text:
papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1359},
rating = {0}
}

@article{Wang:1987p6276,
author = {Y J Wang and G Y Wong},
journal = {JAMA},
title = {Stochastic Blockmodels for Directed Graphs},
abstract = {Holland	and	Leinhardt	(1981)	proposed	t h e p ,	model	for	the	analysis	of binary directed graph data in network studies. Such a model provides information about the "attractiveness" and "expansiveness" of the in- dividual nodes in the network, as well as the tendency of a pair of nodes to reciprocate relational ties. When the nodes are a priori partitioned into subgroups based on attributes such as race and sex, the density of ties from one subgroup to another can differ considerably from that relating another pair of subgroups, thus creating a situation called block- ing in social networks. Thep, model completely ignores this extra piece of information and is, therefore, unable to explain the block structure. Blockmodels that are simple extensions of the p, model are proposed specifically for such data. An iterative scaling algorithm is presented for fitting the model parameters by maximum likelihood. The methodology is illustrated in detail on two empirical examples.},
number = {397},
pages = {8--19},
volume = {82},
year = {1987},
date-added = {2010-02-20 17:39:09 +0100},
date-modified = {2010-07-29 20:01:35 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Wang-1987-JAMA_Stochastic%20Blockmode.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6276},
rating = {0}
}

@article{Ai:2000p4114,
author = {C Ai and EC Norton},
title = {Interaction Terms in Nonlinear Models},
abstract = {Although applied economists often estimate interaction terms to infer how the effect of one independent variable on the dependent variable depends on the magnitude of another independent variable, most researchers misinterpret the coefficient in nonlinear models. The magnitude of the interaction effect does not equal the coefficient on the interaction term, can be of opposite sign, and is conditional on all the independent variables. The statistical significance of the interaction effect may change substantially with changes in the independent variable. Implications are discussed for difference in difference models. We illustrate with an empirical example.},
year = {2000},
date-added = {2010-01-20 00:01:56 +0100},
date-modified = {2010-01-20 00:02:31 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Ai-2000-_Interaction%20Terms%20in.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4114},
rating = {0}
}

@article{Crowley:2009p9620,
author = {Michael J Crowley and Jia Wu and Clifford Crutcher and Christopher A Bailey and C W Lejuez and Linda C Mayes},
journal = {Dev Neurosci},
title = {Risk-taking and the feedback negativity response to loss among at-risk adolescents},
abstract = {Event-related brain potentials were examined in 32 adolescents (50% female) from a high-risk sample, who were exposed to cocaine and other drugs prenatally. Adolescents were selected for extreme high- or low-risk behavior on the Balloon Analog Risk Task, a measure of real-world risk-taking propensity. The feedback error-related negativity (fERN), an event-related potential (ERP) that occurs when an expected reward does not occur, was examined in a game in which choices lead to monetary gains and losses with feedback delayed 1 or 2 s. The fERN was clearly visible in the fronto-central scalp region in this adolescent sample. Feedback type, feedback delay, risk status, and sex were all associated with fERN variability. Monetary feedback also elicited a P300-like component, moderated by delay and sex. Delaying reward feedback may provide a means for studying complementary functioning of dopamine and norepinephrine systems.},
affiliation = {Yale Child Study Center, Yale School of Medicine, New Haven, CT 06473, USA. michael.crowley@yale.edu},
note = {genim},
number = {1-2},
pages = {137--48},
volume = {31},
year = {2009},
month = {Jan},
language = {eng},
keywords = {Risk-Taking, Event-Related Potentials: P300, Sex Characteristics, Male, Adolescent, Psychometrics, Female, Reward, Humans, Evoked Potentials, Feedback: Psychological, Neuropsychological Tests, Motivation, Electroencephalography, Risk},
date-added = {2010-03-25 14:41:53 +0100},
date-modified = {2010-03-25 18:17:28 +0100},
doi = {10.1159/000207501},
pii = {000207501},
pmid = {19372694},
URL = {http://content.karger.com/produktedb/produkte.asp?typ=fulltext&file=000207501},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Crowley-2009-Dev%20Neurosci_Risk-taking%20and%20the.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9620},
rating = {0}
}

@article{Tuerlinckx:2001,
author = {F Tuerlinckx and Paul De Boeck},
journal = {Methods of Psychological Research Online},
title = {Non-modeled item interactions can lead to distorted discrimination parameters: A case study},
pages = {159--174},
volume = {6},
year = {2001},
date-added = {2010-01-10 11:33:23 +0100},
date-modified = {2010-07-29 20:46:12 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Tuerlinckx-2001-Methods%20of%20Psychological%20Research%20Online_Non-modeled%20item%20int.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2004},
rating = {0}
}

@article{Kankaras:2009p13443,
author = {M Kankaras and J K Vermunt and G Moors},
title = {Measurement Equivalence of Ordinal Items: A Comparison of Factor Analytic, Item Response Theory, and Latent Class Approaches},
abstract = {Three distinctive methods of assessing measurement equivalence of ordinal items, i.e. confirmatory factor analysis, differential item functioning using item response theory and latent class factor analysis, make different modeling assumptions and adopt different procedures. Simulation data are used to compare the performance of these three approaches in detecting the sources of measurement inequivalence. For this purpose, we simulated Likert-type data using two non-linear models, one with categorical and one with continuous latent variables. Inequivalence was set up in the slope parameters (loadings) as well as in the item intercept parameters in a form resembling agreement and extreme response styles. Results indicate that the item response theory and latent class factor models can relatively accurately detect and locate inequivalence in the intercept and slope parameters both at the scale and the item level. Confirmatory factor analysis performs well when inequivalence is located in the slope parameters, but wrongfully indicates inequivalence in the slope parameters when inequivalence is located in the intercept parameters. Influences of sample size, number of inequivalent items in a scale, and model fit criteria on the performance of the three methods are also analysed.},
year = {2009},
date-added = {2010-07-01 20:13:40 +0200},
date-modified = {2010-07-01 20:14:21 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Kankaras-2009-_Measurement%20Equivale.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13443},
rating = {5}
}

@misc{Birkett:1986,
author = {N J Birkett},
journal = {Miscellaneous},
title = {Selecting the number of response categories for a Lickert-type scale},
year = {1986},
date-added = {2010-01-10 11:33:20 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Birkett-1986-Miscellaneous_Selecting%20the%20number.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2155},
rating = {0}
}

@article{Verstralen:1996p1849,
author = {H H F M Verstralen},
title = {Estimating Integer Parameters in IRT Models for Polytomous Items},
year = {1996},
date-added = {2010-01-10 11:17:57 +0100},
date-modified = {2010-01-10 11:18:24 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Verstralen-1996-_Estimating%20Integer%20P.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1849},
rating = {0}
}

@article{Hardoon:2009p916,
author = {David R Hardoon and Ulrich Ettinger and Janaina Mour{\~a}o-Miranda and Elena Antonova and David Collier and Veena Kumari and Steven C R Williams and Michael Brammer},
journal = {Neurosci Lett},
title = {Correlation-based multivariate analysis of genetic influence on brain volume},
abstract = {Considerable research effort has focused on achieving a better understanding of the genetic correlates of individual differences in volumetric and morphological brain measures. The importance of these efforts is underlined by evidence suggesting that brain changes in a number of neuropsychiatric disorders are at least partly genetic in origin. The currently used methods to study these relationships are mostly based on single-genotype univariate analysis techniques. These methods are limited as multiple genes are likely to interact with each other in their influences on brain structure and function. In this paper we present a feasibility study where we show that by using kernel correlation analysis, with a new genotypes representation, it is possible to analyse the relative associations of several genetic polymorphisms with brain structure. The implementation of the method is demonstrated on genetic and structural magnetic resonance imaging (MRI) data acquired from a group of 16 healthy subjects by showing the multivariate genetic influence on grey and white matter.},
affiliation = {Computational Statistics {\&} Machine Learning Centre, Dept. of Computer Science, University College London, London WC1E 6BT, United Kingdom. D.Hardoon@cs.ucl.ac.uk},
number = {3},
pages = {281--6},
volume = {450},
year = {2009},
month = {Feb},
language = {eng},
keywords = {Brain, Adolescent, Magnetic Resonance Imaging, Genotype, Nerve Fibers: Myelinated, Male, Multivariate Analysis, Genetic Variation, Pattern Recognition: Automated, Phenotype, Organ Size, Female, Gene Expression Regulation: Developmental, Humans, Polymorphism: Genetic, Image Processing: Computer-Assisted, Polymorphism: Single Nucleotide, Anthropometry, Adult, Young Adult},
date-added = {2010-01-03 19:01:34 +0100},
date-modified = {2010-01-03 19:01:34 +0100},
doi = {10.1016/j.neulet.2008.11.035},
pii = {S0304-3940(08)01604-2},
pmid = {19028548},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hardoon-2009-Neurosci%20Lett_Correlation-based%20mu.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p916},
read = {Yes},
rating = {0}
}

@article{Ding:2004p2927,
author = {B Ding and R Gentleman},
journal = {Bioconductor Project Working Papers},
title = {Classification Using Generalized Partial Least Squares},
abstract = {The advances in computational biology have made simultaneous monitoring of thousands of features possible. The high throughput technologies not only bring about a much richer information context in which to study various aspects of gene functions but they also present challenge of analyzing data with large number of covariates and few samples. As an integral part of machine learning, classification of samples into two or more categories is almost always of interest to scientists. In this paper, we address the question of classification in this setting by extending partial least squares (PLS), a popular dimension reduction tool in chemometrics, in the context of generalized linear regression based on a previous approach, Iteratively ReWeighted Partial Least Squares, i.e. IRWPLS (Marx, 1996). We compare our results with two-stage PLS (Nguyen and Rocke, 2002A; Nguyen and Rocke, 2002B) and other classifiers. We show that by phrasing the problem in a generalized linear model setting and by applying bias correction to the likelihood to avoid (quasi)separation, we often get lower classification error rates.},
number = {5},
year = {2004},
date-added = {2010-01-13 22:15:22 +0100},
date-modified = {2010-01-13 22:16:13 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Ding-2004-Bioconductor%20Project%20Working%20Papers_Classification%20Using.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2927},
rating = {0}
}

@article{Guttman:1977p7066,
author = {L Guttman},
journal = {The Statistician},
title = {What is Not What in Statistics},
number = {2},
pages = {81--107},
volume = {26},
year = {1977},
date-added = {2010-03-06 20:10:14 +0100},
date-modified = {2010-07-29 19:53:47 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Guttman-1977-The%20Statistician_What%20is%20Not%20What%20in.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7066},
rating = {0}
}

@article{Reeve:2010p11578,
author = {B Reeve},
title = {Applications of Item Response Theory (IRT) Modeling for Building and Evaluating Questionnaires Measuring Patient-Reported Outcomes},
date-added = {2010-05-09 18:22:51 +0200},
date-modified = {2010-05-09 18:23:10 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Reeve--_Applications%20of%20Item.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11578},
rating = {4}
}

@article{Wickham:2006p10902,
author = {H Wickham and D Caragea and D Cook},
title = {Exploring high-dimensional classification boundaries},
year = {2006},
date-added = {2010-04-11 13:48:37 +0200},
date-modified = {2010-04-11 13:49:07 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Wickham-2006-_Exploring%20high-dimen.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10902},
rating = {0}
}

@article{Woodruff:1997p11296,
author = {D Woodruff and B A Hanson},
journal = {Annual Meeting of the Psychometric Society},
title = {Estimation for Item Response Models using the EM Algorithm for Finite Mixtures},
abstract = {This paper presents a detailed description of maximum likelihood parameter estima- tion for item response models using the general EM algorithm. In this paper the models are specified using a univariate discrete latent ability variable. When the latent ability variable is discrete the distribution of the observed item responses is a finite mixture, and the EM algorithm for finite mixtures can be used. Maximum likelihood estimates of the item parameters and of the discrete probabilities of the latent ability distribution are given using the EM algorithm for finite mixtures. Results are presented in general for both di- chotomous and polytomous item response models. The relation between the EM estimates and Bock-Aitken marginal maximum likelihood estimates is discussed.},
year = {1997},
date-added = {2010-04-26 22:29:11 +0200},
date-modified = {2010-04-26 22:29:57 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Woodruff-1997-Annual%20Meeting%20of%20the%20Psychometric%20Society_Estimation%20for%20Item.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11296},
rating = {0}
}

@article{Park:2007p3889,
author = {Ae Kyung Park and Ho Kim},
journal = {Journal of preventive medicine and public health = Yebang {\u U}ihakhoe chi},
title = {[A review of power and sample size estimation in genomewide association studies.]},
abstract = {Power and sample size estimation is one of the crucially important steps in planning a genetic association study to achieve the ultimate goal, identifying candidate genes for disease susceptibility, by designing the study in such a way as to maximize the success possibility and minimize the cost. Here we review the optimal two-stage genotyping designs for genomewide association studies recently investigated by Wang et al(2006). We review two mathematical frameworks most commonly used to compute power in genetic association studies prior to the main study: Monte-Carlo and non-central chi-square estimates. Statistical powers are computed by these two approaches for case-control genotypic tests under one-stage direct association study design. Then we discuss how the linkage disequilibrium strength affects power and sample size, and how to use empirically-derived distributions of important parameters for power calculations. We provide useful information on publicly available software developed to compute power and sample size for various study designs.},
affiliation = {Graduate School of Public Health, Seoul National University, Korea.},
number = {2},
pages = {114--21},
volume = {40},
year = {2007},
month = {Mar},
language = {kor},
keywords = {Sample Size, Humans, Genetic Testing, Models: Statistical, Genome: Human, Research Design},
date-added = {2010-01-16 21:04:20 +0100},
date-modified = {2010-01-16 21:04:20 +0100},
pii = {200703114},
pmid = {17426422},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3889},
rating = {3}
}

@article{Fleischhacker:2005p5378,
author = {W Wolfgang Fleischhacker and Jonathan Rabinowitz and Georg Kemmler and Mari{\"e}lle Eerdekens and Angelika Mehnert},
journal = {Br J Psychiatry},
title = {Perceived functioning, well-being and psychiatric symptoms in patients with stable schizophrenia treated with long-acting risperidone for 1 year},
abstract = {BACKGROUND: The extent to which antipsychotics improve patients' well-being is uncertain. AIMS: To examine psychopathology and patient-rated functioning and well-being in patients treated with risperidone. METHOD: In a 1-year, open-label, international multicentre trial of long-acting risperidone in 615 stable adult patients with schizophrenia, self-rated functioning and well-being were measured every 3 months using the Short Form 36-item questionnaire (SF-36). Psychopathology was quantified using the Positive and Negative Syndrome Scale (PANSS). RESULTS: Significant improvements were found on the SF-36 mental component summary score and vitality and social functioning scales. PANSS and mental component summary scores were moderately correlated. CONCLUSIONS: Patient-reported functioning and well-being appear to differ from investigator-rated psychotic symptoms. Patient-rated well-being should be assessed with symptoms to help measure treatment outcomes.},
affiliation = {Department of Biological Psychiatry, Medical University Innsbruck, Anichstrasse 35, 6020 Innsbruck, Austria. wolfgang.fleischhacker@uibk.ac.at},
pages = {131--6},
volume = {187},
year = {2005},
month = {Aug},
language = {eng},
keywords = {Female, Schizophrenia, Male, Adult, Time Factors, Treatment Outcome, Health Status, Quality of Life, Aged, Patient Satisfaction, Humans, Adolescent, Schizophrenic Psychology, Aged: 80 and over, Antipsychotic Agents, Self Assessment (Psychology), Injections: Intramuscular, Depression, Middle Aged, Anxiety, Risperidone, Administration: Oral},
date-added = {2010-02-11 10:29:52 +0100},
date-modified = {2010-07-29 19:52:08 +0200},
doi = {10.1192/bjp.187.2.131},
pii = {187/2/131},
pmid = {16055823},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Fleischhacker-2005-Br%20J%20Psychiatry_Perceived%20functionin.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5378},
rating = {0}
}

@article{Stanfield:2008p11150,
author = {Andrew C Stanfield and Andrew M McIntosh and Michael D Spencer and Ruth Philip and Sonia Gaur and Stephen M Lawrie},
journal = {Eur Psychiatry},
title = {Towards a neuroanatomy of autism: a systematic review and meta-analysis of structural magnetic resonance imaging studies},
abstract = {BACKGROUND: Structural brain abnormalities have been described in autism but studies are often small and contradictory. We aimed to identify which brain regions can reliably be regarded as different in autism compared to healthy controls. METHOD: A systematic search was conducted for magnetic resonance imaging studies of regional brain size in autism. Data were extracted and combined using random effects meta-analysis. The modifying effects of age and IQ were investigated using meta-regression. RESULTS: The total brain, cerebral hemispheres, cerebellum and caudate nucleus were increased in volume, whereas the corpus callosum area was reduced. There was evidence for a modifying effect of age and IQ on the cerebellar vermal lobules VI-VII and for age on the amygdala. CONCLUSIONS: Autism may result from abnormalities in specific brain regions and a global lack of integration due to brain enlargement. Inconsistencies in the literature partly relate to differences in the age and IQ of study populations. Some regions may show abnormal growth trajectories.},
affiliation = {Division of Psychiatry, School of Molecular and Clinical Medicine, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK. andrew.stanfield@ed.ac.uk},
number = {4},
pages = {289--99},
volume = {23},
year = {2008},
month = {Jun},
language = {eng},
keywords = {Sex Factors, Magnetic Resonance Imaging, Dominance: Cerebral, Cerebellum, Humans, Corpus Callosum, Autistic Disorder, Caudate Nucleus, Image Processing: Computer-Assisted, Intelligence, Age Factors, Amygdala, Brain},
date-added = {2010-04-14 13:59:22 +0200},
date-modified = {2010-04-14 13:59:23 +0200},
doi = {10.1016/j.eurpsy.2007.05.006},
pii = {S0924-9338(07)01334-X},
pmid = {17765485},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Stanfield-2008-Eur%20Psychiatry_Towards%20a%20neuroanato.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11150},
rating = {0}
}

@article{Hwang:2007p2720,
author = {H Hwang and Y Takane and N Malhotra},
title = {Multilevel Generalized Structured Component Analysis},
abstract = {Generalized structured component analysis has been proposed as an alternative to partial least squares for path analysis with latent variables. In practice, observed and latent variables may often be hierarchically structured in that their individual-level scores are grouped within higher-level units. The observed and latent variable scores nested within the same higher-level group are likely to be more similar than those in different groups, thereby giving rise to the interdependence of the scores within the same group. Unless this interdependence is taken into account, obtained solutions are likely to be biased. In this paper, generalized structured component analysis is extended so as to account for the nested structures of both observed and latent variables. An alternating least-squares procedure is developed for parameter estimation. An empirical application concerning the measurements of customer-level customer satisfaction nested within different companies is presented to illustrate the usefulness of the proposed method.},
year = {2007},
date-added = {2010-01-13 14:06:35 +0100},
date-modified = {2010-01-13 14:07:12 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hwang-2007-_Multilevel%20Generaliz.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2720},
rating = {0}
}

@article{Hedeker:1997p3614,
author = {D Hedeker and R D Gibbons},
journal = {Psychological Methods},
title = {Application of Random-Effects Pattern-Mixture Models for Missing Data in Longitudinal Studies},
abstract = {Random-effects regression models have become increasingly popular for analysis of longitudinal data. A key advantage of the random-effects approach is that it can be applied when subjects are not measured at the same number of timepoints. In this article we describe use of random-effects pattern-mixture models to further handle and describe the influence of missing data in longitudinal studies. For this ap- proach, subjects are first divided into groups depending on their missing-data pattern and then variables based on these groups are used as model covariates. In this way, researchers are able to examine the effect of missing-data patterns on the outcome (or outcomes) of interest. Furthermore, overall estimates can be obtained by averaging over the missing-data patterns. A psychiatric clinical trials data set is used to illustrate the random-effects pattern-mixture approach to longitudinal data analysis with missing data.},
number = {1},
pages = {64--78},
volume = {2},
year = {1997},
date-added = {2010-01-16 18:31:29 +0100},
date-modified = {2010-01-16 18:32:40 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hedeker-1997-Psychological%20Methods_Application%20of%20Rando.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3614},
rating = {0}
}

@article{Srensen:1997p5052,
author = {H T S{\o}rensen and S Sabroe and J Olsen and K J Rothman and M W Gillman and P Fischer},
journal = {BMJ},
title = {Birth weight and cognitive function in young adult life: historical cohort study},
abstract = {OBJECTIVE: To examine the relation between birth weight and cognitive function in young adult life. DESIGN: Retrospective cohort study based on birth registry data and cognitive function measured during evaluation for military service. SUBJECTS: 4300 Danish conscripts born between 1973 and 1975. MAIN OUTCOME MEASURES: Mean score in the Boerge Prien test of cognitive function; score is the number of correct answers to 78 questions and correlates with full scale intelligence quotient (IQ). RESULTS: Mean score in the Boerge Prien test increased from 39.9 at a birth weight of < or = 2500 g to 44.6 at a birth weight of 4200 g even after adjustment for gestational age and length at birth, maternal age and parity, and other variables. Above a birth weight of 4200 g the test score decreased slightly. CONCLUSION: Birth weight is associated with cognitive performance in young adult life. Interference with fetal growth may influence adult cognitive performance.},
affiliation = {Department of Internal Medicine V, Aarhus University Hospital, Denmark. HTS@soci.aau.dk},
number = {7105},
pages = {401--3},
volume = {315},
year = {1997},
month = {Aug},
language = {eng},
keywords = {Male, Infant: Newborn, Birth Weight, Retrospective Studies, Cognition, Humans, Cohort Studies, Adolescent, Intelligence Tests, Intelligence, Adult, Denmark},
date-added = {2010-02-05 20:01:41 +0100},
date-modified = {2010-02-05 20:01:41 +0100},
pmid = {9277604},
local-url = {file://localhost/Users/chl/Dropbox/Papers/S%C3%B8rensen-1997-BMJ_Birth%20weight%20and%20cog.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5052},
rating = {0}
}

@article{Iacono:2009p6043,
author = {T Iacono and D West and K Bloomberg and H Johnson},
journal = {J Intellect Disabil Res},
title = {Reliability and validity of the revised Triple C: Checklist of Communicative Competencies for adults with severe and multiple disabilities},
abstract = {AIMS: Few tools are available to assess the communication skills of adults with severe and multiple disabilities functioning at unintentional to early symbolic levels. An exception is the Triple C: Checklist of Communicative Competencies. In this study, aspects of support worker and clinician agreement, internal consistency and construct validity of a revised version of the Triple C were explored. METHOD: Triple C checklists were completed for 72 adults with severe intellectual disabilities (ID) by 118 support workers and stages were assigned by the researchers. Two support workers completed checklists for each of 68 adults with ID. Three researchers also conducted direct observations of 20 adults with ID. RESULTS: The average support worker agreement for items across the five stages of the Triple C ranged from 81% to 87%; agreement for stage assignment based on first and second support worker checklists was moderate to high (k = 0.63). Internal consistency was high (KR20 = 0.97); the stages were found to tap one factor (accounting for approximately 74% of variance), interpreted to be unintentional to early symbolic communication. Agreements between stages based on researcher observations and support worker-completed checklists were 35% and 71% across first and second support workers. CONCLUSION: The revised Triple C provides a reliable means of gathering data on which to determine the communication skills of adults with severe and multiple disabilities. The results support a collaborative use of the Triple C, such that a speech-language pathologist or other communication specialist works with a support worker to ensure understanding of the skills observed and development of appropriate intervention strategies.},
affiliation = {Centre for Developmental Disability Health Victoria, Monash University, Melbourne, Victoria, Australia. teresa.iacono@med.monash.edu.au},
number = {1},
pages = {44--53},
volume = {53},
year = {2009},
month = {Jan},
language = {eng},
keywords = {Caregivers, Reproducibility of Results, Aged, Autistic Disorder, Male, Questionnaires, Mental Retardation, Australia, Communication, Severity of Illness Index, Humans, Disabled Persons, Down Syndrome, Young Adult, Female, Comorbidity, Adult, Communication Disorders, Observer Variation, Middle Aged, Cerebral Palsy},
date-added = {2010-02-19 17:01:02 +0100},
date-modified = {2010-02-19 17:01:02 +0100},
doi = {10.1111/j.1365-2788.2008.01121.x},
pii = {JIR1121},
pmid = {18759959},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6043},
rating = {0}
}

@article{Cannon:2006p10210,
author = {Tyrone D Cannon and Matthew C Keller},
journal = {Annual review of clinical psychology},
title = {Endophenotypes in the genetic analyses of mental disorders},
abstract = {Common mental disorders such as schizophrenia, bipolar disorder, and severe major depression are highly heritable, but differ from single-gene (Mendelian) diseases in that they are the end products of multiple causes. Although this fact may help explain their prevalence from an evolutionary perspective, the complexity of the causes of these disorders makes identification of disease-promoting genes much more difficult. The "endophenotype" approach is an alternative method for measuring phenotypic variation that may facilitate the identification of susceptibility genes for complexly inherited traits. Here we examine the endophenotype construct in context of psychiatric genetics. We first develop an evolutionary theoretical framework for common mental disorders and differentiate them from simpler, single-gene disorders. We then provide a definition and description of endophenotypes, elucidating several features that will make a proposed endophenotype useful in psychiatric genetic research and evaluating the methods for detecting and validating such endophenotypes. We conclude with a review of recent results in the schizophrenia literature that illustrate the usefulness of endophenotypes in genetic analyses of mental disorders, and discuss implications of these findings for models of disease causation and nosology. Given that in mental disorders as in behavior generally, the pathways from genotypes to phenotypes are circuitous at best, discernment of endophenotypes more proximal to the effects of genetic variation will aid attempts to link genes to disorders.},
affiliation = {Department of Psychology, University of California, Los Angeles, California 90095, USA. cannon@psych.ucla.edu},
pages = {267--90},
volume = {2},
year = {2006},
month = {Jan},
language = {eng},
keywords = {Mental Disorders, Chromosome Mapping, Genetic Predisposition to Disease, Models: Genetic, Genetic Techniques, Schizophrenia, Gene Expression, Genetic Markers, Social Environment, Genetic Variation, Humans, Phenotype, Family},
date-added = {2010-04-02 10:46:48 +0200},
date-modified = {2010-04-02 10:47:20 +0200},
doi = {10.1146/annurev.clinpsy.2.022305.095232},
pmid = {17716071},
URL = {http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.clinpsy.2.022305.095232?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%253dncbi.nlm.nih.gov},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Cannon-2006-Annual%20review%20of%20clinical%20psychology_Endophenotypes%20in%20th.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10210},
rating = {4}
}

@article{Newcomb:1981p8236,
author = {M D Newcomb and G J Huba and Peter M Bentler},
journal = {Journal of Health and Social Behavior},
title = {A Multidimensional Assessment of Stressful Life Events among Adolescents: Derivation and Correlates},
abstract = {A 39-item life-event questionnaire was administered to 1,018 adolescents, who indicated the perceived desirability of each event and whether rhe event had actually happened to them either during the past year or more than one year earlier. A multidimensional scaling revealed seven interpretable dimensions of stress: FamilylParents, Accidentllllness, Sexuality, Autonomy, Deviance, Relocation, and Distress. Each dimension was scored for desirability, and occur- rence was summed using unit weighting. Sex, race, and grade-level differences were evaluated for each item and scale score. The scales calculated for the two different time periods revealed that stress is correlated over time only for corresponding areas. Finally, the stress scales were related to measures of health and psychological functioning through canonical and product- moment correlation analyses; distinct patterns of association were revealed. Alternative methods of scoring life events are evaluated.},
note = {psytools},
number = {4},
pages = {400--415},
volume = {22},
year = {1981},
date-added = {2010-03-20 20:00:36 +0100},
date-modified = {2010-07-29 20:44:53 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Newcomb-1981-Journal%20of%20Health%20and%20Social%20Behavior_A%20Multidimensional%20A.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8236},
rating = {0}
}

@article{Zhao:2005p3942,
author = {Jinying Zhao and Eric Boerwinkle and Momiao Xiong},
journal = {Am J Hum Genet},
title = {An entropy-based statistic for genomewide association studies},
abstract = {Efficient genotyping methods and the availability of a large collection of single-nucleotide polymorphisms provide valuable tools for genetic studies of human disease. The standard chi2 statistic for case-control studies, which uses a linear function of allele frequencies, has limited power when the number of marker loci is large. We introduce a novel test statistic for genetic association studies that uses Shannon entropy and a nonlinear function of allele frequencies to amplify the differences in allele and haplotype frequencies to maintain statistical power with large numbers of marker loci. We investigate the relationship between the entropy-based test statistic and the standard chi2 statistic and show that, in most cases, the power of the entropy-based statistic is greater than that of the standard chi2 statistic. The distribution of the entropy-based statistic and the type I error rates are validated using simulation studies. Finally, we apply the new entropy-based test statistic to two real data sets, one for the COMT gene and schizophrenia and one for the MMP-2 gene and esophageal carcinoma, to evaluate the performance of the new method for genetic association studies. The results show that the entropy-based statistic obtained smaller P values than did the standard chi2 statistic.},
affiliation = {Human Genetic Center, University of Texas, Health Science Center at Houston, Houston, TX 77225, USA.},
number = {1},
pages = {27--40},
volume = {77},
year = {2005},
month = {Jul},
language = {eng},
keywords = {Genetic Markers, Statistics as Topic, Linkage Disequilibrium, Entropy, Humans, Gene Frequency, Haplotypes},
date-added = {2010-01-16 21:05:55 +0100},
date-modified = {2010-01-16 21:05:55 +0100},
doi = {10.1086/431243},
pii = {S0002-9297(07)60899-4},
pmid = {15931594},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3942},
rating = {0}
}

@article{Pollard:2004,
author = {K S Pollard and S Dudoit and M J van der Laan},
journal = {U.C. Berkeley Division of Biostatistics Working Paper Series},
title = {Multiple Testing Procedures R},
abstract = {The Bioconductor R package multtest implements widely applicable resampling-based single-step and stepwise multiple testing procedures (MTP) for controlling a broad class of Type I error rates, in testing problems involving general data generating distributions (with arbitrary dependence structures among variables), null hypotheses, and test statistics. The current version of multtest provides MTPs for tests concerning means, differences in means, and regression parameters in linear and Cox proportional hazards models. Procedures are provided to control Type I error rates defined as tail probabilities for arbitrary functions of the numbers of false positives and rejected hypotheses. These error rates include tail probabilities for the number of false positives (generalized family-wise error rate, gFWER) and the proportion of false positives among the rejected hypotheses (TPPFP). Single-step and step-down common-cut-off (maxT) and common-quantile (minP) procedures, that take into account the joint distribution of the test statistics, are proposed to control the family-wise error rate (FWER), or chance of at least one Type I error. In addition, augmentation multiple testing procedures are provided to control the gFWER and TPPFP, based on any initial FWER-controlling procedure. The results of a multiple testing procedure can be summarized using rejection regions for the test statistics, confidence regions for the parameters of interest, or adjusted p-values. A key ingredient of our proposed MTPs is the test statistics null distribution (and estimator thereof) used to derive rejection regions and corresponding confidence regions and adjusted p-values. Both bootstrap and permutation estimators of the test statistics null distribution are available. The S4 class/method object-oriented programming approach was adopted to summarize the results of a MTP. The modular design of multtest allows interested users to readily extend the package's functionality. Typical testing scenarios are illustrated by applying various MTPs implemented in multtest to the Acute Lymphoblastic Leukemia (ALL) dataset of Chiaretti et al. (2004), with the aim of identifying genes whose expression measures are associated with (possibly censored) biological and clinical outcomes.},
affiliation = {Center for Biomolecular Science and Engineering, University of California, Santa Cruz},
number = {Working Paper 164},
pages = {1--46},
year = {2004},
month = {Jul},
date-added = {2009-12-29 10:29:25 +0100},
date-modified = {2009-12-29 10:40:58 +0100},
URL = {http://www.google.com/search?client=safari&rls=en-us&q=Multiple+Testing+Procedures+R&ie=UTF-8&oe=UTF-8},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Pollard-2004-U.C.%20Berkeley%20Division%20of%20Biostatistics%20Working%20Paper%20Series_Multiple%20Testing%20Pro.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p262},
read = {Yes},
rating = {0}
}

@article{Verschoor:2004aa,
author = {Angela J Verschoor},
title = {IRT Test Assembly Using Genetic Algorithms},
abstract = {This paper intro duces a new class of ptimisation methods in test assembly: Genetic Algorithms (GAs). In the first part an overview is given of the concepts and principles of GAs, in the second part they are applied to three commonly used test assembly models using Item Response Theory. Simulation studies are performed in order to find conditions under which GAs can be successfully used.},
year = {2004},
month = {Apr},
date-added = {2010-01-03 19:39:02 +0100},
date-modified = {2010-01-03 19:39:03 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Verschoor-2004-_IRT%20Test%20Assembly%20Us.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1194},
rating = {0}
}

@article{Hu:2009p2951,
author = {Jianhua Hu and Adarsh Joshi and Valen E Johnson},
journal = {JAMA},
title = {Log-Linear Models for Gene Association},
abstract = {We describe a class of log-linear models for the detection of interactions in high-dimensional genomic data. This class of models leads to a Bayesian model selection algorithm that can be applied to data that have been reduced to contingency tables using ranks of observations within subjects, and discretization of these ranks within gene/network components. Many normalization issues associated with the analysis of genomic data are thereby avoided. A prior density based on Ewens' sampling distribution is used to restrict the number of interacting components assigned high posterior probability, and the calculation of posterior model probabilities is expedited by approximations based on the likelihood ratio statistic. Simulation studies are used to evaluate the efficiency of the resulting algorithm for known interaction structures. Finally, the algorithm is validated in a microarray study for which it was possible to obtain biological confirmation of detected interactions.},
affiliation = {Jianhua Hu is Assistant Professor of Biostatistics, Department of Biostatistics, University of Texas M. D. Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030 (E-mail: jhu@mdanderson.org ). Adarsh Joshi is graduate student, Department of Statistics, Texas A{\&}M University, College Station, TX 77030 (E- mail: adarsh@stat.tamu.edu ). Valen E. Johnson is Professor of Biostatistics, Department of Biostatistics, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 447, Houston, TX 77030 (E-mail: vejohnson@mdanderson.org ).},
number = {486},
pages = {597--607},
volume = {104},
year = {2009},
month = {Jan},
language = {ENG},
date-added = {2010-01-13 23:05:09 +0100},
date-modified = {2010-07-29 20:01:34 +0200},
doi = {10.1198/jasa.2009.0025},
pmid = {19655032},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hu-2009-JAMA_Log-Linear%20Models%20fo.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2951},
rating = {0}
}

@article{McGrath:2010p13500,
author = {Clare McGrath and Diana Rofail and Elizabeth Gargon and Linda Abetz},
journal = {Health Qual Life Outcomes},
title = {Using qualitative methods to inform the trade-off between content validity and consistency in utility assessment: the example of type 2 diabetes and Alzheimer's disease},
abstract = {BACKGROUND: Key stakeholders regard generic utility instruments as suitable tools to inform health technology assessment decision-making regarding allocation of resources across competing interventions. These instruments require a 'descriptor', a 'valuation' and a 'perspective' of the economic evaluation. There are various approaches that can be taken for each of these, offering a potential lack of consistency between instruments (a basic requirement for comparisons across diseases). The 'reference method' has been proposed as a way to address the limitations of the Quality-Adjusted Life Year (QALY). However, the degree to which generic measures can assess patients' specific experiences with their disease would remain unresolved. This has been neglected in the discussions on methods development and its impact on the QALY values obtained and resulting cost per QALY estimate underestimated. This study explored the content of utility instruments relevant to type 2 diabetes and Alzheimer's disease (AD) as examples, and the role of qualitative research in informing the trade-off between content coverage and consistency. METHOD: A literature review was performed to identify qualitative and quantitative studies regarding patients' experiences with type 2 diabetes or AD, and associated treatments. Conceptual models for each indication were developed. Generic- and disease-specific instruments were mapped to the conceptual models. RESULTS: Findings showed that published descriptions of relevant concepts important to patients with type 2 diabetes or AD are available for consideration in deciding on the most comprehensive approach to utility assessment. While the 15-dimensional health related quality of life measure (15D) seemed the most comprehensive measure for both diseases, the Health Utilities Index 3 (HUI 3) seemed to have the least coverage for type 2 diabetes and the EuroQol-5 Dimensions (EQ-5D) for AD. Furthermore, some of the utility instruments contained items that could not be mapped onto either of the proposed conceptual models. CONCLUSIONS: Content of the utility measure has a significant impact on the treatment effects that can be observed. This varies from one disease to the next and as such contributes to lack of consistency in observable utility effects and incremental utility scores. This observation appears to have been omitted from the method development considerations such as reference methods. As a result, we recommend that patients' perspectives obtained via qualitative methods are taken into consideration in the ongoing methods development in health state descriptions for generic utility instruments. Also, as a more immediate contribution to improving decision making, we propose that a content map of the chosen utility measure with patient-reported domains be provided as standard reporting in utility measurement in order to improve the transparency of the trade-offs in relation to patient relevance and consistency.},
affiliation = {Health Technology Assessment Policy, Medical Division, Worldwide Pharmaceutical Operations, 3-1-60 Walton Oaks, Tadworth, Surrey KT20 7NS, UK.},
pages = {23},
volume = {8},
year = {2010},
month = {Jan},
language = {eng},
date-added = {2010-07-07 20:39:30 +0200},
date-modified = {2010-07-07 20:39:36 +0200},
doi = {10.1186/1477-7525-8-23},
pii = {1477-7525-8-23},
pmid = {20152041},
local-url = {file://localhost/Users/chl/Dropbox/Papers/McGrath-2010-Health%20and%20Quality%20of%20Life%20Outcomes_Using%20qualitative%20me.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13500},
rating = {5}
}

@article{Noortgate:2003,
author = {W Van den Noortgate and Paul De Boeck and M Meulders},
journal = {Journal of Educational and Behavioral Statistics},
title = {Cross-classification multilevel logistic models in psychometrics},
pages = {369--386},
volume = {28},
year = {2003},
date-added = {2010-01-10 11:33:23 +0100},
date-modified = {2010-07-29 20:46:12 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Noortgate-2003-Journal%20of%20Educational%20and%20Behavioral%20Statistics_Cross-classification.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2024},
rating = {0}
}

@article{Ponocny:2002p14104,
author = {I Ponocny},
journal = {Psychometrika},
title = {ERRATA FOR "NONPARAMETRIC GOODNESS-OF-FIT TESTS FOR THE RASCH MODEL"},
abstract = {A Monte Carlo-algorithm realizing a family of nonpaxametric tests for the Rasch model is intro- duced which are conditional on the item and subject marginals. The algorithmis based on random changes of elements of data matrices without changing the maxginals; most powerful tests against all alternative hypotheses are given for which a monotone characteristic may be computed from the data matrix; alterna- tives may also be composed. Computation times are long, but exact p-values are approximated with the quality of approximation only depending on calculation time, but not on the number of persons. The power and the flexibility of the procedure is demonstrated by means of an empirical example where, among oth- ers, indicators for increased item similarities, the existence of subscales, violations of sufficiency of the raw score as well as learning processes were found. Many of the features described are implemented in theprogramT-Rasch1.0byPonocnyandPonocny-Seliger (1999).},
number = {2},
pages = {315},
volume = {67},
year = {2002},
date-added = {2010-08-18 11:20:25 +0200},
date-modified = {2010-08-18 11:21:14 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Ponocny-2002-Psychometrika_ERRATA%20FOR%20%22NONPARAM.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p14104},
rating = {0}
}

@article{Bechger:2004p14017,
author = {Timo M Bechger and Gunter Maris},
journal = {Psicologica},
title = {Structural equation modelling of multiple facet data: Extending models for multitrait-multimethod data},
number = {2},
volume = {25},
year = {2004},
date-added = {2010-08-04 09:45:55 +0200},
date-modified = {2010-08-04 09:47:07 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bechger-2004-Psicologica_Structural%20equation.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p14017},
rating = {0}
}

@article{Zou2006,
author = {H Zou and T Hastie and R Tibshirani},
journal = {Journal of Computational and Graphical Statistics},
title = {Sparse principal component analysis},
pages = {265--286},
volume = {15},
year = {2006},
date-added = {2010-01-12 14:26:48 +0100},
date-modified = {2010-01-12 14:26:52 +0100},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2521},
rating = {0}
}

@article{DelPino:1989p3605,
author = {G Del Pino},
journal = {Statistical Science},
title = {The unifying role of iterative generalized least squares in statistical algorithms},
number = {4},
pages = {394--408},
volume = {4},
year = {1989},
date-added = {2010-01-15 21:46:33 +0100},
date-modified = {2010-01-15 21:47:43 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Del%20Pino-1989-Statistical%20Science_The%20unifying%20role%20of.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3605},
rating = {0}
}

@article{deZubicaray:2008p3006,
author = {Greig I de Zubicaray and Ming-Chang Chiang and Katie L McMahon and David W Shattuck and Arthur W Toga and Nicholas G Martin and Margaret J Wright and Paul M Thompson},
journal = {Brain imaging and behavior},
title = {Meeting the Challenges of Neuroimaging Genetics},
abstract = {As research encompassing neuroimaging and genetics gains momentum, extraordinary information will be uncovered on the genetic architecture of the human brain. However, there are significant challenges to be addressed first. Not the least of these challenges is to accomplish the sample size necessary to detect subtle genetic influences on the morphometry and function of the healthy brain. Aside from sample size, image acquisition and analysis methods need to be refined in order to ensure optimum sensitivity to genetic and complementary environmental influences. Then there is the vexing issue of interpreting the resulting data. We describe how researchers from the east coast of Australia and the west coast of America have embarked upon a collaboration to meet these challenges using data currently being collected from a large-scale twin study, and offer some opinions about future directions in the field.},
affiliation = {Centre for Magnetic Resonance, University of Queensland, Brisbane, Australia.},
number = {4},
pages = {258--263},
volume = {2},
year = {2008},
month = {Dec},
language = {ENG},
date-added = {2010-01-13 23:15:51 +0100},
date-modified = {2010-01-13 23:15:54 +0100},
doi = {10.1007/s11682-008-9029-0},
pmid = {20016769},
local-url = {file://localhost/Users/chl/Dropbox/Papers/de%20Zubicaray-2008-Brain%20imaging%20and%20behavior_Meeting%20the%20Challeng.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3006},
read = {Yes},
rating = {4}
}

@article{Schwarz:2006,
author = {N Schwarz and H Bless and G Bohner and U Harlacher and M Kellenbenz},
journal = {Applied Cognitive Psychology},
title = {Response scales as frames of reference: The impact of frequency range on diagnostic judgements},
abstract = {In social and psychological research, respondents are often asked to report the frequency of a behaviour by checking the appropriate alternative from a list of response categories provided to them. Previous research indicated that respondents extract comparison information from the range of the response alternatives, assuming that the average respondent is represented by values in the middle range of the scale, and that the extremes of the scale represent the extremes of the distribution. Extending this line of research, the present studies demonstrate that the users of a respondent's report are also likely to use the range of the response alternatives as a frame of reference in evaluating the implications of the report. Specifically, subjects are found to draw different conclusions about the respondent's personality (Experiment l ), or the severity of his or her medical condition (Experiment 21, from the same absolute frequency report, depending upon the range of the response scale on which the frequency was checked. Moreover, experienced medical doctors were as likely to be influenced by scale range as first-year medical students, suggesting that the phenomenon is of considerable applied importance. Implications for the use of response alternatives in psychological research and diagnostic judgement are discussed.},
number = {1},
pages = {37--49},
volume = {5},
year = {2006},
date-added = {2010-01-03 19:34:17 +0100},
date-modified = {2010-07-29 19:15:39 +0200},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p983},
rating = {0}
}

@article{Barrowman:2002p2907,
author = {Nicholas J Barrowman},
journal = {CMAJ},
title = {Missing the point (estimate)? Confidence intervals for the number needed to treat},
affiliation = {Chalmers Research Group, Children's Hospital of Eastern Ontario Research Institute, Ottawa. nbarrowman@exchange.cheo.on.ca},
number = {13},
pages = {1676--7},
volume = {166},
year = {2002},
month = {Jun},
language = {eng},
keywords = {Fibrinolytic Agents, Stroke, Confidence Intervals, Sample Size, Severity of Illness Index, Clinical Trials as Topic, Humans, Tissue Plasminogen Activator},
date-added = {2010-01-13 15:02:06 +0100},
date-modified = {2010-01-13 15:02:06 +0100},
pmid = {12126323},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Barrowman-2002-CMAJ_Missing%20the%20point%20(e.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2907},
rating = {0}
}

@article{Ludlow:1986p2691,
author = {L H Ludlow},
journal = {Applied Psychological Measurement},
title = {Graphical Analysis of Item Response Theory Residuals},
number = {3},
pages = {217--229},
volume = {10},
year = {1986},
date-added = {2010-01-13 10:11:41 +0100},
date-modified = {2010-07-29 19:16:53 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Ludlow-1986-Applied%20Psychological%20Measurement_Graphical%20Analysis%20o.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2691},
rating = {0}
}

@article{Conneely:2007p1371,
author = {Karen N Conneely and Michael Boehnke},
journal = {Am J Hum Genet},
title = {So Many Correlated Tests, So Little Time! Rapid Adjustment of P Values for Multiple Correlated Tests},
abstract = {Contemporary genetic association studies may test hundreds of thousands of genetic variants for association, often with multiple binary and continuous traits or under more than one model of inheritance. Many of these association tests may be correlated with one another because of linkage disequilibrium between nearby markers and correlation between traits and models. Permutation tests and simulation-based methods are often employed to adjust groups of correlated tests for multiple testing, since conventional methods such as Bonferroni correction are overly conservative when tests are correlated. We present here a method of computing P values adjusted for correlated tests (P(ACT)) that attains the accuracy of permutation or simulation-based tests in much less computation time, and we show that our method applies to many common association tests that are based on multiple traits, markers, and genetic models. Simulation demonstrates that P(ACT) attains the power of permutation testing and provides a valid adjustment for hundreds of correlated association tests. In data analyzed as part of the Finland-United States Investigation of NIDDM Genetics (FUSION) study, we observe a near one-to-one relationship (r2>.999) between P(ACT) and the corresponding permutation-based P values, achieving the same precision as permutation testing but thousands of times faster.},
affiliation = {Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, GA 30322, USA. kconneely@genetics.emory.edu.},
number = {6},
pages = {},
volume = {81},
year = {2007},
month = {Oct},
language = {ENG},
date-added = {2010-01-07 12:15:49 +0100},
date-modified = {2010-07-29 19:13:31 +0200},
doi = {10.1086/522036},
pii = {S0002929707637665},
pmid = {17966093},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Conneely-2007-Am%20J%20Hum%20Genet_So%20Many%20Correlated%20T.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1371},
rating = {0}
}

@article{Simon:2008p12088,
author = {M K Simon},
title = {Comparison of concurrent and separate multidimensional irt linking of item parameters},
year = {2008},
date-added = {2010-05-24 12:32:31 +0200},
date-modified = {2010-05-24 12:33:02 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Simon-2008-_Comparison%20of%20concur.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12088},
rating = {0}
}

@article{Daniel:2009p12789,
author = {D B Daniel and D A Poole},
journal = {Perspectives on Psychological Science},
title = {Learning for Life. An Ecological Approach to Pedagogical Research},
abstract = {The trend to convert laboratory findings on the conditions associated with optimal memory into recom- mendations for teaching strategies and learning aids will harm students if findings fail to generalize to students' usual learning environments. Moreover, it is likely that pedagogies function differently for students with different degrees of background knowledge, time, and interest in the subject matter; that some support activities will prevent students from honing their ability learn from narrative material without guided learning; and that an overuse of learning aids will tax students' ability to use them effectively. We contrast two approaches to developing pedagogy---memory first and pedagogical ecology---and explain how the human factors approach of pedagogical ecology could be a more satisfying model for the scholar- ship of teaching and learning.},
number = {1},
pages = {91--96},
volume = {4},
year = {2009},
date-added = {2010-06-18 21:04:55 +0200},
date-modified = {2010-06-18 21:07:15 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Daniel-2009-Perspectives%20on%20Psychological%20Science_Learning%20for%20Life.%20A.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12789},
rating = {0}
}

@article{Rushton:2010p13804,
author = {J P Rushton and A R Jensen},
journal = {Intelligence},
title = {The rise and fall of the Flynn Effect as a reason to expect a narrowing of the Black--White IQ gap},
abstract = {In this Editorial we correct the false claim that g loadings and inbreeding depression scores correlate with the secular gains in IQ. This claim has been used to render the logic of heritable g a ``red herring'' and an ``absurdity'' as an explanation of Black--White differences because secular gains are environmental in origin. In point of fact, while g loadings and inbreeding depression scores on the 11 subtests of the Wechsler Intelligence Scale for Children correlate significantly positively with Black--White differences (0.61 and 0.48, Pb0.001), they correlate significantly negatively (or not at all) with the secular gains (mean r=−0.33, Pb0.001; and 0.13, ns, respectively). Moreover, heritabilities calculated from twins also correlate with the g loadings (r=0.99, Pb0.001 for the estimated true correlation), providing biological evidence for a true genetic g, as opposed to a mere statistical g. While the secular gains are on g-loaded tests (such as the Wechsler), they are negatively correlated with the most g-loaded components of those tests. Also, the tests lose their g loadedness over time with training, retesting, and familiarity. In an analysis of mathematics and reading scores from tests such as the NAEP and Coleman Report over the last 54 years, we show that there has been no narrowing of the gap in either IQ scores or in educational achievement. From 1954 to 2008, Black 17-year-olds have consistently scored at about the level of White 14-year-olds, yielding IQ equivalents of 85 for 1954, 82 for 1965, 70 for 1975, and 81 for 2008. We conclude that predictions about the Black--White IQ gap narrowing as a result of the secular rise are unsupported. The (mostly heritable) cause of the one is not the (mostly environmental) cause of the other. The Flynn Effect (the secular rise in IQ) is not a Jensen Effect (because it does not occur on g).},
pages = {213--219},
volume = {38},
year = {2010},
date-added = {2010-07-29 12:20:19 +0200},
date-modified = {2010-07-29 19:29:16 +0200},
doi = {10.1016/j.intell.2009.12.002},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Rushton-2010-Intelligence_The%20rise%20and%20fall%20of.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13804},
rating = {0}
}

@book{Quinlan1993,
author = {R Quinlan},
journal = {Book},
title = {C4.5: Programs for Machine Learning},
year = {1993},
date-added = {2010-01-12 14:26:51 +0100},
date-modified = {2010-01-12 14:26:52 +0100},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2534},
rating = {0}
}

@article{Wang:2006p3419,
author = {L Wang and J Zhu and H Zou},
journal = {Statistica Sinica},
title = {The doubly regularized support vector machine},
abstract = {The standard L2-norm support vector machine (SVM) is a widely used tool for classification problems. The L1-norm SVM is a variant of the standard L2- norm SVM, that constrains the L1-norm of the fitted coefficients. Due to the nature of the L1-norm, the L1-norm SVM has the property of automatically selecting variables, not shared by the standard L2-norm SVM. It has been argued that the L1-norm SVM may have some advantage over the L2-norm SVM, especially with high dimensional problems and when there are redundant noise variables. On the other hand, the L1-norm SVM has two drawbacks: (1) when there are several highly correlated variables, the L1-norm SVM tends to pick only a few of them, and remove the rest; (2) the number of selected variables is upper bounded by the size of the training data. A typical example where these occur is in gene microarray analysis. In this paper, we propose a doubly regularized support vector machine (DrSVM). The DrSVM uses the elastic-net penalty, a mixture of the L2-norm and the L1-norm penalties. By doing so, the DrSVM performs automatic variable selection in a way similar to the L1-norm SVM. In addition, the DrSVM encourages highly correlated variables to be selected (or removed) together. We illustrate how the DrSVM can be particularly useful when the number of variables is much larger than the size of the training data (p ≫ n). We also develop efficient algorithms to compute the whole solution paths of the DrSVM.},
pages = {589--615},
volume = {16},
year = {2006},
date-added = {2010-01-15 14:54:47 +0100},
date-modified = {2010-01-15 14:55:48 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Wang-2006-Statistica%20Sinica_The%20doubly%20regulariz.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3419},
rating = {0}
}

@article{Isaacs:2009p5013,
author = {Elizabeth B Isaacs and Bruce R Fischl and Brian T Quinn and Wui K Chong and David G Gadian and Alan Lucas},
journal = {Pediatric research},
title = {Impact of breast milk on IQ, brain size and white matter development},
abstract = {Although observational findings linking breast milk to higher scores on cognitive tests may be confounded by factors associated with mothers' choice to breastfeed, it has been suggested that one or more constituents of breast milk facilitate cognitive development, particularly in preterms. Because cognitive scores are related to head size, we hypothesised that breast milk mediates cognitive effects by affecting brain growth. We used detailed data from a randomized feeding trial to calculate percentage of breast milk (%EBM) in the infant diet of 50 adolescents. MRI scans were obtained (mean age=15y9m), allowing volumes of total brain (TBV), white and grey matter (WMV, GMV) to be calculated. In the total group %EBM correlated significantly with Verbal IQ (VIQ); in boys, with all IQ scores, TBV and WMV. VIQ was, in turn, correlated with WMV and, in boys only, additionally with TBV. No significant relationships were seen in girls or with grey matter. These data support the hypothesis that breast milk promotes brain development, particularly white matter growth. The selective effect in males accords with animal and human evidence regarding gender effects of early diet. Our data have important neurobiological and public health implications and identify areas for future mechanistic study.},
affiliation = {Childhood Nutrition Research Centre [E.B.I., A.L.], Radiology and Physics Unit [D.G.G.], University College London Institute of Child Health, London WC1N 1EH, United Kingdom; Athinoula A. Martinos Center for Biomedical Imaging [B.R.F., B.T.Q.], Harvard Medical School, Charlestown, MA 02129; Computer Science and Artificial Intelligence Laboratory [B.R.F.], Massachusetts Institute of Technology, Charlestown, MA 02129; New York University Center for Neural Science [B.T.Q.], New York, NY 10003; Department of Radiology [W.K.C.], Great Ormond Street Hospital for Children NHS Trust, London WC1N 3JH, United Kingdom.},
pages = {},
year = {2009},
month = {Dec},
language = {ENG},
date-added = {2010-02-05 19:57:35 +0100},
date-modified = {2010-02-05 19:57:35 +0100},
doi = {10.1203/PDR.0b013e3181d026da},
pmid = {20035247},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5013},
rating = {0}
}

@article{Rush:2003p12763,
author = {A John Rush and Madhukar H Trivedi and Hicham M Ibrahim and Thomas J Carmody and Bruce Arnow and Daniel N Klein and John C Markowitz and Philip T Ninan and Susan Kornstein and Rachel Manber and Michael E Thase and James H Kocsis and Martin B Keller},
journal = {Biol Psychiatry},
title = {The 16-Item Quick Inventory of Depressive Symptomatology (QIDS), clinician rating (QIDS-C), and self-report (QIDS-SR): a psychometric evaluation in patients with chronic major depression},
abstract = {The 16-item Quick Inventory of Depressive Symptomatology (QIDS), a new measure of depressive symptom severity derived from the 30-item Inventory of Depressive Symptomatology (IDS), is available in both self-report (QIDS-SR(16)) and clinician-rated (QIDS-C(16)) formats. This report evaluates and compares the psychometric properties of the QIDS-SR(16) in relation to the IDS-SR(30) and the 24-item Hamilton Rating Scale for Depression (HAM-D(24)) in 596 adult outpatients treated for chronic nonpsychotic, major depressive disorder. Internal consistency was high for the QIDS-SR(16) (Cronbach's alpha =.86), the IDS-SR(30) (Cronbach's alpha =.92), and the HAM-D(24) (Cronbach's alpha =.88). QIDS-SR(16) total scores were highly correlated with IDS-SR(30) (.96) and HAM-D(24) (.86) total scores. Item-total correlations revealed that several similar items were highly correlated with both QIDS-SR(16) and IDS-SR(30) total scores. Roughly 1.3 times the QIDS-SR(16) total score is predictive of the HAM-D(17) (17-item version of the HAM-D) total score. The QIDS-SR(16) was as sensitive to symptom change as the IDS-SR(30) and HAM-D(24), indicating high concurrent validity for all three scales. The QIDS-SR(16) has highly acceptable psychometric properties, which supports the usefulness of this brief rating of depressive symptom severity in both clinical and research settings.},
affiliation = {Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9086, USA.},
number = {5},
pages = {573--83},
volume = {54},
year = {2003},
month = {Sep},
language = {eng},
keywords = {Female, Chronic Disease, Adult, Psychiatric Status Rating Scales, Male, Middle Aged, Depressive Disorder: Major, Self Assessment (Psychology), Psychometrics, Severity of Illness Index, Aged, Humans, Treatment Outcome, Adolescent},
date-added = {2010-06-15 22:53:12 +0200},
date-modified = {2010-06-15 22:53:12 +0200},
pii = {S0006322302018668},
pmid = {12946886},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Rush-2003-Biol%20Psychiatry_The%2016-Item%20Quick%20In.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12763},
rating = {0}
}

@article{Fiorillo:2003,
author = {Christopher D Fiorillo and Philippe N Tobler and Wolfram Schultz},
journal = {Science},
title = {Discrete coding of reward probability and uncertainty by dopamine neurons.},
abstract = {Uncertainty is critical in the measure of information and in assessing the accuracy of predictions. It is determined by probability P, being maximal at P = 0.5 and decreasing at higher and lower probabilities. Using distinct stimuli to indicate the probability of reward, we found that the phasic activation of dopamine neurons varied monotonically across the full range of probabilities, supporting past claims that this response codes the discrepancy between predicted and actual reward. In contrast, a previously unobserved response covaried with uncertainty and consisted of a gradual increase in activity until the potential time of reward. The coding of uncertainty suggests a possible role for dopamine signals in attention-based learning and risk-taking behavior.},
affiliation = {Institute of Physiology, University of Fribourg, CH-1700 Fribourg, Switzerland. cdf28@cam.ac.uk},
number = {5614},
pages = {1898--1902},
volume = {299},
year = {2003},
month = {Mar},
language = {eng},
date-added = {2010-01-03 19:38:21 +0100},
date-modified = {2010-07-29 19:50:10 +0200},
doi = {10.1126/science.1077349},
pii = {299/5614/1898},
pmid = {12649484},
URL = {http://dx.doi.org/10.1126/science.1077349},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1182},
rating = {0}
}

@article{Hardigan:2007p5886,
author = {P Hardigan and M Carvajal},
journal = {IJAHSP},
title = {Job Satisfaction Among Practicing Pharmacists: A Rasch Analysis},
abstract = {Purpose: through the application of a Rasch rating scale model, the researchers investigated the effect of gender, ethnicity, practice site, income, and age on levels of job satisfaction among practicing pharmacists. Method: The data consist of responses to a survey questionnaire mailed to a random sample of 5,000 registered pharmacists throughout the United States. A total of 820 individuals mailed back their completed form for a response rate of 16.4 percent. Results: Older, higher-wage earning pharmacists working at independent practice sites experience the greatest amount of job satisfaction. Conclusion: The most significant finding from this study is that age, income, and practice site can predict job satisfaction among practicing pharmacists. Additionally, the results provide empirical evidence for the variables inclusion in future models and they demonstrate the usefulness of Rasch techniques.},
number = {4},
volume = {5},
year = {2007},
date-added = {2010-02-17 15:16:34 +0100},
date-modified = {2010-02-17 15:17:51 +0100},
URL = {http://ijahsp.nova.edu},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hardigan-2007-IJAHSP_Job%20Satisfaction%20Amo.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5886},
rating = {0}
}

@article{Wu:2008p2934,
author = {L Y Wu and X Zhou and C C Chang and S T C Wong},
journal = {The Second International Symposium on Optimization and Systems Biology (OSB'08)},
title = {Model Based Probe Fitting and Selection for SNP Array},
abstract = {Recent advances of high-throughput SNP arrays such as Affymetrix's GeneChip Human Mapping 500K array set have made it possible to genotype large samples in a fast and cheap manner. A lot of algorithms were developed to call the genotypes from SNP array. When considering the low level preprocessing of SNP array, most algorithms just borrow the techniques from the gene expression microarray. As in the analysis of gene expression microarray, the low level preprocessing of SNP array, e.g. probe summarization, is very important in the analysis of SNP array such as genotyping, loss of heterozygous (LOH) inference, and copy number inference. In this paper, we present a model based method for probe fitting and selection of SNP array. This method exploits the abundant high quality genotypes such as HapMap data, which were genotyped and validated by several independent genotyping techniques. The new probe summarization method can be used with the existing genotyping methods to improve the accuracy.},
year = {2008},
date-added = {2010-01-13 22:55:26 +0100},
date-modified = {2010-01-13 22:56:36 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Wu-2008-The%20Second%20International%20Symposium%20on%20Optimization%20and%20Systems%20Biology%20(OSB%E2%80%9908)_Model%20Based%20Probe%20Fi.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2934},
rating = {0}
}

@article{Wang:2010p12806,
author = {X Wang and S Baldwin and H Wainer and E T Bradlow and B B Reeve and A W Smith and K M Bellizzi and K B Baumgartner},
journal = {Stat Med},
title = {Using Testlet Response Theory to analyze data from a survey of attitude change among breast cancer survivors},
abstract = {In this paper we examine alternative measurement models for fitting data from health surveys. We show why a testlet-based latent trait model that includes covariate information, embedded within a fully Bayesian framework, can allow multiple simultaneous inferences and aid interpretation. We illustrate our approach with a survey of breast cancer survivors that reveals how the attitudes of those patients change after diagnosis toward a focus on appreciating the here-and-now, and away from consideration of longer-term goals. Using the covariate information, we also show the extent to which individual-level variables such as race, age and Tamoxifen treatment are related to a patient's change in attitude.
The major contribution of this research is to demonstrate the use of a hierarchical Bayesian IRT model with covariates in this application area; hence a novel case study, and one that is certainly closely aligned with but distinct from the educational testing applications that have made IRT the dominant test scoring model.},
year = {2010},
date-added = {2010-06-18 22:50:36 +0200},
date-modified = {2010-06-18 22:52:00 +0200},
doi = {10.1002/sim.3945},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Wang-2010-Stat%20Med_Using%20Testlet%20Respon.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12806},
rating = {0}
}

@article{Hennig:2006p3550,
author = {C Hennig},
title = {Cluster-wise assessment of cluster stability},
abstract = {Stability in cluster analysis is strongly dependent on the data set, especially on how well separated and how homogeneous the clusters are. In the same clustering, some clusters may be very stable and others may be extremely unstable.
The Jaccard coefficient, a similarity measure between sets, is used as a cluster- wise measure of cluster stability, which is assessed by the bootstrap distribution of the Jaccard coefficient for every single cluster of a clustering compared to the most similar cluster in the bootstrapped data sets. This can be applied to very general cluster analysis methods.
Some alternative resampling methods are investigated as well, namely subsetting, jittering the data points and replacing some data points by artificial noise points. The different methods are compared by means of a simulation study.
A data example illustrates the use of the cluster-wise stability assessment to distinguish between meaningful stable and spurious clusters, but it is also shown that clusters are sometimes only stable because of the inflexibility of certain clustering methods.},
year = {2006},
date-added = {2010-01-15 21:02:41 +0100},
date-modified = {2010-01-15 21:03:58 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hennig-2006-_Cluster-wise%20assessm.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3550},
rating = {0}
}

@article{Waaijenborg:2008p2588,
author = {Sandra Waaijenborg and Philip C Verselewel de Witt Hamer and Aeilko H Zwinderman},
journal = {Statistical Applications in Genetics and Molecular Biology},
title = {Quantifying the association between gene expressions and DNA-markers by penalized canonical correlation analysis},
abstract = {Multiple changes at the DNA level are at the basis of complex diseases. Identifying the genetic networks that are influenced by these changes might help in understanding the development of these diseases. Canonical correlation analysis is used to associate gene expressions with DNA-markers and thus reveals sets of co-expressed and co-regulated genes and their associating DNA-markers. However, when the number of variables gets high, e.g. in the case of microarray studies, interpretation of these results can be difficult. By adapting the elastic net to canonical correlation analysis the number of variables reduces, and interpretation becomes easier, moreover, due to the grouping effect of the elastic net co-regulated and co-expressed genes cluster. Additionally, our adaptation works well in situations where the number of variables exceeds by far the number of subjects.},
affiliation = {Academic Medical Center / University of Amsterdam. s.waaijenborg@amc.uva.nl},
number = {1},
pages = {Article3},
volume = {7},
year = {2008},
month = {Jan},
language = {eng},
keywords = {Cluster Analysis, Genetic Markers, Gene Expression, DNA},
date-added = {2010-01-12 22:29:12 +0100},
date-modified = {2010-07-29 19:50:47 +0200},
doi = {10.2202/1544-6115.1329},
pmid = {18241193},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Waaijenborg-2008-Statistical%20Applications%20in%20Genetics%20and%20Molecular%20Biology_Quantifying%20the%20asso.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2588},
rating = {0}
}

@article{Grosbras:2006p4872,
author = {Marie-H{\'e}l{\`e}ne Grosbras and Tom{\'a}s Paus},
journal = {Cereb Cortex},
title = {Brain networks involved in viewing angry hands or faces},
abstract = {Most neuropsychological research on the perception of emotion concerns the perception of faces. Yet in everyday life, hand actions are also modulated by our affective state, revealing it, in turn, to the observer. We used functional magnetic resonance imaging (fMRI) to identify brain regions engaged during the observation of hand actions performed either in a neutral or an angry way. We also asked whether these are the same regions as those involved in perceiving expressive faces. During the passive observation of emotionally neutral hand movements, the fMRI signal increased significantly in dorsal and ventral premotor cortices, with the exact location of the 'peaks' distinct from those induced by face observation. Various areas in the extrastriate visual cortex were also engaged, overlapping with the face-related activity. When the observed hand action was performed with emotion, additional regions were recruited including the right dorsal premotor, the right medial prefrontal cortex, the left anterior insula and a region in the rostral part of the supramarginal gyrus bilaterally. These regions, except for the supramarginal gyrus, were also activated during the perception of angry faces. These results complement the wealth of studies on the perception of affect from faces and provide further insights into the processes involved in the perception of others underlying, perhaps, social constructs such as empathy.},
affiliation = {Cognitive Neuroscience Unit, Montreal Neurological Institute, McGill University, Montreal, Canada.},
number = {8},
pages = {1087--96},
volume = {16},
year = {2006},
month = {Aug},
language = {eng},
keywords = {Visual Cortex, Gestures, Anger, Hand, Visual Pathways, Female, Middle Aged, Emotions, Adult, Empathy, Nerve Net, Facial Expression, Male, Humans, Visual Perception},
date-added = {2010-02-01 20:27:39 +0100},
date-modified = {2010-07-29 19:22:58 +0200},
doi = {10.1093/cercor/bhj050},
pii = {bhj050},
pmid = {16221928},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Grosbras-2006-Cereb%20Cortex_Brain%20networks%20invol.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4872},
rating = {0}
}

@article{Candes:2008p14225,
author = {E J Cand{\`e}s and Y Plan},
title = {Near-ideal model selection by l1 minimization},
abstract = {We consider the fundamental problem of estimating the mean of a vector y = Xβ+z, where X is an n × p design matrix in which one can have far more variables than observations and z is a stochastic error term---the so-called `p > n' setup. When β is sparse, or more generally, when there is a sparse subset of covariates providing a close approximation to the unknown mean vector, we ask whether or not it is possible to accurately estimate Xβ using a computationally tractable algorithm.
We show that in a surprisingly wide range of situations, the lasso happens to nearly select the best subset of variables. Quantitatively speaking, we prove that solving a simple quadratic program achieves a squared error within a logarithmic factor of the ideal mean squared error one would achieve with an oracle supplying perfect information about which variables should be included in the model and which variables should not. Interestingly, our results describe the average performance of the lasso; that is, the performance one can expect in an vast majority of cases where Xβ is a sparse or nearly sparse superposition of variables, but not in all cases.
Our results are nonasymptotic and widely applicable since they simply require that pairs of predictor variables are not too collinear.},
year = {2008},
date-added = {2010-08-22 21:09:04 +0200},
date-modified = {2010-08-22 21:09:49 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Cand%C3%A8s-2008-_Near-ideal%20model%20sel.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p14225},
rating = {0}
}

@article{Finch:2007p2686,
author = {H Finch and B Habing},
journal = {Applied Psychological Measurement},
title = {Performance of DIMTEST- and NOHARM-Based Statistics for Testing Unidimensionality},
abstract = {This Monte Carlo study compares the ability of the parametric bootstrap version of DIMTEST with three goodness-of-fit tests calculated from a fitted NOHARM model to detect violations of the assumption of unidimensionality in testing data. The effectiveness of the procedures was evaluated for different numbers of items, numbers of examinees, correlations between underlying ability dimensions, skewness of underlying ability distributions, and the presence or absence of a guessing parameter. In the absence of guessing, DIMTEST and the NOHARM-based statistics had similar power, with the w2 statistic having a very low Type I error rate. In the presence of guessing, however, two of the NOHARM-based statistics had unacceptably high Type I error rates, while the third performed similarly to DIMTEST. Given this inflated error rate, the study compares the empirical powers after adjusting for the discrepancy in Type I error rates.},
number = {4},
pages = {292--307},
volume = {31},
year = {2007},
date-added = {2010-01-13 10:03:22 +0100},
date-modified = {2010-07-29 19:16:52 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Finch-2007-Applied%20Psychological%20Measurement_Performance%20of%20DIMTE.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2686},
rating = {0}
}

@article{Thirion:2007p2325,
author = {B Thirion and P Pinel and A Tucholka and A Roche and P Ciuciu and J F Mangin and Poline J B},
journal = {IEEE Transactions on Medical Imaging},
title = {Structural Analysis of fMRI Data Revisited:
Improving the Sensitivity and Reliability of
fMRI Group Studies},
abstract = {Group studies of functional MRI datasets are usually based on the computation of the mean signal across subjects at each voxel (Random Effects Analyses), assuming that all subjects have been set in the same anatomical space (normalization). Although this approach allows for a correct specificity (rate of false detections), it is not very efficient, for three reasons: i) its underlying hypotheses, perfect coregistration of the individual datasets and normality of the measured signal at the group level, are frequently violated ; ii) the group size is small in general, so that asymptotic approximations on the parameters distributions do not hold ; iii) the large size of the images requires some conservative strategies to control the false detection rate, at the risk of increasing the number of false negatives. Given that it is still very challenging to build generative or parametric models of inter-subject variability, we rely on a rule based, bottom-up approach: we present a set of procedures that detect structures of interest from each subject's data, then search for correspondences across subjects and outline the most reproducible activation regions in the group studied. This framework enables a strict control on the number of false detections. It is shown here that this analysis demonstrates increased validity and improves both the sensitivity and reliability of group analyses compared with standard methods. Moreover, it directly provides information on the spatial position correspondence or variability of the activated regions across subjects, which is difficult to obtain in standard voxel-based analyses.},
number = {9},
pages = {1256--1269},
volume = {26},
year = {2007},
date-added = {2010-01-10 12:51:19 +0100},
date-modified = {2010-01-19 23:09:29 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Thirion-2007-IEEE%20Transactions%20on%20Medical%20Imaging_Structural%20Analysis.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2325},
read = {Yes},
rating = {0}
}

@article{Jansen:1986p5951,
author = {P G W Jansen and E E Roskam},
journal = {Psychometrika},
title = {Latent trait models and dichotomization of graded responses},
abstract = {This paper discusses the compatibility of the polychotomous Rasch model with dichot$\,^{\circ}$ omization of the response continuum. It is argued that in the case of graded responses, the re- sponse categories presented to the subject are essentially an arbitrary polychotomization of the response continuum, ranging for example from total rejection or disagreement to total acceptance or agreement of an item or statement. Because of this arbitrariness, the measurement outcome should be independent of the specificpolychotomization applied, for example, presenting a specif- ic multicategory response format should not affect the measurement outcome. When such is the case, the original polychotomous model is called "compatible" with dichotomization.
A distinction is made between polychotomization or dichotomization "before the fact," that is, in constructing the response format, and polycho- or dichotomization "after the fact," for examplein dichotomizingexistinggraded responsedata.
It isshownthat, at leastineaseofdichotomizationafter-the-fact,the polychotomousRasch model is not compatible with dichotomization, unless a rather special condition of the model parameters is met. Insofar as it may be argued that dichotomization before the fact is not essen- tially different from dichotomization after the fact, the value of the unidimensional poly- chotomous Rasch model is consequently questionable. The impact of our conclusion on related models is also discussed.},
number = {1},
pages = {69--91},
volume = {51},
year = {1986},
date-added = {2010-02-18 23:21:18 +0100},
date-modified = {2010-07-11 09:49:32 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Jansen-1986-Psychometrika_Latent%20trait%20models-1.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5951},
rating = {0}
}

@article{Cremeens:2006p8492,
author = {Joanne Cremeens and Christine Eiser and Mark Blades},
journal = {Qual Life Res},
title = {Characteristics of health-related self-report measures for children aged three to eight years: a review of the literature},
abstract = {AIMS: To review and make recommendations about the format and quality of health-related self-report measures for children aged 3-8 years. METHODS: Literature searches used to identify measures of QOL, self-esteem, self-concept and mental health. The format (i.e., scale type, presentation style) and quality (i.e., item generation, reliability, validity, responsiveness) of measures were compared and evaluated. RESULTS: Fifty three measures were identified: QOL (n = 25, 47%), self-esteem/concept (n = 15, 28%), mental health (n = 13, 25%). Likert scales were used most frequently to represent response choices (n = 34, 64%). The authors of 11 (21%) measures provided justification for their scale choice. Items were most commonly presented in written format (n = 24, 45%). Item content was generated from the respondent population in only 21 (40%) measures. Twenty-seven (51%) measures reported internal reliability between 0.70 and 0.90, and 12 (23%) reported reproducibility in this range. Although validity was reported for 48 (91%) measures, evidence for three or more aspects occurred for only 9 (17%). Eleven (21%) measures evidenced responsiveness to change. CONCLUSION: Authors should provide clearer evidence for reliability and responsiveness. Newly developed instruments need to meet established standards, and further studies should assess the impact of scale and presentation types on the psychometrics of measures.},
affiliation = {Division of Behavioral Medicine, St. Jude Children's Research Hospital, Memphis, TN 38105-2794, USA. Joanne.Cremeens@stjude.org},
number = {4},
pages = {739--54},
volume = {15},
year = {2006},
month = {May},
language = {eng},
keywords = {Attitude to Health, Reproducibility of Results, Child: Preschool, Humans, Mental Health, Child, Self Efficacy, Quality of Life, Psychometrics, Health Status Indicators},
date-added = {2010-03-21 18:01:02 +0100},
date-modified = {2010-07-29 19:48:28 +0200},
doi = {10.1007/s11136-005-4184-x},
pmid = {16688506},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8492},
rating = {0}
}

@article{Ioannidis:2009p3190,
author = {John P A Ioannidis and Gilles Thomas and Mark J Daly},
journal = {Nat Rev Genet},
title = {Validating, augmenting and refining genome-wide association signals},
abstract = {Studies using genome-wide platforms have yielded an unprecedented number of promising signals of association between genomic variants and human traits. This Review addresses the steps required to validate, augment and refine such signals to identify underlying causal variants for well-defined phenotypes. These steps include: large-scale exact replication across both similar and diverse populations; fine mapping and resequencing; determination of the most informative markers and multiple independent informative loci; incorporation of functional information; and improved phenotype mapping of the implicated genetic effects. Even in cases for which replication proves that an effect exists, confident localization of the causal variant often remains elusive.},
affiliation = {Department of Hygiene and Epidemiology, University of Ioannina School of Medicine and Biomedical Research Institute, Foundation for Research and Technology - Hellas, Ioannina 45110, Greece. jioannid@cc.uoi.gr},
number = {5},
pages = {318--29},
volume = {10},
year = {2009},
month = {May},
language = {eng},
keywords = {Reproducibility of Results, Genome, Humans, Linkage (Genetics), Animals, Genome-Wide Association Study, Genetic Heterogeneity, Phenotype},
date-added = {2010-01-14 20:49:17 +0100},
date-modified = {2010-07-29 19:40:47 +0200},
doi = {10.1038/nrg2544},
pii = {nrg2544},
pmid = {19373277},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Ioannidis-2009-Nat%20Rev%20Genet_Validating%20augmenti.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3190},
rating = {4}
}

@article{Henoch:2010p8677,
author = {Ingela Henoch and Bertil Axelsson and Bengt Bergman},
journal = {Qual Life Res},
title = {The Assessment of Quality of life at the End of Life (AQEL) questionnaire: a brief but comprehensive instrument for use in patients with cancer in palliative care},
abstract = {PURPOSE: The aim of the study was to further validate the Assessment of Quality of life at the End of Life (AQEL) questionnaire, to explore whether conceptually consistent scales could be confirmed and how the instrument relates to other widely used and validated HRQL instruments. METHODS: A total of 106 patients with lung cancer in palliative care completed the 20-item AQEL, the EORTC QLQ-C30, Hospital Anxiety and Depression Scale (HADS), Sense of Coherence (SOC-13) and Social Support Survey (SSS). Construct validity of the AQEL was tested by multitrait scaling, principal components analysis, inter-scale correlations and known-groups comparisons. RESULTS: Five scales were supported by multitrait scaling: Basic function, Activity, Emotional function, Cognitive function and Existential needs, with satisfactory (>.7) internal consistency for the latter three and intermediate (>.5) for the remaining two. A Social support scale was supported by principal components analysis, but exhibited a low internal consistency. Items on health care issues and physical symptoms worked best as individual items. Expected correlations with other instruments were found for all scales. Activity was sensitive to different levels of functioning as defined by performance status. CONCLUSIONS: This study provided some evidence for the validity of the AQEL and its feasibility in patients with cancer in palliative care.},
affiliation = {Br{\"a}cke Diakoni Foundation, Research Unit, Box 210 62, 418 04, G{\"o}teborg, Sweden, ihh_gbg@hotmail.com.},
pages = {},
year = {2010},
month = {Mar},
language = {ENG},
date-added = {2010-03-22 11:59:38 +0100},
date-modified = {2010-07-29 19:48:29 +0200},
doi = {10.1007/s11136-010-9623-7},
pmid = {20229190},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8677},
rating = {0}
}

@article{Gernsbacher:2005p11055,
author = {Morton A Gernsbacher and Cheryl Dissanayake and H Hill Goldsmith and Peter C Mundy and Sally J Rogers and Marian Sigman},
journal = {Science},
title = {Autism and deficits in attachment behavior},
number = {5713},
pages = {1201-3; author reply 1201--3},
volume = {307},
year = {2005},
month = {Feb},
language = {eng},
keywords = {Mice, Humans, Autistic Disorder, Object Attachment, Mothers, Animals, Receptors: Opioid: mu, Child, Caregivers},
date-added = {2010-04-14 13:46:54 +0200},
date-modified = {2010-07-29 19:50:10 +0200},
doi = {10.1126/science.307.5713.1201},
pii = {307/5713/1201},
pmid = {15731426},
URL = {http://www.sciencemag.org/cgi/content/full/307/5713/1201},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Gernsbacher-2005-Science_Autism%20and%20deficits.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11055},
rating = {0}
}

@article{Kieffer:2002,
author = {K M Kieffer and R J Reese},
journal = {Educational and Psychological Measurement},
title = {A Reliability Generalization study of the Geriatric Depression Scale (GDS)},
volume = {62},
year = {2002},
date-added = {2010-01-10 11:33:21 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2022},
rating = {0}
}

@article{Smits:2007p12893,
author = {D J M Smits and Paul De Boeck},
journal = {Personality and Individual Differences},
title = {From anger to verbal aggression: Inhibition at different levels},
abstract = {A factor-analytic-based method to measure the inhibition of three verbally aggressive behaviours was inves- tigated in two studies on self-report data. Inhibition was subdivided into two types: inhibition of the tendency to become verbally aggressive and inhibition of the verbally aggressive behaviour. In Study 1, it was investigated whether both kinds can be separated and measured by using a factor-analytic model. In Study 2, the approach was validated by relating both types of inhibition to broad and specific trait measures, either related to behav- iour regulation or not. Inhibition of the tendency to become verbally aggressive was negatively related to Extra- version and Anger Out, and positively to hostility and a general inhibition measure. The inhibition of verbally aggressive behaviour was positively related to Agreeableness, Anger In (keeping anger inside) and anger out control (control of outward expression of anger), and negatively to Verbal Aggression and Anger Out.},
pages = {47--57},
volume = {43},
year = {2007},
date-added = {2010-06-24 13:30:29 +0200},
date-modified = {2010-07-29 20:46:12 +0200},
doi = {10.1016/j.paid.2006.11.006},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Smits-2007-Personality%20and%20Individual%20Differences_From%20anger%20to%20verbal.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12893},
rating = {0}
}

@article{Timko:2009p11975,
author = {Christine Timko and Bernice S Moos and Rudolf H Moos},
journal = {Addict Behav},
title = {Gender differences in 16-year trends in assault- and police-related problems due to drinking},
abstract = {This study examined the frequency and predictors of physical assault and having trouble with the police due to drinking over 16 years among women and men who, at baseline, were untreated for their alcohol use disorder. Predictors examined were the personal characteristics of impulsivity, self-efficacy, and problem-solving and emotional-discharge coping, as well as outpatient treatment and Alcoholics Anonymous (AA) participation. Women and men were similar on rates of perpetrating assault due to drinking, but men were more likely to have had trouble with the police due to drinking. Respondents who, at baseline, were more impulsive and relied more on emotional discharge coping, and less on problem-solving coping, assaulted others more frequently during the first year of follow-up. Similarly, less problem-solving coping at baseline was related to having had trouble with the police more often at one and 16 years due to drinking. The association between impulsivity and more frequent assault was stronger for women, whereas associations of self-efficacy and problem-solving coping with less frequent assault and police trouble were stronger for men. Participation in AA was also associated with a lower likelihood of having trouble with the police at one year, especially for men. Interventions aimed at decreasing impulsivity and emotional discharge coping, and bolstering self-efficacy and problem-solving coping, during substance abuse treatment, and encouragement to become involved in AA, may be helpful in reducing assaultive and other illegal behaviors.},
affiliation = {Center for Health Care Evaluation, Department of Veterans Affairs Health Care System (152-MPD), 795 Willow Road, Menlo Park, CA 94025, USA. ctimko@stanford.edu},
number = {9},
pages = {744--50},
volume = {34},
year = {2009},
month = {Sep},
language = {eng},
keywords = {Violence, Follow-Up Studies, Alcohol Drinking, Adaptation: Psychological, Humans, Alcohol-Related Disorders, Police, Adult, Impulsive Behavior, Male, Self Efficacy, California, Sex Factors, Alcoholics Anonymous, Female, Aged, Young Adult, Problem Solving, Adolescent, Middle Aged},
date-added = {2010-05-23 17:20:28 +0200},
date-modified = {2010-05-23 17:20:28 +0200},
doi = {10.1016/j.addbeh.2009.04.013},
pii = {S0306-4603(09)00095-1},
pmid = {19446963},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11975},
rating = {0}
}

@article{Linden:2000,
author = {W J van der Linden and C A W Glas},
journal = {Applied Measurement in Education},
title = {Capitalization on item calibration error in adaptive testing},
pages = {35--53},
volume = {13},
year = {2000},
date-added = {2010-01-10 11:33:18 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Linden-2000-Applied%20Measurement%20in%20Education_Capitalization%20on%20it.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2006},
rating = {0}
}

@article{Cai:2010p11307,
author = {B Cai and D B Dunson},
title = {Bayesian Covariance Selection in Generalized Linear Mixed Models},
abstract = {The generalized linear mixed model (GLMM), which extends the generalized linear model (GLM) to incorporate random effects characterizing heterogeneity among subjects, is widely used in analyzing correlated and longitudinal data. Although there is often interest in identify- ing the subset of predictors that have random effects, random effects selection can be challenging, particularly when outcome distributions are non-normal. This article proposes a fully Bayesian approach to the problem of simultaneous selection of fixed and random effects in GLMMs. Inte- grating out the random effects induces a covariance structure on the multivariate outcome data, and an important problem which we also consider is that of covariance selection. Our approach relies on variable selection-type mixture priors for the components in a special LDU decomposition of the random effects covariance. A stochastic search MCMC algorithm is developed, which relies on Gibbs sampling, with Taylor series expansions used to approximate intractable integrals. Simu- lated data examples are presented for different exponential family distributions, and the approach is applied to discrete survival data from a time-to-pregnancy study.},
date-added = {2010-04-26 23:04:29 +0200},
date-modified = {2010-04-26 23:05:17 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Cai--_Bayesian%20Covariance.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11307},
rating = {0}
}

@article{Rannou:2007p5879,
author = {F Rannou and I Boutron and M Jardinaud-Lopez and G Meric and M Revel and J Fermanian and S Poiraudeau},
journal = {Osteoarthr Cartil},
title = {Should aggregate scores of the Medical Outcomes Study 36-item Short Form Health Survey be used to assess quality of life in knee and hip osteoarthritis? A national survey in primary care},
abstract = {OBJECTIVE: To assess the relevance of using the aggregate physical component score (PCS) and mental component score (MCS) of the Medical Outcomes Study 36-item Short Form Health Survey (SF-36) for patients with knee and hip osteoarthritis (OA). METHODS: We conducted a cross-sectional national survey in a primary care setting in France. A total of 1474 general practitioners enrolled 4183 patients with hip or knee OA. Construct validity of PCS and MCS was assessed by convergent and divergent validity and factor analysis. RESULTS: Records of 4133 patients (98.8%) were analyzed (2540 knee, 1593 hip OA). PCS mean scores were 32.0+/-8.4 and 31.8+/-8.4 and MCS scores 47.1+/-11.0 and 46.8+/-11.1, for knee and hip OA, respectively. Acceptable convergent and divergent validity was observed, and correlation between PCS and MCS mean scores was low (r=0.14). However, factor analysis performed on the eight subscale scores failed to support the use of PCS and MCS aggregate scores. It extracted two factors which were similar for both OA types and differed from the a priori stratification. Scores for two subscales usually attributed to MCS - emotional role and social functioning - were shared between factors, and scores for another subscale - general health perception - usually belonging to the PCS was in the mental component factor. CONCLUSIONS: Our results suggest that aggregate scores from the PCS and MCS of the SF-36 as they are currently defined may not be optimal for used in hip and knee OA patients to assess health-related quality of life.},
affiliation = {Service de M{\'e}decine Physique et R{\'e}adaptation, H{\^o}pital Cochin (AP-HP), Universit{\'e} Paris 5, Institut F{\'e}d{\'e}ratif de Recherche sur le Handicap (IFR 25) INSERM, Paris, France.},
number = {9},
pages = {1013--8},
volume = {15},
year = {2007},
month = {Sep},
language = {eng},
keywords = {Quality of Life, Female, Osteoarthritis: Hip, Outcome Assessment (Health Care), Health Status, Middle Aged, Health Surveys, Osteoarthritis: Knee, Humans, Cross-Sectional Studies, Factor Analysis: Statistical, Family Practice, Male, Aged},
date-added = {2010-02-17 15:05:54 +0100},
date-modified = {2010-07-29 19:42:29 +0200},
doi = {10.1016/j.joca.2007.02.012},
pii = {S1063-4584(07)00078-7},
pmid = {17387025},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Rannou-2007-Osteoarthr%20Cartil_Should%20aggregate%20sco.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5879},
rating = {0}
}

@article{Macgregor:2006p7514,
author = {Stuart Macgregor and Imtiaz A Khan},
journal = {BMC Med Genet},
title = {GAIA: an easy-to-use web-based application for interaction analysis of case-control data},
abstract = {BACKGROUND: The advent of cheap, large scale genotyping has led to widespread adoption of genetic association mapping as the tool of choice in the search for loci underlying susceptibility to common complex disease. Whilst simple single locus analysis is relatively trivial to conduct, this is not true of more complex analysis such as those involving interactions between loci. The importance of testing for interactions between loci in association analysis has been highlighted in a number of recent high profile publications. RESULTS: Genetic Association Interaction Analysis (GAIA) is a web-based application for testing for statistical interactions between loci. It is based upon the widely used case-control study design for genetic association analysis and is designed so that non-specialists may routinely apply tests for interaction. GAIA allows simple testing of both additive and additive plus dominance interaction models and includes permutation testing to appropriately correct for multiple testing. The application will find use both in candidate gene based studies and in genome-wide association studies. For large scale studies GAIA includes a screening approach which prioritizes loci (based on the significance of main effects at one or both loci) for further interaction analysis. CONCLUSION: GAIA is available at http://www.bbu.cf.ac.uk/html/research/biostats.htm.},
affiliation = {Genetic Epidemiology, Queensland Institute of Medical Research, Brisbane, Australia. stuart.macgregor@qimr.edu.au},
pages = {34},
volume = {7},
year = {2006},
month = {Jan},
language = {eng},
keywords = {Genetic Predisposition to Disease, Polymorphism: Single Nucleotide, Genetic Techniques, Humans, Internet, Logistic Models, Schizophrenia, Case-Control Studies, Epistasis: Genetic},
date-added = {2010-03-10 20:53:52 +0100},
date-modified = {2010-03-10 20:53:52 +0100},
doi = {10.1186/1471-2350-7-34},
pii = {1471-2350-7-34},
pmid = {16595019},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Macgregor-2006-BMC%20Med%20Genet_GAIA%20an%20easy-to-use.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7514},
rating = {0}
}

@article{BelMufti:2005p11915,
author = {G Bel Mufti and P Bertrand and L El Moubarki},
journal = {ASMDA Proceedings},
title = {Determining the number of groups from measures of cluster stability},
abstract = {Animportantlineofinquiryinclustervalidationinvolvesmeasuringthe stability of a partition with respect to perturbations of the data set. Several authors have recently suggested that the `correct' number of clusters in a partition can be determined simply by examining the partition stability measures for different values of numbers of clusters. In this paper, we consider the clustering stability measures that were recently proposed in [Bertrand and Bel Mufti, 2005], and we present experiments that compare the method for predicting the number of clusters that is derived from these stability measures with two of the most successful methods reported in recent surveys.},
year = {2005},
date-added = {2010-05-23 16:39:01 +0200},
date-modified = {2010-05-23 16:40:14 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bel%20Mufti-2005-ASMDA%20Proceedings_Determining%20the%20numb.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11915},
rating = {5}
}

@article{Meng:2009p4361,
author = {Yan A Meng and Yi Yu and L Adrienne Cupples and Lindsay A Farrer and Kathryn L Lunetta},
journal = {BMC Bioinformatics},
title = {Performance of random forest when SNPs are in linkage disequilibrium},
abstract = {BACKGROUND: Single nucleotide polymorphisms (SNPs) may be correlated due to linkage disequilibrium (LD). Association studies look for both direct and indirect associations with disease loci. In a Random Forest (RF) analysis, correlation between a true risk SNP and SNPs in LD may lead to diminished variable importance for the true risk SNP. One approach to address this problem is to select SNPs in linkage equilibrium (LE) for analysis. Here, we explore alternative methods for dealing with SNPs in LD: change the tree-building algorithm by building each tree in an RF only with SNPs in LE, modify the importance measure (IM), and use haplotypes instead of SNPs to build a RF. RESULTS: We evaluated the performance of our alternative methods by simulation of a spectrum of complex genetics models. When a haplotype rather than an individual SNP is the risk factor

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