bluuebunny/crossref_metadata_2025 huggingface dataset:
Analog of the Peter-Weyl expansion for Lorentz group
Authors: Perlov Leonid
Published: November 2015

The expansion of a square integrable function on SL(2, C) into the sum of the principal series matrix coefficients with the specially selected representation parameters was recently used in the Loop Quantum Gravity [C. Rovelli and F. Vidotto, Covariant Loop Quantum Gravity: An Elementary Introduction to Quantum Gravity and Spinfoam Theory (Cambridge University Press, Cambridge, 2014) and C. Rovelli, Classical Quantum Gravity 28(11), 114005 (2011)]. In this paper, we prove that the sum used originally in the Loop Quantum Gravity: ∑j=0∞∑m≤j∑n≤jDjm,jn(j,τj)(g), where j, m, n ∈ Z, τ ∈ C is convergent to a function on SL(2, C); however, the limit is not a square integrable function; therefore, such sums cannot be used for the Peter-Weyl like expansion. We propose the alternative expansion and prove that for each fixed m: ∑j=m∞Djm,jm(j,τj)(g) is convergent and that the limit is a square integrable function on SL(2, C). We then prove the analog of the Peter-Weyl expansion: any ψ(g) ∈ L2(SL(2, C)) can be decomposed into the sum: ψ(g)=∑j=m∞j2(1+τ2)cjmmDjm,jm(j,τj)(g), with the Fourier coefficients cjmm=∫SL(2,C)ψ(g)Djm,jmj,τj(g)¯dg, g ∈ SL(2, C), τ ∈ C, τ ≠ i, − i, j, m ∈ Z, m is fixed. We also prove convergence of the sums ∑j=p∞∑m≤j∑n≤jdpmj2Djm,jn(j,τj)(g), where dpmj2=(j+1)12∫SU(2)ϕ(u)Dpmj2(u)¯du is ϕ(u)’s Fourier transform and p, j, m, n ∈ Z, τ ∈ C, u ∈ SU(2), g ∈ SL(2, C), thus establishing the map between the square integrable functions on SU(2) and the space of the functions on SL(2, C). Such maps were first used in Rovelli [Class. Quant. Grav. 28, 11 (2011)].
Electron- and photon-impact ionization of furfural
Authors: Jones D. B. , Ali E. , Nixon K. L. , Limão-Vieira P. , Hubin-Franskin M.-J. , Delwiche J. , Ning C. G. , Colgan J. , Murray A. J. , Madison D. H. , Brunger M. J.
Published: November 2015

The He(i) photoelectron spectrum of furfural has been investigated, with its vibrational structure assigned for the first time. The ground and excited ionized states are assigned through ab initio calculations performed at the outer-valence Green’s function level. Triple differential cross sections (TDCSs) for electron-impact ionization of the unresolved combination of the 4a″  +  21a′ highest and next-highest occupied molecular orbitals have also been obtained. Experimental TDCSs are recorded in a combination of asymmetric coplanar and doubly symmetric coplanar kinematics. The experimental TDCSs are compared to theoretical calculations, obtained within a molecular 3-body distorted wave framework that employed either an orientation average or proper TDCS average. The proper average calculations suggest that they may resolve some of the discrepancies regarding the angular distributions of the TDCS, when compared to calculations employing the orbital average.
High-entropy alloys as high-temperature thermoelectric materials
Authors: Shafeie Samrand , Guo Sheng , Hu Qiang , Fahlquist Henrik , Erhart Paul , Palmqvist Anders
Published: November 2015

Thermoelectric (TE) generators that efficiently recycle a large portion of waste heat will be an important complementary energy technology in the future. While many efficient TE materials exist in the lower temperature region, few are efficient at high temperatures. Here, we present the high temperature properties of high-entropy alloys (HEAs), as a potential new class of high temperature TE materials. We show that their TE properties can be controlled significantly by changing the valence electron concentration (VEC) of the system with appropriate substitutional elements. Both the electrical and thermal transport properties in this system were found to decrease with a lower VEC number. Overall, the large microstructural complexity and lower average VEC in these types of alloys can potentially be used to lower both the total and the lattice thermal conductivity. These findings highlight the possibility to exploit HEAs as a new class of future high temperature TE materials.
A critical analysis of the feasibility of pure strain-actuated giant magnetostrictive nanoscale memories
Authors: Gowtham P. G. , Rowlands G. E. , Buhrman R. A.
Published: November 2015

Concepts for memories based on the manipulation of giant magnetostrictive nanomagnets by stress pulses have garnered recent attention due to their potential for ultra-low energy operation in the high storage density limit. Here, we discuss the feasibility of making such memories in light of the fact that the Gilbert damping of such materials is typically quite high. We report the results of numerical simulations for several classes of toggle precessional and non-toggle dissipative magnetoelastic switching modes. Material candidates for each of the several classes are analyzed and forms for the anisotropy energy density and ranges of material parameters appropriate for each material class are employed. Our study indicates that the Gilbert damping as well as the anisotropy and demagnetization energies are all crucial for determining the feasibility of magnetoelastic toggle-mode precessional switching schemes. The roles of thermal stability and thermal fluctuations for stress-pulse switching of giant magnetostrictive nanomagnets are also discussed in detail and are shown to be important in the viability, design, and footprint of magnetostrictive switching schemes.
Spectroscopic properties and radiation damage investigation of a diamond based Schottky diode for ion-beam therapy microdosimetry
Authors: Verona C. , Magrin G. , Solevi P. , Grilj V. , Jakšić M. , Mayer R. , Marinelli Marco , Verona-Rinati G.
Published: November 2015

In this work, a detailed analysis of the properties of a novel microdosimeter based on a synthetic single crystal diamond is reported. Focused ion microbeams were used to investigate the device spectropscopic properties as well as the induced radiation damage effects. A diamond based Schottky diode was fabricated by chemical vapor deposition with a very thin detecting region, about 400 nm thick (approximately 1.4 μm water equivalent thickness), corresponding to the typical size in microdosimetric measurements. A 200 × 200 μm2 square metallic contact was patterned on the diamond surface by standard photolithography to define the sensitive area. Experimental measurements were carried out at the Ruder Boškovic′ Institute microbeam facility using 4 MeV carbon and 5 MeV silicon ions. Ion beam induced charge maps were employed to characterize the microdosimeter response in terms of its charge collection properties. A stable response with no evidence of polarization or memory effects was observed up to the maximum investigated ion beam flux of about 1.7 × 109 ions·cm−2·s−1. A homogeneity of the response about 6% was found over the sensitive region with a well-defined confinement of the response within the active area. Tests of the radiation damage effect were performed by selectively irradiating small areas of the device with different ion fluences, up to about 1012 ions/cm2. An exponential decrease of the charge collection efficiency was observed with a characteristic decay constant of about 4.8 MGy and 1 MGy for C and Si ions, respectively. The experimental data were analyzed by means of GEANT4 Monte Carlo simulations. A direct correlation between the diamond damaging effect and the Non Ionizing Energy Loss (NIEL) fraction was found. In particular, an exponential decay of the charge collection efficiency with an exponential decay as a function of NIEL is observed, with a characteristic constant of about 9.3 kGy-NIEL for both carbon and silicon ions.
Novel silicon allotropes: Stability, mechanical, and electronic properties
Authors: Fan Qingyang , Chai Changchun , Wei Qun , Yan Haiyan , Zhao Yingbo , Yang Yintang , Yu Xinhai , Liu Yang , Xing Mengjiang , Zhang Junqin , Yao Ronghui
Published: November 2015

One quasi-direct gap phase (Amm2) and three indirect gap phases (C2/m-16, C2/m-20, and I-4) of silicon allotropes are proposed. The detailed theoretical study on the structure, density of states, elastic properties, sound velocities, and Debye temperature of these four phases is carried out by using first principles calculations. The elastic constants of these four phases are calculated by strain-stress method. The elastic constants and the phonon calculations manifest all novel silicon allotropes in this paper are mechanically and dynamically stable at ambient condition. The B/G values indicate that these four phases of silicon are brittle materials at ambient pressure. The anisotropy properties show that C2/m-20 phase exhibits a larger anisotropy in its elastic modulus, shear elastic anisotropic factors, and several anisotropic indices than others. We have found that the Debye temperature of the four novel silicon allotropes gradually reduces in the order of C2/m-20 > Amm2 > C2/m-16 > I-4 at ambient pressure.
Influence of magnetic field on electric-field-induced local polar states in manganites
Authors: Mamin R. F. , Strle J. , Bizyaev D. A. , Yusupov R. V. , Kabanov V. V. , Kranjec A. , Borovsak M. , Mihailovic D. , Bukharaev A. A.
Published: November 2015

It is shown that creation of local charged states at the surface of the lanthanum-strontium manganite single crystals by means of bias application via a conducting atomic force microscope tip is strongly affected by magnetic field. Both a charge and a size of created structures increase significantly on application of the magnetic field during the induction. We argue that the observed phenomenon originates from a known tendency of manganites toward charge segregation and its intimate relation to magnetic ordering.
Ferroelectric transition in compressively strained SrTiO3 thin films
Authors: Verma Amit , Raghavan Santosh , Stemmer Susanne , Jena Debdeep
Published: November 2015

We report the temperature dependent capacitance-voltage characteristics of Pt/SrTiO3 Schottky diodes fabricated using compressively strained SrTiO3 thin films grown on (LaAlO3)0.3(Sr2AlTaO6)0.7 (LSAT) substrates. The measurements reveal a divergence of the out of plane dielectric constant of SrTiO3 peaked at ∼140 K, implying a ferroelectric transition. A Curie-Weiss law fit to the zero-bias dielectric constant suggests a Curie temperature of ∼56 K. This observation provides experimental confirmation of the theoretical prediction of out of plane ferroelectricity in compressively strained SrTiO3 thin films grown on LSAT substrate. We also discuss the roles of the field-dependent dielectric constant and the interfacial layer in SrTiO3 on the extraction of the Curie temperature.
An optically transparent membrane supports shear stress studies in a three-dimensional microfluidic neurovascular unit model
Authors: Sellgren Katelyn L. , Hawkins Brian T. , Grego Sonia
Published: November 2015

We report a microfluidic blood-brain barrier model that enables both physiological shear stress and optical transparency throughout the device. Brain endothelial cells grown in an optically transparent membrane-integrated microfluidic device were able to withstand physiological fluid shear stress using a hydrophilized polytetrafluoroethylene nanoporous membrane instead of the more commonly used polyester membrane. A functional three-dimensional microfluidic co-culture model of the neurovascular unit is presented that incorporates astrocytes in a 3D hydrogel and enables physiological shear stress on the membrane-supported endothelial cell layer.
Experimental determination of next-nearest-neighbor interlayer exchange coupling in ferromagnetic GaMnAs/GaAs:Be multilayers
Authors: Lee Hakjoon , Bac Seul-Ki , Lee Sangyeop , Choi Seonghoon , Yoo Taehee , Lee Sanghoon , Liu Xinyu , Furdyna Jacek K.
Published: November 2015

We report direct experimental determination of next-nearest-neighbor (NNN) interlayer exchange coupling (IEC) in antiferromagnetically coupled GaMnAs/GaAs:Be multilayers. Magnetoresistance in such multilayers shows step-like transitions as a function of applied magnetic field that corresponds to abrupt changes of spin configuration. By adjusting the field range, one obtains minor hysteresis loops that allow one to determine spin configurations occurring in the multilayer, which in turn can be used to obtain the ratio of NNN IEC to NN IEC. By using this method on a series of GaMnAs/GaAs:Be with different numbers of GaMnAs layers, we obtain this ratio to be 0.23, in good agreement with theoretical predictions.
Unusual isotope effect on thermal transport of single layer molybdenum disulphide
Authors: Wu Xufei , Yang Nuo , Luo Tengfei
Published: November 2015

Thermal transport in single layer molybdenum disulfide (MoS2) is critical to advancing its applications. In this paper, we use molecular dynamics simulations with first-principles force constants to study the isotope effect on the thermal transport of single layer MoS2. Through phonon modal analysis, we found that isotopes can strongly scatter phonons with intermediate frequencies, and the scattering behavior can be radically different from that predicted by conventional scattering model based on perturbation theory, where Tamura's formula is combined with Matthiessen's rule to include isotope effects. Such a discrepancy becomes smaller for low isotope concentrations. Natural isotopes can lead to a 30% reduction in thermal conductivity for large size samples. However, for small samples where boundary scattering becomes significant, the isotope effect can be greatly suppressed. It was also found that the Mo isotopes, which contribute more to the phonon eigenvectors in the intermediate frequency range, have stronger impact on thermal conductivity than S isotopes.
III-nitride disk-in-nanowire 1.2 μm monolithic diode laser on (001)silicon
Authors: Hazari Arnab , Aiello Anthony , Ng Tien-Khee , Ooi Boon S. , Bhattacharya Pallab
Published: November 2015

III-nitride nanowire diode heterostructures with multiple In0.85Ga0.15N disks and graded InGaN mode confining regions were grown by molecular beam epitaxy on (001)Si substrates. The aerial density of the 60 nm nanowires is ∼3 × 1010 cm−2. A radiative recombination lifetime of 1.84 ns in the disks is measured by time-resolved luminescence measurements. Edge-emitting nanowire lasers have been fabricated and characterized. Measured values of Jth, T0, and dg/dn in these devices are 1.24 kA/cm2, 242 K, and 5.6 × 10−17 cm2, respectively. The peak emission is observed at ∼1.2 μm.
Elimination of surface band bending on N-polar InN with thin GaN capping
Authors: Kuzmík J. , Haščík Š. , Kučera M. , Kúdela R. , Dobročka E. , Adikimenakis A. , Mičušík M. , Gregor M. , Plecenik A. , Georgakilas A.
Published: November 2015

0.5–1 μm thick InN {0001} films grown by molecular-beam epitaxy with N- or In-polarity are investigated for the presence of native oxide, surface energy band bending, and effects introduced by 2 to 4 monolayers of GaN capping. Ex situ angle-resolved x-ray photo-electron spectroscopy is used to construct near-surface (GaN)/InN energy profiles, which is combined with deconvolution of In3d signal to trace the presence of InN native oxide for different types of polarity and capping. Downwards surface energy band bending was observed on bare samples with native oxide, regardless of the polarity. It was found that the In-polar InN surface is most readily oxidized, however, with only slightly less band bending if compared with the N-polar sample. On the other hand, InN surface oxidation was effectively mitigated by GaN capping. Still, as confirmed by ultra-violet photo-electron spectroscopy and by energy band diagram calculations, thin GaN cap layer may provide negative piezoelectric polarization charge at the GaN/InN hetero-interface of the N-polar sample, in addition to the passivation effect. These effects raised the band diagram up by about 0.65 eV, reaching a flat-band profile.
Temperature dependence of broadband near-infrared luminescence from Ni2+-doped Ba0.5Sr0.5TiO3
Authors: Bai Gongxun , Jie Wenjing , Yang Zhibin , Hao Jianhua
Published: November 2015

The dielectric and photoluminescence properties of Ni2+-doped Ba0.5Sr0.5TiO3 (BST) were studied at different temperatures. Under 350 nm excitation, the NIR luminescence band from 1200 nm to >1600 nm covers the optical communication window (O-L bands), with a typical bandwidth exceeding 200 nm. The crystal structure of Ni2+-doped BST evolves from rhombohedral to cubic when the temperature increases from 100 to 300 K. The luminescence properties are tightly correlated with the crystal structure of the host BST. The luminescence variations are mainly affected by phase transition induced crystal field change and nonradiative relaxation.
Phase-dependent deterministic switching of magnetoelectric spin wave detector in the presence of thermal noise via compensation of demagnetization
Authors: Dutta Sourav , Nikonov Dmitri E. , Manipatruni Sasikanth , Young Ian A. , Naeemi Azad
Published: November 2015

The possibility of achieving phase-dependent deterministic switching of the magnetoelectric spin wave detector in the presence of thermal noise has been discussed. The proposed idea relies on the modification of the energy landscape by partially canceling the out-of-plane demagnetizing field and the resultant change in the intrinsic magnetization dynamics to drive the nanomagnet towards a preferential final magnetization state. The remarkable increase in the probability of successful switching can be accounted for by the shift in the location of the saddle point in the energy landscape and a resultant change in the nature of the relaxation dynamics of the magnetization from a highly precessional to a fairly damped one and an increased dependence on the initial magnetization values, a crucial requirement for phase-dependent spin wave detection.
Flexo- and piezo-electric polarization of smectic layers in ferroelectric and antiferroelectric liquid crystals
Authors: Kuczyński W. , Hoffmann J. , Dardas D. , Nowicka K. , Bielejewska N.
Published: November 2015

In this paper, we report on how flexoelectric and piezoelectric polarization components can be determined by a method based on simultaneous studies of dielectric and electrooptic properties of the chiral smectic liquid crystal in the regime of weak electric fields. As a rule, the measurements of spontaneous polarization are performed using switching experiments. The polarization measured in this way is not complete—it contains the piezoelectric component only. However, the knowledge of the entire local polarization of a single smectic layer is of great importance—it is necessary for correct determination of some material parameters, for instance elastic constants. Our experiments performed in a helical smectic mixture demonstrated that flexoelectric contribution to the local spontaneous polarization is significant in both ferroelectric and antiferroelectric phases. In the antiferroelectric phase, the flexoelectric polarization is less due to higher helical pitch.
Plug-in nanoliter pneumatic liquid dispenser with nozzle design flexibility
Authors: Choi In Ho , Kim Hojin , Lee Sanghyun , Baek Seungbum , Kim Joonwon
Published: November 2015

This paper presents a novel plug-in nanoliter liquid dispensing system with a plug-and-play interface for simple and reversible, yet robust integration of the dispenser. A plug-in type dispenser was developed to facilitate assembly and disassembly with an actuating part through efficient modularization. The entire process for assembly and operation of the plug-in dispenser is performed via the plug-and-play interface in less than a minute without loss of dispensing quality. The minimum volume of droplets pneumatically dispensed using the plug-in dispenser was 124 nl with a coefficient of variation of 1.6%. The dispensed volume increased linearly with the nozzle size. Utilizing this linear relationship, two types of multinozzle dispensers consisting of six parallel channels (emerging from an inlet) and six nozzles were developed to demonstrate a novel strategy for volume gradient dispensing at a single operating condition. The droplet volume dispensed from each nozzle also increased linearly with nozzle size, demonstrating that nozzle size is a dominant factor on dispensed volume, even for multinozzle dispensing. Therefore, the proposed plug-in dispenser enables flexible design of nozzles and reversible integration to dispense droplets with different volumes, depending on the application. Furthermore, to demonstrate the practicality of the proposed dispensing system, we developed a pencil-type dispensing system as an alternative to a conventional pipette for rapid and reliable dispensing of minute volume droplets.
Microstencils to generate defined, multi-species patterns of bacteria
Authors: Timm Collin M. , Hansen Ryan R. , Doktycz Mitchel J. , Retterer Scott T. , Pelletier Dale A.
Published: November 2015

Microbial communities are complex heterogeneous systems that are influenced by physical and chemical interactions with their environment, host, and community members. Techniques that facilitate the quantitative evaluation of how microscale organization influences the morphogenesis of multispecies communities could provide valuable insights into the dynamic behavior and organization of natural communities, the design of synthetic environments for multispecies culture, and the engineering of artificial consortia. In this work, we demonstrate a method for patterning microbes into simple arrangements that allow the quantitative measurement of growth dynamics as a function of their proximity to one another. The method combines parylene-based liftoff techniques with microfluidic delivery to simultaneously pattern multiple bacterial species with high viability using low-cost, customizable methods. Quantitative measurements of bacterial growth for two competing isolates demonstrate that spatial coordination can play a critical role in multispecies growth and structure.
Biogeographical regionalisation of the world: a reappraisal
Authors: Morrone Juan J.
Published: November 2015

Some phytogeographical, zoogeographical and biogeographical regionalisations of the world are reviewed qualitatively. A biogeographical regionalisation attempting some consensus is proposed, recognising the following three kingdoms and nine regions: Holarctic kingdom (Nearctic and Palearctic regions), Holotropical kingdom (Neotropical, Ethiopian and Oriental regions) and Austral kingdom (Cape, Andean, Australian and Antarctic regions). Additionally, the following five transition zones are recognised: Mexican (Nearctic–Neotropical transition), Saharo-Arabian (Palearctic–Ethiopian transition), Chinese (Palearctic–Oriental transition), Indo-Malayan (Oriental–Australian transition) and South American (Neotropical–Andean transition).
Why we should retain Nothofagus sensu lato
Authors: Hill Robert S. , Jordan Gregory J. , Macphail Michael K.
Published: November 2015

We present the case that the fossil record of Nothofagaceae, which is much more extensive in terms of species numbers than the living species, cannot be dealt with in a productive way by the recent proposal by Heenan and Smissen to split Nothofagus into four genera (Phytotaxa, vol. 146, http://dx.doi.org/10.11646/phytotaxa.146.1.1). Such a proposal will render the fossil record almost unworkable, and will lead to a major split in the approach taken by palynologists in comparison to other researchers. We believe the case for the new generic names, while valid, is weak, and is far outweighed by the utility of retaining Nothofagus sensu lato.
Identification of differentially methylated loci using wavelet-based functional mixed models
Authors: Lee Wonyul , Morris Jeffrey S.
Published: November 2015

Motivation: DNA methylation is a key epigenetic modification that can modulate gene expression. Over the past decade, a lot of studies have focused on profiling DNA methylation and investigating its alterations in complex diseases such as cancer. While early studies were mostly restricted to CpG islands or promoter regions, recent findings indicate that many of important DNA methylation changes can occur in other regions and DNA methylation needs to be examined on a genome-wide scale. In this article, we apply the wavelet-based functional mixed model methodology to analyze the high-throughput methylation data for identifying differentially methylated loci across the genome. Contrary to many commonly-used methods that model probes independently, this framework accommodates spatial correlations across the genome through basis function modeling as well as correlations between samples through functional random effects, which allows it to be applied to many different settings and potentially leads to more power in detection of differential methylation.

Results: We applied this framework to three different high-dimensional methylation data sets (CpG Shore data, THREE data and NIH Roadmap Epigenomics data), studied previously in other works. A simulation study based on CpG Shore data suggested that in terms of detection of differentially methylated loci, this modeling approach using wavelets outperforms analogous approaches modeling the loci as independent. For the THREE data, the method suggests newly detected regions of differential methylation, which were not reported in the original study.

Availability and implementation: Automated software called WFMM is available at https://biostatistics.mdanderson.org/SoftwareDownload. CpG Shore data is available at http://rafalab.dfci.harvard.edu. NIH Roadmap Epigenomics data is available at http://compbio.mit.edu/roadmap.

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  jefmorris@mdanderson.org
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization
Authors: Misirli Goksel , Cavaliere Matteo , Waites William , Pocock Matthew , Madsen Curtis , Gilfellon Owen , Honorato-Zimmer Ricardo , Zuliani Paolo , Danos Vincent , Wipat Anil
Published: November 2015

Motivation: Biological systems are complex and challenging to model and therefore model reuse is highly desirable. To promote model reuse, models should include both information about the specifics of simulations and the underlying biology in the form of metadata. The availability of computationally tractable metadata is especially important for the effective automated interpretation and processing of models. Metadata are typically represented as machine-readable annotations which enhance programmatic access to information about models. Rule-based languages have emerged as a modelling framework to represent the complexity of biological systems. Annotation approaches have been widely used for reaction-based formalisms such as SBML. However, rule-based languages still lack a rich annotation framework to add semantic information, such as machine-readable descriptions, to the components of a model.

Results: We present an annotation framework and guidelines for annotating rule-based models, encoded in the commonly used Kappa and BioNetGen languages. We adapt widely adopted annotation approaches to rule-based models. We initially propose a syntax to store machine-readable annotations and describe a mapping between rule-based modelling entities, such as agents and rules, and their annotations. We then describe an ontology to both annotate these models and capture the information contained therein, and demonstrate annotating these models using examples. Finally, we present a proof of concept tool for extracting annotations from a model that can be queried and analyzed in a uniform way. The uniform representation of the annotations can be used to facilitate the creation, analysis, reuse and visualization of rule-based models. Although examples are given, using specific implementations the proposed techniques can be applied to rule-based models in general.

Availability and implementation: The annotation ontology for rule-based models can be found at http://purl.org/rbm/rbmo. The krdf tool and associated executable examples are available at http://purl.org/rbm/rbmo/krdf.

Contact:  anil.wipat@newcastle.ac.uk   or  vdanos@inf.ed.ac.uk
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS
Authors: Hoff Katharina J. , Lange Simone , Lomsadze Alexandre , Borodovsky Mark , Stanke Mario
Published: November 2015

Motivation: Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction tool that incorporates RNA-Seq data into unsupervised training and subsequently generates ab initio gene predictions. AUGUSTUS is a gene finder that usually requires supervised training and uses information from RNA-Seq reads in the prediction step. Complementary strengths of GeneMark-ET and AUGUSTUS provided motivation for designing a new combined tool for automatic gene prediction.

Results: We present BRAKER1, a pipeline for unsupervised RNA-Seq-based genome annotation that combines the advantages of GeneMark-ET and AUGUSTUS. As input, BRAKER1 requires a genome assembly file and a file in bam-format with spliced alignments of RNA-Seq reads to the genome. First, GeneMark-ET performs iterative training and generates initial gene structures. Second, AUGUSTUS uses predicted genes for training and then integrates RNA-Seq read information into final gene predictions. In our experiments, we observed that BRAKER1 was more accurate than MAKER2 when it is using RNA-Seq as sole source for training and prediction. BRAKER1 does not require pre-trained parameters or a separate expert-prepared training step.

Availability and implementation: BRAKER1 is available for download at http://bioinf.uni-greifswald.de/bioinf/braker/ and http://exon.gatech.edu/GeneMark/.

Contact:  katharina.hoff@uni-greifswald.de or borodovsky@gatech.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
WormExp: a web-based application for a Caenorhabditis elegans-specific gene expression enrichment analysis
Authors: Yang Wentao , Dierking Katja , Schulenburg Hinrich
Published: November 2015

Motivation: A particular challenge of the current omics age is to make sense of the inferred differential expression of genes and proteins. The most common approach is to perform a gene ontology (GO) enrichment analysis, thereby relying on a database that has been extracted from a variety of organisms and that can therefore only yield reliable information on evolutionary conserved functions.

Results: We here present a web-based application for a taxon-specific gene set exploration and enrichment analysis, which is expected to yield novel functional insights into newly determined gene sets. The approach is based on the complete collection of curated high-throughput gene expression data sets for the model nematode Caenorhabditis elegans, including 1786 gene sets from more than 350 studies.

Availability and implementation: WormExp is available at http://wormexp.zoologie.uni-kiel.de.

Contacts:  hschulenburg@zoologie.uni-kiel.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Effects of Atorvastatin on Serum High-Sensitive C-Reactive Protein and Total Cholesterol Levels in Asian Patients With Atrial Fibrillation
Authors: Wang Jing , Wang Ai-Rong , Zhang Ming-Juan , Li Yu
Published: November 2015

Elevated serum levels of high-sensitive C-reactive protein (hs-CRP) and total cholesterol (TC) correlate with atherosclerotic vascular disease and increased frequency of vascular events. In this study, we investigated the effect of atorvastatin treatment on serum hs-CRP and TC levels, and the recurrence rate of atrial fibrillation (AF) in patients. Furthermore, a meta-analysis was performed to confirm the findings in this study. A total of 105 patients with AF were recruited to this study, including 55 patients with AF who were treated with amiodarone and atorvastatin (the treatment group) and 50 patients with AF who were treated with only amiodarone (the control group). Patients were treated for 12 months and followed up regularly for 1 year. Serum hs-CRP and TC levels in patients before and after treatment were recorded, and AF recurrence rate at 3, 6, and 12 months of treatment was obtained. Statistical analyses were performed with R 3.1.0 software and STATA 12.0 software. For patients in both treatment and control groups, serum hs-CRP and TC levels were high before the treatments began (both P < 0.05). However, after 12 months of treatment, serum hs-CRP and TC levels in the treatment group was dramatically reduced compared with the control group (hs-CRP: 3.63 ± 2.14 mg/L vs. 2.75 ± 1.89 mg/L, t = 2.24, P = 0.027; TC: 4.66 ± 1.13 mmol/L vs. 4.20 ± 1.06 mmol/L, t = 2.15, P = 0.034). After 12 months of treatment, the AF recurrence rate in the treatment group was significantly lower than the control group (16.4% vs. 34.0%; χ2 = 4.37; P = 0.037). In addition, 13 studies were selected for meta-analysis. Pooled results of the meta-analysis showed that serum hs-CRP and TC levels decreased significantly in the treatment group compared with the case group [hs-CRP: SMD = 0.95, 95% confidence interval (CI) = 0.62–1.29, and P < 0.001; TC: SMD = 1.39, 95% CI = 0.65–2.13, and P < 0.001]. Our study presents compelling evidence that atorvastatin is highly effective in reducing serum hs-CRP and TC levels and lowering the recurrence rate of AF.
Solvents and sustainable chemistry
Authors: Welton Tom
Published: November 2015

Solvents are widely recognized to be of great environmental concern. The reduction of their use is one of the most important aims of green chemistry. In addition to this, the appropriate selection of solvent for a process can greatly improve the sustainability of a chemical production process. There has also been extensive research into the application of so-called green solvents, such as ionic liquids and supercritical fluids. However, most examples of solvent technologies that give improved sustainability come from the application of well-established solvents. It is also apparent that the successful implementation of environmentally sustainable processes must be accompanied by improvements in commercial performance.
Favourable outcome of combined medical surgical treatment of cerebral aspergillosis of pulmonary origin
Authors: Ruiz-Santana Sergio , Cabrera-Arrocha Jesús , Hernández-Socorro Carmen-Rosa , Paz-Cruz Inmaculada , Campos-Herrero María-Isolina , León-Gil Cristóbal
Published: November 2015

Introduction:

Cerebral aspergillosis is a highly fatal infection. Its origin is most likely blood-borne from the lungs and most patients are immunosuppressed. Mortality is over 90 % and the treatment chosen is key for survival.

Case presentation:

We report a 32-year-old female with a history of acute myeloid leukaemia (M3) who was admitted to the hospital due to a nodular infiltrate in the right superior lobe. A lung computed tomography (CT) scan displayed a right upper lobe cavitated nodule. A brain CT scan showed a right hemisphere deep abscess. Pulmonary aspergillosis was diagnosed after bronchoalveolar lavage. Three weeks later, while on antifungal treatment with voriconazole and liposomal amphotericin B, she suffered left motor focal deficits, and brain abscess puncture and aspiration by neuronavigation were performed for diagnosis and decompression. A PCR assay was positive for Aspergillus fumigatus. One week later, she developed an intraventricular brain haemorrhage requiring external ventricular drainage and intrathecal fibrinolysis with recombinant tissue plasminogen activator. She eventually achieved a good neurological outcome. A control brain CT showed an important reduction in mass size.

Conclusion:

Antifungal treatment is the mainstay for brain abscess treatment, and its combination with stereotactic needle aspiration is a better option compared with open surgery, particularly in abscesses located in deep motor areas.
Evolutionary responses to conditionality in species interactions across environmental gradients
Authors: O’Brien Anna M. , Sawers Ruairidh J.H. , Ross-Ibarra Jeffrey , Strauss Sharon Y.
Published: November 2015

The outcomes of many species interactions are conditional on the environments in which they occur. A common pattern is that outcomes grade from being more positive under stressful conditions to more antagonistic or neutral under benign conditions. The evolutionary implications of conditionality in interactions have received much less attention than the documentation of conditionality itself, with a few notable exceptions. Here, we predict patterns of adaptation and co-adaptation between partners along abiotic gradients, positing that when interactions become more positive in stressful environments, fitness outcomes for mutations affecting interactions align across partners and selection should favor greater mutualistic adap-tation and co-adaptation between interacting species. As a corollary, in benign environments, if interactions are strongly antagonistic, we predict antagonistic co-adaptation resulting in Red Queen or arms-race dynamics, or reduction of antagonism through character displacement and niche partitioning. We predict no adaptation if interactions are more neutral. We call this the CoCoA hypothesis: (Co)-adaptation and Conditionality across Abiotic gradients. We describe experimental designs and statistical models that allow testing predictions of CoCoA, with a focus on positive interactions. While only one study has included all the elements to test CoCoA, we briefly review the literature and summarize study findings relevant to CoCoA and highlight opportunities to test CoCoA further.
Adding value to value stocks in Indian stock market: an empirical analysis
Authors: Singh Jaspal , Kaur Kiranpreet
Published: November 2015

Purpose

– The purpose of this study is to examine the relevance of an accounting-based fundamental strategy in adding value to value stocks in Indian stock market. The fundamentals-based investment strategy “F-score”, given by Joseph Piotroski, has been used on stocks having high book-to-market ratio to eliminate the firms with poor future prospects from the entire portfolio of value stocks.

Design/methodology/approach

– The market adjusted performance of all the firms in the sample is examined using one samplet-test. Further, F-score of all the firms in the sample is calculated and the independent samplet-test has been used to examine the significance of mean difference between high-score and low-score firms. Finally, the predictive ability of F-score in explaining the overall stock returns is examined using panel data regression analysis.

Findings

– Results reveal that the mean market-adjusted return of stocks, meeting all constructs of F-score is significantly larger than the entire portfolio of value stocks by 18.402 per cent annually across the period of study. The results of panel data regression made it evident that one-point improvement in aggregate F-score is associated with an about 4.93 per cent increase in one-year market-adjusted return.

Practical implications

– The significant mean return difference found between the high-F-score firms and the low-score firms suggests that an investor could constitute a hedge portfolio that generates positive return by selling expected losers stocks and buying expected winners.

Originality/value

– The present study is the first attempt made in emerging economy like India to enrich the literature on value investing strategies by examining the performance of F-score strategy to separate winners from losers in Indian stock market.
Retaining older workers – analysis of company surveys from 2005 and 2010
Authors: Hermansen Åsmund , Midtsundstad Tove
Published: November 2015

Purpose

– The purpose of this paper is to shed light on developments in Norwegian companies’ active-ageing policies, and hence offer insight into what characterises those Norwegian companies offering measures to retain their older workers.

Design/methodology/approach

– The research questions are investigated using data from two surveys carried out among a representative sample of Norwegian companies in 2005 and 2010. The two data sets are analysed both separately and jointly, being merged to obtain a pooled cross-section data set. Both multivariate logistic and linear regression are applied.

Findings

– The proportion of companies offering retention measures, as well as the extensiveness of their retention efforts (the number of different measures offered), has increased considerably from 2005 to 2010. What characterises these companies however is surprisingly similar in 2005 and 2010. The retention efforts of Norwegian companies seem to be part of a holistic approach to active ageing. Offering a number of different retention measures is more common among companies having initiated “measures to facilitate lifelong learning” and “measures to prevent health problems or reduced work capacity”. The financial incentives embedded in the contractual early retirement scheme seem also to have a significant impact on retention efforts.

Originality/value

– The employers’ perspective has received little attention in previous research and the authors are the first to report on developments in Norwegian companies’ retention efforts over time. Knowledge about what characterises employers offering such measures will be important for future efforts to increase employments rates among older workers, which is an aim for most European countries.
Minoritynationals
Authors: Mullen Cormac , Berrill Jenny
Published: November 2015

Purpose

– This paper aims to conduct a longitudinal analysis of the patterns of internationalisation of multinational corporations and provide a measure of their degree of globalisation at the firm-level. There is much debate in the literature on the regional nature of the globalisation of multinational corporations (Rugman and Oh, 2013).

Design/methodology/approach

– The authors use firm-level sales data to analyse the location of sales and patterns of globalisation of 1,276 companies across ten countries and ten industries from 1998-2012.

Findings

– The results show that while international sales are rising and the proportion of home region-oriented firms is falling, the majority of sales of the companies in our data set continues to be in the Triad, with little growth in non-Triad regions. The authors find one common theme for the majority of countries, an increase in sales to Asia yet concentrated in just four industries, financials, basic materials, oil and gas and technology. Despite an increase in the percentage of host-region, bi-regional and global companies, 62.6 per cent of the firms have not changed multinational classification over the 15-year period, 43.1 per cent have not expanded out of their home region and 16.4 per cent have not expanded out of their home market. The authors find some evidence of liabilities of interregional foreignness at the industry and country level. The authors show regional sales are moving towards matching global economic activity for the 50 most globalised firms in our study but less so for the other firms in our sample. Overall, the results show that the majority of the growth in internationalisation comes from a small minority of firms.

Originality/value

– The authors make several advances across the literature on internationalisation, including a more in-depth longitudinal analysis of firm-level multinationality than exists to date and a novel method of measuring firm-level globalisation.
Regionalization and risk
Authors: Seno-Alday Sandra
Published: November 2015

Purpose

– The purpose of this study is to examine the nature of regional macroeconomic risk by examining the trade networks formed by regional multinational enterprise (MNE) activity at the aggregate level, and exploring the subsequent implications on the vulnerability of those networks to economic shocks.

Design/methodology/approach

– The study draws on contemporary developments in graph theory to revisit the nature and dynamics of complex trade networks in the Southeast Asian region from 1990 to 2012.

Findings

– Findings indicate that the topology of the regional trade network has changed significantly in the period examined, in that it has become denser, more connected and more clustered. Analysis further indicates that disruptions to the trade network during periods of shock have exhibited decreasing levels of magnitude, pointing to greater robustness over time.

Research limitations/implications

– The results show that intra-regional MNE activity has the effect of reducing risk in the region. If MNEs aim to reduce their risk exposure, they must first deepen their commitment to the regional market.

Originality/value

– This paper enriches current understanding of the changing nature of regional risk, and represents one of the first efforts to examine international trade networks in light of recent developments in the understanding of networks beyond the conventional random graph.
Fund manager trust and information complexity
Authors: Henningsson Johan , Johanson Ulf , Almqvist Roland
Published: November 2015

Purpose

– This study aims to explore fund manager use of trust to reduce information complexity concerning corporate intangible resources and sustainability and what consequences this have for corporates as providers of information. Analytically, fund managers are considered part of a system with social meaning.

Design/methodology/approach

– A qualitative research approach is used. Data are obtained from two focus group discussions that occurred on two separate occasions. The first discussion was between four communications executives at leading Swedish companies. The second discussion was between four experienced fund managers in the Swedish financial market.

Findings

– The results suggest that fund managers oscillate between exhibiting trust and distrust when reducing the complexity of information on intangible resources and sustainability. Fund managers tend to trust the stable context of company information and strive to trust top management. Communicative dilemmas emerge when fund managers oscillate between trust and distrust. The fund manager disinterest in details emerges because of a reliance on a stable information context and company management. The representation dilemma emerges when narratives are used in corporate reporting.

Research limitations/implications

– This study contributes empirically to the knowledge concerning the social complexity of fund management.

Practical implications

– The paper increases the understanding of communicative difficulties for corporates to communicate with actors on the financial markets through narratives on intangible resources and sustainability.

Originality/value

– By focusing on the social meaning in the communication between companies and financial markets, we have contrasted the dominant view of financial economics of financial market actors as rational agents and the individualistic mode of theorizing in accordance with rational choice theory.