text:
individuals may utilize to regulate their emotions. We will then point to evidence that suggests genetic contributions (alongside environmental contributions) to individual differences in emotion regulation. To date, efforts to identify specific genetic mechanisms involved in emotion regulation have focused on common gene variants (i.e. variants that exist in >1% of the population, referred to as polymorphisms) and their association with specific emotion regulation strategies or the neural substrate mediating these strategies. We will discuss these efforts, and conclude with a call to expand the set of experimental paradigms and putative molecular mechanisms, in order to significantly advance our understanding of the molecular mechanisms by which genes are involved in emotion regulation.},
affiliation = {Department of Psychology, Stony Brook University, Stony Brook, NY 11794-2500, USA. turhan.canli@sunysb.edu},
number = {1},
pages = {43--54},
volume = {164},
year = {2009},
month = {Nov},
language = {eng},
keywords = {Humans, Phenotype, Animals, Emotions, Environment},
date-added = {2010-02-17 10:08:31 +0100},
date-modified = {2010-02-17 10:08:31 +0100},
doi = {10.1016/j.neuroscience.2009.06.049},
pii = {S0306-4522(09)01074-4},
pmid = {19559759},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Canli-2009-Neuroscience_Genetics%20of%20emotion.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5777},
rating = {0}
}

@article{Smith:2004p3557,
author = {Michael W Smith and Nick Patterson and James A Lautenberger and Ann L Truelove and Gavin J McDonald and Alicja Waliszewska and Bailey D Kessing and Michael J Malasky and Charles Scafe and Ernest Le and Philip L De Jager and Andre A Mignault and Zeng Yi and Guy De The and Myron Essex and Jean-Louis Sankale and Jason H Moore and Kwabena Poku and John P Phair and James J Goedert and David Vlahov and Scott M Williams and Sarah A Tishkoff and Cheryl A Winkler and Francisco M De La Vega and Trevor Woodage and John J Sninsky and David A Hafler and David M Altshuler and Dennis A Gilbert and Stephen J O'Brien and David Reich},
journal = {Am J Hum Genet},
title = {A high-density admixture map for disease gene discovery in african americans},
abstract = {Admixture mapping (also known as "mapping by admixture linkage disequilibrium," or MALD) provides a way of localizing genes that cause disease, in admixed ethnic groups such as African Americans, with approximately 100 times fewer markers than are required for whole-genome haplotype scans. However, it has not been possible to perform powerful scans with admixture mapping because the method requires a dense map of validated markers known to have large frequency differences between Europeans and Africans. To create such a map, we screened through databases containing approximately 450000 single-nucleotide polymorphisms (SNPs) for which frequencies had been estimated in African and European population samples. We experimentally confirmed the frequencies of the most promising SNPs in a multiethnic panel of unrelated samples and identified 3011 as a MALD map (1.2 cM average spacing). We estimate that this map is approximately 70% informative in differentiating African versus European origins of chromosomal segments. This map provides a practical and powerful tool, which is freely available without restriction, for screening for disease genes in African American patient cohorts. The map is especially appropriate for those diseases that differ in incidence between the parental African and European populations.},
affiliation = {Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD, USA.},
number = {5},
pages = {1001--13},
volume = {74},
year = {2004},
month = {May},
language = {eng},
keywords = {Haplotypes, Genetics: Population, Genetic Markers, Gene Frequency, Alleles, Polymorphism: Single Nucleotide, Linkage Disequilibrium, Genetic Diseases: Inborn, African Americans, Chromosome Mapping, European Continental Ancestry Group, Microsatellite Repeats, Humans, Ethnic Groups, Genome: Human},
date-added = {2010-01-15 21:12:36 +0100},
date-modified = {2010-07-29 20:21:03 +0200},
doi = {10.1086/420856},
pii = {S0002-9297(07)64364-X},
pmid = {15088270},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Smith-2004-Am%20J%20Hum%20Genet_A%20high-density%20admix.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3557},
rating = {0}
}

@article{Rouder:2005,
author = {J N Rouder and J Lu and P Speckman and D Sun and Y Jiang},
journal = {Psychon Bull Rev},
title = {A hierarchical model for estimating response time distributions},
number = {2},
pages = {195--223},
volume = {12},
year = {2005},
date-added = {2010-01-10 11:33:19 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Rouder-2005-Psychonomic%20Bulletin%20&%20Review_A%20hierarchical%20model.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1972},
rating = {0}
}

@article{Verstralen:2000ab,
author = {H H F M Verstralen and N D Verhelst and Timo M Bechger},
title = {A DOUBLE HAZARD MODEL FOR MENTAL SPEED},
abstract = {The administration of tests via the computer allows the registration of response times along with the actual response. This paper describes a model that combines these two kinds of data to estimate a subject latent variable usually called mental speed, but more appropriately called mental power. The model implies that the expected item score increases with invested time. Nevertheless, it allows for a decreasing expected item score with response time, which is sometimes found in experiments. This paradox is obtained by assuming that a subject not only stops working on a problem because of time pressure, but also when he has solved the problem. The model builds on a familiar framework of IRT models. An MML estimation procedure is developed, and model fit on the item level is evaluated using Lagrange multiplier tests.},
year = {2000},
month = {Mar},
date-added = {2010-01-03 19:39:03 +0100},
date-modified = {2010-07-29 20:43:29 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Verstralen-2000-_A%20DOUBLE%20HAZARD%20MODE.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1201},
rating = {0}
}

@article{Prestwich:2001p4277,
author = {S Prestwich},
title = {Balanced incomplete block design as satisfiability},
year = {2001},
date-added = {2010-01-23 22:05:57 +0100},
date-modified = {2010-01-23 22:06:34 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Prestwich-2001-_Balanced%20incomplete.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4277},
rating = {0}
}

@article{Adams:2002p13981,
author = {P Adams and M D Hurd and D McFadden and A Merrill and T Ribeiro},
journal = {Journal of Econometrics},
title = {Healthy, Wealthy, and Wise? Tests for Direct Causal Paths between Health and Socioeconomic Status},
abstract = {This paper provides statistical methods that permit the association of socioeconomic status and health to be partially unraveled in panel data by excluding some postulated causal paths, or delimiting their range of action. These methods are applied to the Asset and Health Dynamics of the Oldest Old (AHEAD) Panel to test for the absence of causal links from socioeconomic status (SES) to health innovations and mortality, and from health conditions to innovations in wealth. We conclude that in this elderly American population, where Medicare covers most acute care and pension income is not affected by ability to work, the evidence supports the hypothesis of no direct causal link from SES to mortality and to incidence of most sudden onset health conditions (accidents and some acute conditions), once initial health conditions are controlled, but there is some association of SES with incidence of gradual onset health conditions (mental conditions, and some degenerative and chronic conditions), due either to causal links or to persistent unobserved behavioral or genetic factors that have a common influence on both SES and innovations in health. There is mixed evidence for an association of health conditions and innovations in wealth. The death of a spouse appears to have a negative effect on the wealth of the survivor; this is plausibly a direct causal effect. There is evidence for some association of health conditions with increased dissaving from liquid wealth for intact couples and singles. From these findings, we conclude that there is no evidence that SES-linked therapies for acute diseases induce mortality differentials. The question of whether SES-linked preventative care influences onset of chronic and mental diseases remains open. The Appendix to this paper containing the detailed model estimates, the data, and the programs used for data preparation and estimation, can be found at http://elsa.berkeley.edu/wp/hww/hww202.html .},
year = {2002},
date-added = {2010-07-30 21:31:33 +0200},
date-modified = {2010-07-30 21:32:39 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Adams-2002-Journal%20of%20Econometrics_Healthy%20Wealthy%20an.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13981},
rating = {0}
}

@article{Grice:1975p3639,
author = {H P Grice},
title = {Logic and Conversation},
year = {1975},
date-added = {2010-01-16 19:42:17 +0100},
date-modified = {2010-01-16 19:43:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Grice-1975-_Logic%20and%20Conversati.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3639},
rating = {0}
}

@article{Lecoutre:2005p11763,
author = {B Lecoutre and J Poitevineau and M P Lecoutre},
journal = {Modulad},
title = {Une raison pour ne pas abandonner les tests de signification de l'hypoth{\`e}se nulle},
abstract = {On montre que l'on peut directement calculer un intervalle pour un contraste entre moyennes,  ́etant donn ́e seulement la valeur observ ́ee du contraste et la statistique de test t ou F associ ́e (ou encore, de mani`ere  ́equivalente le seuil observ ́e correspondant : ``p-value''). Cet intervalle peut ˆetre vu comme un intervalle de confiance fr ́equentiste ou comme un intervalle de cr ́edibilit ́e bay ́esien ou comme un intervalle fiduciaire. Cela donne aux utilisateurs des tests de signification usuels la possibilit ́e d'une transition facile vers des pratiques statistiques plus appropri ́ees. On met en avant les liens conceptuels entre les tests et les intervalles de confiance ou de cr ́edibilit ́e},
number = {33},
pages = {243--248},
year = {2005},
date-added = {2010-05-23 10:10:58 +0200},
date-modified = {2010-07-29 19:40:18 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Lecoutre-2005-Modulad_Une%20raison%20pour%20ne%20p.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11763},
rating = {0}
}

@article{Boelle:2005p3343,
author = {P Y Bo{\"e}lle},
title = {Statistical and computational methods for haplotype reconstruction},
year = {2005},
date-added = {2010-01-15 12:17:37 +0100},
date-modified = {2010-01-15 12:18:14 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bo%C3%ABlle-2005-_Statistical%20and%20comp.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3343},
rating = {0}
}

@article{Naqvi:2007p1294,
author = {N Naqvi and B Shiv and A Bechara},
journal = {Current Directions in Psychological Science},
title = {The role of emotion in decision making. A cognitive neuroscience perspective},
abstract = {Decision making often occurs in the face of uncertainty about whether one's choices will lead to benefit or harm. The somatic-marker hypothesis is a neurobiological theory of how decisions are made in the face of uncertain outcome. This theory holds that such decisions are aided by emotions, in the form of bodily states, that are elicited during the deliberation of future consequences and that mark different options for behavior as being advantageous or disadvantageous. This process involves an interplay between neural systems that elicit emotional/ bodily states and neural systems that map these emotional/ bodily states.},
affiliation = {Division of Cognitive Neuroscience, Department of Neurology, University of Iowa College of Medicine},
number = {5},
pages = {260--264},
volume = {15},
year = {2007},
keywords = {frontal lobes, decision making, emotion, neuropsychology, neuroeconomics},
date-added = {2010-01-07 11:27:36 +0100},
date-modified = {2010-01-07 11:31:09 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Naqvi-2007-Current%20Directions%20in%20Psychological%20Science_The%20role%20of%20emotion.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1294},
rating = {0}
}

@article{Middeldorp:2007p12628,
author = {Christel M Middeldorp and Eco J C de Geus and A Leo Beem and Nico Lakenberg and Jouke-Jan Hottenga and P Eline Slagboom and Dorret I Boomsma},
journal = {Behav Genet},
title = {Family based association analyses between the serotonin transporter gene polymorphism (5-HTTLPR) and neuroticism, anxiety and depression},
abstract = {We studied the association between the short/long promotor-based length polymorphism of the serotonin transporter gene (5-HTTLPR) and neuroticism, anxiety and depression. Subjects included twins, their siblings and parents from the Netherlands Twin Register (559 parents and 1,245 offspring). Subjects had participated between one and five times in a survey study measuring neuroticism, anxiety and depression. Offspring of these families were also approached to participate in a psychiatric interview diagnosing DSM-IV major depression. Within-family and total association between 5-HTTLPR and these traits were tested. Only three of the 36 tests showed a significant effect of 5-HTTLPR (P<0.05). These effects were in opposite directions, i.e. both negative and positive regression coefficients were found for the s allele. No additive effect of the s allele was found for DSM-IV depression. Our results strongly suggest that there is no straightforward association between 5-HTTLPR and neuroticism, anxiety and depression.},
affiliation = {Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 1, Amsterdam, 1081 BT, The Netherlands. cm.middeldorp@psy.vu.nl},
number = {2},
pages = {294--301},
volume = {37},
year = {2007},
month = {Mar},
language = {eng},
keywords = {Depression, Polymorphism: Genetic, Female, Adult, Male, Anxiety, Serotonin Plasma Membrane Transport Proteins, Regression Analysis, Humans, Genotype, Family, Polymerase Chain Reaction, Longitudinal Studies, Neurotic Disorders},
date-added = {2010-06-15 22:39:21 +0200},
date-modified = {2010-07-29 20:09:07 +0200},
doi = {10.1007/s10519-006-9139-7},
pmid = {17216342},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Middeldorp-2007-Behav%20Genet_Family%20based%20associa.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12628},
rating = {0}
}

@article{Storer:1993p6261,
author = {B E Storer},
journal = {Biometrics},
title = {Small-sample confidence sets for the MTD in a phase I clinical trial},
abstract = {Properties of procedures for interval estimation of the maximum tolerable dose (MTD) in a Phase I clinical trial are examined, using a two-stage stochastic sampling scheme (Storer, 1989) as a paradigm for development. Although the likelihood function for the data arising from such a scheme is identical to one arising under a conditional binomial sampling assumption, intervals based on the exact distribution of the usual large-sample statistics under this assumption do not offer improvement over unadjusted intervals. However, consideration of the distribution of these statistics based on the true stochastic sampling scheme can lead to the construction of intervals with correct coverage probabilities that do not depend on the true values of the model parameters. Membership in the confidence set can be evaluated by Monte Carlo simulation at a restricted maximum likelihood estimate of the nuisance slope parameter, despite upward bias in its estimation from the up-and-down sampling scheme. The lack of information in the small-sample setting is reflected in a large proportion of confidence intervals that include infinite values for the MTD, especially when the dose-response curve is shallow. Intervals based on a likelihood ratio criterion perform best in this regard.},
affiliation = {Department of Statistics, University of Wisconsin-Madison 53792.},
number = {4},
pages = {1117--25},
volume = {49},
year = {1993},
month = {Dec},
language = {eng},
keywords = {Humans, Neoplasms, Likelihood Functions, Confidence Intervals, Drug Tolerance, Algorithms, Clinical Trials: Phase I as Topic, Biometry, Antineoplastic Agents, Monte Carlo Method},
date-added = {2010-02-19 21:51:04 +0100},
date-modified = {2010-02-19 21:51:04 +0100},
pmid = {8117905},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6261},
rating = {0}
}

@article{Tucker:2006p11934,
author = {K L Tucker and D J Ozer and S Lyubomirsky and J K Boehm},
journal = {Social Indicators Research},
title = {Testing For Measurement Invariance In The Satisfaction With Life Scale: A Comparison Of Russians And North Americans},
abstract = {This study examined the comparability of Satisfaction With Life Scale (SWLS) [Diener, Emmons, Larsen, {\&} Griffin, 1985, Social Indicators Research, 34: 7-- 32] scores across U.S. and Russian student and community groups. Criteria for weak measurement invariance were met when comparing U.S. and Russian groups (combining student and community samples). Criteria for weak and strong mea- surement invariance were met when comparing the U.S. and Russian student sam- ples. However, when comparing the U.S. and Russian community samples, the results showed a significant statistic for a baseline model, indicating a lack of com- parability across samples. The costs of failing to meet criteria for weak, strong, and strict measurement invariance are discussed.},
pages = {341--360},
volume = {78},
year = {2006},
date-added = {2010-05-23 16:51:47 +0200},
date-modified = {2010-05-23 16:52:52 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Tucker-2006-Social%20Indicators%20Research_Testing%20For%20Measurem.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11934},
rating = {4}
}

@misc{Honaker:2006,
author = {James Honaker and Gary King},
journal = {Miscellaneous},
title = {What to do about missing values in time series cross-section data},
year = {2006},
month = {Sep},
date-added = {2010-01-03 19:37:35 +0100},
date-modified = {2010-01-03 19:37:35 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Honaker-2006-Miscellaneous_What%20to%20do%20about%20mis.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1119},
rating = {0}
}

@article{Cheung:1990p11645,
author = {Y W Cheung},
journal = {Int J Addict},
title = {Ethnicity and alcohol/drug use revisited: a framework for future research},
abstract = {Despite the large pool of research findings pertaining to ethnic and racial variations in the use of drugs (including alcohol), the relationship between ethnicity and drug use has not been thoroughly examined. This paper describes some of the major findings regarding ethnic and racial variations in drug use, and examines the methodological limitations of such studies. Moreover, this paper addresses the problem of shortage of theoretical explanations for ethnic variations in drug use. It is argued that the variable of ethnicity has not been properly conceptualized and measured in most studies. Cultural and structural aspects of ethnicity at both the individual and collective levels are examined, and their possible contributions to more rigorous research on the relationship between ethnicity and drug use are discussed.},
affiliation = {Prevention and Health Promotion Research and Development Department, Addiction Research Foundation, Toronto, Ontario, Canada.},
number = {5A-6A},
pages = {581--605},
volume = {25},
year = {1990},
month = {Jan},
language = {eng},
keywords = {Alcoholism, Risk Factors, Cross-Sectional Studies, Humans, Ethnic Groups, Cross-Cultural Comparison, Research, Canada, Incidence, Substance-Related Disorders},
date-added = {2010-05-11 22:47:30 +0200},
date-modified = {2010-05-11 22:47:30 +0200},
pmid = {2101394},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11645},
rating = {0}
}

@article{Bombardieri:2010p10980,
author = {Roberta Bombardieri and Mariangela Pinci and Romina Moavero and Caterina Cerminara and Paolo Curatolo},
journal = {Eur J Paediatr Neurol},
title = {Early control of seizures improves long-term outcome in children with tuberous sclerosis complex},
abstract = {Epilepsy associated with tuberous sclerosis complex (TSC) is characterized by early onset and intractable seizures in the majority of children. There is a solid evidence of clinical efficacy of vigabatrin in interrupting infantile spasms associated with TSC. Due to an early diagnosis we were able to start vigabatrin at the very early onset of seizures in 10 children, who subsequently underwent a long-term neurodevelopmental follow-up. At the final evaluation, a seizure free status was achieved in 50% of patients; 30% of individuals had a normal or borderline mental development, with no patients developing severe mental retardation and/or autism. Early control of seizures has a crucial role in preventing subsequent epileptic encephalopathy, and in reducing the cognitive/behavioural consequences of seizures, but does not guarantee for a normal mental outcome in children with TSC.},
affiliation = {Department of Neurosciences, Pediatric Neurology Unit, Tor Vergata University, via Montpellier 1, Rome 00133, Italy.},
number = {2},
pages = {146--9},
volume = {14},
year = {2010},
month = {Mar},
language = {eng},
date-added = {2010-04-13 16:26:14 +0200},
date-modified = {2010-04-13 16:26:14 +0200},
doi = {10.1016/j.ejpn.2009.03.003},
pii = {S1090-3798(09)00056-7},
pmid = {19369101},
URL = {http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WF2-4W2M6V8-1&_user=2432700&_coverDate=03%252F31%252F2010&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000057263&_version=1&_urlVersion=0&_userid=2432700&md5=bf2d822215b7b18246dd37a2cb166464},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bombardieri-2010-Eur%20J%20Paediatr%20Neurol_Early%20control%20of%20sei.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10980},
rating = {0}
}

@article{Earleywine:1994p6830,
author = {M Earleywine},
journal = {Addict Behav},
title = {Cognitive bias covaries with alcohol consumption},
abstract = {Cognitive models of behavior led to the prediction that ambiguous stimuli would be interpreted as alcohol-relevant in heavier drinkers. Women were asked to define words that could be interpreted as alcohol-relevant or not (e.g., shot). Two measures served as indicators of a latent construct of cognitive bias: the number of words construed to be related to alcohol, and the position of the first word in the series that was defined as alcohol-relevant. Average quantity, average frequency, and maximum number of drinks imbibed in a single episode served as indicators of a latent construct of alcohol consumption. These two constructs covaried significantly (.44) in a two-factor latent variable analysis that fit the data better than alternative models. These findings support an alcohol-related interpretive bias and suggest hypotheses concerning the types of interpretive preferences that may contribute to alcohol consumption.},
affiliation = {Department of Psychology, University of Southern California, Los Angeles 90089-1061.},
number = {5},
pages = {539--44},
volume = {19},
year = {1994},
month = {Jan},
language = {eng},
keywords = {Attention, Models: Statistical, Female, Adult, Word Association Tests, Alcoholism, Humans, Vocabulary, Alcohol Drinking, Adolescent},
date-added = {2010-03-06 09:31:25 +0100},
date-modified = {2010-07-29 19:12:35 +0200},
pii = {0306-4603(94)90009-4},
pmid = {7832012},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6830},
rating = {0}
}

@article{Steyer:1989p6235,
author = {R Steyer},
journal = {Methodica},
title = {Models of classical psychometric Test Theory as stochastic measurement models: Representation, uniqueness, meaningfulness, identifiability, and testability},
pages = {25--60},
volume = {III},
year = {1989},
date-added = {2010-02-19 21:05:17 +0100},
date-modified = {2010-02-19 21:07:52 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Steyer-1989-Methodica_Models%20of%20classical.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6235},
rating = {0}
}

@article{Lubke:2003p11601,
author = {G H Lubke and C V Dolan},
journal = {Structural Equation Modeling},
title = {Can Unequal Residual Variances Across Groups Mask Differences in Residual Means in the Common Factor Model?},
abstract = {Equality of residual variances across groups is one of the necessary conditions of measurement invariance. The main argument for not applying this restriction in the analysis of empirical data is that unequal residual variances across groups are differ- ences in reliability of the observed variables rather than a violation of measurement invariance. A power study is carried out to investigate the conditions under which vi- olations of measurement invariance can be masked by unequal residual variances across groups. Increasing group differences in residual variance are combined with mean differences in the item-specific residual. Sample sizes needed for rejection of a model with free residual variances across groups are computed for different model sizes and varying group sample size ratios. Increasing group differences in residual variance decreases the power to detect differences in specific means if the residual variances are not held equal across groups. This is especially the case for small mean differences, unequal group sample sizes, and if differences in residual means are ac- companied by correlated residuals.},
number = {2},
pages = {175--192},
volume = {10},
year = {2003},
date-added = {2010-05-09 21:30:24 +0200},
date-modified = {2010-07-29 19:51:13 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Lubke-2003-Structural%20Equation%20Modeling_Can%20Unequal%20Residual.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11601},
rating = {0}
}

@article{Regier:2002p5583,
author = {Darrel A Regier and William E Narrow and Michael B First and Tina Marshall},
journal = {Psychopathology},
title = {The APA classification of mental disorders: future perspectives},
abstract = {After 8-10 years of experience with the fourth edition of the Diagnostic and Statistical Manual (DSM-IV) and the tenth edition of the International Classification of Diseases (ICD-10), it is an ideal time to begin looking at the clinical and research consequences of these diagnostic systems. The American Psychiatric Association, in conjunction with the National Institutes of Health, has initiated a research development process intended to accelerate an evaluation of existing criteria while developing and testing hypotheses that would improve the validity of our diagnostic concepts. Over the past year, a multidisciplinary, international panel has developed a series of six white papers which define research opportunities in the following broad areas: Nomenclature, Disability and Impairment, Personality Disorders, Relational Disorders, Developmental Psychopathology, Neuroscience, and Cross-Cultural aspects of Psychopathology. Recommendations for future national and international research in each of these areas will be discussed.},
affiliation = {Division of Research, American Psychiatric Association, Washington, DC 20005, USA. dregier@psych.org},
number = {2-3},
pages = {166--70},
volume = {35},
year = {2002},
month = {Jan},
language = {eng},
keywords = {Reproducibility of Results, Psychiatric Status Rating Scales, International Classification of Diseases, Mental Disorders, Forecasting, Humans, Societies: Medical, Psychometrics, Psychiatry},
date-added = {2010-02-12 15:38:41 +0100},
date-modified = {2010-02-12 15:38:41 +0100},
pii = {psp35166},
pmid = {12145504},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5583},
rating = {0}
}

@article{Gama:2009p430,
author = {Helena Gama and Sofia Correia and Nuno Lunet},
journal = {BMC Med Res Methodol},
title = {Effect of questionnaire structure on recall of drug utilization in a population of university students},
abstract = {BACKGROUND: Self-reported data are a common source of information about drug exposure. Modes of data collection differ considerably and the questionnaire's structure may affect prevalence estimates. We compared the recall of medication use evaluated by means of two questionnaires differing in structure and length. METHODS: Drug utilization was assessed by two alternative versions of a questionnaire (A - 4 pages, including specific questions for 12 indications/pharmacological groups and one question for "other medicines"; B - 1 page, including 1 open-ended question to cover overall drug consumption). Each of 32 classes in a private University in Maputo, Mozambique, was randomly assigned questionnaire A (233 participants) or B (276 participants). Logistic regression (allowing for clustering by classroom) was used to compare the two groups in terms of socio-demographic characteristics and medication used during the previous month. RESULTS: Overall, 67.4% of the subjects had used at least one drug during the previous month. The following prevalences were greater among participants completing questionnaire A: use of drugs from two or more pharmacological groups (60.5% vs. 34.4%, p < 0.001), use of two or more drugs (66.2% vs. 43.0%, p < 0.001), and use of antibiotics (14.6% vs. 6.9%, p = 0.001), antifungals (9.4% vs. 4.0%, p = 0.013), antiparasitics (5.6% vs. 1.8%, p = 0.031) and antacids (8.6% vs. 3.6%, p = 0.024). Information about duration of treatment and medical advice was more complete with version A. CONCLUSION: The indication/drug-specific questions (questionnaire A) revealed a significantly higher prevalence of use of medicines - antibiotics, antifungals, antiparasitics and antacids - without compromising the completeness of the information.},
affiliation = {Department of Hygiene and Epidemiology, University of Porto Medical School, Porto, Portugal. helena.gama@bial.com},
pages = {45},
volume = {9},
year = {2009},
month = {Jan},
language = {eng},
keywords = {Universities, Male, Humans, Students, Socioeconomic Factors, Female, Young Adult, Mozambique, Logistic Models, Drug Utilization, Questionnaires, Mental Recall},
date-added = {2010-01-03 12:26:06 +0100},
date-modified = {2010-01-03 12:26:09 +0100},
doi = {10.1186/1471-2288-9-45},
pii = {1471-2288-9-45},
pmid = {19563651},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Gama-2009-BMC%20Med%20Res%20Methodol_Effect%20of%20questionna.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p430},
rating = {3}
}

@article{Berman:2009p8841,
author = {Steven M Berman and Ernest P Noble and Parvaneh Mohammadian and Terry Ritchie and Mark A Mandelkern and Edythe D London},
journal = {Synapse},
title = {Laterality of cortical response to ethanol is moderated by TaqIA A1 allele},
affiliation = {Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, USA. sberman@ucla.edu},
number = {9},
pages = {817--21},
volume = {63},
year = {2009},
month = {Sep},
language = {eng},
keywords = {Central Nervous System Depressants, Brain Mapping, Mood Disorders, Young Adult, DNA Mutational Analysis, Cerebral Cortex, Reward, Adult, Ethanol, Glucose, Brain Chemistry, Gene Frequency, Receptors: Dopamine D2, Dopamine, Alcohol-Induced Disorders: Nervous System, Acoustic Stimulation, Arousal, Genetic Testing, Neuropsychological Tests, Positron-Emission Tomography, Male, Genetic Predisposition to Disease, Polymorphism: Genetic, Humans, Alcoholism, Functional Laterality, Reinforcement (Psychology)},
date-added = {2010-03-22 12:36:34 +0100},
date-modified = {2010-03-22 12:36:34 +0100},
doi = {10.1002/syn.20687},
pmid = {19504620},
URL = {http://www3.interscience.wiley.com/journal/122441909/abstract},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Berman-2009-Synapse_Laterality%20of%20cortic.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8841},
rating = {0}
}

@article{Hirschhorn:2009p1412,
author = {Joel N Hirschhorn},
journal = {N Engl J Med},
title = {Genomewide association studies--illuminating biologic pathways},
affiliation = {Division of Genetics, Children's Hospital, Boston, MA, USA.},
number = {17},
pages = {1699--701},
volume = {360},
year = {2009},
month = {Apr},
language = {eng},
keywords = {Genetic Variation, Disease, Genetic Predisposition to Disease, Biophysical Processes, Genome-Wide Association Study, Humans},
date-added = {2010-01-07 12:18:59 +0100},
date-modified = {2010-07-29 19:53:14 +0200},
doi = {10.1056/NEJMp0808934},
pii = {NEJMp0808934},
pmid = {19369661},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hirschhorn-2009-N%20Engl%20J%20Med_Genomewide%20associati.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1412},
rating = {0}
}

@article{Edgell:1996p7276,
author = {E T Edgell and S J Coons and W B Carter and J D Kallich and D Mapes and T M Damush and R D Hays},
journal = {Clin Ther},
title = {A review of health-related quality-of-life measures used in end-stage renal disease},
abstract = {Health-related quality of life (HRQOL) is a critical issue in the treatment of end-stage renal disease (ESRD) patients. The variety of symptoms, comorbidities, and treatments of ESRD over the course of its chronic disease trajectory necessitate comprehensive assessment of the impact of interventions on HRQOL. A literature review of ESRD HRQOL studies was performed to provide an overview of the instruments used and to provide recommendations for HRQOL assessment in future studies. Instruments were classified based on the health domains they assess and whether they are generic or disease targeted. The instruments were judged in terms of their comprehensiveness, reliability, and validity.},
affiliation = {Eli Lilly and Company, Indianapolis, Indiana, USA.},
number = {5},
pages = {887--938},
volume = {18},
year = {1996},
month = {Jan},
language = {eng},
keywords = {Sexual Behavior, Quality of Life, Employment, Mental Health, Questionnaires, Karnofsky Performance Status, Humans, Self Concept, Depression, Affect, Kidney Failure: Chronic, Social Adjustment, Internal-External Control, Personal Satisfaction},
date-added = {2010-03-10 20:14:13 +0100},
date-modified = {2010-03-10 20:14:13 +0100},
pii = {S0149-2918(96)80049-X},
pmid = {8930432},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Edgell-1996-Clin%20Ther_A%20review%20of%20health-r.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7276},
rating = {0}
}

@article{Lee:2008p4687,
author = {Jae K Lee and Paul D Williams and Sooyoung Cheon},
journal = {Clin Lab Med},
title = {Data mining in genomics},
abstract = {This article reviews important emerging statistical concepts, data mining techniques, and applications that have been recently developed and used for genomic data analysis. First, general background and some critical issues in genomic data mining are summarized. A novel concept of statistical significance is described, the so-called "false discovery rate"-the rate of false-positives among all positive findings-which has been suggested to control the error rate of numerous false-positives in large screening biological data analysis. Two recent statistical testing methods are then introduced: significance analysis of microarray and local pooled error tests. Statistical modeling in genomic data analysis is then presented, such as analysis of variance and heterogeneous error modeling approaches that have been suggested for analyzing microarray data obtained from multiple experimental or biological conditions. Two sections then describe data exploration and discovery tools largely termed as supervised learning and unsupervised learning. The former approaches include several multivariate statistical methods to investigate coexpression patterns of multiple genes, and the latter are the classification methods to discover genomic biomarker signatures for predicting important subclasses of human diseases. The last section briefly summarizes various genomic data mining approaches in biomedical pathway analysis and patient outcome or chemotherapeutic response prediction.},
affiliation = {Division of Biostatistics and Epidemiology, Department of Public Health Sciences, Box 800717, University of Virginia, Charlottesville, VA 22908, USA. jaeklee@virginia.edu},
number = {1},
pages = {145--66, viii},
volume = {28},
year = {2008},
month = {Mar},
language = {eng},
keywords = {Artificial Intelligence, Software, Computational Biology, Databases: Genetic, Pattern Recognition: Automated, Data Interpretation: Statistical, Models: Genetic, Genomics},
date-added = {2010-01-30 16:13:14 +0100},
date-modified = {2010-01-30 16:13:14 +0100},
doi = {10.1016/j.cll.2007.10.010},
pii = {S0272-2712(07)00119-9},
pmid = {18194724},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4687},
rating = {0}
}

@article{Lin:2005p3361,
author = {D Y Lin},
journal = {Bioinformatics},
title = {An efficient Monte Carlo approach to assessing statistical significance in genomic studies},
abstract = {MOTIVATION: Multiple hypothesis testing is a common problem in genome research, particularly in microarray experiments and genomewide association studies. Failure to account for the effects of multiple comparisons would result in an abundance of false positive results. The Bonferroni correction and Holm's step-down procedure are overly conservative, whereas the permutation test is time-consuming and is restricted to simple problems. RESULTS: We developed an efficient Monte Carlo approach to approximating the joint distribution of the test statistics along the genome. We then used the Monte Carlo distribution to evaluate the commonly used criteria for error control, such as familywise error rates and positive false discovery rates. This approach is applicable to any data structures and test statistics. Applications to simulated and real data demonstrate that the proposed approach provides accurate error control, and can be substantially more powerful than the Bonferroni and Holm methods, especially when the test statistics are highly correlated.},
affiliation = {Department of Biostatistics, University of North Carolina, McGavran-Greenberg Hall, CB {\#}7420, Chapel Hill, NC 27599-7420, USA. lin@bios.unc.edu},
number = {6},
pages = {781--7},
volume = {21},
year = {2005},
month = {Mar},
language = {eng},
keywords = {Sensitivity and Specificity, Genomics, Humans, Algorithms, Sequence Analysis: DNA, Data Interpretation: Statistical, Reproducibility of Results, Chromosome Mapping, Neoplasm Proteins, Models: Genetic, Oligonucleotide Array Sequence Analysis, Tumor Markers: Biological, Lung Neoplasms, Models: Statistical, Monte Carlo Method, Gene Expression Profiling},
date-added = {2010-01-15 14:38:45 +0100},
date-modified = {2010-01-15 14:38:45 +0100},
doi = {10.1093/bioinformatics/bti053},
pii = {bti053},
pmid = {15454414},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3361},
rating = {0}
}

@article{Gutteling:2007p4533,
author = {J J Gutteling and R A de Man and J J V Busschbach and A-S E Darlington},
journal = {Neth J Med},
title = {Overview of research on health-related quality of life in patients with chronic liver disease},
abstract = {Health-related quality of life (HRQoL) has become an important outcome measure in patients with chronic liver disease (CLD). In this article, an overview is given of the most common measurement instruments of HRQoL, determinants of HRQoL in patients with CLD, and current developments in the implementation of routine measurement of HRQoL in daily clinical practice. Well-developed generic instruments of HRQoL are the Short Form-36 (SF-36), the Nottingham Health Profile (NHP) and the Sickness Impact Profile (SIP). Well-developed liver disease-specific HRQoL instruments are the Hepatitis Quality of Life Questionnaire (HQLQ), the Chronic Liver Disease Questionnaire (CLDQ), the Liver Disease Quality Of Life Questionnaire (LDQOL ), and the Liver Disease Symptom Index 2.0 (LDSI 2.0). Commonly used HRQoL measures in cost-effectiveness studies are the Health Utilities Index (HUI), Short Form-6D (SF-6D) and the EuroQol-5D (EQ-5D). HRQoL of patients with chronic liver disease has been shown to be impaired, with patients with hepatitis C showing the worst HRQoL. Disease severity, pruritus, joint pain, abdominal pain, muscle cramps, fatigue, depression and anxiety have been associated with HRQoL in patients with CLD. Recently, studies assessing the feasibility and effectiveness of measuring HRQoL in daily clinical practice have been performed, generally showing positive results regarding the discussion of HRQoL-related topics, but mixed results regarding the added value of actual improvement in HRQoL. Furthermore, logistic and attitudinal barriers seem to impede successful implementation. Nevertheless, given the importance of HRQoL in liver patients, we should persist in measuring and subsequently improving HRQoL in clinical practice.},
affiliation = {Department of Gastroenterology and Hepatology, Erasmus Medical Centre, Rotterdam, the Netherlands. j.gutteling@erasmusmc.nl},
number = {7},
pages = {227--34},
volume = {65},
year = {2007},
month = {Jan},
language = {eng},
keywords = {Liver Diseases, Chronic Disease, Humans, Psychometrics, Sickness Impact Profile, Quality of Life, Outcome Assessment (Health Care), Questionnaires},
date-added = {2010-01-29 22:16:46 +0100},
date-modified = {2010-01-29 22:16:46 +0100},
pmid = {17656809},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Gutteling-2007-Neth%20J%20Med_Overview%20of%20research.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4533},
rating = {0}
}

@article{Carey:2003p5239,
author = {G Carey},
title = {Cholesky Problems},
abstract = {Behavioral geneticists commonly parameterize a genetic or environmental covariance matrix as the product of a nonsingular, lower diagonal matrix postmultiplied by its transpose---a technique commonly referred to as ``fitting a Cholesky.'' Here, simulations demonstrate that this procedure: (1) may not produce likelihood ratio test statistics that are distributed as a c2; or (2) if the distribution of the test statistic appears to be c2, then the degrees of freedom (df) are not always the difference between the number of parameters in the general model less the number of parameters in the constrained model. It is hypothesized that the problem is related to the fact that the Cholesky parameterization requires that the covariance matrix formed by its product be positive definite. Even though a population covariance matrix may be positive definite, the combination of sampling error and the derived---as opposed to directly observed---nature of some matrices in behavioral genetics allow matrices that are not positive definite. Hence, fitting a Cholesky constrains the area of search and may compromise maximum likelihood theory. Until the reason for this phenomenon is understood and a satisfactory solution is developed, the Cholesky parameterization should be used with caution. An alternate strategy of fitting a lower diagonal matrix to data that avoids the Cholelsky problem is proposed.},
year = {2003},
date-added = {2010-02-08 20:13:44 +0100},
date-modified = {2010-02-08 20:14:12 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Carey-2003-_Cholesky%20Problems.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5239},
rating = {0}
}

@article{Meijer:2004p6590,
author = {Rob R Meijer and Joost J Baneke},
journal = {Psychological Methods},
title = {Analyzing psychopathology items: a case for nonparametric item response theory modeling},
abstract = {The authors discuss the applicability of nonparametric item response theory (IRT) models to the construction and psychometric analysis of personality and psychopathology scales, and they contrast these models with parametric IRT models. They describe the fit of nonparametric IRT to the Depression content scale of the Minnesota Multiphasic Personality Inventory--2 (J. N. Butcher, W. G. Dahlstrom, J. R. Graham, A. Tellegen, {\&} B. Kaemmer, 1989). They also show how nonparametric IRT models can easily be applied and how misleading results from parametric IRT models can be avoided. They recommend the use of nonparametric IRT modeling prior to using parametric logistic models when investigating personality data.},
affiliation = {Department of Research Methodology, Measurement and Data Analysis, University of Twente, Enschede, the Netherlands. r.r.meijer@utwente.nl},
number = {3},
pages = {354--68},
volume = {9},
year = {2004},
month = {Sep},
language = {eng},
keywords = {Personality Tests, Male, MMPI, Psychometrics, Models: Statistical, Psychopathology, Reproducibility of Results, Female, Algorithms, Analysis of Variance, Adult, Depressive Disorder, Humans, Mathematical Computing, Statistics: Nonparametric},
date-added = {2010-02-24 20:38:11 +0100},
date-modified = {2010-03-07 11:07:47 +0100},
doi = {10.1037/1082-989X.9.3.354},
pii = {2004-17801-005},
pmid = {15355153},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Meijer-2004-Psychological%20Methods_Analyzing%20psychopath.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6590},
rating = {4}
}

@article{Elkan:2003p4623,
author = {C Elkan},
journal = {Proceedings of the Twentieth International Conference on Machine Learning (ICML-2003)},
title = {Using the Triangle Inequality to Accelerate k-Means},
year = {2003},
date-added = {2010-01-30 15:31:39 +0100},
date-modified = {2010-01-30 15:32:17 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Elkan-2003-Proceedings%20of%20the%20Twentieth%20International%20Conference%20on%20Machine%20Learning%20(ICML-2003)_Using%20the%20Triangle%20I.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4623},
rating = {0}
}

@article{Smith:1996p9559,
author = {M Y Smith and J Feldman and P Kelly and J A DeHovitz and K Chirgwin and H Minkoff},
journal = {Qual Life Res},
title = {Health-related quality of life of HIV-infected women: evidence for the reliability, validity and responsiveness of the Medical Outcomes Study Short-Form 20},
abstract = {The purpose of this study was to assess the reliability, validity and responsiveness of a health-related quality of life (HRQOL) instrument, the Medical Outcomes Short-Form 20-Item General Health Survey (MOS SF-20), in a sample of women with the human immunodeficiency virus (HIV). Longitudinal data were collected on 202 HIV-infected women without AIDS who were receiving care at Kings County Hospital or SUNY Health Sciences Center, Brooklyn, New York. Internal consistency results showed acceptable reliability for the four multi-item MOS scales (role function, physical function, general health perceptions and mental health). Symptomatic patients and patients with lower Karnofsky Performance Status (KPS) ratings reported lower HRQOL than those who were asymptomatic or who had higher KPS scores. Patients who were older, unemployed or who had a history of injection drug use (IDU) also reported lower HRQOL than those who were younger, employed or who had no drug use history. Adjusted mean scores on the MOS role and physical functioning scales proved sensitive to differences in clinical status over time. The MOS SF-20 is a reliable and valid instrument of HRQOL for women with HIV infection. Its sensitivity to differences in clinical status over time suggest that it may be useful as an HRQOL indicator for HIV/AIDS clinical trials.},
affiliation = {Memorial Sloan-Kettering Cancer Centre, New York, New York, 10021, USA.},
number = {1},
pages = {47--55},
volume = {5},
year = {1996},
month = {Feb},
language = {eng},
keywords = {Quality of Life, Longitudinal Studies, Female, New York, Adult, Health Surveys, Reproducibility of Results, Humans, Psychometrics, HIV Infections},
date-added = {2010-03-23 20:53:46 +0100},
date-modified = {2010-07-29 19:48:31 +0200},
pmid = {8901366},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9559},
rating = {0}
}

@article{Gennaro:2010p10866,
author = {Leonarda Gennaro and Luigi Russo and Luciana Losito and Alessia Zaccaria and Marta De Rinaldis and Antonio Trabacca},
journal = {Res Dev Disabil},
title = {Movement disorders in a twins pair: a casual expression or genetic determination?},
abstract = {A twin study is an excellent means of assessing the contribution of heritability to motor behaviour. We present a movement video-analysis of a monozygotic twins pair with a motor repertoire which is almost totally constituted by persistent and subcontinuous motor stereotypies. PURPOSE: The specific aim of this study is to verify the heritable quantum of motor behaviour and to determine which among the motor patterns we analysed are more likely to be conditioned by inheritance. METHODS: Stereotyped movements were videotaped in two standardized sessions: at rest and in relation to preordained sensory stimulations. We estimated the concordance index (CI) between the observers to evaluate the reliability of the observations. The validity was accepted as being CI>0.80. RESULTS: The results showed a very high concordance rate (>90%) for all the stereotypies analysed. An almost superimposable trend of the stereotyped movements was found both at rest and in relation to the sensory stimulations. CONCLUSIONS: Such strong data suggest that genetic factors have a primary influence on all the movement disorders analysed. This study contributes to a better understanding of the complex relationships between genes and functions.},
affiliation = {Unit of Neurorehabilitation I-Developmental Neurology and Functional Rehabilitation, I.R.C.C.S. E. Medea Scientific Institute-La Nostra Famiglia Association, Ostuni, Brindisi, Italy.},
number = {3},
pages = {692--7},
volume = {31},
year = {2010},
month = {Jan},
language = {eng},
date-added = {2010-04-10 03:35:32 +0200},
date-modified = {2010-04-10 03:35:32 +0200},
doi = {10.1016/j.ridd.2010.01.009},
pii = {S0891-4222(10)00010-7},
pmid = {20153949},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Gennaro-2010-Res%20Dev%20Disabil_Movement%20disorders%20i.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10866},
rating = {0}
}

@article{Lyles:2007p6954,
author = {Robert H Lyles and Hung-Mo Lin and John M Williamson},
journal = {Stat Med},
title = {A practical approach to computing power for generalized linear models with nominal, count, or ordinal responses},
abstract = {Data analysts facing study design questions on a regular basis could derive substantial benefit from a straightforward and unified approach to power calculations for generalized linear models. Many current proposals for dealing with binary, ordinal, or count outcomes are conceptually or computationally demanding, limited in terms of accommodating covariates, and/or have not been extensively assessed for accuracy assuming moderate sample sizes. Here, we present a simple method for estimating conditional power that requires only standard software for fitting the desired generalized linear model for a non-continuous outcome. The model is fit to an appropriate expanded data set using easily calculated weights that represent response probabilities given the assumed values of the parameters. The variance-covariance matrix resulting from this fit is then used in conjunction with an established non-central chi square approximation to the distribution of the Wald statistic. Alternatively, the model can be re-fit under the null hypothesis to approximate power based on the likelihood ratio statistic. We provide guidelines for constructing a representative expanded data set to allow close approximation of unconditional power based on the assumed joint distribution of the covariates. Relative to prior proposals, the approach proves particularly flexible for handling one or more continuous covariates without any need for discretizing. We illustrate the method for a variety of outcome types and covariate patterns, using simulations to demonstrate its accuracy for realistic sample sizes.},
affiliation = {Department of Biostatistics, The Rollins School of Public Health of Emory University, 1518 Clifton Rd. N.E., Atlanta, GA 30322, USA. rlyles@sph.emory.edu},
number = {7},
pages = {1632--48},
volume = {26},
year = {2007},
month = {Mar},
language = {eng},
keywords = {Humans, Linear Models, Data Interpretation: Statistical, Sample Size, Computer Simulation},
date-added = {2010-03-06 12:24:27 +0100},
date-modified = {2010-03-06 12:24:27 +0100},
doi = {10.1002/sim.2617},
pmid = {16817148},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Lyles-2007-Stat%20Med_A%20practical%20approach.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6954},
rating = {0}
}

@article{Lehtonen:2002p4103,
author = {R Lehtonen and K Djerf and T H{\"a}rk{\"a}nen and J Laiho},
title = {M{\'e}thodes d'analyse des donn{\'e}es d'enqu{\^e}tes complexes sur la sant{\'e} bas{\'e}es sur le plan d'{\'e}chantillonnage ou sur un mod{\`e}le : Une {\'e}tude de cas},
abstract = {Le pr{\'e}sent article traite de l'analyse des donn{\'e}es d'enqu{\^e}tes complexes sur la sant{\'e} par des m{\'e}thodes multivari{\'e}es de mod{\'e}lisation. Nous nous concentrons sur les m{\'e}thodes bas{\'e}es sur le plan d'{\'e}chantillonnage et celles bas{\'e}es sur un mod{\`e}le qui visent {\`a} tenir compte des effets de la mise en grappes, de la stratification et de la pond{\'e}ration. Nous nous int{\'e}ressons avant tout aux effets de la mise en grappes. Les m{\'e}thodes {\'e}tudi{\'e}es incluent la mod{\'e}lisation lin{\'e}aire g{\'e}n{\'e}ralis{\'e}e fond{\'e}e sur la pseudo-vraisemblance et les {\'e}quations d'estimation g{\'e}n{\'e}ralis{\'e}es, les mod{\`e}les lin{\'e}aires mixtes estim{\'e}s par le maximum de vraisemblance restreints et les techniques hi{\'e}rarchiques bay{\'e}siennes bas{\'e}es sur les m{\'e}thodes de Monte Carlo par cha{\^\i}ne de Markov (MCCM). Nous comparons empiriquement ces m{\'e}thodes sur des donn{\'e}es provenant d'une enqu{\^e}te comprenant une entrevue sur la sant{\'e} et un examen physique r{\'e}alis{\'e}e en Finlande en 2000 (Health-2000 Study). Les donn{\'e}es de la Health-2000 Study ont {\'e}t{\'e} recueillies au moyen d'entrevues personnelles, de questionnaires et d'examens cliniques. L'enqu{\^e}te a {\'e}t{\'e} r{\'e}alis{\'e}e aupr{\`e}s d'un {\'e}chantillon en grappes stratifi{\'e} {\`a} deux degr{\'e}s. Le plan d'{\'e}chantillonnage a produit des corr{\'e}lations intra-grappes positives pour nombre de variables {\'e}tudi{\'e}es. Nous avons s{\'e}lectionn{\'e} en vue d'une {\'e}tude plus approfondie les variables pression sanguine systolique et morbidit{\'e} chronique, tir{\'e}es des volets de l'entrevue sur la sant{\'e} et de l'examen clinique. Dans de nombreux cas, les diverses m{\'e}thodes ont produit des r{\'e}sultats num{\'e}riques comparables et appuy{\'e} des conclusions statistiques similaires. Celles qui ne tenaient pas compte de la complexit{\'e} du plan d'{\'e}chantillonnage ont parfois produit des conclusions contradictoires. Nous discutons aussi de l'application des m{\'e}thodes lors de l'utilisation de logiciels statistiques standards.},
year = {2002},
date-added = {2010-01-19 23:38:52 +0100},
date-modified = {2010-07-11 09:54:24 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Lehtonen-2002-_Me%CC%81thodes%20d%E2%80%99analyse-1.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4103},
rating = {0}
}

@article{Stitziel:2003p3525,
author = {Nathan O Stitziel and Yan Yuan Tseng and Dimitri Pervouchine and David Goddeau and Simon Kasif and Jie Liang},
journal = {J Mol Biol},
title = {Structural location of disease-associated single-nucleotide polymorphisms},
abstract = {Non-synonymous single-nucleotide polymorphism (nsSNP) of genes introduces amino acid changes to proteins, and plays an important role in providing genetic functional diversity. To understand the structural characteristics of disease-associated SNPs, we have mapped a set of nsSNPs derived from the online mendelian inheritance in man (OMIM) database to the structural surfaces of encoded proteins. These nsSNPs are disease-associated or have distinctive phenotypes. As a control dataset, we mapped a set of nsSNPs derived from SNP database dbSNP to the structural surfaces of those encoded proteins. Using the alpha shape method from computational geometry, we examine the geometric locations of the structural sites of these nsSNPs. We classify each nsSNP site into one of three categories of geometric locations: those in a pocket or a void (type P); those on a convex region or a shallow depressed region (type S); and those that are buried completely in the interior (type I). We find that the majority (88%) of disease-associated nsSNPs are located in voids or pockets, and they are infrequently observed in the interior of proteins (3.2% in the data set). We find that nsSNPs mapped from dbSNP are less likely to be located in pockets or voids (68%). We further introduce a novel application of hidden Markov models (HMM) for analyzing sequence homology of SNPs on various geometric sites. For SNPs on surface pocket or void, we find that there is no strong tendency for them to occur on conserved residues. For SNPs buried in the interior, we find that disease-associated mutations are more likely to be conserved. The approach of classifying nsSNPs with alpha shape and HMM developed in this study can be integrated with additional methods to improve the accuracy of predictions of whether a given nsSNP is likely to be disease-associated.},
affiliation = {Department of Bioengineering SEO, MC-063, University of Illinois at Chicago, Room 218, 851, S. Morgan Street, Chicago, IL 60607-7052, USA.},
number = {5},
pages = {1021--30},
volume = {327},
year = {2003},
month = {Apr},
language = {eng},
keywords = {Polymorphism: Single Nucleotide, Models: Molecular, Disease, Humans},
date-added = {2010-01-15 15:47:53 +0100},
date-modified = {2010-01-15 15:47:53 +0100},
pii = {S0022283603002407},
pmid = {12662927},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Stitziel-2003-J%20Mol%20Biol_Structural%20location.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3525},
rating = {0}
}

@article{Maris:2008p7761,
author = {G Maris},
journal = {Psychometrika},
title = {A NOTE ON ``CONSTANT LATENT ODDS-RATIOS MODELS AND THE MANTEL--HAENSZEL NULL HYPOTHESIS'' HESSEN, 2005},
abstract = {In a recent paper, Hessen (Psychometrika 70(3):497--516, 2005) introduces the class of constant latent odds-ratios models as an extension of the Rasch model for which the sum score is still the sufficient statistic for ability. In this paper the relation between both the general and the general parametric constant latent odds-ratios model and the Rasch model is considered.},
number = {1},
pages = {153--157},
volume = {73},
year = {2008},
date-added = {2010-03-17 20:56:25 +0100},
date-modified = {2010-03-17 20:57:06 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Maris-2008-Psychometrika_A%20NOTE%20ON%20%E2%80%9CCONSTANT.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7761},
rating = {0}
}

@article{Song:2004p2349,
author = {J Song and H X Barnhart and R H Lyles},
journal = {Journal of Data Science},
title = {A GEE Approach for Estimating Correlation Coefficients Involving Left-censored Variables},
abstract = {HIV (Human Immunodeficiency Virus) researchers are often con- cerned with the correlation between HIV viral load measurements and CD4+ lymphocyte counts. Due to the lower limits of detection (LOD) of the avail- able assays, HIV viral load measurements are subject to left-censoring. Mo- tivated by these considerations, the maximum likelihood (ML) method under normality assumptions was recently proposed for estimating the correlation between two continuous variables that are subject to left-censoring. In this paper, we propose a generalized estimating equations (GEE) approach as an alternative to estimate such a correlation coefficient. We investigate the robustness to the normality assumption of the ML and the GEE approaches via simulations. An actual HIV data example is used for illustration.},
pages = {245--257},
volume = {2},
year = {2004},
date-added = {2010-01-10 13:32:34 +0100},
date-modified = {2010-01-10 13:33:34 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Song-2004-Journal%20of%20Data%20Science_A%20GEE%20Approach%20for%20E.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2349},
rating = {0}
}

@article{Bureau2005,
author = {A Bureau and J Dupuis and K Falls and K Lunetta and B Hayward and T Keith and P Van Eerdewegh},
journal = {Genet Epidemiol},
title = {Identifying SNPs predictive of phenotype using random forests},
pages = {171--182},
volume = {28},
year = {2005},
date-added = {2010-01-12 14:26:52 +0100},
date-modified = {2010-01-12 14:26:52 +0100},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2543},
rating = {0}
}

@article{Dorn:2006,
author = {S Dorn},
journal = {Educationa Policy Analysis Archives},
title = {No More Aggregate NAEP Studies?},
number = {31},
volume = {14},
year = {2006},
date-added = {2010-01-10 11:33:09 +0100},
date-modified = {2010-07-29 19:25:37 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Dorn-2006-Educationa%20Policy%20Analysis%20Archives_No%20More%20Aggregate%20NA.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1905},
rating = {0}
}

@article{Guillemin:2007p3996,
author = {Francis Guillemin},
journal = {Nature clinical practice Rheumatology},
title = {Primer: the fallacy of subgroup analysis},
abstract = {The identification of subgroups of patients from randomized clinical trials that are of specific interest for guiding clinical decisions can be an attractive idea; however, since such trials are designed for the comparison of groups of patients, performing subgroup analyses can result in misinterpretation of the data. Such analyses must, therefore, be performed and evaluated with caution: these should be pre-planned and included in the design of a suitably powered trial. Data obtained should be analyzed using formal statistical tests of interaction on proper subgroups rather than improper subgroups of patients, the results obtained should be delineated carefully, and details of how these analyses were performed, and how the data should be interpreted, should be reported in the trial paper. The caveats associated with this approach, such as the occurrence of false positive or false negative effects, chance differences in observed effects, lack of power to perform the analysis, floor or ceiling effects, issues relating to multiple statistical testing, and over-reporting and under-reporting are discussed in this review. Subgroup analyses can, however, provide valuable, albeit predominantly exploratory, information on which to base clinical decisions if they are performed in accordance with recommendations and guidelines, and do, therefore, have a legitimate place in rheumatology clinical trials.},
affiliation = {School of Public Health, Nancy University, and Clinical Epidemiology Centre Inserm CIE6, Nancy-University Hospital, France. francis.guillemin@medecine.uhp-nancy.fr},
number = {7},
pages = {407--13},
volume = {3},
year = {2007},
month = {Jul},
language = {eng},
keywords = {Rheumatology, Sample Size, Reproducibility of Results, Data Interpretation: Statistical, Sensitivity and Specificity, Humans, Randomized Controlled Trials as Topic, Treatment Outcome, Selection Bias, Research Design},
date-added = {2010-01-17 23:24:20 +0100},
date-modified = {2010-01-17 23:24:20 +0100},
doi = {10.1038/ncprheum0528},
pii = {ncprheum0528},
pmid = {17599075},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3996},
rating = {0}
}

@article{State:2000p10344,
author = {M W State and P J Lombroso and D L Pauls and J F Leckman},
journal = {J Am Acad Child Adolesc Psychiatry},
title = {The genetics of childhood psychiatric disorders: a decade of progress},
abstract = {OBJECTIVE: To review the literature over the past decade on the genetics of childhood neuropsychiatric disorders. METHOD: A computerized search was performed for articles published in the past decade, and selected papers were highlighted. RESULTS: The past decade of research has illuminated the complex genetics of early-onset mental disorders. Advances in statistical methodologies and laboratory-based gene-hunting techniques are laying the foundation for a deeper understanding of both the biological and environmental factors that contribute to mental illness. Researchers are on the verge of identifying and characterizing genetic vulnerabilities involved in common childhood psychiatric syndromes. CONCLUSIONS: Although the study of the genetics of childhood psychiatric disorders has advanced significantly over the past decade, considerable work remains. The identification of genes conferring vulnerability to psychiatric illnesses will have the potential to transform the field by providing insight into both biological and environmental determinants that contribute to serious developmental and psychiatric disorders in children and adolescents. These advances promise new understanding and new avenues for prevention and treatment. They will also present physicians and families with significant clinical and ethical challenges.},
affiliation = {Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-7900, USA.},
number = {8},
pages = {946--62},
volume = {39},
year = {2000},
month = {Aug},
language = {eng},
keywords = {Gene Expression Regulation, Chromosome Mapping, Humans, Genotype, Mental Disorders, Genetic Predisposition to Disease, Syndrome, Phenotype, Child, Mutation},
date-added = {2010-04-02 18:18:40 +0200},
date-modified = {2010-04-02 18:18:40 +0200},
pmid = {10939224},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10344},
rating = {0}
}

@article{Prieto:2004p8398,
author = {Luis Prieto and Jos{\'e} A Sacrist{\'a}n},
journal = {BMC Med Res Methodol},
title = {What is the value of social values? The uselessness of assessing health-related quality of life through preference measures},
abstract = {BACKGROUND: The use of preference-based measures in the evaluation of health outcomes has extended considerably over the last decade. Their alleged advantage over other types of general instruments in the evaluation of health related quality of life (HRQOL), supposedly lies in the fact that preference measures incorporate values or utilities that reflects the value of social preferences through health states. The objective of this study was to determine whether the use of social preference weights or utilities makes any real difference when calculating scores for the Euroqol (EQ5-D) questionnaire, a HRQOL preference-based measure. METHODS: Responses to the EQ5-D of a sample of 10,972 patients from 10 countries enrolled in an observational study of the treatment of schizophrenia in Europe were used for this purpose. Two different methods of scoring the EQ-5D where compared: 'weighting the items' of the questionnaire through the UK official weight coefficients, and 'non-weighting the items'. Pearson's, Spearman's, and two-way mixed parametric intraclass correlation coefficients were used to estimate the association of the scores obtained in both ways. RESULTS: The association between weighted and unweighted Euroqol scores was extremely high (Pearson's r = 0.91), as was the association between their ranks (Spearman's rho = 0.93). The intraclass correlation coefficient obtained (0.89) also suggested that the concordance between the score distributions was prominent. CONCLUSIONS: A non-weighted approach to score the EQ5-D is enough to explain a high proportion of variance in scores obtained through the use of utilities. The differential contribution of weights based on population preference values is therefore minimal and, in our opinion, negligible.},
affiliation = {Health Outcomes Research Unit, Eli Lilly {\&} Co, Spain, Av, de la Industria, 30, 28108 Alcobendas, SPAIN. prieto_luis@lilly.com},
pages = {10},
volume = {4},
year = {2004},
month = {Apr},
language = {eng},
keywords = {Humans, Questionnaires, Health Status Indicators, Social Values, Quality of Life, Data Interpretation: Statistical},
date-added = {2010-03-21 13:36:24 +0100},
date-modified = {2010-03-21 13:36:24 +0100},
doi = {10.1186/1471-2288-4-10},
pii = {1471-2288-4-10},
pmid = {15117417},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Prieto-2004-BMC%20Med%20Res%20Methodol_What%20is%20the%20value%20of.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8398},
rating = {0}
}

@article{Csardi:2010p12805,
author = {G Csardi and T Nepusz},
title = {The igraph software package for complex network research},
date-added = {2010-06-18 22:49:36 +0200},
date-modified = {2010-06-18 22:50:09 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Csardi--_The%20igraph%20software.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12805},
rating = {0}
}

@article{Savitz:2009p5838,
author = {J B Savitz and W C Drevets},
journal = {Neuroscience},
title = {Imaging phenotypes of major depressive disorder: genetic correlates},
abstract = {Imaging techniques are a potentially powerful method of identifying phenotypes that are associated with, or are indicative of, a vulnerability to developing major depressive disorder (MDD). Here we identify seven promising MDD-associated traits identified by magnetic resonance imaging (MRI) or positron emission tomography (PET). We evaluate whether these traits are state-independent, heritable endophenotypes, or state-dependent phenotypes that may be useful markers of treatment efficacy. In MDD, increased activity of the amygdala in response to negative stimuli appears to be a mood-congruent phenomenon, and is likely moderated by the 5-HT transporter gene (SLC6A4) promoter polymorphism (5-HTTLPR). Hippocampal volume loss is characteristic of elderly or chronically-ill samples and may be impacted by the val66met brain-derived neurotrophic factor (BDNF) gene variant and the 5-HTTLPR SLC6A4 polymorphism. White matter pathology is salient in elderly MDD cohorts but is associated with cerebrovascular disease, and is unlikely to be a useful marker of a latent MDD diathesis. Increased blood flow or metabolism of the subgenual anterior cingulate cortex (sgACC), together with gray matter volume loss in this region, is a well-replicated finding in MDD. An attenuation of the usual pattern of fronto-limbic connectivity, particularly a decreased temporal correlation in amygdala-anterior cingulate cortex (ACC) activity, is another MDD-associated trait. Concerning neuroreceptor PET imaging, decreased 5-HT(1A) binding potential in the raphe, medial temporal lobe, and medial prefrontal cortex (mPFC) has been strongly associated with MDD, and may be impacted by a functional single nucleotide polymorphism in the promoter region of the 5-HT(1A) gene (HTR1A: -1019 C/G; rs6295). Potentially indicative of inter-study variation in MDD etiology or mood state, both increased and decreased binding potential of the 5-HT transporter has been reported. Challenges facing the field include the problem of phenotypic and etiological heterogeneity, technological limitations, the confounding effects of medication, and non-disease related inter-individual variation in brain morphology and function. Further advances are likely as epigenetic, copy-number variant, gene-gene interaction, and genome-wide association (GWA) approaches are brought to bear on imaging data.},
affiliation = {Mood and Anxiety Disorders Program, NIH/NIMH, Bethesda, MD 20892, USA. savitzj@mail.nih.gov},
number = {1},
pages = {300--30},
volume = {164},
year = {2009},
month = {Nov},
language = {eng},
keywords = {Animals, Brain Mapping, Phenotype, Humans, Depressive Disorder: Major, Models: Genetic, Brain},
date-added = {2010-02-17 10:12:59 +0100},
date-modified = {2010-02-17 10:12:59 +0100},
doi = {10.1016/j.neuroscience.2009.03.082},
pii = {S0306-4522(09)00579-X},
pmid = {19358877},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Savitz-2009-Neuroscience_Imaging%20phenotypes%20o.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5838},
rating = {0}
}

@article{Moore:2010p3106,
author = {Jason H Moore and Folkert W Asselbergs and Scott M Williams},
journal = {Bioinformatics},
title = {Bioinformatics Challenges for Genome-Wide Association Studies},
abstract = {MOTIVATION: The sequencing of the human genome has made it possible to identify an informative set of more than one million single nucleotide polymorphisms (SNPs) across the genome that can be used to carry out genome-wide association studies (GWAS). The availability of massive amounts of GWAS data has necessitated the development of new biostatistical methods for quality control, imputation, and analysis issues including multiple testing. This work has been successful and has enabled the discovery of new associations that have been replicated in multiple studies. However, it is now recognized that most SNPs discovered via GWAS have small effects on disease susceptibility and thus may not be suitable for improving healthcare through genetic testing. One likely explanation for the mixed results of GWAS is that the current biostatistical analysis paradigm is by design agnostic or unbiased in that it ignores all prior knowledge about disease pathobiology. Further, the linear modeling framework that is employed in GWAS often considers only one SNP at a time thus ignoring their genomic and environmental context. There is now a shift away from the biostatistical approach toward a more holistic approach that recognizes the complexity of the genotype-phenotype relationship that is characterized by significant heterogeneity and gene-gene and gene-environment interaction. We argue here that bioinformatics has an important role to play in addressing the complexity of the underlying genetic basis of common human diseases. The goal of this review is to identify and discuss those GWAS challenges that will require computational methods.},
affiliation = {Departments of Genetics and Community and Family Medicine, Dartmouth Medical School, Lebanon, NH 03756.},
pages = {},
year = {2010},
month = {Jan},
language = {ENG},
date-added = {2010-01-14 20:21:18 +0100},
date-modified = {2010-01-14 20:21:18 +0100},
doi = {10.1093/bioinformatics/btp713},
pii = {btp713},
pmid = {20053841},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Moore-2010-Bioinformatics_Bioinformatics%20Chall.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3106},
read = {Yes},
rating = {3}
}

@article{deLeeuw:1982p4263,
author = {Jan de Leeuw},
journal = {COMPSTAT 1982},
title = {Nonlinear principal component analysis},
abstract = {Two quite different forms of nonlinear principal component analysis have been proposed in the literature. The first one is associated with the names of Guttman, Burt, Hayashi, Benz{\'e}cri, McDonald, De Leeuw, Hill, Nishisato. We call it multiple correspondence analysis. The second form has been discussed by Kruskal, Shepard, Roskam, Takane, Young, De Leeuw, Winsberg, Ramsay. We call it nonmetric principal component analysis. The two forms have been related and combined, both geometrically and computationally, by Albert Gifi. In this paper we discuss the relationships in more detail, and propose an alternative algorithm for nonlinear principal component analysis which combines features of both previous approaches.},
pages = {77--86},
year = {1982},
date-added = {2010-01-23 21:21:50 +0100},
date-modified = {2010-07-29 20:45:39 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/de%20Leeuw-1982-COMPSTAT%201982_Nonlinear%20principal.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4263},
rating = {0}
}

@article{Zhao:2003p1777,
author = {L Zhao and K Chan},
journal = {CJIM},
title = {Quality of Life Assessment: An Outcome Estimation of Chinese Medical Treatment},
number = {4},
pages = {299--301},
volume = {9},
year = {2003},
date-added = {2010-01-09 21:44:49 +0100},
date-modified = {2010-01-09 21:45:36 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Zhao-2003-CJIM_Quality%20of%20Life%20Asse.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1777},
rating = {0}
}

@article{Hand:2010p4220,
author = {David J Hand},
journal = {Stat Med},
title = {Evaluating diagnostic tests: The area under the ROC curve and the balance of errors},
abstract = {Because accurate diagnosis lies at the heart of medicine, it is important to be able to evaluate the effectiveness of diagnostic tests. A variety of accuracy measures are used. One particularly widely used measure is the AUC, the area under the receiver operating characteristic (ROC) curve. This measure has a well-understood weakness when comparing ROC curves which cross. However, it also has the more fundamental weakness of failing to balance different kinds of misdiagnoses effectively. This is not merely an aspect of the inevitable arbitrariness in choosing a performance measure, but is a core property of the way the AUC is defined. This property is explored, and an alternative, the H measure, is described. Copyright (c) 2010 John Wiley {\&} Sons, Ltd.},
affiliation = {Imperial College, London.},
pages = {},
year = {2010},
month = {Jan},
language = {ENG},
date-added = {2010-01-21 10:58:26 +0100},
date-modified = {2010-01-21 10:58:26 +0100},
doi = {10.1002/sim.3859},
pmid = {20087877},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hand-2010-Stat%20Med_Evaluating%20diagnosti.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4220},
rating = {0}
}

@article{Houseman:2007,
author = {E Andres Houseman and Carmen Marsit and Margaret Karagas and Louise M Ryan},
journal = {Biometrics},
title = {Penalized item response theory models: application to epigenetic alterations in bladder cancer.},
abstract = {Increasingly used in health-related applications, latent variable models provide an appealing framework for handling high-dimensional exposure and response data. Item response theory (IRT) models, which have gained widespread popularity, were originally developed for use in the context of educational testing, where extremely large sample sizes permitted the estimation of a moderate-to-large number of parameters. In the context of public health applications, smaller sample sizes preclude large parameter spaces. Therefore, we propose a penalized likelihood approach to reduce mean square error and improve numerical stability. We present a continuous family of models, indexed by a tuning parameter, that range between the Rasch model and the IRT model. The tuning parameter is selected by cross validation or approximations such as Akaike Information Criterion. While our approach can be placed easily in a Bayesian context, we find that our frequentist approach is more computationally efficient. We demonstrate our methodology on a study of methylation silencing of gene expression in bladder tumors. We obtain similar results using both frequentist and Bayesian approaches, although the frequentist approach is less computationally demanding. In particular, we find high correlation of methylation silencing among 16 loci in bladder tumors, that methylation is associated with smoking and also with patient survival.},
affiliation = {Department of Work Environment, University of Massachusetts Lowell, Kitson Hall, 202E, One University Ave., Lowell, Massachusetts 01854, USA. andres_houseman@uml.edu},
number = {4},
pages = {1269--1277},
volume = {63},
year = {2007},
month = {Dec},
language = {eng},
date-added = {2010-01-03 19:38:22 +0100},
date-modified = {2010-01-03 19:38:22 +0100},
doi = {10.1111/j.1541-0420.2007.00806.x},
pii = {BIOM806},
pmid = {17484774},
URL = {http://dx.doi.org/10.1111/j.1541-0420.2007.00806.x},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1171},
rating = {0}
}

@article{Agresti:1992p6265,
author = {Alan Agresti},
journal = {Statistical Science},
title = {A Survey of Exact Inference for Contingency Tables},
abstract = {The past decade has seen substantial research on exact infer- ence for contingency tables, both in terms of developing new analyses and developing efficient algorithms for computations. Coupled with concomitant improvements in computer power, this research has re- sulted in a greater variety of exact procedures becoming feasible for practical use and a considerable increase in the size of data sets to which the procedures can be applied. For some basic analyses of contin- gency tables, it is unnecessary to use large-sample approximations to sampling distributions when their adequacy is in doubt. This article surveys the current theoretical and computational developments of exact methods for contingency tables. Primary attention is given to the exact conditional approach, which eliminates nuisance parameters by conditioning on their sflicient statistics. The presentation of various exact inferences is unified by expressing them in terms of parameters and their sufficient statistics in loglinear models. Exact approaches for many inferences are not yet addressed in the literature, particularly for multidimensional contingency tables, and this article also suggests additional research for the next decade that would make exact methods yet more widely applicable.},
number = {1},
pages = {131--153},
volume = {7},
year = {1992},
date-added = {2010-02-19 21:55:51 +0100},
date-modified = {2010-07-29 20:17:57 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Agresti-1992-Statistical%20Science_A%20Survey%20of%20Exact%20In.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6265},
rating = {0}
}

@article{Yu:2005p3537,
author = {S Yu and K Yu and V Tresp and H P Kriegel},
title = {A Probabilistic Clustering-Projection Model for Discrete Data},
abstract = {For discrete co-occurrence data like documents and words, calculating optimal projections and clustering are two different but re- lated tasks. The goal of projection is to find a low-dimensional latent space for words, and clustering aims at grouping documents based on their feature representations. In general projection and clustering are studied independently, but they both represent the intrinsic structure of data and should reinforce each other. In this paper we introduce a probabilistic clustering-projection (PCP) model for discrete data, where they are both represented in a unified framework. Clustering is seen to be performed in the projected space, and projection explicitly considers clustering structure. Iterating the two operations turns out to be exactly the variational EM algorithm under Bayesian model inference, and thus is guaranteed to improve the data likelihood. The model is evaluated on two text data sets, both showing very encouraging results.},
year = {2005},
date-added = {2010-01-15 20:53:22 +0100},
date-modified = {2010-01-15 20:54:02 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Yu-2005-_A%20Probabilistic%20Clus.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3537},
rating = {0}
}

@article{Lubinski:2009p7608,
author = {David Lubinski},
journal = {Behav Genet},
title = {Exceptional cognitive ability: the phenotype},
abstract = {Characterizing the outcomes related to the phenotype of exceptional cognitive abilities has been feasible in recent years due to the availability of large samples of intellectually precocious adolescents identified by modern talent searches that have been followed-up longitudinally over multiple decades. The level and pattern of cognitive abilities, even among participants within the top 1% of general intellectual ability, are related to differential developmental trajectories and important life accomplishments: The likelihood of earning a doctorate, earning exceptional compensation, publishing novels, securing patents, and earning tenure at a top university (and the academic disciplines within which tenure is most likely to occur) all vary as a function of individual differences in cognitive abilities assessed decades earlier. Individual differences that distinguish the able (top 1 in 100) from the exceptionally able (top 1 in 10,000) during early adolescence matter in life, and, given the heritability of general intelligence, they suggest that understanding the genetic and environmental origins of exceptional abilities should be a high priority for behavior genetic research, especially because the results for extreme groups could differ from the rest of the population. In addition to enhancing our understanding of the etiology of general intelligence at the extreme, such inquiry may also reveal fundamental determinants of specific abilities, like mathematical versus verbal reasoning, and the distinctive phenotypes that contrasting ability patterns are most likely to eventuate in at extraordinary levels.},
affiliation = {Department of Psychology and Human Development, Vanderbilt University, Nashville, TN 37203, USA. david.lubinski@vanderbilt.edu},
number = {4},
pages = {350--8},
volume = {39},
year = {2009},
month = {Jul},
language = {eng},
keywords = {Adolescent, Child, Concept Formation, Intelligence, Cognition, Achievement, Adult, Humans, Aptitude Tests, Longitudinal Studies, Creativeness, Aptitude, Child: Gifted, Phenotype},
date-added = {2010-03-15 23:10:11 +0100},
date-modified = {2010-07-29 20:09:06 +0200},
doi = {10.1007/s10519-009-9273-0},
pmid = {19424784},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Lubinski-2009-Behav%20Genet_Exceptional%20cognitiv.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7608},
rating = {0}
}

@article{Guyon2002,
author = {I Guyon and J Weston and S Barnhill and V N Vapnik},
journal = {Machine Learning},
title = {Gene selection for cancer classification using Support Vector Machines},
number = {1-3},
pages = {389--422},
volume = {46},
year = {2002},
date-added = {2010-01-12 14:26:46 +0100},
date-modified = {2010-07-29 19:38:49 +0200},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2530},
rating = {0}
}

@article{Bruggink:2010p7932,
author = {J L M Bruggink and K Van Braeckel and A F Bos},
title = {In children born preterm the quality of the motor repertoire during early infancy is associated with intelligence at school age},
abstract = {Background: The quality of general movements (GMs) during early infancy has consistently been found to be a powerful predictor of motor disorders in later childhood. The question arises whether the quality of GMs is also associated with later cognition. Aim: To determine whether quality of GMs in preterm children has predictive value for cognitive development at school age.
Study design: Prospective cohort study. Subjects: The study group consisted of 60 preterm infants (36 boys, 24 girls) without cerebral palsy. The median gestational age was 30.0 weeks (range 25-33 weeks), median birth weight was 1130 grams (595-1800g). The educational level of both parents ranged from elementary to tertiary level (mothers: median 10 years, range 6-17 years, fathers: median 11 years, range 8-17 years). The quality of GMs was prospectively assessed as normal or abnormal from video- recordings that were made at regular intervals: at preterm age, term, three to eight weeks' post-term, and at eleven to seventeen weeks' post-term age. Outcome measures: At seven to eleven years of age, the children's intelligence was tested using the WISC-IIINL. The total (TIQ), verbal (VIQ) and performance (PIQ) intelligence quotient scores were calculated. Results: The median TIQ was 93 (67-113), VIQ 96 (68-117), and PIQ 92 (65-119). Fifteen children (25%) had a low TIQ (<85). The longitudinal course of the quality of GMs was associated with TIQ, VIQ, and PIQ. If the quality of GMs had normalised before eight weeks' post-term, TIQ, VIQ, and PIQ fell within the normal range. A consistently abnormal quality of GMs before eight weeks' post-term was associated with a lower TIQ, VIQ, and PIQ. The likelihood ratio of consistently abnormal GMs up to eight weeks post-term for a low TIQ was 4.9 (95%CI: 1.4-17.2). The educational levels of the parents were not associated with IQ scores. Conclusions: The quality of GMs during the early post-term period is a predictor for intelligence at school age. Abnormal quality of GMs during the early post-term period may reflect injury or developmental disruptions of brain areas involved in cognitive development. It may also reflect the crucial role of motor activity in normal cognitive development.},
date-added = {2010-03-20 19:23:36 +0100},
date-modified = {2010-03-20 19:24:54 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bruggink--_In%20children%20born%20pre.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7932},
rating = {5}
}

@article{Boeck:2005,
author = {Paul De Boeck and M Wilson and G Scott Acton},
journal = {Psychological Review},
title = {Conceptual and psychometric framework for distinguishing categories and dimensions},
number = {1},
pages = {129--158},
volume = {112},
year = {2005},
date-added = {2010-01-10 11:33:22 +0100},
date-modified = {2010-07-29 20:46:12 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/De%20Boeck-2005-Psychological%20Review_Conceptual%20and%20psych.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1986},
rating = {0}
}

@article{Clark:1991p5441,
author = {L A Clark and D Watson},
journal = {J Abnorm Psychol},
title = {Tripartite model of anxiety and depression: psychometric evidence and taxonomic implications},
abstract = {We review psychometric and other evidence relevant to mixed anxiety-depression. Properties of anxiety and depression measures, including the convergent and discriminant validity of self- and clinical ratings, and interrater reliability, are examined in patient and normal samples. Results suggest that anxiety and depression can be reliably and validly assessed; moreover, although these disorders share a substantial component of general affective distress, they can be differentiated on the basis of factors specific to each syndrome. We also review evidence for these specific factors, examining the influence of context and scale content on ratings, factor analytic studies, and the role of low positive affect in depression. With these data, we argue for a tripartite structure consisting of general distress, physiological hyperarousal (specific anxiety), and anhedonia (specific depression), and we propose a diagnosis of mixed anxiety-depression.},
affiliation = {Department of Psychology, Southern Methodist University, Dallas, Texas 75275-0442.},
number = {3},
pages = {316--36},
volume = {100},
year = {1991},
month = {Aug},
language = {eng},
keywords = {Syndrome, Depressive Disorder, Psychometrics, Diagnosis: Differential, Humans, Psychiatric Status Rating Scales, Anxiety Disorders},
date-added = {2010-02-11 17:23:52 +0100},
date-modified = {2010-02-11 17:23:52 +0100},
pmid = {1918611},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5441},
rating = {0}
}

@article{Lesch:1996p11599,
author = {K P Lesch and D Bengel and A Heils and S Z Sabol and B D Greenberg and S Petri and J Benjamin and C R M{\"u}ller and D H Hamer and D L Murphy},
journal = {Science},
title = {Association of anxiety-related traits with a polymorphism in the serotonin transporter gene regulatory region},
abstract = {Transporter-facilitated uptake of serotonin (5-hydroxytryptamine or 5-HT) has been implicated in anxiety in humans and animal models and is the site of action of widely used uptake-inhibiting antidepressant and antianxiety drugs. Human 5-HT transporter (5-HTT) gene transcription is modulated by a common polymorphism in its upstream regulatory region. The short variant of the polymorphism reduces the transcriptional efficiency of the 5-HTT gene promoter, resulting in decreased 5-HTT expression and 5-HT uptake in lymphoblasts. Association studies in two independent samples totaling 505 individuals revealed that the 5-HTT polymorphism accounts for 3 to 4 percent of total variation and 7 to 9 percent of inherited variance in anxiety-related personality traits in individuals as well as sibships.},
affiliation = {Department of Psychiatry, University of W{\"u}rzburg, F{\"u}chsleinstrasse 15, 97080 W{\"u}rzburg, Germany. kplesch@rzbox.uni-wuerzburg.de},
number = {5292},
pages = {1527--31},
volume = {274},
year = {1996},
month = {Nov},
language = {eng},
keywords = {Polymorphism: Genetic, Membrane Transport Proteins, Neurotic Disorders, Phenotype, Genetic Markers, Male, Adult, Humans, Cell Line, Anxiety Disorders, Nuclear Family, Promoter Regions: Genetic, Personality Tests, Membrane Glycoproteins, Serotonin, Female, Transfection, Nerve Tissue Proteins, Serotonin Plasma Membrane Transport Proteins, Carrier Proteins, Genotype, Alleles, Middle Aged, Adolescent},
date-added = {2010-05-09 21:23:41 +0200},
date-modified = {2010-07-29 19:50:10 +0200},
pmid = {8929413},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Lesch-1996-Science_Association%20of%20anxie.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11599},
rating = {4}
}

@article{Drieling:2006p11470,
author = {Tobias Drieling and Dietrich van Calker and Heidemarie Hecht},
journal = {J Affect Disord},
title = {Stress, personality and depressive symptoms in a 6.5 year follow-up of subjects at familial risk for affective disorders and controls},
abstract = {BACKGROUND: The aim of the study was to identify risk factors in subjects at risk for depressive disorders and controls. METHODS: In a 6.5 year follow-up study we examined the effects of personality (neuroticism, frustration intolerance, rigidity, melancholic type), adverse life events and chronic difficulties on depressive symptoms in 89 high-risk subjects (HRS, siblings and children of patients suffering from an affective disorder), without any mental illness at wave 1 (T1), and 49 controls without any personal and family history of psychiatric disorder at T1. To this end, regression analysis and path analysis using a structural equation model (only for HRS) were performed. RESULTS: Risk factors for depressive symptoms at wave 2 (T2) in HRS comprised acute adverse life events, frustration intolerance (T1) and depressive symptoms (T1). Risk factors for depressive symptoms in controls included chronic difficulties, neuroticism and rigidity. HRS had less stressful life events and the same risk for chronic difficulties, but perceived adverse events as more stressful. LIMITATION: The sample size of the control group is too small for identifying slight effects. CONCLUSION: Our results indicate that the impact on the emergence of depressive symptoms of various risk factors is different in high-risk subjects and controls. High-risk subjects are more sensitive to the depressogenic effects of acute stress and thus avoid potential stressful changes in their life to a higher extent. On the other hand, the influence of persistent factors such as personality traits (neuroticism, rigidity) and chronic difficulties on subsequent depressive symptoms was less pronounced in HRS as compared to controls.},
affiliation = {Department of Psychiatry and Psychotherapy, University of Freiburg, Hauptstr. 5, 79104 Freiburg, Germany. toias_drieling@psyallg.ukl.uni-freiburg.de},
number = {2-3},
pages = {195--203},
volume = {91},
year = {2006},
month = {Apr},
language = {eng},
keywords = {Male, Genetic Predisposition to Disease, Mood Disorders, Risk Factors, Female, Follow-Up Studies, Questionnaires, Adult, Stress: Psychological, Depression, Personality, Humans},
date-added = {2010-05-01 17:24:28 +0200},
date-modified = {2010-05-01 17:24:28 +0200},
doi = {10.1016/j.jad.2006.01.004},
pii = {S0165-0327(06)00005-X},
pmid = {16488022},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11470},
rating = {0}
}

@article{Zhao:2008p2286,
author = {Zhenming Zhao and Nadia Timofeev and Stephen W Hartley and David Hk Chui and Supan Fucharoen and Thomas T Perls and Martin H Steinberg and Clinton T Baldwin and Paola Sebastiani},
journal = {BMC Genet},
title = {Imputation of missing genotypes: an empirical evaluation of IMPUTE},
abstract = {BACKGROUND: Imputation of missing genotypes is becoming a very popular solution for synchronizing genotype data collected with different microarray platforms but the effect of ethnic background, subject ascertainment, and amount of missing data on the accuracy of imputation are not well understood. RESULTS: We evaluated the accuracy of the program IMPUTE to generate the genotype data of partially or fully untyped single nucleotide polymorphisms (SNPs). The program uses a model-based approach to imputation that reconstructs the genotype distribution given a set of referent haplotypes and the observed data, and uses this distribution to compute the marginal probability of each missing genotype for each individual subject that is used to impute the missing data. We assembled genome-wide data from five different studies and three different ethnic groups comprising Caucasians, African Americans and Asians. We randomly removed genotype data and then compared the observed genotypes with those generated by IMPUTE. Our analysis shows 97% median accuracy in Caucasian subjects when less than 10% of the SNPs are untyped and missing genotypes are accepted regardless of their posterior probability. The median accuracy increases to 99% when we require 0.95 minimum posterior probability for an imputed genotype to be acceptable. The accuracy decreases to 86% or 94% when subjects are African Americans or Asians. We propose a strategy to improve the accuracy by leveraging the level of admixture in African Americans. CONCLUSION: Our analysis suggests that IMPUTE is very accurate in samples of Caucasians origin, it is slightly less accurate in samples of Asians background, but substantially less accurate in samples of admixed background such as African Americans. Sample size and ascertainment do not seem to affect the accuracy of imputation.},
affiliation = {Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue, Boston MA 02118, USA.},
pages = {85},
volume = {9},
year = {2008},
month = {Jan},
language = {eng},
keywords = {Genotype, African Americans, Humans, Computational Biology, Models: Genetic, Sensitivity and Specificity, Polymorphism: Single Nucleotide, Genome-Wide Association Study, Software, Mathematical Computing, European Continental Ancestry Group, Asian Continental Ancestry Group},
date-added = {2010-01-10 12:02:20 +0100},
date-modified = {2010-01-10 12:02:20 +0100},
doi = {10.1186/1471-2156-9-85},
pii = {1471-2156-9-85},
pmid = {19077279},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Zhao-2008-BMC%20Genet_Imputation%20of%20missin.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2286},
rating = {0}
}

@article{Dome:2010p5267,
author = {Peter Dome and Judit Lazary and Miklos Peter Kalapos and Zoltan Rihmer},
journal = {Neurosci Biobehav Rev},
title = {Smoking, nicotine and neuropsychiatric disorders},
abstract = {Tobacco smoking is an extremely addictive and harmful form of nicotine (NIC) consumption, but unfortunately also the most prevalent. Although disproportionately high frequencies of smoking and its health consequences among psychiatric patients are widely known, the neurobiological background of this epidemiological association is still obscure. The diverse neuroactive effects of NIC and some other major tobacco smoke constituents in the central nervous system may underlie this association. This present paper summarizes the pharmacology of NIC and its receptors (nAChR) based on a systematic review of the literature. The role of the brain's reward system(s) in NIC addiction and the results of functional and structural neuroimaging studies on smoking-related states and behaviors (i.e. dependence, craving, withdrawal) are also discussed. In addition, the epidemiological, neurobiological, and genetic aspects of smoking in several specific neuropsychiatric disorders are reviewed and the clinical relevance of smoking in these disease states addressed.},
affiliation = {Department of Clinical and Theoretical Mental Health, Kutvolgyi Clinical Center, Semmelweis University, Faculty of Medicine, Kutvolgyi ut 4, 1125 Budapest, Hungary. dome_peter@yahoo.co.uk},
number = {3},
pages = {295--342},
volume = {34},
year = {2010},
month = {Mar},
language = {eng},
date-added = {2010-02-09 22:27:51 +0100},
date-modified = {2010-02-09 22:27:51 +0100},
doi = {10.1016/j.neubiorev.2009.07.013},
pii = {S0149-7634(09)00111-0},
pmid = {19665479},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5267},
rating = {0}
}

@article{Palmer:2005p3275,
author = {Lyle J Palmer and Lon R Cardon},
journal = {Lancet},
title = {Shaking the tree: mapping complex disease genes with linkage disequilibrium},
abstract = {Much effort and expense are being spent internationally to detect genetic polymorphisms contributing to susceptibility to complex human disease. Concomitantly, the technology for detecting and genotyping single nucleotide polymorphisms (SNPs) has undergone rapid development, yielding extensive catalogues of these polymorphisms across the genome. Population-based maps of the correlations amongst SNPs (linkage disequilibrium) are now being developed to accelerate the discovery of genes for complex human diseases. These genomic advances coincide with an increasing recognition of the importance of very large sample sizes for studying genetic effects. Together, these new genetic and epidemiological data hold renewed promise for the identification of susceptibility genes for complex traits. We review the state of knowledge about the structure of the human genome as related to SNPs and linkage disequilibrium, discuss the potential applications of this knowledge to mapping complex disease genes, and consider the issues facing whole genome association scanning using SNPs.},
affiliation = {Western Australian Institute for Medical Research and University of Western Australia Centre for Medical Research, University of Western Australia. lyle.palmer@cyllene.uwa.edu.au},
number = {9492},
pages = {1223--34},
volume = {366},
year = {2005},
month = {Oct},
language = {eng},
keywords = {Haplotypes, Humans, Genetics: Population, Polymorphism: Single Nucleotide, Genotype, Gene Frequency, Linkage Disequilibrium, Chromosome Mapping},
date-added = {2010-01-14 21:08:47 +0100},
date-modified = {2010-07-29 19:38:44 +0200},
doi = {10.1016/S0140-6736(05)67485-5},
pii = {S0140-6736(05)67485-5},
pmid = {16198771},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Palmer-2005-Lancet_Shaking%20the%20tree%20ma.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3275},
read = {Yes},
rating = {0}
}

@article{Hwang:2006p2721,
author = {H Hwang and W S DeSarbo and Y Takane},
title = {Fuzzy Clusterwise Generalized Structured Component Analysis},
abstract = {Generalized Structured Component Analysis (GSCA) was recently introduced by Hwang and Takane (2004) as a component-based approach to path analysis with latent variables. The parameters of GSCA are estimated by pooling data across respondents under the implicit assumption that they all come from a single, homogenous group. However, as has been empirically demonstrated by various researchers across a number of areas of inquiry, such aggregate analyses can often mask the true structure in data when respondent heterogeneity is present. In this paper, GSCA is generalized to a fuzzy clustering framework so as to account for potential group-level respondent heterogeneity. An alternating least-squares procedure is developed and technically described for parameter estimation. A small-scale Monte Carlo study involving synthetic data is carried out to compare the performance between the proposed method and an extant approach. In addition, an empirical application concerning alcohol use among adolescents from US northwestern urban areas is presented to illustrate the usefulness of the proposed method. Finally, a number of directions for future research are provided.},
year = {2006},
date-added = {2010-01-13 14:10:53 +0100},
date-modified = {2010-07-24 11:35:04 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hwang-2006-_Fuzzy%20Clusterwise%20Ge.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2721},
read = {Yes},
rating = {4}
}

@article{Liu:2009p13158,
author = {Qingzhong Liu and Andrew H Sung and Zhongxue Chen and Jianzhong Liu and Xudong Huang and Youping Deng},
journal = {PLoS ONE},
title = {Feature selection and classification of MAQC-II breast cancer and multiple myeloma microarray gene expression data},
abstract = {Microarray data has a high dimension of variables but available datasets usually have only a small number of samples, thereby making the study of such datasets interesting and challenging. In the task of analyzing microarray data for the purpose of, e.g., predicting gene-disease association, feature selection is very important because it provides a way to handle the high dimensionality by exploiting information redundancy induced by associations among genetic markers. Judicious feature selection in microarray data analysis can result in significant reduction of cost while maintaining or improving the classification or prediction accuracy of learning machines that are employed to sort out the datasets. In this paper, we propose a gene selection method called Recursive Feature Addition (RFA), which combines supervised learning and statistical similarity measures. We compare our method with the following gene selection methods: Support Vector Machine Recursive Feature Elimination (SVMRFE), Leave-One-Out Calculation Sequential Forward Selection (LOOCSFS), Gradient based Leave-one-out Gene Selection (GLGS). To evaluate the performance of these gene selection methods, we employ several popular learning classifiers on the MicroArray Quality Control phase II on predictive modeling (MAQC-II) breast cancer dataset and the MAQC-II multiple myeloma dataset. Experimental results show that gene selection is strictly paired with learning classifier. Overall, our approach outperforms other compared methods. The biological functional analysis based on the MAQC-II breast cancer dataset convinced us to apply our method for phenotype prediction. Additionally, learning classifiers also play important roles in the classification of microarray data and our experimental results indicate that the Nearest Mean Scale Classifier (NMSC) is a good choice due to its prediction reliability and its stability across the three performance measurements: Testing accuracy, MCC values, and AUC errors.},
affiliation = {Department of Computer Science and Institute for Complex Additive Systems Analysis, New Mexico Tech, Socorro, New Mexico, United States of America.},
number = {12},
pages = {e8250},
volume = {4},
year = {2009},
month = {Jan},
language = {eng},
keywords = {Multiple Myeloma, Receptors: Estrogen, Databases: Genetic, Gene Expression Profiling, Genes: Neoplasm, Treatment Outcome, Female, Quality Control, Breast Neoplasms, Humans, Oligonucleotide Array Sequence Analysis, Gene Expression Regulation: Neoplastic},
date-added = {2010-06-26 11:17:17 +0200},
date-modified = {2010-06-26 11:17:18 +0200},
doi = {10.1371/journal.pone.0008250},
pmid = {20011240},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Liu-2009-PLoS%20ONE_Feature%20selection%20an.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13158},
rating = {0}
}

@article{Hu:2007p6891,
author = {Yongjian Hu and Sarah Stewart-Brown and Liz Twigg and Scott Weich},
journal = {Psychol Med},
title = {Can the 12-item General Health Questionnaire be used to measure positive mental health?},
abstract = {BACKGROUND: Well-being is an important determinant of health and social outcomes. Measures of positive mental health states are needed for population-based research. The 12-item General Health Questionnaire (GHQ-12) has been widely used in many settings and languages, and includes positively and

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib