bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling Epidemics in Seed Systems to Guide Management Strategies: The Case of Sweetpotato in Northern Uganda
Authors: Andersen K. F. , Buddenhagen C. E. , Rachkara P. , Gibson R. , Kalule S. , Phillips D. , Garrett K. A.
Published: February 2017

Seed systems are critical for deployment of improved varieties, but also serve as major conduits for the spread of seed-borne pathogens. We evaluated the structure of an informal sweetpotato seed system for its vulnerability to the spread of epidemics, and its utility for disseminating improved varieties. During the 2014 growing season, vine sellers were surveyed weekly in the Gulu Region of Northern Uganda. Our analysis draws on tools from network theory to evaluate the potential for epidemic spread in this region. Using empirical seed transaction data and estimated spatial spread, we constructed a network of seed and pathogen movement. We modeled the introduction of a pathogen, and evaluated the influence of both epidemic starting point and quarantine treatments on epidemic progress. Quarantine of 30 out of 99 villages reduced epidemic progress by up to 66%, when compared to the control (no quarantine), over 20 time steps. The starting position in the network was critical for epidemic progress and final epidemic outcomes, and influenced the percent control conferred by quarantine treatments. Considering equal likelihood of any node being an introduction point for a new epidemic, villages of particular utility for disease monitoring were identified. Sensitivity analysis identified important parameters and priorities for future data collection. The efficacy of node degree, closeness, and eigenvector centrality was similar for selecting quarantine locations, while betweenness had more limited utility. This analysis framework can be applied to provide recommendations for a wide variety of seed systems.
A memory of recent oxygen experience switches pheromone valence inC. elegans
Authors: Fenk Lorenz A. , de Bono Mario
Published: February 2017

Animals adjust their behavioral priorities according to momentary needs and prior experience. We show thatC. eleganschanges how it processes sensory information according to the oxygen environment it experienced recently.C.elegansacclimated to 7% O2are aroused by CO2and repelled by pheromones that attract animals acclimated to 21% O2. This behavioral plasticity arises from prolonged activity differences in a circuit that continuously signals O2levels. A sustained change in the activity of O2sensing neurons reprograms the properties of their post-synaptic partners, the RMG hub interneurons. RMG is gap-junctionally coupled to the ASK and ADL pheromone sensors that respectively drive pheromone attraction and repulsion. Prior O2experience has opposite effects on the pheromone responsiveness of these neurons. These circuit changes provide a physiological correlate of altered pheromone valence. Our results suggestC. elegansstores a memory of recent O2experience in the RMG circuit and illustrate how a circuit is flexibly sculpted to guide behavioral decisions in a context-dependent manner.
Enzymatic production of single molecule FISH and RNA capture probes
Authors: Gaspar Imre , Wippich Frank , Ephrussi Anne
Published: February 2017

Arrays of singly-labelled short oligonucleotides that hybridize to a specific target revolutionized RNA biology, enabling quantitative, single molecule microscopy analysis and high efficiency RNA/RNP capture. Here, we describe a simple and efficient method that allows flexible functionalization of inexpensive DNA oligonucleotides by different fluorescent dyes or biotin using terminal deoxynucleotidyl transferase and custom-made functional group conjugated dideoxy-UTP. We show that 1) all steps of the oligonucleotide labelling – including conjugation, enzymatic synthesis and product purification – can be performed in a standard biology laboratory, 2) the process yields >90 %, often >95 % labeled product with minimal carry-over of impurities and 3) the oligonucleotides can be labeled with different dyes or biotin, allowing single molecule FISH or RNA affinity purification to be performed.

Graphical abstract
Inhibition of histone deacetylase 1 or 2 reduces microglia activation through a gene expression independent mechanism
Authors: Durham Benjamin S. , Grigg Ronald , Wood Ian C.
Published: February 2017

Histone deacetylase (HDAC) inhibitors prevent neural cell death inin vivomodels of cerebral ischaemia, brain injury and neurodegenerative disease. One mechanism by which HDAC inhibitors may do this is by suppressing the excessive inflammatory response of chronically activated microglia. However, the molecular mechanisms underlying this anti-inflammatory effect and the specific HDAC responsible are not fully understood. Recent data fromin vivorodent studies has shown that inhibition of class I HDACs suppresses neuroinflammation and is neuroprotective. In our study we have identified that selective HDAC inhibition with inhibitors apicidin, MS-275 or MI-192, or specific knockdown of HDAC1 or 2 using siRNA, suppresses the expression of cytokines interleukin-6 (IL-6) and tumour necrosis factor-alpha (TNF-α) in BV2 murine microglia activated with lipopolysaccharide (LPS). Furthermore, we found that in the absence of HDAC1, HDAC2 is upregulated and these increased levels are compensatory, suggesting these two HDACs have redundancy in regulating the inflammatory response of microglia. Investigating the possible underlying anti-inflammatory mechanisms suggests an increase in protein expression is not important. Taken together, this study supports the idea that inhibitors selective towards HDAC1 or HDAC2, may be therapeutically useful for targeting neuroinflammation in brain injuries and neurodegenerative disease.

Significance Statement

The number of patients suffering a stroke or a neurodegenerative disease, such as Alzheimer’s is increasing These conditions are severely debilitating and are leading causes of mortality, with neural cell death and loss of brain tissue being a major feature. A number of mechanisms contribute to neuronal death, including inflammation in the brain, but we still lack clinical therapies to inhibit this. The work presented here provides further insight into potential molecular therapeutic targets called histone deacetylases (HDACs), which are thought to contribute to neural cell death by promoting inflammation. We show that down regulation of HDAC1 and 2 is sufficient to reduce this inflammatory response. Our findings have clinical relevance because they identify HDAC1 and 2 as promising targets for therapy.
Contextual diversity of the human cell-essential proteome
Authors: Bertomeu Thierry , Coulombe-Huntington Jasmin , Chatr-Aryamontri Andrew , Bourdages Karine , Xia Yu , Tyers Mike
Published: February 2017

Essential genes define central biological functions required for cell growth, proliferation and survival, but the nature of gene essentiality across human cell types is not well understood. We assessed essential gene function in a Cas9-inducible human B-cell lymphoma cell line using an extended knockout (EKO) library of 278,754 sgRNAs that targeted 19,084 RefSeq genes, 20,852 alternatively-spliced exons and 3,872 hypothetical genes. A new statistical analysis tool called RANKS identified 2,280 essential genes, 234 of which had not been reported previously. Essential genes exhibited a bimodal distribution across 10 cell lines screened in different studies, consistent with a continuous variation in essentiality as a function of cell type. Genes essential in more lines were associated with more severe fitness defects and encoded the evolutionarily conserved structural cores of protein complexes. Genes essential in fewer lines tended to form context-specific modules and encode subunits at the periphery of essential complexes. The essentiality of individual protein residues across the proteome correlated with evolutionary conservation, structural burial, modular domains, and protein interaction interfaces. Many alternatively-spliced exons in essential genes were dispensable and tended to encode disordered regions. We also detected a significant fitness defect for 44 newly evolved hypothetical reading frames. These results illuminate the nature and evolution of essential gene functions in human cells.
Sparse synaptic connectivity is required for decorrelation and pattern separation in feedforward networks
Authors: Cayco-Gajic N. Alex , Clopath Claudia , Silver R. Angus
Published: February 2017

Pattern separation is a fundamental function of the brain. Divergent feedforward networks separate overlapping activity patterns by mapping them onto larger numbers of neurons, aiding learning in downstream circuits. However, the relationship between the synaptic connectivity within these circuits and their ability to separate patterns is poorly understood. To investigate this we built simplified and biologically detailed models of the cerebellar input layer and systematically varied the spatial correlation of their inputs and their synaptic connectivity. Performance was quantified by the learning speed of a classifier trained on either the mossy fiber input or granule cell output patterns. Our results establish that the extent of synaptic connectivity governs the pattern separation performance of feedforward networks by counteracting the beneficial effects of expanding coding space and threshold-mediated decorrelation. The sparse synaptic connectivity in the cerebellar input layer provides an optimal solution to this trade-off, enabling efficient pattern separation and faster learning.
Prospects for genomic selection in cassava breeding
Authors: Wolfe Marnin D. , Carpio Dunia Pino Del , Alabi Olumide , Egesi Chiedozie , Ezenwaka Lydia C. , Ikeogu Ugochukwu N. , Kawuki Robert S. , Kayondo Ismail S. , Kulakow Peter , Lozano Roberto , Rabbi Ismail Y. , Williams Esuma , Ozimati Alfred A. , Jannink Jean-Luc
Published: February 2017

Cassava (Manihot esculentaCrantz) is a clonally propagated staple food crop in the tropics. Genomic selection (GS) reduces selection cycle times by the prediction of breeding value for selection of unevaluated lines based on genome-wide marker data. GS has been implemented at three breeding programs in sub-Saharan Africa. Initial studies provided promising estimates of predictive abilities in single populations using standard prediction models and scenarios. In the present study we expand on previous analyses by assessing the accuracy of seven prediction models for seven traits in three prediction scenarios: (1) cross-validation within each population, (2) cross-population prediction and (3) cross-generation prediction. We also evaluated the impact of increasing training population size by phenotyping progenies selected either at random or using a genetic algorithm. Cross-validation results were mostly consistent across breeding programs, with non-additive models like RKHS predicting an average of 10% more accurately. Accuracy was generally associated with heritability. Cross-population prediction accuracy was generally low (mean 0.18 across traits and models) but prediction of cassava mosaic disease severity increased up to 57% in one Nigerian population, when combining data from another related population. Accuracy across-generation was poorer than within (cross-validation) as expected, but indicated that accuracy should be sufficient for rapid-cycling GS on several traits. Selection of prediction model made some difference across generations, but increasing training population (TP) size was more important. In some cases, using a genetic algorithm, selecting one third of progeny could achieve accuracy equivalent to phenotyping all progeny. Based on the datasets analyzed in this study, it was apparent that the size of a training population (TP) has a significant impact on prediction accuracy for most traits. We are still in the early stages of GS in this crop, but results are promising, at least for some traits. The TPs need to continue to grow and quality phenotyping is more critical than ever. General guidelines for successful GS are emerging. Phenotyping can be done on fewer individuals, cleverly selected, making for trials that are more focused on the quality of the data collected.

Abbreviations

(GS)

Genomic selection

(GBS)

genotype-by-sequencing

(IITA)

International Institute of Tropical Agriculture

(NRCRI)

National Root Crops Research Institute

(NaCRRI)

National Crops Resources Research Institute

(GEBVs)

genomic estimated breeding values

(TP)

training population

(RTWT)

fresh root weight

(RTNO)

root number

(SHTWT)

fresh shoot weight

(HI)

harvest index

(DM)

dry matter

(CMD)

content cassava mosaic disease

(MCMDS)

mean CMD severity

(VIGOR)

early vigor
Sorting out adipocyte precursors and their role in physiology and disease
Authors: Hepler Chelsea , Vishvanath Lavanya , Gupta Rana K.
Published: February 2017

The ability to maintain and expand the pool of adipocytes in adults is integral to the regulation of energy balance, tissue/stem cell homeostasis, and disease pathogenesis. For decades, our knowledge of adipocyte precursors has relied on cellular models. The identity of native adipocyte precursors has remained unclear. Recent studies have identified distinct adipocyte precursor populations that are physiologically regulated and contribute to the development, maintenance, and expansion of adipocyte pools in mice. With new tools available, the properties of adipocyte precursors can now be defined, and the regulation and function of adipose plasticity in development and physiology can be explored.
In search of the mechanism that shapes the neutrophil's nucleus
Authors: Georgopoulos Katia
Published: February 2017

The organization of the genome within the confines of the nuclear compartment is considered a key contributor to transcription and DNA replication, repair, and recombination. A typical higher eukaryotic cell has a spherical nucleus that is ∼10 µm in diameter. This is not the case for a neutrophil, a short-lived innate immune cell with an unusual multilobular nuclear structure that may serve purposes outside nuclear functions. In this issue of Genes & Development, Zhu and colleagues (pp. 141–153) investigate the neutrophil's genome organization and the mechanisms that contribute to its unique nuclear shape.
Chemical reaction, radiation and slip effects on MHD mixed convection stagnation-point flow in a porous medium with convective boundary condition
Authors: Sivasankaran S. , Niranjan H. , Bhuvaneswari M.
Published: February 2017

Purpose

The purpose of this paper is to investigate the Newtonian heating and slip effect on mixed convective flow near a stagnation point in a porous medium with thermal radiation in the presence of magnetohydrodynamic (MHD), heat generation/absorption and chemical reaction.

Design/methodology/approach

The governing nonlinear coupled equations are converted into ordinary differential equations by similarity transformation. These equations are solved numerically using a Runge–Kutta–Fehlberg method with shooting technique and analytically using the homotopy analysis method (HAM).

Findings

The effects of different parameters on the fluid flow and heat transfer are investigated. It is found that the velocity and temperature profiles increase on an increase in the Biot number. The velocity and concentration profiles increase on decreasing the chemical reaction parameter.

Practical implications

This paper is helpful to the engineers and scientists in the field of thermal and manufacturing engineering.

Originality/value

The two-dimensional boundary layer flow over a vertical plate with slip and convective boundary conditions near the stagnation-point is analysed in the presence of magnetic field, radiation and heat generation/absorption. This paper is helpful to the engineers and scientists in the field of thermal and manufacturing engineering.
A numerical approach for a class of astrophysics equations using piecewise spectral-variational iteration method
Authors: Heydari Mohammad , Barid Loghmani Ghasem , Wazwaz Abdul-Majid
Published: February 2017

Purpose

The main purpose of this paper is to implement the piecewise spectral-variational iteration method (PSVIM) to solve the nonlinear Lane-Emden equations arising in mathematical physics and astrophysics.

Design/methodology/approach

This method is based on a combination of Chebyshev interpolation and standard variational iteration method (VIM) and matching it to a sequence of subintervals. Unlike the spectral method and the VIM, the proposed PSVIM does not require the solution of any linear or nonlinear system of equations and analytical integration.

Findings

Some well-known classes of Lane-Emden type equations are solved as examples to demonstrate the accuracy and easy implementation of this technique.

Originality/value

In this paper, a new and efficient technique is proposed to solve the nonlinear Lane-Emden equations. The proposed method overcomes the difficulties arising in calculating complicated and time-consuming integrals and terms that are not needed in the standard VIM.
Entropy generation optimization for MHD natural convection of a nanofluid in porous media-filled enclosure with active parts and viscous dissipation
Authors: Mansour M.A. , Ahmed Sameh Elsayed , Chamkha Ali J.
Published: February 2017

Purpose

This paper aims to investigate the entropy generation due to magnetohydrodynamic natural convection flow and heat transfer in a porous enclosure filled with Cu-water nanofluid in the presence of viscous dissipation effect. The left and right walls of the cavity are thermally insulated. There are heated and cold parts, and these are placed on the bottom and top wall, respectively, whereas the remaining parts are thermally insulated.

Design/methodology/approach

The finite volume method is used to solve the dimensionless partial differential equations governing the problem. A comparison with previously published woks is presented and is found to be in an excellent agreement.

Findings

The minimization of entropy generation and local heat transfer according to different values of the governing parameters are presented in details. It is found that the presence of magnetic field has negative effects on the local entropy generation because of heat transfer and the local total entropy generation. Also, the increase in the heated part length leads to a decrease in the local Nusselt number.

Originality/value

This problem is original, as it has not been considered previously.
A highly efficient operator-splitting finite element method for 2D/3D nonlinear Allen–Cahn equation
Authors: Xiao Xufeng , Gui Dongwei , Feng Xinlong
Published: February 2017

Purpose

This study aims to present a highly efficient operator-splitting finite element method for the nonlinear two-dimensional/three-dimensional (2D/3D) Allen–Cahn (AC) equation which describes the anti-phase domain coarsening in a binary alloy. This method is presented to overcome the higher storage requirements, computational complexity and the nonlinear term in numerical computation for the 2D/3D AC equation.

Design/methodology/approach

In each time interval, the authors first split the original equation into a heat equation and a nonlinear equation. Then, they split the high-dimensional heat equation into a series of one-dimensional (1D) heat equations. By solving each 1D subproblem, the authors obtain a numerical solution for heat equation and take it as an initial for the nonlinear equation, which is solved analytically.

Findings

The authors show that the proposed method is unconditionally stable. Finally, various numerical experiments are presented to confirm the high accuracy and efficiency of this method.

Originality/value

A new operator-splitting method is presented for solving the 2D/3D parabolic equation. The 2D/3D parabolic equation is split into a sequence of 1D parabolic equations. In comparison with standard finite element method, the present method can save much central processing unit time. Stability analysis and error estimates are derived and numerical results are presented to support the theoretical analysis.
Perceived justice, service satisfaction and behavior intentions following service recovery efforts in a South African retail banking context
Authors: Petzer Daniel J. , De Meyer-Heydenrych Christine F. , Svensson Göran
Published: February 2017

Purpose

The interactional and distributive dimensions of perceived justice as one of its objectives are to reveal the link between perceived justice and service satisfaction (SS). The purpose of this paper is to consider the influence of the perceived justice that South African retail bank customers experience based on the service recovery efforts of these banks in response to their complaints, the customers’ SS, and, consequently, the behavioral intention (BI) toward these banks.

Design/methodology/approach

This study focuses on the perceived justice construct where a service failure has occurred followed by a customer complaint and a resultant service provider response. In total, 281 respondents completed a structured self-administered questionnaire.

Findings

The study found that interactional and distributive justice (DJ) experienced in response to the service recovery efforts of a bank significantly and positively influence SS, and that SS in turn significantly and positively influences the BI of these customers. However, it was found that interactional and DJ had no direct effect on BI.

Research limitations/implications

The research model tested addresses the interfaces between service receivers’ perception of interactional justice, distributional justice and SS as well as the interface between SS and BI. The tested research model indicates that both are interrelated through SS.

Practical implications

It is evident from the findings that retail banks should utilize the service encounter that follows a customer complaint as a desirable prospect to implement strategies to recover from service failures in an effort to bring about perceived justice that will ultimately influence customers’ levels of SS and BI.

Originality/value

This study makes a complementary contribution to previous studies and existing theory building a nomological framework of constructs in service encounters consisting of service receivers’ perceived justice, SS and BI.
Public leadership in the United Arab Emirates: towards a research agenda
Authors: Mathias Megan
Published: February 2017

Purpose

To date, public leadership has been conceptualised for Western systems while leadership discourse has spread across governments globally. The purpose of this paper is to begin the task of conceptualising public leadership in the United Arab Emirates (UAE), a federal monarchy in the Arabian Gulf, and proposes a forward research agenda.

Design/methodology/approach

The paper employs a qualitative, interview-based design to elicit top government officials’ personal interpretations of the purpose and challenges of public leadership, the practices they engage in, and the arenas across which leadership is performed.

Findings

The study finds that whilst notions of public leadership as conceptualised to date are present, cultural and institutional differences result in distinct localised characteristics that belie the managerial presentation of public leadership. Stimulated by these initial findings, three points of departure for future research are suggested: public leaders’ scope for discretion, values and trust.

Research limitations/implications

The research relies on a relatively small, though élite, sample; findings are therefore preliminary, informing ideas for a forward research agenda.

Originality/value

The paper presents a first conceptualisation of public leadership in the UAE, an Arab-Muslim federal monarchy.
The effect of experience and innovativeness of entrepreneurial opportunities on the new venture emergence in China
Authors: Long Dan , Dong Nan
Published: February 2017

Purpose

The purpose of this paper is to identify the model that explains the new venture emergence in China by examining the effects of experience and innovativeness of entrepreneurial opportunities on the new venture emergence, as well as the moderating effect of munificence.

Design/methodology/approach

Based on the dynamic data from the Chinese Panel Study of Entrepreneurial Dynamics (CPSED) where nascent entrepreneurs were randomly sampled and were followed for three years, this paper uses the COX proportional hazard model to answer the research questions.

Findings

Those who have successful entrepreneurial experience are able to more rapidly create new ventures, whereas the relevant industry experience and innovativeness of entrepreneurial opportunities have a negative effect on the new venture emergence. Moreover, munificence negatively moderates the effects of entrepreneurial experience and innovativeness of entrepreneurial opportunities on the new venture emergence.

Research limitations/implications

This paper only measures whether entrepreneurs have relevant industry experience, and does not reflect on the different degrees of it. In addition, small time interval of dynamic follow-up survey may bias the results.

Practical implications

This paper revealed that not all kinds of experience promote the venture emergence, and a more innovative entrepreneurial opportunity is not always better. Entrepreneurs should accumulate experience and evaluate innovativeness of entrepreneurial opportunities rationally.

Originality/value

New venture emergence relies on the mutual influence of entrepreneurs, entrepreneurial opportunities and entrepreneurial environment. However, most studies explored the new venture emergence from a single perspective which led to a plethora of conflicting conclusions. This paper attempts to examine the effects of experience and innovativeness of entrepreneurial opportunities on the venture emergence, as well as the moderate effect of munificence.
Aboriginal entrepreneurship financing in Canada
Authors: Pinto Laura Elizabeth , Blue Levon Ellen
Published: February 2017

Purpose

This paper aims to explore Canadian in/exclusion of Aboriginal groups to/from access to mainstream business resources and opportunities. The focus is one prominent non-governmental program, the Canadian Aboriginal Prosperity and Entrepreneurship (CAPE) Fund, designed to provide equity to Aboriginal businesses. Do programs such as CAPE Fund promote Aboriginal entrepreneurship that liberates “others” on their own terms? or are they “civilizing missions” that attempt to impose Euro-centric practices and values?

Design/methodology/approach

The authors critically analyze the “promises” of entrepreneurship through CAPE Fund using TribalCrit, a framework rooted in critical race theory (CRT) and postcolonialism. The authors used a CRT research method highlighting two organizational narratives, describing CAPE Fund financing in two separate ventures. The research allowed to test the theory’s use in practical situations.

Findings

This paper develops a postcolonial conception of entrepreneurship to address the realities and needs of Aboriginal communities. Analysis of Canada’s CAPE Fund within two organizational narratives identified aspects of promise (active Aboriginal business ownership) and shortcomings (practices that attempted to erase inequity in ways that led to neocolonial subjugation).

Research limitations/implications

This paper attempts to build theory while engaging in CRT research that relies on organizational narratives. Narrative approaches offer depth of understanding but are not generalizable because of the limited scope of organizations studied.

Practical implications

The research methods used and framework developed offer researchers new approaches to better understand Indigenous and Aboriginal entrepreneurship outcomes. The findings point to specific Aboriginal funding issues that can be addressed by other funding agencies who wish to create more inclusive structures.

Social implications

Financial programs that might improve the possibility of self-determination of Aboriginal peoples within the postcolonial ideal must “hold both economic and non-economic objectives in tension” (Overall et al., 2010 p. 157) in ways that typically disadvantage Aboriginal entrepreneurs.

Originality/value

This is the first, fully articulated framework for postcolonial entrepreneurship, grounded in CRT and applied to analyze Canada’s CAPE Fund.
Communal and student-centered
Authors: Woxland Conrad M. , Cochran Dory , Davis Erin L. , Lundstrom Kacy
Published: February 2017

Purpose

This paper aims to investigate how teaching information creation as a process in a decentralized library classroom impacts student learning and engagement.

Design/methodology/approach

By using mobile technologies (iPads) and a targeted lesson design, the authors explored how these devices can be incorporated into threshold pedagogy. The study took place in a second-year composition course and was taught by librarians during a class session.

Findings

The findings supported by pre- and post-test scores, textual analysis and observations show that iPads did add to the engagement and learning of some students. The discussion includes student responses to the iPads, the decentralized roles of the librarian and instructor, the use of social media as an engagement tool and possible adaptations to the lesson.

Originality/value

This paper provides practical ideas for using iPads in higher education to engage students, particularly in targeting learning outcomes that emphasize on the changing nature and impact of the information creation process.
Meta‐analysis of the human gut microbiome from urbanized and pre‐agricultural populations
Authors: Mancabelli Leonardo , Milani Christian , Lugli Gabriele Andrea , Turroni Francesca , Ferrario Chiara , van Sinderen Douwe , Ventura Marco
Published: February 2017

Metagenomic studies of the human gut microbiome have only recently begun to explore the differences in taxonomic composition between subjects from diverse geographical origins. Here, we compared taxonomy, resistome and functional metabolic properties of publicly available shotgun datasets of human fecal samples collected from different geographical regions (Europe, North America, Asia and Oceania). Such datasets encompassed gut microbiota information corresponding to 13 developed/industrialized societies, as well as two traditional hunter‐gatherer, pre‐agricultural communities (Tanzanian and Peruvian individuals). Assessment of the retrieved taxonomic profiles allowed the most updated reconstruction of the global core‐microbiome as based on currently available data, as well as the identification and targeted genome reconstruction of bacterial taxa that appear to have been lost and/or acquired during urbanization/industrialization. Functional characterization of these metagenomic datasets indicates that the urbanization/industrialization process which occurred in recent human history has shaped the gut microbiota through the acquisition and/or loss of specific gut microbes, thereby potentially impacting on the overall functionality of the gut microbiome.
Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA
Authors: Sproul John S. , Maddison David R.
Published: February 2017

Despite advances that allow DNA sequencing of old museum specimens, sequencing small‐bodied, historical specimens can be challenging and unreliable as many contain only small amounts of fragmented DNA. Dependable methods to sequence such specimens are especially critical if the specimens are unique. We attempt to sequence small‐bodied (3–6 mm) historical specimens (including nomenclatural types) of beetles that have been housed, dried, in museums for 58–159 years, and for which few or no suitable replacement specimens exist. To better understand ideal approaches of sample preparation and produce preparation guidelines, we compared different library preparation protocols using low amounts of input DNA (1–10 ng). We also explored low‐cost optimizations designed to improve library preparation efficiency and sequencing success of historical specimens with minimal DNA, such as enzymatic repair of DNA. We report successful sample preparation and sequencing for all historical specimens despite our low‐input DNA approach. We provide a list of guidelines related to DNA repair, bead handling, reducing adapter dimers and library amplification. We present these guidelines to facilitate more economical use of valuable DNA and enable more consistent results in projects that aim to sequence challenging, irreplaceable historical specimens.
How can we conceptualize behavioural addiction without pathologizing common behaviours?
Authors: Kardefelt‐Winther Daniel , Heeren Alexandre , Schimmenti Adriano , van Rooij Antonius , Maurage Pierre , Carras Michelle , Edman Johan , Blaszczynski Alexander , Khazaal Yasser , Billieux Joël
Published: February 2017

Following the recent changes to the diagnostic category for addictive disorders in DSM‐5, it is urgent to clarify what constitutes behavioural addiction to have a clear direction for future research and classification. However, in the years following the release of DSM‐5, an expanding body of research has increasingly classified engagement in a wide range of common behaviours and leisure activities as possible behavioural addiction. If this expansion does not end, both the relevance and the credibility of the field of addictive disorders might be questioned, which may prompt a dismissive appraisal of the new DSM‐5 subcategory for behavioural addiction. We propose an operational definition of behavioural addiction together with a number of exclusion criteria, to avoid pathologizing common behaviours and provide a common ground for further research. The definition and its exclusion criteria are clarified and justified by illustrating how these address a number of theoretical and methodological shortcomings that result from existing conceptualizations. We invite other researchers to extend our definition under an Open Science Foundation framework.
The role of dual categorization and relative ingroup prototypicality in reparations to a minority group: An examination of empathy and collective guilt as mediators
Authors: Mashuri Ali , Zaduqisti Esti , Alroy‐Thiberge Daphne
Published: February 2017

In the current study, we investigate factors that facilitate or otherwise obstruct reparations of a perpetrating group (i.e. Muslims) to a victim group (i.e. Christians). The study (N = 200) reveals that among Muslim participants, the role of dual Abrahamic categorization in positively predicting reparation attitude towards Christians was mediated by the first group's prosocial emotions of empathy and collective guilt towards the latter group. In addition, relative Muslim prototypicality negatively predicted dual Abrahamic categorization and each of the two prosocial emotions. Empathy and collective guilt in turn mediated the role of relative ingroup prototypicality in negatively predicting reparation attitude. Moreover, as hypothesized, we found that the roles of empathy and collective guilt in predicting reparation intention, as manifested in participants' willingness to engage in collective action on behalf of the victim group, were not significant on their own, but were mediated by reparation attitude. These findings shed light on the importance of the relationship between the perpetrating group's shared identity with the victim group, reduced ingroup focus and its support for making reparations to the victim group. Theoretical implications, study limitations and practical strategies highlighting how to decrease relative Muslim prototypicality are discussed.
Does religious priming increase the prosocial behaviour of a Japanese sample in an anonymous economic game?
Authors: Miyatake Sanae , Higuchi Masataka
Published: February 2017

We examined the effect of religious priming on a Japanese sample in an anonymous dictator game whereas previous studies on religious priming on prosociality had mainly been conducted within Western contexts. The current study attempted to examine whether religion increases prosocial behaviour in a Japanese sample through the replication of ‘God is Watching You’ (Shariff & Norenzayan, 2007) where it was found that participants primed with religion‐related words and secular justice‐related words behaved more prosocially than participants primed with neutral words in an anonymous dictator game. The current experiment was conducted with Japanese students (n = 106) to examine whether the results of the original study could be applied to Japanese people. The results showed that among the three priming conditions (control, religion, secular justice), there was no difference in the amount of money participants allocated to anonymous strangers, although in the secular justice priming condition, theists allocated more money than atheists. The results might be due to the fact that the religious priming words used in the original study did not precisely activate the propositional network of religion that Japanese participants have. More culture‐specific studies are necessary to examine how religious priming works for non‐Westerners.
Does midwife experience affect the rate of severe perineal tears?
Authors: Mizrachi Yossi , Leytes Sophia , Levy Michal , Hiaev Zvia , Ginath Shimon , Bar Jacob , Kovo Michal
Published: February 2017

Background

Our aim was to study whether midwife experience affects the rate of severe perineal tears (3rd and 4th degree).

Methods

A retrospective cohort study of all women with term vertex singleton pregnancies, who underwent normal vaginal deliveries, in a single tertiary hospital, between 2011 and 2015, was performed. Exclusion criteria were instrumental deliveries and stillbirth. All midwives used a “hands on” technique for protecting the perineum. The midwife experience at each delivery was calculated as the time interval between her first delivery and current delivery. A comparison was performed between deliveries in which midwife experience was less than 2 years (inexperienced), between 2 and 10 years (moderately experienced), and more than 10 years (highly experienced). A multivariate regression analysis was performed to assess the association between midwife experience and the incidence of severe perineal tears, after controlling for confounders.

Results

Overall, 15 146 deliveries were included. Severe perineal tears were diagnosed in 51 (0.33%) deliveries. Women delivered by inexperienced midwives had a higher rate of severe perineal tears compared with women delivered by highly experienced midwives (0.5% vs 0.2%, respectively, P=.024). On multivariate regression analysis, midwife experience was independently associated with a lower rate of severe perineal tears, after controlling for confounding factors. Each additional year of experience was associated with a 4.7% decrease in the risk of severe perineal tears (adjusted OR 0.95 [95% CI 0.91–0.99, P=.03).

Conclusion

More experienced midwives had a lower rate of severe perineal tears, and may be preferred for managing deliveries of women at high risk for such tears.
Sentinel node biopsy for prostate cancer: report from a consensus panel meeting
Authors: van der Poel Henk G. , Wit Esther M. , Acar Cenk , van den Berg Nynke S. , van Leeuwen Fijs W. B. , Valdes Olmos Renato A. , Winter Alexander , Wawroschek Friedhelm , Liedberg Fredrik , Maclennan Steven , Lam Thomas ,   the Sentinel Node Prostate Cancer Consensus Panel Group members
Published: February 2017

Objective

To explore the evidence and knowledge gaps in sentinel node biopsy (SNB) in prostate cancer through a consensus panel of experts.

Methods

A two‐round Delphi survey among experts was followed by a consensus panel meeting of 16 experts in February 2016. Agreement voting was performed using the research and development project/University of California, Los Angeles Appropriateness Methodology on 150 statements in nine domains. The disagreement index based on the interpercentile range, adjusted for symmetry score, was used to assess consensus and non‐consensus among panel members.

Results

Consensus was obtained on 91 of 150 statements (61%). The main outcomes were: (1) the results from an extended lymph node dissection (eLND) are still considered the ‘gold standard’, and sentinel node (SN) detection should be combined with eLND, at least in patients with intermediate‐ and high‐risk prostate cancer; (2) the role of SN detection in low‐risk prostate cancer is unclear; and (3) future studies should contain oncological endpoints as number of positive nodes outside the eLND template, false‐negative and false‐positive SN procedures, and recurrence‐free survival. A high rate of consensus was obtained regarding outcome measures of future clinical trials on SNB (89%). Consensus on tracer technology was only obtained in 47% of statements, reflecting a need for further research and standardization in this area. The low‐level evidence in the available literature and the composition of mainly SNB users in the panel constitute the major limitations of the study.

Conclusions

Consensus on a majority of elementary statements on SN detection in prostate cancer was obtained.; therefore, the results from this consensus report will provide a basis for the design of further studies in the field. A group of experts identified evidence and knowledge gaps on SN detection in prostate cancer and its application in daily practice. Information from the consensus statements can be used to direct further studies.
Orthosteric and allosteric potentiation of heteromeric neuronal nicotinic acetylcholine receptors
Authors: Wang Jingyi , Lindstrom Jon
Published: February 2017

Heteromeric nicotinic ACh receptors (nAChRs) were thought to have two orthodox agonist‐binding sites at two α/β subunit interfaces. Highly selective ligands are hard to develop by targeting orthodox agonist sites because of high sequence similarity of this binding pocket among different subunits. Recently, unorthodox ACh‐binding sites have been discovered at some α/α and β/α subunit interfaces, such as α4/α4, α5/α4 and β3/α4. Targeting unorthodox sites may yield subtype‐selective ligands, such as those for (α4β2)2α5, (α4β2)2β3 and (α6β2)2β3 nAChRs. The unorthodox sites have unique pharmacology. Agonist binding at one unorthodox site is not sufficient to activate nAChRs, but it increases activation from the orthodox sites. NS9283, a selective agonist for the unorthodox α4/α4 site, was initially thought to be a positive allosteric modulator (PAM). NS9283 activates nAChRs with three engineered α4/α4 sites. PAMs, on the other hand, act at allosteric sites where ACh cannot bind. Known PAM sites include the ACh‐homologous non‐canonical site (e.g. morantel at β/α), the C‐terminus (e.g. Br‐PBTC and 17β‐estradiol), a transmembrane domain (e.g. LY2087101) or extracellular and transmembrane domain interfaces (e.g. NS206). Some of these PAMs, such as Br‐PBTC and 17β‐estradiol, require only one subunit to potentiate activation of nAChRs. In this review, we will discuss differences between activation from orthosteric and allosteric sites, their selective ligands and clinical implications. These studies have advanced understanding of the structure, assembly and pharmacology of heteromeric neuronal nAChRs.

Linked Articles

This article is part of a themed section on Nicotinic Acetylcholine Receptors. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.11/issuetoc
Suppressors of cytokine signaling: Potential immune checkpoint molecules for cancer immunotherapy
Authors: Chikuma Shunsuke , Kanamori Mitsuhiro , Mise‐Omata Setsuko , Yoshimura Akihiko
Published: February 2017

Inhibition of immune checkpoint molecules, PD‐1 and CTLA4, has been shown to be a promising cancer treatment. PD‐1 and CTLA4 inhibit TCR and co‐stimulatory signals. The third T cell activation signal represents the signals from the cytokine receptors. The cytokine interferon‐γ (IFNγ) plays an important role in anti‐tumor immunity by activating cytotoxic T cells (CTLs). Most cytokines use the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway, and the suppressors of cytokine signaling (SOCS) family of proteins are major negative regulators of the JAK/STAT pathway. Among SOCS proteins, CIS, SOCS1, and SOCS3 proteins can be considered the third immunocheckpoint molecules since they regulate cytokine signals that control the polarization of CD4+ T cells and the maturation of CD8+ T cells. This review summarizes recent progress on CIS, SOCS1, and SOCS3 in terms of their anti‐tumor immunity and potential applications.
Sox2‐dependent inhibition of p21 is associated with poor prognosis of endometrial cancer
Authors: Yamawaki Kaoru , Ishiguro Tatsuya , Mori Yutaro , Yoshihara Kosuke , Suda Kazuaki , Tamura Ryo , Yamaguchi Masayuki , Sekine Masayuki , Kashima Katsunori , Higuchi Masaya , Fujii Masahiro , Okamoto Koji , Enomoto Takayuki
Published: February 2017

Sex‐determining region Y‐box 2 (SOX2) is an essential factor involved in the self‐renewal and pluripotency of embryonic stem cells and has functions in cell survival and progression in many types of cancers. Here, we found that several endometrial cancer cell lines expressed SOX2, which was required for cell growth. Additionally, SOX2 overexpression regulated the expression of cyclin‐dependent kinase inhibitor 1A (CDKN1A), and SOX2 specifically bound to p21 promoter DNA in endometrial cancer cell lines expressing SOX2. Expressions of SOX2 in endometrial cancer patients were significantly correlated with histological grade and poor prognosis. Moreover, low p21 together with high SOX2 expressions in advanced endometrial cancer patients were associated with the most unfavorable outcomes of patients. These results indicated that simultaneous measurement of SOX2 and p21 expression in endometrial cancer patients may be a useful biomarker for patient prognosis.
Serum carotenoid and tocopherol concentrations and risk of asthma in childhood: a nested case–control study
Authors: Hämäläinen N. , Nwaru B. I. , Erlund I. , Takkinen H.‐M. , Ahonen S. , Toppari J. , Ilonen J. , Veijola R. , Knip M. , Kaila M. , Virtanen S. M.
Published: February 2017

Background

The antioxidant hypothesis regarding the risk of asthma in childhood has resulted in inconsistent findings. Some data indicate that the role of antioxidants in childhood asthma risk may have a critical time window of effect, but only a well‐designed longitudinal cohort study can clarify this hypothesis.

Objective

To study the longitudinal associations between serum carotenoid and tocopherol concentrations during the first 4 years of life and asthma risk by the age of 5 years.

Methods

Based on a case–control design nested within a Finnish birth cohort, 146 asthma cases were matched to 270 controls on birth time, sex, genetic risk, and birth place. Non‐fasting blood samples were collected at the ages of 1, 1.5, 2, 3, and 4 years and serum carotenoids and tocopherols were analysed. Parents reported the presence and age at start of persistent doctor‐diagnosed asthma in the child at the age of 5 years. Data analyses were conducted using generalized estimating equations.

Results

We did not find strong associations between serum carotenoids and tocopherols and the risk of asthma based on age‐specific and longitudinal analyses. Both lower and higher quarters of α‐carotene and γ‐tocopherol increased the risk of asthma.

Conclusions

The current findings do not support the suggestion that the increased prevalence of asthma may be a consequence of decreased intake of antioxidant nutrients. Moreover, we did not confirm any critical time window of impact of antioxidants on asthma risk. Replication of these findings in similar longitudinal settings will strengthen this evidence base.