cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8320220.v1
title: Supplementary Material for: β-Catenin Expression and Activation in Conjunctival Melanoma

description: <b><i>Purpose:</i></b> To assess the role of the canonical Wnt pathway via activation of β-catenin in tumor progression of conjunctival melanoma. <b><i>Methods:</i></b> β-Catenin localization was assessed by immunohistochemistry in 43 conjunctival nevi, 48 primary acquired melanoses (PAM; conjunctival melanocytic intraepithelial neoplasia), and 44 conjunctival melanomas. Activation of the canonical or the noncanonical Wnt pathway was tested in vitro in 4 conjunctival melanoma cell lines with stimulation of either Wnt5a or Wnt3a. Wound healing assays were performed with Wnt5a. <b><i>Results:</i></b> Nuclear β-catenin expression was found in 16% of the nevi, in 15% of the melanomas, and in 4% of the PAM. Membranous β-catenin expression was identified in all the nevi and PAM and in 97.7% of the melanomas. In vitro, Wnt5a stimulation in the 4 conjunctival melanomas and in 1 skin melanoma cell line did not induce nuclear translocation of β-catenin, nor did it increase cell motility in the wound healing assays. Wnt3a stimulation did not induce nuclear localization of β-catenin in any of the cell lines tested. <b><i>Conclusions:</i></b> In conjunctival melanoma, nuclear localization and activation of β-catenin appear to be limited, suggesting that inhibition of ARF6, responsible for β-catenin activation, in subsets of skin melanoma may not represent a treatment option for this tumor. In vitro, Wnt3a or Wnt5a did not induce nuclear β-catenin localization.
DOI: 10.6084/m9.figshare.8320214.v1
title: Supplementary Material for: Variability in Palliative Care Use after Intracerebral Hemorrhage at US Hospitals: A Multilevel Analysis

description: <b><i>Background:</i></b> Palliative care (PC) is an essential component of comprehensive care of patients with intracerebral hemorrhage (ICH). In the present study, we sought to characterize the variability of PC use after ICH among US hospitals. <b><i>Methods:</i></b> ICH admissions from hospitals with at least 12 annual ICH cases were identified in the Nationwide Inpatient Sample between 2008 and 2011. We used multilevel logistic regression modeling to estimate between-hospital variance in PC use. We calculated the intraclass correlation coefficient (ICC), proportional variance change, and median OR after accounting for individual-level and hospital-level covariates. <b><i>Results:</i></b> Among 26,791 ICH admissions, 12.5% received PC (95% CI 11.5–13.5). Among the 629 included hospitals, the median rate of PC use was 9.1 (interquartile range 1.5–19.3) per 100 ICH admissions, and 150 (23.9%) hospitals had no recorded PC use. The ICC of the random intercept (null) model was 0.274, suggesting that 27.4% of the overall variability in PC use was due to between-hospital variability. Adding hospital-level covariates to the model accounted for 25.8% of the between-hospital variance observed in the null model, with 74.2% of between-hospital variance remaining unexplained. The median OR of the fully adjusted model was 2.62 (95% CI 2.41–2.89), indicating that a patient moving from 1 hospital to another with a higher intrinsic propensity of PC use had a 2.63-fold median increase in the odds of receiving PC, independent of patient and hospital factors. <b><i>Conclusions:</i></b> Substantial variation in PC use after ICH exists among US hospitals. A substantial proportion of this between-hospital variability remains unexplained even after accounting for patient and hospital characteristics.
DOI: 10.6084/m9.figshare.8320151
title: Basic statistical considerations for physiology: The journal <i>Temperature</i> toolbox

description: The average environmental and occupational physiologist may find statistics are difficult to interpret and use since their formal training in statistics is limited. Unfortunately, poor statistical practices can generate erroneous or at least misleading results and distorts the evidence in the scientific literature. These problems are exacerbated when statistics are used as thoughtless ritual that is performed after the data are collected. The situation is worsened when statistics are then treated as strict judgements about the data (i.e., significant versus non-significant) without a thought given to how these statistics were calculated or their practical meaning. We propose that researchers should consider statistics at every step of the research process whether that be the designing of experiments, collecting data, analysing the data or disseminating the results. When statistics are considered as an integral part of the research process, from start to finish, several problematic practices can be mitigated. Further, proper practices in disseminating the results of a study can greatly improve the quality of the literature. Within this review, we have included a number of reminders and statistical questions researchers should answer throughout the scientific process. Rather than treat statistics as a strict rule following procedure we hope that readers will use this review to stimulate a discussion around their current practices and attempt to improve them. The code to reproduce all analyses and figures within the manuscript can be found at https://doi.org/10.17605/OSF.IO/BQGDH.
DOI: 10.6084/m9.figshare.8320142
title: Pantagruel phylogenomic analysis of a bacterial pangenome covering 571 Rhizobiaceae genomes, with a focus on 41 Pseudorhizobium and Neorhizobium genomes

description: Comparative gebnomic analysis of 571 Rhizobiaceae genomes was conducted using the <i>Pantagruel</i> pipeline under the default settings as described by Lassalle et al. (2019). This pipeline is designed for the analysis of bacterial pangenomes, including the inference of a species tree, gene trees, and the detection of horizontal gene transfers (HGT) through species tree/gene tree reconciliations (Szöllősi et al. 2015).<br>The whole set of information derived from the <i>Pantagruel</i> processing of the 571 Rhizobiaceae pangenome is stored into a SQLite 3 database. This includes:- metadata on the 571 organisms and their genome assemblies;- annotation of 3,370,771 coding sequences (CDSs);- their classification into 50,792 homologous gene families.<br>In addition, for a subset of 41 genomes of strains of the genera <i>Pseudorhizobium</i> and <i>Neorhizobium</i> and their close relatives, a robust species tree and gene trees were reconstructed for 6,629 gene families represented in these genomes (covering 757,162 CDSs). For these gene families, species tree/gene tree reconciliation was used to infer evolutionary scenarios for each gene lineage, with events of gene duplication, origination, HGT and loss. This allowed the classification of genes into orthologous groups (i.e. a sub-clustering of the homologous 6,629 gene families). The database thus also hold information on:- 3,038,614 gene lineage events;- 19,016 orthologous groups.<br>
DOI: 10.6084/m9.figshare.8320151.v2
title: Basic statistical considerations for physiology: The journal <i>Temperature</i> toolbox

description: The average environmental and occupational physiologist may find statistics are difficult to interpret and use since their formal training in statistics is limited. Unfortunately, poor statistical practices can generate erroneous or at least misleading results and distorts the evidence in the scientific literature. These problems are exacerbated when statistics are used as thoughtless ritual that is performed after the data are collected. The situation is worsened when statistics are then treated as strict judgements about the data (i.e., significant versus non-significant) without a thought given to how these statistics were calculated or their practical meaning. We propose that researchers should consider statistics at every step of the research process whether that be the designing of experiments, collecting data, analysing the data or disseminating the results. When statistics are considered as an integral part of the research process, from start to finish, several problematic practices can be mitigated. Further, proper practices in disseminating the results of a study can greatly improve the quality of the literature. Within this review, we have included a number of reminders and statistical questions researchers should answer throughout the scientific process. Rather than treat statistics as a strict rule following procedure we hope that readers will use this review to stimulate a discussion around their current practices and attempt to improve them. The code to reproduce all analyses and figures within the manuscript can be found at https://doi.org/10.17605/OSF.IO/BQGDH.
DOI: 10.6084/m9.figshare.8320151.v1
title: Basic statistical considerations for physiology: The journal <i>temperature</i> toolbox

description: The average environmental and occupational physiologist may find statistics are difficult to interpret and use since their formal training in statistics is limited. Unfortunately, poor statistical practices can generate erroneous or at least misleading results and distorts the evidence in the scientific literature. These problems are exacerbated when statistics are used as thoughtless ritual that is performed after the data are collected. The situation is worsened when statistics are then treated as strict judgements about the data (i.e., significant versus non-significant) without a thought given to how these statistics were calculated or their practical meaning. We propose that researchers should consider statistics at every step of the research process whether that be the designing of experiments, collecting data, analysing the data or disseminating the results. When statistics are considered as an integral part of the research process, from start to finish, several problematic practices can be mitigated. Further, proper practices in disseminating the results of a study can greatly improve the quality of the literature. Within this review, we have included a number of reminders and statistical questions researchers should answer throughout the scientific process. Rather than treat statistics as a strict rule following procedure we hope that readers will use this review to stimulate a discussion around their current practices and attempt to improve them. The code to reproduce all analyses and figures within the manuscript can be found at https://doi.org/10.17605/OSF.IO/BQGDH.
DOI: 10.6084/m9.figshare.8320118
title: Air pollution, respiratory illness and behavioral adaptation: evidence from South Korea

description: The data set used in the paper as well as figures presented in the paper are provided.
DOI: 10.6084/m9.figshare.8320115
title: IAPs Imagery Data

description: Images for the convolutional neural networks training and testing.
DOI: 10.6084/m9.figshare.8320010
title: Qingre-Qushi Recipe (QRQS) ameliorated atopic skin inflammation in Th17-dominated mice via regulating the STAT3/STAT5 pathway

description: Flaky tail mice, a spontaneous Th17-dominated AD-model, were treated with different concentrations of QRQS and Cetirizine. The dermatitis score and scratching frequency were evaluated, and histological evaluation was performed according to a standard protocol. Changes in the T-helper cell population were analysed by flow cytometry. The serum levels of IgE and IgG1 were determined by ELISAs. The levels of T helper (Th) cell associated cytokines in serum and skin lesions were determined by ELISAs and RT-PCR. STAT5 and STAT3 were assessed by Immunoblotting.<br> QRQS ameliorated AD-like symptoms and decreased dermatitis scores and scratching frequencies. The middle dose of QRQS had the optimal effect, we study the potential mechanism based on this. After QRQS treatment, the imbalance of Th17/Treg was corrected. In addition. inhibited STAT5 was activated, and the associated cytokines were up-regulated. STAT3 overexpression was reversed, and the associated cytokines were downregulated. Moreover, the expression of Th2 cytokines was suppressed, and Th1 cytokines were overexpressed which may be attributed to changes in the STAT5 and STAT3 pathways <br>
DOI: 10.6084/m9.figshare.8320007
title: Array of buildings with incoming stratification

description: Experimental study of the influence of incoming stratification on flow and dispersion in an array of rectangular buildings
DOI: 10.6084/m9.figshare.8320010.v1
title: Qingre-Qushi Recipe (QRQS) ameliorated atopic skin inflammation in Th17-dominated mice via regulating the STAT3/STAT5 pathway

description: Flaky tail mice, a spontaneous Th17-dominated AD-model, were treated with different concentrations of QRQS and Cetirizine. The dermatitis score and scratching frequency were evaluated, and histological evaluation was performed according to a standard protocol. Changes in the T-helper cell population were analysed by flow cytometry. The serum levels of IgE and IgG1 were determined by ELISAs. The levels of T helper (Th) cell associated cytokines in serum and skin lesions were determined by ELISAs and RT-PCR. STAT5 and STAT3 were assessed by Immunoblotting.<br> QRQS ameliorated AD-like symptoms and decreased dermatitis scores and scratching frequencies. The middle dose of QRQS had the optimal effect, we study the potential mechanism based on this. After QRQS treatment, the imbalance of Th17/Treg was corrected. In addition. inhibited STAT5 was activated, and the associated cytokines were up-regulated. STAT3 overexpression was reversed, and the associated cytokines were downregulated. Moreover, the expression of Th2 cytokines was suppressed, and Th1 cytokines were overexpressed which may be attributed to changes in the STAT5 and STAT3 pathways <br>
DOI: 10.6084/m9.figshare.8320001
title: The alignment and tree files of phylogenetic analysis

description: the alignment and tree files of phylogenetic analysis
DOI: 10.6084/m9.figshare.8320001.v2
title: The alignment and tree files of phylogenetic analysis

description: the alignment and tree files of phylogenetic analysis
DOI: 10.6084/m9.figshare.8320004.v1
title: A database of functional traits of spiders from native forest of the Iberian Peninsula and Macaronesia

description: Spiders traits measurements: Detailed morphometric measurements dataset including all specimens (2841) of 505 spider species.<br>Aggregate Species Functional Traits: Summary of morphometric and ecological traits for 505 spider species
DOI: 10.6084/m9.figshare.8320001.v1
title: the alignment and tree files of phylogenetic analysis

description: the alignment and tree files of phylogenetic analysis
DOI: 10.6084/m9.figshare.8319980
title: The real-world economic impact of home-based video electroencephalography: the payer perspective

description: <b>Aims:</b> Electroencephalography (EEG) is an established method to evaluate and manage epilepsy; video EEG (VEEG) has significantly improved its diagnostic value. This study compared healthcare costs and diagnostic-related outcomes associated with outpatient vs inpatient VEEG among patients with epilepsy in the US. <b>Materials and methods:</b> This study used Truven MarketScan Commercial and Medicare Supplemental claims databases. Patients with a VEEG between July 1, 2013 and December 31, 2016 were identified. Index event was the first VEEG claim, which was used to determine inpatient and outpatient cohorts. Continuous health plan enrollment 6 months pre- and 12 months post-index VEEG was required. Primary outcomes were costs during the index event and 12 months post index. A generalized linear model with gamma distribution and a log link was used to estimate adjusted index and post-index costs. <b>Results:</b> Controlling for baseline differences, epilepsy-related cost of index VEEG was significantly lower for the outpatient ($4,098) vs the inpatient cohort ($13,821; <i>p</i> p p <b>Limitations:</b> Administrative claims data have limitations, including lack of data on clinical presentation, disease severity, and comprehensive health plan information. Generalizability may be limited to a US insured population of patients who met study criteria. <b>Conclusions:</b> Index VEEG was less costly in an outpatient vs inpatient cohort, and costs were lower during the follow-up period of 12 months, suggesting that outpatient VEEG can be provided to appropriate patients as a less costly option. There were fewer follow-up tests in the outpatient cohort with similar pre- and post-index diagnoses.
DOI: 10.6084/m9.figshare.8320004.v2
title: Spiders Functional Traits Dataset. Macaronesia_Iberian Peninsula

description: Individual Spiders traits measurements: Detailed morphometric measurements dataset including all specimens (2841) of 505 spider species.<br>Aggregate Species Functional Traits: Summary of morphometric and ecological traits for 505 spider species
DOI: 10.6084/m9.figshare.8319980.v1
title: The real-world economic impact of home-based video electroencephalography: the payer perspective

description: <b>Aims:</b> Electroencephalography (EEG) is an established method to evaluate and manage epilepsy; video EEG (VEEG) has significantly improved its diagnostic value. This study compared healthcare costs and diagnostic-related outcomes associated with outpatient vs inpatient VEEG among patients with epilepsy in the US. <b>Materials and methods:</b> This study used Truven MarketScan Commercial and Medicare Supplemental claims databases. Patients with a VEEG between July 1, 2013 and December 31, 2016 were identified. Index event was the first VEEG claim, which was used to determine inpatient and outpatient cohorts. Continuous health plan enrollment 6 months pre- and 12 months post-index VEEG was required. Primary outcomes were costs during the index event and 12 months post index. A generalized linear model with gamma distribution and a log link was used to estimate adjusted index and post-index costs. <b>Results:</b> Controlling for baseline differences, epilepsy-related cost of index VEEG was significantly lower for the outpatient ($4,098) vs the inpatient cohort ($13,821; <i>p</i> p p <b>Limitations:</b> Administrative claims data have limitations, including lack of data on clinical presentation, disease severity, and comprehensive health plan information. Generalizability may be limited to a US insured population of patients who met study criteria. <b>Conclusions:</b> Index VEEG was less costly in an outpatient vs inpatient cohort, and costs were lower during the follow-up period of 12 months, suggesting that outpatient VEEG can be provided to appropriate patients as a less costly option. There were fewer follow-up tests in the outpatient cohort with similar pre- and post-index diagnoses.
DOI: 10.6084/m9.figshare.8319965
title: Supplementary Material for: Glucagon-Like Peptide-1-, but not Growth and Differentiation Factor 15-, Receptor Activation Increases the Number of Interleukin-6-Expressing Cells in the External Lateral Parabrachial Nucleus

description: Interleukin (IL)-6 in the hypothalamus and hindbrain is an important downstream mediator of suppression of body weight and food intake by glucagon-like peptide-1 (GLP-1) receptor stimulation. CNS GLP-1 is produced almost exclusively in prepro-glucagon neurons in the nucleus of the solitary tract. These neurons innervate energy balance-regulating areas, such as the external lateral parabrachial nucleus (PBNel); essential for induction of anorexia. Using a validated novel IL-6-reporter mouse strain, we investigated the interactions in PBNel between GLP-1, IL-6, and calcitonin gene-related peptide (CGRP, a well-known mediator of anorexia). We show that PBNel GLP-1R-containing cells highly (to about 80%) overlap with IL-6-containing cells on both protein and mRNA level. Intraperitoneal administration of a GLP-1 analogue exendin-4 to mice increased the proportion of IL-6-containing cells in PBNel 3-fold, while there was no effect in the rest of the lateral parabrachial nucleus. In contrast, injections of an anorexigenic peptide growth and differentiation factor 15 (GDF15) markedly increased the proportion of CGRP-containing cells, while IL-6-containing cells were not affected. In summary, GLP-1R are found on IL-6-producing cells in PBNel, and GLP-1R stimulation leads to an increase in the proportion of cells with IL-6-reporter fluorescence, supporting IL-6 mediation of GLP-1 effects on energy balance.
DOI: 10.15131/shef.data.8319956
title: Data used in the study "A new method to monitor bone geometry changes at different spatial scales in the longitudinal in vivo μCT studies of mice bones"

description: Link to the data used in:<br>Yang Z, Dall’Ara E, Viceconti M, Kadirkamanathan V (2019) <br><i>An approach to split bone growth and remodelling from longitudinal in vivo microCT imaging of the mouse tibia;</i> Plos One 2019.<br>The folder includes examples of microCT images cropped for the analyses that are used as input of the computational frameworks. In the folder there are dicom files of:<br>1x Wild Type Mouse scanned at week 16 of age (WildM5W2N1228cropped)1x Wild Type Mouse scanned at week 14 of age (WildM5W20N1228cropped)<br>The "Code" used to process the images can be found in:https://doi.org/10.15131/shef.data.8397989<br><br>The whole dataset is stored in the University of Sheffield file-store at the link:https://web-unidrive.sheffield.ac.uk/shared/multisim2/WP6/YangZhang<br>For further information please contact Dr Enrico Dall'Ara: e.dallara@sheffield.ac.uk p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica}
DOI: 10.15131/shef.data.8319956.v1
title: Data used in the study "A new method to monitor bone geometry changes at different spatial scales in the longitudinal in vivo μCT studies of mice bones"

description: Link to the data used in:<br>Yang Z, Dall’Ara E, Viceconti M, Kadirkamanathan V (2019) <br><i>An approach to split bone growth and remodelling from longitudinal in vivo microCT imaging of the mouse tibia;</i> Plos One 2019.<br>The folder includes examples of microCT images cropped for the analyses that are used as input of the computational frameworks. In the folder there are dicom files of:<br>1x Wild Type Mouse scanned at week 16 of age (WildM5W2N1228cropped)1x Wild Type Mouse scanned at week 14 of age (WildM5W20N1228cropped)<br>The "Code" used to process the images can be found in:https://doi.org/10.15131/shef.data.8397989<br><br>The whole dataset is stored in the University of Sheffield file-store at the link:https://web-unidrive.sheffield.ac.uk/shared/multisim2/WP6/YangZhang<br>For further information please contact Dr Enrico Dall'Ara: e.dallara@sheffield.ac.uk p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica}