cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6969863
title: Detailed data of serum proteins(High-flux HD versus Low-flux HD)..xlsx

description: 目的：本研究旨在使用蛋白质组学方法研究血清蛋白的变化高通量和低通量血液透析（HD）后的水平。方法：在HD前后，从两名选择的患者中获取血清样本用Polyflux 140H高通量透析器和Polyflux 14 L低通量透析器治疗两个连续Q5治疗会议。液相色谱 - 串联质谱（LC-MS / MS）进行了鉴定蛋白质。结果：高通量和低通量HD后共鉴定出212和203种血清蛋白，分别。高通量HD后，21种蛋白质增加，132种蛋白质减少。低通量后HD，87种蛋白质增加，45种蛋白质减少。高通量HD导致显着增加蛋白质水平比低通量HD降低（0.73±0.13 vs. 0.84±0.18，p = 0.00）。之间蛋白质增加和减少，等电点（pI）值主要在5到7之间，并且分子量（Mws）大多小于30kDa。血清蛋白显示对于高通量和低通量HD，pI或Mw没有差异。基因本体论（GO）分析表明检测到的蛋白质与免疫系统过程和补体激活有关。结论：高通量和低通量HD后血清蛋白水平差异有所改变。长期在未来的研究中应该观察到效果。
DOI: 10.6084/m9.figshare.6969875
title: Supplementary Material for: A Novel Strategy to Identify Placebo Responders: Prediction Index of Clinical and Biological Markers in the EMBARC Trial

description: <b><i>Background:</i></b> One in three clinical trial patients with major depressive disorder report symptomatic improvement with placebo. Strategies to mitigate the effect of placebo responses have focused on modifying study design with variable success. Identifying and excluding or controlling for individuals with a high likelihood of responding to placebo may improve clinical trial efficiency and avoid unnecessary medication trials. <b><i>Methods:</i></b> Participants included those assigned to the placebo arm (<i>n</i> = 141) of the Establishing Moderators and Biosignatures for Antidepressant Response in Clinical Care (EMBARC) trial. The elastic net was used to evaluate 283 baseline clinical, behavioral, imaging, and electrophysiological variables to identify the most robust yet parsimonious features that predicted depression severity at the end of the double-blind 8-week trial. Variables retained in at least 50% of the 100 imputed data sets were used in a Bayesian multiple linear regression model to simultaneously predict the probabilities of response and remission. <b><i>Results:</i></b> Lower baseline depression severity, younger age, absence of melancholic features or history of physical abuse, less anxious arousal, less anhedonia, less neuroticism, and higher average theta current density in the rostral anterior cingulate predicted a higher likelihood of improvement with placebo. The Bayesian model predicted remission and response with an actionable degree of accuracy (both AUC &gt; 0.73). An interactive calculator was developed predicting the likelihood of placebo response at the individual level. <b><i>Conclusion:</i></b> Easy-to-measure clinical, behavioral, and electrophysiological assessments can be used to identify placebo responders with a high degree of accuracy. Development of this calculator based on these findings can be used to identify potential placebo responders.
DOI: 10.6084/m9.figshare.6969875.v1
title: Supplementary Material for: A Novel Strategy to Identify Placebo Responders: Prediction Index of Clinical and Biological Markers in the EMBARC Trial

description: <b><i>Background:</i></b> One in three clinical trial patients with major depressive disorder report symptomatic improvement with placebo. Strategies to mitigate the effect of placebo responses have focused on modifying study design with variable success. Identifying and excluding or controlling for individuals with a high likelihood of responding to placebo may improve clinical trial efficiency and avoid unnecessary medication trials. <b><i>Methods:</i></b> Participants included those assigned to the placebo arm (<i>n</i> = 141) of the Establishing Moderators and Biosignatures for Antidepressant Response in Clinical Care (EMBARC) trial. The elastic net was used to evaluate 283 baseline clinical, behavioral, imaging, and electrophysiological variables to identify the most robust yet parsimonious features that predicted depression severity at the end of the double-blind 8-week trial. Variables retained in at least 50% of the 100 imputed data sets were used in a Bayesian multiple linear regression model to simultaneously predict the probabilities of response and remission. <b><i>Results:</i></b> Lower baseline depression severity, younger age, absence of melancholic features or history of physical abuse, less anxious arousal, less anhedonia, less neuroticism, and higher average theta current density in the rostral anterior cingulate predicted a higher likelihood of improvement with placebo. The Bayesian model predicted remission and response with an actionable degree of accuracy (both AUC &gt; 0.73). An interactive calculator was developed predicting the likelihood of placebo response at the individual level. <b><i>Conclusion:</i></b> Easy-to-measure clinical, behavioral, and electrophysiological assessments can be used to identify placebo responders with a high degree of accuracy. Development of this calculator based on these findings can be used to identify potential placebo responders.
DOI: 10.17028/rd.lboro.6969851
title: 500uL Mould FDM

description: Mould for the creation of tissue engineered skeletal muscle in 500uL construct volumes. To be 3D printed using fused deposition modelling (FDM).
DOI: 10.17028/rd.lboro.6969848
title: 250uL Mould FDM and LS

description: Mould for the creation of tissue engineered skeletal muscle in 250uL construct volumes. To be 3D printed using fused deposition modelling (FDM) or Laser Sintering (LS).
DOI: 10.6084/m9.figshare.6969842
title: Fecal cortisol concentration

description: When an individual defecates during a behavioral observation the name of the individual, defecation time, date and place were noted down on a map of the enclosure. Feces were collected in 50 mL tubes during the feeding and cleaning of the enclosure. To obtain the fecal cortisol concentration an immunosassay(IEA) was used with the DetectX® Cortisol Immunoassay kit of Arbor Assays.
DOI: 10.6084/m9.figshare.6969839
title: behavior

description: This study used a continuous focal sampling method with a sampling time of 10 minutes per individual to measure behavior (Martin & Bateson 2012). This means one individual at the time is observed while noting down the exact duration of one type of behavior for 10 minutes straight. When the sampling time is over the next individual was observed. One observation of the whole group takes 50 minutes. Observations of the entire group were done three times per day. The first two observations were done from 10:00-12:00 and the last one after the feeding time (ca. 12:00-14:00). The observation times were chosen because of the need to be present during the feeding time, and periods with the highest behavioral complexity as well as the time when the spider monkeys most likely to defecate. Because of the variable feeding time the time of the observations are also slightly variable. The observations took place around five days per week. Five types of behaviors were observed: possible stereotypic, obviously stereotypic, group size and social behavior (appendix 4). Possible stereotypic behavior for example scratching can be stereotypic but it can also be normal behavior. Obvious stereotypic behavior is always stereotypic for example gnashing the teeth. The preference of the location of the spider monkeys determined the location of the observer.
DOI: 10.6084/m9.figshare.6969839.v1
title: behavior

description: This study used a continuous focal sampling method with a sampling time of 10 minutes per individual to measure behavior (Martin & Bateson 2012). This means one individual at the time is observed while noting down the exact duration of one type of behavior for 10 minutes straight. When the sampling time is over the next individual was observed. One observation of the whole group takes 50 minutes. Observations of the entire group were done three times per day. The first two observations were done from 10:00-12:00 and the last one after the feeding time (ca. 12:00-14:00). The observation times were chosen because of the need to be present during the feeding time, and periods with the highest behavioral complexity as well as the time when the spider monkeys most likely to defecate. Because of the variable feeding time the time of the observations are also slightly variable. The observations took place around five days per week. Five types of behaviors were observed: possible stereotypic, obviously stereotypic, group size and social behavior (appendix 4). Possible stereotypic behavior for example scratching can be stereotypic but it can also be normal behavior. Obvious stereotypic behavior is always stereotypic for example gnashing the teeth. The preference of the location of the spider monkeys determined the location of the observer.
DOI: 10.6084/m9.figshare.6969821
title: Supplementary Material for: The Progression of the Stargardt Disease Type 4 (ProgStar-4) Study: Design and Baseline Characteristics (ProgStar-4 Report No. 1)

description: <b><i>Background/Aims:</i></b> To describe the design and baseline characteristics of patients enrolled in the multicenter, prospective natural history study of Stargardt disease type 4. <b><i>Methods:</i></b> Fifteen eligible patients aged 6 years and older at baseline, harboring disease-causing variants in the <i>PROM1</i> gene, and with specified ocular lesions were enrolled. They were examined at baseline using a standard protocol, with 6 monthly follow-up visits for a 2-year period including best-corrected ETDRS visual acuity, spectral-domain optical coherence tomography, fundus autofluorescence (FAF), mesopic and scotopic microperimetry (MP). Areas of definitely decreased FAF (DDAF) and questionably decreased FAF were outlined and quantified on FAF images. <b><i>Results:</i></b> Amongst the 15 patients (29 eyes) that were enrolled at 5 centers in the USA and Europe, 10 eyes (34.5%) had areas of DDAF with an average lesion area of 3.2 ± 3.5 mm<sup>2</sup> (range 0.36–10.39 mm<sup>2</sup>) at baseline. The mean retinal sensitivity of the posterior pole derived from mesopic MP was 8.8 ± 5.8 dB. <b><i>Conclusions:</i></b> Data on disease progression in <i>PROM1</i>-related retinopathy from this study will contribute to the characterization of the natural history of disease and the exploration of the utility of several modalities to track progression and therefore to potentially be used in future interventional clinical trials.
DOI: 10.6084/m9.figshare.6969833
title: Supplementary Material for: Assessment of Placental Cortisol Pathway Gene Expression in Term Pregnant Women with Anxiety

description: <b><i>Introduction:</i></b> The aim of this study was to expand on this field of work by examining, within a cohort of pregnant women with diagnosed clinical anxiety, the mRNA expression of a panel of genes associated with the cortisol pathway and comparing them to controls. <b><i>Methods:</i></b> Placental samples were obtained from 24 pregnant women, 12 with a diagnosed anxiety disorder and 12 with no psychiatric history, within 30 min of delivery. Differential expression analysis of 85 genes known to be involved in glucocorticoid synthesis, metabolism or signalling was conducted for the: (1) full sample, (2) those at term without labour (5 cases, 7 controls) and (3) those at term with labour (7 cases, 5 controls). Correlation analyses between gene expression and measures of anxiety and depressive symptom severity were also conducted. <b><i>Results:</i></b> No robust difference in placental gene expression between pregnant women with and without anxiety disorder was found nor did we detect robust differences by labour status. However, correlational analyses putatively showed a decrease in <i>PER1</i> expression was associated with an increase in anxiety symptom severity, explaining up to 32% of the variance in anxiety symptom severity. <b><i>Discussion:</i></b> Overall, the strongest correlation was found between a decrease in placental <i>PER1</i> expression and increased anxiety scores. Labour status was found to have a profound effect on mRNA expression. The placental samples obtained from women following labour produced greater numbers of significant differences in mRNA species expression suggesting that in long-standing anxiety the placenta may respond differently under conditions of chronic stress.
DOI: 10.6084/m9.figshare.6969833.v1
title: Supplementary Material for: Assessment of Placental Cortisol Pathway Gene Expression in Term Pregnant Women with Anxiety

description: <b><i>Introduction:</i></b> The aim of this study was to expand on this field of work by examining, within a cohort of pregnant women with diagnosed clinical anxiety, the mRNA expression of a panel of genes associated with the cortisol pathway and comparing them to controls. <b><i>Methods:</i></b> Placental samples were obtained from 24 pregnant women, 12 with a diagnosed anxiety disorder and 12 with no psychiatric history, within 30 min of delivery. Differential expression analysis of 85 genes known to be involved in glucocorticoid synthesis, metabolism or signalling was conducted for the: (1) full sample, (2) those at term without labour (5 cases, 7 controls) and (3) those at term with labour (7 cases, 5 controls). Correlation analyses between gene expression and measures of anxiety and depressive symptom severity were also conducted. <b><i>Results:</i></b> No robust difference in placental gene expression between pregnant women with and without anxiety disorder was found nor did we detect robust differences by labour status. However, correlational analyses putatively showed a decrease in <i>PER1</i> expression was associated with an increase in anxiety symptom severity, explaining up to 32% of the variance in anxiety symptom severity. <b><i>Discussion:</i></b> Overall, the strongest correlation was found between a decrease in placental <i>PER1</i> expression and increased anxiety scores. Labour status was found to have a profound effect on mRNA expression. The placental samples obtained from women following labour produced greater numbers of significant differences in mRNA species expression suggesting that in long-standing anxiety the placenta may respond differently under conditions of chronic stress.
DOI: 10.6084/m9.figshare.6969815
title: normalized UMI cout table post cell filtering

description: normalized UMI cout table post cell filtering
DOI: 10.17028/rd.lboro.6969806
title: 100uL Mould LS

description: Mould for the creation of tissue engineered skeletal muscle in 100uL construct volumes. To be 3D printed using Laser Sintering (LS).<br>
DOI: 10.6084/m9.figshare.6969815.v1
title: normalized UMI cout table post cell filtering

description: normalized UMI cout table post cell filtering
DOI: 10.6084/m9.figshare.6969821.v1
title: Supplementary Material for: The Progression of the Stargardt Disease Type 4 (ProgStar-4) Study: Design and Baseline Characteristics (ProgStar-4 Report No. 1)

description: <b><i>Background/Aims:</i></b> To describe the design and baseline characteristics of patients enrolled in the multicenter, prospective natural history study of Stargardt disease type 4. <b><i>Methods:</i></b> Fifteen eligible patients aged 6 years and older at baseline, harboring disease-causing variants in the <i>PROM1</i> gene, and with specified ocular lesions were enrolled. They were examined at baseline using a standard protocol, with 6 monthly follow-up visits for a 2-year period including best-corrected ETDRS visual acuity, spectral-domain optical coherence tomography, fundus autofluorescence (FAF), mesopic and scotopic microperimetry (MP). Areas of definitely decreased FAF (DDAF) and questionably decreased FAF were outlined and quantified on FAF images. <b><i>Results:</i></b> Amongst the 15 patients (29 eyes) that were enrolled at 5 centers in the USA and Europe, 10 eyes (34.5%) had areas of DDAF with an average lesion area of 3.2 ± 3.5 mm<sup>2</sup> (range 0.36–10.39 mm<sup>2</sup>) at baseline. The mean retinal sensitivity of the posterior pole derived from mesopic MP was 8.8 ± 5.8 dB. <b><i>Conclusions:</i></b> Data on disease progression in <i>PROM1</i>-related retinopathy from this study will contribute to the characterization of the natural history of disease and the exploration of the utility of several modalities to track progression and therefore to potentially be used in future interventional clinical trials.
DOI: 10.6084/m9.figshare.6969800
title: scaled gene-cell matrix when the cell cycle effect is not removed

description: scaled gene-cell matrix when the cell cycle effect is not removed
DOI: 10.6084/m9.figshare.6969800.v1
title: scaled gene-cell matrix when the cell cycle effect is not removed

description: scaled gene-cell matrix when the cell cycle effect is not removed
DOI: 10.17028/rd.lboro.6969797
title: 50uL Mould LS

description: Mould for the creation of tissue engineered skeletal muscle in 50uL construct volumes. To be 3D printed via laser sintering (LS).
DOI: 10.17028/rd.lboro.6969797.v1
title: 50uL Mould LS

description: Mould for the creation of tissue engineered skeletal muscle in 50uL construct volumes. To be 3D printed via laser sintering (LS).
DOI: 10.17028/rd.lboro.6969710
title: 50uL Mould FDM

description: Mould for the creation of tissue engineered skeletal muscle in 50uL construct volumes. To be 3D printed via fused deposition modelling (FDM).
DOI: 10.17028/rd.lboro.6969707
title: 50uL FDM removable insert

description: Removable insert for 50uL mould to be 3D printed via fused deposition modelling (FDM).
DOI: 10.17028/rd.lboro.6969683
title: 25uL Mould LS

description: Mould for the creation of tissue engineered skeletal muscle in 25uL construct volumes. To be 3D printed using Laser Sintering (LS).
DOI: 10.17028/rd.lboro.6969683.v1
title: 25uL Mould LS

description: Mould for the creation of tissue engineered skeletal muscle in 25uL construct volumes. To be 3D printed using Laser Sintering (LS).
DOI: 10.6084/m9.figshare.6969593
title: Supplementary Material for: Uric Acid as a Predictor of Immunoglobulin A Nephropathy Progression: A Cohort Study of 1965 Cases

description: <b><i>Background:</i></b> The role of serum uric acid (SUA) level in the progression of Immunoglobulin A nephropathy (IgAN) remains controversial. <b><i>Methods:</i></b> In a cohort of 1,965 cases with biopsy-proven IgAN, we examined the associations of SUA concentration with the primary outcome of a composite of all-cause mortality or kidney failure (defined as a reduction of estimated glomerular filtration rate [eGFR] by 40% from baseline, requirements for dialysis and transplantation), or the outcome of kidney failure alone, assessed using Cox and logistic regression models, respectively, with adjustment for confounders. <b><i>Results:</i></b> At baseline, the mean age was 33.37 ± 11.07 years, eGFR was 101.30 ± 30.49 mL/min/1.73 m<sup>2</sup>, and mean uric acid level was 5.32 ± 1.76 mg/dL. During a median of 7-year follow-up, 317 cases reached the composite outcome of all-cause mortality (5 deaths) or kidney failure (36 cases of dialysis, 5 cases of renal transplantation, and 271 cases with reduction of eGFR by 40% from baseline). After adjustment for demographic and IgAN specific covariates and treatments, a higher quartile of uric acid was linearly associated with an increased risk of the primary outcome (highest versus lowest quartile, hazard ratio [HR] 2.39; 95% CI 1.52–3.75) and kidney failure (highest versus lowest quartile, HR 2.55; 95% CI 1.62–4.01) in the Cox proportional hazards regression models. In the continuous analysis, a 1 mg/dL greater uric acid level was associated with 16% increased risk of primary outcome (HR 1.16, 95% CI 1.07–1.25) and 17% increased risk of kidney failure (HR 1.17, 95% CI 1.08–1.27), respectively, in the fully adjusted model. The multivariate ­logistic regression analyses for the sensitive analyses drew consistent results. In the subgroup analyses, significant interactions were detected that patients with mean arterial pressure (MAP) &lt; 90 mm Hg or mesangial hypercellularity had a higher association of SUA with the incidence of the primary outcome than those with MAP ≥90 mm Hg or those without mesangial hypercellularity respectively. Hyperuricemia was not significantly associated with the risk of developing the primary outcome in elder patients (≥32 years old), patients with eGFR &lt; 90 mL/min or with tubular atrophy/interstitial fibrosis. <b><i>Conclusions:</i></b> SUA level may be positively associated with the progression of IgAN. It was noticeable that the association of hyperuricemia with IgAN progression was less significant in patients with elder age, lower eGFR, or tubular atrophy/interstitial fibrosis, which may be due to some more confounders in association with the IgA progression in these patients. Future prospective studies are warranted to confirm these findings and to investigate the underlying mechanisms.
DOI: 10.6084/m9.figshare.6969533
title: Supplementary Material for: Serum Creatinine and Chronic Kidney Disease-Epidemiology Estimated Glomerular Filtration Rate: Independent Predictors of Renal Replacement Therapy following Cardiac Surgery

description: <b><i>Background:</i></b> Most studies evaluating predictors of renal replacement therapy (RRT) following cardiac surgery use arbitrary defined limits of preoperative serum creatinine. The aim of this study was to evaluate the effect of preoperative renal function using either estimated-glomerular filtration rate (eGFR) derived using Chronic Kidney Disease-Epidemiology (CKD-EPI) or serum creatinine alone as a predictor for RRT after cardiac surgery. <b><i>Methods:</i></b> In this prospective cohort study, baseline, intraoperative, and postoperative data of all patients who underwent an elective, urgent, or emergency cardiac surgery between 2012 and 2016 in a single center were analyzed in order to identify multivariate parameters determining the need for RRT after surgery. For preoperative renal function, we used serum creatinine levels and eGFR-derived CKD-EPI equation. We also divided our cohort into eGFR groups following the thresholds of the currently proposed CKD classification. <b><i>Results:</i></b> From the 1,614 patients (mean age: 65.4 ± 10.6 years; male: 77.6%) that constituted the study population, 42 (2.6%) underwent RRT postoperatively. EUROSCORE II, cardiopulmonary bypass time, cross clamp time, red blood cell (RBC) units transfused, type and urgency of surgery, combined/non combined operation, peripheral vascular disease, heart failure, chronic obstructive pulmonary disease, dyslipidemia, and preoperative renal function were all univariately associated with RRT use. Multivariate regression with bootstrap utilization indicated that CKD-EPI eGFR (OR 0.979; 95% CI 0.956–0.998), heart failure with the New York Heart Association class ≥2 (OR 4.695; 95% CI 1.756–14.061) and RBC units transfused (OR 1.287; 95% CI 1.081–1.850) were independently associated with RRT need. When serum creatinine (OR 2.920, 95% CI1.056–8.074) was used in the model, the associations with RRT were also significant. <b><i>Conclusion:</i></b> Preoperative renal function, defined by serum creatinine or eGFR by CKD-EPI, NYHA class II–IV, and the number of blood units transfused were all independent predictors of RRT postoperatively.