text:
doi = {10.1016/j.paid.2005.04.006},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bastian-2005-Personality%20and%20Individual%20Differences_Emotional%20intelligen.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13125},
rating = {0}
}

@article{Bock:1970,
author = {R Darrell Bock and Marcus Lieberman},
journal = {Psychometrika},
title = {Fitting a response model for n dichotomously scored items},
number = {2},
pages = {179--197},
volume = {35},
year = {1970},
date-added = {2010-01-10 11:33:24 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bock-1970-Psychometrika_Fitting%20a%20response%20m.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1883},
rating = {0}
}

@article{Sterne:2001p3601,
author = {J A Sterne and M Egger and G D Smith},
journal = {BMJ},
title = {Systematic reviews in health care: Investigating and dealing with publication and other biases in meta-analysis},
affiliation = {Medical Research Council Health Services Research Collaboration, Department of Social Medicine, University of Bristol, Bristol BS8 2PR. jonathan.sterne@bristol.ac.uk},
number = {7304},
pages = {101--5},
volume = {323},
year = {2001},
month = {Jul},
language = {eng},
keywords = {Statistics as Topic, Mathematics, Meta-Analysis as Topic, Bias (Epidemiology), Homeopathy, Humans, Placebo Effect},
date-added = {2010-01-15 21:41:34 +0100},
date-modified = {2010-01-15 21:41:34 +0100},
pmid = {11451790},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Sterne-2001-BMJ_Systematic%20reviews%20i.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3601},
rating = {0}
}

@article{Smyth:1996p13485,
author = {P Smyth},
journal = {KDD-96 Proceedings},
title = {CLustering using Monte Carlo cross-validation},
year = {1996},
date-added = {2010-07-01 22:18:11 +0200},
date-modified = {2010-07-01 22:19:42 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Smyth-1996-KDD-96%20Proceedings_CLustering%20using%20Mon.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13485},
rating = {5}
}

@article{Rubio:2007p11862,
author = {Gabriel Rubio and M{\'o}nica Jim{\'e}nez and Roberto Rodr{\'\i}guez-Jim{\'e}nez and Isabel Mart{\'\i}nez and Martin Miguel Iribarren and Miguel Angel Jim{\'e}nez-Arriero and Guillermo Ponce and Cesar Avila},
journal = {Alcohol Clin Exp Res},
title = {Varieties of impulsivity in males with alcohol dependence: the role of Cluster-B personality disorder},
abstract = {BACKGROUND/RATIONALE: Impulsivity has been associated with alcohol dependence, but impulsivity in alcohol-dependent subjects with a Cluster-B personality disorder (PD) has not been well characterized. Using a variety of laboratory measures of impulsivity, we assessed whether alcohol-dependent patients (ADP) with borderline personality disorder (BPD) exhibited the same pattern of behavioral impulsivity than ADP with antisocial personality disorder (AntPD). Also, differences between ADP without PDs and healthy controls were assessed. METHODS: A cross-sectional patient survey with a community comparison group. Diagnoses were made using the Structured Interview for DSM-IV. Sustained attention and rapid-response impulsivity were assessed using the continuous performance test. Inhibitory control was measured by the stop-signal task. Ability to delay reward task was assessed using differential reinforcement for low-rate responding (DRLR). A final sample of 247 males with alcohol-dependence recruited from 2 alcoholism treatment centers was compared with a matched nonsubstance-abusing comparison group (n = 96). RESULTS: Alcohol-dependent patients with BPD made more omission errors than ADP with AntPD, but individuals with AntPD exhibited the poorest efficiency in DRLR. ADPs with a Cluster-B PD displayed more impairment across all behavioral measures than ADP without PD and than controls. In contrast, with respect to controls ADP without a Cluster-B PD showed more impairment only in DRLR. CONCLUSIONS: Our findings support the suggestion of 2 paradigms in alcohol dependence. The first, based on inability to delay gratification, might be a vulnerability marker for alcohol dependence. The second was related to inhibitory control and might be specific for AntPD and BPDs.},
affiliation = {Alcoholism Research Program, Retiro Mental Health Center, Madrid, Spain. garuva@inicia.es},
number = {11},
pages = {1826--32},
volume = {31},
year = {2007},
month = {Nov},
language = {eng},
keywords = {Neuropsychological Tests, Cross-Sectional Studies, Middle Aged, Borderline Personality Disorder, Adult, Case-Control Studies, Humans, Impulsive Behavior, Alcoholism, Antisocial Personality Disorder, Male, Health Surveys},
date-added = {2010-05-23 11:45:35 +0200},
date-modified = {2010-07-29 19:13:02 +0200},
doi = {10.1111/j.1530-0277.2007.00506.x},
pii = {ACER506},
pmid = {17850221},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Rubio-2007-Alcohol%20Clin%20Exp%20Res_Varieties%20of%20impulsi.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11862},
rating = {4}
}

@article{Heinze:2004p3622,
author = {G Heinze and M Ploner},
title = {A SAS macro, S-PLUS library and R package to perform logistic regression without convergence problems},
abstract = {The phenomenon of separation is observed in the fitting process of a logistic model if the likelihood converges while at least one parameter estimate diverges to $\pm$ infinity. Separation primarily occurs in small samples with several unbalanced and highly predictive covariates (cf. Heinze, 1999). A procedure by Firth (1993) originally developed to reduce the bias of maximum likelihood estimates provides an ideal solution to monotone likelihood (cf. Heinze {\&} Schemper, 2002). It produces finite parameter estimates by means of penalized maximum likelihood estimation. Corresponding Wald tests and confidence intervals are available but it was shown that penalized likelihood ratio tests and profile penalized likelihood confidence intervals are often preferable.
This Technical Report presents a SAS macro, an S-PLUS library and an R package to apply Firth's procedure to logistic regression. The present report contains the complete User's Guide to these programs including syntax, computational methods and examples.},
year = {2004},
date-added = {2010-01-16 18:42:21 +0100},
date-modified = {2010-01-16 18:42:52 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Heinze-2004-_A%20SAS%20macro%20S-PLUS.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3622},
rating = {0}
}

@article{Kim:2008p12122,
author = {Kyung In Kim and Mark A van de Wiel},
journal = {BMC Bioinformatics},
title = {Effects of dependence in high-dimensional multiple testing problems},
abstract = {BACKGROUND: We consider effects of dependence among variables of high-dimensional data in multiple hypothesis testing problems, in particular the False Discovery Rate (FDR) control procedures. Recent simulation studies consider only simple correlation structures among variables, which is hardly inspired by real data features. Our aim is to systematically study effects of several network features like sparsity and correlation strength by imposing dependence structures among variables using random correlation matrices. RESULTS: We study the robustness against dependence of several FDR procedures that are popular in microarray studies, such as Benjamin-Hochberg FDR, Storey's q-value, SAM and resampling based FDR procedures. False Non-discovery Rates and estimates of the number of null hypotheses are computed from those methods and compared. Our simulation study shows that methods such as SAM and the q-value do not adequately control the FDR to the level claimed under dependence conditions. On the other hand, the adaptive Benjamini-Hochberg procedure seems to be most robust while remaining conservative. Finally, the estimates of the number of true null hypotheses under various dependence conditions are variable. CONCLUSION: We discuss a new method for efficient guided simulation of dependent data, which satisfy imposed network constraints as conditional independence structures. Our simulation set-up allows for a structural study of the effect of dependencies on multiple testing criterions and is useful for testing a potentially new method on pi0 or FDR estimation in a dependency context.},
affiliation = {Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, The Netherlands. k.i.kim@tue.nl},
pages = {114},
volume = {9},
year = {2008},
month = {Jan},
language = {eng},
keywords = {Sensitivity and Specificity, Reproducibility of Results, Statistics as Topic, Gene Expression Profiling, Artifacts, Algorithms, Oligonucleotide Array Sequence Analysis},
date-added = {2010-05-30 10:06:36 +0200},
date-modified = {2010-05-30 10:06:40 +0200},
doi = {10.1186/1471-2105-9-114},
pii = {1471-2105-9-114},
pmid = {18298808},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Kim-2008-BMC%20Bioinformatics_Effects%20of%20dependenc.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12122},
rating = {3}
}

@article{Jin:2009p7856,
author = {C Jin and G Zhao and F Zhang and L Feng and N Wu},
journal = {HIV Med},
title = {The psychological status of HIV-positive people and their psychosocial experiences in eastern China},
abstract = {Objectives The aim of the study was to investigate the psychological status and the psychosocial experiences of HIV-positive people using Symptom Check List 90 (SCL-90) in eastern China. Methods Two hundred and fourteen HIV-positive people and 200 controls were recruited to the study. Participants were given an anonymous questionnaire which included questions pertaining to demography, SCL-90 and psychosocial experiences. Results The mean subscale scores for SCL-90 in the HIV-positive group were all higher than those of the control group (P<0.001), especially for depression, anxiety, obsessive-compulsive disorder and hostility. Female HIV-positive individuals had significantly higher depression and anxiety scores (P<0.05) and more scores higher than 2.0 than male HIV-positive individuals. The average number of subscales with mean scores higher than 2.0 was 4.1 for female HIV-positive individuals and 3.7 for male HIV-positive individuals. The most common psychosocial experiences related to HIV infection were fear (36.9%) and helplessness (31.8%). 90.2% of HIV-positive people would not tell others about their disease because of fear of discrimination against family members (42.2%), exclusion by community members (26.9%) and abandonment (23.3%). Discrimination from acquaintances (38.8%) was a main stressor in the HIV-positive individuals' daily life. Most members of HIV-positive individuals' communities expressed negative attitudes: alienation, coldness, aversion and fear. 38.3% of the HIV-positive participants reported that their family members had been discriminated against. Conclusions The results demonstrate that HIV-positive people in eastern China live in a negative psychosocial environment and suffer from psychological distress. It is necessary to provide psychological interventions for people living with AIDS and to educate community members in order to improve the psychosocial environment.},
affiliation = {State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.},
pages = {},
year = {2009},
month = {Dec},
language = {ENG},
date-added = {2010-03-18 21:06:56 +0100},
date-modified = {2010-07-29 19:27:54 +0200},
doi = {10.1111/j.1468-1293.2009.00770.x},
pii = {HIV770},
pmid = {20002782},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Jin-2009-HIV%20Med_The%20psychological%20st.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7856},
rating = {3}
}

@article{Vacha-Haase:2001,
author = {T Vacha-Haase and L Kogan and C R Tani and R A Woodall},
journal = {Educational and Psychological Measurement},
title = {Reliability generalization: Exploring reliability coefficients of MMPI clinical scales scores},
pages = {45--59},
volume = {61},
year = {2001},
date-added = {2010-01-10 11:33:21 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1895},
rating = {0}
}

@article{Hothorn:2005p4618,
author = {T Hothorn and F Leisch and A Zeilis and K Hornik},
journal = {Journal of Computational and Graphical Statistics},
title = {The Design and Analysis of Benchmark Experiments},
abstract = {The assessment of the performance of learners by means of benchmark experiments is an established exercise. In practice, benchmark studies are a tool to compare the performance of several competing algorithms for a certain learning problem. Cross-validation or resampling techniques are commonly used to derive point estimates of the performances which are com- pared to identify algorithms with good properties. For several benchmarking problems, test procedures taking the variability of those point estimates into account have been suggested. Most of the recently proposed inference procedures are based on special variance estimators for the cross-validated performance.
We introduce a theoretical framework for inference problems in benchmark experiments and show that standard statistical test procedures can be used to test for differences in the performances. The theory is based on well defined distributions of performance measures which can be compared with established tests. To demonstrate the usefulness in practice, the theoretical results are applied to regression and classification benchmark studies based on artificial and real world data.},
number = {3},
pages = {675--699},
volume = {14},
year = {2005},
date-added = {2010-01-30 15:25:08 +0100},
date-modified = {2010-01-30 15:26:27 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hothorn-2005-Journal%20of%20Computational%20and%20Graphical%20Statistics_The%20Design%20and%20Analy.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4618},
rating = {0}
}

@misc{Leeuw:2003,
author = {Jan de Leeuw},
journal = {Miscellaneous},
title = {Principal component analysis with binary data. Applications to roll-call analysis},
year = {2003},
month = {Aug},
date-added = {2010-01-10 11:33:24 +0100},
date-modified = {2010-07-29 20:45:39 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/de%20Leeuw-2003-Miscellaneous_Principal%20component.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2071},
rating = {0}
}

@article{Deerwester:1990,
author = {Scott Deerwester and Susan T Dumais and Richard Harshman},
journal = {Journal of the American Society for Information Science},
title = {Indexing by latent semantic analysis},
number = {6},
pages = {391--407},
volume = {41},
year = {1990},
date-added = {2010-01-10 11:33:24 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Deerwester-1990-Journal%20of%20the%20American%20Society%20for%20Information%20Science_Indexing%20by%20latent%20s.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1963},
rating = {0}
}

@article{Luciano:2008p5755,
author = {Michelle Luciano and Penelope A Lind and Ian J Deary and Antony Payton and Danielle Posthuma and Lee M Butcher and Zoltan Bochdanovits and Lawrence J Whalley and Peter M Visscher and Sarah E Harris and Tinca J C Polderman and Oliver S P Davis and Margaret J Wright and John M Starr and Eco J C de Geus and Timothy C Bates and Grant W Montgomery and Dorret I Boomsma and Nicholas G Martin and Robert Plomin},
journal = {Eur J Hum Genet},
title = {Testing replication of a 5-SNP set for general cognitive ability in six population samples},
abstract = {A 5-single nucleotide polymorphism (SNP) set has been associated with general cognitive ability in 5000 7-year-old children from the Twins Early Development Study (TEDS). Four of these SNPs were identified through a 10 K microarray analysis and one was identified through a targeted analysis of brain-expressed genes. The present study tested this association with general cognitive ability in six population samples of varying size and age from Australia, the UK (Scotland and England) and the Netherlands. Results from the largest sample (N=1310) approached significance (P=0.06) in the direction of the original finding, but results from the other samples (N=205-758) were mixed. A meta-analysis of the results--allowing for effect size heterogeneity between samples--yielded a non-significant correlation (r=-0.01, P=0.57), indicating that this SNP set was not associated with general cognitive ability in the populations studied.},
affiliation = {Department of Psychology, MRC Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK. michelle.luciano@ed.ac.uk},
number = {11},
pages = {1388--95},
volume = {16},
year = {2008},
month = {Nov},
language = {eng},
keywords = {Humans, Cognition, Polymorphism: Single Nucleotide, Child, Twins: Monozygotic, Child: Preschool, Follow-Up Studies, Meta-Analysis as Topic, Adult, Female, Twins: Dizygotic, Male, Adolescent},
date-added = {2010-02-15 20:29:45 +0100},
date-modified = {2010-02-15 20:29:45 +0100},
doi = {10.1038/ejhg.2008.100},
pii = {ejhg2008100},
pmid = {18493267},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5755},
rating = {0}
}

@article{Ioannidis:2006p9158,
author = {John P A Ioannidis and Marta Gwinn and Julian Little and Julian P T Higgins and Jonine L Bernstein and Paolo Boffetta and Melissa Bondy and Molly S Bray and Paul E Brenchley and Patricia A Buffler and Juan Pablo Casas and Anand Chokkalingam and John Danesh and George Davey Smith and Siobhan Dolan and Ross Duncan and Nelleke A Gruis and Patricia Hartge and Mia Hashibe and David J Hunter and Marjo-Riitta Jarvelin and Beatrice Malmer and Demetrius M Maraganore and Julia A Newton-Bishop and Thomas R O'Brien and Gloria Petersen and Elio Riboli and Georgia Salanti and Daniela Seminara and Liam Smeeth and Emanuela Taioli and Nic Timpson and Andre G Uitterlinden and Paolo Vineis and Nick Wareham and Deborah M Winn and Ron Zimmern and Muin J Khoury and Human Genome Epidemiology Network and the Network of Investigator Networks},
journal = {Nat Genet},
title = {A road map for efficient and reliable human genome epidemiology},
abstract = {Networks of investigators have begun sharing best practices, tools and methods for analysis of associations between genetic variation and common diseases. A Network of Investigator Networks has been set up to drive the process, sponsored by the Human Genome Epidemiology Network. A workshop is planned to develop consensus guidelines for reporting results of genetic association studies. Published literature databases will be integrated, and unpublished data, including 'negative' studies, will be captured by online journals and through investigator networks. Systematic reviews will be expanded to include more meta-analyses of individual-level data and prospective meta-analyses. Field synopses will offer regularly updated overviews.},
affiliation = {Clinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, and Biomedical Research Institute, Foundation for Research and Technology-Hellas, Ioannina 45110, Greece. jioannid@cc.uoi.gr},
number = {1},
pages = {3--5},
volume = {38},
year = {2006},
month = {Jan},
language = {eng},
keywords = {MEDLINE, Research Design, Genome: Human, Human Genome Project, Epidemiologic Methods, Databases: Factual, Humans, Genetic Predisposition to Disease},
date-added = {2010-03-22 13:34:39 +0100},
date-modified = {2010-03-22 13:34:43 +0100},
pmid = {16468121},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Ioannidis-2006-Nat%20Genet_A%20road%20map%20for%20effic.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9158},
rating = {4}
}

@article{Flynn:2008p13510,
author = {Terry N Flynn and Jordan J Louviere and Anthony Aj Marley and Joanna Coast and Tim J Peters},
journal = {Popul Health Metr},
title = {Rescaling quality of life values from discrete choice experiments for use as QALYs: a cautionary tale},
abstract = {ABSTRACT: BACKGROUND: Researchers are increasingly investigating the potential for ordinal tasks such as ranking and discrete choice experiments to estimate QALY health state values. However, the assumptions of random utility theory, which underpin the statistical models used to provide these estimates, have received insufficient attention. In particular, the assumptions made about the decisions between living states and the death state are not satisfied, at least for some people. Estimated values are likely to be incorrectly anchored with respect to death (zero) in such circumstances. METHODS: Data from the Investigating Choice Experiments for the preferences of older people CAPability instrument (ICECAP) valuation exercise were analysed. The values (previously anchored to the worst possible state) were rescaled using an ordinal model proposed previously to estimate QALY-like values. Bootstrapping was conducted to vary artificially the proportion of people who conformed to the conventional random utility model underpinning the analyses. RESULTS: Only 26% of respondents conformed unequivocally to the assumptions of conventional random utility theory. At least 14% of respondents unequivocally violated the assumptions. Varying the relative proportions of conforming respondents in sensitivity analyses led to large changes in the estimated QALY values, particularly for lower-valued states. As a result these values could be either positive (considered to be better than death) or negative (considered to be worse than death). CONCLUSION: Use of a statistical model such as conditional (multinomial) regression to anchor quality of life values from ordinal data to death is inappropriate in the presence of respondents who do not conform to the assumptions of conventional random utility theory. This is clearest when estimating values for that group of respondents observed in valuation samples who refuse to consider any living state to be worse than death: in such circumstances the model cannot be estimated. Only a valuation task requiring respondents to make choices in which both length and quality of life vary can produce estimates that properly reflect the preferences of all respondents.},
affiliation = {Department of Health Economics, Public Health Building, University of Birmingham, Birmingham B15 2TT, UK. j.coast@bham.ac.uk.},
pages = {6},
volume = {6},
year = {2008},
month = {Jan},
language = {eng},
date-added = {2010-07-07 21:03:00 +0200},
date-modified = {2010-07-29 19:44:07 +0200},
doi = {10.1186/1478-7954-6-6},
pii = {1478-7954-6-6},
pmid = {18945358},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Flynn-2008-Popul%20Health%20Metr_Rescaling%20quality%20of.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13510},
rating = {0}
}

@article{Smith:2005,
author = {A B Smith and E P Wright and R Rush and D P Stark and G Velikova and P J Selby},
journal = {Psycho-Oncology},
title = {Rasch analysis of the dimensional structure of the hospital anxiety and depression scale},
year = {2005},
date-added = {2010-01-10 11:33:23 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Smith-2005-Psycho-Oncology_Rasch%20analysis%20of%20th.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1888},
rating = {0}
}

@article{Roberson:2009p1621,
author = {Elisha D O Roberson and Jonathan Pevsner},
journal = {PLoS ONE},
title = {Visualization of shared genomic regions and meiotic recombination in high-density SNP data},
abstract = {BACKGROUND: A fundamental goal of single nucleotide polymorphism (SNP) genotyping is to determine the sharing of alleles between individuals across genomic loci. Such analyses have diverse applications in defining the relatedness of individuals (including unexpected relationships in nominally unrelated individuals, or consanguinity within pedigrees), analyzing meiotic crossovers, and identifying a broad range of chromosomal anomalies such as hemizygous deletions and uniparental disomy, and analyzing population structure. PRINCIPAL FINDINGS: We present SNPduo, a command-line and web accessible tool for analyzing and visualizing the relatedness of any two individuals using identity by state. Using identity by state does not require prior knowledge of allele frequencies or pedigree information, and is more computationally tractable and is less affected by population stratification than calculating identity by descent probabilities. The web implementation visualizes shared genomic regions, and generates UCSC viewable tracks. The command-line version requires pedigree information for compatibility with existing software and determining specified relationships even though pedigrees are not required for IBS calculation, generates no visual output, is written in portable C++, and is well-suited to analyzing large datasets. We demonstrate how the SNPduo web tool identifies meiotic crossover positions in siblings, and confirm our findings by visualizing meiotic recombination in synthetic three-generation pedigrees. We applied SNPduo to 210 nominally unrelated Phase I / II HapMap samples and, consistent with previous findings, identified six undeclared pairs of related individuals. We further analyzed identity by state in 2,883 individuals from multiplex families with autism and identified a series of anomalies including related parents, an individual with mosaic loss of chromosome 18, an individual with maternal heterodisomy of chromosome 16, and unexplained replicate samples. CONCLUSIONS: SNPduo provides the ability to explore and visualize SNP data to characterize the relatedness between individuals. It is compatible with, but distinct from, other established analysis software such as PLINK, and performs favorably in benchmarking studies for the analyses of genetic relatedness.},
affiliation = {Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America.},
number = {8},
pages = {e6711},
volume = {4},
year = {2009},
month = {Jan},
language = {eng},
date-added = {2010-01-08 21:49:56 +0100},
date-modified = {2010-01-08 21:49:56 +0100},
doi = {10.1371/journal.pone.0006711},
pmid = {19696932},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Roberson-2009-PLoS%20ONE_Visualization%20of%20sha.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1621},
rating = {0}
}

@article{Altman:1996p5845,
author = {J Altman and B J Everitt and S Glautier and A Markou and D Nutt and R Oretti and G D Phillips and T W Robbins},
journal = {Psychopharmacology (Berl)},
title = {The biological, social and clinical bases of drug addiction: commentary and debate},
abstract = {This article summarizes the main discussions at a meeting on the biological, social and clinical bases of drug addiction focused on contemporary topics in drug dependence. Four main domains are surveyed, reflecting the structure of the meeting: psychological and pharmacological factors; neurobiological substrates; risk factors (including a consideration of vulnerability from an environmental and genetic perspective); and clinical treatment. Among the topics discussed were tolerance, sensitization, withdrawal, craving and relapse; mechanisms of reinforcing actions of drugs at the behavioural, cognitive and neural levels; the role of subjective factors in drug dependence; approaches to the behavioural and molecular genetics of drug dependence; the use of functional neuroimaging; pharmaceutical and psychosocial strategies for treatment; epidemiological and sociological aspects of drug dependence. The survey takes into account the considerable disagreements and controversies arising from the discussions, but also reaches a degree of consensus in certain areas.},
affiliation = {Department of Experimental Psychology, University of Cambridge, UK.},
number = {4},
pages = {285--345},
volume = {125},
year = {1996},
month = {Jun},
language = {eng},
keywords = {Ethanol, Narcotics, Substance-Related Disorders, Brain, Humans, Drug Tolerance, Nicotine, Substance Withdrawal Syndrome, Risk Factors},
date-added = {2010-02-17 10:19:02 +0100},
date-modified = {2010-07-29 19:47:40 +0200},
pmid = {8826538},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5845},
rating = {0}
}

@article{Michailidis:2010p4268,
author = {G Michailidis and Jan de Leeuw},
title = {Homogeneity analysis using absolute deviations},
abstract = {Homogeneity analysis is a technique for making graphical representations of categor- ical multivariate data sets. Such data sets can also be represented by the adjacency matrix of a bipartite graph. Homogeneity analysis optimizes a weighted least squares criterion and the optimal graph drawing is computed by an alternating least squares algorithm. Heiser (1987) looked at homo- geneity analysis under a weighted least absolute deviations criterion. In this paper, we take a closer look at the mathematical structure of this problem and show that the graph drawings are created by reciprocal computation of multivariate medians. Several algorithms for computing the solution are investigated and applications to actual data suggest that the resulting	-dimensional drawings
are degenerate, in the sense that all object points are clustered in	locations. We also examine some variations of the criterion used and conclude that the generate solutions observed are a consequence of the normalization constraint employed in this class of problems.},
date-added = {2010-01-23 21:32:21 +0100},
date-modified = {2010-07-29 20:45:39 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Michailidis--_Homogeneity%20analysis.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4268},
rating = {0}
}

@article{Carskadon:1993p10135,
author = {M A Carskadon and C Acebo},
journal = {J Adolesc Health},
title = {A self-administered rating scale for pubertal development},
abstract = {The purpose of this study was to assess the reliability and validity of a new self-rating scale to measure children's pubertal status without pictorial representations or interviews. The scale is an adaptation of an interview-based puberty-rating scale by Petersen, and included scores for each of five items rating physical development, an overall maturation measure, and a categorical maturation score designed to be similar to Tanner staging categories. Each measure was obtained from independent ratings by students and parents, and a 3-point categorical scale was also obtained from teachers. Subjects included 698 5th- and 6th-grade students (323 boys and 375 girls) from 61 schools and their parents and teachers. Fifth-grade students rated themselves and were rated by parents as less mature than 6th graders; 6th-grade girls were consistently rated more mature than boys of the same age. Significant correlations were found between parents and students for all of the measures for 6th-graders and 5th-grade girls and several measures for 5th-grade boys. This new scale is a useful tool for assessing pubertal status in settings that require noninvasive measures.},
affiliation = {E. P. Bradley Hospital, Department of Psychiatry and Human Behavior, Brown University School of Medicine, East Providence, Rhode Island 02915.},
number = {3},
pages = {190--5},
volume = {14},
year = {1993},
month = {May},
language = {eng},
keywords = {Puberty, Adolescent, Human Development, Female, Teaching, Male, Evaluation Studies as Topic, Reproducibility of Results, Parents, Humans, Questionnaires, Child, Data Collection, Sex Characteristics},
date-added = {2010-03-31 20:38:30 +0200},
date-modified = {2010-03-31 20:38:30 +0200},
pmid = {8323929},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Carskadon-1993-J%20Adolesc%20Health_A%20self-administered.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10135},
rating = {0}
}

@article{Hunter:2002p2724,
author = {M A Hunter and Y Takane},
journal = {Journal of Educational and Behavioral Statistics},
title = {Constrained Principal Component Analysis: Various applications},
number = {2},
pages = {105--145},
volume = {27},
year = {2002},
date-added = {2010-01-13 14:14:08 +0100},
date-modified = {2010-01-13 14:15:05 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hunter-2002-Journal%20of%20Educational%20and%20Behavioral%20Statistics_Constrained%20Principa.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2724},
rating = {0}
}

@article{Bickel:2008p5662,
author = {P J Bickel and E Levina},
journal = {The Annals of Statistics},
title = {COVARIANCE REGULARIZATION BY THRESHOLDING},
abstract = {This paper considers regularizing a covariance matrix of p variables estimated from n observations, by hard thresholding. We show that the thresholded estimate is consistent in the operator norm as long as the true covariance matrix is sparse in a suitable sense, the variables are Gaussian or sub-Gaussian, and (log p)/n → 0, and obtain explicit rates. The results are uniform over families of covariance matrices which satisfy a fairly natural no- tion of sparsity. We discuss an intuitive resampling scheme for threshold se- lection and prove a general cross-validation result that justifies this approach. We also compare thresholding to other covariance estimators in simulations and on an example from climate data.},
number = {6},
pages = {2577--2604},
volume = {36},
year = {2008},
date-added = {2010-02-12 20:26:44 +0100},
date-modified = {2010-02-12 20:27:42 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bickel-2008-The%20Annals%20of%20Statistics_COVARIANCE%20REGULARIZ.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5662},
rating = {0}
}

@article{Lloyd:2009p925,
author = {Jennifer E V Lloyd and Bruno D Zumbo and Linda S Siegel},
journal = {Journal of Educational Research {\&} Policy Studies},
title = {When Measures Change over Time: A Workable Solution for Analysing Change and Growth across Multiple Waves},
abstract = {In the past 20 years, the analysis of individual change has become a key focus in educational research. There are several parametric analyses that centre upon quantifying change. Some researchers state that such analyses should only occur if the measure itself remains completely unchanged across waves, arguing that it is not possible to link or connect the scores, either methodologically or conceptually, of measures whose content, wording, response categories, or response formats vary across waves. Because it is not always possible or warranted to use the exact same measure over time, however, it is vital to explore more fully the problem of analysing change and growth with measures that vary across waves. To this end, the primary objective of this paper is to expand upon the statistical work of Lloyd and Zumbo (2007) by introducing the non- parametric hierarchical linear model (NPAR-HLM), a workable solution to the problem of analysing change/growth with measures that change over multiple waves. An example of the implementation of the solution is provided, as is a discussion of the solution's assumptions, strengths, and limitations.},
affiliation = {University of British Columbia},
number = {2},
pages = {81--100},
volume = {9},
year = {2009},
date-added = {2010-01-03 19:19:41 +0100},
date-modified = {2010-07-29 20:46:35 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Lloyd-2009-Journal%20of%20Educational%20Research%20&%20Policy%20Studies_When%20Measures%20Change.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p925},
rating = {0}
}

@article{Rivas:2010p11226,
author = {M A Rivas and M J Daly and I Pe'er},
title = {Age, Sex, and Genetic Architecture of Human Gene Expression in EBV Transformed Cell Line},
abstract = {Individual expression profiles from EBV transformed cell lines are an emerging resource for genomic investigation. In this study we characterize the effects of age, sex, and genetic variation on gene expression by surveying public datasets of such profiles. We establish that the expression space of cell lines maintains genetic as well as non-germline information, in an individual-specific and cross-tissue manner. Age of donor is associated with the expression of 949 genes in the derived cell line. Age-associated genes include over-representation of immune-related genes, specifically MHC Class I genes, a phenomenon that replicates across tissues and organisms. Sex associated genes in these cell lines include likely candidates, such as genes that escape X-inactivation, testis specific expressed genes, androgen and estrogen specific genes, but also gene families previously unknown to be sex associated such as common microRNA targets (MIR-490, V_ARP1_01, MIR-489). Finally, we report 494 transcripts whose expression levels are associated with a genetic variant in cis, overlapping and validating previous reports. Incorporating age in analysis of association facilitates additional discovery of trans-acting regulatory genetic variants. Our findings promote expression profiling of transformed cell lines as a vehicle for understanding cellular systems beyond the specific lines.},
date-added = {2010-04-25 21:29:26 +0200},
date-modified = {2010-04-25 21:30:05 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Rivas--_Age%20Sex%20and%20Geneti.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11226},
rating = {0}
}

@article{Nicodemus:2007p5842,
author = {Kristin K Nicodemus and Bhaskar S Kolachana and Radhakrishna Vakkalanka and Richard E Straub and Ina Giegling and Michael F Egan and Dan Rujescu and Daniel R Weinberger},
journal = {Hum Genet},
title = {Evidence for statistical epistasis between catechol-O-methyltransferase (COMT) and polymorphisms in RGS4, G72 (DAOA), GRM3, and DISC1: influence on risk of schizophrenia},
abstract = {Catechol-O-methyltransferase (COMT) regulates dopamine degradation and is located in a genomic region that is deleted in a syndrome associated with psychosis, making it a promising candidate gene for schizophrenia. COMT also has been shown to influence prefrontal cortex processing efficiency. Prefrontal processing dysfunction is a common finding in schizophrenia, and a background of inefficient processing may modulate the effect of other candidate genes. Using the NIMH sibling study (SS), a non-independent case-control set, and an independent German (G) case-control set, we performed conditional/unconditional logistic regression to test for epistasis between SNPs in COMT (rs2097603, Val158Met (rs4680), rs165599) and polymorphisms in other schizophrenia susceptibility genes. Evidence for interaction was evaluated using a likelihood ratio test (LRT) between nested models. SNPs in RGS4, G72, GRM3, and DISC1 showed evidence for significant statistical epistasis with COMT. A striking result was found in RGS4: three of five SNPs showed a significant increase in risk [LRT P-values: 90387 = 0.05 (SS); SNP4 = 0.02 (SS), 0.02 (G); SNP18 = 0.04 (SS), 0.008 (G)] in interaction with COMT; main effects for RGS4 SNPs were null. Significant results for SNP4 and SNP18 were also found in the German study. We were able to detect statistical interaction between COMT and polymorphisms in candidate genes for schizophrenia, many of which had no significant main effect. In addition, we were able to replicate other studies, including allelic directionality. The use of epistatic models may improve replication of psychiatric candidate gene studies.},
affiliation = {Clinical Brain Disorders Branch, National Institute of Mental Health, National Institute of Health, Bethesda, MD 20892, USA.},
number = {6},
pages = {889--906},
volume = {120},
year = {2007},
month = {Feb},
language = {eng},
keywords = {Middle Aged, Alleles, Case-Control Studies, Schizophrenia, Genetic Predisposition to Disease, Risk Factors, Epistasis: Genetic, Genotype, Haplotypes, Carrier Proteins, Humans, Catechol O-Methyltransferase, Models: Genetic, Receptors: Metabotropic Glutamate, RGS Proteins, Female, Adolescent, Polymorphism: Single Nucleotide, Adult, Male, Siblings, Nerve Tissue Proteins},
date-added = {2010-02-17 10:17:40 +0100},
date-modified = {2010-07-29 19:28:44 +0200},
doi = {10.1007/s00439-006-0257-3},
pmid = {17006672},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Nicodemus-2007-Hum%20Genet_Evidence%20for%20statist.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5842},
rating = {0}
}

@article{Sulek:2007p1319,
author = {S Sulek and Z Lacinov{\'a} and M Dolinkov{\'a} and M Haluzik},
journal = {Prague Med Rep},
title = {Genetic polymorphisms as a risk factor for anorexia nervosa},
abstract = {Anorexia nervosa (AN) is an eating disorder affecting mostly young people which could lead to serious complications and consequences. There are ethnical and gender differences in the incidence and prevalence of AN, but the influence of urbanization has not yet been proved. The relationship of genetic background to the risk of AN is still being investigated. In this review we summarize current knowledge about the relationship between AN and polymorphism of substances known to be regulating eating behaviour or metabolic pathways e.g. serotonin, ghrelin, catechol-O-methyl transferase, neuropeptide Y, brain-derived neurotrophic factor and adipokines.},
affiliation = {Department of Paediatrics and Adolescent Medicine, Charles University in Prague, First Faculty of Medicine and General Teaching Hospital, Prague, Czech Republic. stepan.sulek@gmail.com},
number = {3},
pages = {215--25},
volume = {108},
year = {2007},
month = {Jan},
language = {eng},
keywords = {Ghrelin, Catechol O-Methyltransferase, Genetic Predisposition to Disease, Humans, Polymorphism: Genetic, Anorexia Nervosa, Adipokines, Serotonin, Neuropeptide Y, Risk Factors},
date-added = {2010-01-07 11:36:39 +0100},
date-modified = {2010-01-07 11:36:39 +0100},
pmid = {18399059},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1319},
rating = {0}
}

@article{Abdo:2008p4588,
author = {Ayman A Abdo},
journal = {Saudi J Gastroenterol},
title = {Hepatitis C and poor quality of life: is it the virus or the patient?},
abstract = {Hepatitis C is a systemic disease that has many extrahepatic manifestations in addition to hepatic inflammation and fibrosis, some of which may result in a poor health-related quality of life (HRQOL). Fatigue is perhaps the most frequent and disabling extrahepatic symptom of hepatitis C virus (HCV), reported in almost one-half of all chronically infected individuals. Many other factors are associated with a poor quality of life in patients with HCV, including a number of physical and psychological factors. The objective of this article is to review the association between HCV and impaired HRQOL due to fatigue and psychological disturbances.},
affiliation = {Division of Gastroenterology, Department of Medicine, King Saud University, Riyadh, Saudi Arabia. aabdo@ksu.edu.sa},
number = {3},
pages = {109--13},
volume = {14},
year = {2008},
month = {Jul},
language = {eng},
date-added = {2010-01-29 22:33:23 +0100},
date-modified = {2010-01-29 22:33:23 +0100},
doi = {10.4103/1319-3767.41727},
pmid = {19568517},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Abdo-2008-Saudi%20J%20Gastroenterol_Hepatitis%20C%20and%20poor.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4588},
read = {Yes},
rating = {0}
}

@article{CostaSantos:2010p6657,
author = {Cristina Costa-Santos and Jo{\~a}o Bernardes and Diogo Ayres-de-Campos and Ant{\'o}nia Costa and C{\'e}lia Costa},
journal = {Journal of Clinical Epidemiology},
title = {The limits of agreement and the intraclass correlation coefficient may be inconsistent in the interpretation of agreement},
abstract = {OBJECTIVE: To compare the interpretation of agreement in the prediction of neonatal outcome variables, using the limits of agreement (LA) and the intraclass correlation coefficient (ICC). STUDY DESIGN AND SETTING: Three obstetricians were asked to predict neonatal outcomes independently based on the evaluation of intrapartum cardiotocographic tracings. Interobserver agreement was assessed with the LA and the ICC, and the results obtained were interpreted by six clinicians and six statisticians on a scale that established agreement as very poor, poor, fair, good, or very good. RESULTS: Interpretation of the LA results was less consensual than the ICC results, with proportions of agreement of 0.36 (95% confidence interval [CI]: 0.28-0.44) vs. 0.63 (95% CI: 0.54-0.73), respectively. LA results suggested a fair to good agreement among obstetricians, whereas interpretation of ICC results suggested a poor to fair agreement. LA results were more plausible with reality, suggesting that obstetricians predicted neonatal outcomes better than randomly generated values, whereas it was not always the case with the ICC. CONCLUSIONS: LA and ICC can provide inconsistent results in agreement studies. Accordingly, in the absence of better strategies to assess agreement, both should be used for this purpose, but their results need to be interpreted with caution keeping their respective limitations in mind.},
affiliation = {Biostatistics and Medical Informatics Department, Faculty of Medicine, University of Porto, Porto, Portugal; Center for Research in Health Technologies and Information Systems, Faculty of Medicine, University of Porto, Porto, Portugal.},
pages = {},
year = {2010},
month = {Feb},
language = {ENG},
date-added = {2010-03-03 20:40:39 +0100},
date-modified = {2010-03-03 20:40:41 +0100},
doi = {10.1016/j.jclinepi.2009.11.010},
pii = {S0895-4356(09)00364-3},
pmid = {20189765},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Costa-Santos-2010-Journal%20of%20Clinical%20Epidemiology_The%20limits%20of%20agreem-1.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6657},
rating = {3}
}

@article{GonzalezRoma:2003p5888,
author = {V Gonzalez-Roma and B Espejo},
journal = {Psicothema},
title = {Testing the middle response categories «Not sure», «In between» and «?» in polytomous items},
abstract = {The first aim of this study is to test two assumptions of integer scoring (the assumption of ordered res- ponse categories, and the assumption of ordered thresholds). We tested these assumptions using a set of items extracted from the social boldness scale of the 16PF questionnaire that were presented with three different middle response categories: «Not sure», «In between» and «?». The second aim was to compare a 3-point response scale with a dichotomous response scale in terms of the information func- tion and correlations with external criteria. The sample was composed of 816 undergraduate students. The results obtained showed that both assumptions were met only when the middle response category was «In between». The results also revealed that a 3-point response scale including «In between» pro- vided more information than a dichotomous response scale. Both scales showed similar correlations with the considered external criteria.},
number = {2},
pages = {278--284},
volume = {15},
year = {2003},
date-added = {2010-02-17 20:59:50 +0100},
date-modified = {2010-02-17 21:00:59 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Gonzalez-Roma-2003-Psicothema_Testing%20the%20middle%20r.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5888},
rating = {0}
}

@article{Gray:2002p10560,
author = {Jeremy R Gray and Todd S Braver and Marcus E Raichle},
journal = {Proc Natl Acad Sci USA},
title = {Integration of emotion and cognition in the lateral prefrontal cortex},
abstract = {We used functional MRI to test the hypothesis that emotional states can selectively influence cognition-related neural activity in lateral prefrontal cortex (PFC), as evidence for an integration of emotion and cognition. Participants (n = 14) watched short videos intended to induce emotional states (pleasant/approach related, unpleasant/withdrawal related, or neutral). After each video, the participants were scanned while performing a 3-back working memory task having either words or faces as stimuli. Task-related neural activity in bilateral PFC showed a predicted pattern: an Emotion x Stimulus crossover interaction, with no main effects, with activity predicting task performance. This highly specific result indicates that emotion and higher cognition can be truly integrated, i.e., at some point of processing, functional specialization is lost, and emotion and cognition conjointly and equally contribute to the control of thought and behavior. Other regions in lateral PFC showed hemispheric specialization for emotion and for stimuli separately, consistent with a hierarchical and hemisphere-based mechanism of integration.},
affiliation = {Department of Psychology, Washington University, One Brookings Drive, St. Louis, MO 63130, USA.},
number = {6},
pages = {4115--20},
volume = {99},
year = {2002},
month = {Mar},
language = {eng},
keywords = {Prefrontal Cortex, Behavior, Male, Memory, Cognition, Photic Stimulation, Functional Laterality, Emotions, Videotape Recording, Pattern Recognition: Visual, Female, Magnetic Resonance Imaging, Language, Humans, Adult},
date-added = {2010-04-07 11:32:38 +0200},
date-modified = {2010-04-07 11:32:38 +0200},
doi = {10.1073/pnas.062381899},
pii = {99/6/4115},
pmid = {11904454},
URL = {http://www.pnas.org/content/99/6/4115.long},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Gray-2002-Proc%20Natl%20Acad%20Sci%20USA_Integration%20of%20emoti.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10560},
rating = {0}
}

@article{Greenland:1991p1684,
author = {S Greenland and J M Robins},
title = {Empirical-Bayes adjustments for multiple comparisons are sometimes useful},
year = {1991},
date-added = {2010-01-08 22:30:37 +0100},
date-modified = {2010-01-09 18:24:01 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Greenland-1991-_Empirical-Bayes%20adju.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1684},
rating = {0}
}

@article{Williams:2009p8911,
author = {Leanne M Williams and Justine M Gatt and Peter R Schofield and Gloria Olivieri and Anthony Peduto and Evian Gordon},
journal = {Neuroimage},
title = {'Negativity bias' in risk for depression and anxiety: brain-body fear circuitry correlates, 5-HTT-LPR and early life stress},
abstract = {The INTEGRATE Model draws on the framework of 'integrative neuroscience' to bring together brain-body and behavioral concepts of emotion, thinking and feeling and their regulation. The key organizing principle is the drive to 'minimize danger and maximize reward' that determines what is significant to us at each point in time. Traits of 'negativity bias' reflect the tendency to perceive danger rather than reward related information, and this bias influences emotion, thinking and feeling processes. Here, we examined a self-report measure of Negativity Bias in relation to its impact on brain and body correlates of emotion processing. The contributions of the serotonin transporter (5-HTT-LPR) allelic variants and early life stress to both negativity bias and these correlates were also examined. Data were accessed in collaboration with the Brain Resource International Database (BRID) which provides standardized data across these domains of measurement. From an initial sample of 303 nonclinical subjects from the BRID, subjects scoring one standard deviation below (n=55) and above (n=47) the mean on the measure of negativity bias were identified as 'Negativity Bias' and 'Positivity Bias' groups for analysis, respectively. These subjects had been genotyped for 5-HTT-LPR Short allele versus LL homozygote status, and completed the early life stress scale, and recording of startle responses and heart rate for conscious and nonconscious fear conditions. A matched subset (n=39) of BRID subjects completed functional MRI with the same facial emotion tasks. The Negativity Bias (compared to Positivity Bias) group was distinguished by both arousal and brain function correlates: higher startle amplitude, higher heart rate for conscious and nonconscious fear conditions, and heightened activation in neural circuitry for both fear conditions. Regions of heightened activation included brainstem and bilateral amygdala, anterior cingulate and ventral and dorsal medial prefrontal cortex (mPFC) for conscious fear, and brainstem and right-sided amygdala, anterior cingulate and ventral, mPFC for nonconscious fear. The 5-HTT-LPR Short allele (versus LL) conferred a similar pattern of arousal and neural activation. For those with the 5-HTT-LPR Short allele, the addition of early life stress contributed to enhanced negativity bias, and to further effects on heart rate and neural activation for nonconscious fear in particular. These findings suggest that traits of negativity bias impact brain-body arousal correlates of fear circuitry. Both genetic variation and life stressors contribute to the impact of negativity bias. Given that negativity bias is a feature of conditions such as depression and associated biological alterations, the findings have implications for translation into clinical decision support.},
affiliation = {Brain Dynamics Centre, Westmead Millennium Institute and University of Sydney at Westmead Hospital, Westmead, NSW 2145, Australia. lea_williams@wmi.usyd.edu.au},
number = {3},
pages = {804--14},
volume = {47},
year = {2009},
month = {Sep},
language = {eng},
keywords = {Brain Mapping, Brain, Young Adult, Heart Rate, Emotions, Fear, Adult, Middle Aged, Risk Factors, Depression, Electromyography, Personality, Stress: Psychological, Male, Female, Adolescent, Humans, Arousal, Genetic Predisposition to Disease, Startle Reaction, Anxiety, Serotonin Plasma Membrane Transport Proteins, Magnetic Resonance Imaging},
date-added = {2010-03-22 12:57:13 +0100},
date-modified = {2010-03-22 12:57:13 +0100},
doi = {10.1016/j.neuroimage.2009.05.009},
pii = {S1053-8119(09)00491-1},
pmid = {19446647},
URL = {http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNP-4W91PVH-2&_user=2432700&_coverDate=09%252F30%252F2009&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000057263&_version=1&_urlVersion=0&_userid=2432700&md5=77ce2f8319f094e029373ae1069c935a},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Williams-2009-Neuroimage_'Negativity%20bias'%20in.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8911},
rating = {0}
}

@article{vanBuuren:2006p13984,
author = {Stef van Buuren and J P L Brand and C G M Groothuis-Oudshoorn and D B Rubin},
journal = {Journal of Statistical Computation and Simulation},
title = {Fully conditional specification in multivariate imputation},
abstract = {The use of the Gibbs sampler with fully conditionally specified models, where the distribution of each variable given the other variables is the starting point, has become a popular method to create imputations in incomplete multivariate data. The theoretical weakness of this approach is that the specified conditional densities can be incompatible, and therefore the stationary distribution to which the Gibbs sampler attempts to converge may not exist. This study investigates practical consequences of this problem by means of simulation. Missing data are created under four different missing data mechanisms. Attention is given to the statistical behavior under compatible and incompatible models. The results indicate that multiple imputation produces essentially unbiased estimates with appropriate coverage in the simple cases investigated, even for the incompatible models. Of particular interest is that these results were produced using only five Gibbs iterations starting from a simple draw from observed marginal distributions. It thus appears that, despite the theoretical weaknesses, the actual performance of conditional model specification for multivariate imputation can be quite good, and therefore deserves further study.},
number = {12},
pages = {1049--1064},
volume = {76},
year = {2006},
date-added = {2010-07-30 21:33:53 +0200},
date-modified = {2010-07-30 21:35:33 +0200},
doi = {10.1080/10629360600810434},
local-url = {file://localhost/Users/chl/Dropbox/Papers/van%20Buuren-2006-Journal%20of%20Statistical%20Computation%20and%20Simulation_Fully%20conditional%20sp.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13984},
rating = {0}
}

@article{Singh:2009p11625,
author = {K Singh},
journal = {Journal of the Indian Academy of Applied Psychology},
title = {NEO-PI-R Factor Structure in College Students},
abstract = {Little is known about the effectiveness and validity of the revised NEO personality inventory (NEO-PI-R) for identifying the personality traits of the big five in Indian context on students' sample. The main objectives of this study were to examine the replicability of the five-factor model and to establish external validity for personality traits in this population. A total of 205 technology students completed the NEO-PI-R, Emotional intelligence scale and Oxford Happiness Questionnaire. Using principal component analysis with varimax rotation, the dimensions of personality in the Indian students sample clearly replicate the five-factor structure for N,C, and A except A5 facet. Whereas, O and E did not get high loading of their all facets. Psychometric properties of	NEO-PI-R have been discussed in this paper.},
number = {1},
pages = {17--25},
volume = {35},
year = {2009},
date-added = {2010-05-11 22:45:37 +0200},
date-modified = {2010-05-11 22:46:22 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Singh-2009-Journal%20of%20the%20Indian%20Academy%20of%20Applied%20Psychology_NEO-PI-R%20Factor%20Stru.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11625},
rating = {0}
}

@article{Sluyter:2010p12086,
author = {Ronald Sluyter and Leanne Stokes and Stephen J Fuller and Kristen K Skarratt and Ben J Gu and James S Wiley},
journal = {J Psychiatr Res},
title = {Functional significance of P2RX7 polymorphisms associated with affective mood disorders},
affiliation = {School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia.},
pages = {},
year = {2010},
month = {May},
language = {ENG},
date-added = {2010-05-24 12:31:37 +0200},
date-modified = {2010-05-24 12:31:37 +0200},
doi = {10.1016/j.jpsychires.2010.04.013},
pii = {S0022-3956(10)00123-8},
pmid = {20462595},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Sluyter-2010-J%20Psychiatr%20Res_Functional%20significa.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12086},
rating = {0}
}

@techreport{Wang:1998,
author = {Wen-Chung Wang},
journal = {Techreport},
title = {An ANOVA-like Rasch analysis of differential item functioning},
affiliation = {National Chung Cheng University},
year = {1998},
date-added = {2010-01-10 11:33:25 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Wang-1998-Techreport_An%20ANOVA-like%20Rasch.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1870},
rating = {0}
}

@article{Pan:2005p9851,
author = {Zhiying Pan and D Y Lin},
journal = {Biometrics},
title = {Goodness-of-fit methods for generalized linear mixed models},
abstract = {We develop graphical and numerical methods for checking the adequacy of generalized linear mixed models (GLMMs). These methods are based on the cumulative sums of residuals over covariates or predicted values of the response variable. Under the assumed model, the asymptotic distributions of these stochastic processes can be approximated by certain zero-mean Gaussian processes, whose realizations can be generated through Monte Carlo simulation. Each observed process can then be compared, both visually and analytically, to a number of realizations simulated from the null distribution. These comparisons enable one to assess objectively whether the observed residual patterns reflect model misspecification or random variation. The proposed methods are particularly useful for checking the functional form of a covariate or the link function. Extensive simulation studies show that the proposed goodness-of-fit tests have proper sizes and are sensitive to model misspecification. Applications to two medical studies lead to improved models.},
affiliation = {Department of Biostatistics, University of North Carolina, CB 7420, McGavran-Greenberg Hall, Chapel Hill, 27599-7420, USA.},
number = {4},
pages = {1000--9},
volume = {61},
year = {2005},
month = {Dec},
language = {eng},
keywords = {HIV Infections, Female, Vitamin A, Data Interpretation: Statistical, Humans, Monte Carlo Method, Male, Zidovudine, CD4 Lymphocyte Count, Linear Models, Computer Simulation, Indonesia, Child: Preschool, Respiratory Tract Infections, Anti-HIV Agents},
date-added = {2010-03-26 19:29:49 +0100},
date-modified = {2010-03-26 19:29:49 +0100},
doi = {10.1111/j.1541-0420.2005.00365.x},
pii = {BIOM365},
pmid = {16401273},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Pan-2005-Biometrics_Goodness-of-fit%20meth.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9851},
rating = {0}
}

@article{Rabe-Hesketh:2001a,
author = {Sophia Rabe-Hesketh and Anders Skrondal and Andrew Pickles},
journal = {The Stata Joumal},
title = {Maximum likelihood estimation of generalized linear model with covariate measurement error},
number = {1},
volume = {1},
year = {2001},
date-added = {2010-01-03 19:37:35 +0100},
date-modified = {2010-07-29 19:53:39 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Rabe-Hesketh-2001-The%20Stata%20Joumal_Maximum%20likelihood%20e.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1101},
rating = {0}
}

@article{Soto:2008p13864,
author = {Christopher J Soto and Oliver P John and Samuel D Gosling and Jeff Potter},
journal = {J Pers Soc Psychol},
title = {The developmental psychometrics of big five self-reports: acquiescence, factor structure, coherence, and differentiation from ages 10 to 20},
abstract = {How do youths' personality reports differ from those of adults? To identify the year-by-year timing of developmental trends from late childhood (age 10) to early adulthood (age 20), the authors examined Big Five self-report data from a large and diverse Internet sample. At younger ages within this range, there were large individual differences in acquiescent responding, and acquiescence variability had pronounced effects on psychometric characteristics. Beyond the effects of acquiescence, self-reports generally became more coherent within domains, and better differentiated across domains, at older ages. Importantly, however, different Big Five domains showed different developmental trends. Extraversion showed especially pronounced age gains in coherence but no gains in differentiation. In contrast, Agreeableness and Conscientiousness showed large age gains in differentiation but only trivial gains in coherence. Neuroticism and Openness showed moderate gains in both coherence and differentiation. Comparisons of items that were relatively easy versus difficult to comprehend indicated that these patterns were not simply due to verbal comprehension. These findings have important implications for the study of personality characteristics and other psychological attributes in childhood and adolescence.},
affiliation = {Department of Psychology, University of California, Berkeley, CA 94720-5050, USA. cjsoto@berkeley.edu},
number = {4},
pages = {718--37},
volume = {94},
year = {2008},
month = {Apr},
language = {eng},
keywords = {Patient Selection, Humans, Informed Consent, Self Concept, Child, Psychometrics, Language Development, Male, Vocabulary, Data Collection, Reproducibility of Results, Adolescent, Extraversion (Psychology), Adult, Personality Development, Internet, Personality Inventory, Comprehension, Female},
date-added = {2010-07-29 17:44:35 +0200},
date-modified = {2010-07-29 19:35:33 +0200},
doi = {10.1037/0022-3514.94.4.718},
pii = {2008-02998-010},
pmid = {18361680},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13864},
rating = {0}
}

@article{Nering:1995p2698,
author = {M L Nering},
journal = {Applied Psychological Measurement},
title = {The Distribution of Person Fit Using True and Estimated Person Parameters},
number = {2},
pages = {121--129},
volume = {19},
year = {1995},
date-added = {2010-01-13 10:16:54 +0100},
date-modified = {2010-07-29 19:16:53 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Nering-1995-Applied%20Psychological%20Measurement_The%20Distribution%20of.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2698},
rating = {0}
}

@article{Felsted:2010p8906,
author = {Jennifer A Felsted and Xueying Ren and Francois Chouinard-Decorte and Dana M Small},
journal = {J Neurosci},
title = {Genetically determined differences in brain response to a primary food reward},
abstract = {Combining genetic and neuroimaging techniques may elucidate the biological underpinnings of individual differences in neurophysiology and potential vulnerabilities to disease. The TaqIA A1 variant is associated with diminished dopamine D(2) receptor density, higher body mass, and food reinforcement. It also moderates the relationship between brain response to food and future weight gain. This suggests that the polymorphism is associated with a fundamental difference in the neurophysiology of food that may predispose toward overeating. An alternative possibility is that factors, such as impulsivity, eating style, reward drive, and perception, which may covary with the polymorphism, influence reward coding and eating behavior. To distinguish between these alternatives, we used functional magnetic resonance imaging to measure neural response to the ingestion of palatable and caloric milkshakes in healthy subjects with (A1+; n = 13) and without (A1-; n = 13) the TaqIA A1 allele. The groups were selected from a larger group to be matched for linked individual factors such as age, gender, education, body mass index, impulsivity, eating style, and perceptual responses to the milkshake. We demonstrate an interaction between genotype (A1+ vs A1-) and stimulus (milkshake vs a tasteless/odorless baseline) in the midbrain, thalamus, and orbital frontal cortex; whereas A1- shows increased responses to milkshake, A1+ shows decreased responses to milkshake relative to baseline. This interaction occurs despite similar ratings of milkshake pleasantness, intensity, and familiarity. We therefore conclude that there is a specific association between the TaqIA A1 polymorphism and brain response during ingestion of a palatable food.},
affiliation = {The John B. Pierce Laboratory, New Haven, Connecticut 06519, USA.},
number = {7},
pages = {2428--32},
volume = {30},
year = {2010},
month = {Feb},
language = {eng},
keywords = {Body Mass Index, Gene Frequency, Receptors: Dopamine D2, Brain, Image Processing: Computer-Assisted, Eating, Analysis of Variance, Oxygen, Reward, Taste, Magnetic Resonance Imaging, Polymorphism: Genetic, Feeding Behavior, Personality Inventory, Genotype, Brain Mapping, Food Preferences, Humans},
date-added = {2010-03-22 12:53:23 +0100},
date-modified = {2010-07-29 19:52:28 +0200},
doi = {10.1523/JNEUROSCI.5483-09.2010},
pii = {30/7/2428},
pmid = {20164326},
URL = {http://www.jneurosci.org/cgi/content/full/30/7/2428},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Felsted-2010-J%20Neurosci_Genetically%20determin.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8906},
rating = {0}
}

@article{RevahLevy:2007p2916,
author = {Anne Revah-Levy and Boris Birmaher and Isabelle Gasquet and Bruno Falissard},
journal = {BMC Psychiatry},
title = {The Adolescent Depression Rating Scale (ADRS): a validation study},
abstract = {BACKGROUND: To examine the psychometric properties of the Adolescent Depression Rating Scale (ADRS), a new measure was specifically designed to evaluate adolescent depression. METHODS: The 11-item clinician-report and 44-item self-report versions of the ADRS were developed from a qualitative phase involving interviews of experts and adolescents. These two instruments were then administered to 402 French speaking adolescents with and without depressive disorders. Item distribution, internal consistency, convergent validity, discriminant validity and factorial structure were assessed. RESULTS: After reduction procedures, a 10-item clinician version and a 10-item self-report version were obtained. The ADRS demonstrated good internal consistency (alpha Cronbach coefficient >.70). It also discriminated better between adolescents with and without depression than the Hamilton Depressive Rating Scale and the Beck Depression Inventory (BDI-13). CONCLUSION: The ADRS is a useful, short, clinician-report and self-report scale to evaluate adolescent depression. Further studies to replicate our findings and evaluate ADRS sensitivity to effects of treatment and psychometric properties in populations of adolescents with several psychiatric disorders are warranted.},
affiliation = {INSERM U669, Universit{\'e} Paris Sud 11, Centre Hospitalier V, Dupouy, 95107 Argenteuil, France. anne.revah-levy@ch-argenteuil.fr},
pages = {2},
volume = {7},
year = {2007},
month = {Jan},
language = {eng},
keywords = {Female, Sensitivity and Specificity, Adolescent, Psychometrics, Depressive Disorder, Adult, Adolescent Psychiatry, Male, Humans, Psychiatric Status Rating Scales},
date-added = {2010-01-13 21:50:48 +0100},
date-modified = {2010-01-13 21:50:51 +0100},
doi = {10.1186/1471-244X-7-2},
pii = {1471-244X-7-2},
pmid = {17222346},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Revah-Levy-2007-BMC%20Psychiatry_The%20Adolescent%20Depre-1.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2916},
rating = {3}
}

@article{Beguin:2001p2771,
author = {A A B{\'e}guin and C A W Glas},
journal = {Psychometrika},
title = {MCMC estimation and some model-fit analysis of multidimensional IRT models},
number = {4},
pages = {541--562},
volume = {66},
year = {2001},
date-added = {2010-01-13 14:27:37 +0100},
date-modified = {2010-01-13 14:28:30 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/B%C3%A9guin-2001-Psychometrika_MCMC%20estimation%20and-1.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2771},
rating = {0}
}

@article{Denny:2010p11433,
author = {Joshua C Denny and Marylyn D Ritchie and Melissa A Basford and Jill M Pulley and Lisa Bastarache and Kristin Brown-Gentry and Deede Wang and Dan R Masys and Dan M Roden and Dana C Crawford},
journal = {Bioinformatics},
title = {PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations},
abstract = {MOTIVATION: Emergence of genetic data coupled to longitudinal electronic medical records (EMRs) offers the possibility of phenome-wide association scans (PheWAS) for disease-gene associations. We propose a novel method to scan phenomic data for genetic associations using International Classification of Disease (ICD9) billing codes, which are available in most EMR systems. We have developed a code translation table to automatically define 776 different disease populations and their controls using prevalent ICD9 codes derived from EMR data. As a proof of concept of this algorithm, we genotyped the first 6005 European-Americans accrued into BioVU, Vanderbilt's DNA biobank, at five single nucleotide polymorphisms (SNPs) with previously reported disease associations: atrial fibrillation, Crohn's disease, carotid artery stenosis, coronary artery disease, multiple sclerosis, systemic lupus erythematosus and rheumatoid arthritis. The PheWAS software generated cases and control populations across all ICD9 code groups for each of these five SNPs, and disease-SNP associations were analyzed. The primary outcome of this study was replication of seven previously known SNP-disease associations for these SNPs. RESULTS: Four of seven known SNP-disease associations using the PheWAS algorithm were replicated with P-values between 2.8 x 10(-6) and 0.011. The PheWAS algorithm also identified 19 previously unknown statistical associations between these SNPs and diseases at P < 0.01. This study indicates that PheWAS analysis is a feasible method to investigate SNP-disease associations. Further evaluation is needed to determine the validity of these associations and the appropriate statistical thresholds for clinical significance. AVAILABILITY: The PheWAS software and code translation table are freely available at http://knowledgemap.mc.vanderbilt.edu/research.},
affiliation = {Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA. josh.denny@vanderbilt.edu},
number = {9},
pages = {1205--10},
volume = {26},
year = {2010},
month = {May},
language = {eng},
date-added = {2010-05-01 17:16:17 +0200},
date-modified = {2010-05-01 17:16:17 +0200},
doi = {10.1093/bioinformatics/btq126},
pii = {btq126},
pmid = {20335276},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Denny-2010-Bioinformatics_PheWAS%20demonstratin.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11433},
rating = {0}
}

@article{vandenWollenberg:1982p2678,
author = {A L van den Wollenberg},
journal = {Applied Psychological Measurement},
title = {A Simple and Effective Method to Test the Dimensionality Axiom of the Rasch Model},
number = {1},
pages = {83--91},
volume = {6},
year = {1982},
date-added = {2010-01-13 09:52:47 +0100},
date-modified = {2010-07-29 19:16:53 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/van%20den%20Wollenberg-1982-Applied%20Psychological%20Measurement_A%20Simple%20and%20Effecti.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2678},
rating = {0}
}

@article{Leeuw:1986,
author = {Jan de Leeuw and I Kreft},
journal = {Journal of Educational Statistics},
title = {Random coefficient models for multilevel analysis},
pages = {57--85},
volume = {11},
year = {1986},
date-added = {2010-01-10 11:33:20 +0100},
date-modified = {2010-07-29 20:45:39 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/de%20Leeuw-1986-Journal%20of%20Educational%20Statistics_Random%20coefficient%20m.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2077},
rating = {0}
}

@article{deWit:2007p9735,
author = {H de Wit and J D Flory and A Acheson and M McCloskey and S B Manuck},
journal = {Personality and Individual Differences},
title = {IQ and nonplanning impulsivity are independently associated with delay discounting in middle-aged adults},
abstract = {Impulsivity is a complex and multidimensional construct measured using both self-report measures and objective behavioral tasks. However, most studies using behavioral tasks have utilized relatively small homogeneous populations. In this project we examined both self-reported impulsivity, using the Barratt Impulsiveness Scale (BIS), and delay discounting, a behavioral measure of preference for immediate over delayed rewards, in a large sample of adults (N = 606). Performance on the self-report and behavioral mea- sures was examined in relation to demographic characteristics including age, sex, race, IQ, years of school and family income. Using hierarchical multiple regression we found that preference for immediate rewards was related to the Nonplanning impulsiveness subscale of the BIS and, after controlling for other variables, also related to intelligence. The finding that delay discounting, or preference for immediate rewards, is related to intelligence even after taking into account other variables, including socioeconomic indicators, suggests that there may be previously unrecognized links between this form of impulsivity and intelligence. This also suggests that intelligence should be taken into account in studies designed to measure impulsive behaviors.},
pages = {111--121},
volume = {42},
year = {2007},
date-added = {2010-03-25 15:16:42 +0100},
date-modified = {2010-03-25 15:17:41 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/de%20Wit-2007-Personality%20and%20Individual%20Differences_IQ%20and%20nonplanning%20i.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9735},
rating = {0}
}

@article{Nicodemus:2009p3393,
author = {Kristin K Nicodemus and James D Malley},
journal = {Bioinformatics},
title = {Predictor correlation impacts machine learning algorithms: implications for genomic studies},
abstract = {MOTIVATION: The advent of high-throughput genomics has produced studies with large numbers of predictors (e.g. genome-wide association, microarray studies). Machine learning algorithms (MLAs) are a computationally efficient way to identify phenotype-associated variables in high-dimensional data. There are important results from mathematical theory and numerous practical results documenting their value. One attractive feature of MLAs is that many operate in a fully multivariate environment, allowing for small-importance variables to be included when they act cooperatively. However, certain properties of MLAs under conditions common in genomic-related data have not been well-studied--in particular, correlations among predictors pose a problem. RESULTS: Using extensive simulation, we showed considering correlation within predictors is crucial in making valid inferences using variable importance measures (VIMs) from three MLAs: random forest (RF), conditional inference forest (CIF) and Monte Carlo logic regression (MCLR). Using a case-control illustration, we showed that the RF VIMs--even permutation-based--were less able to detect association than other algorithms at effect sizes encountered in complex disease studies. This reduction occurred when 'causal' predictors were correlated with other predictors, and was sharpest when RF tree building used the Gini index. Indeed, RF Gini VIMs are biased under correlation, dependent on predictor correlation strength/number and over-trained to random fluctuations in data when tree terminal node size was small. Permutation-based VIM distributions were less variable for correlated predictors and are unbiased, thus may be preferred when predictors are correlated. MLAs are a powerful tool for high-dimensional data analysis, but well-considered use of algorithms is necessary to draw valid conclusions. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
affiliation = {Department of Statistical Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. kristin.nicodemus@well.ox.ac.uk},
number = {15},
pages = {1884--90},
volume = {25},
year = {2009},
month = {Aug},
language = {eng},
keywords = {Artificial Intelligence, Genome-Wide Association Study, Polymorphism: Single Nucleotide, Phenotype, Genome, Oligonucleotide Array Sequence Analysis, Genomics, Algorithms},
date-added = {2010-01-15 14:40:21 +0100},
date-modified = {2010-01-15 14:40:27 +0100},
doi = {10.1093/bioinformatics/btp331},
pii = {btp331},
pmid = {19460890},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3393},
rating = {3}
}

@article{Borenstein:2005p3615,
author = {M Borenstein},
title = {Software for Publication Bias},
year = {2005},
date-added = {2010-01-16 18:33:12 +0100},
date-modified = {2010-01-16 18:33:37 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Borenstein-2005-_Software%20for%20Publica.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3615},
rating = {0}
}

@article{McCrae:2005p8312,
author = {Robert R McCrae and Paul T Costa Jr and Thomas A Martin},
journal = {J Pers Assess},
title = {The NEO-PI-3: a more readable revised NEO Personality Inventory},
abstract = {Use of the Revised NEO Personality Inventory (NEO-PI-R; Costa {\&} McCrae, 1992) in adolescent samples has shown that a few respondents have difficulty with a subset of items. We identified 30 items that were not understood by at least 2% of adolescent respondents and 18 additional items with low item-total correlations, and we wrote 2 trial replacement items for each. We used self-report and observer rating data from 500 respondents aged 14 to 20 to select replacement items. The modified instrument retained the intended factor structure and showed slightly better internal consistency, cross-observer agreement, and readability (Flesch-Kincaid grade level = 5.3). The NEO-PI-3 appears to be useful in high school and college samples and may have wider applicability to adults as well.},
affiliation = {National Institute on Aging, National Institutes of Health, Department of Health and Human Services, Baltimore, Maryland 21224-6825, USA. mccraej@grc.nia.nih.gov},
note = {psytools},
number = {3},
pages = {261--70},
volume = {84},
year = {2005},
month = {Jun},
language = {eng},
keywords = {Adolescent Behavior, Male, Terminology as Topic, Female, Adult, Humans, Psychometrics, Adolescent, Comprehension, Personality Inventory},
date-added = {2010-03-20 20:10:05 +0100},
date-modified = {2010-03-20 20:10:25 +0100},
doi = {10.1207/s15327752jpa8403_05},
pmid = {15907162},
local-url = {file://localhost/Users/chl/Dropbox/Papers/McCrae-2005-Journal%20of%20Personality%20Assessment_The%20NEO-PI-3%20a%20more.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8312},
read = {Yes},
rating = {0}
}

@article{Bergsma:1997p1618,
author = {W P Bergsma},
title = {Marginal Models},
year = {1997},
date-added = {2010-01-07 17:18:43 +0100},
date-modified = {2010-01-07 17:19:12 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bergsma-1997-_Marginal%20Models.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1618},
read = {Yes},
rating = {3}
}

@article{Lachman:2007p3873,
author = {Herbert M Lachman and Cathy S J Fann and Michael Bartzis and Oleg V Evgrafov and Richard N Rosenthal and Edward V Nunes and Christian Miner and Maria Santana and Jebediah Gaffney and Amy Riddick and Chia-Lin Hsu and James A Knowles},
journal = {Hum Mol Genet},
title = {Genomewide suggestive linkage of opioid dependence to chromosome 14q},
abstract = {The genetic predisposition to addiction to opioids and other substances is transmitted as a complex genetic trait, which investigators are attempting to characterize using genetic linkage and association. We now report a high-density genome-wide linkage study of opioid dependence. We ascertained 305 DSM-IV opioid dependent affected sibling pairs from an ethnically mixed population of methadone maintained subjects and genotyped their DNA using Affymetrix 10K v2 arrays. Analysis with MERLIN identified a region on chromosome 14q with a non-parametric lod (NPL) of 3.30. Secondary analyses indicated that this locus was relatively specific to the self-identified Puerto Rican subset, as the NPL increased from 3.30 to 5.00 (NPL(Caucasian) = 0.05 and NPL(African Amer.) = 0.15). The 14q peak encompasses the NRXN3 gene (neurexin 3), which was previously identified as a potential candidate gene for addiction. Secondary analyses also identified several regions with gender-specific NPL scores greater than 2.00. The most significant was a peak on (10q) that increased from 0.90 to 3.22 when only males were considered (NPL(female) = 0.05). Our linkage data suggest specific chromosomal loci for future fine-mapping genetic analysis and support the hypothesis that ethnic and gender specific genes underlie addiction susceptibility.},
affiliation = {Division of Basic Research, Department of Psychiatry and Behavioral Sciences, Albert Einstein College of MedicineBronx, NY 10461, USA. lachman@aecom.yu.edu},
number = {11},
pages = {1327--34},
volume = {16},
year = {2007},
month = {Jun},
language = {eng},
keywords = {Substance-Related Disorders, Genome: Human, Female, Linkage (Genetics), Analgesics: Opioid, Genetic Predisposition to Disease, Male, Humans, Siblings, Chromosomes: Human: Pair 14},
date-added = {2010-01-16 21:03:24 +0100},
date-modified = {2010-01-16 21:03:25 +0100},
doi = {10.1093/hmg/ddm081},
pii = {ddm081},
pmid = {17409192},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3873},
rating = {0}
}

@article{Bacanu:2002p4956,
author = {Silviu-Alin Bacanu and Bernie Devlin and Kathryn Roeder},
journal = {Genet Epidemiol},
title = {Association studies for quantitative traits in structured populations},
abstract = {Association between disease and genetic polymorphisms often contributes critical information in our search for the genetic components of common diseases. Devlin and Roeder [1999: Biometrics 55:997-1004] introduced genomic control, a statistical method that overcomes a drawback to the use of population-based samples for tests of association, namely spurious associations induced by population structure. In essence, genomic control (GC) uses markers throughout the genome to adjust for any inflation in test statistics due to substructure. To date, genomic control (GC) has been developed for binary traits and bi- or multiallelic markers. Tests of association using GC have been limited to single genes. In this report, we generalize GC to quantitative traits (QT) and multilocus models. Using statistical analysis and simulations, we show that GC controls spurious associations in reasonable settings of population substructure for QT models, including gene-gene interaction. Through simulations, we explore GC power for both random and selected samples, assuming the QT locus tested is causal and its specific heritability is 2.5-5%. We find that GC, combined with either random or selected samples, has good power in this setting, and that more complex models induce smaller GC corrections. The latter suggests greater power can be achieved by specifying more complex genetic models, but this observation only follows when such models are largely correct and specified a priori.},
affiliation = {Department of Psychiatry, University of Pittsburgh School of Medicine, 3811 O'Hara Street, Pittsburgh, PA 15213, USA. roeder@stat.cmu.edu},
number = {1},
pages = {78--93},
volume = {22},
year = {2002},
month = {Jan},
language = {eng},
keywords = {Genetic Predisposition to Disease, Quantitative Trait: Heritable, Genome: Human, Humans, Phenotype, Genotype, Probability, Models: Genetic, Polymorphism: Genetic, Genetic Markers, Alleles},
date-added = {2010-02-03 21:01:26 +0100},
date-modified = {2010-02-03 21:01:26 +0100},
doi = {10.1002/gepi.1045},
pii = {10.1002/gepi.1045},
pmid = {11754475},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bacanu-2002-Genet%20Epidemiol_Association%20studies.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4956},
rating = {0}
}

@article{Diaz2006,
author = {R D\'iaz-Uriarte and Sara Alvarez de Andr{\'e}s},
journal = {BMC Bioinformatics},
title = {Gene selection and classification of microarray data using random forest},
number = {3},
volume = {7},
year = {2006},
date-added = {2010-01-12 14:26:51 +0100},
date-modified = {2010-07-29 20:21:27 +0200},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2562},
rating = {0}
}

@article{Gelhorn:2005p9524,
author = {Heather L Gelhorn and Michael C Stallings and Susan E Young and Robin P Corley and Soo Hyun Rhee and John K Hewitt},
journal = {J Child Psychol Psychiatry},
title = {Genetic and environmental influences on conduct disorder: symptom, domain and full-scale analyses},
abstract = {BACKGROUND: We used variable threshold models which accounted for age and gender differences to investigate the genetic and environmental influences on DSM-IV conduct disorder (CD) at the level of symptoms, aggressive versus non-aggressive domains, and full-scale. METHOD: A community sample of 1100 twin pairs (age 11-18) was interviewed using the Diagnostic Interview Schedule for Children. RESULTS: Behavior genetic model fitting suggested that genetic and environmental influences on individual symptoms varied by symptom. The best-fitting models for aggressive and non-aggressive domains, and full-scale CD included additive genetic effects and unique environmental effects only (AE models). These effects could be constrained across age cohorts and sex. The results suggest that using models that incorporate age- and gender-appropriate thresholds specific to each subject we can account for prevalence differences between cohorts. Heritability estimates were .49, .55 and .53 for the aggressive domain, non-aggressive domain, and full-scales, respectively. These results are in contrast to previous research on antisocial behavior measured with the CBCL reporting higher heritability for aggressive versus non-aggressive domains. CONCLUSIONS: Results suggest that individual symptoms of CD may be differentially heritable. Additionally, CD assessed using DSM-IV criteria may show differing patterns of heritability compared with estimates obtained for other measures of antisocial behavior such as the CBCL.},
affiliation = {Institute for Behavioral Genetics, University of Colorado, Boulder, CO 80309-0447, USA. gelhorn@colorado.edu},
number = {6},
pages = {580--91},
volume = {46},
year = {2005},
month = {Jun},
language = {eng},
keywords = {Conduct Disorder, Female, Sex Factors, Phenotype, Antisocial Personality Disorder, Humans, Child, Diagnostic and Statistical Manual of Mental Disorders, Models: Psychological, Male, Interviews as Topic, Chi-Square Distribution, Environment, Genetic Heterogeneity, Adolescent, Age Factors, Aggression},
date-added = {2010-03-23 19:44:05 +0100},
date-modified = {2010-07-29 19:32:47 +0200},
doi = {10.1111/j.1469-7610.2004.00373.x},
pii = {JCPP373},
pmid = {15877764},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9524},
rating = {0}
}

@article{Cremeens:2006p8496,
author = {Joanne Cremeens and Christine Eiser and Mark Blades},
journal = {Health Qual Life Outcomes},
title = {Factors influencing agreement between child self-report and parent proxy-reports on the Pediatric Quality of Life Inventory 4.0 (PedsQL) generic core scales},
abstract = {BACKGROUND: In situations where children are unable or unwilling to respond for themselves, measurement of quality of life (QOL) is often obtained by parent proxy-report. However the relationship between child self and parent proxy-reports has been shown to be poor in some circumstances. Additionally the most appropriate statistical method for comparing ratings between child and parent proxy-reports has not been clearly established. The objectives of this study were to assess the: 1) agreement between child and parent proxy-reports on an established child QOL measure (the PedsQL) using two different statistical methods; 2) effect of chronological age and domain type on agreement between children's and parents' reports on the PedsQL; 3) relationship between parents' own well-being and their ratings of their child's QOL. METHODS: One hundred and forty-nine healthy children (5.5 - 6.5, 6.5 - 7.5, and 7.5 - 8.5 years) completed the PedsQL. One hundred and three of their parents completed these measures in relation to their child, and a measure of their own QOL (SF-36). RESULTS: Consistency between child and parent proxy-reports on the PedsQL was low, with Intra-Class correlation coefficients ranging from 0.02 to 0.23. Correlations were higher for the oldest age group for Total Score and Psychosocial Health domains, and for the Physical Health domain in the youngest age group. Statistically significant median differences were found between child and parent-reports on all subscales of the PedsQL. The largest median differences were found for the two older age groups. Statistically significant correlations were found between parents' own QOL and their proxy-reports of child QOL across the total sample and within the middle age group. CONCLUSION: Intra-Class correlation coefficients and median difference testing can provide different information on the relationship between parent proxy-reports and child self-reports. Our findings suggest that differences in the levels of parent-child agreement previously reported may be an artefact of the statistical method used. In addition, levels of agreement can be affected by child age, domains investigated, and parents' own QOL. Further studies are needed to establish the optimal predictors of levels of parent-child agreement.},
affiliation = {Division of Behavioral Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA. Joanne.Cremeens@stjude.org},
pages = {58},
volume = {4},
year = {2006},
month = {Jan},
language = {eng},
keywords = {Self Assessment (Psychology), Parents, Quality of Life, Adolescent, Middle Aged, Adult, Proxy, Age Factors, Child: Preschool, Male, Child Psychology, Attitude to Health, Pediatrics, Child, Consensus, Psychometrics, Female, Humans, Health Status},
date-added = {2010-03-21 18:01:02 +0100},
date-modified = {2010-03-21 18:01:02 +0100},
doi = {10.1186/1477-7525-4-58},
pii = {1477-7525-4-58},
pmid = {16942613},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Cremeens-2006-Health%20and%20Quality%20of%20Life%20Outcomes_Factors%20influencing.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8496},
read = {Yes},
rating = {0}
}

@article{Gibson:1960p12006,
author = {W A Gibson},
journal = {Psychometrika},
title = {Remarks on Tucker's inter-battery method of factor analysis},
number = {1},
pages = {19--25},
volume = {25},
year = {1960},
date-added = {2010-05-23 17:34:16 +0200},
date-modified = {2010-05-23 17:35:03 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Gibson-1960-Psychometrika_Remarks%20on%20Tucker's.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12006},
rating = {0}
}

@article{Huang:2006p12327,
author = {J Huang and S Ma and C-H Zhang},
title = {Adaptive lasso for sparse high-dimensional regression models},
abstract = {We study the asymptotic properties of adaptive LASSO estimators in sparse, high-dimensional, linear regression models when the number of covariates may increase with the sample size. We consider variable selection using the adaptive LASSO, where the L1 norms in the penalty are re-weighted by data-dependent weights. We show that, if a reasonable initial estimator is available, then under appropriate conditions, adaptive LASSO correctly select covariates with nonzero coefficients with probability converging to one and that the estimators of nonzero coefficients have the same asymptotic dis- tribution that they would have if the zero coefficients were known in advance. Thus, the adaptive LASSO has an oracle property in the sense of Fan and Li (2001) and Fan and Peng (2004). In addition, under a partial orthogonality condition in which the covariates with zero coefficients are weakly correlated with the covariates with nonzero coefficients, univariate regression can be used to obtain the initial estimator. With this initial estimator, adaptive LASSO has the oracle property even when the number of covariates is greater than the sample size.},
year = {2006},
date-added = {2010-06-12 09:46:04 +0200},
date-modified = {2010-06-12 09:46:52 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Huang-2006-_Adaptive%20lasso%20for%20s.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12327},
rating = {0}
}

@article{Bonkovsky:1999p4528,
author = {H L Bonkovsky and J M Woolley},
journal = {Hepatology},
title = {Reduction of health-related quality of life in chronic hepatitis C and improvement with interferon therapy. The Consensus Interferon Study Group},
abstract = {The natural history, prognosis, and clinical significance of chronic hepatitis C are highly variable and somewhat controversial. The purpose of this study was to evaluate the effect of chronic hepatitis C infection on patients' perceptions of health-related quality of life (HRQOL) and to evaluate whether treatment with interferon improves HRQOL. A total of 642 patients with compensated liver disease who were enrolled in a multicenter trial of interferon therapy for chronic hepatitis C had evaluation of HRQOL using the SF-36 and other instruments derived from the Medical Outcomes Study (MOS). These instruments were self-administered by patients at baseline and at the end of a 24-week post-treatment observation period after 24 weeks of interferon treatment. Patients with chronic hepatitis C were compared with healthy controls (n = 750) selected from a representative sample of adults in the United States. Unadjusted and age/gender-adjusted results were similar, as were analyses using parametric or nonparametric methods. Compared with healthy controls, patients with chronic hepatitis C at baseline had lower HRQOL on all eight scales of the SF-36 (P <.001 for all). Patients without cirrhosis (n = 284 ) showed similar although slightly smaller differences. The differences were highly significant, clinically and socially relevant, and greatest for those scales that were more reflective of physical than mental or emotional disease. Patients who had a sustained viral response to interferon therapy (n = 41) exhibited marked improvements in HRQOL, and these improvements exceeded those of nonresponders on 13 of 14 HRQOL scales (8 were statistically significant). Similar improvements were noted in patients with sustained biochemical responses. The authors concluded that patients with chronic hepatitis C with or without cirrhosis have markedly reduced HRQOL. Patients who had a sustained response (virological or biochemical) to interferon therapy experienced significant improvements in perceived wellness and functional status. Successful interferon therapy provides meaningful improvements in HRQOL in patients with chronic hepatitis C.},
affiliation = {Departments of Medicine, Biochemistry and Molecular Biology, UMass/Memorial Health Care and The University of Massachusetts Medical School, Worcester, MA, USA. Herbert.Bonkovsky@ummc.ummed.edu},
number = {1},
pages = {264--70},
volume = {29},
year = {1999},
month = {Jan},
language = {eng},
keywords = {Male, Double-Blind Method, Adult, Humans, Antiviral Agents, Alanine Transaminase, Female, Hepatitis C: Chronic, Interferon Type I: Recombinant, Quality of Life},
date-added = {2010-01-29 22:15:45 +0100},
date-modified = {2010-07-29 20:00:05 +0200},
doi = {10.1002/hep.510290124},
pii = {S027091399900035X},
pmid = {9862876},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bonkovsky-1999-Hepatology_Reduction%20of%20health.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4528},
rating = {0}
}

@article{Pell:2010p9776,
author = {Gaby S Pell and Regula S Briellmann and Kate M Lawrence and Deborah Glencross and R Mark Wellard and Samuel F Berkovic and Graeme D Jackson},
journal = {Neuroimage},
title = {Reduced variance in monozygous twins for multiple MR parameters: implications for disease studies and the genetic basis of brain structure},
abstract = {Twin studies offer the opportunity to determine the relative contribution of genes versus environment in traits of interest. Here, we investigate the extent to which variance in brain structure is reduced in monozygous twins with identical genetic make-up. We investigate whether using twins as compared to a control population reduces variability in a number of common magnetic resonance (MR) structural measures, and we investigate the location of areas under major genetic influences. This is fundamental to understanding the benefit of using twins in studies where structure is the phenotype of interest. Twenty-three pairs of healthy MZ twins were compared to matched control pairs. Volume, T2 and diffusion MR imaging were performed as well as spectroscopy (MRS). Images were compared using (i) global measures of standard deviation and effect size, (ii) voxel-based analysis of similarity and (iii) intra-pair correlation. Global measures indicated a consistent increase in structural similarity in twins. The voxel-based and correlation analyses indicated a widespread pattern of increased similarity in twin pairs, particularly in frontal and temporal regions. The areas of increased similarity were most widespread for the diffusion trace and least widespread for T2. MRS showed consistent reduction in metabolite variation that was significant in the temporal lobe N-acetylaspartate (NAA). This study has shown the distribution and magnitude of reduced variability in brain volume, diffusion, T2 and metabolites in twins. The data suggest that evaluation of twins discordant for disease is indeed a valid way to attribute genetic or environmental influences to observed abnormalities in patients since evidence is provided for the underlying assumption of decreased variability in twins.},
affiliation = {Brain Research Institute, Neurosciences Building, Austin Health, Heidelberg West, Victoria 3081, Australia.},
number = {2},
pages = {1536--44},
volume = {49},
year = {2010},
month = {Jan},
language = {eng},
keywords = {Diffusion Magnetic Resonance Imaging, Australia, Twins: Monozygotic, Anisotropy, Brain, Female, Magnetic Resonance Spectroscopy, Male, Humans, Magnetic Resonance Imaging, Adult, Nerve Fibers: Unmyelinated, Nerve Fibers: Myelinated, Aspartic Acid, Organ Size},
date-added = {2010-03-26 19:20:13 +0100},
date-modified = {2010-03-26 19:20:13 +0100},
doi = {10.1016/j.neuroimage.2009.09.003},
pii = {S1053-8119(09)00979-3},
pmid = {19747554},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9776},
rating = {0}
}

@article{Foulkes:2005p6643,
author = {A S Foulkes and M Reilly and L Zhou and M Wolfe and D J Rader},
journal = {Stat Med},
title = {Mixed modelling to characterize genotype-phenotype associations},
abstract = {We propose using mixed effects models to characterize the association between multiple gene polymorphisms, environmental factors and measures of disease progression. Characterizing high-order gene-gene and gene-environment interactions presents an analytic challenge due to the large number of candidate genes and the complex, undescribed interactions among them. Several approaches have been proposed recently to reduce the number of candidate genes and post hoc approaches to identify gene-gene interactions are described. However, these approaches may be inadequate for identifying high-order interactions in the absence of main effects and generally do not permit us to control for potential confounders. We describe how mixed effects models and related testing procedures overcome these limitations and apply this approach to data from a cohort of subjects at risk for cardiovascular disease. Four (4) genetic polymorphisms in three genes of the same gene family are considered. The proposed modelling approach allows us first to test whether there is a significant genetic contribution to the variability observed in our disease outcome. This contribution may be through main effects of multi-locus genotypes or through an interaction between genotype and environmental factors. This approach also enables us to identify specific multi-locus genotypes that interact with environmental factors in predicting the outcome. Mixed effects models provide a flexible statistical framework for controlling for potential confounders and identifying interactions among multiple genes and environmental factors that explain the variability in measures of disease progression.},
affiliation = {Department of Biostatistics, University of Massachusetts, School of Public Health, 404 Arnold House, 715N. Pleasant Street, Amherst, MA 01003-9304, USA. foulkes@schoolph.umass.edu},
number = {5},
pages = {775--89},
volume = {24},
year = {2005},
month = {Mar},
language = {eng},
keywords = {Lipase, Models: Statistical, Coronary Artery Disease, Female, Phenotype, Middle Aged, Genotype, Male, Aged, Humans, Genetic Predisposition to Disease, Adult, Polymorphism: Single Nucleotide, Obesity, Models: Genetic},
date-added = {2010-03-03 20:35:24 +0100},
date-modified = {2010-03-03 20:35:24 +0100},
doi = {10.1002/sim.1965},
pmid = {15696502},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6643},
rating = {0}
}

@article{Takeuchi:2009p2300,
author = {Fumihiko Takeuchi and Ralph McGinnis and Stephane Bourgeois and Chris Barnes and Niclas Eriksson and Nicole Soranzo and Pamela Whittaker and Venkatesh Ranganath and Vasudev Kumanduri and William McLaren and Lennart Holm and Jonatan Lindh and Anders Rane and Mia Wadelius and Panos Deloukas},
journal = {PLoS Genet},
title = {A genome-wide association study confirms VKORC1, CYP2C9, and CYP4F2 as principal genetic determinants of warfarin dose},
abstract = {We report the first genome-wide association study (GWAS) whose sample size (1,053 Swedish subjects) is sufficiently powered to detect genome-wide significance (p<1.5 x 10(-7)) for polymorphisms that modestly alter therapeutic warfarin dose. The anticoagulant drug warfarin is widely prescribed for reducing the risk of stroke, thrombosis, pulmonary embolism, and coronary malfunction. However, Caucasians vary widely (20-fold) in the dose needed for therapeutic anticoagulation, and hence prescribed doses may be too low (risking serious illness) or too high (risking severe bleeding). Prior work established that approximately 30% of the dose variance is explained by single nucleotide polymorphisms (SNPs) in the warfarin drug target VKORC1 and another approximately 12% by two non-synonymous SNPs (*2, *3) in the cytochrome P450 warfarin-metabolizing gene CYP2C9. We initially tested each of 325,997 GWAS SNPs for association with warfarin dose by univariate regression and found the strongest statistical signals (p<10(-78)) at SNPs clustering near VKORC1 and the second lowest p-values (p<10(-31)) emanating from CYP2C9. No other SNPs approached genome-wide significance. To enhance detection of weaker effects, we conducted multiple regression adjusting for known influences on warfarin dose (VKORC1, CYP2C9, age, gender) and identified a single SNP (rs2108622) with genome-wide significance (p = 8.3 x 10(-10)) that alters protein coding of the CYP4F2 gene. We confirmed this result in 588 additional Swedish patients (p<0.0029) and, during our investigation, a second group provided independent confirmation from a scan of warfarin-metabolizing genes. We also thoroughly investigated copy number variations, haplotypes, and imputed SNPs, but found no additional highly significant warfarin associations. We present power analysis of our GWAS that is generalizable to other studies, and conclude we had 80% power to detect genome-wide significance for common causative variants or markers explaining at least 1.5% of dose variance. These GWAS results provide further impetus for conducting large-scale trials assessing patient benefit from genotype-based forecasting of warfarin dose.},
affiliation = {Wellcome Trust Sanger Institute, Hinxton, UK.},
number = {3},
pages = {e1000433},
volume = {5},
year = {2009},
month = {Mar},
language = {eng},
keywords = {Pharmacogenetics, Warfarin, Mixed Function Oxygenases, Metabolism, Humans, Cytochrome P-450 Enzyme System, Genome-Wide Association Study, Sweden, Aryl Hydrocarbon Hydroxylases, Polymorphism: Single Nucleotide},
date-added = {2010-01-10 12:12:58 +0100},
date-modified = {2010-01-10 12:12:58 +0100},
doi = {10.1371/journal.pgen.1000433},
pmid = {19300499},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Takeuchi-2009-PLoS%20Genet_A%20genome-wide%20associ.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2300},
rating = {0}
}

@article{Meyners:2000p12017,
author = {M Meyners and J Kunert and E M Qannari},
journal = {Food Qualify and Prefrence},
title = {Comparing generalized procrustes analysis and statis},
abstract = {We consider a model for sensory pro{\textregistered}ling data including translation, rotation and scaling. We compare two methods to calculate an overall consensus from several data matrices: Generalized Procrustes Analysis (GPA) and STATIS (Structuration des Tableaux a{\'A} Trois Indices de la Statistique). These methods are brie ̄y illustrated and explained under our model. A series of simulations to compare their performance has been carried out. We found signi{\textregistered}cant differences in performance depending on the variance of random errors and on the dimensionality of the true underlying consensus. Therefore, we investigated on the dimensionality of the calculated group averages. We found both methods gave too many dimensions compared to the true consensus. This {\textregistered}nding is supported by some theoretical considerations. Finally we propose a combined approach which takes advantage of both methods and which gave better results in the simulations.},
pages = {77--83},
volume = {11},
year = {2000},
date-added = {2010-05-23 22:40:35 +0200},
date-modified = {2010-07-29 19:26:49 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Meyners-2000-Food%20Qualify%20and%20Prefrence_Comparing%20generalize.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12017},
rating = {4}
}

@article{Norman:2010p11002,
author = {Richard Norman and Madeleine T King and Dushyant Clarke and Rosalie Viney and Paula Cronin and Deborah Street},
journal = {Qual Life Res},
title = {Does mode of administration matter? Comparison of online and face-to-face administration of a time trade-off task},
abstract = {PURPOSE: Developments in electronic data collection methods have allowed researchers to generate larger datasets at lower costs, but relatively little is known about the comparative performance of the new methods. This paper considers the comparability

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