bluuebunny/crossref_metadata_2025 huggingface dataset:
Modelling of lucerne (Medicago sativa L.) for livestock production in diverse environments
Authors: Smith Andrew P. , Moore Andrew D. , Boschma Suzanne P. , Hayes Richard C. , Nie Zhongnan , Pembleton Keith G.
Published: February 2017

Several models exist to predict lucerne (Medicago sativa L.) dry matter production; however, most do not adequately represent the ecophysiology of the species to predict daily growth rates across the range of environments in which it is grown. Since it was developed in the late 1990s, the GRAZPLAN pasture growth model has not been updated to reflect modern genotypes and has not been widely validated across the range of climates and farming systems in which lucerne is grown in modern times. Therefore, the capacity of GRAZPLAN to predict lucerne growth and development was assessed. This was done by re-estimating values for some key parameters based on information in the scientific literature. The improved GRAZPLAN model was also assessed for its capacity to reflect differences in the growth and physiology of lucerne genotypes with different winter activity. Modifications were made to GRAZPLAN to improve its capacity to reflect changes in phenology due to environmental triggers such as short photoperiods, declining low temperatures, defoliation and water stress. Changes were also made to the parameter governing the effect of vapour pressure on the biomass-transpiration ratio and therefore biomass accumulation. Other developments included the representation of root development and partitioning of canopy structure, notably the ratio leaf : stem dry matter. Data from replicated field experiments across Australia were identified for model validation. These data were broadly representative of the range of climate zones, soil types and farming systems in which lucerne is used for livestock grazing. Validation of predicted lucerne growth rates was comprehensive owing to plentiful data. Across a range of climate zones, soils and farming systems, there was an overall improvement in the capacity to simulate pasture dry matter production, with a reduction in the mean prediction error of 0.33 and the root-mean-square deviation of 9.6 kg/ha.day. Validation of other parts of the model was restricted because information relating to plant roots, soil water, plant morphology and phenology was limited. This study has highlighted the predictive power, versatility and robust nature of GRAZPLAN to predict the growth, development and nutritive value of perennial species such as lucerne.
Habitat selection by two sympatric rodent species in an alpine resort
Authors: Beilharz Lisa V. , Whisson Desley A.
Published: February 2017

Conservation of small mammal species relies on an understanding of their habitat use. We used trapping surveys and telemetry to examine habitat selection and use by the broad-toothed rat (Mastacomys fuscus mordicus) and the bush rat (Rattus fuscipes) in an alpine resort in Victoria. M. fuscus occurred at low numbers, nesting in subalpine wet heathland and foraging in that habitat as well as small patches of disturbed woodland. In contrast, R. fuscipes was more common and nested in woodlands. Although foraging primarily in woodlands, R. fuscipes also foraged in all other available habitats. Both species showed strong selection for woodland fragments within ski runs. Although highly disturbed, these habitats may provide important habitat and connectivity between less disturbed and larger habitat patches.
Bordetella
PlrSR regulatory system controls BvgAS activity and virulence in the lower respiratory tract
Authors: Bone M. Ashley , Wilk Aaron J. , Perault Andrew I. , Marlatt Sara A. , Scheller Erich V. , Anthouard Rebecca , Chen Qing , Stibitz Scott , Cotter Peggy A. , Julio Steven M.
Published: February 2017

Significance

Bordetella
spp. includes
Bordetella pertussis
, the causal agent of whooping cough. The
Bordetella
virulence gene (BvgAS) two-component regulatory system (TCS) is considered the “master virulence regulator” in
Bordetella
, as it controls expression of all known virulence factor-encoding genes. We show here that another TCS, PlrSR, is required for BvgAS activity in the lower respiratory tract (LRT) and for virulence even when BvgAS is rendered constitutively active, suggesting that it controls critical functions for bacterial survival in the LRT independently of BvgAS. Our data introduce a new layer of complexity to a paradigm of
Bordetella
virulence control that has held for more than 30 y, and they indicate the existence of previously unknown bacterial factors that may serve as vaccine components and therapeutic targets.
TGF-β inhibitor Smad7 regulates dendritic cell-induced autoimmunity
Authors: Lukas Dominika , Yogev Nir , Kel Junda M. , Regen Tommy , Mufazalov Ilgiz A. , Tang Yilang , Wanke Florian , Reizis Boris , Müller Werner , Kurschus Florian C. , Prinz Marco , Kleiter Ingo , Clausen Björn E. , Waisman Ari
Published: February 2017

Significance

Smad7 is a negative regulator of TGF-β signaling, a cytokine with anti-inflammatory properties. Although TGF-β was implicated in the development and function of dendritic cells (DCs), the in vivo role of Smad7 in DCs remains elusive. Here, we demonstrate that DC-specific Smad7 deletion affects the development of splenic CD8+CD103+DCs by regulating expression of the transcription factors Batf3 and IRF8. In addition, Smad7 directs DC function by regulating the expression of indoleamine 2,3-dioxygenase in response to IFN-γ signaling. Hence, absent Smad7 in DCs mediates resistance of mice to the development of autoimmunity via protective regulatory T-cell induction. These findings demonstrate that Smad7 expression governs splenic DC subset differentiation and affects tolerogenic DC function in vivo.
Reaction dynamics analysis of a reconstituted
Escherichia coli
protein translation system by computational modeling
Authors: Matsuura Tomoaki , Tanimura Naoki , Hosoda Kazufumi , Yomo Tetsuya , Shimizu Yoshihiro
Published: February 2017

Significance

Biological systems are driven by multiple components and interactions that form a complex reaction network. We developed a method to analyze their dynamics by focusing on the component in temporal plateaus, or a quasi-stationary state (QSS). The analyses, using a computational model of a minimal in vitro protein synthesis system, showed that components in a QSS form clusters that grow over time. However, the growth is not in a linear fashion: The process involved collapse and regrowth of the formed clusters, where the collapse was closely related to the phase transition in the reaction network. These observations suggest that the studies focusing on the QSS might be useful for understanding of complex reaction dynamics.
Crystal structure of the adenosine A
2A
receptor bound to an antagonist reveals a potential allosteric pocket
Authors: Sun Bingfa , Bachhawat Priti , Chu Matthew Ling-Hon , Wood Martyn , Ceska Tom , Sands Zara A. , Mercier Joel , Lebon Florence , Kobilka Tong Sun , Kobilka Brian K.
Published: February 2017

Significance

The A
2A
R is a G protein-coupled receptor (GPCR) that plays important roles in cardiovascular physiology and immune function. The A
2A
R is also a target for the treatment of Parkinson’s disease, where A
2A
R antagonists have been shown to enhance signaling through the D2 dopamine receptor. Here we present the crystal structure of the A
2A
R bound to a novel bitopic antagonist. As a result of structural changes needed to accommodate the bound antagonist, crystals could not be grown in lipidic cubic phase. Instead, crystals were grown in detergent with a type II packing rarely observed in GPCR crystals. The structure revealed a potential allosteric pocket that that can be exploited to develop subtype-selective allosteric modulators.
MicroRNA-10a is crucial for endothelial response to different flow patterns via interaction of retinoid acid receptors and histone deacetylases
Authors: Lee Ding-Yu , Lin Ting-Er , Lee Chih-I , Zhou Jing , Huang Yi-Hsuan , Lee Pei-Ling , Shih Yu-Tsung , Chien Shu , Chiu Jeng-Jiann
Published: February 2017

Significance

This study demonstrates that hormone receptor RARα plays a vital role in the selective activation of proinflammatory and anti-inflammatory signaling to modulate the miR-10a/GATA6/VCAM-1 cascade in endothelial cells in response to proatherogenic oscillatory shear stress (OS) vs. atheroprotective pulsatile shear stress (PS). HDAC-3/5/7 and RXRα are induced by OS and PS to serve as mechanosensitive “repressors” and “enhancers,” respectively, to associate with RARα to modulate its binding to RA-responsive element (RARE) to switch miR-10a expression. Our findings provide insight into the relationship between two different epigenetic factors (HDACs and miRs) and hormone receptors (RARα and RXRα) in the regulation of endothelial functions and elucidate new mechanisms of hemodynamic-based pathophysiology of the atherosclerotic vascular wall.
The VDAC2–BAK axis regulates peroxisomal membrane permeability
Authors: Hosoi Ken-ichiro , Miyata Non , Mukai Satoru , Furuki Satomi , Okumoto Kanji , Cheng Emily H. , Fujiki Yukio
Published: February 2017

Peroxisomal biogenesis disorders (PBDs) are fatal genetic diseases consisting of 14 complementation groups (CGs). We previously isolated a peroxisome-deficient Chinese hamster ovary cell mutant, ZP114, which belongs to none of these CGs. Using a functional screening strategy, VDAC2 was identified as rescuing the peroxisomal deficiency of ZP114 where VDAC2 expression was not detected. Interestingly, knockdown of BAK or overexpression of the BAK inhibitors BCL-XL and MCL-1 restored peroxisomal biogenesis in ZP114 cells. Although VDAC2 is not localized to the peroxisome, loss of VDAC2 shifts the localization of BAK from mitochondria to peroxisomes, resulting in peroxisomal deficiency. Introduction of peroxisome-targeted BAK harboring the Pex26p transmembrane region into wild-type cells resulted in the release of peroxisomal matrix proteins to cytosol. Moreover, overexpression of BAK activators PUMA and BIM permeabilized peroxisomes in a BAK-dependent manner. Collectively, these findings suggest that BAK plays a role in peroxisomal permeability, similar to mitochondrial outer membrane permeabilization.
Discussion Networks
Authors: McClurg Scott D. , Klofstad Casey A. , Sokhey Anand Edward
Published: February 2017

While political network research is often a holistic enterprise, the network paradigm can also be used to study individual behavior. Specifically, rather than focusing on full network structures, a well-established area of research considers individuals’ “core” networks, their perceptions of interpersonal connections, and the consequences of said micro-social environments for myriad political outcomes and processes. This chapter examines this research tradition, tracing the history of its use in the study of political behavior. It begins with discussion of network research, paying specific attention to “egocentric” network name generator techniques. It then outlines several challenges to this research paradigm: (1) the difficulty of making causal inferences, (2) debates over concept and measurement, and (3) questions about mechanisms of influence. The chapter concludes by reviewing advances in the field that have developed from these challenges and points toward next steps in this research agenda, focused on the connected citizenry.
Rock Art, Music, and Acoustics
Authors: Díaz-Andreu Margarita , Mattioli Tommaso
Published: February 2017

This chapter reviews evidence for relationships between acoustics and rock art by examining the antiquity and nature of such relationships, then examining evidence for music depicted or engraved in rock art. This is followed by a summary of the remains of actual musical instruments found at rock art sites, including lithophones found at or close to rock art. The sonority of rock art landscapes is then assessed, first in those cases where natural elements can unleash special sonorous effects and then in places where exceptional acoustics have been selected for the creation of artworks. The authors conclude that a consideration of sound is common in the placement of rock art and that it should therefore be more routinely considered when recording rock art. The significance of sound in social relations and religious activities makes this aspect of rock art sites essential for understanding the societies that produced it.
Spirituality
Authors: Pargament Kenneth I. , Mahoney Annette
Published: February 2017

This chapter reviews the growing literature on spirituality. Spirituality is defined as a search for the sacred. The term search indicates that spirituality is a process, one that involves efforts to discover the sacred, hold onto the sacred once it has been found, and transform the sacred when necessary. Spirituality is a process that unfolds in different ways, depending on a unique blend of biological, social, psychological, situational, and transcendent forces. At its best, spirituality is broad and deep, responsive to life’s situations, nurtured by the larger social context, capable of flexibility and continuity, and oriented toward a life-enhancing destination. At its worst, spirituality lacks scope and depth, clashes unnecessarily with the surrounding social system, changes and shifts too easily or not at all, and misdirects the individual in the pursuit of spiritual value. Social scientists and health professionals have begun to develop spiritually integrated interventions, with some promising results.
Frequentism
Authors: La Caze Adam
Published: February 2017

This chapter introduces the key frequentist interpretation of probability as developed by Venn, von Mises and Reichenbach. Frequentists identify probabilities with frequencies; but there are problems with this identification. Finite frequentism is beset with problems, including the problem of the single case. Hypothetical frequentism, identifying probability with limiting relative frequencies in infinitely repeated trials, provides a response to the problems of finite frequentism and is consistent with the interpretation of probability in many areas of science. But identifying probability with hypothetical frequencies raises new questions. The chapter focuses on the main criticisms leveled against frequentism. The problems of frequentism raise interesting questions for the role of frequentist probabilities in science. Throughout the chapter an attempt is made to identify the different criteria by which frequentism is assessed as an interpretation of probability in contrast to the instrumental focus of many frequentists in assessing the role of probabilities in science.
The Improbable Journeys of Epiphytic Plants Across The Andes: Historical Biogeography ofCycnoches(Catasetinae, Orchidaceae)
Authors: Pérez-Escobar Oscar Alejandro , Gottschling Marc , Chomicki Guillaume , Condamine Fabien L. , Klitgård Bente , Pansarin Emerson , Gerlach Günter
Published: February 2017

The Andean uplift is one of the major orographic events in the New World and has impacted considerably the diversification of numerous Neotropical organisms. Despite its importance for biogeography, the specific role of mountain ranges as a dispersal barrier between South and Central American lowland plant lineages is still poorly understood. The swan orchids (Cycnoches) compriseca34 epiphytic species distributed in lowland and pre-montane forests of Central and South America. Here, we study the historical biogeography ofCycnochesto better understand the impact of the Andean uplift on the diversification of Neotropical lowland plant lineages. Using novel molecular sequences (five nuclear and plastid regions) and twelve biogeographic models with and without founder-event speciation, we infer that the most recent common ancestor ofCycnochesmay have originated in Amazoniaca5 Mya. The first colonization of Central America occurred from a direct migration event from Amazonia, and multiple bidirectional trans-Andean migrations between Amazonia and Central America took place subsequently. Notably, such biological exchange occurred well after major mountain building periods. The Andes have not acted as an impassable barrier for epiphytic lowland lineages such as orchids having a great potential for effortless dispersal because of the very light, anemochorous seeds.
miRNAs cooperate in apoptosis regulation during C. elegans development
Authors: Sherrard Ryan , Luehr Sebastian , Holzkamp Heinke , McJunkin Katherine , Memar Nadin , Conradt Barbara
Published: February 2017

Programmed cell death occurs in a highly reproducible manner during Caenorhabditis elegans development. We demonstrate that, during embryogenesis, miR-35 and miR-58 bantam family microRNAs (miRNAs) cooperate to prevent the precocious death of mothers of cells programmed to die by repressing the gene egl-1, which encodes a proapoptotic BH3-only protein. In addition, we present evidence that repression of egl-1 is dependent on binding sites for miR-35 and miR-58 family miRNAs within the egl-1 3′ untranslated region (UTR), which affect both mRNA copy number and translation. Furthermore, using single-molecule RNA fluorescent in situ hybridization (smRNA FISH), we show that egl-1 is transcribed in the mother of a cell programmed to die and that miR-35 and miR-58 family miRNAs prevent this mother from dying by keeping the copy number of egl-1 mRNA below a critical threshold. Finally, miR-35 and miR-58 family miRNAs can also dampen the transcriptional boost of egl-1 that occurs specifically in a daughter cell that is programmed to die. We propose that miRNAs compensate for lineage-specific differences in egl-1 transcriptional activation, thus ensuring that EGL-1 activity reaches the threshold necessary to trigger death only in daughter cells that are programmed to die.
Finite element analysis of flexible functionally graded beams with variable Poisson’s ratio
Authors: Pascon João Paulo
Published: February 2017

Purpose

The purpose of this paper is to deal with large deformation analysis of plane beams composed of functionally graded (FG) elastic material with a variable Poisson’s ratio.

Design/methodology/approach

The material is assumed to be linear elastic, with a Poisson’s ratio varying according to a power law along the thickness direction. The finite element used is a plane beam of any-order of approximation along the axis, and with four transverse enrichment schemes, which can describe constant, linear, quadratic and cubic variation of the strain along the thickness direction. Regarding the constitutive law, five materials are adopted: two homogeneous limiting cases, and three intermediate FG cases. The effect of both finite element kinematics and distribution of Poisson’s ratio on the mechanical response of a cantilever is investigated.

Findings

In accordance with the scientific literature, the second scheme, in which the transverse strain is linearly variable, is sufficient for homogeneous long (or thin) beams under bending. However, for FG short (or moderate thick) beams, the third scheme, in which the transverse strain variation is quadratic, is needed for a reliable strain or stress distribution.

Originality/value

In the scientific literature, there are several studies regarding nonlinear analysis of functionally graded materials (FGMs) via finite elements, analysis of FGMs with constant Poisson’s ratio, and geometrically linear problems with gradually variable Poisson’s ratio. However, very few deal with finite element analysis of flexible beams with gradually variable Poisson’s ratio. In the present study, a reliable formulation for such beams is presented.
Predictive modeling of surface roughness in ultrasonic machining of cryogenic treated Ti-6Al-4V
Authors: Dhuria Gaurav , Singh Rupinder , Batish Ajay
Published: February 2017

Purpose

The purpose of this paper is to study the effect of ultrasonic machining process parameters on surface quality while machining titanium alloy Ti-6Al-4V.

Design/methodology/approach

Effect of cryogenic treatment (CT) of tool and work material was also explored in the study. Taguchi’s L18 orthogonal array was chosen for design of experiments and average surface roughness was measured.

Findings

Different modes of fracture were detected at work surface corresponding to varied input process parameters. Slurry grit size, power rating and tool material along with CT of work material were found to be the significant parameters affecting surface quality.

Originality/value

The results obtained have been modelled using artificial neural network approach.
Generational perceptions at work: in-group favoritism and out-group stereotypes
Authors: Weeks Kelly Pledger , Weeks Matthew , Long Nicolas
Published: February 2017

Purpose

The purpose of this paper is to examine the relationship between stereotypes, in-group favoritism, and in-group bolstering effects across generations.

Design/methodology/approach

Based on the trends found in a qualitative study on generational stereotypes, questions on work ethic, work-life balance, and use of technology were administered to 255 participants identified as Millennials, Generation X, and Baby Boomers. Hypotheses predicted that with a strong stereotype, traditional in-group favoritism will not be found; however, an in-group bolstering effect will emerge. In the absence of a strong stereotype, traditional in-group favoritism is expected.

Findings

Generally, there was a strong stereotype that Baby Boomers are worse at technology than Generation X and Generation X is worse than Millennials. There was also a strong stereotype that Millennials do not do what it takes to get the job done as much as other generations. In the presence of these stereotypes, traditional in-group favoritism was not found, but in-groups bolstered themselves by rating themselves more favorably than other groups rated them. Although these findings did not hold for every item studied, there was moderate support for all three hypotheses.

Practical implications

As employees become aware of their biases, they can collaborate better with employees who are different than they are. Practical recommendations are suggested.

Originality/value

The paper applies theory of in-group favoritism to the perceptions of generational cohorts.
Cross-sectional variation of market efficiency
Authors: Jiang Jing
Published: February 2017

Purpose

This paper aims to provide evidence that market efficiency varies greatly across individual stock, and across market exchanges.

Design/methodology/approach

Three approaches, partial adjustment model, Dimson beta model and variance ratio test, are used on a large sample of US stocks.

Findings

This paper finds prices are closer to random walk benchmarks (i.e. more efficient) for stocks with better liquidity provision, frequent trading, greater return volatility, higher prices, larger market capitalizations and smaller trade sizes. These findings suggest that liquidity stimulates arbitrage activity, which, in turn, enhances market efficiency. Market efficiency also varies with information environment. The results show that stocks with greater information-based trading exhibit higher level of efficiency. Finally, market structure influences market efficiency. New York Stock Exchange stocks achieve higher level of efficiency than NASDAQ stocks do. The empirical results are robust and not driven by differences in stock attributes between the two markets.

Research limitations/implications

Overall, these results indicate that liquidity provision, stock attributes and market structure exert a significant impact on the realization of market efficiency.

Practical implications

In addition, this paper is also relevant to both stock exchanges facing increased competition and to market regulators.

Originality/value

Prior studies offer little evidence on the speed at which new information is impounded into the price. There is also limited evidence regarding how liquidity provision and market structure affect market efficiency. Using a transformation of the speed of price adjustment and other measurements as proxies for individual stock efficiency, this study may shed further lights on our understanding of market efficiency.
Corporate governance and executive perquisites
Authors: Andrews Angela , Linn Scott , Yi Han
Published: February 2017

Purpose

The purpose of this paper is to examine the relation between executive perquisite consumption and indicators of corporate governance after the Securities and Exchange Commission (SEC) expanded the disclosure requirements related to perquisites.

Design/methodology/approach

This study uses ordinary least squares and Tobit regressions to examine the dollar value of perquisites consumed, the number of perquisites consumed and the types of perquisites consumed.

Findings

The analysis shows that firms with weak corporate governance are more likely to award perquisites to executives. Firms characterized as being more prone to the presence of agency problems are associated with greater levels of perquisite consumption. Finally, there is evidence that not all perquisite consumptions can be attributed to an agency problem. Efficiently operating firms are associated with greater levels of perquisite consumption as are larger firms.

Research limitations/implications

The authors examine firms in the period immediately after the SEC initiated the expanded disclosures. This may limit the generalizability of the results to other exchange-listed firms that changed their perquisite policy as a result of the rule change.

Originality/value

The paper extends the literature on corporate governance and mandatory corporate disclosure by investigating the association between corporate governance characteristics and perquisite consumption. This paper examines this relation immediately after the SEC expanded the disclosures surrounding perquisites to provide the public with more transparent disclosures.
‘Post‐Third‐World City' or Neoliberal ‘City of Exception'? Rio de Janeiro in the Olympic Era
Authors: Aaron Richmond Matthew , Garmany Jeff
Published: February 2017

This article considers processes of urban development within the context of mega‐event preparations in Rio de Janeiro. We begin with a brief overview of these development processes, highlighting their connections to political and economic change in recent years. Proponents of these mega‐event‐led initiatives argue that Rio is undergoing a period of inclusive growth and integration: a perspective we call here a ‘post‐Third‐World city' narrative of urban renewal. Critics, however, contend that urban officials are harnessing mega‐events (e.g. the 2014 World Cup and the 2016 Olympic Games) to push forward a neoliberal agenda of socially unjust policies benefiting the interests of capital and marginalizing the city's poor and especially its favelas (i.e. the ‘city‐of‐exception' thesis). In this article we explore the insights of these two perspectives and consider why they have grown popular in recent years. Though we side generally with the city‐of‐exception thesis, we argue that important geographic and historical particularities must also be accounted for. Without carefully situating analytical perspectives empirically—in particular, cases in which theoretical models are drawn from European and North American contexts—urban researchers risk concealing more than they reveal in analyses of rapidly developing countries like Brazil.
Sexual Dimorphism of the First Rib: A Comparative Approach Using Metric and Geometric Morphometric Analyses
Authors: Lynch Jeffrey James , Cross Peter , Heaton Vivienne
Published: February 2017

This research investigated the sexual dimorphism of the first human rib using geometric morphometric and metric approaches on a sample of 285 specimens containing European Americans and African Americans from the Hamann‐Todd collection. Metric measurements were investigated for sexual dimorphism and ancestral differences using univariate statistics. Four type II landmarks and 40 sliding semi‐landmarks were placed outlining the dorsal and ventral curvatures of the ribs. Landmark data were processed using Generalized Procrustes Analyses with Procrustes distance sliding, and the subsequent coordinates were investigated for sexual dimorphism and ancestral differences using Procrustes ANOVAs. Both geometric morphometric and metric data were analyzed using cross‐validated discriminant function analyses to test the hypothesis that variables from both approaches can be combined to increase sex classification rate. European Americans had sex correctly classified as high as 88.05% and African Americans as high as 70.86% using a combination of metric and geometric morphometric variables.
Application of the Stephan et al. Chest Radiograph Comparison Method to Decomposed Human Remains
Authors: Isa Mariyam I. , Hefner Joseph T. , Markey Michael A.
Published: February 2017

This manuscript describes the use of comparative radiography of the chest to facilitate positive identification of human remains in advanced stages of decomposition. The method reported by Stephan et al. for positive identification of dry, disarticulated skeletal elements was used on semifleshed, decomposing remains. Positive identification was established through multiple points of concordance observed in radiographs of the left and right clavicles and the C5‐T1 vertebrae. This case study demonstrates the applicability of the Stephan et al.'s method in cases involving decomposing remains.
The impact of firm size on dynamic incentives and investment
Authors: Chi Chang‐Koo , Choi Kyoung Jin
Published: February 2017

Recent studies conclude that small firms have higher but more variable growth rates than large firms. To explore how this empirical regularity affects moral hazard and investment, we develop an agency model with a firm size process having two features: the drift is controlled by the agent's effort and the principal's investment decision, and the volatility is proportional to the square root of size. The firm improves on production efficiency as it grows, and wages are back‐loaded when size is small but front‐loaded when it is large. Furthermore, there is underinvestment in a small firm but overinvestment in a large firm.
HAX1 mutation positive children presenting with haemophagocytic lymphohistiocytosis
Authors: Karapınar Tuba H. , Yılmaz Karapinar Deniz , Oymak Yeşim , Ay Yılmaz , Demirağ Bengü , Aykut Ayça , Onay Hüseyin , Hazan Filiz , Aydınok Yeşim , Özkınay Ferda , Vergin Canan
Published: February 2017

The genetic basis of haemophagocytic lymphohistiocytosis (HLH) has not been elucidated in 10% of affected patients. In this study, we report four HLH episodes in three patients with HAX1 gene mutations. We screened the mutations associated with congenital neutropenia (CN) because the neutropenia persisted following HLH treatment. There were homozygous HAX1 mutations detected in all patients. This is the first case series of patients with CN caused by HAX1 mutation who presented with HLH. We hypothesize that severe neutropenia persists after an HLH episode in children without HLH mutations (especially infants) because these patients have CN caused by HAX1 mutations.
Burial and exhumation of the western border of the Ukrainian Shield (Podolia): a multi‐disciplinary approach
Authors: Schito Andrea , Andreucci Benedetta , Aldega Luca , Corrado Sveva , Di Paolo Lea , Zattin Massimiliano , Szaniawski Rafal , Jankowski Leszek , Mazzoli Stefano
Published: February 2017

The Podolia region is located along the western border of the Eastern European Craton, which is also known as Ukrainian Shield. From the Ordovician to the Miocene, this area formed part of an epicontinental basin system. In order to investigate the effects of orogenic cycles occurring along the plate margin, a multi‐disciplinary approach was used in this study. Paleotemperature analysis and low‐temperature thermochronometry were combined with stratigraphic data to obtain a burial model for the Paleozoic succession exposed in the study area. Maximum burial for Silurian and Devonian rocks occurred during the Devonian and Early Carboniferous at depths of 4–5 km, as constrained by vitrinite reflectance and illite content in mixed illite‐smectite layers. Thermochronometric data indicate that exhumation through the 45–120 °C temperature range took place between the Late Triassic and the Early Jurassic, and that no significant burial occurred afterwards (temperatures characterising the stratigraphically lowermost units remaining below ca. 60 °C). These results point to a major exhumation event coeval with the Cimmerian orogenesis, which took place a few hundreds of kilometres away from the study area. On the other hand, no significant effect of the Alpine orogenesis was recorded, although the collisional front was located <100 km from the Podolia region. This work shows how paleothermal and thermochronometric analyses can be successfully integrated with stratigraphic data to reconstruct the burial history, and how the burial history of a basin located on a plate margin can, in some cases, be independent from the distance of the margin from the collisional fronts.
Industry sponsorship in trials on fluoride varnish or gels for caries prevention
Authors: Reda Seif , Elhennawy Karim , Meyer‐Lückel Hendrik , Paris Sebastian , Schwendicke Falk
Published: February 2017

Objectives

Fluoride is effective for caries prevention, but trials on fluoride varnish or gels are often industry‐sponsored. We assessed trial design and findings in sponsored and nonsponsored trials on fluoride varnish and fluoride gels for caries prevention.

Methods

Data on trials included in the most recent Cochrane Reviews on fluoride varnish and fluoride gels were extracted. Sample sizes/age/dentition, year/country of publication, follow‐up, test and control, risk of bias and spin (claims of a beneficial effect that were not supported by reported data) were assessed. Studies were categorized as certainly, possibly and not sponsored, and statistically compared. Inverse‐generic meta‐analysis and multivariable weighted least‐squares meta‐regression were used to assess impact of sponsorship status on effect estimates.

Results

Based on 19 nonsponsored, 14 possibly sponsored and 11 certainly sponsored trials, sponsored studies were published significantly earlier, always had >1 test group, and had significantly lower risk of spin. Caries‐preventive effects were higher in earlier trials, without indication for sponsorship bias in trials published until 1990 (there were no sponsored trials afterwards). If assessing the overall body of evidence and accounting for confounders, the caries‐preventive effect was significantly associated with year of publication (β: −0.06, 95% CI: −0.10/−0.02), but not sponsorship status.

Conclusions

Industry‐sponsorship bias had limited impact on the overall evidence.
Debunking Occam's razor: Diagnosing multiple genetic diseases in families by whole‐exome sequencing
Authors: Balci T.B. , Hartley T. , Xi Y. , Dyment D.A. , Beaulieu C.L. , Bernier F.P. , Dupuis L. , Horvath G.A. , Mendoza‐Londono R. , Prasad C. , Richer J. , Yang X.‐R. , Armour C.M. , Bareke E. , Fernandez B.A. , McMillan H.J. , Lamont R.E. , Majewski J. , Parboosingh J.S. , Prasad A.N. , Rupar C.A. , Schwartzentruber J. , Smith A.C. , Tétreault M. ,   FORGE Canada Consortium,   Care4Rare Canada Consortium, Innes A.M. , Boycott K.M.
Published: February 2017

Background

Recent clinical whole exome sequencing (WES) cohorts have identified unanticipated multiple genetic diagnoses in single patients. However, the frequency of multiple genetic diagnoses in families is largely unknown.

Aims

We set out to identify the rate of multiple genetic diagnoses in probands and their families referred for analysis in two national research programs in Canada.

Materials & Methods

We retrospectively analyzed WES results for 802 undiagnosed probands referred over the past 5 years in either the FORGE or Care4Rare Canada WES initiatives.

Results

Of the 802 probands, 226 (28.2%) were diagnosed based on mutations in known disease genes. Eight (3.5%) had two or more genetic diagnoses explaining their clinical phenotype, a rate in keeping with the large published studies (average 4.3%; 1.4 ‐ 7.2%). Seven of the 8 probands had family members with one or more of the molecularly diagnosed diseases. Consanguinity and multisystem disease appeared to increase the likelihood of multiple genetic diagnoses in a family.

Conclusion

Our findings highlight the importance of comprehensive clinical phenotyping of family members to ultimately provide accurate genetic counseling.
Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)
Authors: Lu Limin , Cox Cymon J. , Mathews Sarah , Wang Wei , Wen Jun , Chen Zhiduan
Published: February 2017

Evolutionary rate heterogeneity and rapid radiations are common phenomena in organismal evolution and represent major challenges for reconstructing deep‐level phylogenies. Here we detected substantial conflicts in and among data sets as well as uncertainty concerning relationships among lineages of Vitaceae from individual gene trees, supernetworks and tree certainty values. Congruent deep‐level relationships of Vitaceae were retrieved by comprehensive comparisons of results from optimal partitioning analyses, multispecies coalescent approaches and the Bayesian concordance method. We found that partitioning schemes selected by PartitionFinder were preferred over those by gene or by codon position, and the unpartitioned model usually performed the worst. For a data set with conflicting signals, however, the unpartitioned model outperformed models that included more partitions, demonstrating some limitations to the effectiveness of concatenation for these data. For a transcriptome data set, fast coalescent methods (STAR and MP‐EST) and a Bayesian concordance approach yielded congruent topologies with trees from the concatenated analyses and previous studies. Our results highlight that well‐resolved gene trees are critical for the effectiveness of coalescent‐based methods. Future efforts to improve the accuracy of phylogenomic analyses should emphasize the development of new methods that can accommodate multiple biological processes and tolerate missing data while remaining computationally tractable.
Oesophageal Doppler guided optimization of cardiac output does not increase visceral microvascular blood flow in healthy volunteers
Authors: Heinink Thomas P. , Read David J. , Mitchell William K. , Bhalla Ashish , Lund Jonathan N. , Phillips Bethan E. , Williams John P.
Published: February 2017

Background

Oesophageal Doppler monitoring (ODM) is used clinically to optimize cardiac output (CO) and guide fluid therapy. Despite limited experimental evidence, it is assumed that increasing CO increases visceral microvascular blood flow (MBF). We used contrast‐enhanced ultrasound (CEUS) to assess whether ODM‐guided optimization of CO altered MBF.

Methods

Sixteen healthy male volunteers (62 ± 3·4 years) were studied. Baseline measurements of CO were recorded via ODM. Hepatic and renal MBF was assessed via CEUS. Saline 0·9% was administered to optimize CO according to a standard protocol and repeat CEUS performed. Time–intensity curves were constructed, allowing organ perfusion calculation via time to 5% perfusion (TT5). MBF was assessed via organ perfusion rise time (RT) (5–95%).

Results

CO increased (4535 ± 241 ml/min versus 5442 ± 329 ml/min, P<0·0001) following fluid administration, whilst time to renal (22·48 ± 1·19 s versus 20·79 ± 1·31 s; P = 0·03), but not hepatic (28·13 ± 4·48 s versus 26·83 ± 1·53 s; P = 0·15) perfusion decreased. Time to renal perfusion was related to CO (renal: r = −0·43, P = 0·01). Hepatic nor renal RT altered following fluid administration (renal: 9·03 ± 0·86 versus 8·93 ± 0·85 s P = 0·86; hepatic: 27·86 ± 1·60 s versus 30·71 ± 2·19 s, P = 0·13). No relationship was observed between changes in CO and MBF in either organ (renal: r = −0·17, P = 0·54; hepatic: r = −0·07, P = 0·80).

Conclusions

ODM‐optimized CO reduces time to renal perfusion but does not alter renal or hepatic MBF. A lack of relationship between microvascular visceral perfusion and CO following ODM‐guided optimization may explain the absence of improved clinical outcome with ODM monitoring.
Competition under Diseconomies of Scale: The Role of Subcontracting and Single‐Sourcing Commitment
Authors: Shao Lusheng
Published: February 2017

This article studies a supplier competition model in situations with flexible resources where suppliers face diseconomies of scale. Under such a situation, it is generally believed that a buyer may split an order across different suppliers; and even if the buyer chooses only one supplier, the winning supplier may subcontract part of the work to the others. My results, however, show that the buyer always prefers to commit to single‐sourcing prior to running a procurement auction. This is because such commitment eliminates the “assurance” of getting a positive order from the buyer, thus intensifying supplier competition. I also find that subcontracting may be beneficial (detrimental) to the buyer if the subcontract is determined by the winning (losing) supplier of the bidding game. Finally, I show that, for the case with linear costs, the buyer is always better off when subcontracting is considered.
Parasitic association of the mycetophagous wood nematode, Bursaphelenchus fraudulentus with the honey fungus Armillaria ostoyae
Authors: Tomalak M.
Published: February 2017

Honey fungi, Armillaria spp. are common and economically important pathogens of a wide range of tree species grown both in the forest and orchard cultures worldwide. Our field research in 73 forest stands across Poland has shown a common association of the mycetophagous wood nematode, Bursaphelenchus fraudulentus with Armillaria‐infected trees. The data reported here provide the first insight into the parasitic interaction of a nematode and Armillaria ostoyae. In laboratory conditions, B. fraudulentus reproduced on A. ostoyae, caused substantial damage to its mycelium and, finally, killed the whole colony within a short time. In ageing cultures, the nematode produced resting (dauer) juveniles. After artificial inoculation to Armillaria‐infected trees, the nematode population persisted under the bark, continued feeding and mass reproduction on the mycelium, and dispersed over the mycelial fans. The ability of B. fraudulentus to develop and reproduce on the surface and inside the fungal rhizomorphs suggests that these structures could facilitate the nematode dispersion in the environment. Since B. fraudulentus is not pathogenic to the host tree, its parasitic association with A. ostoyae may contribute to natural regulation of this fungus in the environment. The observed characteristics of this nematode suggest that it could potentially be used as a biocontrol agent of honey fungi in forest and orchard trees.
New and unexpected host associations for Diplodia sapinea in the Western Balkans
Authors: Zlatković M. , Keča N. , Wingfield M. J. , Jami F. , Slippers B.
Published: February 2017

Diplodia sapinea is an important pathogen of pine trees in plantations and urban areas in many parts of the world. This pathogen has recently also been isolated from diseased Cedrus atlantica, C. deodara and Picea omorika planted as ornamentals across the Western Balkans. The aim of this study was to consider the host range of D. sapinea in Serbia and Montenegro. Diplodia sapinea was identified from a broader collection of Botryosphaeriaceae from the Western Balkans region, based on the DNA sequence data for the internal transcribed spacer (ITS) rDNA and the translation elongation factor 1α (TEF 1‐ α). The D. sapinea isolates were obtained from sixteen tree species in the genera Abies, Cedrus, Chamaecyparis, Juniperus, Picea, Pinus, Pseudotsuga and Fagus. Four species represented new hosts in the Balkans, and this is the first report of D. sapinea from F. sylvatica anywhere in the world. Pathogenicity tests were conducted on the tree hosts from which D. sapinea was isolated, as well as on P. abies, Thuja occidentalis, Prunus laurocerasus, Eucalyptus grandis and P. patula. Inoculations were made on seedlings in the field, in the greenhouse or on freshly detached branches. Inoculations on P. pungens, P. omorika, P. abies, P. menziesii, A. concolor, P. nigra and P. sylvestris resulted in death of the seedlings 5–16 weeks after inoculation. Diplodia sapinea produced lesions on J. horizontalis and P. patula seedlings and F. sylvatica cut branches. Reciprocal inoculations showed that D. sapinea is not a pine‐specific pathogen, causing disease on tree species, including those from which it had not been isolated. Not surprisingly, the pathogen was most aggressive on some species of Pinaceae.
Evidence for the role of histaminergic pathways in neuroprotective mechanism of ischemic postconditioning in mice
Authors: Kaur Indresh , Kumar Amit , Jaggi Amteshwar S. , Singh Nirmal
Published: February 2017

The present study has been designed to investigate the possible role of histaminergic pathway in neuroprotective mechanism of ischemic postconditioning (iPoCo). Bilateral carotid artery occlusion (BCAO) for 12 min followed by reperfusion for 24 h was employed to produce I/R‐induced cerebral injury in National Institutes of Health mice mice. iPoCo involving three episodes of carotid artery occlusion and reperfusion of 10 sec each was instituted immediately after BCAO just before prolonged reperfusion. Cerebral infarct size was measured using triphenyltetrazolium chloride staining. Memory was evaluated using Morris water maze test. Rotarod test, inclined beam‐walking test, and neurological severity score (NSS) were performed to assess motor incoordination and sensorimotor abilities. Brain acetylcholine esterase (AChE) activity, brain myeloperoxidase (MPO) activity, brain thiobarbituric acid‐reactive species (TBARS), and glutathione level (GSH) were also estimated. BCAO produced a significant rise in cerebral infarct size and NSS along with impairment of memory and motor coordination and biochemical alteration (↑AChE, ↑MPO ↓GSH, and ↑TBARS). iPoCo attenuated the deleterious effect of BCAO on infarct size, memory, NSS, motor coordination, and biochemical markers. Pretreatment of carnosine (a histamine [HA] precursor) potentiated the neuroprotective effects of iPoCo, whereas pretreatment of ketotifen (HA H1 receptor blocker and mast cell stabilizer) abolished the protective effects of iPoCo as well as that of carnosine on iPoCo. It may be concluded that neuroprotective effect of iPoCo probably involves activation of histaminergic pathways.
The predictive validity of individual psychological assessments in selecting UK public sector senior managers
Authors: Weldon Paul T. , Fletcher Clive , MacIver Rab
Published: February 2017

Individual Psychological Assessment (IPA) is a very widely offered service in Organizational Psychology. It generally consists of a psychologist or HR practitioner using a combination of interview and psychometrics to arrive at a detailed assessment of an individual's capabilities in relation to a job they are being considered for. Although much used, this practice has limited supporting evidence of its validity—not least because of the methodological difficulties in conducting research on this subject—and has been criticized accordingly. The current study examines the use of IPAs with 115 middle and senior management level candidates in a civil service context. All candidates completed a set of psychometric measures and had an in‐depth interview with a psychologist as part of a standardized process. The ratings made by the assessors were correlated with a criterion measure of potential for promotion derived from multisource feedback ratings obtained on these candidates some months later. Analysis of the results indicated that three of the four attributes rated by assessors correlated significantly with the criterion measure. Further, assessors’ ratings were found to show incremental validity over that provided by psychometric test scores alone. These findings are discussed in terms of the use of IPAs in senior level assessment.