bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel framework for spatio-temporal prediction of environmental data using deep learning
Authors: Amato Federico , Guignard Fabian , Robert Sylvain , Kanevski Mikhail 
Published: December 2020

AbstractAs the role played by statistical and computational sciences in climate and environmental modelling and prediction becomes more important, Machine Learning researchers are becoming more aware of the relevance of their work to help tackle the climate crisis. Indeed, being universal nonlinear function approximation tools, Machine Learning algorithms are efficient in analysing and modelling spatially and temporally variable environmental data. While Deep Learning models have proved to be able to capture spatial, temporal, and spatio-temporal dependencies through their automatic feature representation learning, the problem of the interpolation of continuous spatio-temporal fields measured on a set of irregular points in space is still under-investigated. To fill this gap, we introduce here a framework for spatio-temporal prediction of climate and environmental data using deep learning. Specifically, we show how spatio-temporal processes can be decomposed in terms of a sum of products of temporally referenced basis functions, and of stochastic spatial coefficients which can be spatially modelled and mapped on a regular grid, allowing the reconstruction of the complete spatio-temporal signal. Applications on two case studies based on simulated and real-world data will show the effectiveness of the proposed framework in modelling coherent spatio-temporal fields.
Comparison of computational chemistry methods for the discovery of quinone-based electroactive compounds for energy storage
Authors: Zhang Qi , Khetan Abhishek , Er Süleyman 
Published: December 2020

AbstractHigh-throughput computational screening (HTCS) is a powerful approach for the rational and time-efficient design of electroactive compounds. The effectiveness of HTCS is dependent on accuracy and speed at which the performance descriptors can be estimated for possibly millions of candidate compounds. Here, a systematic evaluation of computational methods, including force field (FF), semi-empirical quantum mechanics (SEQM), density functional based tight binding (DFTB), and density functional theory (DFT), is performed on the basis of their accuracy in predicting the redox potentials of redox-active organic compounds. Geometry optimizations at low-level theories followed by single point energy (SPE) DFT calculations that include an implicit solvation model are found to offer equipollent accuracy as the high-level DFT methods, albeit at significantly lower computational costs. Effects of implicit solvation on molecular geometries and SPEs, and their overall effects on the prediction accuracy of redox potentials are analyzed in view of computational cost versus prediction accuracy, which outlines the best choice of methods corresponding to a desired level of accuracy. The modular computational approach is applicable for accelerating the virtual studies on functional quinones and the respective discovery of candidate compounds for energy storage.
Time-resolved RIXS experiment with pulse-by-pulse parallel readout data collection using X-ray free electron laser
Authors: Lu H. , Gauthier A. , Hepting M. , Tremsin A. S. , Reid A. H. , Kirchmann P. S. , Shen Z. X. , Devereaux T. P. , Shao Y. C. , Feng X. , Coslovich G. , Hussain Z. , Dakovski G. L. , Chuang Y. D. , Lee W. S. 
Published: December 2020

AbstractTime-resolved resonant inelastic X-ray scattering (RIXS) is one of the developing techniques enabled by the advent of X-ray free electron laser (FEL). It is important to evaluate how the FEL jitter, which is inherent in the self-amplified spontaneous emission process, influences the RIXS measurement. Here, we use a microchannel plate (MCP) based Timepix soft X-ray detector to conduct a time-resolved RIXS measurement at the Ti L3-edge on a charge-density-wave material TiSe2. The fast parallel Timepix readout and single photon sensitivity enable pulse-by-pulse data acquisition and analysis. Due to the FEL jitter, low detection efficiency of spectrometer, and low quantum yield of RIXS process, we find that less than 2% of the X-ray FEL pulses produce signals, preventing acquiring sufficient data statistics while maintaining temporal and energy resolution in this measurement. These limitations can be mitigated by using future X-ray FELs with high repetition rates, approaching MHz such as the European XFEL in Germany and LCLS-II in the USA, as well as by utilizing advanced detectors, such as the prototype used in this study.
Alteration of serum amino acid profiles by dietary adenine supplementation inhibits fatty liver development in rats
Authors: Nishi Hiroki , Yamanaka Daisuke , Masuda Masato , Goda Yuki , Ito Koichi , Hakuno Fumihiko , Takahashi Shin-Ichiro 
Published: December 2020

AbstractStudies on animal models have demonstrated that feeding a low-arginine diet inhibits triacylglycerol (TAG) secretion from the liver, resulting in marked fatty liver development in rats. Here, we first showed that culturing hepatocytes in the medium mimicking the serum amino acid profile of low-arginine diet-fed rats induced TAG accumulation in the cells, indicating that the specific amino acid profile caused TAG accumulation in hepatocytes. Dietary adenine supplementation completely recovered hepatic TAG secretion and abolished hepatic TAG accumulation in rats. A comprehensive non-linear analysis revealed that inhibition of hepatic TAG accumulation by dietary adenine supplementation could be predicted using only serum amino acid concentration data. Comparison of serum amino acid concentrations indicated that histidine, methionine, and branched-chain amino acid (BCAA) concentrations were altered by adenine supplementation. Furthermore, when the serum amino acid profiles of low-arginine diet-fed rats were altered by modifying methionine or BCAA concentrations in their diets, their hepatic TAG accumulation was abolished. Altogether, these results suggest that an increase in methionine and BCAA levels in the serum in response to dietary arginine deficiency is a key causative factor for hepatic TAG accumulation, and dietary adenine supplementation could disrupt this phenomenon by altering serum amino acid profiles.
Single-walled carbon nanotubes as a photo-thermo-acoustic cancer theranostic agent: theory and proof of the concept experiment
Authors: Golubewa L. , Timoshchenko I. , Romanov O. , Karpicz R. , Kulahava T. , Rutkauskas D. , Shuba M. , Dementjev A. , Svirko Yu. , Kuzhir P. 
Published: December 2020

AbstractTheranostics is the emerging field of medicine that uniquely combines diagnostic techniques and active agents to diagnose and treat medical conditions simultaneously or sequentially. Finding a theranostic agent capable to cure the affected cells and being safe for the healthy ones is the key for successful treatment. Here, we demonstrate that agglomerated single-walled carbon nanotubes (SWCNTs) are promising theranostic agent that enables photo-activated ‘cold’ destruction of the cancer cells keeping their environment alive. The absorption of picosecond pulses by SWCNT agglomerates results in the mechanical (due to photoacoustic effect) rather than photothermal cancer cell destruction, which was visualized by micro-Raman and ultrafast near-infrared CARS. The developed theoretical model allows us to distinguish photothermal, photoacoustic, and photothermoacoustic regimes of the cancer cell destruction, and also to optimize SWCNT-based theranostics recipe.
The novel rexinoid MSU-42011 is effective for the treatment of preclinical Kras-driven lung cancer
Authors: Moerland Jessica A. , Zhang Di , Reich Lyndsey A. , Carapellucci Sarah , Lockwood Beth , Leal Ana S. , Krieger-Burke Teresa , Aleiwi Bilal , Ellsworth Edmund , Liby Karen T. 
Published: December 2020

AbstractEffective drugs are needed for lung cancer, as this disease remains the leading cause of cancer-related deaths. Rexinoids are promising drug candidates for cancer therapy because of their ability to modulate genes involved in inflammation, cell proliferation or differentiation, and apoptosis through activation of the retinoid X receptor (RXR). The only currently FDA-approved rexinoid, bexarotene, is ineffective as a single agent for treating epithelial cancers and induces hypertriglyceridemia. Here, we used a previously validated screening paradigm to evaluate 23 novel rexinoids for biomarkers related to efficacy and safety. These biomarkers include suppression of inducible nitric oxide synthase (iNOS) and induction of sterol regulatory element-binding protein (SREBP). Because of its potent iNOS suppression, low SREBP induction, and activation of RXR, MSU-42011 was selected as our lead compound. We next used MSU-42011 to treat established tumors in a clinically relevant Kras-driven mouse model of lung cancer. KRAS is one of the most common driver mutations in human lung cancer and correlates with aggressive disease progression and poor patient prognosis. Ultrasound imaging was used to detect and monitor tumor development and growth over time in the lungs of the A/J mice. MSU-42011 markedly decreased the tumor number, size, and histopathology of lung tumors compared to the control and bexarotene groups. Histological sections of lung tumors in mice treated with MSU-42011 exhibited reduced cell density and fewer actively proliferating cells compared to the control and bexarotene-treated tumors. Although bexarotene significantly (p < 0.01) elevated plasma triglycerides and cholesterol, treatment with MSU-42011 did not increase these biomarkers, demonstrating a more favorable toxicity profile in vivo. The combination of MSU-42011 and carboplatin and paclitaxel reduced macrophages in the lung and increased activation markers of CD8+T cells compared to the control groups. Our results validate our screening paradigm for in vitro testing of novel rexinoids and demonstrate the potential for MSU-42011 to be developed for the treatment of KRAS-driven lung cancer.
Molecular determinant of substrate binding and specificity of cytochrome P450 2J2
Authors: Xu Liang , Chen Liao Y. 
Published: December 2020

AbstractCytochrome P450 2J2 (CYP2J2) is responsible for the epoxidation of endogenous arachidonic acid, and is involved in the metabolism of exogenous drugs. To date, no crystal structure of CYP2J2 is available, and the proposed structural basis for the substrate recognition and specificity in CYP2J2 varies with the structural models developed using different computational protocols. In this study, we developed a new structural model of CYP2J2, and explored its sensitivity to substrate binding by molecular dynamics simulations of the interactions with chemically similar fluorescent probes. Our results showed that the induced-fit binding of these probes led to the preferred active poses ready for the catalysis by CYP2J2. Divergent conformational dynamics of CYP2J2 due to the binding of each probe were observed. However, a stable hydrophobic clamp composed of residues I127, F310, A311, V380, and I487 was identified to restrict any substrate access to the active site of CYP2J2. Molecular docking of a series of compounds including amiodarone, astemizole, danazol, ebastine, ketoconazole, terfenadine, terfenadone, and arachidonic acid to CYP2J2 confirmed the role of those residues in determining substrate binding and specificity of CYP2J2. In addition to the flexibility of CYP2J2, the present work also identified other factors such as electrostatic potential in the vicinity of the active site, and substrate strain energy and property that have implications for the interpretation of CYP2J2 metabolism.
siRNA biogenesis and advances in topically applied dsRNA for controlling virus infections in tomato plants
Authors: Rego-Machado Camila M. , Nakasu Erich Y. T. , Silva João M. F. , Lucinda Natália , Nagata Tatsuya , Inoue-Nagata Alice K. 
Published: December 2020

AbstractA non-transgenic approach based on RNA interference was employed to induce protection against tomato mosaic virus (ToMV) infection in tomato plants. dsRNA molecules targeting the cp gene of ToMV were topically applied on plants prior to virus inoculation. Protection was dose-dependent and sequence-specific. While no protection was achieved when 0–16 µg dsRNA were used, maximum rates of resistance (60 and 63%) were observed in doses of 200 and 400 µg/plant, respectively. Similar rates were also obtained against potato virus Y when targeting its cp gene. The protection was quickly activated upon dsRNA application and lasted for up to 4 days. In contrast, no detectable antiviral response was triggered by the dsRNA from a begomovirus genome, suggesting the method is not effective against phloem-limited DNA viruses. Deep sequencing was performed to analyze the biogenesis of siRNA populations. Although long-dsRNA remained in the treated leaves for at least 10 days, its systemic movement was not observed. Conversely, dsRNA-derived siRNA populations (mainly 21- and 22-nt) were detected in non-treated leaves, which indicates endogenous processing and transport through the plant. Altogether, this study provides critical information for the development of novel tools against plant viruses; strengths and limitations inherent to the systems are discussed.
Measuring spontaneous and automatic processing of magnitude and parity information of Arabic digits by frequency-tagging EEG
Authors: Guillaume Mathieu , Poncin Alexandre , Schiltz Christine , Van Rinsveld Amandine 
Published: December 2020

AbstractArabic digits (1–9) are everywhere in our daily lives. These symbols convey various semantic information, and numerate adults can easily extract from them several numerical features such as magnitude and parity. Nonetheless, since most studies used active processing tasks to assess these properties, it remains unclear whether and to what degree the access to magnitude and especially to parity is automatic. Here we investigated with EEG whether spontaneous processing of magnitude or parity can be recorded in a frequency-tagging approach, in which participants are passively stimulated by fast visual sequences of Arabic digits. We assessed automatic magnitude processing by presenting a stream of frequent small digit numbers mixed with deviant large digits (and the reverse) with a sinusoidal contrast modulation at the frequency of 10 Hz. We used the same paradigm to investigate numerical parity processing, contrasting odd digits to even digits. We found significant brain responses at the frequency of the fluctuating change and its harmonics, recorded on electrodes encompassing right occipitoparietal regions, in both conditions. Our findings indicate that both magnitude and parity are spontaneously and unintentionally extracted from Arabic digits, which supports that they are salient semantic features deeply associated to digit symbols in long-term memory.
Non-aqueous green solvents improve alpha-amylase induced fiber opening in leather processing
Authors: Ramamoorthi Poornima , Rathinam Aravindhan , Jonnalagadda Raghava Rao , Palanisamy Thanikaivelan 
Published: December 2020

AbstractSevere water deficit and highly polluting effluent generation from leather industries have constantly been pressurizing the tanners to adopt cleaner leather processing systems. The present study aims to minimize the use of water by substituting it with non-aqueous green solvents and also to enhance the enzyme action in alpha-amylase based fiber opening process. The activity of alpha-amylase in select non-aqueous green solvents namely, heptane, polyethylene glycol 200 and propylene glycol is considerably higher by 62, 38 and 31% than in water, respectively. Comparable results are obtained for the catalytic efficiency of alpha-amylase and hence it is further validated in collagen fiber opening trials as well. Scanning electron micrographs, histological images and proteoglycan estimation supported the above findings at 1% alpha-amylase dosage. The final quality of the experimental leathers in terms of physical and bulk properties is comparable to that of control leathers. Recycling studies indicate that it is possible to replace water with green solvents for enzymatic fiber opening with the feasibility to recover more than 85% solvent-enzyme mixture and reuse without any additional alpha-amylase usage. Reduction in pollution load coupled with the efficient catalytic action of enzyme in non-aqueous media favors the present protocol for industrial applications.
Metagenomic characterisation of additional and novel avian viruses from Australian wild ducks
Authors: Vibin Jessy , Chamings Anthony , Klaassen Marcel , Alexandersen Soren 
Published: December 2020

AbstractBirds, notably wild ducks, are reservoirs of pathogenic and zoonotic viruses such as influenza viruses and coronaviruses. In the current study, we used metagenomics to detect and characterise avian DNA and RNA viruses from wild Pacific black ducks, Chestnut teals and Grey teals collected at different time points from a single location. We characterised a likely new species of duck aviadenovirus and a novel duck gyrovirus. We also report what, to the best of our knowledge, is the first finding of an avian orthoreovirus from Pacific black ducks and a rotavirus F from Chestnut teals. Other viruses characterised from the samples from these wild ducks belong to the virus families Astroviridae, Caliciviridae and Coronaviridae. Some of the viruses may have potential cross-species transmissibility, while others indicated a wide genetic diversity of duck viruses within a genus. The study also showed evidence of potential transmission of viruses along the East Asian—Australasian Flyway; potentially facilitated by migrating shorebirds. The detection and characterisation of several avian viruses not previously described, and causing asymptomatic but potentially also symptomatic infections suggest the need for more virus surveillance studies for pathogenic and potential zoonotic viruses in wildlife reservoirs.
Possibility of concentration of nonvolatile species near the surface of comet 67P/Churyumov-Gerasimenko
Authors: Suzuki T. , Shinnaka Y. , Majumdar L. , Shibata T. , Shibaike Y. , Nomura H. , Minamoto H. 
Published: December 2020

Context. Cometary materials are thought to be the reservoir of the primitive materials of the Solar System. The recent detection of glycine and CH3NH2 by the ROSINA mass spectrometer in the coma of 67P/Churyumov-Gerasimenko suggests that amino acids and their precursors may have formed in an early evolutionary phase of the Solar System.
Aims. We aim to investigate the evolution of the interior of comets considering the evaporation process of water followed by the concentration of nonvolatile species.
Methods. We developed a Simplified Cometary Concentration Model (SCCM) to simulate the evaporation and concentration processes on the cometary surface. We use 67P/Churyumov-Gerasimenko as the benchmark of the SCCM. We investigated the depth of the layer where nonvolatile species concentrate after the numerous passages of perihelion after the formation of the Solar System.
Results. We find that the SCCM explains the observed production rates of water and CH3NH2 at 100 comet years. Results from the SCCM suggest that the nonvolatile species would concentrate in the top 100 cm of the comet surface within 10 comet years. Our results also suggest that the nonvolatile species would concentrate several meters beneath the surface before it hit the early Earth. This specific mass of nonvolatile species may provide unique chemical conditions for the volcanic hot spring pools.
Characterization of activation induced [18]F-FDG uptake in Dendritic Cells
Authors: Pektor Stefanie , Lawaczeck Laura , Tenzer Stephan , Bausbacher Nicole , Hoffmann Manuela Andrea , Schreckenberger Mathias , Miederer Matthias 
Published: December 2020

Abstract
Aim Activation of immune cells leads to enhanced glucose uptake that can be visualized by [18]F-Fluorodeoxyglucose ([18]F-FDG) positron emission tomography/computed tomography (PET/CT). Dendritic cells (DC) are essential for the function of the adaptive immune system. In contrast to other immune cells metabolic changes leading to an increase of [18]F-FDG uptake are poorly investigated. Here, we analysed the impact of different DC activation pathways on their [18]F-FDG uptake. This effect was then used to radiolabel DC with [18]F-FDG and track their migration in vivo.
Methods DC were generated from bone marrow progenitors (BMDC) or isolated from spleens (SPDC) of C57BL/6 mice. After stimulation with the TLR ligands LPS and CpG or anti-CD40 antibody for up to 72 hours activation markers and glucose transporters (GLUTs) were measured by flow cytometry. Uptake of [18]F-FDG was measured by gamma-counting. DC lysates were analysed for expression of glycolysis relevant proteins by mass spectrometry (MS). [18]F-FDG-labeled DC were injected into footpads of mice to image DC migration.
Results BMDC and SPDC showed strong upregulation of activation markers predominantly 24 hours after TLR stimulation followed by higher uptake of [18]F-FDG. In line with this, the expression of GLUTs was upregulated during the course of activation. Furthermore, MS analyses of DC lysates revealed differential regulation of glycolysis relevant proteins according to the stimulatory pathway. As a proof of principle, DC were labeled with [18]F-FDG upon activation to follow their migration in vivo via PET/MRI.
Conclusion Immune stimulation of DC leads to enhanced [18]F-FDG uptake into DC, representing the typical shift to aerobic glycolysis in immune cells after activation.
Nachweis von relevanten Veränderungen der Sprechstimme bei Frauen, gemessen im Sprechstimmprofil
Authors: Berger Thomas , Meuret Sylvia , Engel Christoph , Vogel Mandy , Kiess Wieland , Fuchs Michael , Poulain Tanja 
Published: December 2020

Zusammenfassung
Hintergrund Eine gesunde Stimme dient uns als Basis für Kommunikation und unverzichtbares Werkzeug in einer modernen Gesellschaft mit einer wachsenden Anzahl an stimmintensiven Berufen. Es gibt Hinweise, dass sich die mittlere Sprechstimmlage von Frauen in den letzten Jahren gesenkt hat und sich im Sinne einer Soziophonie der von Männern annähert. Im Rahmen einer epidemiologischen prospektiven Kohortenstudie sollen die Einflüsse des Alters, soziodemografischer Faktoren und von Persönlichkeitsmerkmalen auf die Sprechstimme von Frauen untersucht werden.
Material und Methoden Im Rahmen eines standardisierten Untersuchungsablaufs wurde bei 2478 stimmgesunden weiblichen Teilnehmerinnen zwischen 5 und 83 Jahren die Sprechstimme in 4 unterschiedlichen Intensitätsstufen (leiseste Stimme, Gesprächsstimme, Vortragsstimme und Rufstimme) registriert. Anschließend wurden Assoziationen zwischen den erhobenen Werten für die Frequenz und Lautstärke der unterschiedlichen Intensitätsstufen und dem Lebensalter sowie Befunden aus Fragebögen zur Persönlichkeit (FFFK und BFI-10), zur (mentalen) Gesundheit (Patient-Health-Questionnaire, PHQ) sowie dem sozioökonomischen Status (SES) untersucht.
Ergebnisse Es konnten für alle Stimmintensitäten signifikante altersbedingte Einflüsse auf die Sprechstimme gezeigt werden. Für die untersuchten Persönlichkeitsmerkmale zeigten sich signifikant positive Zusammenhänge zwischen der Lautstärke der Ruf- und Vortragsstimme und Extraversion. Für die Frequenz der leisesten Stimme und Gesprächsstimme ergaben sich signifikante Zusammenhänge mit den Persönlichkeitsmerkmalen Extraversion und Verträglichkeit. Während sich bei der Betrachtung der Stimmparameter der Sprechstimme mit dem PHQ keine signifikanten Assoziationen beobachten ließen, zeigte sich, dass der SES einen signifikanten Einfluss sowohl auf die Frequenz als auch auf die Intensität hat.
Schlussfolgerung Neben altersbedingten Veränderungen bestätigen sich relevante Einflüsse von Persönlichkeitsmerkmalen und dem SES auf Parameter der Sprechstimme der Frau, die in der klinischen Betreuung von Patientinnen mit Stimmstörungen Berücksichtigung finden sollten.