cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7869119
title: Supplementary Material for: Withdrawal Confounding in Randomized Controlled Trials of Antipsychotic, Antidepressant, and Stimulant Drugs, 2000–2017

description: <b><i>Background:</i></b> Results of relapse prevention randomized controlled trials (RCTs) which discontinue psychotropic drug treatment from some participants may be confounded by drug withdrawal symptoms. We test for the confound by calculating whether ≥50% of the difference in relapse risk between drug-discontinued and drug-maintained groups is present at discontinuation time points (DCTs) with “short” and “long” assumptions regarding onset and duration of withdrawal symptoms. <b><i>Methods:</i></b> In eligible RCTs of antidepressants, antipsychotics, and stimulants from 2000 to 2017 (<i>n</i> = 30) selected from a systematic review, differences in relapse risk were examined by arithmetic and graphical comparison of mean behavioral scores or survival plots. <b><i>Results:</i></b> Only 14 studies (46.6%) with 15 analyses of relapse risk provided sufficient data. Under short and long DCTs, 9 of 13 (69.2%) and 7 of 9 (77.8%) interpretable analyses, respectively, suggested a withdrawal confound. The proportion of endpoint placebo-maintenance group difference present by the DCT averaged 69.1% (range, 58.7–148.0%, <i>n</i> = 13) for short DCT assumptions, and 79.0% (range, 51.5–183.3%, <i>n</i> = 9) under long DCTs.<b><i></i></b> One study (3.33%) controlled for withdraw al effects, and 1 yielded inconclusive results. <b><i>Conclusions:</i></b> These results support suggestions that withdrawal symptoms confound the results of relapse prevention RCTs. Accounting for such symptoms in RCTs is an ethical, scientific, and clinical imperative. Justifications for relapse prevention RCTs employing a discontinuation procedure require more scrutiny.
DOI: 10.6084/m9.figshare.7869119.v1
title: Supplementary Material for: Withdrawal Confounding in Randomized Controlled Trials of Antipsychotic, Antidepressant, and Stimulant Drugs, 2000–2017

description: <b><i>Background:</i></b> Results of relapse prevention randomized controlled trials (RCTs) which discontinue psychotropic drug treatment from some participants may be confounded by drug withdrawal symptoms. We test for the confound by calculating whether ≥50% of the difference in relapse risk between drug-discontinued and drug-maintained groups is present at discontinuation time points (DCTs) with “short” and “long” assumptions regarding onset and duration of withdrawal symptoms. <b><i>Methods:</i></b> In eligible RCTs of antidepressants, antipsychotics, and stimulants from 2000 to 2017 (<i>n</i> = 30) selected from a systematic review, differences in relapse risk were examined by arithmetic and graphical comparison of mean behavioral scores or survival plots. <b><i>Results:</i></b> Only 14 studies (46.6%) with 15 analyses of relapse risk provided sufficient data. Under short and long DCTs, 9 of 13 (69.2%) and 7 of 9 (77.8%) interpretable analyses, respectively, suggested a withdrawal confound. The proportion of endpoint placebo-maintenance group difference present by the DCT averaged 69.1% (range, 58.7–148.0%, <i>n</i> = 13) for short DCT assumptions, and 79.0% (range, 51.5–183.3%, <i>n</i> = 9) under long DCTs.<b><i></i></b> One study (3.33%) controlled for withdraw al effects, and 1 yielded inconclusive results. <b><i>Conclusions:</i></b> These results support suggestions that withdrawal symptoms confound the results of relapse prevention RCTs. Accounting for such symptoms in RCTs is an ethical, scientific, and clinical imperative. Justifications for relapse prevention RCTs employing a discontinuation procedure require more scrutiny.
DOI: 10.6084/m9.figshare.7868681
title: Supplementary Table S2.2

description: Supplementary Table S1. 2 : Patient, PAM50 and TNBC molecular subtypes before and after reclassification.
DOI: 10.6084/m9.figshare.7868666
title: Supplementary Table S2.1

description: Supplementary Table S1. 1 : Types of genomic data available for each patient.
DOI: 10.6084/m9.figshare.7868681.v1
title: Supplementary Table S1.2

description: Supplementary Table S1. 2 : Patient, PAM50 and TNBC molecular subtypes before and after reclassification.
DOI: 10.6084/m9.figshare.7868657
title: Data for segments 1,2,3,5,7,8 - 10279 taxa from A brief history of bird flu

description: Subsampled sequences in fasta format, corresponding trees in newick format and sequence information as tables
DOI: 10.6084/m9.figshare.7868666.v2
title: Supplementary Table S2.1

description: Supplementary Table S1. 1 : Types of genomic data available for each patient.
DOI: 10.6084/m9.figshare.7868681.v3
title: Supplementary Table S2.2

description: Supplementary Table S1. 2 : Patient, PAM50 and TNBC molecular subtypes before and after reclassification.
DOI: 10.6084/m9.figshare.7868651
title: Data for segment 4 subtype H5 - 1177 taxa from A brief history of bird flu

description: Subsampled HA H5 sequences in fasta format, BEAST MCC tree, BEAUTI/BEAST xml configuration file, and sequence information as tables
DOI: 10.6084/m9.figshare.7868654
title: Data for segments 1,2,3,5,7,8 - 8809 taxa for display from A brief history of bird flu

description: Subsampled sequences in fasta format, corresponding trees in newick format, and sequence information for the display data sets as tables
DOI: 10.6084/m9.figshare.7868666.v1
title: Supplementary Table S1.1

description: Supplementary Table S1. 1 : Types of genomic data available for each patient.
DOI: 10.6084/m9.figshare.7868651.v1
title: Data for segment 4 subtype H5 - 1177 taxa from A brief history of bird flu

description: Subsampled HA H5 sequences in fasta format, BEAST MCC tree, BEAUTI/BEAST xml configuration file, and sequence information as tables
DOI: 10.6084/m9.figshare.7868654.v1
title: Data for segments 1,2,3,5,7,8 - 8809 taxa for display from A brief history of bird flu

description: Subsampled sequences in fasta format, corresponding trees in newick format, and sequence information for the display data sets as tables
DOI: 10.6084/m9.figshare.7868657.v1
title: Data for segments 1,2,3,5,7,8 - 10279 taxa from A brief history of bird flu

description: Subsampled sequences in fasta format, corresponding trees in newick format and sequence information as tables
DOI: 10.6084/m9.figshare.7868681.v2
title: Supplementary Table S1.2

description: Supplementary Table S1. 2 : Patient, PAM50 and TNBC molecular subtypes before and after reclassification.
DOI: 10.6084/m9.figshare.7868573
title: Workshop Zoeken naar Onderzoeksdata_VOGIN-IP 2019

description: Slides en opdrachten van de workshop 'Zoeken naar onderzoeksdata', gegeven op de VOGIN-IP lezing van 2019.
DOI: 10.6084/m9.figshare.7868606
title: Matlab code to generate all figures from Modular structure within groups causes information loss but can improve decision accuracy

description: Many animal groups exhibit signatures of persistent internal modular structure, whereby individuals consistently interact with certain groupmates more than others. In such groups, information relevant to a collective decision may spread unevenly through the group, but how this impacts the quality of the resulting decision is not well understood. Here, we explicitly model modularity within animal groups and examine how it affects the amount of information represented in collective decisions, as well as the accuracy of those decisions. We find that modular structure necessarily causes a loss of information, effectively silencing the input from a fraction of the group. However, the effect of this information loss on collective accuracy depends on the informational environment in which the decision is made. In simple environments, the information loss is detrimental to collective accuracy. By contrast, in complex environments, modularity tends to improve accuracy. This is because small group sizes typically maximize collective accuracy in such environments, and modular structure allows a large group to behave like a smaller group (in terms of its decision-making). These results suggest that in naturalistic environments containing correlated information, large animal groups may be able to exploit modular structure to improve decision accuracy while retaining other benefits of large group size.
DOI: 10.6084/m9.figshare.7868606.v1
title: Matlab code to generate all figures from Modular structure within groups causes information loss but can improve decision accuracy

description: Many animal groups exhibit signatures of persistent internal modular structure, whereby individuals consistently interact with certain groupmates more than others. In such groups, information relevant to a collective decision may spread unevenly through the group, but how this impacts the quality of the resulting decision is not well understood. Here, we explicitly model modularity within animal groups and examine how it affects the amount of information represented in collective decisions, as well as the accuracy of those decisions. We find that modular structure necessarily causes a loss of information, effectively silencing the input from a fraction of the group. However, the effect of this information loss on collective accuracy depends on the informational environment in which the decision is made. In simple environments, the information loss is detrimental to collective accuracy. By contrast, in complex environments, modularity tends to improve accuracy. This is because small group sizes typically maximize collective accuracy in such environments, and modular structure allows a large group to behave like a smaller group (in terms of its decision-making). These results suggest that in naturalistic environments containing correlated information, large animal groups may be able to exploit modular structure to improve decision accuracy while retaining other benefits of large group size.
DOI: 10.6084/m9.figshare.7868282
title: Supplementary Material for: Enhancement of Tissue Factor Expression in Monocyte-Derived Dendritic Cells by Pentraxin 3 and Its Modulation by C1 Esterase Inhibitor

description: <b><i>Background:</i></b> We have previously shown that human monocyte-derived dendritic cells (moDCs) may participate in immune system-mediated hypercoagulable state through enhanced tissue factor (TF) expression and that the complement system may be involved in this process. <b><i>Objectives:</i></b> The aim of this study was to explore the role of pentraxin 3 (PTX3) and the complement system in enhanced TF expression in moDCs. <b><i>Methods:</i></b> moDCs were generated from isolated human monocytes. PTX3 levels in whole human blood supplemented with moDCs were determined after lipopolysaccharide (LPS) stimulation. PTX3 release by the generated moDCs upon LPS stimulation was also assessed. The effect of PTX3 on whole blood coagulation was investigated using thromboelastometric analysis. TF expression in stationary moDCs treated with LPS and/or PTX3 was determined by measuring TF activity. The effect of complement inhibitors on TF activity in moDCs treated with LPS and/or PTX3 under low-shear conditions was evaluated. <b><i>Results:</i></b> PTX3 levels were higher in whole blood supplemented with moDCs than in the presence of monocytes and were further elevated by LPS stimulation. PTX3 release from generated moDCs was also increased by LPS stimulation. PTX3 reduced whole blood coagulation time in a dose-dependent manner. However, PTX3 did not increase TF expression in stationary moDCs. Under low-shear conditions, PTX3 increased TF expression in moDCs. C1 esterase inhibitor (C1-inh) suppressed this effect. <b><i>Conclusions:</i></b> PTX3 might have a thrombophilic activity and enhance TF expression in moDCs under low-shear conditions. Furthermore, suppression of moDC-associated hypercoagulability by C1-inh might be partly ascribed to its inhibitory effect on PTX3.
DOI: 10.6084/m9.figshare.7868282.v1
title: Supplementary Material for: Enhancement of Tissue Factor Expression in Monocyte-Derived Dendritic Cells by Pentraxin 3 and Its Modulation by C1 Esterase Inhibitor

description: <b><i>Background:</i></b> We have previously shown that human monocyte-derived dendritic cells (moDCs) may participate in immune system-mediated hypercoagulable state through enhanced tissue factor (TF) expression and that the complement system may be involved in this process. <b><i>Objectives:</i></b> The aim of this study was to explore the role of pentraxin 3 (PTX3) and the complement system in enhanced TF expression in moDCs. <b><i>Methods:</i></b> moDCs were generated from isolated human monocytes. PTX3 levels in whole human blood supplemented with moDCs were determined after lipopolysaccharide (LPS) stimulation. PTX3 release by the generated moDCs upon LPS stimulation was also assessed. The effect of PTX3 on whole blood coagulation was investigated using thromboelastometric analysis. TF expression in stationary moDCs treated with LPS and/or PTX3 was determined by measuring TF activity. The effect of complement inhibitors on TF activity in moDCs treated with LPS and/or PTX3 under low-shear conditions was evaluated. <b><i>Results:</i></b> PTX3 levels were higher in whole blood supplemented with moDCs than in the presence of monocytes and were further elevated by LPS stimulation. PTX3 release from generated moDCs was also increased by LPS stimulation. PTX3 reduced whole blood coagulation time in a dose-dependent manner. However, PTX3 did not increase TF expression in stationary moDCs. Under low-shear conditions, PTX3 increased TF expression in moDCs. C1 esterase inhibitor (C1-inh) suppressed this effect. <b><i>Conclusions:</i></b> PTX3 might have a thrombophilic activity and enhance TF expression in moDCs under low-shear conditions. Furthermore, suppression of moDC-associated hypercoagulability by C1-inh might be partly ascribed to its inhibitory effect on PTX3.
DOI: 10.6084/m9.figshare.7868267
title: Supplementary Material for: Evidence for a Role of TGF-β-Activated Kinase 1 and MAP3K7 Binding Protein 3 in Peanut-Specific T-Cell Responses

description: Peanut allergy is considered to be the most common cause for food-induced anaphylaxis. Currently, no approved treatment is available. Avoidance is the only measure to prevent anaphylactic reactions to peanuts. T-helper cells are of special importance for the sensitization process and the maintenance of allergic inflammation. Identifying markers of allergen-specific T-cell responses may help to develop novel treatment approaches. Therefore, we aimed to define new T-cell target genes in Ara h 2-specific T cells and to investigate the possibility of using them as biomarkers of peanut allergy in peripheral blood mononuclear cells (PBMCs). We performed whole mRNA array analysis (whole human genome oligo microarray) of in vitro expanded Ara h 2-specific T cells (CFSE<sup>low</sup>CD3<sup>+</sup>CD4<sup>+</sup>) from 5 peanut-allergic (PA) and 5 non-peanut-sensitized individuals. Expression of selected genes as a result of a two-step bioinformatic approach was confirmed in a second cohort by quantitative PCR. TGF-β- activated kinase 1 and MAP3K7 binding protein 3 (TAB3), calcium/calmodulin-dependent protein kinase type IV (CAMK4) and HemK methyltransferase family member 1 (HEMK1) were significantly upregulated in Ara h 2-specific T cells of PA patients. In addition, the expression of these genes was also assessed in unstimulated PBMCs from a cohort (<i>n</i> = 43) of PA, atopic non-PA, and nonatopic controls. Interestingly, in unstimulated PBMCs, TAB3 expression was significantly downregulated in PA patients compared to atopic non-PA individuals. Thus, TAB3 may play a significant role at the level of T-cell activation and may also be a candidate biomarker for PA.
DOI: 10.6084/m9.figshare.7868261
title: Supplementary Material for: Clinical Monitoring of Sacrococcygeal Teratoma

description: <b><i>Background:</i></b> Sacrococcygeal teratomas (SCT) are often highly vascularized and may result in high-output cardiac failure, polyhydramnios, fetal hydrops, and demise. Delivery is guided by the SCT to fetus volume ratio (SCTratio), SCT growth rate, and cardiac output indexed for weight (CCOi). <b><i>Methods:</i></b> We compared measurements and outcome in 12 consecutive fetuses referred with SCT. Adverse outcomes were: fetal surgery, delivery &lt; 32 gestational weeks or neonatal demise. Only SCTratio and CCOi were used to manage the cases. SCT vascularization index (VI%) was derived from the 3D virtual organ computer-aided analysis (VOCAL) software. The SCTModel (modified from acardiac twins) calculated a hypothetical SCT draining vein size and derived a risk line, using diameters of the superior and inferior vena cava, the azygous and umbilical veins. VI% and a model of systemic and umbilical venous volumes (SCTModel) were tested as indicators for outcome in SCT. <b><i>Results:</i></b> Fetuses were monitored from 20.1 to 36.4 gestational weeks and 5/12 had adverse outcomes: 1 had successful open fetal surgery at 23.8 weeks and delivered at term, 4 delivered at &lt; 32 weeks with 3/4 having neonatal demise between 25 and 29 weeks. VI% was significantly higher in cases with adverse outcomes (mean 10.3 [8.9–11.6] vs. 4.4 [3.4–5.3], <i>p</i> &lt; 0.0001). The additional fraction of the fetal cardiac output required to perfuse the SCT-draining vein (XSCO%) (<i>p</i> = 0.46), SCTratio (<i>p</i> = 0.08), and CCOi (<i>p</i> = 0.64) were not significant. All cases with adverse outcome had VI% &gt; 8%. The SCTModel risk line predicted nonadverse outcomes well but lacked data in 2/5 cases with adverse outcomes. <b><i>Conclusions:</i></b> VI% is a significant indicator of SCT cases with adverse outcomes and combined with SCTratio may guide timing of delivery better than current measures.
DOI: 10.25387/g3.12869627
title: Supplemental Material for Laimbeer et al., 2020

description: <b>Supplementary Tables and Figures</b><br>
DOI: 10.25387/g3.12869627.v1
title: Supplemental Material for Laimbeer et al., 2020

description: <b>Supplementary Tables and Figures</b><br>
DOI: 10.6084/m9.figshare.7868048
title: Assessing Collaborative Conservation: A Case Survey of Output, Outcome, and Impact Measures Used in the Empirical Literature

description: Much existing research on collaborative conservation has focused on process, even as researchers have called for greater attention to explaining what results these processes yield. It is time to take stock of collaborative conservation research by mapping what kinds of variables researchers are including in analyses. Here we conduct a case survey from the SCAPE database of environmental decision-making cases. We include cases involving collaboration across government, environmental protection, and resource exploitation interests in western democratic countries. Results reveal patterns in what researchers include in their outputs, outcomes, and impacts measures of collaborative conservation. While there is little difference by publication type (peer-reviewed journals, scholarly book chapters, or gray literature) or over time, we find significant differences in explicit measures across variable types. In particular, variables more proximate to process in a logic chain are more often measured, as are social rather than ecological variables.
DOI: 10.6084/m9.figshare.7868048.v1
title: Assessing Collaborative Conservation: A Case Survey of Output, Outcome, and Impact Measures Used in the Empirical Literature

description: Much existing research on collaborative conservation has focused on process, even as researchers have called for greater attention to explaining what results these processes yield. It is time to take stock of collaborative conservation research by mapping what kinds of variables researchers are including in analyses. Here we conduct a case survey from the SCAPE database of environmental decision-making cases. We include cases involving collaboration across government, environmental protection, and resource exploitation interests in western democratic countries. Results reveal patterns in what researchers include in their outputs, outcomes, and impacts measures of collaborative conservation. While there is little difference by publication type (peer-reviewed journals, scholarly book chapters, or gray literature) or over time, we find significant differences in explicit measures across variable types. In particular, variables more proximate to process in a logic chain are more often measured, as are social rather than ecological variables.
DOI: 10.6084/m9.figshare.7867949
title: Data from: Cooney et al. Sexual selection predicts the rate and direction of colour evolution in a large avian radiation. Nature Communications.

description: <b>Contents</b><br><br><b>Analysis_Data.zip</b>Core processed datasets and phylogenies used to conduct the analyses.<br><b>Photography_Data.zip</b>Raw specimen photographs, coordinates of plumage patch locations and scripts used to process images and generate colour data.<br><b>Spec_Data.zip</b>Raw and processed spectrometer measurements used to test the accuracy of image-based colour estimates.<br><br><b>Correspondence</b><b><br></b>Chris Cooney (c.cooney@sheffield.ac.uk)Gavin Thomas (gavin.thomas@sheffield.ac.uk)<br>
DOI: 10.6084/m9.figshare.7867952
title: Exp1

description: Repetition task<br>
DOI: 10.6084/m9.figshare.7867961
title: Exp2

description: Pairing task<br>
DOI: 10.6084/m9.figshare.7867967
title: Exp3

description: MEG exp.<br>
DOI: 10.6084/m9.figshare.7867961.v1
title: Exp2

description: Pairing task<br>
DOI: 10.6084/m9.figshare.7867949.v1
title: Data from: Cooney et al. Sexual selection predicts the rate and direction of colour evolution in a large avian radiation. Nature Communications.

description: <b>Contents</b><br><br><b>Analysis_Data.zip</b>Core processed datasets and phylogenies used to conduct the analyses.<br><b>Photography_Data.zip</b>Raw specimen photographs, coordinates of plumage patch locations and scripts used to process images and generate colour data.<br><b>Spec_Data.zip</b>Raw and processed spectrometer measurements used to test the accuracy of image-based colour estimates.<br><br><b>Correspondence</b><b><br></b>Chris Cooney (c.cooney@sheffield.ac.uk)Gavin Thomas (gavin.thomas@sheffield.ac.uk)<br>
DOI: 10.6084/m9.figshare.7867967.v1
title: Exp3

description: MEG exp.<br>
DOI: 10.6084/m9.figshare.7867919
title: Evaluation of anti-inflammatory impact of dexamethasone-loaded PCL-PEG-PCL micelles on endotoxin-induced uveitis in rabbits

description: The aim of this study was to investigate the capability of polycaprolactone-polyethylene glycol-polycaprolactone (PCL-PEG-PCL) micelles in improving the anti-inflammatory effects of dexamethasone (DEX). A film hydration method was used for the preparation of the DEX-loaded PCL-PEG-PCL micelles. <i>In vitro</i> cytotoxicity of the micelles obtained was investigated on L929 cells. Cellular uptake was studied by using flow cytometry and fluorescence microscopy. Anterior uveitis was induced in a group of rabbits by intravitreal injection of endotoxin from <i>Salmonella typhimurium</i>. The severity of inflammation-induced was clinically graded by using Hogan’s classification method. Protein concentration in the aqueous humor was also measured. The micelles exhibited suitable compatibility on L929 cells and were taken up by the cells in a concentration- and time-dependent manner. The DEX-loaded micelles could reduce the clinical symptoms of uveitis after a lag-time. At 24 and 36 h after the LPS injection, the PCL-PEG-PCL micelles showed a better inhibitory effect on uveitis than the marketed eye drop, the differences did not reach significant levels though. This study demonstrated the potential of the PCL-PEG-PCL micelles as carriers for DEX in treating anterior uveitis. However, this concept is still to be further investigated.