bluuebunny/crossref_metadata_2025_split huggingface dataset:
A facile one-pot oxidation-assisted dealloying protocol to massively synthesize monolithic core-shell architectured nanoporous copper@cuprous oxide nanonetworks for photodegradation of methyl orange
Authors: Liu Wenbo , Chen Long , Dong Xin , Yan Jiazhen , Li Ning , Shi Sanqiang , Zhang Shichao 
Published: November 2016

AbstractIn this report, a facile and effective one-pot oxidation-assisted dealloying protocol has been developed to massively synthesize monolithic core-shell architectured nanoporous copper@cuprous oxide nanonetworks (C-S NPC@Cu2O NNs) by chemical dealloying of melt-spun Al 37 at.% Cu alloy in an oxygen-rich alkaline solution at room temperature, which possesses superior photocatalytic activity towards photodegradation of methyl orange (MO). The experimental results show that the as-prepared nanocomposite exhibits an open, bicontinuous interpenetrating ligament-pore structure with length scales of 20 ± 5 nm, in which the ligaments comprising Cu and Cu2O are typical of core-shell architecture with uniform shell thickness of ca. 3.5 nm. The photodegradation experiments of C-S NPC@Cu2O NNs show their superior photocatalytic activities for the MO degradation under visible light irradiation with degradation rate as high as 6.67 mg min−1gcat−1, which is a diffusion-controlled kinetic process in essence in light of the good linear correlation between photodegradation ratio and square root of irradiation time. The excellent photocatalytic activity can be ascribed to the synergistic effects between unique core-shell architecture and 3D nanoporous network with high specific surface area and fast mass transfer channel, indicating that the C-S NPC@Cu2O NNs will be a promising candidate for photocatalysts of MO degradation.
Novel amperometric glucose biosensor based on MXene nanocomposite
Authors: Rakhi R. B. , Nayak Pranati , Xia Chuan , Alshareef Husam N. 
Published: November 2016

AbstractA biosensor platform based on Au/MXene nanocomposite for sensitive enzymatic glucose detection is reported. The biosensor leverages the unique electrocatalytic properties and synergistic effects between Au nanoparticles and MXene sheets. An amperometric glucose biosensor is fabricated by the immobilization of glucose oxidase (GOx) enzyme on Nafion solubilized Au/ MXene nanocomposite over glassy carbon electrode (GCE). The biomediated Au nanoparticles play a significant role in facilitating the electron exchange between the electroactive center of GOx and the electrode. The GOx/Au/MXene/Nafion/GCE biosensor electrode displayed a linear amperometric response in the glucose concentration range from 0.1 to 18 mM with a relatively high sensitivity of 4.2 μAmM−1cm−2and a detection limit of 5.9 μM (S/N = 3). Furthermore, the biosensor exhibited excellent stability, reproducibility and repeatability. Therefore, the Au/MXene nanocomposite reported in this work is a potential candidate as an electrochemical transducer in electrochemical biosensors.
Effect of Heme Oxygenase-1 on Mitofusin-1 protein in LPS-induced ALI/ARDS in rats
Authors: Yu Jianbo , Wang Ying , Li Zhen , Dong Shuan , Wang Dan , Gong Lirong , Shi Jia , Zhang Yuan , Liu Daquan , Mu Rui 
Published: November 2016

AbstractAcute lung injury (ALI)/acute respiratory distress syndrome (ARDS) is a common and important oxidative stress in the lung. Mitochondrial fusion responds to the normal morphology and function of cells and is finely regulated by mitochondrial fusion proteins, such as mitofusin-1 protein (Mfn1), mitofusin-2 protein (Mfn2) and optical atrophy 1 (OPA1). Additionally, Mfn1 has been identified as the most important protein in mitochondrial fusion. Heme oxygenase-1 (HO-1) is a stress-inducible protein that plays a critical role in protecting against oxidative stress. However, whether the protection of HO-1 is related to mitochondrial fusion is still a question. Thus, ourin vitroandin vivoexperiments aimed to identify the relationship between HO-1 and Mfn1. Here, we used Hemin and ZnPP-IX as treatments in anin vivoexperiment. Then, HO-1 and Mfn1 were measured using RT-PCR and Western blotting. Supernatants were analyzed for MDA, SOD, and ROS. Our results implied that HO-1 upregulation suppressed oxidative stress induced by LPS, and the possible mechanism could be associated with Mfn1 and the PI3K/Akt pathway.
Inhibition of Epac1 suppresses mitochondrial fission and reduces neointima formation induced by vascular injury
Authors: Wang Hui , Robichaux William G. , Wang Ziqing , Mei Fang C. , Cai Ming , Du Guangwei , Chen Ju , Cheng Xiaodong 
Published: November 2016

AbstractVascular smooth muscle cell (VSMC) activation in response to injury plays an important role in the development of vascular proliferative diseases, including restenosis and atherosclerosis. The aims of this study were to ascertain the physiological functions of exchange proteins directly activated by cAMP isoform 1 (Epac1) in VSMC and to evaluate the potential of Epac1 as therapeutic targets for neointima formation during vascular remodeling. In a mouse carotid artery ligation model, genetic knockdown of the Epac1 gene led to a significant reduction in neointima obstruction in response to vascular injury. Pharmacologic inhibition of Epac1 with an Epac specific inhibitor, ESI-09, phenocopied the effects of Epac1 null by suppressing neointima formation and proliferative VSMC accumulation in neointima area. Mechanistically, Epac1 deficient VSMCs exhibited lower level of PI3K/AKT signaling and dampened response to PDGF-induced mitochondrial fission and reactive oxygen species levels. Our studies indicate that Epac1 plays important roles in promoting VSMC proliferation and phenotypic switch in response to vascular injury, therefore, representing a therapeutic target for vascular proliferative diseases.
A dynamic in vivo-like organotypic blood-brain barrier model to probe metastatic brain tumors
Authors: Xu Hui , Li Zhongyu , Yu Yue , Sizdahkhani Saman , Ho Winson S. , Yin Fangchao , Wang Li , Zhu Guoli , Zhang Min , Jiang Lei , Zhuang Zhengping , Qin Jianhua 
Published: November 2016

AbstractThe blood-brain barrier (BBB) restricts the uptake of many neuro-therapeutic molecules, presenting a formidable hurdle to drug development in brain diseases. We proposed a new and dynamicin vivo-like three-dimensional microfluidic system that replicates the key structural, functional and mechanical properties of the blood-brain barrierin vivo. Multiple factors in this system work synergistically to accentuate BBB-specific attributes–permitting the analysis of complex organ-level responses in both normal and pathological microenvironments in brain tumors. The complex BBB microenvironment is reproduced in this system via physical cell-cell interaction, vascular mechanical cues and cell migration. This model possesses the unique capability to examine brain metastasis of human lung, breast and melanoma cells and their therapeutic responses to chemotherapy. The results suggest that the interactions between cancer cells and astrocytes in BBB microenvironment might affect the ability of malignant brain tumors to traverse between brain and vascular compartments. Furthermore, quantification of spatially resolved barrier functions exists within a single assay, providing a versatile and valuable platform for pharmaceutical development, drug testing and neuroscientific research.
Intermediate scattering function of an anisotropic active Brownian particle
Authors: Kurzthaler Christina , Leitmann Sebastian , Franosch Thomas 
Published: November 2016

AbstractVarious challenges are faced when animalcules such as bacteria, protozoa, algae, or sperms move autonomously in aqueous media at low Reynolds number. These active agents are subject to strong stochastic fluctuations, that compete with the directed motion. So far most studies consider the lowest order moments of the displacements only, while more general spatio-temporal information on the stochastic motion is provided in scattering experiments. Here we derive analytically exact expressions for the directly measurable intermediate scattering function for a mesoscopic model of a single, anisotropic active Brownian particle in three dimensions. The mean-square displacement and the non-Gaussian parameter of the stochastic process are obtained as derivatives of the intermediate scattering function. These display different temporal regimes dominated by effective diffusion and directed motion due to the interplay of translational and rotational diffusion which is rationalized within the theory. The most prominent feature of the intermediate scattering function is an oscillatory behavior at intermediate wavenumbers reflecting the persistent swimming motion, whereas at small length scales bare translational and at large length scales an enhanced effective diffusion emerges. We anticipate that our characterization of the motion of active agents will serve as a reference for more realistic models and experimental observations.
Multiscale description of avian migration: from chemical compass to behaviour modeling
Authors: Pedersen J. Boiden , Nielsen Claus , Solov’yov Ilia A. 
Published: November 2016

AbstractDespite decades of research the puzzle of the magnetic sense of migratory songbirds has still not been unveiled. Although the problem really needs a multiscale description, most of the individual research efforts were focused on single scale investigations. Here we seek to establish a multiscale link between some of the scales involved, and in particular construct a bridge between electron spin dynamics and migratory bird behaviour. In order to do that, we first consider a model cyclic reaction scheme that could form the basis of the avian magnetic compass. This reaction features a fast spin-dependent process which leads to an unusually precise compass. We then propose how the reaction could be realized in a realistic molecular environment, and argue that it is consistent with the known facts about avian magnetoreception. Finally we show how the microscopic dynamics of spins could possibly be interpreted by a migrating bird and used for the navigational purpose.
Ethnic Differences in Glucose Homeostasis Markers between the Kyushu-Okinawa Population Study and the Framingham Offspring Study
Authors: Ikezaki Hiroaki , Ai Masumi , Schaefer Ernst J. , Otokozawa Seiko , Asztalos Bela F. , Nakajima Katsuyuki , Zhou Yanhua , Liu Ching-Ti , Jacques Paul F. , Cupples L. Adrienne , Furusyo Norihiro 
Published: November 2016

AbstractWe compared markers of glucose homeostasis and their association with diabetes and impaired fasting glucose (IFG) in Fukuoka, Japanese subjects (n = 1108) and age-, gender- and menopausal status-matched participants in the Framingham Offspring Study (n = 1096). The markers examined included fasting glucose, insulin, adiponectin, and glycated albumin, as well as body mass index (BMI), use of medications, and history of diabetes. The results showed that IFG prevalence in Japanese men (15.9%) and women (7.4%) were 50% less than those observed in Framingham men (34.5%) and women (21.4%) (P < 0.001). However, the diabetes prevalence in Japanese men at 13.3% was twice as high (P < 0.01) as the rate in Framingham men at 6.5%, while these rates were similar in women. Median insulin levels in Japanese men (4.6 μIU/mL) and women (4.3 μIU/mL) were about 50% lower (P < 0.001) than those in Framingham men (10.8 μIU/mL) and women (9.9 μIU/mL), as were insulin resistance values (P < 0.001). These population differences were also observed after subjects were stratified by glucose levels. In conclusion, our data indicate that there is significantly less IFG, lower insulin levels, and insulin resistance, but higher diabetes prevalence in Fukuoka men than in Framingham men, indicating that insulin deficiency may be an important cause of diabetes in Japan.
Population genomic analysis uncovers environmental stress-driven selection and adaptation of Lentinula edodes population in China
Authors: Xiao Yang , Cheng Xuanjin , Liu Jun , Li Chuang , Nong Wenyan , Bian Yinbing , Cheung Man Kit , Kwan Hoi Shan 
Published: November 2016

AbstractThe elucidation of genome-wide variations could help reveal aspects of divergence, domestication, and adaptation of edible mushrooms. Here, we resequenced the whole genomes of 39 wild and 21 cultivated strains of ChineseLentinula edodes, the shiitake mushroom. We identified three distinct genetic groups in the ChineseL. edodespopulation with robust differentiation. Results of phylogenetic and population structure analyses suggest that the cultivated strains and most of the wild trains ofL. edodesin China possess different gene pools and two outlier strains show signatures of hybridization between groups. Eighty-four candidate genes contributing to population divergence were detected in outlier analysis, 18 of which are involved in response to environmental stresses. Gene enrichment analysis of group-specific single nucleotide polymorphisms showed that the cultivated strains were genetically diversified in biological processes related to stress response. As the formation of fruiting bodies is a stress-response process, we postulate that environment factors, such as temperature, drove the population divergence ofL. edodesin China by natural or artificial selection. We also found phenotypic variations between groups and identified some wild strains that have potential to diversify the genetic pool for improving agricultural traits ofL. edodescultivars in China.
Viral vector vaccines expressing nucleoprotein and phosphoprotein genes of avian bornaviruses ameliorate homologous challenge infections in cockatiels and common canaries
Authors: Olbert Marita , Römer-Oberdörfer Angela , Herden Christiane , Malberg Sara , Runge Solveig , Staeheli Peter , Rubbenstroth Dennis 
Published: November 2016

AbstractAvian bornaviruses are causative agents of proventricular dilatation disease (PDD), an often fatal disease of parrots and related species (order Psittaciformes) which is widely distributed in captive psittacine populations and may affect endangered species. Here, we established a vaccination strategy employing two different well described viral vectors, namely recombinant Newcastle disease virus (NDV) and modified vaccinia virus Ankara (MVA) that were engineered to express the phosphoprotein and nucleoprotein genes of two avian bornaviruses, parrot bornavirus 4 (PaBV-4) and canary bornavirus 2 (CnBV-2). When combined in a heterologous prime/boost vaccination regime, NDV and MVA vaccine viruses established self-limiting infections and induced a bornavirus-specific humoral immune response in cockatiels (Nymphicus hollandicus) and common canaries (Serinus canaria forma domestica). After challenge infection with a homologous bornavirus, shedding of bornavirus RNA and viral loads in tissue samples were significantly reduced in immunized birds, indicating that vaccination markedly delayed the course of infection. However, cockatiels still developed signs of PDD if the vaccine failed to prevent viral persistence. Our work demonstrates that avian bornavirus infections can be repressed by vaccine-induced immunity. It represents a first crucial step towards a protective vaccination strategy to combat PDD in psittacine birds.
Causal Evidence for the Role of Specific GABAergic Interneuron Types in Entorhinal Recruitment of Dentate Granule Cells
Authors: Lee Cheng-Ta , Kao Min-Hua , Hou Wen-Hsien , Wei Yu-Ting , Chen Chin-Lin , Lien Cheng-Chang 
Published: November 2016

AbstractThe dentate gyrus (DG) is the primary gate of the hippocampus and controls information flow from the cortex to the hippocampus proper. To maintain normal function, granule cells (GCs), the principal neurons in the DG, receive fine-tuned inhibition from local-circuit GABAergic inhibitory interneurons (INs). Abnormalities of GABAergic circuits in the DG are associated with several brain disorders, including epilepsy, autism, schizophrenia, and Alzheimer disease. Therefore, understanding the network mechanisms of inhibitory control of GCs is of functional and pathophysiological importance. GABAergic inhibitory INs are heterogeneous, but it is unclear how individual subtypes contribute to GC activity. Using cell-type-specific optogenetic perturbation, we investigated whether and how two major IN populations defined by parvalbumin (PV) and somatostatin (SST) expression, regulate GC input transformations. We showed that PV-expressing (PV+) INs, and not SST-expressing (SST+) INs, primarily suppress GC responses to single cortical stimulation. In addition, these two IN classes differentially regulate GC responses to θ and γ frequency inputs from the cortex. Notably, PV+ INs specifically control the onset of the spike series, whereas SST+ INs preferentially regulate the later spikes in the series. Together, PV+ and SST+ GABAergic INs engage differentially in GC input-output transformations in response to various activity patterns.
Origin of the Photoluminescence Quantum Yields Enhanced by Alkane-Termination of Freestanding Silicon Nanocrystals: Temperature-Dependence of Optical Properties
Authors: Ghosh Batu , Takeguchi Masaki , Nakamura Jin , Nemoto Yoshihiro , Hamaoka Takumi , Chandra Sourov , Shirahata Naoto 
Published: November 2016

AbstractOn the basis of the systematic study on temperature dependence of photoluminescence (PL) properties along with relaxation dynamics we revise a long-accepted mechanism for enhancing absolute PL quantum yields (QYs) of freestanding silicon nanocrystals (ncSi). A hydrogen-terminated ncSi (ncSi:H) of 2.1 nm was prepared by thermal disproportination of (HSiO1.5)n, followed by hydrofluoric etching. Room-temperature PL QY of the ncSi:H increased twentyfold only by hydrosilylation of 1-octadecene (ncSi-OD). A combination of PL spectroscopic measurement from cryogenic to room temperature with structural characterization allows us to link the enhanced PL QYs with the notable difference in surface structure between the ncSi:H and the ncSi-OD. The hydride-terminated surface suffers from the presence of a large amount of nonradiative relaxation channels whereas the passivation with alkyl monolayers suppresses the creation of the nonradiative relaxation channels to yield the high PL QY.
Milan's Studio di Fonologia: Voice Politics in the City, 1955–8
Authors: Casadei Delia 
Published: November 2016

ABSTRACTThe Studio di Fonologia Musicale of Milan, Italy's first electronic music studio, opened in 1955. Housed in the national broadcasting (RAI) studios in Milan, the studio was founded by two celebrated Italian composers: Luciano Berio and Bruno Maderna. The institution is often remembered nowadays for being the first electronic music studio to focus its activity on the human voice. As I argue, this focus was not only of an aesthetic nature, but rather reflected long-standing political and intellectual conceptions of voice, speech and public space that were rooted in Italy's early days as a republic, and in mid-twentieth-century Milan as the flagship city for this newly achieved political modernity.
Do Water Level Fluctuations Influence Production of Walleye and Yellow Perch Young-of-the-Year in Large Northern Lakes?
Authors: Larson James H. , Staples David F. , Maki Ryan P. , Vallazza Jon M. , Knights Brent C. , Peterson Kevin E. 
Published: November 2016

Abstract
Many ecological processes depend on the regular rise and fall of water levels (WLs), and artificial manipulations to WL regimes can impair important ecosystem services. Previous research has suggested that differences in WL between late summer and early spring may alter the suitability of shoals used by Walleyes Sander vitreus for spawning. Other species, such as the Yellow Perch Perca flavescens, are unlikely to be affected in the same way by WL fluctuations because their spawning requirements are quite different. We used 11–23 years of data from six northern Minnesota lakes to assess the effects of WL fluctuations on the abundances of young-of-the-year (age-0) Walleyes and Yellow Perch. In two lakes (Rainy Lake and Lake Kabetogama), a change in WL management occurred in 2000, after which these lakes saw increased age-0 Walleye abundance, while the other study lakes experienced decreases or no change. Rainy Lake and Lake Kabetogama also had increases in age-0 Yellow Perch, but another study lake did also. We used partial least-squares regression to assess whether WL metrics were associated with variation in age-0 Walleye and Yellow Perch abundances, but WL metrics were seldom associated with age-0 abundance for either species. Our analysis suggested a potential influence of WL regulation on age-0 Walleye abundance, but we found no evidence that early spring access to spawning shoals was the mechanism by which this occurred.
Received August 19, 2015; accepted July 15, 2016 Published online November 10, 2016
Health and Women’s Role in Agricultural Production Efficiency
Authors: Gkiza Ioanna G. , Nastis Stefanos A. 
Published: November 2016

AbstractThe aim of this article is to examine the direct and indirect links between production efficiency and farmers’ health. Using a sample of male farm leaders, the role of both genders’ health in production efficiency is measured. More specifically, the effect of the farm household’s health through the direct effect of the male farmer’s health and the indirect effect of the woman’s health on production efficiency is examined. An increase in the frequency of illness of the female in the family farm decreases production efficiency, suggesting distinct gender roles in the agricultural household.
Recycler: an algorithm for detecting plasmids from de novo assembly graphs
Authors: Rozov Roye , Brown Kav Aya , Bogumil David , Shterzer Naama , Halperin Eran , Mizrahi Itzhak , Shamir Ron 
Published: November 2016

Abstract

Motivation
Plasmids and other mobile elements are central contributors to microbial evolution and genome innovation. Recently, they have been found to have important roles in antibiotic resistance and in affecting production of metabolites used in industrial and agricultural applications. However, their characterization through deep sequencing remains challenging, in spite of rapid drops in cost and throughput increases for sequencing. Here, we attempt to ameliorate this situation by introducing a new circular element assembly algorithm, leveraging assembly graphs provided by a conventional de novo assembler and alignments of paired-end reads to assemble cyclic sequences likely to be plasmids, phages and other circular elements.

Results
We introduce Recycler, the first tool that can extract complete circular contigs from sequence data of isolate microbial genomes, plasmidome and metagenome sequence data. We show that Recycler greatly increases the number of true plasmids recovered relative to other approaches while remaining highly accurate. We demonstrate this trend via simulations of plasmidomes, comparisons of predictions with reference data for isolate samples, and assessments of annotation accuracy on metagenome data. In addition, we provide validation by DNA amplification of 77 plasmids predicted by Recycler from the different sequenced samples in which Recycler showed mean accuracy of 89% across all data types—isolate, microbiome and plasmidome.

Availability and Implementation
Recycler is available at http://github.com/Shamir-Lab/Recycler

Supplementary information
Supplementary data are available at Bioinformatics online.