bluuebunny/crossref_metadata_2025 huggingface dataset:
Aberrant DNA methylation of miRNAs in Fuchs endothelial corneal dystrophy
Authors: Pan Peipei , Weisenberger Daniel J. , Zheng Siyu , Wolf Marie , Hwang David G. , Rose-Nussbaumer Jennifer R. , Jurkunas Ula V. , Chan Matilda F.
Published: May 2019

Homeostatic maintenance of corneal endothelial cells is essential for maintenance of corneal deturgescence and corneal transparency. In Fuchs endothelial corneal dystrophy (FECD), an accelerated loss and dysfunction of endothelial cells leads to progressively severe visual impairment. An abnormal accumulation of extracellular matrix is a distinctive hallmark of the disease, however the molecular pathogenic mechanisms underlying this phenomenon are not fully understood. We recently reported characteristic patterns of DNA methylation changes in the corneal endothelial cells of patients with FECD. Here, we investigate genome-wide and sequence-specific DNA methylation changes of miRNA genes in corneal endothelial samples derived from patients with FECD. We show that the majority of miRNA genes are hypermethylated at their promoter regions in FECD. More specifically, miR-199B is an extensively hypermethylated miRNA gene at its promoter region and its mature transcript miR-199b-5p was previously found to be almost completely silenced in FECD. Using a cell-based assay, we find that miR-199b-5p directly inhibits the expression of two epithelial mesenchymal transition (EMT)-inducing genes, Snai1 and ZEB1. Taken together, these findings suggest a novel regulatory mechanism of matrix protein production by corneal endothelial cells in which miR-199b-5p hypermethylation leads to its down-regulated expression and thereby the decreased expression of miR-199b-5p target genes, including Snai1 and ZEB1. Our results support miR-199b-5p as a potential therapeutic target to prevent or slow down the progression of FECD disease.

Author summary

Fuchs endothelial corneal dystrophy (FECD) due to corneal endothelial cell degeneration is one of the most common heritable causes of corneal visual loss and a leading indication for corneal transplantation. The progressive loss of corneal endothelial cells is accompanied by an abnormal deposition of extracellular matrix in the form of guttae. Here we discover that miRNA gene promoters are frequent targets of aberrant DNA methylation in FECD. In particular, we describe a novel epigenetic mechanism used by corneal endothelial cells to regulate extracellular matrix production. We find that miRNA-199b-5p functions as a negative regulator of Snai1 and ZEB1, two zinc finger transcription factors that have been shown to lead to increased production of extracellular matrix proteins. Furthermore, miR-199B was extensively hypermethylated in FECD and its mature transcript miR-199b-5p directly binds to the 3′-UTRs of Snai1 and ZEB1 genes. Ultimately, this may negatively modulate Snai1- and ZEB1-mediated production of extracellular matrix proteins. This work is the first to identify an important role of DNA methylation in the epigenetic regulation of miRNA-target genes in FECD and to describe a potential epigenetic biomarker for the treatment of FECD patients.
Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions
Authors: Sieberts Solveig K. , Perumal Thanneer , Carrasquillo Minerva M. , Allen Mariet , Reddy Joseph S. , Hoffman Gabriel E. , Dang Kristen K. , Calley John , Ebert Philip J. , Eddy James , Wang Xue , Greenwood Anna K. , Mostafavi Sara ,   the AMP-AD Consortium,   the CommonMind Consortium (CMC), Omberg Larsson , Peters Mette , Logsdon Benjamin A. , De Jager Philip L. , Ertekin-Taner Nilüfer , Mangravite Lara M. ,   AMP-AD Consortium,   CommonMind Consortium
Published: May 2019

The availability of high-quality RNA-sequencing and genotyping data of post-mortem brain collections from consortia such as CommonMind Consortium (CMC) and the Accelerating Medicines Partnership for Alzheimer’s Disease (AMP-AD) Consortium enable the generation of a large-scale brain cis-eQTL meta-analysis. Here we generate cerebral cortical eQTL from 1433 samples available from four cohorts (identifying >4.1 million significant eQTL for >18,000 genes), as well as cerebellar eQTL from 261 samples (identifying 874,836 significant eQTL for >10,000 genes), and provide the results as a community resource. We find substantially improved power in the meta-analysis over individual cohort analyses, particularly in comparison to the Genotype-Tissue Expression (GTEx) Project eQTL. In addition, we observed differences in eQTL patterns between cerebral and cerebellar brain regions. We provide these brain eQTL as a common resource for use across the community in research programs. As a proof of principle for their utility, we apply a colocalization analysis to identify genes underlying the GWAS association peaks for schizophrenia and identify a potentially novel gene colocalization with lncRNA RP11-677M14.2 (posterior probability of colocalization 0.975).
Cellular reprogramming for successful CNS axon regeneration is driven by a temporally changing cast of transcription factors
Authors: Dhara Sumona P. , Rau Andrea , Flister Michael J. , Recka Nicole M. , Laiosa Michael D. , Auer Paul L. , Udvadia Ava J.
Published: May 2019

In contrast to mammals, adult fish display a remarkable ability to fully regenerate central nervous system (CNS) axons, enabling functional recovery from CNS injury. Both fish and mammals normally undergo a developmental downregulation of axon growth activity as neurons mature. Fish are able to undergo damage-induced “reprogramming” through re-expression of genes necessary for axon growth and guidance, however, the gene regulatory mechanisms remain unknown. Here we present the first comprehensive analysis of gene regulatory reprogramming in zebrafish retinal ganglion cells at specific time points along the axon regeneration continuum from early growth to target reinnervation. Our analyses reveal a regeneration program characterized by sequential activation of stage-specific pathways, regulated by a temporally changing cast of transcription factors that bind to stably accessible DNA regulatory regions. Strikingly, we also find a discrete set of regulatory regions that change in accessibility, consistent with higher-order changes in chromatin organization that mark (1) the beginning of regenerative axon growth in the optic nerve, and (2) the re-establishment of synaptic connections in the brain. Together, these data provide valuable insight into the regulatory logic driving successful vertebrate CNS axon regeneration, revealing key gene regulatory candidates for therapeutic development.
Mouse and human microglial phenotypes in Alzheimer’s disease are controlled by amyloid plaque phagocytosis through Hif1α
Authors: Grubman Alexandra , Choo Xin Yi , Chew Gabriel , Ouyang John F. , Sun Guizhi , Croft Nathan P. , Rossello Fernando J. , Simmons Rebecca , Buckberry Sam , Landin Dulce Vargas , Pflueger Jahnvi , Vandekolk Teresa H. , Abay Zehra , Liu Xiaodong , Haynes John M. , McLean Catriona , Williams Sarah , Chai Siew Yeen , Wilson Trevor , Lister Ryan , Pouton Colin W. , Purcell Anthony W. , Rackham Owen J. L. , Petretto Enrico , Polo Jose M.
Published: May 2019

The important role of microglia, the brain’s resident immune cells, in Alzheimer’s disease (AD) is now well recognized, however their molecular and functional diversity and underlying mechanisms still remain controversial. To transcriptionally and functionally characterize the diversity of microglia in AD and aging, we isolated the amyloid plaque-containing (XO4+) and non-containing (XO4−) microglia from an AD mouse model. Transcriptomics analysis unveiled independent transcriptional trajectories in ageing and AD. XO4+ microglial transcriptomes linked plaque phagocytosis to altered expression of bona fide late onset AD genetic risk factors. We further revealed that the XO4+ transcriptional program is present in a subset of human microglia from AD patients and is a direct and reversible consequence of Aβ plaque phagocytosis. Conversely, XO4− microglia in AD displayed an accelerated ageing signature and contained more intracellular post synaptic material than plaque-containing microglia, despite reduced active synaptosome phagocytosis. Mechanistically, we predicted HIF1α as a core regulator of the XO4−/XO4+ axis, and further validated the mechanism in vitro using human stem cell-derived microglia like cells and primary human microglia. Together these findings unveiled the molecular mechanism underpinning the functional diversity of microglia in AD, providing opportunities to develop treatments targeted at subset specific manipulation of the microglial niche.
The soursop genome and comparative genomics of basal angiosperms provide new insights on evolutionary incongruence
Authors: Strijk Joeri S. , Hinsinger Damien D. , Roeder Mareike M. , Chatrou Lars W. , Couvreur Thomas L. P. , Erkens Roy H. J. , Sauquet Hervé , Pirie Michael D. , Thomas Daniel C. , Cao Kunfang
Published: May 2019

Deep relationships and the sequence of divergence among major lineages of angiosperms (magnoliids, monocots and eudicots) remain ambiguous and differ depending on analytical approaches and datasets used. Complete genomes potentially provide opportunities to resolve these uncertainties, but two recently published magnoliid genomes instead deliver further conflicting signals. To disentangle key angiosperm relationships, we report a high-quality draft genome for the soursop (Annona muricata, Annonaceae). We reconstructed phylogenomic trees and show that the soursop represents a genomic mosaic supporting different histories, with scaffolds almost exclusively supporting single topologies. However, coalescent methods and a majority of genes support magnoliids as sister to monocots and eudicots, where previous whole genome-based studies remained inconclusive. This result is clear and consistent with recent studies using plastomes. The soursop genome highlights the need for more early diverging angiosperm genomes and critical assessment of the suitability of such genomes for inferring evolutionary history.
Detecting Novel Sequence Signals in Targeting Peptides Using Deep Learning
Authors: Almagro Armenteros J.J. , Salvatore M. , Emanuelsson O. , Winther O. , von Heijne G. , Elofsson A. , Nielsen H.
Published: May 2019

In bioinformatics, machine learning methods have been used to predict features embedded in the sequences. In contrast to what is generally assumed, machine learning approaches can also provide new insights into the underlying biology. Here, we demonstrate this by presenting TargetP 2.0, a novel state of art method to identify N-terminal sorting signals, which direct proteins to the secretory pathway, mitochondria and chloroplasts or other plastids.

By examining the strongest signals from the attention layer in the network, we find that the second residue in the protein, i.e. the one following the initial methionine, has a strong influence on the classification. When subsequently examining all targeting peptides, we observe that two-thirds of chloroplast and thylakoid transit peptides have an alanine in position two, but only 20% of other plant proteins. Further highlighting the importance of the second residue, we also note that in fungi and single-celled eukaryotes, less than 30% of the targeting peptides have an amino acid that allows the removal of the N-terminal methionine compared with 60% for the proteins without targeting peptide.

TargetP 2.0 is available at http://www.cbs.dtu.dk/services/TargetP-2.0/index.php
Topographic preservation of functional connectivity among the association areas in the human cerebral cortex
Authors: Koide-Majima Naoko , Nishimoto Shinji
Published: May 2019

In the human sensorimotor cortex, some long-range corticocortical connections appear to preserve a fine-scale topology, in which physically close locations in the cortical region are functionally connected to physically close locations in other cortical regions. However, little is known about whether such topography preservation is unique to the sensorimotor areas or is general across other cortical areas. To investigate this question, we measured voxel-level functional connectivity using functional magnetic resonance imaging (fMRI) and visualized the fine-scale spatial organization of the connectivity patterns across the cortical surface. We found topographical preservation across regions, including the default mode network. Our results suggest that the topographical preservation of functional connectivity is not restricted to the sensorimotor cortex but also occurs in the association cortex.
Synergy pattern of short cationic antimicrobial peptides against multidrug-resistantPseudomonas aeruginosa
Authors: Ruden Serge , Rieder Annika , Schwartz Thomas , Mikut Ralf , Hilpert Kai
Published: May 2019

With the rise of various multi-drug resistance pathogenic bacteria, worldwide health care is under pressure to respond. Conventional antibiotics are failing and the development of novel classes or alternative strategies is a major priority. Antimicrobial peptides (AMPs) can not only kill multi-drug resistant bacteria, but also can be used synergistically with conventional antibiotics. We selected 30 short AMPs from different origins and measured their synergy in combination with Polymyxin B, Piperacillin, Ceftazidime, Cefepime, Meropenem, Imipenem, Tetracycline, Erythromycin, Kanamycin, Tobramycin, Amikacin, Gentamycin, and Ciprofloxacin. In total 403 unique combinations were tested against a multi-drug resistantPseudomonas aeruginosaisolate (PA910). As a measure of the synergistic effects, fractional inhibitory concentrations (FICs) were determined using microdilution assays with FICs ranges between 0.25 and 2. A high number of combinations between peptides and Polymyxin B, Erythromycin and Tetracycline were found to be synergistic. Novel variants of Indolicidin also showed a high frequency in synergist interaction.
An aphid effector promotes barley susceptibility through suppression of defence gene expression
Authors: Escudero-Martinez Carmen , Rodriguez Patricia A. , Santos Pablo A. , Stephens Jennifer , Bos Jorunn I.B.
Published: May 2019

Aphids secrete diverse repertoires of effectors into their hosts to promote the infestation process. While “omics”-approaches facilitated the identification and comparison of effector repertoires from a number of aphid species, the functional characterization of these proteins has been limited to dicot (model) plants. The bird cherry-oat aphid Rhopalosiphum padi is a pest of cereal crops, including barley. Here, we extended efforts to characterize aphid effectors with regards to their role in promoting susceptibility to the R. padi-barley interaction. We selected 3 R. padi effectors based on sequences similarity to previously characterized M. persicae effectors and assessed their subcellular localisation, expression, and role in promoting plant susceptibility. Expression of R. padi effectors RpC002 and Rp1 in transgenic barley lines enhanced plant susceptibility to R. padi but not M. persicae, for which barley is a poor host. Characterization of Rp1 transgenic barley lines revealed reduced gene expression of plant hormone signalling genes relevant to plant-aphid interactions, indicating this effector enhances susceptibility by suppressing plant defences in barley. Our data suggests that some aphid effectors specifically function when expressed in host species, and feature activities that benefit their corresponding aphid species.
Fungal communities living within leaves of native Hawaiian dicots are structured by landscape-scale variables as well as by host plants
Authors: Darcy JL , Switf SOI , Cobian GM , Zahn G , Perry BA , Amend AS
Published: May 2019

A phylogenetically diverse array of fungi live within healthy leaf tissue of dicotyledonous plants. Many studies have examined these endophytes within a single plant species and/or at small spatial scales, but landscape-scale variables that determine their community composition are not well understood, either across geographic space, across climatic conditions, or in the context of host plant phylogeny. Here, we evaluate the contributions of these variables to endophyte beta diversity using a survey of foliar endophytic fungi in native Hawaiian dicots sampled across the Hawaiian archipelago. We used Illumina technology to sequence fungal ITS1 amplicons to characterize foliar endophyte communities across five islands and 80 host plant genera. We found that communities of foliar endophytic fungi showed strong geographic structuring between distances of seven and 36 km. Endophyte community structure was most strongly associated with host plant phylogeny and evapotranspiration, and was also significantly associated with NDVI, elevation, and solar radiation. Additionally, our bipartite network analysis revealed that the five islands we sampled each harbored significantly specialized endophyte communities. These results demonstrate how the interaction of factors at large and small spatial and phylogenetic scales shape fungal symbiont communities.
Development of a Covalent Inhibitor of Gut Bacterial Bile Salt Hydrolases
Authors: Adhikari Arijit A. , Seegar Tom C. , Ficarro Scott B. , McCurry Megan D. , Ramachandran Deepti , Yao Lina , Chaudhari Snehal N. , Ndousse-Fetter Sula , Banks Alexander S. , Marto Jarrod A. , Blacklow Stephen C. , Devlin A. Sloan
Published: May 2019

Bile salt hydrolase (BSH) enzymes are widely expressed by human gut bacteria and catalyze the gateway reaction leading to secondary bile acid formation. Bile acids regulate key metabolic and immune processes by binding to host receptors. There is an unmet need for a potent tool to inhibit BSHs across all gut bacteria in order to study the effects of bile acids on host physiology. Here, we report the development of a covalent pan-inhibitor of gut bacterial BSH. From a rationally designed candidate library, we identified a lead compound bearing an alpha-fluoromethyl ketone warhead that modifies BSH at the catalytic cysteine residue. Strikingly, this inhibitor abolished BSH activity in conventional mouse feces. Mice gavaged with a single dose of this compound displayed decreased BSH activity and decreased deconjugated bile acid levels in feces. Our studies demonstrate the potential of a covalent BSH inhibitor to modulate bile acid composition in vivo.
An automated model reduction tool to guide the design and analysis of synthetic biological circuits
Authors: Pandey Ayush , Murray Richard M.
Published: May 2019

We present an automated model reduction algorithm that uses quasi-steady state approximation to minimize the error between the desired outputs. Additionally, the algorithm minimizes the sensitivity of the error with respect to parameters to ensure robust performance of the reduced model in the presence of parametric uncertainties. We develop the theory for this model reduction algorithm and present the implementation of the algorithm that can be used to perform model reduction of given SBML models. To demonstrate the utility of this algorithm, we consider the design of a synthetic biological circuit to control the population density and composition of a consortium consisting of two different cell strains. We show how the model reduction algorithm can be used to guide the design and analysis of this circuit.
Complex ecological phenotypes on phylogenetic trees: a hidden Markov model for comparative analysis of multivariate count data
Authors: Grundler Michael C. , Rabosky Daniel L.
Published: May 2019

The evolutionary dynamics of complex ecological traits – including multistate representations of diet, habitat, and behavior – remain poorly understood. Reconstructing the tempo, mode, and historical sequence of transitions involving such traits poses many challenges for comparative biologists, owing to their multidimensional nature and intraspecific variability. Continuous-time Markov chains (CTMC) are commonly used to model ecological niche evolution on phylogenetic trees but are limited by the assumption that taxa are monomorphic and that states are univariate categorical variables. Thus, a necessary first step when using standard CTMC models is to categorize species into a pre-determined number of ecological states. This approach potentially confounds interpretation of state assignments with effects of sampling variation because it does not directly incorporate empirical observations of resource use into the statistical inference model. The neglect of sampling variation, along with univariate representations of true multivariate phenotypes, potentially leads to the distortion and loss of information, with substantial implications for downstream macroevolutionary analyses. In this study, we develop a hidden Markov model using a Dirichlet-multinomial framework to model resource use evolution on phylogenetic trees. Unlike existing CTMC implementations, states are unobserved probability distributions from which observed data are sampled. Our approach is expressly designed to model ecological traits that are intra-specifically variable and to account for uncertainty in state assignments of terminal taxa arising from effects of sampling variation. The method uses multivariate count data for individual species to simultaneously infer the number of ecological states, the proportional utilization of different resources by different states, and the phylogenetic distribution of ecological states among living species and their ancestors. The method is general and may be applied to any data expressible as a set of observational counts from different categories.
Non-replication of functional connectivity differences in autism spectrum disorder across multiple sites and denoising strategies
Authors: He Ye , Byrge Lisa , Kennedy Daniel P
Published: May 2019

A rapidly growing number of studies on autism spectrum disorder (ASD) have used resting-state fMRI to identify alterations of functional connectivity, with the hope of identifying clinical biomarkers or underlying neural mechanisms. However, results have been largely inconsistent across studies, and there is therefore a pressing need to determine the primary factors influencing replicability. Here, we used resting-state fMRI data from the Autism Brain Imaging Data Exchange to investigate two potential factors: denoising strategy and data site (which differ in terms of sample, data acquisition, etc.). We examined the similarity of both group-average functional connectomes and group-level differences (ASD vs. control) across 33 denoising pipelines and four independently-acquired datasets. The group-average connectomes were highly consistent across pipelines (r = 0.92±0.06) and sites (r = 0.88±0.02). However, the group differences, while still consistent within site across pipelines (r = 0.76±0.12), were highly inconsistent across sites regardless of choice of denoising strategies (r = 0.07±0.04), suggesting lack of replication may be strongly influenced by site and/or cohort differences. Across-site similarity remained low even when considering the data at a large-scale network level or when considering only the most significant edges. We further show through an extensive literature survey that the parameters chosen in the current study (i.e., sample size, age range, preprocessing methods) are quite representative of the published literature. These results highlight the importance of examining replicability in future studies of ASD, and, more generally, call for extra caution when interpreting alterations in functional connectivity across groups of individuals.
Characterization of an enhancer element that regulates FOXP2 expression in human cerebellum
Authors: Madurga Julen , Novo Francisco J.
Published: May 2019

Human cerebellum is involved not only in motor control but also in several cognitive skills. In this work, our goal was to identify genomic enhancers responsible for the regulation of genes implicated in the development of this brain region. From an initial collection of Vista elements showing specific enhancer activity in mouse hindbrain, we found an enhancer element located within the final intron of FOXP2, a gene expressed in cerebellum and implicated in vocal communication and speech and language disorders in humans. Analysis of this enhancer using various computational resources suggests that it is a strong candidate to account for FOXP2 expression during cerebellar development. Two blocks within this region are deeply conserved in vertebrates; they are separated by a microsatellite sequence present only in eutherian mammals, and expanded in human genomes.
Sequence and immunologic conservation ofAnaplasma marginaleOmpA within strains from Ghana as compared to the predominant OmpA variant
Authors: Futse JE , Buami G , Kayang BB , Koku R , Palmer GH , Graça T , Noh SM
Published: May 2019

A primary challenge in developing effective vaccines against obligate, intracellular, bacterial tick-borne pathogens that establish persistent infection is the identification of antigens that cross protect against multiple strains. In the case ofAnaplasma marginale, the most prevalent tick-borne pathogen of cattle found worldwide, OmpA is an adhesin and thus a promising vaccine candidate. We sequencedompAfrom cattle throughout Ghana naturally infected withA. marginalein order to determine the degree of variation in this gene in an area of suspected high genetic diversity. We compared the Ghanaian sequences with those available from N. America, Mexico, Australia and Puerto Rico. When considering only amino acid changes, three unique Ghanaian OmpA variants were identified. In comparison, strains from all other geographic regions, except one, shared a single OmpA variant, Variant 1, which differed from the Ghanaian variants. Next, using recombinant OmpA based on Variant 1, we determined that amino acid differences in OmpA in Ghanaian cattle as compared to OmpA Variant 1 did not alter the binding capacity of antibody directed against OmpA Variant 1, supporting the value of OmpA as a highly conserved vaccine candidate.
4q-D4Z4 chromatin architecture regulates the transcription of muscle atrophic genes in facioscapulohumeral muscular dystrophy
Authors: Cortesi Alice , Pesant Matthieu , Sinha Shruti , Marasca Federica , Sala Eleonora , Gregoretti Francesco , Antonelli Laura , Oliva Gennaro , Chiereghin Chiara , Soldà Giulia , Bodega Beatrice
Published: May 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 muscular 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 gene up-regulation. 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 that 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 up-regulation 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.
Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes
Authors: Cakiroglu Aylin , Clapier Cedric R. , Ehrensberger Andreas H. , Darbo Elodie , Cairns Bradley R. , Luscombe Nicholas M. , Svejstrup Jesper Q.
Published: May 2019

Chromatin transactions are typically studied in vivo, or in vitro using artificial chromatin lacking the epigenetic complexity of the natural material. Attempting to bridge the gap between these approaches, we established a system for isolating the yeast genome as a library of mononucleosomes harboring the natural epigenetic signature, suitable for biochemical manipulation. Combined with deep sequencing, this library was used to investigate the stability of individual nucleosomes and, as proof of principle, the nucleosome preference of the chromatin remodeling complex, RSC. This approach uncovered a distinct preference of RSC for nucleosomes derived from regions with a high density of histone variant H2AZ, and this preference is indeed markedly diminished using nucleosomes from cells lacking H2AZ. The preference for H2AZ remodeling/nucleosome ejection can also be reconstituted with recombinant nucleosome arrays. Together, our data indicate that, despite being separated from their genomic context, individual nucleosomes can retain their original identity as promoter- or transcription start site (TSS)-nucleosomes. Besides shedding new light on substrate preference of the chromatin remodeler RSC, the simple experimental system outlined here should be generally applicable to the study of chromatin transactions.
Full-profile search–match by the Rietveld method
Authors: Lutterotti Luca , Pillière Henry , Fontugne Christophe , Boullay Philippe , Chateigner Daniel
Published: May 2019

A new search–match procedure has been developed and tested which, in contrast to previously existing methods, does not use a set of lines identified from a diffraction pattern, but an optimized Rietveld fitting on the raw data. Modern computers with multicore processors allow the routine to be fast enough to perform the entire search in a reasonable time using quite large databases of crystal structures. The search–match is done using the crystal structures for all phases and the instrumental geometry, and as such can be applied to every kind of diffraction experiment, including X-rays, thermal/time-of-flight neutrons and electrons. The methodology can also be applied to nanocrystalline samples for which peak identification may be a problem. A web interface has been developed to permit easy testing and evaluation of the procedure. The quality of the results mainly depends on the availability of the sought phase in the structure database. The method permits not only phase identification but also a rapid quantification of the phases and their gross microstructural features, provided the instrumental function is known.
Hard and soft X-ray imaging to resolve human ovarian cortical structures
Authors: Pascolo Lorella , Sena Gabriela , Gianoncelli Alessandra , Cernogoraz Alice , Kourousias Geroge , Metscher Brian D. , Romano Federico , Zito Gabriella , Pacilè Serena , Barroso Regina , Tromba Giuliana , Zweyer Marina , Ricci Giuseppe
Published: May 2019

Laboratory and synchrotron X-ray tomography are powerful tools for non-invasive studies of biological samples at micrometric resolution. In particular, the development of phase contrast imaging is enabling the visualization of sample details with a small range of attenuation coefficients, thus allowing in-depth analyses of anatomical and histological structures. Reproductive medicine is starting to profit from these techniques, mainly applied to animal models. This study reports the first imaging of human ovarian tissue where the samples consisted of surgically obtained millimetre fragments, properly fixed, stained with osmium tetroxide and included in epoxydic resin. Samples were imaged by the use of propagation phase contrast synchrotron radiation micro-computed tomography (microCT), obtained at the SYRMEP beamline of Elettra light source (Trieste, Italy), and X-ray absorption microCT at the Theoretical Biology MicroCT Imaging Laboratory in Vienna, Austria. The reconstructed microCT images were compared with the soft X-ray absorption and phase contrast images acquired at the TwinMic beamline of Elettra in order to help with the identification of structures. The resulting images allow the regions of the cortex and medulla of the ovary to be distinguished, identifying early-stage follicles and visualizing the distribution of blood vessels. The study opens to further application of micro-resolved 3D imaging to improve the understanding of human ovary's structure and support diagnostics as well as advances in reproductive technologies.
Conformational analysis of the disaccharide methyl α-D-mannopyranosyl-(1→3)-2-O-acetyl-β-D-mannopyranoside monohydrate
Authors: Zhang Wenhui , Wu Qingquan , Oliver Allen G. , Serianni Anthony S.
Published: May 2019

The crystal structure of methyl α-D-mannopyranosyl-(1→3)-2-O-acetyl-β-D-mannopyranoside monohydrate, C15H26O12·H2O, (II), has been determined and the structural parameters for its constituent α-D-mannopyranosyl residue compared with those for methyl α-D-mannopyranoside. Mono-O-acetylation appears to promote the crystallization of (II), inferred from the difficulty in crystallizing methyl α-D-mannopyranosyl-(1→3)-β-D-mannopyranoside despite repeated attempts. The conformational properties of the O-acetyl side chain in (II) are similar to those observed in recent studies of peracetylated mannose-containing oligosaccharides, having a preferred geometry in which the C2—H2 bond eclipses the C=O bond of the acetyl group. The C2—O2 bond in (II) elongates by ∼0.02 Å upon O-acetylation. The phi (φ) and psi (ψ) torsion angles that dictate the conformation of the internal O-glycosidic linkage in (II) are similar to those determined recently in aqueous solution by NMR spectroscopy for unacetylated (II) using the statistical program MA′AT, with a greater disparity found for ψ (Δ = ∼16°) than for φ (Δ = ∼6°).
6-Amino-2-iminiumyl-4-oxo-1,2,3,4-tetrahydropyrimidin-5-aminium sulfate monohydrate
Authors: Tapmeyer Lukas , Prill Dragica
Published: May 2019

The title compound, C4H9N5O2+·SO4
2−·H2O, is the monohydrate of the commercially available compound `C4H7N5O·H2SO4·xH2O'. It is obtained by reprecipitation of C4H7N5O·H2SO4·xH2O from dilute sodium hydroxide solution with dilute sulfuric acid. The crystal structure of anhydrous 2,4,5-triamino-1,6-dihydropyrimidin-6-one sulfate is known, although called by the authors 5-amminium-6-amino-isocytosinium sulfate [Bieri et al. (1993). Private communication (refcode HACDEU). CCDC, Cambridge, England]. In the structure, the sulfate group is deprotonated, whereas one of the amino groups is protonated (R
2C—NH3
+) and one is rearranged to a protonated imine group (R
2C=NH2
+). This arrangement is very similar to the known crystal structure of the anhydrate. Several tautomeric forms of the investigated molecule are possible, which leads to questionable proton attributions. The measured data allowed the location of all hydrogen atoms from the residual electron density. In the crystal, ions and water molecules are linked into a three-dimensional network by N—H...O and O—H...O hydrogen bonds.
Substantive and symbolic strategies sustaining the environmentally friendly ideology
Authors: Chelli Mohamed , Durocher Sylvain , Fortin Anne
Published: May 2019

Purpose

The purpose of this paper is to longitudinally explore the symbolic and substantive ideological strategies located in ENGIE’s environmental discourse while considering the specific negative media context surrounding the company’s environmental activities.

Design/methodology/approach

Thompson’s (2007) and Eagleton’s (2007) theorizations are used to build an extended ideological framework to analyze ENGIE’s environmental talk from 2001 to 2015.

Findings

ENGIE drew extensively on a combination of symbolic and substantive ideological strategies in its annual and sustainability reports while ignoring several major issues raised in the press. Its substantive ideological mode of operation included actions for the environment, innovation, partnerships and educating stakeholders/staff, while its symbolic ideological mode of operation used issue identification, legal compliance, rationalization, stakeholders’ responsibilization and unification. Both ideological modes of operation worked synergistically to cast a positive light on ENGIE’s environmental activities, sustaining the ideology of a company that reconciles the irreconcilable despite negative press coverage.

Originality/value

This paper develops the notion of environmentally friendly ideology to analyze the environmental discourse of a polluting company. It is the first to use both Thompson’s and Eagleton’s ideological frameworks to make sense of corporate environmental discourse. Linking corporate discourse with media coverage, it further contributes to the burgeoning literature that interpretively distinguishes between symbolic and substantive ideological strategies by highlighting the company’s progressive shift from symbolic to more substantive disclosure.
Adoption of Big Data analytics in construction: development of a conceptual model
Authors: Ram Jiwat , Afridi Numan Khan , Khan Khawar Ahmed
Published: May 2019

Purpose

Big Data (BD) is being increasingly used in a variety of industries including construction. Yet, little research exists that has examined the factors which drive BD adoption in construction. The purpose of this paper is to address this gap in knowledge.

Design/methodology/approach

Data collected from literature (55 articles) were analyzed using content analysis techniques. Taking a two-pronged approach, first study presents a systematic perspective of literature on BD in construction. Then underpinned by technology–organization–environment theory and supplemented by literature, a conceptual model of five antecedent factors of BD adoption for use in construction is proposed.

Findings

The results show that BD adoption in construction is driven by a number of factors: first, technological: augmented BD–BIM integration and BD relative advantage; second, organizational: improved design and execution efficiencies, and improved project management capabilities; and third, environmental: augmented availability of BD-related technology for construction. Hypothetical relationships involving these factors are then developed and presented through a new model of BD adoption in construction.

Research limitations/implications

The study proposes a number of adoption factors and then builds a new conceptual model advancing theories on technologies adoption in construction.

Practical implications

Findings will help managers (e.g. chief information officers, IT/IS managers, business and senior managers) to understand the factors that drive adoption of BD in construction and plan their own BD adoption. Results will help policy makers in developing policy guidelines to create sustainable environment for the adoption of BD for enhanced economic, social and environmental benefits.

Originality/value

This paper develops a new model of BD adoption in construction and proposes some new factors of adoption process.
KEFST: a knowledge extraction framework using finite-state transducers
Authors: Mahmood Ahsan , Khan Hikmat Ullah , Rehman Zahoor Ur , Iqbal Khalid , Faisal Ch. Muhmmad Shahzad
Published: May 2019

Purpose

The purpose of this research study is to extract and identify named entities from Hadith literature. Named entity recognition (NER) refers to the identification of the named entities in a computer readable text having an annotation of categorization tags for information extraction. NER is an active research area in information management and information retrieval systems. NER serves as a baseline for machines to understand the context of a given content and helps in knowledge extraction. Although NER is considered as a solved task in major languages such as English, in languages such as Urdu, NER is still a challenging task. Moreover, NER depends on the language and domain of study; thus, it is gaining the attention of researchers in different domains.

Design/methodology/approach

This paper proposes a knowledge extraction framework using finite-state transducers (FSTs) – KEFST – to extract the named entities. KEFST consists of five steps: content extraction, tokenization, part of speech tagging, multi-word detection and NER. An extensive empirical analysis using the data corpus of Urdu translation of Sahih Al-Bukhari, a widely known hadith book, reveals that the proposed method effectively recognizes the entities to obtain better results.

Findings

The significant performance in terms of f-measure, precision and recall validates that the proposed model outperforms the existing methods for NER in the relevant literature.

Originality/value

This research is novel in this regard that no previous work is proposed in the Urdu language to extract named entities using FSTs and no previous work is proposed for Urdu hadith data NER.
Multifocus image fusion based on coefficient significance of redundant discrete wavelet transform
Authors: Liu Jianhua , Geng Peng , Ma Hongtao
Published: May 2019

Purpose

This study aims to obtain the more precise decision map to fuse the source images by Coefficient significance method. In the area of multifocus image fusion, the better decision map is very important the fusion results. In the processing of distinguishing the well-focus part with blur part in an image, the edge between the parts is more difficult to be processed. Coefficient significance is very effective in generating the better decision map to fuse the multifocus images.

Design/methodology/approach

The energy of Laplacian is used in the approximation coefficients of redundant discrete wavelet transform. On the other side, the coefficient significance based on statistic property of covariance is proposed to merge the detail coefficient.

Findings

Due to the shift-variance of the redundant discrete wavelet and the effectiveness of fusion rule, the presented fusion method is superior to the region energy in harmonic cosine wavelet domain, pixel significance with the cross bilateral filter and multiscale geometry analysis method of Ripplet transform.

Originality/value

In redundant discrete wavelet domain, the coefficient significance based on statistic property of covariance is proposed to merge the detail coefficient of source images.
Insider trading – unsolved issues
Authors: Teichmann Fabian Maximilian Johannes
Published: May 2019

Purpose

This paper aims to show that, despite the development of prevention mechanisms for banks, undetected insider trading remains highly feasible. It, thereby, highlights that the current anti-insider-trading mechanisms, on which previous literature has extensively focused, can be easily circumvented.

Design/methodology/approach

A two-step research process was employed. First, informal interviews were conducted with illegal financial services providers. Second, 50 compliance experts and law enforcement officers were formally interviewed. Responses from both sets of interviewees were subjected to quantitative content analysis to yield empirical findings.

Findings

Concrete and specific methods of insider trading and limiting the risks of being prosecuted were reported by interviewees. They suggested that the use of strawmen and offshore banks greatly facilitate insider trading.

Research limitations/implications

The perspectives of the 100 interviewees have not been quantitatively tested.

Practical implications

Suggestions on how to more effectively combat insider trading are provided for financial institutions and compliance officers.

Originality/value

Although the empirical findings are based on conditions in Europe, the results have potential global application.
The effect of corruption on bank profitability
Authors: Bolarinwa Segun Thompson , Soetan Funmi
Published: May 2019

Purpose

This paper aims to investigate the effect of corruption on bank profitability.

Design/methodology/approach

The paper adopts panel cointegration, differenced generalized method of moments (GMM) and system GMM.

Findings

The empirical results show that corruption is important in explaining the profitability of commercial banks in both developed and emerging countries. While it has mixed effects in emerging countries, only positive effect is validated in developed countries.

Research limitations/implications

Macroeconomic measures of corruption are adopted in the study.

Originality/value

The paper contributes to the literature on corruption and bank profitability by reporting evidence from both developed and developing countries. Existing papers have only concentrated on developing countries.
Anti-corruption reporting in emerging country multinationals
Authors: Vale José , Branco Manuel Castelo
Published: May 2019

Purpose

Based on a lens of analysis combining legitimacy and stakeholder theories, this paper aims to explore some factors which influence anti-corruption (AC) reporting in large multinationals from emerging countries.

Design/methodology/approach

An ordinal logistic regression is used to assess the relation between the AC reporting and multinationals’ industrial affiliation, number of countries of operations, membership of the United Nations Global Compact (UNGC) and public ownership. The sample was drawn from the 2016 Transparency International Report “Transparency in Corporate Reporting – Assessing Emerging Market Multinationals”.

Findings

Evidence suggests that in emerging countries, listed multinationals, which operate in a large number of countries or are members of the UNGC, present significant levels of AC reporting. Unexpectedly, results also suggest that such reporting is not significantly affected by the corruption risk level of the industries to which the multinationals belong. Finally, results suggest that in emerging markets, the dependency for resources may also affect AC reporting.

Originality/value

This paper contributes to the extant literature, by exploring different determinants of AC reporting, namely, a thus far unexplored one: public vs private ownership. This paper also contributes to the literature by providing insights into the relationships in a specific context: that of emerging countries. Finally, the reliance on the international community for the provision of resources is shown as a factor that potentially affects AC reporting.
Subjective norm vs dogmatism: Christian consumer attitude towards Islamic TV advertising
Authors: Aji Hendy Mustiko , Dharmmesta Basu Swastha
Published: May 2019

Purpose

With concern on cross-religion research, this study aims to examine Christian consumer attitude towards Islamic TV advertising in Indonesia. This study includes together both subjective norm and dogmatism in an analysis as moderating variables.

Design/methodology/approach

An online survey for 186 sample respondents was conducted to test nine hypotheses. Multi-group moderation test was conducted to test the moderation effect of subjective norms and dogmatism on the model.

Findings

The results indicate that Christian intrinsic religiosity has a significant negative relationship with Islamic TV advertising credibility. Consumers’ attitudes towards Islamic TV advertising are proven to be the consequence of Islamic TV advertising credibility, even if the relationship is inverted. Moreover, this study concludes that subjective norms and dogmatism significantly moderate the relationship between Islamic TV advertising credibility and attitudes towards Islamic TV advertising differently. Subjective norms tend to weaken the relationship, while dogmatism strengthens it.

Research limitations/implications

During the process of this study, the authors uncovered three research limitations. First, too many measurement items for dogmatism eliminated from the analysis. Second, having balanced proportion for the high and low group has become the concern of this study, Third, a sample size of 186 is not adequate for such a complex model.

Practical implications

Managers should employ endorsers with multi-faceted images who can be accepted by all segments of society to combat the negative perception and attitudes of Christian consumers on Islamic attributes in TV advertising.

Originality/value

This paper contributes to the literature on cross-religion marketing research, especially on the topic of advertising, by comparing the internal influence (dogmatism) and external influence (subjective norm) on attitude towards Islamic TV advertising.