bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNN-assisted statistical analysis of a model of local cortical circuits
Authors: Zhang Yaoyu , Young Lai-Sang 
Published: November 2020

AbstractIn neuroscience, computational modeling is an effective way to gain insight into cortical mechanisms, yet the construction and analysis of large-scale network models—not to mention the extraction of underlying principles—are themselves challenging tasks, due to the absence of suitable analytical tools and the prohibitive costs of systematic numerical exploration of high-dimensional parameter spaces. In this paper, we propose a data-driven approach assisted by deep neural networks (DNN). The idea is to first discover certain input-output relations, and then to leverage this information and the superior computation speeds of the well-trained DNN to guide parameter searches and to deduce theoretical understanding. To illustrate this novel approach, we used as a test case a medium-size network of integrate-and-fire neurons intended to model local cortical circuits. With the help of an accurate yet extremely efficient DNN surrogate, we revealed the statistics of model responses, providing a detailed picture of model behavior. The information obtained is both general and of a fundamental nature, with direct application to neuroscience. Our results suggest that the methodology proposed can be scaled up to larger and more complex biological networks when used in conjunction with other techniques of biological modeling.
The effect of hypoxia on the proteomic signature of pig adipose-derived stromal/stem cells (pASCs)
Authors: Bukowska Joanna , Słowińska Mariola , Cierniak Patrycja , Kopcewicz Marta , Walendzik Katarzyna , Frazier Trivia , Gawrońska-Kozak Barbara 
Published: November 2020

AbstractHuman adipose-derived stem cells (ASCs) have potential to improve wound healing; however, their equivalents from domestic animals have received less attention as an alternative cell-based therapy for animals or even humans. Hypoxia is essential for maintaining stem cell functionality in tissue-specific niches. However, a cellular response to low oxygen levels has not been demonstrated in pig ASCs. Hence, the goal of our study was to characterize ASCs isolated from the subcutaneous fat of domestic pigs (pASCs) and examine the effect of hypoxia on their proteome and functional characteristics that might reproduce pASCs wound healing ability. Analysis of immunophenotypic and functional markers demonstrated that pASCs exhibited characteristics of mesenchymal stem cells. Proteomic analysis revealed 70 differentially abundant proteins between pASCs cultured under hypoxia (1% O2) or normoxia (21% O2). Among them, 42 proteins were enriched in the cells exposed to low oxygen, whereas 28 proteins showed decrease expression following hypoxia. Differentially expressed proteins were predominantly involved in cell metabolism, regulation of focal and intracellular communication, and attributed to wound healing. Functional examination of hypoxic pASCs demonstrated acquisition of contractile abilities in vitro. Overall, our results demonstrate that hypoxia pre-conditioning impacts the pASC proteome signature and contractile function in vitro and hence, they might be considered for further cell-based therapy study on wound healing.
Motor learning in real-world pool billiards
Authors: Haar Shlomi , van Assel Camille M. , Faisal A. Aldo 
Published: November 2020

AbstractThe neurobehavioral mechanisms of human motor-control and learning evolved in free behaving, real-life settings, yet this is studied mostly in reductionistic lab-based experiments. Here we take a step towards a more real-world motor neuroscience using wearables for naturalistic full-body motion-tracking and the sports of pool billiards to frame a real-world skill learning experiment. First, we asked if well-known features of motor learning in lab-based experiments generalize to a real-world task. We found similarities in many features such as multiple learning rates, and the relationship between task-related variability and motor learning. Our data-driven approach reveals the structure and complexity of movement, variability, and motor learning, enabling an in-depth understanding of the structure of motor learning in three ways: First, while expecting most of the movement learning is done by the cue-wielding arm, we find that motor learning affects the whole body, changing motor-control from head to toe. Second, during learning, all subjects decreased their movement variability and their variability in the outcome. Subjects who were initially more variable were also more variable after learning. Lastly, when screening the link across subjects between initial variability in individual joints and learning, we found that only the initial variability in the right forearm supination shows a significant correlation to the subjects’ learning rates. This is in-line with the relationship between learning and variability: while learning leads to an overall reduction in movement variability, only initial variability in specific task-relevant dimensions can facilitate faster learning.
Characterization of a new cell line from ornamental fish Amphiprion ocellaris (Cuvier, 1830) and its susceptibility to nervous necrosis virus
Authors: Yashwanth B. S. , Goswami Mukunda , Kooloth Valappil Rajendran , Thakuria Dimpal , Chaudhari Aparna 
Published: November 2020

AbstractAmphiprion ocellaris(ocellaris clownfish) is one of the most commercially important marine ornamental fish. A cell line designated as OCF was developed for the first time from the caudal fin of this fish species. The cell line was maintained in Leibovitz’s—15 medium supplemented with 15% FBS (Fetal Bovine Serum) and was successfully subcultured up to 34 passages. The cell line was authenticated by sequencing mitochondrial cytochrome C oxidase subunit I (COI) and 16S rRNA genes. The growth rate of the OCF cell line was maximum in medium containing 20% FBS and 1% of 0.2 M NaCl at 28 °C. Chromosome analysis revealed 48 diploid chromosomes. The OCF cell line was transfected with the pMaxGFP plasmid vector with 7% efficiency and GFP expression was observed. The OCF cell line was used for testing nervous necrosis virus (NNV) susceptibility. Cytopathic effect (CPE) was observed in terms of plaque formation after virus inoculation. Nested PCR confirmed the susceptibility of the OCF cell line to NNV. The cell line was successfully cryopreserved by a slow freezing procedure at − 80 °C with a revival efficiency of 70–75%. The study revealed that the OCF cell line would be useful for virological studies. In addition, the cell line would play an important role as an in vitro tool for carrying out toxicological and biotechnological studies.
Multilevel and spatial analyses of childhood malnutrition in Uganda: examining individual and contextual factors
Authors: Amegbor Prince M. , Zhang Zhaoxi , Dalgaard Rikke , Sabel Clive E. 
Published: November 2020

AbstractIn this study, we examine the concepts of spatial dependence and spatial heterogeneity in the effect of macro-level and micro-level factors on stunting among children aged under five in Uganda. We conducted a cross-sectional analysis of 3624 Ugandan children aged under five, using data from the 2016 Ugandan Demographic and Health Survey. Multilevel mixed-effect analysis, spatial regression methods and multi-scale geographically weight regression (MGWR) analysis were employed to examine the association between our predictors and stunting as well as to analyse spatial dependence and variability in the association. Approximately 28% of children were stunted. In the multilevel analysis, the effect of drought, diurnal temperature and livestock per km2 on stunting was modified by child, parent and household factors. Likewise, the contextual factors had a modifiable effect on the association between child’s sex, mother’s education and stunting. The results of the spatial regression models indicate a significant spatial error dependence in the residuals. The MGWR suggests rainfall and diurnal temperature had spatial varying associations with stunting. The spatial heterogeneity of rainfall and diurnal temperature as predictors of stunting suggest some areas in Uganda might be more sensitive to variability in these climatic conditions in relation to stunting than others.
Medicinal potential of mycelium and fruiting bodies of an arboreal mushroom Fomitopsis officinalis in therapy of lifestyle diseases
Authors: Fijałkowska Agata , Muszyńska Bożena , Sułkowska-Ziaja Katarzyna , Kała Katarzyna , Pawlik Anna , Stefaniuk Dawid , Matuszewska Anna , Piska Kamil , Pękala Elżbieta , Kaczmarczyk Piotr , Piętka Jacek , Jaszek Magdalena 
Published: November 2020

AbstractFomitopsis officinalis is a medicinal mushroom used in traditional European eighteenth and nineteenth century folk medicine. Fruiting bodies of F. officinalis were collected from the natural environment of Świętokrzyskie Province with the consent of the General Director for Environmental Protection in Warsaw. Mycelial cultures were obtained from fragments of F. officinalis fruiting bodies. The taxonomic position of the mushroom mycelium was confirmed using the PCR method. The presence of organic compounds was determined by HPLC–DAD analysis. Bioelements were determined by AF-AAS. The biochemical composition of the tested mushroom material was confirmed with the FTIR method. Antioxidant properties were determined using the DPPH method, and the antiproliferative activity was assessed with the use of the MTT test. The presence of indole compounds (l-tryptophan, 6-methyl-d,l-tryptophan, melatonin, 5-hydroxy-l-tryptophan), phenolic compounds (p-hydroxybenzoic acid, gallic acid, catechin, phenylalanine), and sterols (ergosterol, ergosterol peroxide) as well as trace elements was confirmed in the mycelium and fruiting bodies of F. officinalis. Importantly, a high level of 5-hydroxy-l-tryptophan in in vitro mycelium cultures (517.99 mg/100 g d.w) was recorded for the first time. The tested mushroom extracts also showed antioxidant and antiproliferative effects on the A549 lung cancer cell line, the DU145 prostate cancer cell line, and the A375 melanoma cell line.
17α-ethynylestradiol prevents the natural male-to-female sex change in gilthead seabream (Sparus aurata L.)
Authors: García Hernández M. Pilar , Cabas Isabel , Rodenas M. Carmen , Arizcun Marta , Chaves-Pozo Elena , Power Deborah M. , García Ayala Alfonsa 
Published: November 2020

AbstractExposure to 17α-ethynylestradiol (EE2, 5 μg/g food) impairs some reproductive events in the protandrous gilthead seabream and a short recovery period does not allow full recovery. In this study, spermiating seabream males in the second reproductive cycle (RC) were fed a diet containing 5 or 2.5 μg EE2/g food for 28 days and then a commercial diet without EE2 for the remaining RC. Individuals were sampled at the end of the EE2 treatment and then at the end of the RC and at the beginning of the third RC, 146 and 333 days after the cessation of treatment, respectively. Increased hepatic transcript levels of the gene coding for vitellogenin (vtg) and plasma levels of Vtg indicated both concentrations of EE2 caused endocrine disruption. Modifications in the histological organization of the testis, germ cell proliferation, plasma levels of the sex steroids and pituitary expression levels of the genes coding for the gonadotropin β-subunits, fshβ and lhβ were detected. The plasma levels of Vtg and most of the reproductive parameters were restored 146 days after treatments. However, although 50% of the control fish underwent sex reversal as expected at the third RC, male-to female sex change was prevented by both EE2 concentrations.
High prevalence of undiagnosed comorbidities among adolescents with obesity
Authors: Leong Karen S. W. , Jayasinghe Thilini N. , Wilson Brooke C. , Derraik José G. B. , Albert Benjamin B. , Chiavaroli Valentina , Svirskis Darren M. , Beck Kathryn L. , Conlon Cathryn A. , Jiang Yannan , Schierding William , Vatanen Tommi , Holland David J. , O’Sullivan Justin M. , Cutfield Wayne S. 
Published: November 2020

AbstractMetabolic diseases are increasing among adolescents with obesity. Although the reported prevalence of metabolic syndrome is approximately 30% worldwide, its prevalence is largely unknown among New Zealand adolescents. Therefore, we assessed the health of adolescents with obesity (BMI ≥ 30 kg/m2) enrolled in a randomised clinical trial (Gut Bugs Trial), to identify the prevalence of undiagnosed comorbidities. Assessments included anthropometry, 24-h ambulatory blood pressure monitoring, and insulin sensitivity. We report on baseline data (pre-randomisation) on 87 participants (14–18 years; 59% females), with mean BMI 36.9 ± 5.3 kg/m2 (BMI SDS 3.33 ± 0.79). Approximately 40% of participants had undiagnosed metabolic syndrome, which was twice as common among males. Half (53%) had pre-diabetes and 92% a reduction in insulin sensitivity. Moreover, 31% had pre-hypertension/hypertension, 69% dyslipidaemia, and 25% abnormal liver function. Participants with class III obesity had a greater risk of metabolic syndrome than those with classes I/II [relative risk 1.99 (95% CI 1.19, 3.34)]. Risks for pre-hypertension/hypertension and inflammation were also greater among those with class III obesity. We identified a high prevalence of undiagnosed comorbidities among adolescents with obesity in New Zealand. As adolescent obesity tracks into adulthood, early interventions are needed to prevent progression to overt cardiometabolic diseases.
Using quantitative trait in adults with ADHD to test predictions of dual-process theory
Authors: Persson Emil , Heilig Markus , Tinghög Gustav , Capusan Andrea J. 
Published: November 2020

AbstractDual-process theory is a widely utilized modelling tool in the behavioral sciences. It conceptualizes decision-making as an interaction between two types of cognitive processes, some of them fast and intuitive, others slow and reflective. We make a novel contribution to this literature by exploring differences between adults with clinically diagnosed ADHD and healthy controls for a wide range of behaviors. Given the clinical picture and nature of ADHD symptoms, we had a strong a priori reason to expect differences in intuitive vs reflective processing; and thus an unusually strong case for testing the predictions of dual-process theory. We found mixed results, with overall weaker effects than expected, except for risk taking, where individuals with ADHD showed increased domain sensitivity for gains vs losses. Some of our predictions were supported by the data but other patterns are more difficult to reconcile with theory. On balance, our results provide only limited empirical support for using dual-process theory to understand basic social and economic decision-making.
JavaCyte, a novel open-source tool for automated quantification of key hallmarks of cardiac structural remodeling
Authors: Winters J. , von Braunmuhl M. Edler , Zeemering S. , Gilbers M. , Brink T. Ten , Scaf B. , Guasch E. , Mont L. , Batlle M. , Sinner M. , Hatem S. , Mansour M. K. , Fabritz L. , Sommerfeld L. C. , Kirchhof P. , Isaacs A. , Stoll M. , Schotten U. , Verheule S. 
Published: November 2020

AbstractMany cardiac pathologies involve changes in tissue structure. Conventional analysis of structural features is extremely time-consuming and subject to observer bias. The possibility to determine spatial interrelations between these features is often not fully exploited. We developed a staining protocol and an ImageJ-based tool (JavaCyte) for automated histological analysis of cardiac structure, including quantification of cardiomyocyte size, overall and endomysial fibrosis, spatial patterns of endomysial fibrosis, fibroblast density, capillary density and capillary size. This automated analysis was compared to manual quantification in several well-characterized goat models of atrial fibrillation (AF). In addition, we tested inter-observer variability in atrial biopsies from the CATCH-ME consortium atrial tissue bank, with patients stratified by their cardiovascular risk profile for structural remodeling. We were able to reproduce previous manually derived histological findings in goat models for AF and AV block (AVB) using JavaCyte. Furthermore, strong correlation was found between manual and automated observations for myocyte count (r = 0.94, p < 0.001), myocyte diameter (r = 0.97, p < 0.001), endomysial fibrosis (r = 0.98, p < 0.001) and capillary count (r = 0.95, p < 0.001) in human biopsies. No significant variation between observers was observed (ICC = 0.89, p < 0.001). We developed and validated an open-source tool for high-throughput, automated histological analysis of cardiac tissue properties. JavaCyte was as accurate as manual measurements, with less inter-observer variability and faster throughput.
RNA sequencing as an alternative tool for detecting measurable residual disease in core-binding factor acute myeloid leukemia
Authors: Kim TaeHyung , Moon Joon Ho , Ahn Jae-Sook , Ahn Seo-Yeon , Jung Sung-Hoon , Yang Deok-Hwan , Lee Je-Jung , Shin Myung-Geun , Choi Seung Hyun , Lee Ja-yeon , Tyndel Marc S. , Lee Hui Young , Kim Kyoung Ha , Cai Yu , Lee Yoo Jin , Sohn Sang Kyun , Min Yoo Hong , Cheong June-Won , Kim Hyeoung-Joon , Zhang Zhaolei , Kim Dennis Dong Hwan 
Published: November 2020

AbstractDNA sequencing-based measurable residual disease (MRD) detection has shown to be clinically relevant in AML. However, the same methodology cannot be applied to fusion gene-driven subtypes of AML such as core-binding factor AML (CBF-AML). Here in this study, we evaluated the effectiveness of using DNA and RNA sequencing in MRD detection and in tracking clonal dynamics in CBF-AML. Using RNA-seq, we were able to quantify expression levels of RUNX1-RUNX1T1 and CBFB-MYH11 at diagnosis and their levels of reduction during remission (P < 6.3e−05 and P < 2.2e−13). The level of reduction of RUNX1-RUNX1T1 as measured by RNA-seq and qPCR were highly correlated (R2 = 0.74, P < 5.4e−05). A decision tree analysis, based on 3-log reduction of RUNX1-RUNX1T1 and cKIT-D816mut at diagnosis, stratified RUNX1-RUNX1T1 AML patients into three subgroups. These three subgroups had 2-year overall survival rates at 87%, 74%, and 33% (P < 0.08) and 2-year relapse incidence rates at 13%, 42%, and 67% (P < 0.05). On the other hand, although low residual allelic burden was common, it was not associated with long-term outcome, indicating that mutation clearance alone cannot be interpreted as MRD-negative. Overall, our study demonstrates that the clinical utility of RNA sequencing as a potential tool for MRD monitoring in fusion gene-driven AML such as RUNX1-RUNX1T1 AML.
Galectin-3 gene deletion results in defective adipose tissue maturation and impaired insulin sensitivity and glucose homeostasis
Authors: Blasetti Fantauzzi Claudia , Iacobini Carla , Menini Stefano , Vitale Martina , Sorice Gian Pio , Mezza Teresa , Cinti Saverio , Giaccari Andrea , Pugliese Giuseppe 
Published: November 2020

AbstractAdiposopathy is a pathological adipose tissue (AT) response to overfeeding characterized by reduced AT expandability due to impaired adipogenesis, which favors inflammation, insulin resistance (IR), and abnormal glucose regulation. However, it is unclear whether defective adipogenesis causes metabolic derangement also independently of an increased demand for fat storage. As galectin-3 has been implicated in both adipocyte differentiation and glucose homeostasis, we tested this hypothesis in galectin-3 knockout (Lgal3−/−) mice fed a standard chow. In vitro, Lgal3−/− adipocyte precursors showed impaired terminal differentiation (maturation). Two-month-old Lgal3−/− mice showed impaired AT maturation, with reduced adipocyte size and expression of adipogenic genes, but unchanged fat mass and no sign of adipocyte degeneration/death or ectopic fat accumulation. AT immaturity was associated with AT and whole-body inflammation and IR, glucose intolerance, and hyperglycemia. Five-month-old Lgal3−/− mice exhibited a more mature AT phenotype, with no difference in insulin sensitivity and expression of inflammatory cytokines versus WT animals, though abnormal glucose homeostasis persisted and was associated with reduced β-cell function. These data show that adipogenesis capacity per se affects AT function, insulin sensitivity, and glucose homeostasis independently of increased fat intake, accumulation and redistribution, thus uncovering a direct link between defective adipogenesis, IR and susceptibility to diabetes.
Risk prediction for malignant intraductal papillary mucinous neoplasm of the pancreas: logistic regression versus machine learning
Authors: Kang Jae Seung , Lee Chanhee , Song Wookyeong , Choo Wonho , Lee Seungyeoun , Lee Sungyoung , Han Youngmin , Bassi Claudio , Salvia Roberto , Marchegiani Giovanni , Wolfgang Cristopher L. , He Jin , Blair Alex B. , Kluger Michael D. , Su Gloria H. , Kim Song Cheol , Song Ki-Byung , Yamamoto Masakazu , Higuchi Ryota , Hatori Takashi , Yang Ching-Yao , Yamaue Hiroki , Hirono Seiko , Satoi Sohei , Fujii Tsutomu , Hirano Satoshi , Lou Wenhui , Hashimoto Yasushi , Shimizu Yasuhiro , Del Chiaro Marco , Valente Roberto , Lohr Matthias , Choi Dong Wook , Choi Seong Ho , Heo Jin Seok , Motoi Fuyuhiko , Matsumoto Ippei , Lee Woo Jung , Kang Chang Moo , Shyr Yi-Ming , Wang Shin-E. , Han Ho-Seong , Yoon Yoo-Seok , Besselink Marc G. , van Huijgevoort Nadine C. M. , Sho Masayuki , Nagano Hiroaki , Kim Sang Geol , Honda Goro , Yang Yinmo , Yu Hee Chul , Do Yang Jae , Chung Jun Chul , Nagakawa Yuichi , Seo Hyung Il , Choi Yoo Jin , Byun Yoonhyeong , Kim Hongbeom , Kwon Wooil , Park Taesung , Jang Jin-Young 
Published: November 2020

AbstractMost models for predicting malignant pancreatic intraductal papillary mucinous neoplasms were developed based on logistic regression (LR) analysis. Our study aimed to develop risk prediction models using machine learning (ML) and LR techniques and compare their performances. This was a multinational, multi-institutional, retrospective study. Clinical variables including age, sex, main duct diameter, cyst size, mural nodule, and tumour location were factors considered for model development (MD). After the division into a MD set and a test set (2:1), the best ML and LR models were developed by training with the MD set using a tenfold cross validation. The test area under the receiver operating curves (AUCs) of the two models were calculated using an independent test set. A total of 3,708 patients were included. The stacked ensemble algorithm in the ML model and variable combinations containing all variables in the LR model were the most chosen during 200 repetitions. After 200 repetitions, the mean AUCs of the ML and LR models were comparable (0.725 vs. 0.725). The performances of the ML and LR models were comparable. The LR model was more practical than ML counterpart, because of its convenience in clinical use and simple interpretability.