bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting Genetic Interactions in Pathway‐Based Genome‐Wide Association Studies
Authors: Huang Anhui , Martin Eden R. , Vance Jeffery M. , Cai Xiaodong 
Published: April 2014

ABSTRACTPathway‐based genome‐wide association studies (GWAS) can exploit collective effects of causal variants in a pathway to increase power of detection. However, current methods for pathway‐based GWAS do not consider epistatic effects of genetic variants, although interactions between genetic variants may play an important role in influencing complex traits. In this paper, we employed a Bayesian Lasso logistic regression model for pathway‐based GWAS to include all possible main effects and a large number of pairwise interactions of single nucleotide polymorphisms (SNPs) in a pathway, and then inferred the model with an efficient group empirical Bayesian Lasso (EBLasso) method. Using the inferred model, the statistical significance of a pathway was tested with the Wald statistics. Reliable effects in a significant pathway were selected using the stability selection technique. Extensive computer simulations demonstrated that our group EBlasso method significantly outperformed two competitive methods in most simulation setups and offered similar performance in other simulation setups. When applying to a GWAS dataset for Parkinson disease, EBLasso identified three significant pathways including the primary bile acid biosynthesis pathway, the neuroactive ligand–receptor interaction, and the MAPK signaling pathway. All effects identified in the primary bile acid biosynthesis pathway and many of effects in the other two pathways were epistatic effects. The group EBLasso method provides a valuable tool for pathway‐based GWAS to identify main and epistatic effects of genetic variants.
Detection of Mendelian Consistent Genotyping Errors in Pedigrees
Authors: Cheung Charles Y.K. , Thompson Elizabeth A. , Wijsman Ellen M. 
Published: April 2014

ABSTRACTDetection of genotyping errors is a necessary step to minimize false results in genetic analysis. This is especially important when the rate of genotyping errors is high, as has been reported for high‐throughput sequence data. To detect genotyping errors in pedigrees, Mendelian inconsistent (MI) error checks exist, as do multi‐point methods that flag Mendelian consistent (MC) errors for sparse multi‐allelic markers. However, few methods exist for detecting MC genotyping errors, particularly for dense variants on large pedigrees. Here, we introduce an efficient method to detect MC errors even for very dense variants (e.g., SNPs and sequencing data) on pedigrees that may be large. Our method first samples inheritance vectors (IVs) using a moderately sparse but informative set of markers using a Markov chain Monte Carlo‐based sampler. Using sampled IVs, we considered two test statistics to detect MC genotyping errors: the percentage of IVs inconsistent with observed genotypes (A1) or the posterior probability of error configurations (A2). Using simulations, we show that this method, even with the simpler A1 statistic, is effective for detecting MC genotyping errors in dense variants, with sensitivity almost as high as the theoretical best sensitivity possible. We also evaluate the effectiveness of this method as a function of parameters, when including the observed pattern for genotype, density of framework markers, error rate, allele frequencies, and number of sampled inheritance vectors. Our approach provides a line of defense against false findings based on the use of dense variants in pedigrees.
Rapid expansion of glacial lakes caused by climate and glacier retreat in the Central Himalayas
Authors: Wang Weicai , Xiang Yang , Gao Yang , Lu Anxin , Yao Tandong 
Published: April 2014

AbstractGlacial lake outburst floods are among the most serious natural hazards in the Himalayas. Such floods are of high scientific and political importance because they exert trans‐boundary impacts on bordering countries. The preparation of an updated inventory of glacial lakes and the analysis of their evolution are an important first step in assessment of hazards from glacial lake outbursts. Here, we report the spatiotemporal developments of the glacial lakes in the Poiqu River basin, a trans‐boundary basin in the Central Himalayas, from 1976 to 2010 based on multi‐temporal Landsat images. Studied glacial lakes are classified as glacier‐fed lakes and non‐glacier‐fed lakes according to their hydrologic connection to glacial watersheds. A total of 119 glacial lakes larger than 0.01 km2 with an overall surface area of 20.22 km2 (±10.8%) were mapped in 2010, with glacier‐fed lakes being predominant in both number (69, 58.0%) and area (16.22 km2, 80.2%). We found that lakes connected to glacial watersheds (glacier‐fed lakes) significantly expanded (122.1%) from 1976 to 2010, whereas lakes not connected to glacial watersheds (non‐glacier‐fed lakes) remained stable (+2.8%) during the same period. This contrast can be attributed to the impact of glaciers. Retreating glaciers not only supply meltwater to lakes but also leave space for them to expand. Compared with other regions of the Hindu Kush Himalayas (HKH), the lake area per glacier area in the Poiqu River basin was the highest. This observation might be attributed to the different climate regimes and glacier status along the HKH. The results presented in this study confirm the significant role of glacier retreat on the evolution of glacial lakes. Copyright © 2014 John Wiley & Sons, Ltd.
Using new mass balance methods to estimate gross surface water and groundwater exchange with naturally occurring tracer 222Rn in data poor regions: a case study in northwest China
Authors: Su Xiaosi , Xu Wei , Yang Fengtian , Zhu Pucheng 
Published: April 2014

AbstractGiven that the concentration of 222Rn in groundwater is much higher than that in surface water and that its radioactive half‐life (3.83 d) is short, 222Rn is an effective tracer of groundwater–surface water interactions. In this study, a new mass balance method is presented, which can be used to estimate specific groundwater–surface water interactions within a river reach. Three possible situations of interaction between groundwater and surface water are considered, and equations based on the mass conservation of 222Rn are formulated for judging specific groundwater–surface water interaction processes and for calculating water flux. A case study was conducted for the Nalenggele River, Northwest China, to demonstrate the usefulness of this method. Samples of river water and groundwater containing 222Rn were collected from the study area to estimate the interactions between groundwater and surface water. The amount of water exchanged during these interactions was estimated and the results show that transformations between groundwater and surface water are frequent along the stream. The 222Rn mass balance method is highly sensitive for studying such interactions, even in areas for which conventional hydrologic data are sparse. Copyright © 2014 John Wiley & Sons, Ltd.
Effects of four different cooking methods on anthocyanins, total phenolics and antioxidant activity of black rice
Authors: Surh Jeonghee , Koh Eunmi 
Published: April 2014

AbstractBACKGROUNDTwo cultivars of black rice were investigated for the effects of different cooking methods on anthocyanins, total phenolic compounds and antioxidant activities.RESULTSThere was a significant loss of anthocyanins during cooking: roasting resulted in the greatest decrease (94%), followed by steaming (88%), pan‐frying (86%) and boiling (77%). Contents of phenolic compounds decreased drastically after cooking, with significantly lower retention in the black rice cultivar that had higher amylose content. DPPH radical‐scavenging activity of black rice decreased after cooking. In contrast, metal‐chelating activity increased significantly after cooking. Anthocyanins showed a high positive correlation with total phenolic compounds (r2 = 0.936) but a significant negative correlation with metal‐chelating activity (r2 = 0.6107).CONCLUSIONThe results indicate that cooking degraded anthocyanins and other phenolic compounds, but with a concomitant increase in phenolics from possible degradation of anthocyanins, which resulted in the enhancement of metal‐chelating activity. © 2014 Society of Chemical Industry
Multivariate optimization of a headspace solid‐phase microextraction method followed by gas chromatography with mass spectrometry for the determination of terpenes in Nicotiana langsdorffii
Authors: Ardini Francisco , Carro Marina Di , Abelmoschi Maria Luisa , Grotti Marco , Magi Emanuele 
Published: April 2014

A simple and sensitive procedure based on headspace solid‐phase microextraction and gas chromatography with mass spectrometry was developed for the determination of five terpenes (α‐pinene, limonene, linalool, α‐terpineol, and geraniol) in the leaves of Nicotiana langsdorffii. The microextraction conditions (extraction temperature, equilibration time, and extraction time) were optimized by means of a Doehlert design. The experimental design showed that, for α‐pinene and limonene, a low temperature and a long extraction time were needed for optimal extraction, while linalool, α‐terpineol, and geraniol required a high temperature and a long extraction time. The chosen compromise conditions were temperature 60°C, equilibration time 15 min and extraction time 50 min. The main analytical figures of the optimized method were evaluated; LODs ranged from 0.07 ng/g (α‐pinene) to 8.0 ng/g (geraniol), while intraday and interday repeatability were in the range 10–17% and 9–13%, respectively. Finally, the procedure was applied to in vitro wild‐type and transgenic specimens of N. langsdorffii subjected to abiotic stresses (chemical and heat stress). With the exception of geraniol (75–374 ng/g), low concentration levels of terpenes were measured (ng/g level or lower); some interesting variations in terpene concentration induced by abiotic stress were observed.
Latest Advances in High Brightness Disk Lasers
Authors: Schad Sven‐Silvius , Stolzenburg Christian , Michel Knut , Sutter Dirk 
Published: April 2014

AbstractFor years disk lasers have been an ideal choice for the vast majority of high power material processing applications in the CW as well as short and ultra short pulse regime since they combine high output power with high beam quality at low investment and running cost. Ease of operation combined with highest efficiency, precision and robustness have established the disk laser as a standard tool throughout industrial applications. Tailoring laser based manufacturing chains has opened up a manifold of different areas such as high speed cutting, remote welding, brazing, cladding and hybrid welding.
Associations of drug burden index with falls, general practitioner visits, and mortality in older people
Authors: Nishtala Prasad S. , Narayan Sujita W. , Wang Ting , Hilmer Sarah N. 
Published: April 2014

ABSTRACTAimOn a population level in people aged ≥65 years old living in New Zealand, the aim of this study is to quantify each individual's cumulative exposure to anticholinergic and sedative medicines using the Drug Burden Index (DBI) and examine the impact of DBI on fall‐related hospitalisations, general practitioner (GP) visits, and all‐cause mortality.MethodThe study used data extracted from Pharmaceutical Claims Data Mart (2011), National Minimum Data set (2012), Births, Death and Marriages (2012) and GP Visits (2012) for patient demographics, hospitalisations and mortality. Cumulative anticholinergic and sedative exposure was measured using the DBI. Polypharmacy was defined as greater than or equal to five medicines dispensed concurrently at any time during the study period.ResultsAmongst the study population (n = 537 387; 45% male), 43.22% were exposed to DBI drugs (95% confidence intervals (CIs) = 43.09–43.35). The odds of DBI exposure for individuals with polypharmacy are 4.92 (95%CI = 4.86–4.98) times greater than that for individuals without polypharmacy. DBI drugs were associated with fall‐related hospitalisations (incidence rate ratio (IRR) 1.56, 95%CI = 1.47–1.65) and greater number of GP visits (IRR 1.13, 95%CI = 1.12–1.13). Individuals with DBI > 0 had a 1.29 times higher mortality risk (95%CI = 1.25–1.33). Polypharmacy is also associated with a higher mortality risk with a hazard ratio (HR) of 1.66 (95%CI = 1.59–1.73).ConclusionPolypharmacy and exposure to DBI drugs were independently associated with fall‐related hospitalisations, frequency of GP visits, and risk of mortality. On a population level, DBI may be useful as a quality indicator to guide policy to improve prescribing and optimize clinical outcomes in older people. Copyright © 2014 John Wiley & Sons, Ltd.
Magnetism induced by iron impurities in the overdoped superconductor La2–xSrxCuO4
Authors: Arzhnikov A. K. , Dobysheva L. V. 
Published: April 2014

AbstractWe have performed first‐principles calculations of the magnetic properties of the overdoped (x=0.25) LSCO and Fe‐LSCO systems. Originally, without impurities of iron, La1.75Sr0.25CuO4 is nonmagnetic.Replacing one of Cu atoms in a unit cell with an Fe atom (3 or 6% of Fe relatively to the Cu content) results in lowering the total energy of the magnetic state in comparison to the nonmagnetic one. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Re‐estimating sample size in cluster randomised trials with active recruitment within clusters
Authors: van Schie S. , Moerbeek M. 
Published: April 2014

AbstractOften only a limited number of clusters can be obtained in cluster randomised trials, although many potential participants can be recruited within each cluster. Thus, active recruitment is feasible within the clusters. To obtain an efficient sample size in a cluster randomised trial, the cluster level and individual level variance should be known before the study starts, but this is often not the case. We suggest using an internal pilot study design to address this problem of unknown variances. A pilot can be useful to re‐estimate the variances and re‐calculate the sample size during the trial. Using simulated data, it is shown that an initially low or high power can be adjusted using an internal pilot with the type I error rate remaining within an acceptable range. The intracluster correlation coefficient can be re‐estimated with more precision, which has a positive effect on the sample size. We conclude that an internal pilot study design may be used if active recruitment is feasible within a limited number of clusters. Copyright © 2014 John Wiley & Sons, Ltd.
Redefining the design objectives of large offshore wind turbine rotors
Authors: Buck James A. , Garvey Seamus D. 
Published: April 2014

AbstractWind turbine rotors are normally designed such that rotor power coefficient is maximized. Much of this methodology has been inherited from the aviation industry. This paper points out that designing machines for maximum rotor aerodynamic efficiency does not necessarily lead to a lower levelized cost of energy. The argument sits on the premise that levelized cost of energy is strongly influenced by machine capital expenditure (CAPEX) and annual energy production (AEP). We therefore assume that the true design objective is to minimize the CAPEX/AEP ratio. The basis of an alternative design path is presented, which centres on the minimization of total volume of structural material in the wind turbine. This is done whilst maintaining a given rated power. This alternative methodology requires the removal of conventional pre‐set design variables and assumptions which relate to the maximization of rotor power coefficient. We examine how changing chord length, axial induction factor and aerofoil lift coefficient affect material volume in the blade. Following this, we use a custom‐made blade element momentum programme to explore the relative CAPEX of machines with varying design axial induction factor and varying lift coefficient. This relative cost is calibrated to the 5 MW National Renewable Energy Laboratory offshore reference turbine. The effects on the rotor, drivetrain and tower are considered. For a 5 MW offshore machine, it is shown that an overall CAPEX/AEP reduction of over 2% can be achieved by using a low‐induction rotor with blades possessing aerofoils operating at non‐peak lift to drag ratios. This economy is delivered notwithstanding a 2.3% drop in design rotor power coefficient. Copyright © 2014 John Wiley & Sons, Ltd.
Disclosure of Surgeon Experience
Authors: Ganai Sabha 
Published: April 2014

AbstractIt is uncertain whether there is an ethical obligation to disclose surgical experience. This article explores the impact of principles including respect for patient autonomy, nonmaleficence, and justice, as well as professional duties including truth‐telling on the decision‐making relevant to the process of informed consent, taking into account surgeon experience, training, and the expected risk and uncertainty surrounding the disease process and operation. Issues such as the integrity of the doctor–patient relationship, difficulties with access to complex surgical services, and limitations in applying statistics to the future outcomes of individual surgeons are explored.
The Extent of Surgical Patients’ Understanding
Authors: Pugliese Omar Talhouk , Solari Juan Lombardi , Ferreres Alberto R. 
Published: April 2014

AbstractThe notion that consent to surgery must be informed implies not only that information should be provided by the surgeon but also that the information should be understood by the patient in order to give a foundation to his or her decision to accept or refuse treatment and thus, achieve autonomy for the patient. Nonetheless, this seems to be an idyllic situation, since most patients do not fully understand the facts offered and thus the process of surgical informed consent, as well as the patient’s autonomy, may be jeopardized. Informed consent does not always mean rational consent.
The association of physiological cortisol and IVF treatment outcomes: a systematic review
Authors: Massey Adam J. , Campbell Bruce , Raine‐Fenning Nick , Aujla Navneet , Vedhara Kavita 
Published: April 2014

AbstractPurposeA systematic review was conducted to (1) collate and synthesise the available evidence for the role of cortisol in relation to IVF treatment outcomes; (2) to establish the strength of an association between cortisol and IVF; and (3) to assess the overall quality of the studies and guide future research in this area.MethodsSeven electronic databases, including the reference lists of published papers, were searched. Inclusion criteria qualified any prospective/observational cohort study that reported original data. Quality assessment of eligible studies was conducted using the STROBE statement, which was used to assess the risk of bias and the quality of observational studies included in this review.Result(s)A total of eight studies reported a significant association between cortisol and IVF outcomes. Three studies found that higher cortisol may be associated with more favourable IVF outcomes, whereas five studies found that lower cortisol levels may be conducive to IVF success. Eleven of all studies included in this review were regarded as low quality publications.Conclusion(s)Study findings were that the evidence for the role of cortisol in relation to IVF outcomes is currently mixed. Future researchers are encouraged to consider the methodological limitations highlighted in this review and to utilise more robust assessment methods when examining the influence that chronic, rather than acute, stress may have on IVF outcomes.
Validation of the Griffith Empathy Measure in the Chinese Context
Authors: Zhang Qi , Wang Yi , Lui Simon S.Y. , Cheung Eric F.C. , Neumann David L. , Shum David H.K. , Chan Raymond C.K. 
Published: April 2014

Objectives: The Griffith Empathy Measure (GEM) is a self-report measure of empathy. The current study aimed to explore the reliability and validity of the Chinese version of the GEM. It also aimed to compare individuals with and without schizotypal personality disorder (SPD) features on various components of empathy.Methods: 420 college students from Beijing and 526 college students from Guangzhou completed a set of questionnaires that measured empathy and schizotypal personality disorder traits. Cronbach's coefficient alpha was used to evaluate the internal consistency of the GEM. Construct validity was evaluated using exploratory and confirmatory factor analyses (EFA and CFA). Construct validity was also examined by looking at the relationship between the GEM and the Interpersonal Reactivity Index (IRI). Finally, the sensitivity of the GEM was evaluated by comparing the total and factor GEM scores between individuals with and without SPD traits.Results: The Chinese GEM showed good internal consistency (Cronbach's alpha = 0.83). Results of an exploratory factor analysis suggested a three-factor model consisting of cognitive, affective and behavioural empathy components. Results of a confirmatory factor analysis showed that the three-factor model, as well as the two-factor model found in the English version, were both acceptable. Construct validity (specifically convergent validity) was also corroborated by significant correlations between the IRI subscales and GEM (personal distress: r = .09, p > .05; perspective taking: r = .34, p < .01; fantasy: r = .44, p < .01; empathic concern: r = .51, p < .01). Individuals with SPD traits showed lower scores on the GEM than individuals without SPD traits (t(1,250) = −1.99, p = .05), thus confirming discriminative validity.Conclusions: These preliminary findings suggest that the Chinese version of the GEM demonstrated satisfactory internal consistency and construct validity. In addition, the findings suggest that the GEM is culturally appropriate and researchers can use it to study empathy in healthy and clinical Chinese participants.
Disturbance energy growth in core–annular flow
Authors: Orazzo A. , Coppola G. , de Luca L. 
Published: April 2014

AbstractThe linear stability of the horizontal pipe flow of an equal density oil–water mixture, arranged as acore–annular flow(CAF), is here reconsidered from the point of view of non-modal analysis in order to assess the effects of non-normality of the linearized Navier–Stokes operator on the transient evolution of small disturbances. The aim of this investigation is to give insight into physical situations in which poor agreement occurs between the predictions of linear modal theory and classical experiments. The results exhibit high transient amplifications of the energy of three-dimensional perturbations and, in analogy with single-fluid pipe flow, the largest amplifications arise for non-axisymmetric disturbances of vanishing axial wavenumber. Energy analysis shows that the mechanisms leading to these transient phenomena mostly occur in the annulus, occupied by the less viscous fluid. Consequently, higher values of energy amplifications are obtained by increasing the gap between the core and the pipe wall and the annular Reynolds number. It is argued that these linear transient mechanisms of disturbance amplification play a key role in explaining the transition to turbulence of CAF.