bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel multi-target regression framework for time-series prediction of drug efficacy
Authors: Li Haiqing , Zhang Wei , Chen Ying , Guo Yumeng , Li Guo-Zheng , Zhu Xiaoxin 
Published: January 2017

AbstractExcavating from small samples is a challenging pharmacokinetic problem, where statistical methods can be applied. Pharmacokinetic data is special due to the small samples of high dimensionality, which makes it difficult to adopt conventional methods to predict the efficacy of traditional Chinese medicine (TCM) prescription. The main purpose of our study is to obtain some knowledge of the correlation in TCM prescription. Here, a novel method named Multi-target Regression Framework to deal with the problem of efficacy prediction is proposed. We employ the correlation between the values of different time sequences and add predictive targets of previous time as features to predict the value of current time. Several experiments are conducted to test the validity of our method and the results of leave-one-out cross-validation clearly manifest the competitiveness of our framework. Compared with linear regression, artificial neural networks, and partial least squares, support vector regression combined with our framework demonstrates the best performance, and appears to be more suitable for this task.
Wind Wave Behavior in Fetch and Depth Limited Estuaries
Authors: Karimpour Arash , Chen Qin , Twilley Robert R. 
Published: January 2017

AbstractWetland dominated estuaries serve as one of the most productive natural ecosystems through their ecological, economic and cultural services, such as nursery grounds for fisheries, nutrient sequestration, and ecotourism. The ongoing deterioration of wetland ecosystems in many shallow estuaries raises concerns about the contributing erosive processes and their roles in restraining coastal restoration efforts. Given the combination of wetlands and shallow bays as landscape components that determine the function of estuaries, successful restoration strategies require knowledge of wind wave behavior in fetch and depth limited water as a critical design feature. We experimentally evaluate physics of wind wave growth in fetch and depth limited estuaries. We demonstrate that wave growth rate in shallow estuaries is a function of wind fetch to water depth ratio, which helps to develop a new set of parametric wave growth equations. We find that the final stage of wave growth in shallow estuaries can be presented by a product of water depth and wave number, whereby their product approaches 1.363 as either depth or wave energy increases. Suggested wave growth equations and their asymptotic constraints establish the magnitude of wave forces acting on wetland erosion that must be included in ecosystem restoration design.
Hydrocarbons in phlogopite from Kasenyi kamafugitic rocks (SW Uganda): cross-correlated AFM, confocal microscopy and Raman imaging
Authors: Moro Daniele , Valdrè Giovanni , Mesto Ernesto , Scordari Fernando , Lacalamita Maria , Ventura Giancarlo Della , Bellatreccia Fabio , Scirè Salvatore , Schingaro Emanuela 
Published: January 2017

AbstractThis study presents a cross-correlated surface and near surface investigation of two phlogopite polytypes from Kasenyi kamafugitic rocks (SW Uganda) by means of advanced Atomic Force Microscopy (AFM), confocal microscopy and Raman micro-spectroscopy. AFM revealed comparable nanomorphology and electrostatic surface potential for the two mica polytypes. A widespread presence of nano-protrusions located on the mica flake surface was also observed, with an aspect ratio (maximum height/maximum width) from 0.01 to 0.09. Confocal microscopy showed these features to range from few nm to several μm in dimension, and shapes from perfectly circular to ellipsoidic and strongly elongated. Raman spectra collected across the bubbles showed an intense and convolute absorption in the range 3000–2800 cm−1, associated with weaker bands at 1655, 1438 and 1297 cm−1, indicating the presence of fluid inclusions consisting of aliphatic hydrocarbons, alkanes and cycloalkanes, with minor amounts of oxygenated compounds, such as carboxylic acids. High-resolution Raman images provided evidence that these hydrocarbons are confined within the bubbles. This work represents the first direct evidence that phlogopite, a common rock-forming mineral, may be a possible reservoir for hydrocarbons.
Electrocatalytic activity of lithium polysulfides adsorbed into porous TiO2 coated MWCNTs hybrid structure for lithium-sulfur batteries
Authors: He Xiulin , Hou Huijie , Yuan Xiqing , Huang Long , Hu Jingping , Liu Bingchuan , Xu Jingyi , Xie Jia , Yang Jiakuan , Liang Sha , Wu Xu 
Published: January 2017

AbstractLithium-sulfur batteries have attracted great attention because of their high energy density, environmental friendliness, natural abundance and intrinsically low cost of sulfur. However, their commercial applications are greatly hindered by rapid capacity decay due to poor conductivity of electrode, fast dissolution of the intermediate polysulfides into the electrolyte, and the volume expansion of sulfur. Herein, we report a novel composite MWCNTs@TiO2-S nanostructure by grafting TiO2 onto the surface of MWCNTs, followed by incorporating sulfur into the composite. The inner MWCNTs improved the mechanical strength and conductivity of the electrode and the outer TiO2 provided the adsorption sites to immobilize polysulfides due to bonding interaction between TiO2 and polysulfides. The MWCNTs@TiO2-S composite with a mass ratio of 50% (MWCNTs in MWCNTs@TiO2) exhibited the highest electrochemistry performance among all compositing ratios of MWCNTs/TiO2. The performance improvement might be attributed to the downward shift of the apparent Fermi level to a more positive potential and electron rich space region at the interface of MWCNTs-TiO2 that facilitates the reduction of lithium polysulfide at a higher potential. Such a novel hybrid structure can be applicable for electrode design in other energy storage applications.
Seasonal and regional presence of hymenopteran parasitoids of Drosophila in Switzerland and their ability to parasitize the invasive Drosophila suzukii
Authors: Knoll Valery , Ellenbroek Thomas , Romeis Jörg , Collatz Jana 
Published: January 2017

AbstractSince its introduction into Europe the invasive Drosophila suzukii has established and spread widely, thereby entering habitats populated by native Drosophila species and their natural enemies. The highly prolific D. suzukii will likely interact with these species as a competitor, host or prey. To investigate potential interactions of D. suzukii with parasitoids, a field survey was conducted across several fruit-growing regions in Switzerland in two consecutive years. Eight species of hymenopteran parasitoids were collected using D. melanogaster as sentinel hosts in field-traps. Parasitoid capture was much higher in 2015 than in 2014 and varied among regions, time of the growing season, and habitat type. Laboratory no-choice assays with the field-collected species demonstrated that the larval parasitoids Asobara tabida, Leptopilina boulardi, and L. heterotoma could not use D. suzukii for reproduction, although the latter two reduced the number of emerging D. suzukii. In contrast, the pupal parasitoids Pachycrepoideus vindemmiae, Trichopria drosophilae, Vrestovia fidenas and Spalangia erythromera all developed with D. suzukii as hosts. Regional differences between strains were generally not evident, with the exception of two T. drosophilae strains that differed in parasitization rate. Thus, native parasitoids may interact with D. suzukii and should be regarded when implementing pest control measures.
High Efficiency Hydrodynamic DNA Fragmentation in a Bubbling System
Authors: Li Lanhui , Jin Mingliang , Sun Chenglong , Wang Xiaoxue , Xie Shuting , Zhou Guofu , van den Berg Albert , Eijkel Jan C. T. , Shui Lingling 
Published: January 2017

AbstractDNA fragmentation down to a precise fragment size is important for biomedical applications, disease determination, gene therapy and shotgun sequencing. In this work, a cheap, easy to operate and high efficiency DNA fragmentation method is demonstrated based on hydrodynamic shearing in a bubbling system. We expect that hydrodynamic forces generated during the bubbling process shear the DNA molecules, extending and breaking them at the points where shearing forces are larger than the strength of the phosphate backbone. Factors of applied pressure, bubbling time and temperature have been investigated. Genomic DNA could be fragmented down to controllable 1–10 Kbp fragment lengths with a yield of 75.30–91.60%. We demonstrate that the ends of the genomic DNAs generated from hydrodynamic shearing can be ligated by T4 ligase and the fragmented DNAs can be used as templates for polymerase chain reaction. Therefore, in the bubbling system, DNAs could be hydrodynamically sheared to achieve smaller pieces in dsDNAs available for further processes. It could potentially serve as a DNA sample pretreatment technique in the future.
Enhanced removal of As (V) from aqueous solution using modified hydrous ferric oxide nanoparticles
Authors: Huo Lijuan , Zeng Xibai , Su Shiming , Bai Lingyu , Wang Yanan 
Published: January 2017

AbstractHydrous ferric oxide (HFO) is most effective with high treatment capacity on arsenate [As(V)] sorption although its transformation and aggregation nature need further improvement. Here, HFO nanoparticles with carboxymethyl cellulose (CMC) or starch as modifier was synthesized for the purpose of stability improvement and As(V) removal from water. Comparatively, CMC might be the optimum stabilizer for HFO nanoparticles because of more effective physical and chemical stability. The large-pore structure, high surface specific area, and the non-aggregated nature of CMC-HFO lead to increased adsorption sites, and thus high adsorption capacities of As(V) without pre-treatment (355 mg·g−1), which is much greater than those reported in previous studies. Second-order equation and dual-mode isotherm model could be successfully used to interpret the sorption kinetics and isotherms of As(V), respectively. FTIR, XPS and XRD analyses suggested that precipitation and surface complexation were primary mechanisms for As(V) removal by CMC modified HFO nanoparticles. A surface complexation model (SCM) was used to simulate As adsorption over pH 2.5–10.4. The predominant adsorbed arsenate species were modeled as bidentate binuclear surface complexes at low pH and as monodentate complexes at high pH. The immobilized arsenic remained stable when aging for 270 d at room temperature.
Deep-sea crustacean trawling fisheries in Portugal: quantification of effort and assessment of landings per unit effort using a Vessel Monitoring System (VMS)
Authors: Bueno-Pardo Juan , Ramalho Sofia P. , García-Alegre Ana , Morgado Mariana , Vieira Rui P. , Cunha Marina R. , Queiroga Henrique 
Published: January 2017

AbstractMapping and quantifying bottom trawling fishing pressure on the seafloor is pivotal to understand its effects on deep-sea benthic habitats. Using data from the Vessel Monitoring System of crustacean trawlers along the Portuguese margin, we have identified the most exploited areas and characterized the most targeted habitats and water depths. We estimated a total trawling effort of 69596, 66766, and 63427 h y−1 for the years 2012, 2013, and 2014 respectively which, considering the total landings estimated for this gear, yield values of 20.76, 21.06, and 19.11 kg of landed fish per trawled hour. The main trawling pressure is exerted in the South and Southwest Portuguese margins, on muddy and muddy-sand bottoms between 200 and 700 m water depths, while in the North and Central-West coasts a minor effort, at shallower waters and across a wider range of habitats, is also applied. The most landed species are crustaceans such as rose shrimp and Norway lobster, although this varies importantly between the different regions of Portugal, being fish and cephalopods the main captures in the Northern ports. We discuss the consequences of trawling for the impacted communities as well as the characteristics of the commercialization of these captures in Portugal.
Solving Large-Scale Inverse Magnetostatic Problems using the Adjoint Method
Authors: Bruckner Florian , Abert Claas , Wautischer Gregor , Huber Christian , Vogler Christoph , Hinze Michael , Suess Dieter 
Published: January 2017

AbstractAn efficient algorithm for the reconstruction of the magnetization state within magnetic components is presented. The occurring inverse magnetostatic problem is solved by means of an adjoint approach, based on the Fredkin-Koehler method for the solution of the forward problem. Due to the use of hybrid FEM-BEM coupling combined with matrix compression techniques the resulting algorithm is well suited for large-scale problems. Furthermore the reconstruction of the magnetization state within a permanent magnet as well as an optimal design application are demonstrated.
Cullin 7 mediates proteasomal and lysosomal degradations of rat Eag1 potassium channels
Authors: Hsu Po-Hao , Ma Yu-Ting , Fang Ya-Ching , Huang Jing-Jia , Gan Yu-Ling , Chang Pei-Tzu , Jow Guey-Mei , Tang Chih-Yung , Jeng Chung-Jiuan 
Published: January 2017

AbstractMammalian Eag1 (Kv10.1) potassium (K+) channels are widely expressed in the brain. Several mutations in the gene encoding human Eag1 K+ channel have been associated with congenital neurodevelopmental anomalies. Currently very little is known about the molecules mediating protein synthesis and degradation of Eag1 channels. Herein we aim to ascertain the protein degradation mechanism of rat Eag1 (rEag1). We identified cullin 7 (Cul7), a member of the cullin-based E3 ubiquitin ligase family, as a novel rEag1 binding partner. Immunoprecipitation analyses confirmed the interaction between Cul7 and rEag1 in heterologous cells and neuronal tissues. Cul7 and rEag1 also exhibited significant co-localization at synaptic regions in neurons. Over-expression of Cul7 led to reduced protein level, enhanced ubiquitination, accelerated protein turn-over, and decreased current density of rEag1 channels. We provided further biochemical and morphological evidence suggesting that Cul7 targeted endoplasmic reticulum (ER)- and plasma membrane-localized rEag1 to the proteasome and the lysosome, respectively, for protein degradation. Cul7 also contributed to protein degradation of a disease-associated rEag1 mutant. Together, these results indicate that Cul7 mediates both proteasomal and lysosomal degradations of rEag1. Our findings provide a novel insight to the mechanisms underlying ER and peripheral protein quality controls of Eag1 channels.
Climate change influences on crop mix shifts in the United States
Authors: Cho Sung Ju , McCarl Bruce A. 
Published: January 2017

AbstractWe examine the impact of current and future climate on crop mixes over space in the US. We find using historical data that temperature and precipitation are among the causal factors for shits in crop production location and mixes, with some crops being more sensitive than others. In particular, we find that when temperature rises, cotton, rice, sorghum and winter wheat are more likely to be chosen. We also find that barley, sorghum, winter wheat, spring wheat and hay are more likely to be chosen as regions become drier, and corn, cotton, rice and soybeans are more likely to be selected in wetter regions. Additionally, we assess how much of the observed crop mix shifts between 1970 and 2010 were contributed to by climate change. There we find climate explains about 7–50% of the shift in latitude, 20–36% in longitude and 4–28% of that in elevation. Finally, we estimate climate change impacts on future crop mix under CMIP5 scenarios. There we find shifts in US production regions for almost all major crops with the movement north and east. The estimates describe how the farmers respond to altering climate and can be used for planning future crop allocations.
Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression
Authors: Ma Ding , Yang Laurence , Fleming Ronan M. T. , Thiele Ines , Palsson Bernhard O. , Saunders Michael A. 
Published: January 2017

AbstractConstraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many orders of magnitude. Data values also have greatly varying magnitudes. Standard double-precision solvers may return inaccurate solutions or report that no solution exists. Exact simplex solvers based on rational arithmetic require a near-optimal warm start to be practical on large problems (current ME models have 70,000 constraints and variables and will grow larger). We have developed a quadruple-precision version of our linear and nonlinear optimizer MINOS, and a solution procedure (DQQ) involving Double and Quad MINOS that achieves reliability and efficiency for ME models and other challenging problems tested here. DQQ will enable extensive use of large linear and nonlinear models in systems biology and other applications involving multiscale data.
Combined LRRK2 mutation, aging and chronic low dose oral rotenone as a model of Parkinson’s disease
Authors: Liu Hui-Fang , Ho Philip Wing-Lok , Leung Gideon Chi-Ting , Lam Colin Siu-Chi , Pang Shirley Yin-Yu , Li Lingfei , Kung Michelle Hiu-Wai , Ramsden David Boyer , Ho Shu-Leong 
Published: January 2017

AbstractAging, genetics and environmental toxicity are important etiological factors in Parkinson’s disease (PD). However, its pathogenesis remains unclear. A major obstacle is the lack of an appropriate experimental model which incorporates genetic susceptibility, aging and prolonged environmental toxicity. Here, we explored the interplay amongst these factors using mutant LRRK2R1441G (leucine-rich-repeat-kinase-2) knockin mice. We found that mutant primary cortical and mesencephalic dopaminergic neurons were more susceptible to rotenone-induced ATP deficiency and cell death. Compared with wild-type controls, striatal synaptosomes isolated from young mutant mice exhibited significantly lower dopamine uptake after rotenone toxicity, due to reduced striatal synaptosomal mitochondria and synaptic vesicular proton pump protein (V-ATPase H) levels. Mutant mice developed greater locomotor deficits in open-field tests than wild-type mice following low oral rotenone doses given twice weekly over 50 weeks (half their lifespan). The increased locomotor deficit was associated with specific reduction in striatal mitochondrial Complex-I (NDUFS4) in rotenone-treated mutant but not in similarly treated wild-type mice. Our unique experimental model which incorporates genetic effect, natural aging and prolonged oral environmental toxicity administered to mutant knockin LRRK2 mice over half their life span, with observable and measurable phenotype, is invaluable in further studies of the pathogenic process and therapeutics of PD.
Unsaturated lipid bodies as a hallmark of inflammation studied by Raman 2D and 3D microscopy
Authors: Czamara K. , Majzner K. , Selmi A. , Baranska M. , Ozaki Y. , Kaczor A. 
Published: January 2017

AbstractEndothelial HMEC-1 cells incubated with pro-inflammatory cytokine TNF-α for 6 and 24 hours were studied as a model of inflammation using Raman imaging. Striking changes in distribution, composition and concentration of cellular lipids were observed after exposure to TNF-α compared to the control. In particular, 3D Raman imaging revealed a significant increase in the amount of lipid entities formed under inflammation. Lipid bodies were randomly distributed in the cytoplasm and two types of droplets were assembled: more saturated one, in spectral characteristics resembling phosphatidylcholine and saturated cholesteryl esters, observed also in the control, and highly unsaturated one, containing also cholesterols, being a hallmark of inflamed cells. The statistical analysis showed that the number of lipid bodies was significantly dependent on the exposure time to TNF-α. Overall, observed formation of unsaturated lipid droplets can be directly correlated with the increase in production of prostacyclins - endogenous inflammation mediators.
Wafer-scale Thermodynamically Stable GaN Nanorods via Two-Step Self-Limiting Epitaxy for Optoelectronic Applications
Authors: Kum Hyun , Seong Han-Kyu , Lim Wantae , Chun Daemyung , Kim Young-il , Park Youngsoo , Yoo Geonwook 
Published: January 2017

AbstractWe present a method of epitaxially growing thermodynamically stable gallium nitride (GaN) nanorods via metal-organic chemical vapor deposition (MOCVD) by invoking a two-step self-limited growth (TSSLG) mechanism. This allows for growth of nanorods with excellent geometrical uniformity with no visible extended defects over a 100 mm sapphire (Al2O3) wafer. An ex-situ study of the growth morphology as a function of growth time for the two self-limiting steps elucidate the growth dynamics, which show that formation of an Ehrlich-Schwoebel barrier and preferential growth in the c-plane direction governs the growth process. This process allows monolithic formation of dimensionally uniform nanowires on templates with varying filling matrix patterns for a variety of novel electronic and optoelectronic applications. A color tunable phosphor-free white light LED with a coaxial architecture is fabricated as a demonstration of the applicability of these nanorods grown by TSSLG.
Direct Observation of the Layer-by-Layer Growth of ZnO Nanopillar by In situ High Resolution Transmission Electron Microscopy
Authors: Li Xing , Cheng Shaobo , Deng Shiqing , Wei Xianlong , Zhu Jing , Chen Qing 
Published: January 2017

AbstractCatalyst-free methods are important for the fabrication of pure nanowires (NWs). However, the growth mechanism remains elusive due to the lack of crucial information on the growth dynamics at atomic level. Here, the noncatalytic growth process of ZnO NWs is studied through in situ high resolution transmission electron microscopy. We observe the layer-by-layer growth of ZnO nanopillars along the polar [0001] direction under electron beam irradiation, while no growth is observed along the radial directions, indicating an anisotropic growth mechanism. The source atoms are mainly from the electron beam induced damage of the sample and the growth is assisted by subsequent absorption and then diffusion of atoms along the side "Equation missing" surface to the top (0002) surface. The different binding energy on different ZnO surface is the main origin for the anisotropic growth. Additionally, the coalescence of ZnO nanocrystals related to the nucleation stage is uncovered to realize through the rotational motions and recrystallization. Our in situ results provide atomic-level detailed information about the dynamic growth and coalescence processes in the noncatalytic synthesis of ZnO NW and are helpful for understanding the vapor-solid mechanism of catalyst-free NW growth.