bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanically Resolved Imaging of Bacteria using Expansion Microscopy
Authors: Lim Youngbin , Khariton Margarita , Lane Keara M. , Shiver Anthony L. , Ng Katharine M. , Bray Samuel R. , Qin Jian , Huang Kerwyn Casey , Wang Bo
Published: April 2019

Imaging dense and diverse microbial communities has broad applications in basic microbiology and medicine, but remains a grand challenge due to the fact that many species adopt similar morphologies. While prior studies have relied on techniques involving spectral labeling, we have developed an expansion microscopy method (μExM) in which cells are physically expanded prior imaging and their expansion patterns depend on the structural and mechanical properties of their cell walls, which vary across species and conditions. We use this phenomenon as a quantitative and sensitive phenotypic imaging contrast orthogonal to spectral separation in order to resolve bacterial cells of different species or in distinct physiological states. Focusing on host-microbe interactions that are difficult to quantify through fluorescence alone, we demonstrate the ability of μExM to distinguish species within a dense community throughin vivoimaging of a model gut microbiota, and to sensitively detect cell-envelope damage caused by antibiotics or previously unrecognized cell-to-cell phenotypic heterogeneity among pathogenic bacteria as they infect macrophages.
Morphogenesis and dynamics of slime molds in various environments
Authors: Patino-Ramirez Fernando , Boussard Aurèle , Arson Chloé , Dussutour Audrey
Published: April 2019

Cells, including unicellulars, are highly sensitive to external constraints from their environment. Amoeboid cells change their cell shape during locomotion and in response to external stimuli. Physarum polycephalum is a large multinucleated amoeboid cell that extends and develops pseudopods. In this paper, changes in cell behavior and shape were measured during the exploration of homogenous and non-homogenous environments that presented neutral, and nutritive and/or adverse substances. In the first place, we developed a fully automated image analysis method to measure quantitatively changes in both migration and shape. Then we measured various metrics that describe the area covered, the exploration dynamics, the migration rate and the slime mold shape. Our results show that: 1) Not only the nature, but also the spatial distribution of chemical substances affect the exploration behavior of slime molds; 2) Nutritive and adverse substances both slow down the exploration and prevent the formation of pseudopods; and 3) Slime mold placed in an adverse environment preferentially occupies previously explored areas rather than unexplored areas using mucus secretion as a buffer. Our results also show that slime molds migrate at a rate governed by the substrate up until they get within a critical distance to chemical substances.

Author summary

Physarum polycephalum, also called slime mold, is a giant single-celled organism that can grow to cover several square meters, forming search fronts that are connected to a system of intersecting veins. An original experimental protocol allowed tracking the shape of slime mold placed in homogenous substrates containing an attractant (glucose) or a repellent (salt), or inhomogeneous substrates that contained an attractive spot (glucose), an eccentric slime mold and a repulsive spot (salt) in between. For the first time, the rate of exploration of unexplored areas (primary growth) and the rate of extension in previously explored areas (secondary growth) were rigorously measured, by means of a sophisticated image analysis program. This paper shows that the chemical composition of the substrate has more influence on the morphology and growth dynamics of slime mold than that of concentrated spots of chemicals. It was also found that on a repulsive substrate, slime mold exhibits a bias towards secondary growth, which suggests that the mucus produced during slime mold migration acts as a protective shell in adverse environments.
Artifact-free, high-temporal-resolutionin vivoopto-electrophysiology with microLED optoelectrodes
Authors: Kim Kanghwan , Vöröslakos Mihály , Seymour John P. , Wise Kensall D. , Buzsáki György , Yoon Euisik
Published: April 2019

The combination ofin vivoextracellular recording and genetic-engineering-assisted optical stimulation is a powerful tool for the study of neuronal circuits. Precise analysis of complex neural circuits requires high-density integration of multiple cellular-size light sources and recording electrodes. However, high-density integration inevitably introduces stimulation artifact. We present minimal-stimulation-artifact (miniSTAR) µLED optoelectrodes that enable effective elimination of stimulation artifact. A multi-metal-layer structure with a shielding layer effectively suppresses capacitive coupling of stimulation signals. A heavily-boron-doped silicon substrate silences the photovoltaic effect induced from LED illumination. With transient stimulation pulse shaping, we reduced stimulation artifact on miniSTAR µLED optoelectrodes to below 50 µVpp, much smaller than a typical spike detection threshold, at optical stimulation of > 50 mW mm-2irradiance. We demonstrated high-temporal resolution (< 1 ms) opto-electrophysiology without any artifact-induced signal quality degradation duringin vivoexperiments. MiniSTAR µLED optoelectrodes will facilitate functional mapping of local circuits and discoveries in the brain.
Phase-specific microstimulation in brain machine interface setting differentially modulates beta oscillations and affects behavior
Authors: Peles Oren , Werner-Reiss Uri , Bergman Hagai , Israel Zvi , Vaadia Eilon
Published: April 2019

It is widely accepted that beta-band oscillations play a role in sensorimotor behavior. To further explore this role, we developed a novel hybrid platform to combine operant conditioning and phase-specific intracortical microstimulation (ICMS). We trained monkeys, implanted with 96 electrodes arrays in motor cortex, to volitionally enhance local field potential (LFP) beta-band (20-30Hz) activity at selected sites using a brain-machine interface (BMI). We demonstrate that beta oscillations of LFP and single-unit spiking activity increased dramatically with BMI training, and that pre-movement Beta-power was anti-correlated with task performance. We also show that phase-specific ICMS modulated the power and phase of oscillations, shifting local networks between oscillatory and non-oscillatory states. Furthermore, ICMS induced phase-dependent effects in animal reaction times and success rates. These findings contribute to unraveling of the functional role of cortical oscillations, and to future development of clinical tools for ameliorating abnormal neuronal activities in brain diseases.
Acquisition of Temporal Order Involves a Reverberating Network in Hippocampal Field CA3
Authors: Gunn B.G. , Cox B.M. , Cox C.D. , Le A.A. , Inshishian V.C. , Gall C.M. , Lynch G.
Published: April 2019

Here we report that hippocampal field CA3 maintains self-sustained activity for remarkable periods following a brief input and that this effect is extremely sensitive to minor perturbations. Using novel behavioral tests, that as with human episodic learning do not involve training or explicit rewards, we show that partial silencing of the network in mice blocks acquisition of temporal order, but not the identity or location, of odors. These results suggest a solution to the question of how hippocampus adds time to episodic memories.
Structural and Functional Characterization of G Protein-Coupled Receptors with Deep Mutational Scanning
Authors: Jones Eric M. , Lubock Nathan B. , Venkatakrishnan AJ , Wang Jeffrey , Tseng Alex M. , Paggi Joseph M. , Latorraca Naomi R. , Cancilla Daniel , Satyadi Megan , Davis Jessica E. , Babu M. Madan , Dror Ron O. , Kosuri Sriram
Published: April 2019

In humans, the 813 G protein-coupled receptors (GPCRs) are responsible for transducing diverse chemical stimuli to alter cell state, and are the largest class of drug targets. Their myriad structural conformations and various modes of signaling make it challenging to understand their structure and function. Here we developed a platform to characterize large libraries of GPCR variants in human cell lines with a barcoded transcriptional reporter of G-protein signal transduction. We tested 7,800 of 7,828 possible single amino acid substitutions to the beta-2 adrenergic receptor (β2AR) at four concentrations of the agonist isoproterenol. We identified residues specifically important for β2AR signaling, mutations in the human population that are potentially loss of function, and residues that modulate basal activity. Using unsupervised learning, we resolve residues critical for signaling, including all major structural motifs and molecular interfaces. We also find a previously uncharacterized structural latch spanning the first two extracellular loops that is highly conserved across Class A GPCRs and is conformationally rigid in both the inactive and active states of the receptor. More broadly, by linking deep mutational scanning with engineered transcriptional reporters, we establish a generalizable method for exploring pharmacogenomics, structure and function across broad classes of drug receptors.
Long noncoding RNAAVANpromotes antiviral innate immunity by interacting with TRIM25 and enhancing the transcription of FOXO3a
Authors: Lai Chengcai , Liu Lihui , Liu Qinghua , Cheng Sijie , Wang Keyu , Zhao Lingna , Xia Min , Wang Cheng , Gu Hongjing , Duan Yueqiang , Zhao Zhongpeng , Zhang Lili , Liu Ziyang , Luo Jianjun , Song Jianxun , Yang Penghui , Chen Runsheng , Wang Xiliang
Published: April 2019

Accumulating evidence has shown that long noncoding RNAs (lncRNAs) are involved in several biological processes, including immune responses. However, the role of lncRNAs in antiviral innate immune responses remains largely unexplored. Here, we identify an uncharacterized human lncRNA from influenza A virus (IAV) patients, antivirus and activate neutrophil (AVAN), that is significantly up-regulated upon virus infection. Mechanistically, nuclear lncRNA-AVANpositively regulates the transcription of forkhead box O3A (FOXO3a) by associating with its promoter and inducing chromatin remodeling to promote neutrophil chemotaxis. Furthermore, we also found that cytoplasmic lncRNA-AVANdirectly binds tripartite motif containing 25 (TRIM25) and enhances the association of TRIM25 and Retinoic acid inducible gene-1 proteins (RIG-I) and the ubiquitylation of RIG-I, thereby promoting TRIM25- and RIG-I-mediated antiviral innate immune signaling. More importantly, we enforced the expression of AVAN in transgenic mice and found that it significantly alleviated IAV virulence and virus production. Collectively, these findings highlight the potential clinical implications of lncRNA-AVANas a key positive regulator of the antiviral innate immune response and a promising target for developing broad antiviral therapeutics.
Hierarchical Network Exploration using Gaussian Mixture Models
Authors: Mathews James , Nadeem Saad , Pouryahya Maryam , Belkhatir Zehor , Deasy Joseph O. , Tannenbaum Allen
Published: April 2019

We present a framework based on optimal mass transport to construct, for a given network, a reduction hierarchy which can be used for interactive data exploration and community detection. Given a network and a set of numerical data samples for each node, we calculate a new computationally-efficient comparison metric between Gaussian Mixture Models, the Gaussian Mixture Transport distance, to determine a series of merge simplifications of the network. If only a network is given, numerical samples are synthesized from the network topology. The method has its basis in the local connection structure of the network, as well as the joint distribution of the data associated with neighboring nodes.

The analysis is benchmarked on networks with known community structures. We also analyze gene regulatory networks, including the PANTHER curated database and networks inferred from the GTEx lung and breast tissue RNA profiles. Gene Ontology annotations from the EBI GOA database are ranked and superimposed to explain the salient gene modules. We find that several gene modules related to highly specific biological processes are well-coordinated in such tissues. We also find that 18 of the 50 genes of the PAM50 breast-tumor prognostic signature appear among the highly coordinated genes in a single gene module, in both the breast and lung samples. Moreover these 18 are precisely the subset of the PAM50 recently identified as the basal-like markers.
Acquired loss of cardiac vagal activity is associated with myocardial injury in patients undergoing non-cardiac surgery: prospective observational mechanistic cohort study
Authors: May Shaun M. , Reyes Anna , Martir Gladys , Reynolds Joseph , Paredes Laura Gallego , Karmali Shamir , Stephens Robert CM , Brealey David , Ackland Gareth L.
Published: April 2019

Background

Myocardial injury is more frequent after non-cardiac surgery in patients with preoperative cardiac vagal dysfunction as quantified by delayed heart rate recovery after cessation of cardiopulmonary exercise testing. Here, we hypothesised that serial and dynamic measures of perioperative cardiac vagal activity should also be associated with myocardial injury after non-cardiac surgery.

Methods

Serial measures in cardiac vagal activity were quantified preoperatively and daily using heart rate variability and a standardised orthostatic challenge in patients undergoing elective non-cardiac surgery. The primary outcome was myocardial injury (high-sensitivity troponin (hsTnT) ≥15ng.L−1) within 48h of surgery. Clinicians, patients and investigators were blinded to hsTnT. The exposure of interest was cardiac vagal activity (high-frequency power spectral analysis [HFlog]) and heart rate recovery after a standardised orthostatic challenge.

Results

hsTnT≥15ng.L−1 occurred in 48/189 [25%] patients, of whom 41/48 [85%] had a revised cardiac risk index score <2. Patients with a post surgery troponin HsTnT ≥15ng.L−1 were associated with an early loss (within 24h) of cardiac vagal activity (HFLog) post surgery compared to day of surgery (4.19 [95%CI:3.62-4.75] vs 5.22 [95%CI:4.64-5.81]; p<0.001). Heart rate recovery after a standardised orthostatic challenge after surgery was slower in patients with hsTnT≥15ng.L−1 (5 beats minute−1 (95% CI: 3 −7), compared to heart rate recovery in patients who remained free of myocardial injury (10 beats minute−1 (95%CI:7 to 12]; p = 0.02).

Conclusions

Real-time, serial heart rate measures indicating loss of cardiac vagal activity are associated with perioperative myocardial injury in lower-risk patients undergoing non-cardiac surgery.
The neural basis for response latency in a sensory-motor behavior
Authors: Lee Joonyeol , Darlington Timothy R. , Lisberger Stephen G.
Published: April 2019

We seek a neural circuit explanation for sensory-motor reaction times. We have found evidence that two of three possible mechanisms could contribute to reaction times in smooth pursuit eye movements. In the smooth eye movement region of the frontal eye fields (FEFSEM), an area that causally affects the initiation of smooth pursuit eye movement, neural and behavioral latencies have significant trial-by-trial correlations that can account for 40% to 100% of the variation in behavioral latency. The amplitude of preparatory activity, which represents the motor system’s expectations for target motion, shows negative trial-by-trial correlations with behavioral latency and could contribute to the neural computation of reaction time. In contrast, the traditional “ramp-to-threshold” model is contradicted by the responses of many, but not all FEFSEM neurons. As evidence of neural processing that determines reaction time, the local field potential in FEFSEM includes a brief wave in the 5-15 Hz frequency range that precedes pursuit initiation and whose phase is correlated with the latency of pursuit in individual trials. We suggest that the latency of the incoming visual motion signals combines with the state of preparatory activity to determine the latency of the transient response that drives eye movement.
4q-D4Z4 chromatin architecture regulates the transcription of muscle atrophic genes in FSHD
Authors: Cortesi Alice , Pesant Matthieu , Sinha Shruti , Marasca Federica , Sala Eleonora , Gregoretti Francesco , Antonelli Laura , Oliva Gennaro , Chiereghin Chiara , Soldà Giulia , Bodega Beatrice
Published: April 2019

Despite increasing insights in genome structure organization, the role of DNA repetitive elements, accounting for more than two thirds of the human genome, remains elusive. Facioscapulohumeral Dystrophy (FSHD) is associated with deletion of D4Z4 repeat array below 11 units at 4q35.2. It is known that the deletion alters chromatin structure in cis, leading to genes upregulation. Here we show a genome-wide role of 4q-D4Z4 array in modulating gene expression via 3D nuclear contacts. We have developed an integrated strategy of 4q-D4Z4 specific 4C-seq and chromatin segmentation analyses, showing that 4q-D4Z4 3D interactome and chromatin states of interacting genes are impaired in FSHD1 condition; in particular, genes which have lost the 4q-D4Z4 interaction and with a more active chromatin state are enriched for muscle atrophy transcriptional signature. Expression level of these genes is restored by the interaction with an ectopic 4q-D4Z4 array, suggesting that the repeat directly modulates the transcription of contacted targets.

Of note, the upregulation of atrophic genes is a common feature of several FSHD1 and FSHD2 patients, indicating that we have identified a core set of deregulated genes involved in FSHD pathophysiology.
Persistence of learning-induced synapses depends on neurotrophic-priming of glucocorticoid receptors
Authors: Arango-Lievano M. , Borie A. , Dromard Y. , Murat M. , Desarménien M.G. , Garabedian M.J. , Jeanneteau F.
Published: April 2019

Stress can either promote or impair learning and memory. Such opposing effects depend on whether synapses persist or decay after learning. Maintenance of new synapses formed at the time of learning upon neuronal network activation depends on the stress hormone activated glucocorticoid receptor (GR) and neurotrophic factor release. Whether and how concurrent GR and neurotrophin signaling integrate to modulate synaptic plasticity and learning is unknown. Here we show that deletion of the neurotrophin BDNF-dependent GR phosphorylation sites (GR-PO4) impairs long-term memory retention and maintenance of newly formed postsynaptic dendritic spines in the mouse cortex after motor skills training. Chronic stress and the BDNF polymorphism Val66Met disrupt the BDNF-dependent GR-PO4 pathway necessary for preserving training-induced spines and previously acquired memories. Conversely, enrichment living promotes spine formation but fails to salvage training-related spines in mice lacking BDNF-dependent GR-PO4 sites, suggesting it is essential for spine consolidation and memory retention. Mechanistically, spine maturation and persistence in the motor cortex depend on synaptic mobilization of the glutamate receptor GluA1 mediated by GR-PO4. Together, these findings indicate that regulation of GR-PO4 via activity-dependent BDNF signaling is important for learning-dependent synapses formation and maintenance. They also define a new signaling mechanism underlying these effects.

SIGNIFICANCE STATEMENT

Signal transduction of receptors tyrosine kinase and nuclear receptors is essential for homeostasis. Phosphorylation is one of the currencies used by these receptors to support homeostatic reactions in learning and memory. Here we show that consolidation of learning-induced neuroplasticity is made possible via stress activated glucocorticoid nuclear receptor phosphorylation through the brain-derived neurotrophic tyrosine kinase pathway. Crosstalk between these pathways is specific of cell types and behavioral experience (e.g. learning, stress and enrichment living). Disruption of this response may contribute to the pathophysiology of stress-related disorders and treatment resistance.
Larval growth and survival in Indian Butter Catfish, Ompok bimaculatus (Bloch): effect of light intensity and photoperiod
Authors: Arambam Kalpana , Biswas Pradyut , Singh Soibam Khogen , Patel A. B. , Jena Alok Kumar , Singh Rajkumar Debarjeet , Pandey P. K.
Published: April 2019

Two sequential indoor rearing trials each of 21 days duration were conducted to investigate the effect of light intensity and photoperiod respectively on the growth and survival of Ompok bimaculatus larvae. In first trial, five different light intensities viz. 0, 300, 500, 900, 1200 lx were applied randomly to 800 larvae (0.003 g; 0.51 cm) stocked in triplicate following a completely randomized design into aquarium (30.0 x 15.0 x 15.0 cm) tanks. Sequentially, in second trial, five photoperiod cycles (light: dark, L: D) namely, 24L: 0D, 16L: 8D, 12L: 12D, 8L: 16D and 0L: 24D in combination with the best performing light intensity (300 lx) as observed from the first trial were employed in triplicates in similar set up. From the first trial, significantly higher survival was observed in 0 and 300 lx, whereas growth was highest in 900 lx (P < 0.05). In the second trial, survival was higher in continuous darkness (0L: 24D), whereas, maximum growth was recorded in 24L: 0D and 16L: 8D groups (P < 0.05). Performance index (PI) showed no significant difference (P > 0.05) among 0 and 300 lx light intensities, but were reduced at higher light intensities. The lowest PI was found in 12L: 12D and 8L: 16D condition but did not have any effect in other photoperiod cycles. Overall, from the present study it can be concluded that growth of the larvae is found to be higher in higher light intensity (900lx) and longer photoperiodic cycles (24L: 0D and 16L: 8D), however, better survival was recorded in total dark conditions suggesting that continuous dark condition is recommended for better hatchery performance of the larvae.
Effects of artificially introduced Enterococcus faecalis strains in experimental necrotizing enterocolitis
Authors: Delaplain Patrick T. , Bell Brandon A. , Wang Jin , Isani Mubina , Zhang Emily , Gayer Christopher P. , Grishin Anatoly V. , Ford Henri R.
Published: April 2019

Enterococcus faecalis is a ubiquitous intestinal symbiont and common early colonizer of the neonatal gut. Although colonization with E. faecalis has been previously associated with decreased NEC pathology, these bacteria have been also implicated as opportunistic pathogens. Here we characterized 21 strains of E. faecalis, naturally occurring in 4-day-old rats, for potentially pathogenic properties and ability to colonize the neonatal gut. The strains differed in hemolysis, gelatin liquefaction, antibiotic resistance, biofilm formation, and ability to activate the pro-inflammatory transcription factor NF-κB in cultured enterocytes. Only 3 strains appreciably colonized the neonatal intestine on day 4 after artificial introduction with the first feeding. The best colonizer, strain BB70, effectively displaced maternal E. faecalis and significantly increased NEC pathology. Our results show that colonization with E. faecalis may predispose neonates to NEC.
Survey of intertidal ecosystem reveals a legacy of potentially toxic elements from industrial activity in the Skeena Estuary, British Columbia, Canada
Authors: Sizmur Tom , Campbell Lily , Dracott Karina , Jones Megan , O’Driscoll Nelson J. , Gerwing Travis
Published: April 2019

Relationships between concentrations of Potentially Toxic Elements (PTEs) in estuarine sediments and their impact benthic invertebrate communities are poorly understood. We sampled and analysed PTEs in sediments and benthic invertebrates from five sites surrounding the Skeena Estuary, including sites adjacent to an abandoned cannery and a decommissioned papermill. There was no indication that sediments of the salmon cannery are polluted, but acidic sediments adjacent to the papermill contained elevated concentrations of Cd, Cr, Hg and Pb. Benthic invertebrate community assemblages confirm that sediments have recovered from prior disturbances associated with discharge of papermill sludge. Oregon pill bugs (Gnorimosphaeroma oregonensis), observed at all five sites, feed on the fibers associated with the papermill discharge. Thus, G. oregonensis are useful biomonitors for quantifying the impact of the decommissioned papermill, and similar industrial development projects, on intertidal ecosystems along the north coast of British Columbia, Canada.
Transcriptional programs define intratumoral heterogeneity of Ewing sarcoma at single cell resolution
Authors: Aynaud M-M , Mirabeau O , Gruel N , Grossetête S , Boeva V , Durand S , Surdez D , Saulnier O , Zaïdi S , Gribkova S , Kairov U , Raynal V , Tirode F , Grünewald TGP , Bohec M , Baulande S , Janoueix-Lerosey I , Vert J-P , Barillot E , Delattre O , Zinovyev A
Published: April 2019

EWSR1-FLI1, the chimeric oncogene specific for Ewing sarcoma (EwS), induces a cascade of signaling events leading to cell transformation. However, it remains elusive how genetically homogeneous EwS cells can drive heterogeneity of transcriptional programs. Here, we combined independent component analysis of single cell RNA-sequencing data from diverse cell types and model systems with time-resolved mapping of EWSR1-FLI1 binding sites and of open chromatin regions to characterize dynamic cellular processes associated with EWSR1-FLI1 activity. We thus defined an exquisitely specific and direct, super-enhancer-driven EWSR1-FLI1 program. In EwS tumors, cell proliferation was associated with a well-defined range of EWSR1-FLI1 activity; moreover, cells with a high EWSR1-FLI1 activity presented a strong oxidative phosphorylation metabolism. In contrast, a subpopulation of cells from below and above optimal EWSR1-FLI1 activity was characterized by increased hypoxia. Overall, our study reveals sources of intratumoral heterogeneity within Ewing tumors.
Model-independent recovery of interfacial structure from multi-contrast neutron reflectivity data
Authors: Koutsioubas Alexandros
Published: April 2019

Neutron specular reflectivity at soft interfaces provides sub-nanometre information concerning the molecular distribution of thin films, while the application of contrast variation can highlight the scattering from different parts of the system and lead to an overall reduction in fitting ambiguity. Traditional modelling approaches involve the construction of a trial scattering length density profile based on initial speculation and the subsequent refinement of its parameters through minimization of the discrepancy between the calculated and measured reflectivity. In practice this might produce an artificial bias towards specific sets of solutions. On the other hand, direct inversion of reflectivity data, despite its ability to provide a unique solution, is subject to limitations and experimental complications. Presented here is an integrated indirect Fourier transform/simulated annealing method that, when applied to multiple solvent contrast reflectivity data and within the limits of finite spatial resolution, leads to reliable reconstructions of the interfacial structure without the need for any a priori assumptions. The generality of the method permits its straightforward application in common experimental contrast-variation investigations at the solid/liquid and air/liquid interface.
The polytopes of the H
3 group with 60 vertices and their orbit decompositions
Authors: Bourret Emmanuel , Grabowiecka Zofia
Published: April 2019

The goal of this article is to compare the geometrical structure of polytopes with 60 vertices, generated by the finite Coxeter group H
3, i.e. an icosahedral group in three dimensions. The method of decorating a Coxeter–Dynkin diagram is used to easily read the structure of the reflection-generated polytopes. The decomposition of the vertices of the polytopes into a sum of orbits of subgroups of H
3 is given and presented as a `pancake structure'.
Experimentally obtained and computer-simulated X-ray asymmetric eight-beam pinhole topographs for a silicon crystal
Authors: Okitsu Kouhei , Imai Yasuhiko , Yoda Yoshitaka , Ueji Yoshinori
Published: April 2019

In this study, experimentally obtained eight-beam pinhole topographs for a silicon crystal using synchrotron X-rays were compared with computer-simulated images, and were found to be in good agreement. The experiment was performed with an asymmetric all-Laue geometry. However, the X-rays exited from both the bottom and side surfaces of the crystal. The simulations were performed using two different approaches: one was the integration of the n-beam Takagi–Taupin equation, and the second was the fast Fourier transformation of the X-ray amplitudes obtained by solving the eigenvalue problem of the n-beam Ewald–Laue theory as reported by Kohn & Khikhlukha [Acta Cryst. (2016), A72, 349–356] and Kohn [Acta Cryst. (2017), A73, 30–38].
Automatic calculation of symmetry-adapted tensors in magnetic and non-magnetic materials: a new tool of the Bilbao Crystallographic Server
Authors: Gallego Samuel V. , Etxebarria Jesus , Elcoro Luis , Tasci Emre S. , Perez-Mato J. Manuel
Published: April 2019

Two new programs, MTENSOR and TENSOR, hosted on the open-access website known as the Bilbao Crystallographic Server, are presented. The programs provide automatically the symmetry-adapted form of tensor properties for any magnetic or non-magnetic point group or space group. The tensor is chosen from a list of 144 known tensor properties gathered from the scientific literature or, alternatively, the user can also build a tensor that possesses an arbitrary intrinsic symmetry. Four different tensor types are considered: equilibrium, transport, optical and nonlinear optical susceptibility tensors. For magnetically ordered structures, special attention is devoted to a detailed discussion of the transformation rules of the tensors under the time-reversal operation 1′. It is emphasized that for non-equilibrium properties it is the Onsager theorem, and not the constitutive relationships, that indicates how these tensors transform under 1′. In this way it is not necessary to restrict the validity of Neumann's principle. New Jahn symbols describing the intrinsic symmetry of the tensors are introduced for several transport and optical properties. In the case of some nonlinear optical susceptibilities of practical interest, an intuitive method is proposed based on simple diagrams, which allows easy deduction of the action of 1′ on the susceptibilities. This topic has not received sufficient attention in the literature and, in fact, it is usual to find published results where the symmetry restrictions for such tensors are incomplete.
Fast analytical evaluation of intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density. II. The Fourier transform method
Authors: Nguyen Daniel , Volkov Anatoliy
Published: April 2019

The Fourier transform method for analytical determination of the two-center Coulomb integrals needed for evaluation of the electrostatic interaction energies between pseudoatom-based charge distributions is presented, and its Fortran-based implementation using the 128-bit floating-point arithmetic in theXDPROPmodule of theXDsoftware is described. In combination with mathematical libraries included in the Lahey/Fujitsu LF64 Linux compiler, the new implementation outperforms the previously reported Löwdin α-function technique [Nguyenet al.(2018).Acta Cryst.A74, 524–536] in terms of precision of the determined individual Coulomb integrals regardless of whether the latter uses the 64-, 80- or 128-bit precision floating-point format, all the while being only marginally slower. When the Löwdin α-function or Fourier transform method is combined with a multipole moment approximation for large interatomic separations (such a hybrid scheme is called the analytical exact potential and multipole moment method, aEP/MM) the resulting electrostatic interaction energies are evaluated with a precision of ≤5 × 10−5 kJ mol−1for the current set of benchmark systems composed of H, C, N and O atoms and ranging in size from water–water to dodecapeptide–dodecapeptide dimers. Using a 2012 4.0 GHz AMD FX-8350 computer processor, the two recommended aEP/MM implementations, the 80-bit precision Löwdin α-function and 128-bit precision Fourier transform methods, evaluate the total electrostatic interaction energy between two 225-atom monomers of the benchmark dodecapeptide molecule in 6.0 and 7.9 s, respectively, versus 3.1 s for the previously reported 64-bit Löwdin α-function approach.
Solving the disordered structure of β-Cu2−xSe using the three-dimensional difference pair distribution function
Authors: Roth Nikolaj , Iversen Bo B.
Published: April 2019

High-performing thermoelectric materials such as Zn4Sb3and clathrates have atomic disorder as the root to their favorable properties. This makes it extremely difficult to understand and model their properties at a quantitative level, and thus effective structure–property relations are challenging to obtain. Cu2−xSe is an intensely studied, cheap and non-toxic high performance thermoelectric, which exhibits highly peculiar transport properties, especially near the β-to-α phase transition around 400 K, which must be related to the detailed nature of the crystal structure. Attempts to solve the crystal structure of the low-temperature phase, β-Cu2−xSe, have been unsuccessful since 1936. So far, all studies have assumed that β-Cu2−xSe has a three-dimensional periodic structure, but here we show that the structure is ordered only in two dimensions while it is disordered in the third dimension. Using the three-dimensional difference pair distribution function (3D-ΔPDF) analysis method for diffuse single-crystal X-ray scattering, the structure of the ordered layer is solved and it is shown that there are two modes of stacking disorder present which give rise to an average structure with higher symmetry. The present approach allows for a direct solution of structures with disorder in some dimensions and order in others, and can be thought of as a generalization of the crystallographic Patterson method. The local and extended structure of a solid determines its properties and Cu2−xSe represents an example of a high-performing thermoelectric material where the local atomic structure differs significantly from the average periodic structure observed from Bragg crystallography.
Teaching metadiscourse features and IELTS writing performance of Iranian EFL learners
Authors: Vasheghani Farahani Mehrdad , Pahlevansadegh Vahid
Published: April 2019

Purpose

In spite of the growing interest in using corpora in language teaching and learning, applying computers and software (especially corpora software) is still new in second language teaching and learning. In addition, employing a learner corpus-based perspective in teaching metadiscourse features in International English Language Testing System (IELTS) writing tasks is not reported to the best knowledge of the researchers. Understanding and spotting this gap, the purpose of this paper is to utilize a learner corpus-based approach in teaching metadiscourse features and investigate its possible impacts on IELTS writing performance of the Iranian second language learners. Therefore, this study addressed the following research questions and hypotheses.

Design/methodology/approach

The current research utilized a quasi-experimental research design. In addition, this research used a learner corpus-based methodology. The corpus-based methodology was exploited to enable the researchers to have access to a large body of authentic language materials. In other words, a corpus-based methodology was used due to the fact that it made it possible for the researchers to elicit the metadiscourse features from a large number of authentic writing materials and to employ them during the treatment process with authentic examples.

Findings

The findings showed that there was a positive correlation between teaching metadiscourse features and writing performance of IELTS learners; in that, teaching metadiscourse features could soar the writing performance of the subjects. In addition, interactional metadiscourse features had more impact than interactive metadiscourse features on writing performance.

Practical implications

The results of this research can have useful implications for second language teachers and learners as well as researchers in learner corpus as they can learn the creation and application of learner corpora in second language teaching and learning.

Originality/value

This paper is value in that it uses corpus software and methodology in teaching metadiscourse features in writing section of IELTS test.
Board composition and corporate reporting on internet: Indian evidence
Authors: Sandhu Akasha , Singh Balwinder
Published: April 2019

Purpose

The purpose of this paper is to investigate the impact of board composition on the level of corporate internet reporting (CIR) practices.

Design/methodology/approach

This study uses content analysis to examine the CIR practices of 140 Indian companies selected from the Bombay Stock Exchange 200 index for the year 2015. CIR was measured on a comprehensive internet disclosure index of 136 items capturing both content and presentation dimensions. Regression analysis was used to explore the impact of board composition (board size, board independence, frequency of board meetings, CEO duality and family members on the board) and audit committee characteristics on CIR while controlling the impact of variables firm size, leverage, profitability and industry type.

Findings

The findings reveal that larger boards, boards with less family members and audit committees that meet more frequently are more likely to engage in CIR practices. In addition, larger firms and firms that make less use of debt tend to disclose more information on their websites.

Research limitations/implications

The focus of the study has been on one aspect of corporate governance mechanisms i.e. board characteristics. Future studies can explore the impact of ownership structure on CIR practices.

Originality/value

This study extends the prior CIR research by demonstrating the effectiveness of corporate governance mechanisms in particular board characteristics in adopting internet reporting practices for Indian companies. The examination of the relationship between corporate reporting on the internet and corporate governance aids regulators in evaluating and enhancing the effectiveness of the boards.
Do globalisation and adoption of IFRS by banks in Africa lead to less earnings management?
Authors: Amidu Mohammed , Issahaku Haruna
Published: April 2019

Purpose

This paper aims to analyse the implications of globalisation and the adoption of international standards (International Financial Reporting Standards [IFRS]) for accounting information quality.

Design/methodology/approach

This paper uses a sample of 329 banks across 29 countries leading up to and beyond the implementation of IFRS to test for related hypotheses.

Findings

First, banks’ financial statements are prepared on the basis of international standards as national economies are integrated when social norms are diffused. Building on these results, the second test suggests that the relatively high-quality earnings among banks in Africa during the period is attributable to the adoption of and interaction of IFRS with globalisation and the strategy of banks to diversify within and across interest and non-interest income.

Originality/value

The authors investigate how globalisation and the adoption of IFRS affect accounting information quality.
The relationship between the extent of online financial disclosure and profitability of Islamic banks
Authors: Al-Sartawi Abdalmuttaleb M.A Musleh , Reyad Sameh M. Reda
Published: April 2019

Purpose

This study aims to examine the relationship between online financial disclosure (OFD) and profitability of Islamic banks in the Gulf Cooperation Council (GCC) countries.

Design/methodology/approach

An extensive review of the literature was carried out and a checklist of 90 items (71 for content and 19 for presentation) was adopted to measure the level of OFD for the Islamic banks that are listed on the GCC stock exchanges. Additionally, the study used three indicators to measure profitability, namely, return on equity, return on assets and earnings per share.

Findings

The findings show that the overall OFD by Islamic banks in the GCC is 72.5 per cent, and a negative and insignificant relationship between OFD and profitability.

Practical implications

The study recommends that regulatory bodies should develop a guideline of disclosing information through the internet to enhance the transparency and performance among Islamic banks, which leads to reasonable economic decision-making.

Originality/value

The study contributes to the financial reporting and the Islamic economy literature relating to the GCC countries as previous studies gave no attention to Islamic banks.
Female directors and the cost of debt: does gender diversity in the boardroom matter to lenders?
Authors: Usman Muhammad , Farooq Muhammad Umar , Zhang Junrui , Makki Muhammad Abdul Majid , Khan Muhammad Kaleem
Published: April 2019

Purpose

This paper aims to investigate the question concerning whether gender diversity in the boardroom matters to lenders or not?

Design/methodology/approach

To answer this question, the authors use the data from 2009 to 2015 of all A-share listed companies on the Shanghai and Shenzhen stock exchanges. The authors use ordinary least squares regression and firm fixed effect regression to draw our inferences. To check and control the issue of endogeneity the authors use one-year lagged gender diversity regression, two-stage least squares regression, propensity score matching method and Heckman two-stage regression.

Findings

The results suggest that the presence of female directors on the board reduces managerial opportunistic behavior and information asymmetry and, consequently, creditors’ perceptions about the probability of loan default and the cost of debt. The authors find that lenders charge 4 per cent less from borrowers that have at least one female board member than they do from borrowers with no female board members. The authors also find that the board structure (i.e. gender diversity) of government-owned firms also matters to lenders, as government-owned firms that have gender-diverse boards have a lower cost of debt (i.e. 5 per cent lower interest rate).

Practical Implications

The findings have implications for individual borrowers and for regulators. For example, borrowers can get debt financing at lower rates by altering their boards’ composition (i.e. through gender diversity). From the regulatory perspective, the results support recent legislative initiatives around the world regarding female directors’ representation on boards.

Originality Value

This paper makes several contributions. First, beyond the recent studies on boardroom gender, the authors investigate the relationship between gender diversity in the boardroom and the cost of debt. Second, the authors extend the literature on the association between government ownership and cost of debt by first time providing evidence that the board composition (e.g. gender diversity) of government-owned firms also matters to the lenders. The other contributions are discussed in the introduction section.
Optimal Contract Design in Residential Brokerage
Authors: Liu Peng , Xie Jia
Published: April 2019

We introduce a principal–agent model where a real estate agent has private information that is important for a home seller to make decisions on marketing strategies. The seller designs a commission contract that motivates the agent to acquire information and then truthfully reveal it. We find that fixed commission rates are optimal if the agent has no private information or if his private information is given. If the agent's private information is acquired endogenously, the optimal commission rate should vary with the information revealed by the agent. The varying commission rate, however, is associated with distorted decisions on marketing strategies.
Putting the “We” Into Well‐being: Using Collectivism‐Themed Measures of Well‐Being Attenuates Well‐being's Association With Individualism
Authors: Krys Kuba , Zelenski John M. , Capaldi Colin A. , Park Joonha , van Tilburg Wijnand , van Osch Yvette , Haas Brian W. , Bond Michael H. , Dominguez‐Espinoza Alejandra , Xing Cai , Igbokwe David O. , Kwiatkowska Anna , Luzniak‐Piecha Magdalena , Nader Martin , Rizwan Muhammad , Zhu Zichen , Uchida Yukiko
Published: April 2019

Studies repeatedly have documented that societal well‐being is associated with individualism. Most of these studies, however, have conceptualized/measured well‐being as individual life satisfaction—a type of well‐being that originates in Western research traditions. Drawing from the latest research on interdependent happiness and on family well‐being, we posit that people across cultures pursue different types of well‐being, and test whether more collectivism‐themed types of well‐being that originate in Confucian traditions also are associated with individualism. Based on data collected from 2,036 participants across 12 countries, we find support for the association between individual life satisfaction and individualism at the societal level, but show that well‐being's association with individualism is attenuated when some collectivism‐themed measures of well‐being are considered. Our article advances knowledge on the flourishing of societies by suggesting that individualism may not always be strongly linked with societal well‐being. Implications for public policies are signaled.
Targets to improve quality of care for patients with hepatic encephalopathy: data from a multi‐centre cohort
Authors: Bajaj Jasmohan S. , O’Leary Jacqueline G. , Tandon Puneeta , Wong Florence , Kamath Patrick S. , Biggins Scott W. , Garcia‐Tsao Guadalupe , Lai Jennifer , Fallon Michael B. , Thuluvath Paul J. , Vargas Hugo E. , Maliakkal Benedict , Subramanian Ram M. , Thacker Leroy R. , Reddy K. Rajender
Published: April 2019

Background

Hepatic encephalopathy (HE) can adversely affect outcomes in both in‐patients and out‐patients with cirrhosis.

Aim

To define targets for improving quality of care in HE management in the multi‐centre North American Consortium for End‐Stage Liver Disease (NACSELD) cohort.

Method

NACSELD in‐patient cohort was analysed for (a) medication‐associated precipitants, (b) aspiration pneumonia development, (c) HE medication changes, and (d) 90‐day HE recurrence/readmissions. Comparisons were made between patients on no‐therapy, lactulose only, rifaximin only or both. Ninety‐day HE‐readmission analysis was adjusted for MELD score.

Results

Two thousand eight hundred and ten patients (1102 no‐therapy, 659 lactulose, 154 rifaximin, 859 both) were included. HE on admission, and HE rates during hospitalisation were highest in those on lactulose only or dual therapy compared to no‐therapy or rifaximin only (P < 0.001). Medications were the most prevalent precipitants (32%; 21% lactulose over/underuse, 5% benzodiazepines, 4% opioids, 1% rifaximin underuse, 1% hypnotics). Patients with medication‐associated precipitants had a better prognosis compared to other precipitants. A total of 23% (n = 217) reached grade 3/4 HE, of which 16% developed HE‐related aspiration pneumonia. Two thousand four hundred and twenty patients were discharged alive without liver transplant (790 no‐therapy, 639 lactulose, 136 rifaximin, 855 both); 12.5% (n = 99) of no‐therapy patients did not receive a discharge HE therapy renewal. Ninety‐day HE‐related readmissions were seen in 16% of patients (9% no‐therapy, 9% rifaximin only, lactulose only 18%, dual 21%, <0.001), which persisted despite MELD adjustment (P = 0.009).

Conclusion

Several targets to improve HE management were identified in a large cohort of hospitalised cirrhotic patients. Interventions to decrease medication‐precipitated HE, prevention of aspiration pneumonia, and optimisation of HE medications are warranted.