cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23659587.v1
title: Epitomics: Analysis of Plasma C9 Epitope Heterogeneity in the Plasma of Lung Cancer Patients and Control Subjects

description: The human proteome is more complex than genetic code have predicted it. Sub-protein level provides us a more complex point of view in proteomics and an opportunity to examine epitopes biomarkers values. Epitomics is a recently emerging omics technology that monitors dynamic changes of protein details, epitopes in health and disease. In this study we examined three different complement C9 epitopes via monoclonal antibodies (BSI0449, BSI0581, BSI0639) in control and lung cancerous plasma with ELISA and LC MS/MS methods. Our results suggest that the immunoprecipitated complement C9 is structurally same but we found differences in posttranslational modification ratio and coprecipitated protein composition in control and lung cancerous plasma. We demonstrated that C9 protein heterogeneity exists and shows cancer association at the sub-molecular epitope level.
DOI: 10.25345/c53b5wj8k
title: MassIVE MSV000092560 - The proteomic landscape of genotoxic stress-induced micronuclei
title: Micronuclei (MN) are induced by various genotoxic stressors and amass nuclear- and cytoplasmic-resident proteins, priming the cell for MN-driven signalling cascades. Here, we measure the proteome of micronuclear, cytoplasmic, and nuclear fractions from human cells exposed to a panel of six genotoxins, comprehensively profiling their MN protein landscape. This dataset represents a unique resource detailing the proteomic landscape of MN, guiding mechanistic studies of MN generation and MN-associated outcomes of genotoxic stress.
DOI: 10.18112/openneuro.ds004648.v1.0.0
title: Sympathovagal quotient and functional connectivity of control networks are related to gut Ruminococcaceae abundance in healthy men
DOI: 10.6084/m9.figshare.22132931.v1
title: PIP5K1C Phosphoinositide Kinase Deficiency Distinguishes PIKFYVE-Dependent Cancer Cells from Non-Malignant Cells

description: Although PIKFYVE phosphoinositide kinase inhibitors can selectively eliminate PIKFYVE-dependent human cancer cells <i>in vitro</i> and <i>in vivo</i>, the basis for this selectivity has remained elusive. Here we show that the sensitivity of cells to the PIKFYVE inhibitor WX8 is not linked to PIKFYVE expression, macroautophagic/autophagic flux, the BRAF<sup>V600E</sup> mutation, or ambiguous inhibitor specificity. PIKYVE dependence results from a deficiency in the PIP5K1C phosphoinositide kinase, an enzyme required for conversion of phosphatidylinositol-4-phosphate (PtdIns4P) into phosphatidylinositol-4,5-bisphosphate (PtdIns[4,5]P<sub>2</sub>/PIP2), a phosphoinositide associated with lysosome homeostasis, endosome trafficking, and autophagy. PtdIns(4,5)P<sub>2</sub> is produced via two independent pathways. One requires PIP5K1C; the other requires PIKFYVE and PIP4K2C to convert PtdIns3P into PtdIns(4,5)P<sub>2</sub>. In PIKFYVE-dependent cells, low concentrations of WX8 specifically inhibit PIKFYVE <i>in situ</i>, thereby increasing the level of its substrate PtdIns3P while suppressing PtdIns(4,5)P<sub>2</sub> synthesis and inhibiting lysosome function and cell proliferation. At higher concentrations, WX8 inhibits both PIKFYVE and PIP4K2C <i>in situ</i>, which amplifies these effects to further disrupt autophagy and induce cell death. WX8 did not alter PtdIns4P levels. Consequently, inhibition of PIP5K1C in WX8-resistant cells transformed them into sensitive cells, and overexpression of PIP5K1C in WX8-sensitive cells increased their resistance to WX8. This discovery suggests that PIKFYVE-dependent cancers could be identified clinically by low levels of PIP5K1C and treated with PIKFYVE inhibitors.
DOI: 10.6084/m9.figshare.23515592.v1
title: High-order methods for the simulation of unsteady counterflow flames subject to stochastic forcing of large amplitude

description: Unsteady counterflows are employed to understand and model the effect of turbulence on flames. We present a novel numerical approach for the simulation of one-dimensional unsteady counterflow flames with fourth order spatial discretization and up to fourth order time discretization. The approach couples a three-stage Lobatto IIIa formula for boundary value problems and variable-order, variable time step size Backward Differentiation Formulas for time integration. The framework is explained in detail, its computational performance is analysed, and its use is demonstrated for the case of stochastic forcing of premixed counterflow flames, whereby the imposed rate of strain is a multi-scale lognormal discrete random process with exponential autocorrelation. High-order spatial and temporal discretization make the approach well-suited for the accurate and computationally efficient simulation of the effect of turbulence on flames, which are characterised by large amplitude stochastic fluctuations of the local rate of strain.
DOI: 10.6084/m9.figshare.23515592
title: High-order methods for the simulation of unsteady counterflow flames subject to stochastic forcing of large amplitude

description: Unsteady counterflows are employed to understand and model the effect of turbulence on flames. We present a novel numerical approach for the simulation of one-dimensional unsteady counterflow flames with fourth order spatial discretization and up to fourth order time discretization. The approach couples a three-stage Lobatto IIIa formula for boundary value problems and variable-order, variable time step size Backward Differentiation Formulas for time integration. The framework is explained in detail, its computational performance is analysed, and its use is demonstrated for the case of stochastic forcing of premixed counterflow flames, whereby the imposed rate of strain is a multi-scale lognormal discrete random process with exponential autocorrelation. High-order spatial and temporal discretization make the approach well-suited for the accurate and computationally efficient simulation of the effect of turbulence on flames, which are characterised by large amplitude stochastic fluctuations of the local rate of strain.
DOI: 10.5281/zenodo.7678682
title: Practices of Poster Preparation in Biological Sciences - Datasets

description: <em>Poster sessions are important for the scientific dialogue at conferences and widely used in biology. Preparing a concise and legible poster is however challenging and posters currently are often overloaded with data, text, have inconsistent colour schemes or unintuitive layouts, all of which hinder communication. We performed a qualitative survey and interviews to understand how currently biologist prepare their conference posters. This revealed that biologist spend on average two days preparation a single poster, with half of the time devoted to design aspects. The majority of interviewees state that they received no training for poster design or with professional software tools. Additionally, most participants stated that they had little or no feedback from co-authors and colleagues. </em> <em>Manuscript: </em>https://www.biorxiv.org/content/10.1101/2020.10.08.331413v1
DOI: 10.5281/zenodo.7678681
title: Practices of Poster Preparation in Biological Sciences - Datasets

description: <em>Poster sessions are important for the scientific dialogue at conferences and widely used in biology. Preparing a concise and legible poster is however challenging and posters currently are often overloaded with data, text, have inconsistent colour schemes or unintuitive layouts, all of which hinder communication. We performed a qualitative survey and interviews to understand how currently biologist prepare their conference posters. This revealed that biologist spend on average two days preparation a single poster, with half of the time devoted to design aspects. The majority of interviewees state that they received no training for poster design or with professional software tools. Additionally, most participants stated that they had little or no feedback from co-authors and colleagues. </em> <em>Manuscript: </em>https://www.biorxiv.org/content/10.1101/2020.10.08.331413v1
DOI: 10.5281/zenodo.8199952
title: Practices of Poster Preparation in Biological Sciences - Datasets

description: <em>Poster sessions are important for the scientific dialogue at conferences and widely used in biology. Preparing a concise and legible poster is however challenging and posters currently are often overloaded with data, text, have inconsistent colour schemes or unintuitive layouts, all of which hinder communication. We performed a qualitative survey and interviews to understand how currently biologist prepare their conference posters. This revealed that biologist spend on average two days preparation a single poster, with half of the time devoted to design aspects. The majority of interviewees state that they received no training for poster design or with professional software tools. Additionally, most participants stated that they had little or no feedback from co-authors and colleagues. </em> <em>Manuscript: </em>https://www.biorxiv.org/content/10.1101/2020.10.08.331413v1
DOI: 10.5255/ukda-sn-856621
title: The Effectiveness of Fully Automated Digital Interventions to Promote Mental Well-being in the General Population: A Systematic Review and Meta-analysis, 2022

description: Recent years have highlighted the increasing need to promote mental well-being in the general population. This has led to a rapidly growing market of fully automated digital mental well-being tools. Although many individuals have started using these tools in their daily lives, evidence on the overall effectiveness of digital mental well-being tools is currently lacking. The objective of the current study was therefore to review evidence on the effectiveness of fully automated digital interventions to promote mental well-being in the general population. Following preregistration of the systematic review protocol on PROSPERO (registration: CRD42022310702), searches were carried out in: Medline, Web of Science, Cochrane, PsychINFO, PsychEXTRA, Scopus and ACM Digital (initial searches in February 2022; updated in October 2022). Studies were included if they contained a general population sample and a fully automated digital intervention that exclusively employed psychological mental well-being promotion activities. Two reviewers, blinded to each other’s decisions, conducted data selection, extraction and quality assessment of the included studies. A narrative synthesis and a random-effects model of Per Protocol (PP) data were adopted. A total of 7,243 participants in 19 studies were included. These studies contained 24 fully automated digital mental well-being interventions of which 15 were included in the meta-analysis. Compared with no intervention, there was a significant small effect of fully automated digital mental well-being interventions on mental well-being in the general population (SMD = 0.19, 95% CI ranging from 0.04 to 0.33). Specifically, mindfulness, acceptance & commitment, and compassion-based interventions significantly promoted mental well-being in the general population; insufficient evidence was available for positive psychology and Cognitive Behavioural Therapy (CBT)-based interventions; and contraindications were found for integrative approaches. Overall, there was substantial heterogeneity which could partially be explained by the intervention duration, comparator and study outcome. Risk of bias was high and confidence in quality of the evidence very low (GRADE), primarily due to the high rates of study dropout (averaging 37%, ranging from 0-85%) and suboptimal intervention adherence (averaging 40%).
DOI: 10.6084/m9.figshare.23808441
title: Extended Data File 5.xlsx

description: a spreadsheet in the MS Excel format used to capture GPX4 transcriptional profiles from multiple datasets. Each table represents a disease and dataset. Data was used to compute significance of differences in abundance observed between cases and controls.
DOI: 10.6084/m9.figshare.23808441.v1
title: Extended Data File 5.xlsx

description: a spreadsheet in the MS Excel format used to capture GPX4 transcriptional profiles from multiple datasets. Each table represents a disease and dataset. Data was used to compute significance of differences in abundance observed between cases and controls.
DOI: 10.15468/cht6nd
title: Vascular plants on Surtsey 1965-1990, point distribution data

description: The data come from monitoring activities carried out on Surtsey between 1965-1990.
DOI: 10.5255/ukda-sn-856306
title: Comparison of Devices Used to Measure Blood Pressure, Grip Strength and Lung Function, 2015-2016

description: Blood pressure, grip strength and lung function are frequently assessed in longitudinal population studies, but the measurement devices used differ between studies and within studies over time. Despite efforts to promote standardisation of measurement devices, various studies have opted for different devices due to practical considerations. Additionally, in long-term longitudinal studies, the devices used often need to be replaced with more technologically advanced ones that offer improved or extended measurement capabilities, cost-effectiveness, portability, or ease of use as outdated models become obsolete. This poses significant challenges for research that aims to compare findings across studies or track functional changes over time. A randomised, repeated measurements cross-over trial was conducted to compare measurements ascertained from different commonly used devices. Participants were recruited from London and the South East – N=118 men and women (age 45-74 years), whose blood pressure, grip strength and lung function were assessed by two sphygmomanometers (Omron 705-CP and Omron HEM-907), four handheld dynamometers (Jamar Hydraulic, Jamar Plus+ Digital, Nottingham Electronic and Smedley) and two spirometers (Micro Plus by Micro Medical and Easy on-PC by NDD), respectively, in a randomly allocated order. We identified that there are differences in measurement of blood pressure, grip strength and lung when assessed using different devices. For blood pressure, the new Omron HEM-907 measured higher than the older Omron 705-CP. For grip strength, the electronic dynamometers (Jamar Plus+ Digital and Nottingham Electronic) recorded higher measurements than either the hydraulic (Jamar Hydraulic) or spring gauge (Smedley) dynamometer. For lung function, the ndd Easy on-PC measures of FVC were higher than for the Micromedical, but there was no significant difference between measures of FEV1.
DOI: 10.5281/zenodo.8194906
title: Italian Polarity Lexicon

description: <strong>Italian polarity lexicon</strong> Annotator: Susanna Tron <br> Prefixes from the appraisal theory: A appreciation <br> F emotion<br> J judgement <br> Polarity Labels: A_POS, F_POS, J_POS positive<br> A_NEG, F_NEG, J_NEG negative INT intensifier<br> DIM diminisher<br> SHI shifter <br> Statistics: 1'626 nouns (370 POS, 1242 NEG, 7 INT, 2 DIM, 5 SHI) <br> 1'549 adjectives (421 POS, 1060 NEG, 55 INT,8 DIM,5 SHI)<br> 206 adverbs (76 POS, 78 NEG, 44 INT, 5 DIM, 3 SHI)<br> 156 verbs (29 POS, 126 NEG, 0 INT, 1 DIM, 0 SHI) alltogether 3538 entries <br> Format: lemma,polarity,part of speech <br> Part of Speech: noun<br> adjective<br> adverb<br> verb Examples: allegrissimo,F_POS,adjective<br> allergia,A_NEG,noun<br> altamente,INT,adjective<br> alterigia,J_NEG,noun
DOI: 10.5281/zenodo.8194905
title: Italian Polarity Lexicon

description: <strong>Italian polarity lexicon</strong> Annotator: Susanna Tron <br> Prefixes from the appraisal theory: A appreciation <br> F emotion<br> J judgement <br> Polarity Labels: A_POS, F_POS, J_POS positive<br> A_NEG, F_NEG, J_NEG negative INT intensifier<br> DIM diminisher<br> SHI shifter <br> Statistics: 1'626 nouns (370 POS, 1242 NEG, 7 INT, 2 DIM, 5 SHI) <br> 1'549 adjectives (421 POS, 1060 NEG, 55 INT,8 DIM,5 SHI)<br> 206 adverbs (76 POS, 78 NEG, 44 INT, 5 DIM, 3 SHI)<br> 156 verbs (29 POS, 126 NEG, 0 INT, 1 DIM, 0 SHI) alltogether 3538 entries <br> Format: lemma,polarity,part of speech <br> Part of Speech: noun<br> adjective<br> adverb<br> verb Examples: allegrissimo,F_POS,adjective<br> allergia,A_NEG,noun<br> altamente,INT,adjective<br> alterigia,J_NEG,noun
DOI: 10.5281/zenodo.8174176
title: EU legislation published between 1971-2022

description: <strong>EU Legislation Documents and Metadata from 1971 to 2022 (English language)</strong> This is the set of full text regulation, decision and directive documents in PDF and HTML format, in the English language, downloaded from EURLEX, together with metadata in CSV format about these documents. The documents were downloaded using this Python script, and the metadata was extracted from the CELLAR SPARQL endpoint using this Python script. During the download process, HTML versions for the legislative documents were extracted if they were available. If there was no HTML version available for a particular document, the PDF version was downloaded (HTML versions were preferred because it is generally simpler to extract and process the text with software because of the added structure the format provides). If there was neither an HTML nor PDF version available, we made a note of the unique identifier (CELEX number) for those documents. The archive in this Zenodo repository which contains all the full text documents consists of three directories "htmls/", "pdfs/" and "problems/", which contain all the downloaded documents in that particular format. The "problems/" directory contains a list of blank .txt files where the name of each file is the CELEX number for a legislative document that was not available on EURLEX for download. For more information about the scripts and a description of the metadata extracted, please see this Github repository. The data was extracted as part of the Nature of EU Rules project which seeks to analyse the "strictness" and density of EU regulations over time and by legal policy area.
DOI: 10.5281/zenodo.8174175
title: EU legislation published between 1971-2022

description: <strong>EU Legislation Documents and Metadata from 1971 to 2022 (English language)</strong> This is the set of full text regulation, decision and directive documents in PDF and HTML format, in the English language, downloaded from EURLEX, together with metadata in CSV format about these documents. The documents were downloaded using this Python script, and the metadata was extracted from the CELLAR SPARQL endpoint using this Python script. During the download process, HTML versions for the legislative documents were extracted if they were available. If there was no HTML version available for a particular document, the PDF version was downloaded (HTML versions were preferred because it is generally simpler to extract and process the text with software because of the added structure the format provides). If there was neither an HTML nor PDF version available, we made a note of the unique identifier (CELEX number) for those documents. The archive in this Zenodo repository which contains all the full text documents consists of three directories "htmls/", "pdfs/" and "problems/", which contain all the downloaded documents in that particular format. The "problems/" directory contains a list of blank .txt files where the name of each file is the CELEX number for a legislative document that was not available on EURLEX for download. For more information about the scripts and a description of the metadata extracted, please see this Github repository. The data was extracted as part of the Nature of EU Rules project which seeks to analyse the "strictness" and density of EU regulations over time and by legal policy area.
DOI: 10.6084/m9.figshare.21499045
title: A Look into the Problem of Preferential Sampling through the Lens of Survey Statistics

description: An evolving problem in the field of spatial and ecological statistics is that of preferential sampling, where biases may be present due to a relationship between sample data locations and a response of interest. This field of research bears a striking resemblance to the longstanding problem of informative sampling within survey methodology, although with some important distinctions. With the goal of promoting collaborative effort within and between these two problem domains, we make comparisons and contrasts between the two problem statements. Specifically, we review many of the solutions available to address each of these problems, noting the important differences in modeling techniques. Additionally, we construct a series of simulation studies to examine some of the methods available for preferential sampling, as well as a comparison analyzing heavy metal biomonitoring data.
DOI: 10.6084/m9.figshare.21420412
title: Bayes Factors and Posterior Estimation: Two Sides of the Very Same Coin

description: Recently, several researchers have claimed that conclusions obtained from a Bayes factor (or the posterior odds) may contradict those obtained from Bayesian posterior estimation. In this article, we wish to point out that no such “contradiction” exists if one is willing to consistently define one’s priors and posteriors. The key for congruence is that the (implied) prior model odds used for testing are the same as those used for estimation. Our recommendation is simple: If one reports a Bayes factor comparing two models, then one should also report posterior estimates which appropriately acknowledge the uncertainty with regards to which of the two models is correct.
DOI: 10.6084/m9.figshare.21499045.v2
title: A Look into the Problem of Preferential Sampling through the Lens of Survey Statistics

description: An evolving problem in the field of spatial and ecological statistics is that of preferential sampling, where biases may be present due to a relationship between sample data locations and a response of interest. This field of research bears a striking resemblance to the longstanding problem of informative sampling within survey methodology, although with some important distinctions. With the goal of promoting collaborative effort within and between these two problem domains, we make comparisons and contrasts between the two problem statements. Specifically, we review many of the solutions available to address each of these problems, noting the important differences in modeling techniques. Additionally, we construct a series of simulation studies to examine some of the methods available for preferential sampling, as well as a comparison analyzing heavy metal biomonitoring data.
DOI: 10.6084/m9.figshare.21420412.v1
title: Bayes factors and posterior estimation: Two sides of the very same coin

description: Recently, several researchers have claimed that conclusions obtained from a Bayes factor (or the posterior odds) may contradict those obtained from Bayesian posterior estimation. In this paper, we wish to point out that no such “contradiction” exists if one is willing to consistently define one’s priors and posteriors. The key for congruence is that the (implied) prior model odds used for testing are the same as those used for estimation. Our recommendation is simple: If one reports a Bayes factor comparing two models, then one should also report posterior estimates which appropriately acknowledge the uncertainty with regards to which of the two models is correct.
DOI: 10.6084/m9.figshare.21420412.v2
title: Bayes Factors and Posterior Estimation: Two Sides of the Very Same Coin

description: Recently, several researchers have claimed that conclusions obtained from a Bayes factor (or the posterior odds) may contradict those obtained from Bayesian posterior estimation. In this article, we wish to point out that no such “contradiction” exists if one is willing to consistently define one’s priors and posteriors. The key for congruence is that the (implied) prior model odds used for testing are the same as those used for estimation. Our recommendation is simple: If one reports a Bayes factor comparing two models, then one should also report posterior estimates which appropriately acknowledge the uncertainty with regards to which of the two models is correct.