text:
the same period, a number of matrix methods have also been developed, particularly in the theory of g-inverses and projection matrices. In this chapter, we integrated these two lines of developments, matrix methods and some important topics of factor analysis such as identifiability conditions, communality problems, analysis of image and anti-image variables, estimation of factor scores, and equivalence conditions on canonical factor analysis, thereby extending some of the earlier theories. In particular, we developed the conditions under which the SMC of a variable is equal to the communality of the variable, and some equivalent conditions under which the eigenvalues resulting from canonical factor analysis are either 1 or 0. We also introduced methods for estimating factor score matrices when the uniqueness variance matrix is singular.},
year = {2008},
date-added = {2010-07-24 11:35:45 +0200},
date-modified = {2010-07-24 11:36:51 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Yanai-2008-_Matrix%20Methods%20and%20T.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13732},
rating = {0}
}

@article{Hung:2004p1679,
author = {Rayjean J Hung and Paul Brennan and Christian Malaveille and Stefano Porru and Francesco Donato and Paolo Boffetta and John S Witte},
journal = {Cancer Epidemiol Biomarkers Prev},
title = {Using hierarchical modeling in genetic association studies with multiple markers: application to a case-control study of bladder cancer},
abstract = {BACKGROUND: Genetic association studies are generating much information, usually in the form of single nucleotide polymorphisms in candidate genes. Analyzing such data is challenging, and raises issues of multiple comparisons and potential false-positive associations. Using data from a case-control study of bladder cancer, we showed how to use hierarchical modeling in genetic epidemiologic studies with multiple markers to control overestimation of effects and potential false-positive associations. METHODS: The data were first analyzed with the conventional approach of estimating each main effect individually. We subsequently employed hierarchical modeling by adding a second stage (prior) model that incorporated information on the potential function of the genes. We used an empirical-Bayes approach, estimating the residual effects of the genes from the data. When the residual effect was set to zero, we instead used a semi-Bayes approach, in which they were pre-specified. We also explored the impact of using different second-stage design matrices. Finally, we used two approaches for assessing gene-environment interactions. The first approach added product terms into the first-stage model. The second approach used three indicators for subjects exposed to gene-only, environment-only, and both genetic and environmental factors. RESULTS: By pre-specifying the prior second-stage covariates, the estimates were shrunk to the mean of each pathway. The conventional model detected a number of positive associations, which were reduced with the hierarchical model. For example, the odds ratio for myeloperoxidase (G/G, G/A) genotype changed from 3.17 [95% confidence interval (CI), 1.32-7.59] to 1.64 (95% CI, 0.81-3.34). A similar phenomenon was observed for the gene-environment interactions. The odds ratio for the gene-environment interaction between tobacco smoking and N-acetyltransferase 1 fast genotype was 2.74 (95% CI, 0.68-11.0) from the conventional analysis and 1.24 (95% CI, 0.80-1.93) from the hierarchical model. CONCLUSION: Adding a second-stage hierarchical modeling can reduce the likelihood of false positive via shrinkage toward the prior mean, improve the risk estimation by increasing the precision, and, therefore, represents an alternative to conventional methods for genetic association studies.},
affiliation = {Internal Agency for Research on Cancer Epidemiology, 150 cours Albert-Thomas, 69008 Lyon, France. hung@iarc.fr},
number = {6},
pages = {1013--21},
volume = {13},
year = {2004},
month = {Jun},
language = {eng},
keywords = {Regression Analysis, Occupational Exposure, Smoking, Case-Control Studies, Environmental Exposure, Urinary Bladder Neoplasms, Genetic Markers, Peroxidase, Genotype, Polycyclic Hydrocarbons: Aromatic, Male, Arylamine N-Acetyltransferase, Bayes Theorem, Humans, Genetics: Population, Italy, Models: Genetic},
date-added = {2010-01-08 22:23:49 +0100},
date-modified = {2010-01-08 22:23:49 +0100},
pii = {13/6/1013},
pmid = {15184258},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1679},
rating = {0}
}

@phdthesis{Youness:2004,
author = {Genane Youness},
journal = {PhD Thesis},
title = {Contributions {\`a} une m{\'e}thodologie de comparaison de partitions},
affiliation = {Universit{\'e} Paris 6},
year = {2004},
date-added = {2010-01-10 11:33:25 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Youness-2004-PhD%20Thesis_Contributions%20%C3%A0%20une.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2232},
rating = {0}
}

@article{Davidian:1993p2358,
author = {M Davidian and D M Giltinan},
journal = {J Biopharm Stat},
title = {Some general estimation methods for nonlinear mixed-effects models},
abstract = {A nonlinear mixed-effects model suitable for characterizing repeated measurement data is described. The model allows dependence of random coefficients on covariate information and accommodates general specifications of a common intraindividual covariance structure, such as models for variance within individuals that depend on individual mean response and autocorrelation. Two classes of procedures for estimation in this model are described, which incorporate estimation of unknown parameters in the assumed intraindividual covariance structure. The procedures are straightforward to implement using standard statistical software. The techniques are illustrated by examples in growth analysis and assay development.},
affiliation = {Department of Statistics, North Carolina State University, Raleigh 27695-8203.},
number = {1},
pages = {23--55},
volume = {3},
year = {1993},
month = {Mar},
language = {eng},
keywords = {Computer Simulation, Humans, Likelihood Functions, Relaxin, Soybeans, Female, Data Interpretation: Statistical, Software, Dose-Response Relationship: Drug, Least-Squares Analysis, Models: Biological, Models: Statistical, Calibration},
date-added = {2010-01-10 13:38:44 +0100},
date-modified = {2010-01-10 13:38:44 +0100},
pmid = {8485535},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2358},
rating = {0}
}

@article{Gao:2004p8723,
author = {Fei Gao and Nan Luo and Julian Thumboo and Calvin Fones and Shu-Chuen Li and Yin-Bun Cheung},
journal = {Health Qual Life Outcomes},
title = {Does the 12-item General Health Questionnaire contain multiple factors and do we need them?},
abstract = {BACKGROUND: The 12-item General Health Questionnaire (GHQ-12) is widely used as a unidimensional instrument, but factor analyses tended to suggest that it contains two or three factors. Not much is known about the usefulness of the GHQ-12 factors, if they exist, in revealing between-patient differences in clinical states and health-related quality of life. METHODS: We addressed this issue in a cross-sectional survey of out-patients with psychological disorders in Singapore. The participants (n = 120) completed the GHQ-12, the Beck Anxiety Inventory, and the Short-Form 36 Health Survey. Confirmatory factor analysis was used to compare six previously proposed factor structures for the GHQ-12. Factor scores of the best-fitting model, as well as the overall GHQ-12 score, were assessed in relation to clinical and health-related quality of life variables. RESULTS: The 3-factor model proposed by Graetz fitted the data better than a unidimensional model, two 2-factor models, and two other 3-factor models. However, the three factors were strongly correlated. Their values varied in a similar fashion in relation to clinical and health-related quality of life variables. CONCLUSIONS: The 12-item General Health Questionnaire contains three factors, namely Anxiety and Depression, Social Dysfunction, and Loss of Confidence. Nevertheless, using them separately does not offer many practical advantages in differentiating clinical groups or identifying association with clinical or health-related quality of life variables.},
affiliation = {Clinical Trials and Epidemiological Sciences, National Cancer Centre, 11 Hospital Drive, 169610, Singapore. ctegfe@nccs.com.sg},
pages = {63},
volume = {2},
year = {2004},
month = {Jan},
language = {eng},
keywords = {Factor Analysis: Statistical, Quality of Life, Social Behavior Disorders, Adult, Middle Aged, Personality Inventory, Mental Disorders, Anxiety Disorders, Cross-Sectional Studies, Psychiatric Department: Hospital, Depressive Disorder, Sickness Impact Profile, Male, Self Efficacy, Singapore, Female, Severity of Illness Index, Humans, Hospitals: Teaching, Questionnaires},
date-added = {2010-03-22 12:02:04 +0100},
date-modified = {2010-03-22 12:02:04 +0100},
doi = {10.1186/1477-7525-2-63},
pii = {1477-7525-2-63},
pmid = {15538951},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Gao-2004-Health%20and%20Quality%20of%20Life%20Outcomes_Does%20the%2012-item%20Gen.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8723},
rating = {0}
}

@article{Laloe:2007p12015,
author = {Denis Lalo{\"e} and Thibaut Jombart and Anne-B{\'e}atrice Dufour and Katayoun Moazami-Goudarzi},
journal = {Genet Sel Evol},
title = {Consensus genetic structuring and typological value of markers using multiple co-inertia analysis},
abstract = {Working with weakly congruent markers means that consensus genetic structuring of populations requires methods explicitly devoted to this purpose. The method, which is presented here, belongs to the multivariate analyses. This method consists of different steps. First, single-marker analyses were performed using a version of principal component analysis, which is designed for allelic frequencies (%PCA). Drawing confidence ellipses around the population positions enhances %PCA plots. Second, a multiple co-inertia analysis (MCOA) was performed, which reveals the common features of single-marker analyses, builds a reference structure and makes it possible to compare single-marker structures with this reference through graphical tools. Finally, a typological value is provided for each marker. The typological value measures the efficiency of a marker to structure populations in the same way as other markers. In this study, we evaluate the interest and the efficiency of this method applied to a European and African bovine microsatellite data set. The typological value differs among markers, indicating that some markers are more efficient in displaying a consensus typology than others. Moreover, efficient markers in one collection of populations do not remain efficient in others. The number of markers used in a study is not a sufficient criterion to judge its reliability. "Quantity is not quality".},
affiliation = {Station de g{\'e}n{\'e}tique quantitative et appliqu{\'e}e UR337, INRA, 78352 Jouy-en-Josas, France. denis.laloe@jouy.inra.fr},
number = {5},
pages = {545--67},
volume = {39},
year = {2007},
month = {Jan},
language = {eng},
keywords = {France, Microsatellite Repeats, Cattle, Multivariate Analysis, Gene Frequency, Principal Component Analysis, Models: Genetic, Animals, Africa: Western, Genetics: Population, Breeding, Genetic Markers, Alleles, Biodiversity},
date-added = {2010-05-23 22:38:52 +0200},
date-modified = {2010-07-29 19:27:17 +0200},
doi = {10.1051/gse:2007021},
pii = {g06098},
pmid = {17897596},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Lalo%C3%AB-2007-Genet%20Sel%20Evol_Consensus%20genetic%20st.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12015},
rating = {5}
}

@article{Lang:1996p6269,
author = {J B Lang},
journal = {Journal of the Royal Society, Serie B},
title = {On the comparison of Multinomial and Poisson log-linear models},
number = {1},
pages = {253--266},
volume = {58},
year = {1996},
date-added = {2010-02-19 22:08:09 +0100},
date-modified = {2010-07-29 19:38:24 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Lang-1996-Journal%20of%20the%20Royal%20Society%20Serie%20B_On%20the%20comparison%20of.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6269},
rating = {0}
}

@article{Boulesteix:2004p12029,
author = {A-L Boulesteix},
title = {Dimension Reduction and Classification with High-Dimensional Microarray Data},
year = {2004},
date-added = {2010-05-24 10:25:00 +0200},
date-modified = {2010-05-24 10:25:29 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Boulesteix-2004-_Dimension%20Reduction.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12029},
rating = {0}
}

@article{Ghahramani:2006p12776,
author = {Z Ghahramani and T L Griffiths and P Sollich},
journal = {ISBA 8th World Meeting on Bayesian Statistics},
title = {Bayesian nonparametric latent feature models},
abstract = {We describe a flexible nonparametric approach to latent variable modelling in which the number of latent variables is unbounded. This approach is based on a probability distribution over equivalence classes of binary matrices with a finite number of rows, corresponding to the data points, and an unbounded number of columns, corresponding to the latent variables. Each data point can be associated with a subset of the possible latent variables, which we re- fer to as the latent features of that data point. The binary variables in the matrix indicate which latent feature is possessed by which data point, and there is a potentially infinite array of features. We derive the distribution over unbounded binary matrices by taking the limit of a distribution over N × K binary matrices as K → ∞. We define a simple generative processes for this distribution which we call the Indian buffet process (IBP; Griffiths and Ghahramani, 2005, 2006) by analogy to the Chinese restaurant process (Aldous, 1985; Pitman, 2002). The IBP has a single hyperparameter which controls both the number of feature per object and the total number of fea- tures. We describe a two-parameter generalization of the IBP which has addi- tional flexibility, independently controlling the number of features per object and the total number of features in the matrix. The use of this distribution as a prior in an infinite latent feature model is illustrated, and Markov chain Monte Carlo algorithms for inference are described.},
year = {2006},
date-added = {2010-06-18 20:42:15 +0200},
date-modified = {2010-06-18 20:43:28 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Ghahramani-2006-ISBA%208th%20World%20Meeting%20on%20Bayesian%20Statistics_Bayesian%20nonparametr.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12776},
rating = {0}
}

@article{Weitkunat:2010p12306,
author = {Rolf Weitkunat and Etienne Kaelin and Gregory Vuillaume and Gerd Kallischnigg},
journal = {BMC Med Res Methodol},
title = {Effectiveness of strategies to increase the validity of findings from association studies: size vs. replication},
abstract = {ABSTRACT: BACKGROUND: The capacity of multiple comparisons to produce false positive findings in genetic association studies is abundantly clear. To address this issue, the concept of false positive report probability (FPRP) measures "the probability of no true association between a genetic variant and disease given a statistically significant finding". This concept involves the notion of prior probability of an association between a genetic variant and a disease, making it difficult to achieve acceptable levels for the FPRP when the prior probability is low. Increasing the sample size is of limited efficiency to improve the situation. METHODS: To further clarify this problem, the concept of true report probability (TRP) is introduced by analogy to the positive predictive value (PPV) of diagnostic testing. The approach is extended to consider the effects of replication studies. The formula for the TRP after k replication studies is mathematically derived and shown to be only dependent on prior probability, alpha, power, and number of replication studies. RESULTS: Case-control association studies are used to illustrate the TRP concept for replication strategies. Based on power considerations, a relationship is derived between TRP after k replication studies and sample size of each individual study. That relationship enables study designers optimization of study plans. Further, it is demonstrated that replication is efficient in increasing the TRP even in the case of low prior probability of an association and without requiring very large sample sizes for each individual study. CONCLUSIONS: True report probability is a comprehensive and straightforward concept for assessing the validity of positive statistical testing results in association studies. By its extension to replication strategies it can be demonstrated in a transparent manner that replication is highly effective in distinguishing spurious from true associations. Based on the generalized TRP method for replication designs, optimal research strategy and sample size planning become possible.},
number = {1},
pages = {47},
volume = {10},
year = {2010},
month = {May},
language = {ENG},
date-added = {2010-06-09 21:06:21 +0200},
date-modified = {2010-06-09 21:06:22 +0200},
doi = {10.1186/1471-2288-10-47},
pii = {1471-2288-10-47},
pmid = {20509879},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Weitkunat-2010-BMC%20Med%20Res%20Methodol_Effectiveness%20of%20str.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12306},
rating = {0}
}

@article{DiMaggio:2008p12886,
author = {Peter A DiMaggio and Scott R McAllister and Christodoulos A Floudas and Xiao-Jiang Feng and Joshua D Rabinowitz and Herschel A Rabitz},
journal = {BMC Bioinformatics},
title = {Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies},
abstract = {BACKGROUND: The analysis of large-scale data sets via clustering techniques is utilized in a number of applications. Biclustering in particular has emerged as an important problem in the analysis of gene expression data since genes may only jointly respond over a subset of conditions. Biclustering algorithms also have important applications in sample classification where, for instance, tissue samples can be classified as cancerous or normal. Many of the methods for biclustering, and clustering algorithms in general, utilize simplified models or heuristic strategies for identifying the "best" grouping of elements according to some metric and cluster definition and thus result in suboptimal clusters. RESULTS: In this article, we present a rigorous approach to biclustering, OREO, which is based on the Optimal RE-Ordering of the rows and columns of a data matrix so as to globally minimize the dissimilarity metric. The physical permutations of the rows and columns of the data matrix can be modeled as either a network flow problem or a traveling salesman problem. Cluster boundaries in one dimension are used to partition and re-order the other dimensions of the corresponding submatrices to generate biclusters. The performance of OREO is tested on (a) metabolite concentration data, (b) an image reconstruction matrix, (c) synthetic data with implanted biclusters, and gene expression data for (d) colon cancer data, (e) breast cancer data, as well as (f) yeast segregant data to validate the ability of the proposed method and compare it to existing biclustering and clustering methods. CONCLUSION: We demonstrate that this rigorous global optimization method for biclustering produces clusters with more insightful groupings of similar entities, such as genes or metabolites sharing common functions, than other clustering and biclustering algorithms and can reconstruct underlying fundamental patterns in the data for several distinct sets of data matrices arising in important biological applications.},
affiliation = {Department of Chemical Engineering, Princeton University, Princeton, NJ, USA. pete@titan.princeton.edu},
pages = {458},
volume = {9},
year = {2008},
month = {Jan},
language = {eng},
keywords = {cluster analysis, Database Management Systems, Yeasts, Image Processing: Computer-Assisted, Databases: Genetic, Humans, Models: Theoretical, Algorithms, Pattern Recognition: Automated, Saccharomyces cerevisiae, Colonic Neoplasms, Artificial Intelligence, Systems Biology, Oligonucleotide Array Sequence Analysis, Breast Neoplasms, Information Storage and Retrieval, Escherichia coli},
date-added = {2010-06-24 13:14:55 +0200},
date-modified = {2010-06-24 13:14:55 +0200},
doi = {10.1186/1471-2105-9-458},
pii = {1471-2105-9-458},
pmid = {18954459},
local-url = {file://localhost/Users/chl/Dropbox/Papers/DiMaggio-2008-BMC%20Bioinformatics_Biclustering%20via%20opt.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12886},
rating = {0}
}

@article{Taylor:2005p3696,
author = {J Taylor},
title = {Scale Parameter Modelling of the t-distribution},
year = {2005},
date-added = {2010-01-16 20:47:54 +0100},
date-modified = {2010-01-16 20:48:24 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Taylor-2005-_Scale%20Parameter%20Mode.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3696},
rating = {0}
}

@inproceedings{Landauer:1997,
author = {T K Landauer and D Laham and B Rehder and M E Schreiner},
journal = {Proceedings},
title = {How Well Can Passage Meaning be Derived without Using Word Order? A Comparison of Latent Semantic Analysis and Humans},
year = {1997},
date-added = {2010-01-10 11:33:25 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Landauer-1997-Proceedings_How%20Well%20Can%20Passage.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1956},
rating = {0}
}

@article{Malzahn:2009p9321,
author = {D{\"o}rthe Malzahn and Yesilda Balavarca and Jingky P Lozano and Heike Bickeb{\"o}ller},
journal = {BMC Proc},
title = {Tests for candidate-gene interaction for longitudinal quantitative traits measured in a large cohort},
abstract = {ABSTRACT : For the Framingham Heart Study (FHS) and simulated FHS (FHSsim) data, we tested for gene-gene interaction in quantitative traits employing a longitudinal nonparametric association test (LNPT) and, for comparison, a survival analysis. We report results for the Offspring Cohort by LNPT analysis and on all longitudinal cohorts by survival analysis with cohort effect adjustment. We verified that type I errors were not inflated. We compared the power of both methods to detect in FHSsim data two sets of gene pairs that interact for the trait coronary artery calcification. In FHS, we tested eight gene pairs from a list of candidate genes for interaction effects on body mass index. Both methods found evidence for pairwise non-additive effects of mutations in the genes FTO, PON1, and PFKP on body mass index.},
affiliation = {Department of Genetic Epidemiology, University Medical Center, University of Goettingen, Humboldtallee 32, D-37073 Goettingen, Germany. dmalzah@gwdg.de.},
pages = {S80},
volume = {3 Suppl 7},
year = {2009},
month = {Jan},
language = {eng},
date-added = {2010-03-23 18:33:12 +0100},
date-modified = {2010-07-29 19:21:18 +0200},
pmid = {20018076},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Malzahn-2009-BMC%20Proc_Tests%20for%20candidate.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9321},
rating = {0}
}

@article{Ponce:2008p2491,
author = {G Ponce and J Hoenicka and M A Jim{\'e}nez-Arriero and R Rodr{\'\i}guez-Jim{\'e}nez and M Arag{\"u}{\'e}s and N Mart{\'\i}n-Su{\~n}{\'e} and E Huertas and T Palomo},
journal = {Br J Psychiatry},
title = {DRD2 and ANKK1 genotype in alcohol-dependent patients with psychopathic traits: association and interaction study},
abstract = {BACKGROUND: The TaqI-A polymorphism of the ANKK1 gene, adjacent to the DRD2 gene, has been associated with alcoholism and other psychiatric conditions, although other DRD2 gene variants, such as the C957T polymorphism, could be related to these phenotypic traits. AIMS: To investigate the contribution of the TaqI-A and the C957T polymorphisms to the presence of psychopathic traits in patients with alcoholism. METHOD: We performed association and interaction analyses of the polymorphisms in 150 controls and 176 male alcohol-dependent patients assessed for the presence of dissocial personal disorder, using the Psychopathy Checklist-Revised (PCL-R). RESULTS: There was a significant association of the TaqI-A and C957T polymorphisms when both genotypes were present, with PCL-R scores of F(1-171=0.13) (P=0.01) and a frequency of dissocial personal disorder OR=10.52, P<0.001. CONCLUSIONS: The TaqI-A of the ANKK1 gene and the C957T of the DRD2 gene are epistatically associated with psychopathic traits in alcohol-dependent patients.},
affiliation = {Servicio de Psiquiatr{\'\i}a, Hospital 12 de Octubre, Madrid, Spain.},
number = {2},
pages = {121--5},
volume = {193},
year = {2008},
month = {Aug},
language = {eng},
keywords = {Polymorphism: Genetic, Protein-Serine-Threonine Kinases, Spain, Genotype, Humans, Antisocial Personality Disorder, Statistics as Topic, Genetic Predisposition to Disease, Psychiatric Status Rating Scales, Receptors: Dopamine D2, Adult, Aged, Alcoholism, Case-Control Studies, Middle Aged, Male},
date-added = {2010-01-12 13:33:28 +0100},
date-modified = {2010-01-12 13:33:28 +0100},
doi = {10.1192/bjp.bp.107.041582},
pii = {193/2/121},
pmid = {18669994},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2491},
rating = {0}
}

@article{Liu:2009p1568,
author = {H Liu and J Zhang},
journal = {Proceedings of the 12th International Conference on Artificial Intelligence and Statistics (AISTATS) 2009},
title = {Estimation Consistency of the Group Lasso and its Applications},
abstract = {We extend the l2-consistency result of (Mein- shausen and Yu 2008) from the Lasso to the group Lasso. Our main theorem shows that the group Lasso achieves estimation consis- tency under a mild condition and an asymp- totic upper bound on the number of selected variables can be obtained. As a result, we can apply the nonnegative garrote procedure to the group Lasso result to obtain an estimator which is simultaneously estimation and vari- able selection consistent. In particular, our setting allows both the number of groups and the number of variables per group increase and thus is applicable to high-dimensional problems. We also provide estimation con- sistency analysis for a version of the sparse additive models with increasing dimensions. Some finite-sample results are also reported.},
year = {2009},
date-added = {2010-01-07 16:54:59 +0100},
date-modified = {2010-01-07 16:55:46 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Liu-2009-Proceedings%20of%20the%2012th%20International%20Conference%20on%20Artificial%20Intelligence%20and%20Statistics%20(AISTATS)%202009_Estimation%20Consisten.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1568},
rating = {0}
}

@article{Donaldson:2005p6627,
author = {Gary W Donaldson},
journal = {Qual Life Res},
title = {Structural equation models for quality of life response shifts: promises and pitfalls},
affiliation = {Pain Research Center, Department of Anesthesiology, School of Medicine, University of Utah, USA. Gary.Donaldson@hsc.utah.edu},
number = {10},
pages = {2345--51},
volume = {14},
year = {2005},
month = {Dec},
language = {eng},
keywords = {Patients, Questionnaires, Models: Statistical, Humans, United States, Quality of Life, Health Status},
date-added = {2010-03-03 20:33:50 +0100},
date-modified = {2010-07-29 19:48:29 +0200},
doi = {10.1007/s11136-005-3977-2},
pmid = {16328915},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Donaldson-2005-Qual%20Life%20Res_Structural%20equation.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6627},
rating = {0}
}

@article{Wolinsky:2004p303,
author = {Fredric D Wolinsky and Douglas K Miller and Elena M Andresen and Theodore K Malmstrom and J Philip Miller},
journal = {J Gerontol B Psychol Sci Soc Sci},
title = {Health-Related Quality of Life in Middle-Aged African Americans},
abstract = {Objectives. In this article we explore the measurement properties of the Medical Outcomes Study 36-Item Short-Form Health Survey (SF-36) in 49- to 65-year-old African Americans, compare their health-related quality of life (HRQoL) with that of the nation, and evaluate the association of selected covariates with HRQoL.

Methods. A probability sample of 998 African Americans in St. Louis received comprehensive in-home assessments. We used an item analysis, exploratory and confirmatory factor analysis, and internal consistency reliability to evaluate the measurement properties of the eight SF-36 scales and their interrelationships. We used a multiple linear regression analysis to characterize the effects of the demographic, socioeconomic status, psychosocial attributes, and biomedical markers.

Results. Assessments averaged 2.5 hr. Each SF-36 scale was unidimensional, all items had robust factor loadings, and all but one scale achieved excellent ( .80) internal consistency reliability levels. The overall factor structure of the SF-36 scales was generally consistent with national norms. Substantial variance was explained by the covariates, mostly attributable to socioeconomic status and the biomedical markers.

Conclusions. The SF-36 is a reliable and valid measure of HRQoL for use with African Americans. In this sample, the HRQoL was below national averages. Future social epidemiologic studies should include grip strength, vision, and hearing assessments, which had substantial and consistent associations with the SF-36 scale scores.},
affiliation = {College of Public Health, University of Iowa, Iowa City},
pages = {S118--S123},
volume = {59},
year = {2004},
date-added = {2010-01-03 11:31:33 +0100},
date-modified = {2010-07-29 19:53:56 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Wolinsky-2004-J%20Gerontol%20B%20Psychol%20Sci%20Soc%20Sci_Health-Related%20Quali.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p303},
read = {Yes},
rating = {0}
}

@article{Wray:2009p2501,
author = {Naomi R Wray and Michael R James and Scott D Gordon and Troy Dumenil and Leanne Ryan and William L Coventry and Dixie J Statham and Michele L Pergadia and Pamela A F Madden and Andrew C Heath and Grant W Montgomery and Nicholas G Martin},
journal = {Biol Psychiatry},
title = {Accurate, Large-Scale Genotyping of 5HTTLPR and Flanking Single Nucleotide Polymorphisms in an Association Study of Depression, Anxiety, and Personality Measures},
abstract = {BACKGROUND: The length polymorphism repeat in the promoter region of the serotonin transporter gene (5HTTLPR) is one of the most studied polymorphisms for association with a range of psychiatric and personality phenotypes. However, the original 5HTTLPR assay is prone to bias toward short allele calling. METHODS: We designed new assays for the 5HTTLPR suitable for large-scale genotyping projects and we genotyped 13 single nucleotide polymorphisms (SNPs) in a 38-kilobase region around the 5HTTLPR, including SNP rs25531, a polymorphism of the 5HTTLPR long allele. Association analysis was conducted for major depression and/or anxiety disorder in unrelated cases (n = 1161) and control subjects (n = 1051) identified through psychiatric interviews administered to a large population sample of Australian twin families. Participants had been scored for personality traits several years earlier (n > or = 2643 unrelated individuals). RESULTS: We identified a two-SNP haplotype proxy for 5HTTLPR; the CA haplotype of SNPs rs4251417 and rs2020934 is coupled with the short allele of 5HTTLPR (r(2) = .72). We found evidence for association (p = .0062, after accounting for multiple testing) for SLC6A4 SNPs rs6354 and rs2020936 (positioned in a different linkage disequilibrium [LD] block about 15.5 kb from 5HTTLPR) with anxiety and/or depression and neuroticism, with the strongest association for recurrent depression with onset in young adulthood (odds ratio = 1.55, 95% confidence interval = 1.16-2.06). CONCLUSIONS: The associated SNPs are in the same LD block as the variable number of tandem repeats serotonin transporter intron 2 marker, for which association has previously been reported.},
affiliation = {Genetic and Molecular Epidemiology Laboratories, Queensland Institute of Medical Research, 300 Herston Road, Brisbane 4006, Australia. naomi.wray@qimr.edu.au.},
number = {5},
pages = {468--76},
volume = {66},
year = {2009},
month = {Sep},
language = {eng},
keywords = {Polymorphism: Single Nucleotide, Serotonin Plasma Membrane Transport Proteins, Genotype, Humans, Adult, Models: Genetic, Linkage Disequilibrium, Case-Control Studies, Anxiety Disorders, Female, Genome-Wide Association Study, Depressive Disorder: Major, Personality, Male},
date-added = {2010-01-12 13:36:03 +0100},
date-modified = {2010-01-12 13:36:03 +0100},
doi = {10.1016/j.biopsych.2009.04.030},
pii = {S0006-3223(09)00533-2},
pmid = {19541292},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Wray-2009-Biol%20Psychiatry_Accurate%20Large-Scal.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2501},
rating = {0}
}

@article{Hawthorne:2009p11770,
author = {Graeme Hawthorne},
journal = {Value Health},
title = {Assessing utility where short measures are required: development of the short Assessment of Quality of Life-8 (AQoL-8) instrument},
abstract = {OBJECTIVES: As researchers seek to include clinical outcomes, the health-related quality of life (HRQoL) of participants and meet economic evaluation demands, they are confronted with collecting disparate outcome data where parsimony is imperative. This study addressed this through construction of a short HRQoL measure, the Assessment of Quality of Life (AQoL)-8 from the original AQoL. METHODS: Data from the AQoL validation database (N = 996) were reanalyzed using item response theory (IRT) to identify the least fitting items, which were removed. The standard AQoL scoring algorithm and weights were applied. Validity, reliability, and sensitivity tests were carried out using the 2004 South Australian Health Omnibus Survey (N = 3015), including direct comparisons with other short utility measures, the EQ5D and SF6D. RESULTS: The IRT analysis showed that the AQoL was a weak scale (Loevinger H = 0.36) but reliable (Mokken rho = 0.84). Removal of the four weakest items led to an 8-item instrument with two items per subscale, the AQoL-8. The AQoL-8 Loevinger H = 0.38 and Mokken rho = 0.80 suggested similar psychometric properties to the AQoL. It correlated (intraclass correlation coefficient) 0.95 (or 90% of shared variance) with the AQoL. The AQoL-8 was as sensitive to six common health conditions as the AQoL, EQ5D, and SF6D. CONCLUSIONS: The utility scores fall on the same life-death scale as those of the AQoL. Where parsimony is imperative, researchers may consider use of the AQoL-8 to collect participant self-report HRQoL data that is suitable for use either as reported outcomes or for the calculation of quality-adjusted life-years for cost-utility analysis.},
affiliation = {Department of Psychiatry, The University of Melbourne, Melbourne, Australia. graemeeh@unimelb.edu.au},
number = {6},
pages = {948--57},
volume = {12},
year = {2009},
month = {Sep},
language = {eng},
keywords = {Algorithms, Female, Middle Aged, Young Adult, Databases: Factual, Outcome Assessment (Health Care), Linear Models, Adult, Aged: 80 and over, Quality of Life, Chronic Disease, Sickness Impact Profile, Questionnaires, Victoria, Psychometrics, Humans, Male, Aged},
date-added = {2010-05-23 10:39:48 +0200},
date-modified = {2010-05-23 10:39:48 +0200},
doi = {10.1111/j.1524-4733.2009.00526.x},
pii = {VHE526},
pmid = {19490558},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hawthorne-2009-Value%20Health_Assessing%20utility%20wh.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11770},
rating = {0}
}

@article{Morales:2006p7860,
author = {Leo S Morales and Claudia Flowers and Peter Gutierrez and Marjorie Kleinman and Jeanne A Teresi},
journal = {Med Care},
title = {Item and scale differential functioning of the Mini-Mental State Exam assessed using the Differential Item and Test Functioning (DFIT) Framework},
abstract = {OBJECTIVES: To illustrate the application of the Differential Item and Test Functioning (DFIT) method using English and Spanish versions of the Mini-Mental State Examination (MMSE). SUBJECTS: Study participants were 65 years of age or older and lived in North Manhattan, New York. Of the 1578 study participants who were administered the MMSE 665 completed it in Spanish. MEASURES:: The MMSE contains 20 items that measure the degree of cognitive impairment in the areas of orientation, attention and calculation, registration, recall and language, as well as the ability to follow verbal and written commands. RESEARCH DESIGN: After assessing the dimensionality of the MMSE scale, item response theory person and item parameters were estimated separately for the English and Spanish sample using Samejima's 2-parameter graded response model. Then the DFIT framework was used to assess differential item functioning (DIF) and differential test functioning (DTF). RESULTS: Nine items were found to show DIF; these were items that ask the respondent to name the correct season, day of the month, city, state, and 2 nearby streets, recall 3 objects, repeat the phrase no ifs, no ands, no buts, follow the command, "close your eyes," and the command, "take the paper in your right hand, fold the paper in half with both hands, and put the paper down in your lap." At the scale level, however, the MMSE did not show differential functioning. CONCLUSIONS: Respondents to the English and Spanish versions of the MMSE are comparable on the basis of scale scores. However, assessments based on individual MMSE items may be misleading.},
affiliation = {Department of Health Services and Division of General Internal Medicine and Health Services Research at UCLA, Los Angeles, CA 90095-1772, USA. lsmorales@mednet.ucla.edu},
number = {11 Suppl 3},
pages = {S143--51},
volume = {44},
year = {2006},
month = {Nov},
language = {eng},
keywords = {Hispanic Americans, Aged, Data Interpretation: Statistical, Ethnic Groups, New York City, Bias (Epidemiology), Neuropsychological Tests, Dementia, Translating, Humans, Psychometrics, Models: Statistical, Cross-Cultural Comparison},
date-added = {2010-03-20 18:59:54 +0100},
date-modified = {2010-07-29 19:39:29 +0200},
doi = {10.1097/01.mlr.0000245141.70946.29},
pii = {00005650-200611001-00020},
pmid = {17060821},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Morales-2006-Med%20Care_Item%20and%20scale%20diffe.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7860},
rating = {0}
}

@article{Moncrieff:2001,
author = {J Moncrieff and R Churchill and DC Drummond and H McGuire},
journal = {International Journal of Methods in Psychiatric Research},
title = {Development of a quality assessment instrument for trials of treatments of depression and neurosis},
abstract = {There is evidence that the quality of controlled clinical trials affects the results that are obtained. A systematic approach to the assessment of quality is required for psychiatric research. This study set out to develop an instrument for the assessment of the quality of controlled trials of interventions for depressive and non-psychotic conditions. A pilot study led to the development of a scale containing 23 items covering a wide range of aspects of quality including objective formulation, design, presentation of results, analysis and quality of conclusions. Scoring criteria were devised and the scale was then subjected to reliability testing using a random sample of trials of treatment for depression and neurosis. The scale showed moderate inter-rater reliability and results were comparable to those obtained with shorter instruments. It was quick and easy to use. There were significant correlations between year of publication and overall quality score with later studies showing higher quality. The instrument developed here provides a systematic approach to the assessment of quality for use in critical appraisal of individual studies and meta-analysis. However, the scoring process should be used cautiously since inter-rater agreement was only moderate.},
pages = {126--133},
volume = {10},
year = {2001},
date-added = {2010-01-03 19:36:10 +0100},
date-modified = {2010-01-03 19:36:10 +0100},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1026},
rating = {0}
}

@article{Gibbons:2007p11577,
author = {R D Gibbons and R D Bock and D Hedeker and D J Weiss and E Segawa and D K Bhaumik and D J Kupfer and E Frank and V J Grochocinski and A Stover},
journal = {Applied Psychological Measurement},
title = {Full-Information Item Bifactor Analysis of Graded Response Data},
abstract = {A plausible factorial structure for many types of psychological and educational tests exhibits a general factor and one or more group or method factors. This structure can be represented by a bifactor model. The bifactor structure results from the constraint that each item has a nonzero loading on the primary dimension and, at most, one of the group factors. The authors develop estimation procedures for fitting the graded response model when the data follow the bifactor structure. Using maximum marginal likelihood estimation of item parameters, the bifactor
restriction leads to a major simplification of the likelihood equations and (a) permits analysis of models with large numbers of group factors, (b) permits conditional dependence within identified subsets of items, and (c) provides more parsimonious factor solutions than an unrestricted full-information item factor analysis in some cases. Analysis of data obtained from 586 chronically mentally ill patients revealed a clear bifactor structure.},
number = {4},
volume = {31},
year = {2007},
date-added = {2010-05-09 18:20:19 +0200},
date-modified = {2010-05-09 18:22:12 +0200},
doi = {10.1177/0146621606289485},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Gibbons-2007-Applied%20Psychological%20Measurement_Full-Information%20Ite.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11577},
rating = {0}
}

@article{Schumann:2008p7565,
author = {Gunter Schumann and Monika Johann and Josef Frank and Ulrich Preuss and Norbert Dahmen and Manfred Laucht and Marcella Rietschel and Dan Rujescu and Anbarasu Lourdusamy and Toni-Kim Clarke and Kristina Krause and Anne Dyer and Martin Depner and Stefan Wellek and Jens Treutlein and Armin Szegedi and Ina Giegling and Sven Cichon and Dorothea Blomeyer and Andreas Heinz and Simon Heath and Mark Lathrop and Norbert Wodarz and Michael Soyka and Rainer Spanagel and Karl Mann},
journal = {Arch Gen Psychiatry},
title = {Systematic analysis of glutamatergic neurotransmission genes in alcohol dependence and adolescent risky drinking behavior},
abstract = {CONTEXT: Glutamatergic neurotransmission is implicated in alcohol-drinking behavior in animal models. OBJECTIVE: To investigate whether genetic variations in glutamatergic neurotransmission genes, which are known to alter alcohol effects in rodents, contribute to the genetic basis of alcoholism in humans. DESIGN: Association analysis of alcohol dependence and haplotype-tagging single nucleotide polymorphisms (SNPs) covering 10 glutamatergic genes. Resequencing of functional domains of these genes identified 204 SNPs. Haplotypes with a frequency of 5% or greater could be discriminated by 21 haplotype-tagging SNPs analyzed for association in 2 independent samples of alcohol-dependent adult patients and controls as well as adolescent trios. SETTING: Four university medical centers in the south of Germany. PARTICIPANTS: One thousand three hundred thirty-seven patients and 1555 controls (study 1: 544 patients, 553 controls; study 2: 793 patients, 1002 controls). One hundred forty-four trios of 15-year-old adolescents assessed for risky drinking behavior. MAIN OUTCOME MEASURES: Genotype profiles for GLAST; N-methyl-d-aspartate-receptor subunits NR1, NR2A, and NR2B; MGLUR5; NNOS; PRKG2; CAMK4; the regulatory subunit of PI3K; and CREB were analyzed for association with alcohol dependence using multivariate statistical analysis. Risky adolescent drinking was tested using the transmission disequilibrium test. RESULTS: Analysis of study 1 revealed that NR2A and MGLUR5 have the greatest relevance for human alcohol dependence among the genes selected with odds ratios of 2.35 and 1.69, respectively. Replication analysis in study 2 confirmed an association of alcohol dependence with NR2A (odds ratio, 2.01) but showed no association with MGLUR5. Combined analysis of study 1 and study 2 exhibited a more significant association on the Cochran-Mantel-Haenszel test (P < .001) for NR2A; NR2A was associated with positive family history, early onset of alcoholism, and maximum number of drinks in adults as well as risky drinking patterns in adolescents. CONCLUSION: Genetic variations in NR2A have the greatest relevance for human alcohol dependence among the glutamatergic genes selected for their known alteration of alcohol effects in animal models.},
affiliation = {Interdisciplinary Research Group Addiction, MRC-SGDP Center, Institute of Psychiatry at King's College, POB 080, London SE5 8AF, England. g.schumann@iop.kcl.ac.uk},
number = {7},
pages = {826--38},
volume = {65},
year = {2008},
month = {Jul},
language = {eng},
keywords = {Adult, Receptors: Glutamate, Risk-Taking, Male, Synaptic Transmission, Alcohol Drinking, Female, Genetic Markers, Adolescent, Alcoholism, Sequence Tagged Sites, Humans, Case-Control Studies, Catchment Area (Health), Excitatory Amino Acid Transporter 1, DNA, Polymorphism: Single Nucleotide, Genotype, Haplotypes, Gene Expression, Diagnostic and Statistical Manual of Mental Disorders, Germany},
date-added = {2010-03-14 10:57:17 +0100},
date-modified = {2010-03-14 10:57:18 +0100},
doi = {10.1001/archpsyc.65.7.826},
pii = {65/7/826},
pmid = {18606955},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Schumann-2008-Arch%20Gen%20Psychiatry_Systematic%20analysis.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7565},
rating = {0}
}

@article{Pearlson:2009p3014,
author = {Godfrey D Pearlson and Vince D Calhoun},
journal = {Frontiers in human neuroscience},
title = {Convergent approaches for defining functional imaging endophenotypes in schizophrenia},
abstract = {In complex genetic disorders such as schizophrenia, endophenotypes have potential utility both in identifying risk genes and in illuminating pathophysiology. This is due to their presumed status as closer in the etiopathological pathway to the causative genes than is the currently defining clinical phenomenology of the illness and thus their simpler genetic architecture than that of the full syndrome. There, many genes conferring slight individual risk are additive or epistatic (interactive) with regard to cumulative schizophrenia risk. In addition the use of endophenotypes has encouraged a conceptual shift away from the exclusive study of categorical diagnoses in manifestly ill patients, towards the study of quantitative traits in patients, unaffected relatives and healthy controls. A more recently employed strategy is thus to study unaffected first-degree relatives of schizophrenia patients, who share some of the genetic diathesis without illness-related confounds that may themselves impact fMRI task performance. Consistent with the multiple biological abnormalities associated with the disorder, many candidate endophenotypes have been advanced for schizophrenia, including measures derived from structural brain imaging, EEG, sensorimotor integration, eye movements and cognitive performance (Allen et al., 2009), but recent data derived from quantitative functional brain imaging measures present additional attractive putative endophenotypes. We will review two major, conceptually different approaches that use fMRI in this context. One, the dominant paradigm, employs defined cognitive tasks on which schizophrenia patients perform poorly as "cognitive stress tests". The second uses very simple probes or "task-free" approaches where performance in patients and controls is equal. We explore the potential advantages and disadvantages of each method, the associated data analytic approaches and recent studies exploring their interface with the genetic risk architecture of schizophrenia.},
affiliation = {Olin Neuropsychiatry Research Center, Institute of Living Hartford, CT 06106, USA. godfrey.pearlson@yale.edu},
pages = {37},
volume = {3},
year = {2009},
month = {Jan},
language = {eng},
date-added = {2010-01-14 11:23:16 +0100},
date-modified = {2010-01-14 11:23:16 +0100},
doi = {10.3389/neuro.09.037.2009},
pmid = {19956400},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Pearlson-2009-Frontiers%20in%20human%20neuroscience_Convergent%20approache.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3014},
rating = {0}
}

@article{Pearlson:2007p3459,
author = {Godfrey D Pearlson and Vince Calhoun},
journal = {Can J Psychiatry},
title = {Structural and functional magnetic resonance imaging in psychiatric disorders},
abstract = {OBJECTIVE: To report on recent advances in both structural and functional brain imaging studies in psychiatry and to highlight their importance for the field. METHOD: We reviewed recently published articles dealing with such advances and abstracted them into a selective review of the field. RESULTS: Some of the more important trends include integration of genetic information into research studies, use of novel quantitative image measurement techniques, studies of new subject populations, the use of pharmacologic probes in functional magnetic resonance imaging (fMRI) studies, the incorporation of elements of virtual reality into fMRI task stimuli, and the methodological innovation of hyperscanning. CONCLUSIONS: A whole series of new approaches and techniques are resulting in rapid advances in neuroimaging in psychiatry. Several of these show the potential for clinical translation.},
affiliation = {Olin Neuropsychiatry Research Center, Institute of Living, Hartford, Connecticut 06106, USA. godfrey.pearlson@yale.edu},
number = {3},
pages = {158--66},
volume = {52},
year = {2007},
month = {Mar},
language = {eng},
keywords = {Magnetic Resonance Imaging, Catechol O-Methyltransferase, Electroencephalography, Brain-Derived Neurotrophic Factor, Brain, Mental Disorders, Prefrontal Cortex, Humans, Genomics},
date-added = {2010-01-15 15:19:37 +0100},
date-modified = {2010-07-29 19:22:44 +0200},
pmid = {17479523},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Pearlson-2007-Can%20J%20Psychiatry_Structural%20and%20funct.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3459},
rating = {0}
}

@article{Kamvar:2002p3307,
author = {Sepandar D Kamvar and Dan Klein and Christopher D Manning},
title = {Interpreting and Extending Classical Agglomerative Clustering Algorithms Using a Model-Based Approach},
abstract = {We present two results which arise from amodel-based approach to hierarchical agglomerativeclustering. First, we show formally thatthe common heuristic agglomerative clusteringalgorithms -- Ward's method, single-link,complete-link, and a variant of group-average --are each equivalent to a hierarchical model-basedmethod. This interpretation gives a theoreticalexplanation of the empirical behavior of thesealgorithms, as well as a principled approach toresolving practical issues, such as number ofclusters or the choice of method. Second, weshow how a model-based viewpoint can suggestvariations on these basic agglomerative algorithms.},
affiliation = {Department of Computer Science , Stanford University},
year = {2002},
month = {Sep},
language = {eng},
date-added = {2010-01-15 12:10:09 +0100},
date-modified = {2010-01-15 12:10:09 +0100},
pmid = {551792},
URL = {http://citeseer.ist.psu.edu/551792},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Kamvar-2002-_Interpreting%20and%20Ext.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3307},
rating = {0}
}

@article{Philip:2009,
author = {EJ Philip and TV Merluzzi and A Peterman and LB Cronk},
journal = {Qual Life Res},
title = {Measurement accuracy in assessing patient's quality of life: to weight or not to weight domains of quality of life.},
abstract = {PURPOSE: Health-related quality of life (HRQOL) measures typically do not incorporate patients' preferences for domains such as physical, emotional, functional and social/family well-being, which may compromise precision. METHOD: A forced-choice domain-preference measure was developed to assess the importance of HRQOL domains. About 194 cancer patients completed the domain-preference measure, along with measures of HRQOL, coping, adjustment, and life satisfaction. RESULTS: Patients ranked emotional well-being as most important and the loss of social-family well-being as the most difficult to do without. A weighting algorithm revealed no advantage to incorporating individuals' domain preferences in HRQOL assessment; however, preliminary evidence suggested that HRQOL measurement may be more accurate in predicting outcomes for individuals with no distinct domain preferences than those with distinct preference profiles. CONCLUSION: This study provides preliminary evidence for the validity of current measures of HRQOL, which may inherently take into account patients' domain preferences.},
affiliation = {Department of Psychology, University of Notre Dame, Notre Dame, IN, 46556, USA, ephilip@nd.edu.},
year = {2009},
month = {Jun},
language = {ENG},
date-added = {2010-01-03 19:38:21 +0100},
date-modified = {2010-07-29 19:48:29 +0200},
doi = {10.1007/s11136-009-9492-0},
pmid = {19496020},
URL = {http://dx.doi.org/10.1007/s11136-009-9492-0},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1187},
rating = {4}
}

@article{Freedle:1988p4255,
author = {R Freedle and I Kostin},
title = {Relationship between item characteristics and an index of differential item functioning (DIF) for the GRE verbal item types},
year = {1988},
date-added = {2010-01-23 21:02:47 +0100},
date-modified = {2010-01-23 21:03:53 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Freedle-1988-_Relationship%20between.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4255},
rating = {0}
}

@article{Dudoit:2008p7868,
author = {S Dudoit and S Keles and M J van der Laan},
journal = {IMS Collections Probability and Statistics: Essays in Honor of David A. Freedman},
title = {Multiple tests of association with biological annotation metadata},
abstract = {Weproposeageneralandformalstatisticalframeworkformultiple tests of association between known fixed features of a genome and unknown parameters of the distribution of variable features of this genome in a popu- lation of interest. The known gene-annotation profiles, corresponding to the fixed features of the genome, may concern Gene Ontology (GO) annotation, pathway membership, regulation by particular transcription factors, nucleotide sequences, or protein sequences. The unknown gene-parameter profiles, corre- sponding to the variable features of the genome, may be, for example, re- gression coefficients relating possibly censored biological and clinical outcomes to genome-wide transcript levels, DNA copy numbers, and other covariates. A generic question of great interest in current genomic research regards the detec- tion of associations between biological annotation metadata and genome-wide expression measures. This biological question may be translated as the test of multiple hypotheses concerning association measures between gene-annotation profiles and gene-parameter profiles. A general and rigorous formulation of the statistical inference question allows us to apply the multiple hypothesis test- ing methodology developed in [Multiple Testing Procedures with Applications to Genomics (2008) Springer, New York] and related articles, to control a broad class of Type I error rates, defined as generalized tail probabilities and expected values for arbitrary functions of the numbers of Type I errors and rejected hypotheses. The resampling-based single-step and stepwise multiple testing procedures of [Multiple Testing Procedures with Applications to Ge- nomics (2008) Springer, New York] take into account the joint distribution of the test statistics and provide Type I error control in testing problems involv- ing general data generating distributions (with arbitrary dependence structures among variables), null hypotheses, and test statistics.
The proposed statistical and computational methods are illustrated using the acute lymphoblastic leukemia (ALL) microarray dataset of [Blood 103 (2004) 2771--2778], with the aim of relating GO annotation to differential gene expression between B-cell ALL with the BCR/ABL fusion and cytogenetically normal NEG B-cell ALL. The sensitivity of the identified lists of GO terms to the choice of association parameter between GO annotation and differen- tial gene expression demonstrates the importance of translating the biological question in terms of suitable gene-annotation profiles, gene-parameter profiles, and association measures. In particular, the results reveal the limitations of binary gene-parameter profiles of differential expression indicators, which are still the norm for combined GO annotation and microarray data analyses. Pro- cedures based on such binary gene-parameter profiles tend to be conservative and lack robustness with respect to the estimator for the set of differentially expressed genes. Our proposed statistical framework, with general definitions for the gene-annotation and gene-parameter profiles, allows consideration of a much broader class of inference problems, that extend beyond GO annotation
and microarray data analysis.},
pages = {153--218},
volume = {2},
year = {2008},
date-added = {2010-03-20 19:08:43 +0100},
date-modified = {2010-03-20 19:10:15 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Dudoit-2008-IMS%20Collections%20Probability%20and%20Statistics%20Essays%20in%20Honor%20of%20David%20A.%20Freedman_Multiple%20tests%20of%20as.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7868},
rating = {0}
}

@article{Baldwin:2009p12550,
author = {Peter Baldwin and Joseph Bernstein and Howard Wainer},
journal = {Stat Med},
title = {Hip psychometrics},
abstract = {When data are abundant relative to the number of questions asked of them, answers can be formulated using little more than those data. But when data grow more sparse, so too does our tendency to lean on strong models to help us draw inferences. In this research we show how a strong item response model embedded within a fully Bayesian framework allows us to answer two important questions about the reliability and consistency of the clinical diagnosis of hip fractures from very limited data. We also show how the model automatically adjusts diagnoses for biases among the surgeons judging the radiographs. This research illustrates how a Bayesian approach expands the range of problems on which item response models can profitably be used.},
affiliation = {National Board of Medical Examiners, Philadelphia, PA, USA. pbaldwin@nbme.org},
number = {17},
pages = {2277--92},
volume = {28},
year = {2009},
month = {Jul},
language = {eng},
keywords = {Biometry, Humans, Orthopedics, Bayes Theorem, Psychometrics, Observer Variation, Models: Statistical, Sample Size, Hip Fractures},
date-added = {2010-06-15 22:06:10 +0200},
date-modified = {2010-06-15 22:06:10 +0200},
doi = {10.1002/sim.3616},
pmid = {19507196},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Baldwin-2009-Stat%20Med_Hip%20psychometrics.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12550},
rating = {0}
}

@article{Molko:2004p4971,
author = {N Molko and A Cachia and D Riviere and J F Mangin and M Bruandet and D LeBihan and L Cohen and S Dehaene},
journal = {Cereb Cortex},
title = {Brain anatomy in Turner syndrome: evidence for impaired social and spatial-numerical networks},
abstract = {Analysis of brain structure in Turner syndrome (TS) provides the opportunity to identify the consequences of the loss of one X chromosome on brain anatomy and to characterize the neural bases underlying the specific cognitive profile of TS subjects which includes deficits in spatial-numerical processing and social cognition. Fourteen subjects with TS and fourteen controls were investigated using voxel-based analysis of high resolution anatomical and diffusion tensor images and using sulcal morphometry. The analysis of anatomical images provided evidence for macroscopical changes in cortical regions involved in social cognition such as the left superior temporal sulcus and orbito-frontal cortex and in a region involved in spatial and numerical cognition such as the right intraparietal sulcus. Diffusion tensor images showed a displacement of the grey-white matter interface of the left and right superior temporal sulcus and revealed bilateral microstructural anomalies in the temporal white matter. The analysis of fiber orientation suggests specific alterations of fiber tracts connecting posterior to anterior temporal regions. Last, sulcal morphometry confirmed the anomalies of the left and right superior temporal sulci and of the right intraparietal sulcus. Our results thus provide converging evidence of regionally specific structural changes in TS that are highly consistent with the hallmark symptoms associated with TS.},
affiliation = {INSERM U 562, Service Hospitalier Fr{\'e}d{\'e}ric Joliot, CEA/DSV, IFR 49, Orsay cedex, France. molko@wanadoo.fr},
number = {8},
pages = {840--50},
volume = {14},
year = {2004},
month = {Aug},
language = {eng},
keywords = {Turner Syndrome, Spatial Behavior, Adolescent, Brain, Magnetic Resonance Imaging, Adult, Female, Humans, Cognition Disorders, Image Interpretation: Computer-Assisted, Evidence-Based Medicine, Nerve Net, Social Behavior},
date-added = {2010-02-05 00:05:57 +0100},
date-modified = {2010-07-29 19:22:58 +0200},
doi = {10.1093/cercor/bhh042},
pii = {bhh042},
pmid = {15054057},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Molko-2004-Cereb%20Cortex_Brain%20anatomy%20in%20Tur.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4971},
rating = {0}
}

@article{Kadouri:2007p5621,
author = {Alane Kadouri and Emmanuelle Corruble and Bruno Falissard},
journal = {BMC Psychiatry},
title = {The improved Clinical Global Impression Scale (iCGI): development and validation in depression},
abstract = {BACKGROUND: The Clinical Global Impression scale (CGI) is frequently used in medical care and clinical research because of its face validity and practicability. This study proposes to improve the reliability of the Clinical Global Impression (CGI) scale in depressive disorders by the use of a semi-standardized interview, a new response format, and a Delphi procedure. METHODS: Thirty patients hospitalised for a major depressive episode were filmed at T1 (first week in hospital) and at T2 (2 weeks later) during a 5' specific interview. The Hamilton Depressive Rating Scale and the Symptom Check List were also rated. Eleven psychiatrists rated these videos using either the usual CGI response format or an improved response format, with or without a Delphi procedure. RESULTS: The new response format slightly improved (but not significantly) the interrater agreement, the Delphi procedure did not. The best results were obtained when ratings by 4 independent raters were averaged. In this situation, intraclass correlation coefficients were about 0.9. CONCLUSION: The Clinical Global Impression is a useful approach in psychiatry since it apprehends patients in their entirety. This study shows that it is possible to quantify such impressions with a high level of interrater agreement.},
affiliation = {Inserm, U669, Paris, France. akadouri@free.fr <akadouri@free.fr>},
pages = {7},
volume = {7},
year = {2007},
month = {Jan},
language = {eng},
keywords = {Depressive Disorder: Major, Humans, Aged, Female, Male, Psychometrics, Delphi Technique, Observer Variation, Aged: 80 and over, Middle Aged, Interview: Psychological, Adult, Psychiatric Status Rating Scales},
date-added = {2010-02-12 20:16:47 +0100},
date-modified = {2010-02-12 20:16:47 +0100},
doi = {10.1186/1471-244X-7-7},
pii = {1471-244X-7-7},
pmid = {17284321},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Kadouri-2007-BMC%20Psychiatry_The%20improved%20Clinica-1.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5621},
rating = {0}
}

@article{Weeks:2010p13821,
author = {J P Weeks},
journal = {Journal of Statistical Software},
title = {plink: An R Package for Linking Mixed-Format Tests Using IRT-Based Methods},
abstract = {The R package plink has been developed to facilitate the linking of mixed-format tests for multiple groups under a common item design using unidimensional and multidimen- sional IRT-based methods. This paper presents the capabilities of the package in the context of the unidimensional methods. The package supports nine unidimensional item response models (the Rasch model, 1PL, 2PL, 3PL, graded response model, partial credit and generalized partial credit model, nominal response model, and multiple-choice model) and four separate calibration linking methods (mean/sigma, mean/mean, Haebara, and Stocking-Lord). It also includes functions for importing item and/or ability parameters from common IRT software, conducting IRT true-score and observed-score equating, and plotting item response curves and parameter comparison plots.},
number = {12},
volume = {35},
year = {2010},
date-added = {2010-07-29 12:44:48 +0200},
date-modified = {2010-07-29 12:48:14 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Weeks-2010-Journal%20of%20Statistical%20Software_plink%20An%20R%20Package.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13821},
rating = {0}
}

@inbook{Thompson:2008,
author = {B Thompson},
journal = {Book},
title = {Research in organizations: Foundational principles, processes, and methods of inquiry},
chapter = {Effect sizes vs statistical significance},
year = {2008},
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/p2139},
rating = {0}
}

@inproceedings{Komarek:2003,
author = {P R Komarek and A W Moore},
journal = {Proceedings},
title = {Fast robust logistic regression for large sparse datasets with binary outputs},
year = {2003},
date-added = {2010-01-10 11:33:22 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Komarek-2003-Proceedings_Fast%20robust%20logistic.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2234},
rating = {0}
}

@article{Kraemer:2009p2939,
author = {Nicole Kraemer and Juliane Schaefer and Anne-Laure Boulesteix},
journal = {arXiv},
title = {Regularized estimation of large-scale gene association networks using  graphical Gaussian models},
abstract = { Graphical Gaussian models are popular tools for the estimation of (undirected) gene association networks from microarray data. A key issue when the number of variables greatly exceeds the number of samples is the estimation of the matrix of partial correlations. Since the (Moore-Penrose) inverse of the sample covariance matrix leads to poor estimates in this scenario, standard methods are inappropriate and adequate regularization techniques are needed. In this article, we investigate a general framework for combining regularized regression methods with the estimation of Graphical Gaussian models. This framework includes various existing methods as well as two new approaches based on ridge regression and adaptive lasso, respectively. These methods are extensively compared both qualitatively and quantitatively within a simulation study and through an application to six diverse real data sets. In addition, all proposed algorithms are implemented in the R package "parcor", available from the R repository CRAN. },
note = {added additional experiments},
eprint = {0905.0603v2},
volume = {stat.ME},
year = {2009},
month = {Jan},
keywords = {stat.AP, stat.ME, stat.CO},
date-added = {2010-01-13 23:00:04 +0100},
date-modified = {2010-01-13 23:00:04 +0100},
pmid = {0905.0603v2},
URL = {http://arxiv.org/abs/0905.0603v2},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Kraemer-2009-arXiv_Regularized%20estimati.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2939},
rating = {0}
}

@article{Krantz:1999p7068,
author = {D H Krantz},
journal = {JAMA},
title = {The Null Hypothesis Testing Controversy in Psychology},
number = {448},
pages = {1372--1381},
volume = {94},
year = {1999},
date-added = {2010-03-06 20:11:28 +0100},
date-modified = {2010-07-29 20:01:35 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Krantz-1999-JAMA_The%20Null%20Hypothesis.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7068},
rating = {4}
}

@article{Guillemot:2008p1528,
author = {V Guillemot and L Le Brusquet and A Tenenhaus and V Frouin},
title = {Analyse diff{\'e}rentielle de puces {\`a} ADN. Comparaison entre m{\'e}thodes wrapper et filter},
abstract = {Dans le cadre de donn{\'e}es d'expression g{\'e}n{\'e}tique, nous nous int{\'e}ressons aux m{\'e}thodes qui permettent d'identifier les g{\`e}nes significativement diff{\'e}rentiellement exprim{\'e}s entre deux situations biologiques. Nous allons comparer une m{\'e}thode classique d'analyse par tests d'hypoth{\`e}ses {\`a} des m{\'e}thodes d'analyse diff{\'e}rentielle par r{\'e}gression r{\'e}gularis{\'e}e. La difficult{\'e} de ce genre de jeu de donn{\'e}es est la profusion de variables (les g{\`e}nes) pour assez peu d'individus (les profils d'expression). La strat{\'e}gie usuelle consiste {\`a} mettre en {\oe}uvre autant de tests qu'il y a de variables et de consid{\'e}rer que les variables principales sont celles qui ont la « meilleure » p-value. Une strat{\'e}gie alternative pourrait consister {\`a} choisir de classer les variables non plus en fonction de leur significativit{\'e} (pour un test), mais plut{\^o}t de le classer suivant leur poids dans le mod{\`e}le r{\'e}gularis{\'e} obtenu. Dans la bibliographie, les premi{\`e}res m{\'e}thodes sont dites filter 1 , les deuxi{\`e}mes sont plut{\^o}t dites wrapper 2 . Un bon aper{\c c}u de ce que sont les m{\'e}thodes wrapper et filter est donn{\'e} dans [9]. Le cadre ressemble {\`a} celui de l'apprentissage supervis{\'e}, car on dispose de profils d'expression g{\'e}niques pour si possible l'ensemble du g{\'e}nome d'un organisme, chaque puce appartenant {\`a} une classe (situation biologique particuli{\`e}re).
L'impl{\'e}mentation des m{\'e}thodes {\'e}voqu{\'e}es dans ce rapport a {\'e}t{\'e} effectu{\'e}e sous R [16].},
affiliation = {CEA, iRCM, Laboratoire d'Exploration Fonctionnelle des G{\'e}nomes, F-91000, France},
year = {2008},
date-added = {2010-01-07 16:03:50 +0100},
date-modified = {2010-01-07 16:05:24 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Guillemot-2008-_Analyse%20diffe%CC%81rentie.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1528},
rating = {0}
}

@article{Lukasiewicz:2008p1369,
author = {M Lukasiewicz and X Neveu and L Blecha and B Falissard and M Reynaud and I Gasquet},
journal = {Alcohol Alcohol},
title = {Pathways to substance-related disorder: a structural model approach exploring the influence of temperament, character, and childhood adversity in a national cohort of prisoners},
abstract = {Aims: Using Cloninger's model of personality, we aimed to specify the relative influence of the more biologically determined variables, temperament and character and more environmentally driven influence, childhood adversity in the development of addiction; and to compare patterns found among alcoholics with those found among drug addicts. Methods: We studied a group of prisoners, at a high risk of substance abuse and past history of childhood adversity. Using a stratified random strategy we selected (i) 23 prisons among the different types of prison in France, (ii) 998 prisoners. Each prisoner was assessed by two psychiatrists---one junior, using a structured interview (MINI 5 plus), and one senior, completing the procedure with an open clinical interview. At the end of the interview the clinicians met and agreed on a list of diagnoses. Cloninger's Temperament and Character Inventory was used to measure personality. Structural equations models, which have been advocated to disentangle the respective influence of complex risk factors, were used. Results: the "novelty seeking" temperament was a crucial vulnerability factor, for both alcoholics and drug addicts, in the same proportion. Character and childhood adversity played a significant part only in the development of drug abuse. Conclusions: In a prison population, a common biological loaded factor, novelty seeking is found both at the core of alcohol- and drug-related disorder whereas environmentally loaded factors play a greater role in drug problems.},
affiliation = {INSERM, U669, Paris, F-75014 France, Universite ́ Paris-Sud 11, Le Kremlin Biceˆtre, F-94000 France, University of Paris 5, Paris, F-75015 France, AP-HP, Villejuif, F-94804, France},
number = {3},
pages = {287--295},
volume = {43},
year = {2008},
date-added = {2010-01-07 12:11:52 +0100},
date-modified = {2010-07-29 19:12:56 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Lukasiewicz-2008-Alcohol%20Alcohol_Pathways%20to%20substanc.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1369},
rating = {0}
}

@article{Sung:2006p2766,
author = {H J Sung and T Kang},
journal = {National Council on Measurement in Education},
title = {Choosing a Polytomous IRT Model using Bayesian Model Selection Methods},
abstract = {Model selection is the process by which a specific statistical model is chosen to represent the data. In order to get the benefits of item response theory (IRT), it is important to choose appropriate model which fit the data well. In this study, four model selection methods based on Bayesian estimation process will be com- pared in terms of their relative performances in choosing the best model to analyze Likert-type data. Among lots of polytomous IRT models already suggested, the rating scale model (RSM; Andrich, 1978), the partial credit model (PCM; Masters, 1982), the generalized partial credit model (GPCM; Muraki, 1992), and the graded response model (GRM; Samejima, 1969) are used to compare the utility of the four model selection methods. Results indicate that model selection was dependent to some extent on the particular conditions simulated.},
year = {2006},
date-added = {2010-01-13 14:23:06 +0100},
date-modified = {2010-07-29 19:40:24 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Sung-2006-National%20Council%20on%20Measurement%20in%20Education_Choosing%20a%20Polytomou.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2766},
rating = {0}
}

@article{Thompson:1998p1717,
author = {B Thompson},
journal = {Research in the Schools},
title = {Statistical Significance and Effect Size Reporting: Portrait of a Possible Future},
abstract = {The present paper comments on the matters raised regarding statistical significance tests by three sets of authors in this issue. These articles are placed within the context of contemporary literature. Next, additional empirical evidence is cited showing that the APA publication manual's "encouraging" effect size reporting has had no appreciable effect. Editorial policy will be required to affect change, and some model policies are quoted. Science will move forward to the extent that both effect size and replicability evidence of one or more sorts are finally seriously considered within our inquiry.},
affiliation = {Texas A{\&}M University and Baylor College of Medicine},
number = {2},
pages = {33--38},
volume = {5},
year = {1998},
date-added = {2010-01-09 20:24:29 +0100},
date-modified = {2010-01-09 20:25:31 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Thompson-1998-Research%20in%20the%20Schools_Statistical%20Signific.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1717},
rating = {0}
}

@article{Pettit:2008p12975,
author = {Lewis Pettit and Jennifer Charles and Andrew D Wilson and Mandy S Plumb and Anne Brockman and Justin H G Williams and Mark Mon-Williams},
journal = {Human Movement Science},
title = {Constrained action selection in children with developmental coordination disorder},
abstract = {The effect of advance ('precue') information on short aiming movements was explored in adults, high school children, and primary school children with and without developmental coordination disorder (n=10, 14, 16, 10, respectively). Reaction times in the DCD group were longer than in the other groups and were more influenced by the extent to which the precue constrained the possible action space. In contrast, reaction time did not alter as a function of precue condition in adults. Children with DCD showed greater inaccuracy of response (despite the increased RT). We suggest that the different precue effects reflect differences in the relative benefits of priming an action prior to definitive information about the movement goal. The benefits are an interacting function of the task and the skill level of the individual. Our experiment shows that children with DCD gain a benefit from advance preparation in simple aiming movements, highlighting their low skill levels. This result suggests that goal-directed RTs may have diagnostic potential within the clinic.},
affiliation = {College of Medicine and Life Sciences, University of Aberdeen, Aberdeen, Scotland AB24 2UB, UK.},
number = {2},
pages = {286--95},
volume = {27},
year = {2008},
month = {Apr},
language = {eng},
keywords = {Female, Reaction Time, Male, Motor Skills Disorders, Choice Behavior, Child, Humans, Movement, Adolescent},
date-added = {2010-06-25 22:36:10 +0200},
date-modified = {2010-06-25 22:36:10 +0200},
doi = {10.1016/j.humov.2008.02.014},
pii = {S0167-9457(08)00018-3},
pmid = {18406486},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Pettit-2008-Human%20Movement%20Science_Constrained%20action%20s.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12975},
rating = {0}
}

@article{Gelman:2009p912,
author = {Andrew Gelman and Jennifer Hill and Masanao Yajima},
title = {Why we (usually) don't have to worry about multiple comparisons},
abstract = {Applied researchers often find themselves making statistical inferences in settings that would seem to require multiple comparisons adjustments. We challenge the Type I error paradigm that underlies these corrections. Moreover we posit that the problem of multiple comparisons can disappear entirely when viewed from a hierarchical Bayesian perspective. We propose building multilevel models in the settings where multiple comparisons arise.
Multilevel models perform partial pooling (shifting estimates toward each other), whereas classical procedures typically keep the centers of intervals stationary, adjusting for multiple comparisons by making the intervals wider (or, equivalently, adjusting the p-values corresponding to intervals of fixed width). Thus, multilevel models address the multiple comparisons problem and also yield more efficient estimates, especially in settings with low group-level variation, which is where multiple comparisons are a particular concern.},
affiliation = {Department of Statistics and Department of Political Science, Columbia University, New York},
year = {2009},
keywords = {Bayesian inference, multiple comparisons, Type S error, statistical significance, hierarchical modeling},
date-added = {2010-01-03 18:55:41 +0100},
date-modified = {2010-01-03 18:57:09 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Gelman-2009-_Why%20we%20(usually)%20don.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p912},
rating = {0}
}

@article{Roiser:2009p8924,
author = {Jonathan P Roiser and Benedetto de Martino and Geoffrey C Y Tan and Dharshan Kumaran and Ben Seymour and Nicholas W Wood and Raymond J Dolan},
journal = {J Neurosci},
title = {A genetically mediated bias in decision making driven by failure of amygdala control},
abstract = {Genetic variation at the serotonin transporter-linked polymorphic region (5-HTTLPR) is associated with altered amygdala reactivity and lack of prefrontal regulatory control. Similar regions mediate decision-making biases driven by contextual cues and ambiguity, for example the "framing effect." We hypothesized that individuals hemozygous for the short (s) allele at the 5-HTTLPR would be more susceptible to framing. Participants, selected as homozygous for either the long (la) or s allele, performed a decision-making task where they made choices between receiving an amount of money for certain and taking a gamble. A strong bias was evident toward choosing the certain option when the option was phrased in terms of gains and toward gambling when the decision was phrased in terms of losses (the frame effect). Critically, this bias was significantly greater in the ss group compared with the lala group. In simultaneously acquired functional magnetic resonance imaging data, the ss group showed greater amygdala during choices made in accord, compared with those made counter to the frame, an effect not seen in the lala group. These differences were also mirrored by differences in anterior cingulate-amygdala coupling between the genotype groups during decision making. Specifically, lala participants showed increased coupling during choices made counter to, relative to those made in accord with, the frame, with no such effect evident in ss participants. These data suggest that genetically mediated differences in prefrontal-amygdala interactions underpin interindividual differences in economic decision making.},
affiliation = {Institute of Cognitive Neuroscience, University College London, London WC1N 3AR, UK.},
number = {18},
pages = {5985--91},
volume = {29},
year = {2009},
month = {May},
language = {eng},
keywords = {Reaction Time, Bias (Epidemiology), Brain Mapping, Young Adult, Adult, Image Processing: Computer-Assisted, Psychophysics, Personality, Male, Oxygen, Regression Analysis, Female, Decision Making, Neuropsychological Tests, Analysis of Variance, Amygdala, Humans, Serotonin Plasma Membrane Transport Proteins, Genotype, Magnetic Resonance Imaging},
date-added = {2010-03-22 13:01:12 +0100},
date-modified = {2010-07-29 19:52:28 +0200},
doi = {10.1523/JNEUROSCI.0407-09.2009},
pii = {29/18/5985},
pmid = {19420264},
URL = {http://www.jneurosci.org/cgi/content/full/29/18/5985},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Roiser-2009-J%20Neurosci_A%20genetically%20mediat.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8924},
rating = {0}
}

@article{Wade:2006p13726,
author = {Tracey D Wade and Ross D Crosby and Nicholas G Martin},
journal = {Arch Gen Psychiatry},
title = {Use of latent profile analysis to identify eating disorder phenotypes in an adult Australian twin cohort},
abstract = {CONTEXT: The relationships among the different eating disorders that exist in the community are poorly understood, especially for residual disorders in which bingeing or purging occurs in the absence of other behaviors. OBJECTIVE: To examine a community sample for the number of mutually exclusive weight and eating profiles. DESIGN: Data regarding lifetime eating disorder symptoms and weight range were submitted to a latent profile analysis. Profiles were compared regarding personality, current eating and weight, retrospectively reported life events, and lifetime depressive psychopathology. SETTING: Longitudinal study among female twins from the Australian Twin Registry in whom eating was assessed by a telephone interview. PARTICIPANTS: A community sample of 1002 twins (individuals) who had participated in earlier waves of data collection. MAIN OUTCOME MEASURES: Number and clinical character of latent profiles. RESULTS: The best fit was a 5-profile solution with women who were (1) of normal weight with few lifetime eating disorders (4.3%), (2) overweight (10.6% had a lifetime eating disorder), (3) underweight and generally had no eating disorders except for 5.3% who had restricting anorexia nervosa, (4) of low to normal weight (89.0% had a lifetime eating disorder), and (5) obese (37.0% had a lifetime eating disorder). Each profile contained more than 1 type of lifetime eating disorder except for the third profile. Women in the first and third profiles had the best functioning, with women in the fourth and fifth profiles having similarly poorer functioning. The women in the fourth group had a symptom profile distinctive from the other 4 groups in terms of severity; they were also more likely to have had lifetime major depression and suicidality. CONCLUSION: Lifetime weight ranges and the severity of eating disorder symptoms affected clustering more than the type of eating disorder symptom.},
affiliation = {School of Psychology, Flinders University, PO Box 2100, Adelaide, SA 5001, Australia. tracey.wade@flinders.edu.au},
number = {12},
pages = {1377--84},
volume = {63},
year = {2006},
month = {Dec},
language = {eng},
keywords = {Models: Statistical, Australia, Feeding Behavior, Psychiatric Status Rating Scales, Depressive Disorder: Major, Personality, Longitudinal Studies, Interviews as Topic, Humans, Eating Disorders, Data Collection, Diseases in Twins, Phenotype, Female, Severity of Illness Index, Sex Factors, Adult, Registries, Anorexia Nervosa, Body Weight, Reproducibility of Results, Life Change Events, Suicide: Attempted},
date-added = {2010-07-24 11:19:15 +0200},
date-modified = {2010-07-24 11:19:33 +0200},
doi = {10.1001/archpsyc.63.12.1377},
pii = {63/12/1377},
pmid = {17146012},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Wade-2006-Arch%20Gen%20Psychiatry_Use%20of%20latent%20profil.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13726},
rating = {4}
}

@article{Klimstra:2010p9977,
author = {Theo A Klimstra and William W Hale and Quinten A W Raaijmakers and Susan J T Branje and Wim H J Meeus},
journal = {J Youth Adolesc},
title = {Identity formation in adolescence: change or stability?},
abstract = {The aim of this five-wave longitudinal study of 923 early to middle adolescents (50.7% boys; 49.3% girls) and 390 middle to late adolescents (43.3% boys and 56.7% girls) is to provide a comprehensive view on change and stability in identity formation from ages 12 to 20. Several types of change and stability (i.e., mean-level change, rank-order stability, and profile similarity) were assessed for three dimensions of identity formation (i.e., commitment, in-depth exploration, and reconsideration), using adolescent self-report questionnaires. Results revealed changes in identity dimensions towards maturity, indicated by a decreasing tendency for reconsideration, increasingly more in-depth exploration, and increasingly more stable identity dimension profiles. Mean levels of commitment remained stable, and rank-order stability of commitment, in-depth exploration, and reconsideration did not change with age. Overall, girls were more mature with regard to identity formation in early adolescence, but boys had caught up with them by late adolescence. Taken together, our findings indicate that adolescent identity formation is guided by progressive changes in the way adolescents deal with commitments, rather than by changes in the commitments themselves.},
affiliation = {Research Centre Adolescent Development, Utrecht University, P.O. Box 80.140, 3508 TC, Utrecht, The Netherlands. t.a.klimstra@uu.nl},
number = {2},
pages = {150--62},
volume = {39},
year = {2010},
month = {Feb},
language = {eng},
keywords = {Personality Inventory, Child, Sex Factors, Adolescent Psychology, Adolescent, Self Concept, Identification (Psychology), Male, Personality Development, Models: Psychological, Awareness, Young Adult, Psychometrics, Netherlands, Female, Social Support, Longitudinal Studies, Humans, Social Control: Informal, Interpersonal Relations},
date-added = {2010-03-31 19:46:59 +0200},
date-modified = {2010-03-31 19:46:59 +0200},
doi = {10.1007/s10964-009-9401-4},
pmid = {20084561},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9977},
rating = {0}
}

@article{Titman:2009p13625,
author = {Andrew C Titman and Linda D Sharples},
journal = {Stat Methods Med Res},
title = {Model diagnostics for multi-state models},
abstract = {Multi-state models are a popular method of describing medical processes that can be represented as discrete states or stages. They have particular use when the data are panel-observed, meaning they consist of discrete snapshots of disease status at irregular time points which may be unique to each patient. However, due to the difficulty of inference in more complicated cases, strong assumptions such as the Markov property, patient homogeneity and time homogeneity are applied. It is important that the validity of these assumptions is tested. A review of methods for diagnosing model fit for panel-observed continuous-time Markov and misclassification-type hidden Markov models is given, with illustrative application to a dataset on cardiac allograft vasculopathy progression in post-heart transplant patients.},
affiliation = {Department of Mathematics and Statistics, Lancaster University, UK.},
pages = {},
year = {2009},
month = {Aug},
language = {ENG},
date-added = {2010-07-11 09:00:24 +0200},
date-modified = {2010-07-11 09:00:25 +0200},
doi = {10.1177/0962280209105541},
pii = {0962280209105541},
pmid = {19654169},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Titman-2009-Stat%20Methods%20Med%20Res_Model%20diagnostics%20fo.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13625},
rating = {0}
}

@article{Zou:2005p2425,
author = {H Zou and T Hastie},
journal = {Journal of the Royal Society, Serie B},
title = {Regularization and variable selection via the elastic net},
abstract = {We propose the elastic net, a new regularization and variable selection method. Real world data and a simulation study show that the elastic net often outperforms the lasso, while enjoying a similar sparsity of representation. In addition, the elastic net encourages a grouping effect, where strongly correlated predictors tend to be in or out of the model together. The elastic net is particularly useful when the number of predictors (p) is much bigger than the number of observations (n). By contrast, the lasso is not a very satisfactory variable selection method in the p >> n case. An algorithm called LARS-EN is proposed for computing elastic net regularization paths efficiently, much like algorithm LARS does for the lasso.},
number = {2},
pages = {301--320},
volume = {67},
year = {2005},
date-added = {2010-01-11 23:23:08 +0100},
date-modified = {2010-07-29 19:38:24 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Zou-2005-Journal%20of%20the%20Royal%20Society%20Serie%20B_Regularization%20and%20v.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2425},
rating = {0}
}

@article{Thompson:2002a,
author = {B Thompson},
journal = {Educational Researcher},
title = {What future quantitative social science research could look like: Confidence intervals for effect sizes},
number = {3},
pages = {24--31},
volume = {31},
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/p2198},
rating = {0}
}

@article{Filzmoser:2005p1363,
author = {P Filzmoser},
journal = {Austrian Journal of Statistics},
title = {Identification of Multivariate Outliers: A Performance Study},
abstract = {Three methods for the identification of multivariate outliers (Rousseeuw and Van Zomeren, 1990; Becker and Gather, 1999; Filzmoser et al., 2005) are compared. They are based on the Mahalanobis distance that will be made resistant against outliers and model deviations by robust estimation of location and covariance. The comparison is made by means of a simulation study. Not only the case of multivariate normally distributed data, but also heavy tailed and asymmetric distributions will be considered. The simulations are focused on low dimensional (p = 5) and high dimensional (p = 30) data.},
number = {2},
pages = {127--138},
volume = {34},
year = {2005},
keywords = {Outlier Detection, Ro- bustness, Mahalanobis distance, MCD Estimator},
date-added = {2010-01-07 11:57:16 +0100},
date-modified = {2010-01-07 11:59:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Filzmoser-2005-Austrian%20Journal%20of%20Statistics_Identification%20of%20Mu.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1363},
rating = {0}
}

@article{Hsieh:1998p6603,
author = {F Y Hsieh and D A Bloch and M D Larsen},
journal = {Stat Med},
title = {A simple method of sample size calculation for linear and logistic regression},
abstract = {A sample size calculation for logistic regression involves complicated formulae. This paper suggests use of sample size formulae for comparing means or for comparing proportions in order to calculate the required sample size for a simple logistic regression model. One can then adjust the required sample size for a multiple logistic regression model by a variance inflation factor. This method requires no assumption of low response probability in the logistic model as in a previous publication. One can similarly calculate the sample size for linear regression models. This paper also compares the accuracy of some existing sample-size software for logistic regression with computer power simulations. An example illustrates the methods.},
affiliation = {CSPCC, Department of Veterans Affairs, Palo Alto Health Care System (151-K), California 94304, USA.},
number = {14},
pages = {1623--34},
volume = {17},
year = {1998},
month = {Jul},
language = {eng},
keywords = {Mathematical Computing, Humans, Software, Sample Size, Logistic Models},
date-added = {2010-03-03 20:20:19 +0100},
date-modified = {2010-03-03 20:20:40 +0100},
pii = {10.1002/(SICI)1097-0258(19980730)17:14<1623::AID-SIM871>3.0.CO;2-S},
pmid = {9699234},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hsieh-1998-Stat%20Med_A%20simple%20method%20of%20s.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6603},
rating = {3}
}

@article{Amirkhanian:2003p8188,
author = {Yuri A Amirkhanian and Jeffrey A Kelly and Timothy L McAuliffe},
journal = {AIDS},
title = {Psychosocial needs, mental health, and HIV transmission risk behavior among people living with HIV/AIDS in St Petersburg, Russia},
abstract = {OBJECTIVES: The number of new HIV infections in Russia has doubled annually since 1996. A total of 232 424 HIV infections have been officially recorded but the actual number probably exceeds one million. Very little is known about the social, psychological, behavioral, and health care service access of persons living with HIV in Russia. DESIGN: A cross-sectional sample of 470 persons with HIV/AIDS recruited in 2002 using a representative sampling plan in major St. Petersburg HIV care and service agencies. METHODS: Participants completed anonymous self-administered questionnaires that elicited detailed information about social and psychological characteristics, HIV serostatus disclosure and discrimination experiences, and risk practices since learning of their HIV positive status. RESULTS: Most participants were young (mean age, 25.3 years), knew of their HIV positive status for about 2 years, and had histories of injecting drug use as well as sexual risk behavior. A large proportion reported encountering discrimination including being forced to sign documents acknowledging their HIV status (47.9%), refusal of general health care (29.6%), being fired from their jobs (9.9%), and being forced from their family homes (9.0%). Over one-third had probable clinical depression. Most remained sexually active since learning of their HIV positive serostatus, approximately half engaged in unprotected sex with HIV negative partners, and condoms were not used one-third of the time with discordant partners. A majority of injecting drug users in the sample still shared needles. CONCLUSIONS: HIV-infected persons in Russia experience a wide range of social, psychological, and care access problems. Improved services are urgently needed for persons living with HIV/AIDS in Russia.},
affiliation = {Center for AIDS Intervention Research (CAIR), Department of Psychiatry and Behavioral Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. yuri@mcw.edu},
number = {16},
pages = {2367--74},
volume = {17},
year = {2003},
month = {Nov},
language = {eng},
keywords = {Russia, Social Support, HIV Infections, Sexual Behavior, Adult, Condoms, Discrimination (Psychology), Cross-Sectional Studies, Safe Sex, Substance Abuse: Intravenous, Adaptation: Psychological, Male, Health Services Needs and Demand, Humans, Needle Sharing, Depressive Disorder, Risk-Taking, Female},
date-added = {2010-03-20 19:53:26 +0100},
date-modified = {2010-03-20 19:53:26 +0100},
doi = {10.1097/01.aids.0000076355.20434.7b},
pmid = {14571189},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Amirkhanian-2003-AIDS_Psychosocial%20needs.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8188},
rating = {0}
}

@article{Hedeker:1994p13474,
author = {D Hedeker and R D Gibbons and B R Flay},
journal = {Journal of Consulting and Clinical Psychology},
title = {Random-effects regression models for clustered data with an example from smoking prevention research},
number = {4},
pages = {757--765},
volume = {62},
year = {1994},
date-added = {2010-07-01 20:32:00 +0200},
date-modified = {2010-07-01 20:33:17 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hedeker-1994-Journal%20of%20Consulting%20and%20Clinical%20Psychology_Random-effects%20regre.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13474},
rating = {0}
}

@article{Hebiri:2008p12332,
author = {M Hebiri},
title = {Regularization with the Smooth-Lasso procedure},
abstract = {We consider the linear regression problem. We propose the S-Lasso proce- dure to estimate the unknown regression parameters. This estimator enjoys sparsity of the representation while taking into account correlation between successive covariates (or predictors). The study covers the case when p ≫ n, i.e. the number of covariates is much larger than the number of observations. In the theoretical point of view, for fixed p, we establish asymptotic normality and consistency in variable selection results for our procedure. When p ≥ n, we provide variable selection consistency results and show that the S-Lasso achieved a Sparsity Inequality, i.e., a bound in term of the number of non-zero components of the oracle vector. It appears that the S-Lasso has nice variable selection properties compared to its challengers. Furthermore, we provide an estimator of the effective degree of freedom of the S-Lasso estimator. A simu- lation study shows that the S-Lasso performs better than the Lasso as far as variable selection is concerned especially when high correlations between suc- cessive covariates exist. This procedure also appears to be a good challenger to the Elastic-Net [36].},
year = {2008},
date-added = {2010-06-12 10:10:47 +0200},
date-modified = {2010-06-12 10:11:16 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hebiri-2008-_Regularization%20with.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12332},
rating = {0}
}

@article{Fox:2003a,
author = {J P Fox and C A W Glas},
journal = {Psychometrika},
title = {Bayesian modeling of measurement error in predictor variables},
pages = {169--191},
volume = {68},
year = {2003},
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/Fox-2003-Psychometrika_Bayesian%20modeling%20of.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1944},
rating = {0}
}

@article{Eiser:2004p8498,
author = {Christine Eiser},
journal = {Ambul Pediatr},
title = {Use of quality of life measures in clinical trials},
abstract = {To be useful in clinical trials, quality of life (QOL) measures must meet basic criteria related to psychometric properties (reliability, validity, and sensitivity), length and acceptability to patients, and availability of parallel child and proxy versions. This paper examines the adequacy of several current measures, with special reference to childhood cancer. We identified 10 such measures of varying length, age-appropriateness, and content. We also discerned a number of obstacles to inclusion of QOL measures in trials. These include clinician bias, financial cost, and time required to inform families and to obtain informed consent from parents. We noted some methodological difficulties associated with measuring QOL over time. These include allowing for maturation and accounting for response shift, or children's propensity to change their internal standards for assessing QOL.},
affiliation = {CR-UK Child and Family Research Group, Department of Psychology, University of Sheffield, Sheffield, UK. C.Eiser@shef.ac.uk},
number = {4 Suppl},
pages = {395--9},
volume = {4},
year = {2004},
month = {Jan},
language = {eng},
keywords = {Data Collection, Clinical Trials as Topic, Child, Humans, Quality of Life, Health Status, Time Factors},
date-added = {2010-03-21 18:00:26 +0100},
date-modified = {2010-03-21 18:00:26 +0100},
doi = {10.1367/A03-112R.1},
pii = {A03-112R},
pmid = {15264945},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8498},
rating = {0}
}

@misc{Fox:2007,
author = {J-P Fox and C A W Glas},
journal = {Miscellaneous},
title = {Modeling Measurement Error in Structural Multilevel Models},
year = {2007},
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/Fox-2007-Miscellaneous_Modeling%20Measurement.PDF},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1960},
rating = {0}
}

@article{Cheung:2008p3196,
author = {M W L Cheung},
journal = {Psychological Methods},
title = {A Model for Integrating Fixed-, Random-, and Mixed-Effects Meta- Analyses Into Structural Equation Modeling},
abstract = {Meta-analysis and structural equation modeling (SEM) are two important statistical methods in the behavioral, social, and medical sciences. They are generally treated as two unrelated topics in the literature. The present article proposes a model to integrate fixed-, random-, and mixed-effects meta-analyses into the SEM framework. By applying an appropriate transfor- mation on the data, studies in a meta-analysis can be analyzed as subjects in a structural equation model. This article also highlights some practical benefits of using the SEM approach to conduct a meta-analysis. Specifically, the SEM-based meta-analysis can be used to handle missing covariates, to quantify the heterogeneity of effect sizes, and to address the heterogeneity of effect sizes with mixture models. Examples are used to illustrate the equivalence between the conventional meta-analysis and the SEM-based meta-analysis. Future directions on and issues related to the SEM-based meta-analysis are discussed.},
number = {3},
pages = {182--202},
volume = {13},
year = {2008},
date-added = {2010-01-14 20:54:39 +0100},
date-modified = {2010-01-14 20:55:54 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Cheung-2008-Psychological%20Methods_A%20Model%20for%20Integrat.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3196},
rating = {0}
}

@article{BoutetdeMonvel:1999p1685,
author = {A Boutet de Monvel and A Khorunzhy},
journal = {The Annals of Probability},
title = {On the norm and eigenvalue distribution of large random matrices},
affiliation = {Universit ́e Paris 7 and Verkin Institute},
number = {2},
pages = {913--944},
volume = {27},
year = {1999},
date-added = {2010-01-09 18:29:21 +0100},
date-modified = {2010-01-09 18:30:34 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Boutet%20de%20Monvel-1999-The%20Annals%20of%20Probability_On%20the%20norm%20and%20eige.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1685},
rating = {0}
}

@article{Pan:2002p13227,
author = {Wei Pan and Jizhen Lin and Chap T Le},
journal = {Genome Biol},
title = {Model-based cluster analysis of microarray gene-expression data},
abstract = {BACKGROUND: Microarray technologies are emerging as a promising tool for genomic studies. The challenge now is how to analyze the resulting large amounts of data. Clustering techniques have been widely applied in analyzing microarray gene-expression data. However, normal mixture model-based cluster analysis has not been widely used for such data, although it has a solid probabilistic foundation. Here, we introduce and illustrate its use in detecting differentially expressed genes. In particular, we do not cluster gene-expression patterns but a summary statistic, the t-statistic. RESULTS: The method is applied to a data set containing expression levels of 1,176 genes of rats with and without pneumococcal middle-ear infection. Three clusters were found, two of which contain more than 95% genes with almost no altered gene-expression levels, whereas the third one has 30 genes with more or less differential gene-expression levels. CONCLUSIONS: Our results indicate that model-based clustering of t-statistics (and possibly other summary statistics) can be a useful statistical tool to exploit differential gene expression for microarray data.},
affiliation = {Division of Biostatistics, School of Public Health, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN 55455-0378, USA. weip@biostat.umn.edu},
number = {2},
pages = {RESEARCH0009},
volume = {3},
year = {2002},
month = {Jan},
language = {eng},
keywords = {Gene Expression Profiling, Rats, Rats: Sprague-Dawley, Animals, Ear: Middle, Ear Diseases, Models: Genetic, Streptococcus pneumoniae, Oligonucleotide Array Sequence Analysis, Pneumococcal Infections, Cluster Analysis},
date-added = {2010-07-01 17:24:44 +0200},
date-modified = {2010-07-29 19:27:22 +0200},
pmid = {11864371},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Pan-2002-Genome%20Biol_Model-based%20cluster.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13227},
rating = {0}
}

@article{Purcell:2002p1623,
author = {Shaun Purcell},
journal = {Twin Res},
title = {Variance components models for gene-environment interaction in twin analysis},
abstract = {Gene-environment interaction is likely to be a common and important source of variation for complex behavioral traits. Often conceptualized as the genetic control of sensitivity to the environment, it can be incorporated in variance components twin analyses by partitioning genetic effects into a mean part, which is independent of the environment, and a part that is a linear function of the environment. The model allows for one or more environmental moderator variables (that possibly interact with each other) that may i). be continuous or binary ii). differ between twins within a pair iii). interact with residual environmental as well as genetic effects iv) have nonlinear moderating properties v). show scalar (different magnitudes) or qualitative (different genes) interactions vi). be correlated with genetic effects acting upon the trait, to allow for a test of gene-environment interaction in the presence of gene-environment correlation. Aspects and applications of a class of models are explored by simulation, in the context of both individual differences twin analysis and, in a companion paper (Purcell {\&} Sham, 2002) sibpair quantitative trait locus linkage analysis. As well as elucidating environmental pathways, consideration of gene-environment interaction in quantitative and molecular studies will potentially direct and enhance gene-mapping efforts.},
affiliation = {Social, Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, King's College, London, UK. s.purcell@iop.kcl.ac.uk},
number = {6},
pages = {554--71},
volume = {5},
year = {2002},
month = {Dec},
language = {eng},
keywords = {Models: Genetic, Computer Simulation, Twins, Genetics: Behavioral, Environment, Humans},
date-added = {2010-01-08 21:51:00 +0100},
date-modified = {2010-01-08 21:51:00 +0100},
doi = {10.1375/136905202762342026},
pmid = {12573187},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Purcell-2002-Twin%20Res_Variance%20components.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib