bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the starch-acting MaAmyB enzyme from Microbacterium aurum B8.A representing the novel subfamily GH13_42 with an unusual, multi-domain organization
Authors: Valk Vincent , van der Kaaij Rachel M. , Dijkhuizen Lubbert 
Published: November 2016

AbstractThe bacterium Microbacterium aurum strain B8.A degrades granular starches, using the multi-domain MaAmyA α-amylase to initiate granule degradation through pore formation. This paper reports the characterization of the M. aurum B8.A MaAmyB enzyme, a second starch-acting enzyme with multiple FNIII and CBM25 domains. MaAmyB was characterized as an α-glucan 1,4-α-maltohexaosidase with the ability to subsequently hydrolyze maltohexaose to maltose through the release of glucose. MaAmyB also displays exo-activity with a double blocked PNPG7 substrate, releasing PNP. In M. aurum B8.A, MaAmyB may contribute to degradation of starch granules by rapidly hydrolyzing the helical and linear starch chains that become exposed after pore formation by MaAmyA. Bioinformatics analysis showed that MaAmyB represents a novel GH13 subfamily, designated GH13_42, currently with 165 members, all in Gram-positive soil dwelling bacteria, mostly Streptomyces. All members have an unusually large catalytic domain (AB-regions), due to three insertions compared to established α-amylases, and an aberrant C-region, which has only 30% identity to established GH13 C-regions. Most GH13_42 members have three N-terminal domains (2 CBM25 and 1 FNIII). This is unusual as starch binding domains are commonly found at the C-termini of α-amylases. The evolution of the multi-domain M. aurum B8.A MaAmyA and MaAmyB enzymes is discussed.
Origin of multiple band gap values in single width nanoribbons
Authors: Deepika  , Kumar Shailesh , Shukla Alok , Kumar Rakesh 
Published: November 2016

AbstractDeterministic band gap in quasi-one-dimensional nanoribbons is prerequisite for their integrated functionalities in high performance molecular-electronics based devices. However, multiple band gaps commonly observed in graphene nanoribbons of the same width, fabricated in same slot of experiments, remain unresolved, and raise a critical concern over scalable production of pristine and/or hetero-structure nanoribbons with deterministic properties and functionalities for plethora of applications. Here, we show that a modification in the depth of potential wells in the periodic direction of a supercell on relative shifting of passivating atoms at the edges is the origin of multiple band gap values in nanoribbons of the same width in a crystallographic orientation, although they carry practically the same ground state energy. The results are similar when calculations are extended from planar graphene to buckled silicene nanoribbons. Thus, the findings facilitate tuning of the electronic properties of quasi-one-dimensional materials such as bio-molecular chains, organic and inorganic nanoribbons by performing edge engineering.
Periodic protein adsorption at the gold/biotin aqueous solution interface: evidence of kinetics with time delay
Authors: Neff H. , Laborde H. M. , Lima A. M. N. 
Published: November 2016

AbstractAn oscillatory molecular adsorption pattern of the protein neutravidin from aqueous solution onto gold, in presence of a pre-deposited self assembled mono-molecular biotin film, is reported. Real time surface Plasmon resonance sensing was utilized for evaluation of the adsorption kinetics. Two different fractions were identified: in the initial phase, protein molecules attach irreversibly onto the Biotin ligands beneath towards the jamming limit, forming a neutravidin-biotin fraction. Afterwards, the growth rate exhibits distinct, albeit damped adsorption-desorption oscillations over an extended time span, assigned to a quasi reversibly bound fraction. These findings agree with, and firstly confirm a previously published model, proposing macro-molecular adsorption with time delay. The non-linear dynamic model is applicable to and also resembles non-damped oscillatory binding features of the hetero-catalytic oxidation of carbon monoxide molecules on platinum in the gas phase. An associated surface residence time can be linked to the dynamics and time scale required for self-organization.
Multi-phasic bi-directional chemotactic responses of the growth cone
Authors: Naoki Honda , Nishiyama Makoto , Togashi Kazunobu , Igarashi Yasunobu , Hong Kyonsoo , Ishii Shin 
Published: November 2016

AbstractThe nerve growth cone is bi-directionally attracted and repelled by the same cue molecules depending on the situations, while other non-neural chemotactic cells usually show uni-directional attraction or repulsion toward their specific cue molecules. However, how the growth cone differs from other non-neural cells remains unclear. Toward this question, we developed a theory for describing chemotactic response based on a mathematical model of intracellular signaling of activator and inhibitor. Our theory was first able to clarify the conditions of attraction and repulsion, which are determined by balance between activator and inhibitor, and the conditions of uni- and bi-directional responses, which are determined by dose-response profiles of activator and inhibitor to the guidance cue. With biologically realistic sigmoidal dose-responses, our model predicted tri-phasic turning response depending on intracellular Ca2+ level, which was then experimentally confirmed by growth cone turning assays and Ca2+ imaging. Furthermore, we took a reverse-engineering analysis to identify balanced regulation between CaMKII (activator) and PP1 (inhibitor) and then the model performance was validated by reproducing turning assays with inhibitions of CaMKII and PP1. Thus, our study implies that the balance between activator and inhibitor underlies the multi-phasic bi-directional turning response of the growth cone.
Functional variants of the 5-methyltetrahydrofolate-homocysteine methyltransferase gene significantly increase susceptibility to prostate cancer: Results from an ethnic Han Chinese population
Authors: Qu Yuan-Yuan , Zhou Shu-Xian , Zhang Xuan , Zhao Rui , Gu Cheng-Yuan , Chang Kun , Yang Xiao-Qun , Gan Hua-Lei , Dai Bo , Zhang Hai-Liang , Shi Guo-Hai , Zhu Yao , Ye Ding-Wei , Zhao Jian-Yuan 
Published: November 2016

AbstractAberrant DNA methylation has been implicated in prostate carcinogenesis. The one-carbon metabolism pathway and related metabolites determine cellular DNA methylation and thus is thought to play a pivotal role in PCa occurrence. This study aimed to investigate the contribution of genetic variants in one-carbon metabolism genes to prostate cancer (PCa) risk and the underlying biological mechanisms. In this hospital-based case-control study of 1817 PCa cases and 2026 cancer-free controls, we genotyped six polymorphisms in three one-carbon metabolism genes and assessed their association with the risk of PCa. We found two noncoding MTR variants, rs28372871 T > G and rs1131450 G > A, were independently associated with a significantly increased risk of PCa. The rs28372871 GG genotype (adjusted OR = 1.40, P = 0.004) and rs1131450 AA genotype (adjusted OR = 1.64, P = 0.007) exhibited 1.40-fold and 1.64-fold higher risk of PCa, respectively, compared with their respective homozygous wild-type genotypes. Further functional analyses revealed these two variants contribute to reducing MTR expression, elevating homocysteine and SAH levels, reducing methionine and SAM levels, increasing SAH/SAM ratio, and promoting the invasion of PCa cells in vitro. Collectively, our data suggest regulatory variants of the MTR gene significantly increase the PCa risk via decreasing methylation potential. These findings provide a novel molecular mechanism for the prostate carcinogenesis.
Faster poleward range shifts in moths with more variable colour patterns
Authors: Forsman Anders , Betzholtz Per-Eric , Franzén Markus 
Published: November 2016

AbstractRange shifts have been documented in many organisms, and climate change has been implicated as a contributing driver of latitudinal and altitudinal range modifications. However, little is known about what species trait(s) allow for faster environmental tracking and improved capacity for distribution expansions. We used data for 416 species of moths, and show that range limits in Sweden have shifted to the north by on average 52.4 km per decade between 1973 and 2014. When also including non-expanding species, average expansion rate was 23.2 km per decade. The rate of boundary shifts increased with increasing levels of inter-individual variation in colour patterns and decreased with increasing latitude. The association with colour patterns indicate that variation in this functionally important trait enables species to cope with novel and changing conditions. Northern range limits also increased with average abundance and decreased with increasing year-to-year abundance fluctuations, implicating production of dispersers as a driver of range dynamics. Studies of terrestrial animals show that rates of poleward shifts differ between taxonomic groups, increase over time, and depend on study duration and latitude. Knowledge of how distribution shifts change with time, location, and species characteristics may improve projections of responses to climate change and aid the protection of biodiversity.
Decoding of top-down cognitive processing for SSVEP-controlled BMI
Authors: Min Byoung-Kyong , Dähne Sven , Ahn Min-Hee , Noh Yung-Kyun , Müller Klaus-Robert 
Published: November 2016

AbstractWe present a fast and accurate non-invasive brain-machine interface (BMI) based on demodulating steady-state visual evoked potentials (SSVEPs) in electroencephalography (EEG). Our study reports an SSVEP-BMI that, for the first time, decodes primarily based ontop-downand notbottom-upvisual information processing. The experimental setup presents a grid-shaped flickering line array that the participants observe while intentionally attending to a subset of flickering lines representing the shape of a letter. While the flickering pixels stimulate the participant’s visual cortex uniformly with equal probability, the participant’s intention groups the strokes and thus perceives a ‘letter Gestalt’. We observed decoding accuracy of 35.81% (up to 65.83%) with a regularized linear discriminant analysis; on average 2.05-fold, and up to 3.77-fold greater than chance levels in multi-class classification. Compared to the EEG signals, an electrooculogram (EOG) did not significantly contribute to decoding accuracies. Further analysis reveals that the top-down SSVEP paradigm shows the most focalised activation pattern around occipital visual areas; Granger causality analysis consistently revealed prefrontal top-down control over early visual processing. Taken together, the present paradigm provides the first neurophysiological evidence for the top-down SSVEP BMI paradigm, which potentially enables multi-class intentional control of EEG-BMIs without using gaze-shifting.
Assessing the effectiveness of problem-based learning in physical diagnostics education in China: a meta-analysis
Authors: Wang Jianmiao , Xu Yongjian , Liu Xiansheng , Xiong Weining , Xie Jungang , Zhao Jianping 
Published: November 2016

AbstractProblem-based learning (PBL) has been extensively applied as an experimental educational method in Chinese medical schools over the past decade. A meta-analysis was performed to assess the effectiveness of PBL on students’ learning outcomes in physical diagnostics education. Related databases were searched for eligible studies evaluating the effects of PBL compared to traditional teaching on students’ knowledge and/or skill scores of physical diagnostics. Standardized mean difference (SMD) with 95% confidence interval (CI) was estimated. Thirteen studies with a total of 2086 medical students were included in this meta-analysis. All of these studies provided usable data on knowledge scores, and the pooled analysis showed a significant difference in favor of PBL compared to the traditional teaching (SMD = 0.76, 95%CI = 0.33–1.19). Ten studies provided usable data on skill scores, and a significant difference in favor of PBL was also observed (SMD = 1.46, 95%CI = 0.89–2.02). Statistically similar results were obtained in the sensitivity analysis, and there was no significant evidence of publication bias. These results suggested that PBL in physical diagnostics education in China appeared to be more effective than traditional teaching method in improving knowledge and skills.
Past climate changes facilitated homoploid speciation in three mountain spiny fescues (Festuca, Poaceae)
Authors: Marques I. , Draper D. , López-Herranz M. L. , Garnatje T. , Segarra-Moragues J. G. , Catalán P. 
Published: November 2016

AbstractApart from the overwhelming cases of allopolyploidization, the impact of speciation through homoploid hybridization is becoming more relevant than previously thought. Much less is known, however, about the impact of climate changes as a driven factor of speciation. To investigate these issues, we selected Festuca picoeuropeana, an hypothetical natural hybrid between the diploid species F. eskia and F. gautieri that occurs in two different mountain ranges (Cantabrian Mountains and Pyrenees) separated by more than 400 km. To unravel the outcomes of this mode of speciation and the impact of climate during speciation we used a multidisciplinary approach combining genome size and chromosome counts, data from an extensive nuclear genotypic analysis, plastid sequences and ecological niche models (ENM). Our results show that the same homoploid hybrid was originated independently in the two mountain ranges, being currently isolated from both parents and producing viable seeds. Parental species had the opportunity to contact as early as 21000 years ago although niche divergence occurs nowadays as result of a climate-driven shift. A high degree of niche divergence was observed between the hybrid and its parents and no recent introgression or backcrossed hybrids were detected, supporting the current presence of reproductive isolation barriers between these species.
Nanostructured MoS2/BiVO4 Composites for Energy Storage Applications
Authors: Arora Yukti , Shah Amit P. , Battu Shateesh , Maliakkal Carina B. , Haram Santosh , Bhattacharya Arnab , Khushalani Deepa 
Published: November 2016

AbstractWe report the optimized synthesis and electrochemical characterization of a composite of few-layered nanostructured MoS2 along with an electroactive metal oxide BiVO4. In comparison to pristine BiVO4, and a composite of graphene/BiVO4, the MoS2/BiVO4 nanocomposite provides impressive values of charge storage with longer discharge times and improved cycling stability. Specific capacitance values of 610 Fg−1 (170 mAhg−1) at 1 Ag−1 and 166 Fg−1 (46 mAhg−1) at 10 Ag−1 were obtained for just 2.5 wt% MoS2 loaded BiVO4. The results suggest that the explicitly synthesized small lateral-dimensioned MoS2 particles provide a notable capacitive component that helps augment the specific capacitance. We discuss the optimized synthesis of monoclinic BiVO4, and few-layered nanostructured MoS2. We report the discharge capacities and cycling performance of the MoS2/BiVO4 nanocomposite using an aqueous electrolyte. The data obtained shows the MoS2/BiVO4 nanocomposite to be a promising candidate for supercapacitor energy storage applications.
Giant Gyroid and Templates from High-Molecular-Weight Block Copolymer Self-assembly
Authors: Park Sungmin , Kim Yeongsik , Ahn Hyungju , Kim Jong Hak , Yoo Pil J. , Ryu Du Yeol 
Published: November 2016

AbstractWe present a feasible approach to the direct development of three-dimensionally (3D) bicontinuous gyroid (GYR) nanostructure in high-molecular-weight, composition-controlled polystyrene-b-poly(methyl methacrylate) (PS-b-PMMA) films. The use of a neutral solvent vapor to elaborately control the swelling of block copolymer (BCP) films is essential to generate a direct pathway to GYR (or giant GYR) structure through a hexagonal (HEX) cylindrical morphology in the same material, because the thermal ordering of highly entangled BCP imposes the limit on the chain mobility. Along with the improved mechanical strength arising from the high molecular weight property of the polymers, the structural integrity and overall excellence of a large-scale GYR morphology were confirmed by the results of membrane performance, which showed greater permeability through the nanoporous GYR structure up to by a factor of three than that through the HEX structure. Moreover, a 3D nanoporous GYR template was applied to an affordable material to reproduce an inverse skeletal replica of the GYR structure with its structure being uniformly interconnected. This simple approach to the GYR template, owing to its structural tunability in a controlled composition of BCP, is anticipated to be applicable to a wide range of materialization for practical systems.
α-Synuclein enhances histone H3 lysine-9 dimethylation and H3K9me2-dependent transcriptional responses
Authors: Sugeno Naoto , Jäckel Sandra , Voigt Aaron , Wassouf Zinah , Schulze-Hentrich Julia , Kahle Philipp J. 
Published: November 2016

Abstractα-Synuclein (αS) is a protein linked to Parkinson’s disease (PD) and related neurodegenerative disorders. It is mostly localized within synapses, but αS has also been suggested to play a role in the nucleus. We used transgenicDrosophilaand inducible SH-SY5Y neuroblastoma cells to investigate the effects of αS on chromatin with a particular focus on histone modifications. Overexpression of αS in male flies as well as in retinoic acid pre-treated neuroblastoma cells led to an elevation of histone H3K9 methylations, mostly mono- (H3K9me1) and di- (H3K9me2). The transient increase of H3K9 methylation in αS-induced SH-SY5Y cells was preceded by mRNA induction of the euchromatic histone lysineN-methyltransferase 2 (EHMT2). EHMT2 and H3K9me2 can function within the REST complex. Chromatin immunoprecipitation (ChIP) analyses of selected candidate, REST regulated genes showed significantly increased H3K9me2 promoter occupancy of genes encoding the L1CAM cell adhesion molecule and the synaptosomal-associated protein SNAP25, whose reduced expression levels were confirmed by RT-qPCR in αS induced cells. Treatment with EHMT inhibitor UNC0638 restored the mRNA levels ofL1CAMandSNAP25. Thus, αS overexpression enhances H3K9 methylations via ΕΗΜΤ2 resulting in elevated H3K9me2 at theSNAP25promoter, possibly affecting SNARE complex assembly and hence synaptic vesicle fusion events regulated by αS.
Physical interactions between DNA and sepiolite nanofibers, and potential application for DNA transfer into mammalian cells
Authors: Castro-Smirnov Fidel Antonio , Piétrement Olivier , Aranda Pilar , Bertrand Jean-Rémi , Ayache Jeanne , Le Cam Eric , Ruiz-Hitzky Eduardo , Lopez Bernard S. 
Published: November 2016

AbstractNanofibers of sepiolite, a natural silicate belonging to the clay minerals family, might constitute a potential promising nanocarrier for the non-viral transfer of bio-molecules. We show here that sepiolite nanofibers efficiently bind different types of DNA molecules through electrostatic interactions, hydrogen bonding, cation bridges, and van der Waals forces. Moreover, Fourier-transform infrared spectroscopy identified the external silanol groups as the main sites of interaction with the DNA. Furthermore, as a proof of concept, we show that sepiolite is able to stably transfer plasmid DNA into mammalian cells and that the efficiency can be optimized. Indeed, sonication of sepiolite 100-fold stimulated DNA transfection efficiency. These results open the way to the use of sepiolite-based biohybrids as a novel class of nanoplatform for gene transfer with potential clinical applications.
Origin and Quenching of Novel ultraviolet and blue emission in NdGaO3: Concept of Super-Hydrogenic Dopants
Authors: Ghosh Siddhartha , Saha Surajit , Liu Zhiqi , Motapothula M. , Patra Abhijeet , Yakovlev Nikolai , Cai Yao , Prakash Saurav , Huang Xiao Hu , Tay Chuan Beng , Cong Chun Xiao , Bhatt Thirumaleshwara , Dolmanan Surani B. , Chen Jianqiang , Lü Weiming , Huang Zhen , Tripathy Sudhiranjan , Chua Soo Jin , Yu Ting , Asta Mark , Ariando A. , Venkatesan T. 
Published: November 2016

AbstractIn this study we report the existence of novel ultraviolet (UV) and blue emission in rare-earth based perovskite NdGaO3 (NGO) and the systematic quench of the NGO photoluminescence (PL) by Ce doping. Study of room temperature PL was performed in both single-crystal and polycrystalline NGO (substrates and pellets) respectively. Several NGO pellets were prepared with varying Ce concentration and their room temperature PL was studied using 325 nm laser. It was found that the PL intensity shows a systematic quench with increasing Ce concentration. XPS measurements indicated that nearly 50% of Ce atoms are in the 4+ state. The PL quench was attributed to the novel concept of super hydrogenic dopant (SHD)”, where each Ce4+ ion contributes an electron which forms a super hydrogenic atom with an enhanced Bohr radius, due to the large dielectric constant of the host. Based on the critical Ce concentration for complete quenching this SHD radius was estimated to be within a range of 0.85 nm and 1.15 nm whereas the predicted theoretical value of SHD radius for NdGaO3 is ~1.01 nm.
Population assessment of tropical tuna based on their associative behavior around floating objects
Authors: Capello M. , Deneubourg J. L. , Robert M. , Holland K. N. , Schaefer K. M. , Dagorn L. 
Published: November 2016

AbstractEstimating the abundance of pelagic fish species is a challenging task, due to their vast and remote habitat. Despite the development of satellite, archival and acoustic tagging techniques that allow the tracking of marine animals in their natural environments, these technologies have so far been underutilized in developing abundance estimations. We developed a new method for estimating the abundance of tropical tuna that employs these technologies and exploits the aggregative behavior of tuna around floating objects (FADs). We provided estimates of abundance indices based on a simulated set of tagged fish and studied the sensitivity of our method to different association dynamics, FAD numbers, population sizes and heterogeneities of the FAD-array. Taking the case study of yellowfin tuna (Thunnus albacares) acoustically-tagged in Hawaii, we implemented our approach on field data and derived for the first time the ratio between the associated and the total population. With more extensive and long-term monitoring of FAD-associated tunas and good estimates of the numbers of fish at FADs, our method could provide fisheries-independent estimates of populations of tropical tuna. The same approach can be applied to obtain population assessments for any marine and terrestrial species that display associative behavior and from which behavioral data have been acquired using acoustic, archival or satellite tags.