bluuebunny/crossref_metadata_2025_split huggingface dataset:
On Sample Size and Power Calculation for Variant Set‐Based Association Tests
Authors: Wu Baolin , Pankow James S. 
Published: February 2016

SummarySample size and power calculations are an important part of designing new sequence‐based association studies. The recently developed SEQPower and SPS programs adopted computationally intensive Monte Carlo simulations to empirically estimate power for a series of variant set association (VSA) test methods including the sequence kernel association test (SKAT). It is desirable to develop methods that can quickly and accurately compute power without intensive Monte Carlo simulations. We will show that the computed power for SKAT based on the existing analytical approach could be inflated especially for small significance levels, which are often of primary interest for large‐scale whole genome and exome sequencing projects. We propose a new χ2‐approximation‐based approach to accurately and efficiently compute sample size and power. In addition, we propose and implement a more accurate “exact” method to compute power, which is more efficient than the Monte Carlo approach though generally involves more computations than the χ2 approximation method. The exact approach could produce very accurate results and be used to verify alternative approximation approaches. We implement the proposed methods in publicly available R programs that can be readily adapted when planning sequencing projects.
Macular pigmentation of uncertain aetiology revisited: two case reports and a proposed algorithm for clinical classification
Authors: Chandran Veena , Kumarasinghe Sujith Prasad 
Published: February 2016

AbstractAshy dermatosis, erythema dyschromicum perstans, lichen planus pigmentosus and idiopathic eruptive macular pigmentation are various types of acquired macular hyperpigmentation disorders of the skin described in literature. However, a global consensus on the definitions of these entities is lacking. We report two cases of acquired macular (hyper)pigmentation of uncertain aetiology diagnosed as ashy dermatosis and attempt to clarify the various confusing nosologies based on existing literature. We infer that acquired small and large macular pigmentation of uncertain aetiology should be considered separate from that associated with lichen planus. We also propose a diagnostic algorithm for patients with acquired macular hyperpigmentation.
Comparing motion capture cameras versus human observer monitoring of mammal movement through fence gaps: a case study from Kenya
Authors: Dupuis‐Desormeaux Marc , Davidson Zeke , Mwololo Mary , Kisio Edwin , MacDonald Suzanne E. 
Published: February 2016

AbstractMonitoring the movement and distribution of wildlife is a critical tool of an adaptive management framework for wildlife conservation. We installed motion‐triggered cameras to capture the movement of mammals through two purpose‐built migration gaps in an otherwise fenced conservancy in northern Kenya. We compared the results to data gathered over the same time period (1 Jan 2011–31 Dec 2012) by the human observers monitoring mammal tracks left at the same fence gaps in a sandy loam detection strip. The camera traps detected more crossing events, more species and more individuals of each species per crossing event than did the human track observers. We tested for volume detection differences between methods for the five most common species crossing each gap and found that all detection rates were heavily weighted towards the camera‐trap method. We review some of the discrepancies between the methods and conclude that although the camera traps record more data, the management of that data can be time‐consuming and ill‐suited to some time‐sensitive decision‐making. We also discuss the importance of daily track monitoring for adaptive management conservation and community security.
On the Correlation Structure of Gaussian Copula Models for Geostatistical Count Data
Authors: Han Zifei , De Oliveira Victor 
Published: February 2016

SummaryWe describe a class of random field models for geostatistical count data based on Gaussian copulas. Unlike hierarchical Poisson models often used to describe this type of data, Gaussian copula models allow a more direct modelling of the marginal distributions and association structure of the count data. We study in detail the correlation structure of these random fields when the family of marginal distributions is either negative binomial or zero‐inflated Poisson; these represent two types of overdispersion often encountered in geostatistical count data. We also contrast the correlation structure of one of these Gaussian copula models with that of a hierarchical Poisson model having the same family of marginal distributions, and show that the former is more flexible than the latter in terms of range of feasible correlation, sensitivity to the mean function and modelling of isotropy. An exploratory analysis of a dataset of Japanese beetle larvae counts illustrate some of the findings. All of these investigations show that Gaussian copula models are useful alternatives to hierarchical Poisson models, specially for geostatistical count data that display substantial correlation and small overdispersion.
Form and Function in the Evolution of Grammar
Authors: Newmeyer Frederick J. 
Published: February 2016

AbstractThis article focuses on claims about the origin and evolution of language from the point of view of the formalist–functionalist debate in linguistics. In linguistics, an account of a grammatical phenomenon is considered “formal” if it accords center stage to the structural properties of that phenomenon, and “functional” if it appeals to the language user's communicative needs or to domain‐general human capacities. The gulf between formalism and functionalism has been bridged in language evolution research, in that some leading formalists, Ray Jackendoff for one, appeal to functional mechanisms such as natural selection. In Jackendoff's view, the biological evolution of language has proceeded in stages, each stage improving communicative efficiency. This article calls into question that idea, pointing to the fact that well‐understood purely historical processes suffice to explain the emergence of many grammatical properties. However, one central aspect of formalist linguistic theorizing—the idea of the autonomy of syntax—poses a challenge to the idea, central to most functionalist approaches, that the nature of grammar is a product of purely historical (as opposed to biological) evolution. The article concludes with a discussion of the origins of the autonomy of syntax, speculating that it may well have arisen over evolutionary (as opposed to historical) time.
Conditionals, Context, and the Suppression Effect
Authors: Cariani Fabrizio , Rips Lance J. 
Published: February 2016

AbstractModus ponens is the argument from premises of the formIf A, then BandAto the conclusionB(e.g., fromIf it rained, Alicia got wetandIt rainedtoAlicia got wet). Nearly all participants agree that the modus ponens conclusion logically follows when the argument appears in this Basic form. However, adding a further premise (e.g.,If she forgot her umbrella, Alicia got wet) can lower participants’ rate of agreement—an effect calledsuppression. We propose a theory of suppression that draws on contemporary ideas about conditional sentences in linguistics and philosophy. Semantically, the theory assumes that people interpret an indicative conditional as a context‐sensitive strict conditional: true if and only if its consequent is true in each of a contextually determined set of situations in which its antecedent is true. Pragmatically, the theory claims that context changes in response to new assertions, including new conditional premises. Thus, the conclusion of a modus ponens argument may no longer be accepted in the changed context. Psychologically, the theory describes people as capable of reasoning about broad classes of possible situations, ordered by typicality, without having to reason about individual possible worlds. The theory accounts for the main suppression phenomena, and it generates some novel predictions that new experiments confirm.
Corporate Governance in Banks
Authors: John Kose , De Masi Sara , Paci Andrea 
Published: February 2016

AbstractManuscript TypeReviewResearch Question/IssueWe survey the literature on corporate governance in banks in the US and international settings. We discuss how the specialness of banks, deposit insurance, high bank leverage, and bank regulation interact with bank governance. We evaluate bank governance from three perspectives: (1) maximizing bank equity value, (2) maximizing total enterprise value, and (3) maximizing social objectives. Our survey includes evidence on how bank governance differs from that of manufacturing firms. We also survey studies on managerial incentives in banks and their implications for bank performance and risk taking before and during the 2007–2008 financial crisis.Research Findings/InsightsThe high leverage (usually above 90 percent) of banking institutions gives rise to a trade‐off between strengthening equity governance and maximizing enterprise value. Aligning managers very closely with shareholders can give rise to strong incentives for risk shifting to the detriment of firm value. The bank risk choices might also go against the societal objectives of a stable financial system.Theoretical/Academic ImplicationsWe provide a framework for the optimal design of bank governance and bank regulation, considering the objectives of both depositors and society‐at‐large in addition to those of bank shareholders. This framework could be especially important in determining risk choices by banks and the effects of such on the stability of the financial system.Practitioner/Policy ImplicationsOur analysis of the literature surveyed has policy implications for bank regulation, top‐management compensation in banks, and directives for design of governance in banks. We discuss implications for direct regulation of banks and regulation of bank governance. The findings surveyed provide guidance for board independence, board size, board composition, and incentive features in top‐management compensation.
Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression
Authors: van der Voort Menno , Kempenaar Marcel , van Driel Marc , Raaijmakers Jos M. , Mendes Rodrigo 
Published: February 2016

AbstractThe rhizosphere microbiome offers a range of ecosystem services to the plant, including nutrient acquisition and tolerance to (a)biotic stress. Here, analysing the data by Mendes et al. (2011), we show that short heat disturbances (50 or 80 °C, 1 h) of a soil suppressive to the root pathogenic fungus Rhizoctonia solani caused significant increase in alpha diversity of the rhizobacterial community and led to partial or complete loss of disease protection. A reassembly model is proposed where bacterial families that are heat tolerant and have high growth rates significantly increase in relative abundance after heat disturbance, while temperature‐sensitive and slow‐growing bacteria have a disadvantage. The results also pointed to a potential role of slow‐growing, heat‐tolerant bacterial families from Actinobacteria and Acidobacteria phyla in plant disease protection. In conclusion, short heat disturbance of soil results in rearrangement of rhizobacterial communities and this is correlated with changes in the ecosystem service disease suppression.
Acquired phototrophy stabilises coexistence and shapes intrinsic dynamics of an intraguild predator and its prey
Authors: Moeller Holly V. , Peltomaa Elina , Johnson Matthew D. , Neubert Michael G. 
Published: February 2016

AbstractIn marine ecosystems, acquired phototrophs – organisms that obtain their photosynthetic ability by hosting endosymbionts or stealing plastids from their prey – are omnipresent. Such taxa function as intraguild predators yet depend on their prey to periodically obtain chloroplasts. We present a new theory for the effects of acquired phototrophy on community dynamics by analysing a mathematical model of this predator–prey interaction and experimentally verifying its predictions with a laboratory model system. We show that acquired phototrophy stabilises coexistence, but that the nature of this coexistence exhibits a ‘paradox of enrichment’: as light increases, the coexistence between the acquired phototroph and its prey transitions from a stable equilibrium to boom‐bust cycles whose amplitude increases with light availability. In contrast, heterotrophs and mixotrophic acquired phototrophs (that obtain < 30% of their carbon from photosynthesis) do not exhibit such cycles. This prediction matches field observations, in which only strict ( > 95% of carbon from photosynthesis) acquired phototrophs form blooms.
Enabling cell–cell communication via nanopore formation: structure, function and localization of the unique cell wall amidase AmiC2 of Nostoc punctiforme
Authors: Büttner Felix M. , Faulhaber Katharina , Forchhammer Karl , Maldener Iris , Stehle Thilo 
Published: February 2016

To orchestrate a complex life style in changing environments, the filamentous cyanobacterium Nostoc punctiforme facilitates communication between neighboring cells through septal junction complexes. This is achieved by nanopores that perforate the peptidoglycan (PGN) layer and traverse the cell septa. The N‐acetylmuramoyl‐l‐alanine amidase AmiC2 (Npun_F1846; EC 3.5.1.28) in N. punctiforme generates arrays of such nanopores in the septal PGN, in contrast to homologous amidases that mediate daughter cell separation after cell division in unicellular bacteria. Nanopore formation is therefore a novel property of AmiC homologs. Immunofluorescence shows that native AmiC2 localizes to the maturing septum. The high‐resolution crystal structure (1.12 Å) of its catalytic domain (AmiC2‐cat) differs significantly from known structures of cell splitting and PGN recycling amidases. A wide and shallow binding cavity allows easy access of the substrate to the active site, which harbors an essential zinc ion. AmiC2‐cat exhibits strong hydrolytic activity in vitro. A single point mutation of a conserved glutamate near the zinc ion results in total loss of activity, whereas zinc removal leads to instability of AmiC2‐cat. An inhibitory α‐helix, as found in the Escherichia coli AmiCE. coli structure, is absent. Taken together, our data provide insight into the cell‐biological, biochemical and structural properties of an unusual cell wall lytic enzyme that generates nanopores for cell–cell communication in multicellular cyanobacteria. The novel structural features of the catalytic domain and the unique biological function of AmiC2 hint at mechanisms of action and regulation that are distinct from other amidases.DatabaseThe AmiC2‐cat structure has been deposited in the Protein Data Bank under accession number 5EMI.
Biogeographic ranges do not support niche theory in radiating Canary Island plant clades
Authors: Steinbauer Manuel J. , Field Richard , Fernández‐Palacios José María , Irl Severin D. H. , Otto Rüdiger , Schaefer Hanno , Beierkuhnlein Carl 
Published: February 2016

AbstractAimEcological niche concepts, in combination with biogeographic history, underlie our understanding of biogeographic ranges. Two pillars of this understanding are competitive displacement and niche conservatism. The competitive displacement hypothesis holds that very similar (e.g. closely related) co‐occurring species should diverge, forced apart by competition. In contrast, according to the niche conservatism hypothesis, closely related species should have similar niches. If these are fundamental structuring forces, they should be detectable when comparing the climatic niches of endemic species in radiating clades in oceanic archipelagos, where closely related species exist in both sympatry and allopatry and the species' entire ranges are known. We took advantage of this natural experimental system to test whether the climatic niche relationships predicted by the two hypotheses are found.LocationCanary Islands.MethodsFor the plant clades Aeonium, Argyranthemum, Descurainia, Echium, Lotus and Sonchus, separately, we tested relationships between phylogenetic distance and climatic niche differentiation (in temperature, precipitation and their combination), using a high‐resolution dataset. We also tested for niche conservatism using Blomberg's K and Pagel's λ. We compared climatic niche differentiation between pairs of species existing in sympatry with that for pairs of species in allopatry. For each comparison, we focused on the climatic niche space available to both species.ResultsThe relationships between phylogenetic distance and climatic niche differentiation were mostly non‐significant; some weak but significant positive relationships were found, mainly for Aeonium and Sonchus. Where differences between sympatry and allopatry were found, niche differentiation tended to be greater in allopatry.Main conclusionsThe expectations from niche conservatism were frequently not met; instead our results suggest considerable climatic niche lability. All significant differences in climatic niche differentiation were opposite to the predictions from competitive displacement. These forces may be less important in structuring biogeographic ranges than is commonly thought, at least on islands.
lincRNA‐p21 inhibits invasion and metastasis of hepatocellular carcinoma through Notch signaling‐induced epithelial–mesenchymal transition
Authors: Jia Meng , Jiang Li , Wang Ya‐Dong , Huang Jin‐Zhao , Yu Miao , Xue Huan‐Zhou 
Published: February 2016

AimEmerging evidence has showed that long non‐coding RNA (lncRNA) play an important role in the occurrence and development of various cancers. In the present study, the expression level of lincRNA‐p21 was investigated in hepatocellular carcinoma (HCC), and its role in invasion of HCC was also explored.MethodsThe lincRNA‐p21 levels in human HCC tumor tissue and cell lines HepG2 and SMMC‐7721 were determined by real‐time polymerase chain reaction. Transfected HCC cells with pcDNA‐lincRNA‐p21 or si‐lincRNA‐p21 for overexpression or downregulation of lincRNA‐p21, the Notch signaling and epithelial–mesenchymal transition (EMT)‐related proteins and cell invasion were measured by western blot and Transwell assay, respectively. A tumor xenotransplant mouse model was also established to investigate the role of lincRNA‐p21 in tumor metastasis in vivo.ResultsThe lincRNA‐p21 expression was downregulated in HCC tissue and cells. Overexpression of lincRNA‐p21 inhibited Notch singling and EMT, while its downregulation led to the reverse result. The invasion of HCC cell was also inhibited by pcDNA‐lincRNA‐p21, and activation of Notch signaling reversed this effect. In vivo, overexpression of lincRNA‐p21 decreased the tumor metastasis, as well.ConclusionlincRNA‐p21 was downregulated in HCC and lincRNA‐p21 overexpression contributed to the inhibition of tumor invasion through mediating Notch signaling induced EMT.
Impact of chemical peeling combined with negative pressure on human skin
Authors: Kim S. J. , Kang I. J. , Shin M. K. , Jeong K. H. , Baek J. H. , Koh J. S. , Lee S. J. 
Published: February 2016

AbstractObjectiveIn vivo changes in skin barrier function after chemical peeling with alpha hydroxyacids (AHAs) have been previously reported. However, the additional effects of physical treatment with chemical agents on skin barrier function have not been adequately studied. This study measured the degree of acute skin damage and the time required for skin barrier repair using non‐invasive bioengineering methods in vivo with human skin to investigate the additional effect of a 4% AHA chemical jet accelerated at supersonic velocities.MethodsThirteen female subjects (average age: 29.54 ± 4.86 years) participated in this study. The faces of the subjects were divided into half according to the block randomization design and were then assigned to receive AHA peeling alone or AHA peeling combined with pneumatic pressure on each side of the face. Transepidermal water loss (TEWL), skin colour and skin blood flow were evaluated at baseline and at 30 min, 2, 5 and 7 days after treatment.ResultsThe TEWL and skin blood flow were significantly increased after 30 min in chemodermabrasion compared with chemical peeling alone (P < 0.05). The TEWL and skin blood flow recovered to baseline after 2 days, and TEWL was significantly decreased at 7 days compared with chemical peeling alone (P < 0.05).ConclusionsChemodermabrasion can temporarily impair skin barriers, but it is estimated that it can enhance the skin barrier function after 7 days compared to the use of a chemical agent alone. In addition, chemodermabrasion has a more effective impact in the dermis and relatively preserves the skin barrier.
What Moves the Highly Skilled and Why? Comparing Turkish Nationals in Canada and Germany
Authors: Ozcurumez Saime , Yetkin Aker Deniz 
Published: February 2016

AbstractBased on in‐depth interviews with highly skilled and business Turkish nationals (HSBTN) in Canada and Germany, this study aims to explore why HSBTN decide to move and whether migration policy differences among the countries of destination affect recent migration motivations of HSBTN. It mainly focuses on the reasons and rationale of HSBTN and their explanations. This study argues that the high skilled and business migrants in general and HSBTN in particular move internationally as a consequence of individual‐level gain beyond economic prospects.
A Simple Drought‐Sensitive Model for Leaf : Stem Partitioning of Wheat
Authors: Ratjen A. M. , Neukam D. , Kage H. 
Published: February 2016

AbstractWe investigated the leaf : stem partitioning of winter wheat (Triticum aestivum L. varieties ‘Dekan’ and ‘Batis’) with and without drought influence. Irrigated and drought‐stressed winter wheat, grown in a rainout shelter in 2009/10 and 2013/14, were sampled during shoot elongation phase at the experimental Farm Hohenschulen located in Northern Germany. The data set contains leaf (DML) and stem dry masses (DMS), as well as measured water contents for several soil layers. A reduced relative dry matter allocation to leaves was observed under drought stress. Our results clearly show that, if simulated leaf : stem partitioning is not sensitive to drought, this will cause a positive bias in simulated leaf and a negative bias in simulated stem dry matter under water‐limited conditions. This is in accordance with previous studies which revealed that crop simulators often overestimate the impact of drought on light‐use efficiency, whereas the consequences on leaf area development are underestimated. However, the drought stress‐induced shift in leaf : stem partitioning is yet not considered by most common wheat crop simulators. Our aim was to fill the gap in simulation of drought stress implications on leaf area development. A simple allometric model for leaf : stem partitioning () was parameterized. Starting from the allometric leaf : stem relationship observed under optimum water supply, a correction term was introduced, which allows to adapt the partitioning to drought stress conditions. The lg‐transformed root‐weighted soil water potential in the rooting zone (lgψroot, lg(hPa)), calculated as a function of measured water contents and simulated root distribution, was used as a drought stress indicator. The linear correction term assumes an increase of the stem fraction, proportional to the difference between lgψroot and a drought stress threshold (pFcrit, lg(hPa)). The analysis revealed that the shift in allometric partitioning towards stem fraction starts with lgψroot greater than 1.92 [lg(hPa)]. The slope of the relative increase of dry matter allocated to the stem fraction was determined with 0.26 [lg(hPa)−1]. Both parameters of the correction term were found to be highly significant. Implications for crop modelling are discussed.