cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5589916.v2
title: Does more favourable handling of the cerebrospinal fluid increase the diagnostic sensitivity of <i>Borrelia burgdorferi</i> sensu lato-specific PCR in Lyme neuroborreliosis?

description: <b>Background:</b> Tests for direct detection of <i>Borrelia burgdorferi</i> sensu lato <i>(Bb)</i> in Lyme neuroborreliosis (LNB) are needed. Detection of <i>Bb</i> DNA using PCR is promising, but clinical utility is hampered by low diagnostic sensitivity. We aimed to examine whether diagnostic sensitivity can be improved by the use of larger cerebrospinal fluid (CSF) volumes and faster handling of samples. <b>Methods:</b> Patients who underwent CSF examination for LNB were included. We collected two millilitres of CSF for PCR analysis, extracted DNA from the pellets within 24 h and analysed the eluate by two real-time PCR protocols (16S rRNA and OspA). Patients who fulfilled diagnostic criteria for LNB were classified as LNB cases and the rest as controls. <b>Results:</b><i>Bb</i> DNA in CSF was detected by PCR in seven of 28 adults with LNB. Two were <i>Bb</i> antibody negative. No <i>Bb</i> DNA was detected in CSF from 137 controls. Diagnostic sensitivity was 25% and specificity 100%. There was a non-significant trend towards larger CSF sample volume, faster handling of the sample, shorter duration of symptoms, and higher CSF cell count in the PCR-positive cases. <b>Conclusion:</b> We did not find that optimized handling of CSF increased diagnostic sensitivity of PCR in adults with LNB. However, our case series is small and we hypothesize that the importance of these factors will be clarified in further studies with larger case series and altered study design. PCR for diagnosis of LNB may be useful in cases without <i>Bb</i> antibodies due to short duration of symptoms.
DOI: 10.6084/m9.figshare.5589883
title: Core and surface temperature measurements of experimental animals

description: Core and surface temperature measurements of experimental animals. The dataset included core temperature measurements of 177 temperature-transponder-implanted animals and surface temperature measurements of 435 animals.<br>
DOI: 10.6084/m9.figshare.5589892
title: Information about experimental animals

description: Information about all experimental animals (n=435) used in the study.
DOI: 10.6084/m9.figshare.5589859
title: BiomTable_MiSeq_Pferschy-Wenzig_et_al_2017.xlsx

description: Text-formatted biom table of MiSeq sequencing data produced in the study published as:Pferschy-Wenzig, E-M, Koskinen, K, Moissl-Eichinger, C, Bauer, R. <b>A combined LC-MS metabolomics- and 16S rRNA sequencing platform to assess interactions between herbal medicinal products and human gut bacteria <i>in vitro</i>: A pilot study on willow bark extract" </b><b>in Frontiers in Pharmacology, 2017. doi: 10.3389/fphar.2017.00893</b><br>
DOI: 10.6084/m9.figshare.5589859.v1
title: BiomTable_MiSeq_Pferschy-Wenzig_et_al_2017.xlsx

description: Text-formatted biom table of MiSeq sequencing data produced in the study published as:Pferschy-Wenzig, E-M, Koskinen, K, Moissl-Eichinger, C, Bauer, R. <b>A combined LC-MS metabolomics- and 16S rRNA sequencing platform to assess interactions between herbal medicinal products and human gut bacteria <i>in vitro</i>: A pilot study on willow bark extract" </b><b>in Frontiers in Pharmacology, 2017. doi: 10.3389/fphar.2017.00893</b><br>
DOI: 10.6084/m9.figshare.5589841
title: EEG and BIS raw data

description: the dataset is used for estimation of depth of anesthesia. There are 24 case in total.
DOI: 10.6084/m9.figshare.5589883.v1
title: Core and surface temperature measurements of experimental animals

description: Core and surface temperature measurements of experimental animals. The dataset included core temperature measurements of 177 temperature-transponder-implanted animals and surface temperature measurements of 435 animals.<br>
DOI: 10.6084/m9.figshare.5589775
title: Phylogenetic tree used in analysis from Variation in recombination frequency and distribution across eukaryotes: patterns and processes

description: Recombination, the exchange of DNA between maternal and paternal chromosomes during meiosis, is an essential feature of sexual reproduction in nearly all multicellular organisms. While the role of recombination in the evolution of sex has received theoretical and empirical attention, less is known about how recombination rate <i>itself</i> evolves and what influence this has on evolutionary processes within sexually reproducing organisms. Here, we explore the patterns of, and processes governing recombination in eukaryotes. We summarize patterns of variation, integrating current knowledge with an analysis of linkage map data in 353 organisms. We then discuss proximate and ultimate processes governing recombination rate variation and consider how these influence evolutionary processes. Genome-wide recombination rates (cM/Mb) can vary more than tenfold across eukaryotes, and there is large variation in the distribution of recombination events across closely related taxa, populations and individuals. We discuss how variation in rate and distribution relates to genome architecture, genetic and epigenetic mechanisms, sex, environmental perturbations and variable selective pressures. There has been great progress in determining the molecular mechanisms governing recombination, and with the continued development of new modelling and empirical approaches, there is now also great opportunity to further our understanding of how and why recombination rate varies.This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.
DOI: 10.6084/m9.figshare.5589883.v2
title: Core and surface temperature measurements of experimental animals

description: Core and surface temperature measurements of experimental animals. The dataset included core temperature measurements of 177 temperature-transponder-implanted animals and surface temperature measurements of 435 animals.<br>
DOI: 10.6084/m9.figshare.5589766
title: Mental well-being of HCPs in Pakistan

description: This data set was compiled to assess mental well-being, dietary pattern and physical health parameters of health care professionals in Pakistan.
DOI: 10.6084/m9.figshare.5589766.v2
title: Mental well-being of HCPs in Pakistan

description: This data set was compiled to assess mental well-being, dietary pattern and physical health parameters of health care professionals in Pakistan.
DOI: 10.6084/m9.figshare.12901211
title: Relationships between pollinator quantity and position with fruit setting of Camellia oleifera .xlsx

description: this datas aimed to identify (1) which color pan trap is most suitable for attracting pollinators in <i>C. oleifera </i>fields; (2) the differences in fruit setting at different canopy positions; (3) how pollinator abundance differs across canopy levels; and (4) whether other landscape-scale factors such as crown size or total plant height also influence fruit setting (as they do budding and other life stages).
DOI: 10.6084/m9.figshare.5588917
title: Sample size planning methods in post-GWAS breast cancer eQTL studies

description: (Unfunded) NIH F32 grant application and reviewer comments.
DOI: 10.6084/m9.figshare.5588917.v1
title: Sample size planning methods in post-GWAS breast cancer eQTL studies

description: (Unfunded) NIH F32 grant application and reviewer comments.
DOI: 10.6084/m9.figshare.5588911
title: BH EEG Results (All data)

description: All data generate by using Black Hole Algorithm
DOI: 10.6084/m9.figshare.5588899
title: Open in order to... Dream, remake nature

description: Beyond making the findings discoverable and accessible to non-academics, what else can be done to broaden the cultural legacy of digital research projects when they are finished? How might the afterlives of digital research be experienced, how, by whom and for what purpose? How might digital data get immersive, fuel people’s imaginations, shape identities, right wrongs? Erinma will illustrate some of the creative ways that staff, students and the public can get involved in bringing scientific research data to life through virtual reality experiences, live performance and citizen science.
DOI: 10.6084/m9.figshare.5588896
title: BH EEG Results (Summary)

description: Results of Black Hole Algorithm.
DOI: 10.6084/m9.figshare.5588881
title: Tree-level distribution of a novel insect-pathogen complex and its potential contribution to eastern white pine dieback

description: Raw data. Includes branch segments and bole samples.
DOI: 10.6084/m9.figshare.5588881.v1
title: Tree-level distribution of a novel insect-pathogen complex and its potential contribution to eastern white pine dieback

description: Raw data. Includes branch segments and bole samples.
DOI: 10.6084/m9.figshare.5588848
title: Dataset for: Data generating models of dichotomous outcomes: Heterogeneity in simulation studies for a random-effects meta-analysis

description: Simulation studies to evaluate performance of statistical methods require a well specified Data Generating Model. Details of these models are essential to interpret the results and arrive at proper conclusions. A case in point is random-effects meta-analysis of dichotomous outcomes. We reviewed a number of simulation studies that evaluated approximate normal models for meta-analysis of dichotomous outcomes and we assessed the data generating models that were used to generate events for a series of (heterogeneous) trials. We demonstrate that the performance of the statistical methods, as assessed by simulation, differs between these three alternative Data Generating Models, with larger differences apparent in the small population setting. Our findings are relevant to multilevel binomial models in general.
DOI: 10.6084/m9.figshare.5588848.v1
title: Dataset for: Data generating models of dichotomous outcomes: Heterogeneity in simulation studies for a random-effects meta-analysis

description: Simulation studies to evaluate performance of statistical methods require a well specified Data Generating Model. Details of these models are essential to interpret the results and arrive at proper conclusions. A case in point is random-effects meta-analysis of dichotomous outcomes. We reviewed a number of simulation studies that evaluated approximate normal models for meta-analysis of dichotomous outcomes and we assessed the data generating models that were used to generate events for a series of (heterogeneous) trials. We demonstrate that the performance of the statistical methods, as assessed by simulation, differs between these three alternative Data Generating Models, with larger differences apparent in the small population setting. Our findings are relevant to multilevel binomial models in general.
DOI: 10.6084/m9.figshare.5588842
title: Citations with contexts in Wikipedia

description: This dataset represents <b>structured metadata and contextual information about references added to Wikipedia articles</b> in a JSON format. <br>Each record represents an individual Wikipedia article revision with all the tags parsed, as stored in Wikipedia's XML dumps, including information about: <br>1) the context(s) in which the reference occurs within the article – such as the surrounding text, parent section title, and section level – <br>2) structured data and bibliographic metadata included within the reference itself (such as: any citation template used, external links, any known persistent identifiers) <br>3) additional data/metadata about the reference itself (the reference name, its raw content, and if applicable, revision ID associated with reference addition/deletion/change)<br>The data is available as a set of compressed JSON files, extracted from the July 1, 2017 XML dump of English Wikipedia. Other languages may be added to this dataset in the future.<br>The JSON schema and Python parsing libraries used to generate the data are in the references.
DOI: 10.6084/m9.figshare.5588839
title: Dataset for: Joint mixed-effects models for causal inference with longitudinal data

description: Causal inference with observational longitudinal data and time-varying exposures is complicated due to the potential for time-dependent confounding and unmeasured confounding. Most causal inference methods that handle time-dependent confounding rely on either the assumption of no unmeasured confounders or the availability of an unconfounded variable that is associated with the exposure (e.g., an instrumental variable). Furthermore, when data are incomplete, validity of many methods often depends on the assumption of missing at random. We propose an approach that combines a parametric joint mixed-effects model for the study outcome and the exposure with g-computation to identify and estimate causal effects in the presence of time-dependent confounding and unmeasured confounding. G-computation can estimate participant-specific or population-average causal effects using parameters of the joint model. The joint model is a type of shared parameter model where the outcome and exposure-selection models share common random effect(s). We also extend the joint model to handle missing data and truncation by death when missingness is possibly not at random. We evaluate the performance of the proposed method using simulation studies and compare the method to both linear mixed-effects models and fixed-effects models combined with g-computation as well as to targeted maximum likelihood estimation. We apply the method to an epidemiologic study of vitamin D and depressive symptoms in older adults and include code using SAS PROC NLMIXED software to enhance the accessibility of the method to applied researchers.
DOI: 10.6084/m9.figshare.5588839.v1
title: Dataset for: Joint mixed-effects models for causal inference with longitudinal data

description: Causal inference with observational longitudinal data and time-varying exposures is complicated due to the potential for time-dependent confounding and unmeasured confounding. Most causal inference methods that handle time-dependent confounding rely on either the assumption of no unmeasured confounders or the availability of an unconfounded variable that is associated with the exposure (e.g., an instrumental variable). Furthermore, when data are incomplete, validity of many methods often depends on the assumption of missing at random. We propose an approach that combines a parametric joint mixed-effects model for the study outcome and the exposure with g-computation to identify and estimate causal effects in the presence of time-dependent confounding and unmeasured confounding. G-computation can estimate participant-specific or population-average causal effects using parameters of the joint model. The joint model is a type of shared parameter model where the outcome and exposure-selection models share common random effect(s). We also extend the joint model to handle missing data and truncation by death when missingness is possibly not at random. We evaluate the performance of the proposed method using simulation studies and compare the method to both linear mixed-effects models and fixed-effects models combined with g-computation as well as to targeted maximum likelihood estimation. We apply the method to an epidemiologic study of vitamin D and depressive symptoms in older adults and include code using SAS PROC NLMIXED software to enhance the accessibility of the method to applied researchers.
DOI: 10.6084/m9.figshare.5588704
title: Glyburide study data

description: Raw data from safety trial; serum glyburide and blood glucose in pharmacokinetic study
DOI: 10.6084/m9.figshare.5588704.v1
title: Glyburide study data

description: Raw data from safety trial; serum glyburide and blood glucose in pharmacokinetic study
DOI: 10.6084/m9.figshare.5588584
title: Instrumente zur Messung von Einstellungen zur Inklusion

description: A database of instruments measuring attitudes towards Inclusion.<br><br>Inclusion Criteria:<br>-Published in German or English<br>
DOI: 10.6084/m9.figshare.5588584.v2
title: Instrumente zur Messung von Einstellungen zur Inklusion

description: A database of instruments measuring attitudes towards Inclusion.<br>
DOI: 10.23645/epacomptox.5588635.v1
title: PubMed Abstract Sifter 07/06/2017

description: The Abstract Sifter is a Microsoft Excel based tool that greatly enhances literature searching in PubMed. The tool implements a novel “sifter” functionality for relevance ranking, giving the researcher a way to find articles of interest quickly. The Sifter assists researchers to triage results and keep track of articles of interest. The tool also gives researchers a view of the literature landscape for a set of entities such as chemicals or genes and makes it easy to dive deeper into areas of interest.
DOI: 10.6084/m9.figshare.5588584.v1
title: Instrumente zur Messung von Einstellungen zur Inklusion

description: A database of instruments measuring attitudes towards Inclusion.<br>
DOI: 10.23645/epacomptox.5588512
title: OPERA Model Paper Data

description: Data associated with the OPERA Model paper authored by Kamel Mansouri and Tony Williams.
DOI: 10.23645/epacomptox.5588635.v2
title: Chemistry Dashboard Data: Abstract Sifter Files

description: The Abstract Sifter is a Microsoft Excel based tool that greatly enhances literature searching in PubMed. The tool implements a novel “sifter” functionality for relevance ranking, giving the researcher a way to find articles of interest quickly. The Sifter assists researchers to triage results and keep track of articles of interest. The tool also gives researchers a view of the literature landscape for a set of entities such as chemicals or genes and makes it easy to dive deeper into areas of interest.
DOI: 10.6084/m9.figshare.5585371
title: Smart Residential Thermal Environment Data (SRTED)

description: SRTED is a unique open-source dataset with 15-minute thermal and occupancy behavior data acquired from 310 apartments in two New York City multi-family buildings, during the period July 2015 to Dec 2016. The dataset comprises approximately 20 million readings, which represent the instantaneous thermal environment of monitored rooms. Weather data in SRTED is from NSRDB (LaGuardia Airport, New York for the first building and Central Park, New York for the second building).<br> p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px 'Helvetica Neue'; color: #454545} Cite SRTED as: S. Abrol, A. Mehmani, M. Kerman, C. J. Meinrenken, and P. J. Culligan. "Data-Enabled Building Energy Savings (DE BES)." <i>Proceedings of the IEEE</i> 106, no. 4 (2018): 661-679.<br>
DOI: 10.6084/m9.figshare.5585305
title: Digital Preservation Management and Access

description: From “Digital Preservation Planning Workshop.” Society of Southwest Archivists Annual Meeting, Fayetteville, AR. May 24 2017.
DOI: 10.6084/m9.figshare.5585371.v1
title: Smart Residential Thermal Environment Data (SRTED)

description: SRTED is a unique open-source dataset with 15-minute thermal and occupancy behavior data acquired from 310 apartments in two New York City multi-family buildings, during the period July 2015 to Dec 2016. The dataset comprises approximately 20 million readings, which represent the instantaneous thermal environment of monitored rooms. Weather data in SRTED is from NSRDB (LaGuardia Airport, New York for the first building and Central Park, New York for the second building).<br> p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px 'Helvetica Neue'; color: #454545} Cite SRTED as: S. Abrol, A. Mehmani, M. Kerman, C. J. Meinrenken, and P. J. Culligan. "Data-Enabled Building Energy Savings (DE BES)." <i>Proceedings of the IEEE</i> 106, no. 4 (2018): 661-679.<br>
DOI: 10.6084/m9.figshare.5585293
title: Dataset for: Peptide fragments of Hsp70 modulate its chaperone activity and sensitize tumor cells to anti-cancer drug

description: Most of Hsp70 chaperone inhibitors exert anti-cancer effects and though their toxicity prompted us to employ peptide fragments of the chaperone as its safer modulators and as complements to customary drugs. One of such peptides, ICit-2 was found to inhibit substrate-binding and refolding activities of the chaperone. Using various approaches, we established that ICit-2 binds Hsp70 that may explain the compound inhibitory action. ICit-2 penetrates living A-431 cancer cells and in combination with doxorubicin enhances the drug cytotoxicity and growth inhibitory effect. Similarly, using B16 mouse melanoma model we found that ICit-2 inhibited the rate of tumor growth by 48% compared with the doxorubicin alone proving that the peptide can be employed to sensitize resistant tumors to cytostatic medicines.
DOI: 10.6084/m9.figshare.5585293.v1
title: Dataset for: Peptide fragments of Hsp70 modulate its chaperone activity and sensitize tumor cells to anti-cancer drug

description: Most of Hsp70 chaperone inhibitors exert anti-cancer effects and though their toxicity prompted us to employ peptide fragments of the chaperone as its safer modulators and as complements to customary drugs. One of such peptides, ICit-2 was found to inhibit substrate-binding and refolding activities of the chaperone. Using various approaches, we established that ICit-2 binds Hsp70 that may explain the compound inhibitory action. ICit-2 penetrates living A-431 cancer cells and in combination with doxorubicin enhances the drug cytotoxicity and growth inhibitory effect. Similarly, using B16 mouse melanoma model we found that ICit-2 inhibited the rate of tumor growth by 48% compared with the doxorubicin alone proving that the peptide can be employed to sensitize resistant tumors to cytostatic medicines.
DOI: 10.6084/m9.figshare.5585230
title: Supplementary Material for: Early Nutrition and Growth until the Corrected Age of 2 Years in Extremely Preterm Infants

description: <b><i>Background:</i></b> Extremely preterm birth is associated with a high risk of extrauterine growth retardation, which has been linked with adverse developmental outcomes. <b><i>Objective:</i></b> We investigated whether nutritional management during the first 7 days of life affects growth patterns until the corrected age of 2 years in extremely preterm infants. <b><i>Study Design:</i></b> A retrospective study of 78 extremely preterm (&lt;28 weeks' gestation) neonates was conducted. Data regarding parenteral and enteral intake of energy, protein, lipids, and carbohydrates during the first 7 days of life were collected from patient records. The outcome measures included weight, height, and head circumference with <i>Z</i> scores at term-equivalent age and the corrected ages of 1 and 2 years. Analyses were performed with hierarchical-linear mixed models. <b><i>Results:</i></b> Nutritional intake during the first week of life did not reach the current recommendations. The total energy intake during the first 7 days of life was statistically significantly associated with weight, length, and head circumference until the corrected age of 2 years after adjusting for potential confounding factors. Individual macronutrient intake displayed no association with growth patterns. <b><i>Conclusions:</i></b> Energy intake during the first 7 days of life is associated with growth until the corrected age of 2 years. These results provide support for the aggressive early nutritional management of extremely preterm infants.