cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6989846
title: Supplementary Material for: Prevalence of Atopy following Mass Drug Administration with Albendazole: A Study in School Children on Flores Island, Indonesia

description: <b><i>Background:</i></b> In many rural areas of tropical countries such as Indonesia, the prevalence of soil-transmitted helminths (STH) infections remains high. At the same time, the burden of allergic disorders in such rural areas is reported to be low and inversely associated with helminth infections. To reduce the morbidity and transmission of helminth infections, the world health organization recommends preventive treatment of school children by providing mass drug administration (MDA) with albendazole. Here, we had an opportunity to evaluate the prevalence of skin reactivity to allergens before and after albendazole treatment to get an indication of the possible impact of MDA on allergic sensitization. <b><i>Methods:</i></b> A study was conducted among 150 school children living in an area endemic for STH infections. Before and 1 year after anthelminthic treatment with albendazole, stool samples were examined for the presence of STH eggs, skin prick tests (SPT) for cockroach and house dust mites were performed, blood eosinophilia was assessed, and total immunoglobulin E (IgE) and C-reactive protein (CRP) were measured in plasma. <b><i>Results:</i></b> Anthelminthic treatment significantly reduced the prevalence of STH from 19.6 before treatment to 6% after treatment (<i>p</i> &lt; 0.001). Levels of total IgE (estimate: 0.30; 95% CI 0.22–0.42, <i>p</i> &lt; 0.0001), CRP (estimate: 0.60; 95% CI 0.42–0.86, <i>p</i> = 0.006), and eosinophil counts (estimate: 0.70; 95% CI 0.61–0.80, <i>p</i> &lt; 0.001) decreased significantly. The prevalence of SPT positivity increased from 18.7 to 32.7%. Multivariate analysis adjusted for confounding factors showed an increased risk of being SPT positive to any allergen (OR 3.04; 95% CI 1.338–6.919, <i>p</i> = 0.008). <b><i>Conclusions:</i></b> This study indicates that 1 year of MDA with albendazole was associated with a reduced prevalence of STH infections. This study shows that the prevalence of allergic sensitization increases after 1 year of albendazole treatment. Placebo-controlled and larger studies are needed to further substantiate a role of deworming treatment in an increased risk of allergic sensitization.
DOI: 10.6084/m9.figshare.6989873.v1
title: prepared matrices

description: Prepared feature matrices ready for ingestion by the prediction model.
DOI: 10.6084/m9.figshare.6989846.v1
title: Supplementary Material for: Prevalence of Atopy following Mass Drug Administration with Albendazole: A Study in School Children on Flores Island, Indonesia

description: <b><i>Background:</i></b> In many rural areas of tropical countries such as Indonesia, the prevalence of soil-transmitted helminths (STH) infections remains high. At the same time, the burden of allergic disorders in such rural areas is reported to be low and inversely associated with helminth infections. To reduce the morbidity and transmission of helminth infections, the world health organization recommends preventive treatment of school children by providing mass drug administration (MDA) with albendazole. Here, we had an opportunity to evaluate the prevalence of skin reactivity to allergens before and after albendazole treatment to get an indication of the possible impact of MDA on allergic sensitization. <b><i>Methods:</i></b> A study was conducted among 150 school children living in an area endemic for STH infections. Before and 1 year after anthelminthic treatment with albendazole, stool samples were examined for the presence of STH eggs, skin prick tests (SPT) for cockroach and house dust mites were performed, blood eosinophilia was assessed, and total immunoglobulin E (IgE) and C-reactive protein (CRP) were measured in plasma. <b><i>Results:</i></b> Anthelminthic treatment significantly reduced the prevalence of STH from 19.6 before treatment to 6% after treatment (<i>p</i> &lt; 0.001). Levels of total IgE (estimate: 0.30; 95% CI 0.22–0.42, <i>p</i> &lt; 0.0001), CRP (estimate: 0.60; 95% CI 0.42–0.86, <i>p</i> = 0.006), and eosinophil counts (estimate: 0.70; 95% CI 0.61–0.80, <i>p</i> &lt; 0.001) decreased significantly. The prevalence of SPT positivity increased from 18.7 to 32.7%. Multivariate analysis adjusted for confounding factors showed an increased risk of being SPT positive to any allergen (OR 3.04; 95% CI 1.338–6.919, <i>p</i> = 0.008). <b><i>Conclusions:</i></b> This study indicates that 1 year of MDA with albendazole was associated with a reduced prevalence of STH infections. This study shows that the prevalence of allergic sensitization increases after 1 year of albendazole treatment. Placebo-controlled and larger studies are needed to further substantiate a role of deworming treatment in an increased risk of allergic sensitization.
DOI: 10.6084/m9.figshare.6989684
title: search metadata

description: Counts of remaining articles after searching PubMed and cleaning the results.
DOI: 10.6084/m9.figshare.6989684.v1
title: search metadata

description: Counts of remaining articles after searching PubMed and cleaning the results.
DOI: 10.6084/m9.figshare.6989678
title: NMR data for BATMAN

description: 2000 1D CPMG NMR spectra of blood serum from MESA cohort.
DOI: 10.6084/m9.figshare.6989678.v1
title: NMR data for BATMAN

description: 2000 1D CPMG NMR spectra of blood serum from MESA cohort.
DOI: 10.6084/m9.figshare.6989645
title: journal verdicts

description: Final verdicts on which journals to include in our analysis.
DOI: 10.6084/m9.figshare.6989660
title: Dataset for: Bayesian model-data synthesis with an application to global Glacio-Isostatic Adjustment

description: Glacial isostatic adjustment (GIA) is a crucial component in evaluating sea level change. The GIA process has been simulated globally from various physical forward models and it can also be measured locally at some GPS stations. In this paper we combine the physical model simulations and GPS measurements in a Bayesian hierarchical modelling framework to update global GIA. In common with many large-scale spatial modelling applications, there are two major challenges. One is the scale of the update, which is too large for naive Gaussian conditioning. The other is the need to represent non-stationarity in the prior. We address the first challenge with the now well-established stochastic partial differential equations (SPDE) and integrated nested Laplace approximation (INLA) approach. For non-stationary global process, we propose two general models that accommodate commonly-seen geospatial patterns. We present and compare the GIA result for the two models, alongside the default option of assuming stationarity.
DOI: 10.6084/m9.figshare.6989645.v1
title: journal verdicts

description: Final verdicts on which journals to include in our analysis.
DOI: 10.6084/m9.figshare.6989660.v1
title: Dataset for: Bayesian model-data synthesis with an application to global Glacio-Isostatic Adjustment

description: Glacial isostatic adjustment (GIA) is a crucial component in evaluating sea level change. The GIA process has been simulated globally from various physical forward models and it can also be measured locally at some GPS stations. In this paper we combine the physical model simulations and GPS measurements in a Bayesian hierarchical modelling framework to update global GIA. In common with many large-scale spatial modelling applications, there are two major challenges. One is the scale of the update, which is too large for naive Gaussian conditioning. The other is the need to represent non-stationarity in the prior. We address the first challenge with the now well-established stochastic partial differential equations (SPDE) and integrated nested Laplace approximation (INLA) approach. For non-stationary global process, we propose two general models that accommodate commonly-seen geospatial patterns. We present and compare the GIA result for the two models, alongside the default option of assuming stationarity.
DOI: 10.6084/m9.figshare.6989633
title: match_cleaned.db

description: Final database with the cleaned articles.
DOI: 10.6084/m9.figshare.6989636
title: matched datasets

description: 100 matched datasets to account for variability in the datasets and therefore the outcome of the prediction models.
DOI: 10.6084/m9.figshare.6989633.v1
title: match_cleaned.db

description: Final database with the cleaned articles.
DOI: 10.6084/m9.figshare.6989624
title: Appendectomy and ulcerative colitis in Chinese patients.rar

description: This study examined the associations between appendectomy performed before UC diagnosis and the occurrence and clinical course of UC in Chinese patients.
DOI: 10.6084/m9.figshare.6989627
title: Dataset for: Route of exposure has a major impact on uptake of silver nanoparticles in Atlantic salmon (Salmo salar)

description: The potential impact of Ag nanoparticles on aquatic organisms is to a large extent determined by their bioavailability through different routes of exposure. In the present study juvenile Atlantic salmon (Salmo salar) were exposed to different sources of radiolabeled Ag (radiolabeled 110mAg nanoparticles and 110mAgNO3). After 48 h waterborne exposure to 3 µg/L citrate stabilized 110mAg nanoparticles or 110mAgNO3, or a dietary exposure to 0.6 mg Ag/kg fish (given as citrate stabilized or uncoated 110mAg nanoparticles, or 110mAgNO3), Ag had been taken up in fish regardless of route of exposures and source of Ag (Ag nanoparticles or AgNO3). Waterborne exposure led to high Ag concentrations on the gills, and dietary exposure to high concentrations in the gastrointestinal tract. Silver distribution to the target organs was similar for both dietary and waterborne exposure, with liver as the main target organ. The accumulation level of Ag was 2-3 times higher for AgNO3 than for Ag nanoparticles when exposed through water, whereas dietary exposure led to no significant differences. The transfer (Bq/g liver/g food or water) from exposure through water was four orders of magnitude higher than from feed using the smallest, citrate stabilized Agnanoparticles (4 nm). The smallest nanoparticles had a five times higher bioavailability in food compared to the larger and uncoated Ag nanoparticles (20 nm). Despite the relatively low transfer of Ag from diet to fish, the short lifetime of Ag nanoparticles in water and transfer to sediment, feed or sediment dwelling food sources such as larvae and worms, could make diet a significant long-term exposure route.
DOI: 10.6084/m9.figshare.6989624.v1
title: Appendectomy and ulcerative colitis in Chinese patients.rar

description: This study examined the associations between appendectomy performed before UC diagnosis and the occurrence and clinical course of UC in Chinese patients.
DOI: 10.6084/m9.figshare.6989627.v1
title: Dataset for: Route of exposure has a major impact on uptake of silver nanoparticles in Atlantic salmon (Salmo salar)

description: The potential impact of Ag nanoparticles on aquatic organisms is to a large extent determined by their bioavailability through different routes of exposure. In the present study juvenile Atlantic salmon (Salmo salar) were exposed to different sources of radiolabeled Ag (radiolabeled 110mAg nanoparticles and 110mAgNO3). After 48 h waterborne exposure to 3 µg/L citrate stabilized 110mAg nanoparticles or 110mAgNO3, or a dietary exposure to 0.6 mg Ag/kg fish (given as citrate stabilized or uncoated 110mAg nanoparticles, or 110mAgNO3), Ag had been taken up in fish regardless of route of exposures and source of Ag (Ag nanoparticles or AgNO3). Waterborne exposure led to high Ag concentrations on the gills, and dietary exposure to high concentrations in the gastrointestinal tract. Silver distribution to the target organs was similar for both dietary and waterborne exposure, with liver as the main target organ. The accumulation level of Ag was 2-3 times higher for AgNO3 than for Ag nanoparticles when exposed through water, whereas dietary exposure led to no significant differences. The transfer (Bq/g liver/g food or water) from exposure through water was four orders of magnitude higher than from feed using the smallest, citrate stabilized Agnanoparticles (4 nm). The smallest nanoparticles had a five times higher bioavailability in food compared to the larger and uncoated Ag nanoparticles (20 nm). Despite the relatively low transfer of Ag from diet to fish, the short lifetime of Ag nanoparticles in water and transfer to sediment, feed or sediment dwelling food sources such as larvae and worms, could make diet a significant long-term exposure route.
DOI: 10.6084/m9.figshare.6989615
title: Resting shear elastic modulus as a marker of peripheral fatigue during maximal isometric contractions in humans.xlsx

description: The aim of this study was to investigate whether the resting Vastus Lateralis (VL) muscle shear elastic modulus (µ), evaluated by shear wave elastography, represents peripheral fatigue during repetition of isometric maximal voluntary contractions (MVCs) of the knee extensor (KE) muscles.<br> Eight healthy well-trained males volunteered to repeated 60 isometric MVCs of the KE muscles (6 × 10 MVCs; 5 s on/5 s off). Single and double electrical stimulations were delivered to the femoral nerve every ten MVCs during contraction and at rest. The amplitude and properties of the potentiated torque following single (Twpot) double electrostimulation and the amplitude of the concomitant VL compound action potential were considered to be indicators of peripheral fatigue. The resting VLµ was measured during a 5-s rest period after each MVC and electrical stimulation series.<br><br>
DOI: 10.6084/m9.figshare.6989564
title: Supplementary Material for: Predictive Value of Thompson-Score for Long-Term Neurological and Cognitive Outcome in Term Newborns with Perinatal Asphyxia and Hypoxic-Ischemic Encephalopathy Undergoing Controlled Hypothermia Treatment

description: <b><i>Background:</i></b> The so-called Thompson-score (TS) for newborns with hypoxic-ischemic encephalopathy (HIE) was developed before the introduction of controlled hypothermia as clinical routine. Information on the predictive value of TS in newborns undergoing therapeutic hypothermia to estimate long-term outcome is limited. <b><i>Objectives:</i></b> To determine the predictive value of TS to estimate long-term cognitive and neurological outcome in newborns with perinatal asphyxia treated with controlled hypothermia. <b><i>Methods:</i></b> Thirty-six term newborns with HIE undergoing controlled hypothermia were followed using Wechsler Preschool and Primary Scale of intelligence III test and standardized neurological examination. The primary outcome was survival without cognitive impairment, defined as an IQ ≥85. Secondary outcomes were motor outcomes, survival without relevant neurological impairment, death and epilepsy. <b><i>Results:</i></b> Follow-up was done in 33 out of 36 (91.6%) infants at 53 ± 12 months (mean ± SD). For all investigated parameters, a statistically significant relationship with peak TS was demonstrated. A one-point increase in peak TS indicated an OR (95% CI) of 1.5 (1.1–2.0, <i>p</i> = 0.006) for death or cognitive impairment, an OR (95% CI) of 2.2 (1.3–3.8, <i>p</i> = 0.004) for death or relevant neurologic impairment, an OR (95% CI) of 2.1 (1.3–3.5, <i>p</i> = 0.005) for death or epilepsy and an OR (95% CI) of 1.5 (1.1–2.1, <i>p</i> = 0.02) for death. Although the TS for newborns with adverse outcome (death or cognitive impairment) compared to normal outcome tended to be higher (13 [4–16] vs. 9 [0–13], d1; 15 [5–19] vs. 9 [1–14], d2; 14 [5–21] vs. 8 [2–15], d3; median [range]), there was a considerable overlap during the first 3 days of life between both groups. <b><i>Conclusions:</i></b> The TS seems to be a prognostic tool for predicting the long-term outcome in asphyxiated term newborns undergoing controlled hypothermia after the third day of life. A higher score appears to be significantly associated with an adverse outcome.
DOI: 10.6084/m9.figshare.6989612
title: Supplementary Material for: Dropouts in an Antidepressant Trial: How Do They Fare Afterwards?

description: Medicine
DOI: 10.6084/m9.figshare.6989564.v1
title: Supplementary Material for: Predictive Value of Thompson-Score for Long-Term Neurological and Cognitive Outcome in Term Newborns with Perinatal Asphyxia and Hypoxic-Ischemic Encephalopathy Undergoing Controlled Hypothermia Treatment

description: <b><i>Background:</i></b> The so-called Thompson-score (TS) for newborns with hypoxic-ischemic encephalopathy (HIE) was developed before the introduction of controlled hypothermia as clinical routine. Information on the predictive value of TS in newborns undergoing therapeutic hypothermia to estimate long-term outcome is limited. <b><i>Objectives:</i></b> To determine the predictive value of TS to estimate long-term cognitive and neurological outcome in newborns with perinatal asphyxia treated with controlled hypothermia. <b><i>Methods:</i></b> Thirty-six term newborns with HIE undergoing controlled hypothermia were followed using Wechsler Preschool and Primary Scale of intelligence III test and standardized neurological examination. The primary outcome was survival without cognitive impairment, defined as an IQ ≥85. Secondary outcomes were motor outcomes, survival without relevant neurological impairment, death and epilepsy. <b><i>Results:</i></b> Follow-up was done in 33 out of 36 (91.6%) infants at 53 ± 12 months (mean ± SD). For all investigated parameters, a statistically significant relationship with peak TS was demonstrated. A one-point increase in peak TS indicated an OR (95% CI) of 1.5 (1.1–2.0, <i>p</i> = 0.006) for death or cognitive impairment, an OR (95% CI) of 2.2 (1.3–3.8, <i>p</i> = 0.004) for death or relevant neurologic impairment, an OR (95% CI) of 2.1 (1.3–3.5, <i>p</i> = 0.005) for death or epilepsy and an OR (95% CI) of 1.5 (1.1–2.1, <i>p</i> = 0.02) for death. Although the TS for newborns with adverse outcome (death or cognitive impairment) compared to normal outcome tended to be higher (13 [4–16] vs. 9 [0–13], d1; 15 [5–19] vs. 9 [1–14], d2; 14 [5–21] vs. 8 [2–15], d3; median [range]), there was a considerable overlap during the first 3 days of life between both groups. <b><i>Conclusions:</i></b> The TS seems to be a prognostic tool for predicting the long-term outcome in asphyxiated term newborns undergoing controlled hypothermia after the third day of life. A higher score appears to be significantly associated with an adverse outcome.
DOI: 10.6084/m9.figshare.6989612.v1
title: Supplementary Material for: Dropouts in an Antidepressant Trial: How Do They Fare Afterwards?

description: Medicine
DOI: 10.7284/101353
title: Multibeam Echosounder data collected during research cruise KM0416 using a Kongsberg EM120 instrument system onboard the platform RV Kilo Moana
DOI: 10.6084/m9.figshare.6989549
title: Optic Radiation Tractography

description: Fiber Tracking of the Optic Radiation using DTI and HARDI (with compressed sensing) with all relevant seed/include/exclude ROIs using 4 different data acquisition schemes
DOI: 10.6084/m9.figshare.6989549.v1
title: Optic Radiation Tractography

description: Fiber Tracking of the Optic Radiation using DTI and HARDI (with compressed sensing) with all relevant seed/include/exclude ROIs using 4 different data acquisition schemes
DOI: 10.6084/m9.figshare.6989516
title: Supplementary Material for: Association between Allergic Diseases and Irritable Bowel Syndrome: A Retrospective Study

description: <b><i>Background:</i></b> The relationship between allergic disease and irritable bowel syndrome (IBS) is poorly understood. We aimed to investigate the potential association as well as the underlying immunological mechanisms. <b><i>Methods:</i></b> A retrospective case-control study of 108 atopic patients from among outpatients in an allergy clinic (allergic rhinitis [AR], <i>n</i> = 49; chronic urticaria [CU], <i>n</i> = 59) and 74 controls from among ward companions was conducted from November 2016 to March 2017. The detection rates and related gastrointestinal (GI) symptoms of IBS, as well as immunological indices, were calculated. <b><i>Results:</i></b> CU patients had a trend of increase in the detection of IBS compared to controls (OR = 4.846; 95% CI 0.967–24.279, <i>p</i> = 0.077). Loose stools (OR = 2.406; 95% CI 1.075–5.386, <i>p</i> &lt; 0.05) and viscous stools (OR = 2.665; 95% CI 1.250–5.682, <i>p</i> &lt; 0.05) were more common in CU patients. Atopic patients positive for serum total immunoglobulin E (IgE) (OR = 3.379; 95% CI 1.088–10.498, <i>p</i> &lt; 0.05) or house dust mite (HDM)-specific IgE (OR = 3.640; 95% CI 1.228–10.790, <i>p</i> &lt; 0.05) were more likely to have abdominal bloating. Besides, a positive association between levels of total IgE and severity of abdominal bloating was observed (<i>p</i> &lt; 0.05). An HDM-specific IgE-positive reaction was independently associated with abdominal bloating in atopic patients (<i>p</i> &lt; 0.05). <b><i>Conclusions:</i></b> Allergic disease has a clear clinical association with IBS with more frequent and severe symptoms of IBS. CU patients have a tendency to suffer from IBS, usually with diarrhea. Serum total IgE and HDM-specific IgE are positively correlated with GI symptoms in atopic patients.
DOI: 10.6084/m9.figshare.6989495
title: RF random search items

description: Outcome of the random grid searches for the random forest model.
DOI: 10.6084/m9.figshare.6989498
title: SVM random search items

description: Outcome of the random grid searches for the SVM model.
DOI: 10.6084/m9.figshare.6989483
title: Supplementary Material for: The Clinical Significance of Body Weight Loss in Idiopathic Pulmonary Fibrosis Patients

description: <b><i>Background:</i></b> The significance of the nutritional status in idiopathic pulmonary fibrosis (IPF) is largely unknown. Temporal body weight (BW) change, a dynamic index of nutrition status, can detect the malnutrition more accurately than the conventional single-point body mass index evaluation. <b><i>Objective:</i></b> To investigate how the temporal BW change influences the clinical courses of IPF. <b><i>Methods:</i></b> This multicenter study enrolled IPF patients from four referral hospitals of interstitial lung diseases in Japan (the Japanese cohort, the derivation cohort) and the Royal Brompton Hospital (the UK cohort, the validation cohort). The annual rate of BW change from the initial presentation was evaluated. A &gt; 5% decrease of BW was defined as a significant BW loss. <b><i>Results:</i></b> Twenty-seven out of 124 patients in the Japanese cohort and 13 out of 86 patients in the UK cohort showed significant BW loss. Patients with BW loss showed significantly worse survival in both cohorts. Multivariate analyses revealed that BW loss was an independent factor for decreased survival (Japanese cohort: <i>p</i> = 0.047, UK cohort: <i>p</i> = 0.013). A 6.1% loss of BW was chosen as the optimal cutoff value to predict the 2-year mortality from the initial presentation. The stratified analysis revealed that a 6.1% or greater BW loss could predict worse survival specifically in cases without a greater than 10% decline in forced vital capacity (FVC). <b><i>Conclusions:</i></b> BW loss is independently associated with the survival of IPF patients, particularly when a decline in the FVC was not observed. Further studies are needed to understand the mechanisms underlying BW loss in IPF.
DOI: 10.6084/m9.figshare.6989495.v1
title: RF random search items

description: Outcome of the random grid searches for the random forest model.
DOI: 10.6084/m9.figshare.6989462
title: MRI Images, Subject (b) no MC and no MotionMRI Images

description: Custom 3D FLASH sequence that can apply prospective MC based on the motion estimates.The 3D FLASH sequence has the following parameters: FOV 256 mm × 256 mm × 56 mm with 1 mm × 1 mm × 2 mm voxels (phase/read/slice directions respectively), bandwidth of 1000 Hz/pixel, TR of 15 ms, TE of 2.68 ms, and flip angle 35 degrees.