bluuebunny/crossref_metadata_2025 huggingface dataset:
Raman signatures of inversion symmetry breaking and structural phase transition in type-II Weyl semimetal MoTe2
Authors: Zhang Kenan , Bao Changhua , Gu Qiangqiang , Ren Xiao , Zhang Haoxiong , Deng Ke , Wu Yang , Li Yuan , Feng Ji , Zhou Shuyun
Published: December 2016

Transition metal dichalcogenide MoTe2 is an important candidate for realizing the newly predicted type-II Weyl fermions, for which the breaking of the inversion symmetry is a prerequisite. Here we present direct spectroscopic evidence for the inversion symmetry breaking in the low-temperature phase of MoTe2 by systematic Raman experiments and first-principles calculations. We identify five lattice vibrational modes that are Raman-active only in the low-temperature noncentrosymmetric structure. A hysteresis is also observed in the peak intensity of inversion symmetry-activated Raman modes, confirming a temperature-induced structural phase transition with a concomitant change in the inversion symmetry. Our results provide definitive evidence for the low-temperature noncentrosymmetric Td phase from vibrational spectroscopy, and suggest MoTe2 as an ideal candidate for investigating the temperature-induced topological phase transition.
TRBP ensures efficient Dicer processing of precursor microRNA in RNA-crowded environments
Authors: Fareh Mohamed , Yeom Kyu-Hyeon , Haagsma Anna C. , Chauhan Sweeny , Heo Inha , Joo Chirlmin
Published: December 2016

The RNA-binding protein TRBP is a central component of the Dicer complex. Despite a decade of biochemical and structural studies, the essential functionality of TRBP in microRNA (miRNA) biogenesis remains unknown. Here we show that TRBP is an integral cofactor for time-efficient Dicer processing in RNA-crowded environments. We competed for Dicer processing of pre-miRNA with a large amount of cellular RNA species and found that Dicer-TRBP, but not Dicer alone, remains resilient. To apprehend the mechanism of this substrate selectivity, we use single-molecule fluorescence. The real-time observation reveals that TRBP acts as a gatekeeper, precluding Dicer from engaging with pre-miRNA-like substrates. TRBP acquires the selectivity using the PAZ domain of Dicer, whereas Dicer moderates the RNA-binding affinity of TRBP for fast turnover. This coordinated action between TRBP and Dicer accomplishes an efficient way of discarding pre-miRNA-like substrates.
Multiple signal classification algorithm for super-resolution fluorescence microscopy
Authors: Agarwal Krishna , Macháň Radek
Published: December 2016

Single-molecule localization techniques are restricted by long acquisition and computational times, or the need of special fluorophores or biologically toxic photochemical environments. Here we propose a statistical super-resolution technique of wide-field fluorescence microscopy we call the multiple signal classification algorithm which has several advantages. It provides resolution down to at least 50 nm, requires fewer frames and lower excitation power and works even at high fluorophore concentrations. Further, it works with any fluorophore that exhibits blinking on the timescale of the recording. The multiple signal classification algorithm shows comparable or better performance in comparison with single-molecule localization techniques and four contemporary statistical super-resolution methods for experiments of in vitro actin filaments and other independently acquired experimental data sets. We also demonstrate super-resolution at timescales of 245 ms (using 49 frames acquired at 200 frames per second) in samples of live-cell microtubules and live-cell actin filaments imaged without imaging buffers.
Carbon monoxide in an extremely metal-poor galaxy
Authors: Shi Yong , Wang Junzhi , Zhang Zhi-Yu , Gao Yu , Hao Cai-Na , Xia Xiao-Yang , Gu Qiusheng
Published: December 2016

Extremely metal-poor galaxies with metallicity below 10% of the solar value in the local universe are the best analogues to investigating the interstellar medium at a quasi-primitive environment in the early universe. In spite of the ongoing formation of stars in these galaxies, the presence of molecular gas (which is known to provide the material reservoir for star formation in galaxies such as our Milky Way) remains unclear. Here we report the detection of carbon monoxide (CO), the primary tracer of molecular gas, in a galaxy with 7% solar metallicity, with additional detections in two galaxies at higher metallicities. Such detections offer direct evidence for the existence of molecular gas in these galaxies that contain few metals. Using archived infrared data, it is shown that the molecular gas mass per CO luminosity at extremely low metallicity is approximately one-thousand times the Milky Way value.
Nanoscale assembly of superconducting vortices with scanning tunnelling microscope tip
Authors: Ge Jun-Yi , Gladilin Vladimir N. , Tempere Jacques , Xue Cun , Devreese Jozef T. , Van de Vondel Joris , Zhou Youhe , Moshchalkov Victor V.
Published: December 2016

Vortices play a crucial role in determining the properties of superconductors as well as their applications. Therefore, characterization and manipulation of vortices, especially at the single-vortex level, is of great importance. Among many techniques to study single vortices, scanning tunnelling microscopy (STM) stands out as a powerful tool, due to its ability to detect the local electronic states and high spatial resolution. However, local control of superconductivity as well as the manipulation of individual vortices with the STM tip is still lacking. Here we report a new function of the STM, namely to control the local pinning in a superconductor through the heating effect. Such effect allows us to quench the superconducting state at nanoscale, and leads to the growth of vortex clusters whose size can be controlled by the bias voltage. We also demonstrate the use of an STM tip to assemble single-quantum vortices into desired nanoscale configurations.
Fe3O4 thin films: controlling and manipulating an elusive quantum material
Authors: Liu Xionghua , Chang Chun-Fu , Rata Aurora Diana , Komarek Alexander Christoph , Tjeng Liu Hao
Published: December 2016

Fe3O4 (magnetite) is one of the most elusive quantum materials and at the same time one of the most studied transition metal oxide materials for thin-film applications. The theoretically expected half-metallic behaviour generates high expectations that it can be used in spintronic devices. Yet, despite the tremendous amount of work devoted to preparing thin films, the enigmatic first-order metal–insulator transition, and the hallmark of magnetite known as the Verwey transition, is in thin films extremely broad and occurs at substantially lower temperatures as compared with that in high-quality bulk single crystals. Here we have succeeded in finding and making a particular class of substrates that allows the growth of magnetite thin films with the Verwey transition as sharp as in the bulk. Moreover, we are now able to tune the transition temperature and, using tensile strain, increase it to substantially higher values than in the bulk.
Size effect in thermoelectric materials
Authors: Mao Jun , Liu Zihang , Ren Zhifeng
Published: December 2016

Thermoelectric applications have attracted increasing interest recently due to its capability of converting waste heat into electricity without hazardous emissions. Materials with enhanced thermoelectric performance have been reported in recent two decades. The revival of research for thermoelectric materials began in early 1990s when the size effect is considered. Low-dimensional materials with exceptionally high thermoelectric figure of merit (ZT) have been presented, which broke the limit of ZT around unity. The idea of size effect in thermoelectric materials even inspired the later nanostructuring and band engineering strategies, which effectively enhanced the thermoelectric performance of bulk materials. In this overview, the size effect in low-dimensional thermoelectric materials is reviewed. We first discuss the quantum confinement effect on carriers, including the enhancement of electronic density of states, semimetal to semiconductor transition and carrier pocket engineering. Then, the effect of assumptions on theoretical calculations is presented. Finally, the effect of phonon confinement and interface scattering on lattice thermal conductivity is discussed.
Charge carrier transition in an ambipolar single-molecule junction: Its mechanical-modulation and reversibility
Authors: Shao Jian , Zhang Xiaoyue , Chen Yun , Zheng Yue
Published: December 2016

Precise control from the bottom-up for realizing tunable functionality is of utmost importance to facilitate the development of molecular electronic devices. Until now, however, manipulating charge carriers over single-molecule scale remains intractable. The origin of the problem is that the nature of charge carriers is often hindered by the complexity of the investigated molecular systems. Here, via ab initio simulations, we show a force-modulated and switched ambipolar single-molecule junction with Au/cyclopropane-1,2-dithiol/Au structure. The cyclopropane ring in the molecule can be opened and closed reversibly and repeatedly by the mechanical force. This structural transition from its closed state to open state enables the ambipolarity in charge carriers—from p-type to n-type. Analysis of electronic structure reveals unambiguously the force-dependent correlation between C–S bond order and the nature of charge carriers. Based on this, we design a binary interconnected junction exhibiting resistance, rectification and negative differential resistance functionalities under mechanical modulation, i.e., loading/unloading or pull/push. This interesting phenomenon provides both illuminating insight and feasible controllability into charge carriers in molecules, and a very general idea and useful approach for single-molecule junctions in practical single-molecule devices.
Erratum: Charge density waves in disordered media circumventing the Imry-Ma argument
Authors: Changlani Hitesh J. , Tubman Norm M. , Hughes Taylor L.
Published: December 2016

Scientific Reports 6: Article number: 31897; published online: 24 August 2016; updated: 09 December 2016
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

The 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

Dysfunctional 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

Polyploid 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.
Correction: Corrigendum: The bacterial toxin CNF1 as a tool to induce retinal degeneration reminiscent of retinitis pigmentosa
Authors: Guadagni Viviana , Cerri Chiara , Piano Ilaria , Novelli Elena , Gargini Claudia , Fiorentini Carla , Caleo Matteo , Strettoi Enrica
Published: December 2016

Scientific Reports 6: Article number: 35919; published online: 24 October 2016; updated: 09 December 2016
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

Tubby 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

Punishment 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

Aβ 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

Lake 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

This 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.
Correction: Corrigendum: PAK1 confers chemoresistance and poor outcome in non-small cell lung cancer via β-catenin-mediated stemness
Authors: Chen Ming-Jenn , Wu De-Wei , Wang Yao-Chen , Chen Chi-Yi , Lee Huei
Published: December 2016

Scientific Reports 6: Article number: 34933; published online: 07 October 2016; updated: 09 December 2016
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

Water 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

Light 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

The 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

Inducing 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

Three-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

Bats 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

Accurate 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.
Targeting ASC in NLRP3 inflammasome by caffeic acid phenethyl ester: a novel strategy to treat acute gout
Authors: Lee Hye Eun , Yang Gabsik , Kim Nam Doo , Jeong Seongkeun , Jung Yunjin , Choi Jae Young , Park Hyun Ho , Lee Joo Young
Published: December 2016

Gouty arthritis is caused by the deposition of uric acid crystals, which induce the activation of NOD-like receptor family, pyrin domain containing 3(NLRP3) inflammasome. The NLRP3 inflammasome, composed of NLRP3, the adaptor protein ASC, and caspase-1, is closely linked to the pathogenesis of various metabolic diseases including gouty arthritis. We investigated whether an orally administrable inhibitor of NLRP3 inflammasome was effective for alleviating the pathological symptoms of gouty arthritis and what was the underlying mechanism. In primary mouse macrophages, caffeic acid phenethyl ester(CAPE) blocked caspase-1 activation and IL-1β production induced by MSU crystals, showing that CAPE suppresses NLRP3 inflammasome activation. In mouse gouty arthritis models, oral administration of CAPE suppressed MSU crystals-induced caspase-1 activation and IL-1β production in the air pouch exudates and the foot tissues, correlating with attenuation of inflammatory symptoms. CAPE directly associated with ASC as shown by SPR analysis and co-precipitation, resulting in blockade of NLRP3-ASC interaction induced by MSU crystals. Our findings provide a novel regulatory mechanism by which small molecules harness the activation of NLRP3 inflammasome by presenting ASC as a new target. Furthermore, the results suggest the preventive or therapeutic strategy for NLRP3-related inflammatory diseases such as gouty arthritis using orally available small molecules.
A Predictive Model for Toxicity Effects Assessment of Biotransformed Hepatic Drugs Using Iterative Sampling Method
Authors: Tharwat Alaa , Moemen Yasmine S. , Hassanien Aboul Ella
Published: December 2016

Measuring toxicity is one of the main steps in drug development. Hence, there is a high demand for computational models to predict the toxicity effects of the potential drugs. In this study, we used a dataset, which consists of four toxicity effects:mutagenic, tumorigenic, irritant and reproductive effects. The proposed model consists of three phases. In the first phase, rough set-based methods are used to select the most discriminative features for reducing the classification time and improving the classification performance. Due to the imbalanced class distribution, in the second phase, different sampling methods such as Random Under-Sampling, Random Over-Sampling and Synthetic Minority Oversampling Technique are used to solve the problem of imbalanced datasets. ITerative Sampling (ITS) method is proposed to avoid the limitations of those methods. ITS method has two steps. The first step (sampling step) iteratively modifies the prior distribution of the minority and majority classes. In the second step, a data cleaning method is used to remove the overlapping that is produced from the first step. In the third phase, Bagging classifier is used to classify an unknown drug into toxic or non-toxic. The experimental results proved that the proposed model performed well in classifying the unknown samples according to all toxic effects in the imbalanced datasets.
Extreme Activity of Drug Nanocrystals Coated with A Layer of Non-Covalent Polymers from Self-Assembled Boric Acid
Authors: Zhan Honglei , Liang Jun F.
Published: December 2016

Non-covalent polymers have remarkable advantages over synthetic polymers for wide biomedical applications. In this study, non-covalent polymers from self-assembled boric acid were used as the capping reagent to replace synthetic polymers in drug crystallization. Under acidic pH, boric acid self-assembled on the surface of drug nanocrystals to form polymers with network-like structures held together by hydrogen bonds. Coating driven by boric acid self-assembly had negligible effects on drug crystallinity and structure but resulted in drug nanocrystals with excellent dispersion properties that aided in the formation of a more stable suspension. Boric acid coating improved drug stability dramatically by preventing drug molecules from undergoing water hydrolysis in a neutral environment. More importantly, the specific reactivity of orthoboric groups to diols in cell glycocalyx facilitated a rapid cross-membrane translocation of drug nanocrystals, leading to efficient intracellular drug delivery, especially on cancer cells with highly expressed sialic acids. Boric acid coated nanocrystals of camptothecin, an anticancer drug with poor aqueous solubility and stability, demonstrated extreme cytotoxic activity (IC50 < 5.0 μg/mL) to cancer cells compared to synthetic polymer coated CPT nanocrystals and free CPT. Surface coating using non-covalent polymers from self-assembled boric acid will have wide biomedical applications especially in biomaterials and drug delivery field.
Use of polyvinylpyrrolidone-iodine solution for sterilisation and preservation improves mechanical properties and osteogenesis of allografts
Authors: Zhao Yantao , Hu Xiantong , Li Zhonghai , Wang Fuli , Xia Yang , Hou Shuxun , Zhong Hongbin , Zhang Feimin , Gu Ning
Published: December 2016

Allografts eliminate the disadvantages associated with autografts and synthetic scaffolds but are associated with a disease-transmission risk. Therefore, allograft sterilisation is crucial. We aimed to determine whether polyvinylpyrrolidone-iodine (PVP-I) can be used for sterilisation and as a new wet-preservation method. PVP-I–sterilised and preserved allografts demonstrated improved mechanical property, osteogenesis, and excellent microbial inhibition. A thigh muscle pouch model of nude mice showed that PVP-I–preserved allografts demonstrated better ectopic formation than Co60-sterilised allografts (control) in vivo (P < 0.05). Furthermore, the PVP-I–preserved group showed no difference between 24 h and 12 weeks of allograft preservation (P > 0.05). PVP-I–preserved allografts showed more hydrophilic surfaces and PVP-I–sterilised tendons showed higher mechanical strength than Co60-sterilised tendons (P < 0.05). The level of residual PVP-I was higher without washing and with prolonged preservation (P < 0.05). In vitro cellular tests showed that appropriate PVP-I concentration was nontoxic to preosteoblast cells, and cellular differentiation measured by alkaline phosphatase activity and osteogenic gene markers was enhanced (P < 0.05). Therefore, the improved biological performance of implanted allografts may be attributable to better surface properties and residual PVP-I, and PVP-I immersion can be a simple, easy method for allograft sterilisation and preservation.
Mitigate Cascading Failures on Networks using a Memetic Algorithm
Authors: Tang Xianglong , Liu Jing , Hao Xingxing
Published: December 2016

Research concerning cascading failures in complex networks has become a hot topic. However, most of the existing studies have focused on modelling the cascading phenomenon on networks and analysing network robustness from a theoretical point of view, which considers only the damage incurred by the failure of one or several nodes. However, such a theoretical approach may not be useful in practical situation. Thus, we first design a much more practical measure to evaluate the robustness of networks against cascading failures, termedRcf. Then, adoptingRcfas the objective function, we propose a new memetic algorithm (MA) named MA-Rcfto enhance network the robustness against cascading failures. Moreover, we design a new local search operator that considers the characteristics of cascading failures and operates by connecting nodes with a high probability of having similar loads. In experiments, both synthetic scale-free networks and real-world networks are used to test the efficiency and effectiveness of the MA-Rcf. We systematically investigate the effects of parameters on the performance of the MA-Rcfand validate the performance of the newly designed local search operator. The results show that the local search operator is effective, that MA-Rcfcan enhance network robustness against cascading failures efficiently, and that it outperforms existing algorithms.
Global water cycle amplifying at less than the Clausius-Clapeyron rate
Authors: Skliris Nikolaos , Zika Jan D. , Nurser George , Josey Simon A. , Marsh Robert
Published: December 2016

A change in the cycle of water from dry to wet regions of the globe would have far reaching impact on humanity. As air warms, its capacity to hold water increases at the Clausius-Clapeyron rate (CC, approximately 7% °C−1). Surface ocean salinity observations have suggested the water cycle has amplified at close to CC following recent global warming, a result that was found to be at odds with state-of the art climate models. Here we employ a method based on water mass transformation theory for inferring changes in the water cycle from changes in three-dimensional salinity. Using full depth salinity observations we infer a water cycle amplification of 3.0 ± 1.6% °C−1 over 1950–2010. Climate models agree with observations in terms of a water cycle amplification (4.3 ± 2.0% °C−1) substantially less than CC adding confidence to projections of total water cycle change under greenhouse gas emission scenarios.
Thyroid hormone suppresses expression of stathmin and associated tumor growth in hepatocellular carcinoma
Authors: Tseng Yi-Hsin , Huang Ya-Hui , Lin Tzu-Kang , Wu Sheng-Ming , Chi Hsiang-Cheng , Tsai Chung-Ying , Tsai Ming-Ming , Lin Yang-Hsiang , Chang Wei-Chun , Chang Ya-Ting , Chen Wei-Jan , Lin Kwang-Huei
Published: December 2016

Stathmin (STMN1), a recognized oncoprotein upregulated in various solid tumors, promotes microtubule disassembly and modulates tumor growth and migration activity. However, the mechanisms underlying the genetic regulation of STMN1 have yet to be elucidated. In the current study, we report that thyroid hormone receptor (THR) expression is negatively correlated with STMN1 expression in a subset of clinical hepatocellular carcinoma (HCC) specimens. We further identified the STMN1 gene as a target of thyroid hormone (T3) in the HepG2 hepatoma cell line. An analysis of STMN1 expression profile and mechanism of transcriptional regulation revealed that T3 significantly suppressed STMN1 mRNA and protein expression, and further showed that THR directly targeted the STMN1 upstream element to regulate STMN1 transcriptional activity. Specific knockdown of STMN1 suppressed cell proliferation and xenograft tumor growth in mice. In addition, T3 regulation of cell growth arrest and cell cycle distribution were attenuated by overexpression of STMN1. Our results suggest that the oncogene STMN1 is transcriptionally downregulated by T3 in the liver. This T3-mediated suppression of STMN1 supports the theory that T3 plays an inhibitory role in HCC tumor growth, and suggests that the lack of normal THR function leads to elevated STMN1 expression and malignant growth.
Co-delivery of docetaxel and palmitoyl ascorbate by liposome for enhanced synergistic antitumor efficacy
Authors: Li Junxiu , Guo Chaorui , Feng Fan , Fan Ali , Dai Yu , Li Ning , Zhao Di , Chen Xijing , Lu Yang
Published: December 2016

Palmitoyl ascorbate (PA) as an antioxidant has the potential for the treatment of cancer. In the present study, a nanocarrier system was developed for co-delivery of docetaxel (DOC) with palmitoyl ascorbate and the therapeutic efficacy of a combination drug regimen was investigated. For this purpose, different ratios of docetaxel and palmitoyl ascorbate were co-encapsulated in a liposome and they all showed high encapsulation efficiency. The average diameters of the liposomes ranged from 140 to 170 nm. Negative zeta potential values were observed for all systems, ranged from −40 mV to −56 mV. Studies on drug release and cellular uptake of the co-delivery system demonstrated that both drugs were effectively taken up by the cells and released slowly. Moreover, the liposome loading drugs with DOC/PA concentration ratio of 1:200 showed the highest anti-tumor activity to three different types of tumor cells. The higher in vivo therapeutic efficacy with lower systemic toxicity of the DOC-PA200-LPs was also verified by the H22 tumor bearing mice model. Our results showed that such co-loaded delivery systems could serve as a promising therapeutic approach to improve clinical outcomes against hepatic carcinoma.
Characterization of the first double-stranded RNA bacteriophage infecting Pseudomonas aeruginosa
Authors: Yang Yuhui , Lu Shuguang , Shen Wei , Zhao Xia , Shen Mengyu , Tan Yinling , Li Gang , Li Ming , Wang Jing , Hu Fuquan , Le Shuai
Published: December 2016

Bacteriophages (phages) are widely distributed in the biosphere and play a key role in modulating microbial ecology in the soil, ocean, and humans. Although the role of DNA bacteriophages is well described, the biology of RNA bacteriophages is poorly understood. More than 1900 phage genomes are currently deposited in NCBI, but only 6 dsRNA bacteriophages and 12 ssRNA bacteriophages genome sequences are reported. The 6 dsRNA bacteriophages were isolated from legume samples or lakes with Pseudomonas syringae as the host. Here, we report the first Pseudomonas aeruginosa phage phiYY with a three-segmented dsRNA genome. phiYY was isolated from hospital sewage in China with the clinical P. aeruginosa strain, PAO38, as a host. Moreover, the dsRNA phage phiYY has a broad host range, which infects 99 out of 233 clinical P. aeruginosa strains isolated from four provinces in China. This work presented a detailed characterization of the dsRNA bacteriophage infecting P. aeruginosa.