text:
fraction based on survival functions under the proportional hazards models, and multivariate adaptive splines for the analysis of longitudinal data. The specific scientific questions addressed by these different approaches also varied, ranging from a more precise definition of the phenotype, bias reduction in control selection, estimation of effect sizes and genotype associated risk, to direct incorporation of genetic data into longitudinal modeling approaches and the exploration of population heterogeneity with regard to longitudinal trajectories. The group reached several overall conclusions: (1) The additional information provided by longitudinal data may be useful in genetic analyses. (2) The precision of the phenotype definition as well as control selection in nested designs may be improved, especially if traits demonstrate a trend over time or have strong age-of-onset effects. (3) Analyzing genetic data stratified for high-risk subgroups defined by a unique development over time could be useful for the detection of rare mutations in common multifactorial diseases. (4) Estimation of the population impact of genomic risk variants could be more precise. The challenges and computational complexity demanded by genome-wide single-nucleotide polymorphism data were also discussed.},
affiliation = {Department of Psychiatry, University of California, Los Angeles, California, USA.},
pages = {S93--8},
volume = {33 Suppl 1},
year = {2009},
month = {Jan},
language = {eng},
date-added = {2010-03-15 23:43:58 +0100},
date-modified = {2010-03-15 23:43:58 +0100},
doi = {10.1002/gepi.20479},
pmid = {19924713},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7667},
rating = {0}
}

@article{Dickman:2004p7553,
author = {Paul W Dickman and Andy Sloggett and Michael Hills and Timo Hakulinen},
journal = {Stat Med},
title = {Regression models for relative survival},
abstract = {Four approaches to estimating a regression model for relative survival using the method of maximum likelihood are described and compared. The underlying model is an additive hazards model where the total hazard is written as the sum of the known baseline hazard and the excess hazard associated with a diagnosis of cancer. The excess hazards are assumed to be constant within pre-specified bands of follow-up. The likelihood can be maximized directly or in the framework of generalized linear models. Minor differences exist due to, for example, the way the data are presented (individual, aggregated or grouped), and in some assumptions (e.g. distributional assumptions). The four approaches are applied to two real data sets and produce very similar estimates even when the assumption of proportional excess hazards is violated. The choice of approach to use in practice can, therefore, be guided by ease of use and availability of software. We recommend using a generalized linear model with a Poisson error structure based on collapsed data using exact survival times. The model can be estimated in any software package that estimates GLMs with user-defined link functions (including SAS, Stata, S-plus, and R) and utilizes the theory of generalized linear models for assessing goodness-of-fit and studying regression diagnostics.},
affiliation = {Department of Medical Epidemiology, Karolinska Institutet, Stockholm, Sweden. paul.dickman@mep.ki.se},
number = {1},
pages = {51--64},
volume = {23},
year = {2004},
month = {Jan},
language = {eng},
keywords = {Middle Aged, Neoplasms, Child, Aged, Adolescent, Infant, Child: Preschool, Regression Analysis, Survival Analysis, Humans, Infant: Newborn, Adult, Registries},
date-added = {2010-03-14 10:54:20 +0100},
date-modified = {2010-03-14 10:54:20 +0100},
doi = {10.1002/sim.1597},
pmid = {14695639},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Dickman-2004-Stat%20Med_Regression%20models%20fo.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7553},
rating = {0}
}

@book{Izenman2008,
author = {A J Izenman},
journal = {Book},
title = {Modern Multivariate Statistical Techniques},
year = {2008},
date-added = {2010-01-12 14:26:52 +0100},
date-modified = {2010-01-12 14:26:52 +0100},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2553},
rating = {0}
}

@article{Monni:2010p4928,
author = {S Monni and H Li},
journal = {UPenn Biostatistics Working Papers},
title = {Bayesian Methods for Network-Structured Genomics Data},
abstract = {Graphs and networks are common ways of depicting information. In biology, many different processes are represented by graphs, such as regulatory networks, metabolic pathways and protein-protein interaction networks. This information provides useful supplement to the standard numerical genomic data such as mi- croarray gene expression data. Effectively utilizing such an information can lead to a better identification of biologically relevant genomic features in the context of our prior biological knowledge. In this paper, we present a Bayesian variable selection procedure for network-structured covariates for both Gaussian linear and probit models. The key of our approach is the introduction of a Markov random field prior for the indicator variables that describe which covariates should be in- cluded in the model and the use of the Wolff algorithm for Markov Chain Monte Carlo inference. We illustrate the proposed procedure with simulations and with an analysis of genomic data. Finally, we present some other areas of genomics research where novel Bayesian approaches may play important roles.},
number = {34},
year = {2010},
date-added = {2010-02-02 11:48:45 +0100},
date-modified = {2010-02-02 11:49:18 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Monni-2010-UPenn%20Biostatistics%20Working%20Papers_Bayesian%20Methods%20for.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4928},
rating = {0}
}

@inbook{Eisenhower:1991,
author = {D Eisenhower and NA Mathiowetz and D Morganstein},
journal = {Book},
title = {Measurement errors in sruveys},
chapter = {Recall error: Sources and bias reduction techniques},
pages = {127--144},
year = {1991},
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/p972},
rating = {0}
}

@article{Nichols:2010p12337,
author = {T E Nichols and J-B Poline},
journal = {Perspectives on Psychological Science},
title = {Comment on Vul et al, "Puzzlingly High Correlations in fMRI Studies of Emotion, Personality, and Social Cognition"},
abstract = {Vul et al., ``Puzzlingly High Correlations in fMRI Studies of Emotion, Personality, and Social Cognition'' make a broad case that current practice in neuroimaging methodology is deficient. They go so far as to demand that authors retract or restate results, which we find wrongly casts suspicion on the confirmatory inference methods that form the foundation of neuroimaging statistics. We contend the authors' argument is overstated and that their work can be distilled down to two points already familiar to the neuroimaging community: That the multiple testing problem must be accounted for, and that reporting of methods and results should be improved. We also illuminate their concerns with standard statistical concepts, like the distinction between estimation and inference, and between confirmatory and post hoc inferences, which makes their findings less puzzling.},
date-added = {2010-06-12 10:16:25 +0200},
date-modified = {2010-06-12 10:17:36 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Nichols--Perspectives%20on%20Psychological%20Science_Comment%20on%20Vul%20et%20al.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12337},
rating = {0}
}

@article{Ray:2008p5846,
author = {Riju Ray and James Loughead and Ze Wang and John Detre and Edward Yang and Ruben Gur and Caryn Lerman},
journal = {Behav Brain Res},
title = {Neuroimaging, genetics and the treatment of nicotine addiction},
abstract = {Advances in neuroimaging and genomics provide an unprecedented opportunity to accelerate medication development for nicotine dependence and other addictions. Neuroimaging studies have begun to elucidate the functional neuroanatomy and neurochemistry underlying effects of nicotine and nicotine abstinence. In parallel, genetic studies, including both candidate gene and genome-wide association approaches, are identifying key neurobiological targets and pathways important in addiction to nicotine. To date, only a few neuroimaging studies have explored effects of nicotine or abstinence on brain activity as a function of genotype. Most analyses of genotype are retrospective, resulting in small sample sizes for testing effects of the minor alleles for candidate genes. The purpose of this review is to provide an outline of the work in neuroimaging, genetics, and nicotine dependence, and to explore the potential for increased integration of these approaches to improve nicotine dependence treatment.},
affiliation = {Trandisciplinary Tobacco Use Research Center, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA.},
number = {2},
pages = {159--69},
volume = {193},
year = {2008},
month = {Nov},
language = {eng},
keywords = {Positron-Emission Tomography, Smoking, Behavior: Addictive, Humans, Diagnostic Imaging, Genotype, Genomics, Tobacco Use Disorder, Genetic Predisposition to Disease},
date-added = {2010-02-17 10:19:07 +0100},
date-modified = {2010-02-17 10:19:07 +0100},
doi = {10.1016/j.bbr.2008.05.021},
pii = {S0166-4328(08)00297-0},
pmid = {18599130},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Ray-2008-Behav%20Brain%20Res_Neuroimaging%20geneti.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5846},
rating = {0}
}

@article{RobnikSikonja:2004p1549,
author = {M Robnik-Sikonja},
journal = {Machine Learning, ECML 2004 Proceedings},
title = {Improving Random Forests},
abstract = {Random forests are one of the most successful ensemble methods which exhibits performance on the level of boosting and support vector machines. The method is fast, robust to noise, does not overfit and offers possibilities for explanation and visualization of its output. We investigate some possibilities to increase strength or decrease correlation of individual trees in the forest. Using several attribute evaluation measures instead of just one gives promising results. On the other hand replacement of ordinary voting with voting weighted with mar- gin achieved on most similar instances gives improvements which are statistically highly significant over several data sets.},
year = {2004},
date-added = {2010-01-07 16:33:53 +0100},
date-modified = {2010-01-07 16:34:37 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Robnik-Sikonja-2004-Machine%20Learning%20ECML%202004%20Proceedings_Improving%20Random%20For.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1549},
rating = {0}
}

@article{HardyVallee:2010p4098,
author = {B Hardy-Vall{\'e}e},
title = {D{\'e}cision, strat{\'e}gies et {\'e}changes : une br{\`e}ve introduction {\`a} la rationalit{\'e} pratique},
date-added = {2010-01-19 23:29:48 +0100},
date-modified = {2010-01-19 23:30:07 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hardy-Vall%C3%A9e--_De%CC%81cision%20strate%CC%81gi.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4098},
rating = {0}
}

@article{Hyland:2003p5907,
author = {Michael E Hyland},
journal = {Health Qual Life Outcomes},
title = {A brief guide to the selection of quality of life instrument},
abstract = {There are numerous quality of life (QOL) scales. Because QOL experts are often partial to their own scales, researchers need to be able to select scales for themselves. Scales best suited for longitudinal purposes (clinical trials and audit) have different properties to those suited for cross-sectional studies (population and correlational studies and clinical use). The reason and logic of these differences is explained. For longitudinal use, researchers need to consider the relationship between item set, population and treatment; scales can be short, floor and ceiling effects must be avoided, and there should be extended response options. For cross-sectional use scales should have a wide range of items, should be longer, and there are no adverse floor and ceiling effects, and response options can be simpler to allow a larger set of items.},
affiliation = {Department of Psychology, University of Plymouth, Plymouth PL4 8AA. M.Hyland@plymouth.ac.uk},
pages = {24},
volume = {1},
year = {2003},
month = {Jan},
language = {eng},
keywords = {Reproducibility of Results, Longitudinal Studies, Health Status Indicators, Cross-Sectional Studies, Quality of Life, Psychometrics, Questionnaires, Humans},
date-added = {2010-02-18 23:09:21 +0100},
date-modified = {2010-02-18 23:09:21 +0100},
doi = {10.1186/1477-7525-1-24},
pmid = {12848895},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hyland-2003-Health%20and%20Quality%20of%20Life%20Outcomes_A%20brief%20guide%20to%20the.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5907},
rating = {0}
}

@article{Weich:1998,
author = {S Weich and G Lewis},
journal = {British Medical Journal},
title = {Poverty, unemployment, and common mental disorders: population based cohort study},
abstract = {Objective: To determine whether poverty and unemployment increase the likelihood of or delay recovery from common mental disorders, and whether these associations could be explained by subjective financial strain. Design: Prospective cohort study. Setting: England, Wales, and Scotland. Subjects: 7726 adults aged 16-75 living in private households. Main outcome measures: Common mental disorders were assessed using the general health questionnaire, a self assessed measure of psychiatric morbidity. Results: Poverty and unemployment (odds ratio 1.86, 95% confidence interval 1.18 to 2.94) were associated with the maintenance but not onset of episodes of common mental disorders. Associations between poverty and employment and maintenance of common mental disorders, however, were much smaller than those of cross sectional studies. Financial strain at baseline was independently associated with both onset (1.57, 1.19 to 2.07) and maintenance (1.86, 1.36 to 2.53) even after adjusting for objective indices of standard of living. Conclusions: Poverty and unemployment increased the duration of episodes of common mental disorders but not the likelihood of their onset. Financial strain was a better predictor of future psychiatric morbidity than either of these more objective risk factors though the nature of this risk factor and its relation with poverty and unemployment remain unclear.},
number = {7151},
pages = {115--119},
volume = {317},
year = {1998},
date-added = {2010-01-03 19:36:10 +0100},
date-modified = {2010-01-03 19:36:10 +0100},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1076},
rating = {0}
}

@article{Bowman:2007p4713,
author = {F Dubois Bowman and Ying Guo and Gordana Derado},
journal = {Neuroimaging Clin N Am},
title = {Statistical approaches to functional neuroimaging data},
abstract = {The field of statistics makes valuable contributions to functional neuroimaging research by establishing procedures for the design and conduct of neuroimaging experiments and providing tools for objectively quantifying and measuring the strength of scientific evidence provided by the data. Two common functional neuroimaging research objectives include detecting brain regions that reveal task-related alterations in measured brain activity (activations) and identifying highly correlated brain regions that exhibit similar patterns of activity over time (functional connectivity). This article highlights various statistical procedures for analyzing data from activation studies and functional connectivity studies, focusing on functional magnetic resonance imaging (fMRI) and positron emission tomography (PET) data. Also discussed are emerging statistical methods for prediction using fMRI and PET data, which stand to increase the translational significance of functional neuroimaging data to clinical practice.},
affiliation = {Department of Biostatistics, Center for Biomedical Imaging Statistics, The Rollins School of Public Health, Emory University, 1518 Clifton Road, N.E., Atlanta, GA 30322, USA. dbowma3@sph.emory.edu},
number = {4},
pages = {441--58, viii},
volume = {17},
year = {2007},
month = {Nov},
language = {eng},
keywords = {Brain Mapping, Magnetic Resonance Imaging, Models: Neurological, Humans, Data Interpretation: Statistical, Positron-Emission Tomography},
date-added = {2010-01-30 16:19:44 +0100},
date-modified = {2010-01-30 16:19:44 +0100},
doi = {10.1016/j.nic.2007.09.002},
pii = {S1052-5149(07)00091-3},
pmid = {17983962},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4713},
rating = {0}
}

@article{DelPino:2006p1521,
author = {G Del Pino and E San Martin and J Gonzalez and Paul De Boeck},
title = {On the relationships between sum score based estimation and joint maximum likelihood estimation},
abstract = {This note analyzes the use and limitations of the sum score based (SSB) formulation of the Rasch model, where items and sum scores of persons are considered as factors in a logit model. After reviewing the evolution leading to the rather surprising equality between their maximum likelihood estimates, the SSB model is then discussed from the point of view of pseudo-likelihood and of misspecified models. This is then employed to provide new insights into origin of the known inconsistency of the difficulty parameter estimates in the Rasch model. The main result concerns the relations between the estimated standard errors for both models. It is shown that the equality of the point estimates also holds for the estimated standard errors of the difficulty parameters. For the ability parameters, an exact formula and a useful upper bound are given for the estimated standard errors of the Rasch model in terms of those for the SSB model, which are more easily obtained.},
affiliation = {Department of Statistics, Pontificia Universidad Cato ́lica de Chile, Casilla 302, Santiago 22, Chile},
year = {2006},
keywords = {Rasch model, Pseudo-likelihood, Information Matrix, Standard error, Latent Class Mod- els},
date-added = {2010-01-07 15:50:33 +0100},
date-modified = {2010-07-29 20:46:12 +0200},
URL = {http://www.stat.ucl.ac.be/IAP},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Del%20Pino-2006-_On%20the%20relationships.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1521},
read = {Yes},
rating = {0}
}

@techreport{Fox:2000,
author = {Jean-Paul Fox and Cees A W Glas},
journal = {Techreport},
title = {Bayesian Modeling of Measurement Error in Predictor Variables Using Item Response Theory},
affiliation = {Faculty of Educational Science and Technology, University of Twente},
year = {2000},
date-added = {2010-01-10 11:33:23 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1891},
rating = {0}
}

@article{Carmelli:2002p5055,
author = {Dorit Carmelli and Gary E Swan and Charles DeCarli and Terry Reed},
journal = {Biol Psychol},
title = {Quantitative genetic modeling of regional brain volumes and cognitive performance in older male twins},
abstract = {As part of an ongoing longitudinal twin study, data from both MRI brain scanning and from neuropsychological testing were obtained from 139 male-male twin pairs (72 monozygotic [MZ] and 67 dizygotic [DZ]), 69-80 years old at the time of examination. For descriptive purposes, we examined the MZ and DZ intraclass correlations (ICC) of four lobar brain volumes (frontal, temporal, parietal, and occipital), two cerebrospinal fluid (CSF) volumes (lateral ventricle and temporal horn of the lateral ventricles), and two measures of cognitive functioning (verbal memory and executive function). We found that for lobar brain and CSF space volumes, the MZ ICC were significantly greater than zero (r=0.37-0.77) and greater than the corresponding DZ correlations (r=0.02-0.49). Similarly, within-pair correlations for the two neuropsychological factors were statistically significant and significantly larger in MZ twin pairs than in DZ pairs, suggesting the presence of genetic variance. Bivariate genetic analysis revealed that while close to 60% of individual differences in neuropsychological performance were due to genetic influences, less than 50% of genetic effects were in common with those influencing brain volumes. These data may shed light on the genetic liability for brain diseases that affect the elderly.},
affiliation = {Center for Health Sciences, SRI International (formerly Stanford Research Institute), 333 Ravenswood Avenue, Menlo Park, CA 94025, USA. dorit.carmelli@sri.com},
number = {1-2},
pages = {139--55},
volume = {61},
year = {2002},
month = {Oct},
language = {eng},
keywords = {Longitudinal Studies, Male, Twins: Monozygotic, Aging, Humans, Neuropsychological Tests, Genetic Variation, Image Processing: Computer-Assisted, Reference Values, Models: Genetic, Imaging: Three-Dimensional, Twins: Dizygotic, Aged, Cerebral Cortex, Cerebral Ventricles},
date-added = {2010-02-05 20:02:43 +0100},
date-modified = {2010-02-05 20:02:43 +0100},
pii = {S030105110200056X},
pmid = {12385673},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5055},
rating = {0}
}

@article{Schiffman:2009p5153,
author = {Jason Schiffman and Holger J Sorensen and Justin Maeda and Erik L Mortensen and Jeff Victoroff and Kentaro Hayashi and Niels M Michelsen and Morten Ekstrom and Sarnoff Mednick},
journal = {Am J Psychiatry},
title = {Childhood motor coordination and adult schizophrenia spectrum disorders},
abstract = {OBJECTIVE: The authors examined whether motor coordination difficulties assessed in childhood predict later adult schizophrenia spectrum outcomes. METHOD: A standardized childhood neurological examination was administered to a sample of 265 Danish children in 1972, when participants were 10-13 years old. Adult diagnostic information was available for 244 members of the sample. Participants fell into three groups: children whose mothers or fathers had a psychiatric hospital diagnosis of schizophrenia (N=94); children who had at least one parent with a psychiatric record of hospitalization for a nonpsychotic disorder (N=84); and children with no parental records of psychiatric hospitalization (N=66). Psychiatric outcomes of the offspring were assessed through psychiatric interviews in 1992 when participants were 31-33 years of age, as well as through a scan of national psychiatric registers completed in May 2007. RESULTS: Children who later developed a schizophrenia spectrum disorder (N=32) displayed significantly higher scores on a scale of coordination deficits compared with those who did not develop a mental illness in this category (N=133). CONCLUSIONS: Results from this study provide further support for the neurodevelopmental hypothesis of schizophrenia and underscore the potential role of cerebellar and/or basal ganglia abnormalities in the etiology and pathophysiology of schizophrenia.},
affiliation = {Department of Psychology, University of Maryland, Baltimore County, Baltimore, MD 21250, USA. schiffma@umbc.edu},
number = {9},
pages = {1041--7},
volume = {166},
year = {2009},
month = {Sep},
language = {eng},
keywords = {Male, Denmark, Adult, Fathers, Female, Humans, Cerebellum, Child, Mothers, Schizophrenia, Psychiatric Status Rating Scales, Child of Impaired Parents, Hospitals: Psychiatric, Schizophrenic Psychology, Neurologic Examination, Hospitalization, Mental Disorders, Motor Skills Disorders, Basal Ganglia},
date-added = {2010-02-05 20:19:44 +0100},
date-modified = {2010-07-29 19:51:28 +0200},
doi = {10.1176/appi.ajp.2009.08091400},
pii = {appi.ajp.2009.08091400},
pmid = {19605535},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5153},
rating = {0}
}

@article{Zheng:2010p10331,
author = {M Zheng},
title = {A Biometric Analysis of Twin Data Using PROC MIXED},
abstract = {This paper showed how biometric analyses of twin family data can be easily programmed using SAS PROC MIXED. Previous research has suggested that the mixed-effects modeling approach mighyt be used to estimate biometric parameters in family and twin data. The current study explored this approach by analyzing the twin models with biometric components based on standard maximum likelihood estimation and standard indices of goodness-of-fit. The practical utility of this approach was examined through the application of these techniques to a simulated twin data set. Results showed that twin pair data can be easily accounted for by the mixed-effects approach and the genetic and non-genetic basis of a phenotypic score can be conveniently estimated by PROC MIXED.},
date-added = {2010-04-02 18:14:39 +0200},
date-modified = {2010-04-02 18:15:02 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Zheng--_A%20Biometric%20Analysis.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10331},
rating = {0}
}

@article{Faust:2010p11566,
author = {Karoline Faust and Pierre Dupont and J{\'e}r{\^o}me Callut and Jacques van Helden},
journal = {Bioinformatics},
title = {Pathway discovery in metabolic networks by subgraph extraction},
abstract = {MOTIVATION: Subgraph extraction is a powerful technique to predict pathways from biological networks and a set of query items (e.g. genes, proteins, compounds, etc.). It can be applied to a variety of different data types, such as gene expression, protein levels, operons or phylogenetic profiles. In this article, we investigate different approaches to extract relevant pathways from metabolic networks. Although these approaches have been adapted to metabolic networks, they are generic enough to be adjusted to other biological networks as well. RESULTS: We comparatively evaluated seven sub-network extraction approaches on 71 known metabolic pathways from Saccharomyces cerevisiae and a metabolic network obtained from MetaCyc. The best performing approach is a novel hybrid strategy, which combines a random walk-based reduction of the graph with a shortest paths-based algorithm, and which recovers the reference pathways with an accuracy of approximately 77%. AVAILABILITY: Most of the presented algorithms are available as part of the network analysis tool set (NeAT). The kWalks method is released under the GPL3 license.},
affiliation = {Laboratoire de Bioinformatique des G{\'e}nomes et des R{\'e}seaux (BiGRe), Universit{\'e} Libre de Bruxelles, Bruxelles, Belgium. kfaust@ulb.ac.be},
number = {9},
pages = {1211--8},
volume = {26},
year = {2010},
month = {May},
language = {eng},
date-added = {2010-05-01 17:37:08 +0200},
date-modified = {2010-05-01 17:37:08 +0200},
doi = {10.1093/bioinformatics/btq105},
pii = {btq105},
pmid = {20228128},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Faust-2010-Bioinformatics_Pathway%20discovery%20in.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11566},
rating = {0}
}

@article{Belkhir:2002p13435,
author = {K Belkhir and V Castric and F Bonhomme},
journal = {Mol Ecol Notes},
title = {IDENTIX, a software to test for relatedness in a population using permutation methods},
abstract = {The computer program IDENTIX estimates relatedness in natural populations using multi- locus genotypic data. Queller {\&} Goodnight's (1989) and Lynch {\&} Ritland's (1999) estimators of pairwise relatedness are implemented, as well as the identity index of Mathieu et al. (1990). Estimates of the confidence intervals around these pairwise values are also pro- vided. The null hypothesis of no relatedness (multilocus genotypes are independent draws from a panmictic population) is tested using a permutation method that compares the observed distribution of the moments of pairwise relatedness coefficients to that expected in unstructured population.},
pages = {611--614},
volume = {2},
year = {2002},
date-added = {2010-07-01 19:42:58 +0200},
date-modified = {2010-07-01 19:44:00 +0200},
doi = {10.1046/j.1471-8278 .2002.00273.x},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Belkhir-2002-Mol%20Ecol%20Notes_IDENTIX%20a%20software.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13435},
rating = {0}
}

@article{Curley:2010p7655,
author = {J P Curley and V Rock and A M Moynihan and P Bateson and E B Keverne and F A Champagne},
journal = {Behav Genet},
title = {Developmental shifts in the behavioral phenotypes of inbred mice: the role of postnatal and juvenile social experiences},
abstract = {The interaction between genotype and environment is an important feature of the process of development. We investigate this interaction by examining the influence of postnatal cross-fostering and post-weaning cross-housing on the behavioral development of 129S and B6 mice. Following cross-fostering, we found significant alterations in the frequency of maternal care as a function of maternal strain and pup type as well as interactions between these variables. In adulthood, we find there are sex-specific and strain-specific alterations in anxiety-like behavior as a function of rearing environment, with males exhibiting more pronounced rearing-induced effects. Mixed-strain housing of weanlings was found to lead to alterations in home-cage social and feeding behavior as well as changes in adult anxiety-like responses of 129S mice. Anxiety-like behavior in B6 mice was altered as a function of the interaction between housing condition and weaning weight. These data illustrate the complex pathways through which early and later social experiences may lead to variations in behavior.},
affiliation = {Department of Psychology, Columbia University, Room 406 Schermerhorn Hall, 1190 Amsterdam Avenue, New York, NY, 10027, USA.},
number = {2},
pages = {220--32},
volume = {40},
year = {2010},
month = {Mar},
language = {eng},
date-added = {2010-03-15 23:24:40 +0100},
date-modified = {2010-07-29 20:09:06 +0200},
doi = {10.1007/s10519-010-9334-4},
pmid = {20130977},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Curley-2010-Behav%20Genet_Developmental%20shifts.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7655},
rating = {0}
}

@article{WU:2009p2754,
author = {XueMei WU and HuaSheng XIAO},
journal = {Sci China, C, Life Sci},
title = {Progress in the detection of human genome structural variations},
abstract = {The emerging of high-throughput and high-resolution genomic technologies led to the detection of submicroscopic variants ranging from 1 kb to 3 Mb in the human genome. These variants include copy number variations (CNVs), inversions, insertions, deletions and other complex rearrangements of DNA sequences. This paper briefly reviews the commonly used technologies to discover both genomic structural variants and their potential influences. Particularly, we highlight the array-based, PCR-based and sequencing-based assays, including array-based comparative genomic hybridization (aCGH), representational oligonucleotide microarray analysis (ROMA), multiplex amplifiable probe hybridization (MAPH), multiplex ligation-dependent probe amplification (MLPA), paired-end mapping (PEM), and next-generation DNA sequencing technologies. Furthermore, we discuss the limitations and challenges of current assays and give advices on how to make the database of genomic variations more reliable.},
affiliation = {Center of Functional Genomics, Key Laboratory of System Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.},
number = {6},
pages = {560--7},
volume = {52},
year = {2009},
month = {Jun},
language = {eng},
keywords = {Genomics, Genetics: Population, Genetic Predisposition to Disease, Humans, Genome: Human, Databases: Genetic, Genetic Variation},
date-added = {2010-01-13 14:21:11 +0100},
date-modified = {2010-01-13 14:21:11 +0100},
doi = {10.1007/s11427-009-0078-4},
pmid = {19557334},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2754},
rating = {0}
}

@article{Dehon:2000p1569,
author = {C Dehon and P Filzmoser and C Croux},
title = {Robust Methods for Canonical Correlation Analysis},
abstract = {Canonical correlation analysis studies associations between two sets of random variables. Its standard computation is based on sample covariance matrices, which are however very sensitive to outlying observations. In this note we intro- duce, discuss and compare four different ways for performing a robust canonical correlation analysis. One method uses robust estimators of the involved covariance matrices, another one uses the signs of the observations, a third approach is based on projection pursuit, and finally an alternating regression algorithm for canonical analysis is proposed.},
year = {2000},
date-added = {2010-01-07 16:56:01 +0100},
date-modified = {2010-01-07 16:56:32 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Dehon-2000-_Robust%20Methods%20for%20C.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1569},
rating = {0}
}

@book{Aday:1996,
author = {LA Aday},
journal = {Book},
title = {Designing and conducting health surveys},
abstract = {The book contains sixteen well-written and carefully reasoned chapters that chart the odyssey of a project from conceptualization to publication. The first four chapters cover issues in the general design of a survey, including the formulation of research objectives and specific questions and the development of an analysis plan. Chapters 5--7 cover methodological decisions regarding choices for data collection and the issues in the design and evaluation of sampling plans. Chapters 8--12 focus on the formulation of questions and the construction of the questionnaire. The next two chapters discuss the management of surveys and the preparation of the data for computer entry. Chapter 15 discusses analytical approaches to survey data, and the final chapter completes the cycle by describing effective ways for preparing research reports. [from Journal of Health Politics, Policy and Law 1990 15(3):685-686; DOI:10.1215/03616878-15-3-685]},
year = {1996},
date-added = {2010-01-03 19:34:18 +0100},
date-modified = {2010-07-29 19:21:41 +0200},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1007},
rating = {0}
}

@article{Uhlig:2006p13507,
author = {T Uhlig and E A Haavardsholm and T K Kvien},
journal = {Rheumatology (Oxford)},
title = {Comparison of the Health Assessment Questionnaire (HAQ) and the modified HAQ (MHAQ) in patients with rheumatoid arthritis},
abstract = {OBJECTIVES: Physical disability in patients with rheumatoid arthritis (RA) is often assessed by questionnaires. We compared the Health Assessment Questionnaire (HAQ) with the modified HAQ (MHAQ) in a cohort of RA patients across various levels of disability, and examined correlations with other measures of physical function. METHODS: Patients with RA (n = 182) completed self-report questionnaires assessing functional capacity. Instruments included the MHAQ and HAQ completed separately, as well as SF-36 and the Arthritis Impact Measurement Scales (AIMS). Scores from unadjusted and adjusted HAQ were compared with MHAQ at various disability levels. RESULTS: A clear ceiling effect with aggregation of normal scores for physical function was observed for MHAQ (23%) and HAQ (12%), but not for SF-36 (4%) or AIMS (5%). The correlations between adjusted/unadjusted HAQ and MHAQ scores were 0.85/0.88. A discrepancy in HAQ and MHAQ scores was observed in patients with high levels of disability, especially when MHAQ was compared with the adjusted final HAQ score. Adjustment of HAQ by aids or help increased the final score by an average of 0.15, and both adjusted and unadjusted HAQ scores were numerically clearly higher (mean 0.45 and 0.30, respectively) than the MHAQ score. CONCLUSION: The present findings indicate that MHAQ and HAQ may be applicable as measures of physical capacity in RA patients, but clinicians and researchers should select the appropriate instrument for the setting, and be aware of differences in scores, especially at different disability levels.},
affiliation = {National Resource Center for Rehabilitation in Rheumatology, Department of Rheumatology, Diakonhjemmet Hospital, Box 23 Vinderen, N-0319 Oslo, Norway. till.uhlig@nrrk.no},
number = {4},
pages = {454--8},
volume = {45},
year = {2006},
month = {Apr},
language = {eng},
keywords = {Male, Humans, Female, Quality of Life, Middle Aged, Arthritis: Rheumatoid, Activities of Daily Living, Disability Evaluation, Questionnaires},
date-added = {2010-07-07 21:02:10 +0200},
date-modified = {2010-07-07 21:02:10 +0200},
doi = {10.1093/rheumatology/kei181},
pii = {kei181},
pmid = {16287925},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Uhlig-2006-Rheumatology%20(Oxford)_Comparison%20of%20the%20He.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13507},
rating = {0}
}

@article{Whitney:1996,
author = {P Whitney and D Budd},
journal = {Discourse Processing},
title = {Think-aloud protocols and the study of comprehension},
abstract = {States that although the think-aloud method (TAM) is being used with increasing frequency in studying text comprehension, some skepticism of its value remains. Discusses assumptions behind TAM, aspects of comprehension it can reveal, and directions for research using TAM. Argues that TAM is a useful technique for tracking changes in the contents of working memory during comprehension.},
pages = {341--351},
volume = {21},
year = {1996},
date-added = {2010-01-03 19:34:17 +0100},
date-modified = {2010-07-29 19:25:26 +0200},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p975},
rating = {0}
}

@article{Marenne:2009p3780,
author = {Ga{\"e}lle Marenne and Cyril Dalmasso and Herv{\'e} Perdry and Emmanuelle G{\'e}nin and Philippe Bro{\"e}t},
journal = {Genet Epidemiol},
title = {Impaired performance of FDR-based strategies in whole-genome association studies when SNPs are excluded prior to the analysis},
abstract = {With recent advances in genomewide microarray technologies, whole-genome association (WGA) studies have aimed at identifying susceptibility genes for complex human diseases using hundreds of thousands of single nucleotide polymorphisms (SNPs) genotyped at the same time. In this context and to take into account multiple testing, false discovery rate (FDR)-based strategies are now used frequently. However, a critical aspect of these strAtegies is that they are applied to a collection or a family of hypotheses and, thus, critically depend on these precise hypotheses. We investigated how modifying the family of hypotheses to be tested affected the performance of FDR-based procedures in WGA studies. We showed that FDR-based procedures performed more poorly when excluding SNPs with high prior probability of being associated. Results of simulation studies mimicking WGA studies according to three scenarios are reported, and show the extent to which SNPs elimination (family contraction) prior to the analysis impairs the performance of FDR-based procedures. To illustrate this situation, we used the data from a recent WGA study on type-1 diabetes (Clayton et al. [2005] Nat. Genet. 37:1243-1246) and report the results obtained when excluding or not SNPs located inside the human leukocyte antigen region. Based on our findings, excluding markers with high prior probability of being associated cannot be recommended for the analysis of WGA data with FDR-based strategies.},
affiliation = {Inserm, UMR-S0535, Villejuif, France.},
number = {1},
pages = {45--53},
volume = {33},
year = {2009},
month = {Jan},
language = {eng},
keywords = {Genome-Wide Association Study, Molecular Epidemiology, Case-Control Studies, HLA Antigens, Models: Genetic, Humans, Polymorphism: Single Nucleotide, Models: Statistical, Diabetes Mellitus: Type 1},
date-added = {2010-01-16 21:00:13 +0100},
date-modified = {2010-01-16 21:00:13 +0100},
doi = {10.1002/gepi.20355},
pmid = {18618761},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3780},
rating = {0}
}

@article{DiazUriarte:2005p12870,
author = {Ram{\'o}n Diaz-Uriarte and Sara Alvarez de Andr{\'e}s},
title = {Variable selection from random forests: application to gene expression data},
abstract = {Random forest is a classification algorithm well suited for microarray data: it shows excellent performance even when most predictive variables are noise, can be used when the number of variables is much larger than the number of observations, and returns measures of variable importance. Thus, it is important to understand the performance of random forest with microarray data and its use for gene selection.
We first show the effects of changes in parameters of random forest on the prediction error. Then we present an approach for gene selection that uses measures of variable importance and error rate, and is targeted towards the selection of small sets of genes. Using simulated and real microarray data, we show that the gene selection procedure yields small sets of genes while preserving predictive accuracy.
We first show the effects of changes in parameters of random forest on the prediction error rate with microarray data. Then we present two approaches for gene selection with random forest: 1) comparing variable importance plots of variable importance from original and permuted data sets; 2) using backwards variable elimination. Using simulated and real microarray data, we show: 1) variable importance plots can be used to recover the full set of genes related to the outcome of interest, without being adversely affected by collinearities; 2) backwards variable elimination yields small sets of genes while preserving predictive accuracy (compared to several state-of-the art algorithms). Thus, both methods are useful for gene selection.
All code is available as an R package, varSelRF, from CRAN http://cran.r-project.org/src/contrib/PACKAGES.html or from the supplementary material page.
Supplementary information: http://ligarto.org/rdiaz/Papers/rfVS/randomForestVarSel.html},
year = {2005},
date-added = {2010-06-24 12:52:57 +0200},
date-modified = {2010-07-29 20:21:27 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Diaz-Uriarte-2005-_Variable%20selection%20f.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12870},
rating = {0}
}

@article{Boes:2009p11989,
author = {Aaron D Boes and Antoine Bechara and Daniel Tranel and Steve W Anderson and Lynn Richman and Peg Nopoulos},
journal = {Soc Cogn Affect Neurosci},
title = {Right ventromedial prefrontal cortex: a neuroanatomical correlate of impulse control in boys},
abstract = {Emerging data on the neural mechanisms of impulse control highlight brain regions involved in emotion and decision making, including the ventromedial prefrontal cortex (vmPFC), anterior cingulate cortex (ACC) and amygdala. Variation in the development of these regions may influence one's propensity for impulsivity and, by extension, one's vulnerability to disorders involving low impulse control (e.g. substance abuse). Here we test the hypothesis that lower impulse control is associated with structural differences in these regions, particularly on the right side, in 61 normal healthy boys aged 7-17. We assessed parent- and teacher-reported behavioral ratings of impulse control (motor impulsivity and non-planning behavior) in relation to vmPFC, ACC and amygdala volume, measured using structural magnetic resonance imaging and FreeSurfer. A regression analysis showed that the right vmPFC was a significant predictor of impulse control ratings. Follow-up tests showed (i) a significant correlation between low impulse control and decreased right vmPFC volume, especially the medial sector of the vmPFC and (ii) significantly lower right vmPFC volume in a subgroup of 20 impulsive boys relative to 20 non-impulsive boys. These results are consistent with the notion that right vmPFC provides a neuroanatomical correlate of the normal variance in impulse control observed in boys.},
affiliation = {Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA. aaron-boes@uiowa.edu},
number = {1},
pages = {1--9},
volume = {4},
year = {2009},
month = {Mar},
language = {eng},
keywords = {Image Processing: Computer-Assisted, Child, Gyrus Cinguli, Functional Laterality, Child Behavior, Regression Analysis, Socioeconomic Factors, Amygdala, Adolescent, Impulse Control Disorders, Prefrontal Cortex, Magnetic Resonance Imaging, Humans, Male, Psychometrics, Neuropsychological Tests},
date-added = {2010-05-23 17:26:07 +0200},
date-modified = {2010-07-29 19:50:15 +0200},
doi = {10.1093/scan/nsn035},
pii = {nsn035},
pmid = {19015086},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11989},
rating = {0}
}

@article{Wind:1973p12051,
author = {Y Wind and P E Green and A K Jain},
journal = {Journal of the Market Research Society},
title = {Higher order factor analysis in the classification of psychographic variables},
number = {4},
pages = {224--232},
volume = {15},
year = {1973},
date-added = {2010-05-24 10:35:41 +0200},
date-modified = {2010-05-24 10:36:45 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Wind-1973-Journal%20of%20the%20Market%20Research%20Society_Higher%20order%20factor.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12051},
rating = {0}
}

@article{Merikangas:2000p9241,
author = {K R Merikangas and S Avenevoli},
journal = {Addict Behav},
title = {Implications of genetic epidemiology for the prevention of substance use disorders},
abstract = {Despite advances in characterizing human genotypes, the complex process through which genes exert their influence limits the application of molecular genetics to human diseases. Substance use disorders are necessarily complicated by gene-environment interaction because exposure to an exogenous substance is required for their development. The methods of genetic epidemiology are specifically designed to identify sources of complexity that impede etiologic findings and prevention efforts. The goal of this paper is to illustrate the application of family study methods to identify risk factors for substance abuse and their implications for prevention. The Yale Family Study is a controlled family study of the comorbidity of substance and psychiatric disorders. The sample consists of 223 probands with substance use and/or an anxiety disorders and community controls, 1218 adult first degree relatives and spouses, and 203 offspring (ages 7-17) followed for 8 years. Results indicated familial aggregation of substance disorders in adults and children, independence of familial aggregation of alcoholism and drug dependence, and specificity of familial clustering of some drugs of abuse. Familial factors are more strongly associated with substance dependence than abuse, with an attributable risk of 55%. Premorbid psychiatric disorders--social phobia and bipolar affective disorder in adults, and depression, anxiety, conduct, and oppositional defiant disorders in children--were strongly associated with the subsequent development of substance dependence (attributable risks ranging from 44 to 86%). A family history of substance abuse and premorbid psychopathology are strongly associated with the development of substance use disorders. Implications for primary and secondary prevention are discussed. As specific genetic vulnerability markers for substance use disorders become identified, application of the tools of genetic epidemiology may be employed to identify specific environmental risk factors that may serve as targets for prevention.},
affiliation = {Yale University School of Medicine, Genetic Epidemiology Research Unit, New Haven, Connecticut 06510, USA. Kathleen.merikangas@yale.edu},
number = {6},
pages = {807--20},
volume = {25},
year = {2000},
month = {Jan},
language = {eng},
keywords = {Causality, Mental Disorders, Alcoholism, Humans, Epidemiologic Studies, Adult, Substance-Related Disorders, Male, Adolescent, Child of Impaired Parents, Child, Risk Assessment, Risk Factors, Follow-Up Studies, Genetic Predisposition to Disease, Female, Connecticut, Comorbidity},
date-added = {2010-03-22 13:39:35 +0100},
date-modified = {2010-07-29 19:12:35 +0200},
pii = {S0306460300001295},
pmid = {11125772},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Merikangas-2000-Addict%20Behav_Implications%20of%20gene.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9241},
rating = {3}
}

@article{Gonzalez:2008p12906,
author = {Jorge Gonz{\'a}lez and Paul De Boeck and Francis Tuerlinckx},
journal = {Psychological Methods},
title = {A double-structure structural equation model for three-mode data},
abstract = {Structural equation models are commonly used to analyze 2-mode data sets, in which a set of objects is measured on a set of variables. The underlying structure within the object mode is evaluated using latent variables, which are measured by indicators coming from the variable mode. Additionally, when the objects are measured under different conditions, 3-mode data arise, and with this, the simultaneous study of the correlational structure of 2 modes may be of interest. In this article the authors present a model with a simultaneous latent structure for 2 of the 3 modes of such a data set. They present an empirical illustration of the method using a 3-mode data set (person by situation by response) exploring the structure of anger and irritation across different interpersonal situations as well as across persons.},
affiliation = {Department of Psychology, K. U. Leuven, Leuven, Belgium. jagonzal@uc.cl},
number = {4},
pages = {337--53},
volume = {13},
year = {2008},
month = {Dec},
language = {eng},
keywords = {Frustration, Models: Statistical, Humans, Anger, Irritable Mood, Principal Component Analysis, Data Collection, Psychology: Experimental, Psychometrics, Chi-Square Distribution, Individuality, Social Environment},
date-added = {2010-06-24 17:29:21 +0200},
date-modified = {2010-07-29 20:46:12 +0200},
doi = {10.1037/a0013269},
pii = {2008-17368-003},
pmid = {19071998},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Gonz%C3%A1lez-2008-Psychological%20Methods_A%20double-structure%20s.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12906},
rating = {3}
}

@article{Cachia:2008p5174,
author = {A Cachia},
journal = {Neuronale},
title = {Anomalies du cortex c{\'e}r{\'e}bral dans la schizophr{\'e}nie},
pages = {6--9},
volume = {38},
year = {2008},
date-added = {2010-02-07 12:39:57 +0100},
date-modified = {2010-02-07 12:41:26 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Cachia-2008-Neuronale_Anomalies%20du%20cortex.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5174},
rating = {0}
}

@article{Guo:2006p3688,
author = {F Guo},
journal = {GMAC {\textregistered} Research Reports},
title = {Expected Classification Accuracy Using Latent Distributions},
year = {2006},
date-added = {2010-01-16 20:28:05 +0100},
date-modified = {2010-01-16 20:28:39 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Guo-2006-GMAC%20%C2%AE%20Research%20Reports_Expected%20Classificat.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3688},
rating = {0}
}

@article{Honkela:2007p12863,
author = {A Honkela and J Sepp{\"a} and E Alhoniemi},
journal = {European Symposium on Artificial Neural Networks Proceedings},
title = {Agglomerative Independent Variable Group Analysis},
abstract = {Independent Variable Group Analysis (IVGA) is a principle for grouping dependent variables together while keeping mutually inde- pendent or weakly dependent variables in separate groups. In this paper an agglomerative method for learning a hierarchy of IVGA groupings is presented. The method resembles hierarchical clustering, but the distance measure is based on a model-based approximation of mutual information between groups of variables. The approach also allows determining opti- mal cutoff points for the hierarchy. The method is demonstrated to find sensible groupings of variables that ease construction of a predictive model.},
year = {2007},
date-added = {2010-06-24 12:44:25 +0200},
date-modified = {2010-06-24 12:45:18 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Honkela-2007-European%20Symposium%20on%20Artificial%20Neural%20Networks%20Proceedings_Agglomerative%20Indepe.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12863},
rating = {0}
}

@misc{Hochheiser:1999,
author = {H Hochheiser and B Shneiderman},
journal = {Miscellaneous},
title = {Performance Benefits of Simultaneous over Sequential Menus As Task Complexity Increases},
year = {1999},
date-added = {2010-01-10 11:33:19 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hochheiser-1999-Miscellaneous_Performance%20Benefits.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2016},
rating = {0}
}

@article{Lenth:2010p12771,
author = {R V Lenth},
title = {Two sample-size practices that i don't recommend},
date-added = {2010-06-18 20:35:54 +0200},
date-modified = {2010-06-18 20:36:57 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Lenth--_Two%20sample-size%20prac.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12771},
rating = {0}
}

@article{Brookes:2005p9731,
author = {Keeley-Joanne Brookes and Xiaohui Xu and Chih-Ken Chen and Yu-Shu Huang and Yu-Yu Wu and Philip Asherson},
journal = {BMC Med Genet},
title = {No evidence for the association of DRD4 with ADHD in a Taiwanese population within-family study},
abstract = {BACKGROUND: Attention Deficit Hyperactivity Disorder (ADHD) is a prevalent and highly heritable childhood disorder. The dopamine D4 receptor (DRD4) gene has shown a genetic association with ADHD in Caucasian populations with meta-analysis indicating a small but significant effect across datasets. It remains uncertain whether this association can be generalised to non-Caucasian ethnic groups. Here we investigate two markers within the DRD4 gene in a Taiwanese population, the exon 3 variable number tandem repeat (VNTR) and a 5' 120 base-pair duplication. METHODS: Within-family transmission disequilibrium tests of association of the 5' 120 base-pair duplication, and exon 3 VNTR in a Taiwanese population. RESULTS: No evidence of association of ADHD with either polymorphism in this population was observed. CONCLUSION: The DRD4 gene markers investigated were not found to be associated with ADHD in this Taiwanese sample. Further work in Taiwanese and other Asian populations will therefore be required to establish whether the reports of association of DRD4 genetic variants in Caucasian samples can be generalised to Asian populations.},
affiliation = {MRC Social Genetic Developmental Psychiatry Centre, Institute of Psychiatry, London, UK. k.brookes@iop.kcl.ac.u},
pages = {31},
volume = {6},
year = {2005},
month = {Sep},
language = {eng},
keywords = {Child, Genetic Predisposition to Disease, Family Health, Adolescent, Taiwan, Polymorphism: Genetic, Gene Frequency, Attention Deficit Disorder with Hyperactivity, Receptors: Dopamine D4, Humans, Child: Preschool, Receptors: Dopamine D2, Tandem Repeat Sequences},
date-added = {2010-03-25 15:15:08 +0100},
date-modified = {2010-03-25 15:15:08 +0100},
doi = {10.1186/1471-2350-6-31},
pii = {1471-2350-6-31},
pmid = {16143039},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Brookes-2005-BMC%20Med%20Genet_No%20evidence%20for%20the.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9731},
rating = {0}
}

@article{Moon:2006p4070,
author = {Hojin Moon and Hongshik Ahn and Ralph L Kodell and Chien-Ju Lin and Songjoon Baek and James J Chen},
journal = {Genome Biol},
title = {Classification methods for the development of genomic signatures from high-dimensional data},
abstract = {Personalized medicine is defined by the use of genomic signatures of patients to assign effective therapies. We present Classification by Ensembles from Random Partitions (CERP) for class prediction and apply CERP to genomic data on leukemia patients and to genomic data with several clinical variables on breast cancer patients. CERP performs consistently well compared to the other classification algorithms. The predictive accuracy can be improved by adding some relevant clinical/histopathological measurements to the genomic data.},
affiliation = {Division of Biometry and Risk Assessment, National Center for Toxicological Research, FDA, NCTR Road, Jefferson, AR 72079, USA. hojin.moon@fda.hhs.gov},
number = {12},
pages = {R121},
volume = {7},
year = {2006},
month = {Jan},
language = {eng},
keywords = {Breast Neoplasms, Prognosis, Genome: Human, Humans, Leukemia, Algorithms},
date-added = {2010-01-19 15:50:03 +0100},
date-modified = {2010-07-29 19:27:21 +0200},
doi = {10.1186/gb-2006-7-12-r121},
pii = {gb-2006-7-12-r121},
pmid = {17181863},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Moon-2006-Genome%20Biol_Classification%20metho.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4070},
rating = {0}
}

@article{Bize:2007p7284,
author = {Rapha{\"e}l Bize and Jeffrey A Johnson and Ronald C Plotnikoff},
journal = {Prev Med},
title = {Physical activity level and health-related quality of life in the general adult population: a systematic review},
abstract = {OBJECTIVE: Little is known regarding health-related quality of life and its relation with physical activity level in the general population. Our primary objective was to systematically review data examining this relationship. METHODS: We systematically searched MEDLINE, EMBASE, CINAHL, and PsycINFO for health-related quality of life and physical activity related keywords in titles, abstracts, or indexing fields. RESULTS: From 1426 retrieved references, 55 citations were judged to require further evaluation. Fourteen studies were retained for data extraction and analysis; seven were cross-sectional studies, two were cohort studies, four were randomized controlled trials and one used a combined cross sectional and longitudinal design. Thirteen different methods of physical activity assessment were used. Most health-related quality of life instruments related to the Medical Outcome Study SF-36 questionnaire. Cross-sectional studies showed a consistently positive association between self-reported physical activity and health-related quality of life. The largest cross-sectional study reported an adjusted odds ratio of "having 14 or more unhealthy days" during the previous month to be 0.40 (95% Confidence Interval 0.36-0.45) for those meeting recommended levels of physical activity compared to inactive subjects. Cohort studies and randomized controlled trials tended to show a positive effect of physical activity on health-related quality of life, but similar to the cross-sectional studies, had methodological limitations. CONCLUSION: Cross-sectional data showed a consistently positive association between physical activity level and health-related quality of life. Limited evidence from randomized controlled trials and cohort studies precludes a definitive statement about the nature of this association.},
affiliation = {Centre for Health Promotion Studies, School of Public Health, University of Alberta, Edmonton, Canada. raphael.bize@hospvd.ch},
number = {6},
pages = {401--15},
volume = {45},
year = {2007},
month = {Dec},
language = {eng},
keywords = {Health Status Indicators, Statistics as Topic, Cross-Sectional Studies, Cohort Studies, Randomized Controlled Trials as Topic, Adult, Humans, Longitudinal Studies, Quality of Life, Exercise},
date-added = {2010-03-10 20:15:33 +0100},
date-modified = {2010-07-29 19:44:46 +0200},
doi = {10.1016/j.ypmed.2007.07.017},
pii = {S0091-7435(07)00302-7},
pmid = {17707498},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bize-2007-Prev%20Med_Physical%20activity%20le.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7284},
rating = {0}
}

@article{Durinck:2009p1749,
author = {Steffen Durinck and James Bullard and Paul T Spellman and Sandrine Dudoit},
journal = {BMC Bioinformatics},
title = {GenomeGraphs: integrated genomic data visualization with R},
abstract = {BACKGROUND: Biological studies involve a growing number of distinct high-throughput experiments to characterize samples of interest. There is a lack of methods to visualize these different genomic datasets in a versatile manner. In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses. RESULTS: We developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets. GenomeGraphs uses the biomaRt package to perform on-line annotation queries to Ensembl and translates these to gene/transcript structures in viewports of the grid graphics package. This allows genomic annotation to be plotted together with experimental data. GenomeGraphs can also be used to plot custom annotation tracks in combination with different experimental data types together in one plot using the same genomic coordinate system. CONCLUSION: GenomeGraphs is a flexible and extensible software package which can be used to visualize a multitude of genomic datasets within the statistical programming environment R.},
affiliation = {Life Sciences Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA. steffen@stat.berkeley.edu},
pages = {2},
volume = {10},
year = {2009},
month = {Jan},
language = {eng},
keywords = {Algorithms, Transcription: Genetic, Data Interpretation: Statistical, Genome, Computational Biology, Protein Isoforms, Programming Languages, Models: Statistical, Genomics, Computer Graphics, Humans, User-Computer Interface, Software, Exons},
date-added = {2010-01-09 20:50:55 +0100},
date-modified = {2010-01-09 20:50:57 +0100},
doi = {10.1186/1471-2105-10-2},
pii = {1471-2105-10-2},
pmid = {19123956},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Durinck-2009-BMC%20Bioinformatics_GenomeGraphs%20integr.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1749},
rating = {3}
}

@article{Dray:2003,
author = {S Dray and D Chessel and J Thioulouse},
journal = {Ecology},
title = {Co-inertia analysis and the linking of ecological data tables},
number = {11},
pages = {3078--3089},
volume = {84},
year = {2003},
date-added = {2010-01-10 11:33:20 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Dray-2003-Ecology_Co-inertia%20analysis.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2118},
rating = {0}
}

@article{Resino:2010p7413,
author = {S Resino and D Micheloud and P Miralles and J M Bell{\'o}n and A Vargas and P Catal{\'a}n and E Alvarez and J Cos{\'\i}n and R Lorente and J C L{\'o}pez and M A Mu{\~n}oz-Fern{\'a}ndez and J Berenguer},
journal = {HIV Med},
title = {Diagnosis of advanced fibrosis in HIV and hepatitis C virus-coinfected patients via a new noninvasive index: the HGM-3 index},
abstract = {BACKGROUND: Noninvasive tests are increasingly being used for the assessment of liver fibrosis. We aimed to develop a serum index for the identification of advanced fibrosis (F>or=3) in HIV/hepatitis C virus (HCV)-coinfected patients. METHODS: We carried out a cross-sectional study on a group of 195 patients comprised of an estimation group (EG; n=127) and a validation group (VG; n=68) who all underwent liver biopsy and had not received previous interferon therapy. Liver fibrosis was estimated using the METAVIR score. We developed a new serum index (HGM-3) dependent on levels of platelets, alkaline phosphatase, hepatic growth factor, tissue inhibitor of metalloproteinase-1 and hyaluronic acid. RESULTS: In the EG, the area under the receiver operating characteristic curve (AUC-ROC) of HGM-3 for identification of F>or=3 was 0.939 [95% confidence interval (CI) 0.899, 0.979] which was significantly higher than the AUC-ROC of the HGM-2, FIB-4, aspartate aminotransferase to platelet ratio (APRI) and Forns' indexes. With HGM-3 <0.135 for F<3, 57 patients were correctly identified and two patients were misclassified. We found the presence of F<3 with 96.6% certainty. The negative likelihood ratio (LR) was <0.1 and the diagnostic odds ratio (DOR) was >40. With HGM-3 >0.570 in the EG for F>or=3, 31 patients were correctly identified, and five patients were misclassified. We found the presence of F>or=3 with 86.1% certainty. The positive LR was >12 and the DOR was >40. For the VG, the diagnostic accuracy values were similar to the values for the EG. CONCLUSIONS: HGM-3 appears to be an accurate noninvasive method for the diagnosis of bridging fibrosis and cirrhosis in HIV/HCV-coinfected patients.},
affiliation = {Laboratory of Molecular Epidemiology of Infectious Diseases, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain. sresino@isciii.es},
number = {1},
pages = {64--73},
volume = {11},
year = {2010},
month = {Jan},
language = {eng},
date-added = {2010-03-10 20:37:38 +0100},
date-modified = {2010-03-10 20:37:39 +0100},
doi = {10.1111/j.1468-1293.2009.00745.x},
pii = {HIV745},
pmid = {19686437},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7413},
rating = {0}
}

@article{Schmack:2008p5848,
author = {Katharina Schmack and Florian Schlagenhauf and Philipp Sterzer and Jana Wrase and Anne Beck and Theresa Dembler and Peter Kalus and Imke Puls and Thomas Sander and Andreas Heinz and J{\"u}rgen Gallinat},
journal = {Neuroimage},
title = {Catechol-O-methyltransferase val158met genotype influences neural processing of reward anticipation},
abstract = {Reward processing depends critically on dopaminergic neurotransmission in the ventral striatum. The common polymorphism val(158)met of catechol-O-methyltransferase (COMT) accounts for significant interindividual variations in dopamine (DA) degradation, although the direct effect of COMT on striatal DA might be limited. Using fMRI we assessed the influence of COMT val(158)met genotype on brain activations elicited by the anticipation of monetary gains and losses in forty-four healthy volunteers. We found that the met(158) allele, which is presumably linked to higher synaptic DA levels, was associated with higher responses in ventral striatum to loss incentives. There was a linear relationship between the number of met(158) alleles and ventral striatal activity. Furthermore, we observed a similar gene-dose effect in the anterior temporal cortex, a region that has been linked to the coupling of sensory information with emotional contents. Temporal cortex also showed enhanced connectivity to the ventral striatum during the processing of incentive stimuli. Increased ventral striatal reactivity to loss incentives related to the met(158) allele might contribute to the observed association of the met(158) allele to higher loss aversion behaviour. Current evidence and our results are compatible with an interpretation that construes this effect of COMT genotype on striatal reactivity as a result of a cortico-striatal interaction.},
affiliation = {Department of Psychiatry, Charit{\'e} University Medicine, Charit{\'e}platz 1, 10117 Berlin, Germany. katharina.schmack@charite.de},
note = {genim},
number = {4},
pages = {1631--8},
volume = {42},
year = {2008},
month = {Oct},
language = {eng},
keywords = {Cerebral Cortex, Evoked Potentials, Magnetic Resonance Imaging, Intuition, Genotype, Corpus Striatum, Female, Catechol O-Methyltransferase, Adult, Humans, Attention, Reward, Male},
date-added = {2010-02-17 10:19:46 +0100},
date-modified = {2010-02-17 10:31:51 +0100},
doi = {10.1016/j.neuroimage.2008.06.019},
pii = {S1053-8119(08)00758-1},
pmid = {18634888},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Schmack-2008-Neuroimage_Catechol-O-methyltra.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5848},
rating = {0}
}

@article{Polderman:2006p1337,
author = {Tinca J C Polderman and M Florencia Gosso and Danielle Posthuma and Toos C E M Van Beijsterveldt and Peter Heutink and Frank C Verhulst and Dorret I Boomsma},
journal = {Acta Neurol Belg},
title = {A longitudinal twin study on IQ, executive functioning, and attention problems during childhood and early adolescence},
abstract = {Variation in human behavior may be caused by differences in genotype and by non-genetic differences ("environment") between individuals. The relative contributions of genotype (G) and environment (E) to phenotypic variation can be assessed with the classical twin design. We illustrate this approach with longitudinal data collected in 5 and 12-year-old Dutch twins. At age 5 data on cognitive abilities as assessed with a standard intelligence test (IQ), working memory, selective and sustained attention, and attention problems were collected in 237 twin pairs. Seven years later, 172 twin pairs participated again when they were 12 years old and underwent a similar protocol. Results showed that variation in all phenotypes was influenced by genetic factors. For IQ the heritability estimates increased from 30% at age 5, to 80% at age 12. For executive functioning performance genetic factors accounted for around 50% of the variance at both ages. Attention problems showed high heritabilities (above 60%) at both ages, for maternal and teacher ratings. Longitudinal analyses revealed that executive functioning during childhood was weakly correlated with IQ scores at age 12. Attention problems during childhood, as rated by the mother and the teacher were stronger predictors (r = -0.28 and -0.36, respectively). This association could be attributed to a partly overlapping set of genes influencing attention problems at age 5 and IQ at age 12. IQ performance at age 5 was the best predictor of IQ at age 12. IQ at both ages was influenced by the same genes, whose influence was amplified during development.},
affiliation = {Department of Biological Psychology, Vrije Universiteit Amsterdam, The Netherlands. jc.polderman@psy.vu.nl},
number = {4},
pages = {191--207},
volume = {106},
year = {2006},
month = {Dec},
language = {eng},
keywords = {Child, Developmental Disabilities, Aging, Phenotype, Male, Cognition, Predictive Value of Tests, Child: Preschool, Thinking, Humans, Models: Statistical, Longitudinal Studies, Intelligence, Genotype, Female, Attention Deficit Disorder with Hyperactivity, Genetic Predisposition to Disease, Intelligence Tests, Netherlands, Environment, Inheritance Patterns},
date-added = {2010-01-07 11:39:44 +0100},
date-modified = {2010-01-07 11:39:44 +0100},
pmid = {17323837},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1337},
rating = {0}
}

@article{Falissard:2003,
author = {B Falissard and M Lukasiewicz and E Corruble},
journal = {Journal of Clinical Epidemiology},
title = {The MDP75. A new approach in the determination of the minimal clinically meaningful difference in a scale or a questionnaire},
pages = {618--621},
volume = {56},
year = {2003},
date-added = {2010-01-10 11:33:17 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Falissard-2003-Journal%20of%20Clinical%20Epidemiology_The%20MDP75.%20A%20new%20app.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1892},
rating = {0}
}

@article{Blomeyer:2008p7561,
author = {Dorothea Blomeyer and Jens Treutlein and G{\"u}nter Esser and Martin H Schmidt and Gunter Schumann and Manfred Laucht},
journal = {Biol Psychiatry},
title = {Interaction between CRHR1 gene and stressful life events predicts adolescent heavy alcohol use},
abstract = {BACKGROUND: Recent animal research suggests that alterations in the corticotropin releasing hormone receptor 1 (CRHR1) may lead to heavy alcohol use following repeated stress. The aim of this study was to examine interactions between two haplotype-tagging single nucleotide polymorphisms (SNPs) covering the CRHR1 gene and adverse life events on heavy drinking in adolescents. METHODS: Data were available from the Mannheim Study of Children at Risk, an ongoing cohort study of the long-term outcome of early risk factors followed since birth. At age 15 years, 280 participants (135 males, 145 females) completed a self-report questionnaire measuring alcohol use and were genotyped for two SNPs (rs242938, rs1876831) of CRHR1. Assessment of negative life events over the past three years was obtained by a standardized interview with the parents. RESULTS: Adolescents homozygous for the C allele of rs1876831 drank higher maximum amounts of alcohol per occasion and had greater lifetime rates of heavy drinking in relation to negative life events than individuals carrying the T allele. No gene x environment interactions were found for regular drinking and between rs242938 and stressful life events. CONCLUSIONS: These findings provide first evidence in humans that the CRHR1 gene interacts with exposure to stressful life events to predict heavy alcohol use in adolescents.},
affiliation = {Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Mannheim, Germany.},
number = {2},
pages = {146--51},
volume = {63},
year = {2008},
month = {Jan},
language = {eng},
keywords = {Genotype, Longitudinal Studies, Retrospective Studies, Receptors: Corticotropin-Releasing Hormone, Male, Predictive Value of Tests, Alcohol Drinking, Life Change Events, Female, Risk, Polymorphism: Single Nucleotide, Adolescent, Stress: Psychological, Humans},
date-added = {2010-03-14 10:55:52 +0100},
date-modified = {2010-03-14 10:55:56 +0100},
doi = {10.1016/j.biopsych.2007.04.026},
pii = {S0006-3223(07)00375-7},
pmid = {17597588},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Blomeyer-2008-Biol%20Psychiatry_Interaction%20between.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7561},
rating = {3}
}

@article{Thomas:2009p14095,
author = {Jennifer J Thomas and Lenny R Vartanian and Kelly D Brownell},
journal = {Psychological Bulletin},
title = {The relationship between eating disorder not otherwise specified (EDNOS) and officially recognized eating disorders: meta-analysis and implications for DSM},
abstract = {Eating disorder not otherwise specified (EDNOS) is the most prevalent eating disorder (ED) diagnosis. In this meta-analysis, the authors aimed to inform Diagnostic and Statistical Manual of Mental Disorders revisions by comparing the psychopathology of EDNOS with that of the officially recognized EDs: anorexia nervosa (AN), bulimia nervosa (BN), and binge eating disorder (BED). A comprehensive literature search identified 125 eligible studies (published and unpublished) appearing in the literature from 1987 to 2007. Random effects analyses indicated that whereas EDNOS did not differ significantly from AN and BED on eating pathology or general psychopathology, BN exhibited greater eating and general psychopathology than EDNOS. Moderator analyses indicated that EDNOS groups who met all diagnostic criteria for AN except for amenorrhea did not differ significantly from full syndrome cases. Similarly, EDNOS groups who met all criteria for BN or BED except for binge frequency did not differ significantly from full syndrome cases. Results suggest that EDNOS represents a set of disorders associated with substantial psychological and physiological morbidity. Although certain EDNOS subtypes could be incorporated into existing Diagnostic and Statistical Manual of Mental Disorders (4th ed.; American Psychiatric Association, 1994) categories, others-such as purging disorder and non-fat-phobic AN-may be best conceptualized as distinct syndromes. (PsycINFO Database Record (c) 2009 APA, all rights reserved).},
affiliation = {Department of Psychology, Yale University, USA. jjthomas@partners.org},
number = {3},
pages = {407--33},
volume = {135},
year = {2009},
month = {May},
language = {eng},
keywords = {Eating Disorders, Anorexia Nervosa, Diagnostic and Statistical Manual of Mental Disorders, Bulimia Nervosa, Humans},
date-added = {2010-08-18 11:16:14 +0200},
date-modified = {2010-08-18 11:16:14 +0200},
doi = {10.1037/a0015326},
pii = {2009-05290-006},
pmid = {19379023},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Thomas-2009-Psychological%20Bulletin_The%20relationship%20bet.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p14095},
rating = {0}
}

@article{Revelle:2008p11673,
author = {W Revelle and J Wilt and A Rosenthal},
title = {Individual Differences in Cognition: New methods for examining the Personality-Cognition link},
abstract = {Traditional studies of cognitive ability have examined the component pro- cesses and factor structure of ability tests. Theoretical and empirical studies of non-cognitive dimensions of personality have examined how individual differences in personality interact with situational stressors to affect efficient cognitive performance. Previously reported results have emphasized moti- vational direction and intensity effects upon cognitive performance. Using a new technique of ``Synthetic Aperture Personality Assessment'' (SAPA) which takes advantage of the large subject populations available on the in- ternet, it is possible to study how basic personality dimensions relate to dimensions of cognitive ability. The SAPA procedure presents to partici- pants small subsets of items sampled from large pools of publicly available personality and ability items. Although each participant is given only a small subset of items, with the recognition that subjects (> 65, 000) are randomly sampled and items are missing at random, it is possible to synthesize large (> 350x350) interitem correlation matrices. Individual differences in com- plex pattern recognition, spatial reasoning, and (self reported) standardized ability tests are moderately associated with Big 5 measures. We present the SAPA procedure in some detail and review findings relating dimensions of personality, ability, and interest.},
year = {2008},
date-added = {2010-05-14 21:12:20 +0200},
date-modified = {2010-05-14 21:13:04 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Revelle-2008-_Individual%20Differenc.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11673},
rating = {0}
}

@article{South:2008p9131,
author = {Susan C South and Robert F Krueger and Wendy Johnson and William G Iacono},
journal = {J Pers Soc Psychol},
title = {Adolescent personality moderates genetic and environmental influences on relationships with parents},
abstract = {In contrast with early theories of socialization that emphasized the role of parents in shaping their children's personalities, recent empirical evidence suggests an evocative relationship between adolescent personality traits and the quality of the parent-adolescent relationship. Research using behavior genetic methods suggests that the association between personality and parenting is genetically mediated, such that the genetic effects on adolescent personality traits overlap with the genetic effects on parenting behavior. In the current study, the authors examined whether the etiology of this relationship might change depending on the adolescent's personality. Biometrical moderation models were used to test for gene- environment interaction and correlation between personality traits and measures of conflict, regard, and involvement with parents in a sample of 2,452 adolescents (M age = 17.79 years). They found significant moderation of both positive and negative qualities of the parent-adolescent relationship, such that the genetic and environmental variance in relationship quality varied as functions of the adolescent's levels of personality. These findings support the importance of adolescent personality in the development of the quality of the parent-adolescent relationship.},
affiliation = {Department of Psychology, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA. south088@umn.edu},
number = {5},
pages = {899--912},
volume = {94},
year = {2008},
month = {May},
language = {eng},
keywords = {Phenotype, Social Environment, Personality, Male, Adolescent, Parent-Child Relations, Personality Assessment, Parenting, Twins, Socialization, Female, Humans, Models: Statistical},
date-added = {2010-03-22 13:27:29 +0100},
date-modified = {2010-07-29 19:35:33 +0200},
doi = {10.1037/0022-3514.94.5.899},
pii = {2008-04567-011},
pmid = {18444746},
local-url = {file://localhost/Users/chl/Dropbox/Papers/South-2008-J%20Pers%20Soc%20Psychol_Adolescent%20personali.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9131},
rating = {5}
}

@article{Zhang:2009p419,
author = {Zhongyang Zhang and Kenneth Lange and Chiara Sabatti},
journal = {arXiv},
title = {Reconstructing DNA Copy Number by Penalized Estimation and Imputation},
abstract = { Recent advances in genomics have underscored the surprising ubiquity of DNA copy number variation (CNV). Fortunately, modern genotyping platforms also detect CNVs with fairly high reliability. Hidden Markov models and algorithms have played a dominant role in the interpretation of CNV data. Here we explore CNV reconstruction via estimation with a fused-lasso penalty as suggested by Tibshirani and Wang (2008). We mount a fresh attack on this difficult optimization problem by: (a) changing the penalty terms slightly by substituting a smooth approximation to the absolute value function, (b) designing and implementing a new MM (majorization-minimization) algorithm, and (c) applying a fast version of Newton's method to jointly up-date all model parameters. Together these changes enable us to minimize the fused-lasso criterion in a highly effective way.  We also reframe the reconstruction problem in terms of imputation via discrete optimization. This approach is easier and more accurate than parameter estimation because it relies on the fact that only a handful of possible copy number states exist at each SNP. The dynamic programming framework has the added bonus of exploiting information that the current fused-lasso approach ignores. The accuracy of our imputations is comparable to that of hidden Markov models at a substantially lower computational cost. },
note = {32 pages, 5 figures, 10 tables},
eprint = {0906.2234v2},
volume = {stat.ME},
year = {2009},
month = {Jan},
keywords = {q-bio.GN, stat.ME, stat.AP},
date-added = {2010-01-03 12:13:05 +0100},
date-modified = {2010-01-03 12:13:05 +0100},
pmid = {0906.2234v2},
URL = {http://arxiv.org/abs/0906.2234v2},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Zhang-2009-arXiv_Reconstructing%20DNA%20C.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p419},
rating = {0}
}

@article{Scholz:2002p12049,
author = {U Scholz and B G Dona and S Sud and R Schwarzer},
title = {Is general self-efficacy a universal construct? Psychometric findings from 25 countries},
year = {2002},
date-added = {2010-05-24 10:32:02 +0200},
date-modified = {2010-05-24 10:33:08 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Scholz-2002-_Is%20general%20self-effi.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12049},
rating = {0}
}

@article{Bouchard:2001p12677,
author = {T J Bouchard and J C Loehlin},
journal = {Behav Genet},
title = {Genes, evolution, and personality},
abstract = {There is abundant evidence, some of it reviewed in this paper, that personality traits are substantially influenced by the genes. Much remains to be understood about how and why this is the case. We argue that placing the behavior genetics of personality in the context of epidemiology, evolutionary psychology, and neighboring psychological domains such as interests and attitudes should help lead to new insights. We suggest that important methodological advances, such as measuring traits from multiple viewpoints, using large samples, and analyzing data by modern multivariate techniques, have already led to major changes in our view of such perennial puzzles as the role of "unshared environment" in personality. In the long run, but not yet, approaches via molecular genetics and brain physiology may also make decisive contributions to understanding the heritability of personality traits. We conclude that the behavior genetics of personality is alive and flourishing but that there remains ample scope for new growth and that much social science research is seriously compromised if it does not incorporate genetic variation in its explanatory models.},
affiliation = {Department of Psychology. University of Minnesota, Minneapolis 55455, USA. bouch001@tc.umn.edu},
number = {3},
pages = {243--73},
volume = {31},
year = {2001},
month = {May},
language = {eng},
keywords = {Twin Studies as Topic, Humans, Animals, Individuality, Personality, Genetics: Behavioral, Evolution},
date-added = {2010-06-15 22:40:50 +0200},
date-modified = {2010-07-29 20:09:06 +0200},
pmid = {11699599},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bouchard-2001-Behav%20Genet_Genes%20evolution%20an.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12677},
rating = {5}
}

@article{Emons:2002p2710,
author = {W H M Emons and R R Meijer and K Sijtsma},
journal = {Applied Psychological Measurement},
title = {Comparing Simulated and Theoretical Sampling Distributions of the U3 Person-Fit Statistic},
abstract = {The accuracy with which the theoretical sampling distribution of van der Flier's person-fit statistic U3 approaches the empirical U3 sampling distribution is affected by the item discrimination. A simulation study showed that for tests with a moderate or a strong mean item discrimination, the Type I error rates were either too high or too low to be used in practice. It was concluded that the use of standard normal deviates for the standardized version of the U 3 statistic may be problematic. Nevertheless, the U 3 statistic is suitable for evaluating the relative likelihood of item score patterns, for example, if one wishes to select a fixed percentage of the most improbable patterns.},
number = {1},
pages = {88--108},
volume = {26},
year = {2002},
date-added = {2010-01-13 10:27:53 +0100},
date-modified = {2010-07-29 19:16:52 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Emons-2002-Applied%20Psychological%20Measurement_Comparing%20Simulated.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2710},
rating = {0}
}

@article{Munafo:2003p9054,
author = {M R Munaf{\`o} and T G Clark and L R Moore and E Payne and R Walton and J Flint},
journal = {Mol Psychiatry},
title = {Genetic polymorphisms and personality in healthy adults: a systematic review and meta-analysis},
abstract = {A meta-analysis was conducted on studies reporting data on associations between candidate genes and human personality. Studies reporting data for psychiatric populations (including organic disease and substance abuse) were excluded. A total of 46 studies contributed to the analysis. Pooled data using a fixed-effects model suggested significant associations between the 5HTT LPR, DRD4 c>t, DRD4 length, DRD2 A1/A2, DRD3 A1/A2 polymorphisms and personality traits. A multivariate analysis using a mixed-effects model and including age, sex and predominant ethnicity as covariates was applied to the analyses of 5HTT LPR and DRD4 length polymorphism data. Only the association between the 5HTT LPR polymorphism and avoidance traits remained significant (P=0.038). However, sensitivity analyses excluding data from studies reporting allele frequencies not in Hardy-Weinberg equilibrium and unpublished data resulted in this association no longer being significant. Implications for the design of future association studies of human personality are discussed, including the likely sample sizes that will be required to achieve sufficient power and the potential role of moderating variables such as sex.},
affiliation = {Cancer Research UK GPRG, Institute of Health Sciences, University of Oxford, Oxford, UK. marcus.munafo@dphpc.ox.ac.uk},
number = {5},
pages = {471--84},
volume = {8},
year = {2003},
month = {May},
language = {eng},
keywords = {Personality, Multivariate Analysis, Adult, Sensitivity and Specificity, Serotonin, Genetic Heterogeneity, Dopamine, Polymorphism: Genetic, Humans},
date-added = {2010-03-22 13:17:23 +0100},
date-modified = {2010-03-22 13:17:23 +0100},
doi = {10.1038/sj.mp.4001326},
pii = {4001326},
pmid = {12808427},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Munaf%C3%B2-2003-Mol%20Psychiatry_Genetic%20polymorphism.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9054},
rating = {0}
}

@article{Greene:2008p5832,
author = {Ciara M Greene and Wouter Braet and Katherine A Johnson and Mark A Bellgrove},
journal = {Biol Psychol},
title = {Imaging the genetics of executive function},
abstract = {Recent advances in neuroimaging technologies have allowed ever more detailed studies of the human brain. The combination of neuroimaging techniques with genetics may provide a more sensitive measure of the influence of genetic variants on cognitive function than behavioural measures alone. Here we present a review of functional magnetic resonance imaging (fMRI) studies of genetic links to executive functions, focusing on sustained attention, working memory and response inhibition. In addition to studies in the normal population, we also address findings from three clinical populations: schizophrenia, ADHD and autism spectrum disorders. While the findings in the populations studied do not always converge, they all point to the usefulness of neuroimaging techniques such as fMRI as potential endophenotypes for parsing the genetic aetiology of executive function.},
affiliation = {Trinity College Institute of Neuroscience, Trinity College Dublin, Ireland. cmgreene@gmail.com},
number = {1},
pages = {30--42},
volume = {79},
year = {2008},
month = {Sep},
language = {eng},
keywords = {Psychomotor Performance, Magnetic Resonance Imaging, Molecular Biology, Cognition, Attention Deficit Disorder with Hyperactivity, Brain, Schizophrenic Psychology, Inhibition (Psychology), Phenotype, Autistic Disorder, Schizophrenia, Memory, Mental Disorders, Humans},
date-added = {2010-02-17 10:10:49 +0100},
date-modified = {2010-02-17 10:10:49 +0100},
doi = {10.1016/j.biopsycho.2007.11.009},
pii = {S0301-0511(07)00195-0},
pmid = {18178303},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Greene-2008-Biol%20Psychol_Imaging%20the%20genetics.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5832},
read = {Yes},
rating = {0}
}

@article{Groenvold:1997p12711,
author = {M Groenvold and M C Klee and M A Sprangers and Neil K Aaronson},
journal = {Journal of Clinical Epidemiology},
title = {Validation of the EORTC QLQ-C30 quality of life questionnaire through combined qualitative and quantitative assessment of patient-observer agreement},
abstract = {Patient-rated questionnaires are increasingly used to assess health-related quality of life. We studied one aspect of the validity of such measures that has rarely been investigated do patients interpret questionnaires in the same way as do the researchers reporting the results? If not, there may be a problem. We employed the EORTC QLQ-C30 quality-of-life questionnaire to study 95 cancer patients and measured the agreement between (1) the patient's self-assessment and (2) an observer's rating of the patient's open-ended responses to the same questionnaire administered as an interview. The observer made qualitative recordings describing potential misinterpretations. The agreement between patients' and observers' ratings was high (median kappa = 0.85, range 0.49-1.00). The qualitative data revealed a few minor validity problems. One of these, selective reporting, may lead to systematic errors; some patients reported only what they considered "relevant" symptoms. The combination of quantitative and qualitative methods proved useful for questionnaire validation.},
affiliation = {Department of Social Medicine, University of Copenhagen, Denmark.},
number = {4},
pages = {441--50},
volume = {50},
year = {1997},
month = {Apr},
language = {eng},
keywords = {Female, Health Status Indicators, Adult, Male, Questionnaires, Middle Aged, Quality of Life, Observer Variation, Reproducibility of Results, Aged, Breast Neoplasms, Humans, Chi-Square Distribution, Genital Neoplasms: Female},
date-added = {2010-06-15 22:47:26 +0200},
date-modified = {2010-07-29 20:13:56 +0200},
pii = {S0895-4356(96)00428-3},
pmid = {9179103},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Groenvold-1997-Journal%20of%20Clinical%20Epidemiology_Validation%20of%20the%20EO.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12711},
rating = {0}
}

@article{McGrath:2006p9957,
author = {John J McGrath and Sukanta Saha and Daniel E Lieberman and Stephen Buka},
journal = {Schizophr Res},
title = {Season of birth is associated with anthropometric and neurocognitive outcomes during infancy and childhood in a general population birth cohort},
abstract = {The 'season of birth' effect is one of the most consistently replicated associations in schizophrenia epidemiology. In contrast, the association between season of birth and development in the general population is relatively poorly understood. The aim of this study was to explore the impact of season of birth on various anthropometric and neurocognitive variables from birth to age seven in a large, community-based birth cohort. A sample of white singleton infants born after 37 weeks gestation (n = 22,123) was drawn from the US Collaborative Perinatal Project. Anthropometric variables (weight, head circumference, length/height) and various measures of neurocognitive development, were assessed at birth, 8 months, 4 and 7 years of age. Compared to summer/autumn born infants, winter/spring born infants were significantly longer at birth, and at age seven were significantly heavier, taller and had larger head circumference. Winter/spring born infants were achieving significantly higher scores on the Bayley Motor Score at 8 months, the Graham-Ernhart Block Test at age 4, the Wechsler Intelligence Performance and Full Scale scores at age 7, but had significantly lower scores on the Bender-Gestalt Test at age 7 years. Winter/spring birth, while associated with an increased risk of schizophrenia, is generally associated with superior outcomes with respect to physical and cognitive development.},
affiliation = {Department of Psychiatry, University of Queensland, St Lucia QLD, Australia. john_mcgrath@qcsr.uq.edu.au},
number = {1},
pages = {91--100},
volume = {81},
year = {2006},
month = {Jan},
language = {eng},
keywords = {Brain, Parturition, Cognition, Child: Preschool, Male, Follow-Up Studies, Anthropometry, Seasons, Female, Child, Schizophrenia, Infant, Cohort Studies, Humans, Vitamin D, Risk Factors},
date-added = {2010-03-31 16:10:52 +0200},
date-modified = {2010-07-29 19:50:06 +0200},
doi = {10.1016/j.schres.2005.07.017},
pii = {S0920-9964(05)00307-5},
pmid = {16242917},
local-url = {file://localhost/Users/chl/Dropbox/Papers/McGrath-2006-Schizophr%20Res_Season%20of%20birth%20is%20a.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9957},
rating = {0}
}

@article{Posthuma:2003p5716,
author = {Dani{\"e}lle Posthuma and Wim F C Baar{\'e} and Hilleke E Hulshoff Pol and Ren{\'e} S Kahn and Dorret I Boomsma and Eco J C de Geus},
journal = {Twin Res},
title = {Genetic correlations between brain volumes and the WAIS-III dimensions of verbal comprehension, working memory, perceptual organization, and processing speed},
abstract = {We recently showed that the correlation of gray and white matter volume with full scale IQ and the Working Memory dimension are completely mediated by common genetic factors (Posthuma et al., 2002). Here we examine whether the other WAIS III dimensions (Verbal Comprehension, Perceptual Organization, Processing Speed) are also related to gray and white matter volume, and whether any of the dimensions are related to cerebellar volume. Two overlapping samples provided 135 subjects from 60 extended twin families for whom both MRI scans and WAIS III data were available. All three brain volumes are related to Working Memory capacity (r = 0.27). This phenotypic correlation is completely due to a common underlying genetic factor. Processing Speed was genetically related to white matter volume (r(g) = 0.39). Perceptual Organization was both genetically (r(g) = 0.39) and environmentally (r(e) = -0.71) related to cerebellar volume. Verbal Comprehension was not related to any of the three brain volumes. It is concluded that brain volumes are genetically related to intelligence which suggests that genes that influence brain volume may also be important for intelligence. It is also noted however, that the direction of causation (i.e., do genes influence brain volume which in turn influences intelligence, or alternatively, do genes influence intelligence which in turn influences brain volume), or the presence or absence of pleiotropy has not been resolved yet.},
affiliation = {Department of Biological Psychology, Vrije Universiteit, van der Boechorststraat 1, 1081 BT Amsterdam, the Netherlands. danielle@psy.vu.nl},
number = {2},
pages = {131--9},
volume = {6},
year = {2003},
month = {Apr},
language = {eng},
keywords = {Brain, Phenotype, Reaction Time, Middle Aged, Intelligence, Perception, Wechsler Scales, Verbal Learning, Twins, Memory, Female, Magnetic Resonance Imaging, Likelihood Functions, Male, Humans},
date-added = {2010-02-15 20:25:53 +0100},
date-modified = {2010-02-15 20:25:53 +0100},
doi = {10.1375/136905203321536254},
pmid = {12723999},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Posthuma-2003-Twin%20Res_Genetic%20correlations.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5716},
rating = {0}
}

@article{Epstein:2005p3291,
author = {Michael P Epstein and Colin D Veal and Richard C Trembath and Jonathan N W N Barker and Chun Li and Glen A Satten},
journal = {American Journal of Human Genetics},
title = {Genetic association analysis using data from triads and unrelated subjects},
abstract = {The selection of an appropriate control sample for use in association mapping requires serious deliberation. Unrelated controls are generally easy to collect, but the resulting analyses are susceptible to spurious association arising from population stratification. Parental controls are popular, since triads comprising a case and two parents can be used in analyses that are robust to this stratification. However, parental controls are often expensive and difficult to collect. In some situations, studies may have both parental and unrelated controls available for analysis. For example, a candidate-gene study may analyze triads but may have an additional sample of unrelated controls for examination of background linkage disequilibrium in genomic regions. Also, studies may collect a sample of triads to confirm results initially found using a traditional case-control study. Initial association studies also may collect each type of control, to provide insurance against the weaknesses of the other type. In these situations, resulting samples will consist of some triads, some unrelated controls, and, possibly, some unrelated cases. Rather than analyze the triads and unrelated subjects separately, we present a likelihood-based approach for combining their information in a single combined association analysis. Our approach allows for joint analysis of data from both triad and case-control study designs. Simulations indicate that our proposed approach is more powerful than association tests that are based on each separate sample. Our approach also allows for flexible modeling and estimation of allele effects, as well as for missing parental data. We illustrate the usefulness of our approach using SNP data from a candidate-gene study of psoriasis.},
affiliation = {Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA. mepstein@genetics.emory.edu},
number = {4},
pages = {592--608},
volume = {76},
year = {2005},
month = {Apr},
language = {eng},
keywords = {Humans, Case-Control Studies, Parents, Polymorphism: Single Nucleotide, Algorithms, Likelihood Functions, Research Design, Models: Statistical, Gene Frequency, Linkage (Genetics), Models: Genetic, Psoriasis},
date-added = {2010-01-14 21:22:19 +0100},
date-modified = {2010-01-14 21:22:20 +0100},
doi = {10.1086/429225},
pii = {S0002-9297(07)62871-7},
pmid = {15712104},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Epstein-2005-American%20Journal%20of%20Human%20Genetics_Genetic%20association.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3291},
rating = {0}
}

@article{Guo:2009p3378,
author = {Yan-Fang Guo and Jian Li and Yuan Chen and Li-Shu Zhang and Hong-Wen Deng},
journal = {BMC Bioinformatics},
title = {A new permutation strategy of pathway-based approach for genome-wide association study},
abstract = {ABSTRACT: BACKGROUND: Recently introduced pathway-based approach is promising and advantageous to improve the efficiency of analyzing genome-wide association scan (GWAS) data to identify disease variants by jointly considering variants of the genes that belong to the same biological pathway. However, the current available pathway-based approaches for analyzing GWAS have limited power and efficiency. RESULTS: We proposed a new and efficient permutation strategy based on SNP randomization for determining significance in pathway analysis of GWAS. The developed permutation strategy was evaluated and compared to two previously available methods, i.e. sample permutation and gene permutation, through simulation studies and a study on a real dataset. Results showed that the proposed permutation strategy is more powerful and efficient with greatly reducing the computational complexity. CONCLUSION: Our findings indicate the improved performance of SNP permutation and thus render pathway-based analysis of GWAS more applicable and attractive.},
number = {1},
pages = {429},
volume = {10},
year = {2009},
month = {Dec},
language = {ENG},
date-added = {2010-01-15 14:39:38 +0100},
date-modified = {2010-06-18 21:15:14 +0200},
doi = {10.1186/1471-2105-10-429},
pii = {1471-2105-10-429},
pmid = {20021635},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Guo-2009-BMC%20Bioinformatics_A%20new%20permutation%20st.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3378},
read = {Yes},
rating = {4}
}

@article{Reise:2009p5919,
author = {Steven P Reise and Niels G Waller},
journal = {Annual review of clinical psychology},
title = {Item response theory and clinical measurement},
abstract = {In this review, we examine studies that use item response theory (IRT) to explore the psychometric properties of clinical measures. Next, we consider how IRT has been used in clinical research for: scale linking, computerized adaptive testing, and differential item functioning analysis. Finally, we consider the scale properties of IRT trait scores. We conclude that there are notable differences between cognitive and clinical measures that have relevance for IRT modeling. Future research should be directed toward a better understanding of the metric of the latent trait and the psychological processes that lead to individual differences in item response behaviors.},
affiliation = {Department of Psychology, University of California, Los Angeles, CA 90095, USA. reise@psych.ucla.edu},
pages = {27--48},
volume = {5},
year = {2009},
month = {Jan},
language = {eng},
keywords = {Quality of Life, Mental Disorders, Psychometrics, Psychological Tests, Psychological Theory, Questionnaires, Humans},
date-added = {2010-02-18 23:15:48 +0100},
date-modified = {2010-02-24 09:57:35 +0100},
doi = {10.1146/annurev.clinpsy.032408.153553},
pmid = {18976138},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Reise-2009-Annual%20review%20of%20clinical%20psychology_Item%20response%20theory.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5919},
rating = {4}
}

@article{Bunea:2009p2937,
author = {Florentina Bunea and Adrian Barbu},
journal = {arXiv},
title = {Dimension reduction and variable selection in case control studies via  regularized likelihood optimization},
abstract = { Dimension reduction and variable selection are performed routinely in case-control studies, but the literature on the theoretical aspects of the resulting estimates is scarce. We bring our contribution to this literature by studying estimators obtained via L1 penalized likelihood optimization. We show that the optimizers of the L1 penalized retrospective likelihood coincide with the optimizers of the L1 penalized prospective likelihood. This extends the results of Prentice and Pyke (1979), obtained for non-regularized likelihoods. We establish both the sup-norm consistency of the odds ratio, after model selection, and the consistency of subset selection of our estimators. The novelty of our theoretical results consists in the study of these properties under the case-control sampling scheme. Our results hold for selection performed over a large collection of candidate variables, with cardinality allowed to depend and be greater than the sample size. We complement our theoretical results with a novel approach of determining data driven tuning parameters, based on the bisection method. The resulting procedure offers significant computational savings when compared with grid search based methods. All our numerical experiments support strongly our theoretical findings. },
note = {32 pages, 5 figures, 3 tables},
eprint = {0905.2171v2},
volume = {stat.ML},
year = {2009},
month = {Jan},
keywords = {stat.TH, math.ST, stat.ML},
date-added = {2010-01-13 22:59:06 +0100},
date-modified = {2010-01-13 22:59:06 +0100},
pmid = {0905.2171v2},
URL = {http://arxiv.org/abs/0905.2171v2},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bunea-2009-arXiv_Dimension%20reduction.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2937},
rating = {0}
}

@article{Madore:2001p3644,
author = {D A Madore},
title = {L'infini en math{\'e}matiques},
abstract = {La notion d'infini nous fascine et nous {\'e}chappe {\`a} la fois ; elle est rest{\'e} long- temps mal comprise : lorsque Georg Cantor, {\`a} qui nous devons la vision moderne du concept d'infini en math{\'e}matiques, a pr{\'e}sent{\'e} ses th{\'e}ories, on l'a d'abord pris pour fou. Cependant, les math{\'e}matiques contemporaines ont r{\'e}ussi {\`a} ma{\^\i}triser et {\`a} comprendre l'infini : nous tenterons donc de donner un aper{\c c}u de leur point de vue, en {\'e}voquant au passage les consid{\'e}rations d'ordre philosophique qu'il soul{\`e}ve. Apr{\`e}s un survol du « fini » et de l'infini « inachev{\'e} » (pr{\'e}-Cantorien), nous tente- rons de pr{\'e}senter les deux sortes d'infini qu'on trouve en th{\'e}orie des ensembles : les ordinaux et les cardinaux. Tout au long de l'expos{\'e} se pr{\'e}sentera la question « jusqu'o{\`u} peut-on aller », et la r{\'e}ponse sera toujours « encore tr{\`e}s loin ».},
year = {2001},
date-added = {2010-01-16 19:48:29 +0100},
date-modified = {2010-01-16 19:49:15 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Madore-2001-_L%E2%80%99infini%20en%20mathe%CC%81ma.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3644},
rating = {0}
}

@article{AutismandDevelopmentalDisabilitiesMonitoringNetworkSurveillanceYear2002PrincipalInvestigators:2007p6081,
author = {Autism and Developmental Disabilities Monitoring Network Surveillance Year 2002 Principal Investigators and Centers for Disease Control and Prevention},
journal = {MMWR Surveill Summ},
title = {Prevalence of autism spectrum disorders--autism and developmental disabilities monitoring network, 14 sites, United States, 2002},
abstract = {PROBLEM/CONDITION: Data from a population-based, multisite surveillance network were used to determine the prevalence of autism spectrum disorders (ASDs) among children aged 8 years in 14 areas of the United States and to describe the characteristics of these children. REPORTING PERIOD: 2002. METHODS: Children aged 8 years were identified as having an ASD through screening and abstraction of evaluation records at health facilities for all 14 sites and through information from psychoeducational evaluations for special education services for 10 of the 14 sites. Case status was determined through clinician review of data abstracted from the records. Children whose parent(s) or legal guardian(s) resided in the respective areas in 2002 and whose records documented behaviors consistent with the Diagnostic and Statistical Manual, Fourth Edition, Text Revision (DSM-IV-TR) criteria for autistic disorder; pervasive developmental disorder, not otherwise specified; or Asperger disorder were classified as having ASDs. RESULTS: For 2002, of 407,578 children aged 8 years in the 14 surveillance areas, 2,685 (0.66%) were identified as having an ASD. ASD prevalence per 1,000 children aged 8 years ranged from 3.3 (Alabama) to 10.6 (New Jersey), with the majority of sites ranging from 5.2 to 7.6 (overall mean: 6.6 [i.e., one of every 152 children across all sites). ASD prevalence was significantly lower than all other sites

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib