Strain comparisons in aquaculture species: a manual

When different strains or breeds of a particular species are available, the best choice is seldom immediately obvious for producers. Scientists are also interested in the relative performance of different strains because it provides a basis for recommendations to producers and it often stimulates the conduct of work aimed at unraveling the underlying biological mechanisms involved in the expression of such differences. Hence, strain or breed comparisons of some sort are frequently conducted. This manual is designed to provide general guidelines for the design of strain comparison trials in aquaculture species. Example analyzes are provided using SAS and SPSS. The manual is intended to serve a wide range of readers from developing countries with limited access to information. The users, however, are expected to have a basic knowledge of quantitative genetics and experience in statistical methods and data analysis as well as familiarity with computer software. The manual mainly focuses on the practical aspects of design and data analysis, and interpretation of results.

Controle Gerencial e a Tecnologia da Informação: um estudo de caso na previsão orçamentária em uma organização do setor industrial.

A evolução tecnológica tem feito as empresas se modificarem, e para acompanhar o mercado elas buscam opções que possam ajudar melhor nas tomadas de suas decisões, uma delas é a utilização de tecnologias. A presente pesquisa objetiva analisar a contribuição da tecnologia da informação no orçamento da indústria Alfa. Esta pesquisa é descritiva e exploratória, pois busca descrever a realidade da organização, identificando as características do orçamento da mesma, é quantitativa, pois busca através de métodos estatísticos realizar previsões para o ano de 2013 das demonstrações de resultados advindos dos anos anteriores (2010 a 2012), é também, qualitativa, pois foi elaborado um questionário que pôde auxiliar na interpretação dos dados quantitativos, possibilitando melhores informações sobre o objetivo proposto. Concluiu-se que a tecnologia pode ajudar a melhorar a qualidade da previsão do orçamento da indústria Alfa e o método que melhor se adequou para as estimativas foi a suavização exponencial que demonstrou maior confiabilidade para os resultados.

Do quase nada ao praticamente tudo: uma análise espacial da evolução da votação dos candidatos do Partido dos Trabalhadores à presidência no Nordeste.

Mudanças marcantes no perfil geográfico eleitoral do Brasil, no que diz respeito às eleições para Presidente da República, aconteceram no ano de 2006. Candidatos do Partido dos Trabalhadores (PT) que antes eram bem votados em regiões mais desenvolvidas do país, passaram a ganhar as eleições, com grande margem de preferência, nas regiões mais pobres do país. Entenda por regiões mais pobres as regiões Norte e Nordeste. Esse trabalho pretende traçar um histórico da relação eleitoral da Região Nordeste do Brasil com os candidatos do Partido dos Trabalhadores ao cargo de Presidente da República desde a redemocratização. O objetivo é entender a relação entre a opção de voto em candidatos desse partido e o desenvolvimento socioeconômico ao longo do tempo da região, levando em consideração também o programa Bolsa Família para tentar comprovar a sua racionalidade. Além disso, este trabalho faz um estudo de caso da votação da cidade de Viçosa do Ceará para exemplificar o fato de que a indução do voto para candidatos de âmbito federal por representantes locais não é mais a regra da região e sim a exceção. A investigação usa análise bibliográfica, histórica e métodos de análise estatística, principalmente, técnicas de análise espacial.

Accelerating Bayesian hierarchical clustering of time series data with a randomised algorithm.

We live in an era of abundant data. This has necessitated the development of new and innovative statistical algorithms to get the most from experimental data. For example, faster algorithms make practical the analysis of larger genomic data sets, allowing us to extend the utility of cutting-edge statistical methods. We present a randomised algorithm that accelerates the clustering of time series data using the Bayesian Hierarchical Clustering (BHC) statistical method. BHC is a general method for clustering any discretely sampled time series data. In this paper we focus on a particular application to microarray gene expression data. We define and analyse the randomised algorithm, before presenting results on both synthetic and real biological data sets. We show that the randomised algorithm leads to substantial gains in speed with minimal loss in clustering quality. The randomised time series BHC algorithm is available as part of the R package BHC, which is available for download from Bioconductor (version 2.10 and above) via http://bioconductor.org/packages/2.10/bioc/html/BHC.html. We have also made available a set of R scripts which can be used to reproduce the analyses carried out in this paper. These are available from the following URL. https://sites.google.com/site/randomisedbhc/.

形状填充率的物体识别算法

针对经典形状上下文算法对物体关节相对位置变化敏感的缺点,提出一种基于剪影局部形状填充率的物体识别算法.该算法以物体不同的轮廓控制点为圆心,计算不同半径下物体剪影像素所占总像素的比例,即为控制点的局部形状填充率;将不同控制点、不同半径长度所计算的形状填充率数值构成一个特征矩阵,该矩阵反映了物体整个剪影的统计特性.通过不同数据库的实验结果表明,文中算法对物体的细节有很强的描述能力,对物体关节的相对位置不敏感,并且受剪影轮廓控制点数量影响小.

Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria

Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e. g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.

大气季节内振荡对东亚夏季风活动的影响研究

利用ERA40逐日再分析资料、NCEP/NCAR2逐日再分析资料、中国740个测站日降水资料、上海台风研究所提供的西太平洋热带气旋资料、Kaplan等重建的月平均SSTA资料、NOAA逐日长波辐射（OLR）等资料，应用离散功率谱分析、带通滤波、EOF分析等统计方法，研究了东亚夏季风(EASM）的移动特征、东亚地区季节内振荡(ISO)的基本特征、季节内振荡对东亚夏季风活动的影响、季节内振荡对东亚夏季风异常活动的影响机理。主要结论如下： （1）综合动力和热力因素定义了可动态描述东亚夏季风移动和强度的指数，并利用该指数研究了东亚夏季风的爆发和移动的季节内变化及其年际和年代际变化特征。研究发现，气候平均东亚夏季风前沿分别在28候、33候、36候、38候、40候、44候出现了明显的跳跃。东亚夏季风活动具有显著的年际变率，主要由于季风前沿在某些区域异常停滞和突然跨越北跳或南撤引起，造成中国东部旱涝灾害频繁发生。东亚夏季风的活动具有明显的年代际变化，在1965年、1980年、1994年发生了突变，造成中国东部降水由“南旱北涝”向“南涝北旱”的转变。 （2）东亚季风区季节内变化具有10~25d和30~60d两个波段的季节内振荡周期，以30-60d为主。存在三个主要低频模态，第一模态主要表征了EASM在长江中下游和华北地区活动期间的低频形势；第二模态印度洋-菲律宾由低频气旋式环流控制，主要表现了ISO在EASM爆发期间的低频形势；第三模态主要出现在EASM在华南和淮河活动期间的低频形势。第一模态和第三模态是代表东亚夏季风活动异常的主要低频形势。 （3）热带和副热带地区ISO总是沿垂直切变风的垂直方向传播。因此，在南海-菲律宾东北风垂直切变和副热带西太平洋北风垂直切变下，大气热源激发菲律宾附近交替出现的低频气旋和低频反气旋不断向西北传播，副热带西太平洋ISO以向西传播为主。中高纬度地区，乌拉尔山附近ISO以向东、向南移动或局地振荡为主；北太平洋中部ISO在某些情况下向南、向西传播。 （4）季风爆发期，伴随着热带东印度洋到菲律宾一系列低频气旋和低频反气旋， 冷空气向南输送，10~25天和30~60天季节内振荡低频气旋同时传入南海加快了南海夏季风的爆发。在气候态下，ISO活动表现的欧亚- 太平洋（EAP）以及太平洋-北美（PNA）低频波列分布特征(本文提出的EAP和PNA低频波列与传统意义上的二维定点相关得到的波列不同)。这种低频分布形式使得欧亚和太平洋中高纬度的槽、脊及太平洋副热带高压稳定、加强，东亚地区的低频波列则成为热带和中高纬度ISO相互作用影响东亚夏季风活动的纽带。不同的阶段表现不同的低频模态，30~60d低频模态的转变加快了EASM推进过程中跳跃性；30-60d低频模态的维持使得EASM前沿相对停滞。 （5）30-60d滤波场，菲律宾海域交替出现的低频气旋和低频反气旋不断向西北传播到南海-西太平洋一带。当南海-西太平洋地区低频气旋活跃时，季风槽加强、东伸，季风槽内热带气旋（TC）频数增加；当南海-西太平洋低频反气旋活跃时，季风槽减弱、西退，TC处于间歇期，生成位置不集中。 （6）在El Nino态下，大气季节内振荡偏弱，北传特征不明显，但ISO由中高纬度北太平洋中部向南和副热带西太平洋向西的传播特征显著，东亚地区ISO活动以第三模态为主，EASM集中停滞在华南和淮河流域，常伴随着持续性区域暴雨的出现，易造成华南和江淮流域洪涝灾害，长江和华北持续干旱。在La Nina态下，大气季节内振荡活跃，且具有明显的向北传播特征，PNA低频波列显著，东亚地区ISO活动以第一模态单峰为主；EASM主要停滞在长江中下游和华北地区，这些地区出现异常持续强降水，华南和淮河流域多干旱；在El Nino态向La Nina态转换期，ISO活动以第一模态双峰为主，长江中下游常常出现二度梅。

黄骅坳陷大港探区油气资源潜力与资源结构预测

Facing the problems that Dagang region of Huanghua Depression has high exploration degree and its remaining resource potential and structure are not clear, the theory of Petroleum Accumulation System (PAS) is applied to divide and evaluate the oil/gas systems quantitatively. Then, the petroleum accumulation systems are taken as units to forecast and analyse the oil/gas resources and their structure using statistical methods of sampling analysis of discovery process model and generalized pareto distribution model. The exploration benefit of the unit is estimated using exploration simulation methods. On the basis of the above study, the resource potential of Huanghua Depression is discussed.Huanghua Depression can be diveded into four petroleum accumulation systems, i.e. North PAS5 Middle Qibei PAS, Middle Qinan PAS and South PAS. Each PAS can be diveded futher into several sub- PASs. Using the basic princple of Analytical Hierarchy Process, the method of quantitative evaluation of PAS is established. Then the elements and maturity of PAS are evaluated quantitatively.Taking migration and accumulation units and sub-PASs as prediction units, sampling analysis of discovery process model and generalized pareto distribution model are applied comparatively to forecast the resource structure of eight migration and accumulation units in six PASs of medium-high exploration degree. The results of these two methods are contrasted and analyzed. An examination of X2 data of these two models from exploration samples shows that generalized pareto distribution model is more effective than sampling analysis of discovery process model in Huanghua Depression. It is concluded that minimum and maximum size of reservoir and discovery sequence of reservoirs are the sensitive parameters of these two methods.Aiming at the difficult problem of forecast in low exploration degree, by analysis of relativity between resource parameters and their possible influential geological factors, forecast models for resource parameters were established by liner regressing. Then the resource structure is forecasted in PASs of low exploration degree.Based on the forecast results, beginning with the analysis of exploration history and benefit variation, the exploration benefit variation of the above PASs is fitted effectively using exploration simulation method. The single well exploration benefit of remaining oil resource is also forecasted reasonably.The results of resource forecast show that the total oil resources ofHuanghua Depression amount to 2.28 b illion ton. By the end o f 2 003, the accumulative total proved oil reserve is 0.90 billion ton and the remaining oil resources is 1.38 billion ton. The remaining oil resource is concentrated in Kongdian-Dengmingshi, Banqiao-Beidagang, Qidong-Yangerzhuang and Baidong-Qizhong sub-PASs.

影响生育价值观因素的研究－传统回归分析与多层线性模型分析结果的比较

Based on the research of predictors of VOC, this study explores the predictive effect of factors, such as generation, urban/rural context, collectivism/individualism orientation, family value, independent/interdependent self, adult attachment, on the Emotional and Traditional factors of VOC. Considering the hierarchical data structure of the VOC study, which resulted from the original research design, this dissertation applies Hierarchical Linear Model (HLM) after using traditional regression. A comparison between the results from the tow statistical methods is made, and the results are as follows: 1) Reliability coefficients of questionnaires used in this study are satisfactory, and most of them can be used in further research. 2) Samples from different generation and urban/rural context show significant differences on the score of collectivism/individualism orientation, family value, independent/interdependent self, adult attachment, and VOC. 3) Regression equations with VOC as outcome variable differ from each other when using data from sample with restricted generation or urban/rural context. 4) Results by HLM shows that interdependent self and mother identity have positive effect on emotional factor of VOC. Emotional factor’s variation on family level is not significant. 5) Results by HLM shows that Individualism, Interdependent Self and Grandmother Identity can predict Traditional factor of VOC. Traditional factor’s variation is significant on family level, which can be explained by family income and it’s area-urban or rural. Based on the results above, the researcher concludes that a) generation identity and urban/rural context have important effect on VOC; b) Interdependent Self is an important predictive factor of VOC’s Emotional factor, which is nearly subjective to other factors; d) VOC’s traditional factor varies with other factors, which show its strong relation with culture and tradition; e) more exact results can be gotten from HLM analysis, which beyond tradition regression.

心算年老化的认知心理机制及功能磁共振成像研究

Mechanisms underlying cognitive psychology and cerebral physiological of mental arithmetic with increasing are were studied by using behavioral methods and functional magnetic resonance imaging (fMRI). I. Studies on mechanism underlying cognitive psychology of mental arithmetic with increasing age These studies were accomplished in 172 normal subjects ranging from 20 to 79 years of age with above 12 years of education (Mean = 1.51, SD = 1.5). Five mental arithmetic tasks, "1000-1", "1000-3", "1000-7", "1000-13", "1000-17", were designed with a serial calculation in which subjects sequentially subtracted the same prime number (1, 3, 7, 13, 17) from another number 1000. The variables studied were mental arithmetic, age, working memory, and sensory-motor speed, and four studies were conducted: (1) Aging process of mental arithmetic with different difficulties, (2) mechanism of aging of mental arithmetic processing. (3) effects of working memory and sensory-motor speed on aging process of mental arithmetic, (4) model of cognitive aging of mental arithmetic, with statistical methods such as MANOVA, hierarchical multiple regression, stepwise regression analysis, structural equation modelling (SEM). The results were indicated as following: Study 1: There was an obvious interaction between age and mental arithmetic, in which reaction time (RT) increased with advancing age and more difficult mental arithmetic, and mental arithmetic efficiency (the ratio of accuracy to RT) deceased with advancing age and more difficult mental arithmetic; Mental arithmetic efficiency with different difficulties decreased in power function: Study 2: There were two mediators (latent variables) in aging process of mental arithmetic, and age had an effect on mental arithmetic with different difficulties through the two mediators; Study 3: There were obvious interactions between age and working memory, working memory and mental arithmetic; Working memory and sensory-motor speed had effects on aging process of mental arithmetic, in which the effect of working memory on aging process of mental arithmetic was about 30-50%, and the effect of sensory-motor speed on aging process of mental arithmetic was above 35%. Study 4: Age, working memory, and sensory-motor speed had effects on two latent variables (factor 1 and factor 2), then had effects on mental arithmetic with different difficulties through factor 1 which was relative to memory component, and factor 2 which relative to speed component and had an effect on factor 1 significantly. II. Functional magnetic resonance imaging study on metal arithmetic with increasing age This study was accomplished in 14 normal right-handed subjects ranging from 20 to 29 (7 subjects) and 60 to 69 (7 subjects) years of age by using functional magnetic resonance imaging apparatus, a superconductive Signa Horizon 1.5T MRI system. Two mental arithmetic tasks, "1000-3" and "1000-17", were designed with a serial calculation in which subjects sequentially subtracted the same prime number (3 or 17) from another number 1000 silently, and controlling task, "1000-0", in which subjects continually rehearsed number 1000 silently, was regarded as baseline, based on current "baseline-task" OFF-ON subtraction pattern. Original data collected by fMRI apparatus, were analyzed off-line in SUN SPARC working station by using current STIMULATE software. The analytical steps were composed of within-subject analysis, in which brain activated images about mental arithmetic with two difficulties were obtained by using t-test, and between-subject analysis, in which features of brain activation about mental arithmetic with two difficulties, the relationship between left and right hemisphere during mental arithmetic, and age differences of brain activation in young and elderly adults were examined by using non-parameter Wilcoxon test. The results were as following:

中国企业员工组织承诺研究

The research objectives were to investigate the psychological structure of employees' organizational commitments(OCs), and its antecedents, and to examine the relative effects of employees' OCs to their performances. In order to deeply uncover the nature of OCs, some standard methods, such as in-depth interview, focus-group, semi-open questionnaire, standard questionnaire etc., were employed. In data analysis, not only some common statistical methods, such as multivariate analysis of variance, cross-table analysis, factor analysis, but also some forefront ones, such as confirmatory factor analysis and path analysis of SEM, were used. The paper covers six chapters: 1) In the first chapter, Firstly some previous empirical studies, which examined structures, antecedents, correlates, and/or consequences of organizational commitment in China and Western countries, were summarized. This summary covers most of the respectable researchers' works of this field, such as H.S.Becker, B.Buchanan, L.W.Porter, G. Ritzer, H.M.Trice, J.A.Alutto, L.G.Hrebiniak, R.T.Mowday, J.P.Meyer, N.J.Allen, G.W.McGee, R.C.Ford, R.Eisenberger, etc. Then three theoretical hypothesis were put forward as following: ① In China, OCs should be multidimensional psychological structures, which means there should exist more than one type of OCs; ② There should be some different antecedents to different OCs; ③ Employees with different types of OC should perform differently in their works. Finally the theoretical and practical significance were discussed. 2) In the second chapter, great efforts were made to investigate the OC types. Firstly, in-depth interview with managers and employees, semi-open questionnaire, and some other methods were used in the pilot research to gather much qualitative material. Then OC questionnaire was designed to get quantitative data in about 20 enterprises, including state-owned, collective-owned, wholly foreign-funded, and joint-ventures. During revising of this questionnaire, there were about 5000 samples surveyed. after factor analysis, the data shows that there should be 5 types of OCs in China, which were respectively named as Affective Commitment, Normative commitment, Ideal Commitment, Economic Commitment, Choice Commitment. Thirdly, confirmatory factor analysis method was used to successfully confirm this 5-factor model. Finally, Cronbach a and test-retest correlate indicate that this questionnaire is reliable. Since factor analysis result has show its construct validity, a simple criterion-related validity research was conducted. 3) In order to investigate the correlation between different OC and employee performance and different antecedents of OC, 5 other questionnaires, such as Employee Satisfaction Questionnaire, Perceived Organizational Support Questionnaire, Social Exchange Questionnaire, Altruism Scale, and Leader Confidence Scale were revised in the third chapter. 4)In the fourth chapter, a lot of correlates, cross-table analysis were conducted to show the correlation between different OCs and 10 performances, which indicate employees with different OCs will show different performance in 10 variables, such as altruism, etc. 5) In the fifth chapter, correlate analysis, multivariate of analysis, and path analysis of SEM were used to investigate the antecedents of OC. A satisfactory model showing the correlation between OC and their antecedents was confirmed. 6) In the last chapter, all researches about OC, and its limitations were summarized.

Irish Times coverage of Irish relief and development nongovernmental organisations, legitimacy and accountability, 1994-2009: analysis and implications for the role of nongovernmental organisations

The overall aim of this study was to investigate the extent to which and ways in which Irish relief and development nongovernmental organisations (NGOs) were linked with the concepts of legitimacy and accountability in Irish Times newspaper coverage between 1994 and 2009. This research was based on a quantitative content analysis of 215 Irish Times articles and the results were analysed using statistical methods. Key findings of the research included that NGO accountability received significantly more coverage than NGO legitimacy, "principal-agent" approaches to NGO accountability received significantly more coverage than "stakeholder" approaches to NGO accountability, and questioning of NGOs based on either their accountability or legitimacy was very limited. It is suggested that these findings may indicate both a failure by Irish NGOs to promote "development literacy" and global solidarity among the Irish public, and a limited degree of "development literacy" and global solidarity among the Irish public.

Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies.

A steady increase in knowledge of the molecular and antigenic structure of the gp120 and gp41 HIV-1 envelope glycoproteins (Env) is yielding important new insights for vaccine design, but it has been difficult to translate this information to an immunogen that elicits broadly neutralizing antibodies. To help bridge this gap, we used phylogenetically corrected statistical methods to identify amino acid signature patterns in Envs derived from people who have made potently neutralizing antibodies, with the hypothesis that these Envs may share common features that would be useful for incorporation in a vaccine immunogen. Before attempting this, essentially as a control, we explored the utility of our computational methods for defining signatures of complex neutralization phenotypes by analyzing Env sequences from 251 clonal viruses that were differentially sensitive to neutralization by the well-characterized gp120-specific monoclonal antibody, b12. We identified ten b12-neutralization signatures, including seven either in the b12-binding surface of gp120 or in the V2 region of gp120 that have been previously shown to impact b12 sensitivity. A simple algorithm based on the b12 signature pattern was predictive of b12 sensitivity/resistance in an additional blinded panel of 57 viruses. Upon obtaining these reassuring outcomes, we went on to apply these same computational methods to define signature patterns in Env from HIV-1 infected individuals who had potent, broadly neutralizing responses. We analyzed a checkerboard-style neutralization dataset with sera from 69 HIV-1-infected individuals tested against a panel of 25 different Envs. Distinct clusters of sera with high and low neutralization potencies were identified. Six signature positions in Env sequences obtained from the 69 samples were found to be strongly associated with either the high or low potency responses. Five sites were in the CD4-induced coreceptor binding site of gp120, suggesting an important role for this region in the elicitation of broadly neutralizing antibody responses against HIV-1.

Qualitative analysis of the interdisciplinary interaction between data analysis specialists and novice clinical researchers.

BACKGROUND: The inherent complexity of statistical methods and clinical phenomena compel researchers with diverse domains of expertise to work in interdisciplinary teams, where none of them have a complete knowledge in their counterpart's field. As a result, knowledge exchange may often be characterized by miscommunication leading to misinterpretation, ultimately resulting in errors in research and even clinical practice. Though communication has a central role in interdisciplinary collaboration and since miscommunication can have a negative impact on research processes, to the best of our knowledge, no study has yet explored how data analysis specialists and clinical researchers communicate over time. METHODS/PRINCIPAL FINDINGS: We conducted qualitative analysis of encounters between clinical researchers and data analysis specialists (epidemiologist, clinical epidemiologist, and data mining specialist). These encounters were recorded and systematically analyzed using a grounded theory methodology for extraction of emerging themes, followed by data triangulation and analysis of negative cases for validation. A policy analysis was then performed using a system dynamics methodology looking for potential interventions to improve this process. Four major emerging themes were found. Definitions using lay language were frequently employed as a way to bridge the language gap between the specialties. Thought experiments presented a series of "what if" situations that helped clarify how the method or information from the other field would behave, if exposed to alternative situations, ultimately aiding in explaining their main objective. Metaphors and analogies were used to translate concepts across fields, from the unfamiliar to the familiar. Prolepsis was used to anticipate study outcomes, thus helping specialists understand the current context based on an understanding of their final goal. CONCLUSION/SIGNIFICANCE: The communication between clinical researchers and data analysis specialists presents multiple challenges that can lead to errors.

Assessment of LD matrix measures for the analysis of biological pathway association.

Complex diseases will have multiple functional sites, and it will be invaluable to understand the cross-locus interaction in terms of linkage disequilibrium (LD) between those sites (epistasis) in addition to the haplotype-LD effects. We investigated the statistical properties of a class of matrix-based statistics to assess this epistasis. These statistical methods include two LD contrast tests (Zaykin et al., 2006) and partial least squares regression (Wang et al., 2008). To estimate Type 1 error rates and power, we simulated multiple two-variant disease models using the SIMLA software package. SIMLA allows for the joint action of up to two disease genes in the simulated data with all possible multiplicative interaction effects between them. Our goal was to detect an interaction between multiple disease-causing variants by means of their linkage disequilibrium (LD) patterns with other markers. We measured the effects of marginal disease effect size, haplotype LD, disease prevalence and minor allele frequency have on cross-locus interaction (epistasis). In the setting of strong allele effects and strong interaction, the correlation between the two disease genes was weak (r=0.2). In a complex system with multiple correlations (both marginal and interaction), it was difficult to determine the source of a significant result. Despite these complications, the partial least squares and modified LD contrast methods maintained adequate power to detect the epistatic effects; however, for many of the analyses we often could not separate interaction from a strong marginal effect. While we did not exhaust the entire parameter space of possible models, we do provide guidance on the effects that population parameters have on cross-locus interaction.