bluuebunny/crossref_metadata_2025_split huggingface dataset:
The ER stress regulator Bip mediates cadmium-induced autophagy and neuronal senescence
Authors: Wang Tao , Yuan Yan , Zou Hui , Yang Jinlong , Zhao Shiwen , Ma Yonggang , Wang Yi , Bian Jianchun , Liu Xuezhong , Gu Jianhong , Liu Zongping , Zhu Jiaqiao 
Published: December 2016

AbstractAutophagy is protective in cadmium (Cd)-induced oxidative damage. Endoplasmic reticulum (ER) stress has been shown to induce autophagy in a process requiring the unfolded protein response signalling pathways. Cd treatment significantly increased senescence in neuronal cells, which was aggravated by 3-MA or silencing of Atg5 and abolished by rapamycin. Cd increased expression of ER stress regulators Bip, chop, eIf2α, and ATF4, and activated autophagy as evidenced by upregulated LC3. Moreover, the ER stress inhibitor mithramycin inhibited the expression of ER stress protein chaperone Bip and blocked autophagic flux. Downregulating Bip significantly blocked the conversion of LC3-I to LC3-II, decreased LC3 puncta formation, and prevented the increase of senescence in PC12 cells. Interestingly, knocking down Bip regulated the expression of p-AMPK, p-AKT and p-s6k induced by Cd. BAPTA, a Bip inhibitor, decreased the expression of p-AMPK and LC3-II, but enhanced neuronal senescence. In addition, we found that siRNA for Bip enhanced GATA4 expression after 6 h Cd exposure in PC12 cells, while rapamycin treatment decreased GATA4 levels induced by 24 h Cd exposure. These results indicate that autophagy degraded GATA4 in a Bip-dependent way. Our findings suggest that autophagy regulated by Bip expression after ER stress suppressed Cd-induced neuronal senescence.
Remarkable alterations of Nav1.6 in reactive astrogliosis during epileptogenesis
Authors: Zhu Hongyan , Zhao Yuxiao , Wu Hao , Jiang Nan , Wang Ziyi , Lin Weide , Jin Jiahui , Ji Yonghua 
Published: December 2016

AbstractVoltage-gated sodium channels (VGSCs) play a vital role in controlling neuronal excitability. Nav1.6 is the most abundantly expressed VGSCs subtype in the adult central nervous system and has been found to contribute to facilitate the hyperexcitability of neurons after electrical induction of status epilepticus (SE). To clarify the exact expression patterns of Nav1.6 during epileptogenesis, we examined the expression of Nav1.6 at protein and mRNA levels in two distinct animal models of temporal lobe epilepsy (TLE) including a post-SE model induced by kainic acid (KA) intrahippocampal injection and a kindling model evoked by pentylenetetrazole (PTZ). A prominent, seizure intensity-dependent increase of Nav1.6 expression in reactive astrocytes was observed in ipsilateral hippocampus of post-SE rats, reaching the peak at 21 days after SE, a time point during the latent stage of epileptogenesis. However, Nav1.6 with low expression level was selectively expressed in the hippocampal neurons rather than astrocytes in PTZ-kindled animals. This seizure-related increase of a VGSCs subtype in reactive astrocytes after SE may represent a new mechanism for signal communication between neuron and glia in the course of epileptogenesis, facilitating the neuronal hyperexcitability.
Five key attributes can increase marine protected areas performance for small-scale fisheries management
Authors: Di Franco Antonio , Thiriet Pierre , Di Carlo Giuseppe , Dimitriadis Charalampos , Francour Patrice , Gutiérrez Nicolas L. , Jeudy de Grissac Alain , Koutsoubas Drosos , Milazzo Marco , Otero María del Mar , Piante Catherine , Plass-Johnson Jeremiah , Sainz-Trapaga Susana , Santarossa Luca , Tudela Sergi , Guidetti Paolo 
Published: December 2016

AbstractMarine protected areas (MPAs) have largely proven to be effective tools for conserving marine ecosystem, while socio-economic benefits generated by MPAs to fisheries are still under debate. Many MPAs embed a no-take zone, aiming to preserve natural populations and ecosystems, within a buffer zone where potentially sustainable activities are allowed. Small-scale fisheries (SSF) within buffer zones can be highly beneficial by promoting local socio-economies. However, guidelines to successfully manage SSFs within MPAs, ensuring both conservation and fisheries goals, and reaching a win-win scenario, are largely unavailable. From the peer-reviewed literature, grey-literature and interviews, we assembled a unique database of ecological, social and economic attributes of SSF in 25 Mediterranean MPAs. Using random forest with Boruta algorithm we identified a set of attributes determining successful SSFs management within MPAs. We show that fish stocks are healthier, fishermen incomes are higher and the social acceptance of management practices is fostered if five attributes are present (i.e. high MPA enforcement, presence of a management plan, fishermen engagement in MPA management, fishermen representative in the MPA board, and promotion of sustainable fishing). These findings are pivotal to Mediterranean coastal communities so they can achieve conservation goals while allowing for profitable exploitation of fisheries resources.
Efficient targeted mutagenesis of rice and tobacco genomes using Cpf1 from Francisella novicida
Authors: Endo Akira , Masafumi Mikami , Kaya Hidetaka , Toki Seiichi 
Published: December 2016

AbstractCRISPR/Cas9 systems are nowadays applied extensively to effect genome editing in various organisms including plants. CRISPR from Prevotella and Francisella 1 (Cpf1) is a newly characterized RNA-guided endonuclease that has two distinct features as compared to Cas9. First, Cpf1 utilizes a thymidine-rich protospacer adjacent motif (PAM) while Cas9 prefers a guanidine-rich PAM. Cpf1 could be used as a sequence-specific nuclease to target AT-rich regions of a genome that Cas9 had difficulty accessing. Second, Cpf1 generates DNA ends with a 5′ overhang, whereas Cas9 creates blunt DNA ends after cleavage. “Sticky” DNA ends should increase the efficiency of insertion of a desired DNA fragment into the Cpf1-cleaved site using complementary DNA ends. Therefore, Cpf1 could be a potent tool for precise genome engineering. To evaluate whether Cpf1 can be applied to plant genome editing, we selected Cpf1 from Francisella novicida (FnCpf1), which recognizes a shorter PAM (TTN) within known Cpf1 proteins, and applied it to targeted mutagenesis in tobacco and rice. Our results show that targeted mutagenesis had occurred in transgenic plants expressing FnCpf1 with crRNA. Deletions of the targeted region were the most frequently observed mutations. Our results demonstrate that FnCpf1 can be applied successfully to genome engineering in plants.
Increased hepatocellular carcinoma risk in chronic hepatitis B patients with persistently elevated serum total bile acid: a retrospective cohort study
Authors: Wang Haoliang , Shang Xiaoyun , Wan Xing , Xiang Xiaomei , Mao Qing , Deng Guohong , Wu Yuzhang 
Published: December 2016

AbstractTo investigate the association between long-term changes of serum total bile acid and hepatocellular carcinoma in chronic hepatitis B patients, we did a retrospective cohort study of 2262 chronic hepatitis B patients with regular antiviral treatment using data from the Hepatitis Biobank at Southwest Hospital Program from 2004 to 2014. Patients in the study were classified into 3 groups according to persistence of elevated serum total bile acid during follow-up: none-low, medium, and high persistence of elevated serum total bile acid. The association between persistence of elevated serum total bile acid and hepatocellular carcinoma was estimated using Cox proportional hazard models and Kaplan-Meier analysis including information about patients’ demographic and clinical characteristics. There were 62 hepatocellular carcinoma cases during a total follow-up of 14756.5 person-years in the retrospective study. Compared to patients with none-low persistence of elevated total bile acid, the multivariate adjusted hazard ratios (95% confidence interval) were 2.37 (1.16–4.84), and 2.57 (1.28–5.16) for patients with medium, and high persistence of elevated total bile acid. Our findings identified persistence of elevated serum total bile acid as an independent risk factor of hepatocellular carcinoma in chronic hepatitis B patients.
Inhibition of cystathionine β-synthetase suppresses sodium channel activities of dorsal root ganglion neurons of rats with lumbar disc herniation
Authors: Yan Jun , Hu Shufen , Zou Kang , Xu Min , Wang Qianliang , Miao Xiuhua , Yu Shan Ping , Xu Guang-Yin 
Published: December 2016

AbstractThe pathogenesis of pain in lumbar disc herniation (LDH) remains poorly understood. We have recently demonstrated that voltage-gated sodium channels (VGSCs) in dorsal root ganglion (DRG) neurons were sensitized in a rat model of LDH. However, the detailed molecular mechanism for sensitization of VGSCs remains largely unknown. This study was designed to examine roles of the endogenous hydrogen sulfide synthesizing enzyme cystathionine β-synthetase (CBS) in sensitization of VGSCs in a previously validated rat model of LDH. Here we showed that inhibition of CBS activity by O-(Carboxymethyl) hydroxylamine hemihydrochloride (AOAA) significantly attenuated pain hypersensitivity in LDH rats. Administration of AOAA also reduced neuronal hyperexcitability, suppressed the sodium current density, and right-shifted the V1/2 of the inactivation curve, of hindpaw innervating DRG neurons, which is retrogradely labeled by DiI. In vitro incubation of AOAA did not alter the excitability of acutely isolated DRG neurons. Furthermore, CBS was colocalized with NaV1.7 and NaV1.8 in hindpaw-innervating DRG neurons. Treatment of AOAA markedly suppressed expression of NaV1.7 and NaV1.8 in DRGs of LDH rats. These data suggest that targeting the CBS-H2S signaling at the DRG level might represent a novel therapeutic strategy for chronic pain relief in patients with LDH.
A Parallel Adaboost-Backpropagation Neural Network for Massive Image Dataset Classification
Authors: Cao Jianfang , Chen Lichao , Wang Min , Shi Hao , Tian Yun 
Published: December 2016

AbstractImage classification uses computers to simulate human understanding and cognition of images by automatically categorizing images. This study proposes a faster image classification approach that parallelizes the traditional Adaboost-Backpropagation (BP) neural network using the MapReduce parallel programming model. First, we construct a strong classifier by assembling the outputs of 15 BP neural networks (which are individually regarded as weak classifiers) based on the Adaboost algorithm. Second, we design Map and Reduce tasks for both the parallel Adaboost-BP neural network and the feature extraction algorithm. Finally, we establish an automated classification model by building a Hadoop cluster. We use the Pascal VOC2007 and Caltech256 datasets to train and test the classification model. The results are superior to those obtained using traditional Adaboost-BP neural network or parallel BP neural network approaches. Our approach increased the average classification accuracy rate by approximately 14.5% and 26.0% compared to the traditional Adaboost-BP neural network and parallel BP neural network, respectively. Furthermore, the proposed approach requires less computation time and scales very well as evaluated by speedup, sizeup and scaleup. The proposed approach may provide a foundation for automated large-scale image classification and demonstrates practical value.
Potential and optimization of two-phase anaerobic digestion of oil refinery waste activated sludge and microbial community study
Authors: Wang Qinghong , Liang Ying , Zhao Peng , Li Qing X. , Guo Shaohui , Chen Chunmao 
Published: December 2016

AbstractOil refinery waste activated sludge produced from oil wastewater biological treatment is a major industrial sludge. Two-phase anaerobic digestion of oil refinery waste activated sludge was studied for the first time. Thermal pretreatment under 170 °C is effective on sludge solubilization. At the optimum hydrolytic-acidogenic condition which was pH of 6.5, temperature of 55 °C and HRT of 2 days, 2754 mg/L volatile fatty acids (VFAs) were produced and acetic acid and butyric acid were the key components. Comparative studies of single-phase and two-phase anaerobic digestion in terms of organic removal, biogas production and methane concentration were conducted. The cumulative methane production and soluble COD (SCOD) removal efficiency in the two-phase system were 228 mL/g COD added and 77.8%, respectively, which were 1.6 and 2.1 times higher than those in single-phase anaerobic digestion. Such improved performance is attributed to intensification of dominant microbial population in separated reactors. Caloramator, Ureibacillus, Dechloromonas, Petrobacter, and T78 played important roles in hydrolytic-acidification and oil-organics degradation. Syntrophic bacteria in the family Porphyromonadaceae and the genus Anaerobranca provide acetate for methanogen. The results demonstrated the potential and operating condition of two-phase anaerobic digestion in treatment of oil refinery waste activated sludge.
Neurexin regulates nighttime sleep by modulating synaptic transmission
Authors: Tong Huawei , Li Qian , Zhang Zi Chao , Li Yi , Han Junhai 
Published: December 2016

AbstractNeurexins are cell adhesion molecules involved in synaptic formation and synaptic transmission. Mutations in neurexin genes are linked to autism spectrum disorders (ASDs), which are frequently associated with sleep problems. However, the role of neurexin-mediated synaptic transmission in sleep regulation is unclear. Here, we show that lack of the Drosophila α-neurexin homolog significantly reduces the quantity and quality of nighttime sleep and impairs sleep homeostasis. We report that neurexin expression in Drosophila mushroom body (MB) αβ neurons is essential for nighttime sleep. We demonstrate that reduced nighttime sleep in neurexin mutants is due to impaired αβ neuronal output, and show that neurexin functionally couples calcium channels (Cac) to regulate synaptic transmission. Finally, we determine that αβ surface (αβs) neurons release both acetylcholine and short neuropeptide F (sNPF), whereas αβ core (αβc) neurons release sNPF to promote nighttime sleep. Our findings reveal that neurexin regulates nighttime sleep by mediating the synaptic transmission of αβ neurons. This study elucidates the role of synaptic transmission in sleep regulation, and might offer insights into the mechanism of sleep disturbances in patients with autism disorders.
On the ability of molecular dynamics simulation and continuum electrostatics to treat interfacial water molecules in protein-protein complexes
Authors: Copie Guillaume , Cleri Fabrizio , Blossey Ralf , Lensink Marc F. 
Published: December 2016

AbstractInterfacial waters are increasingly appreciated as playing a key role in protein-protein interactions. We report on a study of the prediction of interfacial water positions by both Molecular Dynamics and explicit solvent-continuum electrostatics based on the Dipolar Poisson-Boltzmann Langevin (DPBL) model, for three test cases: (i) the barnase/barstar complex (ii) the complex between the DNase domain of colicin E2 and its cognate Im2 immunity protein and (iii) the highly unusual anti-freeze protein Maxi which contains a large number of waters in its interior. We characterize the waters at the interface and in the core of the Maxi protein by the statistics of correctly predicted positions with respect to crystallographic water positions in the PDB files as well as the dynamic measures of diffusion constants and position lifetimes. Our approach provides a methodology for the evaluation of predicted interfacial water positions through an investigation of water-mediated inter-chain contacts. While our results show satisfactory behaviour for molecular dynamics simulation, they also highlight the need for improvement of continuum methods.
Coherent Excitation of Optical Phonons in GaAs by Broadband Terahertz Pulses
Authors: Fu Zhengping , Yamaguchi Masashi 
Published: December 2016

AbstractCoherent excitation and control of lattice motion by electromagnetic radiation in optical frequency range has been reported through variety of indirect interaction mechanisms with phonon modes. However, coherent phonon excitation by direct interaction of electromagnetic radiation and nuclei has not been demonstrated experimentally in terahertz (THz) frequency range mainly due to the lack of THz emitters with broad bandwidth suitable for the purpose. We report the experimental observation of coherent phonon excitation and detection in GaAs using ultrafast THz-pump/optical-probe scheme. From the results of THz pump field dependence, pump/probe polarization dependence, and crystal orientation dependence, we attributed THz wave absorption and linear electro-optic effect to the excitation and detection mechanisms of coherent polar TO phonons. Furthermore, the carrier density dependence of the interaction of coherent phonons and free carriers is reported.
Evolution of structural distortion in BiFeO3 thin films probed by second-harmonic generation
Authors: Wang Jie-su , Jin Kui-juan , Guo Hai-zhong , Gu Jun-xing , Wan Qian , He Xu , Li Xiao-long , Xu Xiu-lai , Yang Guo-zhen 
Published: December 2016

AbstractBiFeO3 thin films have drawn much attention due to its potential applications for novel magnetoelectric devices and fundamental physics in magnetoelectric coupling. However, the structural evolution of BiFeO3 films with thickness remains controversial. Here we use an optical second-harmonic generation technique to explore the phase-related symmetry evolution of BiFeO3 thin films with the variation of thickness. The crystalline structures for 60 and 180-nm-thick BiFeO3 thin films were characterized by high-resolution X-ray diffractometry reciprocal space mapping and the local piezoelectric response for 60-nm-thick BiFeO3 thin films was characterized by piezoresponse force microscopy. The present results show that the symmetry of BiFeO3 thin films with a thickness below 60 nm belongs to the point group 4 mm. We conclude that the disappearance of fourfold rotational symmetry in SHG s-out pattern implies for the appearance of R-phase. The fact that the thinner the film is, the closer to 1 the tensor element ratio χ31/χ15 tends, indicates an increase of symmetry with the decrease of thickness for BiFeO3 thin films.
Cognitive individual differences in second language learning and processing
Authors: Granena Gisela , Jackson Daniel O. , Yilmaz Yucel 
Published: December 2016

Abstract
In this introductory chapter, we first describe the rationale for this volume, linking cognitive individual differences (IDs) to previous research in second language acquisition (SLA), and other, related fields. Next, we present a definition of cognitive abilities and illustrate how differences in these abilities may have important implications for several strands of research, including those dealing with second language aptitude, instructed SLA, comprehension and production, novel SLA, bilingualism, cognitive training, and measurement. This collective volume contains 14 additional chapters offering multiple, interdisciplinary perspectives on how individuals process and acquire languages, which incorporate theoretical, methodological, and empirical advances in the study of cognitive IDs. In the last section of this chapter, we summarize these contributions and draw explicit connections between them. The chapter concludes with some thoughts on the practical significance of this volume, in terms of researching cognitive IDs and understanding their implications.
Foreign language aptitude, acquisitional sequences, and psycholinguistic processes
Authors: Skehan Peter 
Published: December 2016

Abstract
This chapter has two broad aims: to relate aptitude tests and recent aptitude research, including that reported in this volume, to proposed second language acquisition stages; and to relate aptitude testing to the contrasts between domain-generality and domain-specificity, on the one hand, and explicit and implicit processes, on the other. Regarding SLA stages, a broad distinction is made between stages concerned with developing knowledge and those concerned with developing control. It is argued that aptitude tests have concentrated on the first and that there is scope to develop more aptitude tests to assess the second. Regarding the two major contrasts, it is argued that analysing aptitude tests in these terms is useful as a means of indicating what underlying theories they have. In that respect it is interesting that the most recent major battery (HiLAB: domain-general, often implicit) contrasts with older batteries (e.g. MLAT: domain specific, explicit). It is argued that aptitude tests, viewed in this way, can make theoretical contributions to second language acquisition more generally in characterising what language learning abilities consist of.
Miniature natural language learning in L2 acquisition research
Authors: Kempe Vera , Brooks Patricia J. 
Published: December 2016

Abstract
Researchers who wish to study mechanisms underlying second language (L2) learning and factors influencing its success face a trade-off between low experimental control in studies of naturalistic language acquisition and low typological and ecological validity in studies of artificial language learning. The methodological solution we propose is a miniature natural language learning paradigm, which exposes participants to selected elements of an unfamiliar L2, in the form of meaningful dialogues, over a period of several laboratory sessions. We show how this methodology allows researchers to understand how various components of learning interact as learners are exposed to vocabulary and grammar simultaneously, and how characteristics of both the learner and the input influence learning outcomes.
Interrelationships among L2 linguistic knowledge, working memory functions, and L2 reading
Authors: Çeçen Sevdeğer , Erçetin Gülcan 
Published: December 2016

Abstract
The main purpose of the current study is to investigate whether L2 reading comprehension is related to the processing and storage functions of working memory (WM) as well as explicit and implicit sources of knowledge in the L2. Byproducts of this question involve (a) whether the relationship between WM and reading comprehension is attributable to the linguistic nature of the complex span task; (b) whether WM is related to explicit and implicit types of linguistic knowledge in the L2. Participants were 84 late adult learners of English with a B2 level of proficiency. WM capacity was measured through reading span tasks (RST) administered in L1 and L2 and an operation span task (OST). An untimed grammaticality judgment test (GJT) and a metalinguistic knowledge test (MKT) were administered to measure explicit linguistic knowledge in the L2 while a timed GJT and an elicited oral imitation test (EOI) were used to measure implicit linguistic knowledge. Reading comprehension scores were obtained from a retired paper-based TOEFL. A principal component analysis (PCA) on the independent variables revealed a three-component model where processing and storage scores obtained from span tasks loaded on separate components reflecting a distinction between processing and storage functions of WM whereas explicit and implicit L2 knowledge measures loaded together on a single component. A regression analysis performed with factor scores from the PCA as independent variables and L2 reading comprehension scores as the dependent variable revealed significant contributions of WM’s processing function and L2 linguistic knowledge to reading comprehension in the L2. This suggests that the variance shared by WM capacity and L2 reading comprehension is not due to the linguistic nature of the span task but to the general processing efficiency of verbal WM capacity.