bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of proteome‐wide binding reagents for research and diagnostics
Authors: Taussig Michael J. , Schmidt Ronny , Cook Elizabeth A. , Stoevesandt Oda
Published: November 2013

Alongside MS, antibodies and other specific protein‐binding molecules have a special place in proteomics as affinity reagents in a toolbox of applications for determining protein location, quantitative distribution and function (affinity proteomics). The realisation that the range of research antibodies available, while apparently vast is nevertheless still very incomplete and frequently of uncertain quality, has stimulated projects with an objective of raising comprehensive, proteome‐wide sets of protein binders. With progress in automation and throughput, a remarkable number of recent publications refer to the practical possibility of selecting binders to every protein encoded in the genome. Here we review the requirements of a pipeline of production of protein binders for the human proteome, including target prioritisation, antigen design, ‘next generation’ methods, databases and the approaches taken by ongoing projects in Europe and the USA. While the task of generating affinity reagents for all human proteins is complex and demanding, the benefits of well‐characterised and quality‐controlled pan‐proteome binder resources for biomedical research, industry and life sciences in general would be enormous and justify the effort. Given the technical, personnel and financial resources needed to fulfil this aim, expansion of current efforts may best be addressed through large‐scale international collaboration.
Seed and feeder use by birds in the United States and Canada
Authors: Horn David J. , Johansen Stacey M. , Wilcoxen Travis E.
Published: November 2013

More people feed birds and other wildlife than hunt and fish combined. Despite its popularity, many bird‐feeding traditions lack scientific data. We examined seed and feeder use by wild birds in the United States and Canada, and how seed use may change by season and geographic region. Between 2005 and 2008, 173 individuals from 38 states and 3 provinces in Canada made 20,077, 45‐minute observations at bird feeders, recording 106 species and 1,282,424 bird visits. Of the 10 seed types most commonly used in bird seed blends, 3 are most attractive to birds: black‐oil sunflower, medium sunflower chips, and white proso millet. Other seeds such as red milo are less attractive. Chickadees (Poecile spp.), nuthatches (Sitta spp.), and larger finches (Carpodacus spp.) were most abundant at black‐oil sunflower, smaller finches (Carduelis spp.) were most abundant at Nyjer® (Wild Bird Feeding Institute, Chicago, IL) and sunflower chips, and sparrows (Spizella spp.) were most abundant at white proso millet. Bird‐feeding traditions have been widely reported in books, magazines, newspaper articles, and websites. These traditions are often conflicting and have not been verified empirically. Studies such as this can be used to develop scientifically based recommendations that can lead to a better bird‐feeding experience and that attract fewer species with known negative ecological consequences. © 2013 The Wildlife Society.
ARP101 inhibits α‐MSH‐stimulated melanogenesis by regulation of autophagy in melanocytes
Authors: Kim Eun Sung , Jo Yoon Kyung , Park So Jung , Chang Huikyoung , Shin Ji Hyun , Choi Eun Sun , Kim Jun Bum , Seok Su Hyeon , Kim Jae-Sung , Oh Jeong Su , Kim Myoung-Hwan , Lee Eunjoo H. , Cho Dong-Hyung
Published: November 2013

Autophagy is a cooperative process between autophagosomes and lysosomes that degrades cellular organelles. Although autophagy regulates the turnover of cellular components, its role in melanogenesis is not clearly established. Previously, we reported that ARP101 induces autophagy in various cancer cells. Here, we show that ARP101 inhibits melanogenesis by regulation of autophagy. ARP101 inhibited α‐MSH‐stimulated melanin synthesis and suppressed the expression of tyrosinase and TRP1 in immortalized mouse melanocytes. ARP101 also induced autophagy in melanocytes. Knockdown of ATG5 reduced both anti‐melanogenic activity and autophagy mediated by ARP101 in α‐MSH treated melanocytes. Electron microscopy analysis further revealed that autophagosomes engulf melanin or melanosome in α‐MSH and ARP101‐treated cells. Collectively, our results suggest that ARP101 inhibits α‐MSH‐stimulated melanogenesis through the activation of autophagy in melanocytes.
Modulation of H+,K+‐ATPase activity by the molecular chaperone ERp57 highly expressed in gastric parietal cells
Authors: Fujii Takuto , Awaka Shun-ya , Takahashi Yuji , Fujita Kyosuke , Tsuji Hiroshi , Shimizu Takahiro , Gomi Tomoharu , Tsukada Kazuhiro , Sakai Hideki
Published: November 2013

ERp57 is a ubiquitous ER chaperone that has disulfide isomerase activity. Here, we found that both ERp57 and gastric H+,K+‐ATPase are expressed in a sample derived from the apical canalicular membranes of parietal cells. Overexpression of ERp57 in HEK293 cells stably expressing H+,K+‐ATPase significantly increased the ATPase activity without changing the expression level of H+,K+‐ATPase. Interestingly, overexpression of a catalytically inactive mutant of ERp57 (C57S/C60S/C406S/C409S) in the cells also increased H+,K+‐ATPase activity. In contrast, knockdown of endogenous ERp57 in H+,K+‐ATPase‐expressing cells significantly decreased ATPase activity without changing the expression level of H+,K+‐ATPase. Overexpression and knockdown of ERp57 had no significant effect on the expression and function of Na+,K+‐ATPase. These results suggest that ERp57 positively regulates H+,K+‐ATPase activity apart from its chaperoning function.
Hax‐1 identified as a two‐pore channel (TPC)‐binding protein
Authors: Lam Andy K.M. , Galione Antony , Lai F. Anthony , Zissimopoulos Spyros
Published: November 2013

Two‐pore channels (TPC1–3) are recently identified endolysosomal ion channels. The mechanism by which these channels are regulated at the molecular level is presently unclear. To identify putative protein regulators of TPCs, we performed unbiased transcriptome‐wide screens using the yeast two‐hybrid technique to identify potential protein–protein interactions with the intracellular domains of human TPC2. We now present biochemical evidence for a novel molecular interaction between human TPC1/2 and the anti‐apoptotic protein Hax‐1 (HCLS‐associated X‐1). The observed binding of Hax‐1 to TPCs may represent a conserved mechanism by which these endolysosomal ion channels are regulated.
Asparagine 42 of the conserved endo‐inulinase INU2 motif WMNDPN from Aspergillus ficuum plays a role in activity specificity
Authors: Vandamme Anne-Michèle , Michaux Catherine , Mayard Aurélie , Housen Isabelle
Published: November 2013

Endo‐inulinase INU2 from Aspergillus ficuum belongs to glycosidase hydrolase family 32 (GH32) that degrades inulin into fructo oligosaccharides consisting mainly of inulotriose and inulotetraose. The 3D structure of INU2 was recently obtained (Pouyez et al., 2012, Biochimie, 94, 2423–2430). An enlarged cavity compared to exo‐inulinase formed by the conserved motif W‐M(I)‐N‐D(E)‐P‐N‐G, the so‐called loop 1 and the loop 4, was identified. In the present study we have characterized the importance of 12 residues situated around the enlarged cavity. These residues were mutated by site‐directed mutagenesis. Comparative activity analysis was done by plate, spectrophotometric and thin‐layer chromatography assay. Most of the mutants were less active than the wild‐type enzyme. Most interestingly, mutant N42G differed in the size distribution of the FOS synthesized.
The Project Management Office: Transforming Healthcare in the Context of a Hospital Redevelopment Project
Authors: Richer Marie-Claire , Marchionni Caroline , Lavoie-Tremblay Melanie , Aubry Monique
Published: November 2013

It has been shown that classifying projects into a typology allows improved allocation of resources and promotes project success. However, a typology of healthcare projects has yet to be developed. The projects encountered by the Transition Support Office at the McGill University Health Centre in Montreal, Quebec, where a major redevelopment project is under way, were classified into a typology unique to the healthcare context. Examples of the 3 project types, Process, People, and Practice, are provided to clarify the specific support strategies and context-adapted interventions that were instrumental to their success.
The aqueous extract from Toona sinensis leaves inhibits microglia‐mediated neuroinflammation
Authors: Wang Chao‐Chuan , Tsai Yee‐Jean , Hsieh Ya‐Ching , Lin Rong‐Jyh , Lin Chih‐Lung
Published: November 2013

The leaves of Toona sinensis, a well‐known traditional oriental medicine, have been prescribed for the treatment of enteritis and infection. Recently, aqueous extracts of Toona sinensis leaves (TSL‐1) have demonstrated many biological effects both in vitro and in vivo. In the central nervous system, microglial activation and their proinflammatory responses are considered an important therapeutic strategy for neuroinflammatory disorders such as cerebral ischemia, Alzheimer's disease, and Parkinson's disease. The present study attempted to validate the effect of TSL‐1 on microglia‐mediated neuroinflammation stimulated by lipopolysaccharide (LPS). As inflammatory parameters, the production of nitric oxide (NO), inducible NO synthase, and tumor necrosis factor‐α were evaluated. Our results demonstrate that TSL‐1 suppresses LPS‐induced NO production, tumor necrosis factor‐α secretion, and inducible NO synthase protein expression in a concentration‐dependent manner, without causing cytotoxicity. In addition, the inhibitory effects of TSL‐1 in LPS‐stimulated BV‐2 microglia were extended to post‐treatment suggesting the therapeutic potential of TSL‐1. Therefore, this work provides the future evaluation of the role of TSL‐1 in the treatment of neurodegenerative diseases by inhibition of inflammatory mediator production in activated microglia.
Unifying binary fluid diffuse-interface models in the sharp-interface limit
Authors: Sibley David N. , Nold Andreas , Kalliadasis Serafim
Published: November 2013

Recent results published by Gugenberger et al. on surface diffusion (Phys. Rev. E, vol. 78, 2008, 016703), show that the sharp-interface limit of the phase field models often adopted in the literature fails to produce the appropriate boundary conditions. With this knowledge, we consider the sharp-interface limit of phase field models for binary fluids, obtained carefully, where hydrodynamic equations are coupled to phase field evolution based on Cahn–Hilliard or Allen–Cahn theories, in a variety of guises, and unify and contrast their forms and behaviours in the sharp-interface limit. In particular, a tensorial mobility model is analysed, which allows the bulk fluids in the outer region to satisfy classical Navier–Stokes type equations to all orders in the Cahn number.
Inertial instability of flows on the inside or outside of a rotating horizontal cylinder
Authors: Benilov E. S. , Lapin V. N.
Published: November 2013

We consider thin liquid films on the inside (rimming flows) or outside (coating flows) of a cylinder with horizontal axis, rotating about this axis. If the liquid’s net volume is small, such films are known to evolve towards a steady state with a smooth surface, whereas, for larger amounts, the flow develops a ‘shock’ similar to a tidal bore. In this work, smooth films are shown to be unstable. Since the strongest instability occurs at wavelengths comparable to the film’s thickness, our analysis is based on the full Navier–Stokes equations, not on the lubrication approximation (which has been traditionally used in this problem). It is also shown that, for cylinders of sufficiently small radii, the instability can be suppressed by surface tension.
Instability regimes in the primary breakup region of planar coflowing sheets
Authors: Fuster D. , Matas J.-P. , Marty S. , Popinet S. , Hoepffner J. , Cartellier A. , Zaleski S.
Published: November 2013

This article investigates the appearance of instabilities in two planar coflowing fluid sheets with different densities and viscosities via experiments, numerical simulation and linear stability analysis. At low dynamic pressure ratios a convective instability is shown to appear for which the frequency of the waves in the primary atomization region is influenced by both liquid and gas velocities. For large dynamic pressure ratios an asymptotic regime is obtained in which frequency is solely controlled by gas velocity and the instability becomes absolute. The transition from convective to absolute is shown to be influenced by the velocity defect induced by the presence of the separator plate. We show that in this regime the splitter plate thickness can also affect the nature of the instability if it is larger than the gas vorticity thickness. Computational and experimental results are in agreement with the predictions of a spatio-temporal stability analysis.
TaqIB polymorphism in the cholesteryl ester transfer protein (CETP) gene influences lipid responses to the consumption of kiwifruit in hypercholesterolaemic men
Authors: Gammon Cheryl S. , Minihane Anne M. , Kruger Rozanne , Conlon Cathryn A. , von Hurst Pamela R. , Jones Beatrix , Stonehouse Welma
Published: November 2013

Fruit and vegetables are key elements of a cardioprotective diet, but benefits on plasma lipids, especially HDL-cholesterol (HDL-C), are inconsistent both within and between studies. In the present study, we investigated whether four selected HDL-C-related polymorphisms (cholesteryl ester transfer protein (CETP) Taq1B, APOA1 − 75G/A, hepatic lipase (LIPC) − 514C → T, and endothelial lipase (LIPG) I24582) modulate the plasma lipid response to a kiwifruit intervention. This is a retrospective analysis of data collected during a 12-week randomised controlled cross-over trial. A total of eighty-five hypercholesterolaemic men completed a 4-week healthy diet run-in period before being randomised to one of two 4-week intervention sequences of two green kiwifruit/d plus healthy diet (kiwifruit intervention) or healthy diet alone (control intervention). The measurement of anthropometric parameters and collection of fasting blood samples were carried out at baseline 1 and after the run-in (baseline 2) and intervention periods. At baseline 2, B1/B1 homozygotes of the CETPTaq1B gene had significantly higher total cholesterol:HDL-C, TAG:HDL-C, and apoB:apoA1 ratios and small-dense LDL concentrations than B2 carriers. A significant CETP Taq1B genotype × intervention interaction was observed for the TAG:HDL-C ratio (P= 0·03). B1/B1 homozygotes had a significantly lower TAG:HDL-C ( − 0·23 (sd 0·58) mmol/l; P= 0·03) ratio after the kiwifruit intervention than after the control intervention, whereas the ratio of B2 carriers was not affected. The lipid response was not affected by other gene polymorphisms. In conclusion, the significant decrease in the TAG:HDL-C ratio in B1/B1 homozygotes suggests that regular inclusion of green kiwifruit as part of a healthy diet may improve the lipid profiles of hypercholesterolaemic men with this genotype.
Risk factors for susceptibility to varicella in newly arrived adult migrants in Canada
Authors: GREENAWAY C. , BOIVIN J. F. , CNOSSEN S. , ROSSI C. , TAPIERO B. , SCHWARTZMAN K. , OLSON S. , MILLER M.
Published: November 2013

Varicella occurs at an older age in tropical compared to cold climates. Migrants from tropical countries provide the opportunity to gain insights into observed global differences in varicella epidemiology. Severity of varicella increases with age thus, description of risk factors for varicella susceptibility will identify those who would benefit most from vaccination. A total of 1480 migrants, with a mean age of 32 years, were recruited in the pre-vaccination period (2002–2004) in Montreal, Canada. A questionnaire was administered and serum varicella antibodies were measured. Overall 6% were susceptible and ranged from 0·8% to 14·1% in subgroups. Risk factors for susceptibility were younger age, recent arrival, and originating from a tropical country. This could be modified by conditions that increased the probability of person-to-person spread of varicella through direct contact in source countries such as larger community size or household crowding. Many new young adult migrants would benefit from targeted varicella vaccination programmes.
Identifying the public health benefits of livestock-dependent, agro-ecosystems under climate change
Authors: Gillette Shana
Published: November 2013

As the demand for meat continues to grow in South Asia and Africa and access to communal sources of water and forage shrinks, intensification of small-scale livestock systems in peri-urban areas is expected to expand. In South East Asia, smallholder transition to livestock intensification has been transformative, increasing economic opportunities while also introducing new disease risks. While we have an understanding of the emerging disease burden from livestock intensification; we have just begun to understand the possible public health benefits of sustainable landscapes and the potential health savings accrued from disease avoidance. To date, few studies have attempted to quantify the health benefits attributable to sustainable agro-ecosystems, especially in regard to livestock systems. In this paper, I will examine what is needed to measure and communicate the public health benefits and cost-savings (from disease avoidance) of sustainable agro-ecosystems.
Anger, Sadness, and Fear Responses to Crime and Accident News Stories
Authors: Solloway Tyler , Slater Michael D. , Chung Adrienne , Goodall Catherine E.
Published: November 2013

Prior research has shown that discrete emotions, notably anger and fear, can explain effects of news articles on health and alcohol-control policy support. This study advances prior work by coding expressed emotional responses to messages (as opposed to directly manipulated emotions or forced responses), incorporating and controlling for central thoughts, including sadness (a particularly relevant response to tragic stories), and examining the mediating role of concern, between emotion and policy support. An experiment with a US national online adult panel had participants read one of 60 violent crime or accident news stories, each manipulated to mention or withhold alcohol’s causal contribution. Multigroup structural equation models suggested that stories not mentioning alcohol had a direct effect on policy support via fear and central thoughts, unmediated by concern. When alcohol was mentioned, sadness and anger affected alcohol-control support through concern. These findings help confirm that emotional responses are key in determining news story effects on public support of health policies.
The cytokine-induced conformational switch of nuclear factor κB p65 is mediated by p65 phosphorylation
Authors: Milanovic Maja , Kracht Michael , Schmitz M. Lienhard
Published: November 2013

The transcription factor NF-κB (nuclear factor κB) serves to up-regulate gene expression in response to precarious signals such as the pro-inflammatory cytokines TNF (tumour necrosis factor) and IL-1 (interleukin 1). In the present study we show that stimulation of cells with TNF or IL-1 results in a profound conformational switch of the NF-κB subunit p65, as revealed by limited proteolysis assays. We also describe the identification of a conformation-specific monoclonal antibody that preferentially immunoprecipitates the inducibly refolded p65 protein. The cytokine-triggered reconfiguration of p65 mainly occurs for p65 contained in the nuclear fraction. Phosphorylations serve as the central driving force for the inducible reconfiguration of p65. Accordingly, mutation of single phosphorylation sites in the C-terminal transactivation domain led to large conformational changes which result in strongly decreased ubiquitination and also in differential protein–protein interactions. Induced conformational changes of p65 thus increase the intramolecular flexibility and therefore expand and specify the repertoire of possible protein–protein interactions. Constitutively bound chaperones of the Hsp (heat-shock protein)/Hsc70 (heat-shock cognate protein, 73 kDa) family are not important for the cytokine-induced conformational switch, but rather control the fidelity of protein rearrangement. Accordingly, pharmacological inhibition of Hsp/Hsc70 interferes with p65-triggered gene expression.
O
2
Vibration Relaxation in Oxygen-Argon Mixtures
Authors: Camac Morton
Published: November 2013

This paper and the one following [M. Camac and A. Vaughan, J. Chem. Phys. 34, 459 (1961)] discuss the use of a new experi-mental technique for the determination of O2 vibration and dissociation rates. The concentration of O2 in the ground vibrational state can be inferred from measurements of ultraviolet light transmission at 1470 A. O2 has a strong continuous absorption band in this vacuum ultraviolet region. The vibrational relaxation rate of O2 in shock-heated O2-Ar mixtures was obtained from 1200 °K to 7000 °K. For Ar-O2 collisions, the measured relaxation time t, can be fit by the Landau-Teller theory [L. Landau and E. Teller, Physik. Z. Sowjetunion 10, 34 (1936)] 1/τv = nC1T1/6[1−exp(−2228T)]exp(−(C/T)1/3), where n is the number of particles/cc and T is the temperature in °K. C1 = 1.2×10−7 cc/particle∼sec-(K)1/6 and C = 1.04×107 (±30%)°K. The observed vibrational relaxation time for O2-O2 collisions is 5.0±0.5 times faster than that for O2-Ar collisions. The experimental results are compared to the theoretical predictions of Schwartz and Herzfeld [R. N. Schwartz, Z. I. Slawsky, and K. F. Herzfeld, J. Chem. Phys. 20, 1591 (1952); R. N. Schwartz and K. F. Herzfeld, ibid. 22, 767 (1954)]. At the lower temperatures, the O2-O2 rates given by Blackman [V. H. Blackman, J. Fluid Mech. 1, 61 (1956)] have a different temperature dependence than the O2-Ar rates obtained in this experiment.
Infrared Spectra of Alkyldiboranes. IV. 1,1-Dimethyl- and 1,1-Diethyldiboranes
Authors: Lehmann Walter J. , Wilson Charles O. , Shapior I.
Published: November 2013

The infrared spectra of five isotopic variants of two 1,1-dialkyldiboranes, viz., (CH3)2B210H4, (CH3)2B2H4, (CH3)2B2D4, (CD3)2B2H4, and (CD3)2B2D4, and the corresponding diethyl compounds, are reported and frequency assignments are made. A method for purification of these compounds also is described. The intensity ratio of the 923 to 2096-cm−1 bands in (CH3)2B2H4 served as a simple preliminary criterion.for the absence of other alkyldiboranes. The strong bridge-stretching frequencies of the 1,1-dialkyldiboranes at 1550 cm−1 are unique in being ca 50 cm−1 lower than corresponding BH′ bands in other alkyldiboranes. Another BH′ absorption, at 2100 cm−1, is quite intense compared with other alkyldiboranes.
Femtosecond two-photon photoassociation of hot magnesium atoms: A quantum dynamical study using thermal random phase wavefunctions
Authors: Amaran Saieswari , Kosloff Ronnie , Tomza Michał , Skomorowski Wojciech , Pawłowski Filip , Moszynski Robert , Rybak Leonid , Levin Liat , Amitay Zohar , Berglund J. Martin , Reich Daniel M. , Koch Christiane P.
Published: November 2013

Two-photon photoassociation of hot magnesium atoms by femtosecond laser pulses, creating electronically excited magnesium dimer molecules, is studied from first principles, combining ab initio quantum chemistry and molecular quantum dynamics. This theoretical framework allows for rationalizing the generation of molecular rovibrational coherence from thermally hot atoms [L. Rybak, S. Amaran, L. Levin, M. Tomza, R. Moszynski, R. Kosloff, C. P. Koch, and Z. Amitay, Phys. Rev. Lett. 107, 273001 (2011)]. Random phase thermal wavefunctions are employed to model the thermal ensemble of hot colliding atoms. Comparing two different choices of basis functions, random phase wavefunctions built from eigenstates are found to have the fastest convergence for the photoassociation yield. The interaction of the colliding atoms with a femtosecond laser pulse is modeled non-perturbatively to account for strong-field effects.
An experimental UHV AFM-STM device for characterizing surface nanostructures under stress/strain at variable temperature
Authors: Nahas Y. , Berneau F. , Bonneville J. , Coupeau C. , Drouet M. , Lamongie B. , Marteau M. , Michel J. , Tanguy P. , Tromas C.
Published: November 2013

A compression setup fully integrated in an ultra high vacuum chamber is presented. The system has been designed to combine in situ mechanical test together with near field microscopy at variable temperature, from 90 to 600 K. Compressive stress can be applied on the samples up to 500 MPa at different strain rates ranging from 10−6 s−1 to 10−2 s−1. The setup performances are highlighted through investigations on Au and Ni3(Al,Ta) single crystals. In particular, it is demonstrated that the high mechanical stability of the original apparatus allows us to follow in situ the evolution of the same area of interest over a large range of temperature and to keep the high spatial resolution offered by near field microscopy, even at high strain levels.
Interfacial exciplex formation in bilayers of conjugated polymers
Authors: Nobuyasu R. S. , Araujo K. A. S. , Cury L. A. , Jarrosson T. , Serein-Spirau F. , Lère-Porte J.-P. , Dias F. B. , Monkman A. P.
Published: November 2013

The donor-acceptor interactions in sequential bilayer and blend films are investigated. Steady-state and time-resolved photoluminescence (PL) were measured to characterize the samples at different geometries of photoluminescence collection. At standard excitation, with the laser incidence at 45° of the normal direction of the sample surface, a band related to the aggregate states of donor molecules appears for both blend and bilayer at around 540 nm. For the PL spectra acquired from the edge of the bilayer, with the laser incidence made at normal direction of the sample surface (90° geometry), a new featureless band emission, red-shifted from donor and acceptor emission regions was observed and assigned as the emission from interfacial exciplex states. The conformational complexity coming from donor/acceptor interactions at the heterojunction interface of the bilayer is at the origin of this interfacial exciplex emission.
Application of evaporative cooling technology in super-high power density magnet
Authors: Xiong B. , Ruan L. , Gu G. B. , Guo S. Q. , Cao R. , Li Z. G. , Lu W. , Zhang X. Z. , Sun L. T. , Zhao H. W.
Published: November 2013

Evaporative cooling technology utilizes phase-change heat transfer mode to achieve the cooling for heating equipment. The heat transfer capacity of evaporative cooling technology is far more than air or water cooling technology. The Electron Cyclotron Resonance ion source magnet is a typical super-high power density magnet, and the evaporative cooling technology is an ideal cooling method for the coils of magnet. In this paper we show the structure and process of coils and the special design of flow channels of coolant for an experiment magnet model. Additionally, the heat transfer circulation is presented and analyzed. By the finite element method, the flow channels are optimized to rationally allocate coolant and to reduce the temperature of coils. For the experiment model, the current density of copper wire of coils is 19 A/mm2, and the coil-windows current density is larger than 12 A/mm2. The max temperature of coils is below 80 °C, and the total heat is about 200 kW.
Anomalous Hall effect in epitaxial permalloy thin films
Authors: Zhang Y. Q. , Sun N. Y. , Shan R. , Zhang J. W. , Zhou S. M. , Shi Z. , Guo G. Y.
Published: November 2013

Anomalous Hall effect (AHE) of epitaxial permalloy thin films grown on MgO (001) substrates is investigated. The longitudinal conductivity independent term (i.e., the sum of intrinsic and side-jump contributions) of the anomalous Hall conductivity (AHC) is found to be much smaller than those of Fe and Ni films. Band theoretical calculations of the intrinsic AHC as a function of the number of valence electrons (band filling) indicate that the AHC of the permalloy is in the vicinity of sign change, thus resulting in the smallness of the intrinsic AHC. The contribution of the phonon scattering is found to be comparable to that of the impurity scattering. This work suggests that the permalloy films are ideal systems to understand the AHE mechanisms induced by impurity scattering.
Influence of AlN layer on electric field distribution in GaN/AlGaN/GaN transistor heterostructures
Authors: Gladysiewicz M. , Kudrawiec R. , Misiewicz J. , Klosek K. , Sobanska M. , Borysiuk J. , Zytkiewicz Z. R.
Published: November 2013

Distribution of built-in electric field in GaN/AlGaN/GaN transistor heterostructures without and with AlN layer was studied theoretically (solving the Schrodinger and Poisson equation) and experimentally (measuring contactless electroreflectance (CER) spectra and analyzing the AlGaN-related Franz-Keldysh oscillation). It is shown that the AlN layer changes very strongly the distribution of electric field in such heterostructures. This change can be very well predicted if the surface boundary conditions for self-consistent Schrodinger-Poisson calculations in GaN/AlGaN/GaN heterostructures are known. These conditions can be determined/verified by CER measurements of AlGaN-related Franz-Keldysh oscillation, which depends on the built-in electric field in AlGaN layer.
Vortex dynamics effects on microwave propagation in high temperature superconducting coplanar waveguides
Authors: Andrews Jolly , Mathew Vincent
Published: November 2013

An analysis of the microwave signal propagation through a High Temperature Superconducting (HTS) transmission line should take into account the vortex dynamics effects of the HTS material used for the study. Taking Coplanar Waveguide (CPW) as a model transmission line, we simulated the transmission characteristics using a field computation method based on Galerkin's procedure. The vortex effects were incorporated into the study using the surface impedance derived from the modified two-fluid model proposed by Coffey and Clem which takes into account the field and thermal effects in a self consistent manner. The increase of temperature and magnetic field significantly affected the attenuation due to the enhanced vortex motion. The observed dip in the value of attenuation of the transmission line at low field values in high temperature range is explained using the vortex effects. It is found that the dispersion is considerably low for the proposed geometrical structures. Simulations were performed for varying strip-to-slot ratios. The impact of vortex motion on the signal propagation is made out for a wide range of temperature, magnetic field, and line geometry.
Note: Parameter-independent bounding of the stochastic Michaelis-Menten steady-state intrinsic noise variance
Authors: Widmer L. A. , Stelling J. , Doyle F. J.
Published: November 2013

Using the (slow-scale) linear noise approximation, we give parameter-independent bounds to the substrate and product intrinsic noise variance for the stochastic Michaelis-Menten approximation at steady state.
Lateral feeding design and selective oxidation process in vertical cavity transistor laser
Authors: Liu M. , Wu M. K. , Feng M. , Holonyak N.
Published: November 2013

Lateral feeding design and selective oxidation process in vertical cavity transistor lasers (oxide-VCTLs) are developed for improving spatial current and optical modes confinement to achieve low threshold operation. Oxide-VCTLs with oxide apertures of 6.4 × 7.4 μm2 and 4.5 × 5.6 μm2 deliver threshold of 1.3 and 1.6 mA, respectively. The smaller oxide-VCTL exhibits a larger mode spacing of 1.02 nm and achieves a better side-mode suppression ratio of 37 dB. The low threshold oxide-VCTL with a high quality factor (Q) cavity shows a gradual current gain (β) compression when the transistor base recombination shifts from spontaneous to coherent stimulated emission as compared with a sharp β compression previously reported in a high threshold edge-emitting transistor laser with a lower “Q” cavity.
Ultra-compact planoconcave zoned metallic lens based on the fishnet metamaterial
Authors: Pacheco-Peña V. , Orazbayev B. , Torres V. , Beruete M. , Navarro-Cía M.
Published: November 2013

A 1.5λ0-thick planoconcave zoned lens based on the fishnet metamaterial is demonstrated experimentally at millimeter wavelengths. The zoning technique applied allows a volume reduction of 60% compared to a full fishnet metamaterial lens without any deterioration in performance. The structure is designed to exhibit an effective refractive index n = −0.25 at f = 56.7 GHz (λ0 = 5.29 mm) with a focal length FL = 47.62 mm = 9λ0. The experimental enhancement achieved is 11.1 dB, which is in good agreement with simulation and also with previous full fishnet metamaterial lenses and opens the door for integrated solutions.
Exciton and multiexciton optical properties of single InAs/GaAs site-controlled quantum dots
Authors: Canet-Ferrer J. , Munoz-Matutano G. , Herranz J. , Rivas D. , Alen B. , Gonzalez Y. , Fuster D. , Gonzalez L. , Martínez-Pastor J.
Published: November 2013

We have studied the optical properties of InAs site-controlled quantum dots (SCQDs) grown on pre-patterned GaAs substrates. Since InAs nucleates preferentially on the lithography motifs, the location of the resulting QDs is determined by the pattern, which is fabricated by local oxidation nanolithography. Optical characterization has been performed on such SCQDs to study the fundamental and excited states. At the ground state different exciton complex transitions of about 500 μeV linewidth have been identified and the fine structure splitting of the neutral exciton has been determined (≈65 μeV). The observed electronic structure covers the demands of future quantum information technologies.
Modeling of nanoscale solar cells: The Green's function formalism
Authors: Cavassilas Nicolas , Michelini Fabienne , Bescond Marc
Published: November 2013

Solar cells incorporating nano-structures represent a promising solution to overtake the Schockley-Queisser limit. On the other hand, the non-equilibrium Green's function formalism provides a sound conceptual basis for the development of quantum simulators that are needed for nanoscale devices. While this approach has already been applied to solar cells, it remains unfamiliar to most photovoltaïc physicists. In this paper we show the main concepts of this formalism and illustrate it with a simple 1D model of solar cell. This model is applied to a thin film GaAs solar cell. Our investigations permit to show and analyze current flowing in the solar cell at the nanometer scale.
Mechanics of finger-tip electronics
Authors: Su Yewang , Li Rui , Cheng Huanyu , Ying Ming , Bonifas Andrew P. , Hwang Keh-Chih , Rogers John A. , Huang Yonggang
Published: November 2013

Tactile sensors and electrotactile stimulators can provide important links between humans and virtual environments, through the sensation of touch. Soft materials, such as low modulus silicones, are attractive as platforms and support matrices for arrays sensors and actuators that laminate directly onto the fingertips. Analytic models for the mechanics of three dimensional, form-fitting finger cuffs based on such designs are presented here, along with quantitative validation using the finite element method. The results indicate that the maximum strains in the silicone and the embedded devices are inversely proportional to the square root of radius of curvature of the cuff. These and other findings can be useful in formulating designs for these and related classes of body-worn, three dimensional devices.
Impact of SiGe source/drain induced-compressive strain on low frequency noise in high-k/metal gate p-channel metal-oxide-semiconductor transistors
Authors: Lein Wu San , Tsai Kai-Shiang , Cheng Osbert
Published: November 2013

In this paper, the properties of dielectric traps induced by SiGe source/drain (SiGe S/D) induced-compressive stress in high-k/metal gate (HK/MG) p-channel metal-oxide-semiconductor field-effect transistors are demonstrated using random telegraph noise (RTN) and 1/f noise analysis. The correlation between RTN and the 1/f noise parameters is presented. Compared with the control devices, the SiGe S/D HK/MG devices show trap positions that are closer to the SiO2 interfacial layer/Si channel, corresponding to a reduced average tunneling attenuation length (λ), and dominate the lower 1/f noise power spectrum.
Resonance broadening and tuning of split ring resonators by top-gated epitaxial graphene on SiC substrate
Authors: Cakmakyapan Semih , Sahin Levent , Pierini Francesco , Strupinski Wlodek , Ozbay Ekmel
Published: November 2013

Split ring resonators (SRRs) are subwavelength structures that are able to localize and enhance the electromagnetic wave. Controlling the plasmonic resonance behavior of metallic nanostructures, such as SRRs, plays an important role in optoelectronics and nanophotonics applications. Electrically tunable carrier concentration of graphene provides hybrid devices, where the plasmonic structures and graphene are combined. In this paper, we report the design, fabrication, and measurement of a device comprising a SRR array on epitaxial graphene. We obtained resonance broadening and tuning of split ring resonators by utilizing an epitaxial graphene transistor with transparent top-gate.
Magnetic mechanisms of magnetic flux leakage nondestructive testing
Authors: Sun Yanhua , Kang Yihua
Published: November 2013

The widely applied magnetic flux leakage (MFL) nondestructive testing for ferrous materials has been simply explained by “MFL escaping from defects and being induced is exactly the MFL testing principle,” with a rough application for evaluation. Hence, we analyze the “escape” course of MFL generation using magnetic refraction and explain the reason why the MFL technology really exists in practice. Furthermore, we also point out that the presently so-called MFL testing technique essentially hides a different signal component arising from bump-shaped defects features unlike the MFL caused by concave-shaped ones, explained by another forming mechanism.
Oxygen ion drift-driven dual bipolar hysteresis curves in a single Pt/Ta2O5−x/TiOxNy framework
Authors: Lee Ah Rahm , Cheol Bae Yoon , Ho Baek Gwang , Bock Chung Je , Sung Kang Tae , Sun Lee Jong , Park Jea-Gun , Sik Im Hyun , Pyo Hong Jin
Published: November 2013

We describe abnormal dual bipolar resistive switching events in simple Pt/Ta2O5−x/TiOxNy and Pt/Ta2O5−x/TiN matrices in which the typical switching directions (SD) are initially clockwise (CW). The negative difference region in a high resistance state before reaching the typical “CW set” process enables the SD transition to a counterclockwise direction. It thereby emphasizes the occurrence of a highly stable secondary bipolar resistive switching curve. The origin of two different switching modes is described by adapting a bias-dependent oxygen ion accumulation and depletion process at TiOxNy and TiN electrode interfaces and by performing various structural analyses.
Modulating optical polarization properties of Al-rich AlGaN/AlN quantum well by controlling wavefunction overlap
Authors: Chen X. J. , Yu T. J. , Lu H. M. , Yuan G. C. , Shen B. , Zhang G. Y.
Published: November 2013

Using modified k·p perturbation method, the optical polarization properties of Al-rich AlGaN/AlN quantum wells (QWs) are studied. It is found that change of wavefunction overlaps between conduction band and valance subbands of heavy hole, light hole, and crystal-field split off hole is different. Such difference leads to the overturn of polarization degree and modulates optical polarization properties as well width and strain vary. This prompts that changing wavefunction overlaps of electron and hole can lead to a way to modulate optical polarization properties of Al-rich AlGaN/AlN QWs, on no condition that valence band order changes.
Prediction and early diagnosis of complex diseases by edge-network
Authors: Yu Xiangtian , Li Guojun , Chen Luonan
Published: November 2013

Motivation: In this article, we develop a novel edge-based network i.e. edge-network, to detect early signals of diseases by identifying the corresponding edge-biomarkers with their dynamical network biomarker score from dynamical network biomarkers. Specifically, we derive an edge-network based on the second-order statistics representation of gene expression profiles, which is able to accurately represent the stochastic dynamics of the original biological system (with Gaussian distribution assumption) by combining with the traditional node-network, which is based only on the first-order statistics representation of the noisy data. In other words, we show that the stochastic network of a biological system can be described by the integration of its node-network and its edge-network in an accurate manner.

Results: By applying edge-network analysis to gene expressions of healthy adults within live influenza experiment sampling at time points before the appearance of infection symptoms, we identified the edge-biomarkers (80 edges with 22 densely connected genes) discovered in edge-networks corresponding to symptomatic adults, which were used to predict the subsequent outcomes of influenza infection. In particular, we not only correctly predict the final infection outcome of each individual at an early time point before his/her clinic symptom but also reveal the key molecules during the disease progression. The prediction accuracy achieves ∼90% under the leave-one-out cross-validation. Furthermore, we demonstrate the superiority of our method on disease classification and predication by comparing with the conventional node-biomarkers. Our edge-network analysis not only opens a new way to understand pathogenesis at a network level due to the new representation for a stochastic network, but also provides a powerful tool to make the early diagnosis of diseases.

Contact: lnchen@sibs.ac.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
The functional therapeutic chemical classification system
Authors: Croset Samuel , Overington John P. , Rebholz-Schuhmann Dietrich
Published: November 2013

Motivation: Drug repositioning is the discovery of new indications for compounds that have already been approved and used in a clinical setting. Recently, some computational approaches have been suggested to unveil new opportunities in a systematic fashion, by taking into consideration gene expression signatures or chemical features for instance. We present here a novel method based on knowledge integration using semantic technologies, to capture the functional role of approved chemical compounds.

Results: In order to computationally generate repositioning hypotheses, we used the Web Ontology Language to formally define the semantics of over 20 000 terms with axioms to correctly denote various modes of action (MoA). Based on an integration of public data, we have automatically assigned over a thousand of approved drugs into these MoA categories. The resulting new resource is called the Functional Therapeutic Chemical Classification System and was further evaluated against the content of the traditional Anatomical Therapeutic Chemical Classification System. We illustrate how the new classification can be used to generate drug repurposing hypotheses, using Alzheimers disease as a use-case.

Availability:  https://www.ebi.ac.uk/chembl/ftc; https://github.com/loopasam/ftc.

Contact:  croset@ebi.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Effect of a High Tunnel, Organic Cropping System on Lettuce Diseases in Western Washington
Authors: Powell Marianne , Cowan Jeremy , Miles Carol , Inglis Debra Ann
Published: November 2013

Incidence of gray mold and lettuce drop, and yield of six cultivars representing market classes Boston/Crisphead, Leaf, and Romaine, were evaluated in open ended high tunnel and open field organic production systems near Mount Vernon, WA from 2010 to 2012. Each year seedlings were transplanted in April and heads harvested in June/July. In 2010, Romaine types had significantly (P < 0.0001) greater incidence of gray mold (caused by Botrytis cinerea) than other types. In 2011, incidence of gray mold was significantly (P = 0.004) greater in high tunnel than open field plots, and greatest in high tunnels when fog persisted. All cultivars were equally susceptible to lettuce drop (caused by Sclerotinia sclerotiorum), although in 2012, incidence was significantly (P < 0.0001) greater in high tunnel than open field plots. ‘Green Star’ (Leaf type) had reduced incidence of gray mold and lettuce drop in 2010 and 2011. Incidence of tipburn was significantly (P = 0.032 and P = 0.001, respectively) greater in the high tunnels in 2011 and 2012 compared to the open field. Total yield (kg) was greater in the open field in 2012, but not in 2011 and 2010.

Accepted for publication 8 July 2013. Published 22 September 2013.
When Do Foliar Pyraclostrobin Fungicide Applications Produce Profitable Soybean Yield Responses?
Authors: Kyveryga Peter M. , Blackmer Tracy M. , Mueller Daren S.
Published: November 2013

From 2005 through 2009, 282 on-farm evaluation trials were conducted in soybean fields across Iowa to identify when a foliar application of pyraclostrobin produced profitable yield responses. Because of a delay in plant maturity, 218 trials exhibited a fungicide-induced “greening effect” documented using the late-season color infrared (CIR) digital aerial imagery of the soybean canopy. These 218 trials were approximately 35% more likely to produce profitable yield responses (65% vs 30%) than those without “the greening effect.” In addition, greater yield responses were observed in trials that received more than 12 inches of cumulative March through May rainfall. Potentially, site-specific observations of spring rainfall could be used to identify fields that are or are not likely to produce above break-even yield responses, and therefore, help farmers avoid unnecessary foliar fungicide applications on soybean.

Accepted for publication 30 July 2013. Published 28 September 2013.
First Report of Geosmithia morbida and Pityophthorus juglandis Causing Thousand Cankers Disease in Butternut
Authors: Serdani Maryna , Vlach Joshua J. , Wallis Kelly L. , Zerillo Marcelo , McCleary Tim , Romero-Severson Jeanne , Tisserat Ned A.
Published: November 2013

To our knowledge, this is the first report of natural infection of butternut by G. morbida and P. juglandis.

Accepted for publication 15 October 2013. Published 18 October 2013.
Fungicide Management of Brown Patch of Tall Turf-type Fescue in the Residential Landscape in Oklahoma
Authors: Smith Damon L. , Walker Nathan R.
Published: November 2013

In the transition zone of the USA, cool-season grasses such as tall fescue are often planted in shaded areas, where warm-season grasses are less adapted. The most damaging disease of tall fescue is brown patch, caused by Rhizoctonia solani. Fungicide applications and cultural practices are often used to manage brown patch in this region. A three-year study was implemented in Oklahoma to evaluate ready-to-use fungicides available to residential lawn owners and compare these to several common commercial fungicide formulations used by professional lawn care applicators. A selection of fungicides representing products commonly available to the residential market and commercial standards were applied to small plots of tall fescue or tall fescue/Kentucky bluegrass mixtures from 2008 to 2010. All products tested, with the exception of azoxystrobin, provided limited or inconsistent control of brown patch and resulted in lower turfgrass quality in all years. Further examination of carrier type (granular vs. liquid) and timing (preventive vs. curative) did not result in strong differences in the level of brown patch control or overall quality. These studies suggest that control of brown patch in tall fescue in the transition zone should focus on integrated disease management principals and not only on applications of fungicides directed at the residential market.

Accepted for publication 5 August 2013. Published 22 October 2013.