bluuebunny/crossref_metadata_2025 huggingface dataset:
Computation of coupled double-diffusive convection–radiation including lattice Boltzmann simulation of fluid flow
Authors: Moufekkir F. , Moussaoui M. A. , Mezrhab A. , Naji H.
Published: July 2013

This paper reports a numerical study of coupled double diffusive convection and radiation in a differentially heated square enclosure filled with non-grey air–CO2(or air–H2O) mixtures. The numerical procedure is based on a hybrid scheme with the multiple relaxation time lattice Boltzmann method and the finite difference method. The fluid velocity is determined by the D2Q9 multiple relaxation time model, and the energy equation is discretized by the finite difference method to compute the temperature field, while the radiative part of the energy equation is calculated by the discrete ordinates method combined with the spectral line-based weighted sum of grey gases model. Depending on the boundary conditions, aiding and opposing flows occur as the result of temperature and concentration gradients. The effects of various parameters, such as the molar fraction on the flow structure, thermal and concentration fields, are investigated for aiding and opposing cases. The numerical results show that, in the presence of non-grey radiation, the heat transfer is decreased and the mass transfer is slightly modified. The gas radiation modifies the structure of the velocity and thermal fields by generating inclined stratifications and promoting instabilities in opposing flows.
Conditional sampling of transitional boundary layers in pressure gradients
Authors: Nolan Kevin P. , Zaki Tamer A.
Published: July 2013

Statistical analysis of transitional boundary layers in pressure gradients is performed using the flow fields from direct numerical simulations of bypass transition. Laminar–turbulent discrimination separates the streaky laminar flow from turbulent regions. Individual streaks are identified and tracked in the flow field in order to obtain statistics of the amplitude of the streak population. An extreme value model is proposed for the distribution of streak amplitudes. It is also possible to differentiate those streaks which break down into turbulent spots from innocuous events. It is shown that turbulence onset is due to high-amplitude streaks, with streamwise perturbation velocity exceeding 20 % of the free stream speed. The resulting turbulent spots are tracked downstream. The current analysis allows for the measurement of the lateral spreading angles of individual spots and their spatial extent and volumes. It is demonstrated that the volumetric growth rate of turbulent spots is insensitive to pressure gradient.
Resonance characteristics of tides in branching channels
Authors: Alebregtse Niels C. , de Swart H. E. , Schuttelaars H. M.
Published: July 2013

Resonance characteristics of tidal waves in a network are investigated with the linearized, one-dimensional shallow water equations. The network comprises a semi-enclosed main channel with an adjacent secondary channel at an arbitrary position. Water motion is forced by a prescribed incoming wave at the entrance of the main channel. The model is used to compute the ratio of sea surface height amplitude in the presence and absence of the secondary channel. Relevance lies in the possible construction of secondary channels to reduce tidal range in the main channel. When $\mu = 2\mathrm{\pi} { l}_{b}^{\ast } / { l}_{t}^{\ast } \gtrsim \mathrm{\pi} $ (${ l}_{b}^{\ast } $ being the length of the main channel, ${ l}_{t}^{\ast } $ the tidal wavelength) and friction is weak, it is found that reduction (amplification) of the tidal range occurs for secondary channels located less (more) than a quarter wavelength from the closed end of the main channel. Furthermore, a minimum is observed halfway between the closed end and the nodal point, and a maximum a quarter wavelength further seaward. With increasing friction and/or decreasing length of the main channel, amplitude ratios become less pronounced and depend weakly on the location of the secondary channel. The mechanism responsible for amplification or reduction of the sea surface height in the main channel is identified and explained in terms of the forced wave and waves radiating away from the secondary channel.
The A to T of historical evidence
Authors: Wolinsky Howard
Published: July 2013

Geneticists and historians collaborated recently to identify the remains of King Richard III of England, found buried under a car park. Genetics has many more contributions to make to history, but scientists and historians must learn to speak each other's languages.
In Situ Breast Cancer and Microchimerism
Authors: Eun Jinny K. , Guthrie Katherine A. , Zirpoli Gary , Gadi V. K.
Published: July 2013

Microchimeric cells of fetal origin persistent in the maternal circulation post-partum are associated with protection against invasive breast cancer. Here using quantitative genomic methods, we evaluated for the presence of male fetal microchimerism in buffy coat cells from women with a prior history of breast carcinomas in situ (CIS) and in healthy controls. Fetal microchimerism was detected in 75 of 88 controls (85%) and in 57 of 89 CIS patients (64%). The odds ratio for protection against non-invasive breast disease was 0.26 (95% confidence interval 0.12–0.56; p < 0.001 adjusted for age and body mass index). Similar to women with invasive breast cancer, women with CIS who are naturally at high risk for future invasive disease were deficient for fetal microchimerism. In addition to autologous anti-tumor immune responses, the maintenance of haploidentical microchimerism may impart an allogeneic edge in immunosurveillance.
From superhydrophobicity to icephobicity: forces and interaction analysis
Authors: Hejazi Vahid , Sobolev Konstantin , Nosonovsky Michael
Published: July 2013

The term “icephobicity” has emerged in the literature recently. An extensive discussion took place on whether the icephobicity is related to the superhydrophobicity and the consensus is that there is no direct correlation. Besides the parallel between the icephobicity and superhydrophobicity for water/ice repellency, there are similarities on other levels including the hydrophobic effect/hydrophobic interactions, mechanisms of protein folding and ice crystal formation. In this paper, we report how ice adhesion is different from water using force balance analysis and why superhydrophobic surfaces are not necessary icephobic. We also present experimental data on anti-icing of various surfaces and suggest a definition of icephobicity, which is broad enough to cover a variety of situations relevant to de-icing including low adhesion strength and delayed ice crystallization and bouncing.
Determination of ferric ions using surface-enhanced Raman scattering based on desferrioxamine-functionalized silver nanoparticles
Authors: Yan Fei , Shrestha Yam K. , Spurgeon Charina L.
Published: July 2013

A simple, robust and reproducible spectroscopic method based on surface-enhanced Raman scattering with nanomolar sensitivity has been developed for selective iron(iii) determination in aqueous solutions.
Preparation and in vivo characterization of a cocaine hydrolase engineered from human butyrylcholinesterase for metabolizing cocaine
Authors: Xue Liu , Hou Shurong , Tong Min , Fang Lei , Chen Xiabin , Jin Zhenyu , Tai Hsin-Hsiung , Zheng Fang , Zhan Chang-Guo
Published: July 2013

Cocaine is a widely abused drug without an FDA (Food and Drug Administration)-approved medication. It has been recognized that an ideal anti-cocaine medication would accelerate cocaine metabolism producing biologically inactive metabolites via a route similar to the primary cocaine-metabolizing pathway, i.e. human BChE (butyrylcholinesterase)-catalysed hydrolysis. However, the native human BChE has a low catalytic activity against cocaine. We recently designed and discovered a BChE mutant (A199S/F227A/S287G/A328W/Y332G) with a high catalytic activity (kcat=5700 min−1, Km=3.1 μM) specifically for cocaine, and the mutant was proven effective in protecting mice from acute cocaine toxicity of a lethal dose of cocaine (180 mg/kg of body weight, LD100). Further characterization in animal models requires establishment of a high-efficiency stable cell line for the BChE mutant production at a relatively larger scale. It has been extremely challenging to develop a high-efficiency stable cell line expressing BChE or its mutant. In the present study, we successfully developed a stable cell line efficiently expressing the BChE mutant by using a lentivirus-based repeated-transduction method. The scaled-up protein production enabled us to determine for the first time the in vivo catalytic activity and the biological half-life of this high-activity mutant of human BChE in accelerating cocaine clearance. In particular, it has been demonstrated that the BChE mutant (administered to mice 1 min prior to cocaine) can quickly metabolize cocaine and completely eliminate cocaine-induced hyperactivity in rodents, implying that the BChE mutant may be developed as a promising therapeutic agent for cocaine abuse treatment.
Molecular Therapy for Disk Degeneration and Pain
Authors: Mwale Fackson
Published: July 2013

The nucleus pulposus of the intervertebral disk contains high amounts of the proteoglycan aggrecan, which confers the disk with a remarkable ability to resist compression. Other molecules such as collagens and noncollagenous proteins in the extracellular matrix are also essential for function. During disk degeneration, aggrecan and other molecules are lost due to proteolysis. This can result in loss of disk height, which can ultimately lead to pain. Biological therapy of intervertebral disk degeneration aims at preventing or restoring primarily aggrecan content and other molecules using therapeutic molecules. The purpose of the article is to review recent advances in biological repair of degenerate disks and pain.
Gendering Creolisation: Creolising Affect
Authors: Anim-Addo Joan
Published: July 2013

Going beyond the creolisation theories of Brathwaite and Glissant, I attempt to develop ideas concerning the gendering of creolisation, and a historicising of affects within it. Addressing affects as ‘physiological things’ contextualised in the history of the Caribbean slave plantation, I seek, importantly, to delineate a trajectory and development of a specific Creole history in relation to affects. Brathwaite's proposition that ‘the most significant (and lasting) inter-cultural creolisation took place’ within the ‘intimate’ space of ‘sexual relations’ is key to my argument. In the light of this, I consider how Creole cultural knowledge about affect—as the primary motivational system inclusive of fear, anger, outrage and so on — might be identified, and what constitutes such Creole knowledge within which affect might be embedded. How might Glissant's relationality and Creole literary texts add to this knowledge? I focus primarily on three texts: Clarke's The Polished Hoe, Collins’ The Colour of Forgetting and Morejón's ‘Amo a mi amo’/‘l Love My Master’. Each text on which I draw is selected for its intersectional representation of gender relations, ‘knowledge about sexual difference’ and its representation of Creole subjectivities within the context problematised here as the ‘demonic ground’. Moreover, as auto-theorising texts, they represent both narrative and meta-narrative of a creolising of affects in and against the economy of the slave plantation. Each represents also a stage or aspect of the development of subjectivities and an affective community that inform this intervention concerned with theorising against consolidated, universalising and Eurocentric conceptualisations of affect. In the process, I attempt to offer a differentiated cartography and literary archaeology of affect.
The Injunctions of the Spectre of Slavery: Affective Memory and the Counterwriting of Community
Authors: Karavanta Mina
Published: July 2013

To rethink history from the perspective of an economy of affects as they are engendered by beings ousted from the definition of the human, I will draw on two Caribbean texts, Anim-Addo's Imoinda: Or She Mho will Lose Her Name and Philip's Z ong!. This essay discusses how these two Caribbean texts counterwrite the history of the slave plantation by staging and embodying the work of what I call an affective memory drawn from the history of the black subject as a history of absence and reconstellated in the present as a history of being and community. This affective memory represents the being of the ‘living corpse’ and her making of a community as the subject of a new polity, the polity of decolonised beings. By drawing on these texts to demonstrate how they write the history of spectres, ruins and other communities, I discuss affective memory not as the absolute possession of a body, but rather as the alienated property of the body that can be reclaimed only by a community that, precarious and tentative as it is for it is a community of slaves and subjected bodies, remains the only promise for the future.
A highly efficient and compact long pulse Nd:YAG rod laser with 540 J of pulse energy for welding application
Authors: Choubey Ambar , Vishwakarma S. C. , Misra Pushkar , Jain R. K. , Agrawal D. K. , Arya R. , Upadhyaya B. N. , Oak S. M.
Published: July 2013

We have developed an efficient and high average power flash lamp pumped long pulse Nd:YAG laser capable of generating 1 kW of average output power with maximum 540 J of single pulse energy and 20 kW of peak power. The laser pulse duration can be varied from 1 to 40 ms and repetition rate from 1 to 100 Hz. A compact and robust laser pump chamber and resonator was designed to achieve this high average and peak power. It was found that this laser system provides highest single pulse energy as compared to other long pulsed Nd:YAG laser systems of similar rating. A slope efficiency of 5.4% has been achieved, which is on higher side for typical lamp pumped solid-state lasers. This system will be highly useful in laser welding of materials such as aluminium and titanium. We have achieved 4 mm deep penetration welding of these metals under optimized conditions of output power, pulse energy, and pulse duration. The laser resonator was optimized to provide stable operation from single shot to 100 Hz of repetition rate. The beam quality factor was measured to be M2 ∼ 91 and pulse-to-pulse stability of ±3% for the multimode operation. The laser beam was efficiently coupled through an optical fiber of 600 μm core diameter and 0.22 numerical aperture with power transmission of 90%.
Numerical simulation of photocurrent generation in bilayer organic solar cells: Comparison of master equation and kinetic Monte Carlo approaches
Authors: Casalegno Mosè , Bernardi Andrea , Raos Guido
Published: July 2013

Numerical approaches can provide useful information about the microscopic processes underlying photocurrent generation in organic solar cells (OSCs). Among them, the Kinetic Monte Carlo (KMC) method is conceptually the simplest, but computationally the most intensive. A less demanding alternative is potentially represented by so-called Master Equation (ME) approaches, where the equations describing particle dynamics rely on the mean-field approximation and their solution is attained numerically, rather than stochastically. The description of charge separation dynamics, the treatment of electrostatic interactions and numerical stability are some of the key issues which have prevented the application of these methods to OSC modelling, despite of their successes in the study of charge transport in disordered system. Here we describe a three-dimensional ME approach to photocurrent generation in OSCs which attempts to deal with these issues. The reliability of the proposed method is tested against reference KMC simulations on bilayer heterojunction solar cells. Comparison of the current-voltage curves shows that the model well approximates the exact result for most devices. The largest deviations in current densities are mainly due to the adoption of the mean-field approximation for electrostatic interactions. The presence of deep traps, in devices characterized by strong energy disorder, may also affect result quality. Comparison of the simulation times reveals that the ME algorithm runs, on the average, one order of magnitude faster than KMC.
Tunability of InGaN/GaN quantum well light emitting diodes through current
Authors: Biswas Dipankar , Panda Siddhartha
Published: July 2013

In the recent years, InGaN/GaN quantum well (QW) light emitting diodes (LEDs) have gathered much importance through the introduction of white LEDs and dual wavelength LEDs. However, the continuous tunability of InGaN/GaN QW LEDs has not been well addressed or discussed. In this paper, we introduce the tunability of an InGaN/GaN QW LED having a well width of 4 nm and In mole fraction of 0.3. The results, obtained from self-consistent solutions of the Schrödinger and Poisson equations, show that the transition energy of the LED may be continuously tuned by the device current. A prominent nonlinearity of the transition energy with the device current is generated, which should be of interest to the research workers in the field of optoelectronics.
Effect of hole shape on spin-wave band structure in one-dimensional magnonic antidot waveguide
Authors: Kumar D. , Sabareesan P. , Wang W. , Fangohr H. , Barman A.
Published: July 2013

We present the possibility of tuning the spin-wave band structure, particularly the bandgaps in a nanoscale magnonic antidot waveguide by varying the shape of the antidots. The effects of changing the shape of the antidots on the spin-wave dispersion relation in a waveguide have been carefully monitored. We interpret the observed variations by analysing the equilibrium magnetic configuration and the magnonic power and phase distribution profiles during spin-wave dynamics. The inhomogeneity in the exchange fields at the antidot boundaries within the waveguide is found to play a crucial role in controlling the band structure at the discussed length scales. The observations recorded here will be important for future developments of magnetic antidot based magnonic crystals and waveguides.
A non-diaphragm type small shock tube for application to a molecular beam source
Authors: Yoshimoto Yuta , Osuka Kenichi , Miyoshi Nobuya , Kinefuchi Ikuya , Takagi Shu , Matsumoto Yoichiro
Published: July 2013

A non-diaphragm type small shock tube was developed for application to a molecular beam source, which can generate beams in the energy range from 1 to several electron volts and beams containing dissociated species such as atomic oxygen. Since repetitive high-frequency operation is indispensable for rapid signal acquisition in beam scattering experiments, the dimensions of the shock tube were miniaturized to reduce the evacuation time between shots. The designed shock tube is 2–4 mm in diameter and can operate at 0.5 Hz. Moreover, a high shock Mach number at the tube end is required for high-energy molecular beam generation. To reduce the shock attenuation caused by the wall boundary layer, which becomes significant in small-diameter tubes, we developed a high-speed response valve employing the current-loop mechanism. The response time of this mechanism is about 100 μs, which is shorter than the rupture time of conventional diaphragms. We show that the current-loop valve generates shock waves with shorter formation distances (about 200–300 mm) than those of conventional shock tubes. In addition, the converging geometry efficiently accelerates shock wave in the small-diameter tubes. The optimal geometry of the shock tube yields shock Mach number around 7, which indicates that the translation energy of molecular beams can exceed 1 eV even in the presence of the real gas effect.
Improvement of the yttrium iron garnet/platinum interface for spin pumping-based applications
Authors: Jungfleisch M. B. , Lauer V. , Neb R. , Chumak A. V. , Hillebrands B.
Published: July 2013

The dependence of the spin pumping efficiency and the spin mixing conductance on the surface processing of yttrium iron garnet (YIG) before the platinum (Pt) deposition has been investigated quantitatively. The ferromagnetic resonance driven spin pumping injects a spin polarized current into the Pt layer, which is transformed into an electromotive force by the inverse spin Hall effect. Our experiments show that the spin pumping effect indeed strongly depends on the YIG/Pt interface condition. We measure an enhancement of the inverse spin Hall voltage and the spin mixing conductance by more than two orders of magnitude with improved sample preparation.
Non-polar m-plane intersubband based InGaN/(Al)GaN quantum well infrared photodetectors
Authors: Pesach A. , Gross E. , Huang C.-Y. , Lin Y.-D. , Vardi A. , Schacham S. E. , Nakamura S. , Bahir G.
Published: July 2013

We demonstrate intersuband InGaN/(Al)GaN quantum well infrared photodetectors grown on a free standing non-polar m-plane GaN substrate. The devices are grown by metal organic chemical vapor deposition and exhibit TM-polarized photocurrent at peak wavelengths of 7.5 and 9.3 μm at temperature of 14 K. Based on the experimental data of intersubband and interband transition energies and 8-band k · p Schrödinger-Poisson solver calculations, we were able to estimate the conduction band offset to valence band offset discontinuity ratio (ΔEc:ΔEv) of 57:43 for In0.1Ga0.9N/GaN and 55:45, for In0.095GA0.905N/Al0.07Ga0.93N non-polar m-plane multi-quantum well structures.
Fabrication and Raman scattering study of epitaxial VO2 films on MgF2 (001) substrates
Authors: Shibuya Keisuke , Tsutsumi Jun’ya , Hasegawa Tatsuo , Sawa Akihito
Published: July 2013

Effects of epitaxial strain on metal–insulator transitions (MITs) of epitaxial VO2 films grown on MgF2 (001) substrates were examined. A partially tensile-strained film deposited at 420 °C showed an MIT temperature (TMI) of 318 K whereas that of a relaxed film deposited at 520 °C was about 331 K. Raman scattering measurements showed that the epitaxial strain affects the V–V vibration modes in the insulating phase. The TMI in the strained film is lower as a result of the shorter V–V distance and the reduced twisting angle of the V–V dimer caused by in-plane tensile strain.
Nanostructured networks of single wall carbon nanotubes for highly transparent, conductive, and anti-reflective flexible electrodes
Authors: Boulanger Nicolas , Barbero David R.
Published: July 2013

Highly transparent, anti-reflective, flexible, and conductive electrodes are produced by nanopatterning of a polymer composite made of single wall carbon nanotubes (SWNTs). The formation of nanostructures creates interconnected nanotubes and vertically aligned SWNT networks which greatly improves charge transport compared to a traditionally mixed composite. These electrodes moreover possess high transparency (98% at 550 nm) and good anti-reflective properties. The use of low nanotube loadings provides an economical solution to make conductive and highly transparent flexible electrodes. The process used is simple and can be easily scaled to large areas by roll to roll processes.
Realization of graphene field-effect transistor with high-κ HCa2Nb3O10 nanoflake as top-gate dielectric
Authors: Li Wenwu , Li Song-Lin , Komatsu Katsuyoshi , Aparecido-Ferreira Alex , Lin Yen-Fu , Xu Yong , Osada Minoru , Sasaki Takayoshi , Tsukagoshi Kazuhito
Published: July 2013

A high-quality HCa2Nb3O10 (HCNO) nanoflake (εr = 9.1) consisting of high-κ perovskite nanosheets is adopted as a gate dielectric for graphene-based electronics. A dual-gated device was physically constructed by directly dry-transferring a 22-nm-thick HCNO nanoflake as a top gate dielectric onto graphene. The fabricated graphene field-effect transistor could be operated at biases <1.5 V with a gate leakage below 1 pA. The top-gate capacitance and mobility of the dual-gated graphene device at room temperature were estimated to be 367 nF/cm2 and 2500 cm2/V · s, respectively. These results show that HCNO can be employed as an alternative dielectric for graphene-based devices.
Performance enhanced piezoelectric ZnO nanogenerators with highly rough Au electrode surfaces on ZnO submicrorod arrays
Authors: Hwan Ko Yeong , Hyun Lee Soo , Su Yu Jae
Published: July 2013

Zinc oxide (ZnO) nanorod arrays (NRAs)-based piezoelectric nanogenerators (NGs) with highly rough gold (Au) film as a top electrode were fabricated by a simple electrochemical deposition. The Au was evaporated mainly onto the discrete top surface of ZnO submicrorod arrays (SMRAs), creating a highly rough Au electrode surface. By applying a pushing force to the ZnO NG, the output current density was increased by ∼1.54 times compared with the Au top electrode deposited without ZnO SMRAs because the larger bending radius of ZnO NRAs leads to increased contribution to the overall piezoelectric charge output due to the roughened top electrode.
Survey of exciton-phonon sidebands by magneto-optical spectroscopy using highly specified (6,5) single-walled carbon nanotubes
Authors: Zhou Weihang , Sasaki Tatsuya , Nakamura Daisuke , Saito Hiroaki , Liu Huaping , Kataura Hiromichi , Takeyama Shojiro
Published: July 2013

We report high-field magneto-optical study on the exciton-phonon sideband of single-walled carbon nanotubes consisting only of (6,5) species. Both energy and intensity of the observed phonon sideband were found to be independent of the external magnetic field. Comparing with theoretical calculations, we confirmed that these sidebands originate from the optically forbidden K-momentum singlet excitons. Energy of these K-momentum dark excitons was estimated to be ∼21.5 meV above the bright Γ-momentum singlet excitons, in close agreement with recent theoretical predictions and experimentally determined values.
Comparing the effects of uniaxial and biaxial strains on the structural stability and electronic structure in wurtzite ZnS
Authors: Lv Dong , Duan Yifeng , Zhao Botao , Qin Lixia , Shi Liwei , Tang Gang , Shi Hongliang
Published: July 2013

Structural stability and electronic structure of wurtzite ZnS under uniaxial and biaxial strains are systematically studied using the HSE hybrid functional. The two types of strain display the markedly different influences on the structural and electronic properties: (I) The newly predicted graphite-like phase is observed at large compressive uniaxial strains, not at large tensile biaxial strains, which is attributed to the different elastic responses to uniaxial and biaxial strains. (II) The direct band structures are obtained in wurtzite ZnS under uniaxial and biaxial strains, whereas the indirect band gaps are only observed in graphite-like ZnS under large uniaxial strain. Our results are different from the widely accepted conclusion but are in good agreement with the available experimental data.
Communication: Fourier-transform infrared probing of remarkable quantities of gas trapped in cold homogeneously nucleated nanodroplets
Authors: Uras-Aytemiz Nevin , Devlin J. Paul
Published: July 2013

Studies of catalyzed all-vapor gas-hydrate formation on a sub-second timescale have been extended with a special focus on liquid-droplet compositions at the instant of hydrate crystallization. This focus has been enabled by inclusion of methanol in the all-vapor mixture. This slows droplet to gas-hydrate conversion near 200 K to a time scale suited for standard FTIR sampling. Such droplet data are sought as a guide to ongoing efforts to reduce the amount of guest catalyst required for instant formation of the gas hydrates. For the same reason, all-vapor sampling has also been extended to the generation of long-lived liquid droplets with reduced or no water content. Observations of single-solvent droplets show that surprising quantities of gas molecules are trapped during rapid droplet growth. For example, CO2 is trapped at levels near 50 mol. % in droplets of acetone, tetrahydrofuran, or trimethylene oxide formed under CO2 pressures of several Torr in a cold-chamber at 170 K. Less but significant amounts of gas are trapped at higher temperatures, or in methanol or water-methanol droplets. The droplet metastability appears to commonly lead to formation of bubbles larger than the original nanodroplets. Besides serving as a guide for the all-vapor gas-hydrate studies, the semiquantitative evidence of extensive trapping of gases is expected to have a role in future studies of atmospheric aerosols.
Design of Sustainable Supply Chains for Sustainable Cities
Authors: Nagurney Anna
Published: July 2013

Supply chains provide the critical infrastructure for the production and distribution of goods and services in our network economy and serve as the conduits for the manufacturing, transportation, and consumption of products ranging from food, clothing, automobiles, and high-technology products, to healthcare products. Cities as major population centers serve not only as the principal demand points but also as the locations of many of the distribution and storage facilities, transportation providers, and even manufacturers. In this paper a new model is developed for the design of sustainable supply chains with a focus on cities that captures the frequency of network link operations, which is especially relevant to cities due to frequent freight deliveries. The model is also related to recent literature on this subject. The goal is to demonstrate how, through the proper design (and operation) of these complex networks, waste can be reduced, along with the environmental impacts, while minimizing operational and frequency costs, and meeting demand.
Characteristics of the clonal propagation of Alhagi sparsifolia Shap. (Fabaceae) under different groundwater depths in Xinjiang, China
Authors: Gui Dongwei , Zeng Fanjiang , Liu Zhen , Zhang Bo
Published: July 2013

Clonal reproduction of plants commonly occurs in arid areas because seedling establishment is rare in such severe environments. The features of clonal architecture differ not only among plant species but also within the same species growing in different environments. The characteristics of clonal propagation of Alhagi sparsifolia Shap. (Fabaceae), growing on the margins of Cele Oasis on the southern rim of the Taklamakan Desert, were investigated in September 2010. The study was conducted on three sites with different groundwater depths (2.5, 4.5, and 11.0 m). The results showed that the root suckering depth and the ability to expand and the biomass of coarse lateral roots of A. sparsifolia significantly increased when the groundwater depth increased. Moreover, the vegetative regeneration capacity of A. sparsifolia significantly declined with increasing groundwater depth, and the canopy cover at the site with a groundwater depth of 2.5 m was significantly greater than at the other two sites. There was no difference in aboveground biomass at the three sites. In such hyper-arid environments with a scarcity of soil nutrients, it was demonstrated that groundwater depth plays an important role in the clonal growth and propagation traits of A. sparsifolia. Increases in the groundwater depth as a result of over-use of oasis water for irrigation could lead to reduced populations of this important species in the interfaces between oases and the surrounding desert.
Quantitative trait analysis in sequencing studies under trait-dependent sampling
Authors: Lin Dan-Yu , Zeng Donglin , Tang Zheng-Zheng
Published: July 2013

It is not economically feasible to sequence all study subjects in a large cohort. A cost-effective strategy is to sequence only the subjects with the extreme values of a quantitative trait. In the National Heart, Lung, and Blood Institute Exome Sequencing Project, subjects with the highest or lowest values of body mass index, LDL, or blood pressure were selected for whole-exome sequencing. Failure to account for such trait-dependent sampling can cause severe inflation of type I error and substantial loss of power in quantitative trait analysis, especially when combining results from multiple studies with different selection criteria. We present valid and efficient statistical methods for association analysis of sequencing data under trait-dependent sampling. We pay special attention to gene-based analysis of rare variants. Our methods can be used to perform quantitative trait analysis not only for the trait that is used to select subjects for sequencing but for any other traits that are measured. For a particular trait of interest, our approach properly combines the association results from all studies with measurements of that trait. This meta-analysis is substantially more powerful than the analysis of any single study. By contrast, meta-analysis of standard linear regression results (ignoring trait-dependent sampling) can be less powerful than the analysis of a single study. The advantages of the proposed methods are demonstrated through simulation studies and the National Heart, Lung, and Blood Institute Exome Sequencing Project data. The methods are applicable to other types of genetic association studies and nongenetic studies.
Inactivating mutations of
RNF43
confer Wnt dependency in pancreatic ductal adenocarcinoma
Authors: Jiang Xiaomo , Hao Huai-Xiang , Growney Joseph D. , Woolfenden Steve , Bottiglio Cindy , Ng Nicholas , Lu Bo , Hsieh Mindy H. , Bagdasarian Linda , Meyer Ronald , Smith Timothy R. , Avello Monika , Charlat Olga , Xie Yang , Porter Jeffery A. , Pan Shifeng , Liu Jun , McLaughlin Margaret E. , Cong Feng
Published: July 2013

A growing number of agents targeting ligand-induced Wnt/β-catenin signaling are being developed for cancer therapy. However, clinical development of these molecules is challenging because of the lack of a genetic strategy to identify human tumors dependent on ligand-induced Wnt/β-catenin signaling. Ubiquitin E3 ligase ring finger 43 (RNF43) has been suggested as a negative regulator of Wnt signaling, and mutations of
RNF43
have been identified in various tumors, including cystic pancreatic tumors. However, loss of function study of RNF43 in cell culture has not been conducted, and the functional significance of
RNF43
mutations in cancer is unknown. Here, we show that RNF43 inhibits Wnt/β-catenin signaling by reducing the membrane level of Frizzled in pancreatic cancer cells, serving as a negative feedback mechanism. Inhibition of endogenous Wnt/β-catenin signaling increased the cell surface level of Frizzled. A panel of 39 pancreatic cancer cell lines was tested for Wnt dependency using LGK974, a selective Porcupine inhibitor being examined in a phase 1 clinical trial. Strikingly, all LGK974-sensitive lines carried inactivating mutations of
RNF43
. Inhibition of Wnt secretion, depletion of β-catenin, or expression of wild-type RNF43 blocked proliferation of RNF43 mutant but not
RNF43
–wild-type pancreatic cancer cells. LGK974 inhibited proliferation and induced differentiation of
RNF43
-mutant pancreatic adenocarcinoma xenograft models. Our data suggest that mutational inactivation of
RNF43
in pancreatic adenocarcinoma confers Wnt dependency, and the presence of
RNF43
mutations could be used as a predictive biomarker for patient selection supporting the clinical development of Wnt inhibitors in subtypes of cancer.
Systems approaches map regulatory networks downstream of the auxin receptor AFB3 in the nitrate response ofArabidopsis thalianaroots
Authors: Vidal Elena A. , Moyano Tomás C. , Riveras Eleodoro , Contreras-López Orlando , Gutiérrez Rodrigo A.
Published: July 2013

Auxin is a key phytohormone regulating central processes in plants. Although the mechanism by which auxin triggers changes in gene expression is well understood, little is known about the specific role of the individual members of the TIR1/AFB auxin receptors, Aux/IAA repressors, and ARF transcription factors and/or molecular pathways acting downstream leading to plant responses to the environment. We previously reported a role for AFB3 in coordinating primary and lateral root growth to nitrate availability. In this work, we used an integrated genomics, bioinformatics, and molecular genetics approach to dissect regulatory networks acting downstream of AFB3 that are activated by nitrate in roots. We found that the NAC4 transcription factor is a key regulatory element controlling a nitrate-responsive network, and thatnac4mutants have altered lateral root growth but normal primary root growth in response to nitrate. This finding suggests that AFB3 is able to activate two independent pathways to control root system architecture. Our systems approach has unraveled key components of the AFB3 regulatory network leading to changes in lateral root growth in response to nitrate.
An integrated toolkit for accurate prediction and analysis ofcis-regulatory motifs at a genome scale
Authors: Ma Qin , Liu Bingqiang , Zhou Chuan , Yin Yanbin , Li Guojun , Xu Ying
Published: July 2013

Motivation: We present an integrated toolkit, BoBro2.0, for prediction and analysis of cis-regulatory motifs. This toolkit can (i) reliably identify statistically significant cis-regulatory motifs at a genome scale; (ii) accurately scan for all motif instances of a query motif in specified genomic regions using a novel method for P-value estimation; (iii) provide highly reliable comparisons and clustering of identified motifs, which takes into consideration the weak signals from the flanking regions of the motifs; and (iv) analyze co-occurring motifs in the regulatory regions.

Results: We have carried out systematic comparisons between motif predictions using BoBro2.0 and the MEME package. The comparison results on Escherichia coli K12 genome and the human genome show that BoBro2.0 can identify the statistically significant motifs at a genome scale more efficiently, identify motif instances more accurately and get more reliable motif clusters than MEME. In addition, BoBro2.0 provides correlational analyses among the identified motifs to facilitate the inference of joint regulation relationships of transcription factors.

Availability: The source code of the program is freely available for noncommercial uses at http://code.google.com/p/bobro/.

Contact:  xyn@bmb.uga.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2013 Recommendations by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM)a
Authors: Baron Ellen Jo , Miller J. Michael , Weinstein Melvin P. , Richter Sandra S. , Gilligan Peter H. , Thomson Richard B. , Bourbeau Paul , Carroll Karen C. , Kehl Sue C. , Dunne W. Michael , Robinson-Dunn Barbara , Schwartzman Joseph D. , Chapin Kimberle C. , Snyder James W. , Forbes Betty A. , Patel Robin , Rosenblatt Jon E. , Pritt Bobbi S.
Published: July 2013

The critical role of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician and the microbiologists who provide enormous value to the health care team. This document, developed by both laboratory and clinical experts, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. Sections are divided into anatomic systems, including Bloodstream Infections and Infections of the Cardiovascular System, Central Nervous System Infections, Ocular Infections, Soft Tissue Infections of the Head and Neck, Upper Respiratory Infections, Lower Respiratory Tract infections, Infections of the Gastrointestinal Tract, Intraabdominal Infections, Bone and Joint Infections, Urinary Tract Infections, Genital Infections, and Skin and Soft Tissue Infections; or into etiologic agent groups, including Tickborne Infections, Viral Syndromes, and Blood and Tissue Parasite Infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. There is redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a reference to guide physicians in choosing tests that will aid them to diagnose infectious diseases in their patients.
Revisiting the Niuzhuang Oil Mill (1868–1870): Transferring Western Technology into China
Authors: Wang Hsien-chun
Published: July 2013

In 1868, the prominent British firm, Jardine, Matheson & Co., opened the Niuzhuang Oil Mill, one of China’s earliest mechanized factories, but closed it in 1870. The mill faced no oppositions from local government officials but suffered from some technical defects. It produced better quality products that obtained higher prices. This essay argues that the mill’s failure had to do with high capital costs and low profitability.
Complete atrioventricular block does not reduce long‐term mortality in patients with permanent atrial fibrillation treated with cardiac resynchronization therapy
Authors: Tolosana José M. , Trucco Emilce , Khatib Malek , Doltra Adelina , Borras Roger , Castel M. Ángeles , Berruezo Antonio , Arbelo Elena , Sitges Marta , Matas Maria , Guasch Eduard , Brugada Josep , Mont Lluís
Published: July 2013

Aims

A maximum percentage of ventricular pacing is mandatory to obtain a good response to CRT. Atrioventricular junction (AVJ) ablation has been recommended to attain this objective in patients with AF. The aims of our study were: (i) to determine whether the presence of complete AVJ block (induced or spontaneous) improves survival in patients with permanent AF treated with CRT and (ii) to analyse the predictors of mortality in AF patients treated with CRT.

Methods and results

From a series of 608 patients treated with CRT in our centre from 2000 to 2011, a cohort of 155 patients with permanent AF was analysed. Patients in AF were divided into two groups, AF + AVJ block [76 (49%)] and AF non‐AVJ block [79 (51%)]. Mean follow‐up was 30 months (interquartile range 13–51 months). During the follow‐up, 62 patients died. Overall and cardiovascular mortality were similar between both groups: hazard ratio (HR) 0.85, 95% confidence interval (CI) 0.51–1.39, P = 0.51 and HR 0.94, 95% CI 0.52–1.68, P = 0.82. Multivariate analysis identified three independent predictors of mortality: basal NYHA functional class IV (HR 2.25, 95% CI 1.12–4.22, P = 0.03), glomerular filtration rate (HR 0.98, 95% CI 0.96–0.99, P = 0.03), and LVEF (HR 0.94, 95% CI 0.89–0.99, P = 0.02).

Conclusions

AVJ block did not improve survival for patients in AF treated with CRT. Basal NYHA functional class IV, poor renal function, and LVEF were the independent predictors of mortality.
Paternal obesity initiates metabolic disturbances in two generations of mice with incomplete penetrance to the F2 generation and alters the transcriptional profile of testis and sperm microRNA content
Authors: Fullston Tod , Teague E. Maria C. Ohlsson , Palmer Nicole O. , DeBlasio Miles J. , Mitchell Megan , Corbett Mark , Print Cristin G. , Owens Julie A. , Lane Michelle
Published: July 2013

Obesity is highly prevalent, and its incidence is increasing. The previous study showing a major effect of paternal obesity on metabolic health of offspring is confounded by comorbidity with diabetes. Therefore, we investigated the effect of diet‐induced paternal obesity, in the absence of diabetes, on the metabolic health of two resultant generations and the molecular profiles of the testes and sperm. Founder (F0) male C57BL6 mice were fed either a high‐fat diet (HFD) or a control diet (CD); n = 10/diet for a period of 10 wk. Testis expression of mRNA/microRNAs was analyzed by microarray and qPCR and sperm microRNA abundance by qPCR Two subsequent generations were generated by mating F0 and then F1 mice to CD mice, and their metabolic health was investigated. All mice, other than F0 males, were maintained on a CD. HFD feeding induced paternal obesity with a 21% increase in adiposity, but not overt diabetes, and initiated intergenerational transmission of obesity and insulin resistance in two generations of offspring. This distinct phenotypic constellation is either partially or fully transmitted to both female and male F1 offspring and further transmitted through both parental lineages to the F2 generation, with a heightened effect on female F1 offspring (+67% in adiposity) and their F2 sons (+24% in adiposity). Founder male obesity altered the testes expression of 414 mRNAs by microarray and 11 microRNAs by qPCR, concomitant with alterations in sperm microRNA content and a 25% reduction in global methylation of germ cell DNA Diet‐induced paternal obesity modulates sperm microRNA content and germ cell methylation status, which are potential signals that program offspring health and initiate the transmission of obesity and impaired metabolic health to future generations. This study implicates paternal obesity in the transgenerational amplification of obesity and type 2 diabetes in humans.—Fullston, T., Ohlsson Teague, E. M. C., Palmer, N. O., DeBlasio, M. J., Mitchell, M., Corbett, M., Print, C. G., Owens, J. A., Lane, M., Paternal obesity initiates metabolic disturbances in two generations of mice with incomplete penetrance to the F2 generation and alters the transcriptional profile of testis and sperm microRNA content. FASEBJ. 27, 4226‐4243 (2013). www.fasebj.org
Potential for Improving Therapy and Defining New Research Targets in Eosinophilic Oesophagitis Based on Understanding of Immunopathogenesis
Authors: Murch Simon H. , Allen Katrina , Chong Sonny , Dias Jorge Amil , Papadopoulou Alexandra ,   Eosinophilic Oesophagitis Working Group of ESPGHAN
Published: July 2013

Objectives:

This review considers the potential for therapeutic advances in the management of eosinophilic oesophagitis (EoE) based on recently increased understanding of the pathophysiology of the disorder.

Methods:

This is a review of publications characterising mucosal changes and leucocyte recruitment patterns in human and experimental EoE.

Results:

EoE, although diagnosed by epithelial infiltration of eosinophils, is actually a transmural inflammation in which eosinophil recruitment occurs via the deeper layers. Penetration of eosinophils into the epithelium is variable, explaining the need for multiple biopsies to diagnose what may be a clearly visible disorder. Fibrosis and neuromuscular dysfunction both occur within the subepithelial tissues. Recent murine studies have identified that T‐cell recruitment underpins antigen‐specific oesophageal eosinophil recruitment. Involvement of innate immunity is also suggested by the role of invariant natural killer T cells in experimental EoE.

Conclusions:

Looking beyond present therapeutic options with a view to future studies, we identify T cells as candidates for “upstream therapy” if antigen specificity or homing markers are determined. Evidence of aeroallergen sensitisation suggests the possibility of lymphocyte priming within nasal‐associated lymphoid tissue or Waldeyer ring, with the potential for topical therapy. We consider acquired neuromuscular dysfunction as a therapeutic target in acute symptomatic deterioration or bolus obstruction. We assess possible similarities with therapeutic stratagems for chronic asthma, recognising at the same time the anatomic specificity of the oesophagus and the difficulty in delivering effective topical medication to subepithelial tissues in this location compared with the airway.