bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pre-diagnostic biomarkers of type 2 diabetes identified in the UAE’s obese national population using targeted metabolomics
Authors: Fikri Asma M. , Smyth Rosemary , Kumar Vijay , Al-Abadla Zainab , Abusnana Salahedeen , Munday Michael R. 
Published: October 2020

AbstractCurrently, type 2 diabetes mellitus (T2DM) and obesity are major global public health issues, and their prevalence in the United Arab Emirates (UAE) are among the highest in the world. In 2019, The UAE diabetes national prevalence was 15.4%. In recent years there has been a considerable investigation of predictive biomarkers associated with these conditions. This study analysed fasting (8 h) blood samples from an obese, normoglycemic cohort and an obese, T2DM cohort of UAE nationals, employing clinical chemistry analysis, 1D 1H NMR and mass spectroscopy (FIA-MS/MS and LC-MS/MS) techniques. The novel findings reported for the first time in a UAE population revealed significant differences in a number of metabolites in the T2DM cohort. Metabolic fingerprints identified by NMR included BCAAs, trimethylamine N-oxide, β-hydroxybutyrate, trimethyl uric acid, and alanine. A targeted MS approach showed significant differences in lysophosphatidylcholines, phosphatidylcholines, acylcarnitine, amino acids and sphingomyelins; Lyso.PC.a.C18.0, PC.ae.C34.2, C3.DC..C4.OH, glutamine and SM.C16.1, being the most significant metabolites. Pearson’s correlation studies showed associations between these metabolites and the clinical chemistry parameters across both cohorts. This report identified differences in metabolites in response to T2DM in agreement with many published population studies. This contributes to the global search for a bank of metabolite biomarkers that can predict the advent of T2DM and give insight to its pathogenic mechanisms.
Efficient trajectory optimization for curved running using a 3D musculoskeletal model with implicit dynamics
Authors: Nitschke Marlies , Dorschky Eva , Heinrich Dieter , Schlarb Heiko , Eskofier Bjoern M. , Koelewijn Anne D. , van den Bogert Antonie J. 
Published: October 2020

AbstractTrajectory optimization with musculoskeletal models can be used to reconstruct measured movements and to predict changes in movements in response to environmental changes. It enables an exhaustive analysis of joint angles, joint moments, ground reaction forces, and muscle forces, among others. However, its application is still limited to simplified problems in two dimensional space or straight motions. The simulation of movements with directional changes, e.g. curved running, requires detailed three dimensional models which lead to a high-dimensional solution space. We extended a full-body three dimensional musculoskeletal model to be specialized for running with directional changes. Model dynamics were implemented implicitly and trajectory optimization problems were solved with direct collocation to enable efficient computation. Standing, straight running, and curved running were simulated starting from a random initial guess to confirm the capabilities of our model and approach: efficacy, tracking and predictive power. Altogether the simulations required 1 h 17 min and corresponded well to the reference data. The prediction of curved running using straight running as tracking data revealed the necessity of avoiding interpenetration of body segments. In summary, the proposed formulation is able to efficiently predict a new motion task while preserving dynamic consistency. Hence, labor-intensive and thus costly experimental studies could be replaced by simulations for movement analysis and virtual product design.
In situ structure of virus capsids within cell nuclei by correlative light and cryo-electron tomography
Authors: Vijayakrishnan Swetha , McElwee Marion , Loney Colin , Rixon Frazer , Bhella David 
Published: October 2020

AbstractCryo electron microscopy (cryo-EM), a key method for structure determination involves imaging purified material embedded in vitreous ice. Images are then computationally processed to obtain three-dimensional structures approaching atomic resolution. There is increasing interest in extending structural studies by cryo-EM into the cell, where biological structures and processes may be imaged in context. The limited penetrating power of electrons prevents imaging of thick specimens (> 500 nm) however. Cryo-sectioning methods employed to overcome this are technically challenging, subject to artefacts or involve specialised and costly equipment. Here we describe the first structure of herpesvirus capsids determined by sub-tomogram averaging from nuclei of eukaryotic cells, achieved by cryo-electron tomography (cryo-ET) of re-vitrified cell sections prepared using the Tokuyasu method. Our reconstructions confirm that the capsid associated tegument complex is present on capsids prior to nuclear egress. We demonstrate that this method is suited to both 3D structure determination and correlative light/electron microscopy, thus expanding the scope of cryogenic cellular imaging.
Anti-GD2-IRDye800CW as a targeted probe for fluorescence-guided surgery in neuroblastoma
Authors: Wellens Lianne M. , Deken Marion M. , Sier Cornelis F. M. , Johnson Hannah R. , de la Jara Ortiz Fàtima , Bhairosingh Shadhvi S. , Houvast Ruben D. , Kholosy Waleed M. , Baart Victor M. , Pieters Annique M. M. J. , de Krijger Ronald R. , Molenaar Jan J. , Wehrens Ellen J. , Dekkers Johanna F. , Wijnen Marc H. W. A. , Vahrmeijer Alexander L. , Rios Anne C. 
Published: October 2020

AbstractNeuroblastoma resection represents a major challenge in pediatric surgery, because of the high risk of complications. Fluorescence-guided surgery (FGS) could lower this risk by facilitating discrimination of tumor from normal tissue and is gaining momentum in adult oncology. Here, we provide the first molecular-targeted fluorescent agent for FGS in pediatric oncology, by developing and preclinically evaluating a GD2-specific tracer consisting of the immunotherapeutic antibody dinutuximab-beta, recently approved for neuroblastoma treatment, conjugated to near-infrared (NIR) fluorescent dye IRDye800CW. We demonstrated specific binding of anti-GD2-IRDye800CW to human neuroblastoma cells in vitro and in vivo using xenograft mouse models. Furthermore, we defined an optimal dose of 1 nmol, an imaging time window of 4 days after administration and show that neoadjuvant treatment with anti-GD2 immunotherapy does not interfere with fluorescence imaging. Importantly, as we observed universal, yet heterogeneous expression of GD2 on neuroblastoma tissue of a wide range of patients, we implemented a xenograft model of patient-derived neuroblastoma organoids with differential GD2 expression and show that even low GD2 expressing tumors still provide an adequate real-time fluorescence signal. Hence, the imaging advancement presented in this study offers an opportunity for improving surgery and potentially survival of a broad group of children with neuroblastoma.
Prevalence and determinants of uterine rupture in Ethiopia: a systematic review and meta-analysis
Authors: Alemu Addisu Alehegn , Bitew Mezinew Sintayehu , Gelaw Kelemu Abebe , Zeleke Liknaw Bewket , Kassa Getachew Mullu 
Published: October 2020

AbstractUterine rupture is a serious public health concern that causes high maternal and perinatal morbidity and mortality in the developing world. Few of the studies conducted in Ethiopia show a high discrepancy in the prevalence of uterine rupture, which ranges between 1.6 and 16.7%. There also lacks a national study on this issue in Ethiopia. This systematic and meta-analysis, therefore, was conducted to assess the prevalence and determinants of uterine rupture in Ethiopia. We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for systematic review and meta-analysis of studies. All observational published studies were retrieved using relevant search terms in Google scholar, African Journals Online, CINHAL, HINARI, Science Direct, Cochrane Library, EMBASE and PubMed (Medline) databases. Newcastle–Ottawa assessment checklist for observational studies was used for critical appraisal of the included articles. The meta-analysis was done with STATA version 14 software. The I2 test statistics were used to assess heterogeneity among included studies, and publication bias was assessed using Begg's and Egger's tests. Odds ratio (OR) with a 95% confidence interval (CI) was presented using forest plots. A total of twelve studies were included in this study. The pooled prevalence of uterine rupture was 3.98% (95% CI 3.02, 4.95). The highest (7.82%) and lowest (1.53%) prevalence were identified in Amhara and Southern Nations, Nationality and Peoples Region (SNNPR), respectively. Determinants of uterine rupture were urban residence (OR = 0.15 (95% CI 0.09, 0.23)), primipara (OR = 0.12 (95% CI 0.06, 0.27)), previous cesarean section (OR = 3.23 (95% CI 2.12, 4.92)), obstructed labor(OR = 12.21 (95% CI 6.01, 24.82)), and partograph utilization (OR = 0.12 (95% CI 0.09, 0.17)). Almost one in twenty-five mothers had uterine rupture in Ethiopia. Urban residence, primiparity, previous cesarean section, obstructed labor and partograph utilization were significantly associated with uterine rupture. Therefore, intervention programs should address the identified factors to reduce the prevalence of uterine rupture.
Improved NDVI based proxy leaf-fall indicator to assess rainfall sensitivity of deciduousness in the central Indian forests through remote sensing
Authors: Singh Beependra , Jeganathan C. , Rathore V. S. 
Published: October 2020

AbstractQuantifying the leaf-fall dynamics in the tropical deciduous forest will help in modeling regional energy balance and nutrient recycle pattern, but the traditional ground-based leaf-fall enumeration is a tedious and geographically limited approach. Therefore, there is a need for a reliable spatial proxy leaf-fall (i.e., deciduousness) indicator. In this context, this study attempted to improve the existing deciduousness metric using time-series NDVI data (MOD13Q1; 250 m; 16 days interval) and investigated its spatio-temporal variability and sensitivity to rainfall anomalies across the central Indian tropical forest over 18 years (2001–2018). The study also analysed the magnitude of deciduousness during extreme (i.e., dry and wet) and normal rainfall years, and compared its variability with the old metric. The improved NDVI based deciduousness metric performed satisfactorily, as its observed variations were in tandem with ground observations in different forest types, and for different pheno-classes. This is the first kind of study in India revealing the spatio-temporal character of leaf-fall in different ecoregions, elevation gradients and vegetation fraction.
A step-down photophobic response in coral larvae: implications for the light-dependent distribution of the common reef coral, Acropora tenuis
Authors: Sakai Yusuke , Kato Kagayaki , Koyama Hiroshi , Kuba Alyson , Takahashi Hiroki , Fujimori Toshihiko , Hatta Masayuki , Negri Andrew P. , Baird Andrew H. , Ueno Naoto 
Published: October 2020

AbstractBehavioral responses to environmental factors at the planktonic larval stage can have a crucial influence on habitat selection and therefore adult distributions in many benthic organisms. Reef-building corals show strong patterns of zonation across depth or underwater topography, with different suites of species aggregating in different light environments. One potential mechanism driving this pattern is the response of free-swimming larvae to light. However, there is little experimental support for this hypothesis; in particular, there are few direct and quantitative observations of larval behavior in response to light. Here, we analyzed the swimming behavior of larvae of the common reef coral Acropora tenuis under various light conditions. Larvae exhibited a step-down photophobic response, i.e. a marked decrease in swimming speed, in response to a rapid attenuation (step-down) of light intensity. Observations of larvae under different wavelengths indicated that only the loss of blue light (wavelengths between 400 and 500 nm) produced a significant response. Mathematical simulations of this step-down photophobic response indicate that larvae will aggregate in the lighter areas of two-dimensional large rectangular fields. These results suggest that the step-down photophobic response of coral larvae may play an important role in determining where larval settle on the reef.
Automatic evaluation of degree of cleanliness in capsule endoscopy based on a novel CNN architecture
Authors: Noorda Reinier , Nevárez Andrea , Colomer Adrián , Pons Beltrán Vicente , Naranjo Valery 
Published: October 2020

AbstractCapsule endoscopy (CE) is a widely used, minimally invasive alternative to traditional endoscopy that allows visualisation of the entire small intestine. Patient preparation can help to obtain a cleaner intestine and thus better visibility in the resulting videos. However, studies on the most effective preparation method are conflicting due to the absence of objective, automatic cleanliness evaluation methods. In this work, we aim to provide such a method capable of presenting results on an intuitive scale, with a relatively light-weight novel convolutional neural network architecture at its core. We trained our model using 5-fold cross-validation on an extensive data set of over 50,000 image patches, collected from 35 different CE procedures, and compared it with state-of-the-art classification methods. From the patch classification results, we developed a method to automatically estimate pixel-level probabilities and deduce cleanliness evaluation scores through automatically learnt thresholds. We then validated our method in a clinical setting on 30 newly collected CE videos, comparing the resulting scores to those independently assigned by human specialists. We obtained the highest classification accuracy for the proposed method (95.23%), with significantly lower average prediction times than for the second-best method. In the validation of our method, we found acceptable agreement with two human specialists compared to interhuman agreement, showing its validity as an objective evaluation method.
Mosaic fungal individuals have the potential to evolve within a single generation
Authors: Tyrrell Maura G. , Peabody Diane C. , Peabody Robert B. , James-Pederson Magdalena , Hirst Rachel G. , Allan-Perkins Elisha , Bickford Heather , Shafrir Amy , Doiron Robert J. , Churchill Amber C. , Ramirez-Tapia Juan Carlos , Seidel Benjamin , Torres Lynes , Fallavollita Kathryn , Hernon Thomas , Wiswell Lindsay , Wilson Sarah , Mondo Erica , Salisbury Kathleen , Peabody Carrie , Cabral Patrick , Presti Lauren , McKenna-Hoffman Kelsey , Flannery Michele , Daly Kaitlin , Haghighat Darius , Lukason Daniel 
Published: October 2020

AbstractAlthough cells of mushroom-producing fungi typically contain paired haploid nuclei (n + n), mostArmillaria gallicavegetative cells are uninucleate. As vegetative nuclei are produced by fusions of paired haploid nuclei, they are thought to be diploid (2n). Here we report finding haploid vegetative nuclei inA. gallicaat multiple sites in southeastern Massachusetts, USA. Sequencing multiple clones of a single-copy gene isolated from single hyphal filaments revealed nuclear heterogeneity both among and within hyphae. Cytoplasmic bridges connected hyphae in field-collected and cultured samples, and we propose nuclear migration through bridges maintains this nuclear heterogeneity. Growth studies demonstrate among- and within-hypha phenotypic variation for growth in response to gallic acid, a plant-produced antifungal compound. The existence of both genetic and phenotypic variation within vegetative hyphae suggests that fungal individuals have the potential to evolve within a single generation in response to environmental variation over time and space.
Quantifying semi-volatile organic contaminants in solution by internal standard addition method requires prompt addition of the internal standards
Authors: Otim Ochan , Rocha Jesus 
Published: October 2020

AbstractThe precision and accuracy of quantifying semi-volatile organic compounds (SVOCs) in solution by GC/MS, particularly when volume errors are unpredictable or difficult to control, are improved by utilizing internal standards (IS). Not obvious though is the extent to which timing IS addition affects measurement. To illustrate this fact, the mean concentrations of 60 SVOCs (40 or 80 μg/mL) in two identical solutions into which IS were added at different times are compared in this study. In one solution, IS were added promptly on preparation (reference); in the other, IS were added after 36 days of incubation (treatment). To investigate the role that temperature might play here as well, equal fractions of each solution were incubated at − 20 °C, 4 °C or 22 °C. Results, as determined by one-way ANOVA, show that there were no differences between the reference solutions at the beginning and after 36 days (F3,236 = 0.244, p = 0.865), but that significant differences exist between the reference solutions collectively and the treatment irrespective of temperature (F6,413 = 6.76, p = 1.99e−06). These results, confirmed by a post hoc analysis, suggest that uncertainty is introduced into SVOC quantitation when internal standards are not added promptly into SVOCs solutions on preparation.
Low prevalence of end plate junction failure in danish patients with lumbar disc herniation
Authors: O’Neill Søren Francis Dyhrberg , Fidelman Jonas Morten , Haarup Linne Steinar , Lund Christian , Konner Mikkel Brunsgaard 
Published: October 2020

AbstractThe present study was undertaken to determine the prevalence of endplate junction failure in a smaller cohort of Danish patients with lumbar disk herniation and compare this to the previously published data from India. Consecutive patients seen in a large regional hospital spine-care unit, with a clinical presentation suggesting a lumbar disk herniation with concomitant radiculopathy and confirmatory recent MRI were included. Additional imaging by CT was performed as part of the study and these were analyzed with specific attention to endplate junction failures. For ethical reasons, the number of participants was kept to a minimum and a total of 26 patients were included. The prevalence (n = 5) of endplate junction failure was found to be statistically significantly lower than that previously reported. Our findings do not echo those previously reported in an Indian population: Endplate junction failure was indeed observed, but at a significantly lower rate. We discuss potential reasons for the difference in findings with due attention to the weaknesses of the current study.
A novel nomogram predicting the risk of positive biopsy for patients in the diagnostic gray area of prostate cancer
Authors: Hou Guang-Dong , Zheng Yu , Zheng Wan-Xiang , Gao Ming , Zhang Lei , Hou Niu-Niu , Yuan Jia-Rui , Wei Di , Ju Dong-En , Dun Xin-Long , Wang Fu-Li , Yuan Jian-Lin 
Published: October 2020

AbstractThe roles played by several inflammatory factors in screening for prostate cancer (PCa) among gray area patients, namely those with serum prostate-specific antigen (PSA) levels between 4 and 10 ng/ml, have not been completely identified, and few effective diagnostic nomograms have been developed exclusively for these patients. We aimed to investigate new independent predictors of positive biopsy (PB) results and develop a novel diagnostic nomogram for this group of patients. The independent predictors of PB results were identified, and a nomogram was constructed using multivariate logistic regression analysis based on a cohort comprising 401 Gy area patients diagnosed at Xijing Hospital (Xi’an, China) between January 2016 and December 2019. The predictive accuracy of the nomogram was assessed using the receiver operating characteristic curve, and the nomogram was calibrated by comparing the prediction with the observation. The performance of the nomogram was further validated using an independent cohort. Finally, lymphocyte-to-monocyte ratio (LMR) > 4.11 and red blood cell distribution width (RDW)-standard deviation (SD) > 42.9 fl were identified as independent protective predictors of PB results, whereas PSA density (PSAD) > 0.141 was identified as an independent risk predictor. The nomogram established using PSAD, LMR, and RDW-SD was perfectly calibrated, and its predictive accuracy was superior to that of PSAD in both internal and external validations (0.827 vs 0.769 and 0.765 vs 0.713, respectively). This study is the first to report the importance of LMR and RDW-SD in screening for PCa among gray area patients and to construct an exclusive nomogram to predict the individual risk of positive 13-core biopsy results in this group of patients. With superior performance over PSAD, our nomogram will help increase the accuracy of PCa screening, thereby avoiding unnecessary biopsy.
Association of short term exposure to Asian dust with increased blood pressure
Authors: Ishii Masanobu , Seki Tomotsugu , Sakamoto Kenji , Kaikita Koichi , Miyamoto Yoshihiro , Tsujita Kenichi , Masuda Izuru , Kawakami Koji 
Published: October 2020

AbstractAir pollution causes hypertension, cardiovascular disease, and mortality. Asian dust (AD) reportedly induces asthma or acute myocardial infarction along with air pollution, but its impact on blood pressure (BP) is unknown. We investigated the association between short-term AD exposure and BP fluctuations in 300,952 individuals whose BP was measured during April 2005–March 2015 and divided them into AD and non-AD groups based on visitation for AD-related events. AD’s occurrence, air pollutants’ concentration (suspended particulate matter, SO2, NO2, photochemical oxidants), and meteorological variables (mean ambient temperature, relative humidity) were obtained from a monitoring station; AD events correlated with decreased visibility (< 10 km). We observed 61 AD days, with 3897 participants undergoing medical check-ups. Short-term AD exposure at lag day-0 was significantly associated with higher systolic BP (SBP), diastolic BP (DBP), and pulse rate (PR) risk (β = 1.85, 95% confidence interval (CI) 1.35–2.35 for SBP, β = 2.24, 95% CI 1.88–2.61 for DBP, β = 0.52, 95% CI 0.14–0.91 for PR) using multi-pollutant model. Population-attributable fractions exposed to AD were 11.5% for those with elevated SBP (SBP ≥ 120 mmHg) and 23.7% for those with hypertension (SBP ≥ 140 mmHg or DBP ≥ 90 mmHg). This study showed a strong association between short-term AD exposure and increased SBP and DBP.