cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4822939
title: Supplementary Material for: Poly-(ADP-Ribose) Polymerase-1 Promotes Prothrombin Gene Transcription and Produces Des-Gamma-Carboxy Prothrombin in Hepatocellular Carcinoma

description: <b><i>Background and Aim:</i></b> Although des-gamma-carboxy prothrombin (DCP) is a well-known tumor marker for hepatocellular carcinoma (HCC), the mechanism of DCP production is unclear. This study aimed to investigate the mechanism how DCP is produced in HCC cells. <b><i>Methods:</i></b> Levels of mRNA and DCP were analyzed by real-time polymerase chain reaction and electro-chemiluminescence immunoassay respectively. Secreted alkaline phosphatase (SEAP) expression vectors including deletion mutants of the prothrombin gene promoter were constructed for reporter gene assay. The transcription factors bound to DNA fragments were analyzed by mass spectrometry. An electrophoretic mobility shift assay (EMSA) was performed using a biotin end-labeled DNA. <b><i>Results:</i></b> The prothrombin mRNA levels in all 5 DCP producing cell lines were appreciably high. However, those in 2 DCP non-producing cell lines were below detectable levels. A SEAP vector with -2985 to +27 showed a very high transcription activity in DCP-producing Huh-1 cells. However, transcription abruptly decreased when the vector with -2955 to +27 was transfected, and then remained at the similar levels with larger deletion mutants, indicating the existence of a cis-element at -2985 to -2955 (31-bp). Mass spectrometry analysis identified the protein that bound to the 31-bp DNA as poly-(ADP-ribose) polymerase-1 (PARP-1). Knockdown of the PARP-1 gene by small interfering RNA in Huh-1 cells induced marked inhibition of prothrombin gene transcription. The EMSA clearly showed that PARP-1 specifically binds to the 31-bp DNA fragment in the prothrombin gene promoter. <b><i>Conclusions:</i></b> Our data suggest that PARP-1 activates prothrombin gene transcription and that the excessive prothrombin gene transcription induces DCP production in DCP-producing HCC cells.
DOI: 10.6084/m9.figshare.4822933
title: Supplementary Material for: Is Reperfusion Useful in Ischaemic Stroke Patients Presenting with a Low National Institutes of Health Stroke Scale and a Proximal Large Vessel Occlusion of the Anterior Circulation?

description: <b><i>Background:</i></b> In population-based studies, patients presenting with minor or mild stroke symptoms represent about two-thirds of stroke patients, and almost one-third of these patients are unable to ambulate independently at the time of discharge. Although mechanical thrombectomy (MT) has become the standard of care for acute ischaemic stroke with proximal large vessel occlusion (LVO) in the anterior circulation, the management of patients harbouring proximal occlusion and minor-to-mild stroke symptoms has not yet been determined by recent trials. The purpose of this study was to evaluate the impact of reperfusion on clinical outcome in low National Institutes of Health Stroke Scale (NIHSS) patients treated with MT. <b><i>Methods:</i></b> We analysed 138 consecutive patients with acute LVO of the anterior circulation (middle cerebral artery M1 or M2 segment, internal carotid artery or tandem occlusion) with NIHSS &lt;8, having undergone MT in 3 different centres. Reperfusion was graded using the modified thrombolysis in cerebral infarction (TICI) score and 3 grades were defined, ranging from failed or poor reperfusion (TICI 0, 1, 2A) to complete reperfusion (TICI 3). The primary clinical endpoint was an excellent outcome defined as a modified Rankin score (mRs) 0-1 at 3-months. The impact of reperfusion grade was assessed in univariate and multivariate analyses. The secondary endpoints included favourable functional outcome (90-day mRS 0-2), death and safety concerns. <b><i>Results:</i></b> Successful reperfusion was achieved in 81.2% of patients (TICI 2B, <i>n</i> = 47; TICI 3, <i>n</i> = 65). Excellent outcome (mRs 0-1) was achieved in 69 patients (65.0%) and favourable outcome (mRs ≤2) in 108 (78.3%). Death occurred in 7 (5.1%). Excellent outcome increased with reperfusion grades, with a rate of 34.6% in patients with failed/poor reperfusion, 61.7% in patients with TICI 2B reperfusion, and 78.5% in patients with TICI 3 reperfusion (<i>p</i> &lt; 0.001). In multivariate analysis adjusted for patient characteristics associated with excellent outcome, the reperfusion grade remained significantly associated with an increase in excellent outcome; the OR (95% CI) was 3.09 (1.06-9.03) for TICI 2B and 6.66 (2.27-19.48) for TICI 3, using the failed/poor reperfusion grade as reference. Similar results were found regarding favourable outcome (90-day mRs 0-2) or overall mRS distribution (shift analysis). <b><i>Conclusion:</i></b> Successful reperfusion is strongly associated with better functional outcome among patients with proximal LVO in the anterior circulation and minor-to-mild stroke symptoms. Randomized controlled studies are mandatory to assess the benefit of MT compared with optimal medical management in this subset of patients.
DOI: 10.6084/m9.figshare.4822912
title: Raw Data

description: Raw data includes the inputs data for the proposed model in three financial markets.Those data is downloaded from WIND database and CSMAR database.
DOI: 10.6084/m9.figshare.12906773
title: Supplementary Material for: Sex Differences in the Control of Social Investigation and Anxiety by Vasopressin Cells of the Paraventricular Nucleus of the Hypothalamus

description: The neuropeptide arginine-vasopressin (AVP) has long been implicated in the regulation of social behavior and communication in diverse taxa, but the source of AVP release relevant for behavior has not been precisely determined. Potential sources include hypothalamic cell populations such as the paraventricular (PVN), supraoptic, and suprachiasmatic nuclei, as well as extrahypothalamic cell groups in the extended amygdala. To address if AVP-expressing cells in the PVN are important for mouse social communication, we deleted PVN AVP-expressing cells using viral-mediated delivery of Cre-dependent caspase-9 cell death construct into the PVN of AVP-Cre-positive mice (expressing Cre-recombinase under the control of the AVP promoter) or AVP-Cre-negative littermate controls, and assessed their levels of social investigation, social communication, anxiety, sex behavior, and aggressive behavior. We found that these lesions increased social investigation in females, but not in males. However, in males but not in females, these lesions increased non-social anxiety-related behaviors in the elevated-plus maze. These results therefore point at differential involvement of PVN AVP-expressing cells in the context of social and emotional behavior in the two sexes, which may contribute to sex differences in social communication and anxiety disorders.
DOI: 10.6084/m9.figshare.4822852
title: Dynamical response properties of neocortical neurons to conductance-driven time-varying inputs

description: Public data repository related to the paper authored by Linaro et al. (2017), published on the European Journal of Neuroscience.<br>Ensembles of cortical neurons can track fast-varying inputs and relay them in their spike trains, far beyond the cutoff imposed by membrane passive electrical properties and mean firing rates. Initially explored in silico and later demonstrated experimentally, investigating how neurons respond to sinusoidally-modulated stimuli provides a deeper insight into spike-initiation mechanisms and information processing than conventional F-I curve methodologies. Besides net membrane currents, physiological synaptic inputs can also induce a stimulus-dependent modulation of the total membrane conductance, which is not reproduced by standard current-clamp protocols.<br>In this work, we investigated whether rat cortical neurons can track fast temporal modulations over a noisy conductance background. We also determined input-output transfer properties over a range of conditions, including: distinct presynaptic activation rates, postsynaptic firing rates and variability, and type of temporal modulations. We found a very broad signal transfer bandwidth across all conditions, similar large cutoff frequencies and power-law attenuations of fast-varying inputs. At slow and intermediate input modulations, the response gain decreased for increasing output mean firing rates. The gain also decreased significantly for increasing intensities of background synaptic activity, thus generalising earlier studies on F-I curves. We also found a direct correlation between the action potentials’ onset rapidness and the neuronal bandwidth. Our novel results extend previous investigations of dynamical response properties to non-stationary and conductance-driven conditions, and provide computational neuroscientists with a novel set of observations that models must capture when aiming to replicate cortical cellular excitability.
DOI: 10.6084/m9.figshare.4822837
title: S1 Table.docx

description: Survival of <i>M. bovis</i> in two soils having contrasted physical and chemical characteristics. Experiments were conducted under laboratory conditions using microcosms containing either fresh soil or desinfected soil.<br>Survival was measured by a culture based approach for sterile soil and using a molecular qPCR assay for both sterile and fresh soils<br>
DOI: 10.6084/m9.figshare.4822843
title: Results

description: The dataset includes the predictive performance and profitability performance of each model. On the top panel, there are quarterly performance. On the bottom panel, there are yearly performance. Each sheet describes the results in each financial market.
DOI: 10.6084/m9.figshare.4822843.v1
title: Results

description: The dataset includes the predictive performance and profitability performance of each model. On the top panel, there are quarterly performance. On the bottom panel, there are yearly performance. Each sheet describes the results in each financial market.
DOI: 10.6084/m9.figshare.12906773.v1
title: Supplementary Material for: Sex Differences in the Control of Social Investigation and Anxiety by Vasopressin Cells of the Paraventricular Nucleus of the Hypothalamus

description: The neuropeptide arginine-vasopressin (AVP) has long been implicated in the regulation of social behavior and communication in diverse taxa, but the source of AVP release relevant for behavior has not been precisely determined. Potential sources include hypothalamic cell populations such as the paraventricular (PVN), supraoptic, and suprachiasmatic nuclei, as well as extrahypothalamic cell groups in the extended amygdala. To address if AVP-expressing cells in the PVN are important for mouse social communication, we deleted PVN AVP-expressing cells using viral-mediated delivery of Cre-dependent caspase-9 cell death construct into the PVN of AVP-Cre-positive mice (expressing Cre-recombinase under the control of the AVP promoter) or AVP-Cre-negative littermate controls, and assessed their levels of social investigation, social communication, anxiety, sex behavior, and aggressive behavior. We found that these lesions increased social investigation in females, but not in males. However, in males but not in females, these lesions increased non-social anxiety-related behaviors in the elevated-plus maze. These results therefore point at differential involvement of PVN AVP-expressing cells in the context of social and emotional behavior in the two sexes, which may contribute to sex differences in social communication and anxiety disorders.
DOI: 10.6084/m9.figshare.4822837.v1
title: S1 Table.docx

description: Survival of <i>M. bovis</i> in two soils having contrasted physical and chemical characteristics. Experiments were conducted under laboratory conditions using microcosms containing either fresh soil or desinfected soil.<br>Survival was measured by a culture based approach for sterile soil and using a molecular qPCR assay for both sterile and fresh soils<br>
DOI: 10.6073/pasta/b01cc58393c5facc46d5ec6cc2a571c6
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 1 meteorological station: 30-minute soil volumetric water content data: 2013 - ongoing

description: 30-minute Soil Moisture data at 10 cm at CSIS Block-1. Collection of soil volumetric water content data at Jornada LTER Cross-scale Interactions Study (CSIS) blocks, New Mexico, supports the environmental monitoring objectives of the Jornada LTER monitoring program that look at plant-soil water dynamics. Soil volumetric water content is measured at 10 cm depth at 3 locations at each of the 4 plots per block. The locations in each plot are under bare soil, under perennial grass, and under shrub. Volumetric water content, bulk electrical conductivity, soil temperature, and bulk dielectric permittivity are recorded every 30 minutes at an automated meteorological station installed at Jornada LTER CSIS Block-1 site. This is an ONGOING dataset.
DOI: 10.15129/8d96c441-f379-4176-b87d-a05d1c837c50
title: Data for: "Investigation of the effect of silica aerogel particle on thermal and mechanical properties of epoxy composite"

description: Data collected during PhD study leading to publication of paper titled "Investigation of the effect of silica aerogel particle on thermal and mechanical properties of epoxy composite" in Composites Part A. Following data includes: Density measurement of silica aerogel/epoxy composites (Aerogel_density_calculations.xlsx) Thermal conductivity measurements (TC_results.xlsx) Summary of mechanical testing data (Aerogel_mech_data.xlsx) BET results (BET_results.zip) Particle Size analysis (Particles_Size_Analysis.zip) SEM images of composites (SEM_images.zip) Raw data for mechanical testing (Compressive_testing_raw_data.zip)
DOI: 10.6084/m9.figshare.4822231
title: Perfect imperfections: Locus of control, self-oriented and socially-prescribed perfectionism, and postpartum depression

description: A sample of 243 women completed an online self-report questionnaires for self-oriented and socially-prescribed perfectionism , locus of control, and postpartum depression.
DOI: 10.6084/m9.figshare.4822243
title: Medaka_Fish_3D_Polygon_Models 3ds-MAX / Color-modified

description: Medaka_Fish_3D_Polygon_Models.<br>3ds-MAX files.
DOI: 10.6084/m9.figshare.4822255.v1
title: Knight DR PhD Thesis - Clostridium difficile ST11 genomes, n=207

description: Genome assemblies<br>
DOI: 10.6084/m9.figshare.4822231.v2
title: Perfect imperfections: Locus of control, self-oriented and socially-prescribed perfectionism, and postpartum depression

description: A sample of 243 women completed an online self-report questionnaires for self-oriented and socially-prescribed perfectionism , locus of control, and postpartum depression.
DOI: 10.6084/m9.figshare.4822231.v1
title: Perfect imperfections: Locus of control, self-oriented and socially-prescribed perfectionism , and postpartum depression

description: A sample of 243 women completed an online self-report questionnaires for self-oriented and socially-prescribed perfectionism , locus of control, and postpartum depression.
DOI: 10.6084/m9.figshare.4822255.v2
title: Supplemental material for Knight et al. 2019 mBio

description: Supplementary FiguresSupplementary TablesGenome assemblies<br>
DOI: 10.6084/m9.figshare.4822177
title: Dataset for: Economic evaluation of factorial randomised controlled trials: Challenges, methods and recommendations

description: Increasing numbers of economic evaluations are conducted alongside randomised controlled trials. Such studies include factorial trials, which randomise patients to different levels of two or more factors and can therefore evaluate the effect of multiple treatments alone and in combination. Factorial trials can provide increased statistical power or assess interactions between treatments, but raise additional challenges for trial-based economic evaluations: interactions may occur more commonly for costs and quality-adjusted life-years (QALYs) than for clinical endpoints; economic endpoints raise challenges for transformation and regression analysis; and both factors must be considered simultaneously to assess which treatment combination represents best value for money. This article aims to examine issues associated with factorial trials that include assessment of costs and/or cost-effectiveness, describe the methods that can be used to analyse such studies; and make recommendations for health economists, statisticians and trialists. A hypothetical worked example is used to illustrate the challenges and demonstrate ways in which economic evaluations of factorial trials may be conducted, and how these methods affect the results and conclusions. Ignoring interactions introduces bias that could result in adopting a treatment that does not make best use of healthcare resources, while considering all interactions avoids bias but reduces statistical power. We also introduce the concept of the opportunity cost of ignoring interactions as a measure of the bias introduced by not taking account of all interactions. We conclude by offering recommendations for planning, analysing and reporting economic evaluations based on factorial trials, taking increased analysis costs into account.
DOI: 10.6084/m9.figshare.4822177.v1
title: Dataset for: Economic evaluation of factorial randomised controlled trials: Challenges, methods and recommendations

description: Increasing numbers of economic evaluations are conducted alongside randomised controlled trials. Such studies include factorial trials, which randomise patients to different levels of two or more factors and can therefore evaluate the effect of multiple treatments alone and in combination. Factorial trials can provide increased statistical power or assess interactions between treatments, but raise additional challenges for trial-based economic evaluations: interactions may occur more commonly for costs and quality-adjusted life-years (QALYs) than for clinical endpoints; economic endpoints raise challenges for transformation and regression analysis; and both factors must be considered simultaneously to assess which treatment combination represents best value for money. This article aims to examine issues associated with factorial trials that include assessment of costs and/or cost-effectiveness, describe the methods that can be used to analyse such studies; and make recommendations for health economists, statisticians and trialists. A hypothetical worked example is used to illustrate the challenges and demonstrate ways in which economic evaluations of factorial trials may be conducted, and how these methods affect the results and conclusions. Ignoring interactions introduces bias that could result in adopting a treatment that does not make best use of healthcare resources, while considering all interactions avoids bias but reduces statistical power. We also introduce the concept of the opportunity cost of ignoring interactions as a measure of the bias introduced by not taking account of all interactions. We conclude by offering recommendations for planning, analysing and reporting economic evaluations based on factorial trials, taking increased analysis costs into account.
DOI: 10.6084/m9.figshare.4822195.v1
title: Medaka_3D_models MP4 Videos

description: Medaka_3D_models MP4 Videos (1920 x 1080, 1 min each)
DOI: 10.6084/m9.figshare.4822255.v3
title: Supplemental material for Knight et al. 2019 mBio

description: Supplementary FiguresSupplementary TablesGenome assemblies<br>
DOI: 10.6084/m9.figshare.4822135
title: Canadian Provincial Spending on Women's Issues, 2001-2016

description: A dataset with 4 Canadian provinces and spending on five women's issues from 2001-2016..
DOI: 10.6084/m9.figshare.4822108
title: Canadian provincial spending on women's issues 2001-2016

description: A dataset of funding by BC, AB, MB, and NS of 5 women's issues from 2001-2016.
DOI: 10.6084/m9.figshare.4822195.v2
title: Medaka_3D_Models MP4 Videos

description: Medaka_3D_models MP4 Videos (1920 x 1080, 60Hz, 1 min each)Gray, Pressed, No-local-motion, No-global-motion, and Normal Models.
DOI: 10.6084/m9.figshare.4822102
title: AKAP95 interacts with nucleoporin TPR in mitosis and is important for the spindle assembly checkpoint

description: Faithful chromosome segregation during mitosis relies on a proofreading mechanism that monitors proper kinetochore-microtubule attachments. The spindle assembly checkpoint (SAC) is based on the concerted action of numerous components that maintain a repressive signal inhibiting transition into anaphase until all chromosomes are attached. Here we show that A-Kinase Anchoring Protein 95 (AKAP95) is necessary for proper SAC function. AKAP95-depleted HeLa cells show micronuclei formed from lagging chromosomes at mitosis. Using a BioID proximity-based proteomic screen, we identify the nuclear pore complex protein TPR as a novel AKAP95 binding partner. We show interaction between AKAP95 and TPR in mitosis, and an AKAP95-dependent enrichment of TPR in the spindle microtubule area in metaphase, then later in the spindle midzone area. AKAP95-depleted cells display faster prometaphase to anaphase transition, escape from nocodazole-induced mitotic arrest and show a partial delocalization from kinetochores of the SAC component MAD1. Our results demonstrate an involvement of AKAP95 in proper SAC function likely through its interaction with TPR.
DOI: 10.6084/m9.figshare.4822135.v1
title: Canadian Provincial Spending on Women's Issues, 2001-2016

description: A dataset with 4 Canadian provinces and spending on five women's issues from 2001-2016..
DOI: 10.6084/m9.figshare.4822093
title: Influence of exercise duration on cardiorespiratory responses, energy cost and tissue oxygenation within a 6 hour treadmill run

description: Dataset for results of 6TR study conducted at the University of the Sunshine Coast
DOI: 10.6084/m9.figshare.4822108.v1
title: Canadian provincial spending on women's issues 2001-2016

description: A dataset of funding by BC, AB, MB, and NS of 5 women's issues from 2001-2016.
DOI: 10.6084/m9.figshare.4822255.v4
title: Supplemental material for Knight et al. 2019 mBio

description: Supplementary FiguresSupplementary TablesGenome assemblies<br>
DOI: 10.6084/m9.figshare.4822093.v1
title: Influence of exercise duration on cardiorespiratory responses, energy cost and tissue oxygenation within a 6 hour treadmill run

description: Dataset for results of 6TR study conducted at the University of the Sunshine Coast
DOI: 10.6084/m9.figshare.4822102.v2
title: AKAP95 interacts with nucleoporin TPR in mitosis and is important for the spindle assembly checkpoint

description: Faithful chromosome segregation during mitosis relies on a proofreading mechanism that monitors proper kinetochore-microtubule attachments. The spindle assembly checkpoint (SAC) is based on the concerted action of numerous components that maintain a repressive signal inhibiting transition into anaphase until all chromosomes are attached. Here we show that A-Kinase Anchoring Protein 95 (AKAP95) is necessary for proper SAC function. AKAP95-depleted HeLa cells show micronuclei formed from lagging chromosomes at mitosis. Using a BioID proximity-based proteomic screen, we identify the nuclear pore complex protein TPR as a novel AKAP95 binding partner. We show interaction between AKAP95 and TPR in mitosis, and an AKAP95-dependent enrichment of TPR in the spindle microtubule area in metaphase, then later in the spindle midzone area. AKAP95-depleted cells display faster prometaphase to anaphase transition, escape from nocodazole-induced mitotic arrest and show a partial delocalization from kinetochores of the SAC component MAD1. Our results demonstrate an involvement of AKAP95 in proper SAC function likely through its interaction with TPR.
DOI: 10.6084/m9.figshare.4822069
title: Annotation table for A. ervi transcriptome, filtered dataset

description: Annotation table (generated with BlastX against NR database, GO terms assigned with Blas2go) of <i>A. ervi</i> transcriptome dataset. <br>
DOI: 10.6084/m9.figshare.4822255.v5
title: Supplemental material for Knight et al. 2019 mBio

description: Supplementary FiguresSupplementary TablesGenome assemblies<br>