bluuebunny/crossref_metadata_2025 huggingface dataset:
Charge mobility in molecules: Charge fluxes from second derivatives of the molecular dipole
Authors: Galimberti Daria , Milani Alberto , Castiglioni Chiara
Published: April 2013

On the basis of the analytical model previously suggested by Dinur, we discuss here a method for the calculation of vibrational charge fluxes in planar molecules, obtained as numerical second derivatives of the molecular dipole moment. This model is consistent with the partitioning of the atomic polar tensors into atomic charge and charge fluxes according to the Equilibrium Charges-Charge Fluxes model and it is directly related to experimentally measurable quantities such as IR intensities. On the basis of density functional theory calculations carried out for several small benchmark molecules, the complete set of charge fluxes is calculated for each molecule and compared with the approximated flux parameters previously derived and reported in the past literature. The degree of localization of charge fluxes is investigated and discussed; in addition, some approximations are analyzed in order to verify the applicability of the method to large and/or non-planar molecules, aimed at obtaining a description of the electron charge mobility in different molecular environments.
Structural, electronic, and linear optical properties of organic photovoltaic PBTTT-C14 crystal
Authors: Li Long-Hua , Kontsevoi Oleg Y. , Rhim S. H. , Freeman Arthur J.
Published: April 2013

Poly(2,5-bis(3-tetradecylthiophen-2yl)thieno(3,2-b)thiophene) (PBTTT-C14) is an important electro-optical polymer, whose three-dimensional crystal structure is somewhat ambiguous and the fundamental electronic and linear optical properties are not well known. We carried out first-principles calculations to model the crystal structure and to study the effect of side-chains on the physical structure and electronic properties. Our calculations suggest that the patterns of side-chain has little direct effect on the valence band maximum and conduction band minimum but they do have impact on the bandgap through changing the π-π stacking distance. By examining the band structure and wave functions, we conclude that the fundamental bandgap of the PBTTT-C14 crystal is determined by the conduction band energy at the Q point. The calculations indicate that the bandgap of PBTTT-C14 crystal may be tunable by introducing different side-chains. The significant peak in the imaginary part of the dielectric function arises from transitions along the polymer backbone axis, as determined by the critical-point analysis and the large optical transition matrix elements in the direction of the backbone.
Numerical studies of the effects of large neutrally buoyant particles on the flow instability and transition to turbulence in pipe flow
Authors: Yu Zhaosheng , Wu Tenghu , Shao Xueming , Lin Jianzhong
Published: April 2013

The effects of large neutrally buoyant particles on the flow instability and turbulence transition in pipe flow are investigated with the fictitious domain method. The periodic boundary condition is introduced in the streamwise direction. The work comprises two parts. In the first part, the pressure gradient is kept constant, and the purpose is to study the particle-induced flow instability. In our previous study [X. Shao, Z. Yu, and B. Sun, Phys. Fluids 20, 103307 (2008)10.1063/1.3005427], it was observed that a particle of a/R = 0.1 (a and R being the radii of the particle and the tube, respectively) induced the flow structure characterized by two pairs of weak and stable streamwise vortices at the Reynolds number of 1000. In the present study, our results show that the flow structure loses stability at the Reynolds number of 1500. However, it is interesting that the system eventually reaches a stable state: the particle spirals forward along the tube wall, accompanied by a stable flow structure for the case of one single particle in the computational domain. In the second part of the present study, the flow flux is kept constant, and the purpose is to examine the effects of particles on the critical Reynolds number based on the mean velocity. Our results show that large particles trigger the turbulence transition at low particle volume fractions, but delay the transition as the particle volume fraction exceeds a critical value, in agreement with the previous experimental observation [J.-P. Matas, J. F. Morris, and É. Guazzelli, Phys. Rev. Lett. 90, 014501 (2003)10.1103/PhysRevLett.90.014501].
Magnonic holographic devices for special type data processing
Authors: Khitun Alexander
Published: April 2013

In this work, we consider the possibility of building magnetic analog logic devices utilizing spin wave interference for special task data processing. As an example, we consider a multi-terminal magnonic matrix switch comprising multiferroic elements and a two-dimensional grid of magnetic waveguides connected via four-terminal cross-junctions. The multiferroic elements are placed on the periphery of the switch and used as input/output ports for signal conversion among the electric and magnetic domains. Data processing is accomplished via the use of spin wave interference within the magnonic matrix. We present the results of numerical modeling illustrating device operation for pattern matching, finding the period of the data string, and image processing. We also present the results of numerical modeling showing the device capabilities as a magnetic holographic memory. Magnonic holographic devices are of great potential to complement the conventional general-type processors in special task data processing and may provide a new direction for functional throughput enhancement. According to estimates, magnonic holographic devices can provide up to 1 Tb/cm2 data storage density and data processing rate exceeding 1018 bits/s/cm2. The physical limitations and practical challenges of the proposed approach are discussed.
Kondo effect and non-Fermi liquid behavior in metallic glasses containing Yb, Ce, and Sm
Authors: Huang B. , Yang Y. F. , Wang W. H.
Published: April 2013

The low temperature properties of metallic glasses containing different concentrations of ytterbium, cerium, and samarium are studied. It is found that the Kondo effect caused by exchange interactions between the conduction and 4f electrons and non-Fermi liquid behavior appear in the strongly disordered alloys. We study the origins for these unique features and demonstrate that the found Kondo effect is inherited from the crystalline counterparts. The results might have significance on investigating the strong electron-electron interaction systems with structural disorder and be helpful for designing new metallic glasses with functional properties.
Quantitative analysis of the quantum dot superlattice by high-resolution x-ray diffraction
Authors: Faleev N. N. , Honsberg C. , Punegov V. I.
Published: April 2013

A new high-resolution x-ray diffraction approach for quantitative analysis of superlattice structures (SLs) with self-assembled quantum dots (QDs) was developed. For numerical simulations of the 2D angular distribution of diffracted x-ray radiation, both the coherent and diffuse scattering components have been calculated. Direct comparison of simulated patterns and experimental results revealed good agreement of the calculated intensity distribution with experimental reciprocal space maps for the superlattice GaAs(001)-AlGaAs-{InAs QDs-GaAs}SL with 20 periods of quantum dots. The simulation procedure allows one to obtain data about the shape, average size, elastic strains around the QDs, average density of the QDs, the presence of short- or long-range order in the arrangement of QDs in the semiconducting matrix, the vertical and lateral correlation lengths of the ensemble of quantum dots, and the parameters of the intermediate GaAs and AlGaAs layers.
Energetic proton generation from intense Coulomb explosion of large-size ethane clusters
Authors: Li Song , Zhou Zili , Tian Ye , Lu Haiyang , Wang Wentao , Ju Jingjing , Li Hongyu , Xu Yi , Leng Yuxin , Ni Guoquan , Wang Cheng , Liu Jiansheng
Published: April 2013

An experimental investigation is performed on the interaction of intense femtosecond laser pulses at the intensity of 6 × 1017 W/cm2 (55 fs, 160 mJ at 800 nm) with ethane cluster (C2H6)N jets prepared under the backing pressure of 30 bars at room temperature (298 K). The experiment results indicate the generation of energetic protons, whose average and maximum kinetic energies are 12.2 and 138.1 keV, respectively, by Coulomb explosion of (C2H6)N clusters. (C2H6)N clusters of 5 nm in radius are generated in the experiment, which are 1.7 times larger than that of (CH4)N clusters prepared in the same conditions. Empirical estimation suggests that (C2H6)N clusters with radius of about 9.6 nm can be prepared at 80-bars backing pressure at 308 K. While (C2H6)N clusters of so large size are irradiated by sufficiently intense laser pulses, the average energy of protons will be increased up to 50 keV. It is inferred that such large-size deuterated ethane clusters (C2D6)N will favor more efficient neutron generation due to the significant increase of the D-D nuclear reaction cross section in laser-driven cluster nuclear fusion.
Ion holes in the hydrodynamic regime in ultracold neutral plasmas
Authors: McQuillen P. , Castro J. , Strickler T. , Bradshaw S. J. , Killian T. C.
Published: April 2013

We describe the creation of localized density perturbations, or ion holes, in an ultracold neutral plasma in the hydrodynamic regime, and show that the holes propagate at the local ion acoustic wave speed. We also observe the process of hole splitting, which results from the formation of a density depletion initially at rest in the plasma. One-dimensional, two-fluid hydrodynamic simulations describe the results well. Measurements of the ion velocity distribution also show the effects of the ion hole and confirm the hydrodynamic conditions in the plasma.
Self-consistent simulations of nonlinear magnetohydrodynamics and profile evolution in stellarator configurations
Authors: Schlutt M. G. , Hegna C. C. , Sovinec C. R. , Held E. D. , Kruger S. E.
Published: April 2013

Self-consistent extended MHD framework is used to investigate nonlinear macroscopic dynamics of stellarator configurations. In these calculations, initial conditions are given by analytical 3-D vacuum solutions. Finite beta discharges in a straight stellarator are simulated. Vacuum magnetic fields are applied to produce stellarator-like rotational transform profiles with iota(0) ≤ 0.5 and iota(0) ≥ 0.5. The vacuum magnetic fields are either helically symmetric or spoiled by the presence of magnetic harmonics of incommensurate helicity. As heat is added to the system, pressure-driven instabilities are excited when a critical β is exceeded. These instabilities may grow to large amplitude and effectively terminate the discharge, or they may saturate nonlinearly as the configuration evolves. In all of these studies, anisotropic heat conduction is allowed with κ∥/κ⊥=104−107.
Structural and magnetic properties of epitaxial CrO2 thin films grown on TiO2 (001) substrates
Authors: Zhang Xueyu , Zhong Xing , Visscher P. B. , LeClair Patrick R. , Gupta Arunava
Published: April 2013

The structural and magnetic properties of epitaxial CrO2 thin films grown on (001)-oriented TiO2 substrates by atmospheric pressure chemical vapor deposition are investigated. Due to the competition between demagnetization and a relatively weak perpendicular magnetocrystalline anisotropy, the deposited CrO2 (001) films exhibit magnetic properties that are significantly different from CrO2 (100) and CrO2 (110) films grown on TiO2 substrates. Based on the thickness dependence of M-H curves, a surface anisotropy is confirmed to exist, likely originating from strain in the film. The out-of-plane hysteresis curves can be well described by a distribution of effective anisotropy that may be due to a varying local demagnetizing field and a distribution of strain across the film. For the in-plane magnetization, the hysteresis curves are consistent with stripe or vortex domain structures of an almost closed flux configuration at remanence.
Optical absorption and photoelectrochemical performance enhancement in Si tube array for solar energy harvesting application
Authors: Zhang Ying , Wang Hui , Liu Zhen , Zou Bin , Duan Chunyang , Yang Tian , Zhang Xiujuan , Zheng Caijun , Zhang Xiaohong
Published: April 2013

We studied large-scale fabrication and photovoltaic properties of Si tube array (SiTA) for solar energy harvesting application. The SiTA is fabricated with photolithography by using Poisson spot effect, followed by investigating its light absorption properties and photoelectrochemical performance to compare its solar energy harvesting property with the well studied Si hole and Si pillar array. It was found that SiTA has the highest onset potential and photocurrent among the three Si micro/nanostructures because of its “hole-in-pillar” hierarchal structures. The result suggests an alternative strategy in enhancing the efficiency of Si photovoltaic devices using this hierarchal structure.
Atomic simulation of the formation and mechanical behavior of carbon nanoscrolls
Authors: Song H. Y. , Geng S. F. , An M. R. , Zha X. W.
Published: April 2013

The process of the formation of a carbon nanoscroll (CNS) from a planar monolayer graphene, initiated by a single-walled carbon nanotube (SWCNT), is investigated by using molecular dynamics simulations. The results show that once the radius of the SWCNT is above a critical value, the SWCNT can activate and guide the rolling of the graphene, and finally form a CNS with the SWCNT inside. During the process of forming the CNS, the van der Waals force plays an important role. The influences of nickel atoms on the formation and mechanical behavior of the CNS are also studied. The results show that there is no appreciable difference between the self scrolling of an ideal graphene (without nickel atoms) and that of a graphene with nickel atoms except for the different times required for the scrolling. The simulations also indicate that adding nickel atoms to two opposite edges (paralleling to the SWCNT axis) of the graphene before rolling is an effective strategy to increase the structural stability and critical buckling load of the CNS.
Current transients in organic field effect transistors
Authors: Juška Gytis , Nekrašas Nerijus , Genevičius Kristijonas , Pivrikas Almantas
Published: April 2013

In this work the detailed charging and extraction current transients in the channel of organic field effect transistors are presented. This allows for precise estimation of the charge carrier mobility along the channel and in the direction perpendicular to the layer. The charge carrier mobility is experimentally obtained by various methods: from the extraction transients (in small charge and space charge limited current modes) as well as from the duration of the gate charging. The results are in good agreement with the results obtained by steady state current, photogenerated carrier extraction by linearly increasing voltage, and time-of-flight.
High contrast ion acceleration at intensities exceeding 1021 Wcm−2
Authors: Dollar F. , Zulick C. , Matsuoka T. , McGuffey C. , Bulanov S. S. , Chvykov V. , Davis J. , Kalinchenko G. , Petrov G. M. , Willingale L. , Yanovsky V. , Maksimchuk A. , Thomas A. G. R. , Krushelnick K.
Published: April 2013

Ion acceleration from short pulse laser interactions at intensities of 2×1021Wcm−2 was studied experimentally under a wide variety of parameters, including laser contrast, incidence angle, and target thickness. Trends in maximum proton energy were observed, as well as evidence of improvement in the acceleration gradients by using dual plasma mirrors over traditional pulse cleaning techniques. Extremely high efficiency acceleration gradients were produced, accelerating both the contaminant layer and high charge state ions from the bulk of the target. Two dimensional particle-in-cell simulations enabled the study of the influence of scale length on submicron targets, where hydrodynamic expansion affects the rear surface as well as the front. Experimental evidence of larger electric fields for sharp density plasmas is observed in simulation results as well for such targets, where target ions are accelerated without the need for contaminant removal.
Orbital-selective single molecule rectifier on graphene-covered Ru(0001) surface
Authors: Lei Shulai , Feng Wei , Li Bin , Li Qunxiang , Zhao Aidi , Wang Bing , Yang Jinlong , Hou J. G.
Published: April 2013

We demonstrate that the tunable molecule-substrate interaction offers possibility to realize a single cobalt phthalocyanine (CoPc) molecule rectifier. CoPc molecule shows a prominent rectifying effect at about −0.30 eV when a monolayer graphene (MG) is intercalated between CoPc and Ru(0001) substrate. First-principles calculations show that CoPc molecule couples with MG/Ru(0001) substrate mainly through the dz2 orbital of Co atom. The tunneling between CoPc molecule and MG/Ru(0001) substrate is mainly intermediated by the Co-dz2 orbital locating at −0.35 eV. The resonant tunneling through this single orbital gives rise to the abrupt current enhancement and hence the rectifying effect.
Perceived Relative Distance Depends on the Size Ratio of Targets in Photographs
Authors: Takezawa Tomomi
Published: April 2013

Focussing on the relationship between distance perception in photographs and the image sizes of the targets on the photographic surface, it is shown that the perceived relative distances between near and far targets depends on their image size ratios. Two targets of the same physical size were placed at fixed distances from each other and their photographs were taken. The image size of the near target was kept constant and the size ratio of the far target image was controlled by manipulating the camera-to-target distances appropriate to the focal lengths of the lenses. Forty undergraduates viewed the photographs and placed an actual target at the same relative distance to the near target as seen in the photographs. The results showed that the smaller the size ratios, the larger the perceived relative distances even when the actual relative distances remained the same. In addition, the perceived relative distance was smaller than the actual relative distance even in the condition where the retinal sizes of the two target images matched the retinal sizes of the actual targets seen from the camera position. However, it was found that the perceived relative distance could approximate the actual relative distance if the size ratio were further reduced.
Olfaction in the Autism Spectrum
Authors: Galle Sara A , Courchesne Valérie , Mottron Laurent , Frasnelli Johannes
Published: April 2013

The autism spectrum (AS) is characterised by enhanced perception in vision and audition, described by the enhanced perceptual functioning (EPF) model. This model predicts enhanced low-level (discrimination of psychophysical dimensions), and mid- and high-level (pattern detection and identification) perception. The EPF model is here tested for olfaction by investigating olfactory function in autistic and Asperger participants. Experiment 1 targeted higher-order olfactory processing by assessing olfactory identification in nine Asperger, ten autistic, and eleven typically developed individuals. Experiment 2 focused on low-level olfactory processing; we assessed odour detection thresholds and odour discrimination in five Asperger, five autistic, and five typically developed males. Olfactory identification was impaired in autistic participants relative to control and Asperger participants. Typical performance in low-level olfactory processing suggests that neural mechanisms involved in the perceptual phenotype of AS do not affect structures implicated in olfactory processing. Reduced olfactory identification is limited to autistic participants who displayed speech delay and may be due to a reduced facility to use verbal labels. The apparent absence of enhanced olfactory perception of AS participants distinguishes the olfactory system from the other sensory modalities and might be caused by the absence of an obligatory thalamic relay.
Ranking Fluctuating Asymmetry in a Dot Figure and the Significant Impact of Imagining a Face
Authors: Neby Magne , Folstad Ivar
Published: April 2013

Fluctuating asymmetry and averageness is correlated with our perception of beauty in human faces. Yet, whether deviations of centrality in the positioning of the eyes, the nose, and the mouth have different effects on our perception of asymmetry in a holistic human face, is still uncertain. In this study we aimed to test the relative effect of decentralising the horizontal position of three sets of paired dots representing eyes, nostrils, or mouth from the vertical midline of ambiguous dot figures, vaguely resembling a face. The figures were ranked according to perceived asymmetry by human observers. When associating the figures with non-facial objects (eg a butterfly), none of the figures' rank distribution differed from each other. However, when observers imagined the figures to represent a human face, the figure with the decentralised pair of dots representing the nostrils was significantly ranked as more asymmetric than the other figures. This result provides indications that the brain may deal with information about facial asymmetry and averageness heavily depending on the centrality of the nasal region.
Face Recognition in Emotional Scenes: Observers Remember the Eye Shape but Forget the Nose
Authors: Ryan Kaitlin F , Schwartz Noah Z
Published: April 2013

Face recognition is believed to be a highly specialized process that allows individuals to recognize faces faster and more accurately than ordinary objects. However, when faces are viewed in highly emotional contexts, the process becomes slower and less accurate. This suggests a change in recognition strategy compared to recognition in non-arousing contexts. Here we explore this finding by using a novel paradigm to determine which face dimensions are most important for recognizing faces that were initially encoded in highly emotional contexts. Participants were asked to recognize faces from a 3-alternative display after viewing a similar face that was embedded in either a neutral, positive, or negative emotional scene. Results showed that individuals rely on eye shape when recognizing faces that were encoded while embedded in either positive or negative emotional contexts, and ignore nose shape when recognizing faces that were encoded while embedded in negative emotional scenes. The findings suggest that, after encoding that face during heightened emotional arousal, individuals are more likely to commit errors when identifying a face on the basis of nose shape, and less likely to commit errors when identifying a face on the basis of eye shape.
‘Classical’ and ‘Abnormal’ Bonding in Tin (II) N-Heterocyclic Carbene Complexes
Authors: Turbervill Robert S. P. , Goicoechea Jose M.
Published: April 2013

Reaction of Sn(OTf)2 (OTf– = OSO2CF3–) with one and two equivalents of the N-heterocyclic carbene (NHC) 1,3-bis(2,6-diisopropylphenyl)-imidazol-2-ylidene (IPr) yielded the complexes [Sn(IPr)(OTf)2] (1) and [Sn(IPr)(aIPr)(OTf)][OTf] (2), respectively. Both species were characterised by single crystal X-ray diffraction, multi-element NMR spectroscopy, and elemental analysis. Both compounds display an NHC ligand bonded to the tin(ii) metal centre via the C2 carbon in a ‘classical’ mode, while 2 also contains an ‘abnormal’ C4/C5-bonded carbene (aIPr). These observations highlight the subtle steric and electronic effects affecting the coordination modes of these ligands. Solution phase NMR experiments on 1 and 2 reveal complex behaviour resulting in the protonation of the IPr ligands to yield the 1,3-bis(2,6-diisopropylphenyl)-imidazolium cation via an unidentified reaction mechanism.
Synaptopodin regulates denervation-induced homeostatic synaptic plasticity
Authors: Vlachos Andreas , Ikenberg Benno , Lenz Maximilian , Becker Denise , Reifenberg Kurt , Bas-Orth Carlos , Deller Thomas
Published: April 2013

Synaptopodin (SP) is a marker and essential component of the spine apparatus (SA), an enigmatic cellular organelle composed of stacked smooth endoplasmic reticulum that has been linked to synaptic plasticity. However, SP/SA-mediated synaptic plasticity remains incompletely understood. To study the role of SP/SA in homeostatic synaptic plasticity we here used denervation-induced synaptic scaling of mouse dentate granule cells as a model system. This form of plasticity is of considerable interest in the context of neurological diseases that are associated with the loss of neurons and subsequent denervation of connected brain regions. In entorhino-hippocampal slice cultures prepared from SP-deficient mice, which lack the SA, a compensatory increase in excitatory synaptic strength was not observed following partial deafferentation. In line with this finding, prolonged blockade of sodium channels with tetrodotoxin induced homeostatic synaptic scaling in wild-type, but not SP-deficient, slice cultures. By crossing SP-deficient mice with a newly generated transgenic mouse strain that expresses GFP-tagged SP under the control of the Thy1.2 promoter, the ability of dentate granule cells to form the SA and to homeostatically strengthen excitatory synapses was rescued. Interestingly, homeostatic synaptic strengthening was accompanied by a compensatory increase in SP cluster size/stability and SA stack number, suggesting that activity-dependent SP/SA remodeling could be part of a negative feedback mechanism that aims at adjusting the strength of excitatory synapses to persisting changes in network activity. Thus, our results disclose an important role for SP/SA in homeostatic synaptic plasticity.
ApoE influences amyloid-β (Aβ) clearance despite minimal apoE/Aβ association in physiological conditions
Authors: Verghese Philip B. , Castellano Joseph M. , Garai Kanchan , Wang Yinong , Jiang Hong , Shah Aarti , Bu Guojun , Frieden Carl , Holtzman David M.
Published: April 2013

Significance

It has been proposed that differential physical interactions of apolipoprotein E (apoE) isoforms with soluble amyloid-β (Aβ) in brain fluids influence the metabolism of Aβ, providing a major mechanism to account for how
APOE
influences Alzheimer’s disease risk. The current study challenges this proposal and clearly shows that lipoproteins containing apoE isoforms are unlikely to play a significant role in Aβ metabolism by binding directly to Aβ in physiological fluids such as cerebrospinal fluid or interstitial fluid. Our in vitro and in vivo results suggest that apoE isoforms influence Aβ metabolism by competing for the same clearance pathways within the brain.
Hippo-Foxa2 signaling pathway plays a role in peripheral lung maturation and surfactant homeostasis
Authors: Chung Chaeuk , Kim Tackhoon , Kim Miju , Kim Minchul , Song Hoogeun , Kim Tae-Shin , Seo Eunjeong , Lee Sang-Hee , Kim Hanbyul , Kim Sang Kyum , Yoo Geon , Lee Da-Hye , Hwang Deog-Su , Kinashi Tatsuo , Kim Jin-Man , Lim Dae-Sik
Published: April 2013

Respiratory distress syndrome (RDS), which is induced by insufficient production of surfactant, is the leading cause of mortality in preterm babies. Although several transcription factors are known to be involved in surfactant protein expression, the molecular mechanisms and signaling pathways upstream of these transcription factors have remained elusive. Here, using mammalian Hippo kinases (Mst1/2, mammalian sterile 20-like kinase 1/2) conditional knockout mice, we demonstrate that Mst1/2 kinases are critical for orchestration of transcription factors involved in surfactant protein homeostasis and prevention of RDS. Mice lacking Mst1/2 in the respiratory epithelium exhibited perinatal mortality with respiratory failure and their lungs contained fewer type I pneumocytes and more immature type II pneumocytes lacking microvilli, lamellar bodies, and surfactant protein expression, pointing to peripheral lung immaturity and RDS. In contrast to previous findings of YAP (Yes-associated protein)-mediated canonical Hippo signaling in the liver and intestine, loss of Mst1/2 kinases induced the defects in pneumocyte differentiation independently of YAP hyperactivity. We instead found that Mst1/2 kinases stabilized and phosphorylated the transcription factor Foxa2 (forkhead box A2), which regulates pneumocyte maturation and surfactant protein expression. Taken together, our results suggest that the mammalian Hippo kinases play crucial roles in surfactant homeostasis and coordination of peripheral lung differentiation through regulation of Foxa2 rather than of YAP.
Janus—a comprehensive tool investigating the two faces of transcription
Authors: Barann Matthias , Esser Daniela , Klostermeier Ulrich C , Lappalainen Tuuli , Luzius Anne , Kuiper Jan W. P. , Ammerpohl Ole , Vater Inga , Siebert Reiner , Amstislavskiy Vyacheslav , Sudbrak Ralf , Lehrach Hans , Schreiber Stefan , Rosenstiel Philip
Published: April 2013

Motivation: Protocols to generate strand-specific transcriptomes with next-generation sequencing platforms have been used by the scientific community roughly since 2008. Strand-specific reads allow for detection of antisense events and a higher resolution of expression profiles enabling extension of current transcript annotations. However, applications making use of this strandedness information are still scarce.

Results: Here we present a tool (Janus), which focuses on the identification of transcriptional active regions in antisense orientation to known and novel transcribed elements of the genome. Janus can compare the antisense events of multiple samples and assigns scores to identify mutual expression of either transcript in a sense/antisense pair, which could hint to regulatory mechanisms. Janus is able to make use of single-nucleotide variant (SNV) and methylation data, if available, and reports the sense to antisense ratio of regions in the vicinity of the identified genetic and epigenetic variation. Janus interrogates positions of heterozygous SNVs to identify strand-specific allelic imbalance.

Availability:  Janus is written in C/C++ and freely available at http://www.ikmb.uni-kiel.de/janus/janus.html under terms of GNU General Public License, for both, Linux and Windows 64×. Although the binaries will work without additional downloads, the software depends on bamtools (https://github.com/pezmaster31/bamtools) for compilation. A detailed tutorial section is included in the first section of the supplemental material and included as brief readme.txt in the tutorial archive.

Contact:  m.barann@mucosa.de or p.rosenstiel@mucosa.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
The MetaboLights repository: curation challenges in metabolomics
Authors: Salek Reza M. , Haug Kenneth , Conesa Pablo , Hastings Janna , Williams Mark , Mahendraker Tejasvi , Maguire Eamonn , González-Beltrán Alejandra N. , Rocca-Serra Philippe , Sansone Susanna-Assunta , Steinbeck Christoph
Published: April 2013

MetaboLights is the first general-purpose open-access curated repository for metabolomic studies, their raw experimental data and associated metadata, maintained by one of the major open-access data providers in molecular biology. Increases in the number of depositions, number of samples per study and the file size of data submitted to MetaboLights present a challenge for the objective of ensuring high-quality and standardized data in the context of diverse metabolomic workflows and data representations. Here, we describe the MetaboLights curation pipeline, its challenges and its practical application in quality control of complex data depositions.

Database URL: http://www.ebi.ac.uk/metabolights
Detection of a novel bunyavirus associated with fever, thrombocytopenia and leukopenia syndrome in Henan Province, China, using real-time reverse transcription PCR
Authors: Huang Xueyong , Liu Licheng , Du Yanhua , Ma Hongxia , Mu Yujiao ,   Pengzhi Wang, Ma Hong , Tang Xiaoyan , Wang Haifeng , Kang Kai , Zhang Shiqiang , Wu Weili , Chen Haomin , Liu Guohua , Yang Yinhui ,   Yongqiangj,   Jiang, Xu Bianli , Chen Weijun
Published: April 2013

A novel bunyavirus associated with fever, thrombocytopenia and leukopenia syndrome (FTLS) was discovered in Henan Province, China. Here, we report the development of an assay for this novel bunyavirus based on real-time reverse transcription PCR (RT-PCR). The assay exhibited high sensitivity and specificity without cross-reactivity towards 13 other viruses that cause similar symptoms. To evaluate the performance of this assay in detecting clinical samples, we analysed 261 serum samples from patients in Henan Province between 2007 and 2010. Of these samples, 91.95 % were bunyavirus positive. Compared with serological assays, the real-time PCR assay was much more sensitive in identifying infected patients 1 to 7 days after the onset of symptoms.
The retinoblastoma protein induces apoptosis directly at the mitochondria
Authors: Hilgendorf Keren I. , Leshchiner Elizaveta S. , Nedelcu Simona , Maynard Mindy A. , Calo Eliezer , Ianari Alessandra , Walensky Loren D. , Lees Jacqueline A.
Published: April 2013

The retinoblastoma protein gene RB-1 is mutated in one-third of human tumors. Its protein product, pRB (retinoblastoma protein), functions as a transcriptional coregulator in many fundamental cellular processes. Here, we report a nonnuclear role for pRB in apoptosis induction via pRB's direct participation in mitochondrial apoptosis. We uncovered this activity by finding that pRB potentiated TNFα-induced apoptosis even when translation was blocked. This proapoptotic function was highly BAX-dependent, suggesting a role in mitochondrial apoptosis, and accordingly, a fraction of endogenous pRB constitutively associated with mitochondria. Remarkably, we found that recombinant pRB was sufficient to trigger the BAX-dependent permeabilization of mitochondria or liposomes in vitro. Moreover, pRB interacted with BAX in vivo and could directly bind and conformationally activate BAX in vitro. Finally, by targeting pRB specifically to mitochondria, we generated a mutant that lacked pRB's classic nuclear roles. This mito-tagged pRB retained the ability to promote apoptosis in response to TNFα and also additional apoptotic stimuli. Most importantly, induced expression of mito-tagged pRB in Rb−/−;p53−/− tumors was sufficient to block further tumor development. Together, these data establish a nontranscriptional role for pRB in direct activation of BAX and mitochondrial apoptosis in response to diverse stimuli, which is profoundly tumor-suppressive.
Changes in relative deprivation and social well‐being
Authors: Sen Jayanta , Prakas Pal Dipti
Published: April 2013

Purpose

Individuals earn their income from different sources in an economy. Persons being engaged with different occupations have different income levels. Welfare level thus varies from person to person. Obviously an indignant feeling arises out of interpersonal shortages of income which is viewed as relative deprivation of the person to whom shortages are inflicted. This paper attempts to analyse geometrically inter‐temporal variations in relative deprivation.

Design/methodology/approach

Temporal movement has been analysed in terms of iso‐deprivation curves.

Findings

Reduction in relative deprivation is the cherished goal of every welfare economy. But how it should be pursued is a matter of concern to the policy makers. In the present analysis five paths are discussed along which the deprivation level may be reduced. The most desirable path is identified.

Originality/value

Different components and their relative contributions to changes in relative deprivation have been identified in a geometrical decomposition framework. The analysis is of use in framing policies for reduction in relative deprivation and increase in social well‐being.
Who are the poor? Who are the rich? Evidence for Portugal
Authors: Crespo Nuno , Moreira Sandrina B. , Simões Nádia
Published: April 2013

Purpose

The purpose of this paper is to identify the main determinants of the probability of a household being poor, middle class, or rich.

Design/methodology/approach

A new and integrated approach to the measurement of inequality in income distribution, poverty, and richness was recently proposed. Based on that approach and considering data for the Portuguese economy, the authors estimate a multinomial model in order to identify the main determinants of the probability of a household being poor, middle class, or rich using a set of characteristics of the households and the household's individual of reference as explanatory variables.

Findings

The evidence obtained indicates that: the determinants of poverty and richness are similar in qualitative terms; and household type, main source of income, education, and labor market state are the most important factors explaining these phenomena.

Originality/value

Following a methodology recently proposed by Crespo et al. toward an integrated measurement of inequality, poverty, and richness, the present study contributes to this line of research by using a micro‐econometric model applied to the Portuguese economy in order to identify the determinants of poverty and richness.
Balanced scorecard: application in the General Panarcadian Hospital of Tripolis, Greece
Authors: Koumpouros Yiannis
Published: April 2013

Purpose

– The purpose of this paper is to discuss the application of the balanced scorecard (BSC) in the Greek public health sector.

Design/methodology/approach

– The basic balanced scorecard theory has been adopted in the characteristics and individualities of the Greek public health system. The theoretical model developed was applied in the General Panarcadian Hospital of Tripolis (GPHT) in Greece. GPHT is a representative paradigm of a big regional Greek public hospital. It has about 300 beds and many clinics and specialties (internal medicine, cardiology, general surgery, intensive care unit, artificial kidney unit, etc.). Strategic management was performed for almost three years. The BSC model was formulated in an appropriate software program. The problems (both technical and managerial) faced during a three-year period along with the results of this management approach are presented in the current paper. The paper highlights some important gaps in the Greek public health system, while proposing actions to be taken.

Findings

– The BSC theory can be very successful under certain conditions.

Originality/value

– Special attention is given to the peculiarities of the Greek public health situation. The paper presents for the first time a real life example of applying BSC in the Greek public health sector.
Educational tug‐of‐war: internal and external accountability of principals in varied contexts
Authors: Gonzalez Raymond A. , Firestone William A.
Published: April 2013

Purpose

Principals face shifting accountability pressures from many sources. The most notable recent change in the USA has been the growing pressure from state and federal government. The purpose of this study is to explore the extent to which the accountability pressures experienced by principals in one American state were the same as those reported in research documenting “objective” changes in those pressures.

Design/methodology/approach

This qualitative study uses interviews with New Jersey middle school principals. The purposeful sample includes principals who had been in their buildings at least three years and enhances variation on socioeconomic status (as measured by New Jersey's rating of “district factor groups”) and school achievement. The authors averaged three years of achievement data and controlled for variation in poverty, ethnicity, language proficiency, and enrollment. A total of 37 principals were contacted; 25 were interviewed. Principals first rank ordered seven sources of accountability. They were then interviewed to learn why the one they ranked highest was most important.

Findings

The most frequent top source of accountability was “your own conscience.” Principals who selected this option highlighted a sense of personal responsibility, responsibility to the children in their charge, and how conscience mediates among competing accountabilities. Accountability to one's conscience was most prevalent in high achieving schools.

Originality/value

Frequent reference to internal responsibility among leaders suggests that they continue to feel a strong sense of internal accountability in spite of increasing external pressures. It also illustrates the range of external, often conflicting pressures that principals face which include pressures from the public and the district office as well as state and federal government. In this increasingly prescriptive and contradictory environment the principal's moral code is important to her or his school.
Developing a planned work process model for housing associations
Authors: Leblanc Hervé , Thomson Craig , Cameron Iain , Nitithamyong Pollaphat
Published: April 2013

Purpose

Improving process management within construction projects has been the source of academic and policy research for decades, and continues to be today. This paper seeks to focuses on the relatively under investigated management of Housing Association (HA) planned works and aims to improve this often ill‐defined process by developing a Planned Work Process Model (PWPM) that aids the definition of the phases and activities.

Design/methodology/approach

First step in developing the process model was through semi‐structured interviews with 11 HA practitioners allowing for the identification of 20 planned works activities. Second step considered the responses of 7 HA practitioners to a set of questions about the 20 activities leading to the development of an initial Process Model (PM). Third step contextualises the PM within four case studies with HAs of different sizes from which the PWPM emerged. Finally, the PWPM was validated by a panel of HA practitioners.

Findings

The PWPM is a process model specific to the practices of HAs in the UK. It represents the first step for process management improvement for planned works by providing a structure to facilitate project planning and performance monitoring.

Research limitations/implications

A panel of HA practitioners recognised the uniqueness and value of the PWPM especially in the context of new staff induction and progress monitoring. Further refinement of the PWPM would be possible through a large survey to help improve its practical applicability and refining the activities description and vocabulary.

Originality/value

This research will be of interest to those responsible for planning and delivering HA planned works since it presents a tailored interpretation of the project process that currently does not exist.
The project insurance option in infrastructure procurement
Authors: Ndekugri Issaka , Daeche Hannah , Zhou Diwei
Published: April 2013

Purpose

Project insurance is designed to get over the perceived deficiencies of the conventional insurance practice. It involves the entire project supply chain being insured under a single policy taken out by the project owner. The purpose of this article is to report the outcomes of a study aimed at developing understanding of project insurance practice and how it compares with the conventional system.

Design/methodology/approach

The study consisted of a questionnaire survey across four sectors of the construction industry.

Findings

Direct experience of project insurance is still very patchy. They also raise doubt whether project insurance offers significant benefits to the supply chain members with direct responsibility for designing or executing projects. The main advantages of project insurance over the traditional fragmented insurance products reported by respondents were: avoidance of litigation to determine which member of the project supply chain should ultimately be liable when loss or damage occurs; the ability to obtain cover for projects too large for the insurance capacity of some members of the supply chain; ability of the project owner to purchase customised cover.

Research limitations/implications

The disadvantages were: there is duplication from contractors, sub‐contractor and designers still having to purchase the traditional products for projects on which project insurance is not implemented; the levels of excess in the available project insurance products are too high; there is little reduction in the annual insurance premium bills of contractors, sub‐contractors and designers.

Practical implications

Universities and other educational institutions can contribute to developing wider awareness by including project insurance in not only their educational curricula but also their research priorities. The UK Government's decision to implement project insurance on some demonstration projects is a step in the right direction but needs to involve the research community who are better able to distil the experience for dissemination to the wider industry. The insurance industry needs to play a more proactive role by reassessing the levels of excesses in their project insurance policies and collaborating with the research community to develop more detailed knowledge of the technique.

Originality/value

This is the only reported empirical study into the use of project insurance in the UK construction industry.
The organisation of innovation in the wine industry
Authors: Doloreux David , Lord‐Tarte Evelyne
Published: April 2013

Purpose

The purpose of this paper is to contribute to the debate on the spatial organisation of the open innovation model in the wine industry in Canada.

Design/methodology/approach

The paper employs a micro‐firm level survey among 146 wine firms in Canada. Descriptive and non‐parametric tests are used in the analysis.

Findings

The results on the occurrence of collaborations depict modest collaborative activities with external sources. Most of the collaborations and information are sourced locally because the local climate and growing conditions are so specific that alternative sources and collaborations are less relevant. The results also show that the firm's openness strategy has a weak influence on innovation capacity but firms that introduce more innovations are those that embrace an open innovation strategy to a greater extent than the less innovative.

Research limitations/implications

The number of respondents is still limited (i.e. about 150). Moreover, only the relationship between some firm‐specific factors related to innovation and the degree of openness is studied.

Practical implications

The paper provides managerial implications because it suggests that firms adopting an open innovation strategy through collaborations have a higher impact on innovation development by means of introducing new types of innovation and on R&D activities.

Originality/value

The paper introduces the spatial dimension of the open innovation strategy in the wine industry in order to understand the link between the geographically‐dispersed open innovation networks and their impacts on innovation capacities and innovation development of winery firms.