bluuebunny/crossref_metadata_2025 huggingface dataset:
Age-Related Progressions in Story Structure in Young Children's Narratives
Authors: Khan Kiren S. , Gugiu Mihaiela R. , Justice Laura M. , Bowles Ryan P. , Skibbe Lori E. , Piasta Shayne B.
Published: December 2016

Purpose

Prior theoretical and empirical work has referenced several broad stages of narrative development, particularly in terms of young children's understanding of story structure. However, there is considerable variation in how story structure has been defined and assessed across these studies. The aims of the present study were threefold: (a) to test the unidimensionality of items designed to assess story-structure knowledge, (b) to examine story-structure item difficulty levels, and (c) to examine age-related progressions on individual story-structure components across 3-, 4-, 5-, and 6-year-olds.

Method

Participants included 386 children (
M
= 4.8 years,
SD
= 11.67 months) from the Narrative Assessment Protocol study (
http://www.narrativeassessment.com/
), which was designed to revise a new narrative assessment tool for children between the ages of 3 and 6 years.

Results

Factor analysis indicated that 16 of 21 items reflecting story-structure knowledge constituted a unidimensional construct. Individual story-structure item analyses further revealed that establishing subgoals and tracking the overall goals in the stories were particularly challenging for 3- and 4-year-olds.

Conclusion

These findings hold implications for refinement of theoretical models of story-structure emergence in early childhood.
Systematic study on dynamic atomic layer epitaxy of InN on/in +c-GaN matrix and fabrication of fine-structure InN/GaN quantum wells: Role of high growth temperature
Authors: Yoshikawa Akihiko , Kusakabe Kazuhide , Hashimoto Naoki , Hwang Eun-Sook , Imai Daichi , Itoi Takaomi
Published: December 2016

The growth kinetics and properties of nominally 1-ML (monolayer)-thick InN wells on/in +c-GaN matrix fabricated using dynamic atomic layer epitaxy (D-ALEp) by plasma-assisted molecular beam epitaxy were systematically studied, with particular attention given to the effects of growth temperature. Attention was also given to how and where the ∼1-ML-thick InN layers were frozen or embedded on/in the +c-GaN matrix. The D-ALEp of InN on GaN was a two-stage process; in the 1st stage, an “In+N” bilayer/monolayer was formed on the GaN surface, while in the 2nd, this was capped by a GaN barrier layer. Each process was monitored in-situ using spectroscopic ellipsometry. The target growth temperature was above 620 °C and much higher than the upper critical epitaxy temperature of InN (∼500 °C). The “In+N” bilayer/monolayer tended to be an incommensurate phase, and the growth of InN layers was possible only when they were capped with a GaN layer. The InN layers could be coherently inserted into the GaN matrix under self-organizing and self-limiting epitaxy modes. The growth temperature was the most dominant growth parameter on both the growth process and the structure of the InN layers. Reflecting the inherent growth behavior of D-ALEp grown InN on/in +c-GaN at high growth temperature, the embedded InN layers in the GaN matrix were basically not full-ML in coverage, and the thickness of sheet-island-like InN layers was essentially either 1-ML or 2-ML. It was found that these InN layers tended to be frozen at the step edges on the GaN and around screw-type threading dislocations. The InN wells formed type-I band line-up heterostructures with GaN barriers, with exciton localization energies of about 300 and 500 meV at 15 K for the 1-ML and 2-ML InN wells, respectively.
Gas viscosity measurement with diamagnetic-levitation viscometer based on electromagnetically spinning system
Authors: Shimokawa Y. , Matsuura Y. , Hirano T. , Sakai K.
Published: December 2016

Utilizing a graphite-disk probe attached with a thin aluminum disk, we have developed a friction-free viscosity measurement system. The probe is levitated above a NdFeB magnet because of diamagnetic effect and rotated by an electromagnetically induced torque. The probe is absolutely free form mechanical friction, and therefore, the accurate measurements of the viscosity of gases can be achieved. To demonstrate the accuracy and sensitivity of our method, we measured the viscosity of 8 kinds of gases and its temperature change from 278 K to 318 K, and we confirmed a good agreement between the obtained values and literature values. This paper demonstrates that our method has the ability to measure the fluid viscosity in the order of μPa ⋅ s.
Bench testing of a heterodyne CO2 laser dispersion interferometer for high temporal resolution plasma density measurements
Authors: Akiyama T. , Van Zeeland M. A. , Boivin R. L. , Carlstrom T. N. , Chavez J. A. , Muscatello C. M. , O’Neill R. C. , Vasquez J. , Watkins M. , Martin W. , Colio A. , Finkenthal D. K. , Brower D. L. , Chen J. , Ding W. X. , Perry M.
Published: December 2016

A heterodyne detection scheme is combined with a 10.59 μm CO2 laser dispersion interferometer for the first time to allow large bandwidth measurements in the 10-100 MHz range. The approach employed utilizes a 40 MHz acousto-optic cell operating on the frequency doubled CO2 beam which is obtained using a high 2nd harmonic conversion efficiency orientation patterned gallium arsenide crystal. The measured standard deviation of the line integrated electron density equivalent phase resolution obtained with digital phase demodulation technique, is 4 × 1017 m−2. Air flow was found to significantly affect the baseline of the phase signal, which an optical table cover was able to reduce considerably. The heterodyne dispersion interferometer (DI) approach is found to be robustly insensitive to motion, with measured phase shifts below baseline drifts even in the presence of several centimeters of retroreflector induced path length variations. Plasma induced dispersion was simulated with a wedged ZnSe plate and the measured DI phase shifts are consistent with expectations.
An ultra-low noise, high-voltage piezo-driver
Authors: Pisenti N. C. , Restelli A. , Reschovsky B. J. , Barker D. S. , Campbell G. K.
Published: December 2016

We present an ultra-low noise, high-voltage driver suited for use with piezoelectric actuators and other low-current applications. The architecture uses a flyback switching regulator to generate up to 250 V in our current design, with an output of 1 kV or more possible with small modifications. A high slew-rate op-amp suppresses the residual switching noise, yielding a total root-mean-square noise of ≈100 μV (1 Hz–100 kHz). A low-voltage (±10 V), high bandwidth signal can be summed with unity gain directly onto the output, making the driver well-suited for closed-loop feedback applications. Digital control enables both repeatable setpoints and sophisticated control logic, and the circuit consumes less than 150 mA at ±15 V.
Strong piezoelectric response in stable TiZnN2, ZrZnN2, and HfZnN2 found by ab initio high-throughput approach
Authors: Tholander C. , Andersson C. B. A. , Armiento R. , Tasnádi F. , Alling B.
Published: December 2016

The phase diagrams of the Ti-Zn-N, Zr-Zn-N, and Hf-Zn-N systems are determined using large-scale high-throughput density functional calculations. Thermodynamically stable ordered phases of TiZnN2, ZrZnN2, and HfZnN2 have been found to be promising candidates in piezoelectric devices/applications for energy harvesting. The identified stable phase of TiZnN2 is an ordered wurtzite superstructure, and the stable phases of ZrZnN2 and HfZnN2 have a layered structure with alternating tetrahedral ZnN and octahedral (Zr, Hf)N layers. All of the TMZnN2 (TM = Ti, Zn, Hf) structures exhibit electronic bandgaps and large piezoelectric constants, d33TiZnN2=14.21, d24ZrZnN2=−26.15, and d24HfZnN2=−21.99 pC/N. The strong piezoelectric responses and their thermodynamical stability make materials with these phases promising candidates for piezoelectric applications.
Strain effects on thermal transport and anisotropy in thin-films of Si and Ge
Authors: Foss Cameron J. , Aksamija Zlatan
Published: December 2016

As dimensions of nanoelectronic devices become smaller, reaching a few nanometers in modern processors, CPU hot spots become increasingly more difficult to manage. Applying mechanical strain in nanostructures provides an additional tuning mechanism for both electronic band structures and phonon dispersions that is independent of other methods such as alloying and dimensional confinement. By breaking crystal symmetry, strain increases anisotropy. We present thermal conductivity calculations, performed in thin Si and Ge strained films, using first principles calculations of vibrational frequencies under biaxial strain, along with a phonon Boltzmann transport equation within the relaxation time approximation. We find that, while in-plane transport is not strongly dependent on strain, the cross-plane component of the thermal conductivity tensor shows a clear strain dependence, with up to 20% increase (decrease) at 4% compressive (tensile) strain in both Si and Ge. We also uncover that strain emphasizes the anisotropy between in-plane and cross-plane thermal conductivity across several orders of magnitude in film thickness.
Comparison of flow-controlled calcium and barium carbonate precipitation patterns
Authors: Schuszter G. , De Wit A.
Published: December 2016

Various precipitation patterns can be obtained in flow conditions when injecting a solution of sodium carbonate in a confined geometry initially filled with a solution of either barium or calcium chloride. We compare here the barium and calcium carbonate precipitate structures as a function of initial concentrations and injection flow rate. We show that, in some part of the parameter space, the patterns are similar and feature comparable properties indicating that barium and calcium behave similarly in the related flow-controlled precipitation conditions. For other values of parameters though, the precipitate structures are different indicating that the cohesive and microscopic properties of barium versus calcium carbonate are then important in shaping the pattern in flow conditions.
Role of oxygen and nitrogen in n-type microcrystalline silicon carbide grown by hot wire chemical vapor deposition
Authors: Pomaska Manuel , Mock Jan , Köhler Florian , Zastrow Uwe , Perani Martina , Astakhov Oleksandr , Cavalcoli Daniela , Carius Reinhard , Finger Friedhelm , Ding Kaining
Published: December 2016

N-type microcrystalline silicon carbide (μc-SiC:H(n)) deposited by hot wire chemical vapor deposition provides advantageous opto-electronic properties for window layer material in silicon-based thin-film solar cells and silicon heterojunction solar cells. So far, it is known that the dark conductivity (σd) increases with the increase in the crystallinity of μc-SiC:H(n)films. However, due to the fact that no active doping source is used, the mechanism of electrical transport in these films is still under debate. It is suggested that unintentional doping by atmospheric oxygen (O) or nitrogen (N) contamination plays an important role in the electrical transport. To investigate the impact of O and N, we incorporated O and N in μc-SiC:H(n) films and compared the influence on the microstructural, electronic, and optical properties. We discovered that, in addition to increasing the crystallinity, it is also possible to increase the σd by several orders of magnitude by increasing the O-concentration or the N-concentration in the films. Combining a high concentration of O and N, along with a high crystallinity in the film, we optimized the σd to a maximum of 5 S/cm.
“Break-junction” technique in application to layered superconductors (Review Article)
Authors: Kuzmichev S. A. , Kuzmicheva T. E.
Published: December 2016

A comprehensive study of superconductor-constriction-superconductor contacts, obtained using the “break-junction” technique in layered superconductors. Depending on the constriction transparency, tunneling and SnS Andreev spectroscopies could be used to directly determine the values of the superconducting gaps, characteristic BCS ratios and temperature dependences of the gaps in cuprates, magnesium diboride and iron pnictides and chalcogenides. Based on these results we can estimate the gap anisotropy and the electron-boson coupling constants. The advantages and drawbacks of “break-junction” technique are discussed, and we demonstrate that this method is powerful enough for the study of optical phonon modes in high-temperature superconducting cuprates and for creating contacts with selective transparency in Mg1-xAlxB2 compounds.
Study on the mutual influence between enterprises: A complex network perspective of China's PV enterprises
Authors: Sun Mei , Zhang Peipei , Gao Cuixia , Ji Jiawen , Ampimah Benjamin Chris
Published: December 2016

With the economic integration of the world, the correlation between enterprises does not only include their cooperative and competitive relationships but also involves their mutual relationship in the market. In this paper, a new index, with considering cooperative, competitive as well as market relationships, is proposed to quantify the mutual influence between any two enterprises. Then, the influence index threshold network is built from a new perspective of complex network theory. Focusing on the empirical research by taking China's photovoltaic (PV) industry as an example, the leading enterprises are identified by their k-shell decomposition analysis in conjunction with their nodal degree. In addition, the reasons for some belong to the leading enterprises are explained using random matrix theory. The results show that leading enterprises with core technologies producing basic products, having complete industrial chain, and owning brand products are likely to have prominent positions during the fierce competition. Finally, some suggestions are made to promote the sustainable development of China's PV market.
Optimal coordination of renewable wind and pumped storage with thermal power generation for maximizing economic profit with considerations for environmental emission based on newly developed heuristic optimization algorithm
Authors: Nazari M. E. , Ardehali M. M.
Published: December 2016

The integration of renewable wind and pumped storage with thermal power generation allows for dispatch of wind energy by generation companies (GENCOs) interested in participation in energy and ancillary services markets. However, to realize the maximum economic profit, optimal coordination and accounting for reduction in cost for environmental emission are essential. The goal of this study is to develop a simulation model for maximizing economic profit from coordination of renewable wind and pumped storage with thermal power generation for a GENCO with the participation in energy and ancillary services markets with considerations for environmental emission and uncertainty associated with wind power based on a newly developed heuristic optimization algorithm. The simulation results for validation of the heuristic optimization algorithm, as compared with those reported in the literature, show profit improvements of 8.58%–14.53% for uncoordinated and coordinated wind-pumped storage systems. It is determined that for a GENCO with 13 MW wind farm capacity and 1662 MW thermal units, for meeting an average demand of 1129 MW, the utilization of 120 MW pumped storage in a coordinated wind-pumped storage-thermal system results in reduction of environmental emission by 13.54%, which leads to an increase in profit by 2.10%, as compared with operation with no pumped storage unit.
Band alignment of MAPb(I1–xBrx)3 thin films by vacuum deposition
Authors: Zhou Xianzhong , Ye Wang , Li Xiaoli , Zheng Wei , Lin Richeng , Huang Feng , Zhong Dingyong
Published: December 2016

In this work, the mixed bromide iodide lead perovskites CH3NH3Pb(I1–xBrx)3 (0 ≤ x ≤ 0.67) thin films were prepared by co-evaporation of CH3NH3I, PbI2, and PbBr2. The electronic properties of CH3NH3Pb(I1–xBrx)3 thin films were investigated by X-ray and ultraviolet photoelectron spectroscopy in-situ. The results of core level binding energy show that there is no chemical shift of the C1s, N1s, Br3d5, and I3d5 when the Br composition changes, while there is an approximately linear chemical shift of Pb4f7 to higher binding energy as the Br composition increases. The density functional theory calculation reveals that there is more charge transfer from Pb to Br than I, which results in the chemical shift of Pb4f states. On the other hand, the valence band maximum increases as the Br composition increases, while the work function shows no obvious change, because the conduction band is dominated by Pb 6p orbitals while the valence band is dominated by halide p orbitals. Our work demonstrates the adjustability of the energy level alignment of MAPb(I1–xBrx)3 by the Br composition.
Barriers to accessing primary health care: comparing Australian experiences internationally
Authors: Corscadden Lisa , Levesque Jean-Frederic , Lewis Virginia , Breton Mylaine , Sutherland Kim , Weenink Jan-Willem , Haggerty Jeannie , Russell Grant
Published: December 2016

Most highly developed economies have embarked on a process of primary health care (PHC) transformation. To provide evidence on how nations vary in terms of accessing PHC, the aim of this study is to describe the extent to which barriers to access were experienced by adults in Australia compared with other countries. Communities participating in an international research project on PHC access interventions were engaged to prioritise questions from the 2013 Commonwealth Fund International Health Policy Survey within a framework that conceptualises access across dimensions of approachability, acceptability, availability, affordability and appropriateness. Logistic regression models, with barriers to access as outcomes, found measures of availability to be a problematic dimension in Australia; 27% of adults experienced difficulties with out-of-hours access, which was higher than 5 of 10 comparator countries. Although less prevalent, affordability was also perceived as a substantial barrier; 16% of Australians said they had forgone health care due to cost in the previous year. After adjusting for age and health status, this barrier was more common in Australia than 7 of 10 countries. Findings of this integrated assessment of barriers to access offer insights for policymakers and researchers on Australia’s international performance in this crucial PHC domain.
Electrotonic coupling of excitable and nonexcitable cells in the heart revealed by optogenetics
Authors: Quinn T. Alexander , Camelliti Patrizia , Rog-Zielinska Eva A. , Siedlecka Urszula , Poggioli Tommaso , O'Toole Eileen T. , Knöpfel Thomas , Kohl Peter
Published: December 2016

Significance

Heart pumping is triggered and coordinated by action potentials (APs) originating in and spreading among electrically excitable heart muscle cells (myocytes) via electrotonic coupling. Cardiac nonmyocytes are thought not to participate in AP conduction in situ, although heterocellular electrotonic coupling is common in cell culture. We used optogenetic tools involving cell-specific expression of a voltage-reporting fluorescent protein to monitor electrical activity in myocytes or nonmyocytes of mouse hearts. We confirm the suitability of this technique for measuring cell type-specific voltage signals and show that, when expressed in nonmyocytes, myocyte AP-like signals can be recorded in cryoinjured scar border tissue. This direct evidence of heterocellular electrotonic coupling in the whole heart necessitates a review of current concepts on cardiac electrical connectivity.
Artemisia annua
mutant impaired in artemisinin synthesis demonstrates importance of nonenzymatic conversion in terpenoid metabolism
Authors: Czechowski Tomasz , Larson Tony R. , Catania Theresa M. , Harvey David , Brown Geoffrey D. , Graham Ian A.
Published: December 2016

Significance

The antimalarial artemisinin is a sesquiterpene lactone produced by glandular secretory trichomes on the leaves of
Artemisia annua
. Using a mutant impaired in artemisinin synthesis, we demonstrate the importance of nonenzymatic conversions in terpenoid metabolism and highlight the ability of
A. annua
glandular secretory trichomes to redirect flux into a sesquiterpene epoxide. The research presented offers insight into the mechanism of the final steps of artemisinin synthesis in
A. annua
, with significant implications for future production of secondary compounds in native versus heterologous host systems.
Cosmc
is an X-linked inflammatory bowel disease risk gene that spatially regulates gut microbiota and contributes to sex-specific risk
Authors: Kudelka Matthew R. , Hinrichs Benjamin H. , Darby Trevor , Moreno Carlos S. , Nishio Hikaru , Cutler Christopher E. , Wang Jianmei , Wu Huixia , Zeng Junwei , Wang Yingchun , Ju Tongzhong , Stowell Sean R. , Nusrat Asma , Jones Rheinallt M. , Neish Andrew S. , Cummings Richard D.
Published: December 2016

Significance

Inflammatory bowel disease (IBD) is a devastating illness that affects 1.6 million people in the United States and disproportionately affects males in early onset disease. However, IBD genes that contribute to sex-specific risk are unexplored. The gut microbiota interfaces the host with its environment and exhibits alterations in spatial organization in IBD with dysbiosis in the mucosa but a relatively unaffected lumen. Core 1 β3GalT-specific molecular chaperone (
Cosmc
) was recently identified as an IBD risk gene on the X chromosome by genome-wide association study. We functionally evaluated Cosmc in IBD and discovered that the loss of
Cosmc
leads to gut inflammation in males but not females and a spatial pattern of dysbiosis resembling IBD. Thus,
Cosmc
contributes to sex bias in IBD and spatially regulates the gut microbiota.
Direct evidence of interaction-induced Dirac cones in a monolayer silicene/Ag(111) system
Authors: Feng Ya , Liu Defa , Feng Baojie , Liu Xu , Zhao Lin , Xie Zhuojin , Liu Yan , Liang Aiji , Hu Cheng , Hu Yong , He Shaolong , Liu Guodong , Zhang Jun , Chen Chuangtian , Xu Zuyan , Chen Lan , Wu Kehui , Liu Yu-Tzu , Lin Hsin , Huang Zhi-Quan , Hsu Chia-Hsiu , Chuang Feng-Chuan , Bansil Arun , Zhou X. J.
Published: December 2016

Significance

Silicene is a one-atom-thick 2D crystal of silicon. The low-energy Dirac cone states in silicene lie at the heart of all novel quantum phenomena and potential applications. However, so far, the evidence of Dirac cones in silicene is highly controversial. We report a direct observation of Dirac cones in monolayer silicene grown on a Ag(111) substrate. We further show that this unusual Dirac cone structure originates from the interaction of silicene with the Ag(111) substrate, establishing the case of a unique type of Dirac fermion generated through the interaction of two different constituents. The observation of Dirac cones in silicene(3 × 3)/Ag(111) opens a unique materials platform for investigating unusual quantum phenomena and for applications based on 2D silicon systems.
Unexpected central role of the androgen receptor in the spontaneous regeneration of myelin
Authors: Bielecki Bartosz , Mattern Claudia , Ghoumari Abdel M. , Javaid Sumaira , Smietanka Kaja , Abi Ghanem Charly , Mhaouty-Kodja Sakina , Ghandour M. Said , Baulieu Etienne-Emile , Franklin Robin J. M. , Schumacher Michael , Traiffort Elisabeth
Published: December 2016

Significance

Myelin allows the rapid conduction of electrical signals and provides axons with metabolic support. It appeared relatively late in evolution in hinge-jawed vertebrates and concomitantly with the emergence of the androgen receptor (AR), hinting at a specific role for androgens in myelination. Here, we show that after demyelination of the central nervous system (CNS), the male gonad, testosterone, and AR favor astrocyte recruitment and myelin regeneration by oligodendrocytes. In their absence, astrocytes remain sparse and peripheral-type remyelination, classically associated with Schwann cells, is predominantly detected. These findings reveal a novel role of androgen signaling in CNS myelin formation and glial cell communication, with possible implications for demyelinating, psychiatric, and age-related disorders.
Simultaneous dimension reduction and adjustment for confounding variation
Authors: Lin Zhixiang , Yang Can , Zhu Ying , Duchi John , Fu Yao , Wang Yong , Jiang Bai , Zamanighomi Mahdi , Xu Xuming , Li Mingfeng , Sestan Nenad , Zhao Hongyu , Wong Wing Hung
Published: December 2016

Significance

With the advancement in high-throughput technologies, analyzing high-dimensional data has become a common task. Dimension reduction methods have been applied to visualize and identify dominant patterns in high-dimensional data. Confounding factors, commonly observed in high-throughput biological experiments, can affect the performance of these methods, and other downstream analysis. Here, we develop a method by coupling dimension reduction with the adjustment for confounder effects. Our method is able to capture the underlying patterns, as demonstrated by a human brain exon array dataset, a model organism ENCODE RNA sequencing dataset, and simulations.
Growth hormone-releasing hormone receptor antagonists inhibit human gastric cancer through downregulation of PAK1–STAT3/NF-κB signaling
Authors: Gan Jinfeng , Ke Xiurong , Jiang Jiali , Dong Hongmei , Yao Zhimeng , Lin Yusheng , Lin Wan , Wu Xiao , Yan Shumei , Zhuang Yixuan , Chu Wai Kit , Cai Renzhi , Zhang Xianyang , Cheung Herman S. , Block Norman L. , Pang Chi Pui , Schally Andrew V. , Zhang Hao
Published: December 2016

Significance

Gastric cancer (GC) is a leading and lethal malignancy in the world. Unfortunately, therapeutics targeting GC lag behind those of many other cancers, and the effective treatment options are limited. Here we report that increased expression of growth hormone-releasing hormone receptor (GHRH-R) in tumor specimens is significantly associated with tumorigenic progression and poor clinical outcome of GC patients. MIA-602, a highly potent GHRH-R antagonist, effectively inhibits GC growth in vitro and in vivo. The anti-neoplastic effects were mediated by blockage of the p21-activated kinase 1 (PAK1)–signal transducer and activator of transcription 3 (STAT3)/nuclear factor-κB (NF-κB) axis. Thus, GHRH-R presents a molecular marker and therapeutic target of GC, and MIA-602 demonstrates excellent therapeutic potential against human GC.
Effects of Cr on stacking-fault energy and damping capacity of FeMn
Authors: Wu B. , Qian B. , Wen Y.
Published: December 2016

Effects of Cr on the stacking-fault energy (SFE) and damping capacity were investigated by experimental and theoretical methods. The effect of Cr on SFE was thermodynamically calculated; the damping capacity, phase composition, microstructure and corrosion resistance were experimentally measured. The results showed that Cr increases the SFE of Fe17MnxCr which resulted in the decay of damping capacity; the increase in α’ martensite with the increasing Cr content above 6% pins the movement of Shockley partials’ dislocation and thus makes the damping capacity even worse; the optimum Cr content of Fe17MnxCr to improve the corrosion resistance in water vapour with a lesser decrease in damping capacity is about 6%.
Electrodeposition and characterisation of Cu–MWCNTs nanocomposite coatings
Authors: Ramalingam S. , Balakrishnan K. , Shanmugasamy S. , Subramania A.
Published: December 2016

The Cu–Multi-walled carbon nanotubes (MWCNTs) nanocomposite coatings were prepared by the electrodeposition process using MWCNTs in an acid copper plating bath under optimised bath composition and process conditions. The Cu–MWCNTs nanocomposite thin film was characterised for structural, mechanical and anti-corrosion properties. The X-ray diffraction confirmed the crystallite structures and texture of pure copper and Cu–MWCNTs nanocomposite coatings. The field emission scanning electron microscopy showed that the MWCNTs were uniformly distributed in the copper matrix as fine crystallites. The Vickers microhardness test results showed that the microhardness of Cu–MWCNTs nanocomposite coating was much higher than that of the pure copper coating. The electrochemical AC-impedance and Tafel polarisation studies confirmed that the Cu–MWCNTs nanocomposite coating was found to have higher corrosion resistance than the pure copper coating in 3.5% NaCl (w/v) solution.
Sonic hedgehog pathway activation increases mitochondrial abundance and activity in hippocampal neurons
Authors: Yao Pamela J. , Manor Uri , Petralia Ronald S. , Brose Rebecca D. , Wu Ryan T. Y. , Ott Carolyn , Wang Ya-Xian , Charnoff Ari , Lippincott-Schwartz Jennifer , Mattson Mark P.
Published: December 2016

Mitochondria are essential organelles whose biogenesis, structure, and function are regulated by many signaling pathways. We present evidence that, in hippocampal neurons, activation of the Sonic hedgehog (Shh) signaling pathway affects multiple aspects of mitochondria. Mitochondrial mass was increased significantly in neurons treated with Shh. Using biochemical and fluorescence imaging analyses, we show that Shh signaling activity reduces mitochondrial fission and promotes mitochondrial elongation, at least in part, via suppression of the mitochondrial fission protein dynamin-like GTPase Drp1. Mitochondria from Shh-treated neurons were more electron-dense, as revealed by electron microscopy, and had higher membrane potential and respiratory activity. We further show that Shh protects neurons against a variety of stresses, including the mitochondrial poison rotenone, amyloid β-peptide, hydrogen peroxide, and high levels of glutamate. Collectively our data suggest a link between Shh pathway activity and the physiological properties of mitochondria in hippocampal neurons.
Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R
Authors: McCarthy Davis J , Campbell Kieran R , Lun Aaron T L , Wills Quin F
Published: December 2016

Motivation

Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene expression at the level of individual cells. However, preparing raw sequence data for further analysis is not a straightforward process. Biases, artifacts and other sources of unwanted variation are present in the data, requiring substantial time and effort to be spent on pre-processing, quality control (QC) and normalization.

Results

We have developed the R/Bioconductor package scater to facilitate rigorous pre-processing, quality control, normalization and visualization of scRNA-seq data. The package provides a convenient, flexible workflow to process raw sequencing reads into a high-quality expression dataset ready for downstream analysis. scater provides a rich suite of plotting tools for single-cell data and a flexible data structure that is compatible with existing tools and can be used as infrastructure for future software development.

Availability and Implementation

The open-source code, along with installation instructions, vignettes and case studies, is available through Bioconductor at http://bioconductor.org/packages/scater.

Supplementary information

Supplementary data are available at Bioinformatics online.
RADER: a RApid DEcoy Retriever to facilitate decoy based assessment of virtual screening
Authors: Wang Ling , Pang Xiaoqian , Li Yecheng , Zhang Ziying , Tan Wen
Published: December 2016

Evaluation of the capacity for separating actives from challenging decoys is a crucial metric of performance related to molecular docking or a virtual screening workflow. The Directory of Useful Decoys (DUD) and its enhanced version (DUD-E) provide a benchmark for molecular docking, although they only contain a limited set of decoys for limited targets. DecoyFinder was released to compensate the limitations of DUD or DUD-E for building target-specific decoy sets. However, desirable query template design, generation of multiple decoy sets of similar quality, and computational speed remain bottlenecks, particularly when the numbers of queried actives and retrieved decoys increases to hundreds or more. Here, we developed a program suite called RApid DEcoy Retriever (RADER) to facilitate the decoy-based assessment of virtual screening. This program adopts a novel database-management regime that supports rapid and large-scale retrieval of decoys, enables high portability of databases, and provides multifaceted options for designing initial query templates from a large number of active ligands and generating subtle decoy sets. RADER provides two operational modes: as a command-line tool and on a web server. Validation of the performance and efficiency of RADER was also conducted and is described.

Availability and Implementation

RADER web server and a local version are freely available at http://rcidm.org/rader/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Structural insight to mutation effects uncover a common allosteric site in class C GPCRs
Authors: Harpsøe Kasper , Boesgaard Michael W , Munk Christian , Bräuner-Osborne Hans , Gloriam David E
Published: December 2016

Motivation

Class C G protein-coupled receptors (GPCRs) regulate important physiological functions and allosteric modulators binding to the transmembrane domain constitute an attractive and, due to a lack of structural insight, a virtually unexplored potential for therapeutics and the food industry. Combining pharmacological site-directed mutagenesis data with the recent class C GPCR experimental structures will provide a foundation for rational design of new therapeutics.

Results

We uncover one common site for both positive and negative modulators with different amino acid layouts that can be utilized to obtain selectivity. Additionally, we show a large potential for structure-based modulator design, especially for four orphan receptors with high similarity to the crystal structures.

Availability and Implementation

All collated mutagenesis data is available in the GPCRdb mutation browser at http://gpcrdb.org/mutations/ and can be analyzed online or downloaded in excel format.

Supplementary information

Supplementary data are available at Bioinformatics online.
Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data
Authors: Shringarpure Suyash S , Mathias Rasika A , Hernandez Ryan D , O’Connor Timothy D , Szpiech Zachary A , Torres Raul , De La Vega Francisco M , Bustamante Carlos D , Barnes Kathleen C , Taub Margaret A ,   CAAPA Consortium
Published: December 2016

Motivation

Variant calling from next-generation sequencing (NGS) data is susceptible to false positive calls due to sequencing, mapping and other errors. To better distinguish true from false positive calls, we present a method that uses genotype array data from the sequenced samples, rather than public data such as HapMap or dbSNP, to train an accurate classifier using Random Forests. We demonstrate our method on a set of variant calls obtained from 642 African-ancestry genomes from the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA), sequenced to high depth (30X).

Results

We have applied our classifier to compare call sets generated with different calling methods, including both single-sample and multi-sample callers. At a False Positive Rate of 5%, our method determines true positive rates of 97.5%, 95% and 99% on variant calls obtained using Illuminas single-sample caller CASAVA, Real Time Genomics multisample variant caller, and the GATK UnifiedGenotyper, respectively. Since NGS sequencing data may be accompanied by genotype data for the same samples, either collected concurrent to sequencing or from a previous study, our method can be trained on each dataset to provide a more accurate computational validation of site calls compared to generic methods. Moreover, our method allows for adjustment based on allele frequency (e.g. a different set of criteria to determine quality for rare versus common variants) and thereby provides insight into sequencing characteristics that indicate call quality for variants of different frequencies.

Availability and Implementation

Code is available on Github at: https://github.com/suyashss/variant_validation

Supplementary information

Supplementary data are available at Bioinformatics online.
SVScore: an impact prediction tool for structural variation
Authors: Ganel Liron , Abel Haley J ,   FinMetSeq Consortium, Hall Ira M
Published: December 2016

Here we present SVScore, a tool for in silico structural variation (SV) impact prediction. SVScore aggregates per-base single nucleotide polymorphism (SNP) pathogenicity scores across relevant genomic intervals for each SV in a manner that considers variant type, gene features and positional uncertainty. We show that the allele frequency spectrum of high-scoring SVs is strongly skewed toward lower frequencies, suggesting that they are under purifying selection, and that SVScore identifies deleterious variants more effectively than alternative methods. Notably, our results also suggest that duplications are under surprisingly strong selection relative to deletions, and that there are a similar number of strongly pathogenic SVs and SNPs in the human population.

Availability and Implementation

SVScore is implemented in Perl and available freely at {{http://www.github.com/lganel/SVScore}} for use under the MIT license.

Supplementary information

Supplementary data are available at Bioinformatics online.
A Cluster-Randomized Trial to Assess the Efficacy of Targeting Trachoma Treatment to Children
Authors: Amza Abdou , Kadri Boubacar , Nassirou Beido , Cotter Sun Y. , Stoller Nicole E. , Zhou Zhaoxia , Bailey Robin L. , Mabey David C. , Porco Travis C. , Keenan Jeremy D. , Gaynor Bruce D. , West Sheila K. , Lietman Thomas M.
Published: December 2016

Background.

The World Health Organization recommends annual treatment of entire trachoma-endemic communities, although children typically have a higher load, longer duration, and greater likelihood of infection.

Methods.

Forty-eight communities in Matameye, Niger, were randomized to annual oral azithromycin treatment of the entire community or biannual treatment of children aged 0–12 years only. Both children and adults were monitored for ocular chlamydial infection by polymerase chain reaction.

Results.

The prevalence of childhood infection was reduced in the annually treated arm from 21.2% (95% confidence interval [CI], 15.2%–28.0%) at baseline to 5.8% (95% CI, 3.2%–9.0%) at 36 months (P < .001) and in the biannual arm from 20.2% (95% CI, 15.5%–25.3%) to 3.8% (95% CI, 2.2%–6.0%; P < .001). Adult infection in the annual arm was reduced from 1.7% (95% CI, .9%–2.7%) to 0.3% (95% CI, .0%–.7%) and in the biannual arm from 1.2% (95% CI, .5%–2.2%) to 0.0% (95% CI, .0%–.7%; P = .005). The effect of biannual treatment of children compared with annual treatment of the entire community in both children (95% CI, –.04% to .02%) and adults (95% CI, .9%–2.7%) excluded the prespecified noninferiority threshold of 6% (P = .003 and P < .001, respectively).

Conclusions.

Periodic distribution of antibiotics to children in trachoma-endemic communities reduces chlamydial infection in both children and untreated adults, suggesting a form of herd protection. Biannual treatment of children was comparable to (specifically, noninferior to) annual treatment of the entire community, and may offer lower antibiotic use and other logistical advantages.

Clinical Trials Registration.

NCT00792922.
Increased Sexually Transmitted Disease Testing Among Sexually Active Persons Receiving Medical Care for Human Immunodeficiency Virus Infection in the United States, 2009–2013
Authors: Mattson Christine L. , Bradley Heather , Beer Linda , Johnson Christopher , Pearson William S. , Shouse R. Luke ,   for the Medical Monitoring Project
Published: December 2016

Background.

Current guidelines recommend that all sexually active human immunodeficiency virus (HIV)–infected persons be tested at least annually for syphilis, chlamydia, and gonorrhea. We examined temporal trends in syphilis, chlamydia, and gonorrhea testing among sexually active HIV-infected adults receiving medical care in the United States during 2009–2013.

Methods.

Using medical record data from the Medical Monitoring Project, a population-based HIV surveillance system, we assessed the proportion of adults receiving HIV medical care who were tested for syphilis, chlamydia, and gonorrhea in the past 12 months by year and stratified by sex and sexual behavior, age, and race/ethnicity.

Results.

During 2009–2013, the proportion of sexually active HIV-infected adults receiving medical care who were tested in the past year for all 3 examined sexually transmitted diseases (STDs) increased from 20% to 36% (PTREND < .01). Overall testing for syphilis increased from 55% to 65% (PTREND < .01), and significant increases were noted for the following subgroups: men who have sex with men (58% to 69%), non-Hispanic whites (48% to 64%), and all age groups with the exception of persons aged 18–29 year. Overall testing for chlamydia and gonorrhea increased from 22% to 42% (PTREND < .01), and significant increases were noted for most subgroups.

Conclusions.

STD testing significantly increased among sexually active HIV-infected adults receiving medical care; however, the majority of persons were not tested for all 3 STDs in 2013. While increased testing indicates progress, testing remained far below recommended guidelines. Our findings suggest enhanced efforts may be warranted to screen all sexually active HIV-infected adults for syphilis, chlamydia, and gonorrhea.
Cajal and Psychology
Authors: Ehrlich Benjamin
Published: December 2016

In the second half of the nineteenth century, psychological inquiry was shifting away from the realm of philosophy and into the natural sciences. The associationalist school believed that the basic elements of the psyche, thoughts, feelings, sensations, and perceptions, were available to study. Cajal’s work affected other disciplines outside of neuroscience. His discovery of distinctly individual cells inside the brain seemed to confirm the associationalist model of psychology. He focused on these spindly, fragile-looking cells as the units of psychological function that he called “the psychic cells.” Even with his work, he was not convinced of the psychological interpretations of the neuron. Cajal knew that contemporary neuroanatomy was ultimately incapable of explaining psychology.
Cajal’s Psyche and His Readings of Freud
Authors: Ehrlich Benjamin
Published: December 2016

Cajal’s interest in hypnosis and suggestion extended into the realm of dreams. After one promising paper, he did not address the subject for the next decade. At sixty-six years of age Cajal started to record a personal dream diary. Although framed as an intellectual project aimed at disproving Freud’s theory, Cajal’s dream diary was deeply personal, as its writing spans a period during which he was acutely depressed, continuing intermittently until his death. In his diary, Cajal notes the interruption of many of his dreams due to intense attacks of emotional anguish. However, Cajal never inquires into the cause of these disturbances; in fact, any traumatic events suggested in his dreams are treated as lacking emotional significance. Cajal treats his dreams as though they were scientific propositions, beholden to the same rules of logic. He claims to see no evidence of repressed desire.
“The Father of Modern Neuroscience” and His Father
Authors: Ehrlich Benjamin
Published: December 2016

This chapter follows the relationship between Cajal and his father, Justo Ramón Casasús. Cajal’s father was his first teacher and, Cajal believed, his true master. When Cajal was four years old, his father started teaching him the basics of reading, writing, arithmetic, geography, physics, and even French. Their classroom was a cave that shepherds had abandoned. Cajal learned how to learn from his father, at a time during which such early academic pursuits were extremely unusual. Cajal’s father treated Cajal’s artistic impulses as symptoms of a psychological disease, which he tried time and again to eradicate. Don Justo never stopped trying to draw his son into medicine, teaching him anatomy and dissection, which inspired him to attend medical school. While Cajal earned his doctorate, inspiring his father’s pride, he also discovered histology, which became his own passion and opened a path toward independence.
The Dream Diary’s Strange Fate
Authors: Ehrlich Benjamin
Published: December 2016

Cajal’s last will and testament bequeathed his scientific materials to his disciples at the Cajal Institute and his personal belongings to his family. The mysterious dream book of Santiago Ramón y Cajal was not among the two thousand extant manuscripts; scholars generally assumed that the unpublished work was lost during the Spanish Civil War. In fact, Cajal’s unfinished dream book was not a formal manuscript but, rather, a collection of loose sheets of used paper and notes composed in the margins of newspapers and magazines. It was never formally published as a book. Just before he died, Cajal surreptitiously handed over this material to José Germain Cebrían, who dutifully typed up the scattered diary into a proper manuscript, although Cajal’s calligraphy often was illegible, including numerous errors, deletions, and blank spaces. The dream diary finally surfaced in November of 2014 when Cajal’s work became public domain.
The Dreams of Cajal
Authors: Ramón y Cajal Santiago , Cebrián José Germain , Romero José Rallo , Ehrlich Benjamin
Published: December 2016

For last five years of his life, Cajal abandoned his own neurobiological research and concentrated on psychological manuscripts, including a new “dream book.” Although his stated intention was to publish, the project was never released. The unfinished work was thought to be lost, until recently, when a Spanish book appeared claiming to feature the dreams of Cajal, along with the untold story of their complex journey into print. The dream diary of Cajal, only recently uncovered and never before read by Anglophones, offers a rare and intimate glimpse into the psyche of its legendary author. The first entry is dated 1918 and the last entry appears in 1934, the year of his death. There are one-hundred-and-three entries, recorded on scraps of used paper and in the margins of books and journals. The manuscript was then transcribed by José Germain Cebrían. This is the first-ever English translation of that work.
Health as the Capacity for Action
Authors: Sullivan Mark D.
Published: December 2016

Objective definitions of health and disease are favored because they promise a value-free measure of health problems and health care needs. But objective health does not simply cause the subjective experience of health. Self-rated health predicts mortality, disability, and hospitalizations for up to a decade after controlling for objective measures of health. Objective tissue abnormalities cannot be discovered to be pathological without reference to the experiences of patients acting in their natural environment. Patients adapt to chronic illness and its functional deficits over time with real improvements in their quality of life. Problems like pain and depression do not distort quality of life assessments, but are at their core. Since neither objective nor subjective models of health are valid, we must derive a different model: health as capacity for action. Any adequate approach to health must foster the patient’s sense of agency, her capacity to achieve her vital goals.