bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards peptide vaccines against Zika virus: Immunoinformatics combined with molecular dynamics simulations to predict antigenic epitopes of Zika viral proteins
Authors: Usman Mirza Muhammad , Rafique Shazia , Ali Amjad , Munir Mobeen , Ikram Nazia , Manan Abdul , Salo-Ahen Outi M. H. , Idrees Muhammad 
Published: December 2016

AbstractThe recent outbreak of Zika virus (ZIKV) infection in Brazil has developed to a global health concern due to its likely association with birth defects (primary microcephaly) and neurological complications. Consequently, there is an urgent need to develop a vaccine to prevent or a medicine to treat the infection. In this study, immunoinformatics approach was employed to predict antigenic epitopes of Zika viral proteins to aid in development of a peptide vaccine against ZIKV. Both linear and conformational B-cell epitopes as well as cytotoxic T-lymphocyte (CTL) epitopes were predicted for ZIKV Envelope (E), NS3 and NS5 proteins. We further investigated the binding interactions of altogether 15 antigenic CTL epitopes with three class I major histocompatibility complex (MHC I) proteins after docking the peptides to the binding groove of the MHC I proteins. The stability of the resulting peptide-MHC I complexes was further studied by molecular dynamics simulations. The simulation results highlight the limits of rigid-body docking methods. Some of the antigenic epitopes predicted and analyzed in this work might present a preliminary set of peptides for future vaccine development against ZIKV.
The Relationship Between Cortical Inhibition and Electroconvulsive Therapy in the Treatment of Major Depressive Disorder
Authors: Voineskos Daphne , Levinson Andrea J. , Sun Yinming , Barr Mera S. , Farzan Faranak , Rajji Tarek K. , Fitzgerald Paul B. , Blumberger Daniel M. , Daskalakis Zafiris J. 
Published: December 2016

AbstractDysfunctional cortical inhibition (CI) is postulated as a key neurophysiological mechanism in major depressive disorder. Electroconvulsive therapy (ECT) is the treatment of choice for resistant depression and ECT has been associated with enhanced CI. The objective of this study was to evaluate the relationship between CI and ECT response in resistant depression. Twenty-five patients with treatment resistant depression underwent an acute course of ECT. CI was indexed by the cortical silent period (CSP) and short-interval cortical inhibition (SICI), through TMS-EMG. CI and clinical response was measured prior to beginning an acute ECT course and within 48 hours of the last ECT treatment in the course. Clinical response to ECT was assessed by HDRS-17 before and after an acute course of ECT. We found that there was a significant difference in CSP at baseline between responder and non-responder groups (p = 0.044). Baseline CSP predicted therapeutic response to ECT with sensitivity of 80% and specificity of 60%. There were no changes in CSP or SICI after administration of the ECT course. Our findings suggest that duration of pre-treatment CSP may be a useful predictor of therapeutic response to ECT in patients with TRD.
An analytical toolkit for polyploid willow discrimination
Authors: Guo Wei , Hou Jing , Yin Tongming , Chen Yingnan 
Published: December 2016

AbstractPolyploid breeding is an important means for creating elite willow cultivars, and therefore provokes an active demand for discriminating the ploidy levels of natural willow stands. In this study, we established an analytical toolkit for polyploid willow identification by combining molecular markers and flow cytometry (FCM). A total of 10 single-copy fully informative SSRs were chosen for marker-aided selection based on a segregation test with a full-sib willow pedigree and a mutability test with a collection of natural willow stands. Aided by these molecular markers, we performed polyploid selection in two tree species and two shrub species of the genus Salix. The ploidy levels of the investigated samples were further examined using a flow cytometer. It was previously shown that results from marker-aided selection were consistent with those from FCM measurements. Based on ploidy level assessment in different willow species, it was found that tree willows were dominantly tetraploid, whereas shrub willows were most frequently diploid. With this analytical toolkit, polyploids can be rapidly screened from a large number of natural stands; thereafter, the exact ploidy levels of the polyploid candidates can be efficiently confirmed by FCM. This analytical toolkit will greatly enhance polyploid breeding programs for willows.
Chickpea transcription factor CaTLP1 interacts with protein kinases, modulates ROS accumulation and promotes ABA-mediated stomatal closure
Authors: Wardhan Vijay , Pandey Aarti , Chakraborty Subhra , Chakraborty Niranjan 
Published: December 2016

AbstractTubby and Tubby-like proteins (TLPs), in mammals, play critical roles in neural development, while its function in plants is largely unknown. We previously demonstrated that the chickpea TLP, CaTLP1, participates in osmotic stress response and might be associated with ABA-dependent network. However, how CaTLP1 is connected to ABA signaling remains unclear. The CaTLP1 was found to be engaged in ABA-mediated gene expression and stomatal closure. Complementation of the yeast yap1 mutant with CaTLP1 revealed its role in ROS scavenging. Furthermore, complementation of Arabidopsis attlp2 mutant displayed enhanced stress tolerance, indicating the functional conservation of TLPs across the species. The presence of ABA-responsive element along with other motifs in the proximal promoter regions of TLPs firmly established their involvement in stress signalling pathways. The CaTLP1 promoter driven GUS expression was restricted to the vegetative organs, especially stem and rosette leaves. Global protein expression profiling of wild-type, attlp2 and complemented Arabidopsis plants revealed 95 differentially expressed proteins, presumably involved in maintaining physiological and biological processes under dehydration. Immunoprecipitation assay revealed that protein kinases are most likely to interact with CaTLP1. This study provides the first demonstration that the TLPs act as module for ABA-mediated stomatal closure possibly via interaction with protein kinase.
Solving the second-order free rider problem in a public goods game: An experiment using a leader support system
Authors: Ozono Hiroki , Jin Nobuhito , Watabe Motoki , Shimizu Kazumi 
Published: December 2016

AbstractPunishment of non-cooperators—free riders—can lead to high cooperation in public goods games (PGG). However, second-order free riders, who do not pay punishment costs, reduce the effectiveness of punishment. Here we introduce a “leader support system,” in which one group leader can freely punish group followers using capital pooled through the support of group followers. In our experiment, participants engage in three stages repeatedly: a PGG stage in which followers decide to cooperate for their group; a support stage in which followers decide whether to support the leader; and a punishment stage in which the leader can punish any follower. We compare a support-present condition with a no-support condition, in which there is an external source for the leader’s punishment. The results show that punishment occurs more frequently in the support-present condition than the no-support condition. Within the former, both higher cooperation and higher support for a leader are achieved under linkage-type leaders—who punish both non-cooperators and non-supporters. In addition, linkage-type leaders themselves earn higher profits than other leader types because they withdraw more support. This means that leaders who effectively punish followers could increase their own benefits and the second-order free rider problem would be solved.
Structural and fluctuational difference between two ends of Aβ amyloid fibril: MD simulations predict only one end has open conformations
Authors: Okumura Hisashi , Itoh Satoru G. 
Published: December 2016

AbstractAβ amyloid fibrils, which are related to Alzheimer’s disease, have a cross-β structure consisting of two β-sheets: β1 and β2. The Aβ peptides are thought to be serially arranged in the same molecular conformation along the fibril axis. However, to understand the amyloid extension mechanism, we must understand the amyloid fibril structure and fluctuation at the fibril end, which has not been revealed to date. Here, we reveal these features by all-atom molecular dynamics (MD) simulations of Aβ42 and Aβ40 fibrils in explicit water. The structure and fluctuation were observed to differ between the two ends. At the even end, the Aβ peptide always took a closed form wherein β1 and β2 were closely spaced. The Aβ peptide fluctuated more at the odd end and took an open form wherein the two β-sheets were well separated. The differences are attributed to the stronger β-sheet formation by the β1 exposed at the even end than the β2 exposed at the odd end. Along with the small fluctuations at the even end, these results explain why the fibril extends from one end only, as observed in experiments. Our MD results agree well with recent observations by high-speed atomic force microscopy.
Modulation of thermal noise and spectral sensitivity in Lake Baikal cottoid fish rhodopsins
Authors: Luk Hoi Ling , Bhattacharyya Nihar , Montisci Fabio , Morrow James M. , Melaccio Federico , Wada Akimori , Sheves Mudi , Fanelli Francesca , Chang Belinda S. W. , Olivucci Massimo 
Published: December 2016

AbstractLake Baikal is the deepest and one of the most ancient lakes in the world. Its unique ecology has resulted in the colonization of a diversity of depth habitats by a unique fauna that includes a group of teleost fish of the sub-order Cottoidei. This relatively recent radiation of cottoid fishes shows a gradual blue-shift in the wavelength of the absorption maximum of their visual pigments with increasing habitat depth. Here we combine homology modeling and quantum chemical calculations with experimental in vitro measurements of rhodopsins to investigate dim-light adaptation. The calculations, which were able to reproduce the trend of observed absorption maxima in both A1 and A2 rhodopsins, reveal a Barlow-type relationship between the absorption maxima and the thermal isomerization rate suggesting a link between the observed blue-shift and a thermal noise decrease. A Nakanishi point-charge analysis of the electrostatic effects of non-conserved and conserved amino acid residues surrounding the rhodopsin chromophore identified both close and distant sites affecting simultaneously spectral tuning and visual sensitivity. We propose that natural variation at these sites modulate both the thermal noise and spectral shifting in Baikal cottoid visual pigments resulting in adaptations that enable vision in deep water light environments.
Effects of dose reduction on bone strength prediction using finite element analysis
Authors: Anitha D. , Subburaj Karupppasamy , Mei Kai , Kopp Felix K. , Foehr Peter , Noel Peter B. , Kirschke Jan S. , Baum Thomas 
Published: December 2016

AbstractThis study aimed to evaluate the effect of dose reduction, by means of tube exposure reduction, on bone strength prediction from finite-element (FE) analysis. Fresh thoracic mid-vertebrae specimens (n = 11) were imaged, using multi-detector computed tomography (MDCT), at different intensities of X-ray tube exposures (80, 150, 220 and 500 mAs). Bone mineral density (BMD) was estimated from the mid-slice of each specimen from MDCT images. Differences in image quality and geometry of each specimen were measured. FE analysis was performed on all specimens to predict fracture load. Paired t-tests were used to compare the results obtained, using the highest CT dose (500 mAs) as reference. Dose reduction had no significant impact on FE-predicted fracture loads, with significant correlations obtained with reference to 500 mAs, for 80 mAs (R2  = 0.997, p < 0.001), 150 mAs (R2 = 0.998, p < 0.001) and 220 mAs (R2 = 0.987, p < 0.001). There were no significant differences in volume quantification between the different doses examined. CT imaging radiation dose could be reduced substantially to 64% with no impact on strength estimates obtained from FE analysis. Reduced CT dose will enable early diagnosis and advanced monitoring of osteoporosis and associated fracture risk.
The world’s road to water scarcity: shortage and stress in the 20th century and pathways towards sustainability
Authors: Kummu M. , Guillaume J. H. A. , de Moel H. , Eisner S. , Flörke M. , Porkka M. , Siebert S. , Veldkamp T. I. E. , Ward P. J. 
Published: December 2016

AbstractWater scarcity is a rapidly growing concern around the globe, but little is known about how it has developed over time. This study provides a first assessment of continuous sub-national trajectories of blue water consumption, renewable freshwater availability, and water scarcity for the entire 20th century. Water scarcity is analysed using the fundamental concepts of shortage (impacts due to low availability per capita) and stress (impacts due to high consumption relative to availability) which indicate difficulties in satisfying the needs of a population and overuse of resources respectively. While water consumption increased fourfold within the study period, the population under water scarcity increased from 0.24 billion (14% of global population) in the 1900s to 3.8 billion (58%) in the 2000s. Nearly all sub-national trajectories show an increasing trend in water scarcity. The concept of scarcity trajectory archetypes and shapes is introduced to characterize the historical development of water scarcity and suggest measures for alleviating water scarcity and increasing sustainability. Linking the scarcity trajectories to other datasets may help further deepen understanding of how trajectories relate to historical and future drivers, and hence help tackle these evolving challenges.
Experimental and theoretical study on the driving force and glass flow by laser-induced metal sphere migration in glass
Authors: Hidai Hirofumi , Wada Jun , Iwamoto Tatsuki , Matsusaka Souta , Chiba Akira , Kishi Tetsuo , Morita Noboru 
Published: December 2016

AbstractLight is able to remotely move matter. Among various driving forces, laser-induced metal sphere migration in glass has been reported. The temperature on the laser-illuminated side of the sphere was higher than that on the non-illuminated side. This temperature gradient caused non-uniformity in the interfacial tension between the glass and the melted metal as the tension decreased with increasing temperature. In the present study, we investigated laser-induced metal sphere migration in different glasses using thermal flow calculations, considering the temperature dependence of the material parameters. In addition, the velocity of the glass flow generated by the metal sphere migration was measured and compared with thermal flow calculations. The migration velocity of the stainless steel sphere increased with increasing laser power density; the maximum velocity was 104 μm/s in borosilicate glass and 47 μm/s in silica glass. The sphere was heated to more than 2000 K. The temperature gradient of the interfacial tension between the stainless steel sphere and the glass was calculated to be −2.29 × 10−5 N/m/K for borosilicate glass and −2.06 × 10−5 N/m/K for silica glass. Glass flowed in the region 15–30 μm from the surface of the sphere, and the 80-μm sphere migrated in a narrow softened channel.
Decadal shifts of East Asian summer monsoon in a climate model free of explicit GHGs and aerosols
Authors: Lin Renping , Zhu Jiang , Zheng Fei 
Published: December 2016

AbstractThe East Asian summer monsoon (EASM) experienced decadal transitions over the past few decades, and the associated "wetter-South-drier-North" shifts in rainfall patterns in China significantly affected the social and economic development in China. Two viewpoints stand out to explain these decadal shifts, regarding the shifts either a result of internal variability of climate system or that of external forcings (e.g. greenhouse gases (GHGs) and anthropogenic aerosols). However, most climate models, for example, the Atmospheric Model Intercomparison Project (AMIP)-type simulations and the Coupled Model Intercomparison Project (CMIP)-type simulations, fail to simulate the variation patterns, leaving the mechanisms responsible for these shifts still open to dispute. In this study, we conducted a successful simulation of these decadal transitions in a coupled model where we applied ocean data assimilation in the model free of explicit aerosols and GHGs forcing. The associated decadal shifts of the three-dimensional spatial structure in the 1990s, including the eastward retreat, the northward shift of the western Pacific subtropical high (WPSH), and the south-cool-north-warm pattern of the upper-level tropospheric temperature, were all well captured. Our simulation supports the argument that the variations of the oceanic fields are the dominant factor responsible for the EASM decadal transitions.
Chiral Sulfoxide-Induced Single Turn Peptide α-Helicity
Authors: Zhang Qingzhou , Jiang Fan , Zhao Bingchuan , Lin Huacan , Tian Yuan , Xie Mingsheng , Bai Guoyun , Gilbert Adam M. , Goetz Gilles H. , Liras Spiros , Mathiowetz Alan A. , Price David A. , Song Kun , Tu Meihua , Wu Yujie , Wang Tao , Flanagan Mark E. , Wu Yun-Dong , Li Zigang 
Published: December 2016

AbstractInducing α-helicity through side-chain cross-linking is a strategy that has been pursued to improve peptide conformational rigidity and bio-availability. Here we describe the preparation of small peptides tethered to chiral sulfoxide-containing macrocyclic rings. Furthermore, a study of structure-activity relationships (SARs) disclosed properties with respect to ring size, sulfur position, oxidation state, and stereochemistry that show a propensity to induce α-helicity. Supporting data include circular dichroism spectroscopy (CD), NMR spectroscopy, and a single crystal X-ray structure for one such stabilized peptide. Finally, theoretical studies are presented to elucidate the effect of chiral sulfoxides in inducing backbone α-helicity.
Tailoring thermal conductivity via three-dimensional porous alumina
Authors: Abad Begoña , Maiz Jon , Ruiz-Clavijo Alejandra , Caballero-Calero Olga , Martin-Gonzalez Marisol 
Published: December 2016

AbstractThree-dimensional anodic alumina templates (3D-AAO) are an astonishing framework with open highly ordered three-dimensional skeleton structures. Since these templates are architecturally different from conventional solids or porous templates, they teem with opportunities for engineering thermal properties. By establishing the mechanisms of heat transfer in these frameworks, we aim to create materials with tailored thermal properties. The effective thermal conductivity of an empty 3D-AAO membrane was measured. As the effective medium theory was not valid to extract the skeletal thermal conductivity of 3D-AAO, a simple 3D thermal conduction model was developed, based on a mixed series and parallel thermal resistor circuit, giving a skeletal thermal conductivity value of approximately 1.25 W·m−1·K−1, which matches the value of the ordinary AAO membranes prepared from the same acid solution. The effect of different filler materials as well as the variation of the number of transversal nanochannels and the length of the 3D-AAO membrane in the effective thermal conductivity of the composite was studied. Finally, the thermal conductivity of two 3D-AAO membranes filled with cobalt and bismuth telluride was also measured, which was in good agreement with the thermal model predictions. Therefore, this work proved this structure as a powerful approach to tailor thermal properties.
Unlocking bat immunology: establishment of Pteropus alecto bone marrow-derived dendritic cells and macrophages
Authors: Zhou Peng , Chionh Yok Teng , Irac Sergio Erdal , Ahn Matae , Jia Ng Justin Han , Fossum Even , Bogen Bjarne , Ginhoux Florent , Irving Aaron T , Dutertre Charles-Antoine , Wang Lin-Fa 
Published: December 2016

AbstractBats carry and shed many emerging infectious disease agents including Ebola virus and SARS-like Coronaviruses, yet they rarely display clinical symptoms of infection. Bat epithelial or fibroblast cell lines were previously established to study the bat immune response against viral infection. However, the lack of professional immune cells such as dendritic cells (DC) and macrophages has greatly limited the significance of current investigations. Using Pteropus alecto (P. alecto) GM-CSF plus IL4, FLT3L and CSF-1, we successfully generated bat bone marrow-derived DC and macrophages. Cells with the phenotype, morphology and functional features of monocyte-derived DC, bona fide DC or macrophages were obtained in GM-CSF/IL4, FLT3L or CSF-1 cultures, respectively. The successful generation of the first bat bone marrow-derived immune cells paves the way to unlocking the immune mechanisms that confer host resilience to pathogens in bats.
Accurate Quantitative Sensing of Intracellular pH based on Self-ratiometric Upconversion Luminescent Nanoprobe
Authors: Li Cuixia , Zuo Jing , Zhang Li , Chang Yulei , Zhang Youlin , Tu Langping , Liu Xiaomin , Xue Bin , Li Qiqing , Zhao Huiying , Zhang Hong , Kong Xianggui 
Published: December 2016

AbstractAccurate quantitation of intracellular pH (pHi) is of great importance in revealing the cellular activities and early warning of diseases. A series of fluorescence-based nano-bioprobes composed of different nanoparticles or/and dye pairs have already been developed for pHi sensing. Till now, biological auto-fluorescence background upon UV-Vis excitation and severe photo-bleaching of dyes are the two main factors impeding the accurate quantitative detection of pHi. Herein, we have developed a self-ratiometric luminescence nanoprobe based on förster resonant energy transfer (FRET) for probing pHi, in which pH-sensitive fluorescein isothiocyanate (FITC) and upconversion nanoparticles (UCNPs) were served as energy acceptor and donor, respectively. Under 980 nm excitation, upconversion emission bands at 475 nm and 645 nm of NaYF4:Yb3+, Tm3+ UCNPs were used as pHi response and self-ratiometric reference signal, respectively. This direct quantitative sensing approach has circumvented the traditional software-based subsequent processing of images which may lead to relatively large uncertainty of the results. Due to efficient FRET and fluorescence background free, a highly-sensitive and accurate sensing has been achieved, featured by 3.56 per unit change in pHi value 3.0–7.0 with deviation less than 0.43. This approach shall facilitate the researches in pHi related areas and development of the intracellular drug delivery systems.