bluuebunny/crossref_metadata_2025 huggingface dataset:
Kinetics and thermodynamics of first-order Markov chain copolymerization
Authors: Gaspard P. , Andrieux D.
Published: July 2014

We report a theoretical study of stochastic processes modeling the growth of first-order Markov copolymers, as well as the reversed reaction of depolymerization. These processes are ruled by kinetic equations describing both the attachment and detachment of monomers. Exact solutions are obtained for these kinetic equations in the steady regimes of multicomponent copolymerization and depolymerization. Thermodynamic equilibrium is identified as the state at which the growth velocity is vanishing on average and where detailed balance is satisfied. Away from equilibrium, the analytical expression of the thermodynamic entropy production is deduced in terms of the Shannon disorder per monomer in the copolymer sequence. The Mayo-Lewis equation is recovered in the fully irreversible growth regime. The theory also applies to Bernoullian chains in the case where the attachment and detachment rates only depend on the reacting monomer.
The water entry of slender axisymmetric bodies
Authors: Bodily Kyle G. , Carlson Stephen J. , Truscott Tadd T.
Published: July 2014

We present a study of the forces, velocities, and trajectories of slender (length/diameter = 10) axisymmetric projectiles using an embedded inertial measurement unit (IMU). Three nose shapes (cone, ogive, and flat) were used. Projectiles were tested at vertical and oblique impact angles with different surface treatments. The trajectory of a half-hydrophobic and half-hydrophilc case impacting vertically was compared to the trajectory of symmetrically coated projectiles impacting the free surface at oblique angles. The oblique impact cases showed significantly more final lateral displacement than the half-and-half case over the same depth. The amount of lateral displacement was also affected by the nose shape, with the cone nose shape achieving the largest lateral displacement for the oblique entry case. Instantaneous lift and drag coefficients were calculated using data from the IMU for the vertical, half-and-half, and oblique entry cases. Impact forces were calculated for each nose shape and the flat nose shape experienced the largest impulsive forces up to 37 N when impacting vertically. The impact force of the flat nose decreased for the oblique entry case. The location of the center of pressure was determined at discrete time steps using a theoretical torque model and values from the IMU. Acoustic spectrograms showed that the sound produced during the water entry event predominately arises from the pinch-off for the cone and ogive nose shapes, with additional sound production from impact for the flat nose shape. Each test run was imaged using two Photron SA3 cameras.
Assessment of subgrid-scale models with a large-eddy simulation-dedicated experimental database: The pulsatile impinging jet in turbulent cross-flow
Authors: Baya Toda Hubert , Cabrit Olivier , Truffin Karine , Bruneaux Gilles , Nicoud Franck
Published: July 2014

Large-Eddy Simulation (LES) in complex geometries and industrial applications like piston engines, gas turbines, or aircraft engines requires the use of advanced subgrid-scale (SGS) models able to take into account the main flow features and the turbulence anisotropy. Keeping this goal in mind, this paper reports a LES-dedicated experiment of a pulsatile hot-jet impinging a flat-plate in the presence of a cold turbulent cross-flow. Unlike commonly used academic test cases, this configuration involves different flow features encountered in complex configurations: shear/rotating regions, stagnation point, wall-turbulence, and the propagation of a vortex ring along the wall. This experiment was also designed with the aim to use quantitative and nonintrusive optical diagnostics such as Particle Image Velocimetry, and to easily perform a LES involving a relatively simple geometry and well-controlled boundary conditions. Hence, two eddy-viscosity-based SGS models are investigated: the dynamic Smagorinsky model [M. Germano, U. Piomelli, P. Moin, and W. Cabot, “A dynamic subgrid-scale eddy viscosity model,” Phys. Fluids A 3(7), 1760–1765 (1991)] and the σ-model [F. Nicoud, H. B. Toda, O. Cabrit, S. Bose, and J. Lee, “Using singular values to build a subgrid-scale model for large eddy simulations,” Phys. Fluids 23(8), 085106 (2011)]. Both models give similar results during the first phase of the experiment. However, it was found that the dynamic Smagorinsky model could not accurately predict the vortex-ring propagation, while the σ-model provides a better agreement with the experimental measurements. Setting aside the implementation of the dynamic procedure (implemented here in its simplest form, i.e., without averaging over homogeneous directions and with clipping of negative values to ensure numerical stability), it is suggested that the mitigated predictions of the dynamic Smagorinsky model are due to the dynamic constant, which strongly depends on the mesh resolution. Indeed, the shear-stress near the wall increases during the vortex-ring impingement leading to a less refined mesh in terms of wall units, y+. This loss of resolution induces a poor damping of the dynamic constant, which is no longer able to adjust itself to ensure the expected y3-behavior near the wall. It is shown that the dynamic constant is never small enough to properly balance the large values of the squared magnitude of the strain-rate tensor, 2SijSij. The experimental database is made available to the community upon request to the authors.
The role of spin exchange in charge transfer in low-bandgap polymer: Fullerene bulk heterojunctions
Authors: Krinichnyi V. I. , Yudanova E. I. , Denisov N. N.
Published: July 2014

Formation, relaxation and dynamics of polarons and methanofullerene anion radicals photoinitiated in poly[N-9″-hepta-decanyl-2,7-carbazole-alt-5,5-(4′,7′-di-2-thienyl-2′,1′,3′-benzothiadiazole)]:-[6,6]-phenyl-C61-butyric acid methyl ester (PCDTBT:PC61BM) bulk heterojunctions were studied mainly by light-induced EPR (LEPR) spectroscopy in wide photon energy and temperature ranges. Some polarons are pinned by spin traps whose number and depth are governed by the composite morphology and photon energy. The proximity of the photon energy and the polymer bandgap reduces the number of such traps, inhibits recombination of mobile charge carriers, and facilitates their mobility in polymer network. Spin relaxation and charge carrier dynamics were studied by the steady-state saturation method at wide range of temperature and photon energy. These processes were shown to be governed by spin exchange as well as by the photon energy. Charge transfer in the composite is governed by the polaron scattering on the lattice phonons of crystalline domains embedded into amorphous polymer matrix and its activation hopping between polymer layers. The energy barrier required for polaron interchain hopping exceeds that of its intrachain diffusion. Anisotropy of polaron dynamics in the PCDTBT:PC61BM composite is less than that of poly(3-alkylthiophenes)-based systems that evidences for better ordering of the former. Lorentzian shape of LEPR lines of both charge carriers, lower concentration of spin traps as well as behaviours of the main magnetic resonance parameters were explained by layer ordered morphology of polymer matrix.
A high-resolution imaging x-ray crystal spectrometer for high energy density plasmas
Authors: Chen Hui , Bitter M. , Hill K. W. , Kerr S. , Magee E. , Nagel S. R. , Park J. , Schneider M. B. , Stone G. , Williams G. J. , Beiersdorfer P.
Published: July 2014

Adapting a concept developed for magnetic confinement fusion experiments, an imaging crystal spectrometer has been designed and tested for HED plasmas. The instrument uses a spherically bent quartz [211] crystal with radius of curvature of 490.8 mm. The instrument was tested at the Titan laser at Lawrence Livermore National Laboratory by irradiating titanium slabs with laser intensities of 1019–1020 W/cm2. He-like and Li-like Ti lines were recorded, from which the spectrometer performance was evaluated. This spectrometer provides very high spectral resolving power (E/dE > 7000) while acquiring a one-dimensional image of the source.
Magnetic anisotropy in ultrathin Fe films on GaAs, ZnSe, and Ge (001) substrates
Authors: Tivakornsasithorn K. , Liu X. , Li X. , Dobrowolska M. , Furdyna J. K.
Published: July 2014

We discuss magnetic anisotropy parameters of ferromagnetic body-centered cubic (bcc) Fe films grown by molecular beam epitaxy (MBE) on (001) substrates of face-centered cubic (fcc) GaAs, ZnSe, and Ge. High-quality MBE growth of these metal/semiconductor combinations is made possible by the fortuitous atomic relationship between the bcc Fe and the underlying fcc semiconductor surfaces, resulting in excellent lattice match. Magnetization measurements by superconducting quantum interference device (SQUID) indicate that the Fe films grown on (001) GaAs surfaces are characterized by a very strong uniaxial in-plane anisotropy; those grown on (001) Ge surfaces have a fully cubic anisotropy; and Fe films grown on ZnSe represent an intermediate case between the preceding two combinations. Ferromagnetic resonance measurements carried out on these three systems provide a strikingly clear quantitative picture of the anisotropy parameters, in excellent agreement with the SQUID results. Based on these results, we propose that the observed anisotropy of cubic Fe films grown in this way results from the surface reconstruction of the specific semiconductor substrate on which the Fe film is deposited. These results suggest that, by controlling surface reconstruction of the substrate during the MBE growth, one may be able to engineer the magnetic anisotropy in Fe, and possibly also in other MBE-grown ferromagnetic films.
Influence of system size on the properties of a fluid adsorbed in a nanopore: Physical manifestations and methodological consequences
Authors: Puibasset Joël , Kierlik Edouard , Tarjus Gilles
Published: July 2014

Hysteresis and discontinuities in the isotherms of a fluid adsorbed in a nanopore in general hamper the determination of equilibrium thermodynamic properties, even in computer simulations. A way around this has been to consider both a reservoir of small size and a pore of small extent in order to restrict the fluctuations of density and approach a classical van der Waals loop. We assess this suggestion by thoroughly studying through Monte Carlo simulations and density functional theory the influence of system size on the equilibrium configurations of the adsorbed fluid and on the resulting isotherms. We stress the importance of pore-symmetry-breaking states that even for modest pore sizes lead to discontinuous isotherms and we discuss the physical relevance of these states and the methodological consequences for computing thermodynamic quantities.
Note: A cubic electromagnetic harvester that convert vibration energy from all directions
Authors: Han Mengdi , Qiu Guolin , Liu Wen , Meng Bo , Zhang Xiao-Sheng , Zhang Haixia
Published: July 2014

We investigate the output performance of a cubic harvester which can scavenge low-frequency vibration energy from all directions. By adjusting the size and shape of the inside magnets, higher induced voltages and output power can be achieved. The optimal magnet is found to be cubic shape with the length of 6.35 mm (25.6% volume ratio), which can generate 4.27 mV root mean square voltage and 2.45 μW average power at the frequency of 28.86 Hz and acceleration of 1.17 g. The device is also demonstrated as a self-powered tilt sensor by measuring induced voltages at different tilt angles.
Phase-mixing of Langmuir oscillations in cold electron-positron-ion plasmas
Authors: Maity Chandan
Published: July 2014

Space-time evolution of Langmuir oscillations in a cold homogeneous electron-positron-ion plasma has been analyzed by employing a straightforward perturbation expansion method, showing phase-mixing and, thus, wave-breaking of excited oscillations at arbitrary amplitudes. Within an assumption of infinitely massive ions, an approximate phase-mixing time is found to scale as ωpetmix∼[(6/δ2){(2−α)5/2/(1−α)}]1/3, where “δ” and “α” (= n0i/n0e) are the amplitude of perturbation and the ratio of equilibrium ion density to equilibrium electron density, respectively, and ωpe∼4πn0ee2/m is the electron plasma frequency. The results presented on phase-mixing of Langmuir modes in multispecies plasmas are expected to be relevant to laboratory and astrophysical environments.
Study of liquid gallium as a function of pressure and temperature using synchrotron x-ray microtomography and x-ray diffraction
Authors: Li Renfeng , Li Liangliang , Yu Tony , Wang Luhong , Chen Jiaxuan , Wang Yanbin , Cai Zhonghou , Chen Jiuhua , Rivers Mark L. , Liu Haozhe
Published: July 2014

The volume change of liquid and solid gallium has been studied as a function of pressure and temperature up to 3.02 GPa at 300 K and up to 3.63 GPa at 330 K using synchrotron x-ray microtomography combined with energy dispersive x-ray diffraction techniques. Two sets of directly measured P-V data at 300 K and 330 K were obtained from 3D tomography reconstruction data, and the corresponding isothermal bulk moduli were determined as 23.6 (0.5) GPa and 24.6 (0.4) GPa, respectively. The existence of a liquid-liquid phase transition region is proposed based on the abnormal compressibility of Ga melt at about 2.44 GPa and 330 K conditions.
Residual ferroelectricity in barium strontium titanate thin film tunable dielectrics
Authors: Garten L. M. , Lam P. , Harris D. , Maria J.-P. , Trolier-McKinstry S.
Published: July 2014

Loss reduction is critical to develop Ba1−xSrxTiO3 thin film tunable microwave dielectric components and dielectric energy storage devices. The presence of ferroelectricity, and hence the domain wall contributions to dielectric loss, will degrade the tunable performance in the microwave region. In this work, residual ferroelectricity—a persistent ferroelectric response above the global phase transition temperature—was characterized in tunable dielectrics using Rayleigh analysis. Chemical solution deposited Ba0.7Sr0.3TiO3 films, with relative tunabilities of 86% over 250 kV/cm at 100 kHz, demonstrated residual ferroelectricity 65 °C above the ostensible paraelectric transition temperature. Frequency dispersion observed in the dielectric temperature response was consistent with the presence of nanopolar regions as one source of residual ferroelectricity. The application of AC electric field for the Rayleigh analysis of these samples led to a doubling of the dielectric loss for fields over 10 kV/cm at room temperature.
Inversion layer on the Ge(001) surface from the four-probe conductance measurements
Authors: Wojtaszek Mateusz , Lis Jakub , Zuzak Rafal , Such Bartosz , Szymonski Marek
Published: July 2014

We report four-probe conductance measurements with sub-micron resolution on atomically clean Ge(001) surfaces. A qualitative difference between n-type and p-type crystals is observed. The scaling behavior of the resistance on n-type samples indicates two-dimensional current flow, while for the p-type crystal a three-dimensional description is appropriate. We interpret this in terms of the formation of an inversion layer at the surface. This result points to the surface states, i.e., dangling bonds, as the driving force behind band bending in germanium. It also explains the intrinsic character of band bending in germanium.
Resonance frequency-retuned quartz tuning fork as a force sensor for noncontact atomic force microscopy
Authors: Ooe Hiroaki , Sakuishi Tatsuya , Nogami Makoto , Tomitori Masahiko , Arai Toyoko
Published: July 2014

Based on a two-prong type quartz tuning fork, a force sensor with a high Q factor, which we call a retuned fork sensor, was developed for non-contact atomic force microscopy (nc-AFM) with atomic resolution. By cutting a small notch and attaching an AFM tip to one prong, its resonance frequency can be retuned to that of the other intact prong. In balancing the two prongs in this manner, a high Q factor (>50 000 in ultrahigh vacuum) is obtained for the sensor. An atomic resolution image of the Si(111)-7 × 7 surface was demonstrated using an nc-AFM with the sensor. The dependence of the Q factor on resonance frequency of the sensor and the long-range force between tip and sample were measured and analyzed in view of the various dissipation channels. Dissipation in the signal detection circuit turned out to be mainly limited by the total Q factor of the nc-AFM system.
Electromagnetic properties of photodefinable barium ferrite polymer composites
Authors: Sholiyi Olusegun , Lee Jaejin , Williams John D.
Published: July 2014

This article reports the magnetic and microwave properties of a Barium ferrite powder suspended in a polymer matrix. The sizes for Barium hexaferrite powder are 3–6 μm for coarse and 0.8–1.0 μm for the fine powder. Ratios 1:1 and 3:1 (by mass) of ferrite to SU8 samples were characterized and analyzed for predicting the necessary combinations of these powders with SU8 2000 Negative photoresist. The magnetization properties of these materials were equally determined and were analyzed using Vibrating Sample Magnetometer (VSM). The Thru, Reflect, Line (TRL) calibration technique was employed in determining complex relative permittivity and permeability of the powders and composites with SU8 between 26.5 and 40 GHz.
Generation of BiFeO3-Fe3O4 Janus particles based on droplet microfluidic method
Authors: Li Shasha , Yu Xiaolei , You Sujian , Cai Bo , Liu Chang , Liu Huiqin , Liu Wei , Guo Shi-Shang , Zhao Xing-Zhong
Published: July 2014

We report on the feasible generation of BiFeO3-Fe3O4 Janus particles (JPs) based on droplet microfluidic method. Utilizing laminar flow and flow-focusing in microchannels, BiFeO3 and Fe3O4 nanoparticles were separately embedded in each hemisphere of one hydrogel particle. The size of the Janus particles showed favorable uniformity at micron scale and could be precisely controlled by flow rate regulation. The magnetism and ferroelectricity of the JPs were confirmed by magnetization and polarization measurements, indicating potential in multiferroic applications.
IFNγ-induced suppression of β-catenin signaling: evidence for roles of Akt and 14.3.3ζ
Authors: Nava Porfirio , Kamekura Ryuta , Quirós Miguel , Medina-Contreras Oscar , Hamilton Ross W. , Kolegraff Keli N. , Koch Stefan , Candelario Aurora , Romo-Parra Hector , Laur Oskar , Hilgarth Roland S. , Denning Timothy L. , Parkos Charles A. , Nusrat Asma
Published: July 2014

The proinflammatory cytokine interferon γ (IFNγ ) influences intestinal epithelial cell (IEC) homeostasis in a biphasic manner by acutely stimulating proliferation that is followed by sustained inhibition of proliferation despite continued mucosal injury. β-Catenin activation has been classically associated with increased IEC proliferation. However, we observed that IFNγ inhibits IEC proliferation despite sustained activation of Akt/β-catenin signaling. Here we show that inhibition of Akt/β-catenin–mediated cell proliferation by IFNγ is associated with the formation of a protein complex containing phosphorylated β-catenin 552 (pβ-cat552) and 14.3.3ζ. Akt1 served as a bimodal switch that promotes or inhibits β-catenin transactivation in response to IFNγ stimulation. IFNγ initially promotes β-catenin transactivation through Akt-dependent C-terminal phosphorylation of β-catenin to promote its association with 14.3.3ζ. Augmented β-catenin transactivation leads to increased Akt1 protein levels, and active Akt1 accumulates in the nucleus, where it phosphorylates 14.3.3ζ to translocate 14.3.3ζ/β-catenin from the nucleus, thereby inhibiting β-catenin transactivation and IEC proliferation. These results outline a dual function of Akt1 that suppresses IEC proliferation during intestinal inflammation.
Rho1 regulates adherens junction remodeling by promoting recycling endosome formation through activation of myosin II
Authors: Yashiro Hanako , Loza Andrew J. , Skeath James B. , Longmore Gregory D.
Published: July 2014

Once adherens junctions (AJs) are formed between polarized epithelial cells they must be maintained because AJs are constantly remodeled in dynamic epithelia. AJ maintenance involves endocytosis and subsequent recycling of E-cadherin to a precise location along the basolateral membrane. In the Drosophila pupal eye epithelium, Rho1 GTPase regulates AJ remodeling through Drosophila E-cadherin (DE-cadherin) endocytosis by limiting Cdc42/Par6/aPKC complex activity. We demonstrate that Rho1 also influences AJ remodeling by regulating the formation of DE-cadherin–containing, Rab11-positive recycling endosomes in Drosophila postmitotic pupal eye epithelia. This effect of Rho1 is mediated through Rok-dependent, but not MLCK-dependent, stimulation of myosin II activity yet independent of its effects upon actin remodeling. Both Rho1 and pMLC localize on endosomal vesicles, suggesting that Rho1 might regulate the formation of recycling endosomes through localized myosin II activation. This work identifies spatially distinct functions for Rho1 in the regulation of DE-cadherin–containing vesicular trafficking during AJ remodeling in live epithelia.
Major alteration in coxsackievirus B3 genomic RNA structure distinguishes a virulent strain from an avirulent strain
Authors: Prusa Jerome , Missak Johanna , Kittrell Jeff , Evans John J. , Tapprich William E.
Published: July 2014

Coxsackievirus B3 (CV-B3) is a cardiovirulent enterovirus that utilizes a 5′ untranslated region (5′UTR) to complete critical viral processes. Here, we directly compared the structure of a 5′UTR from a virulent strain with that of a naturally occurring avirulent strain. Using chemical probing analysis, we identified a structural difference between the two 5′UTRs in the highly substituted stem-loop II region (SLII). For the remainder of the 5′UTR, we observed conserved structure. Comparative sequence analysis of 170 closely related enteroviruses revealed that the SLII region lacks conservation. To investigate independent folding and function, two chimeric CV-B3 strains were created by exchanging nucleotides 104–184 and repeating the 5′UTR structural analysis. Neither the parent SLII nor the remaining domains of the background 5′UTR were structurally altered by the exchange, supporting an independent mechanism of folding and function. We show that the attenuated 5′UTR lacks structure in the SLII cardiovirulence determinant.
Hepatic Steatosis Is Prevalent in Stillborns Delivered to Women With Diabetes Mellitus
Authors: Patel Kalyani R. , White Frances V. , Deutsch Gail H.
Published: July 2014

Objective:

Maternal diabetes is a risk factor for pregnancy complications, including stillbirth and macrosomia. Evolving data suggest that diabetes during pregnancy also has long‐term consequences for offspring, putting them at risk for obesity and the metabolic syndrome in childhood. Because nonalcoholic fatty liver disease is known to occur in adults and children with insulin resistance, we hypothesized that altered lipid metabolism in fetuses of diabetic mothers may manifest with hepatic steatosis.

Methods:

We undertook a retrospective autopsy study to compare the presence and degree of hepatic steatosis between stillborns delivered to women with pregestational or gestational diabetes mellitus (gestational age 20–40 weeks; n = 33) and age‐matched nondiabetic control stillbirth cases (n = 48), the latter enriched for maternal obesity, macrosomia, and similar cause of demise.

Results:

Histopathologic hepatic steatosis was significantly more prevalent and severe in the diabetic subjects (26/33, 78.8%) than in the controls (8/48, 16.6%) (P < 0.001). Within the diabetic cohort, the severity of steatosis was related directly to gestational age, birth weight, and liver weight, with no correlation of presence or severity of steatosis in the control group to maternal or fetal factors, including maternal body mass index or fetal macrosomia. Although macrosomic stillborns were more common in diabetic women with %hemoglobin A1c >6 and body mass index >30 kg/m2, fetal steatosis was independent of glycemic control, maternal obesity, type of diabetes, ethnicity, or fetal sex in our cohort.

Conclusions:

This study is the first to our knowledge to demonstrate a specific association between fetal hepatic steatosis and maternal diabetes.
Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes
Authors: Gilbert C. , Meik J. M. , Dashevsky D. , Card D. C. , Castoe T. A. , Schaack S.
Published: July 2014

We report the discovery of endogenous viral elements (EVEs) from Hepadnaviridae, Bornaviridae and Circoviridae in the speckled rattlesnake,
Crotalus mitchellii
, the first viperid snake for which a draft whole genome sequence assembly is available. Analysis of the draft assembly reveals genome fragments from the three virus families were inserted into the genome of this snake over the past 50 Myr. Cross-species PCR screening of orthologous loci and computational scanning of the python and king cobra genomes reveals that circoviruses integrated most recently (within the last approx. 10 Myr), whereas bornaviruses and hepadnaviruses integrated at least approximately 13 and approximately 50 Ma, respectively. This is, to our knowledge, the first report of circo-, borna- and hepadnaviruses in snakes and the first characterization of non-retroviral EVEs in non-avian reptiles. Our study provides a window into the historical dynamics of viruses in these host lineages and shows that their evolution involved multiple host-switches between mammals and reptiles.
Interspecific signalling between mutualists: food-thieving drongos use a cooperative sentinel call to manipulate foraging partners
Authors: Baigrie Bruce D. , Thompson Alex M. , Flower Tom P.
Published: July 2014

Interspecific communication is common in nature, particularly between mutualists. However, whether signals evolved for communication with other species, or are in fact conspecific signals eavesdropped upon by partners, is often unclear. Fork-tailed drongos (
Dicrurus adsimilis
) associate with mixed-species groups and often produce true alarms at predators, whereupon associating species flee to cover, but also false alarms to steal associating species' food (kleptoparasitism). Despite such deception, associating species respond to drongo non-alarm calls by increasing their foraging and decreasing vigilance. Yet, whether these calls represent interspecific sentinel signals remains unknown. We show that drongos produced a specific sentinel call when foraging with a common associate, the sociable weaver (
Philetairus socius
), but not when alone. Weavers increased their foraging and decreased vigilance when naturally associating with drongos, and in response to sentinel call playback. Further, drongos sentinel-called more often when weavers were moving, and weavers approached sentinel calls, suggesting a recruitment function. Finally, drongos sentinel-called when weavers fled following false alarms, thereby reducing disruption to weaver foraging time. Results therefore provide evidence of an ‘all clear’ signal that mitigates the cost of inaccurate communication. Our results suggest that drongos enhance exploitation of a foraging mutualist through coevolution of interspecific sentinel signals.
Error-prone polymerase activity causes multinucleotide mutations in humans
Authors: Harris Kelley , Nielsen Rasmus
Published: July 2014

About 2% of human genetic polymorphisms have been hypothesized to arise via multinucleotide mutations (MNMs), complex events that generate SNPs at multiple sites in a single generation. MNMs have the potential to accelerate the pace at which single genes evolve and to confound studies of demography and selection that assume all SNPs arise independently. In this paper, we examine clustered mutations that are segregating in a set of 1092 human genomes, demonstrating that the signature of MNM becomes enriched as large numbers of individuals are sampled. We estimate the percentage of linked SNP pairs that were generated by simultaneous mutation as a function of the distance between affected sites and show that MNMs exhibit a high percentage of transversions relative to transitions, findings that are reproducible in data from multiple sequencing platforms and cannot be attributed to sequencing error. Among tandem mutations that occur simultaneously at adjacent sites, we find an especially skewed distribution of ancestral and derived alleles, with GC → AA, GA → TT, and their reverse complements making up 27% of the total. These mutations have been previously shown to dominate the spectrum of the error-prone polymerase Pol ζ, suggesting that low-fidelity DNA replication by Pol ζ is at least partly responsible for the MNMs that are segregating in the human population. We develop statistical estimates of MNM prevalence that can be used to correct phylogenetic and population genetic inferences for the presence of complex mutations.
Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
Authors: Picelli Simone , Björklund Åsa K. , Reinius Björn , Sagasser Sven , Winberg Gösta , Sandberg Rickard
Published: July 2014

Massively parallel DNA sequencing of thousands of samples in a single machine-run is now possible, but the preparation of the individual sequencing libraries is expensive and time-consuming. Tagmentation-based library construction, using the Tn5 transposase, is efficient for generating sequencing libraries but currently relies on undisclosed reagents, which severely limits development of novel applications and the execution of large-scale projects. Here, we present simple and robust procedures for Tn5 transposase production and optimized reaction conditions for tagmentation-based sequencing library construction. We further show how molecular crowding agents both modulate library lengths and enable efficient tagmentation from subpicogram amounts of cDNA. The comparison of single-cell RNA-sequencing libraries generated using produced and commercial Tn5 demonstrated equal performances in terms of gene detection and library characteristics. Finally, because naked Tn5 can be annealed to any oligonucleotide of choice, for example, molecular barcodes in single-cell assays or methylated oligonucleotides for bisulfite sequencing, custom Tn5 production and tagmentation enable innovation in sequencing-based applications.
In situ microfluidic dialysis for biological small-angle X-ray scattering
Authors: Skou Magda , Skou Søren , Jensen Thomas G. , Vestergaard Bente , Gillilan Richard E.
Published: July 2014

Owing to the demand for low sample consumption and automated sample changing capabilities at synchrotron small-angle X-ray (solution) scattering (SAXS) beamlines, X-ray microfluidics is receiving continuously increasing attention. Here, a remote-controlled microfluidic device is presented for simultaneous SAXS and ultraviolet absorption measurements during protein dialysis, integrated directly on a SAXS beamline. Microfluidic dialysis can be used for monitoring structural changes in response to buffer exchange or, as demonstrated, protein concentration. By collecting X-ray data during the concentration procedure, the risk of inducing protein aggregation due to excessive concentration and storage is eliminated, resulting in reduced sample consumption and improved data quality. The proof of concept demonstrates the effect of halted or continuous flow in the microfluidic device. No sample aggregation was induced by the concentration process at the levels achieved in these experiments. Simulations of fluid dynamics and transport properties within the device strongly suggest that aggregates, and possibly even higher-order oligomers, are preferentially retained by the device, resulting in incidental sample purification. Hence, this versatile microfluidic device enables investigation of experimentally induced structural changes under dynamically controllable sample conditions.
Neutron and synchrotron probes in the development of Co–Re-based alloys for next generation gas turbines with an emphasis on the influence of boron additives
Authors: Mukherji D. , Gilles R. , Karge L. , Strunz P. , Beran P. , Eckerlebe H. , Stark A. , Szentmiklosi L. , Mácsik Z. , Schumacher G. , Zizak I. , Hofmann M. , Hoelzel M. , Rösler J.
Published: July 2014

Nickel-based superalloys are the materials of choice in the hot section of current gas turbines, but they are reaching temperature limits constrained by their melting temperature range. Co–Re alloy development was prompted by a search for new materials for future gas turbines, where the temperature of application will be considerably higher. Addition of the very high melting point refractory metal Re to Co can increase the melting range of Co alloys to much higher temperatures than the commercial Co alloys in use today. The alloy development strategy is first discussed very briefly. In this program, model ternary and quaternary compositions were studied in order to develop a basic understanding of the alloy system.In situneutron and synchrotron measurements (small and wide angle) at high temperatures were extensively used for this purpose and some selected results from thein situmeasurements are presented. In particular, the effect of boron doping in Co–Re–Cr alloys and the stability of the TaC precipitates at high temperatures were investigated. A fine dispersion of TaC precipitates strengthens some Co–Re alloys, and their stability at the application temperature is critical for the long-term creep properties.
TomoPy: a framework for the analysis of synchrotron tomographic data
Authors: Gürsoy Dogˇa , De Carlo Francesco , Xiao Xianghui , Jacobsen Chris
Published: July 2014

Analysis of tomographic datasets at synchrotron light sources (including X-ray transmission tomography, X-ray fluorescence microscopy and X-ray diffraction tomography) is becoming progressively more challenging due to the increasing data acquisition rates that new technologies in X-ray sources and detectors enable. The next generation of synchrotron facilities that are currently under design or construction throughout the world will provide diffraction-limited X-ray sources and are expected to boost the current data rates by several orders of magnitude, stressing the need for the development and integration of efficient analysis tools. Here an attempt to provide a collaborative framework for the analysis of synchrotron tomographic data that has the potential to unify the effort of different facilities and beamlines performing similar tasks is described in detail. The proposed Python-based framework is open-source, platform- and data-format-independent, has multiprocessing capability and supports procedural programming that many researchers prefer. This collaborative platform could affect all major synchrotron facilities where new effort is now dedicated to developing new tools that can be deployed at the facility for real-time processing, as well as distributed to users for off-site data processing.
Customer requirements based ERP customization using AHP technique
Authors: Parthasarathy Sudhaman , Daneva Maya
Published: July 2014

Purpose

– Customization is a difficult task for many organizations implementing enterprise resource planning (ERP) systems. The purpose of this paper is to develop a new framework based on customers’ requirements to examine the ERP customization choices for the enterprise. The analytical hierarchy process (AHP) technique has been applied complementarily with this framework to prioritize ERP customization choices.

Design/methodology/approach

– Based on empirical literature, the paper proposed an ERP customization framework anchored on the customer's requirements. A case study research method was used to evaluate the applicability of the framework in a real-life setting. In a case study with 15 practitioners working on the vendor's and the client's sides in an ERP implementation, the paper applied the framework jointly with the AHP technique to prioritize the feasible customization choices for ERP implementation.

Findings

– The paper demonstrates the applicability of the framework in identifying the various feasible choices for the client organization to consider when they decide to customize their selected ERP product.

Research limitations/implications

– Further case studies need to be carried out in various contexts to acquire knowledge about the generalizability of the observations. This will also contribute to refining the proposed ERP customization framework.

Practical implications

– Very few literature sources suggest methods for exploring and evaluating customization options in ERP projects from requirements engineering perspective. The proposed framework helps practitioners and consultants anchor the customization decisions on the customer's requirements and use a well-established prioritization technique, AHP, to identify the feasible customization choices for the implementing enterprise.

Originality/value

– No previously published research studies provide an approach to prioritize customization choices for ERP anchored on the customer's requirements.
An ECRS-based line balancing concept: a case study of a frozen chicken producer
Authors: Ongkunaruk Pornthipa , Wongsatit Wimonrat
Published: July 2014

Purpose

– The purpose of this paper is to improve the productivity of a large-sized frozen chicken manufacturer in Thailand. It analyses the production process based on work study principles and identifies the bottleneck operation. It develops three models for the chicken preparation process.

Design/methodology/approach

– First, analyse the current production system by collecting the cycle time of all operations in the production process based on work study principles. Then, design the production network and identify the bottleneck operation. After that, three methods – based on line balancing (LB), theory of constraints, and JIT concepts or ECRS (eliminate, combine, rearrange and simplify) – are proposed and implemented in the actual production line.

Findings

– With the ECRS concept, the authors implement combine by combining two stations into one station, such as handling and weighing, or weighing batter and mixing it with chicken. Then, Simplify is implemented at job E, or transporting chicken using a cart instead of walking. This method can improve the cycle time and reduce the number of employees. It can increase the line efficiency by up to 94.20 per cent, reduce the number of employees by 14 persons, and reduce the labour cost by 356,160 baht/year.

Originality/value

– Most agro-industry manufacturing processes are labour intensive. Thus, production LB can help increase productivity and reduce costs. The authors found that the case study company designed the production line without aligning it with the production network. A simple improvement can be made by adjusting the sequence of the work. In addition, the current production line was not lean. Implementation of the ECRS concept to improve production can reduce the waiting time and simplify the job.
Business process redesign project success: the role of socio-technical theory
Authors: Xiang Junlian , Archer Norm , Detlor Brian
Published: July 2014

Purpose

– The purpose of this paper is to seek to advance business process redesign (BPR) project research through the generation and testing of a new research model that utilizes formative constructs to model complex BPR project implementation issues. Instead of looking at management principles, the paper examines the activities of improving business processes from the project perspective.

Design/methodology/approach

– A survey of 145 managers and executives from medium and large-sized USA and Canadian companies was used to validate the model.

Findings

– The model, based on socio-technical theory, includes three implementation components (change management, process redesign, and information and communication technology infrastructure improvement), and links the effects of these components to BPR project outcomes. The empirical findings indicated that all three implementation components had a significant impact on BPR project success, with change management having the greatest effect. Interestingly, the results also showed that productivity improvement was no longer the main focus of companies carrying out BPR projects; instead, improvement in operational and organizational quality was more important.

Research limitations/implications

– The main limitation of this study is its generalizability with respect to company size and organizational culture. The sample in this study was drawn from medium- and large-sized companies in Canada and the USA, but small-sized organizations were excluded from this study due to their distinct features (e.g. superior flexibility or ability to reorient themselves quickly). Also, this study controlled the variable of organizational culture by limiting respondents to Canada and US companies. It would be very interesting to investigate BPR project implementations in other countries where the organizational working culture may be different.

Practical implications

– Based on the findings of this study, BPR practitioners can refer to the three BPR project implementation components and then prioritize and sequence the tasks in a BPR project to achieve their preset BPR goals.

Originality/value

– This is the first study which utilizes formative constructs to validate the important BPR project components.
A cross-cultural study of managerial skills and effectiveness
Authors: C. Hoffman Richard , M. Shipper Frank , A. Davy Jeanette , M. Rotondo Denise
Published: July 2014

Purpose

– The purpose of this study is to examine the relationship between managerial skills and effectiveness in a cross-cultural setting to determine their applicability.

Design/methodology/approach

– Data from 7,606 managers in 5 countries from a large multinational firm were analyzed using structural equation modeling to assess all relationships simultaneously and reduce error effects.

Findings

– The results support the cross-cultural validity of the model of managerial skills-effectiveness. Few cross-cultural differences were found. Interactive skills had greater positive impact on attitudes than initiating skills. Pressuring skills had a negative impact on attitudes. None of the skill sets were related to job performance.

Research limitations/implications

– Using a single firm and industry to control for other cultural levels may limit the generalizability of the results. Only three skill sets were assessed and one coarse-grained measure of culture was used. These factors may account for the few cultural differences observed.

Practical implications

– Training programs for managers going overseas should develop both interactive and initiating skills sets, as both had a positive impact on attitudes across cultures.

Originality/value

– The model of managerial skills and effectiveness was validated across five cultures. The use of structural equation modeling ensures that the results are not an artifact of the measures and represents a more direct test for cross-cultural differences. Managing successfully across cultures may require fewer unique skills, with more emphasis placed on using basic management skills having positive impact.
Information security governance implementation within Ghanaian industry sectors
Authors: Yaokumah Winfred
Published: July 2014

Purpose

– The purpose of this study is to assess the levels of information security governance (ISG) implementation among major Ghanaian industry sectors. The intent is to benchmark inter-industry sector ISG implementation and to identify areas that may require improvement.

Design/methodology/approach

– Random sampling strategy was used, and data were collected via Web survey. The data analysis utilized a one-way analysis of variance to determine the differences in means of the levels of implementation of ISG focus areas among five main industry sectors.

Findings

– The results showed that, as a whole, all the industry sectors have only partially implemented ISG. In particular, there existed statistical significant differences in ISG implementation among the industry sectors. Ranking ISG implementation, Financial Institutions were close to completion, Utility Companies, Others (Information Technology, Oil and Gas, Manufacturing) and Public Services had PI ISG and health care and educational institutions were at the planning stages. The result also revealed that all the industry sectors made marginal effort trying to align information security to business strategy, and performance measurement remained the least implemented focus area.

Originality/value

– Organizational leaders could use these findings to benchmark industry sectors’ ISG implementation, which could lead to competitiveness. Again, international enterprises that do businesses with these industry sectors would better understand the level of involvement of the top executives in governing information security toward the protection of valuable information assets.
Understanding the roles of loss-premium comparisons and insurance coverage in customer acceptance of insurance claim frauds
Authors: Tseng Lu-Ming , Kang Yue-Min , Chung Chi-Erh
Published: July 2014

Purpose

– The purpose of this paper is to examine the impacts of loss-premium comparisons (loss-premium comparison refers to the amount of an actual loss compared to the premium level) and insurance coverage on customer acceptance of insurance claim frauds, based on Adams’ equity theory. Customer perceptions of insurance frauds have been studied in recent years.

Design/methodology/approach

– A questionnaire was used as an instrument in the research. The hypotheses were tested using a 3 loss-premium comparisons (the actual loss amount was lower than, or equal to or higher than the annual premium) × 2 insurance coverage (the loss is covered or not covered by the insurance policy) experimental design in a claim application context.

Findings

– The results showed that loss-premium comparisons and insurance coverage significantly affect the final claim amounts. According to the results, age and education may relate to customer acceptance of insurance claim frauds.

Originality/value

– This study proposed a first empirical investigation into the relationship between loss-premium comparisons and customer ethical decision making in the customer frauds. Insurance coverage is also specifically considered in the study.