bluuebunny/crossref_metadata_2025 huggingface dataset:
Wrinkling deformation and thermal conductivity of one graphane sheet under shear
Authors: Shen Haijun
Published: October 2013

Molecular dynamics simulations were performed to investigate the wrinkling deformation of one single‐layer graphane (GA) sheet under shear, and the shear deformation was compared with that of the macromembrane under shear. Furthermore, the thermal conductivity of the wrinkled GA sheet at 300 K was calculated. Moreover, the differences of anti‐shear capability and thermal conductance between the GA and another corresponding graphene sheet are discussed. The results show that the solutions of the macromembrane are applicable to predict the wrinkling deformation of the GA sheet under shear and that both the GA and the graphene sheet under shear have comparable anti‐buckling capability, whereas the GA sheet has much lower post‐buckling load‐carrying capacity. By increasing the shear strain, the thermal conductivity of both the GA and the graphene sheets decreases, and under the same shear strain the graphene sheet has higher thermal conductivity than the GA sheet.
Wetting of carbon nanotube functionalised nylon and its usage as flexible electrode in electrowetting on dielectric
Authors: Zhang Wei , Zuo Xudong , Wu Chengwei
Published: October 2013

The nylons functionalised with single walled carbon nanotubes (SWCNTs) at pH 2.5 and 3.5 display the time dependence of the water droplet contact angle, which is attributed to the adsorption of water molecules onto the nylon–water contact surface and the consequent increase in surface free energy. The contact angle of nylons functionalised at pH 4.5, 6.5 and 8.0 varies marginally with contact time, presumably owing to the presence of a large amount of SWCNTs on the nylon surface. Using the obtained nylon as a flexible electrode, an electrowetting on a dielectric system is designed. The contact angle decreases with the increase of the applied voltage and the electrowetting response is sensitive to the surface free energy of the water droplet. A low surface free energy is preferable for actuating the movement of the water droplet at a low‐driving voltage.
Effects of dopants in InOx-based amorphous oxide semiconductors for thin-film transistor applications
Authors: Aikawa Shinya , Nabatame Toshihide , Tsukagoshi Kazuhito
Published: October 2013

Amorphous metal oxide thin-film transistors (TFTs) are fabricated using InOx-based semiconductors doped with TiO2, WO3, or SiO2. Even at low-dopant densities, the electrical properties of the film strongly depend on the dopant used. We found that this dependence could be reasonably explained by differences in the bond-dissociation energy of the dopants. By incorporating a dopant with a higher bond-dissociation energy, the film became less sensitive to the partial pressure of oxygen used during sputtering and remained electrically stable upon thermal annealing. Thus, choosing a dopant with an appropriate bond-dissociation energy is important when fabricating stable metal-oxide TFTs for flat-panel displays.
Transition between regimes of a vertical channel bubbly upflow due to bubble deformability
Authors: Dabiri Sadegh , Lu Jiacai , Tryggvason Gretar
Published: October 2013

The effect of the deformability of viscous bubbles on the flow rate of bubbly upflow in a vertical channel is examined using direct numerical simulations. A sharp transition between two different flow regimes has been observed. At large bubble deformability, characterized by large Eötvös number (Eo), the flow rate is close to the single phase flow rate, with adjusted pressure gradient, and the bubbles are almost uniformly distributed in the middle of the channel. On the other hand, at low Eo the bubbles are concentrated near channel walls and flow rates are much smaller than the single phase flow. The transition from high flow rate to low flow rate occurs rather abruptly. It is found that the transition occurs when the less deformable bubbles enter the viscous sublayer due to the lateral lift force on the bubbles. This leads to an increase in the viscous dissipation near the wall which leads to a decrease in the flow rate.
Probing pure Lovelock gravity by Nariai and Bertotti-Robinson solutions
Authors: Dadhich Naresh , Pons Josep M.
Published: October 2013

The product spacetimes of constant curvature describe in Einstein gravity, which is linear in Riemann curvature, Nariai metric which is a solution of Λ-vacuum when curvatures are equal, k1 = k2, while it is Bertotti-Robinson metric describing uniform electric field when curvatures are equal and opposite, k1 = −k2. We probe pure Lovelock gravity by these simple product spacetimes and prove that the same characterization of these solutions is indeed true in general for pure Lovelock gravitational equation of order N in d = 2N + 2 dimension. We also consider these solutions for the conventional setting of Einstein-Gauss-Bonnet gravity.
Texture analysis in cubic phase polycrystals by single exposure synchrotron X-ray diffraction
Authors: Xie M. Y. , Baimpas N. , Reinhard C. , Korsunsky A. M.
Published: October 2013

We discuss the possibility of determining orientation distribution function (ODF) of cubic phase polycrystals from single exposure Debye-Scherrer diffraction data by a systematic numerical simulation. The fundamental zone of cubic phase crystals is discretised as 5°× 5° × 5° cubic cells, and the aim is to find out those preferred orientations represented by the cells centres which cannot be determined by single exposure Debye-Scherrer diffraction data. Two simulated ODFs corresponding to two different types of linear combination of single preferred orientations are used to validate if the method is suitable for more complicated textures. A data processing routine as well as experimental procedure that enable texture evaluation in metallic cubic phase polycrystals by single exposure high energy monochromatic synchrotron X-ray diffraction with area detector is presented. MTEX is used to estimate ODFs from both single exposure and multi-exposure 2D diffraction patterns. An extruded tungsten wire and a copper cylinder machined from a rolled plate are used to illustrate the whole method. Careful error comparison is made between the ODFs obtained from single exposure and multi-exposure data. Besides, all the diffraction patterns are processed by MAUD to provide a comparison to the MTEX approach, and good agreement is seen between ODFs produced by MAUD and MTEX.
Dimensional dependence of the Stokes–Einstein relation and its violation
Authors: Charbonneau Benoit , Charbonneau Patrick , Jin Yuliang , Parisi Giorgio , Zamponi Francesco
Published: October 2013

We generalize to higher spatial dimensions the Stokes–Einstein relation (SER) as well as the leading correction to diffusivity in finite systems with periodic boundary conditions, and validate these results with numerical simulations. We then investigate the evolution of the high-density SER violation with dimension in simple hard sphere glass formers. The analysis suggests that this SER violation disappears around dimension du = 8, above which it is not observed. The critical exponent associated with the violation appears to evolve linearly in 8 − d, below d = 8, as predicted by Biroli and Bouchaud [J. Phys.: Condens. Matter 19, 205101 (2007)], but the linear coefficient is not consistent with the prediction. The SER violation with d establishes a new benchmark for theory, and its complete description remains an open problem.
Extension of the non-Markovian Energy-Corrected Sudden model to the case of parallel and perpendicular infrared bands
Authors: Buldyreva Jeanna , Daneshvar Leila
Published: October 2013

The non-Markovian Energy-Corrected Sudden approach [J. Buldyreva and L. Bonamy, Phys. Rev. A 60, 370 (1999)] previously developed for wide-band rototranslational Raman spectra of linear rotors is extended to the case of infrared absorption by linear molecules with stretching and bending modes. Basic relations such as detailed balance and double-sided sum rules for the rotational relaxation matrix are easily satisfied owing to the specific choice of a symmetric metric in the Liouville space. A single set of model parameters deduced from experimental widths of isolated isotropic Raman lines enables calculations of line-shape characteristics and full spectra up to the far wings. Applications to the important but quite complex example of pure carbon dioxide indicate the crucial role of the frequency dependence in the relaxation operator even for calculations of isolated-line characteristics.
Electroosmotic flow of a viscoplastic material through a slit channel with walls of arbitrary zeta potential
Authors: Ng Chiu-On , Qi Cheng
Published: October 2013

Electroosmotic (EO) flow is known to have a nearly uniform velocity profile, but such a plug-flow velocity can be considerably diminished if the fluid is a viscoplastic material having a yield stress. This paper aims to investigate the reduction of EO velocity (also known as Smoluchowski slip velocity) due to a yield stress as a function of the material rheological parameters and the zeta potential. Three rheological models are considered: Casson, Herschel–Bulkley, and Bingham fluids. In the absence of pressure forcing and without the Debye–Hückel approximation, the problems of EO flow of these materials in a slit channel with walls uniformly charged with an arbitrary zeta potential are analytically solved. Analytical expressions are deduced for the reduced Smoluchowski velocity under the limiting conditions of very small and very large zeta potentials. It is shown that qualitatively different asymptotic behaviors will be exhibited by materials of different models.
Development progresses of radio frequency ion source for neutral beam injector in fusion devices
Authors: Chang D. H. , Jeong S. H. , Kim T. S. , Park M. , Lee K. W. , In S. R.
Published: October 2013

A large-area RF (radio frequency)-driven ion source is being developed in Germany for the heating and current drive of an ITER device. Negative hydrogen ion sources are the major components of neutral beam injection systems in future large-scale fusion experiments such as ITER and DEMO. RF ion sources for the production of positive hydrogen (deuterium) ions have been successfully developed for the neutral beam heating systems at IPP (Max-Planck-Institute for Plasma Physics) in Germany. The first long-pulse ion source has been developed successfully with a magnetic bucket plasma generator including a filament heating structure for the first NBI system of the KSTAR tokamak. There is a development plan for an RF ion source at KAERI to extract the positive ions, which can be applied for the KSTAR NBI system and to extract the negative ions for future fusion devices such as the Fusion Neutron Source and Korea-DEMO. The characteristics of RF-driven plasmas and the uniformity of the plasma parameters in the test-RF ion source were investigated initially using an electrostatic probe.
Uncooled detector challenges: Millimeter-wave and terahertz long channel field effect transistor and Schottky barrier diode detectors
Authors: Sakhno M. , Golenkov A. , Sizov F.
Published: October 2013

The model of long channel unbiased field effect transistor (FET) as mm-wave/THz detector is developed with account of some parasitic effects. The model offered is compared with the other known FET detector models and experimental data. The obtained responsivity (R) and noise equivalent power (NEP) estimations were compared with those for Schottky barrier diode (SBD) detectors. Within the framework of the model, R and NEP values for Si FETs can be determined in all inversion regions. Limits for performance of these detectors have been estimated. It has been shown that with advanced FET technology, the performance of FET mm-wave/THz detectors can be made similar to that of SBD ones or in high frequency range can surpass it. Influence of parasitic effects and detector-antenna matching on detector parameters is discussed. It has been ascertained that FETs can be preferable in some applications due to smaller parasitic effects.
High performance thin quantum barrier InGaN/GaN solar cells on sapphire and bulk (0001) GaN substrates
Authors: Young N. G. , Farrell R. M. , Hu Y. L. , Terao Y. , Iza M. , Keller S. , DenBaars S. P. , Nakamura S. , Speck J. S.
Published: October 2013

We demonstrate high performance InGaN/GaN multiple quantum well solar cells with thin quantum barriers and spectral response extending to 460 nm. Devices grown on bulk (0001) GaN substrates with up to 50 quantum wells (QWs) outperform those grown simultaneously on sapphire due to the lower threading dislocation density. Increasing the number of QWs eventually leads to performance degradation of devices grown on both substrates. Solar cells are demonstrated with peak external quantum efficiencies up to 60%, open circuit voltages up to 2.28 V, fill factors up to 80%, and conversion efficiencies up to 2.4% under 1 sun AM0 equivalent illumination.
Enhanced hydrogenation and reduced lattice distortion in size selected Pd-Ag and Pd-Cu alloy nanoparticles
Authors: Sengar Saurabh K. , Mehta B. R. , Kulriya P. K. , Khan S. A.
Published: October 2013

Important correlation between valence band spectra and hydrogenation properties in Pd alloy nanoparticles is established by studying the properties of size selected and monocrystalline Pd, Ag, Cu, Pd-Ag, and Pd-Cu nanoparticles. The X-ray photoelectron spectroscopy and elastic recoil detection analysis show that size induced Pd4d centroid shift is related to enhanced hydrogenation with H/Pd ratio of 0.57 and 0.49 in Pd-Ag and Pd-Cu nanoparticles in comparison to reported bulk values of 0.2 and 0.1, respectively. Pd-alloy nanoparticles show lower hydrogen induced lattice distortion. The reduced distortion and higher hydrogen reactivity of Pd-alloy nanoparticles is important for numerous hydrogen related applications.
Energy-selective multichannel ultraviolet photodiodes based on (Mg,Zn)O
Authors: Zhang Zhipeng , von Wenckstern Holger , Grundmann Marius
Published: October 2013

We report on the fabrication of photodiodes, employing rectifying contacts based on ternary (Mg,Zn)O thin films in wurtzite modification. We utilize a concept for forming a compositionally graded active layer, allowing the design of energy-selective, monolithic, and multichannel ultraviolet metal-semiconductor-metal photodetectors. In our device design, the filter layer blocking high energy irradiation is separated from the active layer and allows the tuning of cutoff energies and bandwidth of the photodiode. Here, the onset of absorption was tuned over 230 meV, and the bandwidth of the photodiodes was varied by 140 meV within the continuous composition spread of the active layer.
Spectral properties of a broad-area diode laser with off-axis external-cavity feedback
Authors: Chi Mingjun , Michael Petersen Paul
Published: October 2013

Spectral properties, both the optical spectrum and the intensity noise spectrum, of a broad-area diode laser with off-axis external-cavity feedback are presented. We show that the optical spectrum of the diode laser system is shifted to longer wavelengths due to the external-cavity feedback. The intensity noise spectrum of the diode laser shows that the intensity noise is increased strongly by the external-cavity feedback. External-cavity modes are excited in the external cavity even in the off-axis configuration. The peak spacing of the intensity noise spectrum shows that single roundtrip external-cavity modes are excited. We believe that the four-wave mixing process in the broad-area diode laser is responsible for the establishment of the external-cavity mode.
Precision quantum Hall resistance measurement on epitaxial graphene device in low magnetic field
Authors: Satrapinski A. , Novikov S. , Lebedeva N.
Published: October 2013

Precision quantum Hall resistance (QHR) measurements were performed on large-area epitaxial graphene device at temperature T = 1.5 K and at magnetic fields B from 8 T down to 2.5 T, that is much lower than typically used in precision QHR measurement. QHR was measured using cryogenic current comparator resistance bridge with relatively large biasing current Isd = 41 μA to reduce measurement uncertainty. The results showed that at B = 8 T, the relative deviation of Hall resistance from the expected quantized value h/2e2 is within experimental uncertainty of 3.5 parts in 108 and remained below 0.35 parts per million (ppm) down to B = 3 T.
Performance of molten salt solar power towers in Chile
Authors: Cáceres G. , Anrique N. , Girard A. , Degrève J. , Baeyens J. , Zhang H. L.
Published: October 2013

Chile is facing important challenges to develop its energy sector. Estimations demonstrate that in its electricity consumption Chile will grow at an annual rate of 4.6% until 2030, despite ongoing efficiency improvements. To satisfy this demand in a sustainable way, the national energy policy promotes the integration of novel and clean power generation into the national power mix, with special emphasis on concentrated solar power (CSP). The present paper assesses the development of solar-based electricity generation in Chile by CSP, achieved by a Solar Power Tower plant (SPT) using molten salt as heat carrier and store. Such SPTs can be installed at different locations in Chile, and connected to the main national grid. Results show that each SPT plant can generate around 76 GWhel of net electricity, when considering solar irradiation as the sole energy source and at a 16% overall efficiency of the SPT process. For operation in a continuous mode, a hybrid configuration with integrated gas backup system increases the generating potential of each SPT to 135 GWhel. A preliminary Levelized Energy Cost (LEC) calculation provides LEC values between 0.15 and 0.18 $/kWh, as function of the overall process efficiency and estimated investment cost. Chile's solar irradiation favors the implementation of SPT plants.
Dynamic relaxation study and experimental verification of dielectric-elastomer minimum-energy structures
Authors: Siu S. , Rhode-Barbarigos L. , Wagner S. , Adriaenssens S.
Published: October 2013

The shape of a dielectric elastomer minimum energy structure (DEMES) depends on the equilibrium between a pre-stretched membrane and an inextensible frame. The authors show that an extended dynamic relaxation method, a technique employed for the form-finding and analysis of pre-stressed structures, can be used to simulate DEMES equilibrium shapes. Physical models show excellent agreement with the shape of computed models. Dynamic relaxation, with its low computational cost, is a powerful form-finding technique that efficiently predicts the equilibrium shape as well as the elastic energy of DEMES.
Electronic transmission in Graphene suppressed by interlayer interference
Authors: Valencia Daniel , Lu Jun-Qiang , Wu Jian , Liu Feng , Zhai Feng , Jiang Yong-Jin
Published: October 2013

We investigate electronic transport property of a graphene monolayer covered by a graphene nanoribbon. We demonstrate that electronic transmission of a monolayer can be reduced when covered by a nanoribbon. The energy at which the transmission reduction occurs depends on the width of nanoribbon. We explain the transmission reduction as interference between wavefunctions in the monolayer and the nanoribbon. Furthermore, we show that the transmission reduction of a monolayer is combinable when covered by more than one nanoribbon and we propose a concept of “combination of control” for possible nano-application designs.
Trigger - and heat-transfer times measured during experimental molten-fuel-interactions
Authors: Spitznagel N. , Dürig T. , Zimanowski B.
Published: October 2013

A modified setup featuring high speed high resolution data and video recording was developed to obtain detailed information on trigger and heat transfer times during explosive molten fuel-coolant-interaction (MFCI). MFCI occurs predominantly in configurations where water is entrapped by hot melt. The setup was modified to allow direct observation of the trigger and explosion onset. In addition the influences of experimental control and data acquisition can now be more clearly distinguished from the pure phenomena. More precise experimental studies will facilitate the description of MFCI thermodynamics.
Configural Gestalts Remain Nothing More Than the Sum of Their Parts in Visual Agnosia
Authors: de-Wit Lee H. , Kubilius Jonas , de Beeck Hans P. Op , Wagemans Johan
Published: October 2013

We report converging evidence that higher stages of the visual system are critically required for the whole to become more than the sum of its parts by studying patient DF with visual agnosia using a configural superiority paradigm. We demonstrate a clear dissociation between this patient and normal controls such that she could more easily report information about parts, demonstrating a striking reversal of the normal configural superiority effect. Furthermore, by comparing DF's performance to earlier neuroimaging and novel modeling work, we found a compelling consistency between her performance and representations in the early visual areas, which are spared in this patient. The reversed pattern of performance in this patient highlights that in some cases visual Gestalts do not emerge early on without processing in higher visual areas. More broadly, this study demonstrates how neuropsychological patients can be used to unmask representations maintained at early stages of processing.
Characterization Methods for Starch-Based Materials: State of the Art and Perspectives
Authors: Wu Alex C. , Witt Torsten , Gilbert Robert G.
Published: October 2013

Improving starch-containing materials, whether food, animal feed, high-tech biomaterials, or engineering plastics, is best done by understanding how biosynthetic processes and any subsequent processing control starch structure, and how this structure controls functional properties. Starch structural characterization is central to this. This review examines how information on the three basic levels of the complex multi-scale structure of starch – individual chains, the branching structure of isolated molecules, and the way these molecules form various crystalline and amorphous arrangements – can be obtained from experiment. The techniques include fluorophore-assisted carbohydrate electrophoresis, multiple-detector size-exclusion chromatography, and various scattering techniques (light, X-ray, and neutron). Some examples are also given to show how these data provide mechanistic insight into how biosynthetic processes control the structure and how the various structural levels control functional properties.
Identification of stay-green and early senescence phenotypes in high-yielding winter wheat, and their relationship to grain yield and grain protein concentration using high-throughput phenotyping techniques
Authors: Kipp Sebastian , Mistele Bodo , Schmidhalter Urs
Published: October 2013

Yield and grain protein concentration (GPC) represent crucial factors in the global agricultural wheat (Triticum aestivum L.) production and are predominantly determined via carbon and nitrogen metabolism, respectively. The maintenance of green leaf area and the onset of senescence (Osen) are expected to be involved in both C and N accumulation and their translocation into grains. The aim of this study was to identify stay-green and early senescence phenotypes in a field experiment of 50 certified winter wheat cultivars and to investigate the relationships among Osen, yield and GPC. Colour measurements on flag leaves were conducted to determine Osen for 20 cultivars and partial least square regression models were used to calculate Osen for the remaining 30 cultivars based on passive spectral reflectance measurements as a high-throughput phenotyping technique for all varieties. Using this method, stay-green and early senescence phenotypes could be clearly differentiated. A significant negative relationship between Osen and grain yield (r2 = 0.81) was observed. By contrast, GPC showed a significant positive relationship to Osen (r2 = 0.48). In conclusion, the high-throughput character of our proposed phenotyping method should help improve the detection of such traits in large field trials as well as help us reach a better understanding of the consequences of the timing of senescence on yield.
Developmental bias in the evolution of phalanges
Authors: Kavanagh Kathryn D. , Shoval Oren , Winslow Benjamin B. , Alon Uri , Leary Brian P. , Kan Akinori , Tabin Clifford J.
Published: October 2013

Significance

It has long been proposed that rules stemming from the mechanisms used during development can constrain the range of evolvable variations in a given form, but few empirical examples are known. We have focused on developmental processes determining proportions of phalanx size along individual digits (fingers/toes) of vertebrates. We find that phalangeal variation seen in nature is indeed constrained by an ancestral developmental program, limiting morphologies to a continuum from nearly equal-sized phalanges to a large-to-small gradient of relative sizes. Nonetheless, later innovations in distal regulation expanded variational possibilities for groups that needed greater grasping ability. These data provide a better understanding of how properties of developmental systems work in combination with natural selection to guide evolution of skeletal proportions.
Argument disrupts interpersonal synchrony
Authors: Paxton Alexandra , Dale Rick
Published: October 2013

Research on interpersonal convergence and synchrony characterizes the way in which interacting individuals come to have more similar affect, behaviour, and cognition over time. Although its dynamics have been explored in many settings, convergence during conflict has been almost entirely overlooked. We present a simple but ecologically valid study comparing how different situational contexts that highlight affiliation and argument impact interpersonal convergence of body movement and to what degree emotional states affect convergence in both conversational settings. Using linear mixed-effect models, we found that in-phase bodily synchrony decreases significantly during argument. However, affective changes did not significantly predict changes in levels of interpersonal synchrony, suggesting that differences in affect valences between affiliation and argument cannot solely explain our results.
On a one-dimensional 𝛼-patch model with nonlocal drift and fractional dissipation
Authors: Dong Hongjie , Li Dong
Published: October 2013

We consider a one-dimensional nonlocal nonlinear equation of the form
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="partial-differential Subscript t Baseline u equals left-parenthesis normal upper Lamda Superscript negative alpha Baseline u right-parenthesis partial-differential Subscript x Baseline u minus nu normal upper Lamda Superscript beta Baseline u">

∂
t

u
=
(

Λ

−
α

u
)

∂
x

u
−
ν

Λ

β

u

\partial _t u = (\Lambda ^{-\alpha } u)\partial _x u - \nu \Lambda ^{\beta }u

, where

Λ
=
(
−

∂

x
x

)

1
2

\Lambda =(-\partial _{xx})^{\frac 12}

is the fractional Laplacian and

ν
≥
0

\nu \ge 0

is the viscosity coefficient. We primarily consider the regime

0
>
α
>
1

0>\alpha >1

and

0
≤
β
≤
2

0\le \beta \le 2

for which the model has nonlocal drift, fractional dissipation, and captures essential features of the 2D

α
\alpha

-patch models. In the critical and subcritical range

1
−
α
≤
β
≤
2

1-\alpha \le \beta \le 2

, we prove global wellposedness for arbitrarily large initial data in Sobolev spaces. In the full supercritical range

0
≤
β
>
1
−
α

0 \le \beta >1-\alpha

, we prove formation of singularities in finite time for a class of smooth initial data. Our proof is based on a novel nonlocal weighted inequality which can be of independent interest.
SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop
Authors: Schumacher André , Pireddu Luca , Niemenmaa Matti , Kallio Aleksi , Korpelainen Eija , Zanetti Gianluigi , Heljanko Keijo
Published: October 2013

Summary: Hadoop MapReduce-based approaches have become increasingly popular due to their scalability in processing large sequencing datasets. However, as these methods typically require in-depth expertise in Hadoop and Java, they are still out of reach of many bioinformaticians. To solve this problem, we have created SeqPig, a library and a collection of tools to manipulate, analyze and query sequencing datasets in a scalable and simple manner. SeqPigscripts use the Hadoop-based distributed scripting engine Apache Pig, which automatically parallelizes and distributes data processing tasks. We demonstrate SeqPig’s scalability over many computing nodes and illustrate its use with example scripts.

Availability and Implementation: Available under the open source MIT license at http://sourceforge.net/projects/seqpig/

Contact:  andre.schumacher@yahoo.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets
Authors: Wang Mingjun , Zhao Xing-Ming , Tan Hao , Akutsu Tatsuya , Whisstock James C. , Song Jiangning
Published: October 2013

Motivation: Caspases and granzyme B (GrB) are important proteases involved in fundamental cellular processes and play essential roles in programmed cell death, necrosis and inflammation. Although a number of substrates for both types have been experimentally identified, the complete repertoire of caspases and granzyme B substrates remained to be fully characterized. Accordingly, systematic bioinformatics studies of known cleavage sites may provide important insights into their substrate specificity and facilitate the discovery of novel substrates.

Results: We develop a new bioinformatics tool, termed Cascleave 2.0, which builds on previous success of the Cascleave tool for predicting generic caspase cleavage sites. It can be efficiently used to predict potential caspase-specific cleavage sites for the human caspase-1, 3, 6, 7, 8 and GrB. In particular, we integrate heterogeneous sequence and protein functional information from various sources to improve the prediction accuracy of Cascleave 2.0. During classification, we use both maximum relevance minimum redundancy and forward feature selection techniques to quantify the relative contribution of each feature to prediction and thus remove redundant as well as irrelevant features. A systematic evaluation of Cascleave 2.0 using the benchmark data and comparison with other state-of-the-art tools using independent test data indicate that Cascleave 2.0 outperforms other tools on protease-specific cleavage site prediction of caspase-1, 3, 6, 7 and GrB. Cascleave 2.0 is anticipated to be used as a powerful tool for identifying novel substrates and cleavage sites of caspases and GrB and help understand the functional roles of these important proteases in human proteolytic cascades.

Availability and implementation: http://www.structbioinfor.org/cascleave2/.

Contact: Jiangning.Song@monash.edu or James.Whisstock@monash.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
From Memory to Mastery: Accounting for Control in America, 1750–1880
Authors: Rosenthal Caitlin C.
Published: October 2013

From Memory to Masteryexplores the development of commercial numeracy and accounting in America and the English-speaking Atlantic world between 1750 and 1880. Most histories of accounting begin in the factories of England and New England, largely ignoring slave economies. I analyze both traditional sites of innovation, including textile mills and iron forges, and also southern and West Indian plantations. Along several dimensions, the calculative practices of slave owners advanced ahead of northern merchants and manufacturers, and many recorded and analyzed the productivity of their human capital with cruel precision. Following threads from Jamaica and Barbados to the American South, I show how plantation power relations stimulated the development of new accounting practices. The control of planters over their slaves made data easier to collect and more profitable to use. Commercial recordkeeping also expanded in free factories, but in different ways than on southern plantations. The mobility of labor made accounting necessary for keeping track of wages but relatively futile for detailed productivity analysis.
Early pathological alterations of lower lumbar cords detected by ultrahigh-field MRI in a mouse multiple sclerosis model
Authors: Mori Yuki , Murakami Masaaki , Arima Yasunobu , Zhu Dasong , Terayama Yasuo , Komai Yutaka , Nakatsuji Yuji , Kamimura Daisuke , Yoshioka Yoshichika
Published: October 2013

Magnetic resonance imaging (MRI) is widely employed for the diagnosis of multiple sclerosis (MS). However, sometimes, the lesions found by MRI do not correlate with the neurological impairments observed in MS patients. We recently showed autoreactive T cells accumulate in the fifth lumbar cord (L5) to pass the blood–brain barrier and cause inflammation in the central nervous system of experimental autoimmune encephalomyelitis (EAE) mice, an MS model. We here investigated this early event using ultrahigh-field MRI. T2-weighted image signals, which conform to the water content, increased in L4 and L5 during the development of EAE. At the same time, the sizes of L4 and L5 changed. Moreover, angiographic images of MRI showed branch positions of the blood vessels in the lower lumbar cords were significantly altered. Interestingly, EAE mice showed occluded and thickened vessels, particularly during the peak phase, followed by reperfusion in the remission phase. Additionally, demyelination regions of some MS patients had increased lactic acid content, suggesting the presence of ischemic events. These results suggest that inflammation-mediated alterations in the lower lumbar cord change the homeostasis of the spinal cord and demonstrate that ultrahigh-field MRI enables the detection of previously invisible pathological alterations in EAE.
Hypoxia-induced and A2A adenosine receptor-independent T-cell suppression is short lived and easily reversible
Authors: Ohta Akio , Madasu Manasa , Subramanian Meenakshi , Kini Radhika , Jones Graham , Choukèr Alexander , Ohta Akiko , Sitkovsky Michail
Published: October 2013

Tissue hypoxia plays a key role in establishing an immunosuppressive environment in vivo by, among other effects, increasing the level of extracellular adenosine, which then signals through A2A adenosine receptor (A2AR) to elicit its immunosuppressive effect. Although the important role of the adenosine–A2AR interaction in limiting inflammation has been established, the current study revisited this issue by asking whether hypoxia can also exert its T-cell inhibitory effects even without A2AR. A similar degree of hypoxia-triggered inhibition was observed in wild-type and A2AR-deficient T cells both in vitro and, after exposure of mice to a hypoxic atmosphere, in vivo. This A2AR-independent hypoxic T-cell suppression was qualitatively and mechanistically different from immunosuppression by A2AR stimulation. The A2AR-independent hypoxic immunosuppression strongly reduced T-cell proliferation, while IFN-γ-producing activity was more susceptible to the A2AR-dependent inhibition. In contrast to the sustained functional impairment after A2AR-mediated T-cell inhibition, the A2AR-independent inhibition under hypoxia was short lived, as evidenced by the quick recovery of IFN-γ-producing activity upon re-stimulation. These data support the view that T-cell inhibition by hypoxia can be mediated by multiple mechanisms and that both A2AR and key molecules in the A2AR-independent T-cell inhibition should be targeted to overcome the hypoxia-related immunosuppression in infected tissues and tumors.
Th2-type inflammation instructs inflammatory dendritic cells to induce airway hyperreactivity
Authors: Iwata Arifumi , Kawashima Saki , Kobayashi Midori , Okubo Ayako , Kawashima Hirotoshi , Suto Akira , Hirose Koichi , Nakayama Toshinori , Nakajima Hiroshi
Published: October 2013

Dendritic cells (DCs) play critical roles in determining the fate of CD4+ T cells. Among DC sub-populations, monocyte-derived inflammatory DCs (iDCs) have been shown to play an important role in the induction of adaptive immune responses under inflammatory conditions. Although previous studies have shown that DCs have an indispensable role in the induction of allergic airway inflammation and airway hyperreactivity (AHR) in murine asthma models, the precise roles of iDCs in the asthmatic responses remain largely unknown. We show here that Th2 cell-mediated inflammation in murine asthma models induces the expression of some markers of alternatively activated macrophage such as arginase 1 and resistin-like molecule-α in iDCs by a mechanism depending on the intrinsic expression of STAT6. In contrast, Th1 cell-mediated inflammation induces iDCs to express TNF-α and inducible nitric oxide synthase (iNOS), markers of TNF-α- and iNOS-producing DCs. Moreover, we show that iDCs under a Th2 environment play an important role in the induction of AHR, independently of allergic airway inflammation. Our results thus indicate the importance of iDCs in the induction of AHR as downstream effector cells in Th2 cell-mediated asthmatic responses.
The double PHD finger domain of MOZ/MYST3 induces α-helical structure of the histone H3 tail to facilitate acetylation and methylation sampling and modification
Authors: Dreveny Ingrid , Deeves Sian E. , Fulton Joel , Yue Baigong , Messmer Marie , Bhattacharya Amit , Collins Hilary M. , Heery David M.
Published: October 2013

Histone tail modifications control many nuclear processes by dictating the dynamic exchange of regulatory proteins on chromatin. Here we report novel insights into histone H3 tail structure in complex with the double PHD finger (DPF) of the lysine acetyltransferase MOZ/MYST3/KAT6A. In addition to sampling H3 and H4 modification status, we show that the DPF cooperates with the MYST domain to promote H3K9 and H3K14 acetylation, although not if H3K4 is trimethylated. Four crystal structures of an extended DPF alone and in complex with unmodified or acetylated forms of the H3 tail reveal the molecular basis of crosstalk between H3K4me3 and H3K14ac. We show for the first time that MOZ DPF induces α-helical conformation of H3K4-T11, revealing a unique mode of H3 recognition. The helical structure facilitates sampling of H3K4 methylation status, and proffers H3K9 and other residues for modification. Additionally, we show that a conserved double glycine hinge flanking the H3 tail helix is required for a conformational change enabling docking of H3K14ac with the DPF. In summary, our data provide the first observations of extensive helical structure in a histone tail, revealing the inherent ability of the H3 tail to adopt alternate conformations in complex with chromatin regulators.
Looking Beyond Demographics: Panel Attrition in the ANES and GSS
Authors: Frankel Laura Lazarus , Hillygus D. Sunshine
Published: October 2013

Longitudinal or panel surveys offer unique benefits for social science research, but they typically suffer from attrition, which reduces sample size and can result in biased inferences. Previous research tends to focus on the demographic predictors of attrition, conceptualizing attrition propensity as a stable, individual-level characteristic—some individuals (e.g., young, poor, residentially mobile) are more likely to drop out of a study than others. We argue that panel attrition reflects both the characteristics of the individual respondent as well as her survey experience, a factor shaped by the design and implementation features of the study. In this article, we examine and compare the predictors of panel attrition in the 2008–2009 American National Election Study, an online panel, and the 2006–2010 General Social Survey, a face-to-face panel. In both cases, survey experience variables are predictive of panel attrition above and beyond the standard demographic predictors, but the particular measures of relevance differ across the two surveys. The findings inform statistical corrections for panel attrition bias and provide study design insights for future panel data collections.
Intrathecal Substance P-Saporin in the Dog
Authors: Brown Dorothy Cimino , Agnello Kimberly
Published: October 2013

Background:

Substance P-saporin (SP-SAP), a chemical conjugate of substance P and a recombinant version of the ribosome-inactivating protein, saporin, when administered intrathecally, acts as a targeted neurotoxin producing selective destruction of superficial neurokinin-1 receptor–bearing cells in the spinal dorsal horn. The goal of this study was to provide proof-of-concept data that a single intrathecal injection of SP-SAP could safely provide effective pain relief in spontaneous bone cancer pain in companion (pet) dogs.

Methods:

In a single-blind, controlled study, 70 companion dogs with bone cancer pain were randomized to standard-of-care analgesic therapy alone (control, n = 35) or intrathecal SP-SAP (20–60 µg) in addition to standard-of-care analgesic therapy (n = 35). Activity, pain scores, and videography data were collected at baseline, 2 weeks postrandomization, and then monthly until death.

Results:

Although the efficacy results at the 2-week postrandomization point were equivocal, the outcomes evaluated beyond 2 weeks revealed a positive effect of SP-SAP on chronic pain management. Significantly, more dogs in the control group (74%) required unblinding and adjustment in analgesic protocol or euthanasia within 6 weeks of randomization than dogs that were treated with SP-SAP (24%; P < 0.001); and overall, dogs in the control group required unblinding significantly sooner than dogs that had been treated with SP-SAP (P < 0.01).

Conclusion:

Intrathecal administration of SP-SAP in dogs with bone cancer produces a time-dependent antinociceptive effect with no evidence of development of deafferentation pain syndrome which can be seen with neurolytic therapies.
Biomechanical regulation of vascular smooth muscle cell functions: from
in vitro
to
in vivo
understanding
Authors: Qiu Juhui , Zheng Yiming , Hu Jianjun , Liao Donghua , Gregersen Hans , Deng Xiaoyan , Fan Yubo , Wang Guixue
Published: October 2013

Vascular smooth muscle cells (VSMCs) have critical functions in vascular diseases. Haemodynamic factors are important regulators of VSMC functions in vascular pathophysiology. VSMCs are physiologically active in the three-dimensional matrix and interact with the shear stress sensor of endothelial cells (ECs). The purpose of this review is to illustrate how haemodynamic factors regulate VSMC functions under two-dimensional conditions
in vitro
or three-dimensional co-culture conditions
in vivo
. Recent advances show that high shear stress induces VSMC apoptosis through endothelial-released nitric oxide and low shear stress upregulates VSMC proliferation and migration through platelet-derived growth factor released by ECs. This differential regulation emphasizes the need to construct more actual environments for future research on vascular diseases (such as atherosclerosis and hypertension) and cardiovascular tissue engineering.
Initiation and propagation of combustion waves with competitive reactions and water evaporation
Authors: Hughes K. J. , Brindley J. , McIntosh A. C.
Published: October 2013

We use a one-dimensional model to present numerical and analytical results on the propagation of combustion waves, driven by competing exothermic and endothermic chemical reactions in parallel with water evaporation. The research was motivated by the phenomenology of emulsion explosives comprising a mixture of fuel and an ammonium nitrate (AN)–water solution. An extensive programme of computational modelling has covered a range of important physical influences, particularly the water fraction and the ambient pressure, on which the endothermic effect of evaporation is critically dependent. A substantial, and not immediately obvious, influence of the evaporation, through its effect on the temperature, is on the fraction of the AN consumed, respectively, by the competing exo- and endothermic reactions, which are controlled by differing, temperature-sensitive kinetics. Self-sustaining travelling combustion waves are initiated for a wide range of parameter values. They are usually oscillatory, regular for small water content and become highly irregular, sometimes causing extinction for larger water content. The numerics are complemented by a brief theoretical analysis, which throws light on the complex and subtle interplay of the two chemical reactions and the evaporation, expressed in the form of a highly convoluted integral over the whole time and space extent of the process.
Geographical range, heat tolerance and invasion success in aquatic species
Authors: Bates Amanda E. , McKelvie Catherine M. , Sorte Cascade J. B. , Morley Simon A. , Jones Nicholas A. R. , Mondon Julie A. , Bird Tomas J. , Quinn Gerry
Published: October 2013

Species with broader geographical ranges are expected to be ecological generalists, while species with higher heat tolerances may be relatively competitive at more extreme and increasing temperatures. Thus, both traits are expected to relate to increased survival during transport to new regions of the globe, and once there, establishment and spread. Here, we explore these expectations using datasets of latitudinal range breadth and heat tolerance in freshwater and marine invertebrates and fishes. After accounting for the latitude and hemisphere of each species’ native range, we find that species introduced to freshwater systems have broader geographical ranges in comparison to native species. Moreover, introduced species are more heat tolerant than related native species collected from the same habitats. We further test for differences in range breadth and heat tolerance in relation to invasion success by comparing species that have established geographically restricted versus extensive introduced distributions. We find that geographical range size is positively related to invasion success in freshwater species only. However, heat tolerance is implicated as a trait correlated to widespread occurrence of introduced populations in both freshwater and marine systems. Our results emphasize the importance of formal risk assessments before moving heat tolerant species to novel locations.
The prevalence and origin of exoprotease-producing cells in the Bacillus subtilis biofilm
Authors: Marlow Victoria L. , Cianfanelli Francesca R. , Porter Michael , Cairns Lynne S. , Dale J. Kim , Stanley-Wall Nicola R.
Published: October 2013

Biofilm formation by the Gram-positive bacteriumBacillus subtilisis tightly controlled at the level of transcription. The biofilm contains specialized cell types that arise from controlled differentiation of the resident isogenic bacteria. DegU is a response regulator that controls several social behaviours exhibited byB. subtilisincluding swarming motility, biofilm formation and extracellular protease (exoprotease) production. Here, for the first time, we examine the prevalence and origin of exoprotease-producing cells within the biofilm. This was accomplished using single-cell analysis techniques including flow cytometry and fluorescence microscopy. We established that the number of exoprotease-producing cells increases as the biofilm matures. This is reflected by both an increase at the level of transcription and an increase in exoprotease activity over time. We go on to demonstrate that exoprotease-producing cells arise from more than one cell type, namely matrix-producing and non-matrix-producing cells.In totothese findings allow us to add exoprotease-producing cells to the list of specialized cell types that are derived duringB. subtilisbiofilm formation and furthermore the data highlight the plasticity in the origin of differentiated cells.