bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic variation/evolution and differential host responses resulting from in-patient adaptation ofMycobacterium avium
Authors: Kannan N. , Lai Y.-P. , Haug M. , Lilleness M. K. , Bakke S. S. , Marstad A. , Hov H. , Naustdal T. , Afset J. E. , Ioerger T. R. , Flo T. H. , Steigedal M.
Published: April 2018

Mycobacterium avium(Mav) complex (MAC) are characterized as non-tuberculosis mycobacteria and are pathogenic mainly in immunocompromised individuals. MAC strains show a wide genetic variability, and there is growing evidence suggesting that genetic differences may contribute to a varied immune response that may impact on the infection outcome. The current study aimed to characterize the genomic changes within Mav isolates collected from single patients over time and test the host immune responses to these clinical isolates. Pulsed field gel electrophoresis and whole genome sequencing was performed on 40 MAC isolates isolated from 15 patients at the Department of Medical Microbiology at St. Olavs Hospital in Trondheim, Norway. Patients (4, 9 and 13) who contributed more than two isolates were selected for further analysis. These isolates exhibited extensive sequence variation in the form of single nucleotide polymorphisms (SNPs), suggesting that Mav accumulates mutations at high rates during persistent infections. Infection of murine macrophages and mice with sequential isolates from patients showed a tendency towards increased persistence and down-regulation of inflammatory cytokines by host-adapted Mav strains. The study revealed rapid genetic evolution of Mav in chronically infected patients accompanied with change in virulence properties of the sequential mycobacterial isolates.

IMPORTANCE

MAC are a group of opportunistic pathogens, consisting of Mav andM. intracellularespecies. Mav is found ubiquitously in the environment. In Mav infected individuals, Mav has been known to persist for long periods of time, and anti-mycobacterial drugs are unable to effectively clear the infection. The continued presence of the bacteria, could be attributed to either a single persistent strain or reinfection with the same or different strain. We examined sequential isolates collected over time from Mav infected individuals and observed that most patients carried the same strain overtime and were not re infected. We observed high rates of mutation within the serial isolates, accompanied with changes in virulence properties. In the light of increase in incidence of MAC related infections, this study highlights the possibility that host adapted Mav undergo genetic modifications to cope with the host environment and thereby persisting longer.
TAC-seq: targeted DNA and RNA sequencing for precise biomarker molecule counting
Authors: Teder Hindrek , Koel Mariann , Paluoja Priit , Jatsenko Tatjana , Rekker Kadri , Laisk-Podar Triin , Kukuškina Viktorija , Velthut-Meikas Agne , Žilina Olga , Peters Maire , Kere Juha , Salumets Andres , Palta Priit , Krjutškov Kaarel
Published: April 2018

Targeted next-generation sequencing based biomarker detection methods have become essential for biomedical diagnostics. In addition to their sensitivity and high-throughput capacity, absolute molecule counting based on unique molecular identifier (UMI) has high potential to increase biomarker detection accuracy even further through the reduction of systematic technical biases. Here, we present TAC-seq, a simple and cost-effective targetedallelecounting bysequencing method that uses UMIs to estimate the original molecule counts of different biomarker types like mRNAs, microRNAs and cell-free DNA. We applied TAC-seq in three different applications and compared the results with standard sequencing technologies. RNA samples extracted from human endometrial biopsies were analyzed using previously described 57 mRNA-based receptivity biomarkers and 49 selected microRNAs at different expression levels. Cell-free DNA aneuploidy testing was based on cell line (47,XX,+21) genomic DNA. TAC-seq mRNA biomarker profiling showed identical clustering results to full transcriptome RNA sequencing, and microRNA detection demonstrated significant reduction in amplification bias, allowing to determine minor expression changes between different samples that remained undetermined by standard sequencing. The mimicking experiment for cell-free DNA fetal aneuploidy analysis showed that TAC-seq can be applied to count highly fragmented DNA, detecting significant (p=4.8×10−11) excess of molecules in case of trisomy 21. Based on three proof-of-principle applications we show that TAC-seq is a highly accurate and universal method for targeted nucleic acid biomarker profiling.
Evolution of the latitudinal diversity gradient in the hyperdiverse ant genus Pheidole
Authors: Economo Evan P. , Huang Jen-Pan , Fischer Georg , Sarnat Eli M. , Narula Nitish , Janda Milan , Guénard Benoit , Longino John T. , Knowles L. Lacey
Published: April 2018

Aim

The latitudinal diversity gradient is the dominant pattern of life on Earth, but a consensus understanding of its origins has remained elusive. The analysis of recently diverged, hyper-rich invertebrate groups provides an opportunity to investigate latitudinal patterns with the statistical power of large trees while minimizing potentially confounding variation in ecology and history. Here, we synthesize global phylogenetic and macroecological data on a hyperdiverse (>1100 species) ant radiation, Pheidole, and evaluate the roles of three general explanations for the latitudinal gradient: variation in diversification rate, tropical conservatism, and ecological regulation.

Location

Global.

Time Period

The past 35 million years.

Major taxa studied

The hyperdiverse ant genus Pheidole Westwood.

Methods

We assembled geographic data for 1499 species and morphospecies, and inferred a dated phylogeny of Pheidole of 449 species, including 150 species newly sequenced for this study. We tested correlations between diversification rate and latitude with BAMM, HiSSE, GeoSSE, and FiSSE, and examined patterns of diversification as Pheidole spread around the globe.

Results

We found that Pheidole diversification occurred in series of bursts when new continents were colonized, followed by a slowdown in each region. There was no evidence of systematic variation of net diversification rates with latitude across any of the methods. Additionally, we found latitudinal affinity is moderately conserved with a Neotropical ancestor and phylogenetic inertia alone is sufficient to produce the gradient pattern.

Main Conclusions

Overall our results are consistent with tropical conservatism explaining the diversity gradient, while providing no evidence that diversification rate varies systematically with latitude. There is evidence of ecological regulation on continental scales through the pattern of diversification after colonization. These results shed light on the mechanisms underlying the diversity gradient, while contributing toward a much-needed invertebrate perspective on global biodiversity dynamics.
The Effect of Productive HPV16 Infection on Global Gene Expression of Cervical Epithelium
Authors: Kang Sa Do , Chatterjee Sreejata , Alam Samina , Salzberg Anna C. , Milici Janice , Burg Sjoerd H. van der , Meyers Craig
Published: April 2018

Human papillomavirus (HPV) infection is the world’s most common sexually transmitted infection, and is responsible for most cases of cervical cancer. Previous studies of global gene expression changes induced by HPV infection have focused on the cancerous stages of infection, and therefore, not much is known about global gene expression changes at early pre-neoplastic stages of infection. We show for the first time, global gene expression changes of early stage HPV16 infection in cervical tissue using 3-dimensional organotypic raft cultures that produce high levels of progeny virions.

cDNA microarray analysis showed that a total of 594 genes were upregulated and 651 genes were downregulated at least 1.5-fold with HPV16 infection. Gene ontology analysis showed that biological processes including cell cycle progression and DNA metabolism were upregulated, while skin development, immune response, and cell death were downregulated with HPV16 infection in cervical keratinocytes. Individual genes were selected for validation at the transcriptional and translational levels including UBC, which was central to the protein association network of immune response genes, and top downregulated genes RPTN, SERPINB4, KRT23, and KLK8. In particular, KLK8 and SERPINB4 have shown to be upregulated in cancer, which contrasts our results.

Organotypic raft cultures that allow full progression of the HPV life-cycle have allowed us to identify novel gene modulations and potential therapeutic targets of early stage HPV infection in cervical tissue. Additionally, our results suggest that early stage productive infection and cancerous stages of infection are distinct disease states expressing different transcriptomes.

Importance

Persistent HPV infection is responsible for most cases of cervical cancer. Transition from precancerous to cancerous stages of HPV infection is marked by a significant reduction in virus production. Most global gene expression studies of HPV infection have focused on the cancerous stages. Therefore, little is known about global gene expression changes at precancerous stages. For the first time, we measured global gene expression changes at precancerous stages of HPV16 infection in human cervical tissue producing high levels of virus. We identified a group of genes that are typically overexpressed in cancerous stages to be significantly downregulated at the precancerous stage. Moreover, we identified significantly modulated genes that have not yet been studied in the context of HPV infection. Studying the role of these genes in HPV infection will help us understand what drives the transition from precancerous to cancerous stages, and may lead to development of new therapeutic targets.
Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken
Authors: Bush Stephen J. , Freem Lucy , MacCallum Amanda J. , O’Dell Jenny , Wu Chunlei , Afrasiabi Cyrus , Psifidi Androniki , Stevens Mark P. , Smith Jacqueline , Summers Kim M. , Hume David A.
Published: April 2018

Background

The domestic chicken (Gallus gallus) is widely used as a model in developmental biology and is also an important livestock species. We describe a novel approach to data integration to generate an mRNA expression atlas for the chicken spanning major tissue types and developmental stages, using a diverse range of publicly-archived RNA-seq datasets and new data derived from immune cells and tissues.

Results

Randomly down-sampling RNA-seq datasets to a common depth and quantifying expression against a reference transcriptome using the mRNA quantitation tool Kallisto ensured that disparate datasets explored comparable transcriptomic space. The network analysis tool Miru was used to extract clusters of co-expressed genes from the resulting expression atlas, many of which were tissue or cell-type restricted, contained transcription factors that have previously been implicated in their regulation, or were otherwise associated with biological processes, such as the cell cycle. The atlas provides a resource for the functional annotation of genes that currently have only a locus ID. We cross-referenced the RNA-seq atlas to a publicly available embryonic Cap Analysis of Gene Expression (CAGE) dataset to infer the developmental time course of organ systems, and to identify a signature of the expansion of tissue macrophage populations during development.

Conclusion

Expression profiles obtained from public RNA-seq datasets – despite being generated by different laboratories using different methodologies – can be made comparable to each other. This meta-analytic approach to RNA-seq can be extended with new datasets from novel tissues, and is applicable to any species.
The cholinergic pesticide imidacloprid impairs contrast and direction sensitivity in motion detecting neurons of an insect pollinator
Authors: Rigosi Elisa , O’Carroll David C.
Published: April 2018

Cholinergic pesticides such as the neonicotinoid imidacloprid are the most important insecticides used for plant protection worldwide. In recent decades concerns have been raised about side effects on non-target insect species, including altered foraging behaviour and navigation. Although pollinators rely on visual cues to forage and navigate their environment, the effect of neonicotinoids on visual processing have been largely overlooked. Here we describe a modified electrophysiological setup that allowed recordings of visually evoked responses while perfusing the brainin vivo. Long-lasting recordings from wide-field motion sensitive neurons of the hoverfly pollinator,Eristalis tenax, revealed that sub-lethal exposure to imidacloprid alters their physiological response to motion stimuli. We observed substantially increased spontaneous firing rate, reduced contrast sensitivity and weaker directional tuning to wide-field moving stimuli. This approach reveals sub-lethal effects of imidacloprid in the visual motion detecting system of an important pollinator with likely implications for flight control, hovering and routing.
theseus - An R package for the analysis and visualization of microbial community data
Authors: Price Jacob R. , Woloszynek Stephen , Rosen Gail , Sales Christopher M.
Published: April 2018

theseus is a collection of functions within the R programming framework [1] to assist microbiologists and molecular biologists in the interpretation of microbial community composition data.
Polygenic risk scores for major depressive disorder and neuroticism as predictors of antidepressant response: meta-analysis of three treatment cohorts
Authors: Ward Joey , Graham Nicholas , Strawbridge Rona , Ferguson Amy , Jenkins Gregory , Chen Wenan , Frye Mark , Weinshilboum Richard , Uher Rudolf , Lewis Cathryn M. , Biernacka Joanna , Smith Daniel J.
Published: April 2018

There are currently no reliable approaches for correctly identifying which patients with major depressive disorder (MDD) will respond well to antidepressant therapy. However, recent genetic advances suggest that Polygenic Risk Scores (PRS) could allow MDD patients to be stratified for antidepressant response. We used PRS for MDD and PRS for neuroticism as putative predictors of antidepressant response within three treatment cohorts: The Genome-based Therapeutic Drugs for Depression (GENDEP) cohort, and 2 sub-cohorts from the Pharmacogenomics Research Network Antidepressant Medication Pharmacogenomics Study PRGN-AMPS (total patient number = 783). Results across cohorts were combined via meta-analysis within a random effects model. Overall, PRS for MDD and neuroticism did not significantly predict antidepressant response but there was a consistent direction of effect, whereby greater genetic loading for both MDD (best MDD result, p < 5*10-5 MDD-PRS at 4 weeks, β = -0.019, S.E = 0.008, p = 0.01) and neuroticism (best neuroticism result, p < 0.1 neuroticism-PRS at 8 weeks, β = -0.017, S.E = 0.008, p = 0.03) were associated with less favourable response. We conclude that the PRS approach may offer some promise for treatment stratification in MDD and should now be assessed within larger clinical cohorts.
Training enhances the ability of listeners to exploit visual information for auditory scene analysis
Authors: Atilgan Huriye , Bizley Jennifer K.
Published: April 2018

The ability to use temporal relationships between cross-modal cues facilitates perception and behavior. Previously we observed that temporally correlated changes in the size of a visual stimulus and the intensity in an auditory stimulus influenced the ability of listeners to perform an auditory selective attention task (Maddox et al., 2015). In this task participants detected timbral changes in a target sound while ignoring those in a simultaneously presented masker. When the visual stimulus was temporally coherent with the target sound, performance was significantly better than when it was temporally coherent with the masker sound, despite the visual stimulus conveying no task-relevant information. Here, we trained observers to detect audiovisual temporal coherence and asked whether this improved their ability to benefit from visual cues during the auditory selective attention task. We observed these listeners improved performance in the auditory selective attention task and changed the way in which they benefited from a visual stimulus: after training performance was better when the visual stimulus was temporally coherent with either the target or the masker stream, relative to the condition in which the visual stimulus was coherent with neither auditory stream. A second group which trained to discriminate modulation rate differences between temporally coherent audiovisual streams improved task performance, but did not change the way in which they used visual information. A control group did not change their performance between pretest and post-test. These results provide insights into how crossmodal experience may optimize multisensory integration.
Phospholipid membranes promote the early stage assembly of α-synuclein aggregates
Authors: Lv Zhengjian , Hashemi Mohtadin , Banerjee Siddhartha , Zagorski Karen , Rochet Jean-Christophe , Lyubchenko Yuri L.
Published: April 2018

Development of Parkinson’s disease is associated with spontaneous self-assembly of α-synuclein (α-syn). Efforts aimed at understanding this process have produced little clarity and the mechanism remains elusive. We report a novel effect of phospholipid bilayers on the catalysis of α-syn aggregation from monomers. We directly visualized α-syn aggregation on supported lipid bilayers using time-lapse atomic force microscopy. We discovered that α-syn assemble in aggregates on bilayer surfaces even at the nanomolar concentration of monomers in solution. The efficiency of the aggregation process depends on the membrane composition, being highest for a negatively charged bilayer. Furthermore, assembled aggregates can dissociate from the surface, suggesting that on-surface aggregation can be a mechanism by which pathological aggregates are produced. Computational modeling revealed that interaction of α-syn with bilayer surface changes the protein conformation and its affinity to assemble into dimers, and these properties depend on the bilayer composition. A model of the membrane-mediated aggregation triggering the assembly of neurotoxic aggregates is proposed.
Molecular basis for voltage sensitivity in membrane proteins
Authors: Kasimova Marina A. , Lindahl Erik , Delemotte Lucie
Published: April 2018

Voltage-sensitive membrane proteins are united by the ability to transform changes in the membrane potential into mechanical work. They are responsible for a spectrum of key physiological processes in living organisms, including electric signaling and progression along the cell cycle. While the voltage-sensing mechanism has been well characterized for some membrane proteins such as voltage-gated ion channels, for others even the location of the voltage-sensing elements remains unknown. The detection of these elements using experimental techniques is complicated due to the large diversity of membrane proteins. Here, we suggest a computational approach to predict voltage-sensing elements in any membrane protein independent of structure or function. It relies on the estimation of the capacity of a protein to respond to changes in the membrane potential. We first show how this property correlates well with voltage sensitivity by applying our approach to a set of membrane proteins including voltage-sensitive and voltage-insensitive ones. We further show that it correctly identifies true voltage-sensitive residues in the voltage sensor domain of voltage-gated ion channels. Finally, we investigate six membrane proteins for which the voltage-sensing elements have not yet been characterized and identify residues and ions potentially involved in the response to voltage. The suggested approach is fast and simple and allows for characterization of voltage sensitivity that goes beyond mere identification of charges. We anticipate that its application prior to mutagenesis experiments will allow for significant reduction of the number of potential voltage-sensitive elements to be tested.
Towards automation of germline variant curation in clinical cancer genetics
Authors: Ravichandran Vignesh , Shameer Zarina , Kernel Yelena , Walsh Michael , Cadoo Karen , Lipkin Steven , Mandelker Diana , Zhang Liying , Stadler Zsofia , Robson Mark , Offit Kenneth , Vijai Joseph
Published: April 2018

Cancer care professionals are confronted with interpreting results from multiplexed gene sequencing of patients at hereditary risk for cancer. Assessments for variant classification now require orthogonal data searches, requiring aggregation of multiple lines of evidence from diverse resources. The burden of evidence for each variant to meet thresholds for pathogenicity or actionability now poses a growing challenge for those seeking to counsel patients and families following germline genetic testing. A computational algorithm that automates, provides uniformity and significantly accelerates this interpretive process is needed. The tool described here, Pathogenicity of Mutation Analyzer (PathoMAN) automates germline genomic variant curation from clinical sequencing based on ACMG guidelines. PathoMAN aggregates multiple tracks of genomic, protein and disease specific information from public sources. We compared expert manually curated variant data from studies on (i) prostate cancer (ii) breast cancer and (iii) ClinVar to assess performance. PathoMAN achieves high concordance (83.1% pathogenic, 75.5% benign) and negligible discordance (0.04% pathogenic, 0.9% benign) when contrasted against expert curation. Some loss of resolution (8.6% pathogenic, 23.64% benign) and gain of resolution (6.6% pathogenic, 1.6% benign) was also observed. We highlight the advantages and weaknesses related to the programmable automation of variant classification. We also propose a new nosology for the five ACMG classes to facilitate more accurate reporting to ClinVar. The proposed refinements will enhance utility of ClinVar to allow further automation in cancer genetics. PathoMAN will reduce the manual workload of domain level experts. It provides a substantial advance in rapid classification of genetic variants by generating robust models using a knowledge-base of diverse genetic data https://pathoman.mskcc.org.
Terrorism and female teacher leadership in girls’ secondary school
Authors: Usman Lantana Martha
Published: April 2018

Purpose

The purpose of this paper is to explore female teachers and vice principal’s leadership on girls attendance and learning, safety and security issues in rural girls’ schools experiencing Boko Haram insurgencies. The secondary purpose is to recommend innovative educational policy initiatives at the school, community and state levels, so as to ameliorate girls and teachers’ challenges, and to sustain girls in schools.

Design/methodology/approach

Qualitative educational research orientation and an ethnographic-narrative research design were used for the study. Purposeful sampling procedure was adopted through the selection of female teachers and a vice principal. Soft qualitative oral data (SQOD) were collected from structured interviews and focus groups and participant observation data. Data analysis engaged hand data analysis (HAD) for transcription, while the coding and theming process involved qualitative computer software data analysis (CSDA) of NVivo 8.0. The measures of validity involved the qualitative process of member checking, while ethical issues of anonymity with participants were addressed in the process of data collection, and reporting.

Findings

Major findings revealed a symbiotic relationship between female teacher’s moral leadership and the application of law of tort in the girls’ school; teachers’ adopted spiritual leadership and moral decision making process on girls’ safety, and learning motivation; and improved school community collaboration for security and safety of the girls and effective communication.

Practical implications

Educational policy options are prescribed. They include the training of teachers and girls on fire safety and conflict crisis; recruitment of female school counsellors; housing incentives for female teachers; support grassroot initiatives on school security; and sustaining school-community/parents involvement.

Originality/value

Boko Haram’s impact on teacher and school leadership in girls’ school(s) has not been studied so far. The paper is the first, thereby filling the gap of the literature on girls’ rural education and terrorism.
An econophysics non-monetized theory of value
Authors: Baer Wolfgang , Bounfour Ahmed , Housel Thomas J.
Published: April 2018

Purpose

Mobile phones are radically transforming micro-finance in Sub-Saharan Africa, and Kenya, in particular. The introduction of the micro-financial transaction mobile phone application, “MPesa,” created a means to facilitate micro-transactions without the need for an intermediary, such as a banking system. The purpose of this paper is to posit an econophysics model to predict the value of Mpesa for Kenyan and South African consumers. The econophysics framework posits several fitness matrices and a distance measure that can account for the concepts of mass, distance, momentum, velocity, action, and force. The authors begin with a table of the match between the physics concepts and the economic concepts followed by the vector model that utilizes these concepts for the MPesa application case. In this paper, the authors will argue that MPesa succeeded in Sub-Saharan African countries, such as Kenya, because the fit between what this group of customers needed and the solutions Safaricom’s MPesa offered was a better fit with a smaller distance to adoption than in the South African case.

Design/methodology/approach

The research develops an econophysics approach to the assessment of micro-finance development in Sub-Saharan countries.

Findings

The research shows clearly the reasons of the success of MPesa in Kenya in comparison of its relative failure in South Africa: the distance between customers’ expectations and the system supply.

Research limitations/implications

The research is limited to two case studies and needs to be extended to other contexts, in order to demonstrate its robustness, especially with regard to the intangible dimension, e.g., the distance between a system potential and what it really offers.

Practical implications

The research shows the importance of system’s characteristics in its success.

Social implications

The social implications are very high, especially in this case, where micro-finance is a high stake for developing societies.

Originality/value

This is one of the first works to develop an econophysics approach for the evaluation of the key characteristics of a system.
A comparative study of intangible investment in Egypt and South Africa
Authors: Chen Wen
Published: April 2018

Purpose

The purpose of this paper is to understand the recent developments and trends of intangible investment in Egypt and South Africa.

Design/methodology/approach

This paper follows the framework pioneered by Corrado, Hulten and Sichel (2005, 2009) and measures investments in scientific R&D, organizational capital, and brand equity using the expenditure-based approach.

Findings

The main findings are that South Africa invests consistently and considerably more in intangible assets than Egypt. Among the three intangible assets examined, namely, scientific R&D, organizational capital, and brand equity, South Africa seems to invest more evenly across these assets, whereas intangible investment in Egypt is predominantly driven by investment in brand equity and very little in R&D.

Originality/value

This is the first paper to formally examine intangible investment in African countries. The ballpark estimate provided in this study is a useful step forward in understanding the trends of intangible investment in Egypt and South Africa.
Does Wall Street buy your growth story? For how long?
Authors: McGrath Rita Gunther , van Putten Alexander B. , Pierantozzi Ron
Published: April 2018

Purpose

The article introduces the authors’ “ Imagination Premium™” metric which assesses the confidence of the investing community in a business’ growth strategy.

Design/methodology/approach

The article explains how the Imagination Premium is calculated and applies it to several cases--Amazon, Tesla and Buffalo Wild Wings.

Findings

Amazon’s implied value of growth was nearly four times its value from operations, a result completely consistent with its “profits are optional” motto. Amazon is a prototypical example of a company that is built to thrive in the ‘transient advantage economy.

Practical implications

Sky-high expectations for growth can be dashed by external events over which businesses have little control as Tesla found out. Unless a business can show, as Amazon has historically done, that it can turn expectations into gold-spun reality, lofty investor expectations can become a liability.

Originality/value

By applying the Imagination Premium concept to successful and problematic cases the authors illustrate the risks and advantages of a bold growth-before-profits strategy.
How industry leaders enhance the value of ecosystems
Authors: Davidson Steven , Giesen Edward , Harmer Martin , Marshall Anthony
Published: April 2018

Purpose

The article explains how industry leaders engage in ecosystems effectively to access new markets and new geographies, and through intensive collaboration within new partnering arrangements, ecosystems have become an essential resource for building their new capabilities.

Design/methodology/approach

Executives of the most successful organizations surveyed embrace their existing ecosystems and expect to pursue new and different partnering arrangements. Outperforming organizations credit their ecosystems with generating value and innovation. The article looks at what they did differently than under-performers.

Findings

Ecosystems can drive a broad range of strategic opportunities including new engagement and monetization models.

Practical implications

Ecosystems help organizations access critical capabilities that would have otherwise been unavailable or very difficult to obtain. 10; 10; 10;

Originality/value

3BLeaders of outperforming organizations recognize the significant opportunity to improve skills by learning alongside ecosystem partners.
China’s “New Silk Road” initiative – implications for competitors and partners, near and far
Authors: Leavy Brian
Published: April 2018

Purpose

The author explains how the story of China geo-political vision has recently taken a new turn under the leadership of Xi Jinping, and signals a major shift towards a more expansive and outward-looking economic policy.

Design/methodology/approach

Understanding more fully what is happening in the latest phase of China’s modern resurgence is a strategic imperative for both public policy analysts and corporate leaders with global interests and ambitions.

Findings

China is now convinced that extending its ‘infrastructure and connectivity” focus outwards in this way will help ‘to dismantle investment barriers, create new trade routes, improve international logistics and deepen financial integration.’

Practical implications

Beijing is ‘adamant’ that it should not be called a ‘plan’ or a ‘strategy’ lest it ‘be interpreted as ruse to build a vast economic empire.’

Originality/value

China's BRI extends beyond ports, railways and highways to other major types of infrastructure including oil and gas pipelines, electricity power plants and telecommunications networks. So the invitation to be part of BRI presents ‘a vast economic carrot,’ and the prospect of becoming major hubs on emerging new pan-regional trade routes is enormously attractive to many of China’s underdeveloped neighbors. 10;
Exploring the role of transformational leadership in human capital effectiveness
Authors: Khan Muhammad Shahid , Sentosa Ilham , Salman Faryal
Published: April 2018

Purpose

Malaysia has set year 2020 as a targeted year to become the most developed nation and to transform the economy into knowledge based. Issue is to become developed nation, but without human capital development (HCD) process, the achievement of this vision would be difficult. Numerous studies articulated the direct impact of human capital on the country economic growth. Human capital is a significant factor to get competitive advantage, which is the need of the day for all countries as well as for organizations to survive in today’s tough competitive environment. Major objective of this research was to find the role of transformational leadership (TL) in human capital effectiveness with the effect of knowledge management (KM) strategies. The paper aims to discuss these issues.

Design/methodology/approach

A mixed research method is deployed in this study. Data are collected with the help of self-administrated questionnaire and a semi-structured interview. The structural equation modeling technique is used in the data; data are analyzed with the help of AMOS and Nvivo software.

Findings

The results revealed that transformation has a positive effect on KM strategies. Further, this study also identified that knowledge codification strategy and personalization strategy have a positive impact on human capital effectiveness.

Research limitations/implications

The results revealed that KM strategies play a vital role in human capital effectiveness. Therefore, the Malaysian healthcare industry should introduce KM strategies in order to enhance employees’ knowledge skills and ability. This study is only conducted in Malaysia; the future researcher can use a different method to test the current research model.

Practical implications

Knowledge codification and knowledge personalization strategy can contribute to the HCD process. This study can be generalized in the Malaysian healthcare industry. This kind of effort will add value into human capital. Hence, organization can get a competitive advantage with the help of human capital. TL style is the most appropriate style in the current era; this leadership has the ability to transform the system, which is the need of the day. Due to rapid changes in technology, a leader who believes in change can meet the challenges of twenty-first century.

Originality/value

KM strategies and their use have been a research issue for some time. Companies have also adopted knowledge management strategies tools to support and stimulate knowledge sharing in their organizations and to help employees to find the expertise they are looking for. But no research has been performed on the importance of KM strategies. This paper describes a unique and new framework that the authors devised to help companies to do just that.
Religion and the Composition of the Commissions of the Peace, 1547–1640
Authors: WALL ALISON
Published: April 2018

Between the Reformation and the Civil War, the crown and its ministers sought to ensure that the JPs who ran county governments would enforce religious policy. The composition of county commissions was adjusted to the religious complexion of the regime, so that justices were appointed or dismissed according to their opinions, Protestant or Catholic. There were some major purges under Edward VI, Mary and Elizabeth, and frequent instability, but there were constraints on the crown's ability to obtain compliance. Under James I, dismissals of JPs were sometimes motivated by official hostility to the more godly Protestants, while from 1617 to 1625 more clergy were nominated as JPs. Under Charles I, some critical of Arminian tendencies and fiscal policy were expelled from the commissions of the peace. The late 1630s saw a new development – JPs leaving the office voluntarily, which, it is argued here, was partly impelled by their religious convictions.
From the Editor
Authors: Smith Tom
Published: April 2018

Report from the Editor as I start a second term. I outline success and otherwise in the first term and encourage authors to engage in the local research conversation when they are writing their papers. I point out that all methodological approaches are welcome including qualitative, survey, systematic literature reviews and experiments. I point out the hot points that Editors now are looking for so that you can pay particular attention to them in advance of submission.
Behavioural repertoire of free‐range laying hens indoors and outdoors, and in relation to distance from the shed
Authors: Thuy Diep A , Larsen H , Rault J‐L
Published: April 2018

Background

Access to an outdoor area is believed to allow free‐range hens to express a greater behavioural repertoire. However, very little research has been done in this area. We hypothesised that the type and frequency of behaviours would differ between areas that vary in their characteristics and distance from the shed.

Methods

This preliminary study investigated the behaviour of free‐range laying hens in indoor and outdoor areas on one commercial free‐range farm, through video recordings and scan sampling of focal hens, with the aim of determining their behavioural repertoire and time budget.

Results

While ranging, hens spent most of their time foraging. Indoors, hens preened and rested. Behaviour in the wintergarden showed similarities to both the indoor and outdoor areas, with preening, resting and foraging behaviours. Differences were not in the main behavioural repertoire, but rather in terms of time budget, with access to the range and wintergarden encouraging exploration.

Conclusion

There was no difference in the types of behaviours that hens performed in the outdoor range compared with inside the shed, but access to a wintergarden and the outdoor range were favoured by the hens for foraging.
Sums of three squares and Noether–Lefschetz loci
Authors: Benoist Olivier
Published: April 2018

We show that the set of real polynomials in two variables that are sums of three squares of rational functions is dense in the set of those that are positive semidefinite. We also prove that the set of real surfaces in $\mathbb{P}^{3}$ whose function field has level 2 is dense in the set of those that have no real points.
Crisis, and the Impacts of Crisis, on the Inhabitants of Rural Space: The Case of a Village in North West Portugal
Authors: Silva Manuel Carlos , Cardoso Antonio
Published: April 2018

In 2011, Portugal, suffering the impact of the 2008 crisis, both for internal and external reasons, requested financial assistance from the Troika (IMF/ECB/EU). The Portuguese experienced company bankruptcies, cuts to salaries and pensions, rising unemployment and job insecurity and difficulties in paying their mortgages. Despite severe austerity programs and formal exit of the Troika, Portugal failed to reduce public debt. In this article, after giving a brief overview of development models, we will focus our attention on the impacts of the crisis in rural areas and the diverse perceptions of crisis by different groups and families. As a case study, we will consider the strategies employed by residents of a parish in the municipality of Barcelos (Braga, Minho), to reduce the damage caused by the crisis. Against the mainstream liberal perspective and the traditional Marxist thesis we sustain that rural people adopt an attitude of resiliency in relation to the austerity program and on the basis of empirical qualitative research methods we can witness creative familial strategies to survive: migration, exploiting the potentialities of the land, taking advantage of artisanal and commercial opportunities in order to cope with the difficulties caused by the crisis.     
Edge of extinction
Authors: Kumar Sanjay
Published: April 2018

India's paleontologists are struggling to save fossil sites—and their own discipline.
Supporting recovery from brain injury
Authors: Rumpel Simon
Published: April 2018

A window of therapeutic opportunity could widen beyond the initial phase of brain injury
ESCRTs offer repair service
Authors: Gutierrez Maximiliano G. , Carlton Jeremy G.
Published: April 2018

A cellular membrane remodeling machinery repairs damaged organelles
Soft Rot Enterobacteriaceae Are Carried by a Large Range of Insect Species in Potato Fields
Authors: Rossmann Simeon , Dees Merete Wiken , Perminow Juliana , Meadow Richard , Brurberg May Bente
Published: April 2018

Pathogenic soft rot
Enterobacteriaceae
(SRE) belonging to the genera
Pectobacterium
and
Dickeya
cause diseases in potato and numerous other crops. Seed potatoes are the most important source of infection, but how pathogen-free tubers initially become infected remains an enigma. Since the 1920s, insects have been hypothesized to contribute to SRE transmission. To validate this hypothesis and to map the insect species potentially involved in SRE dispersal, we have analyzed the occurrence of SRE in insects recovered from potato fields over a period of 2 years. Twenty-eight yellow sticky traps were set up in 10 potato fields throughout Norway to attract and trap insects. Total DNA recovered from over 2,000 randomly chosen trapped insects was tested for SRE, using a specific quantitative PCR (qPCR) TaqMan assay, and insects that tested positive were identified by DNA barcoding. Although the occurrence of SRE-carrying insects varied, they were found in all the tested fields. While
Delia
species were dominant among the insects that carried the largest amount of SRE, more than 80 other SRE-carrying insect species were identified, and they had different levels of abundance. Additionally, the occurrence of SRE in three laboratory-reared insect species was analyzed, and this suggested that SRE are natural members of some insect microbiomes, with herbivorous
Delia floralis
carrying more SRE than the cabbage moth (
Plutella xylostella
) and carnivorous green lacewing larvae (
Chrysoperla carnea
). In summary, the high proportion, variety, and ubiquity of insects that carried SRE show the need to address this source of the pathogens to reduce the initial infection of seed material.

IMPORTANCE
Soft rot
Enterobacteriaceae
are among the most important pathogens of a wide range of vegetables and fruits. The bacteria cause severe rots in the field and in storage, leading to considerable harvest losses. In potato, efforts to understand how soft rot bacteria infect and spread between healthy plants have been made for over a century. Early on, fly larvae were implicated in the transmission of these bacteria. This work aimed at investigating the occurrence of soft rot bacteria in insects present in potato fields and at identifying the species of these insects to better understand the potential of this suspected source of transmission. In all tested potato fields, a large proportion of insects were found to carry soft rot bacteria. This suggests a need to give more weight to the role of insects in soft rot ecology and epidemiology to design more effective pest management strategies that integrate this factor.
Incorporation of IgG Depletion in a Neutralization Assay Facilitates Differential Diagnosis of Zika and Dengue in Secondary Flavivirus Infection Cases
Authors: Calvert Amanda E. , Boroughs Karen L. , Laven Janeen , Stovall Janae L. , Luy Betty E. , Kosoy Olga I. , Huang Claire Y.-H.
Published: April 2018

Zika virus (ZIKV) has emerged as a major global public health concern due to its link as a causative agent of human birth defects. Laboratory diagnosis of suspected ZIKV infections by serological testing of specimens collected a week or more after symptom onset primarily relies on detection of anti-ZIKV-specific IgM antibodies by enzyme-linked immunosorbent assay coupled with detection of ZIKV-specific neutralizing antibody by neutralization tests. A definitive diagnosis based on serological assays is possible during primary ZIKV infections; however, due to the cross-reactivity of antibodies elicited during flaviviral infections, a definitive diagnosis is not always possible, especially among individuals who have previously been exposed to closely related flaviviruses, such as dengue virus (DENV). Here, we investigated the neutralizing IgM antibody profiles of 33 diagnostic specimens collected from individuals with suspected primary and secondary flaviviral infections acquired when visiting areas experiencing active ZIKV transmission in 2015 and 2016. Specimens collected between 1 day and 3 months postexposure were tested for ZIKV and dengue virus type 1 (DENV1) and type 2 (DENV2) by the plaque reduction neutralization test (PRNT) before and after IgG depletion. We found that IgG depletion prior to neutralization testing had little effect in differentiating samples from individuals with secondary infections taken less than 3 weeks postexposure; however, IgG depletion significantly reduced the cross-reactive neutralizing antibody titers and increased the percentage of cases discernible by PRNT from 15.4% (95% confidence interval [CI], 4.3 to 42.2%) to 76.9% (95% CI, 49.7 to 91.8%) for samples collected between roughly 3 and 12 weeks postexposure. These results highlight the potential of IgG depletion to improve the specificity of PRNT for better confirmation and differential diagnosis of flavivirus infections.
Large-Scale Complete-Genome Sequencing and Phylodynamic Analysis of Eastern Equine Encephalitis Virus Reveals Source-Sink Transmission Dynamics in the United States
Authors: Tan Yi , Lam Tommy Tsan-Yuk , Heberlein-Larson Lea A. , Smole Sandra C. , Auguste Albert J. , Hennigan Scott , Halpin Rebecca A. , Fedorova Nadia , Puri Vinita , Stockwell Timothy B. , Shilts Meghan H. , Andreadis Theodore , Armstrong Philip M. , Tesh Robert B. , Weaver Scott C. , Unnasch Thomas R. , Ciota Alexander T. , Kramer Laura D. , Das Suman R.
Published: April 2018

Eastern equine encephalitis virus (EEEV) has a high case-fatality rate in horses and humans, and Florida has been hypothesized to be the source of EEEV epidemics for the northeastern United States. To test this hypothesis, we sequenced complete genomes of 433 EEEV strains collected within the United States from 1934 to 2014. Phylogenetic analysis suggested EEEV evolves relatively slowly and that transmission is enzootic in Florida, characterized by higher genetic diversity and long-term local persistence. In contrast, EEEV strains in New York and Massachusetts were characterized by lower genetic diversity, multiple introductions, and shorter local persistence. Our phylogeographic analysis supported a source-sink model in which Florida is the major source of EEEV compared to the other localities sampled. In sum, this study revealed the complex epidemiological dynamics of EEEV in different geographic regions in the United States and provided general insights into the evolution and transmission of other avian mosquito-borne viruses in this region.

IMPORTANCE
Eastern equine encephalitis virus (EEEV) infections are severe in horses and humans on the east coast of the United States with a >90% mortality rate in horses, an ∼33% mortality rate in humans, and significant brain damage in most human survivors. However, little is known about the evolutionary characteristics of EEEV due to the lack of genome sequences. By generating large collection of publicly available complete genome sequences, this study comprehensively determined the evolution of the virus, described the epidemiological dynamics of EEEV in different states in the United States, and identified Florida as one of the major sources. These results may have important implications for the control and prevention of other mosquito-borne viruses in the Americas.