bluuebunny/crossref_metadata_2025 huggingface dataset:
ZnO-NiO hetero-nanostructures as highly sensitive and selective triethylamine sensor
Authors: Guo Ting , Luo Yidong , Zhang Yujun , Lin Yuan-Hua , Nan Ce-Wen
Published: July 2014

Al-doped ZnO nanorods arrays on NiO nanofibers to construct a typical ZnO-NiO hetero-nanostructure on Al2O3 substrate have been obtained by electrospinning and hydrothermal methods. The sensors based on this hetero-nanostructures exhibit high selectivity and sensitivity towards triethylamine gas under operating temperature of 250 °C, and Al doping has a great influence on the air-sensitive performance of the sensors. Our results indicate that the ZnO-NiO hetero-nanostructure is a potential candidate for gas sensors with good performances for practical applications.
Focused-ion-beam overlay-patterning of three-dimensional diamond structures for advanced single-photon properties
Authors: Jiang Qianqing , Liu Dongqi , Liu Gangqin , Chang Yanchun , Li Wuxia , Pan Xinyu , Gu Changzhi
Published: July 2014

Sources of single photons are of fundamental importance in many applications as to provide quantum states for quantum communication and quantum information processing. Color centers in diamond are prominent candidates to generate and manipulate quantum states of light, even at room temperature. However, the efficiency of photon collection of the color centers in bulk diamond is greatly reduced by refraction at the diamond/air interface. To address this issue, diamond structuring has been investigated by various methods. Among them, focused-ion-beam (FIB) direct patterning has been recognized as the most favorable technique. But it has been noted that diamond tends to present significant challenges in FIB milling, e.g., the susceptibility of forming charging related artifacts and topographical features. In this work, periodically-positioned-rings and overlay patterning with stagger-superimposed-rings were proposed to alleviate some problems encountered in FIB milling of diamond, for improved surface morphology and shape control. Cross-scale network and uniform nanostructure arrays have been achieved in single crystalline diamond substrates. High quality diamond solid immersion lens and nanopillars were sculptured with a nitrogen-vacancy center buried at the desired position. Compared with the film counterpart, an enhancement of about ten folds in single photon collection efficiency was achieved with greatly improved signal to noise ratio. All these results indicate that FIB milling through over-lay patterning could be an effective approach to fabricate diamond structures, potentially for quantum information studies.
Note: A novel design of a microwave feed for a microwave frequency standard with a linear ion trap
Authors: Zhang J. W. , Miao K. , Wang S. G. , Wang Z. B.
Published: July 2014

Linear ion traps are important tools in many applications, particularly in mass spectrum analyzers and frequency standards. Here a novel design of a microwave feed integrated into one electrode of a linear quadrupole ion trap is demonstrated for the application of a microwave frequency standard based on cadmium ions. The mechanical structure of the microwave feed is compact and easy to build. The ion trap integrated with this microwave feed is successfully applied to measure the hyperfine splitting of the ground state of 113Cd+, thus demonstrating the practicality and reliability of the microwave feed.
Instrumentation for a multichord motional Stark effect diagnostic in KSTAR
Authors: Chung J. , Ko J. , De Bock M. F. M. , Jaspers R. J. E.
Published: July 2014

The motional Stark effect (MSE) diagnostic is used to measure the radial magnetic pitch angle profile in neutral beam heated plasmas. This information is used to calculate the safety factor, q, with magnetic equilibrium reconstruction codes such as EFIT. The MSE diagnostic is important during active shaping of the q profile to optimize confinement and stability, and it has become a key diagnostic in high performance tokamaks. A multichord photo-elastic modulator (PEM) based MSE system is being developed for a real-time plasma current profile control in Korea Superconducting Tokamak Advanced Research (KSTAR). The PEM-based approach is a standard method that measures the polarization direction of a single Stark line with narrow tunable bandpass filters. A tangential view of the heating beam provides good spatial resolution of 1–3 cm, which provides an opportunity to install 25 spatial channels spanning the major radius from 1.74 m to 2.84 m. Application of real-time control is a long-term technical goal after commissioning the diagnostic in KSTAR, which is expected in 2015. In this paper, we describe the design of this newly-constructed multichord MSE diagnostic in KSTAR.
Fabrication of SiO2/4H-SiC (0001) interface with nearly ideal capacitance-voltage characteristics by thermal oxidation
Authors: Kikuchi Richard Heihachiro , Kita Koji
Published: July 2014

We fabricated SiO2/4H-SiC (0001) metal-oxide-semiconductor capacitors with nearly ideal capacitance-voltage characteristics, simply by the control of thermal oxidation conditions which were selected based on thermodynamic and kinetic considerations of SiC oxidation. The interface with low interface defect state density <1011 cm−2 eV−1 for the energy range of 0.1–0.4 eV below the conduction band of SiC was obtained by thermal oxidation at 1300 °C in a ramp-heating furnace with a short rise/fall time, followed by low temperature O2 anneal at 800 °C.
Structural origins of morphing in plant tissues
Authors: Bar-On Benny , Sui Xiaomeng , Livanov Konstantin , Achrai Ben , Kalfon-Cohen Estelle , Wiesel Erica , Daniel Wagner H.
Published: July 2014

Plant tissues are able to generate complex movements via shape modifications. These effects are tightly related to distinctive multi-scale composite architectures of the plant material, and can therefore largely be interpreted by composite mechanics principles. Here, we propose a generic framework for the analysis and prediction of the shape morphing of intricate biological composite materials, arising from changes in humidity. We have examined in depth the hierarchical structures of three types of seed pods for which we propose a theoretical scheme that is able to accurately simulate the relevant shape deformations. The validity and generality of this approach are confirmed by means of laboratory scale synthetic models with similar architectures leading to equivalent morphing patterns. Such synthetic configurations could pave the way to future morphing architectures of advanced materials and structures.
Electrical characterization and an equivalent circuit model of a microhollow cathode discharge reactor
Authors: Taylan O. , Berberoglu H.
Published: July 2014

This paper reports the electrical characterization and an equivalent circuit of a microhollow cathode discharge (MHCD) reactor in the self-pulsing regime. A MHCD reactor was prototyped for air plasma generation, and its current-voltage characteristics were measured experimentally in the self-pulsing regime for applied voltages from 2000 to 3000 V. The reactor was modeled as a capacitor in parallel with a variable resistor. A stray capacitance was also introduced to the circuit model to represent the capacitance of the circuit elements in the experimental setup. The values of the resistor and capacitors were recovered from experimental data, and the proposed circuit model was validated with independent experiments. Experimental data showed that increasing the applied voltage increased the current, self-pulsing frequency and average power consumption of the reactor, while it decreased the peak voltage. The maximum and the minimum voltages obtained using the model were in agreement with the experimental data within 2.5%, whereas the differences between peak current values were less than 1%. At all applied voltages, the equivalent circuit model was able to accurately represent the peak and average power consumption as well as the self-pulsing frequency within the experimental uncertainty. Although the results shown in this paper was for atmospheric air pressures, the proposed equivalent circuit model of the MHCD reactor could be generalized for other gases at different pressures.
Origins of interlayer formation and misfit dislocation displacement in the vicinity of InAs/GaAs quantum dots
Authors: Huang S. , Kim S. J. , Pan X. Q. , Goldman R. S.
Published: July 2014

We have examined the origins of interlayer formation and misfit dislocation (MD) displacement in the vicinity of InAs/GaAs quantum dots (QDs). For QDs formed by the Stranski-Krastanov mode, regularly spaced MDs nucleate at the interface between the QD and the GaAs buffer layer. In the droplet epitaxy case, both In island formation and In-induced “nano-drilling” of the GaAs buffer layer are observed during In deposition. Upon annealing under As flux, the In islands are converted to InAs QDs, with an InGaAs interlayer at the QD/buffer interface. Meanwhile, MDs nucleate at the QD/interlayer interface.
Analysis of cancellation exponents in two-dimensional Vlasov turbulence
Authors: De Vita G. , Sorriso-Valvo L. , Valentini F. , Servidio S. , Primavera L. , Carbone V. , Veltri P.
Published: July 2014

Statistical properties of plasma turbulence are investigated by means of two-dimensional Vlasov simulations. In particular, a classical technique called signed measure is used to characterize the scaling behavior and the topology of sign-oscillating structures in simulations of the hybrid Vlasov-Maxwell model. Exploring different turbulence regimes, varying both the plasma β and the level of fluctuations, it is observed that Vlasov turbulence manifests two ranges with different exponents, the transition being observed near the ion skin depth. These results, which may have applications to both laboratory and astrophysical systems, further confirm the singular nature of small scale fluctuations in a plasma, mainly classified as intermittent, narrow, and intense current sheets.
Performance limits of plasmon-enhanced organic photovoltaics
Authors: Karatay Durmus U. , Salvador Michael , Yao Kai , Jen Alex K.-Y. , Ginger David S.
Published: July 2014

We use a combination of experiment and modeling to explore the promise and limitations of using plasmon-resonant metal nanoparticles to enhance the device performance of organic photovoltaics (OPVs). We focus on optical properties typical of the current generation of low-bandgap donor polymers blended with the fullerene (6,6)-phenyl C71-butyric acid methyl ester (PC71BM) and use the polymer poly(indacenodithiophene-co-phenanthro[9,10-b]quinoxaline) (PIDT-PhanQ) as our test case. We model the optical properties and performance of these devices both in the presence and absence of a variety of colloidal silver nanoparticles. We show that for these materials, device performance is sensitive to the relative z-position and the density of nanoparticles inside the active layer. Using conservative estimates of the internal quantum efficiency for the PIDT-PhanQ/PC71BM blend, we calculate that optimally placed silver nanoparticles could yield an enhancement in short-circuit current density of over 31% when used with ∼ 80-nm-thick active layers, resulting in an absolute increase in power conversion efficiency of up to ∼2% for the device based on optical engineering.
Tunable MoS2 bandgap in MoS2-graphene heterostructures
Authors: Ebnonnasir Abbas , Narayanan Badri , Kodambaka Suneel , Ciobanu Cristian V.
Published: July 2014

Using density functional theory calculations with van der Waals corrections, we investigated how the interlayer orientation affects the structure and electronic properties of MoS2-graphene bilayer heterostructures. Changing the orientation of graphene with respect to MoS2 strongly influences the type and the value of the electronic bandgap in MoS2, while not significantly altering the binding energy between the layers or the interlayer spacing. We show that the physical origin of this tunable bandgap arises from variations in the S–S interplanar distance (MoS2 thickness) with the interlayer orientation, variations which are caused by electron transfer away from the Mo–S bonds.
Organic magnetoresistance from deep traps
Authors: Harmon N. J. , Flatté M. E.
Published: July 2014

We predict that singly occupied carrier traps, produced by electrical stress or irradiation within organic semiconductors, can cause spin blockades and the large room-temperature magnetoresistance known as organic magnetoresistance. The blockade occurs because many singly occupied traps can only become as doubly occupied in a spin-singlet configuration. Magnetic-field effects on spin mixing during transport dramatically modify the effects of this blockade and produce magnetoresistance. We calculate the quantitative effects of these traps on organic magnetoresistance from percolation theory and find a dramatic nonlinear dependence of the saturated magnetoresistance on trap density, leading to values ∼20%, within the theory's range of validity.
Electric field manipulation of nonvolatile magnetization in Au/NiO/Pt heterostructure with resistive switching effect
Authors: Xiong Y. Q. , Zhou W. P. , Li Q. , He M. C. , Du J. , Cao Q. Q. , Wang D. H. , Du Y. W.
Published: July 2014

The electrical field manipulation of magnetization is investigated in an Au/NiO/Pt heterostructure, which is fully compatible with the standard complementary metal-oxide semiconductor process. Reversible and stable unipolar resistive switching effects as well as a significant nonvolatile change of the magnetization are observed in this device during the set and reset processes at room temperature. Further analysis indicates that the formation and rupture of metallic Ni conducting filaments caused by the electric field would be responsible for the changes of resistivity and magnetization. The coexistence of the electric field control of magnetization change and resistive switching makes Au/NiO/Pt heterostructure a promising candidate for the multifunctional memory devices.
Induced hydroelectric energy generated by compressing a single-walled carbon nanotube hydrogel
Authors: Tan Zhenquan , Yamamoto Kazuhiro , Qiu Nan , Hashishin Takeshi , Ohara Satoshi
Published: July 2014

Using single-walled carbon nanotubes (SWCNTs) for energy harvesting and storage have attracted much attention recently because SWCNTs have supercapacity performance. In this paper, we report a simple electromechanical approach for the generation of induced electrical potential by the compression of a SWCNT-triggered sodium deoxycholate hydrogel. This hydrogel enhances the electrical potential generated under compression, and this is mainly because of the generation of hydroelectric power by the flow of water over the SWCNTs. The induced voltage was 63.1 mV upon the compression of a 4% SWCNT hydrogel to a compression ratio of 50%, which is superior to values reported previously. The enhancement in hydroelectric potential increased with SWCNT loading in the hydrogel and with the compression ratio because of an enhancement of the impact frequency between water molecules and the SWCNTs.
X-ray induced demagnetization of single-molecule magnets
Authors: Dreiser Jan , Westerström Rasmus , Piamonteze Cinthia , Nolting Frithjof , Rusponi Stefano , Brune Harald , Yang Shangfeng , Popov Alexey , Dunsch Lothar , Greber Thomas
Published: July 2014

Low-temperature x-ray magnetic circular dichroism measurements on the endohedral single-molecule magnet DySc2N@C80 at the Dy M4,5 edges reveal a shrinking of the opening of the observed hysteresis with increasing x-ray flux. Time-dependent measurements show that the exposure of the molecules to x-rays resonant with the Dy M5 edge accelerates the relaxation of magnetization more than off-resonant x-rays. The results cannot be explained by a homogeneous temperature rise due to x-ray absorption. Moreover, the observed large demagnetization cross sections indicate that the resonant absorption of one x-ray photon induces the demagnetization of many molecules.
Micro electro mechanical cantilever with electrostatically controlled tip contact
Authors: Rezadad Imen , Boroumand Javaneh , Smith Evan M. , Peale Robert E.
Published: July 2014

A micro-electro-mechanical system (MEMS) cantilever that lifts from the surface by electrostatic force is described. The design is composed of three conductors: a fixed buried plate, a fixed surface plate, and a moveable cantilever. All have the same square shape and are arranged parallel in a vertical stack with aligned edges. The surface plate and cantilever are biased at the same potential, and the buried plate is oppositely biased. Theoretical analysis based on values of position-dependent coefficients of capacitance and electrostatic induction from finite element method demonstrates the sign of the force on the cantilever and determines its magnitude. Video microscopy and electrical measurements demonstrate the electrostatic lifting of the cantilever in a fabricated MEMS device. The vertical displacement of the cantilever is quantified from changes in optical interference fringes, and the displacement magnitude agrees with expectations based on estimated strengths of upward electrostatic force and downward elastic restoring force.
Experimental study for the feasibility of using hard x-rays for micro-XRF analysis of multilayered metals
Authors: Polese C. , Dabagov S. B. , Esposito A. , Hampai D. , Gorghinian A. , Liedl A. , Ferretti M.
Published: July 2014

Application of polycapillary optical systems to improve a spatial resolution for the μ-XRF analysis by focusing a primary x-ray beam and/or by collecting fluorescence emission is well known. The challenge is to optimize them in combination with x-ray source for exciting K-lines above 20 keV that could allow characterization of many materials composed by heavy elements. To pursue this goal, preliminary studies on possible polycapillary lens employment in thickness determination for multilayer metal materials will be presented in this work. In this paper, the results of first attempts of integrating PyMCA with Monte Carlo simulation code (XMI-MSIM) that takes into account the secondary fluorescence effects on quantitative analysis of homogeneous matrices, in particular, metal alloys, are presented.
“Rings of saturn-like” nanoarrays with high number density of hot spots for surface-enhanced Raman scattering
Authors: Dai Zhigao , Mei Fei , Xiao Xiangheng , Liao Lei , Fu Lei , Wang Jiao , Wu Wei , Guo Shishang , Zhao Xinyue , Li Wei , Ren Feng , Jiang Changzhong
Published: July 2014

The Ag nanoparticles (NPs) surrounding triangular nanoarrays (TNAs) with high number density of surface-enhanced Raman scattering (SERS) hot spots (SERS hot spots ring) are prepared by a combination of NPs deposition and subsequent colloid lithography processing. Owing to the SERS hot spots ring, the Ag NPs surrounding TNAs have been proved an excellent candidate for ultrasensitive molecular sensing for their high SERS signal enhancing capacity in experiments and theories. The Ag NPs surrounding TNAs can be readily used for the quick detection of low concentrations of molecules related to food safety; herein, detection of melamine is discussed.
Coulomb impurity scattering in topological insulator thin films
Authors: Yin Gen , Wickramaratne Darshana , Zhao Yuanyuan , Lake Roger K.
Published: July 2014

Inter-surface coupling in thin-film topological insulators can reduce the surface state mobility by an order of magnitude in low-temperature transport measurements. The reduction is caused by a reduction in the group velocity and an increased sz component of the surface-state spin which weakens the selection rule against large-angle scattering. An intersurface potential splits the degenerate bands into a Rashba-like bandstructure. This reduces the intersurface coupling, it largely restores the selection rule against large angle scattering, and the ring-shaped valence band further reduces backscattering by requiring, on average, larger momentum transfer for backscattering events. The effects of temperature, Fermi level, and intersurface potential on the Coulomb impurity scattering limited mobility are analyzed and discussed.
Native structure of a type IV secretion system core complex essential for
Legionella
pathogenesis
Authors: Kubori Tomoko , Koike Masafumi , Bui Xuan Thanh , Higaki Saori , Aizawa Shin-Ichi , Nagai Hiroki
Published: July 2014

Significance

Bacterial pathogens manipulate host cellular processes using their own proteins. These proteins, so-called effectors, are injected into host cells using specialized nanomachines assembled on the bacterial cell surface. One such nanomachine, the type IV secretion system (T4SS), is evolutionarily related to bacterial conjugation systems. We describe the structure of the T4SS core complex required for effector translocation and virulence in the human pathogen
Legionella pneumophila.
The core complex of this T4SS is larger and more intricate than that of the pKM101 conjugation system. Analysis of premature complexes gives insights into a mechanism for core complex assembly whereby channel components dock in an outer-membrane subcomplex. Our data describing nanomachine assembly will aid toward development of drug therapies for bacterial pathogens.
Direct evidence for a magnetic
f
-electron–mediated pairing mechanism of heavy-fermion superconductivity in CeCoIn
5
Authors: Van Dyke John S. , Massee Freek , Allan Milan P. , Davis J. C. Séamus , Petrovic Cedomir , Morr Dirk K.
Published: July 2014

Significance

In heavy-fermion materials, the magnetic moment of an
f
-electron atom, such as Ce, is screened via the Kondo effect resulting in the splitting of a conventional light band into two heavy bands within few millielectron volts of the Fermi energy. For decades it has been hypothesized that Cooper pairing and superconductivity of the resulting heavy electrons are mediated by the
f
-electron magnetism. By extracting the magnetic interactions of CeCoIn
5
from heavy-fermion scattering interference, and by then predicting quantitatively a variety of characteristics expected for unconventional superconductivity driven by them, we provide direct evidence that the heavy-fermion Cooper pairing in this material is indeed mediated by
f
-electron magnetism.
Big data and other challenges in the quest for orthologs
Authors: Sonnhammer Erik L.L. , Gabaldón Toni , Sousa da Silva Alan W. , Martin Maria , Robinson-Rechavi Marc , Boeckmann Brigitte , Thomas Paul D. , Dessimoz Christophe ,   the Quest for Orthologs consortium
Published: July 2014

Given the rapid increase of species with a sequenced genome, the need to identify orthologous genes between them has emerged as a central bioinformatics task. Many different methods exist for orthology detection, which makes it difficult to decide which one to choose for a particular application.

Here, we review the latest developments and issues in the orthology field, and summarize the most recent results reported at the third ‘Quest for Orthologs’ meeting. We focus on community efforts such as the adoption of reference proteomes, standard file formats and benchmarking. Progress in these areas is good, and they are already beneficial to both orthology consumers and providers. However, a major current issue is that the massive increase in complete proteomes poses computational challenges to many of the ortholog database providers, as most orthology inference algorithms scale at least quadratically with the number of proteomes.

The Quest for Orthologs consortium is an open community with a number of working groups that join efforts to enhance various aspects of orthology analysis, such as defining standard formats and datasets, documenting community resources and benchmarking.

Availability and implementation: All such materials are available at http://questfororthologs.org .

Contact:  erik.sonnhammer@scilifelab.se or c.dessimoz@ucl.ac.uk
Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing
Authors: Papatheodorou Irene , Petrovs Rudolfs , Thornton Janet M.
Published: July 2014

Motivation : A large number of experimental studies on ageing focus on the effects of genetic perturbations of the insulin/insulin-like growth factor signalling pathway (IIS) on lifespan. Short-lived invertebrate laboratory model organisms are extensively used to quickly identify ageing-related genes and pathways. It is important to extrapolate this knowledge to longer lived mammalian organisms, such as mouse and eventually human, where such analyses are difficult or impossible to perform. Computational tools are needed to integrate and manipulate pathway knowledge in different species.

Results: We performed a literature review and curation of the IIS and target of rapamycin signalling pathways in Mus Musculus . We compare this pathway model to the equivalent models in Drosophila melanogaster and Caenorhabtitis elegans . Although generally well-conserved, they exhibit important differences. In general, the worm and mouse pathways include a larger number of feedback loops and interactions than the fly. We identify ‘functional orthologues’ that share similar molecular interactions, but have moderate sequence similarity. Finally, we incorporate the mouse model into the web-service NetEffects and perform in silico gene perturbations of IIS components and analyses of experimental results. We identify sub-paths that, given a mutation in an IIS component, could potentially antagonize the primary effects on ageing via FOXO in mouse and via SKN-1 in worm. Finally, we explore the effects of FOXO knockouts in three different mouse tissues.

Availability and implementation:  http://www.ebi.ac.uk/thornton-srv/software/NetEffects

Contact:  ip8@sanger.ac.uk or thornton@ebi.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Compression and fast retrieval of SNP data
Authors: Sambo Francesco , Di Camillo Barbara , Toffolo Gianna , Cobelli Claudio
Published: July 2014

Motivation: The increasing interest in rare genetic variants and epistatic genetic effects on complex phenotypic traits is currently pushing genome-wide association study design towards datasets of increasing size, both in the number of studied subjects and in the number of genotyped single nucleotide polymorphisms (SNPs). This, in turn, is leading to a compelling need for new methods for compression and fast retrieval of SNP data.

Results: We present a novel algorithm and file format for compressing and retrieving SNP data, specifically designed for large-scale association studies. Our algorithm is based on two main ideas: (i) compress linkage disequilibrium blocks in terms of differences with a reference SNP and (ii) compress reference SNPs exploiting information on their call rate and minor allele frequency. Tested on two SNP datasets and compared with several state-of-the-art software tools, our compression algorithm is shown to be competitive in terms of compression rate and to outperform all tools in terms of time to load compressed data.

Availability and implementation: Our compression and decompression algorithms are implemented in a C++ library, are released under the GNU General Public License and are freely downloadable from http://www.dei.unipd.it/~sambofra/snpack.html .

Contact:  sambofra@dei.unipd.it or cobelli@dei.unipd.it .
Biocellion
: accelerating computer simulation of multicellular biological system models
Authors: Kang Seunghwa , Kahan Simon , McDermott Jason , Flann Nicholas , Shmulevich Ilya
Published: July 2014

Motivation: Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming.

Results: We have developed Biocellion , a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion , modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies.

Availability and implementation:  Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information.

Contact:  seunghwa.kang@pnnl.gov
e-Driver: a novel method to identify protein regions driving cancer
Authors: Porta-Pardo Eduard , Godzik Adam
Published: July 2014

Motivation: Most approaches used to identify cancer driver genes focus, true to their name, on entire genes and assume that a gene, treated as one entity, has a specific role in cancer. This approach may be correct to describe effects of gene loss or changes in gene expression; however, mutations may have different effects, including their relevance to cancer, depending on which region of the gene they affect. Except for rare and well-known exceptions, there are not enough data for reliable statistics for individual positions, but an intermediate level of analysis, between an individual position and the entire gene, may give us better statistics than the former and better resolution than the latter approach.

Results: We have developed e-Driver, a method that exploits the internal distribution of somatic missense mutations between the protein’s functional regions (domains or intrinsically disordered regions) to find those that show a bias in their mutation rate as compared with other regions of the same protein, providing evidence of positive selection and suggesting that these proteins may be actual cancer drivers. We have applied e-Driver to a large cancer genome dataset from The Cancer Genome Atlas and compared its performance with that of four other methods, showing that e-Driver identifies novel candidate cancer drivers and, because of its increased resolution, provides deeper insights into the potential mechanism of cancer driver genes identified by other methods.

Availability and implementation: A Perl script with e-Driver and the files to reproduce the results described here can be downloaded from https://github.com/eduardporta/e-Driver.git

Contact:  adam@godziklab.org or eppardo@sanfordburnham.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations
Authors: Seemayer Stefan , Gruber Markus , Söding Johannes
Published: July 2014

Motivation : Recent breakthroughs in protein residue–residue contact prediction have made reliable de novo prediction of protein structures possible. The key was to apply statistical methods that can distinguish direct couplings between pairs of columns in a multiple sequence alignment from merely correlated pairs, i.e. to separate direct from indirect effects. Two classes of such methods exist, either relying on regularized inversion of the covariance matrix or on pseudo-likelihood maximization (PLM). Although PLM-based methods offer clearly higher precision, available tools are not sufficiently optimized and are written in interpreted languages that introduce additional overheads. This impedes the runtime and large-scale contact prediction for larger protein families, multi-domain proteins and protein–protein interactions.

Results : Here we introduce CCMpred, our performance-optimized PLM implementation in C and CUDA C. Using graphics cards in the price range of current six-core processors, CCMpred can predict contacts for typical alignments 35–113 times faster and with the same precision as the most accurate published methods. For users without a CUDA-capable graphics card, CCMpred can also run in a CPU mode that is still 4–14 times faster. Thanks to our speed-ups ( http://dictionary.cambridge.org/dictionary/british/speed-up ) contacts for typical protein families can be predicted in 15–60 s on a consumer-grade GPU and 1–6 min on a six-core CPU.

Availability and implementation : CCMpred is free and open-source software under the GNU Affero General Public License v3 (or later) available at https://bitbucket.org/soedinglab/ccmpred

Contact : johannes.soeding@mpibpc.mpg.de

Supplementary information : Supplementary data are available at Bioinformatics online.
CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies
Authors: Wood Christopher W. , Bruning Marc , Ibarra Amaurys Á. , Bartlett Gail J. , Thomson Andrew R. , Sessions Richard B. , Brady R Leo , Woolfson Derek N.
Published: July 2014

Motivation: The ability to accurately model protein structures at the atomistic level underpins efforts to understand protein folding, to engineer natural proteins predictably and to design proteins de novo . Homology-based methods are well established and produce impressive results. However, these are limited to structures presented by and resolved for natural proteins. Addressing this problem more widely and deriving truly ab initio models requires mathematical descriptions for protein folds; the means to decorate these with natural, engineered or de novo sequences; and methods to score the resulting models.

Results: We present CCBuilder, a web-based application that tackles the problem for a defined but large class of protein structure, the α-helical coiled coils. CCBuilder generates coiled-coil backbones, builds side chains onto these frameworks and provides a range of metrics to measure the quality of the models. Its straightforward graphical user interface provides broad functionality that allows users to build and assess models, in which helix geometry, coiled-coil architecture and topology and protein sequence can be varied rapidly. We demonstrate the utility of CCBuilder by assembling models for 653 coiled-coil structures from the PDB, which cover >96% of the known coiled-coil types, and by generating models for rarer and de novo coiled-coil structures.

Availability and implementation: CCBuilder is freely available, without registration, at http://coiledcoils.chm.bris.ac.uk/app/cc_builder/

Contact:  D.N.Woolfson@bristol.ac.uk or Chris.Wood@bristol.ac.uk
img2net: automated network-based analysis of imaged phenotypes
Authors: Breuer David , Nikoloski Zoran
Published: July 2014

Summary: Automated analysis of imaged phenotypes enables fast and reproducible quantification of biologically relevant features. Despite recent developments, recordings of complex networked structures, such as leaf venation patterns, cytoskeletal structures or traffic networks, remain challenging to analyze. Here we illustrate the applicability of img2net to automatedly analyze such structures by reconstructing the underlying network, computing relevant network properties and statistically comparing networks of different types or under different conditions. The software can be readily used for analyzing image data of arbitrary 2D and 3D network-like structures.

Availability and Implementation : img2net is open-source software under the GPL and can be downloaded from http://mathbiol.mpimp-golm.mpg.de/img2net/ , where supplementary information and datasets for testing are provided.

Contact : breuer@mpimp-golm.mpg.de
Kotai Antibody Builder: automated high-resolution structural modeling of antibodies
Authors: Yamashita Kazuo , Ikeda Kazuyoshi , Amada Karlou , Liang Shide , Tsuchiya Yuko , Nakamura Haruki , Shirai Hiroki , Standley Daron M.
Published: July 2014

Motivation: Kotai Antibody Builder is a Web service for tertiary structural modeling of antibody variable regions. It consists of three main steps: hybrid template selection by sequence alignment and canonical rules, 3D rendering of alignments and CDR-H3 loop modeling. For the last step, in addition to rule-based heuristics used to build the initial model, a refinement option is available that uses fragment assembly followed by knowledge-based scoring. Using targets from the Second Antibody Modeling Assessment, we demonstrate that Kotai Antibody Builder generates models with an overall accuracy equal to that of the best-performing semi-automated predictors using expert knowledge.

Availability and implementation: Kotai Antibody Builder is available at http://kotaiab.org

Contact:  standley@ifrec.osaka-u.ac.jp
Marketing the Hearth: Ornamental Embroidery and the Building of the Multinational Singer Sewing Machine Company
Authors: De La Cruz-Fernández Paula A.
Published: July 2014

This study examines the Singer Sewing Machine Company’s strategies for selling family sewing machines on a global scale. In marketing the sewing machine, the American-headquartered Singer focused on ornamental embroidery or “fancy” sewing, defining home sewing as art, to distance the company and the appliance from negative perceptions of women’s garment work as industrial manufacturing. Singer created its Embroidery Department in the early 1890s in response to consumers’ sewing preferences. The department reflects how the home became a site where global capitalism was constructed and articulated. Singer’s Embroidery Department had representatives in many countries, coordinating expositions and other advertising. In the case of Singer in Spain and the United States, women who took part in the department’s work were an essential part of the corporate-integrated operation. This article examines the relationship between Singer’s corporate strategies and gender and culture in Spain and the United States.
Spatial interactions between saithe (Pollachius virens) and hake (Merluccius merluccius) in the North Sea
Authors: Cormon Xochitl , Loots Christophe , Vaz Sandrine , Vermard Youen , Marchal Paul
Published: July 2014

Spatial interactions between saithe (Pollachius virens) and hake (Merluccius merluccius) were investigated in the North Sea. Saithe is a well-established species in the North Sea, while occurrence of the less common hake has recently increased in the area. Spatial dynamics of these two species and their potential spatial interactions were explored using binomial generalized linear models (GLM) applied to the International Bottom Trawl Survey (IBTS) data from 1991 to 2012. Models included different types of variables: (i) abiotic variables including sediment types, temperature, and bathymetry; (ii) biotic variables including potential competitors and potential preys presence; and (iii) spatial variables. The models were reduced and used to predict and map probable habitats of saithe, hake but also, for the first time in the North Sea, the distribution of the spatial overlap between these two species. Changes in distribution patterns of these two species and of their overlap were also investigated by comparing species’ presence and overlap probabilities predicted over an early (1991–1996) and a late period (2007–2012). The results show an increase in the probability over time of the overlap between saithe and hake along with an expansion towards the southwest and Scottish waters. These shifts follow trends observed in temperature data and might be indirectly induced by climate changes. Saithe, hake, and their overlap are positively influenced by potential preys and/or competitors, which confirms spatial co-occurrence of the species concerned and leads to the questions of predator–prey relationships and competition. Finally, the present study provides robust predictions concerning the spatial distribution of saithe, hake, and of their overlap in the North Sea, which may be of interest for fishery managers.
Variability of northeast Arctic cod (Gadus morhua) distribution on the main spawning grounds in relation to biophysical factors
Authors: Höffle H. , Solemdal P. , Korsbrekke K. , Johannessen M. , Bakkeplass K. , Kjesbu O. S.
Published: July 2014

Early life stages may on average gain a survival benefit from the regular return of parent fish to the same spawning grounds. Such areas may have a considerable spatial extent, occupation of which varies between spawning seasons. Northeast Arctic cod (Gadus morhua) is an ideal candidate to pinpoint the most influential biophysical factors in these respects due to its data richness and apparently strong “homing” behaviour. Their main spawning grounds, off northern Norway, are split in two by the Lofoten archipelago, and in the previous decade strong spawning activity was observed on the seaward continental shelf (Yttersida), while in recent years spawning activity in the wide fjord (Vestfjorden), that separates the islands from the Norwegian mainland, has again increased. Time-series of egg distribution were available from the 1980s, 1990s, and 2004–2012. We used several fixed and random factors to construct a statistical model for the distribution of recently spawned eggs, and hence, spawning adults in either area. We show that the most relevant covariates for the spatial distribution of eggs in Vestfjorden are local temperature and bathymetry, while at Yttersida influence affecting the whole stock, like regional ocean climate and age structure appear more important. Therefore, spawning inside the fjord may be constrained by suboptimal environmental conditions. Yttersida may be occupied by fish which have been displaced out of Vestfjorden when preferred conditions there are of limited extent.
Indoleamine 2,3-dioxygenase increases p53 levels in alloreactive human T cells, and both indoleamine 2,3-dioxygenase and p53 suppress glucose uptake, glycolysis and proliferation
Authors: Eleftheriadis Theodoros , Pissas Georgios , Antoniadi Georgia , Spanoulis Aginor , Liakopoulos Vassilios , Stefanidis Ioannis
Published: July 2014

Indoleamine 2,3-dioxygenase (IDO) suppresses adaptive immunity by inhibiting T-cell proliferation and altering glucose metabolism. The tumor suppressor p53 also alters these cellular processes with similar results. The effect of IDO on p53 and on glucose metabolism was evaluated in alloreactive T cells. Mixed-lymphocyte reactions (MLRs) were performed in the presence or not of the IDO inhibitor, 1-dl-methyl-tryptophan (1-MT) and/or the p53 inhibitor, pifithrin-α (PFT). Cell proliferation, glucose consumption and lactate production were assessed. 1-MT increased cell proliferation, glucose influx and lactate production, whereas PFT enhanced cell proliferation and glucose influx, leaving lactate production unaffected. In MLR-derived T cells, protein analysis revealed that IDO activated general control non-derepressible 2 kinase and induced p53, p-p53 (p53 phosphorylated at serine 15) and p21. In addition, both IDO and p53 decreased glucose transporter 1 and TP53-induced glycolysis and apoptosis regulator and increased synthesis of cytochrome c oxidase 2. IDO also reduced lactate dehydrogenase-A and glutaminase 2 levels, whereas p53 left them unaffected. Neither 1-MT nor PFT affected glucose-6-phosphate dehydrogenase. In conclusion, in alloreactive T cells, IDO increases p53 levels, and both IDO and p53 inhibit cell proliferation, glucose consumption and glycolysis. Lactate production and glutaminolysis are also suppressed by IDO, but not by p53.
metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA
Authors: Dale Ryan K. , Matzat Leah H. , Lei Elissa P.
Published: July 2014

Here we introduce metaseq, a software library written in Python, which enables loading multiple genomic data formats into standard Python data structures and allows flexible, customized manipulation and visualization of data from high-throughput sequencing studies. We demonstrate its practical use by analyzing multiple datasets related to chromatin insulators, which are DNA–protein complexes proposed to organize the genome into distinct transcriptional domains. Recent studies in Drosophila and mammals have implicated RNA in the regulation of chromatin insulator activities. Moreover, the Drosophila RNA-binding protein Shep has been shown to antagonize gypsy insulator activity in a tissue-specific manner, but the precise role of RNA in this process remains unclear. Better understanding of chromatin insulator regulation requires integration of multiple datasets, including those from chromatin-binding, RNA-binding, and gene expression experiments. We use metaseq to integrate RIP- and ChIP-seq data for Shep and the core gypsy insulator protein Su(Hw) in two different cell types, along with publicly available ChIP-chip and RNA-seq data. Based on the metaseq-enabled analysis presented here, we propose a model where Shep associates with chromatin cotranscriptionally, then is recruited to insulator complexes in trans where it plays a negative role in insulator activity.
High-throughput mutagenesis reveals functional determinants for DNA targeting by activation-induced deaminase
Authors: Gajula Kiran S. , Huwe Peter J. , Mo Charlie Y. , Crawford Daniel J. , Stivers James T. , Radhakrishnan Ravi , Kohli Rahul M.
Published: July 2014

Antibody maturation is a critical immune process governed by the enzyme activation-induced deaminase (AID), a member of the AID/APOBEC DNA deaminase family. AID/APOBEC deaminases preferentially target cytosine within distinct preferred sequence motifs in DNA, with specificity largely conferred by a small 9–11 residue protein loop that differs among family members. Here, we aimed to determine the key functional characteristics of this protein loop in AID and to thereby inform our understanding of the mode of DNA engagement. To this end, we developed a methodology (Sat-Sel-Seq) that couples saturation mutagenesis at each position across the targeting loop, with iterative functional selection and next-generation sequencing. This high-throughput mutational analysis revealed dominant characteristics for residues within the loop and additionally yielded enzymatic variants that enhance deaminase activity. To rationalize these functional requirements, we performed molecular dynamics simulations that suggest that AID and its hyperactive variants can engage DNA in multiple specific modes. These findings align with AID's competing requirements for specificity and flexibility to efficiently drive antibody maturation. Beyond insights into the AID-DNA interface, our Sat-Sel-Seq approach also serves to further expand the repertoire of techniques for deep positional scanning and may find general utility for high-throughput analysis of protein function.