bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural insights into DNA sequence recognition by Arabidopsis ETHYLENE RESPONSE FACTOR 96
Authors: Chen Chun-Yen , Lin Pei-Hsuan , Chen Kun-Hung , Cheng Yi-Sheng
Published: April 2018

The phytohormone ethylene is widely involved in many developmental processes and is a crucial regulator of defense responses against biotic and abiotic stresses in plants. Ethylene-responsive element binding protein (EREBP), a member of the APETALA2/ethylene response factor (AP2/ERF) superfamily, is a transcription factor that regulates stress-responsive genes by recognizing a specific cis-acting element of target DNA. A previous study showed only the NMR structure of the AP2/ERF domain of AtERF100 in complex with a GCC box DNA motif. In this report, we determined the crystal structure of AtERF96 in complex with a GCC box at atomic resolution. We analyzed the binding residues of the conserved AP2/ERF domain in the DNA recognition sequence. In addition to the AP2/ERF domain, an N-terminal α-helix of AtERF96 participates in DNA interaction in the flanking region. We also demonstrated the structure of AtERF96 EDLL motif, a unique conserved motif in the group IX of AP2/ERF family, is critical for the transactivation of defense-related genes. Our study establishes the structural basis of the AtERF96 transcription factor in complex with the GCC box, as well as the DNA binding mechanisms of the N-terminal α-helix and AP2/ERF domain.
Rare non-synonymous germline mutations systematically define the risk of triple negative breast cancer
Authors: Yang Mei , Fan Yanhui , Wu Zhi-Yong , Feng Zhendong , Zhang Qiangzu , Han Shunhua , Li Xiaoling , Zhu Teng , Cheng Minyi , Xu Juntao , Yang Ciqiu , Gao Hongfei , Zhang Chunming , Tan Guangming , Zhang Michael Q. , Song You-Qiang , Niu Gang , Wang Kun
Published: April 2018

Early identification of the risk for triple-negative breast cancer (TNBC) at the asymptomatic phase could lead to better prognosis. Here we developed a machine learning method to quantify systematic impact of all rare germline mutations on each pathway. We collected 106 TNBC patients and 287 elder healthy women controls. The spectra of activity profiles in multiple pathways were mapped and most pathway activities exhibited globally suppressed by the portfolio of individual germline mutations in TNBC patients. Accordingly, all individuals were delineated into two types: A and B. Type A patients could be differentiated from controls (AUC = 0.89) and sensitive to BRCA1/2 damages; Type B patients can be also differentiated from controls (AUC = 0.69) but probably being protected from BRCA1/2 damages. Further we found that Individuals with the lowest activity of selected pathways had extreme high relative risk (up to 21.67 in type A) and increased lymph node metastasis in these patients. Our study showed that genomic DNA contains information of unimaginable pathogenic factors. And this information is in a distributed form that could be applied to risk assessment for more cancer types.

Significance

We identified individuals who are more susceptible to triple negative breast cancer. Our method performs much better than previous assessments based on BRCA1/2 damages, even polygenic risk scores. We disclosed previously unimaginable pathogens in a distributed form on genome and extended risk prediction to scenarios for other cancers.
Inferring Population Structure and Admixture Proportions in Low Depth NGS Data
Authors: Meisner Jonas , Albrechtsen Anders
Published: April 2018

We here present two methods for inferring population structure and admixture proportions in low depth next generation sequencing data. Inference of population structure is essential in both population genetics and association studies and is often performed using principal component analysis or clustering-based approaches. Next-generation sequencing methods provide large amounts of genetic data but are associated with statistical uncertainty for especially low depth sequencing data. Models can account for this uncertainty by working directly on genotype likelihoods of the unobserved genotypes. We propose a method for inferring population structure through principal component analysis in an iterative approach of estimating individual allele frequencies, where we demonstrate improved accuracy in samples with low and variable sequencing depth for both simulated and real datasets. We also use the estimated individual allele frequencies in a fast non-negative matrix factorization method to estimate admixture proportions. Both methods have been implemented in the PCAngsd framework available at http://www.popgen.dk/software/.
PRESTO, a new tool for integrating large-scale -omics data and discovering disease-specific signatures
Authors: McArdle Sara , Buscher Konrad , Ehinger Erik , Pramod Akula Bala , Riley Nicole , Ley Klaus
Published: April 2018

Background

Cohesive visualization and interpretation of hyperdimensional, large-scale -omics data is an ongoing challenge, particularly for biologists and clinicians involved in current highly complex sequencing studies. Multivariate studies are often better suited towards non-linear network analysis than differential expression testing. Here, we present PRESTO, a ‘PREdictive Stochastic neighbor embedding Tool for Omics’, which allows unsupervised dimensionality reduction of multivariate data matrices with thousands of subjects or conditions. PRESTO is intuitively integrated into an interactive user interface that helps to visualize the multidimensional patterns in genome-wide transcriptomic data from basic science and clinical studies.

Results

PRESTO was tested with multiple input omics’ platforms, including microarray and proteomics from both mouse and human clinical datasets. PRESTO can analyze up to tens of thousands of genes and shows no increase in processing time with a large number of samples or patients. In complex datasets, such as those with multiple time points, several patient groups, or diverse mouse strains, PRESTO outperformed conventional methods. Core co-expressed gene networks were intuitively grouped in clusters, or gates, after dimensionality reduction and remained consistent across users. Networks were identified and assigned to physiological and pathological functions that cannot be gleaned from conventional bioinformatics analyses. PRESTO detected gene networks from the natural variations among mouse macrophages and human blood leukocytes. We applied PRESTO to clinical transcriptomic and proteomic data from large patient cohorts and detected disease-defining signatures in antibody-mediated kidney transplant rejection, renal cell carcinoma, and relapsing acute myeloid leukemia (AML). In AML, PRESTO confirmed a previously described gene signature and found a new signature of 10 genes that is highly predictive of patient outcome.

Conclusions

PRESTO offers an important integration of powerful bioinformatics tools with an interactive user interface that increases data analysis accessibility beyond bioinformaticians and ‘coders’. Here, we show that PRESTO out performs conventional methods, such as DE analysis, in multi-dimensional datasets and can identify biologically relevant co-expression gene networks. In paired samples or time points, co-expression networks could be compared for insight into longitudinal regulatory mechanisms. Additionally, PRESTO identified disease-specific signatures in clinical datasets with highly significant diagnostic and prognostic potential.
Discovering epistatic feature interactions from neural network models of regulatory DNA sequences
Authors: Greenside Peyton , Shimko Tyler , Fordyce Polly , Kundaje Anshul
Published: April 2018

Motivation

Transcription factors bind regulatory DNA sequences in a combinatorial manner to modulate gene expression. Deep neural networks (DNNs) can learn the cis-regulatory grammars encoded in regulatory DNA sequences associated with transcription factor binding and chromatin accessibility. Several feature attribution methods have been developed for estimating the predictive importance of individual features (nucleotides or motifs) in any input DNA sequence to its associated output prediction from a DNN model. However, these methods do not reveal higher-order feature interactions encoded by the models.

Results

We present a new method called Deep Feature Interaction Maps (DFIM) to efficiently estimate interactions between all pairs of features in any input DNA sequence. DFIM accurately identifies ground truth motif interactions embedded in simulated regulatory DNA sequences. DFIM identifies synergistic interactions between GATA1 and TAL1 motifs from in vivo TF binding models. DFIM reveals epistatic interactions involving nucleotides flanking the core motif of the Cbf1 TF in yeast from in vitro TF binding models. We also apply DFIM to regulatory sequence models of in vivo chromatin accessibility to reveal interactions between regulatory genetic variants and proximal motifs of target TFs as validated by TF binding quantitative trait loci. Our approach makes significant strides in improving the interpretability of deep learning models for genomics.

Availability

Code is available at: https://github.com/kundajelab/dfim.

Contact: akundaje@stanford.edu
Six species of non-tuberculosis mycobacteria carry non-identical 16S rRNA gene copies
Authors: Takeda Keita , Chikamatsu Kinuyo , Igarashi Yuriko , Morishige Yuta , Murase Yoshiro , Aono Akio , Yamada Hiroyuki , Takaki Akiko , Mitarai Satoshi
Published: April 2018

Non-tuberculosis mycobacteria (NTM) can carry two or more 16S rRNA gene copies that are, in some instances, non-identical. In this study, we used a combined cloning and sequencing approach to analyze the 16S rRNA gene sequences of six NTM species,Mycobacterium cosmeticum, M. pallens, M. hodleri, M. crocinum, M. flavescens, andM. xenopi. The approach facilitated the identification of two distinct gene copies in each species. The twoM. cosmeticumgenes had a single nucleotide difference, whereas two nucleotide polymorphisms were identified inM. hodleri, M. flavescens, andM. xenopi. M. pallenshad a difference in four nucleotides andM. crocinumin 23. Hence, we showed that the six NTM species possess at least two non-identical 16S rRNA gene copies.

Importance

The presence of multiple 16S rRNA gene copies with nucleotide polymorphisms represents a challenge for species identification using 16S rRNA as the target sequence. Our analysis was focused on six NTM species,M. cosmeticum, M. pallens, M. hodleri, M. crocinum, M. flavescens, andM. xenopi. As a result, we generated the full-length sequences of two non-identical 16S rRNA copies for each NTM species. The data will be helpful for the sequence analysis of specimens or other samples.
Fusion expression and anti-Aspergillus flavusactivity of a novel inhibitory protein DN-AflR
Authors: Liang Yuan , Kong Qing , Yao Yao , Xu Shujing , Xie Xiang
Published: April 2018

The regulatory gene (aflR) of aflatoxin encodes AflR, a positive regulator that activates transcriptional pathway of genes in aflatoxin biosynthesis. New L-Asp-L-Asn (DN) extracted fromBacillus megateriuminhibited the growth ofA. flavushad been elucidated in our laboratory. The genes encoding DN and binuclear zinc finger cluster protein of AflR were fused, then fusion protein could compete with the AflS-AflR complex for the AflR binding site and significantly improve anti-A. flavusactivity of DN. The fusion genedn-aflRwas cloned into pET32a and recombinant plasmid was introduced intoEscherichia coliBL21. The highest expression was observed after 10 h induction and purified by affinity chromatography column. Compared with DN, the novel fusion protein DN-AflR significantly inhibited the growth ofA. flavusand biosynthesis of aflatoxin B1. This study promoted the use of competitive inhibition of fusion proteins to reduce the expression of regulatory genes in the biosynthetic pathway of aflatoxin. Moreover, it provided more supports for deep research and industrialization of such novel, anti-A. flavusbio-inhibitors.

IMPORTANCE

Aflatoxin contamination has seriously influence on export of agricultural products, income of farmers and economic development. Biological methods, especially using antagonistic microorganisms to inhibit aflatoxin biosynthesis gradually become the hot spot in recent years. DN (L-Asp-L-Asn) fromBacillus megaterium, which could inhibit growth ofAspergillus flavusand synthesis of aflatoxin, has been identified. In this report, we fused the genes encoding inhibitory peptides (DN) and specific zinc finger cluster protein, and expressed the novel anti-A.flavusprotein inEscherichia coli. Compared with DN, the inhibitory ability of novel protein has been improved significantly. This research showed fusion expression of anti-fungal proteins, such as DN-AflR, is a promising method to economically improve the inhibitory activity of bio-inhibitors forA. flavus.
Sequencing and de novo assembly reveals genomic variations associated with differential responses of Candida albicans ATCC 10231 towards fluconazole, pH and non-invasive growth
Authors: Zore Gajanan , Thakre Archana , Patil Rajendra , Pradeep Chaithra , Balan Bipin
Published: April 2018

The whole genome sequencing generated 8.09 million paired-end reads, which were assembled into 2,262 scaffolds totaling 17,113,050 bp in length. We predict 7,654 coding regions and 7,647 genes, and annotated the coding regions with gene ontology terms based on similarity to other annotated genomes. Genome comparisons revealed variations (including SNP and indels in genes involved in pH response, fluconazole resistance and invasive growth) compared to C. albicans SC5314 and WO1.
Limited Introgression Supports Division of Giraffe into Four Species
Authors: Winter Sven , Fennessy Julian , Janke Axel
Published: April 2018

All giraffe (Giraffa) were previously assigned to a single species (G. camelopardalis) and nine subspecies. However, multi-locus analyses of all subspecies have shown that there are four genetically distinct clades and suggest four giraffe species. This conclusion might not be fully accepted due to limited data and lack of explicit gene flow analyses. Here we present an extended study based on 21 independent nuclear loci from 137 individuals. Explicit gene flow analyses identify less than one migrant per generation, including between the closely related northern and reticulated giraffe. Thus, gene flow analyses and population genetics of the extended dataset confirm four genetically distinct giraffe clades and support four independent giraffe species. The new findings call for a revision of the IUCN classification of giraffe taxonomy. Three of the four species are threatened with extinction, mostly occurring in politically unstable regions, and as such, require the highest conservation support possible.
Genetic divergence and phenotypic plasticity contribute to variation in cuticular hydrocarbons in the seaweed flyCoelopa frigida
Authors: Berdan Emma , Enge Swantje , Nylund Göran M. , Wellenreuther Maren , Martens Gerrit A. , Pavia Henrik
Published: April 2018

Cuticular hydrocarbons (CHCs) form the boundary between insects and their environments and often act as essential cues for species, mate and kin recognition. This complex polygenic trait can be highly variable both among and within species, but the causes of this variation, especially the genetic basis, are largely unknown. In this study, we investigated phenotypic and genetic variation of CHCs in the seaweed fly,C. frigida, and found that composition was affected by both genetic (sex and population) and environmental (larval diet) factors. We subsequently conducted behavioral trials that show CHCs are likely used as a sexual signal. We identified general shifts in CHC chemistry as well as individual compounds and found that the methylated compounds, mean chain length, proportion of alkenes, and normalized total CHCs differed between sexes and populations. We combined this data with whole genome re-sequencing data to examine the genetic underpinnings of these differences. We identified 11 genes related to CHC synthesis and found population level outlier SNPs in 5 that are concordant with phenotypic differences. Together these results reveal that the CHC composition ofC. frigidais dynamic, strongly affected by the larval environment, and likely under natural and sexual selection.
Chromosomal scale length variation of germline DNA can predict individual cancer risk
Authors: Toh Chris , Brody James P.
Published: April 2018

Inherited factors are thought to be responsible for a substantial fraction of many different forms of cancer. However, individual cancer risk cannot currently be well quantified by analyzing germ line DNA. Most analyses of germline DNA focus on the additive effects of single nucleotide polymorphisms (SNPs) found. Here we show that chromosomal-scale length variation of germline DNA can be used to predict whether a person will develop cancer. In two independent datasets, the Cancer Genome Atlas (TCGA) project and the UK Biobank, we could classify whether or not a patient had a certain cancer based solely on chromosomal scale length variation. In the TCGA data, we found that all 32 different types of cancer could be predicted better than chance using chromosomal scale length variation data. We found a model that could predict ovarian cancer in women with an area under the receiver operator curve, AUC=0.89. In the UK Biobank data, we could predict breast cancer in women with an AUC=0.83. This method could be used to develop genetic risk scores for other conditions known to have a substantial genetic component and complements genetic risk scores derived from SNPs.
IRES-mediated ribosome repositioning directs translation of a +1 overlapping ORF that enhances viral infection
Authors: Kerr Craig H , Wang Qing S , Moon Kyung-Mee , Keatings Kathleen , Allan Douglas W , Foster Leonard J , Jan Eric
Published: April 2018

RNA structures can interact with the ribosome to alter translational reading frame maintenance and promote recoding that result in alternative protein products. Here, we show that the internal ribosome entry site (IRES) from the dicistrovirus Cricket paralysis virus drives translation of the 0-frame viral polyprotein and an overlapping +1 open reading frame, called ORFx, via a novel mechanism whereby a subset of ribosomes recruited to the IRES bypasses downstream to resume translation at the +1-frame 13th non-AUG codon. A mutant of CrPV containing a stop codon in the +1 frame ORFx sequence, yet synonymous in the 0-frame, is attenuated compared to wild-type virus in aDrosophilainfection model, indicating the importance of +1 ORFx expression in promoting viral pathogenesis. This work demonstrates a novel programmed IRES-mediated recoding strategy to increase viral coding capacity and impact virus infection, highlighting the diversity of RNA-driven translation initiation mechanisms in eukaryotes.

Significance Statement

Viruses use alternate mechanisms to increase the coding capacity of their viral genomes. Here, we provide biochemical evidence that ribosomes recruited to the dicistrovirus cricket paralysis virus IRES undergo a bypass event to direct translation of a downstream +1 frame overlapping open reading frame, called ORFx. Mutations that block ORFx expression inhibit +1 frame translation and infection in fruit flies. These findings highlight the diversity of RNA-driven translation initiation mechanisms in eukaryotes.
Most human introns are recognized via multiple and tissue-specific branchpoints
Authors: Pineda Jose Mario Bello , Bradley Robert K.
Published: April 2018

Although branchpoint recognition is an essential component of intron excision during the RNA splicing process, the branchpoint itself is frequently assumed to be a basal, rather than regulatory, sequence feature. However, this assumption has not been systematically tested due to the technical difficulty of identifying branchpoints and quantifying their usage. Here, we analyzed ∼1.31 trillion reads from 17,164 RNA sequencing data sets to demonstrate that almost all human introns contain multiple branchpoints. This complexity holds even for constitutive introns, 95% of which contain multiple branchpoints, with an estimated five to six branchpoints per intron. Introns upstream of the highly regulated ultraconserved poison exons of SR genes contain twice as many branchpoints as the genomic average. Approximately three-quarters of constitutive introns exhibit tissue-specific branchpoint usage. In an extreme example, we observed a complete switch in branchpoint usage in the well-studied first intron of HBB (β-globin) in normal bone marrow versus metastatic prostate cancer samples. Our results indicate that the recognition of most introns is unexpectedly complex and tissue-specific and suggest that alternative splicing catalysis typifies the majority of introns even in the absence of differences in the mature mRNA.
An exploration of O—H...O and C—H...π interactions in a long-chain-ester-substituted phenylphenol: methyl 10-[4-(4-hydroxyphenyl)phenoxy]decanoate
Authors: Geiger David K. , Geiger H. Cristina , Morell Dominic L.
Published: April 2018

An understanding of the driving forces resulting in crystallization vs organogel formation is essential to the development of modern soft materials. In the molecular structure of the title compound, methyl 10-[4-(4-hydroxyphenyl)phenoxy]decanoate (MBO10Me), C23H30O4, the aromatic rings of the biphenyl group are canted by 6.6 (2)° and the long-chain ester group has an extended conformation. In the crystal, molecules are linked by O—H...O hydrogen bonds, forming chains along [10\overline{3}]. The chains are linked by C—H...O hydrogen bonds, forming layers parallel to the ac plane. The layers are linked by C—H...π interactions, forming a three-dimensional supramolecular structure. The extended structure exhibits a lamellar sheet arrangement of molecules stacking along the b-axis direction. Each molecule has six nearest neighbors and the seven-molecule bundles stack to form a columnar superstructure. Interaction energies within the bundles are dominated by dispersion forces, whereas intercolumnar interactions have a greater electrostatic component.
An investigation to elucidate the factors dictating the crystal structure of seven ammonium carboxylate molecular salts
Authors: Blignaut Jacques , Lemmerer Andreas
Published: April 2018

The crystal structures of seven ammonium carboxylate salts are reported, namely (RS)-1-phenylethan-1-aminium isonicotinate, C8H12N+·C6H4N1O2
−, (I), (RS)-1-phenylethan-1-aminium flurbiprofenate [or 2-(3-fluoro-4-phenylphenyl)propanoate], C8H12N+·C15H12FO2
−, (II), (RS)-1-phenylethan-1-aminium 2-chloro-4-nitrobenzoate, C8H12N+·C7H3ClNO4
−, (III), (RS)-1-phenylethan-1-aminium 4-iodobenzoate, C8H12N+·C7H4IO2
−, (IV), (S)-1-cyclohexylethan-1-aminium 2-chloro-4-nitrobenzoate, C8H18N+·C7H3ClNO4
−, (V), 2-(cyclohex-1-en-1-yl)ethan-1-aminium 4-bromobenzoate, C8H16N+·C7H4BrO2
−, (VI), and (S)-1-cyclohexylethan-1-aminium 4-bromobenzoate, C8H18N+·C7H4BrO2
−, (VII). Salts (II) to (VII) feature three N+—H...O− hydrogen bonds, which form one-dimensional hydrogen-bonded ladders. Salts (II), (III), (IV), (V) and (VII) have a type II ladder system despite the presence of halogen bonding and other intermolecular interactions, whereas (VI) has a type III ladder system. Salt (I) has a unique hydrogen-bonded system of ladders, featuring both N+—H...O− and N+—H...N hydrogen bonds owing to the presence of the pyridine functional group. The presence of an additional hydrogen-bond acceptor on the carboxylate cation disrupts the formation of the ubiquitous type II and III ladder found predominately in ammonium carboxylate salts. Halogen bonding, however, has no influence on their formation.
Hydrogen bonds and π–π interactions in two new crystalline phases of methylene blue
Authors: Canossa Stefano , Predieri Giovanni , Graiff Claudia
Published: April 2018

Two unprecedented solid phases involving the 3,7-bis(dimethylamino)phenothiazin-5-ium cation, i.e. methylene blue (MB+
), have been obtained and structurally characterized. In the crystals of 3,7-bis(dimethylamino)phenothiazin-5-ium chloride dihydrate, C16H18N3S+·Cl−·2H2O (I) and 3,7-bis(dimethylamino)phenothiazinium bisulfite, C16H18N3S+·HSO4
− (II), the cationic dye molecules are planar and disposed in an antiparallel mode, showing π–π stacking interactions, with mean interplanar distances of 3.326 (4) and 3.550 (3) Å in (I) and (II), respectively. In compound (I), whose phase was found affected by merohedral twinning [BASF = 0.185 (3)], the presence of water molecules allows a network of hydrogen bonds involving MB+
as both a donor and an acceptor, whereas in compound (II), the homo-interaction of the anions causes an effective absence of classical hydrogen-bond donors. This substantial difference has important consequences for the stacking geometry and supramolecular interactions of the MB+
cations, which are analysed by Hirshfeld fingerprint plots and subsequently discussed.
Crystal structure of a supramolecular lithium complex ofp-tert-butylcalix[4]arene
Authors: Yamada Manabu , Gandhi Muniyappan Rajiv , Akimoto Kazuhiko , Hamada Fumio
Published: April 2018

Crystals of a supramolecular lithium complex with a calix[4]arene derivative, namely tetramethanollithium 5,11,17,23-tetra-tert-butyl-25,26,27-trihydroxy-28-oxidocalix[4]arene methanol monosolvate, [Li(CH3OH)4](C44H55O4)·CH3OH or [Li(CH3OH)4]+·(calix[4]arene−)]·CH3OH (where calix[4]arene−represents a mono-anion species because of deprotonation of one H atom of the calixarene hydroxy groups), were obtained fromp-tert-butylcalix[4]arene reacted with LiH in tetrahydrofuran, followed by recrystallization from methanol. The asymmetric unit comprises one mono-anionic calixarene molecule, one Li+cation coordinated to four methanol molecules, and one methanol molecule included in the calixarene cavity. The calixarene molecule maintains a cone conformation by intramolecular hydrogen bonding between one phenoxide (–O−) and three pendent calixarene hydroxy groups (–OH). The coordinated methanol molecules around the metal cation play a significant role in forming the supramolecular assembly. The crystal structure of this assembly is stabilized by three sets of intermolecular interactions: (i) hydrogen bonds involving the –OH and –O−moieties of the calixarene molecules, the –OH groups of the coordinated methanol molecules, and the –OH group of the methanol molecule included in the calixarene cavity; (ii) C—H...π interactions between the calixarene molecules and/or the coordinated methanol molecules; (iii) O—H...π interactions between the calixarene molecule and the included methanol molecule.
Structural characterization and Hirshfeld surface analysis of a CoII complex with imidazo[1,2-a]pyridine
Authors: Seth Saikat Kumar
Published: April 2018

A new mononuclear tetrahedral CoII complex, dichloridobis(imidazo[1,2-a]pyridine-κN
1)cobalt(II), [CoCl2(C7H6N2)2], has been synthesized using a bioactive imidazopyridine ligand. X-ray crystallography reveals that the solid-state structure of the title complex exhibits both C—H...Cl and π–π stacking interactions in building supramolecular assemblies. Indeed, the molecules are linked by C—H...Cl interactions into a two-dimensional framework, with finite zero-dimensional dimeric units as building blocks, whereas π–π stacking plays a crucial role in building a supramolecular layered network. An exhaustive investigation of the diverse intermolecular interactions via Hirshfeld surface analysis enables contributions to the crystal packing of the title complex to be quantified. The fingerprint plots associated with the Hirshfeld surface clearly display each significant interaction involved in the structure, by quantifying them in an effective visual manner.
Redetermination of the crystal structure of bis(tri-2-pyridylamine)iron(II) bis(perchlorate), and a new refinement of the isotypic nickel(II) analogue: treatment of the perchlorate anion disorder
Authors: Setifi Zouaoui , Setifi Fatima , Dege Necmi , El Ati Rafika , Glidewell Christopher
Published: April 2018

The redetermination of the structure of the title compound, [Fe(C15H12N4)2](ClO4)2, (I), confirms the structure previously reported [Kucharski et al. (1978a). Aust. J. Chem. 31, 53–56], but models the perchlorate over four sets of atomic sites, rather than using just one set of sites as in the original report. The supramolecular assembly, not reported previously, takes the form of a complex three-dimensional framework built from C—H...O hydrogen bonds. The isotypic nickel(II) analogue, [Ni(C15H12N4)2](ClO4)2, (III), has been refined using the original data set [Wang et al. (2011). Acta Cryst. E67, m78], again using a four-component disorder model for the anion, rather than a two-component model as in the original report, leading to more satisfactory Cl—O distances and O—Cl—O angles.
Syn and anti conformers of diammonium aquabis(malonato)oxidovanadate(IV) in an anhydrate crystal
Authors: Ohno Keiji , Yoshida Takumi , Nagasawa Akira , Fujihara Takashi
Published: April 2018

The asymmetric unit of the title anhydrate compound, (NH4)2[VO(C3H2O4)2(H2O)], consists of two independent complex anions and four ammonium cations. In the complex anions, the VIV atoms are each coordinated by two malonate ligands, one water molecule and one oxide O atom in a distorted octahedral geometry. The equatorial plane is formed by the malonate O atoms, while the axial positions are occupied by water and oxide O atoms. The difference between the two independent complexes is the relative conformation of the malonate ligands. The two ligands in one complex anion are in a syn conformation, while in the other they adopt an anti conformation. In the crystal, the complex anions interact with the counter-cations and adjacent anions through O—H...O, N—H...O and C—H...O hydrogen bonds. Stacks of alternating layers consisting of either anti or syn isomers, formed with the aid of the hydrogen bonding, are observed. DFT calculations for the anti and syn isomers show a similar thermodynamic stability to each other. The crystal used for this analysis was an inversion twin with the ratio of the twin components being 0.270 (13):0.730 (13).
(1S,4R)-1,11,11-Trimethyl-1,2,3,4-tetrahydro-1,4-methanophenazine N
5-oxide
Authors: Quirion Kevin , Crundwell Guy , Glagovich Neil M.
Published: April 2018

The title compound, C16H18N2O, was synthesized via reaction of (1S,4R)-1,2,3,4-tetrahydro-1,11,11-trimethyl-1,4-methanophenazine with 3-chloroperbenzoic acid in dichloromethane. The absolute configuration for the product was assigned based on the stereochemistry of the camphorquinone reactant.
Political connections and stock price crash risk
Authors: Hu Guoliu , Wang Yu
Published: April 2018

Purpose

The purpose of this paper is to research the impact of firms’ political connections on the stock price crash risk.

Design/methodology/approach

Empirical methodology is used in this study.

Findings

Using a large sample of Chinese firms for the period 2008-2013, the authors find that corporate political connections can reduce the stock price crash risk. When managers are still in politics or firms are in high financial transparency of local governments, the relationship between political connections and the stock price crash risk is weakened. In addition, the authors’ research shows that the corporate political connections influence the stock price crash risk by affecting the speed of confirmation of bad news.

Research limitations/implications

The findings in this study suggest that political connections will affect corporate disclosure.

Practical implications

These results can help senior executives and investors make better decisions to prevent the stock price crash risk.

Originality/value

This paper empirically analyzes the impact of different types of political connections on the stock price crash risk for the first time.
Optimal overcurrent relay coordination in distribution network based on Lightning Flash Algorithm
Authors: Kheshti Mostafa , Kang Xiaoning
Published: April 2018

Purpose

Distribution network protection is a complicated problem and mal-operation of the protective relays due to false settings make the operation of the network unreliable. Besides, obtaining proper settings could be very complicated. This paper aims to discuss an innovative evolutionary Lightning Flash Algorithm (LFA) which is developed for solving the relay coordination problems in distribution networks. The proposed method is inspired from the movements of cloud to ground lightning strikes in a thunderstorm phenomenon. LFA is applied on three case study systems including ring, interconnected and radial distribution networks. The power flow analysis is performed in Digsilent Power Factory software; then the collected data are sent to MATLAB software for optimization process. The proposed algorithm provides optimum time multiplier setting and plug setting of all digital overcurrent relays in each system. The results are compared with other methods such as particle swarm optimization and genetic algorithm. The result comparisons demonstrate that the proposed LFA can successfully obtain proper relay settings in distribution networks with faster speed of convergence and lower total operation time of relays. Also, it shows the superiority and effectiveness of this method against other algorithms.

Design/methodology/approach

A novel LFA is designed based on the movements of cloud to ground lightning strikes in a thunderstorm. This method is used to optimally adjust the time multiplier setting and plug setting of the relays in distribution system to provide a proper coordination scheme.

Findings

The proposed algorithm was tested on three case study systems, and the results were compared with other methods. The results confirmed that the proposed method could optimally adjust the relay settings in the electric distribution system to provide a proper protection scheme.

Practical implications

The practical implications can be conducted on distribution networks. The studies provided in this paper approve the practical application of the proposed method in providing proper relay protection in real power system.

Originality/value

This paper proposes a new evolutionary method derived from the movements of cloud to ground lightning strikes in thunderstorm. The proposed method can be used as an optimization toolbox to solve complex optimization problems in practical engineering systems.
Controllable velocity moment and prediction model for inlet guide vanes of a centrifugal pump
Authors: Liu Ming , Tan Lei , Liu Yabin , Xu Yun , Cao Shuliang
Published: April 2018

Purpose

This paper aims to investigate the effect of three-dimensional (3D) inlet guide vanes (IGVs) on performance of a centrifugal pump.

Design/methodology/approach

A design method for 3D IGVs is proposed based on the controllable velocity moment, which is determined by a fourth-order dimensionless function. Numerical simulation of the centrifugal pump with IGVs is carried out by solving the Reynolds-averaged Navier–Stokes equations. The method of frozen rotor is applied to couple the stationary and rotational domain.

Findings

The efficiency of pump with 3D IGVs is higher than that with 2D IGVs for most prewhirl angles, which validate the advancement of 3D IGVs on prewhirl regulation. The effect of prewhirl regulation at small flow rate is more significant than that at large flow rate.

Originality/value

A prediction model of velocity moment based on the Oseen vortex is proposed to describe the flow pattern downstream the IGVs.
Application of smooth transition regression (STR) model on the relationship between natural gas consumption and economic growth in Nigeria
Authors: Galadima Mukhtar Danladi , Aminu Abubakar Wambai
Published: April 2018

Purpose

The purpose of this paper is to identify the level of natural gas consumption that can be adjudged as capable of improving the growth of the Nigerian economy, to investigate whether natural gas consumption is at optimal level in Nigeria and to examine the nature and rate to which natural gas consumption affects economic growth in Nigeria at low and high regimes.

Design/methodology/approach

The tool used to achieve the objectives of the paper is the smooth transition regression (STR) model.

Findings

The findings of the paper are that the relationship between natural gas consumption and economic growth in Nigeria is asymmetric, where the natural gas consumption threshold value in the country is 9085.36 standard cubic meters, whereas the level of its consumption in the country is below the optimal level. Further, in both low and high regimes, natural gas consumption has been found to have a positive and significant impact on economic growth in Nigeria.

Practical implications

The policy implication of the paper is that natural gas consumption in Nigeria should not be less than 9085.36 standard cubic meters and the country should intensify efforts to increase the level of natural gas consumption, as it is below the optimal level and its consumption bolsters the growth of Nigerian economy.

Originality/value

What is new in this paper is its ability to use the STR model. To the best of the authors’ knowledge, such methodology has not been adopted before in such a relation.
Developing the capability to terminate IT projects when they can no longer deliver business value
Authors: Thornley Clare Victoria , Crowley Catherine Anne
Published: April 2018

Purpose

The purpose of this paper is to address the problem of ensuring that the capabilities are in place to identify when a project can no longer deliver value and to take appropriate action to terminate the project.

Design/methodology/approach

Focus groups with project management practitioners were used to collect in-depth qualitative data. This was then supplemented with a questionnaire, which included both closed questions and the opportunity for free text answers.

Findings

The problem of getting better at stopping projects is both common and difficult to solve. It has many facets, which include complex people and cultural issues, processes and procedures as well as financial reporting and project governance. In order to improve, therefore, it is useful to address these different facets in a coordinated way using a capability approach with a focus on business value.

Research limitations/implications

The data from practitioners are retrospective, as their actions were not actually observed by the researchers as they were happening. This means that faulty recollection may influence the results but, it also allows for insights from reflection to be incorporated.

Practical implications

An organizational capability approach focusing on all three aspects of capability; people, processes and technology, can help organizations get better at stopping projects. Specific recommendations are provided and analyzed in terms of their respective capability focus.

Social implications

If performance in terminating projects is improved, it has the potential for significant benefits and cost saving for society in terms of improved government services and the ability to halt projects around new policy initiatives when emerging evidence shows they will not work.

Originality/value

It provides detailed practitioner input on the problem of stopping projects and suggests recommendations for improvement in the context of a structured organizational capability approach with reference to a particular framework, IT-CMF.
“Superfast!” managing the urgent: case study of telecommunications infrastructure project in Algeria
Authors: Zidane Youcef J-T. , Klakegg Ole Jonny , Andersen Bjorn , Hussein Bassam
Published: April 2018

Purpose

With the aim of furthering the understanding of project speed and how to manage the urgent project, the purpose of this paper is to investigate the management challenges involved in delivering a telecommunications infrastructure project in a period of much shorter duration than a similar project. The authors wanted to understand the reasons behind the urgency and how the project management team succeeds in delivering in such a tight time window. Finally, the authors assessed the consequences (negative and positive, during and after the project delivery), knowing that the project was considered a success at its delivery, but not that it was successful at the post-project evaluation.

Design/methodology/approach

A case study based on qualitative research interviews with management team including the client, the main contractor and some related stakeholders, combined with case archives and internal documentation from the case project.

Findings

The urgency of a project or programme may lead to some negative consequences and impacts. The success seen in a short- and mid-term view is not enough to justify making acceleration decisions: thus holistic thinking and a long-term sustainable approach are needed to ensure continuity and profits.

Research limitations/implications

This research is based on a single case study. There are some limitations regarding how urgent and unexpected the case was managed in comparing to normal case. A second limitation is that there is no clear definition of what are normal practices such that we can say what are a normal case and an urgent case.

Practical implications

There are some lessons learned from this case study about managing the unexpected and the urgent. Practitioners can obtain insight into positive and negative consequences of fast project delivery from this case.

Originality/value

This study is unique in its content and context, since it presents the first-hand insight into a case study that seemed to be successful to some extent (short-term impact); however, negative consequences appeared within a few years of its delivery.
Fashion self-congruity: scale development and validation
Authors: Anand Sahiba , Kaur Harsandaldeep
Published: April 2018

Purpose

The purpose of this paper is to develop and validate measurement properties of a scale measuring fashion self-congruity (FSC).

Design/methodology/approach

Based on the existing literature of self-congruity, and four studies carried out as a part of this research, the FSC scale has been validated in a step-by-step process following the scale validation methodology suggested by Churchill (1979).

Findings

The final version of the scale incorporates nine items classified into three dimensions: actual fashion self-congruity, ideal fashion self-congruity, and ideal social fashion self-congruity. The scale reveals strong psychometric properties based on findings of different reliability and validity tests.

Practical implications

A valid and reliable FSC scale provides a foundation to broaden quantitative inquiry into the types of FSC that consumers seek under different situations. Knowledge of the dominant self-concept driving the consumption of fashion in various situations will enable marketers to position their brands along the desired dimension of FSC.

Originality/value

The value of this research paper lies in validating a scale to measure FSC for the first time in the self-concept/congruity literature.
The sustainability word challenge
Authors: Evans Susan , Peirson-Smith Anne
Published: April 2018

Purpose

The purpose of this paper is to examine user perceptions toward consumer-facing words used by fashion brands to stimulate sustainable consumption and post consumption behavior.

Design/methodology/approach

A self-completion, survey based matching exercise was administered to 100 active fashion-shoppers in Hong Kong aged between 18 and 35 years old. A probability sampling method was used for on-street intercepts to ensure a random selection within the defined population. This was accompanied by 20 individual ethnographic interviews.

Findings

A lack of understanding and comprehension of key green language terminology used frequently in user facing communications is problematic for fashion brand marketers as the impact of their messages is often unclear, distributed and more likely to lead to user frustration rather than positive engaged consumer decision making and action. Further, there is an emerging indication that this approach is highly unlikely to enhance knowledge, engagement and action or to influence brand loyalty.

Research limitations/implications

Data were collected in Hong Kong and is culturally bounded, so while providing a good indication of the findings in situ this can also be replicated in other locations.

Practical implications

Recommended outcomes from the findings suggest that brand messages should be delivered that are intended to stimulate sustainability behaviors that are core to one key brand theme so that user outcome decision making and actions fit with the core brand values. This suggested approach will have a greater likelihood of leading to brand trust, responsible business action and greater clarity about the issue of sustainability and related action to be taken on behalf of the user.

Originality/value

The paper raises concerns about the effectiveness and outcomes of fashion brand marketing communications and findings provide insights into the confusion of understanding and the rise in frustration among targeted fashion shoppers 18-35 years, despite the use of frequently used words in brand communications to promote sustainable fashion consumption behaviors.
Mapping the official discourse of frugality in China between 1979 and 2015
Authors: Gao Zhihong
Published: April 2018

Purpose

This paper aims to examine how the official discourse of frugality evolved in China between 1979 and 2015.

Design/methodology/approach

The study uses historical and textual analysis. It divides the Chinese official discourse on frugality between 1979 and 2015 into four periods: 1979-1992, 1993-2002, 2003-2012 and 2013-2015.

Findings

A Chinese official discourse on frugality persisted between 1979 and 2015, even though during the same period, China transformed from a socialist economy of central planning and insufficient supply to a market economy of excessive supply and weak consumer demand. The intensity of this official discourse frequently vacillated, adjusting to both economic and political conditions of the time as part of the larger political-economic contestation between competing ideas and policies.

Originality/value

There have been calls for more studies on how frugality discourses have evolved in international markets, especially in terms of how they are shaped by local historical antecedents and long-standing tensions. Through the Chinese case, this article illuminates why some traditional values persist and obtain a paradoxical co-existence with consumerist ethos in our modern society.
Will Saudi Arabia get older? Will its pension system be sustainable? Spectral answers
Authors: Rostan Pierre , Rostan Alexandra
Published: April 2018

Purpose

The purpose of this paper is to answer the following two questions: Will Saudi Arabia get older? Will its pension system be sustainable?

Design/methodology/approach

The methodology/approach is to forecast KSA’s population with wavelet analysis combined with the Burg model which fits a pth order autoregressive model to the input signal by minimizing (least squares) the forward and backward prediction errors while constraining the autoregressive parameters to satisfy the Levinson-Durbin recursion, then relies on an infinite impulse response prediction error filter.

Findings

Spectral analysis projections of Saudi age groups are more optimistic than the Bayesian probabilistic model sponsored by the United Nations Population Division: Saudi Arabia will not get older as fast as projected by the United Nations model. The KSA’s pension system will stay sustainable based on spectral analysis, whereas it will not based on the U.N. model.

Originality/value

Spectral analysis will provide better insight and understanding of population dynamics for Saudi government policymakers, as well as economic, health and pension planners.