bluuebunny/crossref_metadata_2025 huggingface dataset:
Bacterial killing by complement requires direct anchoring of Membrane Attack Complex precursor C5b-7
Authors: Doorduijn Dennis J , Bardoel Bart W , Heesterbeek Dani AC , Ruyken Maartje , Benn Georgina , Parsons Edward S , Hoogenboom Bart , Rooijakkers Suzan HM
Published: December 2019

An important effector function of the human complement system is to directly kill Gram-negative bacteria via Membrane Attack Complex (MAC) pores. MAC pores are assembled when surface-bound convertase enzymes convert C5 into C5b, which together with C6, C7, C8 and multiple copies of C9 forms a transmembrane pore that damages the bacterial cell envelope. Recently, we found that bacterial killing by MAC pores requires local conversion of C5 by surface-bound convertases. In this study we aimed to understand why local assembly of MAC pores is essential for bacterial killing. Here, we show that rapid interaction of C7 with C5b6 is required to form bactericidal MAC pores. Binding experiments with fluorescently labelled C6 show that C7 prevents release of C5b6 from the bacterial surface. Moreover, trypsin shaving experiments and atomic force microscopy revealed that this rapid interaction between C7 and C5b6 is crucial to efficiently anchor C5b-7 to the bacterial cell envelope and form complete MAC pores. Using complement-resistant clinicalE. colistrains, we show that bacterial pathogens can prevent complement-dependent killing by interfering with the anchoring of C5b-7. While C5 convertase assembly was unaffected, these resistant strains blocked efficient anchoring of C5b-7 and thus prevented stable insertion of MAC pores into the bacterial cell envelope. Altogether, these findings provide basic molecular insights into how bactericidal MAC pores are assembled and how bacteria evade MAC-dependent killing.
Structural and functional characterization of oligomeric states of proteins in RecFOR pathway
Authors: Chaudhary Santosh Kumar , Elayappan Mohanapriya , Jeyakanthan Jeyaraman , Sekar Kanagaraj
Published: December 2019

RecFOR pathway is the principal repair pathway for double strand break and single strand gap repair inThermus thermophilus. RecF and RecR exist as monomer and dimer in solution, interestingly; they undergo condition-dependent dimerization and tetramerization, respectively during the DNA break repair. However, their importance in protein-protein and protein-DNA interactions remains elusive. In this study, the three-dimensional crystal structures of the wild type RecF and RecR proteins are determined. Thereafter, the structural information is used to mutate the interface residues to cysteine to stabilize the dimeric and tetrameric states of the RecF and RecR proteins, respectively. A comparative study for their interactions with other cognate proteins and ssDNA in native and SSB (single strand binding protein) bound states was performed. RecF or RecFR complex displays a negligible affinity towards ssDNA. Conversely, the RecF mutants and its complexes with wild type RecR showed affinity towards ssDNA, suggesting, distinct modes of interaction of RecF and RecFR complex for ssDNA binding. In the presence of RecO, the stabilized tetrameric RecR showed a lower binding affinity for ssDNA as compared to the SSB bound ssDNA, indicating the importance of tetrameric RecR in stabilizing the RecOR complex on the SSB coated ssDNA. This provides an insight into the reduction of the binding affinity of SSB proteins with the ssDNA, which in turn enhances the recruitment of RecA for strand exchange.
The Tung Tree (Vernicia Fordii) Genome Provides A Resource for Understanding Genome Evolution and Oil Improvement
Authors: Zhang Lin , Liu Meilan , Long Hongxu , Dong Wei , Pasha Asher , Esteban Eddi , Li Wenying , Yang Xiaoming , Li Ze , Song Aixia , Ran Duo , Zhao Guang , Zeng Yanling , Chen Hao , Zou Ming , Li Jingjing , Liang Fan , Xie Meili , Hu Jiang , Wang Depeng , Cao Heping , Provart Nicholas J. , Zhang Liangsheng , Tan Xiaofeng
Published: December 2019

Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil containing a high proportion of eleostearic acid (∼80%). Here we report a high-quality, chromosome-scale tung tree genome sequence of 1.12 Gb with 28,422 predicted genes and over 73% repeat sequences. Tung tree genome was assembled by combining Illumina short reads, PacBio single-molecule real-time long reads and Hi-C sequencing data. Insertion time analysis revealed that the repeat-driven tung tree genome expansion might be due to long standing long terminal repeat (LTR) retrotransposon bursts and lack of efficient DNA deletion mechanisms. An electronic fluorescent pictographic (eFP) browser was generated based on genomic and RNA-seq data from 17 various tissues and developmental stages. We identified 88 nucleotide-binding site (NBS)-encoding resistance genes, of which 17 genes may help the tung tree resist theFusariumwilt shortly after infection. A total of 651 oil-related genes were identified and 88 of them were predicted to be directly involved in tung oil biosynthesis. The fewer phosphoenolpyruvate carboxykinase (PEPC) genes, and synergistic effects between transcription factors and oil biosynthesis-related genes may contribute to high oil content in tung seeds. The tung tree genome should provide valuable resources for molecular breeding and genetic improvement.
Use of thep-valueas a size-dependent function to address practical differences when analyzing large datasets
Authors: Gómez-de-Mariscal Estibaliz , Guerrero Vanesa , Sneider Alexandra , Jayatilaka Hasini , Phillip Jude M. , Wirtz Denis , Muñoz-Barrutia Arrate
Published: December 2019

Biomedical research has come to rely onp-valuesas a deterministic measure for data-driven decision making. In the largely extended null-hypothesis significance testing (NHST) for identifying statistically significant differences among groups of observations, a singlep-valuecomputed from sample data is routinely compared with a threshold, commonly set to 0.05, to assess the evidence against the hypothesis of having non-significant differences among groups, or the null hypothesis. Because the estimatedp-valuetends to decrease when the sample size is increased, applying this methodology to large datasets results in the rejection of the null hypothesis, making it not directly applicable in this specific situation. Herein, we propose a systematic and easy-to-follow method to detect differences based on the dependence of thep-valueon the sample size. The proposed method introduces new descriptive parameters that overcome the effect of the size in thep-valueinterpretation in the framework of large datasets, reducing the uncertainty in the decision about the existence of biological/clinical differences between the compared experiments. This methodology enables both the graphical and quantitative characterization of the differences between the compared experiments guiding the researchers in the decision process. An in-depth study of the proposed methodology is carried out using both simulated and experimentally obtained data. Simulations show that under controlled data, our assumptions on thep-valuedependence on the sample size holds. The results of our analysis in the experimental datasets reflect the large scope of this approach and its interpretability in terms of common decision-making and data characterization tasks. For both simulated and real data, the obtained results are robust to sampling variations within the dataset.
Quantifying the impact of an inference model in Bayesian phylogenetics
Authors: Bilderbeek Richèl J.C. , Laudanno Giovanni , Etienne Rampal S.
Published: December 2019

Phylogenetic trees are currently routinely reconstructed from an alignment of character sequences (usually nucleotide sequences). Bayesian tools, such as MrBayes, RevBayes and BEAST2, have gained much popularity over the last decade, as they allow joint estimation of the posterior distribution of the phylogenetic trees and the parameters of the underlying inference model. An important ingredient of these Bayesian approaches is the species tree prior. In principle, the Bayesian framework allows for comparing different tree priors, which may elucidate the macroevolutionary processes underlying the species tree. In practice, however, only macroevolutionary models that allow for fast computation of the prior probability are used. The question is how accurate the tree estimation is when the real macroevolutionary processes are substantially different from those assumed in the tree prior.

Here we presentpirouette, a free and open-source R package that assesses the inference error made by Bayesian phylogenetics for a given macroevolutionary diversification model.pirouettemakes use of BEAST2, but its philosophy applies to any Bayesian phylogenetic inference tool.

We describepirouette’s usage providing full examples in which we interrogate a model for its power to describe another.

Last, we discuss the results obtained by the examples and their interpretation.
LAVA: a streamlined visualization tool for longitudinal analysis of viral alleles
Authors: Lin Michelle J. , Shean Ryan C. , Makhsous Negar , Greninger Alexander L.
Published: December 2019

With their small genomes, fast evolutionary rates, and clinical significance, viruses have long been fodder for studies of whole genome evolution. One common need in these studies is the analysis of viral evolution over time through longitudinal sampling. However, there exists no simple tool to automate such analyses. We created a simple command-line visualization tool called LAVA (Longitudinal Analysis of Viral Alleles). LAVA allows dynamic and interactive visualization of viral evolution across the genome and over time. Results are easily shared via a single HTML file that also allows interactive analysis based on read depth and allele frequency. LAVA requires minimal input and runs in minutes for most use cases. LAVA is programmed mainly in Python 3 and is compatible with Mac and Linux machines. LAVA is a user-friendly command-line tool for generating, visualizing, and sharing the results of longitudinal viral genome evolution analysis. Instructions for downloading, installing, and using LAVA can be found at https://github.com/michellejlin/lava.
Intelli-NGS: Intelligent NGS, a deep neural network-based artificial intelligence to delineate good and bad variant calls from IonTorrent sequencer data
Authors: Singh Aditya , Bhatia Prateek
Published: December 2019

Background

IonTorrent is a second-generation sequencing platform with smaller capital costs than Illumina but is also prone to higher machine error than later. Given its lower costs, the platform is generally preferred in developing countries where next-generation sequencing is still a very exclusive technique. There are many software tools available for other platforms but IonTorrent. This makes the already tricky analysis part more error-prone.

Motivation

We have been using the IonTorrent platform in our hospital setting for aiding diagnosis or treatment for the past couple of years. Given to our experience, analysis part of IonTorrent data takes the longest time and still, we used to get stuck with certain variants which seemed fine on looking at their metrics but were found to be negative in Sanger sequencing verification. This made us determined to develop a tool that could aid us in reducing false positive and negative rates while still retaining good recall. The artificial intelligence-based technique was our final choice after developing pipelines with less success.

Methodology

The artificial intelligence was developed from scratch in Python 3 using TensorFlow fully connected dense layers. The model takes VCF files as input and solves each variant based on the thirty-five parameters given by the IonTorrent platform, including the flow-space information which is missed by variant callers other than the default torrent variant caller.

Results

The final trained model was able to achieve an accuracy of 93.08% and a ROC-AUC of 0.95 with GIAB validation data. The additional program that was written to run the model annotates each variant using online databases such as dbSNP, ClinVar and others. A probability score for each outcome for each variant is also provided to aid in decision making.

Availability

The model and running code are available for free only for non-commercial users athttps://www.github.com/aditya-88/intelli-ngs.
Transcriptional regulation of MGE progenitor proliferation by PRDM16 controls cortical GABAergic interneuron production
Authors: García Miguel Turrero , Baizabal José-Manuel , Tran Diana , Peixoto Rui , Wang Wengang , Xie Yajun , Adam Manal A. , Brito Salvador , Booker Matthew A. , Tolstorukov Michael Y. , Harwell Corey C.
Published: December 2019

The mammalian cortex is populated by neurons derived from neural progenitors located throughout the embryonic telencephalon. Excitatory neurons are derived from progenitors located in the dorsal telencephalon, while inhibitory interneurons are generated by ventral telencephalic progenitors. The transcriptional regulator PRDM16 is expressed by radial glia, neural progenitors present in both regions; however, its mechanisms of action are still not fully understood. It is unclear if PRDM16 functions plays a role in neurogenesis in both dorsal and ventral progenitor lineages, and if so, whether it does so by regulating common or unique networks of genes. Here, we show thatPrdm16expression in MGE progenitors is required for maintaining their proliferative capacity and for the production of proper numbers of pallial GABAergic interneurons. PRDM16 binds to cis-regulatory elements and represses the expression of region-specific neuronal differentiation genes, thereby controlling the timing of neuronal maturation. Our results highlight the importance of PRDM16 for the development of both excitatory and inhibitory cortical circuits. We demonstrate the existence of convergent developmental gene expression programs regulated by PRDM16, which utilize both common and region-specific sets of genes in the cortex and the MGE to control the proliferative capacity of neural progenitors, ensuring the generation of correct numbers of cortical neurons.
Management of a Walnut Germplasm Collection: Which of SSR or SNP Markers Are Most Suitable to Preserve Biodiversity?
Authors: Bernard Anthony , Barreneche Teresa , Donkpegan Armel , Fabrice Lheureux , Dirlewanger Elisabeth
Published: December 2019

The preservation of the maximum of diversity within the smallest number of accessions is one of the challenges of germplasm management. To construct core-collections, the assessment of the population structure and the relationships between the accessions represents a key step and the choice of suitable molecular markers is the starting point. Since the expansion of available SNP-based genomics tools, a debate has emerged regarding the usefulness of the widely used microsatellites (SSRs) markers. In this study, we analysed a part of the INRAE walnut germplasm collection of 150 accessions, unique in Europe for walnut biodiversity conservation, by comparing the power of both types of marker. We found that the first level of structure is equally detected using 13 SSRs or the Axiom™J. regia700K SNP array, and is in relation with the geographical origin of the accessions. For K=2, there was no exchange of accession between the two groups when both markers were compared. We also highlighted empirically that approximately 100 SNPs are needed to obtain similar clustering to SSRs in Principal Coordinate Analysis (PCoA). The neighbor-joining trees constructed were also consistent between both types of marker. The main differences lied in the upper levels of structure from K=3 to K=6, more powerful using the SNPs, and in the percentage of the explained variation in PCoA for K=2, higher using SSRs. We then constructed core-collections of 50 accessions, a crucial step in genetic resources management to reduce the costs and preserve the allelic diversity. Using two different construction methods, both SSR and SNP markers were suitable and able to keep at least 88.57% of the alleles. 32/50 accessions were in common between the two markers, for both methods. We concluded that the use of either marker is dependent on the researcher’s goal.
Antioxidant, anti-enzymatic, antimicrobial and cytotoxic properties ofEuphorbia tirucalliL
Authors: Altamimi Mohammad , Jaradat Nidal , Alham Saad , Al-Masri Motasem , Bsharat Ala , Alsaleh Rania , Sabobeh Rozan
Published: December 2019

Medicinal properties ofEuphorbia tirucalliL. have been investigated in vitro. Water extract from the plant latex was freeze dried and tested against 3 digestive enzymes and showed IC50 as 39.8±0.22, 79.43±0.38 and 316.22±0.3 for lipase, alpha- glucosidase and alpha- amylase, respectively. These results were incomparable with drugs such as acarbose and orlistat. Antioxidant property showed that the IC50 values ofE. tirucalliand Trolox were 79.43±0.69 and 3.1 ±0.92 respectively. Also, the plant extract exhibited a range of antimicrobial activity against gram-positive and gram-negative bacteria and pathogenic yeast and fungi. Cytotoxicity of the plant extract tested on Caco-2 cells was determined using MTT method. The effect was linear and almost 0.5 mg/ml extract has inhibited 50% of cells relative to the control.Euphorbia tirucallishowed promising activities and is potential source of active ingredient with functional properties.
Evolution of the insecticide targetRdlin AfricanAnophelesis driven by interspecific and interkaryotypic introgression
Authors: Grau-Bové Xavier , Tomlinson Sean , O’Reilly Andrias O. , Harding Nicholas J. , Miles Alistair , Kwiatkowski Dominic , Donnelly Martin J. , Weetman David ,   The Anopheles gambiae 1000 Genomes Consortium
Published: December 2019

The evolution of insecticide resistance mechanisms in natural populations ofAnophelesmalaria vectors is a major public health concern across Africa. Using genome sequence data, we study the evolution of resistance mutations in theresistance to dieldrin locus(Rdl), a GABA receptor targeted by several insecticides, but most notably by the long-discontinued cyclodiene, dieldrin. The twoRdlresistance mutations (296Gand296S) spread across West and Central AfricanAnophelesvia two independent hard selective sweeps that included likely compensatory nearby mutations, and were followed by a rare combination of introgression across species (fromA. gambiaeandA. arabiensistoA. coluzzii) and across non-concordant karyotypes of the 2La chromosomal inversion.Rdlresistance evolved in the 1950s as the first known adaptation to a large-scale insecticide-based intervention, but the evolutionary lessons from this system highlight contemporary and future dangers for management strategies designed to combat development of resistance in malaria vectors.
A polarized nucleus-cytoskeleton-ECM connection controls collective migration and cardioblasts number inDrosophila
Authors: Dondi C , Bertin B , Da Ponte JP , Wojtowicz I , Jagla K , Junion G
Published: December 2019

The formation of the cardiac tube is a remarkable example of complex morphogenetic process conserved from invertebrates to humans. It involves coordinated collective migration of contralateral rows of cardiac cells. The molecular processes underlying the specification of cardioblasts prior to migration are well established and significant advances have been made in understanding the process of lumen formation. However, the mechanisms of collective cardiac cells migration remain elusive. Here we identifiedCAPandMSP-300as novel actors involved in cardioblast migration. They both display highly similar temporal and spatial expression pattern in migrating cardiac cells and are required for the correct number, alignment and coordinated directional migration of cardioblasts. Our data suggest that CAP and MSP-300 are part of a tension-sensitive protein complex linking cardioblast focal adhesion sites to nuclei via actin cytoskeleton and triggering coordinated cardioblast movements.
Visualizing ’omic feature rankings and log-ratios using Qurro
Authors: Fedarko Marcus W. , Martino Cameron , Morton James T. , González Antonio , Rahman Gibraan , Marotz Clarisse A. , Minich Jeremiah J. , Allen Eric E. , Knight Rob
Published: December 2019

Many tools for dealing with compositional “’omics” data produce feature-wise values that can be ranked in order to describe features’ associations with some sort of variation. These values include differentials (which describe features’ associations with specified covariates) and feature loadings (which describe features’ associations with variation along a given axis in a biplot). Although prior work has discussed the use of these “rankings” as a starting point for exploring the log-ratios of particularly high-or low-ranked features, such exploratory analyses have previously been done using custom code to visualize feature rankings and the log-ratios of interest. This approach is laborious, prone to errors, and raises questions about reproducibility. To address these problems we introduce Qurro, a tool that interactively visualizes a plot of feature rankings (a “rank plot”) alongside a plot of selected features’ log-ratios within samples (a “sample plot”). Qurro’s interface includes various controls that allow users to select features from along the rank plot to compute a log-ratio; this action updates both the rank plot (through highlighting selected features) and the sample plot (through displaying the current log-ratios of samples). Here we demonstrate how this unique interface helps users explore feature rankings and log-ratios simply and effectively.
Inhibition of tumor growth by a novel engineered chimeric toxin that cleaves activated mutant and wild-type RAS
Authors: Vidimar Vania , Beilhartz Greg L. , Park Minyoung , Biancucci Marco , Kieffer Matthew B. , Gius David R. , Melnyk Roman A. , Satchell Karla J. F.
Published: December 2019

Despite nearly four decades of effort, broad inhibition of oncogenic RAS using small molecule approaches has proven to be a major challenge. Here we describe the development of a novel pan-RAS biologic inhibitor comprised of the RAS-RAP1-specific endopeptidase fused to the protein delivery machinery of diphtheria toxin. We show that this engineered chimeric toxin irreversibly cleaves and inactivates intracellular RAS at low picomolar concentrations terminating downstream signaling in receptor-bearing cells. Further, we demonstratein vivotarget engagement and reduction of tumor burden in three mouse xenograft models driven by either wild-type or mutantRAS. Intracellular delivery of a potent anti-RAS biologic through a receptor-mediated mechanism represents a promising new approach to developing RAS therapeutics against a broad array of cancers.

Significance

RAS oncoproteins have long been considered among the most elusive drug targets in cancer research. At issue is the lack of accessible drug binding sites and the extreme affinity for its GTP substrate. Covalent inhibitors against the KRAS G12C mutant have shown early clinical promise, however, targeting the other oncogenic RAS mutants across three RAS isoforms has proven challenging. Inhibition of activated wild-type RAS in the absence of canonicalRASmutations is also highly desirable in certain tumors. Here, we demonstrate delivery of an extremely potent pan-RAS and RAP1 cleaving enzyme in therapeutic quantities to specific receptor-bearing cellsin vitroandin vivo. We aim to advance this approach to engineer the first targeted pan-RAS inhibitor for cancer therapy.

One Sentence Summary

Engineered chimeric toxin halts tumor growthin vivovia RAS cleavage
Two distinct mechanisms of small molecule inhibition of LpxA acyltransferase essential for lipopolysaccharide biosynthesis
Authors: Han Wooseok , Ma Xiaolei , Balibar Carl J. , Baxter Rath Christopher M. , Benton Bret , Bermingham Alun , Casey Fergal , Chie-Leon Barbara , Cho Min-Kyu , Frank Andreas O. , Frommlet Alexandra , Ho Chi-Min , Lee Patrick S. , Li Min , Lingel Andreas , Ma Sylvia , Merritt Hanne , Ornelas Elizabeth , de Pascale Gianfranco , Prathapam Ramadevi , Prosen Katherine R. , Rasper Dita , Ruzin Alexey , Sawyer William , Shaul Jacob , Shen Xiaoyu , Shia Steven , Steffek Micah , Subramanian Sharadha , Vo Jason , Wang Feng , Wartchow Charles , Uehara Tsuyoshi
Published: December 2019

The paper with the doi 10.1101/850305 has been removed as a result of a technical error. The paper is available on bioRxiv under this doi: 10.1101/2019.12.14.850305.
Characterizing the nuclear and cytoplasmic transcriptomes in developing and mature human cortex uncovers new insight into psychiatric disease gene regulation
Authors: Price Amanda J. , Hwang Taeyoung , Tao Ran , Burke Emily E. , Rajpurohit Anandita , Shin Joo Heon , Hyde Thomas M. , Kleinman Joel E. , Jaffe Andrew E. , Weinberger Daniel R.
Published: December 2019

Transcriptome compartmentalization by the nuclear membrane provides both stochastic and functional buffering of transcript activity in the cytoplasm, and has recently been implicated in neurodegenerative disease processes. Although many mechanisms regulating transcript compartmentalization are also prevalent in brain development, the extent to which subcellular localization differs as the brain matures has yet to be addressed. To characterize the nuclear and cytoplasmic transcriptomes during brain development, we sequenced both RNA fractions from homogenate prenatal and adult human postmortem cortex using poly(A)+ and Ribo-Zero library preparation methods. We find that while many genes are differentially expressed by fraction and developmental expression changes are similarly detectable in nuclear and cytoplasmic RNA, the compartmented transcriptomes become more distinct as the brain matures, perhaps reflecting increased utilization of nuclear retention as a regulatory strategy in adult brain. We examined potential mechanisms of this developmental divergence including alternative splicing, RNA editing, nuclear pore composition, RNA-binding protein motif enrichment, and RNA secondary structure. Intron retention is associated with greater nuclear abundance in a subset of transcripts, as is enrichment for several splicing factor binding motifs. Finally, we examined disease association with fraction-regulated gene sets and found nuclear-enriched genes were also preferentially enriched in gene sets associated with neurodevelopmental psychiatric disorders. These results suggest that although gene-level expression is globally comparable between fractions, nuclear retention of transcripts may play an underappreciated role in developmental regulation of gene expression in brain, particularly in genes whose dysregulation is related to neuropsychiatric disorders.
Incommensurate crystal structure of PbHfO3
Authors: Bosak Alexei , Svitlyk Volodymyr , Arakcheeva Alla , Burkovsky Roman , Diadkin Vadim , Roleder Krystian , Chernyshov Dmitry
Published: December 2019

Controversy in the description/identification of so-called intermediate phase(s) in PbHfO3, stable in the range ∼420–480 K, has existed for a few decades. A synchrotron diffraction experiment on a partially detwinned crystal allowed the structure to be solved in the superspace groupImma(00γ)s00 (No. 74.2). In contrast to some previously published reports, in the pure compound only one distinct phase was observed betweenPbamPbZrO3-like antiferroelectric andPm3mparaelectric phases. The modulation vector depends only slightly on temperature. The major structure modulation is associated with the displacement of lead ions, which is accompanied by a smaller amplitude modulation for the surrounding O atoms and tilting of HfO6octahedra. Tilting of the octahedra results in a doubling of the unit cell compared with the parent structure.
The solubility and stability of heterocyclic chalcones compared with trans-chalcone
Authors: Sweeting Stephen G. , Hall Charlie L. , Potticary Jason , Pridmore Natalie E. , Warren Stephen D. , Cremeens Matthew E. , D'Ambruoso Gemma D. , Matsumoto Masaomi , Hall Simon R.
Published: December 2019

Heterocyclic chalcones are a recently explored subgroup of chalcones that have sparked interest due to their significant antibacterial and antifungal capabilities. Herein, the structure and solubility of two such compounds, (E)-1-(1H-pyrrol-2-yl)-3-(thiophen-2-yl)prop-2-en-1-one and (E)-3-phenyl-1-(1H-pyrrol-2-yl)prop-2-en-1-one, are assessed. Single crystals of (E)-1-(1H-pyrrol-2-yl)-3-(thiophen-2-yl)prop-2-en-1-one were grown, allowing structural comparisons between the heterocyclic chalcones and (2E)-1,3-diphenylprop-2-en-1-one, trivially known as trans-chalcone. The two heterocyclic chalcones were found to be less soluble in all solvents tested and to have higher melting points than trans-chalcone, probably due to their stronger intermolecular interactions arising from the functionalized rings. Interestingly, however, it was found that the addition of the thiophene ring in (E)-1-(1H-pyrrol-2-yl)-3-(thiophen-2-yl)prop-2-en-1-one increased both the melting point and solubility of the sample compared with (E)-3-phenyl-1-(1H-pyrrol-2-yl)prop-2-en-1-one. This observation may be key for the future crystal engineering of heterocyclic chalcones for pharmaceutical applications.
A combined model of electron density and lattice dynamics refined against elastic diffraction data. Thermodynamic properties of crystalline L-alanine
Authors: Sovago Ioana , Hoser Anna A. , Madsen Anders Ø.
Published: December 2019

Thermodynamic stability is an essential property of crystalline materials, and its accurate calculation requires a reliable description of the thermal motion – phonons – in the crystal. Such information can be obtained from periodic density functional theory (DFT) calculations, but these are costly and in some cases insufficiently accurate for molecular crystals. This deficiency is addressed here by refining a lattice-dynamics model, derived from DFT calculations, against accurate high-resolution X-ray diffraction data. For the first time, a normal-mode refinement is combined with the refinement of aspherical atomic form factors, allowing a comprehensive description and physically meaningful deconvolution of thermal motion and static charge density in the crystal. The small and well diffracting L-alanine system was used. Different lattice-dynamics models, with or without phonon dispersion, and derived from different levels of theory, were tested, and models using spherical and aspherical form factors were compared. The refinements indicate that the vibrational information content in the 23 K data is too small to study lattice dynamics, whereas the 123 K data appear to hold information on the acoustic and lowest-frequency optical phonons. These normal-mode models show slightly larger refinement residuals than their counterparts using atomic displacement parameters, and these features are not removed by considering phonon dispersion in the model. The models refined against the 123 K data, regardless of their sophistication, give calculated heat capacities for L-alanine within less than 1 cal mol−1 K−1 of the calorimetric measurements, in the temperature range 10–300 K. The findings show that the normal-mode refinement method can be combined with an elaborate description of the electron density. It appears to be a promising technique for free-energy determination for crystalline materials at the expense of performing a single-crystal elastic X-ray diffraction determination combined with periodic DFT calculations.
Neural-sliding mode approach-based adaptive estimation, isolation and tolerance of aircraft sensor fault
Authors: Taimoor Muhammad , Aijun Li
Published: December 2019

Purpose

The purpose of this paper is to propose an adaptive neural-sliding mode-based observer for the estimation and reconstruction of unknown faults and disturbances for time-varying nonlinear systems such as aircraft, to ensure preciseness in the diagnosis of fault magnitude as well as the shape without enhancement of system complexity and cost. Fault-tolerant control (FTC) strategy based on adaptive neural-sliding mode is also proposed in the existence of faults for ensuring the stability of the faulty system.

Design/methodology/approach

In this paper, three strategies are presented: adaptive radial basis functions neural network (ARBFNN), conventional radial basis functions neural network (CRBFNN) and integral-chain differentiator. For the purpose of enhancement of fault diagnosis and isolation, a new sliding mode-based concept is introduced for the weight updating parameters of radial basis functions neural network (RBFNN).The main objective of updating the weight parameters adaptively is to enhance the effectiveness of fault diagnosis and isolation without increasing the computational complexities of the system. Results depict the effectiveness of the proposed ARBFNN approach in fault detection (FD) and approximation compared to CRBFNN, integral-chain differentiator and schemes existing in literature. In the second step, the FTC strategy is presented separately for each observer in the presence of unknown faults and failures for ensuring the stability of the system, which is validated on Boeing 747 100/200 aircraft.

Findings

The proposed adaptive neural-sliding mode approach is investigated, which depicts more effectiveness in numerous situations such as faults, disturbances and uncertainties compared to algorithms used in literature. In this paper, both the fault approximation and isolation and the fault tolerance approaches are studied.

Practical implications

For the enhancement of safety level as well as for avoiding any kind of damage, timely FD and fault tolerance have always had a significant role; therefore, the algorithms proposed in this research ensure the tolerance of faults and failures, which plays a vital role in practical life for avoiding any kind of damage.

Originality/value

In this study, a new neural-sliding mode concept is adopted for the adaptive faults approximation and reconstruction, and then the FTC algorithms are studied for each observer separately, whereas in previous studies, only the fault detection and isolation (FDI) or the fault tolerance problems were studied. Results demonstrate the effectiveness of the proposed strategy compared to the approaches given in the literature.
Energy management-based design of a Wankel hybrid-electric UAV
Authors: Donateo Teresa , Ficarella Antonio , De Pascalis Claudia Lucia
Published: December 2019

Purpose

The purpose of this study is to investigate the optimization of design and energy management in a parallel hybrid-electric powertrain to replace the conventional engine of an existing tactical unmanned aerial vehicle (UAV) equipped with a Wankel engine with a pre-defined flight mission. The proposed powertrain can work in four different operating modes: electric, thermal, power-assist and charging.

Design/methodology/approach

The power request at propeller axis of each flight segment is used as input for an in-house model that calculates the overall fuel consumption throughout the mission (Mfuel) and the maximum payload weight (Wpay) by means of an average-point analysis. These outputs depend on the energy management strategy that is expressed by the power-split ratio between engine and electric phase (Uphase) of each mission phase, according to which the components of the hybrid system are sized. The in-house model is integrated into an optimization framework to find the optimal set of Uphase and battery size that minimizes Mfuel and maximizes Wpay.

Findings

It was found a 3.24% saving of the fuel mass burned throughout the mission (or, alternative an improvement of endurance by 4.3%) with about the same maximum-payload mass (+0.2%) of the original configuration, or a smaller fuel saving with +11% more payload. The fuel saving of 3.24% corresponds to −3.25% in total emissions of CO2and a 2.34% reduction of the cost-per-mission.

Practical implications

This study demonstrates that environmental advantages, even if limited, can be already obtained from optimal design and management of the hybrid power system with today technologies while waiting for further benefits from the introduction of advanced technologies for batteries and electric machines.

Originality/value

The main novelties are the design of the powertrain on the basis of the energy management and the application of scalability and hybridization to Wankel engines.
The impact of informal credit on rural agricultural productivity in the savannah ecological zone of Ghana
Authors: Sekyi Samuel , Domanban Paul Bata , Honya George Kwame
Published: December 2019

Purpose

The purpose of this paper is to examine the impact of informal credit access on agricultural productivity in rural Ghana.

Design/methodology/approach

Data sets from the Ghana Feed the Future baseline survey involving a total sample of 2,437 rural farm households were used. In order to address the problem of endogeneity and sample selectivity bias, the endogenous switching regression (ESR) model was employed to examine whether rural farm households’ with access to informal credit and those without access differ in terms of their productivity levels and whether access to informal credit affects agricultural productivity.

Findings

Estimates from the ESR show that access to informal credit significantly promotes agricultural productivity. Specifically, farmers with access to informal credit were able to achieve a yield of 48.42 kg/ha more than their counterparts without informal credit access. In terms of the counterfactual, farmers without informal credit access would have increased their yield by 57.61 kg/ha if they were to have access to informal credit.

Research limitations/implications

The study was restricted to the savannah ecological zone of Ghana. This limits the extent of generalisation of results.

Originality/value

This study provides a rigorous econometric analysis of the impacts of access to informal credit on agricultural productivity in rural Ghana. The study contributes to the current debate on the link between access to informal credit and agricultural productivity and provides valuable input for policymakers.
Pyramid ownership structure and tax avoidance among Canadian firms
Authors: Mindzak Justin , Zeng Tao
Published: December 2019

Purpose

This paper aims to examine the relationship between pyramid ownership structure and tax avoidance.

Design/methodology/approach

This paper is an empirical work using a sample of Canadian listed firms.

Findings

Relying on several proxies for tax avoidance, the authors find that firms affiliated with pyramidal structures generally engage in more tax avoidance activities than non-affiliated firms; firms affiliated with more complex pyramids engage in more tax avoidance practices and firms located at the lower tiers of the pyramids avoid more taxes; and some pyramid-affiliated firms with larger deviation between controlling shareholders’ cash flow rights and control rights engage in more tax avoidance practices.

Social implications

A broader understanding of the relationship between pyramidal structure and tax avoidance can be pursued by including firms in other countries, where the pyramid groups (pyramid structure) are prevalent, but institutional environments differ from that of Canada.

Originality/value

This study highlights the importance of pyramid ownership in shaping tax avoidance activities among Canadian-listed firms. Canada provides an ideal setting for studying the impact of ownership structure, as it contains a diverse corporate ownership structure ranging from widely held freestanding firms to pyramidal business groups.
“Carne Fraca”
Authors: Quevedo-Silva Filipe , Freire Otavio , Spanhol-Finocchio Caroline Pauletto
Published: December 2019

Purpose

Over the last few years, several events have reduced the consumer confidence in relation to food safety. Recently, one event that triggered discussions and concern among consumers in Brazil was the “Carne Fraca” operation which cast doubt on the quality and safety of Brazilian beef. The purpose of this paper is to analyse the impact of the news regarding a national crisis in beef production on consumers’ assessment and purchase intention of beef.

Design/methodology/approach

A quantitative study was conducted involving 417 respondents in Brazil. The procedure for the analysis consisted of the investigation of two models, incorporating mediation and moderation effects.

Findings

The results show that news on the crisis had a positive impact on risk perception. This impact was negatively moderated by consumer scepticism. Risk perception had a negative effect on the assessment of beef and purchase intention. These effects were negatively affected by risk attitude. The news directly affected consumers’ assessment of beef and indirectly affected purchase intention through mediation of perceived risk.

Originality/value

This study proposes two models, analysing the effect of the media on consumers’ assessment of beef and purchase intention, mediated by risk perception. Furthermore, the models analyse the moderating effects of scepticism and consumers’ risk attitude.
Board diversity and corporate risk: evidence from China
Authors: Bhat Kalim Ullah , Chen Yan , Jebran Khalil , Memon Zulfiqar Ali
Published: December 2019

Purpose

The purpose of this study shows how overall board diversity influences corporate risk-taking. Board diversity is quantified into task-oriented diversity (tenure and education) and relation-oriented diversity (age and gender). Further, this study tests whether the association of board diversity and corporate risk varies across state-owned firms (SOEs) and non-state-owned firms (NSOEs).

Design/methodology/approach

The authors used a sample of Chinese listed firms over the period 1999-2017. The results are estimated using the fixed-effects model. To deal with the endogeneity problem and single model bias, the authors use a dynamic model, i.e. two-step generalized method of moment’s model.

Findings

The results show that both task-oriented and relation-oriented diversity reduces corporate risk. Further, the authors document that overall board diversity reduces risk-taking across different types of firms, that is, SOEs and NSOEs. These results are consistent after controlling for endogeneity problems.

Practical implications

The results provide implications for enhancing corporate governance practices by considering overall board diversity as an important factor influencing corporate decisions. The findings suggest that policymakers and shareholders should consider different diversity attributes important for the composition of a board, which can enhance board outcomes.

Originality/value

Most of the prior studies considered only one dimension of diversity, and therefore, have overlooked the overall board diversity. Unlike prior studies, this study considers four board diversity attributes – age, gender, tenure and education, and further tests their association with corporate risk. Further, this study also examines the effect of overall diversity on corporate risk in SOEs and NSOEs.
The influence of strategic alliances on human capital development
Authors: Ferreira António , Franco Mário
Published: December 2019

Purpose

The purpose of this paper is to analyse the influence of strategic alliances (knowledge/learning, efficiency and market motives) on the development of human capital.

Design/methodology/approach

To do so, a quantitative study was chosen, with data on technology-based small and medium-sized enterprises (SMEs) in Portugal, leading to 257 valid answers.

Findings

The results obtained from a structural equation model show that motives for strategic alliances (knowledge/learning, efficiency and market) have a strong influence on the human capital of the SMEs analysed.

Practical implications

These outcomes reveal that strategic alliances are a way for SMEs to overcome resource constraints in terms of human capital, representing an important implication for business practice. As strategic alliances influence human capital, the relations SMEs establish with other firms are increasingly important for their sustainability and development. Acting in isolation in the market can reduce this type of firm’s chances of survival.

Originality/value

Despite some studies relating the formation of strategic alliances and human capital, there is a gap regarding the relationship between the role of strategic alliances and human capital in the technology-based sector. Therefore, this research represents a contribution and innovation in academic terms in this area.
Investigating international strategic brand management and export performance outcomes in the B2B context
Authors: Pyper Keith , Doherty Anne Marie , Gounaris Spiros , Wilson Alan
Published: December 2019

Purpose

Drawing on Resource-based Theory, the purpose of this paper is to empirically examine the effect of International Strategic Brand Management (SBM) on export performance within the Business-to-Business (B2B) context. To be able to purposely assess the relationship, this paper also sets out to discover what antecedent international resources, (financial resources) and international capabilities (market information, branding and marketing planning) contribute to the ability of B2B exporters to effectively manage their brands abroad.

Design/methodology/approach

A mixed method firm-level approach was employed. First, a qualitative study of 34 in-depth interviews explored the focal inter-relationships and constructs identified within the literature. A survey of 208 successful UK exporters was then conducted and the results were analysed using structured equation modelling.

Findings

The results confirm that certain marketing capabilities (branding and marketing planning) are advantageous antecedents to the employment of effective SBM in foreign markets which, in turn, leads to increased financial and market performance internationally.

Practical implications

This paper outlines practical brand management considerations managers need to account for to achieve effective exporting. Practitioners are advised to prioritise the development of robust international branding and marketing planning capabilities which can enable them to exploit their limited financial resources for optimal benefits. Furthermore, by developing these capabilities, firms can focus on the essence of their brand and communicate their brand image through the effective strategic management of their brand to business customers, evoking positive brand associations, enhanced perceived brand value and the achievement of increased export performance.

Originality/value

This paper is the first to focus on international SBM as the deterministic factor leading to improved B2B export performance. An innovative framework is offered which positions the pivotal role of International SBM as the central focus. The construct for international branding capabilities is extended specifically for use in the B2B domain.