bluuebunny/crossref_metadata_2025 huggingface dataset:
LanD-like Flavoprotein-Catalyzed Aminovinyl-Cysteine Formation through Oxidative Decarboxylation and Cyclization of a Peptide at the C-Terminus
Authors: Liu Jingyu , Qiu Yanping , Fu Tao , Li Miao , Li Yuqing , Yang Qian , Tang Zhijun , Tang Haoyu , Li Guangyu , Pan Lifeng , Liu Wen
Published: February 2020

Aminovinyl-cysteine residues arise from processing the C-terminall-Cys and an internall-Ser/l-Thr orl-Cys of a peptide. Formation of these nonproteinogenic amino acids, which occur in a macrocyclic ring of diverse ribosomally synthesized lanthipeptides and non-lanthipeptides, remains poorly understood. Here, we report that LanD-like flavoproteins in the biosynthesis of distinct non-lanthipeptides share an unexpected dual activity for aminovinyl-cysteine formation. Each flavoprotein catalyzes oxidative decarboxylation of the C-terminall-Cys and couples the resulting enethiol nucleophile with the internal residue to afford a thioether linkage for peptide cyclization. The cyclization step, which largely depends on proximity effect by positioning the enethiol intermediate with a bent conformation at the active site, can be substrate-dependent, proceeding inefficiently through nucleophilic substitution for an unmodified peptide or efficiently through Michael addition for a dehydrated/dethiolated peptide. Uncovering this unusual flavin-dependent paradigm for thioether residue formation advances the understanding in the biosynthesis of aminovinyl-cysteine-containing RiPPs and renews interest in flavoproteins, particularly those involved in non-redox transformations. LanD-like flavoproteins activity, which is flexible in peptide substrate and amenable for evolution by engineering, can be combined with different post-translational modifications for structural diversity, thereby holding promise for peptide macrocyclization/functionalization in drug development by chemoenzymatic or synthetic biology approaches.
Identification of potential candidates for drug designing againstKlebsiella Pneumoniaeamong hypothetical proteins of DNA Adenine Methyltransferase through subtractive genomics approach
Authors: Omeershffudin Umairah Natasya Mohd , Kumar Suresh
Published: February 2020

Klebsiella Pneumoniaeis a gram-negative bacterium that is known for causing infection in nosocomial settings. As reported by WHO, this bacterial pathogen is classified as an urgent threat our most concern is that these bacterial pathogens acquired genetic traits that make them resistant towards antibiotics. The last class of antibiotics; carbapenems are not able to combat these bacterial pathogens allowing them to clonally expand their antibiotic-resistant strain. Most antibiotics target the essential pathways of the bacteria cell however these targets are no longer susceptible to the antibiotic. Hence in our study, we focus onKlebsiella Pneumoniaebacterial strains that contain DNA Adenine Methyltransferase domain which suggests a new potential site for a drug target. DNA methylation is seen to regulate the attenuation of bacterial virulence. In this study, all hypothetical proteins ofKlebsiella Pneumoniaecontaining N6 DNA Adenine Methyltransferase domain were analysed for a potential drug target. About 32 hypothetical proteins were retrieved from Uniprot. 19 proteins were selected through a step-wise subtractive genomics approach like a selection of non-homologus proteins against the human host, selection of bacterial proteins contains an essential gene, broad-spectrum analysis, druggability analysis, Non-homology analysis against gut microbiota. Through drug target prioritization like sub-cellular analysis, drug property analysis, anti-target non-homology analysis, virulence factor analysis and protein-protein interaction analysis one drug target protein (Uniprot ID: A0A2U0NNR3) was prioritized. Identified drug target docked with potential inhibitors like are mahanine (PubChem ID: 375151), curcumin (PubChem ID: 969516), EGCG (PubChem ID: 65064), nanaomycin A (PubChem ID: 40586), parthenolide (PubChem ID: 7251185), quercetin (PubChem ID: 5280343) and trimethylaurintricarboxylic acid. Based on the moelcular docking analysis, mahanine has the highest binding affinity. In order to identify novel natural inhibitor based on mahanine fingerprint search is performed against NPASS (Natural Product Activity and Species Source databases) and Koenimbine was identified as a novel natural inhibitor based on virtual screening.
Jointing analysis of scATAC-seq datasets using epiConv
Authors: Lin Li , Zhang Liye
Published: February 2020

Technical improvement in ATAC-seq makes it possible to profile the chromatin states of single cells at high throughput, but currently no method is available to integrate datasets from multiple sources (different batches of same protocol or multiple experimental protocols). Here we present an algorithm to perform joint analyses on scATAC-seq datasets from multiple sources. In addition to batch correction, we also demonstrate that epiConv is capable of aligning co-assay data (simultaneous profiling of transcriptome and chromatin) onto high-quality ATAC-seq reference or integrating cells in different biological conditions (malignantvs. normal), which increases the statistical power of downstream analyses and reveals hidden hierarchy of malignant cells.
Diffusion MRI reveals in vivo and non-invasively changes in astrocyte function induced by an aquaporin-4 inhibitor
Authors: Debaker Clément S. , Djemai Boucif , Ciobanu Luisa , Tsurugizawa Tomokazu , Le Bihan Denis
Published: February 2020

The Glymphatic System (GS) has been proposed as a mechanism to clear brain tissue from waste. Its dysfunction might lead to several brain pathologies, including the Alzheimer’s disease. A key component of the GS and brain tissue water circulation is the astrocyte which is regulated by acquaporin4 (AQP4), a membrane-bound water channel on the astrocytic end-feet. Here we investigated the potential of diffusion MRI to monitor astrocyte activity in a mouse brain model through the inhibition of AQP4 channels with TGN-020. Upon TGN-020 injection, we observed a significant decrease in the Sindex, a diffusion marker of tissue microstructure, and a significant increase of the water diffusion coefficient (sADC) in cerebral cortex and hippocampus compared to saline injection. These results indicate the suitability of diffusion MRI to monitor astrocytic activity in vivo and non-invasively.
Exploring spatiotemporal changes in ecosystem service values and hotspots in Southwest of China, Mekong Region
Authors: Zhang Zhuoya , Yang Junjie , Yang Xin , Xie Fuming
Published: February 2020

Xishuangbanna in the southwestern border of China is located in the upper reaches of the Mekong River between the Indo-China Peninsula and the East Asian continent. It is the largest tropical rain forest and monsoon forest in China. They have an irreplaceable ecological service function and are an important barrier to maintaining the ecological security of the Mekong River transboundary basin of the Lancang River. Based on three sets of remote sensing data (1996, 2003, 2010 and 2016), this study has made an exploration on spatio-temporal changes of Xishuangbanna, and also made an assessment on different ecosystem values of six types of ecosystem in Xishuangbanna based on related theories of ecological economics. Results showed that the values of Xishuangbanna ecosystem services in 1996, 2003, 2010, and 2016 were 70.4014billion yuan, 70.2115 billion yuan, 68.5129 billion yuan and 63.6098 billion yuan, respectively. The total value shows a continuous decreasing trend, reflecting the continuous decline in the ability of the Xishuangbanna ecosystem to provide services to humans. If divided by ecosystem types, forest and rubber were two types that have the greatest proportion of service values. In the perspective of service types, soil formation and protection account for the largest proportion, followed by gas regulation and biodiversity protection. Studying Xishuangbanna’s ecosystem service values is helpful to explore the sustainable development of resources and economy.

Highlight

This paper used coefficient of sensitivity to determine the dependence of ESV on the change of ecosystem value coefficient over time.

The total amount of ESV shows a continuous downward trend, indicating that the ecological environment of Xishuangbanna is still severe.

The temporal-spatial change of ESV was analyzed for two decades.
Drug-adapted cancer cell lines reveal drug-induced heterogeneity and enable the identification of biomarker candidates for the acquired resistance setting
Authors: Michaelis Martin , Wass Mark N. , Reddin Ian , Voges Yvonne , Rothweiler Florian , Hehlgans Stephanie , Cinatl Jaroslav , Mernberger Marco , Nist Andrea , Stiewe Thorsten , Rödel Franz , Cinatl Jindrich
Published: February 2020

Survivin is a drug target and the survivin suppressant YM155 a drug candidate for high-risk neuroblastoma. Findings from one YM155-adapted subline of the neuroblastoma cell line UKF-NB-3 had suggested that increased ABCB1 (mediates YM155 efflux) levels, decreased SLC35F2 (mediates YM155 uptake) levels, decreased survivin levels, andTP53mutations indicate YM155 resistance. Here, the investigation of ten additional YM155-adapted UKF-NB-3 sublines only confirmed the roles of ABCB1 and SLC35F2. However, cellular ABCB1 and SLC35F2 levels did not indicate YM155 sensitivity in YM155-naïve cells, as indicated by drug response data derived from the Cancer Therapeutics Response Portal (CTRP) and the Genomics of Drug Sensitivity in Cancer (GDSC) databases. Moreover, the resistant sublines were characterised by a remarkable heterogeneity. Only seven sublines developed on-target resistance as indicated by resistance to RNAi-mediated survivin depletion. The sublines also varied in their response to other anti-cancer drugs. In conclusion, cancer cell populations of limited intrinsic heterogeneity can develop various resistance phenotypes in response to treatment. Therefore, individualised therapies will require monitoring of cancer cell evolution in response to treatment. Moreover, biomarkers can indicate resistance formation in the acquired resistance setting, even when they are not predictive in the intrinsic resistance setting.
MSH1 is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes
Authors: Wu Zhiqiang , Waneka Gus , Broz Amanda K. , King Connor R. , Sloan Daniel B.
Published: February 2020

Mitochondrial and plastid genomes in land plants exhibit some of the slowest rates of sequence evolution observed in any eukaryotic genome, suggesting an exceptional ability to prevent or correct mutations. However, the mechanisms responsible for this extreme fidelity remain unclear. We tested seven candidate genes involved in cytoplasmic DNA replication, recombination, and repair (POLIA, POLIB, MSH1, RECA3, UNG, FPG, and OGG1) for effects on mutation rates in the model angiosperm Arabidopsis thaliana by applying a highly accurate DNA sequencing technique (duplex sequencing) that can detect newly arisen mitochondrial and plastid mutations still at low heteroplasmic frequencies. We find that disrupting MSH1 (but not the other candidate genes) leads to massive increases in the frequency of point mutations and small indels and changes to the mutation spectrum in mitochondrial and plastid DNA. We also used droplet digital PCR to show transmission of de novo heteroplasmies across generations in msh1 mutants, confirming a contribution to heritable mutation rates. This dual-targeted gene is part of an enigmatic lineage within the mutS mismatch repair family that we find is also present outside of green plants in multiple eukaryotic groups (stramenopiles, alveolates, haptophytes, and cryptomonads), as well as certain bacteria and viruses. MSH1 has previously been shown to limit ectopic recombination in plant cytoplasmic genomes. Our results point to a broader role in recognition and correction of errors in plant mitochondrial and plastid DNA sequence, leading to greatly suppressed mutation rates perhaps via initiation of double-stranded breaks and repair pathways based on faithful homologous recombination.
A Total-Evidence Dated Phylogeny of Echinoids and the Evolution of Body Size across Adaptive Landscape
Authors: Koch Nicolás Mongiardino , Thompson Jeffrey R.
Published: February 2020

Several unique properties of echinoids (sea urchins) make them useful for exploring macroevolutionary dynamics, including their remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. However, this potential cannot be exploited without a robust resolution of the echinoid tree of life. We revisit the phylogeny of crown group Echinoidea using both the largest phylogenomic dataset compiled for the clade, as well as a large-scale morphological matrix with a dense fossil sampling. We also gather a new compendium of both tip and node age constraints, allowing us to combine phylogenomic, morphological and stratigraphic data using a total-evidence dating approach. For this, we develop a novel method for subsampling phylogenomic datasets that selects loci with high phylogenetic signal, low systematic biases and enhanced clock-like behavior. Our approach restructure much of the higher-level phylogeny of echinoids, and demonstrates that combining different data sources increases topological accuracy. We are able to resolve multiple alleged conflicts between molecular and morphological datasets, such as the position of Echinothurioida and Echinoneoida, as well as unravelling the relationships between sand dollars and their closest relatives. We then use this topology to trace the evolutionary history of echinoid body size through more than 270 million years, revealing a complex pattern of convergent evolution to stable peaks in macroevolutionary adaptive landscape. Our efforts show how combining phylogenomic and paleontological evidence offers new ways of exploring evolutionary forces operating across deep timescales.
Second messenger control of mRNA translation by dynamic ribosome modification
Authors: Grenga Lucia , Little Richard Howard , Chandra Govind , Woodcock Stuart Daniel , Saalbach Gerhard , Morris Richard James , Malone Jacob George
Published: February 2020

Control of mRNA translation is a crucial regulatory mechanism used by bacteria to respond to their environment. In the soil bacteriumPseudomonas fluorescens, RimK modifies the C-terminus of ribosomal protein RpsF to influence important aspects of rhizosphere colonisation through proteome remodelling. In this study, we show that RimK activity is itself under complex, multifactorial control by the co-transcribed phosphodiesterase trigger enzyme (RimA) and a polyglutamate-specific protease (RimB). Furthermore, biochemical experimentation and mathematical modelling reveal a role for the nucleotide second messenger cyclic-di-GMP in coordinating these activities. Active ribosome regulation by RimK occurs by two main routes: indirectly, through changes in the abundance of the global translational regulator Hfq and directly, with translation of surface attachment factors, amino acid transporters and key secreted molecules linked specifically to RpsF modification. Our findings show that post-translational ribosomal modification functions as a rapid-response mechanism that tunes global gene translation in response to environmental signals.
The hidden land use cost of upscaling cover crops
Authors: Runck Bryan , Khoury Colin K. , Ewing Patrick M. , Kantar Michael
Published: February 2020

Cover cropping is considered a cornerstone practice in sustainable agriculture; however, little attention has been paid to the cover crop production supply chain. In this Perspective, we estimate land use requirements to supply the United States maize production area with cover crop seed, finding that across 18 cover crops, on average 3.8% (median 2.0%) of current production area would be required, with the popular cover crops rye and hairy vetch requiring as much as 4.5% and 11.9%, respectively. The latter land requirement is comparable to the annual amount of maize grain lost to disease in the U.S. We highlight avenues for reducing these high land use costs.
The marine spongeHymeniacidon perlevisis a globally-distributed invasive species
Authors: Turner Thomas L.
Published: February 2020

In Elkhorn Slough, a tidal estuary draining into Monterey Bay, California, the intertidal is occupied by a conspicuous orange sponge known by the nameHymeniacidon sinapium. This same species is found in the rocky intertidal zone of the outer coast of California, and is described herein from subtidal kelp forests of Southern California. Farther afield, morphologically and ecologically indistinguishable sponges are common in estuaries and intertidal areas in Asia, Europe, South America, and Africa. Here I use morphological, ecological, and genetic data to show that these sponges are all members of the same globally-distributed species, which should be known by the senior synonymH. perlevis. Though previous authors have remarked upon the morphological, ecological, and/or genetic similarity of various distant populations, the true scope of this sponge’s distribution appears to be unrecognized or unacknowledged in the literature. Limited larval dispersal, historically documented range expansion, and low genetic variation all support a hypothesis that this sponge has achieved its extraordinary range via human-mediated dispersal, making it the most widely-distributed invasive sponge known to date.

Declarations

Conflicts of interest/Competing interests: none to declare

Availability of data and material: All raw data is included as supplementary files; georeferenced collection data is available as a supplementary .xls file; genetic data are archived at Genbank; specimen vouchers are archived at the California Academy of Sciences and at the Natural History Museum of Los Angeles; specimen photos will be made available as supplementary files, are also archived by the associated museums in GBIF, and are posted as georeferenced data oniNaturalist.org.

Code availability: n/a
The LUBAC participates in Lysophosphatidic Acid-induced NF-κB Activation
Authors: Douanne Tiphaine , Chapelier Sarah , Rottapel Robert , Gavard Julie , Bidère Nicolas
Published: February 2020

The natural bioactive glycerophospholipid lysophosphatidic acid (LPA) binds to its cognate G protein-coupled receptors (GPCRs) on the cell surface to promote the activation of several transcription factors, including NF-κB. LPA-mediated activation of NF-κB relies on the formation of a signalosome that contains the scaffold CARMA3, the adaptor BCL10 and the paracaspase MALT1 (CBM complex). The CBM has been extensively studied in lymphocytes, where it links antigen receptors to NF-κB activation via the recruitment of the linear ubiquitin assembly complex (LUBAC), a tripartite complex of HOIP, HOIL1 and SHARPIN. Moreover, MALT1 cleaves the LUBAC subunit HOIL1 to further enhance NF-κB activation. However, the contribution of the LUBAC downstream of GPCRs has not been investigated. By using murine embryonic fibroblasts from mice deficient for HOIP, HOIL1 and SHARPIN, we report that the LUBAC is crucial for the activation of NF-κB in response to LPA. Further echoing the situation in lymphocytes, LPA unbridles the protease activity of MALT1, which cleaves HOIL1 at the Arginine 165. The expression of a MALT1-insensitive version of HOIL1 reveals that this processing is required for the optimal production of the NF-κB target cytokine interleukin-6. Lastly, we provide evidence that the guanine exchange factor GEF-H1 activated by LPA favors MALT1-mediated cleavage of HOIL1 and NF-κB signaling. Together, our results unveil a critical role for the LUBAC as a positive regulator of NF-κB signaling downstream of GPCRs.
Inflammation promotes tumor aggression by stimulating stromal cell-dependent collagen crosslinking and stromal stiffening
Authors: Maller Ori , Drain Allison P. , Barrett Alexander S. , Borgquist Signe , Ruffell Brian , Thanh Pham T , Gruosso Tina , Kuasne Hellen , Lakins Johnathon N. , Acerbi Irene , Barnes J. Matthew , Nemkov Travis , Chauhan Aastha , Gruenberg Jessica , Nasir Aqsa , Bjarnadottir Olof , Werb Zena , Kabos Peter , Hwang E. Shelley , Park Morag , Coussens Lisa M. , Nelson Andrew C. , Hansen Kirk C. , Weaver Valerie M.
Published: February 2020

Collagen deposition and stromal stiffening accompany malignancy, compromise treatment, and promote tumor aggression. Clarifying the molecular nature of and the factors that regulate extracellular matrix stiffening in tumors should identify biomarkers to stratify patients for therapy and therapeutic interventions to improve outcome. We profiled lysyl hydroxylase- and lysyl oxidase-mediated collagen crosslinks and quantified the greatest abundance of total and complex collagen crosslinks in more aggressive human breast cancer subtypes with the stiffest stroma. These tissues also harbored the highest number of tumor-associated macrophages (TAM), whose therapeutic ablation not only reduced metastasis, but also concomitantly decreased accumulation of collagen crosslinks and stromal stiffening. Epithelial-targeted expression of the crosslinking enzyme lysyl oxidase had no impact on collagen crosslinking in PyMT mammary tumors, whereas stromal cell targeting did. Consistently, stromal cells in microdissected human tumors expressed the highest level of collagen crosslinking enzymes. Immunohistochemical analysis of a cohort of breast cancer patient biopsies revealed that stromal expression of lysyl hydroxylase two, an enzyme that induces hydroxylysine aldehyde-derived collagen crosslinks and stromal stiffening correlated significantly disease specific mortality. The findings link tissue inflammation, stromal cell-mediated collagen crosslinking and stiffening to tumor aggression and identify lysyl hydroxylase two as a novel stromal biomarker.

Significance

We show infiltrating macrophages induce stromal fibroblast, and not epithelial, expression of collagen crosslinking enzymes that drive tumor stiffening. Stromal enzyme LH2 is significantly upregulated in breast cancer patients with the stiffest stroma, the most trivalent HLCCs and the worst prognosis, underscoring its potential as a biomarker and therapeutic target.
Parallel alpine differentiation inArabidopsis arenosa
Authors: Knotek Adam , Konečná Veronika , Wos Guillaume , Požárová Doubravka , Šrámková Gabriela , Bohutínská Magdalena , Zeisek Vojtěch , Marhold Karol , Kolář Filip
Published: February 2020

Parallel evolution provides powerful natural experiments for studying repeatability of evolution. Well-documented examples from plants are, however, still rare, as are inquiries of mechanisms driving convergence in some traits while divergence in others.Arabidopsis arenosa, a predominantly foothill species with scattered morphologically distinct alpine occurrences is a promising candidate. Yet, the hypothesis of parallelism remained untested. We sampled foothill and alpine populations in all regions known to harbour the alpine ecotype and used SNP genotyping to test for repeated alpine colonisation. Then, we combined field surveys and a common garden experiment to quantify phenotypic parallelism. Genetic clustering by region but not elevation and coalescent simulations demonstrated parallel origin of alpine ecotype in four mountain regions. Alpine populations exhibited parallelism in height and floral traits which persisted after two generations in cultivation. In contrast, leaf traits were distinctive only in certain region(s), reflecting a mixture of plasticity and genetically determined non-parallelism. We demonstrate varying degrees and causes of parallelism and non-parallelism across populations and traits within a plant species. Parallel divergence along a sharp elevation gradient makesA. arenosaa promising candidate for studying genomic basis of adaptation.
The LRRC8A:C Heteromeric Channel Is a cGAMP Transporter and the Dominant cGAMP Importer in Human Vasculature Cells
Authors: Lahey Lauren J. , Wen Xianlan , Mardjuki Rachel E. , Böhnert Volker , Hess Gaelen T. , Ritchie Christopher , Carozza Jacqueline A. , Maduke Merritt , Bassik Michael C. , Li Lingyin
Published: February 2020

Extracellular 2’3’-cyclic-GMP-AMP (cGAMP) is an immunotransmitter secreted by cancer cells and taken up by host cells to activate the anti-cancer STING pathway. No cGAMP exporter has been identified, and SLC19A1, a recently identified cGAMP importer, does not account for the import activity in most cell types. Here, we identify the LRRC8A:C heteromeric channel, a volume-regulated anion channel (VRAC), as a cGAMP transporter. This channel mediates cGAMP import or export depending on the cGAMP chemical gradient, and channel activation or inhibition modulates cGAMP transport. Other 2’3’-cyclic dinucleotides are also transported by LRRC8A:C channels, including the investigational cancer therapeutic ADU-S100. Furthermore, we demonstrate that the LRRC8A-containing channel is the dominant cGAMP importer in primary human vasculature cells. Given tumor vasculature’s regulation of immune infiltration and its disruption in response to STING agonists, we have uncovered a leading molecular mechanism for extracellular cGAMP signaling in this important anti-cancer target.
Generating realistic null hypothesis of cancer mutational landscapes using SigProfilerSimulator
Authors: Bergstrom Erik N. , Barnes Mark , Martincorena Iñigo , Alexandrov Ludmil B.
Published: February 2020

Performing a statistical test requires a null hypothesis. In cancer genomics, a key challenge is the fast generation of accurate somatic mutational landscapes that can be used as a realistic null hypothesis for making biological discoveries. Here we present SigProfilerSimulator, a powerful tool that is capable of simulating the mutational landscapes of thousands of cancer genomes at different resolutions within seconds. Applying SigProfilerSimulator to 2,144 whole-genome sequenced cancers reveals:(i)that most doublet base substitutions are not due to two adjacent single base substitutions but likely occur as single genomic events;(ii)that an extended sequencing context of +/-2bp is required to more completely capture the patterns of substitution mutational signatures in human cancer;(iii)information on false-positive discovery rate of commonly used bioinformatics tools for detecting driver genes. SigProfilerSimulator’s breadth of features allows one to construct a tailored null hypothesis and use it for evaluating the accuracy of other bioinformatics tools or for downstream statistical analysis for biological discoveries.
Relative efficiencies of simple and complex substitution models in estimating divergence times in phylogenomics
Authors: Tao Qiqing , Barba-Montoya Jose , Huuki Louise A. , Durnan Mary Kathleen , Kumar Sudhir
Published: February 2020

The conventional wisdom in molecular evolution is to apply parameter-rich models of nucleotide and amino acid substitutions for estimating divergence times. However, the actual extent of the difference between time estimates produced by highly complex models compared to those from simple models is yet to be quantified for contemporary datasets that frequently contain sequences from many species and genes. In a reanalysis of many large multispecies alignments from diverse groups of taxa using the same tree topologies and calibrations, we found that the use of the simplest models can produce divergence time estimates and credibility intervals similar to those obtained from the complex models applied in the original studies. This result is surprising because the use of simple models underestimates sequence divergence for all the datasets analyzed. We find three fundamental reasons for the observed robustness of time estimates to model complexity in many practical datasets. First, the estimates of branch lengths and node-to-tip distances under the simplest model show an approximately linear relationship with those produced by using the most complex models applied, especially for datasets with many sequences. Second, relaxed clock methods automatically adjust rates on branches that experience considerable underestimation of sequence divergences, resulting in time estimates that are similar to those from complex models. And, third, the inclusion of even a few good calibrations in an analysis can reduce the difference in time estimates from simple and complex models. The robustness of time estimates to models complexity in these empirical data analyses is encouraging, because all phylogenomics studies use statistical models that are oversimplified descriptions of actual evolutionary substitution processes.
X-ray absorption linear dichroism at the Ti K-edge of rutile (001) TiO2 single crystal
Authors: Rossi T. C. , Grolimund D. , Cannelli O. , Mancini G. F. , Bacellar C. , Kinschel D. , Rouxel J. R. , Ohannessian N. , Pergolesi D. , Chergui M.
Published: February 2020

X-ray absorption linear dichroism of rutile TiO2 at the Ti K-edge provides information about the electronic states involved in the pre-edge transitions. Here, linear dichroism with high energy resolution is analyzed in combination with ab initio finite difference method calculations and spherical tensor analysis. It provides an assignment of the three pre-edge peaks beyond the octahedral crystal field splitting approximation and estimates the spatial extension of the corresponding final states. It is then discussed for the first time the X-ray absorption (XAS) of pentacoordinated titanium atoms due to oxygen vacancies and it is found that, similarly to anatase TiO2, rutile is expected to exhibit a transition on the low-energy side of peak A3. Its apparent absence in the experiment is related to the degree of p–d orbital mixing which is small in rutile due to its centrosymmetric point group. A recent XAS linear dichroism study on anatase TiO2 single crystals has shown that peak A2 has an intrinsic origin and is due to a quadrupolar transition to the 3d energy levels. In rutile, due to its centrosymmetric point group, the corresponding peak A2 has a small dipole moment explaining the weak transition. The results are confronted with recent picosecond X-ray absorption spectroscopy on rutile TiO2 nanoparticles.
Synthesis and crystal structure of NaCuIn(PO4)2
Authors: Benhsina Elhassan , Khmiyas Jamal , Ouaatta Said , Assani Abderrazzak , Saadi Mohamed , El Ammari Lahcen
Published: February 2020

Single crystals of sodium copper(II) indium bis[phosphate(V)], NaCuIn(PO4)2, were grown from the melt under atmospheric conditions. The title phosphate crystallizes in the space group P21/n and is isotypic with KCuFe(PO4)2. In the crystal, two [CuO5] trigonal bipyramids share an edge to form a dimer [Cu2O8] that is connected to two PO4 tetrahedra. The obtained [Cu2P2O12] units are interconnected through vertices to form sheets that are sandwiched between undulating layers resulting from the junction of PO4 tetrahedra and [InO6] octahedra. The two types of layers are alternately stacked along [101] and are joined into a three-dimensional framework through vertex- and edge-sharing, leaving channels parallel to the stacking direction. The channels host the sodium cations that are surrounded by four oxygen atoms in form of a distorted disphenoid.
Synthesis, crystal structure, and thermal properties of poly[aqua(μ5-2,5-dicarboxybenzene-1,4-dicarboxylato)strontium]
Authors: Mokhtari Samia , Trifa Chahrazed , Bouacida Sofiane , Boudaren Chaouki , Abdelbaky Mohammed S.M. , García-Granda Santiago
Published: February 2020

A coordination polymer formulated as [Sr(H2BTEC)(H2O)]
n
(H4BTEC = benzene-1,2,4,5-tetracarboxylic acid, C10H6O8), was synthesized hydrothermally and characterized by single-crystal and powder X-ray diffraction, scanning electron microscopy and thermal analysis. Its crystal structure is made up of a zigzag inorganic chain formed by edge-sharing of [SrO8] polyhedra running along [001]. Adjacent chains are connected to each other via the carboxylate groups of the ligand, resulting in a double-layered network extending parallel to (100). O—H...O hydrogen bonds of medium-to-weak strength between the layers consolidate the three-dimensional structure. One of the carboxylic OH functions was found to be disordered over two sets of sites with half-occupancy.
6-Nitro-2,3-bis(thiophen-2-yl)quinoxaline
Authors: Freitas Jorge F. de , Brown Shayne , Oberndorfer James S. , Crundwell Guy
Published: February 2020

The title compound, C16H9N3O2S2, was synthesized via a condensation reaction in refluxing acetic acid. One thienyl ring is nearly coplanar with the quinoxaline unit [dihedral angle = 3.29 (9)°], the other makes an angle of 83.96 (4)°.
Corporate governance and performance of medium-sized firms in Nigeria: does sustainability initiative matter?
Authors: Adedeji Babatunji Samuel , Ong Tze San , Uzir Md Uzir Hossain , Abdul Hamid Abu Bakar
Published: February 2020

Purpose

The non-existence of the corporate governance (CG) concept for practices by non-financial medium-sized firms (MSFs) in Nigeria informed. This study aims to determine whether CG practices influence firms’ performance and whether sustainability initiative (SI) mediates the relationship between CG and MSFs’ performance in Nigeria.

Design/methodology/approach

A total of 300 firms were selected on convenience sampling basis from South Western Nigeria using a structured questionnaire. The authors used Statistical Package for Social Sciences for exploratory data analysis and hypotheses were tested using covariance-based structural equation modelling.

Findings

The results show that CG has a significant positive effect on performance [financial performance (FNP) and non-financial performance (NFP)] and SI. SI has a mixed impact on performance, e.g. a significant positive impact on NFP but insignificant negative impact on FNP. Similarly, SI has a combined mediating effect in the relationship between CG and performance, e.g. fully mediates CG → NFP and does not mediate CG → FNP. Firms are to invest in social and environmental initiatives substantially. CG codes will complement the International Financial Reporting Standards for MSFs.

Research limitations/implications

This study supports the assumptions of theories (institutional, stakeholder and agency) as the basis for the usage of multiple approaches to determine the outcome of hypotheses, especially in developing climes.

Practical implications

The study contributes to CG and performance literature by examining the mediating effects of SI. The paper also shows the necessity to emphasise NFP aspect. Policymakers should evolve CG codes to encourage stakeholders to believe more in the corporate existence of MSFs for strengthening capital-base and quality personnel engagement.

Originality/value

To the best of the authors’ knowledge, this is one of the first empirical attempts showing the evidence on the relationship between CG and NFP in Nigeria.
Social and technical chains-of-effects in business-to-business (B2B) service relationships
Authors: Kingshott Russel P.J. , Sharma Piyush , Nair Smitha Ravindranathan
Published: February 2020

Purpose

This paper aims to combine the social–technical systems and social exchange theories with the resource-based view of the firm, to investigate how business-to-business (B2B) service firms manage their social and technical resources to manage customer relationships.

Design/methodology/approach

An online survey-based study with 321 managers working in Australian small and medium (SME) firms is used to test hypotheses about the sequential and substitutional impact of four social and technical resources (service quality, satisfaction, trust and commitment) on customer loyalty, using both offline and online platforms.

Findings

The findings show that both social and technical chains of effects are viable channels for B2B service firms to build customer loyalty; however, mixing of both social and technical resources results in the weakening of both these chains.

Research limitations/implications

The results based on B2B service relationships between Australian SME firms and their banks may not be generalizable to other contexts.

Practical implications

This research would help managers in B2B service firms understand the pitfalls of combining their social and technical resources because it may hamper their ability to build customer loyalty. Hence, they need to learn how to synergize their marketing resources across both offline and online platforms to achieve optimal results.

Originality/value

This research introduces social and technical chains of effects as a novel way to examine the ability of B2B service firms to optimize their social and technical resources in a synergistic manner to build and nurture stronger customer relationships.
Women in the workforce
Authors: Hartman Rosanne L. , Barber Emily G.
Published: February 2020

Purpose

While women perform as well as their male counterparts at work, women are drastically underrepresented in the onboarding process to senior leadership. The link between occupational self-efficacy and the role it may play in how men and women make decisions about work has not been done. The purpose of this study is to examine potential differences of occupational self-efficacy, career aspirations and work engagement between women and men.

Design/methodology/approach

Online surveys were created and sent out as emails and on social network sites including Facebook, Twitter and LinkedIn.

Findings

Findings indicate that occupational self-efficacy has positive effect on career aspirations of women in the workplace. Further, there was no statistically significant difference between occupational self-efficacy and work engagement between men and women. However, men were found to have statistically significantly higher career aspirations than women do.

Research limitations/implications

While men and women do not differ in occupational self-efficacy or work engagement, men do have higher career aspirations than women do. Although women may believe they can accomplish challenging tasks in the workplace, it does not mean this belief is acted upon.

Practical implications

The study highlights the importance of occupational self-efficacy and its relation to career aspirations. Individuals who are high in occupational self-efficacy may set their own path in advancing within their career. However, individuals who are low or moderate in occupational self-efficacy may require further encouragement and development using additional resources as a catalyst for advancement guidance. While no differences were found between men and women in occupational self-efficacy, human resource practitioners should develop those individuals who are low or moderate in occupational self-efficacy with coaching, training and/or mentoring to build leadership capacity, increase self-efficacy and career-planning acumen.

Social implications

Men and women behave differently when seeking career advancement and in their career aspirations. For men, advancement is linked to performance whereas women use a multi-pronged approach focusing on preparing for career success and building role competency. Differences in strategy for advancement mean men will actively engage in behaviors to advance even when they do not have the knowledge or experience to perform in the new role. Conversely, women seek to feel competent in a work role prior to seeking it out. Finding ways to mentor women toward higher self-efficacy for their next career advancement will benefit organizations overall.

Originality/value

Research examining the role of occupational self-efficacy and its relation to career aspirations does not exist in comparing men and women.
The study of the effect of online review on purchase behavior
Authors: Zhang Jinghuan , Zheng Wenfeng , Wang Shan
Published: February 2020

Purpose

The purpose of this paper is to explain the difference and connection between the network big data analysis technology and the psychological empirical research method.

Design/methodology/approach

This study analyzed the data from laboratory setting first, then the online sales data from Taobao.com to explore how the influential factors, such as online reviews (positive vs negative mainly), risk perception (higher vs lower) and product types (experiencing vs searching), interacted on the online purchase intention or online purchase behavior.

Findings

Compared with traditional research methods, such as questionnaire and behavioral experiment, network big data analysis has significant advantages in terms of sample size, data objectivity, timeliness and ecological validity.

Originality/value

Future study may consider the strategy of using complementary methods and combining both data-driven and theory-driven approaches in research design to provide suggestions for the development of e-commence in the era of big data.
Development of structural equation model for Lean Six Sigma system incorporated with sustainability considerations
Authors: R. Ben Ruben , Vinodh S. , P. Asokan
Published: February 2020

Purpose

The study aims to describe the development of a structural measurement model using structural equation modeling technique to validate the association that exists between Lean Six Sigma (LSS) and sustainable manufacturing strategies.

Design/methodology/approach

Both LSS and sustainable manufacturing aim at improving the firm’s business competitiveness which forms a strategic link that benefits the manufacturing organizations. The study aims to investigate the relationship among constructs that leads to operational excellence while deploying LSS and sustainable manufacturing strategies in organizations.

Findings

Empirical data needed for the study are collected from experts belonging to various industries that are implementing both LSS and sustainable manufacturing practices. Later statistical estimates (hypotheses) are being formulated to confirm the developed measurement model. Based on the obtained results after analysis of the structural model, the statistical estimate is either being accepted or rejected. Results of this study reveal that there exists a strong correlation between LSS and sustainable manufacturing factors that leads to organizational performance.

Research limitations/implications

Additional indicators could be included to deal with technological advancements in sustainable manufacturing.

Practical implications

The study has been done with regard to Indian automotive component manufacturing organizations scenario. Hence, the inferences derived have practical relevance.

Originality/value

The development of structural model for the Lean Six Sigma system with sustainability considerations is the original contribution of the authors.
Using critical discourse analysis to reflect on collaborative professional learning
Authors: Hunt Carolyn S. , MacPhee Deborah
Published: February 2020

Purpose

This article presents a case study of Kelly, a third-grade teacher enrolled in a literacy leadership course within a Master of Reading program. In this course, practicing teachers completed an assignment in which they implemented a literacy coaching cycle with a colleague, video-recorded their interaction, and conducted critical discourse analysis (CDA) of the interaction. The authors explore how engaging in CDA influenced Kelly's enactment of professional identities as she prepared to be a literacy leader.

Design/methodology/approach

Data presented in this article are taken from a larger study of four white, middle-class teachers enrolled in the course. Data sources included the students' final paper and semistructured interviews. The researchers used qualitative coding methods to analyze all data sources, identify prominent themes, and select Kelly as a focal participant for further analysis.

Findings

Findings indicate that Kelly's confidence as a literacy leader grew after participating in the coaching cycle and conducting CDA. Through CDA, Kelly explored how prominent discourses of teaching and learning, particularly those relating to novice and expert status, influenced Kelly in-the-moment coaching interactions.

Originality/value

Previous literacy coaching research suggests that literacy coaches need professional learning opportunities that support a deep understanding of coaching stances and discursive moves to effectively support teachers. The current study suggests that CDA may be one promising method for engaging literacy coaches in such work because it allows coaches to gain understandings about how discourses of teaching and learning function within coaching interactions.
The effect of liner surface texture on journal bearing performance under thermo-hydrodynamic conditions
Authors: Saleh Ahmed M. , Crosby Wael , El Fahham Ibrahim M. , Elhadary M.
Published: February 2020

Purpose

The purpose of this paper is to study the effect of liner surface texture on journal bearing performance. Modeling the profile curvature of the dimples or grooves is planned for different cases of texture surface under thermo-hydrodynamic condition (THD). The aim of this paper is to determine the effect the texture surface on the performance of journal bearing and specify the optimum shape for texture dimples.

Design/methodology/approach

The paper was opted for an exploratory study by applying finite difference method to solve the energy equation, the heat conduction equations and the Reynolds equation numerically. The lubricant film thickness is divided to a mesh of 640,000 points. The equations were solved for each point of the mesh by using a MATLAB code. For texture shape optimization, 24 cases of different texture shapes were selected which includes elliptical, triangle and square curvature shape.

Findings

The paper provides theoretical insights about the effect of texture shape on journal bearing performance. It was concluded that to get a high load-carrying capacity, the direction of curvature is preferably to be perpendicular to the sliding direction. The convex texture has higher load carrying capacity than concave texture. Finally, the surface with textures in channel form yields better overall performance than the surface with several dimples.

Originality/value

This paper fulfils an identified need to study how texture surface affects the performance of journal bearing under thermo-hydrodynamic conditions.
The influence of servicescape and service credibility on older adults' intention to recover
Authors: Lai Kim Piew , Chong Siong Choy
Published: February 2020

Purpose

Based on the stimuli-organism-response (SOR) model and relationship marketing theory, the paper aims to examine whether servicescape influences trust, service credibility and affective commitment amongst older adults, and their effects on the intention to recover in a rehabilitation setting.

Design/methodology/approach

The study takes a quantitative approach, applying confirmatory factor analysis and structural equation model to examine the responses. A total of 400 data were collected using questionnaires distributed to older adults in Malaysia. Respondents were selected based on two criteria: they should be over 65 years, and they should have been visiting the rehabilitation centres in the last 12 months.

Findings

The results suggest that trust and affective commitment play significant roles in increasing the intention of older adults to recover. Contradicting previous research findings, service credibility does not have any significant impact on the intention to recover as hypothesised. The direct effect of service credibility on trust and affective commitment enhances the premise further that the relationship between service credibility and intention to recover is primarily indirect. Even though we expect servicescape to be a significant driver in forming the behaviour of older adults, its impact on intention to recover, trust and affective commitment remain non-significant, with the exception of service credibility.

Originality/value

Past studies have focused on the roles of servicescape and service credibility separately. We have extended the literature by examining the combined effects of both servicescape and service credibility. The findings, therefore, contribute to a deeper understanding of the literature on the intention–behaviour relationship in the context of healthcare, as well as in service marketing.