bluuebunny/crossref_metadata_2025 huggingface dataset:
Nanowire-toughened CVD-SiC coating for C/C composites with surface pre-oxidation
Authors: Jing Jun-Yi , Fu Qian-Gang , Yuan Rui-Mei
Published: February 2017

A combination method of surface pre-treatment and SiC nanowire toughening was proposed to solve the problems of easy cracking and peeling of the SiC coating on carbon/carbon composites. The composition and microstructure of the as-prepared coating were analysed by XRD and SEM. After introducing the buffer layer toughened by SiC nanowire, the bonding force between substrate and coating increased from 6.0 to 18.5 N. After thermal shock between room temperature and 1773 K for 15 cycles, the mass loss of the sample decreased by 67%. The enhancements of interface bonding and thermal shock resistance of the CVD-SiC coating are mainly due to the formation of the nanowire-toughened buffer layer, which could improve the matching compatibility between C/C substrate and CVD-SiC coating.
A Drosophila model of Fragile X syndrome exhibits defects in phagocytosis by innate immune cells
Authors: O’Connor Reed M. , Stone Elizabeth F. , Wayne Charlotte R. , Marcinkevicius Emily V. , Ulgherait Matt , Delventhal Rebecca , Pantalia Meghan M. , Hill Vanessa M. , Zhou Clarice G. , McAllister Sophie , Chen Anna , Ziegenfuss Jennifer S. , Grueber Wesley B. , Canman Julie C. , Shirasu-Hiza Mimi M.
Published: February 2017

Fragile X syndrome, the most common known monogenic cause of autism, results from the loss of FMR1, a conserved, ubiquitously expressed RNA-binding protein. Recent evidence suggests that Fragile X syndrome and other types of autism are associated with immune system defects. We found that Drosophila melanogaster Fmr1 mutants exhibit increased sensitivity to bacterial infection and decreased phagocytosis of bacteria by systemic immune cells. Using tissue-specific RNAi-mediated knockdown, we showed that Fmr1 plays a cell-autonomous role in the phagocytosis of bacteria. Fmr1 mutants also exhibit delays in two processes that require phagocytosis by glial cells, the immune cells in the brain: neuronal clearance after injury in adults and the development of the mushroom body, a brain structure required for learning and memory. Delayed neuronal clearance is associated with reduced recruitment of activated glia to the site of injury. These results suggest a previously unrecognized role for Fmr1 in regulating the activation of phagocytic immune cells both in the body and the brain.
fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy
Authors: Hilsenbeck Oliver , Schwarzfischer Michael , Loeffler Dirk , Dimopoulos Sotiris , Hastreiter Simon , Marr Carsten , Theis Fabian J , Schroeder Timm
Published: February 2017

Motivation

Quantitative large-scale cell microscopy is widely used in biological and medical research. Such experiments produce huge amounts of image data and thus require automated analysis. However, automated detection of cell outlines (cell segmentation) is typically challenging due to, e.g. high cell densities, cell-to-cell variability and low signal-to-noise ratios.

Results

Here, we evaluate accuracy and speed of various state-of-the-art approaches for cell segmentation in light microscopy images using challenging real and synthetic image data. The results vary between datasets and show that the tested tools are either not robust enough or computationally expensive, thus limiting their application to large-scale experiments. We therefore developed fastER, a trainable tool that is orders of magnitude faster while producing state-of-the-art segmentation quality. It supports various cell types and image acquisition modalities, but is easy-to-use even for non-experts: it has no parameters and can be adapted to specific image sets by interactively labelling cells for training. As a proof of concept, we segment and count cells in over 200 000 brightfield images (1388 × 1040 pixels each) from a six day time-lapse microscopy experiment; identification of over 46 000 000 single cells requires only about two and a half hours on a desktop computer.

Availability and Implementation

C ++ code, binaries and data at https://www.bsse.ethz.ch/csd/software/faster.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
Cosmic particle colliders: simulations of self-interacting dark matter with anisotropic scattering
Authors: Robertson Andrew , Massey Richard , Eke Vincent
Published: February 2017

We investigate how self-interacting dark matter (SIDM) with anisotropic scattering affects the evolution of isolated dark matter haloes as well as systems with two colliding haloes. For isolated haloes, we find that the evolution can be adequately captured by treating the scattering as isotropic, as long as the isotropic cross-section is appropriately matched to the underlying anisotropic model. We find that this matching should not be done using the momentum transfer cross-section, as has been done previously. Matching should instead be performed via a modified momentum transfer cross-section that takes into account that dark matter particles can be relabelled after they scatter, without altering the dynamics. However, using cross-sections that are matched to give the same behaviour in isolated haloes, we find that treating dark matter scattering as isotropic underpredicts the effects of anisotropic dark matter scattering when haloes collide. In particular, the DM-galaxy offset induced by SIDM in colliding galaxy clusters is larger when we simulate the underlying particle model, than if we use a matched isotropic model. On the other hand, well-motivated particle models with anisotropic scattering typically have cross-sections with a strong velocity dependence, and we discover a previously unrecognised effect that suppresses DM-galaxy offsets in colliding clusters making it hard for these systems to provide competitive constraints on such particle models.
Phase-resolved pulse propagation through metallic photonic crystal slabs: plasmonic slow light
Authors: Schönhardt Anja , Nau Dietmar , Bauer Christina , Christ André , Gräbeldinger Hedi , Giessen Harald
Published: February 2017

We characterized the electromagnetic field of ultra-short laser pulses after propagation through metallic photonic crystal structures featuring photonic and plasmonic resonances. The complete pulse information, i.e. the envelope and phase of the electromagnetic field, was measured using the technique of cross-correlation frequency resolved optical gating. In good agreement, measurements and scattering matrix simulations show a dispersive behaviour of the spectral phase at the position of the resonances. Asymmetric Fano-type resonances go along with asymmetric phase characteristics. Furthermore, the spectral phase is used to calculate the dispersion of the sample and possible applications in dispersion compensation are investigated. Group refractive indices of 700 and 70 and group delay dispersion values of 90 000 fs
2
and 5000 fs
2
are achieved in transverse electric and transverse magnetic polarization, respectively. The behaviour of extinction and spectral phase can be understood from an intuitive model using the complex transmission amplitude. An associated depiction in the complex plane is a useful approach in this context. This method promises to be valuable also in photonic crystal and filter design, for example, with regards to the symmetrization of the resonances.

This article is part of the themed issue ‘New horizons for nanophotonics’.
Intensity dependences of the nonlinear optical excitation of plasmons in graphene
Authors: Constant T. J. , Hornett S. M. , Chang D. E. , Hendry E.
Published: February 2017

Recently, we demonstrated an all-optical coupling scheme for plasmons, which takes advantage of the intrinsic nonlinear optical response of graphene. Frequency mixing using free-space, visible light pulses generates surface plasmons in a planar graphene sample, where the phase matching condition can define both the wavevector and energy of surface waves and intraband transitions. Here, we also show that the plasmon generation process is strongly intensity-dependent, with resonance features washed out for absorbed pulse fluences greater than 0.1 J m
−2
. This implies a subtle interplay between the nonlinear generation process and sample heating. We discuss these effects in terms of a non-equilibrium charge distribution using a two-temperature model.

This article is part of the themed issue ‘New horizons for nanophotonics’.
Metasurface polarization splitter
Authors: Slovick Brian A. , Zhou You , Yu Zhi Gang , Kravchenko Ivan I. , Briggs Dayrl P. , Moitra Parikshit , Krishnamurthy Srini , Valentine Jason
Published: February 2017

Polarization beam splitters, devices that separate the two orthogonal polarizations of light into different propagation directions, are among the most ubiquitous optical elements. However, traditionally polarization splitters rely on bulky optical materials, while emerging optoelectronic and photonic circuits require compact, chip-scale polarization splitters. Here, we show that a rectangular lattice of cylindrical silicon Mie resonators functions as a polarization splitter, efficiently reflecting one polarization while transmitting the other. We show that the polarization splitting arises from the anisotropic permittivity and permeability of the metasurface due to the twofold rotational symmetry of the rectangular unit cell. The high polarization efficiency, low loss and low profile make these metasurface polarization splitters ideally suited for monolithic integration with optoelectronic and photonic circuits.

This article is part of the themed issue ‘New horizons for nanophotonics’.
Do Candidate Genes Affect the Brain’s White Matter Microstructure? Large-Scale Evaluation of 6,165 Diffusion MRI Scans
Authors: Jahanshad Neda , Ganjgahi Habib , Bralten Janita , den Braber Anouk , Faskowitz Joshua , Knodt Annchen R , Lemaitre Hervé , Nir Talia M , Patel Binish , Richie Stuart , Sprooten Emma , Hoogman Martine , van Hulzen Kimm , Zavaliangos-Petropulu Artemis , Zwiers Marcel P , Almasy Laura , Bastin Mark E , Bernstein Matt A , Blangero John , Curran Joanne , Deary Ian J , de Zubicary Greig I , Duggirala Ravi , Fisher Simon E , Franke Barbara , Fox Peter , Goldman David , Haberg Asta K , Hariri Ahmad , Hong L Elliot , Huentelman Matt , Martin Nicholas G , Martinot Jean-Luc , McIntosh Andrew , McMahon Katie L , Medland Sarah E , Mitchell Braxton D , Muñoz Maniega Susana , Olvera Rene L , Oosterlaan Jaap , Peterson Charles , Royle Natalie , Saykin Andrew J , Schumann Gunter , Starr John , Stein Elliot A , Sussmann Jessika , Valdés Hernández Maria del C. , van’t Ent Dennis , Wardlaw Joanna M , Weiner Michael W , Williamson Douglas E , Winkler Anderson M , Wright Margaret J , Yang Yihong , Thompson Paul M , Glahn David C , Nichols Thomas E , Kochunov Peter
Published: February 2017

Susceptibility genes for psychiatric and neurological disorders - includingAPOE, BDNF, CLU,CNTNAP2, COMT, DISC1, DTNBP1, ErbB4, HFE, NRG1, NTKR3, andZNF804A- have been reported to affect white matter (WM) microstructure in the healthy human brain, as assessed through diffusion tensor imaging (DTI). However, effects of single nucleotide polymorphisms (SNPs) in these genes explain only a small fraction of the overall variance and are challenging to detect reliably in single cohort studies. To date, few studies have evaluated the reproducibility of these results. As part of the ENIGMA-DTI consortium, we pooled regional fractional anisotropy (FA) measures for 6,165 subjects (CEU ancestry N=4,458) from 11 cohorts worldwide to evaluate effects of 15 candidate SNPs by examining their associations with WM microstructure. Additive association tests were conducted for each SNP. We used several meta-analytic and mega-analytic designs, and we evaluated regions of interest at multiple granularity levels. The ENIGMA-DTI protocol was able to detect single-cohort findings as originally reported. Even so, in this very large sample, no significant associations remained after multiple-testing correction for the 15 SNPs investigated. Suggestive associations (1.3×10-4< p < 0.05, uncorrected) were found forBDNF, COMT, andZNF804Ain specific tracts. Meta-and mega-analyses revealed similar findings. Regardless of the approach, the previously reported candidate SNPs did not show significant associations with WM microstructure in this largest genetic study of DTI to date; the negative findings are likely not due to insufficient power. Genome-wide studies, involving large-scale meta-analyses, may help to discover SNPs robustly influencing WM microstructure.
New insights on the pharmacogenomics of antidepressant response from the GENDEP and STAR*D studies: rare variant analysis and high-density imputation
Authors: Fabbri Chiara , Tansey Katherine E. , Perlis Roy H. , Hauser Joanna , Henigsberg Neven , Maier Wolfgang , Mors Ole , Placentino Anna , Rietschel Marcella , Souery Daniel , Breen Gerome , Curtis Charles , Sang-Hyuk Lee , Newhouse Stephen , Patel Hamel , Guipponi Michel , Perroud Nader , Bondolfi Guido , O’Donovan Micheal , Lewis Glyn , Biernacka Joanna M. , Weinshilboum Richard M. , Farmer Anne , Aitchison Katherine J. , Craig Ian , McGuffin Peter , Uher Rudolf , Lewis Cathryn M.
Published: February 2017

Genome-wide association studies have generally failed to identify polymorphisms associated with antidepressant response. Possible reasons include limited coverage of genetic variants that this study tried to address by exome genotyping and dense imputation.

A meta-analysis of Genome-Based Therapeutic Drugs for Depression (GENDEP) and Sequenced Treatment Alternatives to Relieve Depression (STAR*D) studies was performed at SNP, gene and pathway level. Coverage of genetic variants was increased compared to previous studies by adding exome genotypes to previously available genome-wide data and using the Haplotype Reference Consortium panel for imputation. Standard quality control was applied. Phenotypes were symptom improvement and remission after 12 weeks of antidepressant treatment. NEWMEDS consortium samples and Pharmacogenomic Research Network Antidepressant Medication Pharmacogenomic Study (PGRN-AMPS) served for replication.

7,062,950 SNPs were analysed in GENDEP (n=738) and STAR*D (n=1409). rs116692768 (p=1.80e-08,ITGA9(integrin alpha 9)) and rs76191705 (p=2.59e-08,NRXN3(neurexin 3)) were significantly associated with symptom improvement during citalopram/escitalopram treatment. At gene level, no consistent effect was found. At pathway level, the Gene Ontology terms GO:0005694 (chromosome) and GO:0044427 (chromosomal part) were associated with improvement (corrected p=0.007 and 0.045, respectively). The association between rs116692768 and symptom improvement was replicated in PGRN-AMPS (p=0.047), while rs76191705 was not. The two SNPs did not replicate in NEWMEDS.

ITGA9codes for a membrane receptor for neurotrophins andNRXN3is a transmembrane neuronal adhesion receptor involved in synaptic differentiation. Despite their meaningful biological rationale for being involved in antidepressant effect, no convincing replication was achieved. Further studies may help in clarifying their role.
Model-based spike sorting with a mixture of drifting t-distributions
Authors: Shan Kevin Q. , Lubenov Evgueniy V. , Siapas Athanassios G.
Published: February 2017

Chronic extracellular recordings are a powerful tool for systems neuroscience, but spike sorting remains a challenge. A common approach is to fit a generative model, such as a mixture of Gaussians, to the observed spike data. Even if non-parametric methods are used for spike sorting, such generative models provide a quantitative measure of unit isolation quality, which is crucial for subsequent interpretation of the sorted spike trains. We present a spike sorting strategy that models the data as a mixture of drifting t-distributions. This model captures two important features of chronic extracellular recordings—cluster drift over time and heavy tails in the distribution of spikes—and offers improved robustness to outliers. We evaluate this model on several thousand hours of chronic tetrode recordings and show that it fits the empirical data substantially better than a mixture of Gaussians. We also provide a software implementation that can re-fit long datasets (several hours, millions of spikes) in a few seconds, enabling interactive clustering of chronic recordings. Using experimental data, we identify three common failure modes of spike sorting methods that assume stationarity. We also characterize the limitations of several popular unit isolation metrics in the presence of empirically-observed variations in cluster size and scale. We find that the mixture of drifting t-distributions model enables efficient spike sorting of long datasets and provides an accurate measure of unit isolation quality over a wide range of conditions.
A fast and accurate algorithm to test for binary phenotypes and its application to PheWAS
Authors: Dey Rounak , Schmidt Ellen M. , Abecasis Goncalo R. , Lee Seunggeun
Published: February 2017

The availability of electronic health record (EHR)-based phenotypes allows for genome-wide association analyses in thousands of traits, and has great potential to identify novel genetic variants associated with clinical phenotypes. We can interpret the phenome-wide association study (PheWAS) result for a single genetic variant by observing its association across a landscape of phenotypes. Since PheWAS can test 1000s of binary phenotypes, and most of them have unbalanced (case:control = 1:10) or often extremely unbalanced (case:control = 1:600) case-control ratios, existing methods cannot provide an accurate and scalable way to test for associations. Here we propose a computationally fast score test-based method that estimates the distribution of the test statistic using the saddlepoint approximation. Our method is much faster than the state of the art Firth’s test (∼ 100 times). It can also adjust for covariates and control type I error rates even when the case-control ratio is extremely unbalanced. Through application to PheWAS data from the Michigan Genomics Initiative, we show that the proposed method can control type I error rates while replicating previously known association signals even for traits with a very small number of cases and a large number of controls.
Outer membrane lipid homeostasis via retrograde phospholipid transport inEscherichia coli
Authors: Shrivastava Rahul , Jiang Xiang’Er , Chng Shu-Sin
Published: February 2017

Biogenesis of the outer membrane (OM) in Gram-negative bacteria, which is essential for viability, requires the coordinated transport and assembly of proteins and lipids, including lipopolysaccharides (LPS) and phospholipids (PLs), into the membrane. While pathways for LPS and OM protein assembly are well-studied, how PLs are transported to and from the OM is not clear. Mechanisms that ensure OM stability and homeostasis are also unknown. The trans-envelope Tol-Pal complex, whose physiological role has remained elusive, is important for OM stability. Here, we establish that the Tol-Pal complex is required for PL transport and OM lipid homeostasis inEscherichia coli. Cells lacking the complex exhibit defects in lipid asymmetry and accumulate excess phospholipids (PLs) in the OM. This imbalance in OM lipids is due to defective retrograde PL transport in the absence of a functional Tol-Pal complex. Thus, cells ensure the assembly of a stable OM by maintaining an excess flux of PLs to the OM only to return the surplus to the inner membrane. Our findings also provide insights into the mechanism by which the Tol-Pal complex may promote OM invagination during cell division.
Automated 3D Neuron Tracing with Precise Branch Erasing and Confidence Controlled Back-Tracking
Authors: Liu Siqi , Zhang Donghao , Song Yang , Peng Hanchuan , Cai Weidong
Published: February 2017

The automatic reconstruction of single neuron cells from microscopic images is essential to enabling large-scale data-driven investigations in neuron morphology research. However, few previous methods were able to generate satisfactory results automatically from 3D microscopic images without human intervention. In this study, we developed a new algorithm for automatic 3D neuron reconstruction. The main idea of the proposed algorithm is to iteratively track backwards from the potential neuronal termini to the soma centre. An online confidence score is computed to decide if a tracing iteration should be stopped and discarded from the final reconstruction. The performance improvements comparing to the previous methods are mainly introduced by a more accurate estimation of the traced area and the confidence controlled back-tracking algorithm. The proposed algorithm supports large-scale batch-processing by requiring only one hyper-parameter for background segmentation. We bench-tested the proposed algorithm on the images obtained from both the DIADEM challenge and the BigNeuron challenge. Our proposed algorithm achieved the state-of-the-art results.
Bird interactions with drones, from individuals to large colonies
Authors: Lyons Mitchell , Brandis Kate , Callaghan Corey , McCann Justin , Mills Charlotte , Ryall Sharon , Kingsford Richard
Published: February 2017

Drones are rapidly becoming a key part of the toolkit for a range of scientific disciplines, as well as a range of management and commercial applications. This presents a number of challenges in context of how drone use might impact nearby wildlife. Interactions between birds and drones naturally come to mind, since they share the airspace. This paper details initial findings on the interactions between drones and birds for a range of waterbird, passerine and raptor species, across of a range of scientific applications and natural environments. The primary aims of this paper are to provide guidance for those planning or undertaking drone monitoring exercises, as well as provide direction for future research into safe and effective monitoring with drones. Our study sites we all located within Australia and spanned a range of arid, semi-arid, dunefield, floodplain, wetland, woodland, forest, coastal heath and urban environments. We particularly focus on behavioral changes towards drones during breeding season, interactions with raptors, and effects on nesting birds in large colonies – three areas yet to be explored in published literature. In over 70 hours of flight, there were no incidents with birds. Although some aggressive behavior was encountered from solitary breeding birds. Several large breeding bird colonies were surveyed, and included in our observations is monitoring and counting of nests in a colony of over 200,000 Straw-necked Ibis, the largest drone-based bird monitoring exercise to date. In addition to providing observations of interactions with specific bird species, we recommend procedures for flight planning, safe flying and avoidance. This paper also provides a basis for a number of critical and emerging areas of research into bird-drone interactions, most notably, territorial breeding birds, safety around large raptors, and the effect of drones on the behaviour of birds in large breeding colonies.
A cell based, high throughput assay for quantitative analysis of Hedgehog pathway activation using a Smoothened phosphorylation sensor
Authors: Albert Eugene A. , Bökel Christian
Published: February 2017

The Hedgehog (Hh) signalling cascade is conserved across evolution and plays an important role in development and disease. In the absence of Hh, activity of the key signal transducer Smoothened (Smo) is downregulated by the Hh receptor Patched (Ptc). However, the mechanisms underlying this inhibition, and especially its release upon ligand stimulation, are still poorly understood, in part because tools for directly following Smo activation at the subcellular level were long lacking. Here we present a high throughput, cell culture assay based on a fluorescent sensor forDrosophilaSmo phosphorlyation. Using this approach we could first demonstrate that the graded response to increasing Hh levels observed at the population level can be traced back to threshold responses of individual cells exhibiting differential Hh sensitivity. Second, we screened a small molecule inhibitor library for regulators of Smo phosphorylation. We observed increased Smo sensor fluorescence with compounds aimed at two major target groups, the MAPK signalling cascade and polo and aurora kinases. Biochemical validation confirmed the screen results for selected inhibitors (dobrafenib, tak-733, volasertib) and revealed differences in the mode of Smo activation, demonstrating that the assay is in principle suitable for dissecting the cell biological basis of Hh pathway activation.
Meiotic recombination modulates the structure and dynamics of the synaptonemal complex duringC. elegansmeiosis
Authors: Pattabiraman Divya , Roelens Baptiste , Woglar Alexander , Villeneuve Anne M.
Published: February 2017

During meiotic prophase, a structure called the synaptonemal complex (SC) assembles at the interface between aligned pairs of homologous chromosomes, and crossover recombination events occur between their DNA molecules. Here we investigate the inter-relationships between these two hallmark features of the meiotic program in the nematodeC. elegans, revealing dynamic properties of the SC that are modulated by recombination. We demonstrate that the SC incorporates new subunits and switches from a more highly dynamic/labile state to a more stable state as germ cells progress through the pachytene stage of meiotic prophase. We further show that the more dynamic state of the SC is prolonged in mutants where meiotic recombination is impaired. Moreover, in meiotic mutants where recombination intermediates are present in limiting numbers, SC central region subunits become preferentially stabilized on the subset of chromosome pairs that harbor a site where pro-crossover factors COSA-1 and MutSγare concentrated. Polo-like kinase PLK-2 becomes preferentially localized to the SCs of chromosome pairs harboring recombination sites prior to the enrichment of SC central region proteins on such chromosomes, and PLK-2 is required for this enrichment to occur. Further, late pachytene nuclei in aplk-2mutant exhibit the more highly dynamic SC state. Together our data demonstrate that crossover recombination events elicit chromosome-autonomous stabilizing effects on the SC and implicate PLK-2 in this process. We discuss how this recombination-triggered modulation of SC state might contribute to regulatory mechanisms that operate during meiosis to ensure the formation of crossovers while at the same time limiting their numbers.
Evolinc: a comparative transcriptomics and genomics pipeline for quickly identifying sequence conserved lincRNAs for functional analysis
Authors: Nelson Andrew D. L. , Devisetty Upendra K. , Palos Kyle , Haug-Baltzell Asher K. , Lyons Eric , Beilstein Mark A.
Published: February 2017

Long intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class of eukaryotic transcripts. Reported lincRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, covering ~90% of the genome. In addition to elucidating function, there is particular interest in understanding the origin and evolution of lincRNAs. Aside from mammals, lincRNA populations have been sparsely sampled, precluding evolutionary analyses focused on lincRNA emergence and persistence. Here we present Evolinc, a two-module pipeline designed to facilitate lincRNA discovery and characterize aspects of lincRNA evolution. The first module (Evolinc-I) is a lincRNA identification workflow that also facilitates downstream differential expression analysis and genome browser visualization of identified lincRNAs. The second module (Evolinc-II) is a genomic and transcriptomic comparative analyses workflow that determines the phylogenetic depth to which a lincRNA locus is conserved within a user-defined group of related species. Evolinc-II builds families of homologous lincRNA loci, aligns constituent sequences, infers gene trees, and then uses gene tree / species tree reconciliation to reconstruct evolutionary processes such as gain, loss, or duplication of the locus. Here we demonstrate that Evolinc-I is agnostic to target organism by validating against previously annotated Arabidopsis and human lincRNA data. Using Evolinc-II, we examine ways in which conservation can rapidly be used to winnow down large lincRNA datasets to a small set of candidates for functional analysis. Finally, we show how Evolinc-II can be used to recover the evolutionary history of a known lincRNA, the human telomerase RNA (TERC). The analyses revealed unexpected duplication events as well as the loss and subsequent acquisition of a novel TERC locus in the lineage leading to mice and rats. The Evolinc pipeline is currently integrated in CyVerse’s Discovery Environment and is free to use by researchers.
Point focusing with flat and wedged crossed multilayer Laue lenses
Authors: Kubec Adam , Melzer Kathleen , Gluch Jürgen , Niese Sven , Braun Stefan , Patommel Jens , Burghammer Manfred , Leson Andreas
Published: February 2017

Point focusing measurements using pairs of directly bonded crossed multilayer Laue lenses (MLLs) are reported. Several flat and wedged MLLs have been fabricated out of a single deposition and assembled to realise point focusing devices. The wedged lenses have been manufactured by adding a stress layer onto flat lenses. Subsequent bending of the structure changes the relative orientation of the layer interfaces towards the stress-wedged geometry. The characterization at ESRF beamline ID13 at a photon energy of 10.5 keV demonstrated a nearly diffraction-limited focusing to a clean spot of 43 nm × 44 nm without significant side lobes with two wedged crossed MLLs using an illuminated aperture of approximately 17 µm × 17 µm to eliminate aberrations originating from layer placement errors in the full 52.7 µm × 52.7 µm aperture. These MLLs have an average individual diffraction efficiency of 44.5%. Scanning transmission X-ray microscopy measurements with convenient working distances were performed to demonstrate that the lenses are suitable for user experiments. Also discussed are the diffraction and focusing properties of crossed flat lenses made from the same deposition, which have been used as a reference. Here a focal spot size of 28 nm × 33 nm was achieved and significant side lobes were noticed at an illuminated aperture of approximately 23 µm × 23 µm.
XDesign: an open-source software package for designing X-ray imaging phantoms and experiments
Authors: Ching Daniel J. , Gürsoy Dogˇa
Published: February 2017

The development of new methods or utilization of current X-ray computed tomography methods is impeded by the substantial amount of expertise required to design an X-ray computed tomography experiment from beginning to end. In an attempt to make material models, data acquisition schemes and reconstruction algorithms more accessible to researchers lacking expertise in some of these areas, a software package is described here which can generate complex simulated phantoms and quantitatively evaluate new or existing data acquisition schemes and image reconstruction algorithms for targeted applications.
Synthesis, crystal structure, DFT studies and photophysical properties of a copper(I)–triphenylphosphane complex based on trans-(±)-2,4,5-tris(pyridin-2-yl)-2-imidazoline
Authors: Báez-Castro Alberto , Baldenebro-López Jesús , Ceballos-Mendivil Laura , Román-Bravo Perla P. , Höpfl Herbert , Miranda-Soto Valentín , Glossman-Mitnik Daniel , Cruz-Enríquez Adriana , Campos-Gaxiola José J.
Published: February 2017

The possibility of using less expensive and nontoxic metals, such as copper, as substitutes for more expensive heavy metals in the synthesis of new transition-metal complexes to be used as sensitizers in dye-sensitized solar cells (DSSCs) has stimulated research in this field. The novel photoluminescent copper(I) complex bis(triphenylphosphane-κP)[trans-(±)-2,4,5-tris(pyridin-2-yl)-2-imidazoline-κ2
N
2,N
3]copper(I) hexafluorophosphate, [CuI(C18H15N5)(C18H15P)2]PF6, has been successfully synthesized and characterized by IR and 1H NMR spectroscopy, as well as by single-crystal X-ray diffraction and thermogravimetric analysis. The complex showed interesting photophysical properties, which were studied experimentally in solution and in the solid state by UV–Vis and fluorescence spectroscopy. Density functional theory (DFT) calculations with dichloromethane as solvent reproduced reasonably well the HOMO and LUMO orbitals of the title compound.
Crystal structure of full-lengthZika virusNS5 protein reveals a conformation similar toJapanese encephalitis virusNS5
Authors: Upadhyay Anup K. , Cyr Matthew , Longenecker Kenton , Tripathi Rakesh , Sun Chaohong , Kempf Dale J.
Published: February 2017

The rapid spread of the recentZika virus(ZIKV) epidemic across various countries in the American continent poses a major health hazard for the unborn fetuses of pregnant women. To date, there is no effective medical intervention. The nonstructural protein 5 ofZika virus(ZIKV-NS5) is critical for ZIKV replication through the 5′-RNA capping and RNA polymerase activities present in its N-terminal methyltransferase (MTase) and C-terminal RNA-dependent RNA polymerase (RdRp) domains, respectively. The crystal structure of the full-length ZIKV-NS5 protein has been determined at 3.05 Å resolution from a crystal belonging to space groupP21212 and containing two protein molecules in the asymmetric unit. The structure is similar to that reported for the NS5 protein fromJapanese encephalitis virusand suggests opportunities for structure-based drug design targeting either its MTase or RdRp domain.
Crystallization of FcpA fromLeptospira, a novel flagellar protein that is essential for pathogenesis
Authors: San Martin Fabiana , Mechaly Ariel E. , Larrieux Nicole , Wunder Elsio A. , Ko Albert I. , Picardeau Mathieu , Trajtenberg Felipe , Buschiazzo Alejandro
Published: February 2017

The protein FcpA is a unique component of the flagellar filament of spirochete bacteria belonging to the genusLeptospira. Although it plays an essential role in translational motility and pathogenicity, no structures of FcpA homologues are currently available in the PDB. Its three-dimensional structure will unveil the novel motility mechanisms that render pathogenicLeptospiraparticularly efficient at invading and disseminating within their hosts, causing leptospirosis in humans and animals. FcpA fromL. interroganswas purified and crystallized, but despite laborious attempts no useful X ray diffraction data could be obtained. This challenge was solved by expressing a close orthologue from the related saprophytic speciesL. biflexa. Three different crystal forms were obtained: a primitive and a centred monoclinic form, as well as a hexagonal variant. All forms diffracted X-rays to suitable resolutions for crystallographic analyses, with the hexagonal type typically reaching the highest limits of 2.0 Å and better. A variation of the quick-soaking procedure resulted in an iodide derivative that was instrumental for single-wavelength anomalous diffraction methods.
Similarities in the structure of the transcriptional repressor AmtR in two different space groups suggest a model for the interaction with GlnK
Authors: Sevvana Madhumati , Hasselt Kristin , Grau Florian C. , Burkovski Andreas , Muller Yves A.
Published: February 2017

AmtR belongs to the TetR family of transcription regulators and is a global nitrogen regulator that is induced under nitrogen-starvation conditions inCorynebacterium glutamicum. AmtR regulates the expression of transporters and enzymes for the assimilation of ammonium and alternative nitrogen sources, for example urea, amino acidsetc. The recognition of operator DNA by homodimeric AmtR is not regulated by small-molecule effectors as in other TetR-family members but by a trimeric adenylylated PII-type signal transduction protein named GlnK. The crystal structure of ligand-free AmtR (AmtRorth) has been solved at a resolution of 2.1 Å in space groupP21212. Comparison of its quaternary assembly with the previously solved native AmtR structure (PDB entry 5dy1) in a trigonal crystal system (AmtRtri) not only shows how a solvent-content reduction triggers a space-group switch but also suggests a model for how dimeric AmtR might stoichiometrically interact with trimeric adenylylated GlnK.
Crystal structure of bis(μ-3-nitrobenzoato)-κ3O,O′:O;κ3O:O,O′-bis[bis(3-cyanopyridine-κN1)(3-nitrobenzoato-κ2O,O′)cadmium]
Authors: Hökelek Tuncer , Akduran Nurcan , Özen Azer , Uğurlu Güventürk , Necefoğlu Hacali
Published: February 2017

The asymmetric unit of the title compound, [Cd2(C7H4NO4)4(C6H4N2)4], contains one CdIIatom, two 3-nitrobenzoate (NB) anions and two 3-cyanopyridine (CPy) ligands. The two CPy ligands act as monodentate N(pyridine)-bonding ligands, while the two NB anions act as bidentate ligands through the carboxylate O atoms. The centrosymmetric dinuclear complex is generated by application of inversion symmetry, whereby the CdIIatoms are bridged by the carboxylate O atoms of two symmetry-related NB anions, thus completing the distorted N2O5pentagonal–bipyramidal coordination sphere of each CdIIatom. The benzene and pyridine rings are oriented at dihedral angles of 10.02 (7) and 5.76 (9)°, respectively. In the crystal, C—H...N hydrogen bonds link the molecules, enclosingR22(26) ring motifs, in which they are further linkedviaC—H...O hydrogen bonds, resulting in a three-dimensional network. In addition, π–π stacking interactions between parallel benzene rings and between parallel pyridine rings of adjacent molecules [shortest centroid-to-centroid distances = 3.885 (1) and 3.712 (1) Å, respectively], as well as a weak C—H...π interaction, may further stabilize the crystal structure.
Bis(μ2-N-methyl-N-phenyldithiocarbamato)-κ3S,S′:S;κ3S:S,S′-bis[(N-methyl-N-phenyldithiocarbamato-κ2S,S′)cadmium]: crystal structure and Hirshfeld surface analysis
Authors: Suwardi Siti Aisyah Nabilah , Lee See Mun , Lo Kong Mun , Jotani Mukesh M. , Tiekink Edward R. T.
Published: February 2017

The title compound, [Cd2(C8H8NS2)4], is a centrosymmetric dimer with both chelating and μ2-tridentate dithiocarbamate ligands. The resulting S5donor set defines a CdIIcoordination geometry intermediate between square-pyramidal and trigonal–bipyramidal, but tending towards the former. The packing features C—H...S and C—H...π interactions, which generate a three-dimensional network. The influence of these interactions, along with intra-dimer π–π interactions between chelate rings, has been investigated by an analysis of the Hirshfeld surface.
3-Hydroxy-2-[(4-hydroxybenzyl)azaniumyl]propanoate monohydrate
Authors: Gao Min , Lu Li-Ping
Published: February 2017

In the title hydrated zwitterion, C10H13NO4·H2O, the N—C—C—OH side chain shows agaucheconformation [torsion angle = −59.05 (18)°]. In the crystal, the components are linked by O—H...O, N—H...O and C—H...O hydrogen bonds to generate a three-dimensional supramolecular network.
1,4-Bis(1H-1,2,4-triazol-1-yl)benzene
Authors: Du Ran , Meng Li , Lu Li-Ping
Published: February 2017

The complete molecule of the title compound, C10H8N6, is generated by crystallographic inversion symmetry; the dihedral angle between the planes of the benzene and triazole rings is 16.7 (2)°. In the crystal, inversion dimers linked by pairs of weak C—H...N hydrogen bonds generateR22(6) loops. Weak aromatic π–π stacking interactions [centroid–centroid separation = 3.809 (1) Å] are also observed.
An empirical analysis of the relationship between the information quality of CSR reporting and reputation among publicly traded companies in Spain
Authors: Pérez Andrea , Lopez-Gutierrez Carlos
Published: February 2017

Purpose

Supported by the principles of the legitimacy theory, the purpose of this paper is to explore the relationship that exists between the information quality of the corporate social responsibility (CSR) reporting provided by the most liquid companies operating in the Spanish Stock Market and their corporate reputation.

Design/methodology/approach

Three regression models are tested with panel data collected for a sample of the 35 most liquid companies operating in the Spanish Stock Market between 2004 and 2014.

Findings

The findings show that two axes of information quality (i.e. content and management systems) should be necessarily controlled by companies in order to improve their corporate reputation through their CSR reporting. The content axis refers to the compliance of CSR reports with the provision of qualitative, quantitative, and evaluative information concerning the impacts of the CSR of the company on society and the environment. The management systems axis refers to the compliance of CSR reports with the disclosure of details about the policies, plans, and actions that companies implement to assure an effective management of CSR initiatives.

Originality/value

Previous literature exploring the relationship between corporate reporting and reputation has frequently focused on either the impact of the quantity of financial and CSR information reported by companies and the role of information quality, but only in reference to a number of specific themes (environment, customers) and not to the full range of information covered by CSR reports. The authors of this paper extend on previous academic literature by empirically evaluating the relationship between two dimensions of the information quality of CSR reporting (content and management systems) and the corporate reputation of companies operating in the Spanish Stock Market.
Relationship between work-family balance, employee well-being and job performance
Authors: Medina-Garrido José Aurelio , Biedma-Ferrer José María , Ramos-Rodríguez Antonio Rafael
Published: February 2017

Purpose

The purpose of this paper is to assess the impact of the existence of and access to different work-family policies on employee well-being (EWB) and job performance.

Design/methodology/approach

Hypothesis testing was performed using a structural equation model based on a PLS-SEM approach applied to a sample of 1,511 employees of the Spanish banking sector.

Findings

The results obtained demonstrate that the existence and true access to different types of work-family policies such as flexible working hours (flexi-time), long leaves, and flexible work location (flexi-place) are not directly related to job performance, but indirectly so, when mediated by the well-being of employees generated by work-family policies. In a similar vein, true access to employee and family support services also has an indirect positive impact on job performance mediated by the well-being produced. In contrast, the mere existence of employee and family support services does not have any direct or indirect effect on job performance.

Originality/value

This study makes a theoretical and empirical contribution to better understand the impact that of the existence of and access to work-family policies on job performance mediated by EWB. In this sense, the authors posited and tested an unpublished theoretical model where the concept of EWB gains special relevance at academic and organizational level due to its implications for human resource management.
Family involvement and the impact of information and communication technology on performance
Authors: Gargallo Castel Ana Felicitas , Galve Górriz Carmen
Published: February 2017

Purpose

The purpose of this paper is to explore the moderated effect of family involvement on the relationship between information and communication technology (ICT) and firm performance.

Design/methodology/approach

According to agency and transaction cost theories, distinctive family business characteristics provide a unique context that favours a more efficient use of ICT. The authors perform a multivariate analysis that includes the moderating effect of family involvement and considers the possible endogeneity of the ICT variable.

Findings

The results, using a large panel of Spanish manufacturing firms, confirm the importance of family involvement for explaining differences in terms of the impact of this technology in family and non-family businesses. The relationship between ICT and performance is stronger for family firms than for non-family firms.

Research implications

The paper provides new evidence for the academic literature on ICT impact and family firms. It corroborates the importance of using an organizational perspective to explain differences in the effect of ICT on performance.

Practical implications

Family firms should understand the opportunities that family involvement offers regarding ICT impact on performance, and exploit this moderating effect to achieve competitive advantages.

Originality/value

No previous studies deal with the impact of family involvement on ICT-performance analysis. This study fills this gap and increases the understanding of how family business involvement moderates the ICT-performance relationship.
Designing robust model for banks benchmarking based on Rembrandt method and DEA
Authors: Karbassi Yazdi Amir , Abdi Farshid
Published: February 2017

Purpose

The purpose of this paper is to find excellent banks on the basis of identified variables. First of all, banks are evaluated based on operation costs, deposits, staff, investments, net profit, and loans variables. Subsequently, these variables are categorized into inputs and outputs. The performances of the banks based on these variables are analyzed by data envelopment analysis (DEA) method to find efficiency and inefficiency of decision making units (DMUs).

Design/methodology/approach

This research is aimed to determine the best banks based on predetermined indicators. The indicators are categorized into inputs and outputs. DEA method is used to find efficiency and inefficiency of DMU. However, the aim is to find the efficient banks and to implement the model by using AP Super Efficiency method in order to find the most efficient unit for benchmarking. However, some inputs and outputs have more priority for banks than the others, as a result it will require some changes.

Findings

The results indicate that among 13 banks, including ten public and three private, solely five public banks are efficient. Moreover, DEA is used as a benchmarking tool for inefficient banks to be efficient. Among these banks ten of them are public banks and three are private. Among efficient ones, all are public banks. Moreover, five of public banks and three of private are inefficient.

Originality/value

In some cases, inputs and outputs have more priority for DMs than the others, as a result it will require some changes. Also, if one of the inputs or outputs is larger in number than the others, the DMU becomes efficient, despite its low priority. Thus, for solving this problem, the indicators of this research are ranked by Rembrandt method considering the existing ones to find the best banks (best DMU) based on their performance and the relevant indicators.