodegenerative diseases and can be exacerbated by the release of proinflammatory molecules by microglia. These molecules can affect trafficking of AMPARs. The preferential trafficking of calcium-permeable versus impermeable AMPARs can result in disruptions of [Ca<sup>2+</sup>]<sub>i</sub> and alter cellular functions. In striatal neurodegenerative diseases, changes in [Ca<sup>2+</sup>]<sub>i</sub> and L-type voltage-gated calcium channels (VGCCs) have been reported. Therefore, the present study sought to determine whether a proinflammatory environment alters AMPA-stimulated [Ca<sup>2+</sup>]<sub>i</sub> through calcium-permeable AMPARs and/or L-type VGCCs in dopamine-2 and dopamine-1 expressing striatal spiny projection neurons (D2 and D1 SPNs) in the dorsal striatum. Mice expressing the calcium indicator protein, GCaMP in D2 or D1 SPNs, were utilized for calcium imaging. Microglial activation was assessed by morphology analyses. To induce inflammation, acute mouse striatal slices were incubated with lipopolysaccharide (LPS). Here we report that LPS treatment potentiated AMPA responses only in D2 SPNs. When a nonspecific VGCC blocker was included, we observed a decrease of AMPA-stimulated calcium fluorescence in D2 but not D1 SPNs. The remaining agonist induced [Ca<sup>2+</sup>]<sub>i</sub> was mediated by calcium-permeable AMPARs because the responses were completely blocked by a selective calcium-permeable AMPAR antagonist. We used isradipine, the highly selective L-type VGCC antagonist to determine the role of L-type VGCCs in SPNs treated with LPS. Isradipine decreased AMPA-stimulated responses selectively in D2 SPNs after LPS treatment. Our findings suggest that dorsal striatal D2 SPNs are specifically targeted in proinflammatory conditions and that L-type VGCCs and calcium-permeable AMPARs are important mediators of this effect.
DOI: 10.6084/m9.figshare.5400628.v1
title: Widefield GCaMP6f Imaging in Awake and Anesthetized Mice

description: Representative evoked and spontaneous GCaMP6 and HbO2 imaging data in awake and anesthetized mice associated with the manuscript "Functional Connectivity of Calcium Dynamics in Anesthetized and Awake Mice" by Wright et al., 2017 (PLOS ONE). Please see PLOS_DataSharing_Key for descriptions of individual items within this fileset.
DOI: 10.6084/m9.figshare.5400502
title: The perception of Malaysian pedestrians toward the use of footbridges

description: <b>Objective</b>: The footbridge is a vital structure in the road network and a cornerstone among crossing facilities. Yet, it suffers from low usage by pedestrians as they try to cross the street on the level. This study aims to analyze the perceptions of Malaysian pedestrians toward the use of footbridges with the consideration of different factors. <b>Method</b>: The study was carried out by collecting data from field observation and questionnaire distribution on the street among the public. The data were statistically analyzed by applying multiple linear regression models and a series of chi-square tests. <b>Results</b>: The study found that the most influential factor cited by pedestrians in decision making regarding using a footbridge is the existence of an escalator. Being in a hurry and the fear of heights were significantly associated with choosing not to use a footbridge. Zebra crossing was chosen as the most favorable type of crossing facility by the majority of respondents. In addition, installation of a fence and barriers was proposed as an effective procedure to prevent jaywalking. To construct new and efficient footbridges in the future, the study suggests consideration of traffic volume, posted speed limit, and the number of lanes, because these are the most influential factors to predict the usage rate. <b>Conclusions</b>: The study encourages decision makers and stakeholders to consider providing escalators for new footbridges to enhance the safety of pedestrians.
DOI: 10.6084/m9.figshare.5400205
title: multiple ROI h5 files

description: Data file contains data for expanded regions of interest. Data types are 1. per-voxel percent signal change time-courses for 6 runs2. per-voxel percent signal change time-courses for 6 runs, leave-one-out median - name of the array refers to the file that was left out3. per-voxel percent signal change time-course, grand average over runs (median)4. parameters of pRF fits per run (leave-one-out)5. parameters of pRF fits all runs <br># indices into prf output array:# 0: X (position, degrees of visual angle from fixation)# 1: Y (position, degrees of visual angle from fixation)# 2: s (size, standard deviation of gauss)# 3: n (nonlinearity power)# 4: a (amplitude)# 5: b (baseline, intercept value)# 6: rsq# 7: #<br>Github repo for analysis code on this dataset: https://github.com/tknapen/decode_encode<br>The voxel size of these recordings is 2mm isotropic, and the sample duration (TR) is 0.945 s. pRF fits were done using a CSS model implemented in Popeye, using a standard HRF shape.
DOI: 10.6084/m9.figshare.5400502.v2
title: The perception of Malaysian pedestrians toward the use of footbridges

description: <b>Objective</b>: The footbridge is a vital structure in the road network and a cornerstone among crossing facilities. Yet, it suffers from low usage by pedestrians as they try to cross the street on the level. This study aims to analyze the perceptions of Malaysian pedestrians toward the use of footbridges with the consideration of different factors. <b>Method</b>: The study was carried out by collecting data from field observation and questionnaire distribution on the street among the public. The data were statistically analyzed by applying multiple linear regression models and a series of chi-square tests. <b>Results</b>: The study found that the most influential factor cited by pedestrians in decision making regarding using a footbridge is the existence of an escalator. Being in a hurry and the fear of heights were significantly associated with choosing not to use a footbridge. Zebra crossing was chosen as the most favorable type of crossing facility by the majority of respondents. In addition, installation of a fence and barriers was proposed as an effective procedure to prevent jaywalking. To construct new and efficient footbridges in the future, the study suggests consideration of traffic volume, posted speed limit, and the number of lanes, because these are the most influential factors to predict the usage rate. <b>Conclusions</b>: The study encourages decision makers and stakeholders to consider providing escalators for new footbridges to enhance the safety of pedestrians.
DOI: 10.6084/m9.figshare.5398888
title: Entomological Collections in the Age of Big Data

description: Data of survey of 36 entomological collections published in Short, A.E.Z., Dikow, T., and Moreau, C.S. 2018. Entomological Collections in the Age of Big Data. Annual Review of Entomology 63: 513-530.doi: http://dx.doi.org/10.1146/annurev-ento-031616-035536
DOI: 10.6084/m9.figshare.5400502.v1
title: The perception of Malaysian pedestrians towards the use of footbridges

description: <b>Objective</b>: The footbridge is a vital structure in the road network and a cornerstone among crossing facilities. Yet, it suffers from the low usage by pedestrians as they try to cross the street on the level. This study is aimed to analyse the perceptions of Malaysian pedestrians towards the use of footbridges with the consideration of different factors. <b>Method</b>: The study was carried out by collecting data from the field observation and the questionnaire distribution on the street among the public. The data were statistically analysed by applying the multiple linear regression models and a series of Chi square test. <b>Results</b>: The study found that the most influential factor cited by pedestrians in decision making of using footbridge is the existence of an escalator. Hurriedness and the fear of heights were significantly associated with choosing not to use the footbridge. Zebra crossing was chosen as the most favourable type of crossing facility by the majority of respondents. Also, installation of fence and barriers was proposed as an effective procedure to prevent jaywalking. For constructing new and efficient footbridges in the future, the study suggested consideration of traffic volume, posted speed limit and the lanes number, as these are the most influential factors to predict the usage rate. <b>Conclusions</b>: The study encourages the decision makers and the stakeholders to consider providing escalators for the new footbridges to enhance the safety of the pedestrians.
DOI: 10.6084/m9.figshare.5400121
title: Distillability of GHZ Correlations

description: Qip 2016 poster
DOI: 10.6084/m9.figshare.5400121.v1
title: Distillability of GHZ Correlations

description: Qip 2016 poster
DOI: 10.6084/m9.figshare.5398888.v2
title: Entomological Collections in the Age of Big Data

description: Data of survey of 36 entomological collections published in Short, A.E.Z., Dikow, T., and Moreau, C.S. 2018. Entomological Collections in the Age of Big Data. Annual Review of Entomology 63: 513-530.doi: http://dx.doi.org/10.1146/annurev-ento-031616-035536
DOI: 10.6084/m9.figshare.5400328.v1
title: CIVIL RESPONSIBILITY OF THE STATE: BRIEF OVERVIEW OF BRAZILIAN LAW

description: For the last century, civil responsibility, which before used to be based on the agent’s guilt, little by little has been reorganizing since its premises to its reach. In Brazil, after the 1988’s Constitution, all legal order was reorganized and given new interpretation through its principles. A section of Civil Law that was greatly changed with the vision through constitutional principles was the one of civil responsibility, which changed the measurement of the guilt for the risk theory as a rule. Therefore, the government now also answers for its agent’s acts, no matter if they are guilty, and theirs actions must always be based on the principles of legality, impersonality, morality, publicity and efficiency, as stated in the article 37, caput, of Federal Constitution. That being said, it’s necessary a new behavior from the governors, from the agents, as well as from the citizens. This text intends to show an overview about the evolution of the Government’s Civil Responsibility, before social expectations and needs that come with modern times, its premises and exclusiveness.
DOI: 10.6084/m9.figshare.5398888.v1
title: Entomological Collections in the Age of Big Data

description: Data of survey of 36 entomological collections published in Short, A.E.Z., Dikow, T., and Moreau, C.S. 2018. Entomological Collections in the Age of Big Data. Annual Review of Entomology 63.doi: http://dx.doi.org/10.1146/annurev-ento-031616-035536
DOI: 10.6084/m9.figshare.5398600
title: Octopamine-and-Tyramine-play-a-role-in-the-counterregulatory-response-to-sugar-deficit-in-Drosophila: Reagent.table

description: Author reagent table (v2) for the eponymous manuscript. <br>
DOI: 10.6084/m9.figshare.5398618
title: Comparative transcriptomics in two bivalve species offers different perspectives on the evolution of sex-biased genes

description: Comparative genomics has become a central tool for evolutionary biology, and a better knowledge of understudied taxa represents the foundation for future work. In this study we characterized the transcriptome of male and female mature gonads in the European clam <i>Ruditapes decussatus</i>, compared to that in the Manila clam <i>Ruditapes philippinarum</i> providing, for the first time in bivalves, information about transcription dynamics and sequence evolution of sex-biased genes. In both the species we found a relatively low number of sex-biased genes (1,284, corresponding to 41.3 % of the orthologous genes between the two species), probably due to the absence of sexual dimorphism, and the transcriptional bias is maintained in only 33% of the orthologs. The dN/dS is generally low, indicating purifying selection, with genes where the female-biased transcription is maintained between the two species showing a significantly higher dN/dS. Genes involved in embryo development, cell proliferation, and maintenance of genome stability show a faster sequence evolution. Finally, we report a lack of clear correlation between transcription level and evolutionary rate in these species, in contrast with studies that reported a negative correlation. We discuss such discrepancy and call into question some methodological approaches and rationales generally used in this type of comparative studies.<br>
DOI: 10.6084/m9.figshare.5398618.v1
title: Comparative transcriptomics in two bivalve species offers different perspectives on the evolution of sex-biased genes

description: Comparative genomics has become a central tool for evolutionary biology, and a better knowledge of understudied taxa represents the foundation for future work. In this study we characterized the transcriptome of male and female mature gonads in the European clam <i>Ruditapes decussatus</i>, compared to that in the Manila clam <i>Ruditapes philippinarum</i> providing, for the first time in bivalves, information about transcription dynamics and sequence evolution of sex-biased genes. In both the species we found a relatively low number of sex-biased genes (1,284, corresponding to 41.3 % of the orthologous genes between the two species), probably due to the absence of sexual dimorphism, and the transcriptional bias is maintained in only 33% of the orthologs. The dN/dS is generally low, indicating purifying selection, with genes where the female-biased transcription is maintained between the two species showing a significantly higher dN/dS. Genes involved in embryo development, cell proliferation, and maintenance of genome stability show a faster sequence evolution. Finally, we report a lack of clear correlation between transcription level and evolutionary rate in these species, in contrast with studies that reported a negative correlation. We discuss such discrepancy and call into question some methodological approaches and rationales generally used in this type of comparative studies.<br>
DOI: 10.6084/m9.figshare.5398573
title: Model Onychomycosis Training Datasets (JPG thumbnails) and Validation Datasets (JPG images)

description: <b>1. Train dataset (Thumbnails)<br></b><i>A1 - Asan dataset</i> (49567 thumbnail images) - Diagnosis based on image findings +/- clinical diagnosis identified by chart review<i>A2 - Asan dataset</i> (3741 thumbnail images) - Clinical diagnosis identified by chart review<br><b>2. Validation dataset (1358 images)</b><i>B1 - Inje dataset</i> (100 images) - Culture<i>B2 - Inje dataset</i> (194 images) - KOH, or Culture, or Responsiveness to medications (TA ILI or antifungal drugs)<i>C - Hallym dataset</i> (125 images) - KOH, or Culture, or Responsiveness to medications (TA ILI or antifungal drugs)<i>D - Seoul dataset</i> (939 images) - KOH<br>
DOI: 10.6084/m9.figshare.5398537
title: Comparison chart of Vai script

description: This dataset is a comprehensive diachronic comparison of the Vai script of Liberia, as derived from sixteen sources dated between 1834 and 2005. It can be viewed as a webpage at https://ftp.shh.mpg.de/kelly/Vai.html.<br><br>Please note that a subset of these graphemes have been traced as svg vector images. You can download them here: https://doi.org/10.6084/m9.figshare.5897158.v1<br>The same graphemes with a black background can be found here: https://doi.org/10.6084/m9.figshare.5901337.v1
DOI: 10.6084/m9.figshare.5398522
title: Supplementary Material for: An Open-Label Study of the Long-Term Safety of Pirfenidone in Patients with Idiopathic Pulmonary Fibrosis (RECAP)

description: <b><i>Background:</i></b> RECAP (NCT00662038) was an open-label extension study in patients with idiopathic pulmonary fibrosis (IPF) who completed either the Assessment of Pirfenidone to Confirm Efficacy and Safety in Idiopathic Pulmonary Fibrosis (ASCEND) 016 phase 3 trial or the Clinical Studies Assessing Pirfenidone in Idiopathic Pulmonary Fibrosis: Research of Efficacy and Safety Outcomes (CAPACITY) 004/006 phase 3 trials. <b><i>Objective:</i></b> To obtain long-term safety data for pirfenidone in patients with IPF in RECAP. <b><i>Methods:</i></b> Of the 1,334 patients who participated in the phase 3 trials, 1,058 entered RECAP. The final analysis from enrollment (September 2008) to June 2015 is presented. <b><i>Results:</i></b> Mean (SD) and median (range) pirfenidone exposures in RECAP were 122 (98) weeks and 88 (&gt;0 to 349) weeks, respectively, with a mean daily dose of 2,091.1 mg. Cumulative total exposure was 2,482 patient exposure years (PEY). The treatment-emergent adverse event (TEAE) rate was 701.9 per 100 PEY. The serious TEAE rate was 53.5 per 100 PEY, with the most common serious TEAE being IPF (11.1 per 100 PEY). Of the 231 deaths (9.3 per 100 PEY), the most common cause was IPF (5.4 per 100 PEY). The treatment discontinuation rate due to a TEAE was 17.9 per 100 PEY; discontinuations were due to IPF (7.2 per 100 PEY), pneumonia, respiratory failure, acute respiratory failure, rash (0.5 per 100 PEY each), and nausea (0.4 per 100 PEY). For patients from CAPACITY 004/006 who entered RECAP, the mean change in percent predicted forced vital capacity from RECAP baseline at 180 weeks was -9.6%. Median on-treatment survival from the first pirfenidone dose in RECAP was 77.2 months. <b><i>Conclusions:</i></b> RECAP provides long-term follow-up and safety data for pirfenidone that were consistent with the known profile, with no new safety signals observed.
DOI: 10.6084/m9.figshare.5398537.v1
title: Comparison chart of Vai script

description: This dataset is a comprehensive diachronic comparison of the Vai script of Liberia, as derived from sixteen sources dated between ca. 1834 and 2005.