cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4772323
title: Risk and Loss aversion in pathologically anxious and matched control individuals

description: This dataset contains data collected on 25 pathologically anxious individuals (meeting criteria for GAD) and 23 matched healthy controls on a task measuring gambling behavior, its modulation by incidental emotional cues, and working memory for these emotional cues.Computational modelling derived from Prospect Theory was employed to formally estimate risk and loss aversion parameters from the gambling data, revealing that relative to healthy controls, anxious individuals exhibit enhanced levels of risk aversion, but no difference in loss aversion.There was no effect of emotional cues on gambling or working memory (and no group differences on these variables).The dataset shows parameter estimates from the Prospect Theory model: Mu (inverse temperature, free parameter), Lambda (loss aversion), and Rho (risk preference). The parameters were log-transformed because of their distribution (Log Mu, Log Loss Aversion, Log Risk Aversion). A Maximum A Posteriori (MAP) estimation procedure was also run to corroborate the main results, leading to another set of parameter estimates labelled "MAP". The next columns of the data set shows group (anxious vs control), MDD group (whether the anxious individuals also met criteria for Major Depression), Trait anxiety and BDI scores. Log-transformed parameter values are then shown for each emotion condition separately. Then come gamble propensity data, calculated across all trials, separately for each gamble type, and then for each emotion condition; followed by working memory performance and reaction time data.For more details please refer to the published version of the paper:Charpentier CJ, Aylward J, Roiser JP, Robinson OJ (2017) Enhanced Risk Aversion, But Not Loss Aversion, in Unmedicated Pathological Anxiety. <i>Biological Psychiatry</i>. in press
DOI: 10.6084/m9.figshare.4772320
title: Microarray-based analysis of gene expression profiles in peripheral blood of patients with acute primary angle closure

description: <i>Background</i>: We investigated the expression of molecules in peripheral blood mononuclear cells (PBMCs) and plasma of patients with acute primary angle closure (APAC). <i>Materials and methods</i>: Peripheral blood was collected from patients with APAC (<i>n</i> = 10) and age-matched controls (<i>n</i> = 5). The gene transcription profile was analyzed in PBMCs using microarrays and validated by real-time reverse transcription polymerase chain reaction (RT-PCR). The levels of secreted proteins were evaluated in plasma by ELISA. <i>Results</i>: 347 gene transcripts were up-regulated by 2-fold or more, and 696 transcripts down-regulated 2-fold or more in PBMCs from patients compared to controls. The most highly up-regulated gene was thrombospondin-1 (<i>TSP-1</i>, 8.66-fold increase), and the most down-regulated gene was prostaglandin-endoperoxide synthase 2 (<i>PTGS2</i>, 9.09-fold decrease). Real-time RT-PCR assay confirmed the increase of <i>TSP-1</i> and the decrease of <i>PTGS2</i> in PBMCs of patients. ELISA revealed that the levels of <i>TSP-1</i> and active transforming growth factor (TGF)-β1 that is activated by <i>TSP-1</i> were elevated in plasma of patients, while the level of prostaglandin E2 (<i>PGE2</i>) that is converted by <i>PTGS2</i> was reduced. The plasma level of <i>TSP-1</i> was positively correlated with that of active <i>TGF-β1</i>. <i>Conclusions</i>: Our data suggest that the molecular network including <i>TSP-1, TGF-β1</i>, and <i>PGE2</i> might be involved in the pathogenesis of APAC and PACG.
DOI: 10.6084/m9.figshare.4772293
title: Vision-related Quality of Life in Patients with Non-infectious Uveitis: A Cross-sectional Study

description: <i>Purpose</i>: To analyze the influence of socio-demographic, comorbidity, and clinical-related variables in the vision-related quality of life (VR-QoL) of non-infectious uveitis patients. <i>Methods</i>: Cross-sectional study includes 156 consecutive non-infectious uveitis patients from a tertiary uveitis clinic from Madrid (Spain). The main outcome was the log-transformed composite score of the Visual Functioning Questionnaire 25. Bivariate and multivariate ordinary least-squares regression models were performed and results expressed using effect sizes with 95% confidence intervals (95% CI). <i>Results</i>: In the multivariate analysis, one unit increase in the logarithm of the minimum angle of resolution scale [i.e., worse best corrected visual acuity (BCVA)] was associated with a seven times worse VR-QoL (a 0.14-fold change [95% CI: 0.07–0.27]). Patients with ocular comorbidities had a 64% worse VR-QoL (a 0.61-fold change [95% CI: 0.49–0.77]). <i>Conclusions</i>: Lower BCVA and the presence of ocular comorbidities had a significant, independent, and deleterious effect in the VR-QoL of non-infectious uveitis patients.
DOI: 10.6084/m9.figshare.4772305
title: Detection of cytosine and CpG density in proto-oncogenes and tumor suppressor genes in promoter sequences of acute myeloid leukemia

description: Aberrant methylation is one of the driving forces of cancer genome development. Although the rate of methylation appears massively variable across the genome, it is mainly observed in histone modification, chromatin organization, DNA accessibility, or promoter sequence. Methylation of promoter sequence occurs mostly to cytosine nucleotides, which can affect transcription factors' binding affinities. In this study, we demonstrated that cytosine repeats (C types density), consisting of CC, CCC, CCCC, CCCCC, CCCCCC, CCCCCCC motifs and CpG islands density in 25 proto-oncogenes, tumor suppressor genes and control genes may play a role in the pathogenesis of acute myeloid leukemia. The promoter sequences were divided into a 100 nucleotide window from −500 to +100 nucleotides and 20 nucleotide window from −100 to +100. Each window is analyzed to find the higher C type and CpG islands density, which may cause the increased methylation in the promoter sequence. Our novel findings show that promoter sequence cytosine repeats and CpG density increase closer to transcription sites, especially just before and after the transcription start site (TSS). The results demonstrate that cytosine density increases while proto-oncogenes and TSG promoter sequences are closer to TSS 50.8% and 41.0% respectively, if (−500 to −200) and (−100 to +100) windows of the nucleotide sequences are compared. This proves that around TSS location has special nucleotide motifs and could be an important implication for our understanding of potential methylating locations in promoters.
DOI: 10.6084/m9.figshare.4772320.v1
title: Microarray-based analysis of gene expression profiles in peripheral blood of patients with acute primary angle closure

description: <i>Background</i>: We investigated the expression of molecules in peripheral blood mononuclear cells (PBMCs) and plasma of patients with acute primary angle closure (APAC). <i>Materials and methods</i>: Peripheral blood was collected from patients with APAC (<i>n</i> = 10) and age-matched controls (<i>n</i> = 5). The gene transcription profile was analyzed in PBMCs using microarrays and validated by real-time reverse transcription polymerase chain reaction (RT-PCR). The levels of secreted proteins were evaluated in plasma by ELISA. <i>Results</i>: 347 gene transcripts were up-regulated by 2-fold or more, and 696 transcripts down-regulated 2-fold or more in PBMCs from patients compared to controls. The most highly up-regulated gene was thrombospondin-1 (<i>TSP-1</i>, 8.66-fold increase), and the most down-regulated gene was prostaglandin-endoperoxide synthase 2 (<i>PTGS2</i>, 9.09-fold decrease). Real-time RT-PCR assay confirmed the increase of <i>TSP-1</i> and the decrease of <i>PTGS2</i> in PBMCs of patients. ELISA revealed that the levels of <i>TSP-1</i> and active transforming growth factor (TGF)-β1 that is activated by <i>TSP-1</i> were elevated in plasma of patients, while the level of prostaglandin E2 (<i>PGE2</i>) that is converted by <i>PTGS2</i> was reduced. The plasma level of <i>TSP-1</i> was positively correlated with that of active <i>TGF-β1</i>. <i>Conclusions</i>: Our data suggest that the molecular network including <i>TSP-1, TGF-β1</i>, and <i>PGE2</i> might be involved in the pathogenesis of APAC and PACG.
DOI: 10.6084/m9.figshare.4772287
title: Comparing three regularization methods to avoid extreme allocation probability in response-adaptive randomization

description: We examine three variations of the regularization methods for response-adaptive randomization (RAR) and compare their operating characteristics. A power transformation (PT) is applied to refine the randomization probability. The clip method is used to bound the randomization probability within specified limits. A burn-in period of equal randomization (ER) can be added before adaptive randomization (AR). For each method, more patients are assigned to the superior arm and overall response rate increase as the scheme approximates simple AR, while statistical power increases as it approximates ER. We evaluate the performance of the three methods by varying the tuning parameter to control the extent of AR to achieve the same statistical power. When there is no early stopping rule, PT method generally performed the best in yielding higher proportion to the superior arm and higher overall response rate, but with larger variability. The burn-in method showed smallest variability compared with the clip method and the PT method. With the efficacy early stopping rule, all three methods performed more similarly. The PT and clip methods are better than the burn-in method in achieving higher proportion randomized to the superior arm and higher overall response rate but burn-in method required fewer patients in the trial. By carefully choosing the method and the tuning parameter, RAR methods can be tailored to strike a balance between achieving the desired statistical power and enhancing the overall response rate.
DOI: 10.6084/m9.figshare.4772293.v1
title: Vision-related Quality of Life in Patients with Non-infectious Uveitis: A Cross-sectional Study

description: <i>Purpose</i>: To analyze the influence of socio-demographic, comorbidity, and clinical-related variables in the vision-related quality of life (VR-QoL) of non-infectious uveitis patients. <i>Methods</i>: Cross-sectional study includes 156 consecutive non-infectious uveitis patients from a tertiary uveitis clinic from Madrid (Spain). The main outcome was the log-transformed composite score of the Visual Functioning Questionnaire 25. Bivariate and multivariate ordinary least-squares regression models were performed and results expressed using effect sizes with 95% confidence intervals (95% CI). <i>Results</i>: In the multivariate analysis, one unit increase in the logarithm of the minimum angle of resolution scale [i.e., worse best corrected visual acuity (BCVA)] was associated with a seven times worse VR-QoL (a 0.14-fold change [95% CI: 0.07–0.27]). Patients with ocular comorbidities had a 64% worse VR-QoL (a 0.61-fold change [95% CI: 0.49–0.77]). <i>Conclusions</i>: Lower BCVA and the presence of ocular comorbidities had a significant, independent, and deleterious effect in the VR-QoL of non-infectious uveitis patients.
DOI: 10.6084/m9.figshare.4772305.v1
title: Detection of cytosine and CpG density in proto-oncogenes and tumor suppressor genes in promoter sequences of acute myeloid leukemia

description: Aberrant methylation is one of the driving forces of cancer genome development. Although the rate of methylation appears massively variable across the genome, it is mainly observed in histone modification, chromatin organization, DNA accessibility, or promoter sequence. Methylation of promoter sequence occurs mostly to cytosine nucleotides, which can affect transcription factors' binding affinities. In this study, we demonstrated that cytosine repeats (C types density), consisting of CC, CCC, CCCC, CCCCC, CCCCCC, CCCCCCC motifs and CpG islands density in 25 proto-oncogenes, tumor suppressor genes and control genes may play a role in the pathogenesis of acute myeloid leukemia. The promoter sequences were divided into a 100 nucleotide window from −500 to +100 nucleotides and 20 nucleotide window from −100 to +100. Each window is analyzed to find the higher C type and CpG islands density, which may cause the increased methylation in the promoter sequence. Our novel findings show that promoter sequence cytosine repeats and CpG density increase closer to transcription sites, especially just before and after the transcription start site (TSS). The results demonstrate that cytosine density increases while proto-oncogenes and TSG promoter sequences are closer to TSS 50.8% and 41.0% respectively, if (−500 to −200) and (−100 to +100) windows of the nucleotide sequences are compared. This proves that around TSS location has special nucleotide motifs and could be an important implication for our understanding of potential methylating locations in promoters.
DOI: 10.6084/m9.figshare.4772287.v1
title: Comparing three regularization methods to avoid extreme allocation probability in response-adaptive randomization

description: We examine three variations of the regularization methods for response-adaptive randomization (RAR) and compare their operating characteristics. A power transformation (PT) is applied to refine the randomization probability. The clip method is used to bound the randomization probability within specified limits. A burn-in period of equal randomization (ER) can be added before adaptive randomization (AR). For each method, more patients are assigned to the superior arm and overall response rate increase as the scheme approximates simple AR, while statistical power increases as it approximates ER. We evaluate the performance of the three methods by varying the tuning parameter to control the extent of AR to achieve the same statistical power. When there is no early stopping rule, PT method generally performed the best in yielding higher proportion to the superior arm and higher overall response rate, but with larger variability. The burn-in method showed smallest variability compared with the clip method and the PT method. With the efficacy early stopping rule, all three methods performed more similarly. The PT and clip methods are better than the burn-in method in achieving higher proportion randomized to the superior arm and higher overall response rate but burn-in method required fewer patients in the trial. By carefully choosing the method and the tuning parameter, RAR methods can be tailored to strike a balance between achieving the desired statistical power and enhancing the overall response rate.
DOI: 10.17028/rd.lboro.4772275
title: Systematic Literature Review for Consumer Intervention Map

description: Systematic Literature Review for the creation of the Consumer Intervention Map. Forms part of a toolkit developed for the Business As Unusual Feasibility Project under the EPSRC RECODE network.<br>The links below are to "BAU Workshop Materials and Interaction Cards" and a "Consumer Intervention Map".
DOI: 10.17028/rd.lboro.4772275.v1
title: Systematic Literature Review for Consumer Intervention Map

description: Systematic Literature Review for the creation of the Consumer Intervention Map. Forms part of a toolkit developed for the Business As Unusual Feasibility Project under the EPSRC RECODE network.<br>The links below are to "BAU Workshop Materials and Interaction Cards" and a "Consumer Intervention Map".
DOI: 10.6073/pasta/6b3b6af2be1e3d3b8e55c47a55d344d8
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 1 meteorological station: Daily average soil volumetric water content data: 2013 - ongoing

description: Daily Average of 30-minute Soil Volumetric Water Content data at 10 cm at CSIS Block-1. Collection of soil water content data at Jornada LTER Cross-scale Interactions Study (CSIS) blocks, New Mexico, supports the environmental monitoring objectives of the Jornada LTER monitoring program that look at plant-soil water dynamics. Soil volumetric water content is measured every 30 minutes at 10 cm depth at 3 locations at each of the 4 plots per block and averaged for the daily value. The locations in each plot are under bare soil, under perennial grass, and under shrub. Volumetric water content, bulk electrical conductivity, soil temperature, and bulk dielectric permittivity are recorded at an automated meteorological station installed at Jornada LTER CSIS Block-1 site. This is an ONGOING dataset.
DOI: 10.6084/m9.figshare.4772167
title: Multi-omic analysis of the effects of low frequency ventilation (LFV) during cardiopulmonary bypass surgery.

description: Multi-Omic data of lung biopsies taken before and after cardio-pulmonary bypass surgery, either with or without low frequency ventilation.
DOI: 10.6084/m9.figshare.4772170
title: Supplementary Material for: The P-Type ATPase Superfamily

description: P-type ATPases function to provide homeostasis in higher eukaryotes, but they are essentially ubiquitous, being found in all domains of life. Thever and Saier [J Memb Biol 2009;229:115–130] recently reported analyses of eukaryotic P-type ATPases, dividing them into nine functionally characterized and 13 functionally uncharacterized (FUPA) families. In this report, we analyze P-type ATPases in all major prokaryotic phyla for which complete genome sequence data are available, and we compare the results with those for eukaryotic P-type ATPases. Topological type I (heavy metal) P-type ATPases predominate in prokaryotes (approx. tenfold) while type II ATPases (specific for Na<sup>+</sup>,K<sup>+</sup>, H<sup>+</sup> Ca<sup>2+</sup>, Mg<sup>2+</sup> and phospholipids) predominate in eukaryotes (approx. twofold). Many P-type ATPase families are found exclusively in prokaryotes (e.g. Kdp-type K<sup>+</sup> uptake ATPases (type III) and all ten prokaryotic FUPA familes), while others are restricted to eukaryotes (e.g. phospholipid flippases and all 13 eukaryotic FUPA families). Horizontal gene transfer has occurred frequently among bacteria and archaea, which have similar distributions of these enzymes, but rarely between most eukaryotic kingdoms, and even more rarely between eukaryotes and prokaryotes. In some bacterial phyla (e.g. Bacteroidetes, Flavobacteria and Fusobacteria), ATPase gene gain and loss as well as horizontal transfer occurred seldom in contrast to most other bacterial phyla. Some families (i.e. Kdp-type ATPases) underwent far less horizontal gene transfer than other prokaryotic families, possibly due to their multisubunit characteristics. Functional motifs are better conserved across family lines than across organismal lines, and these motifs can be family specific, facilitating functional predictions. In some cases, gene fusion events created P-type ATPases covalently linked to regulatory catalytic enzymes. In one family (FUPA Family 24), a type I ATPase gene (N-terminal) is fused to a type II ATPase gene (C-terminal) with retention of function only for the latter. Several pseudogene-encoded nonfunctional ATPases were identified. Genome minimalization led to preferential loss of P-type ATPase genes. We suggest that in prokaryotes and some unicellular eukaryotes, the primary function of P-type ATPases is protection from extreme environmental stress conditions. The classification of P-type ATPases of unknown function into phylogenetic families provides guides for future molecular biological studies.
DOI: 10.6084/m9.figshare.4772164
title: Internet data sources for disease surveillance: Assessment of suitability

description: This assessment evaluates 34 internet activity data sources for use in disease surveillance. Our goals are to (a) understand the available data on internet usage and activity well enough to (b) identify real-world internet data sources that can be used both for evaluating our theories of disease surveillance and building<br>operational internet data-based disease surveillance systems.<br><br>The assessment (pdf) and raw data (excel spreadsheet) are attached.<br>
DOI: 10.6084/m9.figshare.4772158
title: Supplementary Material for: Early Diagnosis of Intra-Abdominal Inflammation and Sepsis by Neutrophil CD64 Expression in Newborns

description: <i>Background:</i> Newborn infants with intra-abdominal inflammation/sepsis often present with nonspecific signs in the early stages of the disease, but can rapidly develop life-threatening complications. A reliable ‘early’ biomarker would be invaluable. <i>Objective:</i> To evaluate the effectiveness of neutrophil CD64 as an ‘early’ biomarker of intra-abdominal inflammation/sepsis. <i>Methods:</i> Blood was collected from newborns with suspected intra-abdominal pathology for neutrophil CD64 and C-reactive protein (CRP) determination at the onset of clinical presentation and 24 h later. They were classified into three groups: intra-abdominal inflammation/sepsis (group 1), extra-abdominal sepsis (group 2) and nonsepsis (group 3). Between-group comparisons were made by Kruskal-Wallis and χ<sup>2</sup> tests. Receiver-operating characteristic curves and diagnostic utilities for single and combination of tests were determined. <i>Results:</i> 310 infants were recruited (102, 34 and 174 in groups 1, 2 and 3, respectively). CD64 (conventional cutoff = 6,010 antibody-PE molecules bound/cell) had substantially better sensitivity (0.81 vs. 0.56) and negative predictive value (0.90 vs. 0.79) for diagnosing intra-abdominal sepsis than CRP, at presentation. Pairing CD64 with routine abdominal radiograph (AXR) substantially increased the sensitivity and negative predictive value for group 1 to 0.99 and 0.99, respectively. By adjusting the CD64 cutoff to 12,500 units, a substantial improvement in specificity could be achieved (0.62 to 0.80) without significantly compromising sensitivity (0.99 to 0.97). <i>Conclusions:</i> CD64 is a sensitive and ‘early’ biomarker for diagnosing intra-abdominal inflammation/sepsis. Intra-abdominal catastrophes, including necrotizing enterocolitis, intestinal necrosis, perforation and peritonitis can confidently be excluded using CD64 and AXR early in the course of the disease.
DOI: 10.6084/m9.figshare.4772167.v1
title: Multi-omic analysis of the effects of low frequency ventilation (LFV) during cardiopulmonary bypass surgery.

description: Multi-Omic data of lung biopsies taken before and after cardio-pulmonary bypass surgery, either with or without low frequency ventilation.
DOI: 10.6084/m9.figshare.4772131
title: Equine cartilage secretome 5 days IL-1 treatment in vitro;'Neopeptide Analyser' output files

description: Neopeptide Analyser output files.<br>Experiment n=8 equine metacarpophalangeal cartilage explants from grossly normal joints treated in vitro with 10ng/ml IL-1 for 5 days. Secretome samples collected and pooled for 5 days. Media samples tryspin digested and run on an Orbitrap-Velos mass spectrometer. Raw files input into Progenesis QIP and label-free quantification undertaken with Mascot used to search for semi-tryptic peptides. Peptide measurements output file from ProgenesisQIP is then used as the input file into the 'Neopeptide Analyser' for neopeptide identification. The files here are the output files from the 'Neopeptide Analyser'. They are suffixed _filter and _processed.