text:
systems biology analyses are mostly based on microarray data. Although these data often cover genome wide expression, the validity of single microarray experiments remains questionable. However, for systems biology approaches addressing the interactions of molecular networks comprehensive but also highly validated data are necessary. RESULTS: We have therefore generated the first comprehensive database for published molecular associations in human liver diseases. It is based on PubMed published abstracts and aimed to close the gap between genome wide coverage of low validity from microarray data and individual highly validated data from PubMed. After an initial text mining process, the extracted abstracts were all manually validated to confirm content and potential genetic associations and may therefore be highly trusted. All data were stored in a publicly available database, Library of Molecular Associations (http://www.medicalgenomics.org/databases/loma/news), currently holding approximately 1260 confirmed molecular associations for chronic liver diseases such as HCC, CCC, liver fibrosis, NASH/fatty liver disease, AIH, PBC, and PSC. We furthermore transformed these data into a powerful resource for molecular liver research by connecting them to multiple biomedical information resources. CONCLUSION: Together, this database is the first available database providing a comprehensive view and analysis options for published molecular associations on multiple liver diseases.},
number = {1},
pages = {189},
volume = {11},
year = {2010},
month = {Mar},
language = {ENG},
date-added = {2010-03-23 18:43:00 +0100},
date-modified = {2010-03-23 18:43:00 +0100},
doi = {10.1186/1471-2164-11-189},
pii = {1471-2164-11-189},
pmid = {20302666},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Buchkremer-2010-BMC%20Genomics_Library%20of%20molecular-1.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9371},
rating = {0}
}

@article{Jung:2007p1753,
author = {S Jung and Y Takane},
title = {Regularized Common Factor Analysis},
abstract = {In common factor analysis, estimation of unique variances by unweighted least squares (ULS), generalized least squares (GLS), and maximum likelihood (ML) often leads to improper solutions. To deal with this problem, a new estimation method of the unique variances was proposed by applying the idea of generalized ridge regularization. In regularized common factor analysis (RCFA), unique vari- ances are estimated under three alternative assumptions: 1) unique variances are constant across variables (i.e., proportional to the unit variance), 2) unique vari- ances are proportional to variances of anti-image variables, and 3) unique variances are proportional to Ihara-Kano's non-iterative estimates of unique variances. The constant of proportionality (i.e., the regularization parameter λ) is then estimated by ULS, GLS, or ML. Illustrative examples consisting of Monte Carlo studies and a real data set were given to demonstrate the usefulness of the proposed method.},
affiliation = {Department of Psychology, McGill University, 1205 Dr. Penfield Avenue, Montreal, QC, H3A 1B1, Canada},
year = {2007},
date-added = {2010-01-09 20:59:27 +0100},
date-modified = {2010-01-09 21:01:54 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Jung-2007-_Regularized%20Common%20F.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1753},
read = {Yes},
rating = {0}
}

@article{Warrens:2005p5882,
author = {M J Warrens and W J Heiser and D N M de Gruijter},
journal = {Behaviormetrika},
title = {REPARAMETRIZATION OF HOMOGENEITY ANALYSIS TO ACCOMMODATE ITEM RESPONSE FUNCTIONS},
abstract = {Two test theoretical approaches to item analysis are compared, an approach based on homogeneity analysis and one based on item response theory. The literature on the relationship between the two approaches is briefly reviewed. The paper contains a contribution to the relationship between the two approaches for the case that the scores are dichotomous and a single latent variable is assumed to underlie the data. A loss function is proposed for modelling item response functions with two parameters, one for discrimination and one for difficulty. It turns out that the loss of the proposed loss function is related to loss of homogeneity. Demonstrations with simulated data are used to evaluate the proposed method.},
number = {2},
pages = {127--139},
volume = {32},
year = {2005},
date-added = {2010-02-17 15:09:17 +0100},
date-modified = {2010-02-17 15:10:40 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Warrens-2005-Behaviormetrika_REPARAMETRIZATION%20OF.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5882},
rating = {0}
}

@article{Oeseburg:2010p10862,
author = {B Oeseburg and D E M C Jansen and G J Dijkstra and J W Groothoff and S A Reijneveld},
journal = {Res Dev Disabil},
title = {Prevalence of chronic diseases in adolescents with intellectual disability},
abstract = {Valid community-based data on the prevalence of chronic diseases in adolescents (12-18 years) with intellectual disability (ID-adolescents) are scarce. The aim of this study was to assess the prevalence rates and the nature of chronic diseases in a population of ID-adolescents and to compare them with the rates among adolescents in the general population. Therefore, we obtained data on 1083 ID-adolescents attending secondary schools, day care centers or living in residential centers fully covering one region of The Netherlands. Parents of the adolescents completed a questionnaire about the occurrence of chronic diseases in their child during the previous 12 months and about background characteristics. The questionnaire was derived from the Dutch National Permanent Survey on Living Conditions questionnaire periodically administered in a representative population sample (n approximately = 10,000). Prevalence rates of chronic diseases in ID-adolescents were compared with those in adolescents in the Dutch general population. Among ID-adolescents, high prevalence rates of a wide range of chronic diseases were found. The five most prevalent were: ADHD (21.1%), PDD-NOS (14.0%), dyslexia (13.9%), migraine or chronic headache (12.7%), and autistic disorder (10.9%). These prevalence rates were all higher (p<0.05) than among adolescents in the general population. Of all ID-adolescents, 62.9% was reported to have at least one chronic disease. The burden of chronic diseases among ID-adolescents is very high, showing a high need for adequate care. These high prevalence rates should alert policymakers and clinicians regarding the widespread of chronic diseases among ID-adolescents.},
affiliation = {Department of Health Sciences and Graduate School for Health Research (SHARE), University Medical Center Groningen, University of Groningen, The Netherlands. b.oeseburg@med.umcg.nl},
number = {3},
pages = {698--704},
volume = {31},
year = {2010},
month = {Jan},
language = {eng},
date-added = {2010-04-10 03:34:48 +0200},
date-modified = {2010-04-10 03:34:48 +0200},
doi = {10.1016/j.ridd.2010.01.011},
pii = {S0891-4222(10)00012-0},
pmid = {20188511},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Oeseburg-2010-Res%20Dev%20Disabil_Prevalence%20of%20chroni.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10862},
rating = {0}
}

@article{Tversky:1974p4681,
author = {A Tversky and D Kahneman},
journal = {Science},
title = {Judgment under uncertainty: Heuristics and biases},
pages = {1124--1131},
volume = {185},
year = {1974},
date-added = {2010-01-30 16:11:06 +0100},
date-modified = {2010-07-29 19:50:10 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Tversky-1974-Science_Judgment%20under%20uncer.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4681},
rating = {0}
}

@article{CommitteeforMedicinalProductsforHumanUse:2006p6458,
author = {Committee for Medicinal Products for Human Use and Efficacy Working Party and Committee for Release for Consultation},
journal = {Stat Med},
title = {Committee for Medicinal Products for Human Use (CHMP) guideline on the choice of the non-inferiority margin},
number = {10},
pages = {1628--38},
volume = {25},
year = {2006},
month = {May},
language = {eng},
keywords = {European Union, Confidence Intervals, Clinical Trials as Topic, Data Interpretation: Statistical, Humans, Pharmaceutical Preparations, Therapeutic Equivalency},
date-added = {2010-02-23 08:30:38 +0100},
date-modified = {2010-02-23 08:30:38 +0100},
doi = {10.1002/sim.2584},
pmid = {16639773},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Committee%20for%20Medicinal%20Products%20for%20Human%20Use-2006-Stat%20Med_Committee%20for%20Medici.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6458},
rating = {0}
}

@article{Rogers:1996,
author = {SI Rogers and LT Friedhoff},
journal = {Dementia},
title = {The efficacy and safety of donepezil in patients with Alzeihmer's Disease: results of a US multicentre, randomised, double-blind, placebo-controlled trial},
pages = {293--303},
volume = {7},
year = {1996},
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/p1084},
rating = {0}
}

@article{Fears:2009p7711,
author = {Scott C Fears and William P Melega and Susan K Service and Chris Lee and Kelly Chen and Zhuowen Tu and Matthew J Jorgensen and Lynn A Fairbanks and Rita M Cantor and Nelson B Freimer and Roger P Woods},
journal = {J Neurosci},
title = {Identifying heritable brain phenotypes in an extended pedigree of vervet monkeys},
abstract = {The area and volume of brain structural features, as assessed by high-resolution three-dimensional magnetic resonance imaging (MRI), are among the most heritable measures relating to the human CNS. We have conducted MRI scanning of all available monkeys >2 years of age (n = 357) from the extended multigenerational pedigree of the Vervet Research Colony (VRC). Using a combination of automated and manual segmentation we have quantified several correlated but distinct brain structural phenotypes. The estimated heritabilities (h(2)) for these measures in the VRC are higher than those reported previously for such features in humans or in other nonhuman primates: total brain volume (h(2) = 0.99, SE = 0.06), cerebral volume (h(2) = 0.98, SE = 0.06), cerebellar volume (h(2) = 0.86, SE = 0.09), hippocampal volume (h(2) = 0.95, SE = 0.07) and corpus callosum cross-sectional areas (h(2) = 0.87, SE = 0.07). These findings indicate that, in the controlled environment and with the inbreeding structure of the VRC, additive genetic factors account for almost all of the observed variance in brain structure, and suggest the potential of the VRC for genetic mapping of quantitative trait loci underlying such variance.},
affiliation = {Center for Neurobehavioral Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA. fears.scott@gmail.com},
number = {9},
pages = {2867--75},
volume = {29},
year = {2009},
month = {Mar},
language = {eng},
keywords = {Cerebellum, Aging, Female, Atlases as Topic, Phenotype, Corpus Callosum, Cercopithecus aethiops, Brain, Image Processing: Computer-Assisted, Male, Brain Mapping, Genetic Variation, Pedigree, Magnetic Resonance Imaging, Hippocampus, Social Dominance, Animals},
date-added = {2010-03-15 23:51:14 +0100},
date-modified = {2010-03-15 23:51:15 +0100},
doi = {10.1523/JNEUROSCI.5153-08.2009},
pii = {29/9/2867},
pmid = {19261882},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Fears-2009-J%20Neurosci_Identifying%20heritabl.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7711},
rating = {0}
}

@article{Weiss:2009p6029,
author = {Lauren A Weiss and Dan E Arking and Gene Discovery Project of Johns Hopkins {\&} the Autism Consortium and Mark J Daly and Aravinda Chakravarti},
journal = {Nature},
title = {A genome-wide linkage and association scan reveals novel loci for autism},
abstract = {Although autism is a highly heritable neurodevelopmental disorder, attempts to identify specific susceptibility genes have thus far met with limited success. Genome-wide association studies using half a million or more markers, particularly those with very large sample sizes achieved through meta-analysis, have shown great success in mapping genes for other complex genetic traits. Consequently, we initiated a linkage and association mapping study using half a million genome-wide single nucleotide polymorphisms (SNPs) in a common set of 1,031 multiplex autism families (1,553 affected offspring). We identified regions of suggestive and significant linkage on chromosomes 6q27 and 20p13, respectively. Initial analysis did not yield genome-wide significant associations; however, genotyping of top hits in additional families revealed an SNP on chromosome 5p15 (between SEMA5A and TAS2R1) that was significantly associated with autism (P = 2 x 10(-7)). We also demonstrated that expression of SEMA5A is reduced in brains from autistic patients, further implicating SEMA5A as an autism susceptibility gene. The linkage regions reported here provide targets for rare variation screening whereas the discovery of a single novel association demonstrates the action of common variants.},
affiliation = {Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.},
number = {7265},
pages = {802--8},
volume = {461},
year = {2009},
month = {Oct},
language = {eng},
keywords = {Sample Size, Chromosome Mapping, Polymorphism: Single Nucleotide, Genetic Predisposition to Disease, Chromosomes: Human: Pair 5, Brain, Membrane Proteins, Linkage (Genetics), Internationality, Humans, Nerve Tissue Proteins, Genome-Wide Association Study, Autistic Disorder},
date-added = {2010-02-19 17:00:19 +0100},
date-modified = {2010-02-19 17:00:19 +0100},
doi = {10.1038/nature08490},
pii = {nature08490},
pmid = {19812673},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6029},
rating = {0}
}

@article{Hays:2005p5495,
author = {Ron D Hays and Dennis Revicki and Karin S Coyne},
journal = {Eval Health Prof},
title = {Application of structural equation modeling to health outcomes research},
abstract = {This article provides an overview of the basic underlying principles of structural equation modeling (SEM). SEM models have two basic elements: a measurement model and a structural model. The measurement model describes the associations between the indicators (observed measures) of the latent variables, whereas the structural model delineates the direct and indirect substantive effects among latent variables and between measured and latent variables. The application of SEM to health outcomes research is illustrated using two examples: (a) assessing the equivalence of the SF-36 and patient evaluations of care for English- and Spanish-language respondents and (b) evaluating a theoretical model of health in myocardial infarction patients. The results of SEM studies can contribute to better understanding of the validity of health outcome measures and of relationships between physiologic, clinical, and health outcome variables.},
affiliation = {University of California, Los Angeles, USA. drhays@ucla.edu},
number = {3},
pages = {295--309},
volume = {28},
year = {2005},
month = {Sep},
language = {eng},
keywords = {Myocardial Infarction, Cross-Cultural Comparison, Models: Theoretical, Questionnaires, Health Status Indicators, Humans, Translations, Outcome Assessment (Health Care), Software, Models: Econometric, Psychometrics, Factor Analysis: Statistical},
date-added = {2010-02-12 14:45:16 +0100},
date-modified = {2010-02-12 14:45:18 +0100},
doi = {10.1177/0163278705278277},
pii = {28/3/295},
pmid = {16123259},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5495},
rating = {4}
}

@article{deBoer:1993p9560,
author = {J B de Boer and F S van Dam and M A Sprangers and P H Frissen and J M Lange},
journal = {AIDS},
title = {Longitudinal study on the Quality of Life of symptomatic HIV-infected patients in a trial of zidovudine versus zidovudine and interferon-alpha},
abstract = {OBJECTIVES: To compare the effect of treatment with zidovudine (ZDV) or a combination of ZDV and interferon-alpha (IFN-alpha) on patient Quality-of-Life (QoL); and to document changes over time in QoL. DESIGN: This study is part of a longitudinal, randomized, controlled clinical trial comparing the efficacy and tolerance of ZDV monotherapy and ZDV plus IFN-alpha. Patients were followed-up for 1 year. SETTING: Seven academic or general medical hospitals. PARTICIPANTS: Thirty-six symptomatic HIV-infected patients (Centers for Disease Control and Prevention stage IV) with a CD4+ count > or = 150 x 10(6)/l and Karnofsky Performance Status score > or = 60, who had not received ZDV or IFN-alpha before. METHODS: QoL was assessed using two self-report questionnaires (the European Organization for Research and Treatment of Cancer Core Quality-of-Life Questionnaire and an AIDS-specific questionnaire), administered before and every 3 months after the start of the treatment. RESULTS: There were no significant differences in QoL between the two treatment groups over a 1-year period. Emotional, cognitive and social functioning improved in the entire group, and patients reported fewer symptoms (for example, shortness of breath, nausea and vomiting, influenza-like symptoms, diarrhoea, lack of appetite, taste disturbances, dizziness, weight loss, trouble in vision) and a better overall QoL until month 9. Thereafter, emotional, cognitive and social functioning and overall QoL deteriorated and patients reported more symptoms. Major complaints at baseline and follow-up were associated with fatigue and emotional functioning: patients reported a strong need to rest, and felt very tired, worried, tense and irritable. CONCLUSIONS: These results show that both treatments may have a temporary beneficial effect on patient QoL. QoL research may contribute to evaluation of clinical trials and provide patients with information about the effects of treatment on their QoL, thus enabling them to make informed decisions.},
affiliation = {WHO Collaborating Centre on Quality of Life, The Netherlands Cancer Institute, Amsterdam.},
number = {7},
pages = {947--53},
volume = {7},
year = {1993},
month = {Jul},
language = {eng},
keywords = {Female, Quality of Life, Acquired Immunodeficiency Syndrome, Adult, Longitudinal Studies, Drug Therapy: Combination, Interferon-alpha, Humans, Patient Compliance, Demography, Patient Dropouts, Middle Aged, Questionnaires, Male, Zidovudine},
date-added = {2010-03-23 20:53:36 +0100},
date-modified = {2010-07-29 19:12:25 +0200},
pmid = {8357556},
local-url = {file://localhost/Users/chl/Dropbox/Papers/de%20Boer-1993-AIDS_Longitudinal%20study%20o.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9560},
rating = {0}
}

@article{Cordell:2006p5289,
author = {Heather J Cordell},
journal = {Genet Epidemiol},
title = {Estimation and testing of genotype and haplotype effects in case-control studies: comparison of weighted regression and multiple imputation procedures},
abstract = {A popular approach for testing and estimating genotype and haplotype effects associated with a disease outcome is to conduct a population-based case/control study, in which haplotypes are not directly observed but may be inferred probabilistically from unphased genotype data. A variety of methods exist to analyse the resulting data while accounting for the uncertainty in haplotype assignment, but most focus on the issue of testing the global null hypothesis that no genotype or haplotype effects exist. A more interesting question, once a region of disease association has been identified, is to estimate the relevant genotypic or haplotypic effects and to perform tests of complex null hypotheses such as the hypothesis that some loci, but not others, are associated with disease. Here I examine the assumptions behind, and the performance of, two classes of methods for addressing this question. The first is a weighted regression approach in which posterior probabilities of haplotype assignments are used as weights in a logistic regression analysis, generating a test based on either a weighted pseudo-likelihood, or a weighted log-likelihood. The second is a multiple imputation approach using either an improper procedure in which the posterior probabilities are used to generate replicate imputed data sets, or a proper data augmentation procedure. I compare these approaches to a simple expectation substitution (haplotype trend regression) approach. In simulations, all methods gave unbiased parameter estimation but the weighted pseudo-likelihood, expectation substitution and multiple imputation methods had superior confidence interval coverage. For the weighted pseudo-likelihood and expectation substitution methods it was necessary to estimate posterior haplotype assignment probabilities using the combined case/control data, whereas for the multiple imputation approaches it was necessary to estimate these probabilities in the case and control groups separately. Overall, multiple imputation was easiest approach to implement in standard statistical software and to extend to more complex models such as those that include gene-gene or gene-environment interactions.},
affiliation = {Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke's Hospital, Cambridge, UK. heather.cordell@cimr.cam.ac.uk},
number = {3},
pages = {259--75},
volume = {30},
year = {2006},
month = {Apr},
language = {eng},
keywords = {Case-Control Studies, Haplotypes, Humans, Odds Ratio, Genetic Techniques, Genotype, Risk},
date-added = {2010-02-09 22:28:44 +0100},
date-modified = {2010-02-09 22:28:44 +0100},
doi = {10.1002/gepi.20142},
pmid = {16496312},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5289},
rating = {0}
}

@article{Reuband:1995,
author = {KH Reuband},
journal = {European Addiction research},
title = {Drug use and drug policy in Western Europe},
pages = {32--41},
volume = {1},
year = {1995},
date-added = {2010-01-03 19:36:09 +0100},
date-modified = {2010-01-03 19:36:10 +0100},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1091},
rating = {0}
}

@article{Engelen:2010p7295,
author = {Vivian Engelen and Lotte Haverman and Hendrik Koopman and Netteke Schouten-van Meeteren and Esther Meijer-van den Bergh and Jantien Vrijmoet-Wiersma and Elisabeth Maria van Dijk and Bob Last and Symone Detmar and Martha Grootenhuis},
journal = {Patient Education and Counseling},
title = {Development and implementation of a patient reported outcome intervention (QLIC-ON PROfile) in clinical paediatric oncology practice},
abstract = {OBJECTIVE: The use of patient reported outcomes (PRO) in routine clinical practice is becoming increasingly common, but there is limited knowledge about the development and implementation of PRO. The objective of the current paper is to provide a thorough description of the development and implementation of a PRO on health related quality of life (HRQOL) - the QLIC-ON PROfile - in clinical paediatric oncology practice. METHODS: The development of the QLIC-ON PROfile is explained by elucidating important choices: the HRQOL instrument, the professional that uses the QLIC-ON PROfile, the optimal form of HRQOL feedback and whether or not a clinically important difference is reported. The description of the implementation of the QLIC-ON PROfile focuses on the education and commitment of the professional that uses the QLIC-ON PROfile. Study design and outcome measures are also elaborated on. RESULTS: Important considerations regarding the development and implementation of PRO interventions are reported. These considerations have also resulted in educational material. CONCLUSION: Our study adds to current knowledge of PRO research. This paper can be used as a practical guide for researchers and other professionals, who are interested in setting up PRO interventions in any clinical setting.},
affiliation = {Academic Medical Centre/Emma Children's Hospital, Paediatric Psychosocial Department, Amsterdam, The Netherlands.},
pages = {},
year = {2010},
month = {Feb},
language = {ENG},
date-added = {2010-03-10 20:20:13 +0100},
date-modified = {2010-07-29 19:42:37 +0200},
doi = {10.1016/j.pec.2010.02.003},
pii = {S0738-3991(10)00029-7},
pmid = {20189747},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7295},
rating = {0}
}

@article{Kang:2008p3825,
author = {Hyun Min Kang and Noah A Zaitlen and Claire M Wade and Andrew Kirby and David Heckerman and Mark J Daly and Eleazar Eskin},
journal = {Genetics},
title = {Efficient control of population structure in model organism association mapping},
abstract = {Genomewide association mapping in model organisms such as inbred mouse strains is a promising approach for the identification of risk factors related to human diseases. However, genetic association studies in inbred model organisms are confronted by the problem of complex population structure among strains. This induces inflated false positive rates, which cannot be corrected using standard approaches applied in human association studies such as genomic control or structured association. Recent studies demonstrated that mixed models successfully correct for the genetic relatedness in association mapping in maize and Arabidopsis panel data sets. However, the currently available mixed-model methods suffer from computational inefficiency. In this article, we propose a new method, efficient mixed-model association (EMMA), which corrects for population structure and genetic relatedness in model organism association mapping. Our method takes advantage of the specific nature of the optimization problem in applying mixed models for association mapping, which allows us to substantially increase the computational speed and reliability of the results. We applied EMMA to in silico whole-genome association mapping of inbred mouse strains involving hundreds of thousands of SNPs, in addition to Arabidopsis and maize data sets. We also performed extensive simulation studies to estimate the statistical power of EMMA under various SNP effects, varying degrees of population structure, and differing numbers of multiple measurements per strain. Despite the limited power of inbred mouse association mapping due to the limited number of available inbred strains, we are able to identify significantly associated SNPs, which fall into known QTL or genes identified through previous studies while avoiding an inflation of false positives. An R package implementation and webserver of our EMMA method are publicly available.},
affiliation = {Department of Computer Science, University of California, Los Angeles, California 90095-1596, USA.},
number = {3},
pages = {1709--23},
volume = {178},
year = {2008},
month = {Mar},
language = {eng},
keywords = {Chromosome Mapping, Mice: Inbred Strains, Saccharin, Models: Biological, Models: Genetic, Quantitative Trait: Heritable, Phenotype, Body Weight, Polymorphism: Single Nucleotide, Mice, Organ Size, Zea mays, Population Dynamics, Software, Animals, Genome, Inbreeding, Arabidopsis, Flowers},
date-added = {2010-01-16 21:01:44 +0100},
date-modified = {2010-01-16 21:01:44 +0100},
doi = {10.1534/genetics.107.080101},
pii = {178/3/1709},
pmid = {18385116},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3825},
rating = {0}
}

@article{Rudas:2004p13780,
author = {T Rudas and W Bergsma},
journal = {METRON - International Journal of Statistics},
title = {On applications of marginal models for categorical data},
abstract = {The paper considers marginal models for categorical data and after review- ing the most important theoretical results concerning the definition, estimation and testing of such models, discusses a number of common statistical problems. These examples include, among others, the analysis of repeated measurements, panel studies and missing data. Fitting marginal models in these cases has the potential of pro- viding the researcher with substantial new insight. The examples illustrate that the marginal modeling approach may be used more widely than thought before. One of the examples shows how graphical models associated with directed acyclic graphs can be parameterized. A general algorithm is presented to compute maximum likelihood estimates under marginal models.},
number = {1},
volume = {LXII},
year = {2004},
date-added = {2010-07-28 23:10:57 +0200},
date-modified = {2010-07-28 23:12:02 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Rudas-2004-METRON%20-%20International%20Journal%20of%20Statistics_On%20applications%20of%20m.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13780},
rating = {0}
}

@article{Alvord:1988p6684,
author = {W G Alvord and J E Drummond and L O Arthur and R J Biggar and J J Goedert and P H Levine and E L Murphy and S H Weiss and W A Blattner},
journal = {AIDS Res Hum Retroviruses},
title = {A method for predicting individual HIV infection status in the absence of clinical information},
abstract = {Latent structure analysis can be used to determine sensitivity and specificity rates of human immunodeficiency virus antibody assays in the absence of previous clinical or laboratory results. The technique was applied to the analysis of data obtained when a panel of serum samples, collected as part of a large-scale screening project, were subjected to four conventional bioassays (ag121, p24, gp120, and an enzyme-linked immunosorbent assay). To determine the accuracy of this statistical approach, the results of latent structure analysis were compared with the known clinical diagnoses of patients from whom the samples were taken, and nearly 100% agreement was obtained. Although a two-class latent structure model had some predictive value, a three-class model more adequately explained assay patterns. The use of the four standard assays in conjunction with the statistical methods described here would largely reduce the need for confirmatory Western blot assays in analyses of large panels of samples.},
affiliation = {Data Management Services, National Cancer Institute-Frederick Cancer Research Facility, MD 21701.},
number = {4},
pages = {295--304},
volume = {4},
year = {1988},
month = {Aug},
language = {eng},
keywords = {HIV Seropositivity, Models: Statistical, Acquired Immunodeficiency Syndrome, AIDS Serodiagnosis, Humans, Radioimmunoassay, False Positive Reactions, Enzyme-Linked Immunosorbent Assay, False Negative Reactions},
date-added = {2010-03-05 22:07:58 +0100},
date-modified = {2010-03-05 22:07:59 +0100},
pmid = {3207513},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6684},
rating = {0}
}

@article{Pollard:2008p3588,
author = {K S Pollard and M J van der Laan},
journal = {U.C. Berkeley Division of Biostatistics Working Paper Series},
title = {Supervised Distance Matrices: Theory and Applications to Genomics},
abstract = {We propose a new approach to studying the relationship between a very high di- mensional random variable and an outcome. Our method is based on a novel con- cept, the supervised distance matrix, which quantifies pairwise similarity between variables based on their association with the outcome. A supervised distance ma- trix is derived in two stages. The first stage involves a transformation based on a particular model for association. In particular, one might regress the outcome on each variable and then use the residuals or the influence curve from each regres- sion as a data transformation. In the second stage, a choice of distance measure is used to compute all pairwise distances between variables in this transformed data. When the outcome is right-censored, we show that the supervised distance ma- trix can be consistently estimated using inverse probability of censoring weighted (IPCW) estimators based on the mean and covariance of the transformed data. The proposed methodology is illustrated with examples of gene expression data analysis with a survival outcome. This approach is widely applicable in genomics and other fields where high-dimensional data is collected on each subject.},
number = {238},
year = {2008},
date-added = {2010-01-15 21:14:20 +0100},
date-modified = {2010-07-29 19:55:06 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Pollard-2008-U.C.%20Berkeley%20Division%20of%20Biostatistics%20Working%20Paper%20Series_Supervised%20Distance.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3588},
rating = {0}
}

@article{Chachamovich:2007p3413,
author = {J R Chachamovich and E Chachamovich and S Zachia and D Knauth and E P Passos},
journal = {Hum Reprod},
title = {What variables predict generic and health-related quality of life in a sample of Brazilian women experiencing infertility?},
abstract = {BACKGROUND: Infertility is a condition associated with impairment in several areas of life. Questionnaires about quality of life (QoL) allow the examination of the impact of health conditions in a broader way, comprehending outcomes beyond symptomatology, morbidity and mortality. The aim of this study was to identify factors associated with various aspects of QoL. METHODS: Cross-sectional study using the following: a socio-demographic and clinical data form, the Health Survey Short Form (SF-36) which examines health-related QoL and the WHOQOL-BREF which examines general QoL. RESULTS: 177 women seeking fertility assistance were interviewed. The sample was predominantly composed of women between 30 and 40 years old (64%), who had known about their infertility for <5 years (57%) and who had had no previous attempts at assisted reproduction (79%). Logistic regression indicated the following predictor variables: age (for better general health and physical functioning), previous in vitro fertilization (for lower vitality and poor psychological health scores), previous reproductive tract surgery (for worse general health but higher environment scores), advanced education (for higher vitality, mental health and environment scores, but for worse social relationships) and perception of worse sexual life (for lower overall scores). CONCLUSIONS: The identification of factors associated with better or worse QoL, in its different domains, is vital in order to propose and test scientifically based interventions on infertile women.},
affiliation = {Assisted Reproduction Service, Embryology and Genetics Laboratory, Gynecology and Obstetrics Department, Hospital de Clinicas de Porto Alegre, RS, and Federal University of Rio Grande do Sul, Brazil. jurigol@terra.com.br},
number = {7},
pages = {1946--52},
volume = {22},
year = {2007},
month = {Jul},
language = {eng},
keywords = {Humans, Infertility, Health Status, Adult, Treatment Outcome, Questionnaires, Quality of Life, Odds Ratio, Female, Regression Analysis, Cross-Sectional Studies, Brazil, Sickness Impact Profile, Health Surveys},
date-added = {2010-01-15 14:49:11 +0100},
date-modified = {2010-01-15 14:49:11 +0100},
doi = {10.1093/humrep/dem080},
pii = {dem080},
pmid = {17428881},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Chachamovich-2007-Hum%20Reprod_What%20variables%20predi.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3413},
rating = {0}
}

@article{Vermunt:2001,
author = {J K Vermunt},
journal = {Applied Psychological Measurement},
title = {The use restricted latent class models for defining and testing nonparametric and parame tric IRT models},
pages = {283--294},
volume = {25},
year = {2001},
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/Vermunt-2001-Applied%20Psychological%20Measurement_The%20use%20restricted%20l.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2101},
rating = {0}
}

@article{Thomas:2008p4064,
author = {Duncan C Thomas and James W Baurley and Elizabeth E Brown and Jane C Figueiredo and Alisa Goldstein and Aditi Hazra and Robin T Wilson and Nathaniel Rothman and American Association for Cancer Research},
journal = {Cancer Res},
title = {Approaches to complex pathways in molecular epidemiology: summary of a special conference of the American Association for Cancer Research},
affiliation = {Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089-9011, USA. dthomas@usc.edu},
number = {24},
pages = {10028--30},
volume = {68},
year = {2008},
month = {Dec},
language = {eng},
keywords = {Animals, Humans, Molecular Epidemiology, Neoplasms},
date-added = {2010-01-19 15:48:08 +0100},
date-modified = {2010-01-19 15:48:08 +0100},
doi = {10.1158/0008-5472.CAN-08-1690},
pii = {68/24/10028},
pmid = {19074865},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Thomas-2008-Cancer%20Res_Approaches%20to%20comple.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4064},
rating = {0}
}

@article{Gargus:2005p6163,
author = {Regina A Gargus and Yvette Yatchmink},
journal = {Med Health R I},
title = {Early identification and assessment of young children with autism},
affiliation = {Hasbro Children's Hospital, Providence, RI 02903, USA.},
number = {5},
pages = {147--51},
volume = {88},
year = {2005},
month = {May},
language = {eng},
keywords = {Mass Screening, Child, Humans, Child Development, Autistic Disorder},
date-added = {2010-02-19 20:19:14 +0100},
date-modified = {2010-02-19 20:19:14 +0100},
pmid = {16052956},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Gargus-2005-Med%20Health%20R%20I_Early%20identification.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6163},
rating = {0}
}

@article{Kirby:2010p5081,
author = {Amanda Kirby and Lisa Edwards and David Sugden and Sara Rosenblum},
journal = {Res Dev Disabil},
title = {The development and standardization of the Adult Developmental Co-ordination Disorders/Dyspraxia Checklist (ADC)},
abstract = {Developmental Co-ordination Disorder (DCD), also known as Dyspraxia in the United Kingdom (U.K.), is a developmental disorder affecting motor co-ordination. In the past this was regarded as a childhood disorder, however there is increasing evidence that a significant number of children will continue to have persistent difficulties into adulthood. Despite this, there remains little information as to how the difficulties might present at this stage, and additionally the impact on every day functioning. As young people move into further and higher education there is a need for screening and assessment tools. Such tools allow for identification of these difficulties, access to support, and clarification of areas where appropriate support needs to be targeted. This paper describes the first adult screening tool for DCD. The development and the results from testing this tool in two countries, Israel and the U.K. are outlined and the implications for its use in further and higher education discussed.},
affiliation = {The Dyscovery Centre, Allt-yr-yn Campus, University of Wales, Newport, UK. amanda.kirby@newport.ac.uk},
number = {1},
pages = {131--9},
volume = {31},
year = {2010},
month = {Jan},
language = {eng},
keywords = {Male, Disability Evaluation, Female, Israel, Humans, Mass Screening, Activities of Daily Living, Psychometrics, Adolescent, Apraxias, Handwriting, Young Adult, Cross-Cultural Comparison, Reference Values, Great Britain, Adult, Questionnaires, Motor Skills Disorders},
date-added = {2010-02-05 20:16:33 +0100},
date-modified = {2010-02-05 20:16:33 +0100},
doi = {10.1016/j.ridd.2009.08.010},
pii = {S0891-4222(09)00143-7},
pmid = {19819107},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5081},
rating = {0}
}

@book{Oppenheim:1992,
author = {AN Oppenheim},
journal = {Book},
title = {Questionnaire design, interviewing and attitude measurement},
year = {1992},
date-added = {2010-01-03 19:34:17 +0100},
date-modified = {2010-07-29 19:21:41 +0200},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p953},
rating = {0}
}

@article{Dominicus:2006p5216,
author = {Annica Dominicus and Anders Skrondal and H{\aa}kon K Gjessing and Nancy L Pedersen and Juni Palmgren},
journal = {Behav Genet},
title = {Likelihood ratio tests in behavioral genetics: problems and solutions},
abstract = {The likelihood ratio test of nested models for family data plays an important role in the assessment of genetic and environmental influences on the variation in traits. The test is routinely based on the assumption that the test statistic follows a chi-square distribution under the null, with the number of restricted parameters as degrees of freedom. However, tests of variance components constrained to be non-negative correspond to tests of parameters on the boundary of the parameter space. In this situation the standard test procedure provides too large p-values and the use of the Akaike Information Criterion (AIC) or the Bayesian Information Criterion (BIC) for model selection is problematic. Focusing on the classical ACE twin model for univariate traits, we adapt existing theory to show that the asymptotic distribution for the likelihood ratio statistic is a mixture of chi-square distributions, and we derive the mixing probabilities. We conclude that when testing the AE or the CE model against the ACE model, the p-values obtained from using the chi(2)(1 df) as the reference distribution should be halved. When the E model is tested against the ACE model, a mixture of chi(2)(0 df), chi(2)(1 df) and chi(2)(2 df) should be used as the reference distribution, and we provide a simple formula to compute the mixing probabilities. Similar results for tests of the AE, DE and E models against the ADE model are also derived. Failing to use the appropriate reference distribution can lead to invalid conclusions.},
affiliation = {Department of Mathematics, Stockholm University, Stockholm, Sweden. annicad@math.su.se},
number = {2},
pages = {331--40},
volume = {36},
year = {2006},
month = {Mar},
language = {eng},
keywords = {Twin Studies as Topic, Analysis of Variance, Models: Genetic, Genotype, Chi-Square Distribution, Humans, Bayes Theorem, Social Environment, Probability, Genetics: Behavioral, Likelihood Functions},
date-added = {2010-02-08 19:29:05 +0100},
date-modified = {2010-07-29 20:09:06 +0200},
doi = {10.1007/s10519-005-9034-7},
pmid = {16474914},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5216},
rating = {0}
}

@article{Storkey:2010p6301,
author = {A J Storkey and E Simonotto and H Whalley and S Lawrie and L Murray and D McGonigle},
title = {Learning Structural Equation Models for fMRI},
abstract = {Structural equation models can be seen as an extension of Gaussian belief net- works to cyclic graphs, and we show they can be understood generatively as the model for the joint distribution of long term average equilibrium activity of Gaus- sian dynamic belief networks. Most use of structural equation models in fMRI involves postulating a particular structure and comparing learnt parameters across different groups. In this paper it is argued that there are situations where priors about structure are not firm or exhaustive, and given sufficient data, it is worth investigating learning network structure as part of the approach to connectivity analysis. First we demonstrate structure learning on a toy problem. We then show that for particular fMRI data the simple models usually assumed are not supported. We show that is is possible to learn sensible structural equation models that can provide modelling benefits, but that are not necessarily going to be the same as a true causal model, and suggest the combination of prior models and learning or the use of temporal information from dynamic models may provide more benefits than learning structural equations alone.},
date-added = {2010-02-20 20:14:45 +0100},
date-modified = {2010-02-20 20:15:39 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Storkey--_Learning%20Structural.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6301},
rating = {0}
}

@article{Marquis:1986,
author = {KH Marquis and MS Marquis and JM Polich},
journal = {JAMA},
title = {Response bias and reliability in sensitive topic surveys},
abstract = {This discussion focuses on a reexamination of empirical evidence on the direction and size of response biases and estimates of the variance of the response error distributions for sensitive topics (receipt of welfare, income, alcohol use, drug use, criminal history, and embarrassing medical conditions). Partial or unidirectional record check studies are used as evidence of underreporting on specific topics. The estimates suggest that response biases are not uniformly negative but center around zero. Unreliability as measured in response error variance estimates appears to be very high. A response model based on classical test theory and other studies of Hansen, Hurwitz, and Bershad, and Hansen, Hurwitz, and Pritzer is presented. A review is given of empirical studies which estimate response error parameters. Estimates of response bias and error variance are given with a discussion of implications for methodological research and survey design. The conclusion in this review of the literature on response bias and reliability is that modeling of design features and response errors is not possible. There is no apparent link between features such as length of recall period, respondent rules, mode of data collection, working of survey questions, and rules for matching the survey and criterion sources. The results of the review for income show that income studies and welfare studies have a net response bias close to zero or no bias. In the income studies, other sources of potential estimation error from sampling, definitions, treatment of missing observations may cause survey estimates to be less than estimates made from administrative records. The drug and alcohol estimates are more disperse but still are not negative. For example, in the comparison of drug self-reports to urine test reports, 50% of studies show negative estimates, and 50% show positive estimates. Net bias estimates of crime data tend to be positive. For socially embarrassing problems (mental illness, hemorrhoids, and diseases of the genitourinary tract system), the large average response bias estimates are mostly negative, which may be due to poor questionnaire design. Only income estimates are higher than the accepted value of 70%, which means techniques should be used to overcome the bias of random measurement error.},
number = {394},
pages = {381--389},
volume = {81},
year = {1986},
date-added = {2010-01-03 19:34:17 +0100},
date-modified = {2010-07-29 20:01:35 +0200},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p973},
rating = {0}
}

@article{Jelizarow:2010p11610,
author = {M Jelizarow and V Guillemot and A Tenenhaus and K strimmer and A-L Boulesteix},
title = {Over-optimism in bioinformatics: an illustration},
abstract = {In statistical bioinformatics research, different optimization mechanisms potentially lead to ``over-optimism'' in published papers. The present empirical study illustrates these mechanisms through a concrete example from an active research field. The investigated sources of over-optimism include the optimization of the data sets, of the settings, of the competing methods and, most importantly, of the method's characteristics.
We consider a ``promising'' new classification algorithm that turns out to yield disappointing results in terms of error rate, namely linear discriminant analysis incorporating prior knowledge on gene functional groups through an appropriate shrinkage of the within-group covariance matrix. We quantitatively demonstrate that this disappointing method can artificially seem superior to existing approaches if we ``fish for significance''. We conclude that, if the improvement of a quantitative criterion such as the error rate is the main contribution of a paper, the superiority of new algorithms should be validated using ``fresh'' validation data sets.
The R codes and preprocessed versions of the data sets as well as additional files can be downloaded from http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/020− professuren/boulesteix/overoptimism/, such that the study is completely reproducible.},
number = {81},
year = {2010},
date-added = {2010-05-11 21:38:39 +0200},
date-modified = {2010-05-11 21:40:07 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Jelizarow-2010-_Over-optimism%20in%20bio.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11610},
rating = {0}
}

@article{Wickham:2009p488,
author = {Hadley Wickham and Michael Lawrence and Dianne Cook and Andreas Buja and Heike Hofmann and Deborah F Swayne},
journal = {Computational Statistics},
title = {The plumbing of interactive graphics},
abstract = {What is a pipeline, and why do we need one for interactive graphics? This conceptual paper attempts to answer these questions, building on previous work. A pipeline controls the transformation from data to graphical objects on our screens, and we argue that the pipeline must be present, in some form, in all graphics software. The pipeline is made explicit in descendants of DataViewer.},
affiliation = {Iowa State University, Ames, IA, USA},
pages = {207--215},
volume = {24},
year = {2009},
keywords = {dsc 2007, Interactive graphics, Pipeline},
date-added = {2010-01-03 12:38:36 +0100},
date-modified = {2010-07-29 19:24:32 +0200},
doi = {10.1007/s00180-008-0116-x},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Wickham-2009-Computational%20Statistics_The%20plumbing%20of%20inte.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p488},
rating = {0}
}

@article{Tairyan:2009p8813,
author = {K Tairyan and J Illes},
journal = {Neuroscience},
title = {Imaging genetics and the power of combined technologies: a perspective from neuroethics},
abstract = {Imaging genetics has emerged as a powerful and sensitive approach to the study of functional genetic variations and brain responses in psychiatric and neurologic disorders. Ethics issues in contemporary neuroscience as they apply separately to genetics and neuroimaging have been a growing focus for research but, to date, there has not yet been a rigorous exploration of the ethical dimensions of the territory in which they overlap. Here we propose that the ethics challenges associated with the combination of these methods call for an expanded "neuro-space" in which societal and ethical values are closely and explicitly integrated with the new science. We build specifically on the model delivered by Roffman et al. [Roffman JL, Weiss AP, Goff DC, Rauch SL, Weinberger DR (2006) Neuroimaging-genetic paradigms: a new approach to investigate the pathophysiology and treatment of cognitive deficits in schizophrenia. Harv Rev Psychiatry 14:78-91] for neuroimaging, and develop the argument that the ethics issues parallel the heightened discriminative and cumulative power of imaging genetics. In the new combined space, features of discriminative power concern better differentiation of disease, sometimes by ethnicity, and incidental findings. Clinical utility, prediction and intervention, and stigma and labeling reflect a common ground between discriminative and cumulative power. Privacy, autonomy, response sensitivity and attitudes, resource allocation for research and for health care, and commercialization, are features of cumulative power. Parallel to the clinical features highlighted in the Roffman et al. map, the combined space yields additional neuroethics features. These are characterized by new knowledge and new implications for health care, justice, and policy. We conclude by examining these features in the context of public health at the interface of emerging new neurotechnologies.},
affiliation = {National Core for Neuroethics, The University of British Columbia, Vancouver, BC, Canada.},
number = {1},
pages = {7--15},
volume = {164},
year = {2009},
month = {Nov},
language = {eng},
keywords = {Public Health, Neurology, Humans, Genetic Techniques, Psychiatry, Genetics},
date-added = {2010-03-22 12:13:47 +0100},
date-modified = {2010-03-22 12:13:47 +0100},
doi = {10.1016/j.neuroscience.2009.01.052},
pii = {S0306-4522(09)00112-2},
pmid = {19409220},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Tairyan-2009-Neuroscience_Imaging%20genetics%20and.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8813},
read = {Yes},
rating = {0}
}

@article{Nestor:2010p9588,
author = {Liam Nestor and Robert Hester and Hugh Garavan},
journal = {Neuroimage},
title = {Increased ventral striatal BOLD activity during non-drug reward anticipation in cannabis users},
abstract = {Despite an increased understanding of the pharmacology and long-term cognitive effects of cannabis in humans, there has been no research to date examining its chronic effects upon reward processing in the brain. Motivational theories regarding long-term drug use posit contrasting predictions with respect to how drug users are likely to process non-drug incentives. The reward deficiency syndrome (RDS) of addiction posits that there are deficits in dopamine (DA) motivational circuitry for non-drug rewards, such that only drugs of abuse are capable of normalizing DA in the ventral striatum (VS). Alternatively, the opponent process theory (OPT) holds that in individuals prone to drug use, there exists some form of mesolimbic hyperactivity, in which there is a bias towards reward-centred behaviour concomitant with impulsivity. The current study examined BOLD responses during reward and loss anticipation and their outcome deliveries in 14 chronic cannabis users and 14 drug-naive controls during a monetary incentive delay (MID) task. Despite no significant behavioural differences between the two groups, cannabis users had significantly more right VS BOLD activity during reward anticipation. Correlation analyses demonstrated that this right VS BOLD response was significantly correlated with life-time use and reported life-time cannabis joints consumed. No correlations between cannabis abstinence and BOLD responses were observed. We also observed a number of group differences following outcome deliveries, most notably hypoactivity in the left insula cortex in response to loss and loss avoidance outcome notifications in the cannabis group. These results may suggest hypersensitivity during instrumental response anticipation for non-drug rewards and a hyposensitivity to loss outcomes in chronic cannabis users; the implications of which are discussed with respect to the potentially sensitizing effects of cannabis for other rewards.},
affiliation = {School of Psychology and Institute of Neuroscience, Trinity College Dublin, Ireland. lnestor@mednet.ucla.edu},
number = {1},
pages = {1133--43},
volume = {49},
year = {2010},
month = {Jan},
language = {eng},
keywords = {Dopamine, Limbic System, Adult, Substance Withdrawal Syndrome, Male, Marijuana Abuse, Oxygen, Putamen, Female, Reward, Cannabis, Magnetic Resonance Imaging, Cues, Humans, Young Adult, Motivation, Neostriatum, Image Processing: Computer-Assisted},
date-added = {2010-03-25 14:09:38 +0100},
date-modified = {2010-03-25 14:09:38 +0100},
doi = {10.1016/j.neuroimage.2009.07.022},
pii = {S1053-8119(09)00792-7},
pmid = {19631753},
URL = {http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNP-4WV15PV-4&_user=2432700&_coverDate=01%252F01%252F2010&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000057263&_version=1&_urlVersion=0&_userid=2432700&md5=b55c15605b7f87bd17984ed027696c46},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Nestor-2010-Neuroimage_Increased%20ventral%20st.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9588},
rating = {0}
}

@article{Fisher:1999p5857,
author = {W P Fisher},
journal = {J La State Med Soc},
title = {Foundations for health status metrology: the stability of MOS SF-36 PF-10 calibrations across samples},
abstract = {Interest in applying probabilistic conjoint measurement (PCM) models, such as those devised by the late Georg Rasch, to health status and quality of life data has grown significantly in the last few years. Applications have yet, however, to fully realize the opportunities for scientific generalization and practical convenience PCM offers. This article fleshes out the substance of some of these opportunities by comparing eight separate PCM calibrations of the SF-36 ten-item physical functioning scale (PF-10). The initial average correlation across the 28 pairs of calibrations is .84; after taking advantage of the PCM model's capacity to account for missing data by omitting from the comparisons items that vary due to sample idiosyncracies, the average correlation is .90. Opportunities for, and limitations on, generalization from PF-10 measures are explored.},
affiliation = {Department of Biometry {\&} Genetics, Louisiana State University Medical Center, New Orleans, USA.},
number = {11},
pages = {566--78},
volume = {151},
year = {1999},
month = {Nov},
language = {eng},
keywords = {Calibration, Humans, Activities of Daily Living, Health Status Indicators, Models: Statistical, Disability Evaluation},
date-added = {2010-02-17 15:00:51 +0100},
date-modified = {2010-02-23 08:13:38 +0100},
pmid = {10618861},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5857},
rating = {4}
}

@article{Sinharay:2003p4257,
author = {S Sinharay and M S Johnson},
title = {Simulation studies: Applying posterior predictive model checking for assessing fit of the common item response theory models},
year = {2003},
date-added = {2010-01-23 21:05:04 +0100},
date-modified = {2010-01-23 21:06:00 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Sinharay-2003-_Simulation%20studies.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4257},
rating = {0}
}

@article{Hardouin:2008p1819,
author = {J B Hardouin and V S{\'e}bille},
title = {Comparison of sixteen methods for handling missing data in the framework of Patients Reported Outcomes},
year = {2008},
date-added = {2010-01-09 22:57:36 +0100},
date-modified = {2010-01-09 22:58:02 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hardouin-2008-_Comparison%20of%20sixtee.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1819},
rating = {0}
}

@article{Cilibrasi:2005p3495,
author = {R Cilibrasi and P M B Vitanyi},
journal = {IEEE TRANSACTIONS ON INFORMATION THEORY},
title = {Clustering by Compression},
abstract = {We present a new method for clustering based on compression. The method doesn't use subject-specific features or background knowledge, and works as follows: First, we determine a parameter-free, universal, similarity distance, the normalized compression distance or NCD , computed from the lengths of compressed data files (singly and in pairwise concatenation). Second, we apply a hierarchical clustering method. The NCD is not restricted to a specific application area, and works across application area boundaries. A theoretical precursor, the normal- ized information distance, co-developed by one of the authors, is provably optimal. However, the optimality comes at the price of using the non-computable notion of Kolmogorov complexity. We propose axioms to capture the real-world setting, and show that the NCD approximates optimality. To extract a hierarchy of clusters from the distance matrix, we determine a dendrogram (binary tree) by a new quartet method and a fast heuristic to implement it. The method is implemented and available as public software, and is robust under choice of different compressors. To substantiate our claims of universality and robustness, we report evidence of successful application in areas as diverse as genomics, virology, languages, literature, music, handwritten digits, astronomy, and combinations of objects from completely different domains, using statistical, dictionary, and block sorting compressors. In genomics we presented new evidence for major questions in Mammalian evolution, based on whole-mitochondrial genomic analysis: the Eutherian orders and the Marsupionta hypothesis against the Theria hypothesis.},
number = {4},
pages = {1523--1545},
volume = {51},
year = {2005},
date-added = {2010-01-15 15:22:36 +0100},
date-modified = {2010-01-15 15:26:02 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Cilibrasi-2005-IEEE%20TRANSACTIONS%20ON%20INFORMATION%20THEORY_Clustering%20by%20Compre.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3495},
rating = {0}
}

@article{Cumming:2001,
author = {G Cumming and S Finch},
journal = {Educational and Psychological Measurement},
title = {A primer on the understanding, use and calculation of confidence intervals that are based on central and noncentral distributions},
pages = {532--575},
volume = {61},
year = {2001},
date-added = {2010-01-10 11:33:21 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2028},
rating = {0}
}

@article{Rodgers:1988p2307,
author = {J L Rodgers and W A Nicewander},
journal = {The American Statistician},
title = {Thirteen Ways to Look at the Correlation Coefficient},
abstract = {In 1885, Sir Francis Galton first defined the term "regression" and completed the theory of bivariate correlation. A decade later, Karl Pearson developed the index that we still use to measure correlation, Pearson's r . Our article is written in recognition of the 100th anniversary of Galton's first discussion of regression and correlation. We begin with a brief history. Then we present 13 different formulas, each of which represents a different computational and conceptual definition of r. Each formula suggests a different way of thinking about this index, from algebraic, geometric, and trigonometric settings. We show that Pearson's r (or simple functions of r ) may variously be thought of as a special type of mean, a special type of variance, the ratio of two means, the ratio of two variances, the slope of a line, the cosine of an angle, and the tangent to an ellipse, and may be looked at from several other interesting perspectives.},
number = {1},
pages = {59--66},
volume = {42},
year = {1988},
date-added = {2010-01-10 12:20:50 +0100},
date-modified = {2010-01-10 12:21:58 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Rodgers-1988-The%20American%20Statistician_Thirteen%20Ways%20to%20Loo.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2307},
rating = {0}
}

@article{Bajari:2007p3604,
author = {P Bajari and J T Fox and S P Ryan},
title = {Linear regression estimation of discrete choice models with nonparametric distributions of random coefficients},
year = {2007},
date-added = {2010-01-15 21:44:52 +0100},
date-modified = {2010-01-15 21:46:00 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bajari-2007-_Linear%20regression%20es.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3604},
rating = {0}
}

@article{Miles:1998p9159,
author = {D R Miles and M C Stallings and S E Young and J K Hewitt and T J Crowley and D W Fulker},
journal = {Drug Alcohol Depend},
title = {A family history and direct interview study of the familial aggregation of substance abuse: the adolescent substance abuse study},
abstract = {The adolescent substance abuse (ASA) study collected information concerning drug use and psychopathology on male adolescent probands in treatment for substance abuse and also on matched control adolescents, as well as all available family members of both groups. Information was obtained through direct interview and the family history method of assessment. Both methods revealed greater alcohol and drug use, conduct disorder (CD) and antisocial personality disorder (ASP) in the relatives of treatment probands as compared with control relatives. These results suggest familial transmission, not only for alcohol abuse, but also for non-alcohol substance abuse. Familial transmission for CD and ASP is also evident for both male and female relatives, although the prevalence of these disorders is significantly greater in males than females.},
affiliation = {Institute for Behavioral Genetics, University of Colorado, Boulder, 80309, USA.},
number = {2},
pages = {105--14},
volume = {49},
year = {1998},
month = {Jan},
language = {eng},
keywords = {Case-Control Studies, Sensitivity and Specificity, Substance-Related Disorders, Chi-Square Distribution, Adult, Middle Aged, Prevalence, Family Health, Antisocial Personality Disorder, Residential Treatment, Family, Male, Adolescent, Sex Factors, Female, Analysis of Variance, Humans, Comorbidity, Conduct Disorder, Colorado},
date-added = {2010-03-22 13:35:07 +0100},
date-modified = {2010-03-22 13:35:08 +0100},
pii = {S0376-8716(97)00156-7},
pmid = {9543647},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Miles-1998-Drug%20Alcohol%20Depend_A%20family%20history%20and.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9159},
rating = {0}
}

@article{Boulesteix:2007p315,
author = {Anne-Laure Boulesteix and Korbinian Strimmer},
journal = {Brief Bioinformatics},
title = {Partial least squares: a versatile tool for the analysis of high-dimensional genomic data},
abstract = {Partial least squares (PLS) is an efficient statistical regression technique that is highly suited for the analysis of genomic and proteomic data. In this article, we review both the theory underlying PLS as well as a host of bioinformatics applications of PLS. In particular, we provide a systematic comparison of the PLS approaches currently employed, and discuss analysis problems as diverse as, e.g. tumor classification from transcriptome data, identification of relevant genes, survival analysis and modeling of gene networks and transcription factor activities.},
affiliation = {Department of Medical Statistics and Epidemiology, Technical University of Munich, Ismaningerstrasse 22, D-81675 Munich, Germany. anne-laure.boulesteix@tum.de},
number = {1},
pages = {32--44},
volume = {8},
year = {2007},
month = {Jan},
language = {eng},
keywords = {Models: Statistical, Data Interpretation: Statistical, Least-Squares Analysis, Humans, Computational Biology, Multivariate Analysis, Survival Analysis, Genomics, Software, Animals},
date-added = {2010-01-03 11:44:47 +0100},
date-modified = {2010-01-03 11:44:47 +0100},
doi = {10.1093/bib/bbl016},
pii = {bbl016},
pmid = {16772269},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Boulesteix-2007-Brief%20Bioinformatics_Partial%20least%20square.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p315},
rating = {0}
}

@article{Mccrae:2005p11170,
author = {R R Mccrae and A Terracciano},
journal = {J Pers Soc Psychol},
title = {Personality Profiles of Cultures: Aggregate Personality Traits},
abstract = {Personality profiles of cultures can be operationalized as the mean trait levels of culture members. College students from 51 cultures rated an individual from their country whom they knew well (N 􏰀 12,156). Aggregate scores on Revised NEO Personality Inventory (NEO-PI-R) scales generalized across age and sex groups, approximated the individual-level 5-factor model, and correlated with aggregate self-report personality scores and other culture-level variables. Results were not attributable to national differences in economic development or to acquiescence. Geographical differences in scale variances and mean levels were replicated, with Europeans and Americans generally scoring higher in Extraversion than Asians and Africans. Findings support the rough scalar equivalence of NEO-PI-R factors and facets across cultures and suggest that aggregate personality profiles provide insight into cultural differences.},
number = {3},
pages = {407--425},
volume = {89},
year = {2005},
date-added = {2010-04-25 21:17:33 +0200},
date-modified = {2010-07-29 19:35:33 +0200},
doi = {10.1037/0022-3514.89.3.407},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Mccrae-2005-J%20Pers%20Soc%20Psychol_Personality%20Profiles.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11170},
rating = {4}
}

@article{Huopaniemi:2010p12338,
author = {I Huopaniemi and T Suvitaival and J Nikkil{\"a} and M Oresic and S Kaski},
journal = {Bioinformatics},
title = {Multivariate multi-way analysis of multi-source data},
abstract = {Motivation: Analysis of variance (ANOVA)-type methods are the default tool for the analysis of data with multiple covariates. These tools have been generalized to the multivariate analysis of high- throughput biological datasets, where the main challenge is the problem of small samplesize and high dimensionality. However, the existing multi-way analysis methods are not designed for the currently increasingly important experiments where data is obtained from multiple sources. Common examples of such settings include integrated analysis of metabolic and gene expression profiles, or metabolic profiles from several tissues in our case, in a controlled multi-way experimental setup where disease status, medical treatment, gender and time-series are usual covariates. Results: We extend the applicability area of multivariate, multi-way ANOVA-type methods to multi-source cases by introducing a novel Bayesian model. The method is capable of finding covariate-related dependencies between the sources. It assumes the measurements consist of groups of similarly behaving variables, and estimates the multivariate covariate effects and their interaction effects for the discovered groups of variables. In particular, the method partitions the effects to those shared between the sources and to source- specific ones. The method is specifically designed for datasets with small sample sizes and high dimensionality.
We apply the method to a lipidomics dataset from a lung cancer study with two-way experimental setup, where measurements from several tissues with mostly distinct lipids have been taken. The method is also directly applicable to gene expression and proteomics.},
pages = {i391--i398},
volume = {26},
year = {2010},
date-added = {2010-06-12 10:17:49 +0200},
date-modified = {2010-06-12 10:20:34 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Huopaniemi-2010-Bioinformatics_Multivariate%20multi-w.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12338},
rating = {4}
}

@article{Mora:2008p7760,
author = {F Mora and M C Gon{\c c}alves-Vidigal and A I Santos},
journal = {CHILEAN JOURNAL OF AGRICULTURAL RESEARCH},
title = {BAYESIAN ANALYSIS OF THE GENETIC CONTROL OF SURVIVAL IN F3 FAMILIES OF COMMON BEAN},
abstract = {The objectives of this study were to examine the genetic control of survival in segregant families F3 of the common bean (Phaseolus vulgaris L.) in southern Brazil during the 2004-2005 growing season, to identify useful genotypes for the breeding program of this crop, and to determine the genetic association between survival and weight of 100 seeds (production trait; P100). A Bayesian approach was used to predict breeding values and to estimate variance components. Survival was recorded as a binary response: dead plant or live plant during harvest. The total population consisted of 11 520 individual plants. The difference in the magnitude between the best and the worst families was as high as 22%, and varied from 57 to 73%. Survival was found to be highly heritable, with an a posteriori heritability mean and Bayesian credible interval: H2 = 53% (43-65%). The genetic advance by direct selection achieved a value of 18%, considering a selection intensity of 25%. Survival was not correlated with P100 (Pearson = 0.099; Spearman = 0.074), indicating that selection for this trait alone would have little impact on production from a breeding viewpoint. Bayesian analysis, using the Gibbs algorithm, was useful in the genetic evaluation of common bean families based on a binary response variable.},
number = {4},
pages = {334--341},
volume = {68},
year = {2008},
date-added = {2010-03-17 20:55:02 +0100},
date-modified = {2010-03-17 20:56:02 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Mora-2008-CHILEAN%20JOURNAL%20OF%20AGRICULTURAL%20RESEARCH_BAYESIAN%20ANALYSIS%20OF.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7760},
rating = {0}
}

@article{Surguladze:2008p8896,
author = {S A Surguladze and A Elkin and C Ecker and S Kalidindi and A Corsico and V Giampietro and N Lawrence and Q Deeley and D G M Murphy and K Kucharska-Pietura and T A Russell and P McGuffin and R Murray and M L Phillips},
journal = {Genes Brain Behav},
title = {Genetic variation in the serotonin transporter modulates neural system-wide response to fearful faces},
abstract = {A distributed, serotonergically innervated neural system comprising extrastriate cortex, amygdala and ventral prefrontal cortex is critical for identification of socially relevant emotive stimuli. The extent to which a genetic variation of serotonin transporter gene 5-HTTLPR impacts functional connectivity between the amygdala and the other components of this neural system remains little examined. In our study, neural activity was measured using event-related functional magnetic resonance imaging in 29 right-handed, white Caucasian healthy subjects as they viewed mild or prototypical fearful and neutral facial expressions. 5-HTTLPR genotype was classified as homozygous for the short allele (S/S), homozygous for the long allele (L/L) or heterozygous (S/L). S/S showed greater activity than L/L within right fusiform gyrus (FG) to prototypically fearful faces. To these fearful faces, S/S more than other genotype subgroups showed significantly greater positive functional connectivity between right amygdala and FG and between right FG and right ventrolateral prefrontal cortex (VLPFC). There was a positive association between measure of psychoticism and degree of functional connectivity between right FG and right VLPFC in response to prototypically fearful faces. Our data are the first to show that genotypic variation in 5-HTTLPR modulates both the amplitude within and the functional connectivity between different components of the visual object-processing neural system to emotionally salient stimuli. These effects may underlie the vulnerability to mood and anxiety disorders potentially triggered by socially salient, emotional cues in individuals with the S allele of 5-HTTLPR.},
affiliation = {Institute of Psychiatry, King's College London, London, United Kingdom. sphasis@iop.kcl.ac.uk},
number = {5},
pages = {543--51},
volume = {7},
year = {2008},
month = {Jul},
language = {eng},
keywords = {Brain Mapping, Fear, Middle Aged, Adult, Personality, Aged, Facial Expression, Male, Female, Visual Cortex, Photic Stimulation, Genetic Variation, Neural Pathways, Humans, Amygdala, Anxiety, Affect, Serotonin Plasma Membrane Transport Proteins, Genotype, Magnetic Resonance Imaging},
date-added = {2010-03-22 12:51:01 +0100},
date-modified = {2010-03-22 12:51:02 +0100},
doi = {10.1111/j.1601-183X.2008.00390.x},
pii = {GBB390},
pmid = {18266983},
URL = {http://www3.interscience.wiley.com/journal/119879341/abstract},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Surguladze-2008-Genes%20Brain%20Behav_Genetic%20variation%20in.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8896},
rating = {0}
}

@article{From:2006,
author = {S G From and L Li},
journal = {Communications in Statistics -- Theory and Methods},
title = {Estimation of the paramters of the Birnbaum-Saunders distribution},
number = {12},
pages = {2157--2169},
volume = {35},
year = {2006},
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/From-2006-Communications%20in%20Statistics%20--%20Theory%20and%20Methods_Estimation%20of%20the%20pa.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1904},
rating = {0}
}

@article{Cohen:1998p9553,
author = {C Cohen and D A Revicki and A Nabulsi and P W Sarocco and P Jiang},
journal = {AIDS},
title = {A randomized trial of the effect of ritonavir in maintaining quality of life in advanced HIV disease. Advanced HIV Disease Ritonavir Study Group},
abstract = {BACKGROUND: The aim of treatment for HIV disease is prolonging survival and improvement in health-related quality of life. Ritonavir is a potent, orally bioavailable HIV protease inhibitor with demonstrated impact on surrogate endpoints, AIDS-defining disease, and mortality. OBJECTIVES: To evaluate the effect of ritonavir combined with reverse transcriptase inhibitor therapy on patient functioning and well-being. METHODS: An international, multicenter randomized placebo-controlled clinical trial of ritonavir was conducted in HIV-infected patients with CD4 cell counts < or = 100 x 10(6)/l. A total of 1090 patients were randomized to ritonavir and continued treatment with as many as two nucleoside agents (n=543) or placebo and continued treatment with as many as two nucleoside agents (n=547). Health-related quality of life was measured at baseline and after 3 and 6 months of treatment using the Medical Outcomes Study HIV Health Survey (MOS-HIV) and HIV-related symptoms scale. MOS-HIV contains 10 subscales and two summary scores (physical health and mental health). RESULTS: The two treatment groups were comparable on baseline CD4 cell counts, demographic characteristics, and MOS-HIV and HIV symptom subscale scores. After 3 months, statistically significant differences (P < 0.03) favoring the ritonavir-treated patients were seen on the physical health summary, mental health summary, and general health perceptions, social function, mental health, and energy/fatigue subscales. After 6 months of ritonavir therapy, significant differences were observed on physical health and mental health summary scores (P < 0.001), and on measures of general health perceptions, physical function, role function, social function, cognitive function, mental health, health distress, energy/fatigue, and overall ratings of quality of life (P < 0.01). Ritonavir-treated patients reported fewer fever symptoms and neurologic symptoms than the placebo group after 6 months of treatment (P < 0.005). CONCLUSIONS: Ritonavir therapy, combined with other antiretroviral treatments, significantly contributes to maintenance of functioning and well-being over at least 6 months in patients with advanced HIV disease.},
affiliation = {Community Research Initiative of New England, Brookline, Massachusetts, USA.},
number = {12},
pages = {1495--502},
volume = {12},
year = {1998},
month = {Aug},
language = {eng},
keywords = {HIV Infections, Female, Quality of Life, Drug Therapy: Combination, Adult, Middle Aged, Humans, Treatment Outcome, Anti-HIV Agents, Male, Double-Blind Method, Ritonavir},
date-added = {2010-03-23 20:50:25 +0100},
date-modified = {2010-07-29 19:12:25 +0200},
pmid = {9727571},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Cohen-1998-AIDS_A%20randomized%20trial%20o.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9553},
rating = {0}
}

@article{Friedman:2007p12326,
author = {J Friedman and T Hastie and R Tibshirani},
journal = {Biostatistics},
title = {Sparse inverse covariance estimation with the graphical lasso},
abstract = {We consider the problem of estimating sparse graphs by a lasso penalty applied to the inverse covariance
matrix. Using a coordinate descent procedure for the lasso, we develop a simple algorithm---the graphical lasso---that is remarkably fast: It solves a 1000-node problem (∼500 000 parameters) in at most a minute and is 30--4000 times faster than competing methods. It also provides a conceptual link between the exact problem and the approximation suggested by Meinshausen and Bu ̈hlmann (2006). We illustrate the method on some cell-signaling data from proteomics.},
year = {2007},
date-added = {2010-06-12 09:44:47 +0200},
date-modified = {2010-06-12 09:45:54 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Friedman-2007-Biostatistics_Sparse%20inverse%20covar.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12326},
read = {Yes},
rating = {5}
}

@article{Mayo:2004p6364,
author = {Nancy E Mayo and Lise Poissant and Sara Ahmed and Lois Finch and Johanne Higgins and Nancy M Salbach and Judith Soicher and Susan Jaglal},
journal = {J Am Med Inform Assoc},
title = {Incorporating the International Classification of Functioning, Disability, and Health (ICF) into an electronic health record to create indicators of function: proof of concept using the SF-12},
abstract = {OBJECTIVE: The purpose of this proof-of-concept study was to assess the feasibility of using a generic health measure to create coded functional status indicators and compare the characterization of a stroke population using coded functional indicators and using health-related quality-of-life summary measures alone. DESIGN: Multiple raters assigned International Classification of Functioning, Disability, and Health (ICF) codes to the items of the 12-Item Short Form Health Survey (SF-12). Data for comparing the information from the SF-12 and from ICF codes were derived from the Montreal Stroke Cohort Study that was set up to examine the long-term impact of stroke. Available for analysis were data from 604 persons with stroke, average age 69 years, and 488 controls, average age 62 years. MEASUREMENT: The SF-12 provides two summary scores, one for physical health and one for mental health. Domains of the ICF are coded to three digits, before the decimal; specific categorizations of impairments, activity limitations, and participation restrictions are coded to four digits before the decimal. RESULTS: Persons with stroke scored, on average, approximately 10 points lower than controls on physical and mental health. The ICF coding indicated that this was attributed, not surprisingly, to greater difficulty in doing moderate activities including housework, climbing stairs, and working and was not attributed to differences in pain. Differences in mental health were attributed most strongly to greater fatigue (impairment in energy), but all areas of mental health were affected to some degree. CONCLUSION: The ICF coding provided enhanced functional status information in a format compatible with the structure of administrative health databases.},
affiliation = {Division of Clinical Epidemiology, McGill University Health Center, Montreal, Quebec, Canada. nancy.mayo@mcgill.ca},
number = {6},
pages = {514--22},
volume = {11},
year = {2004},
month = {Jan},
language = {eng},
keywords = {Age Factors, Vocabulary: Controlled, Sex Factors, Humans, Activities of Daily Living, Quality of Life, Sickness Impact Profile, Aged: 80 and over, International Classification of Diseases, Middle Aged, Feasibility Studies, Medical Records Systems: Computerized, Mental Health, Female, Case-Control Studies, Regression Analysis, Health Status Indicators, Health Status, Income, Male, Aged, Stroke},
date-added = {2010-02-23 08:21:49 +0100},
date-modified = {2010-02-23 08:21:49 +0100},
doi = {10.1197/jamia.M1462},
pii = {M1462},
pmid = {15298994},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6364},
rating = {0}
}

@article{Ware:2001p3608,
author = {J E Ware},
title = {Using Item Response Theory
To Construct QOL Measures
For Children:
The Dynamic Health Assessment (DynHA) Approach},
year = {2001},
date-added = {2010-01-16 18:23:09 +0100},
date-modified = {2010-02-23 15:00:02 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Ware-2001-_Using%20Item%20Response.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3608},
read = {Yes},
rating = {4}
}

@article{Sarkar:2008p4356,
author = {Sanat K Sarkar},
journal = {arXiv},
title = {Stepup procedures controlling generalized FWER and generalized FDR},
abstract = { In many applications of multiple hypothesis testing where more than one false rejection can be tolerated, procedures controlling error rates measuring at least {\$}k{\$} false rejections, instead of at least one, for some fixed {\$}k\ge 1{\$} can potentially increase the ability of a procedure to detect false null hypotheses. The {\$}k{\$}-FWER, a generalized version of the usual familywise error rate (FWER), is such an error rate that has recently been introduced in the literature and procedures controlling it have been proposed. A further generalization of a result on the {\$}k{\$}-FWER is provided in this article. In addition, an alternative and less conservative notion of error rate, the {\$}k{\$}-FDR, is introduced in the same spirit as the {\$}k{\$}-FWER by generalizing the usual false discovery rate (FDR). A {\$}k{\$}-FWER procedure is constructed given any set of increasing constants by utilizing the {\$}k{\$}th order joint null distributions of the {\$}p{\$}-values without assuming any specific form of dependence among all the {\$}p{\$}-values. Procedures controlling the {\$}k{\$}-FDR are also developed by using the {\$}k{\$}th order joint null distributions of the {\$}p{\$}-values, first assuming that the sets of null and nonnull {\$}p{\$}-values are mutually independent or they are jointly positively dependent in the sense of being multivariate totally positive of order two (MTP{\$}_2{\$}) and then discarding that assumption about the overall dependence among the {\$}p{\$}-values. },
annote = {Published in: Annals of Statistics 2007, Vol. 35, No. 6, 2405-2420

Published in at http://dx.doi.org/10.1214/009053607000000398 the
  Annals of Statistics (http://www.imstat.org/aos/) by the Institute of
  Mathematical Statistics (http://www.imstat.org)},
eprint = {0803.2934v1},
volume = {math.ST},
year = {2008},
month = {Jan},
keywords = {stat.TH, math.ST, 62J15, 62H15 (Primary) 62H99 (Secondary)},
date-added = {2010-01-27 18:29:41 +0100},
date-modified = {2010-01-27 18:29:41 +0100},
doi = {10.1214/009053607000000398},
pmid = {0803.2934v1},
URL = {http://arxiv.org/abs/0803.2934v1},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4356},
rating = {0}
}

@article{Mark:2005p13798,
author = {Barbara A Mark and Thomas T H Wan},
journal = {West J Nurs Res},
title = {Testing measurement equivalence in a patient satisfaction instrument},
abstract = {The purpose of this methodological study was to examine five sources of measurement equivalence (configural invariance, metric invariance, scalar invariance, invariant uniquenesses, and invariant factor variances) in perceptions of patient satisfaction for two groups of patients, whose satisfaction was measured at different times, for men compared with women, and for minority populations compared with Whites. The sample consisted of a total sample of 1,897 patients of whom 1,070 were females, and 1,228 were White. Using confirmatory factor analysis and structural equation modeling, we found that the 10-item Likert-type scale performed well across time but required additional attention if it is to be used to compare satisfaction between genders and racial groups.},
affiliation = {University of North Carolina at Chapel Hill, USA.},
number = {6},
pages = {772--87},
volume = {27},
year = {2005},
month = {Oct},
language = {eng},
keywords = {Texas, Inpatients, District of Columbia, Research Design, Men, Humans, Nursing Staff: Hospital, Sex Factors, Women, Factor Analysis: Statistical, Questionnaires, Patient Satisfaction, Time Factors, Female, Nursing Care, Psychometrics, Minority Groups, Nursing Evaluation Research, Southeastern United States, Male, Regression Analysis, Analysis of Variance},
date-added = {2010-07-29 12:17:55 +0200},
date-modified = {2010-07-29 12:17:55 +0200},
doi = {10.1177/0193945905276336},
pii = {27/6/772},
pmid = {16157947},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13798},
rating = {0}
}

@article{Holmes:2008p4761,
author = {Amanda Holmes and Maria Kragh Nielsen and Simon Green},
journal = {Biol Psychol},
title = {Effects of anxiety on the processing of fearful and happy faces: an event-related potential study},
abstract = {This study investigated the influence of trait anxiety on event-related potentials (ERPs) to fearful, happy, and neutral faces. Fearful faces, relative to neutral, elicited a range of effects in the low-trait anxiety (LTA) group: an enhanced visual P1 component, an early posterior negativity (EPN), and a sustained fronto-central positivity. Emotional expression effects were generally weaker for happy faces. The enhanced fronto-central positivity and EPN triggered by fearful stimuli in LTA participants were less pronounced in the high-trait anxiety (HTA) group, while the enhancement of the visual P1 seen in the LTA group was further augmented in the HTA group. This represents a clear dissociation across anxiety groups between rapid attentional processing as reflected by the visual P1 and later strategic processing as reflected by fronto-central and EPN components. These effects of high-trait anxiety in potentiating initial threat evaluation but attenuating later cognitive processing are discussed in the context of the possible roles of neural systems underlying threat evaluation, cognitive avoidance, and differentiated affective responses.},
affiliation = {School of Human and Life Sciences, Roehampton University, UK. a.holmes@roehampton.ac.uk},
number = {2},
pages = {159--73},
volume = {77},
year = {2008},
month = {Feb},
language = {eng},
keywords = {Personality Tests, Electrocardiography, Electroencephalography, Anxiety, Fear, Female, Data Interpretation: Statistical, Happiness, Adult, Humans, Cerebral Cortex, Evoked Potentials, Cues, Male, Facial Expression, Habituation: Psychophysiologic},
date-added = {2010-02-01 20:18:48 +0100},
date-modified = {2010-02-01 20:18:48 +0100},
doi = {10.1016/j.biopsycho.2007.10.003},
pii = {S0301-0511(07)00162-7},
pmid = {18022310},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Holmes-2008-Biol%20Psychol_Effects%20of%20anxiety%20o.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4761},
rating = {0}
}

@article{Rutgers:2007p11035,
author = {Anna H Rutgers and Marinus H van Ijzendoorn and Marian J Bakermans-Kranenburg and Sophie H N Swinkels and Emma van Daalen and Claudine Dietz and Fabienne B A Naber and Jan K Buitelaar and Herman van Engeland},
journal = {J Abnorm Child Psychol},
title = {Autism, attachment and parenting: a comparison of children with autism spectrum disorder, mental retardation, language disorder, and non-clinical children},
abstract = {Children with Autism Spectrum Disorder (ASD) have severe and pervasive impairments in the development of social interaction, which may affect the attachment relationship with their parents and may have an impact on parenting. In the current investigation 89 families with young children (mean age 26.5 months) were involved, who were diagnosed as ASD, mentally retarded (MR), or language delayed (LD), or part of a non-clinical comparison group. Attachment security was observed with the Brief Attachment Screening Questionnaire, and several parental self-report questionnaires assessed the parenting style, parental efficacy, parental experiences of daily hassles, social support, and psychological problems. Children with ASD were rated as less secure compared to the other clinical and normal comparison groups. Parents of non-clinical children reported higher levels of authoritative parenting than parents in the ASD group and in the total clinical group, and they also received less social support. Parents of children with ASD coped remarkably well with the challenges of raising a child with ASD.},
affiliation = {Centre for Child and Family Studies, Leiden University, PO Box 9555, NL-2300RB, Leiden, The Netherlands.},
number = {5},
pages = {859--70},
volume = {35},
year = {2007},
month = {Oct},
language = {eng},
keywords = {Child: Preschool, Adaptation: Psychological, Language Development Disorders, Mental Retardation, Parenting, Male, Discriminant Analysis, Autistic Disorder, Analysis of Variance, Object Attachment, Parents, Humans, Netherlands, Social Support, Infant, Female},
date-added = {2010-04-14 13:41:11 +0200},
date-modified = {2010-07-29 19:31:18 +0200},
doi = {10.1007/s10802-007-9139-y},
pmid = {17505877},
URL = {http://www.springerlink.com/content/t5t565nj38278765/},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Rutgers-2007-J%20Abnorm%20Child%20Psychol_Autism%20attachment%20a.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11035},
read = {Yes},
rating = {0}
}

@article{Williams:2006,
author = {N J Williams and S N Beretvas},
journal = {Applied Psychological Measurement},
title = {DIF Identification Using HGLM for Polytomous Items},
abstract = {The relationship between the hierarchical generalized linear model (HGLM) and item response theory (IRT) models has been demonstrated for dichotomous items. The current study demonstrated the use of the HGLM for polytomous items (termed PHGLM) for identification of differential item functioning (DIF). First, the algebraic equivalence between parameterizations of a constrained form of Muraki's rating scale model and PHGLM was demonstrated. Next, as a precursor to using the PHGLM for DIF identification, a simulation was conducted to compare estimation of item and person latent trait parameters using HLM 5 and PARSCALE software. The resulting PHGLM and IRT parameter estimates were comparable. Last, a simulation was conducted that compared the performance of PHGLM with that of the generalized Mantel-Haenszel statistic for DIF identification. Both approaches performed similarly. Benefits and limitations of using PHGLM for DIF identification are presented. Index terms: hierarchical linear modeling, item response theory, polytomous items, parameter estimation, differential item functioning, attitude measurement.},
number = {1},
pages = {22--42},
volume = {30},
year = {2006},
date-added = {2010-01-03 19:38:21 +0100},
date-modified = {2010-07-29 19:16:54 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Williams-2006-Applied%20Psychological%20Measurement_DIF%20Identification%20U-1.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1143},
read = {Yes},
rating = {0}
}

@article{Durinck:2005p5049,
author = {Steffen Durinck and Yves Moreau and Arek Kasprzyk and Sean Davis and Bart De Moor and Alvis Brazma and Wolfgang Huber},
journal = {Bioinformatics},
title = {BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis},
abstract = {biomaRt is a new Bioconductor package that integrates BioMart data resources with data analysis software in Bioconductor. It can annotate a wide range of gene or gene product identifiers (e.g. Entrez-Gene and Affymetrix probe identifiers) with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Furthermore biomaRt enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. Fast and up-to-date data retrieval is possible as the package executes direct SQL queries to the BioMart databases (e.g. Ensembl). The biomaRt package provides a tight integration of large, public or locally installed BioMart databases with data analysis in Bioconductor creating a powerful environment for biological data mining.},
affiliation = {Department of Electronical Engineering, ESAT-SCD, K.U.Leuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium. steffen.durinck@esat.kuleuven.ac.be},
number = {16},
pages = {3439--40},
volume = {21},
year = {2005},
month = {Aug},
language = {eng},
keywords = {Databases: Protein, Systems Integration, Software, Gene Expression Profiling, Oligonucleotide Array Sequence Analysis, Database Management Systems, Information Storage and Retrieval, Algorithms},
date-added = {2010-02-05 20:01:09 +0100},
date-modified = {2010-02-05 20:01:09 +0100},
doi = {10.1093/bioinformatics/bti525},
pii = {21/16/3439},
pmid = {16082012},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Durinck-2005-Bioinformatics_BioMart%20and%20Biocondu.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5049},
rating = {0}
}

@article{Hawley:2002p8155,
author = {C J Hawley and T M Gale and T Sivakumaran and Hertfordshire Neuroscience Research group},
journal = {J Affect Disord},
title = {Defining remission by cut off score on the MADRS: selecting the optimal value},
abstract = {BACKGROUND: Remission from major depression may be conceptualised in terms of a cut-off score on an appropriate rating scale. Candidate values proposed hitherto have not been directly validated. METHOD: The relationship between The Clinical Global Impression Scale for Severity (CGI-S) and the Montgomery-Asberg Depression Rating Scale (MADRS) was explored in 684 major depressed patients (1114 observations). The value on the MADRS which had greatest concordance with remission, as defined by the CGI-S, was computed using two models. Concordance between clinician and patient judgements of global illness were also compared. RESULTS AND CONCLUSION: The two models yielded optimal definitions of remission of <9 and <10 on the MADRS. Either value offers a workable operationalisation of remission and there is little to choose between them. CLINICAL RELEVANCE: The data confirm that MADRS <10 should provide the clinician with a valid, and reasonably objectifiable, target for remission},
affiliation = {Department of Psychiatry, QEII Hospital, Hertfordshire AL7 4HQ, Welwyn Garden City, UK. c.l.hawley@herts.ac.uk},
number = {2},
pages = {177--84},
volume = {72},
year = {2002},
month = {Nov},
language = {eng},
keywords = {Depressive Disorder: Major, Severity of Illness Index, Adult, Middle Aged, Psychiatric Status Rating Scales, Remission: Spontaneous, Questionnaires, Aged, Humans, Male, Reproducibility of Results, Female},
date-added = {2010-03-20 19:50:06 +0100},
date-modified = {2010-03-20 19:50:06 +0100},
pii = {S0165032701004517},
pmid = {12200208},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hawley-2002-J%20Affect%20Disord_Defining%20remission%20b.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8155},
rating = {0}
}

@article{Yi:2009p540,
author = {Nengjun Yi and Samprit Banerjee},
journal = {Genetics},
title = {Hierarchical generalized linear models for multiple quantitative trait locus mapping},
abstract = {We develop hierarchical generalized linear models and computationally efficient algorithms for genomewide analysis of quantitative trait loci (QTL) for various types of phenotypes in experimental crosses. The proposed models can fit a large number of effects, including covariates, main effects of numerous loci, and gene-gene (epistasis) and gene-environment (G x E) interactions. The key to the approach is the use of continuous prior distribution on coefficients that favors sparseness in the fitted model and facilitates computation. We develop a fast expectation-maximization (EM) algorithm to fit models by estimating posterior modes of coefficients. We incorporate our algorithm into the iteratively weighted least squares for classical generalized linear models as implemented in the package R. We propose a model search strategy to build a parsimonious model. Our method takes advantage of the special correlation structure in QTL data. Simulation studies demonstrate reasonable power to detect true effects, while controlling the rate of false positives. We illustrate with three real data sets and compare our method to existing methods for multiple-QTL mapping. Our method has been implemented in our freely available package R/qtlbim (www.qtlbim.org), providing a valuable addition to our previous Markov chain Monte Carlo (MCMC) approach.},
affiliation = {Department of Biostatistics, Section on Statistical Genetics, University of Alabama, Birmingham, Alabama 35294-0022, USA. nyi@ms.soph.uab.edu},
number = {3},
pages = {1101--13},
volume = {181},
year = {2009},
month = {Mar},
language = {eng},
keywords = {Male, Chromosome Mapping, Listeria monocytogenes, Animals, Female, Mice, Obesity, Monte Carlo Method, Quantitative Trait Loci, Linear Models, Algorithms, Hordeum, Markov Chains},
date-added = {2010-01-03 14:05:20 +0100},
date-modified = {2010-01-03 14:05:20 +0100},
doi = {10.1534/genetics.108.099556},
pii = {genetics.108.099556},
pmid = {19139143},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Yi-2009-Genetics_Hierarchical%20general.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p540},
rating = {0}
}

@article{Drosler:2008p3603,
author = {S Dr{\"o}sler},
title = {FACILITATING CROSS-NATIONAL COMPARISONS OF INDICATORS FOR PATIENT SAFETY AT THE HEALTH-SYSTEM LEVEL IN THE OECD COUNTRIES},
year = {2008},
date-added = {2010-01-15 21:43:21 +0100},
date-modified = {2010-01-15 21:43:57 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Dr%C3%B6sler-2008-_FACILITATING%20CROSS-N.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3603},
rating = {0}
}

@article{Jacob:2009p6234,
author = {L Jacob and G Obozinski and J-P Vert},
journal = {Proceedings of the 26th International Conference on Machine Learning},
title = {Group Lasso with Overlap and Graph Lasso},
abstract = {We propose a new penalty function which, when used as regularization for empirical risk mini- mization procedures, leads to sparse estimators. The support of the sparse vector is typically a union of potentially overlapping groups of co- variates defined a priori, or a set of covariates which tend to be connected to each other when a graph of covariates is given. We study theo- retical properties of the estimator, and illustrate its behavior on simulated and breast cancer gene expression data.},
year = {2009},
date-added = {2010-02-19 21:03:57 +0100},
date-modified = {2010-02-19 21:04:47 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Jacob-2009-Proceedings%20of%20the%2026th%20International%20Conference%20on%20Machine%20Learning_Group%20Lasso%20with%20Ove.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6234},
rating = {0}
}

@article{Plaze:2009p5006,
author = {Marion Plaze and Marie-Laure Paill{\`e}re-Martinot and Jani Penttil{\"a} and Dominique Januel and Renaud de Beaurepaire and Franck Bellivier and Jamila Andoh and Andr{\'e} Galinowski and Thierry Gallarda and Eric Artiges and Jean-Pierre Oli{\'e} and Jean-Fran{\c c}ois Mangin and Jean-Luc Martinot and Arnaud Cachia},
journal = {Schizophr Bull},
title = {"Where Do Auditory Hallucinations Come From?"--A Brain Morphometry Study of Schizophrenia Patients With Inner or Outer Space Hallucinations},
abstract = {Auditory verbal hallucinations are a cardinal symptom of schizophrenia. Bleuler and Kraepelin distinguished 2 main classes of hallucinations: hallucinations heard outside the head (outer space, or external, hallucinations) and hallucinations heard inside the head (inner space, or internal, hallucinations). This distinction has been confirmed by recent phenomenological studies that identified 3 independent dimensions in auditory hallucinations: language complexity, self-other misattribution, and spatial location. Brain imaging studies in schizophrenia patients with auditory hallucinations have already investigated language complexity and self-other misattribution, but the neural substrate of hallucination spatial location remains unknown. Magnetic resonance images of 45 right-handed patients with schizophrenia and persistent auditory hallucinations and 20 healthy right-handed subjects were acquired. Two homogeneous subgroups of patients were defined based on the hallucination spatial location: patients with only outer space hallucinations (N = 12) and patients with only inner space hallucinations (N = 15). Between-group differences were then assessed using 2 complementary brain morphometry approaches: voxel-based morphometry and sulcus-based morphometry. Convergent anatomical differences were detected between the patient subgroups in the right temporoparietal junction (rTPJ). In comparison to healthy subjects, opposite deviations in white matter volumes and sulcus displacements were found in patients with inner space hallucination and patients with outer space hallucination. The current results indicate that spatial location of auditory hallucinations is associated with the rTPJ anatomy, a key region of the "where" auditory pathway. The detected tilt in the sulcal junction suggests deviations during early brain maturation, when the superior temporal sulcus and its anterior terminal branch appear and merge.},
affiliation = {2INSERM, U797 Research Unit, Neuroimaging and Psychiatry, IFR49, Orsay, France.},
pages = {},
year = {2009},
month = {Aug},
language = {ENG},
date-added = {2010-02-05 00:08:14 +0100},
date-modified = {2010-02-05 00:08:14 +0100},
doi = {10.1093/schbul/sbp081},
pii = {sbp081},
pmid = {19666833},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Plaze-2009-Schizophr%20Bull_%22Where%20Do%20Auditory%20H.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5006},
rating = {0}
}

@article{Hedeker:2003p6515,
author = {Donald Hedeker},
journal = {Stat Med},
title = {A mixed-effects multinomial logistic regression model},
abstract = {A mixed-effects multinomial logistic regression model is described for analysis of clustered or longitudinal nominal or ordinal response data. The model is parameterized to allow flexibility in the choice of contrasts used to represent comparisons across the response categories. Estimation is achieved using a maximum marginal likelihood (MML) solution that uses quadrature to numerically integrate over the distribution of random effects. An analysis of a psychiatric data set, in which homeless adults with serious mental illness are repeatedly classified in terms of their living arrangement, is used to illustrate features of the model.},
affiliation = {Division of Epidemiology {\&} Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, IL 60612, USA. hedeker@uic.edu},
number = {9},
pages = {1433--46},
volume = {22},
year = {2003},
month = {May},
language = {eng},
keywords = {California, Adult, Housing, Cluster Analysis, Logistic Models, Social Welfare, Humans, Public Assistance, Mentally Ill Persons, Longitudinal Studies, Likelihood Functions, Homeless Persons},
date-added = {2010-02-23 08:38:12 +0100},
date-modified = {2010-02-23 08:38:12 +0100},
doi = {10.1002/sim.1522},
pmid = {12704607},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hedeker-2003-Stat%20Med_A%20mixed-effects%20mult.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6515},
rating = {0}
}

@article{Mynarek:2008p11911,
author = {Zb M{\l}ynarek and J Wierzbicki and W Wo{\l}ynski and W Tschuschke},
journal = {International Association for Computer Methods and Advances in Geomechanics (IACMAG)},
title = {Assessment of Efficiency of Different Cluster Analysis Methods for Evaluation of a Stratigraphy of Strongly Laminated Subsoil},
abstract = {Cluster analysis is a statistical method applied with increasing frequency to solve geotechnical problems. Its primary advantage is the possibility to simultaneously consider several parameters describing soil to isolate homogenous subsoil layers. Studies conducted so far pertained mainly to subsoil composed of homogenous layers with thickness of at least several dozen centimeters. This study presents the results of analyses conducted on deposits of different character -- varved clays. These deposits exhibit marked lamination, consisting of alternate clay and silt layers. Individual laminae do not exceed several cm in thickness. Such a structure of deposits may cause marked discrepancies in the assessment of homogenous geotechnical layers, depending on the applied method of cluster analysis. The subject of the paper is the assessment of the effect of the laminar structure on efficiency of isolations performed using different cluster analysis methods.},
year = {2008},
date-added = {2010-05-23 12:00:34 +0200},
date-modified = {2010-05-23 12:02:02 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/M%C5%82ynarek-2008-International%20Association%20for%20Computer%20Methods%20and%20Advances%20in%20Geomechanics%20(IACMAG)_Assessment%20of%20Effici.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11911},
rating = {0}
}

@article{Muthen:2009p13479,
author = {B Muth{\'e}n and T Asparouhov},
title = {Beyond Multilevel Regression Modeling: Multilevel Analysis in a General Latent Variable Framework},
abstract = {Multilevel modeling is often treated as if it concerns only regression analysis and growth modeling. Multilevel modeling, however, is rele- vant for nested data not only with regression and growth analysis but with all types of statistical analyses. This chapter has two aims. First, it shows that already in the traditional multilevel analysis areas of re- gression and growth there are several new modeling opportunities that should be considered. Second, it gives an overview with examples of multilevel modeling for path analysis, factor analysis, structural equa- tion modeling, and growth mixture modeling. Examples include two extensions of two-level regression analysis with measurement error in the level 2 covariate and a level 1 mixture; two-level path analysis and structural equation modeling; two-level exploratory factor analysis of classroom misbehavior; two-level growth modeling using a two-part model for heavy drinking development; an unconventional approach to three-level growth modeling of math achievement; and multilevel latent class mediation of high school dropout using multilevel growth mixture modeling of math achievement development.},
year = {2009},
date-added = {2010-07-01 20:42:32 +0200},
date-modified = {2010-07-01 20:43:08 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Muth%C3%A9n-2009-_Beyond%20Multilevel%20Re.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13479},
rating = {0}
}

@article{Kang:2010p13620,
author = {T Kang and T T Chen},
journal = {Asia Pacific Educ. Rev.},
title = {Performance of the generalized S-X2 item fit index for the graded response model},
abstract = {The utility of Orlando and Thissen's (2000, 2003) S-X2 fit index was

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branch_name: refs/heads/master

extension: bib