bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Modeling Framework for Computationally Efficient and Accurate Real‐Time Ensemble Flood Forecasting With Uncertainty Quantification
Authors: Tran Vinh Ngoc , Dwelle M. Chase , Sargsyan Khachik , Ivanov Valeriy Y. , Kim Jongho 
Published: February 2020

AbstractA novel modeling framework that simultaneously improves accuracy, predictability, and computational efficiency is presented. It embraces the benefits of three modeling techniques integrated together for the first time: surrogate modeling, parameter inference, and data assimilation. The use of polynomial chaos expansion (PCE) surrogates significantly decreases computational time. Parameter inference allows for model faster convergence, reduced uncertainty, and superior accuracy of simulated results. Ensemble Kalman filters assimilate errors that occur during forecasting. To examine the applicability and effectiveness of the integrated framework, we developed 18 approaches according to how surrogate models are constructed, what type of parameter distributions are used as model inputs, and whether model parameters are updated during the data assimilation procedure. We conclude that (1) PCE must be built over various forcing and flow conditions, and in contrast to previous studies, it does not need to be rebuilt at each time step; (2) model parameter specification that relies on constrained, posterior information of parameters (so‐called Selected specification) can significantly improve forecasting performance and reduce uncertainty bounds compared to Random specification using prior information of parameters; and (3) no substantial differences in results exist between single and dual ensemble Kalman filters, but the latter better simulates flood peaks. The use of PCE effectively compensates for the computational load added by the parameter inference and data assimilation (up to ~80 times faster). Therefore, the presented approach contributes to a shift in modeling paradigm arguing that complex, high‐fidelity hydrologic and hydraulic models should be increasingly adopted for real‐time and ensemble flood forecasting.
A New Multiobjective Simulated Annealing Algorithm—MOSA‐GR: Application to the Optimal Design of Water Distribution Networks
Authors: Cunha M. , Marques J. 
Published: February 2020

AbstractThis paper presents a simulated annealing multiobjective algorithm developed to include novel features for promoting the convergence toward the best Pareto front that shows diversity and uniformity in the distribution of solutions. The new algorithm, MultiObjective Simulated Annealing with new Generation and Reannealing procedures (MOSA‐GR), is a trajectory‐based algorithm, where, in a first phase, diversified generation strategies are used to define candidate solutions at different stages of the search procedure. In a second phase a reannealing process starting at low temperature is implemented to intensify the search based on the last solutions of the first phase. An extensive comparison with solutions obtained by various multiobjective evolutionary algorithms (MOEAs) described in the literature is provided. Using a limited budget for the number of function evaluations, the results show that MOSA‐GR has a very good performance and gives rise to better fronts, even compared with those obtained by merging the results from different MOEAs implemented in similar conditions.
Sources and Transformation Processes of Proteinaceous Matter and Free Amino Acids in PM2.5
Authors: Zhu Ren‐guo , Xiao Hua‐Yun , Zhu Yuwen , Wen Zequn , Fang Xiaozheng , Pan Yuanyuan 
Published: February 2020

AbstractAmino acids is an important organic nitrogen compound class in aerosol. Its origins and transformation in the atmosphere remain poorly understood. The concentrations of free amino acids (FAAs) and combined amino acids (CAAs) and δ15N values of free and combined Glycine (Gly) in PM2.5 and main emission sources (plant, soil, and aerosol from biomass burning) were investigated from five sampling sites in Nanchang area (Jiangxi Province, China). Our results showed that the composition profiles of CAAs and FAAs were quite different from each other in PM2.5. For CAAs, percentages of individual combined amino acids were different between biomass burning sources and plant or soil sources, and we found that the composition profiles of aerosol CAAs could reflect the contribution of the main emission sources. For FAAs, a predominance of free Gly was observed in aerosol FAAs pool because atmospheric photooxidative processes could increase free Gly and decrease other reactive FAAs. This implied that the composition of aerosol FAAs could not reflect their origins. A strong correlation between δ15NF‐Gly values in aerosols or sources and the δ15NC‐Gly values in their parent CAAs was observed, indicating that the isotope effect associated with Gly transformation in aerosols may be small. Additionally, we found more positive δ15NGly in aerosols emitted by biomass burning, which was likely due to 15N‐depleted amino‐N loss from Gly molecule. The results suggested that δ15NGly values in aerosols might be used to identify biomass burning sources.
AMPK-dependent activation of the Cyclin Y/CDK16 complex controls autophagy
Authors: Dohmen Marc , Krieg Sarah , Agalaridis Georgios , Zhu Xiaoqing , Shehata Saifeldin N. , Pfeiffenberger Elisabeth , Amelang Jan , Bütepage Mareike , Buerova Elena , Pfaff Carolina M. , Chanda Dipanjan , Geley Stephan , Preisinger Christian , Sakamoto Kei , Lüscher Bernhard , Neumann Dietbert , Vervoorts Jörg 
Published: February 2020

AbstractThe AMP-activated protein kinase (AMPK) is a master sensor of the cellular energy status that is crucial for the adaptive response to limited energy availability. AMPK is implicated in the regulation of many cellular processes, including autophagy. However, the precise mechanisms by which AMPK controls these processes and the identities of relevant substrates are not fully understood. Using protein microarrays, we identify Cyclin Y as an AMPK substrate that is phosphorylated at Serine 326 (S326) both in vitro and in cells. Phosphorylation of Cyclin Y at S326 promotes its interaction with the Cyclin-dependent kinase 16 (CDK16), thereby stimulating its catalytic activity. When expressed in cells, Cyclin Y/CDK16 is sufficient to promote autophagy. Moreover, Cyclin Y/CDK16 is necessary for efficient AMPK-dependent activation of autophagy. This functional interaction is mediated by AMPK phosphorylating S326 of Cyclin Y. Collectively, we define Cyclin Y/CDK16 as downstream effector of AMPK for inducing autophagy.
Uncovering near-free platinum single-atom dynamics during electrochemical hydrogen evolution reaction
Authors: Fang Shi , Zhu Xiaorong , Liu Xiaokang , Gu Jian , Liu Wei , Wang Danhao , Zhang Wei , Lin Yue , Lu Junling , Wei Shiqiang , Li Yafei , Yao Tao 
Published: February 2020

AbstractSingle-atom catalysts offering intriguing activity and selectivity are subject of intense investigation. Understanding the nature of single-atom active site and its dynamics under working state are crucial to improving their catalytic performances. Here, we identify at atomic level a general evolution of single atom into a near-free state under electrocatalytic hydrogen evolution condition, via operando synchrotron X-ray absorption spectroscopy. We uncover that the single Pt atom tends to dynamically release from the nitrogen-carbon substrate, with the geometric structure less coordinated to support and electronic property closer to zero valence, during the reaction. Theoretical simulations support that the Pt sites with weakened Pt–support interaction and more 5d density are the real active centers. The single-atom Pt catalyst exhibits very high hydrogen evolution activity with only 19 mV overpotential in 0.5 M H2SO4 and 46 mV in 1.0 M NaOH at 10 mA cm−2, and long-term durability in wide-pH electrolytes.
Hand posture affects brain-function measures associated with listening to speech
Authors: Tsunoda Koichi , Takazawa Mihiro , Sekimoto Sotaro , Itoh Kenji , Baer Thomas 
Published: February 2020

AbstractA major difficulty in studies of the brain, from the molecular to large-scale network level, is ensuring the accuracy and reliability of results, since repeatability has been a problem in studies utilizing functional magnetic resonance imaging (f-MRI) near-infrared spectroscopy (NIRS), and positron-emission tomography (PET). More generally, an effort to replicate psychological studies has shown that the original results were unambiguously reobtained only 39% of the time. It has been suggested that researchers must undertake studies to identify factors that reduce reliability and conduct more carefully controlled studies to improve reliability. In our previous work, we examined whether changes in hand/arm posture can have a confounding effect on task-related brain activity. Here we show a solution to enhance reproducibility in a NIRS study in a hearing task. The results showed that crossed posture can lead to different results than parallel posture with respect to asymmetric functional connectivity, especially during non-resting state. Even when the only task is listening to speech stimuli, participants should be asked to place their hands on a surface and feet on the floor and keep the same stable posture to increase reproducibility of results. To achieve accurate reliability and reproductively of results, stable hand posture through the experiment is important.
Combined cardio-protective ability of syringic acid and resveratrol against isoproterenol induced cardio-toxicity in rats via attenuating NF-kB and TNF-α pathways
Authors: S. Manjunatha , Shaik Althaf Hussain , E. Maruthi Prasad , Al Omar Suliman Yousef , Mohammad Altaf , Kodidhela Lakshmi Devi 
Published: February 2020

AbstractThe study was conducted to evaluate the cardio-protective activity of combination (COMB) of syringic acid (SA) and resveratrol (RV) against isoproterenol (ISO) induced cardio-toxicity in rats. Rats were pre-treated orally with SA (50 mg/kg), RV (50 mg/kg) and combination of SA (25 mg/kg) and RV (25 mg/kg) along with positive control gallic acid (50 mg/kg) for 30 days. The effects of ISO on cardiac markers, lipid profile and lipid peroxidation marker, anti-oxidant enzymes and m-RNA expression of nuclear factor-kappa B (NF-kB) and tumor necrosis factor-α (TNF-α) were observed along with histopathological observations of simple and transmission electron microscopes (TEM). Serum creatine kinase-MB (CK-MB), lactate dehydrogenase (LDH) and alkaline phosphatase were significantly increased while cardiac tissue CK-MB, LDH, superoxide dismutase and catalase were significantly decreased in ISO administered rats, which also exhibited a significant increase in total cholesterol, triglycerides, low density lipoprotein cholesterol, very low density lipoprotein cholesterol and thiobarbutyric acid reactive substances and significant decrease in high density lipoprotein cholesterol in serum and heart. The m-RNA levels of inflammatory markers NF-kB and TNF-α were significantly increased in ISO treated rats. COMB Pre-treatment significantly reversed the ISO actions. Histopathological studies of simple and TEM were also co-related with the above biochemical parameters. Docking studies with NF-kB were also performed. Evidence has shown for the first time in this approach that COMB pre-treatment ameliorated ISO induced cardio-toxicity in rats and revealed cardio-protection.
Agricultural productivity in relation to climate and cropland management in West Africa
Authors: Mechiche-Alami Altaaf , Abdi Abdulhakim M. 
Published: February 2020

AbstractThe climate of West Africa is expected to become more arid due to increased temperature and uncertain rainfall regimes, while its population is expected to grow faster than the rest of the world. As such, increased demand for food will likely coincide with declines in agricultural production in a region where severe undernutrition already occurs. Here, we attempt to discriminate between the impacts of climate and other factors (e.g. land management/degradation) on crop production across West Africa using satellite remote sensing. We identify trends in the land surface phenology and climate of West African croplands between 2000 and 2018. Using the combination of a an attribution framework and residual trend anlaysis, we discriminate between climate and other impacts on crop productivity. The combined effect of rainfall, land surface temperature and solar radiation explains approximately 40% of the variation in cropland productivity over West Africa at the 95% significance level. The largest proportions of croplands with greening trends were observed in Mali, Niger and Burkina Faso, and the largest proportions with browning trends were in Nigeria, The Gambia and Benin. Climate was responsible for 52% of the greening trends and 25% of the browning trends. Within the other driving factors, changes in phenology explained 18% of the greening and 37% of the browning trends across the region, the use of inputs and irrigation explained 30% of the greening trends and land degradation 38% of the browning trends. These findings have implications for adaptation policies as we map out areas in need of improved land management practices and those where it has proven to be successful.
Analysis of membrane fouling by Brunauer-Emmett-Teller nitrogen adsorption/desorption technique
Authors: Virtanen Tiina , Rudolph Gregor , Lopatina Anastasiia , Al-Rudainy Basel , Schagerlöf Herje , Puro Liisa , Kallioinen Mari , Lipnizki Frank 
Published: February 2020

AbstractMembrane fouling is the major factor limiting the wider applicability of the membrane-based technologies in water treatment and in separation and purification processes of biorefineries, pulp and paper industry, food industry and other sectors. Endeavors to prevent and minimize fouling requires a deep understanding on the fouling mechanisms and their relative effects. In this study, Brunauer-Emmett-Teller (BET) nitrogen adsorption/desorption technique was applied to get an insight into pore-level membrane fouling phenomena occurring in ultrafiltration of wood-based streams. The fouling of commercial polysulfone and polyethersulfone membranes by black liquor, thermomechanical pulping process water and pressurized hot-water extract was investigated with BET analysis, infrared spectroscopy, contact angle analysis and pure water permeability measurements. Particular emphasis was paid to the applicability of BET for membrane fouling characterization. The formation of a fouling layer was detected as an increase in cumulative pore volumes and pore areas in the meso-pores region. Pore blocking was seen as disappearance of meso-pores and micro-pores. The results indicate that the presented approach of using BET analysis combined with IR spectroscopy can provide complementary information revealing both the structure of fouling layer and the chemical nature of foulants.
Quantum dynamics studies of isotope effects in the Mg+(3p) + HD → MgH+/MgD+ + D/H insertion reaction
Authors: Mao Ye , Yuan Jiuchuang , Yang Zijiang , Chen Maodu 
Published: February 2020

AbstractThe time-dependent wave packet quantum dynamics studies for the Mg+(3p) + HD → MgH+/MgD+ + D/H diabatic reaction are carried out for the first time on recently developed diabatic YHWCH potential energy surfaces [Phys. Chem. Chem. Phys., 2018, 20, 6638–6647]. The results of reaction probabilities and total integral cross sections show a dramatic preference to the formation of MgD+ over MgH+ owing to the insertion reaction mechanism in the title reaction. The MgD+/MgH+ branching ratio witnesses a monotonic decrease from 10.58 to 3.88 at collision energy range of 0.01 to 0.20  eV, and at the collision energy of 0.114  eV, it is close to the experimental value of 5. The rovibrational state-resolved ICSs of the two channels show the products MgD+ have higher vibrational excitation and hotter rotational state distributions. The opacity function P(J) suggests that the MgH+ + D channel and MgD+ + H channel are dominated by high-b and low-b collisions, respectively. Both forward and backward scattering peaks are found in the differential cross section curves, whereas the angle distributions of products are not strictly forward-backward symmetric because of the short lifetime of the complex in the reaction.
New perspectives on analysing data from biological collections based on social network analytics
Authors: de Siracusa Pedro C. , Gadelha Luiz M. R. , Ziviani Artur 
Published: February 2020

AbstractBiological collections have been historically regarded as fundamental sources of scientific information on biodiversity. They are commonly associated with a variety of biases, which must be characterized and mitigated before data can be consumed. In this work, we are motivated by taxonomic and collector biases, which can be understood as the effect of particular recording preferences of key collectors on shaping the overall taxonomic composition of biological collections they contribute to. In this context, we propose two network models as the first steps towards a network-based conceptual framework for understanding the formation of biological collections as a result of the composition of collectors’ interests and activities. Building upon the defined network models, we present a case study in which we use our models to explore the community of collectors and the taxonomic composition of the University of Brasília herbarium. We describe topological features of the networks and point out some of the most relevant collectors in the biological collection as well as their taxonomic groups of interest. We also investigate their collaborative behaviour while recording specimens. Finally, we discuss future perspectives for incorporating temporal and geographical dimensions to the models. Moreover, we indicate some possible investigation directions that could benefit from our approach based on social network analytics to model and analyse biological collections.
Plasmonic Manipulation of DNA using a Combination of Optical and Thermophoretic Forces: Separation of Different-Sized DNA from Mixture Solution
Authors: Shoji Tatsuya , Itoh Kenta , Saitoh Junki , Kitamura Noboru , Yoshii Takahiro , Murakoshi Kei , Yamada Yuto , Yokoyama Tomohiro , Ishihara Hajime , Tsuboi Yasuyuki 
Published: February 2020

AbstractWe demonstrate the size-dependent separation and permanent immobilization of DNA on plasmonic substrates by means of plasmonic optical tweezers. We found that a gold nanopyramidal dimer array enhanced the optical force exerted on the DNA, leading to permanent immobilization of the DNA on the plasmonic substrate. The immobilization was realized by a combination of the plasmon-enhanced optical force and the thermophoretic force induced by a photothermal effect of the plasmons. In this study, we applied this phenomenon to the separation and fixation of size-different DNA. During plasmon excitation, DNA strands of different sizes became permanently immobilized on the plasmonic substrate forming micro-rings of DNA. The diameter of the ring was larger for longer DNA (in base pairs). When we used plasmonic optical tweezers to trap DNA of two different lengths dissolved in solution (φx DNA (5.4 kbp) and λ-DNA (48.5 kbp), or φx DNA and T4 DNA (166 kbp)), the DNA were immobilized, creating a double micro-ring pattern. The DNA were optically separated and immobilized in the double ring, with the shorter sized DNA and the larger one forming the smaller and larger rings, respectively. This phenomenon can be quantitatively explained as being due to a combination of the plasmon-enhanced optical force and the thermophoretic force. Our plasmonic optical tweezers open up a new avenue for the separation and immobilization of DNA, foreshadowing the emergence of optical separation and fixation of biomolecules such as proteins and other ncuelic acids.
The association of Chlamydia trachomatis and Mycoplasma genitalium infection with the vaginal metabolome
Authors: Borgogna Joanna-Lynn C. , Shardell Michelle D. , Yeoman Carl J. , Ghanem Khalil G. , Kadriu Herlin , Ulanov Alexander V. , Gaydos Charlotte A. , Hardick Justin , Robinson Courtney K. , Bavoil Patrik M. , Ravel Jacques , Brotman Rebecca M. , Tuddenham Susan 
Published: February 2020

AbstractChlamydia trachomatis (CT) and Mycoplasma genitalium (MG) are two highly prevalent bacterial sexually transmitted infections (STIs) with a significant rate of co-infection in some populations. Vaginal metabolites are influenced by resident vaginal microbiota, affect susceptibility to sexually transmitted infections (STIs), and may impact local inflammation and patient symptoms. Examining the vaginal metabolome in the context of CT mono (CT+) and CT/MG co-infection (CT+/MG+) may identify biomarkers for infection or provide new insights into disease etiology and pathogenesis. Yet, the vaginal metabolome in the setting of CT infection is understudied and the composition of the vaginal metabolome in CT/MG co-infected women is unknown. Therefore, in this analysis, we used an untargeted metabolomic approach combined with 16S rRNA gene amplicon sequencing to characterize the vaginal microbiota and metabolomes of CT+, CT+/MG+, and uninfected women. We found that CT+ and CT+/MG+ women had distinct vaginal metabolomic profiles as compared to uninfected women both before and after adjustment for the vaginal microbiota. This study provides important foundational data documenting differences in the vaginal metabolome between CT+, CT+/MG+ and uninfected women. These data may guide future mechanistic studies that seek to provide insight into the pathogenesis of CT and CT/MG infections.
Aluminosilicate Nanocomposites from Incinerated Chinese Holy Joss Fly Ash: A Potential Nanocarrier for Drug Cargos
Authors: Ramanathan Santheraleka , Gopinath Subash C. B. , Md Arshad M. K. , Poopalan Prabakaran , Anbu Periasamy , Lakshmipriya Thangavel 
Published: February 2020

AbstractAn incredible amount of joss fly ash is produced from the burning of Chinese holy joss paper; thus, an excellent method of recycling joss fly ash waste to extract aluminosilicate nanocomposites is explored. The present research aims to introduce a novel method to recycle joss fly ash through a simple and straightforward experimental procedure involving acidic and alkaline treatments. The synthesized aluminosilicate nanocomposite was characterized to justify its structural and physiochemical characteristics. A morphological analysis was performed with field-emission transmission electron microscopy, and scanning electron microscopy revealed the size of the aluminosilicate nanocomposite to be ~25 nm, while also confirming a uniformly spherical-shaped nanostructure. The elemental composition was measured by energy dispersive spectroscopy and revealed the Si to Al ratio to be 13.24 to 7.96, showing the high purity of the extracted nanocomposite. The roughness and particle distribution were analyzed using atomic force microscopy and a zeta analysis. X-ray diffraction patterns showed a synthesis of faceted and cubic aluminosilicate crystals in the nanocomposites. The presence of silica and aluminum was further proven by X-ray photoelectron spectroscopy, and the functional groups were recognized through Fourier transform infrared spectroscopy. The thermal capacity of the nanocomposite was examined by a thermogravimetric analysis. In addition, the research suggested the promising application of aluminosilicate nanocomposites as drug carriers. The above was justified by an enzyme-linked apta-sorbent assay, which claimed that the limit of the aptasensing aluminosilicate-conjugated ampicillin was two-fold higher than that in the absence of the nanocomposite. The drug delivery property was further justified through an antibacterial analysis against Escherichia coli (gram-negative) and Bacillus subtilis (gram-positive).