bluuebunny/crossref_metadata_2025 huggingface dataset:
Discovery of parvovirus-related sequences in an unexpected broad range of animals
Authors: François S. , Filloux D. , Roumagnac P. , Bigot D. , Gayral P. , Martin D. P. , Froissart R. , Ogliastro M.
Published: September 2016

Our knowledge of the genetic diversity and host ranges of viruses is fragmentary. This is particularly true for the Parvoviridae family. Genetic diversity studies of single stranded DNA viruses within this family have been largely focused on arthropod- and vertebrate-infecting species that cause diseases of humans and our domesticated animals: a focus that has biased our perception of parvovirus diversity. While metagenomics approaches could help rectify this bias, so too could transcriptomics studies. Large amounts of transcriptomic data are available for a diverse array of animal species and whenever this data has inadvertently been gathered from virus-infected individuals, it could contain detectable viral transcripts. We therefore performed a systematic search for parvovirus-related sequences (PRSs) within publicly available transcript, genome and protein databases and eleven new transcriptome datasets. This revealed 463 PRSs in the transcript databases of 118 animals. At least 41 of these PRSs are likely integrated within animal genomes in that they were also found within genomic sequence databases. Besides illuminating the ubiquity of parvoviruses, the number of parvoviral sequences discovered within public databases revealed numerous previously unknown parvovirus-host combinations; particularly in invertebrates. Our findings suggest that the host-ranges of extant parvoviruses might span the entire animal kingdom.
Light-induced rotations of chiral birefringent microparticles in optical tweezers
Authors: Donato M. G. , Mazzulla A. , Pagliusi P. , Magazzù A. , Hernandez R. J. , Provenzano C. , Gucciardi P. G. , Maragò O. M. , Cipparrone G.
Published: September 2016

We study the rotational dynamics of solid chiral and birefringent microparticles induced by elliptically polarized laser light in optical tweezers. We find that both reflection of left circularly polarized light and residual linear retardance affect the particle dynamics. The degree of ellipticity of laser light needed to induce rotations is found. The experimental results are compared with analytical calculations of the transfer of angular moment from elliptically polarized light to chiral birefringent particles.
Camouflage and Clutch Survival in Plovers and Terns
Authors: Stoddard Mary Caswell , Kupán Krisztina , Eyster Harold N. , Rojas-Abreu Wendoly , Cruz-López Medardo , Serrano-Meneses Martín Alejandro , Küpper Clemens
Published: September 2016

Animals achieve camouflage through a variety of mechanisms, of which background matching and disruptive coloration are likely the most common. Although many studies have investigated camouflage mechanisms using artificial stimuli and in lab experiments, less work has addressed camouflage in the wild. Here we examine egg camouflage in clutches laid by ground-nesting Snowy Plovers Charadrius nivosus and Least Terns Sternula antillarum breeding in mixed aggregations at Bahía de Ceuta, Sinaloa, Mexico. We obtained digital images of clutches laid by both species. We then calibrated the images and used custom computer software and edge detection algorithms to quantify measures related to three potential camouflage mechanisms: pattern complexity matching, disruptive effects and background color matching. Based on our image analyses, Snowy Plover clutches, in general, appeared to be more camouflaged than Least Tern clutches. Snowy Plover clutches also survived better than Least Tern clutches. Unexpectedly, variation in clutch survival was not explained by any measure of egg camouflage in either species. We conclude that measures of egg camouflage are poor predictors of clutch survival in this population. The behavior of the incubating parents may also affect clutch predation. Determining the significance of egg camouflage requires further testing using visual models and behavioral experiments.
Probing the causal role of prestimulus interregional synchrony for perceptual integration via tACS
Authors: Stonkus Rolandas , Braun Verena , Kerlin Jess R. , Volberg Gregor , Hanslmayr Simon
Published: September 2016

The phase of prestimulus oscillations at 7–10 Hz has been shown to modulate perception of briefly presented visual stimuli. Specifically, a recent combined EEG-fMRI study suggested that a prestimulus oscillation at around 7 Hz represents open and closed windows for perceptual integration by modulating connectivity between lower order occipital and higher order parietal brain regions. We here utilized brief event-related transcranial alternating current stimulation (tACS) to specifically modulate this prestimulus 7 Hz oscillation, and the synchrony between parietal and occipital brain regions. To this end we tested for a causal role of this particular prestimulus oscillation for perceptual integration. The EEG was acquired at the same time allowing us to investigate frequency specific after effects phase-locked to stimulation offset. On a behavioural level our results suggest that tACS did modulate perceptual integration, however, in an unexpected manner. On an electrophysiological level our results suggest that brief tACS does induce oscillatory entrainment, as visible in frequency specific activity phase-locked to stimulation offset. Together, our results do not strongly support a causal role of prestimulus 7 Hz oscillations for perceptual integration. However, our results suggest that brief tACS is capable of modulating oscillatory activity in a temporally sensitive manner.
Quantifying evolutionary dynamics from variant-frequency time series
Authors: Khatri Bhavin S.
Published: September 2016

From Kimura’s neutral theory of protein evolution to Hubbell’s neutral theory of biodiversity, quantifying the relative importance of neutrality versus selection has long been a basic question in evolutionary biology and ecology. With deep sequencing technologies, this question is taking on a new form: given a time-series of the frequency of different variants in a population, what is the likelihood that the observation has arisen due to selection or neutrality? To tackle the 2-variant case, we exploit Fisher’s angular transformation, which despite being discovered by Ronald Fisher a century ago, has remained an intellectual curiosity. We show together with a heuristic approach it provides a simple solution for the transition probability density at short times, including drift, selection and mutation. Our results show under that under strong selection and sufficiently frequent sampling these evolutionary parameters can be accurately determined from simulation data and so they provide a theoretical basis for techniques to detect selection from variant or polymorphism frequency time-series.
Low serum magnesium levels are associated with impaired peripheral nerve function in type 2 diabetic patients
Authors: Chu Chen , Zhao Weijing , Zhang Yinan , Li Lu , Lu Jingyi , Jiang Lan , Wang Congrong , Jia Weiping
Published: September 2016

The aim of this study was to explore the relationship between serum magnesium and peripheral nerve function in patients with type 2 diabetes (T2DM). A total of 978 T2DM patients were included in the study. Patients were divided into tertiles according to serum magnesium concentration (low tertile: ≤0.85 mmol/L; medium tertile: 0.85 to 0.92 mmol/L; and high tertile: >0.92 mmol/L). All participants underwent nerve conduction (NC) studies. Composite z scores of conduction velocity, latency, and amplitude were constructed, respectively. The serum magnesium levels were significantly lower in patients with abnormal NC than in those with normal NC (0.87 [0.82, 0.92] vs. 0.88 [0.83, 0.93] mmol/L, P = 0.048). The composite z score of amplitude significantly increased with increasing tertiles of magnesium (−0.60 ± 0.02 vs. −0.57 ± 0.02 vs. −0.48 ± 0.03, P for trend = 0.001). After adjusting for all potential confounders, lower serum magnesium levels were still associated with lower composite z score of amplitude (β = 0.095, P = 0.014). In patients with T2DM, lower serum magnesium levels were significantly associated with lower composite z score of amplitude, indicating magnesium might affect peripheral nerve function through axonal degeneration.
Elucidating the Performance Limitations of Lithium-ion Batteries due to Species and Charge Transport through Five Characteristic Parameters
Authors: Jiang Fangming , Peng Peng
Published: September 2016

Underutilization due to performance limitations imposed by species and charge transports is one of the key issues that persist with various lithium-ion batteries. To elucidate the relevant mechanisms, two groups of characteristic parameters were proposed. The first group contains three characteristic time parameters, namely: (1) te, which characterizes the Li-ion transport rate in the electrolyte phase, (2) ts, characterizing the lithium diffusion rate in the solid active materials, and (3) tc, describing the local Li-ion depletion rate in electrolyte phase at the electrolyte/electrode interface due to electrochemical reactions. The second group contains two electric resistance parameters: Re and Rs, which represent respectively, the equivalent ionic transport resistance and the effective electronic transport resistance in the electrode. Electrochemical modeling and simulations to the discharge process of LiCoO2 cells reveal that: (1) if te, ts and tc are on the same order of magnitude, the species transports may not cause any performance limitations to the battery; (2) the underlying mechanisms of performance limitations due to thick electrode, high-rate operation, and large-sized active material particles as well as effects of charge transports are revealed. The findings may be used as quantitative guidelines in the development and design of more advanced Li-ion batteries.
Deep Networks Can Resemble Human Feed-forward Vision in Invariant Object Recognition
Authors: Kheradpisheh Saeed Reza , Ghodrati Masoud , Ganjtabesh Mohammad , Masquelier Timothée
Published: September 2016

Deep convolutional neural networks (DCNNs) have attracted much attention recently, and have shown to be able to recognize thousands of object categories in natural image databases. Their architecture is somewhat similar to that of the human visual system: both use restricted receptive fields, and a hierarchy of layers which progressively extract more and more abstracted features. Yet it is unknown whether DCNNs match human performance at the task of view-invariant object recognition, whether they make similar errors and use similar representations for this task, and whether the answers depend on the magnitude of the viewpoint variations. To investigate these issues, we benchmarked eight state-of-the-art DCNNs, the HMAX model, and a baseline shallow model and compared their results to those of humans with backward masking. Unlike in all previous DCNN studies, we carefully controlled the magnitude of the viewpoint variations to demonstrate that shallow nets can outperform deep nets and humans when variations are weak. When facing larger variations, however, more layers were needed to match human performance and error distributions, and to have representations that are consistent with human behavior. A very deep net with 18 layers even outperformed humans at the highest variation level, using the most human-like representations.
Silver-nanoparticles-modified biomaterial surface resistant to staphylococcus: new insight into the antimicrobial action of silver
Authors: Wang Jiaxing , Li Jinhua , Guo Geyong , Wang Qiaojie , Tang Jin , Zhao Yaochao , Qin Hui , Wahafu Tuerhongjiang , Shen Hao , Liu Xuanyong , Zhang Xianlong
Published: September 2016

Titanium implants are widely used clinically, but postoperative implant infection remains a potential severe complication. The purpose of this study was to investigate the antibacterial activity of nano-silver(Ag)-functionalized Ti surfaces against epidemic Staphylococcus from the perspective of the regulation of biofilm-related genes and based on a bacteria-cell co-culture study. To achieve this goal, two representative epidemic Staphylococcus strains, Staphylococcus epidermidis (S. epidermidis, RP62A) and Staphylococcus aureus (S. aureus, USA 300), were used, and it was found that an Ag-nanoparticle-modified Ti surface could regulate the expression levels of biofilm-related genes (icaA and icaR for S. epidermidis; fnbA and fnbB for S. aureus) to inhibit bacterial adhesion and biofilm formation. Moreover, a novel bacteria-fibroblast co-culture study revealed that the incorporation of Ag nanoparticles on such a surface can help mammalian cells to survive, adhere and spread more successfully than Staphylococcus. Therefore, the modified surface was demonstrated to possess a good anti-infective capability against both sessile bacteria and planktonic bacteria through synergy between the effects of Ag nanoparticles and ion release. This work provides new insight into the antimicrobial action and mechanism of Ag-nanoparticle-functionalized Ti surfaces with bacteria-killing and cell-assisting capabilities and paves the way towards better satisfying the clinical needs.
Association between ABCB1 polymorphisms and haplotypes and Alzheimer’s disease: a meta-analysis
Authors: Zhong Xin , Liu Ming-Yan , Sun Xiao-Hong , Wei Min-Jie
Published: September 2016

Although several epidemiological studies have investigated the association between ATP-binding cassette subfamily B member 1 (ABCB1) gene polymorphisms and Alzheimer’s disease (AD) susceptibility, controversial results exist. Here, we performed a meta-analysis to assess whether ABCB1 polymorphisms 3435C > T (rs1045642), 2677G > T/A (rs2032582), 1236C > T (rs1128503) and haplotypes were associated with AD risk. Nine independent publications were included and analyzed. Crude odds ratio (OR) and 95% confidence interval (CI) were applied to investigate the strength of the association. Sensitivity analysis was conducted to measure the robustness of our analysis. A funnel plot and trim and fill method were used to test and adjust for publication bias. The results showed a significant association between the 3435C > T single nucleotide polymorphism (SNP) and AD susceptibility (CT vs. CC: OR = 1.24, 95% CI = 1.06–1.45, P = 0.01; CT + TT vs. CC: OR = 1.21, 95% CI = 1.04–1.41, P = 0.01) in the total population, as well as in Caucasian subgroup. The 2677G > T/A SNP was related to a decreased AD risk in Caucasian subgroup (TT + TA + AA vs. GT + GA + GG: OR = 0.68, 95% CI = 0.47–0.98, P = 0.04). Moreover, the ABCB1 haplotype analysis showed that the 1236T/2677T/3435C haplotype was associated with a higher risk of AD (OR = 1.99, 95% CI = 1.24–3.18, P = 0.00). Our results suggest that the ABCB1 3435C > T SNP, the 2677G > T/A SNP and 1236T/2677T/3435C haplotype are significantly associated with AD susceptibility.
Origin of the low critical observing temperature of the quantum anomalous Hall effect in V-doped (Bi, Sb)2Te3 film
Authors: Li W. , Claassen M. , Chang Cui-Zu , Moritz B. , Jia T. , Zhang C. , Rebec S. , Lee J. J. , Hashimoto M. , Lu D.-H. , Moore R. G. , Moodera J. S. , Devereaux T. P. , Shen Z.-X.
Published: September 2016

The experimental realization of the quantum anomalous Hall (QAH) effect in magnetically-doped (Bi, Sb)2Te3 films stands out as a landmark of modern condensed matter physics. However, ultra-low temperatures down to few tens of mK are needed to reach the quantization of Hall resistance, which is two orders of magnitude lower than the ferromagnetic phase transition temperature of the films. Here, we systematically study the band structure of V-doped (Bi, Sb)2Te3 thin films by angle-resolved photoemission spectroscopy (ARPES) and show unambiguously that the bulk valence band (BVB) maximum lies higher in energy than the surface state Dirac point. Our results demonstrate clear evidence that localization of BVB carriers plays an active role and can account for the temperature discrepancy.
Clustering drug-drug interaction networks with energy model layouts: community analysis and drug repurposing
Authors: Udrescu Lucreţia , Sbârcea Laura , Topîrceanu Alexandru , Iovanovici Alexandru , Kurunczi Ludovic , Bogdan Paul , Udrescu Mihai
Published: September 2016

Analyzing drug-drug interactions may unravel previously unknown drug action patterns, leading to the development of new drug discovery tools. We present a new approach to analyzing drug-drug interaction networks, based on clustering and topological community detection techniques that are specific to complex network science. Our methodology uncovers functional drug categories along with the intricate relationships between them. Using modularity-based and energy-model layout community detection algorithms, we link the network clusters to 9 relevant pharmacological properties. Out of the 1141 drugs from the DrugBank 4.1 database, our extensive literature survey and cross-checking with other databases such as Drugs.com, RxList, and DrugBank 4.3 confirm the predicted properties for 85% of the drugs. As such, we argue that network analysis offers a high-level grasp on a wide area of pharmacological aspects, indicating possible unaccounted interactions and missing pharmacological properties that can lead to drug repositioning for the 15% drugs which seem to be inconsistent with the predicted property. Also, by using network centralities, we can rank drugs according to their interaction potential for both simple and complex multi-pathology therapies. Moreover, our clustering approach can be extended for applications such as analyzing drug-target interactions or phenotyping patients in personalized medicine applications.
Observations of internal flow inside an evaporating nanofluid sessile droplet in the presence of an entrapped air bubble
Authors: Shin Dong Hwan , Allen Jeffrey S. , Lee Seong Hyuk , Choi Chang Kyoung
Published: September 2016

Using a unique, near-field microscopy technique, fringe patterns and nanoparticle motions are visualized immediately following a nanofluid droplet deposition on a glass substrate in which an air bubble is entrapped. The nanofluid consists of DI-water, 0.10% Aluminum Oxide nanoparticles with an average diameter of 50 nm, and 0.0005% yellow-green polystyrene fluorescent particles of 1 μm diameter. High-speed, fluorescent-mode confocal imaging enables investigation of depth-wise sectioned particle movements in the nanofluid droplet inside which a bubble is entrapped. The static contact angle is increased when a bubble is applied. In the presence of the bubble in the droplet, the observed flow toward the center of the droplet is opposite to the flow observed in a droplet without the bubble. When the bubble is present, the evaporation process is retarded. Also, random motion is observed in the contact line region instead of the typical evaporation-driven flow toward the droplet edge. Once the bubble bursts, however, the total evaporation time decreases due to the change in the contact line characteristics. Moreover, the area of fringe patterns beneath the bubble increases with time. Discussed herein is a unique internal flow that has not been observed in nanofluid droplet evaporation.
Ammonia deposition in the neighbourhood of an intensive cattle feedlot in Victoria, Australia
Authors: Shen Jianlin , Chen Deli , Bai Mei , Sun Jianlei , Coates Trevor , Lam Shu Kee , Li Yong
Published: September 2016

Intensive cattle feedlots are large emission sources of ammonia (NH3), but NH3 deposition to the landscape downwind of feedlots is not well understood. We conducted the first study in Australia to measure NH3 dry deposition within 1 km of a commercial beef cattle feedlot in Victoria. NH3 concentrations and deposition fluxes decreased exponentially with distance away from the feedlot. The mean NH3 concentrations decreased from 419 μg N m−3 at 50 m to 36 μg N m−3 at 1 km, while the mean NH3 dry deposition fluxes decreased from 2.38 μg N m−2 s−1 at 50 m to 0.20 μg N m−2 s−1 at 1 km downwind from the feedlot. These results extrapolate to NH3 deposition of 53.9 tonne N yr−1 in the area within 1 km from the feedlot, or 67.5 kg N ha−1 yr−1 as an area-weighted mean, accounting for 8.1% of the annual NH3-N emissions from the feedlot. Thus NH3 deposition around feedlots is a significant nitrogen input for surrounding ecosystems. Researches need be conducted to evaluate the impacts of NH3 deposition on the surrounding natural or semi-naturals ecosystems and to reduce N fertilizer application rate for the surrounding crops by considering nitrogen input from NH3 deposition.
Quantum optical signatures in strong-field laser physics: Infrared photon counting in high-order-harmonic generation
Authors: Gonoskov I. A. , Tsatrafyllis N. , Kominis I. K. , Tzallas P.
Published: September 2016

We analytically describe the strong-field light-electron interaction using a quantized coherent laser state with arbitrary photon number. We obtain a light-electron wave function which is a closed-form solution of the time-dependent Schrödinger equation (TDSE). This wave function provides information about the quantum optical features of the interaction not accessible by semi-classical theories. With this approach we can reveal the quantum optical properties of high harmonic generation (HHG) process in gases by measuring the photon statistics of the transmitted infrared (IR) laser radiation. This work can lead to novel experiments in high-resolution spectroscopy in extreme-ultraviolet (XUV) and attosecond science without the need to measure the XUV light, while it can pave the way for the development of intense non-classical light sources.
Mechanistic insights from resolving ligand-dependent kinetics of conformational changes at ATP-gated P2X1R ion channels
Authors: Fryatt Alistair G. , Dayl Sudad , Cullis Paul M. , Schmid Ralf , Evans Richard J.
Published: September 2016

Structural studies of P2X receptors show a novel U shaped ATP orientation following binding. We used voltage clamp fluorometry (VCF) and molecular dynamics (MD) simulations to investigate agonist action. For VCF the P2X1 receptor (P2X1R) K190C mutant (adjacent to the agonist binding pocket) was labelled with the fluorophore MTS-TAMRA and changes in fluorescence on agonist treatment provided a real time measure of conformational changes. Studies with heteromeric channels incorporating a key lysine mutation (K68A) in the ATP binding site demonstrate that normally three molecules of ATP activate the receptor. The time-course of VCF responses to ATP, 2′-deoxy ATP, 3′-deoxy ATP, Ap5A and αβmeATP were agonist dependent. Comparing the properties of the deoxy forms of ATP demonstrated the importance of the 2′ hydroxyl group on the ribose ring in determining agonist efficacy consistent with MD simulations showing that it forms a hydrogen bond with the γ-phosphate oxygen stabilizing the U-shaped conformation. Comparison of the recovery of fluorescence on agonist washout, with channel activation to a second agonist application for the partial agonists Ap5A and αβmeATP, showed a complex relationship between conformational change and desensitization. These results highlight that different agonists induce distinct conformational changes, kinetics and recovery from desensitization at P2X1Rs.
Bamboo shoot fiber prevents obesity in mice by modulating the gut microbiota
Authors: Li Xiufen , Guo Juan , Ji Kailong , Zhang Ping
Published: September 2016

Dietary fiber has been shown to prevent high-fat diet induced obesity through modulating the gut microbiota; however, quality difference in fiber type is largely unknown. We performed a 6 week study on C57BL/6J mice fed a macronutrient matched high-fat diet with different fiber types including cellulose (HFC), bamboo shoot fiber (HFBS) and several other commonly consumed fibers. Our results showed that the HFBS group exhibited the lowest weight gain among all diet groups and had improved lipid profiles and glycemic control compared with the HFC group. As revealed by 16S rRNA gene sequencing, loss of diversity in the gut microbiota induced by the HFC diet was largely prevented by the HFBS diet. Moreover, compared with the HFC diet, the HFBS diet resulted in markedly increased relative abundance of Bacteroidetes and strong inhibition of Verrucomicrobia, two divisions strongly correlated with body weight. In conclusion, the present study provides evidence of a quality difference among different types of dietary fibers and shows that bamboo shoot fiber is the most effective in suppressing high-fat diet induced obesity. Our findings indicate that bamboo shoot fiber is a potential prebiotic fiber which modulates the gut microbiota and improves host metabolism.
High-temperature operation of broadband bidirectional terahertz quantum-cascade lasers
Authors: Khanal Sudeep , Gao Liang , Zhao Le , Reno John L. , Kumar Sushil
Published: September 2016

Terahertz quantum cascade lasers (QCLs) with a broadband gain medium could play an important role for sensing and spectroscopy since then distributed-feedback schemes could be utilized to produce laser arrays on a single semiconductor chip with wide spectral coverage. QCLs can be designed to emit at two different frequencies when biased with opposing electrical polarities. Here, terahertz QCLs with bidirectional operation are developed to achieve broadband lasing from the same semiconductor chip. A three-well design scheme with shallow-well GaAs/Al0.10Ga0.90As superlattices is developed to achieve high-temperature operation for bidirectional QCLs. It is shown that shallow-well heterostructures lead to optimal quantum-transport in the superlattice for bidirectional operation compared to the prevalent GaAs/Al0.15Ga0.85As material system. Broadband lasing in the frequency range of 3.1–3.7 THz is demonstrated for one QCL design, which achieves maximum operating temperatures of 147 K and 128 K respectively in opposing polarities. Dual-color lasing with large frequency separation is demonstrated for a second QCL, that emits at ~3.7 THz and operates up to 121 K in one polarity, and at ~2.7 THz up to 105 K in the opposing polarity. These are the highest operating temperatures achieved for broadband terahertz QCLs at the respective emission frequencies, and could lead to commercial development of broadband terahertz laser arrays.
Infiltrating cells from host brain restore the microglial population in grafted cortical tissue
Authors: Wang Cong , Tao Sijue , Fang Yukun , Guo Jing , Zhu Lirui , Zhang Shengxiang
Published: September 2016

Transplantation of embryonic cortical tissue is considered as a promising therapy for brain injury. Grafted neurons can reestablish neuronal network and improve cortical function of the host brain. Microglia is a key player in regulating neuronal survival and plasticity, but its activation and dynamics in grafted cortical tissue remain unknown. Using two-photon intravital imaging and parabiotic model, here we investigated the proliferation and source of microglia in the donor region by transplanting embryonic cortical tissue into adult cortex. Live imaging showed that the endogenous microglia of the grafted tissue were rapidly lost after transplantation. Instead, host-derived microglia infiltrated and colonized the graft. Parabiotic model suggested that the main source of infiltrating cells is the parenchyma of the host brain. Colonized microglia proliferated and experienced an extensive morphological transition and eventually differentiated into resting ramified morphology. Collectively, these results demonstrated that donor tissue has little contribution to the activated microglia and host brain controls the microglial population in the graft.
Factors associated with significant liver necroinflammation in chronic hepatitis B patients with cirrhosis
Authors: Chen Sheng-Sen , Yu Kang-Kang , Ling Qing-Xia , Huang Chong , Li Ning , Zheng Jian-Ming , Bao Su-Xia , Cheng Qi , Zhu Meng-Qi , Chen Ming-Quan
Published: September 2016

We determined the association between various clinical parameters and significant liver necroinflammation in patients with chronic hepatitis B (CHB) related cirrhosis. Two hundred patients with CHB related cirrhosis were recruited in the final analysis. Clinical laboratory values and characteristics were obtained from the medical record. We performed analyses of the relationships between independent variables and significant liver necroinflammation by using binary logistic regression analysis and discriminant analysis. Significant liver necroinflammation (grade≥2) was found in 58.0% (80/138) of antiviral therapy patients and 48.4% (30/62) of non antiviral therapy patients respectively. Also, there were some significant differences in serum hepatitis B surface antigen (HBsAg), serum hepatitis B e antigen (HBeAg) and serum hepatitis B virus (HBV) DNA between antiviral therapy and non antiviral therapy patients. After that, aspartate aminotransferase (AST), total bilirubin (TBIL), total bile acid (TBA), prothrombin time (PT), aspartate aminotransferase to platelet ratio index (APRI) and serum HBV DNA were confirmed as independent predictors of significant liver necroinflammation in CHB patients with cirrhosis by univariate analysis and multivariate analysis (p = 0.002, 0.044, 0.001, 0.014, 0.01 and 0.02 respectively). Finally, receiver operating characteristic (ROC) curve analysis and discriminant analysis validated that these six variables together have strong predictive power to evaluate significant liver necroinflammation.
Homogeneous diet of contemporary Japanese inferred from stable isotope ratios of hair
Authors: Kusaka Soichiro , Ishimaru Eriko , Hyodo Fujio , Gakuhari Takashi , Yoneda Minoru , Yumoto Takakazu , Tayasu Ichiro
Published: September 2016

The globalization of food production and distribution has homogenized human dietary patterns irrespective of geography, but it is uncertain how far this homogenization has progressed. This study investigated the carbon and nitrogen isotope ratios in the scalp hair of 1305 contemporary Japanese and found values of −19.4 ± 0.6‰ and 9.4 ± 0.6‰ (mean ± SD), respectively. Within Japan, the inter-regional differences for both isotope ratios was less than 1‰, which indicates low dietary heterogeneity among prefectural divisions. The carbon and nitrogen isotope ratios of the hair showed a significant correlation with the results of questionnaires on self-reported dietary habits. The carbon isotope ratios from Japan were lower than those in samples from the USA but higher than those in samples from Europe. These differences stem from the varying dietary proportions of food products originally derived from C3and C4plants. The dietary variation of Japan is as small as those of Europe and USA and smaller than those of some Asian countries. These results indicate that dietary homogeneity has progressed in Japan, which may indicate the influence from the spread of the Western-style diet and food globalization, although dietary heterogeneity among countries is still preserved.
Dynamics of surface evolution in semiconductor thin films grown from a chemical bath
Authors: Gupta Indu , Mohanty Bhaskar Chandra
Published: September 2016

Dynamics of surface evolution in CdS thin films grown by chemical bath deposition technique has been studied from time sequence of atomic force micrographs. Detailed scaling analysis of surface fluctuation in real and Fourier space yielded characteristic exponents αloc = 0.78 ± 0.07, α = 2.20 ± 0.08, αs = 1.49 ± 0.22, β = 0.86 ± 0.05 and βloc = 0.43 ± 0.10, which are very different from those predicted by the local growth models and are not related to any known universality classes. The observed anomalous scaling pattern, characterized by power law scaling dependence of interface width on deposition time differently at local and global scale, with rapid roughening of the growth front has been discussed to arise as a consequence of a nonlocal effect in the form of diffusional instability.
Grazing improves C and N cycling in the Northern Great Plains: a meta-analysis
Authors: Wang Xiaoyu , McConkey Brian G. , VandenBygaart A. J. , Fan Jianling , Iwaasa Alan , Schellenberg Mike
Published: September 2016

Grazing potentially alters grassland ecosystem carbon (C) and nitrogen (N) storage and cycles, however, the overall direction and magnitude of such alterations are poorly understood on the Northern Great Plains (NGP). By synthesizing data from multiple studies on grazed NGP ecosystems, we quantified the response of 30 variables to C and N pools and fluxes to grazing using a comprehensive meta-analysis method. Results showed that grazing enhanced soil C (5.2 ± 4.6% relative) and N (11.3 ± 9.1%) pools in the top layer, stimulated litter decomposition (26.8 ± 18.4%) and soil N mineralization (22.3 ± 18.4%) and enhanced soil NH4+(51.5 ± 42.9%) and NO3−(47.5 ± 20.7%) concentrations. Our results indicate that the NGP grasslands have sequestered C and N in the past 70 to 80 years, recovering C and N lost during a period of widespread grassland deterioration that occurred in the first half of the 20thcentury. Sustainable grazing management employed after this deterioration has acted as a critical factor for C and N amelioration of degraded NGP grasslands and about 5.84 Mg C ha−1CO2-equivalent of anthropogenic CO2emissions has been offset by these grassland soils.
STAR: a simple TAL effector assembly reaction using isothermal assembly
Authors: Gogolok Sabine , Garcia-Diaz Claudia , Pollard Steven M.
Published: September 2016

Transcription activator-like effectors (TALEs) contain modular programmable DNA binding domains. Fusing TALEs with effector domains creates synthetic transcription factors (TALE-TFs) or nucleases (TALENs), enabling precise gene manipulations. The construction of TALEs remains challenging due to their repetitive sequences. Here we report a simple TALE assembly reaction (STAR) that enables individual laboratories to generate multiple TALEs in a facile manner. STAR uses an isothermal assembly (‘Gibson assembly’) that is labour- and cost-effective, accessible, rapid and scalable. A small 68-part fragment library is employed, and the specific TALE repeat sequence is generated within ~8 hours. Sequence-verified TALENs or TALE-TF plasmids targeting 17 bp target sequences can be produced within three days, without the need for stepwise intermediate plasmid production. We demonstrate the utility of STAR through production of functional TALE-TFs capable of activating human SOX2 expression. STAR addresses some of the shortcomings of existing Golden Gate or solid-phase assembly protocols and enables routine production of TALE-TFs that will complement emerging CRISPR/Cas9-based reagents across diverse applications in mammalian stem cell and synthetic biology.
Visualization and ligand-induced modulation of dopamine receptor dimerization at the single molecule level
Authors: Tabor Alina , Weisenburger Siegfried , Banerjee Ashutosh , Purkayastha Nirupam , Kaindl Jonas M. , Hübner Harald , Wei Luxi , Grömer Teja W. , Kornhuber Johannes , Tschammer Nuska , Birdsall Nigel J. M. , Mashanov Gregory I. , Sandoghdar Vahid , Gmeiner Peter
Published: September 2016

G protein–coupled receptors (GPCRs), including dopamine receptors, represent a group of important pharmacological targets. An increased formation of dopamine receptor D2 homodimers has been suggested to be associated with the pathophysiology of schizophrenia. Selective labeling and ligand-induced modulation of dimerization may therefore allow the investigation of the pathophysiological role of these dimers. Using TIRF microscopy at the single molecule level, transient formation of homodimers of dopamine receptors in the membrane of stably transfected CHO cells has been observed. The equilibrium between dimers and monomers was modulated by the binding of ligands; whereas antagonists showed a ratio that was identical to that of unliganded receptors, agonist-bound D2 receptor-ligand complexes resulted in an increase in dimerization. Addition of bivalent D2 receptor ligands also resulted in a large increase in D2 receptor dimers. A physical interaction between the protomers was confirmed using high resolution cryogenic localization microscopy, with ca. 9 nm between the centers of mass.
Discovery of novel xylosides in co-culture of basidiomycetes Trametes versicolor and Ganoderma applanatum by integrated metabolomics and bioinformatics
Authors: Yao Lu , Zhu Li-Ping , Xu Xiao-Yan , Tan Ling-Ling , Sadilek Martin , Fan Huan , Hu Bo , Shen Xiao-Ting , Yang Jie , Qiao Bin , Yang Song
Published: September 2016

Transcriptomic analysis of cultured fungi suggests that many genes for secondary metabolite synthesis are presumably silent under standard laboratory condition. In order to investigate the expression of silent genes in symbiotic systems, 136 fungi-fungi symbiotic systems were built up by co-culturing seventeen basidiomycetes, among which the co-culture of Trametes versicolor and Ganoderma applanatum demonstrated the strongest coloration of confrontation zones. Metabolomics study of this co-culture discovered that sixty-two features were either newly synthesized or highly produced in the co-culture compared with individual cultures. Molecular network analysis highlighted a subnetwork including two novel xylosides (compounds 2 and 3). Compound 2 was further identified as N-(4-methoxyphenyl)formamide 2-O-β-D-xyloside and was revealed to have the potential to enhance the cell viability of human immortalized bronchial epithelial cell line of Beas-2B. Moreover, bioinformatics and transcriptional analysis of T. versicolor revealed a potential candidate gene (GI: 636605689) encoding xylosyltransferases for xylosylation. Additionally, 3-phenyllactic acid and orsellinic acid were detected for the first time in G. applanatum, which may be ascribed to response against T.versicolor stress. In general, the described co-culture platform provides a powerful tool to discover novel metabolites and help gain insights into the mechanism of silent gene activation in fungal defense.
Mutation screening of GRIN2B in schizophrenia and autism spectrum disorder in a Japanese population
Authors: Takasaki Yuto , Koide Takayoshi , Wang Chenyao , Kimura Hiroki , Xing Jingrui , Kushima Itaru , Ishizuka Kanako , Mori Daisuke , Sekiguchi Mariko , Ikeda Masashi , Aizawa Miki , Tsurumaru Naoko , Iwayama Yoshimi , Yoshimi Akira , Arioka Yuko , Yoshida Mami , Noma Hiromi , Oya-Ito Tomoko , Nakamura Yukako , Kunimoto Shohko , Aleksic Branko , Uno Yota , Okada Takashi , Ujike Hiroshi , Egawa Jun , Kuwabara Hitoshi , Someya Toshiyuki , Yoshikawa Takeo , Iwata Nakao , Ozaki Norio
Published: September 2016

N-methyl-d-aspartate receptors (NMDARs) play a critical role in excitatory synaptic transmission and plasticity in the central nervous systems. Recent genetics studies in schizophrenia (SCZ) show that SCZ is susceptible to NMDARs and the NMDAR signaling complex. In autism spectrum disorder (ASD), several studies report dysregulation of NMDARs as a risk factor for ASD. To further examine the association between NMDARs and SCZ/ASD development, we conducted a mutation screening study of GRIN2B which encodes NR2B subunit of NMDARs, to identify rare mutations that potentially cause diseases, in SCZ and ASD patients (n = 574 and 152, respectively). This was followed by an association study in a large sample set of SCZ, ASD, and normal healthy controls (n = 4145, 381, and 4432, respectively). We identified five rare missense mutations through the mutation screening of GRIN2B. Although no statistically significant association between any single mutation and SCZ or ASD was found, one of its variant, K1292R, is found only in the patient group. To further examine the association between mutations in GRIN2B and SCZ/ASD development, a larger sample size and functional experiments are needed.
WEE1 inhibition in pancreatic cancer cells is dependent on DNA repair status in a context dependent manner
Authors: Lal Shruti , Zarei Mahsa , Chand Saswati N. , Dylgjeri Emanuela , Mambelli-Lisboa Nicole C. , Pishvaian Michael J. , Yeo Charles J. , Winter Jordan M. , Brody Jonathan R.
Published: September 2016

Pancreatic ductal adenocarcinoma (PDA) is a lethal disease, in part, because of the lack of effective targeted therapeutic options. MK-1775 (also known as AZD1775), a mitotic inhibitor, has been demonstrated to enhance the anti-tumor effects of DNA damaging agents such as gemcitabine. We evaluated the efficacy of MK-1775 alone or in combination with DNA damaging agents (MMC or oxaliplatin) in PDA cell lines that are either DNA repair proficient (DDR-P) or deficient (DDR-D). PDA cell lines PL11, Hs 766T and Capan-1 harboring naturally selected mutations in DNA repair genes FANCC, FANCG and BRCA2 respectively, were less sensitive to MK-1775 as compared to two out of four representative DDR-P (MIA PaCa2 and PANC-1) cell lines. Accordingly, DDR-P cells exhibit reduced sensitivity to MK-1775 upon siRNA silencing of DNA repair genes, BRCA2 or FANCD2, compared to control cells. Only DDR-P cells showed increased apoptosis as a result of early mitotic entry and catastrophe compared to DDR-D cells. Taken together with other recently published reports, our results add another level of evidence that the efficacy of WEE1 inhibition is influenced by the DNA repair status of a cell and may also be dependent on the tumor type and model evaluated.
Endothelial dysfunction correlates with decompression bubbles in rats
Authors: Zhang Kun , Wang Dong , Jiang Zhongxin , Ning Xiaowei , Buzzacott Peter , Xu Weigang
Published: September 2016

Previous studies have documented that decompression led to endothelial dysfunction with controversial results. This study aimed to clarify the relationship between endothelial dysfunction, bubble formation and decompression rate. Rats were subjected to simulated air dives with one of four decompression rates: one slow and three rapid. Bubble formation was detected ultrasonically following decompression for two hours, before measurement of endothelial related indices. Bubbles were found in only rapid-decompressed rats and the amount correlated with decompression rate with significant variability. Serum levels of ET-1, 6-keto-PGF1α, ICAM-1, VCAM-1 and MDA, lung Wet/Dry weight ratio and histological score increased, serum NO decreased following rapid decompression. Endothelial-dependent vasodilatation to Ach was reduced in pulmonary artery rings among rapid-decompressed rats. Near all the above changes correlated significantly with bubble amounts. The results suggest that bubbles may be the causative agent of decompression–induced endothelial damage and bubble amount is of clinical significance in assessing decompression stress. Furthermore, serum levels of ET-1 and MDA may serve as sensitive biomarkers with the capacity to indicate endothelial dysfunction and decompression stress following dives.
Rapid acquisition of mean Raman spectra of eukaryotic cells for a robust single cell classification
Authors: Schie Iwan W. , Kiselev Roman , Krafft Christoph , Popp Jürgen
Published: September 2016

Integrated acquisition of Raman spectra gives better results for classification of tumor and non-tumor cells.
Recent advances in the chemical imaging of human fingermarks (a review)
Authors: Wei Qianhui , Zhang Meiqin , Ogorevc Božidar , Zhang Xueji
Published: September 2016

This review highlights the considerable advances in the chemical imaging of human fingermarks. Additional information about the donor can be obtained from the chemical composition of latent fingermarks besides the physical pattern, such as the age, gender, medical history and possible drug habits.
Comparing surface properties of melanoma cells using time of flight secondary ions mass spectrometry
Authors: Bobrowska J. , Moffat J. , Awsiuk K. , Pabijan J. , Rysz J. , Budkowski A. , Reading M. , Lekka M.
Published: September 2016

Various techniques have been already reported to differentiate between normal (non-malignant) and cancerous cells based on their physico-chemical properties.
Manifesting the sergeants-and-soldiers principle in coadsorber induced homochiral polymorphic assemblies at the liquid/solid interface
Authors: Li Shu-Ying , Chen Ting , Yue Jie-Yu , Wang Lin , Yan Hui-Juan , Wang Dong , Wan Li-Jun
Published: September 2016

Strong hydrogen bonding facilitates a more efficient amplification of chirality because of its critical role in chiral communication.
Supramolecular assembly of cobaloxime on nanoring-coated carbon nanotubes: addressing the stability of the pyridine–cobalt linkage under hydrogen evolution turnover conditions
Authors: Donck Simon , Fize Jennifer , Gravel Edmond , Doris Eric , Artero Vincent
Published: September 2016

A carbon nanotube–cobaloxime H2-evolving nanohybrid catalyst was prepared through supramolecular assembly of tailored polymerizable amphiphiles, leading to the coordination of cobalt on pyridine-coated nanotubes.
Robust onionlike structures with magnetic and photodynamic properties formed by a fullerene C60–POM hybrid
Authors: Zhou Shengju , Feng Yongqiang , Chen Mengjun , Li Qian , Liu Baoyong , Cao Jiamei , Sun Xiaofeng , Li Hongguang , Hao Jingcheng
Published: September 2016

A fullerene C60–Dawson POM hybrid was prepared for the first time, which can aggregate into onionlike structures with magnetic and photodynamic properties.
Simple rules and the emergence of complexity in surface chirality
Authors: Forster M. , Raval R.
Published: September 2016

Surface chirality arising from self-organized molecular monolayers may manifest both a handedness and footedness, leading to a dual level of chiral expression.
Stereoselective synthesis of 2,3,4-highly substituted oxetanes by intramolecular C–C bond forming Michael addition
Authors: Ho Guo-Ming , Li Yu-Jang
Published: September 2016

A wide variety of 2,3,3,4-tetrasubstituted oxetanes and 3-α,β-unsaturated ester substituted oxetanes were synthesized starting from vinylogous urethane derivatives.
Benzoannelated aza-, oxa- and azaoxa[8]circulenes as promising blue organic emitters
Authors: Baryshnikov Gleb V. , Valiev Rashid R. , Karaush Nataliya N. , Minaeva Valentina A. , Sinelnikov Alexandr N. , Pedersen Stephan K. , Pittelkow Michael , Minaev Boris F. , Ågren Hans
Published: September 2016

In the present study, we studied the synergetic effect of benzoannelation and NH/O-substitution for enhancing the absorption intensity in a series of novel designed benzoannelated aza- and oxa[8]circulenes.
DFT global optimisation of gas-phase and MgO-supported sub-nanometre AuPd clusters
Authors: Hussein Heider A. , Davis Jack B. A. , Johnston Roy L.
Published: September 2016

The effect of a MgO support on the structures and energies of Au–Pd clusters is calculated at the DFT level.
Broadband anti-Stokes white emission of Sr2CeO4 nanocrystals induced by laser irradiation
Authors: Strek W. , Tomala R. , Marciniak L. , Lukaszewicz M. , Cichy B. , Stefanski M. , Hreniak D. , Kedziorski A. , Krosnicki M. , Seijo L.
Published: September 2016

The laser induced white emission (LIWE) from Sr2CeO4 nanocrystals upon irradiation with a focused IR laser beam was investigated.
Conductive multi-walled boron nitride nanotubes by catalytic etching using cobalt oxide
Authors: Kim Do-Hyun , Jang Ho-Kyun , Kim Min-Seok , Kim Sung-Dae , Lee Dong-Jin , Kim Gyu Tae
Published: September 2016

Multi-walled boron nitride nanotubes are etched at low temperature by catalytic oxidation and converted to electrical conductors.
Investigation of novel crystal structures of Bi–Sb binaries predicted using the minima hopping method
Authors: Singh Sobhit , Ibarra-Hernández Wilfredo , Valencia-Jaime Irais , Avendaño-Franco Guillermo , Romero Aldo H.
Published: September 2016

In this work, we investigate how different combinations of the crystal structure and the spin-orbit coupling strength (i.e. Sb-concentration) result in different novel properties of Bi–Sb binaries.
The effect of Rhδ+dopant in SrTiO3on the active oxidation state of co-catalytic Pt nanoparticles in overall water splitting
Authors: Zoontjes M. G. C. , Han K. , Huijben M. , van der Wiel W. G. , Mul G.
Published: September 2016

We have shown that the average oxidation state of Pt nanoparticles during water splitting depends on Rhδ+-doping in SrTiO3.