bluuebunny/crossref_metadata_2025 huggingface dataset:
Key data for outbreak evaluation: building on the Ebola experience
Authors: Cori Anne , Donnelly Christl A. , Dorigatti Ilaria , Ferguson Neil M. , Fraser Christophe , Garske Tini , Jombart Thibaut , Nedjati-Gilani Gemma , Nouvellet Pierre , Riley Steven , Van Kerkhove Maria D. , Mills Harriet L. , Blake Isobel M.
Published: April 2017

Following the detection of an infectious disease outbreak, rapid epidemiological assessment is critical for guiding an effective public health response. To understand the transmission dynamics and potential impact of an outbreak, several types of data are necessary. Here we build on experience gained in the West African Ebola epidemic and prior emerging infectious disease outbreaks to set out a checklist of data needed to: (1) quantify severity and transmissibility; (2) characterize heterogeneities in transmission and their determinants; and (3) assess the effectiveness of different interventions. We differentiate data needs into individual-level data (e.g. a detailed list of reported cases), exposure data (e.g. identifying where/how cases may have been infected) and population-level data (e.g. size/demographics of the population(s) affected and when/where interventions were implemented). A remarkable amount of individual-level and exposure data was collected during the West African Ebola epidemic, which allowed the assessment of (1) and (2). However, gaps in population-level data (particularly around which interventions were applied when and where) posed challenges to the assessment of (3). Here we highlight recurrent data issues, give practical suggestions for addressing these issues and discuss priorities for improvements in data collection in future outbreaks.

This article is part of the themed issue ‘The 2013–2016 West African Ebola epidemic: data, decision-making and disease control’.
ICTV Virus Taxonomy Profile: Iflaviridae
Authors: Valles S. M , Chen Y , Firth A. E , Guérin D. M. A , Hashimoto Y , Herrero S , de Miranda J. R , Ryabov E ,   ICTV Report Consortium
Published: April 2017

Iflaviridae is a family of small non-enveloped viruses with monopartite, positive-stranded RNA genomes of approximately 9–11 kilobases. Viruses of all classified species infect arthropod hosts, with the majority infecting insects. Both beneficial and pest insects serve as hosts, and infections can be symptomless (Nilaparvatalugens honeydew virus 1) or cause developmental abnormalities (deformed wing virus), behavioural changes (sacbrood virus) and premature mortality (infectious flacherie virus). The host range has not been examined for most members. The most common route of infection for iflaviruses is the ingestion of virus-contaminated food sources. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Iflaviridae, which is available at www.ictv.global/report/iflaviridae.
First report of fatal disseminated microsporidiosis in two inland bearded dragons Pogona vitticeps in Japan
Authors: Shibasaki Kojiro , Tokiwa Toshihiro , Sukegawa Akihiro , Kondo Hirotaka , Tamukai Kenichi , Haga Yumiko , Ike Kazunori
Published: April 2017

Introduction.
Encephalitozoon pogonae is a newly described pathogen belonging to the phylum Microsporidia. In Austria and the USA, this species has been isolated from fatal and disseminated cases of captive-bred inland bearded dragons. Here, we report the case of fatal disseminated microsporidiosis caused by E. pogonae in two bearded dragons in Japan.

Case Presentation. The two lizards from different private households in Tokyo, Japan, had been brought to an animal hospital for examination. In both cases, the animal presented with a history of weight loss for several weeks. There were no improvements in clinical symptoms and the lizards deteriorated and finally died. Histopathological examination demonstrated necrotizing granulomatous inflammation attributed to disseminated microsporidian infection. Nucleotide sequencing of the nuclear ribosomal internal transcribed spacer region identified the microsporidian as E. pogonae with sequence identity of 100 %.

Conclusion. We report the first case, to our knowledge, of disseminated microsporidiosis caused by E. pogonae in inland bearded dragons in Japan. Although it is difficult to diagnose prenatally since the signs are nonspecific, the disease should be considered in the differential diagnosis of chronic infections that do not respond to antibiotics.
Diagnostic prediction tools for bacteraemia caused by 3rd generation cephalosporin-resistant Enterobacteriaceae in suspected bacterial infections: a nested case-control study
Authors: Rottier Wouter C. , van Werkhoven Cornelis H. , Bamberg Yara R.P. , Dorigo-Zetsma J. Wendelien , van de Garde Ewoudt M. , van Hees Babette C. , Kluytmans Jan A.J.W. , Kuck Emile M. , van der Linden Paul D. , Prins Jan M. , Thijsen Steven F.T. , Verbon Annelies , Vlaminckx Bart J.M. , Ammerlaan Heidi S.M. , Bonten Marc J.M.
Published: April 2017

Objectives

Current guidelines for empirical antibiotic treatment poorly predict the presence of 3rd generation cephalosporin resistant Enterobacteriaceae (3GC-R EB) as a cause of infection, thereby increasing unnecessary carbapenem use. We aimed to develop diagnostic scoring systems to better predict the presence of 3GC-R EB as a cause of bacteraemia.

Methods

A retrospective nested case-control study was performed that included patients ≥18 years in whom blood cultures were obtained and intravenous antibiotics were initiated. Each patient with 3GC-R EB bacteraemia was matched to four control infection episodes within the same hospital, based on blood culture date and onset location (community or hospital). Starting from 32 described clinical risk factors at infection onset, selection strategies were used to derive scoring systems for the probability of community- and hospital-onset 3GC-R EB bacteraemia.

Results

3GC-R EB bacteraemia occurred in 90 of 22,506 (0.4%) community-onset and in 82 of 8,110 (1.0%) hospital-onset infections, and these cases were matched to 360 community-onset and 328 hospital-onset control episodes, respectively. The derived community-onset and hospital-onset scoring system consisted of 6 and 9 predictors, respectively, with c-statistics of 0.807 (95% confidence interval 0.756-0.855) and 0.842 (0.794-0.887). With selected score cutoffs, the models identified 3GC-R EB bacteraemia with equal sensitivity as existing guidelines, but reduced the proportion of patients classified as at risk for 3GC-R EB bacteraemia (i.e. eligible for empiric carbapenem therapy) with 40% in patients with community-onset and 49% in patients with hospital-onset infection.

Conclusions

These prediction rules for 3GC-R EB bacteraemia may reduce unnecessary empiric carbapenem use.
Interactions and collider bias in case-only gene-environment data
Authors: Balazard Félix , Le Fur Sophie , Bougnères Pierre , Valleron Alain-Jacques ,   the Isis-Diab collaborative group
Published: April 2017

Background: Case-only design for gene-environment interaction (CODGEI) relies on the rare disease assumption. A negative association due to collider bias appears between gene and environment when this assumption is not respected. Genetic risk estimation can quantify part of the predisposition of an individual to a disease.
Methods: We introduce Disease As Collider (DAC), a new case-only methodology to discover environmental factors using genetic risk estimation: a negative correlation between genetic risk and environment in cases provides a signature of a genuine environmental risk marker. Simulation of disease occurrence in a source population allows to estimate the statistical power of DAC and the influence of collider bias in CODGEI. We illustrate DAC in 831 type 1 diabetes (T1D) patients.
Results: The power of DAC increases with sample size, prevalence and accuracy of genetic risk estimation. For a prevalence of 1% and a realistic genetic risk estimation, power of 80% is reached for a sample size under 3000. Collider bias offers an alternative interpretation to the results of CODGEI in a published study on breast cancer.
Conclusion: DAC could provide a new line of evidence for discovering which environmental factors play a role in complex diseases or confirming results obtained in case-control studies. We discuss the circumstances needed for DAC to participate in the dissection of environmental determinants of disease. We provide guidance on the use of CODGEI regarding the rare disease assumption.
The Developing Human Connectome Project: a Minimal Processing Pipeline for Neonatal Cortical Surface Reconstruction
Authors: Makropoulos Antonios , Robinson Emma C. , Schuh Andreas , Wright Robert , Fitzgibbon Sean , Bozek Jelena , Counsell Serena J. , Steinweg Johannes , Vecchiato Katy , Passerat-Palmbach Jonathan , Lenz Gregor , Mortari Filippo , Tenev Tencho , Duff Eugene P. , Bastiani Matteo , Cordero-Grande Lucilio , Hughes Emer , Tusor Nora , Tournier Jacques-Donald , Hutter Jana , Price Anthony N. , Teixeira Rui Pedro A. G. , Murgasova Maria , Victor Suresh , Kelly Christopher , Rutherford Mary A. , Smith Stephen M. , Edwards A. David , Hajnal Joseph V. , Jenkinson Mark , Rueckert Daniel
Published: April 2017

The Developing Human Connectome Project (dHCP) seeks to create the first 4-dimensional connectome of early life. Understanding this connectome in detail may provide insights into normal as well as abnormal patterns of brain development. Following established best practices adopted by the WU-MINN Human Connectome Project (HCP), and pioneered by FreeSurfer, the project utilises cortical surface-based processing pipelines. In this paper, we propose a fully automated processing pipeline for the structural Magnetic Resonance Imaging (MRI) of the developing neonatal brain. This proposed pipeline consists of a refined framework for cortical and sub-cortical volume segmentation, cortical surface extraction, and cortical surface inflation, which has been specifically designed to address considerable differences between adult and neonatal brains, as imaged using MRI. Using the proposed pipeline our results demonstrate that images collected from 465 subjects ranging from 28 to 45 weeks post-menstrual age (PMA) can be processed fully automatically; generating cortical surface models that are topologically correct, and correspond well with manual evaluations of tissue boundaries in 85% of cases. Results improve on state-of-the-art neonatal tissue segmentation models and significant errors were found in only 2% of cases, where these corresponded to subjects with high motion. Downstream, these surfaces will enhance comparisons of functional and diffusion MRI datasets, supporting the modelling of emerging patterns of brain connectivity.
“A different gut microbiome linked to inflammation found in cirrhotic patients with and without hepatocellular carcinoma”
Authors: Piñero Federico , Vazquez Martín , Baré Patricia , Rohr Cristian , Mendizabal Manuel , Sciara Mariela , Alonso Cristina , Fay Fabián , Silva Marcelo
Published: April 2017

Background

No specific microbiome in patients with hepatocellular carcinoma (HCC) has been reported to date.

Aim

To compare the gut microbiome found in cirrhotic patients with and without HCC.

Methods

From 407 patients with Child Pugh A/B cirrhosis prospectively followed, 25 with HCC (cases) were matched with 25 without HCC (wo-HCC) in a 1:1 ratio according to age, gender, etiology, Child Pugh and severity of portal hypertension. In addition results were also compared with 25 healthy subjects. Faecal stool samples were collected noninvasively, aliquoted for DNA extraction and sequenced for the V3-V4 region of the microbial 16S rRNA (Illumina MiSeq Platform).

Results

There were no significant clinical differences among cases and controls. We found a differential abundance in family members of Firmicutes with a 3-fold increased of Erysipelotrichaceae and a 5-fold decrease in family Leuconostocaceae in HCC when compared to wo-HCC controls. Genus Fusobacterium was found 5-fold decreased in HCC versus wo-HCC. The ratio bacteriodes/prevotella was increased in HCC due to the significant decrease in the genus prevotella. Genus Odoribacter and Butyricimonas were more differentialy abundant in HCC. This pattern has been previously associated with an inflammatory milieu with a putative increased activation of NOD-like receptor signalling pathways. A Random Forest model trained with differential abundant taxa correctly classifyed HCC individuals with an error of 22%.

Conclusions

A pattern of microbiome linked to inflammation was observed in cirrhotic patients with HCC. These findings open the discussion whether or not microbiota has a physiopathologic role in HCC development in cirrhosis.
Efficient Information Contents Flow Down from Memory to Predict the Identity of Faces
Authors: Zhan Jiayu , Garrod Oliver G. B. , van Rijsbergen Nicola , Schyns Philippe G.
Published: April 2017

In the sciences of cognition, an influential idea is that the brain makes predictions about incoming sensory information to reduce inherent ambiguity. In the visual hierarchy, this implies that information content originating in memory–the identity of a face–propagates down to disambiguate incoming stimulus information. However, understanding this powerful prediction-for-recognition mechanism will remain elusive until we uncover the content of the information propagating down from memory. Here, we address this foundational limitation with a task ubiquitous to humans–familiar face identification. We developed a unique computer graphics platform that combines a generative model of random face identity information with the subjectivity of perception. In 14 individual participants, we reverse engineered the predicted information contents propagating down from memory to identify 4 familiar faces. In a follow-up validation, we used the predicted face information to synthesize the identity of new faces and confirmed the causal role of the predictions in face identification. We show these predictions comprise both local 3D surface patches, such as a particularly thin and pointy nose combined with a square chin and a prominent brow, or more global surface characteristics, such as a longer or broader face. Further analyses reveal that the predicted contents are efficient because they represent objective features that maximally distinguish each identity from a model norm. Our results reveal the contents that propagate down the visual hierarchy from memory, showing this coding scheme is efficient and compatible with norm-based coding, with implications for mechanistic accounts of brain and machine intelligence.
A versatile compressed sensing scheme for faster and less phototoxic 3D fluorescence microscopy
Authors: Woringer Maxime , Darzacq Xavier , Zimmer Christophe , Mir Mustafa
Published: April 2017

Three-dimensional fluorescence microscopy based on Nyquist sampling of focal planes faces harsh trade-offs between acquisition time, light exposure, and signal-to-noise. We propose a 3D compressed sensing approach that uses temporal modulation of the excitation intensity during axial stage sweeping and can be adapted to fluorescence microscopes without hardware modification. We describe implementations on a lattice light sheet microscope and an epifluorescence microscope, and show that images of beads and biological samples can be reconstructed with a 5-10 fold reduction of light exposure and acquisition time. Our scheme opens a new door towards faster and less damaging 3D fluorescence microscopy.

OCIS codes:(110.1758) Computational imaging; (170.2520) Fluorescence microscopy; (170.6900) Three-dimensional microscopy.
Cataloguing over-expressed genes in Epstein Barr Virus immortalized lymphoblastoid cell lines through consensus analysis of PacBio transcriptomes corroborates hypomethylation of chromosome 1
Authors: Chakraborty Sandeep
Published: April 2017

The ability of Epstein Barr Virus (EBV) to transform resting cell B-cells into immortalized lymphoblastoid cell lines (LCL) provides a continuous source of peripheral blood lymphocytes that are used to model conditions in which these lymphocytes play a key role. Here, the PacBio generated transcriptome of three LCLs from a parent-daughter trio (SRAid:SRP036136) provided by a previous study [1] were analyzed using a kmer-based version of YeATS (KEATS). The set of over-expressed genes in these cell lines were determined based on a comparison with the PacBio transcriptome of twenty tissues provided by another study (hOPTRS) [2]. MIR155 long non-coding RNA (MIR155HG), Fc fragment of IgE receptor II (FCER2), T-cell leukemia/lymphoma 1A (TCL1A), and germinal center associated signaling and motility (GCSAM) were genes having the highest expression counts in the three LCLs with no expression in hOPTRS. Other over-expressed genes, having low expression in hOPTRS, were membrane spanning 4-domains A1 (MS4A1) and ribosomal protein S2 pseudogene 55 (RPS2P55). While some of these genes are known to be over-expressed in LCLs, this study provides a comprehensive cataloguing of such genes. A recent work involving a patient with EBV-positive large B-cell lymphoma was ‘unusually lacking various B-cell markers’, but over-expressing CD30 [3] - a gene ranked 79 among uniquely expressed genes here. Hypomethylation of chromosome 1 observed in EBV immortalized LCLs [4, 5] is also corroborated here by mapping the genes to chromosomes. Extending previous work identifying un-annotated genes [6], 80 genes were identified which are expressed in the three LCLs, not in hOPTRS, and missing in the GENCODE, RefSeq and RefSeqGene databases. KEATS introduces a method of determining expression counts based on a partitioning of the known annotated genes, has runtimes of a few hours on a personal workstation and provides detailed reports enabling proper debugging.
The microbiome and metabolome of pre-term infant stool is personalized, and not driven by health outcomes including necrotizing enterocolitis and late-onset sepsis
Authors: Wandro Stephen , Osborne Stephanie , Enriquez Claudia , Bixby Christine , Arrieta Antonio , Whiteson Katrine
Published: April 2017

The assembly and development of the gut microbiome in infants has important consequences for immediate and long-term health. Preterm infants represent an abnormal case for bacterial colonization because of early exposure to bacteria and frequent use of antibiotics. To better understand the assembly of the gut microbiota in preterm infants, fecal samples were collected from 32 very low birthweight preterm infants over the first six weeks of life. Infant health outcomes included healthy, late-onset sepsis, and necrotizing enterocolitis (NEC). We characterized the bacterial composition by 16S rRNA gene sequencing and metabolome by untargeted gas chromatography mass spectrometry. Preterm infant fecal samples lacked beneficialBifidobacteriumand were dominated byEnterobacteriaceae, Enterococcus, andStaphylococcusdue to the near uniform antibiotic administration. Most of the variance between the microbial community compositions could be attributed to which baby the sample came from (Permanova R2=0.48, p<0.001), while clinical status (healthy, NEC, or late-onset sepsis), and overlapping time in the NICU did not explain a significant amount of variation in bacterial composition. Fecal metabolomes were also found to be unique to the individual (Permanova R2=0.43, p<0.001) and weakly associated with bacterial composition (Mantel statistic r = 0.23 ± 0.05 (p = 0.03 ± 0.03). No measured metabolites were found to be associated with necrotizing enterocolitis, late-onset sepsis or a healthy outcome. Overall, preterm infants gut microbial communities were personalized and reflected antibiotic usage.

Importance

Preterm infants face health problems likely related to microbial exposures including sepsis and necrotizing enterocolitis. However, the role of the gut microbiome in preterm infant health is poorly understood. Microbial colonization differs from healthy term babies because it occurs in the NICU and is often perturbed by antibiotics. We measured bacterial compositions and metabolomic profiles of 77 fecal samples from thirty-two preterm infants to investigate the differences between microbiomes in health and disease. Rather than finding microbial signatures of disease, we found the preterm infant microbiome and metabolome were both personalized, and that the preterm infant gut microbiome is enriched in microbes that commonly dominate in the presence of antibiotics. These results contribute to the growing knowledge of the preterm infant microbiome and emphasize that a personalized view will be important to disentangling the health consequences of the preterm infant microbiome.
The Y-chromosome clarifies the evolutionary history ofSus scrofaby large-scale deep genome sequencing
Authors: Ai Huashui , Ren Jun , Ma Junwu , Zhang Zhiyan , Li Wanbo , Yang Bin , Huang Lusheng
Published: April 2017

The genetics and evolution of sex chromosomes are largely distinct from autosomes and mitochondrial DNA (mtDNA). The Y chromosome offers unique genetic perspective on male-line inheritance. Here, we uncover novel evolutionary history ofSus scrofabased on 205 high-quality genomes from worldwide-distributed different wild boars and domestic pig breeds. We find that only two haplotypes exist in the distal and proximal blocks of at least 7.7 Mb on chromosome Y in pigs across European and Asian continents. And the times of most recent common ancestors (TMRCA) within both haplotypes, approximately 0.14 and 0.10 million years, are far smaller than their divergence time of around 1.07 million years. What’s more, the relationship between Sumatran and Eurasian continentSus scrofais much closer than that we knew before. And surprisingly, European pigs share the same haplotype with many Chinese pigs, which is not consistent with their deep splitting status on autosome and mtDNA. Further analyses show that the haplotype in Chinese pigs was likely introduced from European wild boars via ancient gene flow before pig domestication about 24k years ago. Low mutation rates and no recombination in the distal and proximal blocks on chromosome Y help us detect this male-driven ancient gene flow. Taken together, our results update the knowledge of pig demography and evolution, and might shed insight into the genetics and evolution studies on chromosome Y in other mammals.
An Arf6- and caveolae-dependent pathway links hemidesmosome remodeling and mechanoresponse
Authors: Osmani Naël , Pontabry Julien , Comelles Jordi , Fekonja Nina , Goetz Jacky G. , Riveline Daniel , Georges-Labouesse Elisabeth , Labouesse Michel
Published: April 2017

Hemidesmosomes (HDs) are epithelial-specific cell-matrix adhesions, which stably anchor the intracellular keratin network to the extracellular matrix. Although their main role is to protect the epithelial sheet from external mechanical strain, how HDs respond to mechanical stress remains poorly understood. Here we identify a pathway essential for HD remodeling, and outline its role with respect to α6β4 integrin recycling. We find that α6β4 integrin chains localize to the plasma membrane/caveolae and Arf6+ endocytic compartments. Based on FRAP and endocytosis assays, integrin recycling between both sites requires the small GTPase Arf6 and its co-regulators GIT1/βPIX, but neither Caveolin1 (Cav1) nor Cavin1. Strikingly, when keratinocytes are stretched or hypo-osmotically shocked, α6β4 integrin accumulates at cell edges, whereas Cav1 disappears from it. This process, which is isotropic relative to the orientation of stretch, depends on Arf6, Cav1 and Cavin1. We propose that mechanically-induced HD growth involves the isotropic flattening of caveolae (known for their mechanical buffering role) associated with integrin diffusion and turnover.
Large, long range tensile forces drive convergence duringXenopusblastopore closure and body axis elongation
Authors: Shook David R. , Kasprowicz Eric M. , Davidson Lance A. , Keller Ray
Published: April 2017

Indirect evidence suggests that blastopore closure during gastrulation of anamniotes, including amphibians such asXenopus laevis,depends on circumblastoporal convergence forces generated by the marginal zone (MZ), but direct evidence is lacking. We show that explanted MZs generate tensile convergence forces up to 1.5 μN during gastrulation and over 4 μN thereafter. These forces are generated by convergent thickening (CT) until the midgastrula and increasingly by convergent extension (CE) thereafter. Explants from ventralized embryos, which lack tissues expressing CE but close their blastopores, produce up to 2 μN of tensile force, showing that CT alone generates forces sufficient to close the blastopore. Uniaxial tensile stress relaxation assays show stiffening of mesodermal and ectodermal tissues around the onset of neurulation, potentially enhancing long-range transmission of convergence forces. These results illuminate the mechanobiology of early vertebrate morphogenic mechanisms, aid interpretation of phenotypes, and give insight into the evolution of blastopore closure mechanisms.
Cytosine modifications modulate the chromatin architecture of transcriptional enhancers
Authors: Mahé Elise A. , Madigou Thierry , Sérandour Aurélien A. , Bizot Maud , Avner Stéphane , Chalmel Frédéric , Palierne Gaëlle , Métivier Raphaël , Salbert Gilles
Published: April 2017

Epigenetic mechanisms are believed to play key roles in the establishment of cell-specific transcription programs. Accordingly, the modified bases 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) have been observed in DNA of genomic regulatory regions such as enhancers, and oxidation of 5mC into 5hmC by Ten-eleven translocation (TET) proteins correlates with enhancer activation. However, the functional relationship between cytosine modifications and the chromatin architecture of enhancers remains elusive. To gain insights into their function, 5mC and 5hmC levels were perturbed by inhibiting DNA methyltransferases and TETs during differentiation of mouse embryonal carcinoma cells into neural progenitors, and chromatin characteristics of enhancers bound by the pioneer transcription factors FOXA1, MEIS1, and PBX1 were interrogated. In a large fraction of the tested enhancers, inhibition of DNA methylation was associated with a significant increase in monomethylation of H3K4, a characteristic mark of enhancer priming. In addition, at some specific enhancers, 5mC oxidation by TETs facilitated chromatin opening, a process that may stabilize MEIS1 binding to these genomic regions.
High-confidence coding and noncoding transcriptome maps
Authors: You Bo-Hyun , Yoon Sang-Ho , Nam Jin-Wu
Published: April 2017

The advent of high-throughput RNA sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic genomes. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed based on RNA-seq reads that lack their orientations (known as unstranded reads) and certain boundary information. Methods to expand the usability of unstranded RNA-seq data by predetermining the orientation of the reads and precisely determining the boundaries of assembled transcripts could significantly benefit the quality of the resulting transcriptome maps. Here, we present a high-performing transcriptome assembly pipeline, called CAFE, that significantly improves the original assemblies, respectively assembled with stranded and/or unstranded RNA-seq data, by orienting unstranded reads using the maximum likelihood estimation and by integrating information about transcription start sites and cleavage and polyadenylation sites. Applying large-scale transcriptomic data comprising 230 billion RNA-seq reads from the ENCODE, Human BodyMap 2.0, The Cancer Genome Atlas, and GTEx projects, CAFE enabled us to predict the directions of about 220 billion unstranded reads, which led to the construction of more accurate transcriptome maps, comparable to the manually curated map, and a comprehensive lncRNA catalog that includes thousands of novel lncRNAs. Our pipeline should not only help to build comprehensive, precise transcriptome maps from complex genomes but also to expand the universe of noncoding genomes.
New leads for fragment-based design of rhenium/technetium radiopharmaceutical agents
Authors: Brink Alice , Helliwell John R.
Published: April 2017

Multiple possibilities for the coordination offac-[Re(CO)3(H2O)3]+to a protein have been determined and include binding to Asp, Glu, Arg and His amino-acid residues as well as to the C-terminal carboxylate in the vicinity of Leu and Pro. The large number of rhenium metal complex binding sites that have been identified on specific residues thereby allow increased target identification for the design of future radiopharmaceuticals. The core experimental concept involved the use of state-of-art tuneable synchrotron radiation at the Diamond Light Source to optimize the rhenium anomalous dispersion signal to a large value (f′′ of 12.1 electrons) at itsLIabsorption edge with a selected X-ray wavelength of 0.9763 Å. At the Cu Kα X-ray wavelength (1.5418 Å) thef′′ for rhenium is 5.9 electrons. The expected peak-height increase owing to the optimization of the Ref′′ was therefore 2.1. This X-ray wavelength tuning methodology thereby showed the lower occupancy rhenium binding sites as well as the occupancies of the higher occupancy rhenium binding sites.
Selective synthesis of (3-ferrocenylprop-2-en-1-yl)triphenylphosphonium iodide: crystal structure determination of two polymorphs
Authors: Bouchene Rafika , Daran Jean Claude , Merazig Hocine , Manoury Eric , Bouacida Sofiane
Published: April 2017

This work is part of a project studying the reactivity of a new ferrocenyl allylammonium salt, [3-(trimethylazaniumyl)prop-1-en-1-yl]ferrocene iodide, (1+)·I−, with different nucleophiles. With nitrogen-based nucleophiles, different ferrocenyl allylamine isomers have been synthesized successfully in good yield. Optimization of the basicity of the reaction medium has allowed selection of the best operating conditions to obtain the targeted isomer. In a similar way and in order to introduce phosphorus-containing functional groups, the reaction of ammonium salt (1+)·I− with a phosphorus nucleophile, namely triphenylphosphane, was attempted. It was then possible to isolate single crystals of (3-ferrocenylprop-2-en-1-yl)triphenylphosphonium iodide, [Fe(C5H5)(C26H23P)]I, which is shown to crystallize in two concomitant polymorphic forms, viz. a triclinic form, (I), in the space group P\overline{1}, and a monoclinic form, (II), in the space group P21/c. In the inter-ion packing of polymorph (I), the cations form bilayer ribbons via C—H...π and π–π stacking interactions. In polymorph (II), where π–π interactions do not occur, adjacent molecules are joined by C—H...π interactions into a one-dimensional helical arrangement along the b axis.
1,4-Di-n-octyl-1,2,3,4-tetrahydroquinoxaline-2,3-dione
Authors: El Bourakadi Khadija , El Bakri Youness , Sebhaoui Jihad , Rayni Ibtissam , Essassi El Mokhtar , Mague Joel T.
Published: April 2017

In the title compound, C24H38N2O2, the heterocyclic ring (r.m.s. = 0.015 Å) deviates from planarity to a greater extent than the benzene ring (r.m.s. deviation = 0.007 Å). In the crystal, the molecules pack to form polar and non-polar regions. The major intermolecular interaction appears to be complementary π-stacking between oppositely oriented tetrahydroquinoxaline units.
N2,N2,N6,N6-Tetraphenylpyridine-2,6-diamine
Authors: Miki Shintaro , Umezono Satoru , Okuno Tsunehisa
Published: April 2017

In the title compound, C29H23N3, the molecule has an unsymmetrical structure, although it can possessCssymmetry. The NC3units around the amino N atoms are approximately planar and make dihedral angles of 13.41 (5) and 31.05 (5)° with the pyridine ring. In the crystal, C—H...N interactions between the phenyl and pyridyl rings lead to a columnar stack along thebaxis.
Consumer racism: a scale modification
Authors: Abdul-Latif Samshul-Amry , Abdul-Talib Asmat-Nizam
Published: April 2017

Purpose

Consumer racism describes the act of purchase discrimination based on ethnic and/or cultural differences. As the original consumer racism scale was developed based on a western context and environment, most of its items may be unsuitable for use in certain non-western countries. The purpose of this paper is to modify the existing consumer racism scale to include the elements of inter-ethnic relationships, historical occurrences and political situations, which are crucial in shaping and influencing racism in a multi-religion and multi-racial context.

Design/methodology/approach

After generating new items and retaining or removing others for a modified consumer racism scale, exploratory factor analysis (EFA) is performed based on 145 respondents followed by confirmatory factor analysis (CFA) based on 176 respondents. The modified scale, including two other related constructs (consumer ethnocentrism and consumer animosity), is then tested through structural equation modeling (SEM) using WarpPLS 5.0 and data from 495 respondents.

Findings

EFA and CFA results suggest that the modified eight-item consumer racism scale is applicable in a multi-ethnic scenario. However, SEM findings contradict previous studies; thus, discussion of the possible effects of consumer racism is based on two different approaches.

Research limitations/implications

Future research could be expanded into other ethnic groups and countries, and/or to different products, categories and brands.

Originality/value

The main contributions of this study are the validation of the modified measurement scale and demonstration of its applicability in a multi-ethnic scenario. The study is based on data from a multi-ethnic, multi-religion and multi-cultural country: Malaysia.
Price reduction strategy
Authors: Kareem Abdul Waheed
Published: April 2017

Purpose

The purpose of this paper is to address consumers’ post-purchase perceptions toward the brand when it adopts price reduction strategy. The study specifically conceptualizes the effect of consumers’ price unfairness perceptions of past purchase (PUPoPP) on customer-based brand equity (CBBE) with a moderating effects of elapsed time since purchase (ETSP) and magnitude of price reduction (MPR) in situations where consumers were aware of the reduction in price of the product that they had purchased earlier.

Design/methodology/approach

A survey was conducted among consumers who were aware of the reduction in the price of the computer laptop which they had purchased earlier. A sample size of 214 respondents was utilized for the study. The hypotheses were tested by using partial least squares-structural equations modeling.

Findings

The results of the study show that there is a significant negative impact of PUPoPP on CBBE and the ETSP was found to enhance CBBE and also weaken the negative effect of PUPoPP on CBBE. Furthermore, the MPR was found to strengthen the negative effect of PUPoPP on CBBE.

Originality/value

The findings of this study are unique and contribute to both pricing and branding areas of research. While extant research in these areas has focused on price fairness perceptions in situations where the price of future purchase increases, particularly for frequently purchased non-durable goods, this study explored PUPoPP in situations where the firm reduces the price of a durable good such as a computer laptop.
A review of Spanish consumers’ product-country image of China
Authors: Gorostidi-Martinez Haritz , Xu Weimin , Zhao Xiaokang
Published: April 2017

Purpose

The purpose of this paper is to facilitate and clarify the perceptions of Spanish consumers towards China, its people, and its products, while outlining the overall contemporary Chinese product-country image (PCI) within the Spanish market.

Design/methodology/approach

A 52-item construct was adapted from former PCI scales from cross-cultural equivalence, including “country image”, “personal image”, “product image”, “general knowledge about China”, and “personal data”. Overall, 215 valid structured questionnaires were gathered.

Findings

The current study provides: a PCI literature review; hypotheses results concerning Spanish citizens’ views of Chinese products’ price, quality, technicality, inventiveness, and known brands concepts; descriptive statistics and results graphs for each of the PCI sections; and correlations of other variables with the five product image variables within the construct.

Research limitations/implications

Implementing standardized, longitudinal consumer studies that facilitate better comprehension of PCI evolution within a specific market emerged as a future research agenda.

Originality/value

The data informed both the Chinese public and private organizations’ managers of the importance of adapting to the market and non-market environments within Spain to avoid the liability of country of origin effect.
Continuities of influence
Authors: Manuel Jacqueline , Carter Don
Published: April 2017

Purpose

This paper provides a critical interpretative analysis of the first secondary English syllabus for schools in New South Wales (NSW), Australia, contained within theCourses for Study for High Schools(New South Wales Department of Public Instruction, 1911). The purpose of the paper is to examine the “continuities that link English curriculum discourses and practices with previous discourses and practices” in the rhetorical curriculum. The analysis identifies those aspects of the 1911 English syllabus that have since become normative and challenges the appropriateness of certain enduring orthodoxies in a twenty-first century context.

Design/methodology/approach

Focussing on a landmark historical curriculum document from 1911, this paper draws on methods of historical comparative and documentary analysis. It sits within the tradition of historical curriculum research that critiques curriculum documents as a primary source for understanding continuities of discourses and practices. A social constructionist approach informs the analysis.

Findings

The conceptualisation of subject English evident in the structure, content and emphases of the 1911 English syllabus encodes a range of “discourses and practices” that have in some form endured or been “reconstituted and remade” (Cormack, 2008, p. 275) over the course of a century. The analysis draws attention to those aspects of the subject that have remained unproblematised and taken-for-granted, and the implications of this for universal student participation and attainment.

Originality/value

This paper reorients critical attention to a significant historical curriculum document that has not, to date, been explored against the backdrop twenty-first century senior secondary English curriculum. In doing so, it presents extended insights into a range of now normative structures, beliefs, ideas, assumptions and practices and questions the potential impact of these on student learning, access and achievement in senior secondary English in NSW in the twenty-first century.
“Do it this way, not that way”: An exploration of Chinese workplace conflicts
Authors: Guo Yijia , Cionea Ioana A.
Published: April 2017

Purpose

This paper aims to examine the occurrence and management of conflict in Chinese organizations, from an emic perspective. The authors provide an in-depth understanding of Chinese working adults’ lived experiences regarding workplace conflicts.

Design/methodology/approach

The study is a qualitative one, consisting of open-ended questionnaires administered to 55 Chinese nationals who worked in governmental, public or international organizations in China. A thematic analysis of the answers was conducted.

Findings

Chinese participants adopted a normative mental model that defined their preferred “way of doing” things. A skillful balance was expected in conflict management that incorporated integrated open communication and strategic silence. Chinese working adults emphasized maturity in the workplace and the recognition of shared goals.

Research limitations/implications

The online questionnaire format may have constrained participants’ responses. Also, the data were collected from various organizational contexts, but there were not enough participants from each type of organization so that comparisons between institutions could be made.

Practical implications

The results could help expatriate populations better prepare their lives abroad in China. Also, the findings could aid organizational or management consultants who work closely with Chinese partners.

Social implications

The findings enhance our understanding of how Chinese working adults deal with workplace conflicts and the circumstances in which conflicts arise in the workplace, which also reflected the social and cultural contexts of the Chinese workplace experience.

Originality/value

This study provides an alternative interpretation of workplace conflicts and their management in China that is anchored in the unique organizational and national cultural context. They constitute the base for future development of culture-based explanations of Chinese organizational conflict behaviors.
International policies for sustainable development from cultural empowerment
Authors: Froner Yacy-Ara
Published: April 2017

Purpose

The purpose of this paper is to explore the international agenda regarding the discussion on the sustainable development. It asserts the idea that economic growth is a process that embraces the cultural values, human capability, and transnational policies aimed to guide and support the efforts of nations to achieve social security. The paper places the issues of contemporary heritage science theory on the recent debate concerning the cultural heritage preservation based on scientific, legal, social, and management issues.

Design/methodology/approach

The paper selected mainly reports, declarations, resolutions, and recommendations concerning this theme. The framework comprehends almost 30 years: from the first project titled “World Decade of Cultural Development” (1988) to the last conference in Tanzania (2016). Some questions defined the methodological approach of this investigation: how can we generate sustainability in terms of the use, maintenance, and conservation of cultural heritage? How can we adjust the local, national, and international guidelines to a common logic without letting go of the community autonomy?

Findings

The paper provides a historical context about the enlargement of the debate concerning the international policies for sustainable development from cultural empowerment. It suggests that UNESCO, WHC, and ICCROM have been promoting positive projects in vulnerable regions.

Research limitations/implications

Eurocentric models of development and occidental concept of culture exposure in the selected documents should be reviewed mainly in decolonization areas.

Practical implications

The article offers a distinct perspective for the system of international evaluation of cultural heritage, and a different focus of reflection for the academic community.

Originality/value

The study promotes a reflection regarding the international agenda for sustainable development over the last 30 years.
A comprehensive analysis of knowledge management in Indian manufacturing companies
Authors: Uma Mageswari S.D. , Sivasubramanian R. Chitra , Dath T.N. Srikantha
Published: April 2017

Purpose

The purpose of this paper is to ascertain the current status of knowledge management (KM) adoption in the Indian manufacturing organizations and to develop a comprehensive research model to investigate the impact of enabling conditions for KM and the impact of KM on organizational performance through structural equation modelling.

Design/methodology/approach

A descriptive research design is adopted and primary data are collected through structured questionnaire. In total, 251 responses were obtained from the top- and middle-level managers and the structural relationships in the research model were tested using the partial least squares method.

Findings

The results revealed a moderate adoption of KM by the manufacturing companies. Also, a significant impact of the enablers on KM processes is observed. It is found that Indian manufacturing is operating in labour-intensive traditional methods and KM is still in its infancy. The impact of KM on the performance is moderate and contradicting the extant literature, the impact of KM on innovation is found to be weak.

Research limitations/implications

The study is carried out in companies located in India and hence generalizing the findings should be done with caution. The sample is dominated by small- and medium-sized enterprises (SMEs) which may have implications for the findings.

Practical implications

As manufacturing companies in the developing countries such as India experience a greater competition in the globalized economy, adoption of KM will perk up the performance of the organizations. Practicing managers need to create a culture that facilitates KM adoption. Policy makers shall support SMEs in technology adoption, R&D, skill development and so on.

Originality/value

Previous KM studies in India are fragmented and analysed KM processes and KM enablers in isolation. Also, the holistic studies on KM literature focussed only on one or two facets of KM. A study which investigates the interactions between KM enablers, KM processes and organizational performance and innovation is scarce. The scarcity of empirical studies on KM and a dearth of understanding of the KM concept led to this maiden attempt to provide a comprehensive understanding of KM framework in the Indian manufacturing sector. A validated structured questionnaire for exploring KM practices in the Indian context is developed. Though the importance of the influence of external factors is theoretically emphasized, an empirical investigation is first of its kind.
Reproductive biology of Clintonia udensis
Authors: Yoshima Ayako , Ohara Masashi
Published: April 2017

To clarify the life history of Clintonia udensis, we investigated its reproductive systems and spatio‐temporal population structure. Pollination experiments and the observation of floral visitors revealed that C. udensis was compatible with both self‐ and outcross‐pollen, and it potentially produces seeds by insect‐mediated outcrossing in natural conditions. In addition, propagation by clonal reproduction from rhizomes was evident. In this study, it was clarified that C. udensis potentially propagates by sexual and asexual reproduction and maintains its population through a stable frequency of flowering. The differences in the dependence on each reproduction mode could be one of the contributing factors for creating a variety of population sizes and distribution patterns of ramets in populations.