bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental and ab initio studies on sub-lattice ordering and magnetism in Co2Fe(Ge1−xSix) alloys
Authors: Deka Bhargab , Kundu Ashis , Ghosh Subhradip , Srinivasan A.
Published: October 2015

Crystallographic and magnetic properties of bulk Co2Fe(Ge1−xSix) alloys with 0 ≤ x ≤ 1, synthesized by arc melting method, have been studied. Co2FeSi alloy has been found to crystallize with L21 structure, but the super-lattice peaks are absent in the X-ray diffraction patterns of alloys containing high Ge concentration. Unit cell volume of this series of alloys decreased from 185.2 to 178.5 Å3 as Si content was increased from 0 to 1.00. All alloy compositions exhibit ferromagnetic behavior with a high Curie temperature (TC). TC showed a systematic variation with x. A comparison between the values of saturation magnetization (Ms) and effective moment per magnetic atom pc estimated from the temperature dependent susceptibility data above TC, shows that the alloys have half-metallic character. The alloy with x = 0 follows Slater-Pauling (S-P) rule with Ms of 5.99μB. However, Ms for the alloy with x = 1.00 was found to be 5.42μB, which is lower than the value of 6.0μB predicted by S-P rule. Since atomic disorder is known to affect the Ms and electronic structure of these alloys, ab initio calculations were carried out to explain the deviation in observed Ms from S-P rule prediction and the half-metallic character of the alloys. Ab initio calculations reveal that alloys with L21 structure have Ms value as predicted by S-P rule. However, introduction of 12.5% DO3 disorder, which occurs due to swapping of Co and Fe atoms in the unit cell, decreases Ms of alloys with x > 0 from the S-P prediction to values obtained experimentally. The results analyzed from the view point of electronic structure of the alloys in different ordered states bring out the influence of disorder on the observed magnetic properties of these technologically important alloys.
Evidence for enhancement of vortex matching field above 5 T and oxygen-deficient annuli around barium-niobate nanorods
Authors: Horii Shigeru , Haruta Masakazu , Ichinose Ataru , Doi Toshiya
Published: October 2015

We report the dependence of critical temperature (Tc), the irreversibility line, the microstructure of nanorods with perovskite-based barium niobates (BNOs), and the c-axis length of the YBa2Cu3Oy (Y123) superconducting matrix on the BNO-doping level and growth temperature for Y123 thin films with BNO nanorods. The characteristic field (Bcr) determined from the vortex-Bose-glass-like irreversibility lines in Y123+BNO films is strongly correlated to the BNO nanorod density and the growth temperature. Despite a monotonic decrease in Tc with increasing Bcr and nanorod density, the irreversibility fields (Birr) were enhanced up to Bcr ∼ 5 T. From the Bcr value and the mean diameter of the BNO nanorod (∼10 nm), we estimate that a lower Tc matrix annulus with a diameter of 12–14 nm exists around each BNO nanorod due to the strong interface strains. Our present study suggests that generation of this lower Tc region around each BNO nanorod increases the vortex-pinning strength significantly and, moreover, may offer a new way of enhancing Birr for REBa2Cu3Oy film with nanorods.
An excited-state approach within full configuration interaction quantum Monte Carlo
Authors: Blunt N. S. , Smart Simon D. , Booth George H. , Alavi Ali
Published: October 2015

We present a new approach to calculate excited states with the full configuration interaction quantum Monte Carlo (FCIQMC) method. The approach uses a Gram-Schmidt procedure, instantaneously applied to the stochastically evolving distributions of walkers, to orthogonalize higher energy states against lower energy ones. It can thus be used to study several of the lowest-energy states of a system within the same symmetry. This additional step is particularly simple and computationally inexpensive, requiring only a small change to the underlying FCIQMC algorithm. No trial wave functions or partitioning of the space is needed. The approach should allow excited states to be studied for systems similar to those accessible to the ground-state method due to a comparable computational cost. As a first application, we consider the carbon dimer in basis sets up to quadruple-zeta quality and compare to existing results where available.
Millisecond non-melt laser annealing of phosphorus implanted germanium: Influence of nitrogen co-doping
Authors: Stathopoulos S. , Tsetseris L. , Pradhan N. , Colombeau B. , Tsoukalas D.
Published: October 2015

In this work, we present the results obtained using a CO2 laser source at 10.6 μm wavelength for the study of the non-melt annealing of phosphorus doped germanium in the millisecond regime. Main objective of this paper is the demonstration of electrically active n+-p junctions in germanium by implanting phosphorus in p-type substrate while trying to maintain minimal dopant diffusion, which is a critical issue for scaling germanium devices. In addition to the phosphorus diffusion studies, we also explore the presence of nitrogen introduced in the substrate together with phosphorus and we conclude that it can further reduce dopant movement at the expense of lower activation level. The observation is confirmed by both electrical and SIMS measurements. Moreover, density functional theory calculations show that nitrogen-phosphorus co-doping of germanium creates stable N-P complexes that, indeed, are consistent with the deactivation and diffusion suppression of phosphorus.
Position-sensitive change in the transition metal L-edge fine structures
Authors: Gulec Ahmet , Phillips Patrick J. , Klie Robert F.
Published: October 2015

Studying the structure and composition of solid-state materials on the atomic scale has become nearly routine in transmission electron microscopy with the development of novel electron optics and electron sources. In particular, with spatial resolutions better than 0.1 nm and energy resolution smaller than 100 meV, the stoichiometry, bonding, and coordination can now be examined on similar scales. Aberration-corrected scanning transmission electron microscopy and electron energy-loss spectroscopy (EELS) have played a crucial role in identifying charge ordering, valence, and as spin state transitions in transition metal perovskite oxides. In this letter, we investigate the effects of ever-decreasing electron-probe sizes on the measured near-edge fine-structure of the transition metal core-loss edge using EELS. We find that for certain transition metal perovskites, the position of the electron probe with respect to the atomic column is crucial in determining the correct valence state. Several reasons for the observed position-sensitive EELS fine-structure are discussed.
Giant supercurrent states in a superconductor-InAs/GaSb-superconductor junction
Authors: Shi Xiaoyan , Yu Wenlong , Jiang Zhigang , Andrei Bernevig B. , Pan W. , Hawkins S. D. , Klem J. F.
Published: October 2015

Superconductivity in topological materials has attracted a great deal of interest in both electron physics and material sciences since the theoretical predictions that Majorana fermions can be realized in topological superconductors. Topological superconductivity could be realized in a type II, band-inverted, InAs/GaSb quantum well if it is in proximity to a conventional superconductor. Here, we report observations of the proximity effect induced giant supercurrent states in an InAs/GaSb bilayer system that is sandwiched between two superconducting tantalum electrodes to form a superconductor-InAs/GaSb-superconductor junction. Electron transport results show that the supercurrent states can be preserved in a surprisingly large temperature-magnetic field (T – H) parameter space. In addition, the evolution of differential resistance in T and H reveals an interesting superconducting gap structure.
HfO2 dielectric thickness dependence of electrical properties in graphene field effect transistors with double conductance minima
Authors: Zhang Cheng , Xie Dan , Xu Jian-Long , Li Xin-Ming , Sun Yi-Lin , Dai Rui-Xuan , Li Xian , Zhu Hong-Wei
Published: October 2015

We investigate the electrical properties in back-gated graphene field effect transistors (GFETs) with SiO2 dielectric and different thickness of high-k HfO2 dielectric. The results show that transform characteristic (Ids–Vgs) curves of GFETs are uniquely W-shaped with two charge neutrality point (left and right) in both SiO2 and HfO2 dielectric (SiO2-GFETs and HfO2-GFETs). The gate voltage reduces drastically in HfO2-GFETs compared with that in SiO2-GFETs, and it becomes much smaller with the decline of HfO2 thickness. The left charge neutrality point in Id–Vg curves of all HfO2-GFETs is negative, compared to the positive ones in SiO2-GFETs, which means that there exists n-doping in graphene with HfO2 as bottom dielectric. We speculate that this n-doping comes from the HfO2 layer, which brings fixed charged impurities in close proximity to graphene. The carrier mobility is also researched, demonstrating a decreasing trend of hole mobility in HfO2-GFETs contrast to that in SiO2-GFETs. In a series of HfO2-GFETs with different HfO2 dielectric thickness, the hole mobility shows a tendency of rise when the thickness decreases to 7 nm. The possible reason might be due to the introduced impurities into HfO2 film from atomic layer deposition process, the concentration of which varies from the thickness of HfO2 layer.
Mechanisms of electromechanical response in (1 − x)Ba(Zr0.2Ti0.8)O3-x(Ba0.7Ca0.3)TiO3 ceramics
Authors: Acosta Matias , Novak Nikola , Rossetti George A. , Rödel Jürgen
Published: October 2015

Contributions to the piezoelectric response of (1 − x)Ba(Zr0.2Ti0.8)O3-x(Ba0.7Ca0.3)TiO3 ceramics are quantified by small signal measurements made as functions of bias field and temperature. The highest fraction of intrinsic contributions is observed far from phase boundaries, of extrinsic contributions around phase boundaries, and of irreversible switching in the orthorhombic phase. The largest piezoelectric response, d33 = 475 ± 85 pC/N, is found near the orthorhombic to tetragonal phase boundary due to both reversible and irreversible switching. A peak in reversible switching above the Curie temperature for all compositions suggests a line of critical points associated with first order phase transitions, indicating that concurrence of triple and tricritical points in the zero-field phase diagram is not the responsible mechanism of enhanced piezoelectricity.
Substrate wettability requirement for the direct transfer of graphene
Authors: Du F. , Duan H. L. , Xiong C. Y. , Wang J. X.
Published: October 2015

The direct transfer method, wherein graphene is transferred from its growth metal to a soft substrate, is widely used to fabricate various devices, and the interfacial bonding condition between the substrate and the graphene is vital for transfer success. In this letter, we present a theoretical model to derive the wettability requirements of the soft substrate to sustain the direct transfer of graphene, and verify the theoretical analysis with experiments. We find that the surface energy components of the substrate have a crucial effect upon the graphene transfer, and that substrates possessing a strong polar surface energy are not suitable for transfer. The theoretical model predicts the critical water contact angle of the soft substrate for graphene transfer to be about 50°, and the experiments measure it to be about 60°. These results provide guidelines for choosing proper substrates to transfer graphene during the fabrication of graphene-based flexible devices.
Polarization reversal in organic-inorganic ferroelectric composites: Modeling and experiment
Authors: Silibin Maxim V. , Belovickis Jaroslavas , Svirskas Sarunas , Ivanov Maksim , Banys Juras , Solnyshkin Alexandr V. , Gavrilov Sergei A. , Varenyk Olexander V. , Pusenkova Anastasiia S. , Morozovsky Nicholas , Shvartsman Vladimir V. , Morozovska Anna N.
Published: October 2015

Tailoring of ferroelectric properties of copolymer P(VDF-TrFE) by incorporation of ceramic inclusions in the polymer matrix is promising for advanced applications in sensorics. We have observed experimentally that in composites of P(VDF-TrFE) with barium-doped lead zirconate titanate (BPZT), the remanent polarization increases, while the coercive field substantially decreases in comparison with the pure polymer samples. Results of simulation in framework of the modified Weiss model have shown that the changes of the hysteresis loops characteristics are due to increase of the dielectric susceptibility of the composite as compared to pure PVDF-TrFE. This originates from the strong dispersion of the mean field constant α, which describes the feedback of the polarization on the electric field at the location of the dipoles and is closely related with the local increase of composite susceptibility in the vicinity the BPZT inclusions. This phenomenon effectively becomes macro-scale due to the long-range nature of the inhomogeneous elastic and electric fields occurring at the interfaces between the matrix and inclusions.
Holographic characterization of imperfect colloidal spheres
Authors: Hannel Mark , Middleton Christine , Grier David G.
Published: October 2015

We demonstrate precise measurements of the size and refractive index of individual dimpled colloidal spheres using holographic characterization techniques developed for ideal spheres.
A simple method for understanding the triangular growth patterns of transition metal dichalcogenide sheets
Authors: Zhu Siya , Wang Qian
Published: October 2015

Triangular nanoflake growth patterns have been commonly observed in synthesis of transition metal dichalcogenide sheets and their hybrid structures. Triangular nanoflakes not only show exceptional properties, but also can serve as building blocks for two or three dimensional structures. In this study, taking the MoS2 system as a test case, we propose a Matrix method to understand the mechanism of such unique growth pattern. Nanoflakes with different edge types are mathematically described with configuration matrices, and the total formation energy is calculated as the sum of the edge formation energies and the chemical potentials of sulfur and molybdenum. Based on energetics, we find that three triangular patterns with the different edge configurations are energetically more favorable in different ranges of the chemical potential of sulfur, which are in good agreement with experimental observations. Our algorithm has high efficiency and can deal with nanoflakes in microns which are beyond the ability of ab-initio method. This study not only elucidates the mechanism of triangular nanoflake growth patterns in experiment, but also provides a clue to control the geometric configurations in synthesis.
A comparative study about electronic structures at rubrene/Ag and Ag/rubrene interfaces
Authors: Sinha Sumona , Mukherjee M.
Published: October 2015

The contact between the electrode and the organic semiconductor is one of the most crucial factors in determining the organic device performance. The development and production technology of different organic devices require the understanding of different types of metal/organic semiconducting thin film interfaces. Comparisons about the electronic structures at Rubrene/Ag and Ag/Rubrene interfaces have been studied using photoemission spectroscopy. The Ag on rubrene interfaces is found to show more interesting and complex natures than its counterpart. The vacuum level (VL) was shifted about 0.51 eV from push back effect for deposition of 5 Å rubrene onto Ag film whereas the electronic features of silver was only suppressed and no energy shift was resulted. While the deposition of 5 Å Ag onto rubrene film leads to the diffusion of the Ag atoms, as a cluster with quantum size effect, inside the film. Angle dependent XPS measurement indicates that diffused metal clusters were present at entire probed depth of the film. Moreover these clusters dope the uppermost surface of the rubrene film which consequences a shift of the electronic states of thick organic film towards higher binding energy. The VL was found to shift about 0.31 eV toward higher binding energy whereas the shift was around 0.21 eV for the electronic states of rubrene layer.
Assessment and analysis on numerical and experimental performance of the photovoltaic systems for Germany and Turkey
Authors: Yilmaz Saban , Ozcalik Hasan Riza , Dincer Furkan
Published: October 2015

Solar energy plants are popular due to their low cost, and environmental friendly and renewable nature. Germany is the leading country in the solar energy market in the world. Turkey also possesses a very high potential in terms of solar energy among European countries. The present study aims to draw attention to solar energy plants and define its applicability for these two countries. Two identical photovoltaic systems, installed in Turkey and Germany, were analyzed. First, we introduced the experimental results of two installed photovoltaic systems. Second, we numerically modelled two photovoltaic systems and processed the data with PVsyst in order to compare and verify experimental results. Numerical results display a good agreement with the experimental results, indicating that the performance of the modelling system is high, and that it can be used as a tentative photovoltaic system prior to installation. In addition, the solar energy capacities of Turkey and Germany are analyzed and discussed in detail.
Lateral oscillations of the center of mass of bipeds as they walk. Inverted pendulum model with two degrees of freedom
Authors: H Goldsztein Guillermo
Published: October 2015

The use of inverted pendulum models to study the bio-mechanics of biped walkers is a common practice. In its simplest form, the inverted pendulum consists of a point mass, which models the center of mass of the biped, attached to two straight mass-less legs. Most works using the simplest inverted pendulum model constrain the mass and the legs to the sagittal plane (the plane that contains the direction perpendicular to the ground and the direction toward the biped is walking). In this article, we remove this constrain and use this unconstrained inverted pendulum model to study the oscillations the mass experiences in the direction perpendicular to the sagittal plane as the biped walks. While small, these oscillations are unavoidable and of importance in the understanding of balance and stability of walkers, as well as walkers induced oscillations in pedestrian bridges.
Dimethylated sulfur compounds in coral-reef ecosystems
Authors: Deschaseaux Elisabeth , Jones Graham , Swan Hilton
Published: October 2015

Environmental contextDimethylated sulfur compounds can exert multiple biological and environmental effects including climate regulation. Climate change and other anthropogenic factors are predicted to affect coral-reef ecosystems where these sulfur compounds are particularly abundant. We review the processes that regulate the production of dimethylated sulfur compounds in coral reefs and the potential consequences of environmental changes on their biogenic cycle in such fragile ecosystems under future climate change scenarios. AbstractDimethylsulfoniopropionate (DMSP) and its main breakdown products dimethylsulfide (DMS) and dimethylsulfoxide (DMSO) are biogenic species in the marine environment. In coral reefs, these dimethylated sulfur compounds (DSCs) have been reported at greater concentrations than in other marine ecosystems, which is most likely attributable to the extraordinary large biodiversity of coral reef communities (e.g. corals, macroalgae, coralline algae, invertebrates) and to the unique ability of zooxanthellate corals to synthesise DMSP from both the animal host and algal symbionts. Besides the various biological functions that have been attributed to DSCs, including thermoregulation, osmoregulation, chemoattraction and antioxidant response, DMS is suspected to take part in a climate feedback loop that could help counteract global warming. Nowadays, anthropogenic effects such as pollution, overfishing, increased sedimentation and global climate change are imminently threatening the health of coral reef communities around the world, with possible consequences on the natural cycle of DSCs within these ecosystems. This review provides insight into the biogeochemistry of DSCs in coral reefs and discusses the implications of projected changes in DSC production in these increasingly stressed ecosystems under future climate change scenarios. It shows that DSC dynamics will incontestably be affected in the near future, with possible feedback consequences on local climate.
Characterisation and cryopreservation of the ovarian preantral follicle population from Spix’s yellow-toothed cavies (Galea spixii Wagler, 1831)
Authors: Praxedes Érica C. G. , Lima Gabriela L. , Silva Andréia M. , Apolinário Carlos A. C. , Bezerra José A. B. , Souza Ana L. P. , Oliveira Moacir F. , Rodrigues Ana P. R. , Silva Alexandre R.
Published: October 2015

The aim of the present study was to characterise the ovarian preantral follicle (PF) population and to establish a solid surface vitrification (SSV) process using dimethyl sulfoxide (DMSO) as a cryoprotectant for preservation of ovarian tissue from yellow-toothed cavies (Galea spixii). Ovaries were fixed for PF population analysis or were subjected to the SSV process. The mean (± s.e.m.) PF population per ovarian pair was estimated to be 416.0 ± 342.8. There were 140.0 ± 56.0 (63.4%) and 125.0 ± 58.0 (64.0%) primary follicles on the right and left ovaries, respectively. The proportion of this follicle category was significantly greater than that of other follicle categories (P < 0.05). The diameter of follicles (123.7 ± 18.3 µm), oocytes (50.1 ± 5.0 µm) and nuclei (14.27 ± 2.01 µm) was larger for secondary ones when compared with other PFs categories. Most PFs were morphologically normal (94.6%), with light microscopy identifying only a few atretic follicles (5.4%). After SSV, there was a reduction in the proportion of morphologically normal PFs compared with the non-vitrified group (69.5% vs 91.2%, respectively). Transmission electron microscopy revealed preservation of oocytes and granulosa cell membranes and the morphological aspect of follicles; the primary change observed in some vitrified PFs was the presence of vacuoles in the oocytes and granulosa cells cytoplasm and turgid mitochondria. In conclusion, the present study provides an estimative and characterization for the PF population in ovaries of G. spixii. Moreover, we report its PFs cryopreservation using an SSV process.
Higher Body Mass Index is Associated with Episodic Memory Deficits in Young Adults
Authors: Cheke Lucy G. , Simons Jon S. , Clayton Nicola S.
Published: October 2015

Obesity has become an international health crisis. There is accumulating evidence that excess bodyweight is associated with changes to the structure and function of the brain and with a number of cognitive deficits. In particular, research suggests that obesity is associated with hippocampal and frontal lobe dysfunction, which would be predicted to impact memory. However, evidence for such memory impairment is currently limited. We hypothesised that higher body mass index (BMI) would be associated with reduced performance on a test of episodic memory that assesses not only content, but also context and feature integration. A total of 50 participants aged 18–35 years, with BMIs ranging from 18 to 51, were tested on a novel what–where–when style episodic memory test: the “Treasure-Hunt Task”. This test requires recollection of object, location, and temporal order information within the same paradigm, as well as testing the ability to integrate these features into a single event recollection. Higher BMI was associated with significantly lower performance on the what–where–when (WWW) memory task and all individual elements: object identification, location memory, and temporal order memory. After controlling for age, sex, and years in education, the effect of BMI on the individual what, where, and when tasks remained, while the WWW dropped below significance. This finding of episodic memory deficits in obesity is of concern given the emerging evidence for a role for episodic cognition in appetite regulation.
Fabrication of silver nanorods embedded in PDMS film and its application for strain sensing
Authors: Goel Pratibha , Singh J P
Published: October 2015

Highly reflective and surface conductive strain gauges have been prepared by embedding the silver nanorods (AgNRs) into polydimethylsiloxane (PDMS). Thermal curing of PDMS on AgNRs grown Si wafer leads to a flexible, reflective and conductive silver surface. The reflectance of the as prepared films were observed to be 60% with a low value of sheet resistance. The reflectance of the film was able to be tuned from 60% to 15% in the visible region. The fabrication of a parallel plate capacitor strain sensor from AgNRs embedded PDMS, and tuning of the capacitance with respect to the applied strain, leads to a gauge factor of ~1. These mechanically tunable AgNRs/PDMS films demonstrate potential application as a strain sensor.
Pedestal confinement and stability in JET-ILW ELMy H-modes
Authors: Maggi C.F. , Saarelma S. , Casson F.J. , Challis C. , de la Luna E. , Frassinetti L. , Giroud C. , Joffrin E. , Simpson J. , Beurskens M. , Chapman I. , Hobirk J. , Leyland M. , Lomas P. , Lowry C. , Nunes I. , Rimini F. , Sips A.C.C. , Urano H.
Published: October 2015

New experiments in 2013–2014 have investigated the physics responsible for the decrease in H-mode pedestal confinement observed in the initial phase of JET-ILW operation (2012 Experimental Campaigns). The effects of plasma triangularity, global beta and neutrals on pedestal confinement and stability have been investigated systematically. The stability of JET-ILW pedestals is analysed in the framework of the peeling–ballooning model and the model assumptions of the pedestal predictive code EPED. Low D neutrals content in the plasma, achieved either by low D2 gas injection rates or by divertor configurations with optimum pumping, and high beta are necessary conditions for good pedestal (and core) performance. In such conditions the pedestal stability is consistent with the peeling–ballooning paradigm. Moderate to high D2 gas rates, required for W control and stable H-mode operation with the ILW, lead to increased D neutrals content in the plasma and additional physics in the pedestal models may be required to explain the onset of the ELM instability. The changes in H-mode performance associated with the change in JET wall composition from C to Be/W point to D neutrals and low-Z impurities playing a role in pedestal stability, elements which are not currently included in pedestal models. These aspects need to be addressed in order to progress towards full predictive capability of the pedestal height.
Biochemical and biophysical analyses of tight junction permeability made of claudin-16 and claudin-19 dimerization
Authors: Gong Yongfeng , Renigunta Vijayaram , Zhou Yi , Sunq Abby , Wang Jinzhi , Yang Jing , Renigunta Aparna , Baker Lane A. , Hou Jianghui
Published: October 2015

The molecular nature of tight junction architecture and permeability is a long-standing mystery. Here, by comprehensive biochemical, biophysical, genetic, and electron microscopic analyses of claudin-16 and -19 interactions—two claudins that play key polygenic roles in fatal human renal disease, FHHNC—we found that 1) claudin-16 and -19 form a stable dimer through cis association of transmembrane domains 3 and 4; 2) mutations disrupting the claudin-16 and -19 cis interaction increase tight junction ultrastructural complexity but reduce tight junction permeability; and 3) no claudin hemichannel or heterotypic channel made of claudin-16 and -19 trans interaction can exist. These principles can be used to artificially alter tight junction permeabilities in various epithelia by manipulating selective claudin interactions. Our study also emphasizes the use of a novel recording approach based on scanning ion conductance microscopy to resolve tight junction permeabilities with submicrometer precision.
Cell type–dependent mechanisms for formin-mediated assembly of filopodia
Authors: Young Lorna E. , Heimsath Ernest G. , Higgs Henry N.
Published: October 2015

Filopodia are finger-like protrusions from the plasma membrane and are of fundamental importance to cellular physiology, but the mechanisms governing their assembly are still in question. One model, called convergent elongation, proposes that filopodia arise from Arp2/3 complex–nucleated dendritic actin networks, with factors such as formins elongating these filaments into filopodia. We test this model using constitutively active constructs of two formins, FMNL3 and mDia2. Surprisingly, filopodial assembly requirements differ between suspension and adherent cells. In suspension cells, Arp2/3 complex is required for filopodial assembly through either formin. In contrast, a subset of filopodia remains after Arp2/3 complex inhibition in adherent cells. In adherent cells only, mDia1 and VASP also contribute to filopodial assembly, and filopodia are disproportionately associated with focal adhesions. We propose an extension of the existing models for filopodial assembly in which any cluster of actin filament barbed ends in proximity to the plasma membrane, either Arp2/3 complex dependent or independent, can initiate filopodial assembly by specific formins.
The new protein topology graph library web server
Authors: Schäfer Tim , Scheck Andreas , Bruneß Daniel , May Patrick , Koch Ina
Published: October 2015

Summary: We present a new, extended version of the Protein Topology Graph Library web server. The Protein Topology Graph Library describes the protein topology on the super-secondary structure level. It allows to compute and visualize protein ligand graphs and search for protein structural motifs. The new server features additional information on ligand binding to secondary structure elements, increased usability and an application programming interface (API) to retrieve data, allowing for an automated analysis of protein topology.

Availability and implementation: The Protein Topology Graph Library server is freely available on the web at http://ptgl.uni-frankfurt.de. The website is implemented in PHP, JavaScript, PostgreSQL and Apache. It is supported by all major browsers. The VPLG software that was used to compute the protein ligand graphs and all other data in the database is available under the GNU public license 2.0 from http://vplg.sourceforge.net.

Contact:  tim.schaefer@bioinformatik.uni-frankfurt.de; ina.koch@bioinformatik.uni-frankfurt.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy
Authors: Křížek Pavel , Lukeš Tomáš , Ovesný Martin , Fliegel Karel , Hagen Guy M.
Published: October 2015

Summary: SIMToolbox is an open-source, modular set of functions for MATLAB equipped with a user-friendly graphical interface and designed for processing two-dimensional and three-dimensional data acquired by structured illumination microscopy (SIM). Both optical sectioning and super-resolution applications are supported. The software is also capable of maximum a posteriori probability image estimation (MAP-SIM), an alternative method for reconstruction of structured illumination images. MAP-SIM can potentially reduce reconstruction artifacts, which commonly occur due to refractive index mismatch within the sample and to imperfections in the illumination.

Availability and implementation: SIMToolbox, example data and the online documentation are freely accessible at http://mmtg.fel.cvut.cz/SIMToolbox.

Contact:  ghagen@uccs.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
An Informed Forensics Approach to Detecting Vote Irregularities
Authors: Montgomery Jacob M. , Olivella Santiago , Potter Joshua D. , Crisp Brian F.
Published: October 2015

Electoral forensics involves examining election results for anomalies to efficiently identify patterns indicative of electoral irregularities. However, there is disagreement about which, if any, forensics tool is most effective at identifying fraud, and there is no method for integrating multiple tools. Moreover, forensic efforts have failed to systematically take advantage of country-specific details that might aid in diagnosing fraud. We deploy a Bayesian additive regression trees (BART) model–a machine-learning technique–on a large cross-national data set to explore the dense network of potential relationships between various forensic indicators of anomalies and electoral fraud risk factors, on the one hand, and the likelihood of fraud, on the other. This approach allows us to arbitrate between the relative importance of different forensic and contextual features for identifying electoral fraud and results in a diagnostic tool that can be relatively easily implemented in cross-national research.
PROSE Treatment for Ocular Chronic Graft-Versus-Host Disease as a Clinical Network Expands
Authors: DeLoss Karen S. , Le Hong-Gam , Gire Anisa , Chiu Gloria B. , Jacobs Deborah S. , Carrasquillo Karen G.
Published: October 2015

Background:

Keratoconjunctivitis sicca occurs in 40% to 90% of patients with ocular chronic graft-versus-host disease (cGVHD). Ocular symptoms can have profound effects in both the visual function and quality of life of patients with GVHD. We report the impact of prosthetic replacement of the ocular surface ecosystem (PROSE) treatment in patients with cGVHD as a clinical network expands.

Methods:

We queried the BostonSight PROSE manufacturing database from January 2002 to December 2011. Patients treated for ocular cGVHD were reported by age, gender, year, and network site where the treatment was undertaken. The baseline and six-month follow-up scores of visual function using a standardized validated instrument, the National Eye Institute Visual Function Questionnaire (NEI VFQ-25), were evaluated for a period in 2006 and again in 2010 after network expansion had occurred.

Results:

A total of 407 patients with a male:female ratio of 226:181, mean age was 51 years with ocular cGVHD underwent PROSE treatment from January 2002 to December 2011. By 2011, 67% of all cases were treated at network clinics. Baseline characteristics of patients treated throughout the network in 2010 were similar to that of 2006 and 2010 cohorts from the main center. There was a significant improvement of 41 points (P<0.001) in composite NEI VFQ score among patients treated across the network in 2010, similar to the improvement of 30 points (P<0.001) seen among the patients treated at the main center in 2010. There was a trend toward lower baseline self-reported general health status (SRGHS) and VFQ scores among patients treated at network clinics, suggesting that expansion of the network allows treatment of sicker patients (lower general health status) or those more severely affected by ocular cGVHD.

Conclusions:

PROSE treatment of ocular cGVHD has increased in the last decade with the establishment of BostonSight network clinics across the United States. Patients treated at network clinics showed similar levels of baseline visual function and SRGHS, and achieved a similar high level of improvement in visual function as those treated at the main center. Patient-reported measures of functional status are useful in evaluating treatment options for patients with cGVHD. PROSE treatment has significant positive impact on the visual function of patients with ocular cGVHD regardless of whether the patient is treated at the main center or at a network site.
Coronary Artery Disease in Patients With Disorders of Bilirubin Excretion
Authors: Gupta Nancy , Chaudhary Rahul , Krishnamoorthy Parasuram , Mahajan Sugandhi , Bodin Roxana , Sule Sachin
Published: October 2015

We aimed to determine the predictors of coronary artery disease (CAD) in patients with abnormal bilirubin excretion, that is, Gilbert syndrome, Crigler–Najjar syndrome, Dubin–Johnson syndrome, and Rotor syndrome. We analyzed data from the Healthcare Cost and Utilization Project (HCUP) of the Agency for Healthcare Research and Quality, Rockville, MD for the period 2009 to 2010. All patients ≥18 years of age with a primary diagnosis of “disorders of bilirubin excretion” [International Classification of Diseases, Ninth Edition, Clinical Modification (ICD-9CM) code 277.4] were included in the study. Primary outcome was to determine predictors of CAD in adult patients diagnosed with abnormal bilirubin excretion. We identified a total of 12,423 adult patients with bilirubin excretion disorder hospitalized during 2009–2010 (0.03% of all inpatient admissions). CAD was seen in 18% of patients, with a higher prevalence in men (21% in men vs. 13% in women, P < 0.0001). In multivariate logistic regression adjusted for demographic and traditional risk factors, hypertension [odds ratio (OR): 1.74; 95% confidence interval (CI), 1.33–2.27, P < 0.001], hyperlipidemia (OR: 2.49; 95% CI, 1.95–3.18, P < 0.001), diabetes (OR: 1.46; 95% CI, 1.12–1.91, P = 0.01), and age (OR: 1.05; 95% CI, 1.04–1.06, P < 0.001) were found to be independent predictors of CAD in adult patients with abnormal bilirubin excretion. Female sex (OR: 0.49; 95% CI, 0.36–0.65, P < 0.001) demonstrated an inverse association in predicting CAD. There was increased prevalence of CAD in our patient population with increased prevalence of cardiovascular risk factors. Age, diabetes mellitus, hypertension, and hyperlipidemia were found to be independent predictors of CAD.
Distinguishing Classical Hodgkin Lymphoma, Gray Zone Lymphoma, and Large B-cell Lymphoma: A Proposed Scoring System
Authors: O’Malley Dennis P. , Fedoriw Yuri , Weiss Lawrence M.
Published: October 2015

Background:

The diagnosis of “B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and classical Hodgkin lymphoma” represents an indeterminate or equivocal decision in relation to management because there remain differences in the management of Hodgkin and non-Hodgkin lymphomas. We developed a scoring system for this group of lymphomas using markers that are traditionally associated with diagnosis of classical Hodgkin lymphoma (CHL) and immunophenotypic markers associated with the “B-cell program” expressed in normal B cells.

Materials and Methods:

This system emphasized known criteria used to diagnose CHL that are rare in B-cell lymphoma (BCL) [CD15+, CD45−, CD20− or weak/variable, PAX5+ (weak or moderate), CD79a−, OCT-2−/BOB.1− or OCT-2+/BOB.1− or OCT-2−/BOB.1+, EBV+] versus findings that are common in BCL in contrast to CHL (CD15−, CD45+, CD20+ strong, PAX5+ strong, CD79a+, OCT-2+/BOB.1+, EBV−). After a preliminary test trial, MUM1 staining was also added. Results associated with CHL were assigned a score of +1 and score associated with BCL were assigned a score of −1. In the final grading system, a maximum score of +6 is possible for CHL and −6 for BCL.

Results:

An initial series of 38 cases was evaluated using a proprietary system that allows analysis of multiple stains on individual cells in a single section. An additional 23 cases were evaluated with results blinded until after scoring was performed. In general there was high concordance among cases originally diagnosed as CHL with high scores (score +4 to +6). Cases originally diagnosed as gray zone lymphomas exhibited a broader range of scores (+3 to −4). Cases of BCLs had low scores (−3 to −6).

Conclusions:

The primary goal of this study was to create a scoring system that allows a cumulative quantitative measure of immunohistochemical markers, based on expected results to compare cases that might have overlapping features. In most cases, scores that trend to one extreme or another are likely representative of CHL or BCL and do not lie in the gray zone. This scoring system allows for practical resolution of many borderline cases and provide some guidance in difficult cases.
Differential responses of coral larvae to the colour of ambient light guide them to suitable settlement microhabitat
Authors: Strader Marie E. , Davies Sarah W. , Matz Mikhail V.
Published: October 2015

Reef-building corals produce planktonic planula larvae that must select an appropriate habitat to settle and spend the rest of their life, a behaviour that plays a critical role in survival. Here, we report that larvae obtained from a deep-water population of
Pseudodiploria strigosa
settled more readily under blue light and in the dark, which aligns well with the light field characteristics of their natal habitat. By contrast, larvae of the shallow-water coral
Acropora millepora
settled in high proportions under blue and green light while settlement was less in the dark.
Acropora millepora
larvae also showed reduced settlement under red light, which should be abundant at shallow depth. Hypothesizing that this might be a mechanism preventing the larvae from settling on the exposed upwards-facing surfaces, we quantified
A. millepora
settlement in manipulated light chambers
in situ
on the reef. While
A. millepora
larvae naturally preferred settling on vertical rather than exposed horizontal surfaces, swapping the colours of upwards-facing and sideways-facing light fields was sufficient to invert this preference. We also tested if the variation in intrinsic red fluorescence in
A. millepora
larvae correlates with settlement rates, as has been suggested previously. We observed this correlation only in the absence of light, indicating that larval red fluorescent protein is probably not directly involved in light sensing. Our study reveals previously under-appreciated light-sensory capabilities in coral larvae, which could be an important axis of ecological differentiation between coral species and/or populations.
Simulations of ceria nanoparticles
Authors: Cormack A. N. , Lamphier S. , Wang Bu , Gubb T. , Reed K.
Published: October 2015

Atomistic computer simulations, using classical potential models, have been used to model ceria nanoparticles (NPs) with diameters of approximately 1 and 2 nm. Lattice expansion is observed in the stoichiometric 1 nm NP, consistent with experiment, indicating that reduction is not the primary driver for such expansion. Furthermore, on reduction, the 1 nm NP is found to distort significantly, offering a possible explanation for its reduced oxygen storage capacity compared to the 2 nm NP. Point defect calculations on the 2 nm NP indicate that while doping with La is energetically favourable, Fe incorporation is not.
The SOS response increases bacterial fitness, but not evolvability, under a sublethal dose of antibiotic
Authors: Torres-Barceló Clara , Kojadinovic Mila , Moxon Richard , MacLean R. Craig
Published: October 2015

Exposure to antibiotics induces the expression of mutagenic bacterial stress–response pathways, but the evolutionary benefits of these responses remain unclear. One possibility is that stress–response pathways provide a short-term advantage by protecting bacteria against the toxic effects of antibiotics. Second, it is possible that stress-induced mutagenesis provides a long-term advantage by accelerating the evolution of resistance. Here, we directly measure the contribution of the
Pseudomonas aeruginosa
SOS pathway to bacterial fitness and evolvability in the presence of sublethal doses of ciprofloxacin. Using short-term competition experiments, we demonstrate that the SOS pathway increases competitive fitness in the presence of ciprofloxacin. Continued exposure to ciprofloxacin results in the rapid evolution of increased fitness and antibiotic resistance, but we find no evidence that SOS-induced mutagenesis accelerates the rate of adaptation to ciprofloxacin during a 200 generation selection experiment. Intriguingly, we find that the expression of the SOS pathway decreases during adaptation to ciprofloxacin, and this helps to explain why this pathway does not increase long-term evolvability. Furthermore, we argue that the SOS pathway fails to accelerate adaptation to ciprofloxacin because the modest increase in the mutation rate associated with SOS mutagenesis is offset by a decrease in the effective strength of selection for increased resistance at a population level. Our findings suggest that the primary evolutionary benefit of the SOS response is to increase bacterial competitive ability, and that stress-induced mutagenesis is an unwanted side effect, and not a selected attribute, of this pathway.
Early development of rostrum saw-teeth in a fossil ray tests classical theories of the evolution of vertebrate dentitions
Authors: Smith Moya Meredith , Riley Alex , Fraser Gareth J. , Underwood Charlie , Welten Monique , Kriwet Jürgen , Pfaff Cathrin , Johanson Zerina
Published: October 2015

In classical theory, teeth of vertebrate dentitions evolved from co-option of external skin denticles into the oral cavity. This hypothesis predicts that ordered tooth arrangement and regulated replacement in the oral dentition were also derived from skin denticles. The fossil batoid ray
Schizorhiza stromeri
(Chondrichthyes; Cretaceous) provides a test of this theory.
Schizorhiza
preserves an extended cartilaginous rostrum with closely spaced, alternating saw-teeth, different from sawfish and sawsharks today. Multiple replacement teeth reveal unique new data from micro-CT scanning, showing how the ‘cone-in-cone’ series of ordered saw-teeth sets arrange themselves developmentally, to become enclosed by the roots of pre-existing saw-teeth. At the rostrum tip, newly developing saw-teeth are present, as mineralized crown tips within a vascular, cartilaginous furrow; these reorient via two 90° rotations then relocate laterally between previously formed roots. Saw-tooth replacement slows mid-rostrum where fewer saw-teeth are regenerated. These exceptional developmental data reveal regulated order for serial self-renewal, maintaining the saw edge with ever-increasing saw-tooth size. This mimics tooth replacement in chondrichthyans, but differs in the crown reorientation and their enclosure directly between roots of predecessor saw-teeth.
Schizorhiza
saw-tooth development is decoupled from the jaw teeth and their replacement, dependent on a dental lamina. This highly specialized rostral saw, derived from diversification of skin denticles, is distinct from the dentition and demonstrates the potential developmental plasticity of skin denticles.
Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome
Authors: Goodwin Sara , Gurtowski James , Ethe-Sayers Scott , Deshpande Panchajanya , Schatz Michael C. , McCombie W. Richard
Published: October 2015

Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available, and we used this for sequencing the Saccharomyces cerevisiae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Nanocorr specifically for Oxford Nanopore reads, because existing packages were incapable of assembling the long read lengths (5–50 kbp) at such high error rates (between ∼5% and 40% error). With this new method, we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: The contig N50 length is more than ten times greater than an Illumina-only assembly (678 kb versus 59.9 kbp) and has >99.88% consensus identity when compared to the reference. Furthermore, the assembly with the long nanopore reads presents a much more complete representation of the features of the genome and correctly assembles gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in the Illumina-only assembly.