bluuebunny/crossref_metadata_2025 huggingface dataset:
Low-dose cadmium potentiates lung inflammatory response to 2009 pandemic H1N1 influenza virus in mice
Authors: Chandler Joshua D. , Hu Xin , Ko Eunju , Park Soojin , Fernandes Jolyn , Lee Young-Tae , Orr Michael L. , Hao Li , Ryan Smith M. , Neujahr David C. , Uppal Karan , Kang Sang-Moo , Jones Dean P. , Go Young-Mi
Published: June 2018

BACKGROUND

Cadmium (Cd) is a toxic, pro-inflammatory metal ubiquitous in the diet that accumulates in body organs due to inefficient elimination. Many individuals exposed to dietary Cd are also infected by seasonal influenza virus. The H1N1 strain causes mild to severe pneumonia which can be fatal.

OBJECTIVES

To determine the influence of low-dose Cd exposure on inflammatory responses to H1N1 influenza A virus.

METHODS

We exposed mice to low-dose (1 mg CdCl2/l) Cd or vehicle (water) for 16 weeks prior to infection with a sub-lethal dose of H1N1. Lung inflammation was assessed by histopathology and flow cytometry. We used a combination of transcriptomics, metabolomics and bioinformatics to determine the molecular associations of inflammatory cells important in Cd-exacerbated responses.

RESULTS

Cd-treated mice had increased lung tissue inflammatory cells, including neutrophils, monocytes, T lymphocytes and dendritic cells, following H1N1 infection. Lung genetic responses to infection (increasing TNF-a, interferon and complement, and decreasing myogenesis) were also exacerbated. Global correlations with immune cell counts, leading edge gene transcripts and metabolites revealed that Cd increased correlation of myeloid immune cells with pro-inflammatory genes, particularly interferon-γ, and metabolites in amino acid, nucleobase, glycerophospholipid and vitamin B3 pathways.

DISCUSSION

Cd burden in mice increased inflammation in response to sub-lethal H1N1 challenge, which was coordinated by genetic and metabolic responses, and could provide new targets for intervention against lethal inflammatory pathology of clinical H1N1 infection.
Determinants of base-pair substitution patterns revealed by whole-genome sequencing of DNA mismatch repair defectiveEscherichia coli
Authors: Foster Patricia L. , Niccum Brittany A. , Popodi Ellen , Townes Jesse P. , Lee Heewook , MohammedIsmail Wazim , Tang Haixu
Published: June 2018

Mismatch repair (MMR) is a major contributor to replication fidelity, but its impact varies with sequence context and the nature of the mismatch. Mutation accumulation experiments followed by whole-genome sequencing of MMR-defectiveE. colistrains yielded ≈30,000 base-pair substitutions, revealing mutational patterns across the entire chromosome. The base-pair substitution spectrum was dominated by A:T > G:C transitions, which occurred predominantly at the center base of 5′NAC3′+5′GTN3′ triplets. Surprisingly, growth on minimal medium or at low temperature attenuated these mutations. Mononucleotide runs were also hotspots for base-pair substitutions, and the rate at which these occurred increased with run length. Comparison with ≈2000 base-pair substitutions accumulated in MMR-proficient strains revealed that both kinds of hotspots appeared in the wild-type spectrum and so are likely to be sites of frequent replication errors. In MMR-defective strains transitions were strand biased, occurring twice as often when A and C rather than T and G were on the lagging-strand template. Loss of nucleotide diphosphate kinase increases the cellular concentration of dCTP, which resulted in increased rates of mutations due to misinsertion of C opposite A and T. In anmmr ndkdouble mutant strain, these mutations were more frequent when the template A and T were on the leading strand, suggesting that lagging-strand synthesis was more error-prone or less well corrected by proofreading than was leading strand synthesis.
A Statistical Model of Cell Wall Dynamics during Expansive Growth
Authors: Sridhar S. Lalitha , Ortega J.K.E. , Vernerey F.J.
Published: June 2018

Expansive growth is a process by which walled cells found in plants, algae and fungi, use turgor pressure to mediate irreversible wall deformation and regulate their shape and volume. The molecular structure of the primary cell wall must therefore be able to perform multiple function simultaneously such as providing structural support by a combining elastic and irreversible deformation and facilitate the deposition of new material during growth. This is accomplished by a network of microfibrils and tethers composed of complex polysaccharides and proteins that are able to dynamically mediate the network topology via constant detachment and reattachment events. Global biophysical models such as those of Lockhart and Ortega have provided crucial macroscopic understanding of the expansive growth process, but they lack the connection to molecular processes that trigger network rearrangements in the wall. In this context, we propose a statistical approach that describes the population behavior of tethers that have elastic properties and the ability to break and re-form in time. Tether properties such as bond lifetimes and stiffness, are then shown to govern global cell wall mechanics such as creep and stress relaxation. The model predictions are compared with experiments of stress relaxation and turgor pressure step-up from existing literature, for the growing cells of incised pea (Pisum sativus L.), algaeChara corallinaand the sporangiophores of the fungus,Phycomyces blakesleeanus. The molecular parameters are estimated from fits to experimental measurements combined with the information on the dimensionless number Πpethat is unique to each species. To our knowledge, this research is the first attempt to use a statistical approach to model the cell wall during expansive growth and we believe it will provide a better understanding of the cell wall dynamics at a molecular level.
Identifying, understanding, and correcting technical biases on the sex chromosomes in next-generation sequencing data
Authors: Webster Timothy H. , Couse Madeline , Grande Bruno M. , Karlins Eric , Phung Tanya N. , Richmond Phillip A. , Whitford Whitney , Sayres Melissa A. Wilson
Published: June 2018

Mammalian X and Y chromosomes share a common evolutionary origin and retain regions of high sequence similarity. This sequence homology can cause the mismapping of short sequencing reads derived from the sex chromosomes and affect variant calling and other downstream analyses. Understanding and correcting this problem is critical for medical genomics and population genomic inference. Here, we characterize how sequence homology can affect analyses on the sex chromosomes and present XYalign, a new tool that: (1) facilitates the inference of sex chromosome complement from next-generation sequencing data; (2) corrects erroneous read mapping on the sex chromosomes; and (3) tabulates and visualizes important metrics for quality control such as mapping quality, sequencing depth, and allele balance. We show how these metrics can be used to identify XX and XY individuals across diverse sequencing experiments, including low and high coverage whole genome sequencing, and exome sequencing. We also show that XYalign corrects mismapped reads on the sex chromosomes, resulting in more accurate variant calling. Finally, we discuss how the flexibility of the XYalign framework can be leveraged for other use cases including the identification of aneuploidy on the autosomes. XYalign is available open source under the GNU General Public License (version 3).
New insights into human nostril microbiome from the expanded Human Oral Microbiome Database (eHOMD): a resource for the microbiome of the human aerodigestive tract
Authors: Escapa Isabel F. , Chen Tsute , Huang Yanmei , Gajare Prasad , Dewhirst Floyd E. , Lemon Katherine P.
Published: June 2018

The expanded Human Oral Microbiome Database (eHOMD) is a comprehensive microbiome database for sites along the human aerodigestive tract that revealed new insights into the nostril microbiome. The eHOMD provides well-curated 16S rRNA gene reference sequences linked to available genomes and enables assignment of species-level taxonomy to most NextGeneration sequences derived from diverse aerodigestive tract sites, including the nasal passages, sinuses, throat, esophagus and mouth. Using Minimum Entropy Decomposition coupled with the RDP Classifier and our eHOMD V1-V3 training set, we reanalyzed 16S rRNA V1-V3 sequences from the nostrils of 210 Human Microbiome Project participants at the species level revealing four key insights. First, we discovered that Lawsonella clevelandensis, a recently named bacterium, and Neisseriaceae [G-1] HMT-174, a previously unrecognized bacterium, are common in adult nostrils. Second, just 19 species accounted for 90% of the total sequences from all participants. Third, one of these 19 belonged to a currently uncultivated genus. Fourth, for 94% of the participants, two to ten species constituted 90% of their sequences, indicating nostril microbiome may be represented by limited consortia. These insights highlight the strengths of the nostril microbiome as a model system for studying interspecies interactions and microbiome function. Also, in this cohort, three common nasal species (Dolosigranulum pigrum and two Corynebacterium species) showed positive differential abundance when the pathobiont Staphylococcus aureus was absent, generating hypotheses regarding colonization resistance. By facilitating species-level taxonomic assignment to microbes from the human aerodigestive tract, the eHOMD is a vital resource enhancing clinical relevance of microbiome studies.

IMPORTANCE

The eHOMD (ehomd.org) is a valuable resource for researchers, from basic to clinical, who study the microbiomes, and the individual microbes, in health and disease of body sites in the human aerodigestive tract, which includes the nasal passages, sinuses, throat, esophagus and mouth, and the lower respiratory tract. The eHOMD is an actively curated, web-based, open-access resource. eHOMD provides the following: (1) species-level taxonomy based on grouping 16S rRNA gene sequences at 98.5% identity, (2) a systematic naming scheme for unnamed and/or uncultivated microbial taxa, (3) reference genomes to facilitate metagenomic, metatranscriptomic and proteomic studies and (4) convenient cross-links to other databases (e.g., PubMed and Entrez). By facilitating the assignment of species names to sequences, the eHOMD is a vital resource for enhancing the clinical relevance of 16S rRNA gene-based microbiome studies, as well as metagenomic studies.
Re-evaluating the salty divide: phylogenetic specificity of transitions between marine and freshwater systems
Authors: Paver Sara F. , Muratore Daniel J. , Newton Ryan J. , Coleman Maureen L.
Published: June 2018

Marine and freshwater microbial communities are phylogenetically distinct and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages exhibiting notably high or low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA gene tag-sequencing datasets. As expected, marine and freshwater microbial communities differed in the relative abundance of major phyla and contained habitat-specific lineages; at the same time, however, many shared taxa were observed in both environments. Betaproteobacteria and Alphaproteobacteria sequences had the highest similarity between marine and freshwater sample pairs. Gammaproteobacteria and Alphaproteobacteria contained the highest number of Minimum Entropy Decomposition nodes shared by marine and freshwater samples. Shared nodes included lineages of the abundant alphaproteobacterial group SAR11 that have not previously been reported in 16S rRNA gene surveys of freshwater lakes. Our results suggest that shared taxa are numerous, but tend to occur sporadically and at low relative abundance in one habitat type, leading to an underestimation of transition frequency between marine and freshwater habitats. Lineages with a high degree of shared taxa or habitat-specific diversification represent targets for genome-scale investigations into microbial adaptations and evolutionary innovations. Rare taxa with abundances near or below detection, including lineages that appear to have crossed the salty divide relatively recently, may have novel adaptations enabling them to exploit opportunities for niche expansion when environments are disturbed or conditions change.

Importance

The distribution of microbial diversity across environments yields insight into processes that create and maintain this diversity as well as potential to infer how communities will respond to future environmental changes. We integrated datasets from dozens of freshwater lake and marine samples to compare diversity across open water habitats differing in salinity. Our novel combination of sequence-based approaches revealed phyla and proteobacterial classes inferred to include more or less recent transitions across habitat types as well as specific lineages that are shared by marine and freshwater environments at the level of 16S rRNA sequence types. Our findings contribute to understanding the ecological and evolutionary controls on microbial distributions, and open up new questions regarding the plasticity and adaptability of particular lineages.
A metapopulation model of the spread of the Devil Facial Tumour Disease predicts the long term collapse of its host but not its extinction
Authors: Siska Veronika , Eriksson Anders , Mehlig Bernhard , Manica Andrea
Published: June 2018

The Devil Facial Tumour Disease (DFTD), a unique case of a transmissible cancer, had a devastating effect on its host, the Tasmanian Devil. Current estimates of its density are at roughly 20% of the pre-disease state, and single-population epidemiological models have predicted the likely extinction of the host. Here we take advantage of extensive surveys across Tasmania providing data on the spatial and temporal spread of DFTD, and investigate the dynamics of this host-pathogen system using a spatial metapopulation model. We first confirm a most likely origin of DFTD in the north-east corner of the island, and then use the inferred dynamics to predict the fate of the species. We find that our medium-term predictions match additional data not used for fitting, and that on the longterm, Tasmanian Devils are predicted to coexist with the tumour. The key process allowing persistence is the repeated reinvasion of extinct patches from neighbouring areas where the disease has flared up and died out, resulting in a dynamic equilibrium with different levels of spatial heterogeneity. However, this dynamic equilibrium is predicted to keep this apex predator at about 9 % of its original density, with possible dramatic effects on the Tasmanian ecosystem.
Aerobic removal of microcystin-LR by a novel native effective bacterial community designated as YFMCD4 isolated from Lake Taihu
Authors: Yang Fei , Guo Jian , Huang Feiyu , Massey Isaac Yaw , Huang Ruixue , Ding Ping , Zeng Weiming
Published: June 2018

Microcystins (MCs) are a group of monocyclic heptapeptide hepatotoxins produced by species of cyanobacteria. MC-LR is the most toxic and frequently detected MCs variant in water, which poses a great threat to the natural ecosystem and public health. It’s important to seek environment-friendly and cost-efficient methods to remove MC-LR. To investigate the MC-degrading capacities of a novel indigenous bacterial community designated as YFMCD4 and the influence of environmental factors including various temperatures, MC concentrations and pH on the MC-degrading activities, the concentration of MC-LR was measured by high performance liquid chromatography. In addition, the MC-degrading mechanism containing the degradation pathway and products of YFMCD4 was studied using HPLC coupled with an ultra-high resolution LTQ Orbitrap Velos Pro ETD mass spectrometry equipped with electrospray ionization interface. The data showed MC-LR can be removed at the maximum rate of 0.5 µg/(ml·h) by YFMCD4 containingAlcaligenes faecalisandStenotrophomonas acidaminiohila. The MC-degrading rates of YFMCD4 were significantly affected by different temperatures, pH and MC-LR concentrations. Two intermediates of a tetrapeptide and Adda appeared in the degradation process. These results illustrate that the novel bacterial community YFMCD4 can remove MC-LR effectively and completely, which indicates YFMCD4 possesses a significant potential to be used in bioremediation of water bodies contaminated by MC-LR.
High-fat diet suppresses the positive effect of creatine supplementation on skeletal muscle function by reducing protein expression of IGF-PI3K-AKT-mTOR pathway
Authors: Ferretti Renato , Moura Eliezer Guimarães , Carvalho dos Santos Veridiana , Caldeira Eduardo José , Conte Marcelo , Matsumura Cintia Yuri , Pertille Adriana , Mosqueira Matias
Published: June 2018

High-fat (HF) diets in combination with sedentary lifestyle represent one of the major public health concerns predisposing to obesity and diabetes leading to skeletal muscle atrophy, decreased fiber diameter and muscle mass with accumulation of fat tissue resulting in loss of muscle strength. One strategy to overcome the maleficent effects of HF diet is resistance training, a strategy used to improve muscle mass, reverting the negative effects on obesity-related changes in skeletal muscle. Together with resistance training, supplementation with creatine monohydrate (CrM) in the diet has been used to improve muscle mass and strength. Creatine is a non-essential amino acid that is directly involved in the cross-bridge cycle providing a phosphate group to ADP during the initiation of muscle contraction. Besides its antioxidant and anti-inflammatory effects CrM also upregulates IGF-1 resulting in hyperthophy with an increase in muscle function. However, it is unknown whether CrM supplementation during resistance training would revert the negative effects of high-fat diet on the muscle performance. During 8 weeks we measured muscle performance to climb a 1.1m and 80° ladder with increasing load on trained rats that had received standard diet or high-fat diet, supplemented or not with CrM. We observed that the CrM supplementation up-regulated IGF-1 and phospho-AKT protein levels, suggesting an activation of the IGF1-PI3K-Akt/PKB-mTOR pathway. Moreover, despite the CrM supplementation, HF diet down-regulated several proteins of the IGF1-PI3K-Akt/PKB-mTOR pathway, suggesting that diet lipid content is crucial to maintain or improve muscle function during resistance training.
Facility delivery and postnatal care services use among mothers who attended four or more antenatal care visits in Ethiopia: further analysis of the 2016 Demographic and Health Survey
Authors: Fekadu Gedefaw Abeje , Getahun Fentie Ambaw , Kidanie Seblewongiel Ayenalem
Published: June 2018

Introduction

In Ethiopia, many mothers who attend the recommended number of antenatal care visits fail to use facility delivery and postnatal care services. This study identifies factors associated with facility delivery and use of postnatal care among mothers who had four or more antenatal care visits, using data from the 2016 Ethiopian Demographic and Health Survey (EDHS).

Methods

To identify factors associated with facility delivery, we studied background and service-related characteristics among 2,415 mothers who attended four or more antenatal care visits for the most recent birth. In analyzing factors associated with postnatal care within 42 days after delivery, the study included 1,055 mothers who attended four or more antenatal care visits and delivered at home. We focused on women who delivered at home because women who deliver at a health facility are more likely also to receive postnatal care as well. A multivariable logistic regression model was fitted for each outcome to find significant associations between facility delivery and use of postnatal care.

Results

Fifty-six percent of women who had four or more antenatal care visits delivered at a health facility, while 44% delivered at home. Mothers with secondary or above level of education, urban residents, women in the richest wealth quintile, and women who were working at the time of interview had higher odds of delivering in a health facility. High birth order was associated with a lower likelihood of health facility delivery. Among women who delivered at home, only 8% received postnatal care within 42 days after delivery. Quality of antenatal care as measured by the content of care received during antenatal care visits stood out as an important factor that influences both facility delivery and postnatal care. Among mothers who attended four or more antenatal care visits and delivered at home, the content of care received during ANC visits was the only factor that showed a statistically significant association with receiving postnatal care.

Conclusions

The more antenatal care components a mother receives, the higher her probability of delivering at a health facility and of receiving postnatal care. The health care system needs to increase the quality of antenatal care provided to mothers because receiving more components of antenatal care is associated with increased health facility delivery and postnatal care. Further research is recommended to identify other reasons why many women do not use facility delivery and postnatal care services even after attending four or more antenatal care visits.
Mutations in nucleoporinNUP88cause lethal neuromuscular disorder
Authors: Bonnin Edith , Cabochette Pauline , Filosa Alessandro , Jühlen Ramona , Komatsuzaki Shoko , Hezwani Mohammed , Dickmanns Achim , Martinelli Valérie , Vermeersch Marjorie , Supply Lynn , Martins Nuno , Pirenne Laurence , Ravenscroft Gianina , Lombard Marcus , Port Sarah , Spillner Christiane , Janssens Sandra , Roets Ellen , Dorpe Jo Van , Lammens Martin , Kehlenbach Ralph H. , Ficner Ralf , Laing Nigel , Hoffmann Katrin , Vanhollebeke Benoit , Fahrenkrog Birthe
Published: June 2018

Nucleoporins build the nuclear pore complex (NPC), which, as sole gate for nuclear-cytoplasmic exchange, are of outmost importance for normal cell function. Defects in the process of nucleocytoplasmic transport or in its machinery have been frequently described in human diseases, such as cancer and neurodegenerative disorders, but only in a few cases of developmental disorders. Here we report biallelic mutations in the nucleoporinNUP88as a novel cause of lethal fetal akinesia deformation sequence (FADS) in two families. FADS comprises a spectrum of clinically and genetically heterogeneous disorders with congenital malformations related to impaired fetal movement. We show that genetic disruption ofnup88in zebrafish results in pleiotropic developmental defects reminiscent of those seen in affected human fetuses, including locomotor defects as well as defects at neuromuscular junctions. Phenotypic alterations become visible at distinct developmental stages, both in affected human fetuses and in zebrafish, whereas early stages of development are apparently normal. The zebrafish phenotypes caused by nup88 deficiency are only rescued by expressing wild-type nup88 and not the disease-linked mutant forms of nup88. Furthermore, using human and mouse cell lines as well as immunohistochemistry on fetal muscle tissue, we demonstrate that NUP88 depletion affects rapsyn, a key regulator of the muscle nicotinic acetylcholine receptor at the neuromuscular junction. Together, our studies provide the first characterization of NUP88 in vertebrate development, expand our understanding of the molecular events causing FADS, and suggest that variants inNUP88should be investigated in cases of FADS.
Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia
Authors: Arias Leonardo , Schröder Roland , Hübner Alexander , Barreto Guillermo , Stoneking Mark , Pakendorf Brigitte
Published: June 2018

Human populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the non-recombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native-American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic-exogamy, a marital practice in which men are required to marry women speaking a different language.

We identified 2,969 SNPs in the NRY sequences; only 925 SNPs were previously described. The NRY and mtDNA data showed that males and females experienced different demographic histories: the female effective population size has been larger than that of males through time, and both markers show an increase in lineage diversification beginning ~5,000 years ago, with a male-specific expansion occurring ~3,500 years ago. These dates are too recent to be associated with agriculture, therefore we propose that they reflect technological innovations and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, our study provides evidence of the impact of postmarital residence rules and linguistic exogamy on genetic diversity patterns. Finally, we highlight the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between males and females.
Bayesian inference of ancestral dates on bacterial phylogenetic trees
Authors: Didelot Xavier , Croucher Nicholas J , Bentley Stephen D , Harris Simon R , Wilson Daniel J
Published: June 2018

The sequencing and comparative analysis of a collection of bacterial genomes from a single species or lineage of interest can lead to key insights into its evolution, ecology or epidemiology. The tool of choice for such a study is often to build a phylogenetic tree, and more specifically when possible a dated phylogeny, in which the dates of all common ancestors are estimated. Here we propose a new Bayesian methodology to construct dated phylogenies which is specifically designed for bacterial genomics. Unlike previous Bayesian methods aimed at building dated phylogenies, we consider that the phylogenetic relationships between the genomes have been previously evaluated using a standard phylogenetic method, which makes our methodology much faster and scalable. This two-steps approach also allows us to directly exploit existing phylogenetic methods that detect bacterial recombination, and therefore to account for the effect of recombination in the construction of a dated phylogeny. We analysed many simulated datasets in order to benchmark the performance of our approach in a wide range of situations. Furthermore, we present applications to three different real datasets from recent bacterial genomic studies. Our methodology is implemented in a R package called BactDating which is freely available for download athttps://github.com/xavierdidelot/BactDating.
SqueezeMeta, a highly portable, fully automatic metagenomic analysis pipeline
Authors: Tamames Javier , Puente-Sánchez Fernando
Published: June 2018

The improvement of sequencing technologies has allowed the generalization of metagenomic sequencing, which has become a standard procedure for analysing the structure and functionality of microbiomes. The bioinformatic analysis of the sequencing results poses a challenge because it involves many different complex steps. SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes via binning procedures. SqueezeMeta features several unique characteristics: Co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of the abundances of genes in each metagenome. It also includes binning and bin checking for retrieving individual genomes. Internal checks for the assembly and binning steps inform about the consistency of contigs and bins. Also, the results are stored in a mySQL database, where they can be easily exported and shared, and can be inspected anywhere using a flexible web interface allowing the easy creation of complex queries.

We illustrate the potential of SqueezeMeta by analyzing 32 gut metagenomes in a fully automatic way, allowing to retrieve several millions of genes and several hundreds of genomic bins.

One of the motivations in the development of SqueezeMeta was producing a software capable to run in small desktop computers, thus being amenable to all users and all settings. We were also able to co-assemble two of these metagenomes and complete the full analysis in less than one day using a simple laptop computer, illustrating the capacity of SqueezeMeta to run without high-performance computing infrastructure. SqueezeMeta is a complete system covering all steps in the analysis of metagenomes and metatranscriptomes, capable to work even in scarcity of computational resources. It is therefore adequate for in-situ, real time analysis of metagenomes produced by nanopore sequencing.

SqueezeMeta can be downloaded from https://github.com/jtamames/SqueezeMeta
Mind-wandering in Parkinson’s disease hallucinations reflects primary visual and default network coupling
Authors: Walpola Ishan C. , Muller Alana J. , Hall Julie M. , Andrews-Hanna Jessica R. , Irish Muireann , Lewis Simon J. G. , Shine James M. , O’Callaghan Claire
Published: June 2018

A mismatch between top-down expectations and incoming sensory information is thought to be associated with hallucinations across a range of neuropsychiatric disorders. In Parkinson’s disease with visual hallucinations, abnormal activity within the default network, and its pattern of connectivity with early visual regions, has been identified as a potential pathological source of the internally generated expectations that override incoming sensory input. In the context of attention deficits and visual dysfunction, mental imagery and perceptual expectancies generated across the default network are suggested to exert excessive influence over earlier visual regions, leading to aberrant perceptual experiences. Whilst converging neuroimaging evidence has identified unconstrained default network activity in Parkinson’s disease with hallucinations, to date there has been a lack of behavioural evidence to confirm the consequences of an over-engaged default mode network – therefore the contributions it might make to hallucination phenomenology remain speculative. To address this, we administered a validated thought-sampling task to 38 Parkinson’s disease patients (18 with hallucinations; 20 without) and 40 controls, to test the hypothesis that individuals with hallucinations experience an increased frequency of mind-wandering – a form of spontaneous cognition strongly associated with mental imagery and default network activity. The neural correlates of mind-wandering frequency were examined in relation to resting-state functional connectivity. Our results showed that patients with hallucinations exhibited significantly higher mind-wandering frequencies compared to non-hallucinators, who in turn had reduced levels of mind-wandering relative to controls. Inter-network connectivity and seed-to-voxel analyses confirmed that increased mind-wandering in the hallucinating vs. non-hallucinating group was associated with greater coupling between the primary visual cortex and dorsal default network. Taken together, both elevated mind-wandering and increased default-visual network coupling emerged as a distinguishing feature of the hallucinatory phenotype. We propose that the finding of increased mind-wandering reflects unconstrained spontaneous thought and mental imagery, which in turn furnish the content of visual hallucinations. Our findings suggest that primary visual cortex to dorsal default network coupling may provide a neural substrate by which regions of the default network exert disproportionate influence over ongoing visual perception. These findings refine current models of visual hallucinations by identifying a specific cognitive phenomenon and neural substrate consistent with the top-down influences over perception that have been implicated in visual hallucinations.
Supporting progression to HE: the role of colleges and vocational courses
Authors: Gartland Clare Elizabeth , Smith Christine
Published: June 2018

Purpose

Vocational courses in England support the progression to higher education (HE) of large numbers of young people from disadvantaged backgrounds, yet there is little research exploring the college experiences of these young people prior to entering university. The purpose of this paper is to consider the experiences of young people on Level 3 Business and Technology Education Council (BTEC) vocational courses in their progression to HE from differently positioned post-16 colleges in England.

Design/methodology/approach

A qualitative study was undertaken into the experiences of students on BTEC courses in four subject clusters (science, technology, engineering and maths, arts and humanities, social sciences and health) at both a Further Education College and a Sixth Form College in an area of multiple deprivation and low HE participation. Young people’s experiences of BTEC courses and the support and guidance they receive are explored through the conceptual lens of “possible selves” and using Bourdieu’s ideas of capital, habitus and field.

Findings

Pedagogies and practices on BTEC courses are found to support the development of relevant social and cultural capital and help young people formulate well-articulated “possible selves” as university students, even amongst students who previously had not considered university as an option. The findings illustrate how differently positioned colleges support students’ progression and identify challenges presented by an increasingly stratified and marketised system.

Originality/value

The study highlights the transformative potential of BTEC courses and their role in supporting progression to HE amongst young people from economically disadvantaged backgrounds. The current emphasis on standardisation and rigour as mechanisms to better equip students for HE neglects the unique contribution BTEC pedagogies and practices make to encouraging HE participation. A Bourdieusian and “possible selves” theoretical framework has provided new insights into these valuable learning processes.
Entrepreneurial orientation
Authors: Smith Brent , Jambulingam Thanigavelan
Published: June 2018

Purpose

Scholarship in the entrepreneurship and marketing literatures has helped advance thinking about how health care organizations create value for companies and consumers. However, there is an ongoing need for empirical research; hence, the purpose of this paper is to examine how entrepreneurial orientation and customer orientation influence healthcare (retail pharmacy) industry performance.

Design/methodology/approach

Using a sample of the US retail pharmacies, the study applies partial least squares structural equation modeling to identify the direct and indirect effects of the entrepreneurial orientation constructs on company performance. The study also includes importance–performance analyses to prioritize for managers which orientations, dimensions and respective manifest items merit the most critical attention as contributors to pharmacy performance.

Findings

We find that the entrepreneurial orientation has a significant impact on customer orientation and company effectiveness. We also find that three dimensions – innovation, risk-taking, and proactiveness – exhibit stronger importance and performance than autonomy and competitive aggressiveness.

Research limitations/implications

While the present study employs data from firms of various sizes, it is limited to firms in the pharmacy industry. Although this study included established EO measures, one of the risk taking items was dropped from the final analysis. In certain research contexts, this result may or may not be consequential. Finally, this study employed nonfinancial measures for measuring performance. Using such measures is not uncommon and can offer insightful linkages to long-term organizational strategies in ways not afforded by conventional financial measures (Ittner and Larcker 2000); however, future research should, if possible, aim to capture financial and nonfinancial data.

Practical implications

In the dynamic healthcare environment, entrepreneurial pharmacies that have the ability to innovate, take risks and be proactive can provide superior customer orientation and hence better performance.

Social implications

Health care industry in general and pharmacies in particular have to be entrepreneurial to meet customer needs and hence the wellbeing of the society With the aging population and growth of complex diseases, pharmacies can provide better access to care delivery if they have entrepreneurial orientation.

Originality/value

In this study, partial least square modeling technique along with importance performance analysis was adopted for first time in this literature to identify key factors that contribute to EO. The findings will aid pharmacy managers to focus their initiatives on the three key dimensions to succeed in their retail pharmacy business.
The trade and income effects of RCEP: implications for China and Korea
Authors: Li Qiaomin , Moon Hee Cheol
Published: June 2018

Purpose

The purpose of this paper is to simulate the effects of the Regional Comprehensive Economic Partnership (RCEP) on trade and income, with a particular interest in the effect on China and Korea.

Design/methodology/approach

This paper adopts a Computable General Equilibrium (CGE) model developed by Li et al. (2017) to simulate the effect of RCEP. The CGE model is grounded in the firm heterogeneity theory. Within this framework, the feature of dynamic movements of firms allows the CGE model to capture the extensive margin of trade increase. Aside from that, the CGE model separates foreign direct investment (FDI) from domestic investment, which helps to explain the effect of the removal of FDI barriers.

Findings

Results show that RCEP will increase trade of China by 1.5 percent. The income of China will increase by 2.5 percent. The trade increase of Korea will be $8bn, and its income will increase by 0.6 percent. In terms of welfare, China will gain $214bn and Korea will gain $23~35bn, taking 2~3 percent of Korea’s GDP. Also, the reduction of behind-the-border barriers presents very significant effects.

Originality/value

The main contribution of this paper is to quantitatively assess the potential effects of RCEP on trade and income. The positive findings would propel RCEP parties, especially China and Korea, to reach an agreement as soon as possible.
From “clientilism” to transformational leadership? An autoethnographic journey from Soviet Georgia to the UK
Authors: Beattie Liana
Published: June 2018

Purpose

The purpose of this paper is to contribute to the ethnographic tradition in the educational leadership literature through providing an autoethnographic critical analysis of the idiosyncrasies of leadership across two different socio-political environments: a Soviet educational establishment and a contemporary UK higher education institution.

Design/methodology/approach

In a previous issue, Doloriert and Sambrook (2012) argued that autoethnographic approach could help to uncover some experiences and voices that previously were silenced due to the discomfort they caused. In response to this claim and with consideration of three epistemological possibilities of autoethnography as suggested by Doloriert and Sambrook (2012), the author uses narrative accounts of personal experiences of leadership in Soviet Georgia and in the UK as the main source of data in the attempt to demonstrate how the three epistemological positions overlap and complement each other in the context of a critical autoethnography.

Findings

The paper argues that autoethnographic approach can provide a unique opportunity for a simultaneous analysis of the particularities of leadership practice across different socio-political environments, whereas the “three positions” approach could be used as an expedient template for further exploration of educational leadership. The paper also suggests there are some parallels between current leadership practice in the UK higher education and Soviet system of “clientilism”.

Originality/value

This paper is one of the first attempts to use autoethnography as an analytical tool for comparing leadership patterns in two contrasting socio-political structures.
How CSR impact meaning of work and dysfunctional customer behavior
Authors: Kim Jiyoung , Kim Hae-Ryong , Lacey Russell , Suh Jaebeom
Published: June 2018

Purpose

The purpose of this paper is to investigate how frontline service employees’ (FSEs) perceptions of corporate social responsibility (CSR) can enhance meaningful work perceptions as well as help alleviate FSEs’ perceptions of verbal dysfunctional customer behavior.

Design/methodology/approach

The conceptual model is empirically examined through a survey of 306 FSEs of a large insurance company in South Korea and tested via structural equation modeling.

Findings

The results indicate that FSEs’ perceptions of CSR are negatively related to their perceptions of verbal dysfunctional customer conduct, which in turn is shown to be directly linked to emotional exhaustion. FSEs’ CSR perceptions strengthen their view that they are performing meaningful work (i.e. perceived task significance), which in turn strengthens their job satisfaction.

Practical implications

CSR has a preventive effect on workplace stress reduction, as FSE perceptions of CSR may help them cope with the emotional fatigue of dealing with dysfunctional customer behavior. CSR also provides a needs fulfillment effect, as FSEs’ perceptions of CSR foster perceived task significance and helps reduce their emotional exhaustion from work.

Originality/value

This is the first study to examine the potential impact of CSR within the context of FSEs’ boundary spanning emotional labor.
SME ambidexterity during economic recessions: the role of managerial external capabilities
Authors: Alcalde-Heras Henar , Iturrioz-Landart Cristina , Aragon-Amonarriz Cristina
Published: June 2018

Purpose

Most literature on ambidexterity has focused on large firms and on the influence of internal issues in this strategy, that is, organizational structures, top management integration, or internal knowledge management processes (Lutbatkinet al., 2006; Chang et al., 2011; Lee and Huang, 2012). The purpose of this paper is to assess small- to medium-sized enterprises (SMEs)’ ambidexterity strategies during economic recession periods in comparison with those of large firms and identify the managerial external capabilities which are associated with the development of SMEs’ ambidexterity.

Design/methodology/approach

A multinomial logit model and a probit model are proposed and tested using data collected from 2,150 Spanish firms during the period of 2009-2013.

Findings

The data analysis reveals that SMEs develop more ambidextrous innovation strategies in recession periods than larger firms do. Moreover, two managerial external capabilities have been identified as drivers of SMEs’ ambidextrous behavior in crisis periods: first, the capability of top management to anticipate scenarios; and second, the capacity to acquire adequate external resources through co-operation.

Practical implications

The results show that SME managers wanting to develop ambidextrous strategies in recession periods have to forecast scenarios in terms of innovation difficulties and strengthen their resources through co-operation. Implementation of public policy is encouraged to support these capabilities, thus enhancing SME sustainability in uncertain contexts.

Originality/value

Prior studies have paid little attention to the role of external capabilities. Although their role was revealed as a relevant dimension in the study of SME ambidexterity in adverse contexts by Caoet al.(2010), it remained underexplored. This paper aims to fill this gap.
Public–Private Partnerships and the Design Process: Consequences for Architects and City Building
Authors: van den Hurk Martijn , Siemiatycki Matti
Published: June 2018

Governments are increasingly using public–private partnerships (PPPs) to deliver public infrastructures and facilities. The prime motivation to embark on these partnerships is often to deliver products and services on time and on budget. It is generally assumed that by transferring project risks and responsibilities to private‐sector actors, governments can achieve better value for money. This article provides a novel perspective on the standards applied in PPP endeavors as it examines the tensions between the public management rationale behind value for money on the one hand, and conceptions of design and city building on the other. We focus on planning practice in the Canadian province of Ontario to show that governments apply different understandings of value in PPPs which, in turn, affect the way the design process is run. Architects, who are used to playing the role of master builder in a traditional public infrastructure project, are shifted into a less influential position and struggle with their new role. Furthermore, a different set of priorities applies in the new procurement process. The increasing use of PPPs can thus have significant consequences for city building.
Surgery in ovarian cancer – Brazilian Society of Surgical Oncology consensus
Authors: Tsunoda AT , Ribeiro R , Reis RJ , da Cunha Andrade CEM , Moretti Marques R , Baiocchi G , Fin F , Zanvettor PH , Falcao D , Batista TP , Azevedo BRB , Guitmann G , Pessini SA , Nunes JS , Campbell LM , Linhares JC , Carneiro V , Coimbra FJF
Published: June 2018

Surgical management in epithelial ovarian cancer (EOC) has a significant impact in overall survival and progression‐free survival. The Brazilian Society of Surgical Oncology (BSSO) supported a taskforce of experts to reach a consensus: experienced and specialised trained surgeons, in cancer centres, provide the best EOC surgery. Laparoscopic and/or radiological staging prognosticates the possibility of complete cytoreduction (CC0) and helps to reduce unnecessary laparotomies. Surgical techniques were reviewed. Multidisciplinary input is essential for treatment planning. Quality assurance criteria are proposed and require national consensus. Genetic testing is mandatory. This consensus states the final recommendations from BSSO for management of EOC.

Tweetable abstract

Brazilian Society of Surgical Oncology consensus for surgery in epithelial ovarian cancer patients.