bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical modelling of a healthy/malaria-infected erythrocyte in shear flow using dissipative particle dynamics method
Authors: Ye Ting , Phan-Thien Nhan , Cheong Khoo Boo , Teck Lim Chwee
Published: June 2014

In the present paper, the dynamics of healthy and malaria-infected erythrocytes in the shear flow are investigated using dissipative particle dynamics (DPD), a particle-based method. A discrete model is developed, where the computational domain is discretized into a set of particles to represent the suspending liquid, as well as erythrocytes as suspended deformable particles. The particles on an erythrocyte surface are connected into a triangular network to represent the membrane. The interaction between any two particles is modelled by the DPD method, which conserves both mass and momentum. In order to validate this model, the deformation of a spherical capsule in the shear flow is firstly simulated, and a good agreement is found with previously published works. Then, the dynamics of a healthy biconcave erythrocyte in a shear flow is investigated. The results demonstrate that a healthy erythrocyte undergoes a tank-treading motion at a high capillary number, and a tumbling motion at a low capillary number or at a high viscosity ratio, internal (erythrocyte) to external fluids. Two other types of trembling motions, breathing with tumbling and swinging with tank-treading, are also found at an intermediate capillary number or viscosity ratio. Finally, the dynamics of malaria-infected erythrocyte in a shear flow is studied. At the same shear rate, if the healthy erythrocyte undergoes a tumbling motion, the malaria-infected one will exhibit a tumbling motion only. If the healthy erythrocyte undergoes a trembling motion, the malaria-infected one cannot exhibit tank-treading motion. If the healthy erythrocyte undergoes a tank-treading motion, the malaria-infected one will exhibit one of three dynamic motions: tumbling, trembling or tank-treading motion.
Precision large field scanning system for high numerical aperture lenses and application to femtosecond micromachining of ophthalmic materials
Authors: Brooks D. R. , Brown N. S. , Savage D. E. , Wang C. , Knox W. H. , Ellis J. D.
Published: June 2014

A precision, large stroke (nearly 1 cm) scanning system was designed, built, and calibrated for micromachining of ophthalmic materials including hydrogels and cornea (excised and in vivo). This system comprises a flexure stage with an attached objective on stacked vertical and horizontal translation stages. This paper outlines the design process leading to our most current version including the specifications that were used in the design and the drawbacks of other methods that were previously used. Initial measurements of the current version are also given. The current flexure was measured to have a 27 Hz natural frequency with no load.
Photoisomerization among ring-open merocyanines. II. A computational study
Authors: Walter Christof , Ruetzel Stefan , Diekmann Meike , Nuernberger Patrick , Brixner Tobias , Engels Bernd
Published: June 2014

The photochemical isomerization of the trans-trans-cis to the trans-trans-trans isomer of the merocyanine form of 6-nitro BIPS, which has been studied with femtosecond transient absorption spectroscopy [S. Ruetzel, M. Diekmann, P. Nuernberger, C. Walter, B. Engels, and T. Brixner, J. Chem. Phys. 140, 224310 (2014)], is investigated using time-dependent density functional theory in conjunction with polarizable continuum models. Benchmark calculations against SCS-ADC(2) evaluate the applicability of the CAM-B3LYP functional. Apart from a relaxed scan in the ground state with additional computation of the corresponding excitation energies, which produces the excited-state surface vertical to the ground-state isomerization coordinate, a relaxed scan in the S1 gives insight into the geometric changes orthogonal to the reaction coordinate and the fluorescence conditions. The shape of the potential energy surface (PES) along the reaction coordinate is found to be highly sensitive to solvation effects, with the method of solvation (linear response vs. state-specific) being critical. The shape of the PES as well as the computed harmonic frequencies in the S1 minima are in line with the experimental results and offer a straightforward interpretation.
Mechanisms for three kinds of limiting shear stresses appearing in the traction modes of viscous, viscoelastic, and glassy states of lubricants
Authors: Kobayashi H. , Fujita Y.
Published: June 2014

We present that the tractional flow of a lubricant shows three kinds of limiting shear stresses at which the shear stresses take place independently of the shear rates in its viscous, viscoelastic, and glassy states. We propose three models on the mechanisms for the limiting shear stresses, based on the data of Brillouin spectra and viscosity of viscoelastic liquids previously reported by us and based on the data of the deformation of glassy polymers referred from others. The Brillouin spectra of a viscoelastic lubricant measured at up to 5 GPa at 25 and 80 °C show that we could not observe a frequency dispersion in sound waves below 0.8 GPa at 80 °C, while we can observe the frequency dispersion above 0.1 MPa at 25 °C owing to the viscosity of the lubricant. This result predicts the viscous limiting shear stress in the viscous state owing to the disappearance of meso-structures by heating and shearing under pressure. The viscosity of a polymer measured around the glass transition temperature (Tg) shows that Tg determined by the viscosity measurement is 27 K lower than that determined by calorimetry. This result predicts the elastic limiting shear stress in the viscoelastic state near the glass transition pressure (Pg) owing to the shear thinning effect by shearing a lubricant film. In addition, there is the plastic limiting shear stress in the glassy state owing to the yield stress at which the tractional flow of a glassy lubricant behaves as a plastic solid.
Quantum tomography meets dynamical systems and bifurcations theory
Authors: Goyeneche D. , de la Torre A. C.
Published: June 2014

A powerful tool for studying geometrical problems in Hilbert spaces is developed. We demonstrate the convergence and robustness of our method in every dimension by considering dynamical systems theory. This method provides numerical solutions to hard problems involving many coupled nonlinear equations in low and high dimensions (e.g., quantum tomography problem, existence and classification of Pauli partners, mutually unbiased bases, complex Hadamard matrices, equiangular tight frames, etc.). Additionally, this tool can be used to find analytical solutions and also to implicitly prove the existence of solutions. Here, we develop the theory for the quantum pure state tomography problem in finite dimensions but this approach is straightforwardly extended to the rest of the problems. We prove that solutions are always attractive fixed points of a nonlinear operator explicitly given. As an application, we show that the statistics collected from three random orthonormal bases is enough to reconstruct pure states from experimental (noisy) data in every dimension d ⩽ 32.
Enhanced target normal sheath acceleration based on the laser relativistic self-focusing
Authors: Zou D. B. , Zhuo H. B. , Yang X. H. , Shao F. Q. , Ma Y. Y. , Yu T. P. , Wu H. C. , Yin Y. , Ge Z. Y. , Li X. H.
Published: June 2014

The enhanced target normal sheath acceleration of ions in laser target interaction via the laser relativistic self-focusing effect is investigated by theoretical analysis and particle-in-cell simulations. The temperature of the hot electrons in the underdense plasma is greatly increased due to the occurrence of resonant absorption, while the electron-betatron-oscillation frequency is close to its witnessed laser frequency [Pukhov et al., Phys. Plasma 6, 2847 (1999)]. While these hot electrons penetrate through the backside solid target, a stronger sheath electric field at the rear surface of the target is induced, which can accelerate the protons to a higher energy. It is also shown that the optimum length of the underdense plasma is approximately equal to the self-focusing distance.
Note: A gel based imaging technique of the iridocorneal angle for evaluation of angle-closure glaucoma
Authors: Shinoj V. K. , Murukeshan V. M. , Baskaran M. , Aung T.
Published: June 2014

Noninvasive medical imaging techniques have high potential in the field of ocular imaging research. Angle closure glaucoma is a major disease causing blindness and a possible way of detection is the examination of the anterior chamber angle in eyes. Here, a simple optical method for the evaluation of angle-closure glaucoma is proposed and illustrated. The light propagation from the region associated with the iridocorneal angle to the exterior of eye is considered analytically. The design of the gel assisted probe prototype is carried out and the imaging of iridocorneal angle is performed on an eye model.
On-demand hierarchical patterning with electric fields
Authors: Wang Qiming , Robinson Dominick , Zhao Xuanhe
Published: June 2014

We report a method to generate hierarchical topographical patterns on demand under the control of applied voltages. The method is implemented by harnessing the electro-creasing instability in multilayer elastomer films. The critical electric field for electro-creasing instability in a layer of elastomer scales with square root of the elastomer's modulus, while the wavelength of instability pattern scales with the layer's thickness. By rationally designing elastomer films with varied modulus and thickness throughout different layers, we control the formation of surface instability patterns with feature sizes of different scales under prescribed voltages. The method is very versatile, giving various types of hierarchical patterns such as randomly oriented, aligned, and gradient ones. A theoretical model is developed and validated to guide the design of hierarchical patterns.
High blue-near ultraviolet photodiode response of vertically stacked graphene-MoS2-metal heterostructures
Authors: Wi Sungjin , Chen Mikai , Nam Hongsuk , Liu Amy C. , Meyhofer Edgar , Liang Xiaogan
Published: June 2014

We present a study on the photodiode response of vertically stacked graphene/MoS2/metal heterostructures in which MoS2 layers are doped with various plasma species. In comparison with undoped heterostructures, such doped ones exhibit significantly improved quantum efficiencies in both photovoltaic and photoconductive modes. This indicates that plasma-doping-induced built-in potentials play an important role in photocurrent generation. As compared to indium-tin-oxide/ MoS2/metal structures, the presented graphene/MoS2/metal heterostructures exhibit greatly enhanced quantum efficiencies in the blue-near ultraviolet region, which is attributed to the low density of recombination centers at graphene/MoS2 heterojunctions. This work advances the knowledge for making photo-response devices based on layered materials.
Magnetization switching of rare earth orthochromite CeCrO3
Authors: Cao Yiming , Cao Shixun , Ren Wei , Feng Zhenjie , Yuan Shujuan , Kang Baojuan , Lu Bo , Zhang Jincang
Published: June 2014

We report the synthesis of single phase rare earth orthochromite CeCrO3 and its magnetic properties. A canted antiferromagnetic transition with thermal hysteresis at T = 260 K is observed, and a magnetic compensation (zero magnetization) near 133 K is attributed to the antiparallel coupling between Ce3+ and Cr3+ moments. At low temperature, field induced magnetization reversal starting from 43 K for H = 1.2 kOe reveals the spin flip driven by Zeeman energy between the net moments and the applied field. These findings may find potential uses in magnetic switching devices such as nonvolatile magnetic memory which facilitates two distinct states of magnetization.
Storage and on-demand release of microwaves using superconducting resonators with tunable coupling
Authors: Pierre Mathieu , Svensson Ida-Maria , Raman Sathyamoorthy Sankar , Johansson Göran , Delsing Per
Published: June 2014

We present a system which allows to tune the coupling between a superconducting resonator and a transmission line. This storage resonator is addressed through a second, coupling resonator, which is frequency-tunable and controlled by a magnetic flux applied to a superconducting quantum interference device. We experimentally demonstrate that the lifetime of the storage resonator can be tuned by more than three orders of magnitude. A field can be stored for 18 μs when the coupling resonator is tuned off resonance and it can be released in 14 ns when the coupling resonator is tuned on resonance. The device allows capture, storage, and on-demand release of microwaves at a tunable rate.
Photoresponse in thin films of WO3 grown by pulsed laser deposition
Authors: Roy Moulik Samik , Samanta Sudeshna , Ghosh Barnali
Published: June 2014

We report, the photoresponse behaviour of Tungsten trioxide (WO3) films of different surface morphology, grown by using pulsed laser deposition (PLD). The Growth parameters for PLD were changed for two substrates SiO2/Si (SO) and SrTiO3 (STO), such a way which, result nanocrystalline film on SO and needle like structured film on STO. The photoresponse is greatly modified in these two films because of two different surface morphologies. The nanocrystalline film (film on SO) shows distinct photocurrent (PC) ON/OFF states when light was turned on/off, the enhancement of PC is ∼27%. Whereas, the film with needle like structure (film on STO) exhibits significantly enhanced persistent photocurrent even in light off condition, in this case, the enhancement of PC ∼ 50% at room temperature at lowest wavelength (λ = 360 nm) at a nominal bias voltage of 0.1 V.
Theoretical study of InN/GaN short period superlattices to mimic disordered alloys
Authors: Ribeiro M. , Marques M.
Published: June 2014

We carried out ab initio calculations of the (InN)n∕(GaN)m short period superlattices using the LDA-1/2 method in order to obtain approximate quasiparticle electronic structures. We performed calculations for several short period superlattices respecting the concentrations of 33%, 50%, 66%, and 80% of InN, considering different straining possibilities due to lattice mismatches. For the majority of configurations, we find relevant changes on the valence and conduction profiles around bandgap with position plane-by-plane along the superlattices growth direction, with the presence of intrinsic electric fields in the materials, in the case, when strain is applied. Our results show that for small numbers n and m of layers, the band edge states extend over the entire superlattice. For larger n and/or m, the edge states tend to localise on particular subtype layers (InN or GaN). For the former cases, the bandgaps are very close to the random alloys with the same concentrations, providing potential good materials for optoelectronic devices based on nitrides.
Vacancy dynamic in Ni-Mn-Ga ferromagnetic shape memory alloys
Authors: Merida D. , García J. A. , Sánchez-Alarcos V. , Pérez-Landazábal J. I. , Recarte V. , Plazaola F.
Published: June 2014

Vacancies control any atomic ordering process and consequently most of the order-dependent properties of the martensitic transformation in ferromagnetic shape memory alloys. Positron annihilation spectroscopy demonstrates to be a powerful technique to study vacancies in NiMnGa alloys quenched from different temperatures and subjected to post-quench isothermal annealing treatments. Considering an effective vacancy type the temperature dependence of the vacancy concentration has been evaluated. Samples quenched from 1173 K show a vacancy concentration of 1100 ± 200 ppm. The vacancy migration and formation energies have been estimated to be 0.55 ± 0.05 eV and 0.90 ± 0.07 eV, respectively.
Modulation of the electron transport properties in graphene nanoribbons doped with BN chains
Authors: Liu Wu , Zhang Kaiwang , Wang Ru-Zhi , Zhong JianXin , Liu Li-Min
Published: June 2014

Using density-functional theory and the non-equilibrium Green's function method, the electron transport properties of zigzag graphene nanoribbons (ZGNRs) doped with BN chains are studied by systematically calculating the energy band structure, density of states and the transmission spectra for the systems. The BN chains destroyed the electronic transport properties of the ZGNRs, and an energy gap appeared for the ZGNRs, and displayed variations from a metal to a wide-gap semiconductor. With an increase in the number of BN chains, the band gap increased gradually in the band structure and the transmission coefficient decreased near the Fermi surface. Additionally, the doping position had a significant effect on the electronic properties of the ZGNRs.
A Conceptual Outline of Contemporary Magic Practice
Authors: Rolfe Charles
Published: June 2014

This paper offers a conceptual outline of contemporary magic practice that is applicable to magic performed, experienced, and commercialized as a form of entertainment. Magic is defined within a paradoxical dialectics of art and (the nonart of) work. Jacques Rancière's ideas are used to conceive magic as (1) art: where magic is based around dissemblance (operations which alter the given) and theatrical spectacle (drama before an audience); and (2) work: where magic is embodied in the figure of the magician, which knots together ways of doing (practical knowledge; potentialities) and thinking (genealogical; teleological) in order to produce an effect of impossibility and the affect of astonishment. The paper concludes by making an argument for how theorizing magic requires thinking about and expressing paradoxical situations given that magic is enigmatic.
A Question of Perspective: Impact Assessment and the Perceived Costs and Benefits of New Regulations for SMEs
Authors: Chittenden Francis , Ambler Tim
Published: June 2014

Regulation remains a contentious topic between small firms, policy makers, and scholars. Business lobbying organizations persistently claim that regulation acts as a deterrent to economic activity. In contrast, policy makers and some scholars have argued that regulation creates net benefits for society and so may have a modest positive impact on SMEs. This paper seeks to offer at least a partial explanation for these very different perspectives. Through studying the majority of UK Impact Assessments issued over the twelve years from 1998 to 2009 and relevant government publications, we find that differences in the objective decision-making criteria (algorithms and heuristics) of the parties involved provide at least a partial explanation of why their views appear irreconcilable. It is argued that both are acting rationally in pursuit of higher goals and are not simply ‘gaming’ in order to gain the greatest private advantage.
Geometrical Optical Illusionists
Authors: Wade Nicholas J
Published: June 2014

Geometrical optical illusions were given this title by Oppel in 1855. Variants on such small distortions of visual space were illustrated thereafter, many of which bear the names of those who first described them. Some original forms of the geometrical optical illusions are shown together with ‘perceptual portraits’ of those who described them. These include: Roget, Chevreul, Fick, Zöllner, Poggendorff, Hering, Kundt, Delbœuf, Mach, Helmholtz, Hermann, von Bezold, Müller-Lyer, Lipps, Thiéry, Wundt, Münsterberg, Ebbinghaus, Titchener, Ponzo, Luckiesh, Sander, Ehrenstein, Gregory, Heard, White, Shepard, and Lingelbach. The illusions are grouped under the headings of orientation, size, the combination of size and orientation, and contrast. Early theories of illusions, before geometrical optical illusions were so named, are mentioned briefly.
Social support and depressive symptoms among 'money' boys and general men who have sex with men in Shanghai, China
Authors: Yan Huamei , Wong Frank Y. , Zheng Tony , Ning Zhen , Ding Yingying , Nehl Eric J. , Lin Lavinia , He Na
Published: June 2014

The primary objective was to examine prevalence and correlates of social support and depressive symptoms among male sex workers (known as ‘money boys’ (MBs)) and general men who have sex with men (MSM) in Shanghai. The Social Provision Scale (SPS), which consists of 24 items, scored out of 4 for social provision, was used to evaluate the functions of social relationships. The score for each item ranges from 1 to 4, with a higher score indicating more social provision. The overall mean SPS score was 68.1 (s.d. = 6.53) for MBs and 69.3 (s.d. = 6.99) for general MSM. Depression was measured with a 12-item version of the Center for Epidemiological Studies Depression Scale (CES-D), where a score of 9 has been recommended as the cutoff score to indicate possible depressive symptoms. The prevalence of depressive symptoms was 57.9%, with MBs having a higher level of depressive symptoms than general MSM (70.0% v. 46.1%) (odds ratio = 1.86, 95% confidence interval = 1.07–3.24). Social support was a protective factor for depressive symptoms (odds ratio = 0.92, 95% confidence interval = 0.89–0.96). MSM in China, particularly MBs, are vulnerable to low social support and high depressive symptoms, highlighting the need for tailored psychological programs targeting this population.
Pituitary tumor-transforming gene 1 regulates the patterning of retinal mosaics
Authors: Keeley Patrick W. , Zhou Cuiqi , Lu Lu , Williams Robert W. , Melmed Shlomo , Reese Benjamin E.
Published: June 2014

Significance

The spatial distributions of neuronal populations are frequently patterned, but molecular mechanisms underlying their orderliness have received little attention. We used a genetic screen to identify prospective genes participating in the patterning within a population of retinal amacrine cells. We mapped variation in their patterning, assessed using nearest-neighbor analysis across a panel of 25 recombinant inbred strains, to a genomic locus on chromosome 11. There, we identified pituitary tumor-transforming gene 1 (
Pttg1
) as a candidate. Critically,
Pttg1
expression correlated with regularity across these 25 strains, and a variant in
Pttg1
was found to modulate expression. By knocking out
Pttg1
, patterning was selectively disrupted in two types of retinal neuron.
Pitx2
-microRNA pathway that delimits sinoatrial node development and inhibits predisposition to atrial fibrillation
Authors: Wang Jun , Bai Yan , Li Na , Ye Wenduo , Zhang Min , Greene Stephanie B. , Tao Ye , Chen Yiping , Wehrens Xander H. T. , Martin James F.
Published: June 2014

Significance

Atrial Fibrillation (AF) is the most common sustained cardiac arrhythmia in the human population. It is critical to elucidate the molecular mechanisms underlying AF, given that the prevalence of AF is expected to dramatically increase as the human population ages. We identified a microRNA (miR)-regulated genetic pathway that delimits sinoatrial node development and inhibits AF. To our knowledge, our data are the first genetic evidence showing that miR deletion results in AF predisposition. Moreover, to our knowledge, our data are the first demonstration that sinoatrial node regulatory genes are regulated by miRs. Our findings suggest attractive therapeutic targets to treat AF given that miR-based therapeutics are feasible using miR antagonists and mimics.
Divine Spark: The Prelude to the Tobacco Régie of 1890
Authors: Davoudi Leonardo
Published: June 2014

This article looks at the negotiations leading up to the Persian Tobacco Régie of 1890 as well as a previous failed Tobacco Régie in 1886. There exist only a few allusions to these two phases of the tobacco concession in the existing literature. Due to the newly uncovered diaries of the main commercial intermediary in these negotiations, the present article will be able to retrace, with precision, the events leading up to this economic concession of historical significance.
Policy versus ground reality: secondary English language assessment system in Bangladesh
Authors: Das Sharmistha , Shaheen Robina , Shrestha Prithvi , Rahman Arifa , Khan Rubina
Published: June 2014

Any policy reform in education is highly effective when it is planned and implemented ‘holistically’ and yet, it is the most challenging way forward. Many countries in Asia have reformed their English language policies and syllabi in the last two decades due to the increasing value of the language worldwide. Motivated by a ‘communicative approach’ to English language teaching, Bangladesh was one of the countries that launched such a reform in the 1990s. However, this reform has been criticised for imposing the changes on teachers without preparing them sufficiently. More importantly, there is limited evidence as to how much the secondary English language assessment system is aligned with the changes introduced in the curriculum. In order to explore this gap, a medium‐scale study was conducted in 38 secondary schools in Bangladesh, following a mixed methods approach. The findings highlighted a ‘mismatch’ between the intended English language learning outcomes and current assessment practices, including the resulting challenges faced by the teachers. This paper argues that language education reform is likely to fail if the assessment system is not aligned with the curriculum.
MetAssign: probabilistic annotation of metabolites from LC–MS data using a Bayesian clustering approach
Authors: Daly Rónán , Rogers Simon , Wandy Joe , Jankevics Andris , Burgess Karl E. V. , Breitling Rainer
Published: June 2014

Motivation: The use of liquid chromatography coupled to mass spectrometry has enabled the high-throughput profiling of the metabolite composition of biological samples. However, the large amount of data obtained can be difficult to analyse and often requires computational processing to understand which metabolites are present in a sample. This article looks at the dual problem of annotating peaks in a sample with a metabolite, together with putatively annotating whether a metabolite is present in the sample. The starting point of the approach is a Bayesian clustering of peaks into groups, each corresponding to putative adducts and isotopes of a single metabolite.

Results: The Bayesian modelling introduced here combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The results inherently contain a quantitative estimate of confidence in the peak annotations and allow an accurate trade-off between precision and recall. Extensive validation experiments using authentic chemical standards show that this system is able to produce more accurate putative identifications than other state-of-the-art systems, while at the same time giving a probabilistic measure of confidence in the annotations.

Availability and implementation : The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download at http://mzmatch.sourceforge.net/ .

Contact:  Ronan.Daly@glasgow.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Will the Real Businessman/Businesswoman Stand Up?: The Historical Implications of Regendering Business Success in the Early Twentieth Century
Authors: Mandell Nikki
Published: June 2014

This paper compares the corporate network strategies between multinational corporations of two different origins (United States and Spain), business groups, and state-owned enterprises in the public utility sector of a developing country going through economic and political transitions. The transitions we consider are from an import substitution industrialization model to an open market economy and from a democratic regime to a dictatorial one and back to democracy. We analyze the Chilean telecommunications sector between 1958 and 2005 and find that during a democratic regime all firms sought to build more networks with each other, while incentives decrease under an authoritarian regime. In the protectionist era, US investors built links with Chile’s corporate elite, while in times of an open economy, Spanish investors built these links with the government. State-owned corporations did not attempt to build links with other actors at any time, and business groups sought to build most networks among members of the group. Our findings challenge two commonly held assumptions: first, that open economies decrease incentives for domestic actors to build links with each other and, second, that close political regimes increase incentives to build networks among economic actors.
Modelling fuel consumption of fishing vessels for predictive use
Authors: Davie Sarah , Minto Cóilín , Officer Rick , Lordan Colm , Jackson Emmet
Published: June 2014

Fuel costs are an important element in models used to analyse and predict fisher behaviour for application within the wider mixed fisheries and ecosystem approaches to management. This investigation explored the predictive capability of linear and generalized additive models (GAMs) in providing daily fuel consumption estimates for fishing vessels given knowledge of their length, engine power, fleet segment (annual dominant gear type), and fuel prices. Models were fitted to half of the Irish fishing vessel economic data collected between 2003 and 2011. The predictive capabilities of the seven best models were validated against the remaining, previously un-modelled, data. The type of gear used by a fleet segment had an important influence on fuel consumption as did the price of fuel. The passive pot gear and Scottish seine gear segments indicated consistently lower consumptions, whereas dredge and pelagic gears showed consistently higher fuel consumptions. Furthermore, increasing fuel price negatively affected fuel consumption, especially for more powerful, larger vessels. Of the formulated models, the best fit to training data were a GAM with a gear main effect and two smooth functions; standardized vessel length and engine power interacting with fuel price. For prediction, overall, this model showed the closest predictions with the least bias, followed by three linear models. However, all seven models compared for predictive capability performed well for the most sampled segments (demersal and pelagic trawlers).
NF-κB RELA-deficient bone marrow macrophages fail to support bone formation and to maintain the hematopoietic niche after lethal irradiation and stem cell transplantation
Authors: Mise-Omata Setsuko , Alles Neil , Fukazawa Taro , Aoki Kazuhiro , Ohya Keiichi , Jimi Eijiro , Obata Yuichi , Doi Takahiro
Published: June 2014

Bone remodeling and hematopoiesis are interrelated and bone marrow (BM) macrophages are considered to be important for both bone remodeling and maintenance of the hematopoietic niche. We found that NF-κB Rela-deficient chimeric mice, generated by transplanting Rela−/− fetal liver cells into lethally irradiated hosts, developed severe osteopenia, reduced lymphopoiesis and enhanced mobilization of hematopoietic stem and progenitor cells when BM cells were completely substituted by Rela-deficient cells. Rela−/− hematopoietic stem cells from fetal liver had normal hematopoietic ability, but those harvested from the BM of osteopenic Rela−/− chimeric mice had reduced repopulation ability, indicating impairment of the microenvironment for the hematopoietic niche. Osteopenia in Rela−/− chimeric mice was due to reduced bone formation, even though osteoblasts differentiated from host cells. This finding indicates impaired functional coupling between osteoblasts and hematopoietic stem cell-derived cells. Rela-deficient BM macrophages exhibited an aberrant inflammatory phenotype, and transplantation with wild-type F4/80+ BM macrophages recovered bone formation and ameliorated lymphopoiesis in Rela−/− chimeric mice. Therefore, RELA in F4/80+ macrophages is important both for bone homeostasis and for maintaining the hematopoietic niche after lethal irradiation and hematopoietic stem cell transplantation.
Fast radio bursts: constraints on the dispersing medium
Authors: Dennison Brian
Published: June 2014

Fast radio bursts appear to exhibit large dispersion measures, typically exceeding any expected Galactic interstellar contribution, especially along the moderate to high Galactic latitude directions in which such events have been most often observed. The dispersions have been therefore interpreted as extragalactic, with the sources of the bursts at Gpc distances. This then implies that the bursts are extremely energetic events, originating from quite small volumes. To circumvent the energetic difficulties, Loeb et al. propose that the bursts are produced by flares near the surfaces of M stars or contact binaries within a local volume of the Galaxy, with the observed dispersion occurring in the overlying stellar coronae. With the dispersion concentrated in a high-density region, the quadratic dispersion approximation breaks down as the plasma frequency is comparable to (although less than) the propagation frequency. The observed dispersion curves are closely quadratic, however, consistent with a low-density medium, ruling out this model. It thus appears highly likely that the dispersions occur in the intergalactic medium. This medium, probably containing most of the baryon content of the Universe, is expected to be highly structured on large scales. Hot gas within clusters and especially groups of galaxies may contribute significantly to the observed dispersion.
Scattered light correction of Hayabusa/AMICA data and quantitative spectral comparisons of Itokawa
Authors: Ishiguro Masateru
Published: June 2014

The Hayabusa spacecraft rendezvoused with its target asteroid 25143 Itokawa in 2005 and brought an asteroidal sample back to the Earth in 2010. The onboard camera, AMICA, took more than 1400 images of Itokawa during the rendezvous phase. It was reported that the AMICA images were severely contaminated by light scatter inside the optics. The effect made it difficult to produce the color maps at longer wavelengths (> 800 nm). In this paper, we demonstrate a method to subtract the scattered light by investigating the dim halos of Itokawa and the Moon taken by AMICA during the inflight operation. As a result, we found that the overall data reduction scheme including the scattered light correction enables the recognition of 3% regional differences in the relative reflectance spectra of Itokawa. We confirmed that the color variation in Itokawa was largely attributed to space weathering.
Thiopurine Metabolite Ratios for Monitoring Therapy in Pediatric Crohn Disease
Authors: Kopylov U. , Amre D. , Theoret Y. , Deslandres C. , Seidman E.G.
Published: June 2014

Objectives:

Thiopurines (azathioprine, 6‐mercaptopurine) are a mainstay of treatment in Crohn disease (CD). Monitoring intracellular metabolite (6‐thioguanine nucleotides [6‐TGN] and 6‐methylmercaptopurine [6‐MMP]) levels can help optimize therapeutic efficacy and minimize potential toxicity. Determination of 6‐MMP/6‐TGN ratios may provide additional useful information, such as the identification of individuals with excessive thiopurine methyltransferase activity and disadvantageous 6‐MMP overproduction. These patients are at increased risk of therapeutic failure and hepatotoxicity. The aim of the study was to evaluate the correlation of 6‐MMP/6‐TGN ratios with therapeutic efficacy and risk of hepatotoxicity in CD.

Methods:

The present study was a single‐center cross‐sectional study including pediatric patients with CD studied prospectively with clinical and laboratory assessments along with serial measurements of 6‐MMP and 6‐TGN. Clinical response was determined using established clinical indices.

Results:

The study included 238 pediatric patients with CD with a total of 1648 evaluation points. The patients were in steroid‐free remission at 59.1% of the evaluation points. 6‐MMP/6‐TGN ratios of 4 to 24 were protective against relapse (odds ratio [OR] 0.52, 95% confidence interval [CI] −0.39 to 0.69, P = 0.001). Hepatotoxicity was associated with high 6‐MMP levels (>3919 pmol/8 × 108 red blood cell count: OR 7.65, 95% CI 3.7–15.9, P = 0.001) and high 6‐MMP/6‐TGN ratios (>24: OR 5.35, 95% CI −3.43 to 8.43, P = 0.001).

Conclusions:

We observed significant associations between 6‐MMP/6‐TGN ratios and clinical response, and risk of hepatotoxicity. Our results suggest that determination of thiopurine metabolite ratios is a valuable tool for identification of patients at increased risk of therapeutic failure and hepatotoxicity.
K-Pg events facilitated lineage transitions between terrestrial and aquatic ecosystems
Authors: Procheş Şerban , Polgar Gianluca , Marshall David J.
Published: June 2014

We use dated phylogenetic trees for tetrapod vertebrates to identify lineages that shifted between terrestrial and aquatic ecosystems in terms of feeding or development, and to assess the timing of such events. Both stem and crown lineage ages indicate a peak in transition events in correspondence with the K-Pg mass extinction. This meets the prediction that changes in competitive pressure and resource availability following mass extinction events should facilitate such transitions.
A computational method to differentiate normal individuals, osteoarthritis and rheumatoid arthritis patients using serum biomarkers
Authors: Heard Bryan J. , Rosvold Joshua M. , Fritzler Marvin J. , El-Gabalawy Hani , Wiley J. Preston , Krawetz Roman J.
Published: June 2014

The objective of this study was to develop a method for categorizing normal individuals (normal,
n
= 100) as well as patients with osteoarthritis (OA,
n
= 100), and rheumatoid arthritis (RA,
n
= 100) based on a panel of inflammatory cytokines expressed in serum samples. Two panels of inflammatory proteins were used as training sets in the construction of two separate artificial neural networks (ANNs). The first training set consisted of all proteins (38 in total) and the second consisted of only the significantly different proteins expressed (12 in total) between at least two patient groups. Both ANNs obtained high levels of sensitivity and specificity, with the first and second ANN each diagnosing 100% of test set patients correctly. These results were then verified by re-investigating the entire dataset using a decision tree algorithm. We show that ANNs can be used for the accurate differentiation between serum samples of patients with OA, a diagnosed RA patient comparator cohort and normal/control cohort. Using neural network and systems biology approaches to manage large datasets derived from high-throughput proteomics should be further explored and considered for diagnosing diseases with complex pathologies.
From ‘third pole’ to north pole: a Himalayan origin for the arctic fox
Authors: Wang Xiaoming , Tseng Zhijie Jack , Li Qiang , Takeuchi Gary T. , Xie Guangpu
Published: June 2014

The ‘third pole’ of the world is a fitting metaphor for the Himalayan–Tibetan Plateau, in allusion to its vast frozen terrain, rivalling the Arctic and Antarctic, at high altitude but low latitude. Living Tibetan and arctic mammals share adaptations to freezing temperatures such as long and thick winter fur in arctic muskox and Tibetan yak, and for carnivorans, a more predatory niche. Here, we report, to our knowledge, the first evolutionary link between an Early Pliocene (3.60–5.08 Myr ago) fox,Vulpes qiuzhudinginew species, from the Himalaya (Zanda Basin) and Kunlun Mountain (Kunlun Pass Basin) and the modern arctic foxVulpes lagopusin the polar region. A highly hypercarnivorous dentition of the new fox bears a striking resemblance to that ofV. lagopusand substantially predates the previous oldest records of the arctic fox by 3–4 Myr. The low latitude, high-altitude Tibetan Plateau is separated from the nearest modern arctic fox geographical range by at least 2000 km. The apparent connection between an ancestral high-elevation species and its modern polar descendant is consistent with our ‘Out-of-Tibet’ hypothesis postulating that high-altitude Tibet was a training ground for cold-environment adaptations well before the start of the Ice Age.
Rapid transcriptional response to physiological neuronal activityin vivorevealed by transcriptome sequencing
Authors: Katz Yarden , Velho Tarciso , Butty Vincent , Burge Christopher B. , Lois Carlos
Published: June 2014

Neuronal activity serves as a gateway between external stimulus from environment and the brain, often inducing gene expression changes. Alternative splicing (AS) is a widespread mechanism of increasing the number of transcripts produced from a single gene and has been shown to alter properties of neuronal genes, such as ion channels (Xie and Black 2001) and neurotransmitter receptors (Mu et al. 2003). Patterns of neural tissue-specific AS have been identified, often regulated by neuron-specific splicing factors that are essential for survival (Jensen et al. 2000; Li et al. 2007), demonstrating the importance of AS in neurons.In vitrostudies of neuronal activity found AS changes in response to neuronal activity in addition to transcriptional ones, raising the question of whether such changes are recapitulatedin vivoon behaviorally relevant timescales. We developed a paradigm for studying physiological neuronal activity through controlled stimulation of the olfactory bulb, and performed RNA-Seq transcriptome analysis of olfactory bulbs from odor-deprived and stimulated mice. We found that physiological stimulation induces large, rapid and reproducible changes in transcriptionin vivo, and that the activation of a core set of activity-regulated factors is recapitulated in anin vitromodel of neuronal stimulation. However, physiological activity did not induce global changes in post-transcriptional mRNA processing, such as AS or alternative cleavage and polyadenylation. In contrast, analysis of RNA-Seq fromin vitrostimulation models showed rapid activity-dependent changes in both transcription and mRNA processing. Our results provide the first genome-wide look at neuronal activity-dependent mRNA processing and suggest that rapid changes in AS might not be the dominant form of transcriptome alterations that take place during olfactory rodent behavior.
Gene co-expression modules underlying polymorphic and monomorphic zooids in the colonial hydrozoan,Hydractinia symbiolongicarpus
Authors: Plachetzki David C. , Sabrina Pankey M. , Johnson Brian R. , Ronne Eric J. , Kopp Artyom , Grosberg Richard K.
Published: June 2014

Advances in sequencing technology have forced a quantitative revolution in Evolutionary Biology. One important feature of this renaissance is that comprehensive genomic resources can be obtained quickly for almost any taxon, thus speeding the development of new model organisms. Here we analyze 20 RNA-seq libraries from morphologically, sexually, and genetically distinct polyp types from the gonochoristic colonial hydrozoan,Hydractinia symbiolongicarpus(Cnidaria). Analyses of these data using Weighted Gene Co-expression Networks highlights deeply conserved genetic elements of animal spermatogenesis and demonstrate the utility of these methods in identifying modules of genes that correlate with different zooid types across various statistical contrasts. RNAseq data and analytical scripts described here are deposited in publicly available databases.
Validation of methods for Low-volume RNA-seq
Authors: Combs Peter A. , Eisen Michael B.
Published: June 2014

Recently, a number of protocols extending RNA-sequencing to the single-cell regime have been published. However, we were concerned that the additional steps to deal with such minute quantities of input sample would introduce serious biases that would make analysis of the data using existing approaches invalid. In this study, we performed a critical evaluation of several of these low-volume RNA-seq protocols, and found that they performed slightly less well in metrics of interest to us than a more standard protocol, but with at least two orders of magnitude less sample required. We also explored a simple modification to one of these protocols that, for many samples, reduced the cost of library preparation to approximately $20/sample.
Maritime piracy and the cost of world trade*
Authors: Jones Stephanie
Published: June 2014

Purpose

– The aim of this study is to determine the nature and extent of the threat of global maritime piracy. The cost of global piracy has been estimated at USD15-25 billion, reaching an all-time high in 2011, remaining an ongoing threat to world trade and contributing to high commodity costs.

Design/methodology/approach

– Based on a literature review of formal and informal published sources, this exploratory and diagnostic article attempts to approximately quantify global piracy in terms of pirate activity worldwide and shipper response, and looks at global trends and some tentative economic implications.

Findings

– The overall findings are inconclusive due to unreliable and piecemeal data, but global piracy clearly impacts goods carried by sea. The piracy problem may be estimated in terms of ships and crew affected, ransoms paid, the impact on specific commodities in terms of cargoes carried and cost implications of pirate-avoiding rerouting.

Practical implications

– Pirates are getting rich, but their compatriots are poorer than ever. Countries desperate for international aid are corruptly laundering pirate ransom income and continuing to support pirate warlords. Prices are continuing to rise for consumers in all countries. Solutions to the piracy problem remain elusive, and are considered in a follow-up article, Maritime piracy – the challenge of providing long-term solutions.

Originality/value

– Most articles in this field consider specific piracy incidents in particular locations, without an overall analysis of the impact on world trade as a whole. There is a gap in the literature for an up-to-date, analytical study of maritime piracy worldwide.
Limited purpose banking (LPB) and Islamic finance
Authors: Smolo Edib , Mirakhor Abbas
Published: June 2014

Purpose

– This paper primarily aims to review and analyze a new model for Islamic finance based on Laurence J. Kotlikoff's idea of limited purpose banking (LPB). In addition, this paper aims to highlight, explain and discuss various aspects of LPB and how it suits the original aspirations of pioneer writers in Islamic finance.

Design/methodology/approach

– Based on an extensive literature review, this paper aims to highlight, explain and discuss the reform of the Islamic finance industry based on Kotlikoff's model of LPB.

Findings

– Based on a modified LPB model, Islamic financial institutions could be established to provide specific services with clear aims and objectives. These LPB Islamic financial institutions would operate in a similar way to LPB.

Research limitations/implications

– As there is no perfect plan, the proposal of this paper is far from being perfect and is open to discussions and improvements. The paper will, hopefully, spark off quite a discussion on the topic; may result in a better understanding of the model; and provide some alternative solutions to the current structurally ill financial system.

Practical implications

– The paper provides some practical ideas for a better implementation of Shari'ah principles in financial intermediation of the Islamic financial system.

Originality/value

– Kotlikoff's LPB proposal for reforming the financial system is new and has been directed to the conventional financial system. This paper represents the first attempt to apply his proposal to the Islamic finance industry.