bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neoarchean Synmagmatic Crustal Extrusion in the Transpressional Yilgarn Orogen
Authors: Zibra I. , Weinberg R. F. , Peternell M. 
Published: January 2020

AbstractPositive feedback mechanisms between magmatism and transpression allow efficient extraction, transfer, and delivery of synorogenic granitic magma. Although many Archean orogens are dominantly transpressional and record voluminous production of synorogenic granites, the role of crustal magmatism in Archean tectonics has been so far little explored. We detail here the structural evolution of the Ballard shear zone, a major synorogenic, inclined transpressional shear zone from the upper‐crustal granite‐greenstone system of the Neoarchean Yilgarn Orogen (Western Australia). We show that the bulk of the three‐dimensional deformation was efficiently partitioned between greenstones and crystallizing granitic sheets, with the latter accommodating large amounts of orogen‐parallel strain through hypersolidus viscous flow. Other large synorogenic Yilgarn shear zones show a similar structural evolution, allowing the formulation of a general tectonomagmatic model. The positive feedback between protracted magmatism and transpression promoted lower‐ to middle‐crustal extraction and upward transfer of syntectonic magma. In upper‐crustal sink regions, the rheological dichotomy between cold and strong greenstones and hot and weak sheets of crystallizing granite allowed efficient kinematic partitioning, resulting in the extrusion of the partially molten shear zone cores. This sequence of events occurred repeatedly throughout the orogeny, following magma pulses, with the bulk of the shearing along each shear zone waning with the cooling of each syntectonic pluton. Synorogenic magmatism played therefore a major role in promoting and localizing transpressional deformation, and ultimately in shaping the architecture of the whole Yilgarn orogen.
Using Particle Tracking to Understand Flow Paths, Age Distributions, and the Paradoxical Origins of the Inverse Storage Effect in an Experimental Catchment
Authors: Wilusz D. C. , Harman C. J. , Ball W. P. , Maxwell R. M. , Buda A. R. 
Published: January 2020

AbstractMany catchment studies use estimates of stream age distributions, including transit time distributions and StorAge Selection (SAS) functions, to make inferences about hydrologic processes and dominant flow paths. To improve the basis for such inferences, this study examined how different hydrologic flow paths contribute to the age distribution of discharge and evapotranspiration (ET) at the U.S. Department of Agriculture's Mahantango Creek experimental catchment in PA, USA, using the integrated surface‐subsurface hydrology model Parallel Flow‐Common Land Model with SLIM‐FAST particle tracking. The model tracked ET and five flow paths: direct runoff, overland flow, interflow, and shallow and deep groundwater. Over a 1‐year simulation, we found that individual flow paths release generallyolderage‐rank storage under wetting conditions (a direct storage effect). Paradoxically, total discharge originated fromyoungerage‐rank storage under wetting conditions (an inverse storage effect). This inverse storage effect was caused by the disproportionate increase in contributions from younger flow paths, particularly overland flow. This result suggests that where direct storage effects have been observed for individual sources of discharge (such as shallow groundwater), the same may not necessarily hold for total discharge and could in fact be reversed. Other findings include (1) a highly nonunique mapping between water age and flow path, (2) a “middle‐aged depression” in stream ages that cannot be fit by unimodal distributions (e.g., gamma and beta), (3) a taxonomy of transit time distribution shapes that occur during a typical storm, and (4) relatively young ET age distributions with a time‐invariant SAS function shape that reflects the parameterized depth distribution of root‐water uptake.
A Rainfall‐Runoff Model With LSTM‐Based Sequence‐to‐Sequence Learning
Authors: Xiang Zhongrun , Yan Jun , Demir Ibrahim 
Published: January 2020

AbstractRainfall‐runoff modeling is a complex nonlinear time series problem. While there is still room for improvement, researchers have been developing physical and machine learning models for decades to predict runoff using rainfall data sets. With the advancement of computational hardware resources and algorithms, deep learning methods such as the long short‐term memory (LSTM) model and sequence‐to‐sequence (seq2seq) modeling have shown a good deal of promise in dealing with time series problems by considering long‐term dependencies and multiple outputs. This study presents an application of a prediction model based on LSTM and the seq2seq structure to estimate hourly rainfall‐runoff. Focusing on two Midwestern watersheds, namely, Clear Creek and Upper Wapsipinicon River in Iowa, these models were used to predict hourly runoff for a 24‐hr period using rainfall observation, rainfall forecast, runoff observation, and empirical monthly evapotranspiration data from all stations in these two watersheds. The models were evaluated using the Nash‐Sutcliffe efficiency coefficient, the correlation coefficient, statistical bias, and the normalized root‐mean‐square error. The results show that the LSTM‐seq2seq model outperforms linear regression, Lasso regression, Ridge regression, support vector regression, Gaussian processes regression, and LSTM in all stations from these two watersheds. The LSTM‐seq2seq model shows sufficient predictive power and could be used to improve forecast accuracy in short‐term flood forecast applications. In addition, the seq2seq method was demonstrated to be an effective method for time series predictions in hydrology.
ROCK inhibitors upregulate the neuroprotective Parkin-mediated mitophagy pathway
Authors: Moskal Natalia , Riccio Victoria , Bashkurov Mikhail , Taddese Rediet , Datti Alessandro , Lewis Peter N. , Angus McQuibban G. 
Published: January 2020

AbstractThe accumulation of damaged mitochondria causes the death of dopaminergic neurons. The Parkin-mediated mitophagy pathway functions to remove these mitochondria from cells. Targeting this pathway represents a therapeutic strategy for several neurodegenerative diseases, most notably Parkinson’s disease. We describe a discovery pipeline to identify small molecules that increase Parkin recruitment to damaged mitochondria and ensuing mitophagy. We show that ROCK inhibitors promote the activity of this pathway by increasing the recruitment of HK2, a positive regulator of Parkin, to mitochondria. This leads to the increased targeting of mitochondria to lysosomes and removal of damaged mitochondria from cells. Furthermore, ROCK inhibitors demonstrate neuroprotective effects in flies subjected to paraquat, a parkinsonian toxin that induces mitochondrial damage. Importantly, parkin and rok are required for these effects, revealing a signaling axis which controls Parkin-mediated mitophagy that may be exploited for the development of Parkinson’s disease therapeutics.
Accurate quantification of circular RNAs identifies extensive circular isoform switching events
Authors: Zhang Jinyang , Chen Shuai , Yang Jingwen , Zhao Fangqing 
Published: January 2020

AbstractDetection and quantification of circular RNAs (circRNAs) face several significant challenges, including high false discovery rate, uneven rRNA depletion and RNase R treatment efficiency, and underestimation of back-spliced junction reads. Here, we propose a novel algorithm, CIRIquant, for accurate circRNA quantification and differential expression analysis. By constructing pseudo-circular reference for re-alignment of RNA-seq reads and employing sophisticated statistical models to correct RNase R treatment biases, CIRIquant can provide more accurate expression values for circRNAs with significantly reduced false discovery rate. We further develop a one-stop differential expression analysis pipeline implementing two independent measures, which helps unveil the regulation of competitive splicing between circRNAs and their linear counterparts. We apply CIRIquant to RNA-seq datasets of hepatocellular carcinoma, and characterize two important groups of linear-circular switching and circular transcript usage switching events, which demonstrate the promising ability to explore extensive transcriptomic changes in liver tumorigenesis.
Rational design of universal immunotherapy for TfR1-tropic arenaviruses
Authors: Cohen-Dvashi Hadas , Amon Ron , Agans Krystle N. , Cross Robert W. , Borenstein-Katz Aliza , Mateo Mathieu , Baize Sylvain , Padler-Karavani Vered , Geisbert Thomas W. , Diskin Ron 
Published: January 2020

AbstractCertain arenaviruses that circulate in rodent populations can cause life-threatening hemorrhagic fevers when they infect humans. Due to their efficient transmission, arenaviruses pose a severe risk for outbreaks and might be exploited as biological weapons. Effective countermeasures against these viruses are highly desired. Ideally, a single remedy would be effective against many or even all the pathogenic viruses in this family. However, despite the fact that all pathogenic arenaviruses from South America utilize transferrin receptor 1 (TfR1) as a cellular receptor, their viral glycoproteins are highly diversified, impeding efforts to isolate cross-neutralizing antibodies. Here we address this problem using a rational design approach to target TfR1-tropic arenaviruses with high potency and breadth. The pan-reactive molecule is highly effective against all arenaviruses that were tested, offering a universal therapeutic approach. Our design scheme avoids the shortcomings of previous immunoadhesins and can be used to combat other zoonotic pathogens.
Bis(ethylmaltolato)oxidovanadium(iv) inhibited the pathogenesis of Alzheimer’s disease in triple transgenic model mice
Authors: He Zhijun , Han Shuangxue , Wu Chong , Liu Lina , Zhu Huazhang , Liu Ang , Lu Qiying , Huang Jingqiang , Du Xiubo , Li Nan , Xie Qinguo , Wan Lu , Ni Jiazuan , Chen Lingling , Yang Xiaogai , Liu Qiong 
Published: January 2020

Abstract
Vanadium compounds have been reported to mimic the anti-diabetes effects of insulin on rodent models, but their effects on Alzheimer’s disease (AD) have rarely been explored. In this paper, 9-month-old triple transgenic AD model mice (3×Tg-AD) received bis(ethylmaltolato)oxidovanadium(iv) (BEOV) at doses of 0.2 mmol L−1 (68.4 μg mL−1) and 1.0 mmol L−1 (342 μg mL−1) for 3 months. BEOV at both doses was found to improve contextual memory and spatial learning in AD mice. It also improved glucose metabolism and protected neuronal synapses in the AD brain, as evidenced respectively by 18F-labeled fluoro-deoxyglucose positron emission tomography (18F-FDG-PET) scanning and by transmission electron microscopy. Inhibitory effects of BEOV on β-amyloid (Aβ) plaques and neuronal impairment in the cortex and hippocampus of fluorescent AD mice were visualized three-dimensionally by applying optical clearing technology to brain slices before confocal laser scanning microscopy. Western blot analysis semi-quantitatively revealed the altered levels of Aβ42 in the brains of wildtype, AD, and AD treated with 0.2 and 1.0 mmol L−1 BEOV mice (70.3%, 100%, 83.2% and 56.8% in the hippocampus; 82.4%, 100%, 66.9% and 42% in the cortex, respectively). The mechanism study showed that BEOV increased the expression of peroxisome proliferator-activated receptor γ (PPARγ) (140%, 100%, 142% and 160% in the hippocampus; 167%, 100%, 124% and 133% in the cortex) to inactivate the JAK2/STAT3/SOCS-1 pathway and to block the amyloidogenesis cascade, thus attenuating Aβ-induced insulin resistance in AD models. BEOV also reduced protein tyrosine phosphatase 1B (PTP1B) expression (74.8%, 100%, 76.5% and 53.8% in the hippocampus; 71.8%, 100%, 94.2% and 81.8% in cortex) to promote insulin sensitivity and to stimulate the PI3K/Akt/GSK3β pathway, subsequently reducing tau hyperphosphorylation (phosphorylated tau396 levels were 51.1%, 100%, 56.1% and 50.2% in the hippocampus; 22.2%, 100%, 36.1%, and 24% in the cortex). Our results suggested that BEOV reduced the pathological hallmarks of AD by targeting the pathways of PPARγ and PTP1B in 3×Tg AD mice.
Proteomic screening of plasma identifies potential noninvasive biomarkers associated with significant/advanced fibrosis in patients with nonalcoholic fatty liver disease
Authors: Hou Wei , Janech Michael G. , Sobolesky Philip M. , Bland Alison M. , Samsuddin Salma , Alazawi William , Syn Wing-Kin 
Published: January 2020

Abstract
Noninvasive biomarkers are clinically useful for evaluating liver fibrosis stage in patients with nonalcoholic fatty liver disease (NAFLD). The aim of the present study was to compare plasma proteins in patients with early nonalcoholic steatohepatitis (NASH) (F0-F1) versus NASH with significant/advanced fibrosis (F2–F4) to determine whether candidate proteins could be used as potential noninvasive biomarkers. Nineteen biopsy-proven NAFLD patients including ten early NASH patients and nine NASH patients with significant/advanced fibrosis were enrolled in the present study. High-resolution proteomics screening of plasma was performed with the SCIEX TripleTOF 5600 System. Proteins were quantified using two different software platforms, Progenesis Qi and Scaffold Q+, respectively. Progenesis Qi analysis resulted in the discovery of 277 proteins compared with 235 proteins in Scaffold Q+. Five consensus proteins (i.e. Complement component C7; α-2-macroglobulin; Complement component C8 γ chain; Fibulin-1; α-1-antichymotrypsin) were identified. Complement component C7 was three-fold higher in the NASH group with significant/advanced fibrosis (F2–F4) compared with the early NASH (F0-F1) group (q-value = 3.6E-6). Complement component C7 and Fibulin-1 are positively correlated with liver stiffness (P=0.000, P=0.002, respectively); whereas, Complement component C8 γ chain is negatively correlated (P=0.009). High levels of Complement C7 are associated with NASH with significant/advanced fibrosis and Complement C7 is a perfect classifier of patients included in this pilot study. Further studies will be needed in a larger validation cohort to confirm the utility of complement proteins as biomarkers or mechanistic determinants of NASH with significant/advanced fibrosis.
The ratio of exogenous Luteinizing hormone to Follicle stimulating hormone administered for controlled ovarian stimulation is associated with oocytes’ number and competence
Authors: Albu Dragos , Albu Alice 
Published: January 2020

Abstract
We performed a retrospective study aiming to study the relationship between the ratio of the exogenous luteinizing hormone to follicle stimulating hormone (LH/FSH) administrated for controlled ovarian stimulation (COS) and the number and competence of the oocytes retrieved for in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI). Eight hundred sixty-eight consecutive infertile patients (mean age 34.54 ± 4.01 years, mean anti-Müllerian hormone (AMH) 2.94 ± 2.07 ng/ml) treated with long agonist protocol and a mixed gonadotropin protocol (human menopausal gonadotropin in association with recombinant FSH (recFSH)) who performed IVF/ICSI between January 2013 and February 2016, were included. Patients with severe male factor were excluded. LH/FSH was calculated based on total doses of the two gonadotropins. We found, after adjustment for confounders, a positive relationship between LH/FSH and the retrieved oocytes’ (β = 0.229, P&lt;0.0001) and zygotes’ number (β = 0.144, P&lt;0.0001) in the entire study group and in subgroups according to age (&lt;35 and ≥35 years) and ovarian reserve (AMH &lt; 1.1 and ≥ 1.1 ng/ml). The fertilization rate was positively associated with LH/FSH in patients with LH/FSH in the lowest three quartiles (below 0.77) (β = 0.096, P=0.034). However, patients in the fourth quartile of LH/FSH had a lower fertilization rate as compared with patients in quartiles 1–3 which, after adjustment for covariates, was only marginally negatively related with LH/FSH (β = −0.108, P=0.05). In conclusion, our results suggest that the adequate LH/FSH administrated during COS can improve the oocytes’ and zygotes’ number in IVF/ICSI cycles, but also the fertilization rate when a certain proportion of LH/FSH is not exceeded.
Recent Developments in Highly Stereoselective Michael Addition Reactions Catalyzed by Metal Complexes
Authors: Reznikov Alexander N. , Klimochkin Yuri N. 
Published: January 2020

Achieving high enantioselectivity and diastereoselectivity simultaneously­ is a rather challenging task for asymmetric catalytic synthesis­. Thanks to the rapid development of asymmetric transition-metal catalysis, significant progress has been made during recent years in achieving highly enantio- and diastereoselective conjugate addition reactions with a diverse combination of Michael donors and acceptors. This short review surveys the advances in transition-metal-catalyzed asymmetric diastereoselective Michael addition including diastereodivergent catalysis developed between 2015 and 2019. The review is divided into multiple parts according to the type of nucleophiles involved in the reaction.1	Introduction2	Addition of Functionalized Ketones and Dicarbonyl Compounds3	Addition of Aldimino Esters and Their Cyclic Analogues4	Addition of Indolin-2-ones5	Vinylogous Michael Reactions6	Other Michael Donors7	Cascade Reactions Initiated by Michael Addition8	Conclusion
Hydrocortisone for Preventing Mortality and Bronchopulmonary Dysplasia in Preterm Infants with or without Chorioamnionitis Exposure: A Meta-Analysis of Randomized Trials
Authors: Zhou Jianguo , Yu Zhuowen , Chen Chao 
Published: January 2020

Abstract
Objective This study sought to assess whether infants exposed to chorioamnionitis are the optimal population to benefit the most from early postnatal hydrocortisone delivery in preventing bronchopulmonary dysplasia (BPD). This meta-analysis was conducted to discover the efficacy of hydrocortisone in preterm infants with and without chorioamnionitis.
Study Design From the earliest available date until March 2018, studies, review articles, and papers published in PubMed, Ovid, and Web of Science were reviewed. Randomized controlled trials comparing hydrocortisone with placebo/no intervention in preterm infants with a known status of chorioamnionitis exposure were included.
Results Early postpartum low-dose hydrocortisone prevents the combined outcome of neonatal BPD or death in infants weighing less than 1,000 g with chorioamnionitis exposure (odds ratio [95% confidence interval]: 0.52 [0.32–0.79]; risk difference: –0.15 [–0.24 to –0.06]; number needed to treat: 6 [4–16]) but not in infants without chorioamnionitis exposure. Further secondary analysis showed no significant difference between the hydrocortisone group and the placebo group in individual outcomes of BPD or death, regardless of infant exposure to chorioamnionitis.
Conclusion Early application of low-dose hydrocortisone could potentially prevent BPD or death in infants weighing less than 1,000 g with exposure to chorioamnionitis. This finding provides the basis for further study in this target group.
Application of deep neural networks to improve diagnostic accuracy of rheumatoid arthritis using diffuse optical tomography
Authors: Feng Yangqin , Lighter D. , Zhang Lei , Wang Yan , Dehghani H. 
Published: January 2020

Abstract
A set of deep neural network models for rheumatoid arthritis (RA) classification using a highway network, a convolutional neural network and a residual network is proposed based on the data of diffuse optical tomography (DOT) utilising near-infrared light, which ensures early diagnosis of pathophysiological changes resulting from inflammation. A numerical model of the finger is used to generate images to overcome the inherent problem of insufficient clinical DOT images available. The proposed deep neural network models are applied to automatically classify simulated DOT images of inflamed and non-inflamed joints and transfer learning is also used to improve the performance of the classification. The results demonstrate that all three deep neural network methods improve the diagnostic accuracy as compared to the widely applied support vector machine (SVM), especially for high inter-subject variability databases. In cases of distinct modelled severity of disease, residual network achieved the highest accuracy (> 99 %), and both of highway and convolutional neural networks reached 99 %, respectively. However, as the severity of the modelled disease is reduced, this accuracy is reduced to 75.2 % for residual networks. The results indicate that transfer learning can improve the performance of deep neural network methods on RA classification from DOT data and highlight their potential as a computer aided tool in DOT diagnostic systems.
Assessment of the degree of hydration of ocular surface tissues using THz reflectometry
Authors: Kekkonen E.A. , Konovko A.A. , Lee E.S. , Lee I.-M. , Ozheredov I.A. , Park K.H. , Safonova T.N. , Sikach E.I. , Shkurinov A.P. 
Published: January 2020

AbstractUsing the effective medium model, the complex permittivity of the ocular surface system in the THz frequency range is considered. The penetration depth of THz radiation and the sensitivity of the reflected component to the dynamics of evaporation of the tear film are discussed. The results ofin vivoexperiments aimed to determine the reflection coefficient of the ocular surface using continuous THz reflectometers are well described using the developed model.
Control of laser-beam spatial distribution for correcting the shape and refraction of eye cornea
Authors: Baum O.I. , Omelchenko A.I. , Kasianenko E.M. , Skidanov R.V. , Kazanskiy N.L. , Sobol’ E.N. , Bolshunov A.V. , Avetisov S.E. , Panchenko V.Ya. 
Published: January 2020

Abstract
The results of calculation and development of a device aimed at forming a laser beam with an annular intensity distribution and spatial mode homogenisation, as well as approbation of this device for biological phantoms and eyes in ex vivo experiments with laser non-ablative correction of the cornea profile, are presented. The radiation intensities and thermal field distributions on the surfaces of a phantom and isolated rabbit’s eye are investigated. The absence of significant heating in the central region of eye is confirmed. It is shown that this device can be used for laser impact in order to change symmetrically eye’s refraction.
“Going video”
Authors: Pöchhacker Franz 
Published: January 2020

Abstract
This chapter explores the link between interpreting and video
mainly by engaging in a conceptual analysis drawing on insights from social
semiotics and communication studies. Departing from an understanding of
speech as a semiotic mode in the oral-aural modality, the development of
interpreting practices since the early twentieth century is reviewed with
respect to the use of technology as a sign-conveying medium. Special
emphasis is given to the introduction of “telephonic” interpreting and its
implications for “visibility” in interpreter-mediated communication before
the introduction of audiovisual transmission systems. Based on the
examination of some existing models of multimodal language use, and further
theoretical reflection, a conceptual framework is suggested to account more
explicitly for different medium-based forms of interpreting and for the
communicative dynamics shaped by the mediality of these practices. On this
foundation, video is discussed as a technological medium supporting novel
professional practices as well as research approaches.