bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using cases to strengthen inference on the association between single nucleotide polymorphisms and a secondary phenotype in genome‐wide association studies
Authors: Li Huilin , Gail Mitchell H. , Berndt Sonja , Chatterjee Nilanjan 
Published: November 2010

AbstractCase‐control genome‐wide association studies provide a vast amount of genetic information that may be used to investigate secondary phenotypes. We study the situation in which the primary disease is rare and the secondary phenotype and genetic markers are dichotomous. An analysis of the association between a genetic marker and the secondary phenotype based on controls only (CO) is valid, whereas standard methods that also use cases result in biased estimates and highly inflated type I error if there is an interaction between the secondary phenotype and the genetic marker on the risk of the primary disease. Here we present an adaptively weighted (AW) method that combines the case and control data to study the association, while reducing to the CO analysis if there is strong evidence of an interaction. The possibility of such an interaction and the misleading results for standard methods, but not for the AW or CO approaches, are illustrated by data from a case‐control study of colorectal adenoma. Simulations and asymptotic theory indicate that the AW method can reduce the mean square error for estimation with a prespecified SNP and increase the power to discover a new association in a genome‐wide study, compared to CO analysis. Further experience with genome‐wide studies is needed to determine when methods that assume no interaction gain precision and power, thereby can be recommended, and when methods such as the AW or CO approaches are needed to guard against the possibility of nonzero interactions. Genet. Epidemiol. 34:427–433, 2010. Published 2010 Wiley‐Liss, Inc.
An “almost exhaustive” search‐based sequential permutation method for detecting epistasis in disease association studies
Authors: Ma Li , Assimes Themistocles L. , Asadi Narges B. , Iribarren Carlos , Quertermous Thomas , Wong Wing H. 
Published: November 2010

AbstractDue to the complex nature of common diseases, their etiology is likely to involve “uncommon but strong” (UBS) interactive effects—i.e. allelic combinations that are each present in only a small fraction of the patients but associated with high disease risk. However, the identification of such effects using standard methods for testing association can be difficult. In this work, we introduce a method for testing interactions that is particularly powerful in detecting UBS effects. The method consists of two modules—one is a pattern counting algorithm designed for efficiently evaluating the risk significance of each marker combination, and the other is a sequential permutation scheme for multiple testing correction. We demonstrate the work of our method using a candidate gene data set for cardiovascular and coronary diseases with an injected UBS three‐locus interaction. In addition, we investigate the power and false rejection properties of our method using data sets simulated from a joint dominance three‐locus model that gives rise to UBS interactive effects. The results show that our method can be much more powerful than standard approaches such as trend test and multifactor dimensionality reduction for detecting UBS interactions. Genet. Epidemiol. 34:434–443, 2010. © 2010 Wiley‐Liss, Inc.
Analyze multivariate phenotypes in genetic association studies by combining univariate association tests
Authors: Yang Qiong , Wu Hongsheng , Guo Chao‐Yu , Fox Caroline S. 
Published: November 2010

AbstractMultivariate phenotypes are frequently encountered in genome‐wide association studies (GWAS). Such phenotypes contain more information than univariate phenotypes, but how to best exploit the information to increase the chance of detecting genetic variant of pleiotropic effect is not always clear. Moreover, when multivariate phenotypes contain a mixture of quantitative and qualitative measures, limited methods are applicable. In this paper, we first evaluated the approach originally proposed by O'Brien and by Wei and Johnson that combines the univariate test statistics and then we proposed two extensions to that approach. The original and proposed approaches are applicable to a multivariate phenotype containing any type of components including continuous, categorical and survival phenotypes, and applicable to samples consisting of families or unrelated samples. Simulation results suggested that all methods had valid type I error rates. Our extensions had a better power than O'Brien's method with heterogeneous means among univariate test statistics, but were less powerful than O'Brien's with homogeneous means among individual test statistics. All approaches have shown considerable increase in power compared to testing each component of a multivariate phenotype individually in some cases. We apply all the methods to GWAS of serum uric acid levels and gout with 550,000 single nucleotide polymorphisms in the Framingham Heart Study. Genet. Epidemiol. 34:444–454, 2010. © 2010 Wiley‐Liss, Inc.
Housekeepers for accurate transcript expression analysis in Alzheimer's disease autopsy brain tissue
Authors: Gebhardt Florian M. , Scott Heather A. , Dodd Peter R. 
Published: November 2010

BackgroundQuantitative real‐time reverse transcription–polymerase chain reaction (qRT‐PCR) is a popular technique for mRNA expression studies. Normalization to an endogenous reference transcript (housekeeper) is widely used to correct for differences in loading and RNA quality. Alzheimer's disease (AD) alters brain metabolism. The stability of housekeeper transcript expression must be carefully validated.MethodsqRT‐PCR was used to assess eight putative housekeeper transcripts in four brain regions from 15 control, 12 AD, and 10 AD/Lewy body disease (LBD) cases.ResultsRNA quality is lower in AD and AD/LBD than in controls. Frequently used housekeepers such as glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) and β‐actin had lower overall expression in AD and AD/LBD cases than in controls. RPL13 and 18S were the most stably expressed housekeepers tested. Synaptophysin and glial fibrillary acidic protein were used to evaluate normalized quantification. By using different housekeepers we confirmed that synaptophysin expression was down‐regulated in AD cases, whereas glial fibrillary acidic protein expression was increased.ConclusionsAmong all candidates tested, RPL13 was the best housekeeper for qRT‐PCR studies in autopsy brain tissue samples from controls and AD cases. RNA quality should be assessed and data normalized on this index as well.
Exercise and cognition: Results from the National Long Term Care Survey
Authors: Jedrziewski M. Kathryn , Ewbank Douglas C. , Wang Haidong , Trojanowski John Q. 
Published: November 2010

BackgroundAge remains a robust risk factor for Alzheimer's disease as well as other dementias. Therefore, the aging of the population in the United States will result in dramatic increases in the prevalence of dementia if preventative interventions are not identified. The aim of this study was to examine potential associations between exercise and lowering the risk of cognitive impairment.MethodsNational Long Term Care Survey data were used. Level of exercise participation was measured at baseline (1994) and cognitive impairment status was measured at baseline and 5‐ and 10‐year follow‐up. Linear regression was performed, controlling for age, sex, education, baseline score on cognitive test, diabetes, and hypertension.ResultsAt 10‐year follow‐up, the number of different types of exercises performed was inversely associated with the onset of cognitive impairment (P = .002) as was the number of exercise sessions lasting at least 20 minutes (P = .007).ConclusionStudy results from National Long Term Care Survey data provide evidence supporting the potential for exercise to lower the risk of dementia.
High normal fasting blood glucose is associated with dementia in Chinese elderly
Authors: Mortimer James A. , Borenstein Amy R. , Ding Ding , DeCarli Charles , Zhao Qianhua , Copenhaver Cathleen , Guo Qihao , Chu Shugang , Galasko Douglas , Salmon David P. , Dai Qi , Wu Yougui , Petersen Ronald , Hong Zhen 
Published: November 2010

BackgroundDiabetes is a risk factor for mild cognitive impairment (MCI) and dementia. However, the association between high normal fasting blood glucose (FBG) and dementia has not been studied.MethodsPolytomous logistic regression was used to assess the association of dementia and MCI with FBG in an age‐ and sex‐matched sample of 32 dementia patients, 27 amnestic MCI (aMCI) patients, and 31 normal controls (NC). Analyses were repeated for those with normal FBG. Correlations between FBG and cognitive test scores were obtained.ResultsControlling for age, gender, education, body mass index, Hachinski Ischemic Score, magnetic resonance imaging (MRI) stroke, and normalized brain, hippocampal, and white matter hyperintensity MRI volumes; higher FBG was associated with dementia versus aMCI status (OR = 3.13; 95% CI, 1.28–7.69). This association remained (OR = 7.75; 95% CI, 1.10–55.56) when analyses were restricted to subjects with normal FBG. When dementia patients were compared with NC adjusting for age, gender, and education, a significant association with FBG also was seen (OR = 1.83; 95% CI, 1.09–3.08), but it was lost when vascular covariates were added to the model. FBG was not associated with aMCI status versus NC. Higher FBG was correlated with poorer performance on the Trailmaking Test Part B (P = .003). The percentage of dementia patients with high normal FBG (90%) was significantly higher than that of aMCI patients with high normal FBG (32.9%) (χ2 = 13.9, P < .001).ConclusionsHigher FBG was associated with dementia (vs. aMCI) independent of vascular risk factors and MRI indicators of vascular disease, and remained a significant risk factor when analyses were restricted to subjects with normal FBG. The results of this cross‐sectional study suggest that a high normal level of FBG may be a risk factor for dementia.
Predicting cognitive decline in Alzheimer's disease: An integrated analysis
Authors: Lopez Oscar L. , Schwam Elias , Cummings Jeffrey , Gauthier Serge , Jones Roy , Wilkinson David , Waldemar Gunhild , Zhang Richard , Schindler Rachel 
Published: November 2010

BackgroundNumerous patient‐ and disease‐related factors increase the risk of rapid cognitive decline in patients with Alzheimer's disease (AD). The ability of pharmacological treatment to attenuate this risk remains undefined.MethodsPooled data from 14 randomized clinical studies of donepezil in the treatment of AD (N = 3748) were analyzed to identify predictors of fast decline and determine the effect of donepezil on the risk of fast decline.ResultsYoung age and more severe baseline cognitive, global, or behavioral status were identified as independent predictors of faster decline in placebo‐treated patients. Multivariate models indicated that donepezil treatment was associated with a 39% to 63% reduction in the risk of faster decline.ConclusionsThese results correspond with previous findings, indicating relationships between age or baseline disease severity and rates of cognitive decline. Furthermore, they suggest that symptomatic therapy for AD could reduce the likelihood of faster decline in treated patients.
Field optimization of the sex pheromone of Stenoma catenifer (Lepidoptera: Elachistidae): evaluation of lure types, trap height, male flight distances, and number of traps needed per avocado orchard for detection
Authors: Hoddle M.S. , Millar J.G. , Hoddle C.D. , Zou Y. , McElfresh J.S. , Lesch S.M. 
Published: November 2010

AbstractThe sex pheromone of Stenoma catenifer was evaluated in commercial avocado orchards in Guatemala to determine operational parameters, such as optimal lure type, trap height, trap density and estimates of the distances that male moths fly. Of four pheromone dispensers tested, gray and white rubber septa were of equal efficacy, whereas 1-ml low-density polyethylene vials and 2×3-cm polyethylene ziplock bags were least efficacious. The height at which wing traps were hung did not significantly affect the number of adult male S. catenifer captured. For monitoring S. catenifer, these data suggest that the pheromone should be dispensed from gray rubber septa in wing traps hung inside the tree canopy at 1.75 m, a height convenient for trap placement and monitoring. Mark-recapture studies of male S. catenifer indicated that, on average, males flew 67 m in one night. However, it is likely that this is an underestimate of the distance that male moths are capable of flying in a single night. Probabilistic modeling of S. catenifer capture data from different numbers of pheromone traps deployed in seven commercial avocado orchards of varying sizes and infestation levels suggested that 10–13 randomly deployed traps per orchard for a 7-day period are needed to detect at least one male S. catenifer with 90% confidence. These data provide sufficient information to develop effective protocols for using the S. catenifer pheromone to detect and monitor this pest in countries with endemic populations that are exporting fresh avocados, and for quarantine detection and incursion monitoring in countries receiving avocado imports from high risk areas.
PCR-based species identification ofAgrioteslarvae
Authors: Staudacher K. , Pitterl P. , Furlan L. , Cate P.C. , Traugott M. 
Published: November 2010

AbstractClick beetle larvae within the genusAgriotes(Coleoptera: Elateridae), commonly known as wireworms, are abundant ground-dwelling herbivores which can inflict considerable damage to field crops. In Central Europe up to 20 species, which differ in their distribution, ecology and pest status, occur in arable land. However, the identification of these larvae based on morphological characters is difficult or impossible. This hampers progress towards controlling these pests. Here, we present a polymerase chain reaction (PCR)-based approach to identify, for the first time, 17Agriotesspecies typically found in Central Europe. Diagnostic sequence information was generated and submitted to GenBank, allowing the identification of these species via DNA barcoding. Moreover, multiplex PCR assays were developed to identify the nine most abundant species rapidly within a single-step reaction:Agriotes brevis, A. litigiosus, A. obscurus, A. rufipalpis, A. sordidus, A. sputator, A. ustulatus, A. lineatusandA. proximus. The latter two species remain molecularly indistinguishable, questioning their species status. The multiplex PCR assays proved to be highly specific against non-agrioted elaterid beetles and other non-target soil invertebrates. By testing the molecular identification system with over 900 field-collected larvae, our protocol proved to be a reliable, cheap and quick method to routinely identify Central EuropeanAgriotesspecies.
Crop and field boundary influences on the activity of a wide range of beneficial invertebrate groups on a split conventional/organic farm in northern England
Authors: Eyre M.D. , Leifert C. 
Published: November 2010

AbstractActivity of 12 beneficial invertebrate groups was assessed in 2005 and 2006 on a farm in northern England split into conventional and organic management halves, using pitfall and pan traps set in both crops and field boundaries. Management, crop and boundary structure influences on invertebrate activity were assessed, as was the relationship between crop and boundary type. Classification of crop and boundary assemblages produced three and two groups, respectively, in both years. Organic arable crops had well-defined assemblages in both years; and, while grass and grass/clover fields were separated from conventional arable fields in 2005, there was mixing in 2006. One boundary group, in both years, was dominated by conventional arable fields with tall herbaceous boundary vegetation. The other group had more organic arable and grassy fields with shorter boundary vegetation. Redundancy analyses showed that a number of groups (Cantharidae, Coccinellidae, Syrphidae, Ichneumonidae, Braconidae, Proctotrupoidea, Lycosidae) were more active in organic arable fields with more Staphylinidae in conventional arable crops and no obvious trend with Carabidae, Hemiptera, Neuroptera and Linyphiidae. Activity of some groups, especially Coccinellidae, Syrphidae and parasitic wasps, was strongly related to weed cover. Staphylinidae were most active in tall herbaceous boundaries by conventional arable crops with more of a number of groups (Cantharidae, Coccinellidae, parasitic wasps) in short herbaceous boundaries by organic arable crops. Organic management produced most differences in aerially-dispersed invertebrates, and management had a profound effect on activity in field boundaries. Possible management prescriptions to increase invertebrate activity include changing sowing times, weed cover manipulation and field boundary and margin management.
Reproductive incompatibility between the B and Q biotypes of the whitefly Bemisia tabaci in China: genetic and behavioural evidence
Authors: Sun D.B. , Xu J. , Luan J.B. , Liu S.S. 
Published: November 2010

AbstractThe B and Q ‘biotypes’ of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) have been invading many parts of the world and causing severe damage to a range of crops. Recent phylogenetic analyses indicate that B and Q are cryptic species within the B. tabaci species complex. Although various attempts have been made to examine the reproductive compatibility between B and Q, few studies have tested the fertility of the F1 females and so the extent of possible gene flow remains unclear. In this study, we conducted a series of crossing experiments and behavioural observations to examine in detail the reproductive compatibility between the B and Q biotypes collected from Zhejiang, China, a region recently invaded by these whiteflies. Crossing experiments between the two biotypes using either single-pairs or small groups demonstrated that proportions of females in the F1 progeny were only 0–2% in the inter-biotype crosses compared to 58–68% in the intra-biotype treatments. Furthermore, all inter-biotype F1 females were sterile. Continuous video observations showed that B and Q adults very rarely copulated, and copulation occurred only when adults of opposite sex from different biotypes were enclosed in dense cohorts for a relatively long period of time. These data show that the B and Q biotypes examined in this study are completely isolated in reproduction. The isolation was due to mainly a copulation barrier, but post-copulation barriers were also involved.
Edge-induced narrowing of dietary diversity in leaf-cutting ants
Authors: Falcão P.F. , Pinto S.R.R. , Wirth R. , Leal I.R. 
Published: November 2010

AbstractMuch of the ecological alteration faced by human-modified Neotropical forests can be assigned to edge effects, including the proliferation of some voracious herbivores such as leaf-cutting ants. However, the underlying mechanisms/impacts of tropical forest edge on herbivores performance and their foraging behaviour (e.g. dietary diversity) have rarely been investigated. The goal of this study was, therefore, to determine whether and how the annual diet (i.e. species richness, diversity and the relative proportion of pioneer versus non-pioneer species of plant materials) of Atta cephalotes colonies differs in the forest edge versus the interior zone of a large remnant of Atlantic forest in northeastern Brazil. Among the key results was a strong habitat effect on dietary diversity (explaining ca. 40–50% of the variation), which, in edge colonies, decreased approximately by one fourth compared to interior colonies (inverse of Simpson's index: 3.7±0.84 versus 4.99±0.95). There was a predominance of leaf fragments collected from pioneer species in the diet in both habitat (86% in edge and 80.4% in interior). Edge colonies collected proportionally more fragments from pioneer species than colonies located in the forest interior. Our results are the first to demonstrate an edge-mediated relaxation of dietary restrictions in leaf-cutting ants. These findings render robust support to previous evidence indicating the reduction of bottom-up forces as a key factor explaining both edge-induced hyper-abundance and increased herbivory of leaf-cutting ants in human-modified Neotropical landscapes.
Morphometric and gonad maturity of the spider crab Libinia spinosa (Crustacea: Brachyura: Majoidea: Epialtidae) in Argentina
Authors: Sal Moyano M.P. , Gavio M.A. , Maggi M.D. 
Published: November 2010

Morphometric and gonad maturity of Libinia spinosa on the coast of Mar del Plata, Argentina, were assessed. In both sexes various morphometric features were measured to determine the morphometric maturity, and through macroscopic inspection of gonads and analysis of its content, different stages of gonad maturity were described and the physiological maturity was estimated. In females, the carapace width ranged from 8 to 56.5 mm while in males from 4.6 to 81.97 mm. The size at which 50% of females were morphometrically mature was calculated at 40.6 mm. Based on the allometric growth of the abdomen, two morphometric groups of females were recognized as juvenile and adult phases. In males, results of principal component analysis showed that the most suitable variables that efficiently represent the size and sexual differentiation factor were the carapace width and cheliped length respectively. The size at which 50% of males were morphometrically mature was estimated at 58.9 mm. Based on the allometry of the cheliped growth, two morphometric groups were recognized as immature and mature phases. Males maintained under laboratory conditions moulted and growth was related to regular and terminal moults. Males reached their terminal moult at a wide size-range, from 48.5 mm to 61.4 mm of carapace width. This terminal moult coincided with the size of morphometric maturity. In both sexes four stages of gonad development were described, two corresponded to immature phases and two to mature phases. The size at which 50% of females and males reached gonad maturity was LC50 = 40.33 mm and LC50 = 33.6 mm, respectively. In females, both morphometric and gonad maturity occurred at a similar size. In males, gonad maturity is acquired prior to morphometric maturity, thus three different types of males were characterized: (1) those with small carapace width and cheliped, without spermatophores in their vas deferens; (2) those with large carapace width and small cheliped, bearing spermatophores in their vas deferens; and (3) those with large carapace width and cheliped, bearing spermatophores in their vas deferens.
On a class of stable conditional measures
Authors: MIHAILESCU EUGEN 
Published: November 2010

AbstractThe dynamics of endomorphisms (smooth non-invertible maps) presents many differences from that of diffeomorphisms or that of expanding maps; most methods from those cases do not work if the map has a basic set of saddle type with self-intersections. In this paper we study the conditional measures of a certain class of equilibrium measures, corresponding to a measurable partition subordinated to local stable manifolds. We show that these conditional measures are geometric probabilities on the local stable manifolds, thus answering in particular the questions related to the stable pointwise Hausdorff and box dimensions. These stable conditional measures are shown to be absolutely continuous if and only if the respective basic set is a non-invertible repeller. We find also invariant measures of maximal stable dimension, on folded basic sets. Examples are given, too, for such non-reversible systems.