text:
/Dropbox/Papers/Tuerlinckx-2006-British%20Journal%20of%20Mathematical%20&%20Statistical%20Psychology_Statistical%20inferenc.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1980},
rating = {0}
}

@article{Hubbard:2008p3616,
author = {R Hubbard and M M Lindsay},
journal = {Theory {\&} Psychology},
title = {Why P Values Are Not a Useful Measure of Evidence in Statistical Significance Testing},
abstract = {Reporting p values from statistical significance tests is common in psychology's empirical literature. Sir Ronald Fisher saw the p value as playing a useful role in knowledge development by acting as an `objective' measure of inductive evidence against the null hypothesis. We review several reasons why the p value is an unobjective and inadequate measure of evidence when statis- tically testing hypotheses. A common theme throughout many of these reasons is that p values exaggerate the evidence against H0. This, in turn, calls into question the validity of much published work based on comparatively small, including .05, p values. Indeed, if researchers were fully informed about the limitations of the p value as a measure of evidence, this inferential index could not possibly enjoy its ongoing ubiquity. Replication with extension research focusing on sample statistics, effect sizes, and their confidence intervals is a better vehicle for reliable knowledge development than using p values. Fisher would also have agreed with the need for replication research.},
number = {1},
pages = {69--88},
volume = {18},
year = {2008},
date-added = {2010-01-16 18:33:51 +0100},
date-modified = {2010-01-16 18:34:39 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hubbard-2008-Theory%20&%20Psychology_Why%20P%20Values%20Are%20Not.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3616},
rating = {0}
}

@article{Tincello:2009p11806,
author = {Douglas Tincello and Mark Sculpher and Ralf Tunn and Deborah Quail and Huub van der Vaart and Christian Falconer and Martina Manning and Louise Timlin},
journal = {Value Health},
title = {Patient Characteristics Impacting Health State Index Scores, Measured by the EQ-5D of Females with Stress Urinary Incontinence Symptoms},
abstract = {ABSTRACT Objective: To describe the characteristics of women seeking treatment for symptoms of stress urinary incontinence (SUI) and to investigate the association of SUI symptoms with generic health-related quality of life (HRQoL) as measured by the EuroQol (EQ-5D) instrument. Methods: The Stress Urinary Incontinence Treatment (SUIT) study was a 12-month observational study in four European countries that evaluated the cost-effectiveness of duloxetine compared with other forms of nonsurgical intervention in the treatment of the symptoms of SUI. Four hundred thirty-one physicians observed women seeking treatment for their SUI, and recorded the care provided and the outcomes of that care at enrollment and at 3, 6 and 12 months afterward The impact of SUI on baseline HRQoL as expressed by the EQ-5D index score was assessed by linear and logistic regression. Results: Three thousand seven hundred sixty-two women were enrolled into SUIT, with the largest patient group from Germany. Overall, the majority of women were postmenopausal, had a mean age of 58.0 years, were not current smokers, and tended to be overweight (mean body mass index [BMI] = 27.7 kg/m(2)), with at least one comorbidity. The health state index scores were significantly and independently influenced by the presence of comorbidity(ies) affecting quality of life, total number of stress and urge incontinence episodes, urinary incontinence subtype, comorbidity(ies) affecting incontinence, BMI, socioeconomic status, educational status, age, and country. Conclusion: This article describes the characteristics of patients at the SUIT enrollment visit, and demonstrates that the number of incontinence episodes has a significant impact on the EQ-5D index score.},
affiliation = {University of Leicester, Leicester, UK.},
pages = {},
year = {2009},
month = {Sep},
language = {ENG},
date-added = {2010-05-23 10:42:42 +0200},
date-modified = {2010-05-23 10:42:43 +0200},
doi = {10.1111/j.1524-4733.2009.00599.x},
pii = {VHE599},
pmid = {19744293},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Tincello-2009-Value%20Health_Patient%20Characterist.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11806},
rating = {0}
}

@book{Hippler:1987,
author = {H Hippler and N Schwarz and S (Eds Sudman},
journal = {Book},
title = {Social information processing and survey methodology},
year = {1987},
date-added = {2010-01-03 19:34:17 +0100},
date-modified = {2010-07-29 19:21:41 +0200},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p941},
rating = {0}
}

@article{Betjemann:2010p5722,
author = {Rebecca S Betjemann and Erin Phinney Johnson and Holly Barnard and Richard Boada and Christopher M Filley and Pauline A Filipek and Erik G Willcutt and John C DeFries and Bruce F Pennington},
journal = {Behav Genet},
title = {Genetic Covariation Between Brain Volumes and IQ, Reading Performance, and Processing Speed},
abstract = {Although there has been much interest in the relation between brain size and cognition, few studies have investigated this relation within a genetic framework and fewer still in non-adult samples. We analyzed the genetic and environmental covariance between structural MRI data from four brain regions (total brain volume, neocortex, white matter, and prefrontal cortex), and four cognitive measures (verbal IQ (VIQ), performance IQ (PIQ), reading ability, and processing speed), in a sample of 41 MZ twin pairs and 30 same-sex DZ twin pairs (mean age at cognitive test = 11.4 years; mean age at scan = 15.4 years). Multivariate Cholesky decompositions were performed with each brain volume measure entered first, followed by the four cognitive measures. Consistent with previous research, each brain and cognitive measure was found to be significantly heritable. The novel finding was the significant genetic but not environmental covariance between brain volumes and cognitive measures. Specifically, PIQ shared significant common genetic variance with all four measures of brain volume (r (g) = .58-.82). In contrast, VIQ shared significant genetic influence with neocortex volume only (r (g) = .58). Processing speed was significant with total brain volume (r (g) = .79), neocortex (r (g) = .64), and white matter (r (g) = .89), but not prefrontal cortex. The only brain measure to share genetic influence with reading was total brain volume (r (g) = .32), which also shared genetic influences with processing speed.},
affiliation = {Department of Psychology, D-12, Regis University, 3333 Regis Blvd., Denver, CO, 80221, USA, rbetjema@regis.edu.},
pages = {},
year = {2010},
month = {Jan},
language = {ENG},
date-added = {2010-02-15 20:27:17 +0100},
date-modified = {2010-07-29 20:09:07 +0200},
doi = {10.1007/s10519-009-9328-2},
pmid = {20072853},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Betjemann-2010-Behav%20Genet_Genetic%20Covariation.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5722},
rating = {0}
}

@article{Hadfield:2010p4935,
author = {J Hadfield},
journal = {Journal of Statistical Software},
title = {MCMC Methods for Multi-Response Generalized Linear Mixed Models: The MCMCglmm R Package},
abstract = {Generalized linear mixed models provide a flexible framework for modeling a range of data, although with non-Gaussian response variables the likelihood cannot be obtained in closed form. Markov chain Monte Carlo methods solve this problem by sampling from a series of simpler conditional distributions that can be evaluated. The R package MCMCglmm implements such an algorithm for a range of model fitting problems. More than one response variable can be analyzed simultaneously, and these variables are allowed to follow Gaussian, Poisson, multi(bi)nominal, exponential, zero-inflated and censored dis- tributions. A range of variance structures are permitted for the random effects, including interactions with categorical or continuous variables (i.e., random regression), and more complicated variance structures that arise through shared ancestry, either through a pedi- gree or through a phylogeny. Missing values are permitted in the response variable(s) and data can be known up to some level of measurement error as in meta-analysis. All simu- lation is done in C/ C++ using the CSparse library for sparse linear systems.},
number = {2},
volume = {33},
year = {2010},
date-added = {2010-02-03 11:43:13 +0100},
date-modified = {2010-02-03 11:44:07 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hadfield-2010-Journal%20of%20Statistical%20Software_MCMC%20Methods%20for%20Mul.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4935},
rating = {0}
}

@article{Boulesteix:2009p11608,
author = {Anne-Laure Boulesteix and Carolin Strobl},
journal = {BMC Med Res Methodol},
title = {Optimal classifier selection and negative bias in error rate estimation: an empirical study on high-dimensional prediction},
abstract = {BACKGROUND: In biometric practice, researchers often apply a large number of different methods in a "trial-and-error" strategy to get as much as possible out of their data and, due to publication pressure or pressure from the consulting customer, present only the most favorable results. This strategy may induce a substantial optimistic bias in prediction error estimation, which is quantitatively assessed in the present manuscript. The focus of our work is on class prediction based on high-dimensional data (e.g. microarray data), since such analyses are particularly exposed to this kind of bias. METHODS: In our study we consider a total of 124 variants of classifiers (possibly including variable selection or tuning steps) within a cross-validation evaluation scheme. The classifiers are applied to original and modified real microarray data sets, some of which are obtained by randomly permuting the class labels to mimic non-informative predictors while preserving their correlation structure. RESULTS: We assess the minimal misclassification rate over the different variants of classifiers in order to quantify the bias arising when the optimal classifier is selected a posteriori in a data-driven manner. The bias resulting from the parameter tuning (including gene selection parameters as a special case) and the bias resulting from the choice of the classification method are examined both separately and jointly. CONCLUSIONS: The median minimal error rate over the investigated classifiers was as low as 31% and 41% based on permuted uninformative predictors from studies on colon cancer and prostate cancer, respectively. We conclude that the strategy to present only the optimal result is not acceptable because it yields a substantial bias in error rate estimation, and suggest alternative approaches for properly reporting classification accuracy.},
affiliation = {Department of Statistics, University of Munich, Ludwigstr 33, D-80539 Munich, Germany. boulesteix@ibe.med.uni-muenchen.de},
pages = {85},
volume = {9},
year = {2009},
month = {Jan},
language = {eng},
keywords = {Models: Statistical, Predictive Value of Tests, Genetic Testing, Humans, Prostatic Neoplasms, Empirical Research, Colonic Neoplasms, Male, Bias (Epidemiology), Genes: Neoplasm, Microarray Analysis},
date-added = {2010-05-11 17:22:53 +0200},
date-modified = {2010-05-11 17:22:53 +0200},
doi = {10.1186/1471-2288-9-85},
pii = {1471-2288-9-85},
pmid = {20025773},
URL = {http://www.biomedcentral.com/1471-2288/9/85},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Boulesteix-2009-BMC%20Med%20Res%20Methodol_Optimal%20classifier%20s.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11608},
rating = {0}
}

@article{Haber:2008p9842,
author = {Michael Haber and Huiman X Barnhart},
journal = {Stat Methods Med Res},
title = {A general approach to evaluating agreement between two observers or methods of measurement from quantitative data with replicated measurements},
abstract = {We present a general approach to the definition and estimation of coefficients for evaluating agreement between two fixed methods of measurements or human observers. The measured variable is assumed to be continuous with a finite second moment. No other distributional assumptions are made. We introduce the term ;disagreement function' for the function of the observations that is used to quantify the extent of disagreement between the two measurements made on the same subject. The proposed inter-methods agreement coefficients compare the disagreement between measurements made by different methods on the same subject to the corresponding disagreement between replicated measurements made by the same method. Therefore, the new coefficients require data with replications readings. We propose inter-methods agreement coefficients for two practical situations involving two methods that have a measurement error: 1) comparison of a new method to a gold standard (or a reference method), and 2) comparison of two methods where neither method is considered a gold standard. We consider three disagreement functions based on the differences between two measurements: 1) the mean squared difference, 2) the mean absolute difference and 3) the mean relative difference. We then derive non-parametric estimates for the various agreement coefficients. Our approach is illustrated using data from a study comparing systolic blood pressure measurements by a human observer and an automatic monitor. The performance of the new estimates is assessed via stochastic simulations.},
affiliation = {Department of Biostatistics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA. mhaber@sph.emory.edu},
number = {2},
pages = {151--69},
volume = {17},
year = {2008},
month = {Apr},
language = {eng},
keywords = {Reproducibility of Results, Observer Variation},
date-added = {2010-03-26 19:29:09 +0100},
date-modified = {2010-03-26 19:29:09 +0100},
doi = {10.1177/0962280206075527},
pii = {0962280206075527},
pmid = {17698934},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9842},
rating = {0}
}

@article{Alesina:2004p12908,
author = {A Alesina and R Di Tella and R MacCulloch},
journal = {Journal of Public Economics},
title = {Inequality and happiness: are Europeans and Americans different?},
abstract = {We study the effect of the level of inequality in society on individual well-being using a total of 123,668 answers to a survey question about ``happiness''. We find that individuals have a lower tendency to report themselves happy when inequality is high, even after controlling for individual income, a large set of personal characteristics, and year and country (or, in the case of the US, state) dummies. The effect, however, is more precisely defined statistically in Europe than in the US. In addition, we find striking differences across groups. In Europe, the poor and those on the left of the political spectrum are unhappy about inequality; whereas in the US the happiness of the poor and of those on the left is uncorrelated with inequality. Interestingly, in the US, the rich are bothered by inequality. Comparing across continents, we find that left-wingers in Europe are more hurt by inequality than left-wingers in the US. And the poor in Europe are more concerned with inequality than the poor in America, an effect that is large in terms of size but is only significant at the 10% level. We argue that these findings are consistent with the perception (not necessarily the reality) that Americans have been living in a mobile society, where individual effort can move people up and down the income ladder, while Europeans believe that they live in less mobile societies.},
pages = {2009--2042},
volume = {88},
year = {2004},
date-added = {2010-06-24 17:32:26 +0200},
date-modified = {2010-06-24 17:34:03 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Alesina-2004-Journal%20of%20Public%20Economics_Inequality%20and%20happi.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12908},
rating = {0}
}

@article{Hatfield:2007p1813,
author = {J P Hatfield},
journal = {American Educational Research Association Meeting},
title = {Finding a Needle in a Haystack: Detecting Item Disclosure in Large-Scale Testing Programs},
affiliation = {Pearson VUE},
year = {2007},
date-added = {2010-01-09 22:42:04 +0100},
date-modified = {2010-01-09 22:42:45 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hatfield-2007-American%20Educational%20Research%20Association%20Meeting_Finding%20a%20Needle%20in.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1813},
rating = {0}
}

@article{Amin:2007p9870,
author = {Najaf Amin and Cornelia M van Duijn and Yurii S Aulchenko},
journal = {PLoS ONE},
title = {A genomic background based method for association analysis in related individuals},
abstract = {BACKGROUND: Feasibility of genotyping of hundreds and thousands of single nucleotide polymorphisms (SNPs) in thousands of study subjects have triggered the need for fast, powerful, and reliable methods for genome-wide association analysis. Here we consider a situation when study participants are genetically related (e.g. due to systematic sampling of families or because a study was performed in a genetically isolated population). Of the available methods that account for relatedness, the Measured Genotype (MG) approach is considered the 'gold standard'. However, MG is not efficient with respect to time taken for the analysis of genome-wide data. In this context we proposed a fast two-step method called Genome-wide Association using Mixed Model and Regression (GRAMMAR) for the analysis of pedigree-based quantitative traits. This method certainly overcomes the drawback of time limitation of the measured genotype (MG) approach, but pays in power. One of the major drawbacks of both MG and GRAMMAR, is that they crucially depend on the availability of complete and correct pedigree data, which is rarely available. METHODOLOGY: In this study we first explore type 1 error and relative power of MG, GRAMMAR, and Genomic Control (GC) approaches for genetic association analysis. Secondly, we propose an extension to GRAMMAR i.e. GRAMMAR-GC. Finally, we propose application of GRAMMAR-GC using the kinship matrix estimated through genomic marker data, instead of (possibly missing and/or incorrect) genealogy. CONCLUSION: Through simulations we show that MG approach maintains high power across a range of heritabilities and possible pedigree structures, and always outperforms other contemporary methods. We also show that the power of our proposed GRAMMAR-GC approaches to that of the 'gold standard' MG for all models and pedigrees studied. We show that this method is both feasible and powerful and has correct type 1 error in the context of genome-wide association analysis in related individuals.},
affiliation = {Department of Epidemiology and Biostatistics, Erasmus University Medical Center (MC) Rotterdam, Rotterdam, The Netherlands.},
number = {12},
pages = {e1274},
volume = {2},
year = {2007},
month = {Jan},
language = {eng},
keywords = {Male, Polymorphism: Single Nucleotide, Female, Pedigree, Genomics, Animals},
date-added = {2010-03-26 19:31:15 +0100},
date-modified = {2010-03-26 19:31:15 +0100},
doi = {10.1371/journal.pone.0001274},
pmid = {18060068},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Amin-2007-PLoS%20ONE_A%20genomic%20background.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9870},
rating = {0}
}

@article{Kustra:2008p382,
author = {Rafal Kustra and Xiaofei Shi and Duncan J Murdoch and Celia M T Greenwood and Jagadish Rangrej},
journal = {Biostatistics},
title = {Efficient p-value estimation in massively parallel testing problems},
abstract = {We present a new method to efficiently estimate very large numbers of p-values using empirically constructed null distributions of a test statistic. The need to evaluate a very large number of p-values is increasingly common with modern genomic data, and when interaction effects are of interest, the number of tests can easily run into billions. When the asymptotic distribution is not easily available, permutations are typically used to obtain p-values but these can be computationally infeasible in large problems. Our method constructs a prediction model to obtain a first approximation to the p-values and uses Bayesian methods to choose a fraction of these to be refined by permutations. We apply and evaluate our method on the study of association between 2-way interactions of genetic markers and colorectal cancer using the data from the first phase of a large, genome-wide case-control study. The results show enormous computational savings as compared to evaluating a full set of permutations, with little decrease in accuracy.},
affiliation = {Department of Public Health Sciences, University of Toronto, Toronto, ON, Canada. r.kustra@utoronto.ca},
number = {4},
pages = {601--12},
volume = {9},
year = {2008},
month = {Oct},
language = {eng},
keywords = {Humans, Bayes Theorem, Likelihood Functions, Statistical Distributions, Genotype, Polymorphism: Single Nucleotide, Colorectal Neoplasms, Haplotypes, Genome-Wide Association Study, Models: Genetic, Artificial Intelligence, Algorithms, Models: Statistical, Genetic Markers},
date-added = {2010-01-03 11:51:25 +0100},
date-modified = {2010-01-03 11:51:25 +0100},
doi = {10.1093/biostatistics/kxm053},
pii = {kxm053},
pmid = {18304995},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Kustra-2008-Biostatistics_Efficient%20p-value%20es.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p382},
rating = {0}
}

@article{Valdano:2007p13237,
author = {S G Valdano and J A Di Rienzo},
title = {Discovering meaningful groups in hierarchical cluster analysis. An extension to the multivariate case of a multiple comparison method based on cluster analysis},
abstract = {In	the	framework	of	univariate	pairwise	comparison	procedures, Di Rienzo et al.[1] developed a hybrid technique joining a hierarchical clustering method with the principles of hypothesis testing. This paper presents an extension to the multivariate case. The new method gives an answer, on the bases of inferencial statistics, to the problem of determining the number of groups in hierarchical cluster analysis when there are replicates. Although, the method was developed as a test for the general hypothesis of equality of population centroids, it performs very well, considering size and power, as a pairwise comparison algorithm. Moreover it avoids the lack of transitivity of classical pairwise comparisons methods that yields to logical inconsistencies. The method is evaluated and compared, by Monte Carlo simulation, with a partitioning multivariate procedure proposed by Bozdogan and with a multiple comparison algorithm based on the Hotelling's T2 statistic. An example of grouping provenances of a native South American tree is presented.},
year = {2007},
date-added = {2010-07-01 17:47:45 +0200},
date-modified = {2010-07-01 17:48:59 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Valdano-2007-_Discovering%20meaningf-1.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13237},
rating = {0}
}

@article{Schmidt:2010p14020,
author = {Wolf-Peter Schmidt and Bernd Genser and Mauricio L Barreto and Thomas Clasen and Stephen P Luby and Sandy Cairncross and Zaid Chalabi},
journal = {Emerging themes in epidemiology},
title = {Sampling strategies to measure the prevalence of common recurrent infections in longitudinal studies},
abstract = {ABSTRACT: BACKGROUND: Measuring recurrent infections such as diarrhoea or respiratory infections in epidemiological studies is a methodological challenge. Problems in measuring the incidence of recurrent infections include the episode definition, recall error, and the logistics of close follow up. Longitudinal prevalence (LP), the proportion-of-time-ill estimated by repeated prevalence measurements, is an alternative measure to incidence of recurrent infections. In contrast to incidence which usually requires continuous sampling, LP can be measured at intervals. This study explored how many more participants are needed for infrequent sampling to achieve the same study power as frequent sampling. METHODS: We developed a set of four empirical simulation models representing low and high risk settings with short or long episode durations. The model was used to evaluate different sampling strategies with different assumptions on recall period and recall error. RESULTS: The model identified three major factors that influence sampling strategies: (1) the clustering of episodes in individuals; (2) the duration of episodes; (3) the positive correlation between an individual's disease incidence and episode duration. Intermittent sampling (e.g. 12 times per year) often requires only a slightly larger sample size compared to continuous sampling, especially in cluster-randomized trials. The collection of period prevalence data can lead to highly biased effect estimates if the exposure variable is associated with episode duration. To maximize study power, recall periods of 3 to 7 days may be preferable over shorter periods, even if this leads to inaccuracy in the prevalence estimates. CONCLUSION: Choosing the optimal approach to measure recurrent infections in epidemiological studies depends on the setting, the study objectives, study design and budget constraints. Sampling at intervals can contribute to making epidemiological studies and trials more efficient, valid and cost-effective.},
number = {1},
pages = {5},
volume = {7},
year = {2010},
month = {Aug},
language = {ENG},
date-added = {2010-08-07 10:09:27 +0200},
date-modified = {2010-08-07 10:09:28 +0200},
doi = {10.1186/1742-7622-7-5},
pii = {1742-7622-7-5},
pmid = {20678239},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Schmidt-2010-Emerging%20themes%20in%20epidemiology_Sampling%20strategies.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p14020},
rating = {0}
}

@article{Trabasso:1993,
author = {T Trabasso and S Suh},
journal = {Discourse Processing},
title = {Understanding text: Achieving explanatory coherence through on-line inferences and mental operations in working memory},
abstract = {Studies whether global, causal inferences are made during comprehension. Provides verbal protocol data in the form of talking aloud during reading. Discusses the data with reference to processing claims and working-memory models. Considers what verbal protocols reveal about processing.},
pages = {3--34},
volume = {16},
year = {1993},
date-added = {2010-01-03 19:34:17 +0100},
date-modified = {2010-01-03 19:34:18 +0100},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p965},
rating = {0}
}

@article{Nicolae:2010p10910,
author = {Dan L Nicolae and Eric Gamazon and Wei Zhang and Shiwei Duan and M Eileen Dolan and Nancy J Cox},
journal = {PLoS Genet},
title = {Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS},
abstract = {Although genome-wide association studies (GWAS) of complex traits have yielded more reproducible associations than had been discovered using any other approach, the loci characterized to date do not account for much of the heritability to such traits and, in general, have not led to improved understanding of the biology underlying complex phenotypes. Using a web site we developed to serve results of expression quantitative trait locus (eQTL) studies in lymphoblastoid cell lines from HapMap samples (http://www.scandb.org), we show that single nucleotide polymorphisms (SNPs) associated with complex traits (from http://www.genome.gov/gwastudies/) are significantly more likely to be eQTLs than minor-allele-frequency-matched SNPs chosen from high-throughput GWAS platforms. These findings are robust across a range of thresholds for establishing eQTLs (p-values from 10(-4)-10(-8)), and a broad spectrum of human complex traits. Analyses of GWAS data from the Wellcome Trust studies confirm that annotating SNPs with a score reflecting the strength of the evidence that the SNP is an eQTL can improve the ability to discover true associations and clarify the nature of the mechanism driving the associations. Our results showing that trait-associated SNPs are more likely to be eQTLs and that application of this information can enhance discovery of trait-associated SNPs for complex phenotypes raise the possibility that we can utilize this information both to increase the heritability explained by identifiable genetic factors and to gain a better understanding of the biology underlying complex traits.},
affiliation = {Department of Medicine, University of Chicago, Chicago, Illinois, United States of America.},
number = {4},
pages = {e1000888},
volume = {6},
year = {2010},
month = {Jan},
language = {eng},
date-added = {2010-04-11 21:36:35 +0200},
date-modified = {2010-04-11 21:36:36 +0200},
doi = {10.1371/journal.pgen.1000888},
pmid = {20369019},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Nicolae-2010-PLoS%20Genet_Trait-associated%20SNP.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10910},
rating = {0}
}

@article{Goldberg:1995p13840,
author = {L R Goldberg and G Saucier},
journal = {Psychological Bulletin},
title = {So what do you propose we use instead? A reply to Block},
abstract = {Unfortunately, Block's brilliant critique is terribly biased, much like a legal brief that presents only one side of the issues at suit. It does not distinguish between the Big Five model of phenotypic personality attributes from alternative models of the causal underpinnings of personality differences. Ironically, it attempts to explain away the extensive evidence for the Big Five model as largely the result of data prestructuring, with no acknowledgement of the unique contribution of the lexical approach to minimizing such problems. Even more seriously, it omits a good deal of crucial evidence favorable to the Big Five model, including studies of Block's own Q-set and independent investigations of personality-related terms in other languages. Sadly, Block's closing suggestions provide little in the way of specific proposals for alternatives that he would have us use instead.},
affiliation = {University of Oregon.},
number = {2},
pages = {221-5; discussion 226--9},
volume = {117},
year = {1995},
month = {Mar},
language = {eng},
keywords = {Reproducibility of Results, Personality Disorders, Q-Sort, Factor Analysis: Statistical, Personality Assessment, Personality Development, Psychometrics, Humans},
date-added = {2010-07-29 17:21:02 +0200},
date-modified = {2010-07-29 17:21:02 +0200},
pmid = {7724689},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Goldberg-1995-Psychological%20Bulletin_So%20what%20do%20you%20propo.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13840},
rating = {0}
}

@article{Petrowski:2009p428,
author = {Katja Petrowski and Hendrik Berth and Silke Schmidt and J{\"o}rg Schumacher and Andreas Hinz and Elmar Br{\"a}hler},
journal = {BMC Med Res Methodol},
title = {The assessment of recalled parental rearing behavior and its relationship to life satisfaction and interpersonal problems: a general population study},
abstract = {BACKGROUND: Parental rearing behavior is a significant etiological factor for the vulnerability of psychopathology and has been an issue of clinical research for a long time. For this scope instruments are important who asses economically recalled parental rearing behavior in a clinical practice. Therefore, a short German instrument for the assessment of the recalled parental rearing behavior Fragebogen zum erinnerten elterlichen Erziehungsverhalten (FEE) was psychometrically evaluated [Recalled Parental Rearing Behavior]. METHODS: This questionnaire was evaluated in a representative population sample (N = 2.948) in Germany which included 44.2% male and 55.8% female persons with a mean age of M = 47.35 (SD = 17.10, range = 18-92). For the content evaluation of the FEE the Life Satisfaction Questionnaire (FLZ) and the Inventory of Interpersonal Problems (IIP) was filled out by the participants. RESULTS: The FEE scales yielded a good to satisfactory internal consistency and split-half reliability. Its three factors (rejection/punishment, emotional warmth, control/overprotection) correlated positively with most of the areas of life satisfaction. Furthermore, positive associations between interpersonal problems and parental rejection and control could be identified. CONCLUSION: The FEE is a short, reliable and valid instrument that can be applied in the clinical practice. In addition, the data proved an association between recalled parental rearing behavior, life satisfaction and interpersonal problems conform to the literature. Finally, specific problems with the retrospective assessment of parental rearing behavior were addressed as well.},
affiliation = {Department of Psychotherapy and Psychosomatic Medicine, Dresden University of Technology, Dresden, Germany. katja.petrowski@tu-dresden.de},
pages = {17},
volume = {9},
year = {2009},
month = {Jan},
language = {eng},
keywords = {Questionnaires, Maternal Behavior, Aged, Parent-Child Relations, Child, Adult, Germany, Interpersonal Relations, Sex Factors, Middle Aged, Reproducibility of Results, Young Adult, Data Interpretation: Statistical, Male, Personal Satisfaction, Mental Recall, Aged: 80 and over, Humans, Child Rearing, Age Factors, Psychometrics},
date-added = {2010-01-03 12:24:11 +0100},
date-modified = {2010-01-03 12:24:11 +0100},
doi = {10.1186/1471-2288-9-17},
pii = {1471-2288-9-17},
pmid = {19267894},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Petrowski-2009-BMC%20Med%20Res%20Methodol_The%20assessment%20of%20re.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p428},
rating = {0}
}

@article{Plummer:2003p13437,
author = {M Plummer},
journal = {DSC 2003 Working Papers},
title = {JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling},
abstract = {JAGS is a program for Bayesian Graphical modelling which aims for compatibility with Classic BUGS. The program could eventually be developed as an R package. This article explains the motivations for this program, briefly describes the architecture and then discusses some ideas for a vectorized form of the BUGS language.},
note = {/Users/chl/Documents/Help/guide_rjags_dec09.pdf},
year = {2003},
date-added = {2010-07-01 19:48:42 +0200},
date-modified = {2010-07-01 19:50:17 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Plummer-2003-DSC%202003%20Working%20Papers_JAGS%20A%20program%20for.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13437},
rating = {0}
}

@article{Wang:2003p14294,
author = {F-K Wang and E Y Li},
journal = {Total Quality Management},
title = {Confidence intervals in repeatability and reproducibility using the Bootstrap method},
abstract = {The repeatability and reproducibility (R{\&}R) study---also called a gauge capability study---has been employed as part of the statistical process control program in many organizations. The objective of the study is to determine whether a measurement procedure or instrument is adequate for monitoring the performance of a process. The classical control chart method can be easily performed and calculations can be done with a spreadsheet or statistical computer software. However, this approach only provides the point estimates on the variance components of the measurement error study. In many situations, confidence intervals are more useful than point estimates, because an interval estimate enables an engineer to see both how small and how large an effect may be. In this paper, the Bootstrap method is used for obtaining the confidence intervals of the gauge variability when the control chart method is use for finding the point estimates. One real-life example is used to show the application of this control chart with the Bootstrapping method and comparisons are made with three experimental design procedures in terms of point estimates and confidence intervals for repeatability, reproducibility and total gauge variability.},
number = {3},
pages = {341--354},
volume = {14},
year = {2003},
date-added = {2010-08-24 14:11:24 +0200},
date-modified = {2010-08-24 14:12:43 +0200},
doi = {10.1080/1478336032000046643},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Wang-2003-Total%20Quality%20Management_Confidence%20intervals.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p14294},
rating = {0}
}

@article{Hoti:2004p1,
author = {Fabian Hoti and Annamari Tuulio-Henriksson and Jari Haukka and Timo Partonen and Lasse Holmstr{\"o}m and Jouko L{\"o}nnqvist},
journal = {BMC Psychiatry},
title = {Family-based clusters of cognitive test performance in familial schizophrenia},
abstract = {BACKGROUND: Cognitive traits derived from neuropsychological test data are considered to be potential endophenotypes of schizophrenia. Previously, these traits have been found to form a valid basis for clustering samples of schizophrenia patients into homogeneous subgroups. We set out to identify such clusters, but apart from previous studies, we included both schizophrenia patients and family members into the cluster analysis. The aim of the study was to detect family clusters with similar cognitive test performance. METHODS: Test scores from 54 randomly selected families comprising at least two siblings with schizophrenia spectrum disorders, and at least two unaffected family members were included in a complete-linkage cluster analysis with interactive data visualization. RESULTS: A well-performing, an impaired, and an intermediate family cluster emerged from the analysis. While the neuropsychological test scores differed significantly between the clusters, only minor differences were observed in the clinical variables. CONCLUSIONS: The visually aided clustering algorithm was successful in identifying family clusters comprising both schizophrenia patients and their relatives. The present classification method may serve as a basis for selecting phenotypically more homogeneous groups of families in subsequent genetic analyses.},
affiliation = {Department of Mathematical Sciences, University of Oulu, Finland. Fabian.Hoti@helsinki.fi},
pages = {20},
volume = {4},
year = {2004},
month = {Jan},
language = {eng},
keywords = {Cognition Disorders, Middle Aged, Male, Pedigree, Family Health, Registries, Sampling Studies, Genetic Predisposition to Disease, Phenotype, Neuropsychological Tests, Female, Adult, Cluster Analysis, Algorithms, Linkage (Genetics), {\&}psychometrics {\&}epidemiology, Finland, Schizophrenia, Humans},
date-added = {2009-12-28 20:14:49 +0100},
date-modified = {2009-12-29 10:27:46 +0100},
doi = {10.1186/1471-244X-4-20},
pii = {1471-244X-4-20},
pmid = {15271222},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hoti-2004-BMC%20Psychiatry_Family-based%20cluster.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1},
rating = {0}
}

@misc{Yamamoto:1999,
author = {K Yamamoto and E Kulick},
journal = {Miscellaneous},
title = {Scaling Methodology and Procedures for the TIMSS Mathematics and Science Scales},
year = {1999},
date-added = {2010-01-10 11:33:18 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Yamamoto-1999-Miscellaneous_Scaling%20Methodology.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1935},
rating = {0}
}

@article{Ward:2008,
author = {G Ward and T Hastie and S C Barry and J Elith and J R Leathwick},
journal = {Biometrics},
title = {Presence-only data and the EM algorithm},
year = {2008},
date-added = {2010-01-10 11:33:18 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Ward-2008-Biometrics_Presence-only%20data%20a.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2146},
rating = {0}
}

@article{Crosby:2003p7453,
author = {Ross D Crosby and Ronette L Kolotkin and G Rhys Williams},
journal = {Journal of Clinical Epidemiology},
title = {Defining clinically meaningful change in health-related quality of life},
abstract = {This article reviews current approaches to defining clinically meaningful change in health-related quality of life (HRQOL) and provides guidelines for their use. Definitions of clinically meaningful change are discussed. Two broad methods for identifying clinically meaningful change are contrasted: anchor-based methods and distribution-based methods. Anchor-based methods include cross-sectional approaches and longitudinal approaches. Distribution-based methods include those based on statistical significance, sample variability, and measurement precision. Anchor-based and distribution-based methods have advantages and limitations, and neither seems to be superior to the other. An integrated system for defining clinically meaningful change is recommended that combines anchor-based and distribution-based methods. We propose a new terminology for describing meaningful change derived from anchor-based and distribution-based methods.},
affiliation = {Neuropsychiatric Research Institute, 700 First Avenue South, Fargo, ND 58107, USA. rcrosby@nrifargo.com <rcrosby@nrifargo.com>},
number = {5},
pages = {395--407},
volume = {56},
year = {2003},
month = {May},
language = {eng},
keywords = {Statistics as Topic, Quality of Life, Life Style, Humans, Treatment Outcome, Health Status, Prognosis},
date-added = {2010-03-10 20:42:03 +0100},
date-modified = {2010-03-10 20:42:03 +0100},
pii = {S0895435603000441},
pmid = {12812812},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Crosby-2003-Journal%20of%20Clinical%20Epidemiology_Defining%20clinically.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7453},
rating = {0}
}

@article{Zhou:2007p12773,
author = {Xin Zhou and David P Tuck},
journal = {Bioinformatics},
title = {MSVM-RFE: extensions of SVM-RFE for multiclass gene selection on DNA microarray data},
abstract = {MOTIVATION: Given the thousands of genes and the small number of samples, gene selection has emerged as an important research problem in microarray data analysis. Support Vector Machine-Recursive Feature Elimination (SVM-RFE) is one of a group of recently described algorithms which represent the stat-of-the-art for gene selection. Just like SVM itself, SVM-RFE was originally designed to solve binary gene selection problems. Several groups have extended SVM-RFE to solve multiclass problems using one-versus-all techniques. However, the genes selected from one binary gene selection problem may reduce the classification performance in other binary problems. RESULTS: In the present study, we propose a family of four extensions to SVM-RFE (called MSVM-RFE) to solve the multiclass gene selection problem, based on different frameworks of multiclass SVMs. By simultaneously considering all classes during the gene selection stages, our proposed extensions identify genes leading to more accurate classification.},
affiliation = {Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06510, USA.},
number = {9},
pages = {1106--14},
volume = {23},
year = {2007},
month = {May},
language = {eng},
keywords = {Pattern Recognition: Automated, Software, Algorithms, Oligonucleotide Array Sequence Analysis, Artificial Intelligence, Gene Expression Profiling},
date-added = {2010-06-18 20:38:36 +0200},
date-modified = {2010-06-18 20:38:36 +0200},
doi = {10.1093/bioinformatics/btm036},
pii = {23/9/1106},
pmid = {17494773},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Zhou-2007-Bioinformatics_MSVM-RFE%20extensions.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12773},
rating = {0}
}

@article{Zimmerman:2008p14102,
author = {Mark Zimmerman and Caren Francione-Witt and Iwona Chelminski and Diane Young and Christina Tortolani},
journal = {J Clin Psychiatry},
title = {Problems applying the DSM-IV eating disorders diagnostic criteria in a general psychiatric outpatient practice},
abstract = {OBJECTIVE: A substantial number of patients treated in specialized eating disorder programs fail to meet criteria for anorexia nervosa or bulimia nervosa, the 2 eating disorders with specified criteria in DSM-IV, and are diagnosed with eating disorder not otherwise specified (NOS). In a general psychiatric setting, where the severity of eating pathology is likely to be milder than in specialty programs, we predicted that most patients with disordered eating would fail to meet the full criteria for one of the DSM-IV eating disorders and instead would be diagnosed with eating disorder NOS. METHOD: Two thousand five hundred psychiatric outpatients were interviewed with the Structured Clinical Interview for DSM-IV (SCID) upon presentation for treatment. The findings presented in this report were derived from patients interviewed from December 1995 to August 2006. RESULTS: Thirteen percent (N = 330) of the patients were diagnosed with a lifetime history of an eating disorder, 307 of whom received 1 diagnosis and 23 of whom were diagnosed with 2 disorders. Almost half (N = 164) of the disorders were present at the time of presentation, approximately one sixth (N = 60) were considered to be in partial remission, and slightly more than one third (N = 129) were past diagnoses. When binge-eating disorder was combined with the other forms of eating disorder NOS, as it is in DSM-IV, 90.2% (148/164) of the patients with a current eating disorder were diagnosed with eating disorder NOS. CONCLUSIONS: The preponderance of eating-disordered patients in a general psychiatric setting were diagnosed with eating disorder NOS. This finding suggests that there is a problem with the clinical applicability of the diagnostic criteria in the DSM-IV eating disorder category.},
affiliation = {Department of Psychiatry and Human Behavior, Brown University School of Medicine, Rhode Island Hospital, Providence, RI, USA. mzimmerman@lifespan.org},
number = {3},
pages = {381--4},
volume = {69},
year = {2008},
month = {Mar},
language = {eng},
keywords = {Female, Eating Disorders, Male, Ambulatory Care, Diagnostic and Statistical Manual of Mental Disorders, Humans, Adult, Mental Health Services, Interview: Psychological, Psychiatry, Bulimia Nervosa},
date-added = {2010-08-18 11:17:49 +0200},
date-modified = {2010-08-18 11:17:49 +0200},
pii = {ej06m03006},
pmid = {18348598},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Zimmerman-2008-J%20Clin%20Psychiatry_Problems%20applying%20th.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p14102},
rating = {0}
}

@article{Groenvold:1995p12743,
author = {M Groenvold and J B Bjorner and M C Klee and S Kreiner},
journal = {Journal of Clinical Epidemiology},
title = {Test for item bias in a quality of life questionnaire},
abstract = {Item bias (differential item functioning) analysis examines whether the construction of an index from two or more variables results in bias in relation to sex, age, or other criteria. Item bias may lead to erroneous conclusions because of distortion or dilution of the effects measured. In comparing groups, item bias analysis, tests whether the information about possible differences between groups, obtained by the variables constituting an index, are correctly passed on by the index score. We examined a quality of life questionnaire answered by 1189 breast cancer patients. We found age-bias or bias in the comparison of groups receiving different treatments in three out of nine indexes. Recommendations for the interpretation of these indexes are made. Item bias analysis is a useful method examining an issue not covered by traditional psychometric tests.},
affiliation = {Department of Social Medicine, University of Copenhagen, Denmark.},
number = {6},
pages = {805--16},
volume = {48},
year = {1995},
month = {Jun},
language = {eng},
keywords = {Female, Health Status Indicators, Adult, Bias (Epidemiology), Questionnaires, Middle Aged, Quality of Life, Chemotherapy: Adjuvant, Denmark, Aged, Reproducibility of Results, Breast Neoplasms, Humans},
date-added = {2010-06-15 22:48:36 +0200},
date-modified = {2010-06-15 22:48:36 +0200},
pii = {0895-4356(94)00195-V},
pmid = {7769411},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Groenvold-1995-Journal%20of%20Clinical%20Epidemiology_Test%20for%20item%20bias%20i.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12743},
rating = {0}
}

@article{Vermunt:2007p6250,
author = {J K Vermunt and J R van Ginkel and L Andries van der Ark and K Sijtsma},
title = {Multiple imputation of incomplete categorical data using latent class analysis},
abstract = {We propose using latent class analysis as an alternative to log- linear analysis for the multiple imputation of incomplete cate- gorical data. Similar to log-linear models, latent class models can be used to describe complex association structures between the variables used in the imputation model. However, unlike log- linear models, latent class models can be used to build large im- putation models containing more than a few categorical variables. To obtain imputations reflecting uncertainty about the unknown model parameters, we use a nonparametric bootstrap procedure as an alternative to the more common full Bayesian approach. The proposed multiple imputation method, which is implemented in Latent GOLD software for latent class analysis, is illustrated with two examples. In a simulated data example, we compare the new method to well-established methods such as maximum likelihood estimation with incomplete data and multiple imputation using a saturated log-linear model. This example shows that the proposed method yields unbiased parameter estimates and standard errors. The second example concerns an application using a typical social sciences data set. It contains 79 variables that are all included in the imputation model. The proposed method is especially useful for such large data sets because standard methods for dealing with missing data in categorical variables break down when the number of variables is so large.},
year = {2007},
date-added = {2010-02-19 21:25:41 +0100},
date-modified = {2010-07-29 20:42:55 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Vermunt-2007-_Multiple%20imputation-1.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6250},
read = {Yes},
rating = {0}
}

@article{Calson:2007,
author = {A L Calson and A W Meade},
journal = {Educational and Psychological Measurement},
title = {Assessing Gender-Related Differential Item Functioning and Predictive Validity With the Institutional Integration Scale},
abstract = {This study examined the gender-related differential predictive validity of five subscales of the Institutional Integration Scale (IIS) with regard to college student withdrawal. Differential functioning of the IIS across genders was assessed using an item response theory (IRT)---based framework of differential item and test functioning. The results confirmed the absence of differential functioning and supported the predictive validity of two of the five subscales for student withdrawal. IRT analyses revealed that a number of the items did not adequately reflect the construct and should be revised or removed from the measure. A discussion of these results and the implications for higher education institutions focused on preventing student withdrawal are presented.},
number = {3},
pages = {545--559},
volume = {67},
year = {2007},
date-added = {2010-01-03 19:38:21 +0100},
date-modified = {2010-01-03 19:38:22 +0100},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1137},
rating = {0}
}

@article{Kendel:2010p10661,
author = {Friederike Kendel and Markus Wirtz and Anne Dunkel and Elke Lehmkuhl and Roland Hetzer and Vera Regitz-Zagrosek},
journal = {J Affect Disord},
title = {Screening for depression: Rasch analysis of the dimensional structure of the PHQ-9 and the HADS-D},
abstract = {BACKGROUND: Both the depression modules of the Hospital Anxiety and Depression Scale (HADS-D) and the Patient Health Questionnaire (PHQ-9) are widely used for the screening of depression. We analyzed the dimensionality and the item fit of both scales individually and across the scales. Moreover, we sought to identify items which evidenced item response bias associated with age and gender. METHODS: The depression subscales HADS-D and the PHQ-9 were administered to 1271 patients (mean age 67.2; 22.5% women) undergoing coronary artery bypass graft surgery (CABG). Rasch analyses were performed to assess the overall fit of the model, individual item fit and differential item functioning (DIF). RESULTS: Rasch analysis revealed that the HADS-D and the PHQ-9 feature a common core construct containing six items of the HADS-D and three items of the PHQ-9. Two of these items are identical with the 2-item short form of the PHQ-9. In addition, fatigability was the only somatic item that fitted the model. No substantial DIF was observed. LIMITATIONS: The generalizability of these results might be restricted to patients awaiting CABG. CONCLUSIONS: The short form of the PHQ-9 seems to be an economic and valid instrument for the screening of depression, which indicates the same latent construct that is captured by six items of the HADS-D. Further studies are needed to evaluate whether the addition of fatigability might enhance the validity of the PHQ-2 in this patient population.},
affiliation = {Institute of Medical Psychology, Charit{\'e} - Universit{\"a}tsmedizin Berlin, 10117 Berlin, Germany. friederike.kendel@charite.de},
number = {3},
pages = {241--6},
volume = {122},
year = {2010},
month = {May},
language = {eng},
date-added = {2010-04-07 11:48:34 +0200},
date-modified = {2010-04-07 11:48:40 +0200},
doi = {10.1016/j.jad.2009.07.004},
pii = {S0165-0327(09)00325-5},
pmid = {19665236},
URL = {http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T2X-4WY5BCV-1&_user=2432700&_coverDate=05%252F31%252F2010&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000057263&_version=1&_urlVersion=0&_userid=2432700&md5=f0a4d3aeab9ef83ad18279a3e142f45d},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Kendel-2010-J%20Affect%20Disord_Screening%20for%20depres.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10661},
rating = {4}
}

@article{Li:2006p11854,
author = {Chiang-shan Ray Li and Cong Huang and R Todd Constable and Rajita Sinha},
journal = {J Neurosci},
title = {Imaging response inhibition in a stop-signal task: neural correlates independent of signal monitoring and post-response processing},
abstract = {Execution of higher cortical functions requires inhibitory control to restrain habitual responses and meet changing task demands. We used functional magnetic resonance imaging to show the neural correlates of response inhibition during a stop-signal task. The task has a frequent "go" stimulus to set up a pre-potent response tendency and a less frequent "stop" signal for subjects to withhold their response. We contrasted brain activation between successful and failed inhibition for individual subjects and compared groups of subjects with short and long stop-signal reaction times. The two groups of subjects did not differ in their inhibition failure rates or the extent of signal monitoring, error monitoring, or task-associated frustration ratings. The results showed that short stop-signal reaction time or more efficient response inhibition was associated with greater activation in the superior medial and precentral frontal cortices. Moreover, activation of these inhibitory motor areas correlated negatively with stop-signal reaction time. These brain regions may represent the neural substrata of response inhibition independent of other cognitive and affective functions.},
affiliation = {Department of Psychiatry, Magnetic Resonance Research Center, Yale University, New Haven, Connecticut 06519, USA. chiang-shan.li@yale.edu},
number = {1},
pages = {186--92},
volume = {26},
year = {2006},
month = {Jan},
language = {eng},
keywords = {Reaction Time, Monitoring: Physiologic, Brain Mapping, Psychomotor Performance, Regression Analysis, Adult, Neural Pathways, Cerebral Cortex, Inhibition (Psychology), Humans, Magnetic Resonance Imaging, Male, Female},
date-added = {2010-05-23 10:47:51 +0200},
date-modified = {2010-05-23 10:47:51 +0200},
doi = {10.1523/JNEUROSCI.3741-05.2006},
pii = {26/1/186},
pmid = {16399686},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Li-2006-J%20Neurosci_Imaging%20response%20inh.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11854},
rating = {0}
}

@article{Hageman:2008p13184,
author = {Jos A Hageman and Margriet M W B Hendriks and Johan A Westerhuis and Mari{\"e}t J van der Werf and Ruud Berger and Age K Smilde},
journal = {PLoS ONE},
title = {Simplivariate models: ideas and first examples},
abstract = {One of the new expanding areas in functional genomics is metabolomics: measuring the metabolome of an organism. Data being generated in metabolomics studies are very diverse in nature depending on the design underlying the experiment. Traditionally, variation in measurements is conceptually broken down in systematic variation and noise where the latter contains, e.g. technical variation. There is increasing evidence that this distinction does not hold (or is too simple) for metabolomics data. A more useful distinction is in terms of informative and non-informative variation where informative relates to the problem being studied. In most common methods for analyzing metabolomics (or any other high-dimensional x-omics) data this distinction is ignored thereby severely hampering the results of the analysis. This leads to poorly interpretable models and may even obscure the relevant biological information. We developed a framework from first data analysis principles by explicitly formulating the problem of analyzing metabolomics data in terms of informative and non-informative parts. This framework allows for flexible interactions with the biologists involved in formulating prior knowledge of underlying structures. The basic idea is that the informative parts of the complex metabolomics data are approximated by simple components with a biological meaning, e.g. in terms of metabolic pathways or their regulation. Hence, we termed the framework 'simplivariate models' which constitutes a new way of looking at metabolomics data. The framework is given in its full generality and exemplified with two methods, IDR analysis and plaid modeling, that fit into the framework. Using this strategy of 'divide and conquer', we show that meaningful simplivariate models can be obtained using a real-life microbial metabolomics data set. For instance, one of the simple components contained all the measured intermediates of the Krebs cycle of E. coli. Moreover, these simplivariate models were able to uncover regulatory mechanisms present in the phenylalanine biosynthesis route of E. coli.},
affiliation = {Biosystems Data Analysis, Universiteit van Amsterdam, Amsterdam, The Netherlands.},
number = {9},
pages = {e3259},
volume = {3},
year = {2008},
month = {Jan},
language = {eng},
keywords = {Systems Biology, Models: Statistical, Software, Phenylalanine, Computer Simulation, Genomics, Escherichia coli, Models: Biological, Algorithms, Metabolomics, Models: Theoretical, Models: Genetic, Computational Biology},
date-added = {2010-06-26 11:20:09 +0200},
date-modified = {2010-06-26 11:20:09 +0200},
doi = {10.1371/journal.pone.0003259},
pmid = {18810272},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hageman-2008-PLoS%20ONE_Simplivariate%20models.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13184},
rating = {0}
}

@article{Anonymous:2010p4639,
title = {Guidelines for assessing Quality of Life in EORTC clinical trials},
date-added = {2010-01-30 15:46:40 +0100},
date-modified = {2010-01-30 15:46:57 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Guidelines%20for%20asses.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4639},
rating = {0}
}

@article{Ruczinski2003,
author = {I Ruczinski and C Kooperberg and M LeBlanc},
journal = {Journal of Computational and Graphical Statistics},
title = {Logic regression},
pages = {475--511},
volume = {12},
year = {2003},
date-added = {2010-01-12 14:26:46 +0100},
date-modified = {2010-01-12 14:26:52 +0100},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2545},
rating = {0}
}

@article{Sher:2008p12000,
author = {Leo Sher and Barbara H Stanley and Jill M Harkavy-Friedman and Juan J Carballo and Mikkel Arendt and David A Brent and Dahlia Sperling and Dana Lizardi and J John Mann and Maria A Oquendo},
journal = {J Clin Psychiatry},
title = {Depressed patients with co-occurring alcohol use disorders: a unique patient population},
abstract = {OBJECTIVE: Alcohol use and depressive disorders are frequently comorbid. Few studies have assessed the impact of comorbid alcohol use disorders (AUDs) on clinical aspects of major depression. We compared depressed subjects with and without co-occurring AUDs with respect to demographic and clinical parameters. METHOD: 505 individuals participated. 318 subjects had DSM-IV major depressive disorder (MDD) without a history of any alcohol or substance abuse/dependence (MDD only), and 187 individuals had MDD and a history of alcohol abuse/dependence (MDD/AUD). Demographic, clinical, and psychiatric history measures of patients in the 2 groups were examined and compared. The study was conducted from January 1990 to June 2005. RESULTS: MDD/AUD patients were younger at their first psychiatric hospitalization (p = .014), their first major depressive episode (p = .041), and their first suicide attempt (p = .001). They reported more previous major depressive episodes (p = .001), suicide attempts (p = .001), and recent life events (p = .001); and had higher lifetime aggression (p < .001), impulsivity (p < .001), and hostility (p < .001) scores. MDD/AUD patients were also more likely to report tobacco smoking (p < .001), a lifetime history of abuse (p = .004), and a history of AUD among first-degree relatives (p < .001) compared to MDD only patients. MDD/AUD individuals also had higher childhood (p < .001), adolescent (p < .001), and adult (p < .001) aggression scores and reported more behavioral problems during their childhood compared to their counterparts. Logistic regression analysis demonstrates that the number of previous depressive episodes, lifetime aggression, and smoking drive the difference between the groups. CONCLUSIONS: Our findings suggest that comorbid MDD/AUD may result from worse antecedents and lead to early onset, more comorbidity, and a more severe course of illness.},
affiliation = {Department of Psychiatry, Columbia University, and New York State Psychiatric Institute, New York, NY 10032, USA. LS2003@columbia.edu},
number = {6},
pages = {907--15},
volume = {69},
year = {2008},
month = {Jun},
language = {eng},
keywords = {Female, Suicide: Attempted, Demography, Diagnostic and Statistical Manual of Mental Disorders, Depressive Disorder: Major, Adult, Aggression, Comorbidity, Impulse Control Disorders, Humans, Male, Alcoholism, Tobacco Use Disorder},
date-added = {2010-05-23 17:26:15 +0200},
date-modified = {2010-05-23 17:26:15 +0200},
pii = {ej07m03556},
pmid = {18422397},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12000},
rating = {0}
}

@article{Gibson:1961p12005,
author = {W A Gibson},
journal = {Psychometrika},
title = {A retraction on inter-battery factor analysis},
number = {4},
pages = {451--452},
volume = {26},
year = {1961},
date-added = {2010-05-23 17:33:20 +0200},
date-modified = {2010-05-23 17:34:08 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Gibson-1961-Psychometrika_A%20retraction%20on%20inte.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12005},
rating = {0}
}

@article{Crane:2008p6000,
author = {Paul K Crane and Kaavya Narasimhalu and Laura E Gibbons and Otto Pedraza and Kala M Mehta and Yuxiao Tang and Jennifer J Manly and Bruce R Reed and Dan M Mungas},
journal = {J Int Neuropsychol Soc},
title = {Composite scores for executive function items: demographic heterogeneity and relationships with quantitative magnetic resonance imaging},
abstract = {Accurate neuropsychological assessment of older individuals from heterogeneous backgrounds is a major challenge. Education, ethnicity, language, and age are associated with scale level differences in test scores, but item level bias might contribute to these differences. We evaluated several strategies for dealing with item and scale level demographic influences on a measure of executive abilities defined by working memory and fluency tasks. We determined the impact of differential item functioning (DIF). We compared composite scoring strategies on the basis of their relationships with volumetric magnetic resonance imaging (MRI) measures of brain structure. Participants were 791 Hispanic, white, and African American older adults. DIF had a salient impact on test scores for 9% of the sample. MRI data were available on a subset of 153 participants. Validity in comparison with structural MRI was higher after scale level adjustment for education, ethnicity/language, and gender, but item level adjustment did not have a major impact on validity. Age adjustment at the scale level had a negative impact on relationships with MRI, most likely because age adjustment removes variance related to age-associated diseases.},
affiliation = {Department of Medicine, University of Washington, Seattle, Washington, USA. pcrane@u.washington.edu},
number = {5},
pages = {746--59},
volume = {14},
year = {2008},
month = {Sep},
language = {eng},
keywords = {Humans, Geriatric Assessment, Aged, Male, Age Factors, Outcome Assessment (Health Care), Brain, Aged: 80 and over, Educational Status, Middle Aged, Demography, Sex Factors, Ethnic Groups, Magnetic Resonance Imaging, Psychometrics, Problem Solving, Female, Neuropsychological Tests},
date-added = {2010-02-18 23:34:18 +0100},
date-modified = {2010-07-29 19:37:46 +0200},
doi = {10.1017/S1355617708081162},
pii = {S1355617708081162},
pmid = {18764970},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Crane-2008-J%20Int%20Neuropsychol%20Soc_Composite%20scores%20for.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6000},
rating = {0}
}

@article{Scantlebury:2010p10915,
author = {Morris H Scantlebury and Aristea S Galanopoulou and Lenka Chudomelova and Emmanuel Raffo and David Betancourth and Solomon L Mosh{\'e}},
journal = {Neurobiol Dis},
title = {A model of symptomatic infantile spasms syndrome},
abstract = {Infantile spasms are characterized by age-specific expression of epileptic spasms and hypsarrhythmia and often result in significant cognitive impairment. Other epilepsies or autism often ensue especially in symptomatic IS (SIS). Cortical or subcortical damage, including white matter, have been implicated in the pathogenesis of SIS. To generate a model of SIS, we recreated this pathology by injecting rats with lipopolysaccharide and doxorubicin intracerebrally at postnatal day (P) 3 and with p-chlorophenylalanine intraperitoneally at P5. Spasms occurred between P4 and 13 and were associated with ictal EEG correlates, interictal EEG abnormalities and neurodevelopmental decline. After P9 other seizures, deficits in learning and memory, and autistic-like behaviors (indifference to other rats, increased grooming) were observed. Adrenocorticotropic hormone (ACTH) did not affect spasms. Vigabatrin transiently suppressed spasms at P5. This new model of SIS will be useful to study the neurobiology and treatment of SIS, including those that are refractory to ACTH.},
affiliation = {Saul R. Korey Department of Neurology, Laboratory of Developmental Neurology, and Montefiore/Einstein Epilepsy Management Center, USA. moscantl@montefiore.org},
number = {3},
pages = {604--12},
volume = {37},
year = {2010},
month = {Mar},
language = {eng},
date-added = {2010-04-13 16:23:29 +0200},
date-modified = {2010-04-13 16:23:29 +0200},
doi = {10.1016/j.nbd.2009.11.011},
pii = {S0969-9961(09)00333-7},
pmid = {19945533},
URL = {http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNK-4XSVR6D-2&_user=2432700&_coverDate=03%252F31%252F2010&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000057263&_version=1&_urlVersion=0&_userid=2432700&md5=03e3f338c49481058f7c0d23c899340b},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Scantlebury-2010-Neurobiol%20Dis_A%20model%20of%20symptomat.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10915},
read = {Yes},
rating = {0}
}

@inbook{Graesser:1999,
author = {AC Graesser and T Kennedy and P Wiemer-Hastings and V Ottati},
journal = {Book},
title = {Cognition and survey research},
chapter = {The use of computational cognitive models to improve questions on surveys and questionnaires},
pages = {199--216},
year = {1999},
date-added = {2010-01-03 19:34:17 +0100},
date-modified = {2010-07-29 19:21:41 +0200},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p996},
rating = {0}
}

@article{Zhao:2006p3891,
author = {Jinying Zhao and Li Jin and Momiao Xiong},
journal = {Genetics},
title = {Nonlinear tests for genomewide association studies},
abstract = {As millions of single-nucleotide polymorphisms (SNPs) have been identified and high-throughput genotyping technologies have been rapidly developed, large-scale genomewide association studies are soon within reach. However, since a genomewide association study involves a large number of SNPs it is therefore nearly impossible to ensure a genomewide significance level of 0.05 using the available statistics, although the multiple-test problems can be alleviated, but not sufficiently, by the use of tagging SNPs. One strategy to circumvent the multiple-test problem associated with genome-wide association tests is to develop novel test statistics with high power. In this report, we introduce several nonlinear tests, which are based on nonlinear transformation of allele or haplotype frequencies. We investigate the power of the nonlinear test statistics and demonstrate that under certain conditions, some nonlinear test statistics have much higher power than the standard chi2-test statistic. Type I error rates of the nonlinear tests are validated using simulation studies. We also show that a class of similarity measure-based test statistics is based on the quadratic function of allele or haplotype frequencies, and thus they belong to nonlinear tests. To evaluate their performance, the nonlinear test statistics are also applied to three real data sets. Our study shows that nonlinear test statistics have great potential in association studies of complex diseases.},
affiliation = {Human Genetics Center, University of Texas Health Science Center, Houston 77030, USA.},
number = {3},
pages = {1529--38},
volume = {174},
year = {2006},
month = {Nov},
language = {eng},
keywords = {Gene Frequency, Genome: Human, Schizophrenia, Models: Statistical, Membrane Proteins, Esophageal Neoplasms, Polymorphism: Single Nucleotide, Humans, Male, Catechol O-Methyltransferase, Acyltransferases, Reproducibility of Results, Matrix Metalloproteinase 2, Female, Computer Simulation, Alleles, Haplotypes},
date-added = {2010-01-16 21:04:30 +0100},
date-modified = {2010-01-16 21:04:30 +0100},
doi = {10.1534/genetics.106.060491},
pii = {genetics.106.060491},
pmid = {16816420},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3891},
rating = {0}
}

@article{Bell:2001p6116,
author = {M D Bell and T Conway Greig and G Bryson and E Kaplan},
journal = {J Clin Psychol},
title = {Patterns of object relations and reality testing deficits in schizophrenia: clusters and their symptom and personality correlates},
abstract = {Bell Object Relations Reality Testing Inventory (BORRTI) profile scores were used to cluster 222 outpatients with schizophrenia or schizoaffective disorder. An eight-cluster solution was subjected to replication analysis, and six clusters were found valid and replicable. These clusters were sorted into three pairs that were interpreted as follows: Residually Impaired consisted of Sealed-Over Recovery and Integrated Recovery; Socially Withdrawn consisted of Socially Withdrawn and Socially Withdrawn-Autistic; and Psychotically Egocentric consisted of Psychotically Egocentric and Psychotically Egocentric-Severe. Clusters were compared on Positive and Negative Syndrome Scale ratings and on subscales from the Eysenck Personality Questionnaire. MANOVAs indicated significant differences among clusters. These differences provided further interpretations of cluster membership. Implications for the use of BORRTI profiles for treatment and rehabilitation planning are discussed.},
affiliation = {Psychology Service, Connecticut VA Medical Center and Yale University School of Medicine, West Haven, 06516, USA. Bell.Morris_D+@West-Haven.VA.Gov},
number = {12},
pages = {1353--67},
volume = {57},
year = {2001},
month = {Dec},
language = {eng},
keywords = {Severity of Illness Index, Schizophrenic Psychology, Male, Object Attachment, Reality Testing, Adult, Female, Psychometrics, Personality Assessment, Humans, Schizophrenia, Psychiatric Status Rating Scales, Reproducibility of Results},
date-added = {2010-02-19 17:07:43 +0100},
date-modified = {2010-02-19 17:07:43 +0100},
pii = {10.1002/jclp.1102},
pmid = {11745581},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6116},
rating = {0}
}

@article{Vaeth:2004p6972,
author = {Michael Vaeth and Eva Skovlund},
journal = {Stat Med},
title = {A simple approach to power and sample size calculations in logistic regression and Cox regression models},
abstract = {For a given regression problem it is possible to identify a suitably defined equivalent two-sample problem such that the power or sample size obtained for the two-sample problem also applies to the regression problem. For a standard linear regression model the equivalent two-sample problem is easily identified, but for generalized linear models and for Cox regression models the situation is more complicated. An approximately equivalent two-sample problem may, however, also be identified here. In particular, we show that for logistic regression and Cox regression models the equivalent two-sample problem is obtained by selecting two equally sized samples for which the parameters differ by a value equal to the slope times twice the standard deviation of the independent variable and further requiring that the overall expected number of events is unchanged. In a simulation study we examine the validity of this approach to power calculations in logistic regression and Cox regression models. Several different covariate distributions are considered for selected values of the overall response probability and a range of alternatives. For the Cox regression model we consider both constant and non-constant hazard rates. The results show that in general the approach is remarkably accurate even in relatively small samples. Some discrepancies are, however, found in small samples with few events and a highly skewed covariate distribution. Comparison with results based on alternative methods for logistic regression models with a single continuous covariate indicates that the proposed method is at least as good as its competitors. The method is easy to implement and therefore provides a simple way to extend the range of problems that can be covered by the usual formulas for power and sample size determination.},
affiliation = {Department of Biostatistics, University of Aarhus, Vennelyst Boulevard 6, DK-8000 Arhus C, Denmark. vaeth@biostat.au.dk},
number = {11},
pages = {1781--92},
volume = {23},
year = {2004},
month = {Jun},
language = {eng},
keywords = {Breast Neoplasms, Logistic Models, Female, Clinical Trials as Topic, Computer Simulation, Proportional Hazards Models, Humans, Survival Analysis, Sample Size, Psychology},
date-added = {2010-03-06 12:25:12 +0100},
date-modified = {2010-03-06 12:25:12 +0100},
doi = {10.1002/sim.1753},
pmid = {15160408},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Vaeth-2004-Stat%20Med_A%20simple%20approach%20to.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6972},
rating = {0}
}

@article{Takane:2008p2719,
author = {Y Takane and H Hwang and Herv{\'e} Abdi},
journal = {Psychometrika},
title = {Regularized multiple-set canonical correlation analysis},
abstract = {Multiple-set canonical correlation analysis (Generalized CANO or GCANO for short) is an important technique because it subsumes a number of interesting multivari- ate data analysis techniques as special cases. More recently, it has also been recognized as an important technique for integrating information from multiple sources. In this paper we present a simple regularization technique for GCANO and demonstrate its usefulness. Regularization is deemed important as a way of supplementing insufficient data by prior knowledge, and/or of incorporating certain desirable properties in the estimates of parameters in the model. Implications of regularized GCANO for multiple correspondence analysis are also discussed. Examples are given to illustrate the use of the proposed technique.},
year = {2008},
date-added = {2010-01-13 14:05:52 +0100},
date-modified = {2010-07-29 20:14:08 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Takane-2008-Psychometrika_Regularized%20multiple-1.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2719},
read = {Yes},
rating = {4}
}

@article{Anonymous:2001p6264,
journal = {Statistical Science},
title = {Interval Estimation for a Binomial Proportion},
abstract = {We revisit the problem of interval estimation of a binomial proportion. The erratic behavior of the coverage probability of the stan- dardWaldconfidenceintervalhaspreviouslybeenremarkedoninthe literature(BlythandStill,AgrestiandCoull,Santnerandothers).We beginbyshowingthatthechaoticcoveragepropertiesoftheWaldinter- val are far more persistent than is appreciated. Furthermore, common textbook prescriptions regarding its safety are misleading and defective inseveralrespectsandcannotbetrusted.
This leads us to consideration of alternative intervals. A number of natural alternatives are presented, each with its motivation and con- text.Eachintervalisexaminedforitscoverageprobabilityanditslength. Basedonthisanalysis,werecommendtheWilsonintervalortheequal- tailedJeffreyspriorintervalforsmallnandtheintervalsuggestedin AgrestiandCoullforlargern.Wealsoprovideanadditionalfrequentist justification for use of the Jeffreys interval.},
number = {2},
pages = {101--183},
volume = {16},
year = {2001},
date-added = {2010-02-19 21:52:16 +0100},
date-modified = {2010-02-19 21:55:45 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/2001-Statistical%20Science_Interval%20Estimation.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6264},
rating = {0}
}

@article{Schadt:2008p1544,
author = {Eric E Schadt and Cliona Molony and Eugene Chudin and Ke Hao and Xia Yang and Pek Y Lum and Andrew Kasarskis and Bin Zhang and Susanna Wang and Christine Suver and Jun Zhu and Joshua Millstein and Solveig Sieberts and John Lamb and Debraj GuhaThakurta and Jonathan Derry and John D Storey and Iliana Avila-Campillo and Mark J Kruger and Jason M Johnson and Carol A Rohl and Atila van Nas and Margarete Mehrabian and Thomas A Drake and Aldons J Lusis and Ryan C Smith and F Peter Guengerich and Stephen C Strom and Erin Schuetz and Thomas H Rushmore and Roger Ulrich},
journal = {PLoS Biol},
title = {Mapping the genetic architecture of gene expression in human liver},
abstract = {Genetic variants that are associated with common human diseases do not lead directly to disease, but instead act on intermediate, molecular phenotypes that in turn induce changes in higher-order disease traits. Therefore, identifying the molecular phenotypes that vary in response to changes in DNA and that also associate with changes in disease traits has the potential to provide the functional information required to not only identify and validate the susceptibility genes that are directly affected by changes in DNA, but also to understand the molecular networks in which such genes operate and how changes in these networks lead to changes in disease traits. Toward that end, we profiled more than 39,000 transcripts and we genotyped 782,476 unique single nucleotide polymorphisms (SNPs) in more than 400 human liver samples to characterize the genetic architecture of gene expression in the human liver, a metabolically active tissue that is important in a number of common human diseases, including obesity, diabetes, and atherosclerosis. This genome-wide association study of gene expression resulted in the detection of more than 6,000 associations between SNP genotypes and liver gene expression traits, where many of the corresponding genes identified have already been implicated in a number of human diseases. The utility of these data for elucidating the causes of common human diseases is demonstrated by integrating them with genotypic and expression data from other human and mouse populations. This provides much-needed functional support for the candidate susceptibility genes being identified at a growing number of genetic loci that have been identified as key drivers of disease from genome-wide association studies of disease. By using an integrative genomics approach, we highlight how the gene RPS26 and not ERBB3 is supported by our data as the most likely susceptibility gene for a novel type 1 diabetes locus recently identified in a large-scale, genome-wide association study. We also identify SORT1 and CELSR2 as candidate susceptibility genes for a locus recently associated with coronary artery disease and plasma low-density lipoprotein cholesterol levels in the process.},
affiliation = {Rosetta Inpharmatics, Seattle, Washington, United States of America. eric_schadt@merck.com},
number = {5},
pages = {e107},
volume = {6},
year = {2008},
month = {May},
language = {eng},
keywords = {Middle Aged, Aged, Child, Genome: Human, Female, Cholesterol: LDL, Adult, Quantitative Trait Loci, Diabetes Mellitus: Type 1, Genotype, Aged: 80 and over, Oligonucleotide Array Sequence Analysis, Liver, Mice, Transcription: Genetic, Infant, Adolescent, Genetic Predisposition to Disease, Coronary Artery Disease, Genes: MHC Class II, Child: Preschool, Gene Expression Profiling, Animals, Polymorphism: Single Nucleotide, Humans, Male, RNA: Messenger},
date-added = {2010-01-07 16:29:28 +0100},
date-modified = {2010-01-07 16:29:28 +0100},
doi = {10.1371/journal.pbio.0060107},
pii = {07-PLBI-RA-4030},
pmid = {18462017},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Schadt-2008-PLoS%20Biol_Mapping%20the%20genetic.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1544},
rating = {0}
}

@article{Eriksson:2005p4031,
author = {A Eriksson and B Mehlig},
journal = {Genetics},
title = {On the effect of fluctuating recombination rates on the decorrelation of gene histories in the human genome},
abstract = {We show how to incorporate fluctuations of the recombination rate along the chromosome into standard gene-genealogical models for the decorrelation of gene histories. This enables us to determine how small-scale fluctuations (Poissonian hot-spot model) and large-scale variations (Kong et al. 2002) of the recombination rate influence this decorrelation. We find that the empirically determined large-scale variations of the recombination rate give rise to a significantly slower decay of correlations compared to the standard, unstructured gene-genealogical model assuming constant recombination rate. A model with long-range recombination-rate variations and with demographic structure (divergent population) is found to be consistent with the empirically observed slow decorrelation of gene histories. Conversely, we show that small-scale recombination-rate fluctuations do not alter the large-scale decorrelation of gene histories.},
affiliation = {Physics and Engineering Physics, Gothenburg University/Chalmers, 41296 Gothenburg, Sweden.},
number = {2},
pages = {1175--8},
volume = {169},
year = {2005},
month = {Feb},
language = {eng},
keywords = {Recombination: Genetic, Genetic Variation, Polymorphism: Single Nucleotide, Genetics: Population, Genome: Human, Demography, Humans, Models: Genetic, Chromosomes: Human: Pair 5, Poisson Distribution, Pedigree},
date-added = {2010-01-19 15:45:05 +0100},
date-modified = {2010-01-19 15:45:05 +0100},
doi = {10.1534/genetics.103.018002},
pii = {genetics.103.018002},
pmid = {15520270},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Eriksson-2005-Genetics_On%20the%20effect%20of%20flu.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4031},
rating = {0}
}

@article{Lilenfeld:2008p9194,
author = {Lisa R R Lilenfeld and Rebecca Ringham and Melissa A Kalarchian and Marsha D Marcus},
journal = {Compr Psychiatry},
title = {A family history study of binge-eating disorder},
abstract = {Family studies of anorexia nervosa and bulimia nervosa have yielded important information about the etiologies of these eating disorders. By contrast, little is known about familial factors of etiologic importance for binge-eating disorder (BED). The purpose of the current family history study was to assess the prevalence of comorbid psychopathology in a non-treatment seeking female sample of 31 probands with BED, 32 control probands without BED, and their 283 first-degree relatives. In-person semistructured clinical interviews were conducted with the probands, who also served as informants for all of their first-degree relatives. Significantly higher lifetime rates of major depressive disorder, dysthymic disorder, and social phobia were found among women with BED compared with control women. Significantly higher lifetime rates of bipolar (I or II) disorder, any depressive disorder, nearly all anxiety disorders, anorexia nervosa, and BED were reported among the first-degree relatives of women with BED compared with the first-degree relatives of control women. Furthermore, female relatives of women with BED were reported to have higher rates of substance use disorders and dysthymic disorder compared with female relatives of control women without BED. Nearly all disorders that were elevated in relatives of women with BED followed a pattern of independent transmission from BED. The primary exception was substance use disorder among female relatives, whose transmission pattern was consistent with that of a shared etiology with BED. Thus, BED and substance use disorder may share a common mechanism of familial transmission among women.},
affiliation = {Clinical Psychology Program, Argosy University, Washington, DC 22209, USA. llilenfeld@argosy.edu},
number = {3},
pages = {247--54},
volume = {49},
year = {2008},
month = {Jan},
language = {eng},
keywords = {Family, Psychiatric Status Rating Scales, Humans, Case-Control Studies, Interview: Psychological, Mental Disorders, Adult, Comorbidity, Female, Bulimia Nervosa, Sex Factors},
date-added = {2010-03-22 13:37:47 +0100},
date-modified = {2010-07-29 19:24:13 +0200},
doi = {10.1016/j.comppsych.2007.10.001},
pii = {S0010-440X(07)00141-1},
pmid = {18396183},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Lilenfeld-2008-Compr%20Psychiatry_A%20family%20history%20stu.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9194},
rating = {0}
}

@article{Vanderweele:2010p1707,
author = {T J Vanderweele and J M Robins},
title = {Empirical and counterfactual conditions for sufficient cause interactions},
abstract = {Su¢ cient-component causes are discussed within the deterministic potential out- comes framework so as to formalize notions of su¢ cient causes, synergism and su¢ cient cause interactions.	Doing so allows for the derivation of counterfactual and empirical conditions for detecting the presence of su¢ cient cause interactions. The conditions are novel in that, unlike other conditions in the literature, they makenoassumptionsaboutmonotonicity. Theconditionscanalsobegeneralized and the conditions for three-way su¢ cient cause interactions are given explicitly. The statistical tests derived for su¢ cient cause interactions are compared with and contrasted to interaction terms in standard statistical models.},
affiliation = {Department of Health Studies, University of Chicago 5841 South Maryland Avenue, MC 2007, Chicago, IL 60637},
keywords = {Su¢ cient cause, Potential outcome, Counterfactual, Risk difference, Synergism, Interaction, Causal inference},
date-added = {2010-01-09 19:18:24 +0100},
date-modified = {2010-01-09 19:20:15 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Vanderweele--_Empirical%20and%20counte.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1707},
rating = {0}
}

@article{Eisenberg:2007p10134,
author = {Dan T A Eisenberg and Benjamin Campbell and James Mackillop and J Koji Lum and David S Wilson},
journal = {PLoS ONE},
title = {Season of birth and dopamine receptor gene associations with impulsivity, sensation seeking and reproductive behaviors},
abstract = {BACKGROUND: Season of birth (SOB) has been associated with many physiological and psychological traits including novelty seeking and sensation seeking. Similar traits have been associated with genetic polymorphisms in the dopamine system. SOB and dopamine receptor genetic polymorphisms may independently and interactively influence similar behaviors through their common effects on the dopaminergic system. METHODOLOGY/PRINCIPAL FINDINGS: Based on a sample of 195 subjects, we examined whether SOB was associated with impulsivity, sensation seeking and reproductive behaviors. Additionally we examined potential interactions of dopamine receptor genes with SOB for the same set of traits. Phenotypes were evaluated using the Sociosexual Orientation Inventory, the Barratt Impulsivity Scale, the Eysenck Impulsivity Questionnaire, the Sensation Seeking Scale, and the Delay Discounting Task. Subjects were also asked about their age at first sex as well as their desired age at the birth of their first child. The dopamine gene polymorphisms examined were Dopamine Receptor D2 (DRD2) TaqI A and D4 (DRD4) 48 bp VNTR. Primary analyses included factorial genderxSOB ANOVAs or binary logistic regression models for each dependent trait. Secondary analysis extended the factorial models by also including DRD2 and DRD4 genotypes as independent variables. Winter-born males were more sensation seeking than non-winter born males. In factorial models including both genotype and season of birth as variables, two previously unobserved effects were discovered: (1) a SOBxDRD4 interaction effect on venturesomeness and (2) a DRD2xDRD4 interaction effect on sensation seeking. CONCLUSION: These results are consistent with past findings that SOB is related to sensation seeking. Additionally, these results provide tentative support for the hypothesis that SOB modifies the behavioral expression of dopaminergic genetic polymorphism. These findings suggest that SOB should be included in future studies of risky behaviors and behavioral genetic studies of the dopamine system.},
affiliation = {Department of Anthropology, Northwestern University, Evanston, Illinois, United States of America. dtae@dtae.net},
number = {11},
pages = {e1216},
volume = {2},
year = {2007},
month = {Jan},
language = {eng},
keywords = {Adult, Receptors: Dopamine, Parturition, Sensation, Humans, Reproduction, Polymorphism: Genetic, Seasons, Minisatellite Repeats, Questionnaires, Phenotype, Impulsive Behavior},
date-added = {2010-03-31 20:36:01 +0200},
date-modified = {2010-03-31 20:36:08 +0200},
doi = {10.1371/journal.pone.0001216},
pmid = {18030347},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Eisenberg-2007-PLoS%20ONE_Season%20of%20birth%20and.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10134},
rating = {4}
}

@article{HapMap2003,
author = {Consortium The International HapMap},
journal = {Nature},
title = {The International HapMap Project.},
number = {6968},
pages = {789--796},
volume = {426},
year = {2003},
date-added = {2010-01-12 14:26:46 +0100},
date-modified = {2010-07-29 19:40:35 +0200},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2516},
rating = {0}
}

@article{Strobl:2008p2568,
author = {Carolin Strobl and Anne-Laure Boulesteix and Thomas Kneib and Thomas Augustin and Achim Zeileis},
journal = {BMC Bioinformatics},
title = {Conditional variable importance for random forests},
abstract = {BACKGROUND: Random forests are becoming increasingly popular in many scientific fields because they can cope with "small n large p" problems, complex interactions and even highly correlated predictor variables. Their variable importance measures have recently been suggested as screening tools for, e.g., gene expression studies. However, these variable importance measures show a bias towards correlated predictor variables. RESULTS: We identify two mechanisms responsible for this finding: (i) A preference for the selection of correlated predictors in the tree building process and (ii) an additional advantage for correlated predictor variables induced by the unconditional permutation scheme that is employed in the computation of the variable importance measure. Based on these considerations we develop a new, conditional permutation scheme for the computation of the variable importance measure. CONCLUSION: The resulting conditional variable importance reflects the true impact of each predictor variable more reliably than the original marginal approach.},
affiliation = {Department of Statistics, Ludwig-Maximilians-Universit{\"a}t Munchen, Ludwigstrasse 33, D-80539 M{\"u}nchen, Germany. carolin.strobl@stat.uni-muenchen.de},
pages = {307},
volume = {9},
year = {2008},
month = {Jan},
language = {eng},
keywords = {Regression Analysis, Statistics: Nonparametric, Biometry, Amino Acid Sequence, Major Histocompatibility Complex, Research Design, Decision Trees, Factor Analysis: Statistical, Binding Sites, Computational Biology},
date-added = {2010-01-12 22:22:30 +0100},
date-modified = {2010-01-12 22:22:30 +0100},
doi = {10.1186/1471-2105-9-307},
pii = {1471-2105-9-307},
pmid = {18620558},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Strobl-2008-BMC%20Bioinformatics_Conditional%20variable.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2568},
rating = {0}
}

@article{Sinoquet:2008p4679,
author = {C Sinoquet},
title = {Performance analysis of methods to infer missing genotypes},
abstract = {Complex analyses such as genetic mapping, disease association studies, disease mapping in the context of environmental health and environmental epidemiology studies rely on high-throughput genotyping techniques. These analyses thoroughly examine genetic variations between subjects, in particular through Single Nucleotide Polymorphism (SNP). Nonetheless, though nowa- days genotyping techniques impose high-quality standards, one still has to cope with the issues of missing data and genotyping errors. Typically, the percentage of missing data - or missing calls - now ranges in interval [5%, 10%]. Computational inference of missing data represents a challenging alternative to genotyping again the missing regions. This document first briefly reviews the various methods designed to infer missing SNPs. Then, it reports performances published for these inference methods. The present report carefully describes the characteristics of the different benchmarks generated by the designers (missing data per- centage, correlation between SNPs). We show that most methods provide accuracies in the range [90%, 96%]. However, we also emphasize that no algorithm garantees constant high accuracies: an algorithm may perform well on some benchmarks and show in contrast relatively poor results on others.},
year = {2008},
date-added = {2010-01-30 16:08:17 +0100},
date-modified = {2010-01-30 16:08:49 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Sinoquet-2008-_Performance%20analysis.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4679},
rating = {0}
}

@article{Neale2004,
author = {B Neale and P Sham},
journal = {American Journal of Human Genetics},
title = {The future of association studies: Gene-based analysis and replication},
pages = {353--362},
volume = {75},
year = {2004},
date-added = {2010-01-12 14:26:52 +0100},
date-modified = {2010-07-29 19:13:36 +0200},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2554},
rating = {0}
}

@article{Schneider:1999p5890,
author = {B Schneider},
journal = {SUGI 24},
title = {How to Display Correlated ROC Curves with the SAS System},
abstract = {Diagnosis is an essential part of clinical practice. Much medical research is carried out to improve methods of diagnosis. Medical tests are developed for diagnosis purpose. Thus statistical methods of evaluating and comparing the performance of such tests are of great importance. A test is associated with an observed variable which is able to discriminate between a diseased and non- diseased population. If this variable lies on an ordinal or metric scale an assessment of the overall performance of the test can be made through the use of the Receiver Operating Characteristic (ROC) curve. Correlated ROC curves arise when two or more different tests are performed on the same individuals.},
year = {1999},
date-added = {2010-02-17 21:02:20 +0100},
date-modified = {2010-02-17 21:03:55 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Schneider-1999-SUGI%2024_How%20to%20Display%20Corre.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5890},
rating = {0}
}

@article{Lewis:1990,
author = {G Lewis and AJ Pelosi},
journal = {British Journal of Psychiatry},
title = {The case-control in psychiatry},
abstract = {Case-control studies involve 'cases' being compared to 'controls' with respect to 'exposures', possible aetiological (or associated) factors. Associations between a disease and an exposure can be explained by chance, reverse causality, confounding and biases or, lastly, by causality. However, confounders as well as information and selection biases can be adjusted for at the design (or analysis) stage of the study. The strength of an association can be measured by means of relative risk, calculated indirectly using the odds ratio. Well conducted control studies should produce accurate estimates of relative risks in many psychiatric investigations.},
number = {197-207},
volume = {157},
year = {1990},
date-added = {2010-01-03 19:36:09 +0100},
date-modified = {2010-07-29 19:22:27 +0200},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1028},
rating = {0}
}

@article{Kamarajan:2009p9680,
author = {Chella Kamarajan and Madhavi Rangaswamy and Yongqiang Tang and David B Chorlian and Ashwini K Pandey and Bangalore N Roopesh and Niklas Manz and Ramotse Saunders and Arthur T Stimus and Bernice Porjesz},
journal = {J Psychiatr Res},
title = {Dysfunctional reward processing in male alcoholics: An ERP study during a gambling task},
abstract = {OBJECTIVE: A dysfunctional neural reward system has been shown to be associated with alcoholism. The current study aims to examine reward processing in male alcoholics by using event-related potentials (ERPs) as well as behavioral measures of impulsivity and risk-taking. METHODS: Outcome-related negativity (ORN/N2) and positivity (ORP/P3) derived from a single outcome gambling task were analyzed using a mixed model procedure. Current density was compared across groups and outcomes using standardized low resolution electromagnetic tomography (sLORETA). Behavioral scores were also compared across groups. Correlations of ERP factors with behavioral and impulsivity factors were also analyzed. RESULTS: Alcoholics showed significantly lower amplitude than controls during all outcome conditions for the ORP component and decreased amplitude during the loss conditions for the ORN component. Within conditions, gain produced higher amplitudes than loss conditions. Topographically, both groups had an anterior focus during loss conditions and posterior maxima during gain conditions, especially for the ORN component. Decreased ORP current density at cingulate gyrus and less negative ORN current density at sensory and motor areas characterized the alcoholics. Alcoholics had higher levels of impulsivity and risk-taking features than controls. CONCLUSIONS: Deficient outcome/reward processing and increased impulsivity and risk-taking observed in alcoholics may be at least partly due to reward deficiency and/or dysfunctional reward circuitry in the brain, suggesting that alcoholism can be considered as part of the cluster of the reward deficiency syndrome (RDS).},
affiliation = {Henri Begleiter Neurodynamics Laboratory, Department of Psychiatry, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA.},
note = {genim},
pages = {},
year = {2009},
month = {Dec},
language = {ENG},
date-added = {2010-03-25 15:08:18 +0100},
date-modified = {2010-07-29 19:35:54 +0200},
doi = {10.1016/j.jpsychires.2009.11.019},
pii = {S0022-3956(09)00271-4},
pmid = {20035952},
URL = {http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T8T-4Y0THV5-2&_user=2432700&_coverDate=12%252F24%252F2009&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000057263&_version=1&_urlVersion=0&_userid=2432700&md5=82448966fe0c3d36ec7a538be863e1d1},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Kamarajan-2009-J%20Psychiatr%20Res_Dysfunctional%20reward.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9680},
rating = {0}
}

@article{Meeds:2010p12867,
author = {E Meeds and Z Ghahramani and R Neal and S Roweis},
title = {Modeling Dyadic Data with Binary Latent Factors},
abstract = {We introduce binary matrix factorization, a novel model for unsupervised ma- trix decomposition. The decomposition is learned by fitting a non-parametric Bayesian probabilistic model with binary latent variables to a matrix of dyadic data. Unlike bi-clustering models, which assign each row or column to a single cluster based on a categorical hidden feature, our binary feature model reflects the prior belief that items and attributes can be associated with more than one latent cluster at a time. We provide simple learning and inference rules for this new model and show how to extend it to an infinite model in which the number of features is not a priori fixed but is allowed to grow with the size of the data.},
date-added = {2010-06-24 12:49:11 +0200},
date-modified = {2010-06-24 12:49:59 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Meeds--_Modeling%20Dyadic%20Data.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12867},
rating = {0}
}

@article{Buchel:1997p2314,
author = {C B{\"u}chel and K J Friston},
journal = {Cereb Cortex},
title = {Modulation of connectivity in visual pathways by attention: cortical interactions evaluated with structural equation modelling and fMRI},
abstract = {Electrophysiological and neuroimaging studies have shown that attention to visual motion can increase the responsiveness of the motion-selective cortical area V5 and the posterior parietal cortex (PP). Increased or decreased activation in a cortical area is often attributed to attentional modulation of the cortical projections to that area. This leads to the notion that attention is associated with changes in connectivity. We have addressed attentional modulation of effective connectivity using functional magnetic resonance imaging (fMRI). Three subjects were scanned under identical stimulus conditions (visual motion) while varying only the attentional component of the task. Haemodynamic responses defined an occipito-parieto-frontal network, including the, primary visual cortex (V1), V5 and PR A structural equation model of the interactions among these dorsal visual pathway areas revealed increased connectivity between V5 and PP related to attention. On the basis of our analysis and the neuroanatomical pattern of projections from the prefrontal cortex to PP we attributed the source of modulatory influences, on the posterior visual pathway, to the prefrontal cortex (PFC). To test this hypothesis we included the PFC in our model as a 'modulator' of the pathway between V5 and PP, using interaction terms in the structural equation model. This analysis revealed a significant modulatory effect of prefrontal regions on V5 afferents to posterior parietal cortex.},
affiliation = {The Wellcome Department of Cognitive Neurology, Institute of Neurology, London, UK. cbuechel@fil.ion.ucl.ac.uk},
number = {8},
pages = {768--78},
volume = {7},
year = {1997},
month = {Dec},
language = {eng},
keywords = {Brain Mapping, Parietal Lobe, Humans, Analysis of Variance, Visual Cortex, Regression Analysis, Occipital Lobe, Frontal Lobe, Cerebral Cortex, Models: Neurological, Cerebrovascular Circulation, Magnetic Resonance Imaging, Hemodynamics, Visual Pathways},
date-added = {2010-01-10 12:30:04 +0100},
date-modified = {2010-01-10 12:30:04 +0100},
pmid = {9408041},
local-url = {file://localhost/Users/chl/Dropbox/Papers/B%C3%BCchel-1997-Cereb%20Cortex_Modulation%20of%20connec.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2314},
rating = {0}
}

@article{Zupan:2003p1842,
author = {Blaz Zupan and Janez Demsar and Ivan Bratko and Peter Juvan and John A Halter and Adam Kuspa and Gad Shaulsky},
journal = {Bioinformatics},
title = {GenePath: a system for automated construction of genetic networks from mutant data},
abstract = {MOTIVATION: Genetic networks are often used in the analysis of biological phenomena. In classical genetics, they are constructed manually from experimental data on mutants. The field lacks formalism to guide such analysis, and accounting for all the data becomes complicated when large amounts of data are considered. RESULTS: We have developed GenePath, an intelligent assistant that automates the analysis of genetic data. GenePath employs expert-defined patterns to uncover gene relations from the data, and uses these relations as constraints in the search for a plausible genetic network. GenePath formalizes genetic data analysis, facilitates the consideration of all the available data in a consistent manner, and the examination of the large number of possible consequences of planned experiments. It also provides an explanation mechanism that traces every finding to the pertinent data. AVAILABILITY: GenePath can be accessed at http://genepath.org. SUPPLEMENTARY INFORMATION: Supplementary material is available at http://genepath.org/bi-.supp.},
affiliation = {University of Ljubljana, Faculty of Computer and Information Science Jozef Stefan Institute, Ljubljana, Slovenia.},
number = {3},
pages = {383--9},
volume = {19},
year = {2003},
month = {Feb},
language = {eng},
keywords = {Animals, Larva, Sequence Analysis: DNA, Gene Expression Regulation, Caenorhabditis elegans, Dictyostelium, Models: Genetic, Single-Blind Method, DNA Mutational Analysis, Expert Systems, Software},
date-added = {2010-01-10 10:37:03 +0100},
date-modified = {2010-01-10 10:37:03 +0100},
pmid = {12584124},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Zupan-2003-Bioinformatics_GenePath%20a%20system%20f.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1842},
rating = {0}
}

@article{Caspi:1990p10001,
author = {A Caspi and E S Herbener},
journal = {J Pers Soc Psychol},
title = {Continuity and change: assortative marriage and the consistency of personality in adulthood},
abstract = {How is personality stability possible amid the myriad of social changes and transformations that characterize a human life? We argue that by choosing situations that are compatible with their dispositions and by affiliating with similar others, individuals may set in motion processes of social interchange that sustain their dispositions across time and circumstance. To test this proposition we examined mate selection, using data on married couples from two ongoing longitudinal studies at the Institute of Human Development, University of California, Berkeley. Consistent with other research, the results point to homogamy as a basic norm in marriage. More important, the results show that marriage to a similar other promotes consistency in the intraindividual organization of personality attributes across middle adulthood. We offer some speculations for a more relational approach to the problem of individual continuity and change.},
affiliation = {Department of Psychology, University of Wisconsin, Madison 53706.},
number = {2},
pages = {250--8},
volume = {58},
year = {1990},
month = {Feb},
language = {eng},
keywords = {Social Environment, Personality, Adult, Marriage, Longitudinal Studies, Q-Sort, Female, Humans, Individuality, Male},
date-added = {2010-03-31 19:47:41 +0200},
date-modified = {2010-07-29 19:35:33 +0200},
pmid = {2319443},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10001},
rating = {0}
}

@article{Tricot:2000,
author = {J-M Tricot and M Mesbah},
journal = {Revue de Statistique Appliqu{\'e}e},
title = {Un mod{\`e}le de r{\'e}ponses aux items. Propri{\'e}t{\'e}s et comparaison de groupes de traitement en {\'e}pid{\'e}miologie},
number = {4},
pages = {29--39},
volume = {48},
year = {2000},
date-added = {2010-01-10 11:33:18 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Tricot-2000-Revue%20de%20Statistique%20Appliqu%C3%A9e_Un%20mod%C3%A8le%20de%20r%C3%A9ponse.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2199},
rating = {0}
}

@article{Baddeley:2009p10723,
author = {Roland Baddeley and David Attewell},
journal = {Psychol Sci},
title = {The relationship between language and the environment: information theory shows why we have only three lightness terms},
abstract = {The surface reflectance of objects is highly variable, ranging between 4% for, say, charcoal and 90% for fresh snow. When stimuli are presented simultaneously, people can discriminate hundreds of levels of visual intensity. Despite this, human languages possess a maximum of just three basic terms for describing lightness. In English, these are white (or light), black (or dark), and gray. Why should this be? Using information theory, combined with estimates of the distribution of reflectances in the natural world and the reliability of lightness recall over time, we show that three lightness terms is the optimal number for describing surface reflectance properties in a modern urban or indoor environment. We also show that only two lightness terms would be required in a forest or rural environment.},
affiliation = {University of Bristol, Bristol, BS8 1TU, United Kingdom. roland.baddeley@bristol.ac.uk},
number = {9},
pages = {1100--7},
volume = {20},
year = {2009},
month = {Sep},
language = {eng},
keywords = {Concept Formation, Mathematical Concepts, Communication, Lighting, Discrimination (Psychology), Information Theory, Uncertainty, Humans, Social Environment, Semantics, Visual Perception, Entropy, Mental Recall, Contrast Sensitivity},
date-added = {2010-04-10 03:25:49 +0200},
date-modified = {2010-07-29 19:46:15 +0200},
doi = {10.1111/j.1467-9280.2009.02412.x},
pii = {PSCI2412},
pmid = {19656339},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Baddeley-2009-Psychol%20Sci_The%20relationship%20bet.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10723},
rating = {0}
}

@article{Schwarz:1991,
author = {N Schwarz and F Strack and H Mai},
journal = {Public Opinion Quarterly},
title = {Assimilation and contrast effects in part-whole question sequences: A

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib