cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8953559.v1
title: The genetic relationships within <i>Apiognomonia errabunda</i> and related species

description: Species of <i>Apiognomonia</i> are some of the most ubiquitous leaf-associated fungi of broad-leaved trees of the northern temperate zone. Especially widespread and diverse is <i>Apiognomonia errabunda</i>, found mostly on beech, oak, and linden. This species and its closest relatives are known for their complicated phylogenetic relationships that have caused considerable confusion in the past. In the present paper, we describe the results of a three-gene-based reconstruction of phylogenetic relationships between <i>A. errabunda, A. veneta</i>, and <i>A. hystrix</i> for 373 isolates. Using combined information from the nuc rDNA internal transcribed spacer region ITS1‐5.8S‐ITS2 (ITS barcode) and intron regions of actin (<i>ACT</i>) and calmodulin (<i>CAL</i>) genes for 263 isolates, we confirmed the occurrence of host-associated lineages within <i>A. errabunda</i>. However, the clustering of isolates by host species was incomplete: some isolates occurred on the “wrong” hosts and a number of isolates carried mixed genetic profile, indicating substantial level of inter-host group recombination. In addition, a number of isolates were identified as putative, pending further verification, interspecies hybrids between the much more divergent <i>A. errabunda</i> and <i>A. hystrix</i>.
DOI: 10.6084/m9.figshare.8953355
title: Table S3 from Identification of proteins in the adhesive trails of the diatom <i>Amphora coffeaeformis</i>

description: Tabular overview of identified protein hits. NCBI BLAST results are shown for protein hits that returned an E-value less than 1E-06. Top hits are given for both the top diatom and non-diatom species. A hypen (-) indicates the absence of the attribute.
DOI: 10.6084/m9.figshare.8953229
title: Differentially expressed gene lists - Repeats (mapped with a transcriptome reference)

description: Differentially expressed gene lists - Repeats (mapped with a transcriptome reference)<br>Data for Collins et al. 2019 (doi: 10.7554/eLife.30860) p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica} These are files of differentially expressed repeat sequences (as defined by repeatmasker). This is an initial analysis using reads mapped to the genome using a reference transcriptome to see the extent of misregulation of repeats before remapping the reads without a reference transcriptome.<br>see README.md for more details<br>
DOI: 10.6084/m9.figshare.8953229.v1
title: Differentially expressed gene lists - Repeats (mapped with a transcriptome reference)

description: Differentially expressed gene lists - Repeats (mapped with a transcriptome reference)<br>Data for Collins et al. 2019 (doi: 10.7554/eLife.30860) p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica} These are files of differentially expressed repeat sequences (as defined by repeatmasker). This is an initial analysis using reads mapped to the genome using a reference transcriptome to see the extent of misregulation of repeats before remapping the reads without a reference transcriptome.<br>see README.md for more details<br>
DOI: 10.17028/rd.lboro.8953118
title: Pathways of antibiotic use in humans and animals in Bangladesh: transcripts of interviews with household members and healthcare providers

description: The dataset presents transcripts of interviews conducted around antibiotic use in humans and animals in Bangladesh. Interviews examined antibiotic use and behaviours contributing to antibiotic resistance from the perspective of household members and healthcare providers in one urban and one rural site in Bangladesh. Household interviews were carried out with the household decision-maker or main care-giver (total 48 interviews). Healthcare provider interviews were carried out with a range of qualified and unqualified providers from human and veterinary medicine (total 46 interviews). The interviews gathered information on where people sought treatment for illnesses due to infection, what determined their choice of healthcare provider; factors contributing to antibiotic use in humans and animals; knowledge and understanding of antibiotic resistance. Similar questions about antibiotic prescribing and selling practices were asked of healthcare providers.<br>Interviews were conducted in Bangla, audio-recorded and transcribed anonymously. All transcripts are available in Bangla as .pdf files. A proportion of transcripts have been translated to English and are available in word files. <br>Further information on the study as well as details on methods and analysis are available under a CC-BY licence at https://doi.org/10.1136/bmjopen-2018-028215 or https://dspace.lboro.ac.uk/2134/36467<br>The guides used to conduct the interviews are available at: https://doi.org/10.17028/rd.lboro.9333158.v1
DOI: 10.6084/m9.figshare.12869864
title: Aspergillus fumigatus G-protein coupled receptors GprM and GprJ are important for the regulation of the cell wall integrity pathway, secondary metabolite production, and virulence

description: G-protein coupled receptors (GPCRs) are extracellular signalling receptors that sense environmental cues to coordinate a biological response. Fungi sense their environment primarily through GPCR-mediated signalling pathways, which in turn regulate fungal development, metabolism, virulence and mycotoxin biosynthesis. <i>A. fumigatus</i> is an important human pathogen that causes aspergillosis, a heterogeneous group of diseases that presents a wide range of clinical manifestations. Here, we investigate in detail the role of the GPCRs GprM and GprJ in growth and gene expression. GprM and GprJ are important for melanin production and the regulation of the cell wall integrity (CWI) pathway. Overexpression of <i>gprM</i> and <i>gprJ </i>causes a 20 and 50% reduction in growth rate when compared to the wild-type (WT) strain, and increases sensitivity to cell wall-damaging agents. Phosphorylation of the CWI protein kinase MpkA is increased in the Δ<i>gprM</i> and Δ<i>gprJ</i> strains and decreased in the overexpression mutants when compared to the WT strain. Furthermore, differences in cell wall polysaccharide concentrations and organization were observed in these strains. RNA-sequencing suggests that GprM and GprJ negatively regulate genes encoding secondary metabolites (SMs). Mass spectrometry analysis confirmed that the production of fumagillin, pyripyropene, fumigaclavine C, fumiquinazoline, and fumitremorgin is reduced in the Δ<i>gprM</i> and Δ<i>gprJ</i> strains, and that this regulation occurs, at least partially, through the activation of MpkA. Overexpression of <i>grpM</i> also resulted in the regulation of many transcription factors, with AsgA predicted to function downstream of GprM and MpkA signalling. Finally, we show that the Δ<i>gprM</i> and Δ<i>gprJ</i> mutants are reduced in virulence in the <i>Galleria mellonella</i> insect model of invasive aspergillosis. This work further contributes to unravelling functions of <i>A. fumigatus</i> GPCRs and shows that GprM and GprJ are essential for CWI, secondary metabolite production and virulence. <b> </b>
DOI: 10.6084/m9.figshare.8952989
title: Online Supplementary physiology R2.docx

description: Supplementary Tables for AJP-Heart and Circulatory Physiology H-00062-2019<br>
DOI: 10.6084/m9.figshare.8953124
title: Demonstration Tray Data

description: Data stored in a zipped ~1.5Gb MATLAB .mat file.<br>---<br>See [Sena, Howard 2019] for full details on data collection, summary below (link 1 in references).<br>---<br>Data formatted to follow similar internal 's' structure as [Calinon 2015] (link 2 in references).<br><br>----<br>Loads a struct 'groups'. Contains data from a 4 x 3 mixed ANOVA style study.<br>Condition 1: No FeedbackCondition 2: Replay FeedbackCondition 3: Batch FeedbackCondition 4: Selected Feedback<br>See [Sena, Howard 2019] for full details on test conditions (link 1 in references).<br><br>----<br>Data collected from novice participants using a Rethink Robotics Sawyer collaborative robot to perform a horticultural tray sorting manipulation task. <br>---<br>4 groups, one for each condition.Each group contains:- demos : Set of data collected from users-- Each row in demos represents a participant.-- Each column represents an attempt at the assigned condition.-- Contains sub structs containing the experiment data for each attempt (demonstration data trajectories, etc.)- repos : Set of data generated with TP-GMR model, as described in [Sena, Howard 2019]-- Rows and columns same as demos, but all data is generated from the model.-- Same sub structs as demos, except there will be 100 trajectories (one for each target plant in the experiment tray).<br>---<br>This experiment was conducted with ethical approval granted by King's College London Research Ethics Committee under LRS-17/18-5549.<br>
DOI: 10.6084/m9.figshare.8952989.v1
title: Online Supplementary physiology R2.docx

description: Supplementary Tables for AJP-Heart and Circulatory Physiology H-00062-2019<br>
DOI: 10.6084/m9.figshare.8952971
title: Human leukocyte antigen in Japanese patients with idiopathic inflammatory myopathy

description: <b>Objective:</b> The human leukocyte antigen (HLA) is the strongest genetic risk factor for idiopathic inflammatory myopathy (IIM), and different <i>HLA</i> alleles have been reported to be associated with IIM susceptibility among different ethnic groups. In this study, we have investigated HLA alleles associated with IIM in Japanese patients. <b>Methods:</b> Genotyping of <i>HLA-DRB1</i> and <i>DPB1</i> were performed in 252 Japanese IIM patients (166 dermatomyositis [DM] and 86 polymyositis [PM] patients) and the association was analyzed with comparison to controls (<i>n</i> = 1026 for <i>DRB1</i> and <i>n</i> = 413 for <i>DPB1</i>). <b>Results:</b><i>DRB1*08:03</i> was associated with IIM (<i>p</i> = 1.60 × 10<sup>−5</sup>, <i>p</i>c = .0005, odds ratio [OR] 2.11, 95% confidence interval [CI] 1.52–2.92) and DM (<i>p</i> = .0004, <i>p</i>c = .0128, OR 2.06, 95%CI 1.40–3.02). <i>DPB1*05:01</i> was also associated with IIM (<i>p</i> = .0001, <i>p</i>c = .0021, OR 1.96, 95%CI 1.38–2.77) and DM (<i>p</i> = .0005, <i>p</i>c = .0075, OR 2.05, 95%CI 1.37–3.08). <i>DRB1*09:01</i> (<i>p</i> = .0012, <i>p</i>c = .0368, OR 0.35, 95% CI 0.18–0.69) and <i>DPB1*04:01</i>(<i>p</i> = .0004, <i>p</i>c = .0057, OR 0.05, 95% CI 0.00–0.85) were protectively associated with PM. Two locus analyses suggested that <i>DRB1*09:01</i> and <i>DPB1*04:01</i> were independently associated with PM. <b>Conclusion:</b> Protective associations of <i>HLA</i> were detected in Japanese PM patients.
DOI: 10.6084/m9.figshare.8952971.v1
title: Human leukocyte antigen in Japanese patients with idiopathic inflammatory myopathy

description: <b>Objective:</b> The human leukocyte antigen (HLA) is the strongest genetic risk factor for idiopathic inflammatory myopathy (IIM), and different <i>HLA</i> alleles have been reported to be associated with IIM susceptibility among different ethnic groups. In this study, we have investigated HLA alleles associated with IIM in Japanese patients. <b>Methods:</b> Genotyping of <i>HLA-DRB1</i> and <i>DPB1</i> were performed in 252 Japanese IIM patients (166 dermatomyositis [DM] and 86 polymyositis [PM] patients) and the association was analyzed with comparison to controls (<i>n</i> = 1026 for <i>DRB1</i> and <i>n</i> = 413 for <i>DPB1</i>). <b>Results:</b><i>DRB1*08:03</i> was associated with IIM (<i>p</i> = 1.60 × 10<sup>−5</sup>, <i>p</i>c = .0005, odds ratio [OR] 2.11, 95% confidence interval [CI] 1.52–2.92) and DM (<i>p</i> = .0004, <i>p</i>c = .0128, OR 2.06, 95%CI 1.40–3.02). <i>DPB1*05:01</i> was also associated with IIM (<i>p</i> = .0001, <i>p</i>c = .0021, OR 1.96, 95%CI 1.38–2.77) and DM (<i>p</i> = .0005, <i>p</i>c = .0075, OR 2.05, 95%CI 1.37–3.08). <i>DRB1*09:01</i> (<i>p</i> = .0012, <i>p</i>c = .0368, OR 0.35, 95% CI 0.18–0.69) and <i>DPB1*04:01</i>(<i>p</i> = .0004, <i>p</i>c = .0057, OR 0.05, 95% CI 0.00–0.85) were protectively associated with PM. Two locus analyses suggested that <i>DRB1*09:01</i> and <i>DPB1*04:01</i> were independently associated with PM. <b>Conclusion:</b> Protective associations of <i>HLA</i> were detected in Japanese PM patients.
DOI: 10.6084/m9.figshare.8952962
title: Genome annotation of Trilophysa bleekeri

description: These are the gene structure and function annotation file of Trilophysa bleekeri.
DOI: 10.6084/m9.figshare.8952962.v2
title: Genome annotation of Trilophysa bleekeri

description: These are the gene structure and function annotation file of Trilophysa bleekeri.
DOI: 10.6084/m9.figshare.8952938
title: PeerJ_Supplementary Materials

description: Alzheimer's disease (AD) is a prevalent progressive neurodegenerative human disease. Several initially highly hopeful anti-AD drugs based on the amyloid-β (Aβ) hypothesis of AD have failed recent late-phase tests, and the cause of AD remains unclear. Natural aging (AG) is a high-risk factor for AD. Here, we aim to gain insights in AD that may lead to its therapeutic treatment through conducting functional analyses of gene expression microarray data from AG and AD-affected brain. These may add to our understanding of AD pathology.
DOI: 10.6084/m9.figshare.8952962.v1
title: Genome annotation of Trilophysa bleekeri

description: These are the gene structure and function annotation file of Trilophysa bleekeri.
DOI: 10.6084/m9.figshare.8952521
title: A systematic review of the methodological quality of economic studies evaluating ophthalmic drugs

description: <b>Introduction</b>: Innovative drugs have been approved in ophthalmology. Thus, the number and importance of economic evaluation studies of ophthalmic drugs have been growing. This study aims to assess the methodological quality of pharmacoeconomic studies of ophthalmic drugs. <b>Areas covered</b>: A systematic search was conducted in Pubmed/Embase until November 2018 to identify full pharmacoeconomic studies evaluating ophthalmic drugs. The quality of studies was evaluated using the British Medical Journal (BMJ) checklist. Quality indicators were evaluated by Fisher’s exact test. Ninety-five studies were included, 50 (52.6%) cost-utility analysis, 28 (29.5%) cost-effectiveness and 17 (17.9%) cost-effectiveness/cost-utility. All studies presented, at least, three methodological limitations. Cost-utility studies, studies conducted from a health system perspective, with time horizons longer than one-year and that rely on observational or observational and experimental data simultaneously are associated with higher quality. Only eight (8.4%) studies considered two eyes in the economic analysis and only 13 (13.7%) considered the natural history of the disease when extrapolating results for long-term analysis. <b>Expert opinion</b>: The majority of the pharmacoeconomic studies were assessed as having good methodological quality, however, the methodological quality scores were sensitive to several indicators. Therefore, improving the quality of studies would enhance their usefulness in the decision-making processes.
DOI: 10.6084/m9.figshare.8952521.v1
title: A systematic review of the methodological quality of economic studies evaluating ophthalmic drugs

description: <b>Introduction</b>: Innovative drugs have been approved in ophthalmology. Thus, the number and importance of economic evaluation studies of ophthalmic drugs have been growing. This study aims to assess the methodological quality of pharmacoeconomic studies of ophthalmic drugs. <b>Areas covered</b>: A systematic search was conducted in Pubmed/Embase until November 2018 to identify full pharmacoeconomic studies evaluating ophthalmic drugs. The quality of studies was evaluated using the British Medical Journal (BMJ) checklist. Quality indicators were evaluated by Fisher’s exact test. Ninety-five studies were included, 50 (52.6%) cost-utility analysis, 28 (29.5%) cost-effectiveness and 17 (17.9%) cost-effectiveness/cost-utility. All studies presented, at least, three methodological limitations. Cost-utility studies, studies conducted from a health system perspective, with time horizons longer than one-year and that rely on observational or observational and experimental data simultaneously are associated with higher quality. Only eight (8.4%) studies considered two eyes in the economic analysis and only 13 (13.7%) considered the natural history of the disease when extrapolating results for long-term analysis. <b>Expert opinion</b>: The majority of the pharmacoeconomic studies were assessed as having good methodological quality, however, the methodological quality scores were sensitive to several indicators. Therefore, improving the quality of studies would enhance their usefulness in the decision-making processes.
DOI: 10.6084/m9.figshare.8951006
title: Spontaneous astrocytic calcium traces from organotypic hippocampal slices

description: Each column of the file (ROI) corresponds to an individual calcium trace, expressed as ΔF/F0. Recordings were performed using confocal microscopy on organotypic hippocampal slices (Gähwiler type), with a spatial resolution around 175 nm (in x-y) and 450 nm (z). Confocal time-lapse imaging (12.5 x 25 μm, pixel size 100 nm) was performed at 2Hz. For more details, see the associated paper: Simulation of calcium signaling in fine astrocytic processes: effect of spatial properties on spontaneous activity, Denizot et al, PLOS Computational Biology, 2019.<br>
DOI: 10.6084/m9.figshare.8950859
title: Data from "Phylogenomics provides robust support for a two-domains tree of life"

description: Data associated with the paper "Phylogenomics provides robust support for a two-domains tree of life" (including sequence alignments and Newick tree files). Updated 18/12/2019 to add a missing sequence set (family 22).
DOI: 10.6084/m9.figshare.8950859.v1
title: Data from "Phylogenomics provides robust support for a two-domains tree of life"

description: Data associated with the paper "Phylogenomics provides robust support for a two-domains tree of life" (including sequence alignments).
DOI: 10.6084/m9.figshare.8951006.v1
title: Astrocytic calcium traces from organotypic hippocampal slices

description: Each column of the file (ROI) corresponds to an individual calcium trace, expressed as ΔF/F0. Recordings were performed using confocal microscopy on organotypic hippocampal slices (Gähwiler type), with a spatial resolution around 175 nm (in x-y) and 450 nm (z). Confocal time-lapse imaging (12.5 x 25 μm, pixel size 100 nm) was performed at 2Hz. For more details, see the associated paper: Simulation of calcium signaling in fine astrocytic processes: effect of spatial properties on spontaneous activity, Denizot et al, PLOS Computational Biology, 2019.<br>
DOI: 10.6084/m9.figshare.8949410
title: DataExpPosinut

description: Mesocosm experiment assessing temperature and nutrients effects on Posidonia oceanica
DOI: 10.6084/m9.figshare.8949320
title: spikesort_S16.mat

description: Fine-wire intramuscular EMG Subject 14 Protocol: Long Residual Limb Spike-Sorted Data
DOI: 10.6084/m9.figshare.8949317
title: spikesort_S15.mat

description: Fine-wire intramuscular EMG Subject 13 Protocol: Short Residual Limb Spike-Sorted Data
DOI: 10.6084/m9.figshare.8949314
title: Supplementary Material for: Prognostic Value of Pretreatment Lymphocyte-to-Monocyte Ratio in Non-Small Cell Lung Cancer: A Meta-Analysis

description: Past evidence has shown that lymphocyte-to-monocyte ratio (LMR) could be considered as a potential prognostic factor in non-small cell lung cancer (NSCLC). We conducted the current meta-analysis based on published studies to elucidate the prognostic value of pretreatment LMR on survival outcomes in NSCLC. Comprehensive searches of available electronic databases were implemented to identify potentially related studies that focused on the role of pretreatment LMR in predicting the prognosis of NSCLC patients. The hazard ratios (HRs) with 95% confidence intervals (CIs) were combined to assess the association of pretreatment LMR with overall survival (OS) and progression-free survival (PFS). A total of 20 articles including 8,304 patients were analyzed. Compared with patients with higher LMR, patients with lower LMR had poorer OS (HR = 1.63, 95% CI: 1.44–1.85, <i>p</i> &lt; 0.001) and PFS (HR = 1.49, 95% CI: 1.25–1.77, <i>p</i> &lt; 0.001). The subgroup analysis outcomes were similar to the overall analysis. Pretreatment LMR may be a useful prognostic marker in patients with NSCLC. However, more well-designed studies are warranted to confirm our findings.
DOI: 10.6084/m9.figshare.8949317.v1
title: spikesort_S15.mat

description: Fine-wire intramuscular EMG Subject 13 Protocol: Short Residual Limb Spike-Sorted Data
DOI: 10.6084/m9.figshare.8949314.v1
title: Supplementary Material for: Prognostic Value of Pretreatment Lymphocyte-to-Monocyte Ratio in Non-Small Cell Lung Cancer: A Meta-Analysis

description: Past evidence has shown that lymphocyte-to-monocyte ratio (LMR) could be considered as a potential prognostic factor in non-small cell lung cancer (NSCLC). We conducted the current meta-analysis based on published studies to elucidate the prognostic value of pretreatment LMR on survival outcomes in NSCLC. Comprehensive searches of available electronic databases were implemented to identify potentially related studies that focused on the role of pretreatment LMR in predicting the prognosis of NSCLC patients. The hazard ratios (HRs) with 95% confidence intervals (CIs) were combined to assess the association of pretreatment LMR with overall survival (OS) and progression-free survival (PFS). A total of 20 articles including 8,304 patients were analyzed. Compared with patients with higher LMR, patients with lower LMR had poorer OS (HR = 1.63, 95% CI: 1.44–1.85, <i>p</i> &lt; 0.001) and PFS (HR = 1.49, 95% CI: 1.25–1.77, <i>p</i> &lt; 0.001). The subgroup analysis outcomes were similar to the overall analysis. Pretreatment LMR may be a useful prognostic marker in patients with NSCLC. However, more well-designed studies are warranted to confirm our findings.
DOI: 10.6084/m9.figshare.8949218
title: pollen fertility rate data

description: this is the pollen fertility rate data for quantitative trait loci mapping.
DOI: 10.6084/m9.figshare.8949218.v1
title: pollen fertility rate data

description: this is the pollen fertility rate data for quantitative trait loci mapping.
DOI: 10.6084/m9.figshare.8949209
title: Sea Star Wasting Syndrome Modeling: Cox Proportional Hazards Data and Code

description: Sea Star Wasting Syndrome (SSWS) has been ongoing in echinoderm species of the North American Pacific Coast. Previous outbreaks, as well as the most recent one, have reduced sea 21 star populations to near-absence in many locations. To identify potential factors correlated with SSWS appearance, we combined intertidal surveys, citizen scientist disease observations, and environmental data. I modeled relationships between environmental variables and the risk of a site's transition from healthy to infected using a Cox Proportional Hazards Model. More information at www.seastarwasting.org. Sea star observations can be viewed interactively at data.piscoweb.org/marine1/seastardisease.html.If using any of these sea star observations or datasets, please acknowledge the Multi-Agency Rocky Intertidal Network (MARINe) and the Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO).This code was written as part of the doctoral thesis of Monica Moritsch: Moritsch, M. (2018). Ecological causes and consequences of Sea Star Wasting Syndrome on the Pacific coast. UC Santa Cruz. ProQuest ID: Moritsch_ucsc_0036E_11614. Merritt ID: ark:/13030/m5x39vdx. Retrieved from https://escholarship.org/uc/item/9dr8t5kq
DOI: 10.6084/m9.figshare.8949194
title: Data Figure 4: Pharmacological block of excitatory and inhibitory inputs in nob retina blocks or modify both GC and eye-movement oscillations

description: Data Figure 4: Pharmacological block of excitatory and inhibitory inputs in nob retina blocks or modify both GC and eye-movement oscillations