text:
, we find that the original Random Forest method performed on SNPs provides good performance. When individual, genotyped SNPs are the risk factors, we find that the stronger the genetic effect, the stronger the effect LD has on the performance of the original RF. A revised importance measure used with the original RF is relatively robust to LD among SNPs; this revised importance measure used with the revised RF is sometimes inflated. Overall, we find that the revised importance measure used with the original RF is the best choice when the genetic model and the number of SNPs in LD with risk SNPs are unknown. For the haplotype-based method, under a multiplicative heterogeneity model, we observed a decrease in the performance of RF with increasing LD among the SNPs in the haplotype. CONCLUSION: Our results suggest that by strategically revising the Random Forest method tree-building or importance measure calculation, power can increase when LD exists between SNPs. We conclude that the revised Random Forest method performed on SNPs offers an advantage of not requiring genotype phase, making it a viable tool for use in the context of thousands of SNPs, such as candidate gene studies and follow-up of top candidates from genome wide association studies.},
affiliation = {Department of Medicine, Boston University, MA, USA. ymeng@broad.mit.edu},
pages = {78},
volume = {10},
year = {2009},
month = {Jan},
language = {eng},
keywords = {Polymorphism: Single Nucleotide, Computer Simulation, Haplotypes, Algorithms, Alzheimer Disease, Models: Genetic, Genome-Wide Association Study, Linkage Disequilibrium},
date-added = {2010-01-28 13:29:01 +0100},
date-modified = {2010-01-28 13:29:01 +0100},
doi = {10.1186/1471-2105-10-78},
pii = {1471-2105-10-78},
pmid = {19265542},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Meng-2009-BMC%20Bioinformatics_Performance%20of%20rando.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4361},
read = {Yes},
rating = {0}
}

@article{Upton:2008p8495,
author = {Penney Upton and Joanne Lawford and Christine Eiser},
journal = {Qual Life Res},
title = {Parent-child agreement across child health-related quality of life instruments: a review of the literature},
abstract = {AIM: To systematically review the literature published since 1999 on paediatric health-related quality of life (HRQL) in relation to parent-child agreement. METHODS: Literature searches used to identify studies which evaluated parent-child agreement for child HRQL measures. RESULTS: Nineteen studies were identified, including four HRQL instruments. The Pediatric Quality of Life Inventory (PedsQL) was most commonly used. Differences in parent-child agreement were noted between domains for different measures. The impact of child and parent characteristics were not consistently considered; however parents of children in a nonclinical sample tended to report higher child HRQL scores than children themselves, while parents of children with health conditions tended to underestimate child HRQL. CONCLUSION: Despite increasing numbers of studies considering children's HRQL, information about variables contributing to parent-child agreement levels remains limited. Authors need to consistently provide evidence for reliability and validity of measures, and design studies to systematically investigate variables that impact on levels of parent-child agreement.},
affiliation = {Department of Psychology and Health Sciences, University of Worcester, Worcester WR2 6AJ, UK. p.upton@worc.ac.uk},
number = {6},
pages = {895--913},
volume = {17},
year = {2008},
month = {Aug},
language = {eng},
keywords = {Child Welfare, Reproducibility of Results, Child, Humans, Parent-Child Relations, Quality of Life, Psychometrics, Child: Preschool},
date-added = {2010-03-21 18:01:02 +0100},
date-modified = {2010-07-29 19:48:29 +0200},
doi = {10.1007/s11136-008-9350-5},
pmid = {18521721},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8495},
rating = {0}
}

@article{Zyphur:2009p5236,
author = {M J Zyphur and J Narayanan and R D Arvey and G J Alexander},
journal = {Journal of Behavioral Decision Making},
title = {The Genetics of Economic Risk Preferences},
abstract = {We examine the influence of genetics on economic risk preferences by administering a measure of these preferences to monozygotic (MZ) (i.e., identical) and dizygotic (DZ) (i.e., non-identical) twin pairs. Our analysis supports a dominant genetic effect and virtually no additive genetic effect on economic risk preferences, with the heritability of preferences estimated at 0.63. These findings suggest that over half of the variation in such preferences can be explained by genetic factors, with the remainder of the variance explained by environmental influences not shared among sibling twins. We discuss the implications of our findings for the study of individual differences in economic risk preferences.},
pages = {367--377},
volume = {22},
year = {2009},
date-added = {2010-02-08 19:34:07 +0100},
date-modified = {2010-02-08 19:34:58 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Zyphur-2009-Journal%20of%20Behavioral%20Decision%20Making_The%20Genetics%20of%20Econ.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5236},
rating = {0}
}

@article{Korn:2001p1523,
author = {E L Korn and J F Troendle and L M McShane and R Simon},
title = {Controlling the number of false discoveries: Application to high-dimensional genomic data},
abstract = {Detailed genetic characterizations of specimens from healthy or diseased individuals may hold the key to predicting which healthy individuals will develop disease or which diseased individuals will respond to therapy. For example, cDNA microarrays allow simultaneous measurement of expression levels of thousands of genes on a single specimen, producing a ``gene expression profile''. Frequently an objective of such a study is to identify which genes among the thousands measured are differentially expressed in one group as compared to another. Statistically, this presents an enormous multiple comparisons problem. Here we propose two new statistical procedures for controlling the number of spurious findings.
We analyze a microarray data set consisting of measurements on approximately 9000 genes in paired tumor specimens, collected both before and after chemotherapy on 20 breast cancer patients. Our interest was to identify genes that were differentially expressed after chemotherapy as compared to before chemotherapy. A straightforward approach to the identification of differentially expressed genes is to perform a univariate analysis of group mean differences for each gene, and then identify those genes that are most statistically significant. Using nominal significance levels (unadjusted for the multiple comparisons) will lead to the identification of many genes that truly are not differentially expressed, ``false discoveries''. However, control of the familywise error rate (e.g., using the Bonferonni inequality) seems too extreme. Since the identified genes will be further studied for biologic relevance, a reasonable strategy is to allow a small number of false discoveries, or a small proportion of the identified genes to be false discoveries. Although previous work has considered control for the expected proportion of false discoveries, we show these methods may be inadequate. We propose two stepwise permutation-based procedures designed to control the actual number or proportion of false discoveries with specified confidence. Applying these new methods to the breast tumor microarray example, we were able to identify 28 genes (more than twice the number identified by a Bonferroni procedure) that we can state with high confidence are differentially expressed comparing before to after chemotherapy. In addition, simulation studies evaluate the procedures and demonstrate that their use results in substantial gain in sensitivity to detect truly differentially expressed genes even when allowing as few as one or two false discoveries. The methods described are broadly applicable to the problem of identifying which variables of any large set of measured variables differ between pre-specified groups.},
affiliation = {Biometric Research Branch, National Cancer Institute, Bethesda, Maryland 20892, USA},
year = {2001},
keywords = {Stepwise procedure, Microarray, Gene expression, Multiple comparisons, Permutation method, False discovery},
date-added = {2010-01-07 15:55:14 +0100},
date-modified = {2010-01-07 15:57:22 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Korn-2001-_Controlling%20the%20numb.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1523},
rating = {0}
}

@article{Whelan:2008p10851,
author = {R Whelan},
journal = {The Psychological Record},
title = {Effective analysis of reaction time data},
year = {2008},
date-added = {2010-04-10 03:30:52 +0200},
date-modified = {2010-04-10 03:31:31 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Whelan-2008-The%20Psychological%20Record_Effective%20analysis%20o.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10851},
read = {Yes},
rating = {0}
}

@article{Kranzler:1995,
author = {HR Kranzler and JA Burleson and P et al Korner},
journal = {American Journal of Psychiatry},
title = {Placebo-controlled trial of fluoxetine as an adjunct to relapse prevention in alcoholics},
abstract = {OBJECTIVE: The authors tested the hypothesis that fluoxetine, when used in combination with relapse prevention psychotherapy, directly reduces relapse frequency and severity for alcoholics. METHOD: The authors conducted a randomized, placebo-controlled trial of fluoxetine (up to a maximum of 60 mg/day) for 12 weeks in combination with weekly psychotherapy for 101 alcohol-dependent subjects who were not selected on the basis of comorbid major depression. Outcomes were measured at the end of treatment and 6 months after treatment. RESULTS: Placebo- treated subjects were more complaint with the medication regimen and remained in the study longer than fluoxetine-treated subjects. There was significantly less alcohol consumption in both groups during treatment than before treatment. These effects persisted during the posttreatment period. Although fluoxetine treatment had no significant effects on alcohol consumption, it reduced Hamilton Depression Rating Scale scores more than placebo treatment among subjects with current major depression. CONCLUSIONS: Fluoxetine at a dose of 60 mg/day is probably not of use for relapse prevention in alcoholics with mild to moderate alcohol dependence and no comorbid depression. In alcoholics with major depression, the drug may reduce depressive symptoms. Subsequent studies with fluoxetine should probably focus on more severely alcohol-dependent subjects or those with comorbid depression.},
pages = {391--397},
volume = {152},
year = {1995},
date-added = {2010-01-03 19:36:10 +0100},
date-modified = {2010-07-29 19:13:59 +0200},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1081},
rating = {0}
}

@article{Devouche:2000p4642,
author = {E Devouche},
title = {La situation d'imitation {\`a} 8 et 12 mois. Aspects sociaux et cognitifs},
year = {2000},
date-added = {2010-01-30 15:51:42 +0100},
date-modified = {2010-01-30 15:52:27 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Devouche-2000-_La%20situation%20d'imita.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4642},
rating = {0}
}

@article{Iacoboni:1999p14145,
author = {M Iacoboni and E Zaidel},
journal = {Exp Brain Res},
title = {The crossed-uncrossed difference in simple reaction times to lateralized auditory stimuli is not a measure of interhemispheric transmission time: evidence from the split brain},
abstract = {In a complete commissurotomy patient, the difference in simple (detection) reaction times between responses to contralateral and ipsilateral auditory stimuli was found to be small (less than 5 ms) and not reliable, whereas the difference between contralateral and ipsilateral responses to lateralized visual stimuli was found to be large (ranging from 25 ms to 45 ms in different previous studies) and always reliable. This suggests that the reaction times difference in detecting lateralized auditory stimuli is not a valid estimate of interhemispheric transmission time.},
affiliation = {Ahmanson-Lovelace Brain Mapping Center, Room 265, Neuropsychiatric Institute, UCLA School of Medicine, 660 Charles E. Young Drive, Los Angeles, CA 90095, USA, iacoboni@loni.ucla.edu},
number = {3},
pages = {421--4},
volume = {128},
year = {1999},
month = {Oct},
language = {eng},
keywords = {Reaction Time, Adolescent, Male, Corpus Callosum, Acoustic Stimulation, Humans, Analysis of Variance},
date-added = {2010-08-18 17:04:59 +0200},
date-modified = {2010-08-18 17:04:59 +0200},
pii = {91280421.221},
pmid = {10501816},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Iacoboni-1999-Exp%20Brain%20Res_The%20crossed-uncrosse.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p14145},
rating = {0}
}

@article{Carver:2009p344,
author = {Tim Carver and Nick Thomson and Alan Bleasby and Matthew Berriman and Julian Parkhill},
journal = {Bioinformatics},
title = {DNAPlotter: circular and linear interactive genome visualization},
abstract = {DNAPlotter is an interactive Java application for generating circular and linear representations of genomes. Making use of the Artemis libraries to provide a user-friendly method of loading in sequence files (EMBL, GenBank, GFF) as well as data from relational databases, it filters features of interest to display on separate user-definable tracks. It can be used to produce publication quality images for papers or web pages. AVAILABILITY: DNAPlotter is freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/circular/},
affiliation = {Wellcome Trust Sanger Institute, CB10 1SA and European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. artemis@sanger.ac.uk},
number = {1},
pages = {119--20},
volume = {25},
year = {2009},
month = {Jan},
language = {eng},
keywords = {Software, Computational Biology, Genome, Salmonella typhi},
date-added = {2010-01-03 11:47:13 +0100},
date-modified = {2010-01-03 11:47:13 +0100},
doi = {10.1093/bioinformatics/btn578},
pii = {btn578},
pmid = {18990721},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Carver-2009-Bioinformatics_DNAPlotter%20circular.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p344},
rating = {0}
}

@misc{Yeh:2007,
author = {S-T Yeh},
journal = {Miscellaneous},
title = {Using Trapezoidal Rule for the Area Under a Curve Calculation},
year = {2007},
date-added = {2010-01-10 11:33:18 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Yeh-2007-Miscellaneous_Using%20Trapezoidal%20Ru.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2065},
rating = {0}
}

@article{Hedecker:1999p13478,
author = {D Hedecker and R D Gibbons and C Waternaux},
journal = {Journal of Educational and Behavioral Statistics},
title = {Sample size estimation for longitudinal designs with attrition: Comparing time-related contrasts between two groups},
number = {1},
pages = {70--93},
volume = {24},
year = {1999},
date-added = {2010-07-01 20:40:48 +0200},
date-modified = {2010-07-01 20:42:01 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hedecker-1999-Journal%20of%20Educational%20and%20Behavioral%20Statistics_Sample%20size%20estimati.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13478},
rating = {0}
}

@article{Coromina:2004p5172,
author = {L Coromina and G Coenders and T Kogovsek},
journal = {Metodolo{\v s}ki zvezki},
title = {Multilevel Multitrait Multimethod Model. Application to the Measurement of Egocentered Social Networks},
abstract = {Our goal in this paper is to assess reliability and validity of egocentered network data using multilevel analysis (Muth{\'e}n, 1989, Hox, 1993) under the multitrait-multimethod approach. The confirmatory factor analysis model for multitrait-multimethod data (Werts {\&} Linn, 1970; Andrews, 1984) is used for our analyses.
In this study we reanalyse a part of data of another study (Kogov{\v s}ek et al., 2002) done on a representative sample of the inhabitants of Ljubljana. The traits used in our article are the name interpreters. We consider egocentered network data as hierarchical; therefore a multilevel analysis is required. We use Muth{\'e}n's partial maximum likelihood approach, called pseudobalanced solution (Muth{\'e}n, 1989, 1990, 1994) which produces estimations close to maximum likelihood for large ego sample sizes (Hox {\&} Mass, 2001).
Several analyses will be done in order to compare this multilevel analysis to classic methods of analysis such as the ones made in Kogov{\v s}ek et al. (2002), who analysed the data only at group (ego) level considering averages of all alters within the ego.
We show that some of the results obtained by classic methods are biased and that multilevel analysis provides more detailed information that much enriches the interpretation of reliability and validity of hierarchical data. Within and between-ego reliabilities and validities and other related quality measures are defined, computed and interpreted.},
number = {2},
pages = {323--349},
volume = {1},
year = {2004},
date-added = {2010-02-07 12:38:28 +0100},
date-modified = {2010-02-07 12:39:18 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Coromina-2004-Metodolos%CC%8Cki%20zvezki_Multilevel%20Multitrai.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5172},
rating = {0}
}

@article{Quinn:2004p6293,
author = {K M Quinn},
journal = {Political Analysis},
title = {Bayesian Factor Analysis for Mixed Ordinal and Continuous Responses},
abstract = {Many situations exist in which a latent construct has both ordinal and continuous indicators. This presents a problem for the applied researcher because standard measurement models are not designed to accommodate mixed ordinal and continuous data. I address this problem by formulating a measurement model that is appropriate for such mixed multivariate responses. This model unifies standard normal theory factor analysis and item response theory models for ordinal data. I detail a Markov chain Monte Carlo algorithm for model fitting. I apply the model to cross-national data on political-economic risk and find that the model works well. Software for fitting this model is publicly available in the MCMCpack (Martin and Quinn 2004, ``MCMCpack 0.4--8'') R package.},
pages = {338--353},
volume = {12},
year = {2004},
date-added = {2010-02-20 20:04:39 +0100},
date-modified = {2010-02-20 20:05:18 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Quinn-2004-Political%20Analysis_Bayesian%20Factor%20Anal.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6293},
rating = {0}
}

@article{Barrett:2007p11430,
author = {P Barrett},
journal = {Personality and Individual Differences},
title = {Structural equation modelling: Adjudging model fit},
abstract = {For journal editors, reviewers, and readers of research articles, structural equation model (SEM) fit has recently become a confusing and contentious area of evaluative methodology. Proponents of two kinds of approaches to model fit can be identified: those who adhere strictly to the result from a null hypothesis sig- nificance test, and those who ignore this and instead index model fit as an approximation function. Both have principled reasons for their respective course of action. This paper argues that the chi-square exact- fit test is the only substantive test of fit for SEM, but, its sensitivity to discrepancies from expected values at increasing sample sizes can be highly problematic if those discrepancies are considered trivial from an explanatory-theory perspective. On the other hand, suitably scaled indices of approximate fit do not possess this sensitivity to sample size, but neither are they ``tests'' of model fit. The proposed solution to this dilemma is to consider the substantive ``consequences'' of accepting one explanatory model over another in terms of the predictive accuracy of theory-relevant-criteria. If there are none to be evaluated, then it is proposed that no scientifically worthwhile distinction between ``competing'' models can thus be made, which of course begs the question as to why such a SEM application was undertaken in the first place.},
pages = {815--824},
volume = {42},
year = {2007},
date-added = {2010-05-01 17:11:46 +0200},
date-modified = {2010-05-01 17:12:24 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Barrett-2007-Personality%20and%20Individual%20Differences_Structural%20equation.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11430},
rating = {0}
}

@article{Goodman:2000p8277,
author = {R Goodman and T Ford and H Richards and R Gatward and H Meltzer},
journal = {J Child Psychol Psychiatry},
title = {The Development and Well-Being Assessment: description and initial validation of an integrated assessment of child and adolescent psychopathology},
abstract = {The Development and Well-Being Assessment (DAWBA) is a novel package of questionnaires, interviews, and rating techniques designed to generate ICD-10 and DSM-IV psychiatric diagnoses on 5-16-year-olds. Nonclinical interviewers administer a structured interview to parents about psychiatric symptoms and resultant impact. When definite symptoms are identified by the structured questions, interviewers use open-ended questions and supplementary prompts to get parents to describe the problems in their own words. These descriptions are transcribed verbatim by the interviewers but are not rated by them. A similar interview is administered to 11-16-year-olds. Teachers complete a brief questionnaire covering the main conduct, emotional, and hyperactivity symptoms and any resultant impairment. The different sorts of information are brought together by a computer program that also predicts likely diagnoses. These computer-generated summary sheets and diagnoses form a convenient starting point for experienced clinical raters, who decide whether to accept or overturn the computer diagnosis (or lack of diagnosis) in the light of their review of all the data, including transcripts. In the present study, the DAWBA was administered to community (N = 491) and clinic (N = 39) samples. There was excellent discrimination between community and clinic samples in rates of diagnosed disorder. Within the community sample, subjects with and without diagnosed disorders differed markedly in external characteristics and prognosis. In the clinic sample, there was substantial agreement between DAWBA and case note diagnoses, though the DAWBA diagnosed more comorbid disorders. The use of screening questions and skip rules greatly reduced interview length by allowing many sections to be omitted with very little loss of positive information. Overall, the DAWBA successfully combined the cheapness and simplicity of respondent-based measures with the clinical persuasiveness of investigator-based diagnoses. The DAWBA has considerable potential as an epidemiological measure, and may prove to be of clinical value too.},
affiliation = {Department of Child and Adolescent Psychiatry, Institute of Psychiatry, De Crespigny Park, London, UK.},
note = {psytools},
number = {5},
pages = {645--55},
volume = {41},
year = {2000},
month = {Jul},
language = {eng},
keywords = {Sampling Studies, Diagnosis: Computer-Assisted, Psychometrics, London, Psychiatric Status Rating Scales, Interview: Psychological, Follow-Up Studies, Mental Disorders, Questionnaires, Diagnosis: Differential, Humans, Male, Reproducibility of Results, Adolescent, Female, Child, Child: Preschool},
date-added = {2010-03-20 20:03:53 +0100},
date-modified = {2010-07-29 19:32:47 +0200},
pmid = {10946756},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Goodman-2000-J%20Child%20Psychol%20Psychiatry_The%20Development%20and.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8277},
read = {Yes},
rating = {0}
}

@article{Jobe:1991,
author = {JB Jobe and DJ Mingay},
journal = {Applied Cognitive Psychology},
title = {Cognition and survey measurement: History and overview},
abstract = {In 1978 a small group of cognitive psychologists and survey methodologists initiated research in a new and exciting interdisciplinary field. This research applies the methods and theories of cognitive science to the study of respondents' answers to autobiographical and attitude surveys. This article describes the events that led up to the initiation of research, describes the history of the field, and overviews the cutting edge of research. Finally, the article offers perspectives on the benefits of collaborative research to both cognitive science and survey research, and the prospects for future research.},
pages = {175--192},
volume = {5},
year = {1991},
date-added = {2010-01-03 19:34:17 +0100},
date-modified = {2010-07-29 19:15:39 +0200},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p977},
rating = {0}
}

@article{Hipwell:2010p11977,
author = {Alison E Hipwell and Stephanie D Stepp and Kate Keenan and Tammy Chung and Rolf Loeber},
journal = {J Adolesc},
title = {Brief report: Parsing the heterogeneity of adolescent girls' sexual behavior: Relationships to individual and interpersonal factors},
abstract = {Clusters of pre-sexual and sexual behaviors were identified in an urban US sample of 546 mid-adolescent girls. No distinct group of girls engaging in sexually risky behavior was revealed. Sexually active girls were older, lived with a single parent, and reported more substance use and depression, but similar levels of conduct problems, impulsivity and deviant peers to girls engaging in pre-sexual behavior.},
affiliation = {Western Psychiatric Institute {\&} Clinic, University of Pittsburgh Medical Center, 3811 O'Hara Street, Pittsburgh, PA 15213, United States.},
pages = {},
year = {2010},
month = {Mar},
language = {ENG},
date-added = {2010-05-23 17:20:35 +0200},
date-modified = {2010-05-23 17:20:35 +0200},
doi = {10.1016/j.adolescence.2010.03.002},
pii = {S0140-1971(10)00041-2},
pmid = {20359740},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11977},
rating = {0}
}

@article{Kelly:2008p7288,
author = {Brendan D Kelly},
journal = {Health Policy},
title = {The emerging mental health strategy of the European Union: a multi-level work-in-progress},
abstract = {Policy-making in the European Union (EU) is a complex process that can appear impenetrable and opaque. This paper examines the ongoing process of mental health policy-making in the EU. In 2005, the Health and Consumer Protectorate Director-General of the European Commission published a Green Paper and launched a consultation process aimed at mental health service-users, advocates, providers, business, social services and governments. While there were varying levels of participation between member states, a range of trans-national, national and infra-national actors made contributions. Based on these consultations, a 'Consultative Platform' was created and made 10 recommendations centered on the principles of partnership; establishing policy competencies; integrating mental health into national policies; involving stakeholders; and protecting human rights. This ongoing process illustrates many features of EU policy-making: (a) the European Commission generates an initiative; (b) policy focuses on EU standardization, with member states remaining central actors in service-delivery; (c) policy focuses on social inclusion; (d) the European Commission coordinates diverse networks of actors; and (e) there is 'multi-level' involvement, with direct interaction between trans-national, national and infra-national actors. An enhanced focus on epidemiological data and 'evidence-based policy' would increase rigor and focus further attention on this relatively neglected policy area.},
affiliation = {Department of Adult Psychiatry, University College Dublin, Mater Misericordiae University Hospital, 62/63 Eccles Street, Dublin 7, Ireland. brendankelly35@gmail.com},
number = {1},
pages = {60--70},
volume = {85},
year = {2008},
month = {Jan},
language = {eng},
keywords = {European Union, Europe, Politics, Social Values, Decision Making: Organizational, Mental Health Services, Humans, Policy Making, Health Policy, Models: Organizational},
date-added = {2010-03-10 20:18:22 +0100},
date-modified = {2010-03-10 20:18:22 +0100},
doi = {10.1016/j.healthpol.2007.06.005},
pii = {S0168-8510(07)00144-3},
pmid = {17643547},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Kelly-2008-Health%20Policy_The%20emerging%20mental.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7288},
rating = {0}
}

@article{Pepe:2009p5901,
author = {M S Pepe and J W Gu and D E Morris},
journal = {CEBP},
title = {The Potential of Genes and other Markers to Inform about Risk},
abstract = {Background Advances in biotechnology have raised expectations that biomarkers, including genetic profiles, will yield information to accurately predict outcomes for individuals. However, results to date have been disappointing. In addition, statistical methods to quantify the predictive information in markers have not been standardized. Methods We discuss statistical techniques to summarize predictive information including risk distribution curves, receiver operating characteristic curves, R-squared, percent reclassification and net reclassification index. Data are generated from simple models of risk conferred by genetic profiles for individuals in a population. Statistical techniques are illustrated and the risk prediction capacities of different risk models are quantified. Results Risk distribution curves are most informative and relevant to clinical practice. They show proportions of subjects classified into clinically relevant risk categories. In a population in which 10% have the outcome event and subjects are categorized as high risk if their risk exceeds 20%, we found that to identify as high risk more than half of those destined to have an event, either 150 genes each with odds ratio of 1.5 or 250 genes each with odds ratio of 1.25 was required when the minor allele frequencies are 10%. When minor allele frequencies are 30%, either 150 genes with odds ratios equal to 1.25 or 50 genes with odds ratios equal to 1.5 are required.
Conclusions Many highly predictive genes will be required in order to correctly identify substantial numbers of subjects at high risk. A free program is available to calculate risk distributions for alternative scenarios.},
year = {2009},
date-added = {2010-02-17 21:32:47 +0100},
date-modified = {2010-02-17 21:33:44 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Pepe-2009-CEBP_The%20Potential%20of%20Gen.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5901},
rating = {0}
}

@article{Maris:2003aa,
author = {Gunter Maris},
title = {Are attitude items monotone or single peaked? An analysis using bayesian methods},
year = {2003},
month = {Mar},
date-added = {2010-01-03 19:39:02 +0100},
date-modified = {2010-01-03 19:39:03 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Maris-2003-_Are%20attitude%20items%20m.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1225},
rating = {0}
}

@article{Hesse:2008p8351,
author = {Morten Hesse and Joachim Rasmussen and Mads Kjaer Pedersen},
journal = {BMC Psychiatry},
title = {Standardised assessment of personality - a study of validity and reliability in substance abusers},
abstract = {BACKGROUND: Brief screening instruments for co-morbid personality disorders could potentially have great value in substance abuse treatment settings. METHODS: We assessed the psychometric properties of the 8-item Standardised Assessment of Personality - Abbreviated Scale (SAPAS) in a sample of 58 methadone maintenance patients. RESULTS: Internal consistency was modest, but similar to the original value (alpha = 0.62), and test-retest correlation at four months follow-up was moderately encouraging for a short instrument such as this (n = 31, test retest intraclass correlation = 0.58), and change at the mean level was minimal, but marginally significant (from an average of 3.3 to 3.8, p = 0.06). Analyses of nurse ratings of patients' behaviour at the clinic showed that SAPAS was significantly correlated with nurse ratings of externalizing behaviour (r = 0.42, p = 0.001), and Global Assessment of Functioning (r = -0.36, p = 0.006), but unrelated to intoxication (r = 0.02, NS), or withdrawal (r = 0.20, NS). CONCLUSION: There is evidence that the SAPAS is a modestly valid and relatively reliable brief screening measure of personality disorders in patients with ongoing substance abuse undergoing methadone maintenance. It can be used in situations where limited resources are available, and researchers or others wish to get an impression of the degree of personality pathology in a clinical population, as well as for screening purposes.},
affiliation = {Aarhus University, Centre for Alcohol and Drug Research, Copenhagen Division, K{\o}bmagergade 26E, 1150 Copenhagen C, Denmark. mortenhesse@crf.dk},
pages = {7},
volume = {8},
year = {2008},
month = {Jan},
language = {eng},
keywords = {Comorbidity, Male, Middle Aged, Opioid-Related Disorders, Psychometrics, Female, Denmark, Regression Analysis, Reproducibility of Results, Humans, Personality Disorders, Personality Assessment, Interview: Psychological, Substance-Related Disorders, Adult, Multivariate Analysis},
date-added = {2010-03-21 12:53:42 +0100},
date-modified = {2010-03-21 12:53:42 +0100},
doi = {10.1186/1471-244X-8-7},
pii = {1471-244X-8-7},
pmid = {18221511},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hesse-2008-BMC%20Psychiatry_Standardised%20assessm.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8351},
rating = {4}
}

@misc{Komarek:2007,
author = {Arnost Komarek and Emmanuel Lesaffre},
journal = {Miscellaneous},
title = {Generalized linear mixed model with a penalized gaussian mixture as a random effects distribution},
year = {2007},
month = {Jun},
date-added = {2010-01-03 19:37:35 +0100},
date-modified = {2010-07-29 19:40:14 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Komarek-2007-Miscellaneous_Generalized%20linear%20m.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1116},
rating = {0}
}

@article{Held:2010p8164,
author = {Leonhard Held},
journal = {BMC Med Res Methodol},
title = {A nomogram for P values},
abstract = {ABSTRACT: BACKGROUND: P values are the most commonly used tool to measure evidence against a hypothesis. Several attempts have been made to transform P values to minimum Bayes factors and minimum posterior probabilities of the hypothesis under consideration. However, the acceptance of such calibrations in clinical fields is low due to inexperience in interpreting Bayes factors and the need to specify a prior probability to derive a lower bound on the posterior probability. METHODS: I propose a graphical approach which easily translates any prior probability and P value to minimum posterior probabilities. The approach allows to visually inspect the dependence of the minimum posterior probability on the prior probability of the null hypothesis. Likewise, the tool can be used to read off, for fixed posterior probability, the maximum prior probability compatible with a given P value. The maximum P value compatible with a given prior and posterior probability is also available. RESULTS: Use of the nomogram is illustrated based on results from a randomized trial for lung cancer patients comparing a new radiotherapy technique with conventional radiotherapy. CONCLUSION: The graphical device proposed in this paper will enhance the understanding of P values as measures of evidence among non-specialists.},
number = {1},
pages = {21},
volume = {10},
year = {2010},
month = {Mar},
language = {ENG},
date-added = {2010-03-20 19:50:32 +0100},
date-modified = {2010-03-20 19:50:32 +0100},
doi = {10.1186/1471-2288-10-21},
pii = {1471-2288-10-21},
pmid = {20233437},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Held-2010-BMC%20Med%20Res%20Methodol_A%20nomogram%20for%20P%20val.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8164},
rating = {0}
}

@article{Takane:2007p1533,
author = {Y Takane and H Hwang},
journal = {Computational Statistics},
title = {Regularized linear and kernel redundancy analysis},
abstract = {Redundancy analysis (RA) is a versatile technique used to predict multivariate criterion variables from multivariate predictor variables. The reduced-rank feature of RA captures redundant information in the criterion variables in a most parsimonious way. A ridge type of regularization was introduced in RA to deal with the multicollinearity problem among the predictor variables. The regularized linear RA was extended to nonlinear RA using a kernel method to enhance the predictability. The usefulness of the proposed procedures was demonstrated by a Monte Carlo study and through the analysis of two real data sets.},
affiliation = {Department of Psychology, McGill University, 1205 Dr. Penfield Avenue, Montreal, Que., Canada H3A 1B1},
pages = {394--405},
volume = {52},
year = {2007},
keywords = {Bootstrap method, Kernel methods, Permutation tests, Generalized singular value decomposition (GSVD), Reduced rank approximation, J-fold cross validation, Ridge regression, Gaussian kernel},
date-added = {2010-01-07 16:10:25 +0100},
date-modified = {2010-07-29 19:24:30 +0200},
doi = {10.1016/j.csda.2007.02.014},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Takane-2007-Computational%20Statistics_Regularized%20linear%20a.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1533},
rating = {0}
}

@article{Falush:2003p4352,
author = {Daniel Falush and Matthew Stephens and Jonathan K Pritchard},
journal = {Genetics},
title = {Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies},
abstract = {We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations ("admixture linkage disequilibium"). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.},
affiliation = {Department of Molecular Biology, Max-Planck Institut f{\"u}r Infektionsbiologie, Schumann Strasse 21/22, 10117 Berlin, Germany. falush@mpiib-berlin.mpg.de},
number = {4},
pages = {1567--87},
volume = {164},
year = {2003},
month = {Aug},
language = {eng},
keywords = {Animals, African Continental Ancestry Group, Chromosomes, Algorithms, Markov Chains, Genotype, Drosophila melanogaster, Genetic Drift, Evolution: Molecular, Male, Recombination: Genetic, Monte Carlo Method, Models: Genetic, Humans, Linkage (Genetics), Genetic Markers, Alleles, Helicobacter pylori, Computer Simulation, Female, Genetics: Population, Bayes Theorem, Gene Frequency},
date-added = {2010-01-26 13:57:31 +0100},
date-modified = {2010-01-26 13:57:31 +0100},
pmid = {12930761},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Falush-2003-Genetics_Inference%20of%20populat.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4352},
rating = {0}
}

@article{Snapinn:2000p6460,
author = {Steven M Snapinn},
journal = {Curr Control Trials Cardiovasc Med},
title = {Noninferiority trials},
abstract = {Noninferiority trials are intended to show that the effect of a new treatment is not worse than that of an active control by more than a specified margin. These trials have a number of inherent weaknesses that superiority trials do not: no internal demonstration of assay sensitivity, no single conservative analysis approach, lack of protection from bias by blinding, and difficulty in specifying the noninferiority margin. Noninferiority trials may sometimes be necessary when a placebo group can not be ethically included, but it should be recognized that the results of such trials are not as credible as those from a superiority trial.},
affiliation = {Merck Research Laboratories, West Point, Pennsylvania, USA. snapinns@merck.com},
number = {1},
pages = {19--21},
volume = {1},
year = {2000},
month = {Jan},
language = {ENG},
date-added = {2010-02-23 08:31:18 +0100},
date-modified = {2010-02-23 08:31:18 +0100},
pmid = {11714400},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Snapinn-2000-Curr%20Control%20Trials%20Cardiovasc%20Med_Noninferiority%20trial.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6460},
read = {Yes},
rating = {0}
}

@article{Pihur:2007p12246,
author = {Vasyl Pihur and Susmita Datta and Somnath Datta},
journal = {Bioinformatics},
title = {Weighted rank aggregation of cluster validation measures: a Monte Carlo cross-entropy approach},
abstract = {MOTIVATION: Biologists often employ clustering techniques in the explorative phase of microarray data analysis to discover relevant biological groupings. Given the availability of numerous clustering algorithms in the machine-learning literature, an user might want to select one that performs the best for his/her data set or application. While various validation measures have been proposed over the years to judge the quality of clusters produced by a given clustering algorithm including their biological relevance, unfortunately, a given clustering algorithm can perform poorly under one validation measure while outperforming many other algorithms under another validation measure. A manual synthesis of results from multiple validation measures is nearly impossible in practice, especially, when a large number of clustering algorithms are to be compared using several measures. An automated and objective way of reconciling the rankings is needed. RESULTS: Using a Monte Carlo cross-entropy algorithm, we successfully combine the ranks of a set of clustering algorithms under consideration via a weighted aggregation that optimizes a distance criterion. The proposed weighted rank aggregation allows for a far more objective and automated assessment of clustering results than a simple visual inspection. We illustrate our procedure using one simulated as well as three real gene expression data sets from various platforms where we rank a total of eleven clustering algorithms using a combined examination of 10 different validation measures. The aggregate rankings were found for a given number of clusters k and also for an entire range of k. AVAILABILITY: R code for all validation measures and rank aggregation is available from the authors upon request. SUPPLEMENTARY INFORMATION: Supplementary information are available at http://www.somnathdatta.org/Supp/RankCluster/supp.htm.},
affiliation = {Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY 40202, USA.},
number = {13},
pages = {1607--15},
volume = {23},
year = {2007},
month = {Jul},
language = {eng},
keywords = {Artificial Intelligence, Oligonucleotide Array Sequence Analysis, Pattern Recognition: Automated, Monte Carlo Method, Gene Expression Profiling, Entropy, Algorithms, Cluster Analysis},
date-added = {2010-06-09 20:08:10 +0200},
date-modified = {2010-06-25 21:45:16 +0200},
doi = {10.1093/bioinformatics/btm158},
pii = {btm158},
pmid = {17483500},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Pihur-2007-Bioinformatics_Weighted%20rank%20aggreg.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12246},
rating = {4}
}

@article{Clarke:2008p4072,
author = {Robert Clarke and Habtom W Ressom and Antai Wang and Jianhua Xuan and Minetta C Liu and Edmund A Gehan and Yue Wang},
journal = {Nat Rev Cancer},
title = {The properties of high-dimensional data spaces: implications for exploring gene and protein expression data},
abstract = {High-throughput genomic and proteomic technologies are widely used in cancer research to build better predictive models of diagnosis, prognosis and therapy, to identify and characterize key signalling networks and to find new targets for drug development. These technologies present investigators with the task of extracting meaningful statistical and biological information from high-dimensional data spaces, wherein each sample is defined by hundreds or thousands of measurements, usually concurrently obtained. The properties of high dimensionality are often poorly understood or overlooked in data modelling and analysis. From the perspective of translational science, this Review discusses the properties of high-dimensional data spaces that arise in genomic and proteomic studies and the challenges they can pose for data analysis and interpretation.},
affiliation = {Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, 3970 Reservoir Road NW, Washington, DC 20057, USA.},
number = {1},
pages = {37--49},
volume = {8},
year = {2008},
month = {Jan},
language = {eng},
keywords = {Prognosis, Proteins, Models: Genetic, Proteome, Neoplasms, Genome, Models: Statistical, Humans, Genes, Gene Expression Regulation, Transcription: Genetic},
date-added = {2010-01-19 15:50:42 +0100},
date-modified = {2010-01-19 15:50:42 +0100},
doi = {10.1038/nrc2294},
pii = {nrc2294},
pmid = {18097463},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Clarke-2008-Nat%20Rev%20Cancer_The%20properties%20of%20hi.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4072},
rating = {0}
}

@article{Acar:2007p11617,
author = {E Acar and B Yener},
title = {Unsupervised Multiway Data Analysis: A Literature Survey},
abstract = {Multiway data analysis captures multilinear structures in higher-order datasets, where data have more than two modes. Standard two-way methods commonly applied on matrices often fail to find the underlying structures in multiway ar- rays. With increasing number of application areas, multiway data analysis has become popular as an exploratory analy- sis tool. We provide a review of significant contributions in literature on multiway models, algorithms as well as their applications in diverse disciplines including chemometrics, neuroscience, computer vision, and social network analysis.},
year = {2007},
date-added = {2010-05-11 21:46:44 +0200},
date-modified = {2010-05-11 21:47:30 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Acar-2007-_Unsupervised%20Multiwa.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11617},
rating = {4}
}

@article{DeBoeck:2008p1779,
author = {Paul De Boeck},
journal = {Psychometrika},
title = {Random item IRT models},
abstract = {It is common practice in IRT to consider items as fixed and persons as random. Both, continuous and categorical person parameters are most often random variables, whereas for items only continuous parameters are used and they are commonly of the fixed type, although exceptions occur. It is shown in the present article that random item parameters make sense theoretically, and that in practice the random item approach is promising to handle several issues, such as the measurement of persons, the explanation of item difficulties, and trouble shooting with respect to DIF. In correspondence with these issues, three parts are included. All three rely on the Rasch model as the simplest model to study, and the same data set is used for all applications. First, it is shown that the Rasch model with fixed persons and random items is an interesting measurement model, both, in theory, and for its goodness of fit. Second, the linear logistic test model with an error term is introduced, so that the explanation of the item difficulties based on the item properties does not need to be perfect. Finally, two more models are presented: the random item profile model (RIP) and the random item mixture model (RIM). In the RIP, DIF is not considered a discrete phenomenon, and when a robust regression approach based on the RIP difficulties is applied, quite good DIF identification results are obtained. In the RIM, no prior anchor sets are defined, but instead a latent DIF class of items is used, so that posterior anchoring is realized (anchoring based on the item mixture). It is shown that both approaches are promising for the identification of DIF.},
number = {4},
pages = {533--559},
volume = {73},
year = {2008},
keywords = {measurement, DIF, generalizability, LLTM, random effects},
date-added = {2010-01-09 21:46:05 +0100},
date-modified = {2010-07-29 20:46:12 +0200},
doi = {10.1007/S11336-008-9092-X},
local-url = {file://localhost/Users/chl/Dropbox/Papers/De%20Boeck-2008-Psychometrika_Random%20item%20IRT%20mode.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1779},
rating = {4}
}

@article{Beguin:2001,
author = {A A B{\'e}guin and C A W Glas},
journal = {Psychometrika},
title = {MCMC estimation and some fit analysis of multidimensional IRT models},
pages = {471--488},
volume = {66},
year = {2001},
date-added = {2010-01-10 11:33:18 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/B%C3%A9guin-2001-Psychometrika_MCMC%20estimation%20and.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1880},
rating = {0}
}

@article{Horvitz:1952p6324,
author = {D G Horvitz and D J Thompson},
journal = {JAMA},
title = {A Generalization of Sampling Without Replacement From a Finite Universe},
number = {260},
pages = {663--685},
volume = {47},
year = {1952},
date-added = {2010-02-20 21:18:07 +0100},
date-modified = {2010-07-29 20:01:35 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Horvitz-1952-JAMA_A%20Generalization%20of.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6324},
rating = {3}
}

@article{Albert:1993p6278,
author = {J H Albert and S Chib},
journal = {JAMA},
title = {Bayesian Analysis of Binary and Polychotomous Response Data},
number = {422},
pages = {669--679},
volume = {88},
year = {1993},
date-added = {2010-02-20 17:56:34 +0100},
date-modified = {2010-07-29 20:01:35 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Albert-1993-JAMA_Bayesian%20Analysis%20of.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6278},
read = {Yes},
rating = {0}
}

@article{Lee:2007p2946,
author = {Seung Yeoun Lee and Yujin Chung and Robert C Elston and Youngchul Kim and Taesung Park},
journal = {Bioinformatics},
title = {Log-linear model-based multifactor dimensionality reduction method to detect gene gene interactions},
abstract = {MOTIVATION: The identification and characterization of susceptibility genes that influence the risk of common and complex diseases remains a statistical and computational challenge in genetic association studies. This is partly because the effect of any single genetic variant for a common and complex disease may be dependent on other genetic variants (gene-gene interaction) and environmental factors (gene-environment interaction). To address this problem, the multifactor dimensionality reduction (MDR) method has been proposed by Ritchie et al. to detect gene-gene interactions or gene-environment interactions. The MDR method identifies polymorphism combinations associated with the common and complex multifactorial diseases by collapsing high-dimensional genetic factors into a single dimension. That is, the MDR method classifies the combination of multilocus genotypes into high-risk and low-risk groups based on a comparison of the ratios of the numbers of cases and controls. When a high-order interaction model is considered with multi-dimensional factors, however, there may be many sparse or empty cells in the contingency tables. The MDR method cannot classify an empty cell as high risk or low risk and leaves it as undetermined. RESULTS: In this article, we propose the log-linear model-based multifactor dimensionality reduction (LM MDR) method to improve the MDR in classifying sparse or empty cells. The LM MDR method estimates frequencies for empty cells from a parsimonious log-linear model so that they can be assigned to high-and low-risk groups. In addition, LM MDR includes MDR as a special case when the saturated log-linear model is fitted. Simulation studies show that the LM MDR method has greater power and smaller error rates than the MDR method. The LM MDR method is also compared with the MDR method using as an example sporadic Alzheimer's disease.},
affiliation = {Department of Applied Mathematics, Sejong University, 98 Gunja-Dong Kwangjin-Gu, Seoul 143-747, Korea.},
number = {19},
pages = {2589--95},
volume = {23},
year = {2007},
month = {Oct},
language = {eng},
keywords = {Multigene Family, Models: Genetic, Computer Simulation, Risk Assessment, Alzheimer Disease, Algorithms, Protein Interaction Mapping, Genetic Predisposition to Disease, Humans, Statistics as Topic, Nerve Tissue Proteins},
date-added = {2010-01-13 23:05:37 +0100},
date-modified = {2010-01-13 23:05:37 +0100},
doi = {10.1093/bioinformatics/btm396},
pii = {btm396},
pmid = {17872915},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2946},
rating = {0}
}

@article{Vermunt:2009p6243,
author = {J K Vermunt},
title = {Longitudinal Research Using Mixture Models},
abstract = {This chapter provides a state-of-the-art overview of the use of mixture and latent class models for the analysis of longitudinal data. It first describes the three basic types mixture models for longitudinal data: the mixture growth, mixture Markov, and latent Markov model. Subsequently, it presents an integrating frame- work merging various recent developments in software and algorithms, yielding mixture models for longitudinal data that can (1) not only be used with categorical, but also with continuous response variables (as well as combinations of these), (2) be used with very long time series, (3) include covariates (which can be numeric or categorical, as well as time-constant or time-varying), (4) include parameter restric- tions yielding interesting measurement models, and (5) deal with missing values (which is very important in longitudinal research). Moreover, it discusses other ad- vanced models, such as latent Markov models with dependent classification errors across time points, mixture growth and latent Markov models with random effects, and latent Markov models for multilevel data and multiple processes. The appendix shows how the presented models can be defined using the Latent GOLD syntax system (Vermunt and Magidson, 2005, 2008).},
year = {2009},
date-added = {2010-02-19 21:19:37 +0100},
date-modified = {2010-02-19 21:20:05 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Vermunt-2009-_Longitudinal%20Researc.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6243},
rating = {0}
}

@article{Saavalainen:2008p7897,
author = {Pia M Saavalainen and Laila Luoma and Eila Laukkanen and Dermot M Bowler and Sara M{\"a}{\"a}tt{\"a} and Vesa Kiviniemi and Eila Herrg{\aa}rd},
journal = {Eur J Paediatr Neurol},
title = {School performance of adolescents born preterm: neuropsychological and background correlates},
abstract = {In this longitudinal study the development of preterm and control children was followed from infancy until adolescence. School performance at the age of 16 in subjects born very preterm with a gestational age (GA) of <or= 32 weeks was compared with the performance of adolescents born full-term. None of the subjects had major disabilities. The study groups performed similarly in most school subjects, including mathematics, the second foreign language and the native language (Finnish). Subjects in the preterm group achieved significantly higher grade points in the first foreign language than control subjects. In particular, the difference was evident between the preterm and control boys. The extremely preterm group with a GA <or= 29 weeks did not differ from the more mature group with a GA between 30 and 32 weeks in terms of the school grade points. Verbal and performance scale IQs as assessed at the age of 9 were of primary importance in predicting school success in adolescence. The results suggest a good outcome, measured by school grade scores at 16 years of age, of the subjects born very preterm.},
affiliation = {Department of Psychology, University of Joensuu, PO Box 111, 80101 Joensuu, Finland. pia.saavalainen@kuh.fi},
number = {3},
pages = {246--52},
volume = {12},
year = {2008},
month = {May},
language = {eng},
keywords = {Pregnancy, Child Development, Premature Birth, Intelligence, Intelligence Tests, Infant: Newborn, Neuropsychological Tests, Achievement, Humans, Male, Adolescent, Female, Infant: Premature},
date-added = {2010-03-20 19:20:38 +0100},
date-modified = {2010-03-20 19:20:38 +0100},
doi = {10.1016/j.ejpn.2007.08.007},
pii = {S1090-3798(07)00156-0},
pmid = {17933569},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Saavalainen-2008-Eur%20J%20Paediatr%20Neurol_School%20performance%20o.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7897},
rating = {0}
}

@article{Pfeifle:1999p4484,
author = {W G Pfeifle and D E Gussak and C A Keegan},
journal = {J Allied Health},
title = {Perspectives on clinical outcomes assessment: a view for the allied health professions},
abstract = {The purpose of clinical outcomes assessment is well recognized by allied health professionals, but several obstacles have impeded the conduct of such research in the allied health professions. Many professionals have difficulty in determining how to begin. To explore the research possibilities already available within the health care environment, a way to visualize and organize the potential variables is needed. In light of a taxonomy of patient outcomes, an effort is made here to summarize and portray the characteristics of the delivery system, the environmental and structural factors, and both patient and provider attributes. Many of these aspects of outcomes investigations are within the purview and capabilities of allied health professionals. Through a division of labor among the professions, a mosaic can be collectively created that validates what they do and the value they add to patient care.},
affiliation = {College of Allied Health Professionals, University of Kentucky, Lexington 40536-0003, USA.},
number = {4},
pages = {240--6},
volume = {28},
year = {1999},
month = {Dec},
language = {eng},
keywords = {Job Description, Terminology as Topic, Health Services Research, Models: Organizational, Allied Health Personnel, Outcome Assessment (Health Care), Attitude of Health Personnel, Patient Participation, Humans, Health Knowledge: Attitudes: Practice},
date-added = {2010-01-29 21:38:47 +0100},
date-modified = {2010-01-29 21:38:47 +0100},
pmid = {10614557},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Pfeifle-1999-J%20Allied%20Health_Perspectives%20on%20clin.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4484},
rating = {0}
}

@article{Husain:2006p8234,
author = {N Husain and I Bevc and M Husain and I B Chaudhry and N Atif and A Rahman},
journal = {Arch Womens Ment Health},
title = {Prevalence and social correlates of postnatal depression in a low income country},
abstract = {BACKGROUND: Postnatal depression is an important public health problem worldwide. Recent evidence suggests that rates may be relatively higher in developing countries. We aimed to explore the prevalence of postnatal depression and its association with social support and other risk factors in a sample of Pakistani women. METHODS: Population-based survey of 149 women at 12 weeks postnatal using the Edinburgh Postnatal Depression Scale (EPDS), Multidimensional Scale of Perceived Social Support (MSPSS) and Personal Information Questionnaire (PIQ). RESULTS: Thirty six percent women scored > or =12 on EPDS. High depression score was associated with lower social support, increased stressful life events in the preceding year and higher levels of psychological distress in the antenatal period. CONCLUSIONS: There is a high prevalence of postnatal depression in Pakistani women. Early interventions should be developed that target the antenatal period and strengthen social support networks in women at risk.},
affiliation = {Centre for Addiction and Mental Health, Toronto, Canada.},
number = {4},
pages = {197--202},
volume = {9},
year = {2006},
month = {Jul},
language = {eng},
keywords = {Depression: Postpartum, Pregnancy, Poverty, Social Support, Adult, Depression, Questionnaires, Prevalence, Pakistan, Social Class, Humans, Maternal Health Services, Adolescent, Female, Mothers, Risk Assessment},
date-added = {2010-03-20 20:00:30 +0100},
date-modified = {2010-03-20 20:00:31 +0100},
doi = {10.1007/s00737-006-0129-9},
pmid = {16633740},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8234},
rating = {0}
}

@article{Stephens:2009p9933,
author = {Matthew Stephens and David J Balding},
journal = {Nat Rev Genet},
title = {Bayesian statistical methods for genetic association studies},
abstract = {Bayesian statistical methods have recently made great inroads into many areas of science, and this advance is now extending to the assessment of association between genetic variants and disease or other phenotypes. We review these methods, focusing on single-SNP tests in genome-wide association studies. We discuss the advantages of the Bayesian approach over classical (frequentist) approaches in this setting and provide a tutorial on basic analysis steps, including practical guidelines for appropriate prior specification. We demonstrate the use of Bayesian methods for fine mapping in candidate regions, discuss meta-analyses and provide guidance for refereeing manuscripts that contain Bayesian analyses.},
affiliation = {Departments of Statistics and Human Genetics, University of Chicago, Chicago, IL 60637, USA. mstephens@uchicago.edu},
number = {10},
pages = {681--90},
volume = {10},
year = {2009},
month = {Oct},
language = {eng},
keywords = {Genome-Wide Association Study, Polymorphism: Single Nucleotide, Humans, Bayes Theorem},
date-added = {2010-03-31 16:08:58 +0200},
date-modified = {2010-03-31 16:08:58 +0200},
doi = {10.1038/nrg2615},
pii = {nrg2615},
pmid = {19763151},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Stephens-2009-Nat%20Rev%20Genet_Bayesian%20statistical.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9933},
read = {Yes},
rating = {0}
}

@article{Breiman1996,
author = {L Breiman},
journal = {Machine Learning},
title = {Bagging predictors},
number = {2},
pages = {123--140},
volume = {24},
year = {1996},
date-added = {2010-01-12 14:26:51 +0100},
date-modified = {2010-07-29 19:38:49 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Breiman-1996-Machine%20Learning_Bagging%20predictors.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2539},
rating = {0}
}

@article{Maris:2003ac,
author = {Gunter Maris},
title = {Concerning the identification of the 3PL model},
year = {2003},
month = {Mar},
date-added = {2010-01-03 19:39:03 +0100},
date-modified = {2010-01-03 19:39:03 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Maris-2003-_Concerning%20the%20ident.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1216},
rating = {0}
}

@article{Stegle:2010p6661,
author = {O Stegle and K Sharp and M Rattray and J Winn},
title = {A Comparison of Inference Methods for Sparse Factor Analysis Models},
date-added = {2010-03-03 20:42:47 +0100},
date-modified = {2010-03-03 20:43:19 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Stegle--_A%20Comparison%20of%20Infe.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6661},
rating = {0}
}

@article{Neale:2008p9581,
author = {Benjamin M Neale and Shaun Purcell},
journal = {Am J Med Genet B Neuropsychiatr Genet},
title = {The positives, protocols, and perils of genome-wide association},
abstract = {Genome-wide association aims to comprehensively survey genetic variation for the purposes of disease and trait mapping. We provide a brief history of the development of genetic technology necessary to realize genome-wide association. From there we identify and review the publicly available resources for conducting such work including the molecular technologies, genomic databases, and analytic tools. Following on from the analytic tools, we highlight common analytic considerations, ranging from study design, quality control, and data cleaning to association analysis and replication. We conclude with a look toward future developments such as the analysis of copy number variation and integration of expression and epigenetic phenomenon into genome-wide association.},
affiliation = {Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, De Crespigny Park, London, UK. b.neale@iop.kcl.ac.uk},
number = {7},
pages = {1288--94},
volume = {147B},
year = {2008},
month = {Oct},
language = {eng},
keywords = {Genetic Research, Genetic Techniques, Humans, Genome: Human, Genetic Predisposition to Disease, Biotechnology},
date-added = {2010-03-24 22:26:50 +0100},
date-modified = {2010-03-24 22:26:50 +0100},
doi = {10.1002/ajmg.b.30747},
pmid = {18500721},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Neale-2008-Am%20J%20Med%20Genet%20B%20Neuropsychiatr%20Genet_The%20positives%20proto.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9581},
read = {Yes},
rating = {0}
}

@article{Sohn:2008p3402,
author = {I Sohn and S Kim and C Hwang and J W Lee and J Shim},
journal = {Methods Inf Med},
title = {Support vector machine quantile regression for detecting differentially expressed genes in microarray analysis},
abstract = {OBJECTIVES: One of the main objectives of microarray analysis is to identify genes differentially expressed under two distinct experimental conditions. This task is complicated by the noisiness of data and the large number of genes that are examined. Fold change (FC) based gene selection often misleads because error variability for each gene is heterogeneous in different intensity ranges. Several statistical methods have been suggested, but some of them result in high false positive rates because they make very strong parametric assumptions. METHODS: We present support vector quantile regression (SVMQR) using iterative reweighted least squares (IRWLS) procedure based on the Newton method instead of usual quadratic programming algorithms. This procedure makes it possible to derive the generalized approximate cross validation (GACV) method for choosing the parameters which affect the performance of SVMAR. We propose SVMQR based on a novel method for identifying differentially expressed genes with a small number of replicated microarrays. RESULTS: We applied SVMQR to both three biological dataset and simulated dataset and showed that it performed more reliably and consistently than FC-based gene selection, Newton's method based on the posterior odds of change, or the nonparametric t-test variant implemented in significance analysis of microarrays (SAM). CONCLUSIONS: The SVMQR method was an exploratory method for cDNA microarray experiments to identify genes with different expression levels between two types of samples (e.g., tumor versus normal tissue). The SVMQR method performed well in the situation where error variability for each gene was heterogeneous in intensity ranges.},
affiliation = {Skin Research Institute, AmorePacific R{\&}D Center, 314-1 Sanggal-dong, Kiheung-gu, Yongin-si, Kyounggi-do 449-729, Korea. sundance@amorepacific.com},
number = {5},
pages = {459--67},
volume = {47},
year = {2008},
month = {Jan},
language = {eng},
keywords = {Genetic Variation, Gene Expression Profiling, Pattern Recognition: Automated, Algorithms, Humans, Oligonucleotide Array Sequence Analysis},
date-added = {2010-01-15 14:43:18 +0100},
date-modified = {2010-01-15 14:43:18 +0100},
pii = {08050459},
pmid = {18852921},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3402},
rating = {0}
}

@article{Hanmer:2009p11769,
author = {Janel Hanmer},
journal = {Value Health},
title = {Predicting an SF-6D preference-based score using MCS and PCS scores from the SF-12 or SF-36},
abstract = {BACKGROUND: The SF-6D preference-based scoring system was developed several years after the SF-12 and SF-36 instruments. A method to predict SF-6D scores from information in previous reports would facilitate backwards comparisons and the use of these reports in cost-effectiveness analyses. METHODS: This report uses data from the 2001-2003 Medical Expenditures Panel Survey (MEPS), the Beaver Dam Health Outcomes Survey, and the National Health Measurement Study. SF-6D scores were modeled using age, sex, mental component summary (MCS) score, and physical component summary (PCS) score from the 2002 MEPS. The resulting SF-6D prediction equation was tested with the other datasets for groups of different sizes and groups stratified by age, MCS score, PCS score, sum of MCS and PCS scores, and SF-6D score. RESULTS: The equation can be used to predict an average SF-6D score using average age, proportion female, average MCS score, and average PCS score. Mean differences between actual and predicted average SF-6D scores in out-of-sample tests was -0.001 (SF-12 version 1), -0.013 (SF-12 version 2), -0.007 (SF-36 version 1), and -0.010 (SF-36 version 2). Ninety-five percent credible intervals around these point estimates range from +/-0.045 for groups with 10 subjects to +/-0.008 for groups with more than 300 subjects. These results were consistent for a wide range of ages, MCS scores, PCS scores, sum of MCS and PCS scores, and SF-6D scores. SF-6D scores from the SF-36 and SF-12 from the same data set were found to be substantially different. CONCLUSIONS: Simple equation predicts an average SF-6D preference-based score from widely published information.},
affiliation = {Department of Population Health Sciences, University of Wisconsin-Madison, Madison, WI 53726, USA. jehanmer@wisc.edu},
number = {6},
pages = {958--66},
volume = {12},
year = {2009},
month = {Sep},
language = {eng},
keywords = {Aged, Female, Cost-Benefit Analysis, Middle Aged, Young Adult, United States, Adult, Aged: 80 and over, Models: Statistical, Questionnaires, Humans, Male, Health Status Indicators, Sex Factors, Health Surveys},
date-added = {2010-05-23 10:39:11 +0200},
date-modified = {2010-05-23 10:39:11 +0200},
doi = {10.1111/j.1524-4733.2009.00535.x},
pii = {VHE535},
pmid = {19490549},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hanmer-2009-Value%20Health_Predicting%20an%20SF-6D.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11769},
rating = {0}
}

@article{Grossman:2010p5371,
author = {Sharon R Grossman and Ilya Shylakhter and Elinor K Karlsson and Elizabeth H Byrne and Shannon Morales and Gabriel Frieden and Elizabeth Hostetter and Elaine Angelino and Manuel Garber and Or Zuk and Eric S Lander and Stephen F Schaffner and Pardis C Sabeti},
journal = {Science},
title = {A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection},
abstract = {The human genome contains hundreds of regions whose patterns of genetic variation indicate recent positive natural selection, yet for most the underlying gene and the advantageous mutation remain unknown. We developed a method, Composite of Multiple Signals (CMS), that combines tests for multiple signals of selection and increases resolution by up to 100-fold. Applying CMS to candidate regions from the International Haplotype Map, we localized population-specific selective signals to 55 kb (median), identifying known and novel causal variants. CMS can identify not just individual loci but implicates precise variants selected by evolution.},
affiliation = {Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.},
pages = {},
year = {2010},
month = {Jan},
language = {ENG},
date-added = {2010-02-11 09:31:30 +0100},
date-modified = {2010-07-29 19:50:10 +0200},
doi = {10.1126/science.1183863},
pii = {science.1183863},
pmid = {20056855},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5371},
rating = {0}
}

@article{Krosnick:1991,
author = {JA Krosnick},
journal = {Applied Cognitive Psychology},
title = {Response strategies for coping with the cognitive demands on attitude measures in surveys},
abstract = {This paper proposes that when optimally answering a survey question would require substantial cognitive effort, some repondents simply provide a satisfactory answer instead. This behaviour, called satisficing, can take the form of either (1) incomplete or biased information retrieval and/or information integration, or (2) no information retrieval or integration at all. Satisficing may lead respondents to employ a variety of response strategies, including choosing the first response alternative that seems to constitute a reasonable answer, agreeing with an assertion made by a question, endorsing the status quo instead of endorsing social change, failing to differentiate among a set of diverse objects in ratings, saying don't knowinstead of reporting an opinion, and randomly choosing among the response alternatives offered. This paper specifies a wide range of factors that are likely to encourage satisficing, and reviews relevant evidence evaluating these speculations. Many useful directions for future research are suggested.},
pages = {213--236},
volume = {5},
year = {1991},
date-added = {2010-01-03 19:34:17 +0100},
date-modified = {2010-07-29 19:15:39 +0200},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p970},
rating = {0}
}

@article{Trochesset:2004p13481,
author = {M Trochesset and A Bonner},
title = {Clustering Labeled Data and Cross-Validation for Classification with Few Positives in Yeast},
year = {2004},
date-added = {2010-07-01 20:51:37 +0200},
date-modified = {2010-07-01 20:52:10 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Trochesset-2004-_Clustering%20Labeled%20D.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13481},
rating = {0}
}

@article{Frie:2009p5483,
author = {Kirstin Grosse Frie and Christian Janssen},
journal = {International journal of public health},
title = {Social inequality, lifestyles and health - a non-linear canonical correlation analysis based on the approach of Pierre Bourdieu},
abstract = {OBJECTIVES: Based on the theoretical and empirical approach of Pierre Bourdieu, a multivariate non-linear method is introduced as an alternative way to analyse the complex relationships between social determinants and health. METHODS: The analysis is based on face-to-face interviews with 695 randomly selected respondents aged 30 to 59. Variables regarding socio-economic status, life circumstances, lifestyles, health-related behaviour and health were chosen for the analysis. In order to determine whether the respondents can be differentiated and described based on these variables, a non-linear canonical correlation analysis (OVERALS) was performed. RESULTS: The results can be described on three dimensions; Eigenvalues add up to the fit of 1.444, which can be interpreted as approximately 50 % of explained variance. The three-dimensional space illustrates correspondences between variables and provides a framework for interpretation based on latent dimensions, which can be described by age, education, income and gender. CONCLUSION: Using non-linear canonical correlation analysis, health characteristics can be analysed in conjunction with socio-economic conditions and lifestyles. Based on Bourdieus theoretical approach, the complex correlations between these variables can be more substantially interpreted and presented.},
affiliation = {Department of Medical Sociology, Center of Psychosocial Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany. k.grosse-frie@uke.uni-hamburg.de},
number = {4},
pages = {213--21},
volume = {54},
year = {2009},
month = {Jan},
language = {eng},
keywords = {Female, Middle Aged, Adult, Germany, Life Style, Humans, Multivariate Analysis, Interviews as Topic, Nonlinear Dynamics, Social Class, Health Status, Sociology: Medical, Male},
date-added = {2010-02-12 14:43:56 +0100},
date-modified = {2010-02-12 14:43:56 +0100},
doi = {10.1007/s00038-009-8017-5},
pmid = {19418020},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5483},
rating = {0}
}

@article{Shi:2006p12866,
author = {T Shi and S Horvath},
journal = {Journal of Computational and Graphical Statistics},
title = {Unsupervised Learning With Random Forest Predictors},
abstract = {A random forest (RF) predictor is an ensemble of individual tree predictors. As part of their construction, RF predictors naturally lead to a dissimilarity measure between the observations. One can also define an RF dissimilarity measure between unlabeled data: the idea is to construct an RF predictor that distinguishes the ``observed'' data from suitably generated synthetic data. The observed data are the original unlabeled data and the synthetic data are drawn from a reference distribution. Here we describe the properties of the RF dissimilarity and make recommendations on how to use it in practice.
An RF dissimilarity can be attractive because it handles mixed variable types well, is invariant to monotonic transformations of the input variables, and is robust to outlying observations. The RF dissimilarity easily deals with a large number of variables due to its in- trinsic variable selection; for example, the Addcl1 RF dissimilarity weighs the contribution of each variable according to how dependent it is on other variables.
We find that the RF dissimilarity is useful for detecting tumor sample clusters on the basis of tumor marker expressions. In this application, biologically meaningful clusters can often be described with simple thresholding rules.},
number = {1},
pages = {118--138},
volume = {15},
year = {2006},
date-added = {2010-06-24 12:47:23 +0200},
date-modified = {2010-06-24 12:49:06 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Shi-2006-Journal%20of%20Computational%20and%20Graphical%20Statistics_Unsupervised%20Learnin.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12866},
rating = {0}
}

@article{Kissita:2010p12004,
author = {G Kissita and R A Makany and D Miz{\`e}re},
journal = {Afrika Statistika},
title = {L'analyse CONCORG Simultan{\'e}e : La M{\'e}thode CONCORGS},
abstract = {The analysis CONCORG is a method that investigates the link between two multi-tables (partitioned sets of variables measured on the same individuals). It allows to detail the contributions of partial sub-tables form- ing the two tables. CONCORG is an extension of Concor, which itself is an extension of the inter-battery analysis. This new method performs successive determinations of the solution. In this article, we propose three criteria that enables to simultaneously identify solutions. It happens that the three cri- teria are equivalent to the solution. In this sense, our method, denoted as CONCORGS, is a generalization of CONCORG. Finally, we establish a fun- damental property checked at the optimum these three criteria.},
year = {2010},
date-added = {2010-05-23 17:31:46 +0200},
date-modified = {2010-05-23 17:33:02 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Kissita-2010-Afrika%20Statistika_L%E2%80%99analyse%20CONCORG%20Si.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12004},
rating = {0}
}

@article{Regier:2007p10724,
author = {Terry Regier and Paul Kay and Naveen Khetarpal},
journal = {Proc Natl Acad Sci USA},
title = {Color naming reflects optimal partitions of color space},
abstract = {The nature of color categories in the world's languages is contested. One major view holds that color categories are organized around universal focal colors, whereas an opposing view holds instead that categories are defined at their boundaries by linguistic convention. Both of these standardly opposed views are challenged by existing data. Here, we argue for a third view based on a proposal by Jameson and D'Andrade [Jameson KA, D'Andrade RG (1997) in Color Categories in Thought and Language, eds Hardin CL, Maffi L (Cambridge Univ Press, Cambridge, U.K.), pp 295-319]: that color naming across languages reflects optimal or near-optimal divisions of an irregularly shaped perceptual color space. We formalize this idea, test it against color-naming data from a broad range of languages and show that it accounts for universal tendencies in color naming while also accommodating some observed cross-language variation.},
affiliation = {Department of Psychology, University of Chicago, 5848 South University Avenue, Chicago, IL 60637, USA. regier@uchicago.edu},
number = {4},
pages = {1436--41},
volume = {104},
year = {2007},
month = {Jan},
language = {eng},
keywords = {Color, Language},
date-added = {2010-04-10 03:26:16 +0200},
date-modified = {2010-04-10 03:26:16 +0200},
doi = {10.1073/pnas.0610341104},
pii = {0610341104},
pmid = {17229840},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Regier-2007-Proc%20Natl%20Acad%20Sci%20USA_Color%20naming%20reflect.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10724},
rating = {0}
}

@article{DiazUriarte:2007p2577,
author = {Ram{\'o}n Diaz-Uriarte},
journal = {BMC Bioinformatics},
title = {GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest},
abstract = {BACKGROUND: Microarray data are often used for patient classification and gene selection. An appropriate tool for end users and biomedical researchers should combine user friendliness with statistical rigor, including carefully avoiding selection biases and allowing analysis of multiple solutions, together with access to additional functional information of selected genes. Methodologically, such a tool would be of greater use if it incorporates state-of-the-art computational approaches and makes source code available. RESULTS: We have developed GeneSrF, a web-based tool, and varSelRF, an R package, that implement, in the context of patient classification, a validated method for selecting very small sets of genes while preserving classification accuracy. Computation is parallelized, allowing to take advantage of multicore CPUs and clusters of workstations. Output includes bootstrapped estimates of prediction error rate, and assessments of the stability of the solutions. Clickable tables link to additional information for each gene (GO terms, PubMed citations, KEGG pathways), and output can be sent to PaLS for examination of PubMed references, GO terms, KEGG and and Reactome pathways characteristic of sets of genes selected for class prediction. The full source code is available, allowing to extend the software. The web-based application is available from http://genesrf2.bioinfo.cnio.es. All source code is available from Bioinformatics.org or The Launchpad. The R package is also available from CRAN. CONCLUSION: varSelRF and GeneSrF implement a validated method for gene selection including bootstrap estimates of classification error rate. They are valuable tools for applied biomedical researchers, specially for exploratory work with microarray data. Because of the underlying technology used (combination of parallelization with web-based application) they are also of methodological interest to bioinformaticians and biostatisticians.},
affiliation = {Statistical Computing Team, Structural Biology and Biocomputing Programme, Spanish National Cancer Center (CNIO), Melchor Fern{\'a}ndez Almagro 3, Madrid, 28029, Spain. rdiaz02@gmail.com},
pages = {328},
volume = {8},
year = {2007},
month = {Jan},
language = {eng},
keywords = {Gene Expression Profiling, User-Computer Interface, Algorithms, Internet, Oligonucleotide Array Sequence Analysis, Software, Data Interpretation: Statistical},
date-added = {2010-01-12 22:23:46 +0100},
date-modified = {2010-01-12 22:23:47 +0100},
doi = {10.1186/1471-2105-8-328},
pii = {1471-2105-8-328},
pmid = {17767709},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2577},
rating = {0}
}

@article{Adair:2001p8804,
author = {L S Adair},
journal = {Pediatrics},
title = {Size at birth predicts age at menarche},
abstract = {OBJECTIVE: This study examines the relationship of intrauterine growth, measured by size and maturity at birth, to age at menarche, while also considering a wide range of other factors that may affect maturation. The research is motivated by the current debate about the importance of the prenatal environment as a determinant of later disease risk. METHODS: Data were collected during the Cebu Longitudinal Health and Nutrition Survey. This community-based study has followed a cohort of several thousand Filipino infants since their birth in 1983 to 1984. Participants live in urban and rural communities of Metro Cebu, the second largest metropolitan area of the Philippines. The analysis sample includes 997 girls 14 to 15 years of age. The main outcome measure is age at menarche, determined from girls' self-report of the month and year of first menses. Factors that influenced age at menarche were identified using Weibull parametric survival time models. The main exposure variables of interest included weight and length (measured by trained field staff) and gestational age (assessed from mother's reported date of last menstrual period, augmented by clinical assessments at birth). The analysis also takes into account a wide range of other factors that are likely to affect age at menarche. These include the girls' early postnatal growth rates, premenarcheal body composition (body mass index and skinfold thicknesses measured at 8 years), current diet (measured by two 24-hour dietary recalls), and socioeconomic conditions of the household in which they live. We also assessed the contribution of maternal characteristics, including age at menarche, height, and nutritional status while pregnant with the study child. RESULTS: The median age at menarche calculated from the hazard model is 13.1 years, with 50% of girls attaining menarche between 12.4 and 13.9 years. Earlier menarche is characteristic of girls who live in urban, higher socioeconomic status households, as indicated by higher maternal education, better housing quality, and possession of assets, such as a TV or refrigerator. Age at menarche is significantly associated with birth characteristics. Although birth weight alone was not significantly related to age at menarche, girls who were relatively long and thin at birth (>49 cm, <3 kg) attained menarche ~6 months earlier than did girls who were short and light (<49 cm, <3 kg). This effect of thinness at birth is most pronounced among girls with greater than average growth increments in 6 months of life. The effects of birth size are not modified when body mass index and skinfold thicknesses at 8 years are taken into account. Effects of birth size on age at menarche also remain significant when maternal nutritional status during pregnancy and the girl's current diet and socioeconomic indicators are taken into account. CONCLUSIONS: The study provides additional evidence of fetal programming of later health outcomes by showing that future growth and maturation trajectories are established in utero. Furthermore, rapid postnatal growth potentiates the effects of size at birth and is related independently to earlier pubertal maturation.},
affiliation = {Department of Nutrition, University of North Carolina, Schools of Medicine and Public Health, Chapel Hill, North Carolina 27516-3997, USA. linda_adair@unc.edu},
number = {4},
pages = {E59},
volume = {107},
year = {2001},
month = {Apr},
language = {eng},
keywords = {Sexual Maturation, Embryonic and Fetal Development, Seasons, Anthropometry, Infant, Birth Weight, Pregnancy, Adult, Infant: Newborn, Health Surveys, Female, Body Mass Index, Mothers, Age Factors, Adolescent, Child: Preschool, Humans, Menarche, Proportional Hazards Models, Cohort Studies, Skinfold Thickness, Child},
date-added = {2010-03-22 12:08:17 +0100},
date-modified = {2010-03-22 12:08:17 +0100},
pmid = {11335780},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8804},
rating = {0}
}

@article{Ridolfi:2002p4108,
author = {A Ridolfi and J Idier},
title = {Penalized Maximum Likelihood Estimation for Normal Mixture Distributions},
abstract = {Mixture models form the essential basis of data clustering within a statistical framework. Here, the estimation of the parameters of a mixture of Gaussian densities is considered. In this particular context, it is well known that the maximum likelihood approach is statistically ill posed, i.e. the likelihood function is not bounded above, because of singularities at the boundary of the parameter domain. We show that such a degeneracy can be avoided by penalizing the likelihood function using a suited type of penalty function. Recently, the resulting penalized maximum likelihood estimator has been proved to be asymptotically well- behaved. Local maximization of the likelihood function can be performed by mean of Green's modified EM algorithm: provided that an inverse gamma is chosen as penalty function, EM re-estimation equations are still explicit and automatically ensure that the estimates are not singular. Numerical examples are provided in the finite data case, showing the performances of the penalized estimator compared to the standard one. Our penalized approach is also compared to a constrained approach, which, up to the authors knowledge, represents the only alternate solution to likelihood degeneracy. Our contribution mainly addresses the case of an independent, identically distributed mixture of Gaussian densities, but the more general case of dependent classes is also tackled, with a particular reference to the important case of hidden Markov models.},
year = {2002},
date-added = {2010-01-19 23:48:08 +0100},
date-modified = {2010-01-19 23:48:49 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Ridolfi-2002-_Penalized%20Maximum%20Li.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4108},
rating = {0}
}

@article{Pilla:2005p3609,
author = {R S Pilla and D J Kitska and C Loader},
journal = {Journal of Experimental Biology},
title = {STATISTICAL ANALYSIS OF MODIFIED COMPLETE RANDOMIZED DESIGNS: APPLICATIONS TO CHEMO-ORIENTATION STUDIES},
abstract = {Often experimental scientists employ a randomized complete block de- sign (RCBD) to study the effect of treatments on different subjects. Under a complete randomization, the order of the apparatus setups within each block, including all replications of each treatment across all subjects, is completely randomized. However, in many experimental settings complete randomization is impractical due to the cost involved in re-adjusting the devise to administer a new treatment. One typically resorts to a type of restricted randomization in which multiple subjects are tested under each treatment before the devise is re-adjusted. The order of the treatments as well as the assignment of subjects to each block are random. If the data ob- tained under any type of restricted randomization are treated as if the data were collected under an RCBD with complete randomization within each block, then there is potential to increase the risk of false positives (Type I error). This is of concern to animal orientation studies and other areas such as chemical ecology where it is impractical to reset the experimental devise for each subject tested. The goal of the research presented in this article is two fold. First is to demonstrate the consequences of construct- ing an F-statistic based on a mean square error for testing the significance of treatment effects under the restricted randomization. Second is to de- scribe an alternative method, based on split-plot analysis of variance, to analyse designed experiments that yield better power under the restricted randomization. The data analyses from simulated experiments and that in- volving virgin male Periplaneta americana substantiate the benefits of the alternative approach under the restricted randomization. The methodology and analysis employed for the simulated experiment is equally applicable to any organism or artificial agent tested under a restricted randomization protocol.},
pages = {1267--1276},
volume = {208},
year = {2005},
date-added = {2010-01-16 18:23:42 +0100},
date-modified = {2010-01-16 18:26:18 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Pilla-2005-Journal%20of%20Experimental%20Biology_STATISTICAL%20ANALYSIS.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3609},
rating = {0}
}

@misc{Hermann:1999,
author = {Margaret G Hermann},
journal = {Miscellaneous},
title = {Assessing leadership style: A trait analysis},
year = {1999},
month = {Nov},
date-added = {2010-01-10 11:33:24 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hermann-1999-Miscellaneous_Assessing%20leadership.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2079},
rating = {0}
}

@article{Passamonti:2009p8931,
author = {Luca Passamonti and James B Rowe and Christian Schwarzbauer and Michael P Ewbank and Elisabeth von dem Hagen and Andrew J Calder},
journal = {J Neurosci},
title = {Personality predicts the brain's response to viewing appetizing foods: the neural basis of a risk factor for overeating},
abstract = {Eating is not only triggered by hunger but also by the sight of foods. Viewing appetizing foods alone can induce food craving and eating, although there is considerable variation in this "external food sensitivity" (EFS). Because increased EFS is associated with overeating, identifying its neural correlates is important for understanding the current epidemic of obesity. Animal research has identified the ventral striatum, amygdala, hypothalamus, medial prefrontal and premotor cortices as key interacting structures for feeding. However, it is unclear whether a similar network exists in humans and how it is affected by EFS. Using functional magnetic resonance imaging, we showed that viewing appetizing compared with bland foods produced changes in connectivity among the human ventral striatum, amygdala, anterior cingulate and premotor cortex that were strongly correlated with EFS. Differences in the dynamic interactions within the human appetitive network in response to pictures of appetizing foods may determine an individual's risk of obesity.},
affiliation = {Cognition and Brain Sciences Unit, Medical Research Council, Cambridge CB2 7EF, United Kingdom. l.passamonti@isn.cnr.it},
number = {1},
pages = {43--51},
volume = {29},
year = {2009},
month = {Jan},
language = {eng},
keywords = {Young Adult, Brain, Image Processing: Computer-Assisted, Adult, Oxygen, Personality, Food, Male, Pattern Recognition: Visual, Magnetic Resonance Imaging, Hyperphagia, Risk Factors, Appetite, Brain Mapping, Photic Stimulation, Female, Humans},
date-added = {2010-03-22 13:04:12 +0100},
date-modified = {2010-07-29 19:52:28 +0200},
doi = {10.1523/JNEUROSCI.4966-08.2009},
pii = {29/1/43},
pmid = {19129383},
URL = {http://www.jneurosci.org/cgi/content/full/29/1/43},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Passamonti-2009-J%20Neurosci_Personality%20predicts.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8931},
rating = {0}
}

@article{Chen:2010p13423,
author = {Yea-Hung Chen and H Fisher Raymond and Willi McFarland and Hong-Ha M Truong},
journal = {AIDS Behav},
title = {HIV risk behaviors in heterosexual partnerships: female knowledge and male behavior},
abstract = {We initiated a study of high-risk heterosexual females and their male partners. The goal was to characterize the partnerships, quantify the prevalence of high-risk male behaviors and characteristics, and to assess whether females in these partnerships would be able to accurately and consistently describe their partners' risk conditions. Seventy-four percent (73.6%) of partnerships reported frequent unprotected sex (condom use during fewer than half their sexual encounters) and 55.9% reported frequent drug or alcohol use during sex (drug or alcohol use during more than half their sexual encounters). Two-thirds (66.7%) of men reported concurrent sexual partnerships and 40.8% reported a history of STDs. The women's assessments of their partners' behaviors often differed from the behaviors and characteristics reported by the women's male partners.},
affiliation = {HIV Epidemiology Section, San Francisco Department of Public Health, San Francisco, CA 94102-6033, USA.},
number = {1},
pages = {87--91},
volume = {14},
year = {2010},
month = {Feb},
language = {eng},
keywords = {Adult, Heterosexuality, Sexual Behavior, Awareness, Humans, Sex Factors, Prevalence, Ethnic Groups, Male, Middle Aged, HIV Infections, Risk-Taking, Attitude to Health, Sexually Transmitted Diseases, Adolescent, Young Adult, Female},
date-added = {2010-07-01 19:35:31 +0200},
date-modified = {2010-07-01 19:35:31 +0200},
doi = {10.1007/s10461-009-9558-6},
pmid = {19365720},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Chen-2010-AIDS%20Behav_HIV%20risk%20behaviors%20i.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13423},
rating = {0}
}

@article{Mislevy:2003p4251,
author = {R Mislevy},
journal = {Conference on Inference, Culture, and Ordinary Thinking in Dispute Resolution},
title = {Argument Substance and Argument Structure in Educational Assessment},
abstract = {Educational assessment is reasoning from observations of what students do or make in a handful of particular circumstances, to what they know or can do more broadly. Practice has changed a great deal over the past century, in response to evolving conceptions of knowledge and its acquisition, views of schooling and its purposes, and technologies for gathering and evaluating response data. Conceptions of what constitutes assessment data, how it should be interpreted, and what kind of inferences are to be drawn differ radically when cast under different psychological perspectives. If we distinguish the structure of assessment arguments from their substance, we see greater continuity. Developments here have been more in the nature of extension, elaboration, refinement, and explication of argument structures, as they have been prompted by more radically changes in culture and substance.},
year = {2003},
date-added = {2010-01-23 20:54:47 +0100},
date-modified = {2010-01-23 20:55:31 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Mislevy-2003-Conference%20on%20Inference%20Culture%20and%20Ordinary%20Thinking%20in%20Dispute%20Resolution_Argument%20Substance%20a.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4251},
rating = {0}
}

@article{Helms:1999,
author = {J E Helms},
journal = {Measurement and Evaluation in Counseling and Development},
title = {Another meta-analysis of the White Racial Identity Attitude Scale's Cronbach alphas: Implications for validity},
pages = {122--137},
volume = {32},
year = {1999},
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/p2050},
rating = {0}
}

@article{Ehlers:2010p7874,
author = {Cindy L Ehlers and Ian R Gizer and Evelyn Phillips and Kirk C Wilhelmsen},
journal = {BMC Med Genet},
title = {EEG alpha phenotypes: linkage analysis and relation to alcohol dependence in an American Indian community study},
abstract = {ABSTRACT: BACKGROUND: Evidence for a high degree of heritability of EEG alpha phenotypes has been demonstrated in twin and family studies in a number of populations. However, information on linkage of this phenotype to specific chromosome locations is still limited. This study's aims were to map loci linked to EEG alpha phenotypes and to determine if there was overlap with loci previously mapped for alcohol dependence in an American Indian community at high risk for substance dependence. METHODS: Each participant gave a blood sample and completed a structured diagnostic interview using the Semi Structured Assessment for the Genetics of Alcoholism. Bipolar EEGs were collected and spectral power determined in the alpha (7.5-12.0 Hz) frequency band for two composite scalp locations previously identified by principal components analyses (bilateral fronto-central and bilateral centro-parietal-occipital). Genotypes were determined for a panel of 791 micro-satellite polymorphisms in 410 members of multiplex families using SOLAR. RESULTS: Sixty percent of this study population had a lifetime diagnosis of alcohol dependence. Analyses of multipoint variance component LOD scores, for the EEG alpha power phenotype, revealed two loci that had a LOD score of 3.0 or above for the fronto-central scalp region on chromosomes 1 and 6. Additionally, 4 locations were identified with LOD scores above 2.0 on chromosomes 4, 11, 14, 16 for the fronto-central location and one on chromosome 2 for the centro-parietal-occipital location. CONCLUSION: These results corroborate the importance of regions on chromosome 4 and 6 highlighted in prior segregation studies in this and other populations for alcohol dependence-related phenotypes, as well as other areas that overlap with other substance dependence phenotypes identified in previous linkage studies in other populations. These studies additionally support the construct that EEG alpha recorded from fronto-central scalp areas may represent an important endophenotype associated with alcohol and other substance dependence.},
number = {1},
pages = {43},
volume = {11},
year = {2010},
month = {Mar},
language = {ENG},
date-added = {2010-03-20 19:14:31 +0100},
date-modified = {2010-03-20 19:14:31 +0100},
doi = {10.1186/1471-2350-11-43},
pii = {1471-2350-11-43},
pmid = {20298578},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Ehlers-2010-BMC%20Med%20Genet_EEG%20alpha%20phenotypes.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7874},
rating = {0}
}

@article{Dunn:2003p7402,
author = {Kate M Dunn and Kelvin Jordan and Peter R Croft},
journal = {Journal of Clinical Epidemiology},
title = {Does questionnaire structure influence response in postal surveys?},
abstract = {This study tested the effect of questionnaire structure on response, speed of return, and content of answers in a postal survey. All 259 patients aged 30-59 years who consulted with back pain at four UK general practices from March to June 2001 were randomly allocated to receive either a traditionally or chronologically structured self-completion questionnaire. The response was higher and the returns quicker (P =.05) for the chronologic questionnaire. There were no statistically significant differences in completion rates or scores on the SF-36, Chronic Pain Grade, Hospital Anxiety and Depression Scale, or Roland-Morris Disability Questionnaire between the two types of questionnaire, and test-retest reliability was high for all scales. Changing questionnaire structure to make questions chronologic does not substantially affect the answers given, but may make a questionnaire more acceptable and easier to complete and speed up returns.},
affiliation = {Keele University, Primary Care Sciences Research Centre, Hornbeam Building, Keele, Staffordshire ST5 5BG, UK. k.m.dunn@cphc.keele.ac.uk},
number = {1},
pages = {10--6},
volume = {56},
year = {2003},
month = {Jan},
language = {eng},
keywords = {Questionnaires, Reproducibility of Results, Time Factors, Female, Health Status, Adult, Back Pain, Humans, Pilot Projects, Male, Longitudinal Studies, Patient Participation, Sensitivity and Specificity, Health Surveys, Middle Aged},
date-added = {2010-03-10 20:36:28 +0100},
date-modified = {2010-03-10 20:36:28 +0100},
pii = {S089543560200567X},
pmid = {12589865},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Dunn-2003-Journal%20of%20Clinical%20Epidemiology_Does%20questionnaire%20s.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7402},
rating = {0}
}

@article{Rodriguez:2003p14016,
author = {G Rodriguez and I Elo},
journal = {The Stata Joumal},
title = {Intra-class correlation in random-effects models for binary data},
abstract = {We review the concept of intra-class correlation in random-effects mod- els for binary outcomes as estimated by Stata's xtprobit, xtlogit, and xtclog. We consider the usual measures of correlation based on a latent variable formu- lation of these models and note corrections to the last two procedures. We also discuss alternative measures of association based on manifest variables or actual outcomes and introduce a new command xtrho for computing these measures for all three types of models.},
number = {1},
pages = {32--46},
volume = {3},
year = {2003},
date-added = {2010-08-04 09:44:24 +0200},
date-modified = {2010-08-04 09:45:25 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Rodriguez-2003-The%20Stata%20Joumal_Intra-class%20correlat.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p14016},
rating = {0}
}

@article{Kirwan:2009p6346,
author = {John R Kirwan and Stanton Newman and Peter S Tugwell and George A Wells and Sarah Hewlett and Leanne Idzera and Britta Laslo and Lyn M March and Patricia Minnock and Pam Montie and Jo Nicklin and Tamara Rader and Pamela Richards and Tessa C Sanderson and Maria Suarez-Almazor and Elizabeth Tanjong-Ghogomu and Erin Ueffing and Vivian Welch},
journal = {J Rheumatol},
title = {Progress on incorporating the patient perspective in outcome assessment in rheumatology and the emergence of life impact measures at OMERACT 9},
abstract = {The Patient Perspective Workshop included over 100 researchers and 18 patient participants from 8 countries. Following preconference reading and short plenary presentations, breakout groups considered work undertaken on measurement of sleep, assessing interventions to develop the effective consumer, and assessing psychological and educational interventions. The workshop explored the best way to identify other outcome domains (and instruments) that should be measured in observational or interventional studies with broader intentions than simply altering outcomes captured in the traditional "core set" plus fatigue. Four sleep questionnaires showed promise and will be the subject of further study. The Effective Consumer scale (EC-17) was reviewed and the concept Effective Consumer was well received. Participants thought it worthwhile to measure the skills and attributes of an effective consumer and develop an intervention that would include education in all of the scale's categories. Assessment of educational and psychological interventions requires a wider set of instruments than is currently used; these should relate to the purpose of the intervention. This principle was extended to include wider measures of the impact of disease on life, as indicated in the International Classification of Functioning, Disability and Health. Life impact measure sets covering domains appropriate to different rheumatic conditions and focused on different interventions might be defined by future OMERACT consensus. Measurement instruments within these domains that are valid for use in rheumatic conditions can then be identified and, in the case of psychological and educational interventions, chosen to fit with the purpose of the intervention.},
affiliation = {University of Bristol Academic Rheumatology Unit, Bristol Royal Infirmary, Bristol, UK. John.Kirwan@Bristol.ac.uk},
number = {9},
pages = {2071--6},
volume = {36},
year = {2009},
month = {Sep},
language = {eng},
keywords = {Humans, Self Concept, Outcome Assessment (Health Care), Rheumatic Diseases, Sleep, Patient Education as Topic},
date-added = {2010-02-23 08:21:10 +0100},
date-modified = {2010-07-29 19:52:38 +0200},
doi = {10.3899/jrheum.090360},
pii = {36/9/2071},
pmid = {19738216},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6346},
rating = {0}
}

@article{Blair:1987,
author = {EA Blair and S Burton},
journal = {Journal of Consumer Research},
title = {Cognitive processes used by survey respondents in answering behavioral frequency questions},
pages = {280--288},
volume = {14},
year = {1987},
date-added = {2010-01-03 19:34:18 +0100},
date-modified = {2010-01-03 19:34:18 +0100},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p929},
rating = {0}
}

@article{Vermunt:2008p1526,
author = {J K Vermunt and J R van Ginkel and L Andries van der Ark and K Sijstma},
title = {Multiple imputation of incomplete categorical data using latent class analysis},
abstract = {We propose using latent class analysis as an alternative to log- linear analysis for the multiple imputation of incomplete categorical data. Similar to log-linear models, latent class models can be used to describe complex association structures between the variables used in the imputation model. However, unlike log- linear models, latent class models can be used to build large imputation models containing more than a few categorical variables. To obtain imputations reflecting uncertainty about the unknown model parameters, we use a nonparametric bootstrap procedure as an alternative to the more common full Bayesian approach. The proposed multiple imputation method, which is implemented in Latent GOLD software for latent class analysis, is illustrated with two examples. In a simulated data example, we compare the new method to well-established methods such as maximum likelihood estimation with incomplete data and multiple imputation using a saturated log-linear model. This example shows that the proposed method yields unbiased parameter estimates and standard errors. The second example concerns an application using a typical social sciences data set. It contains 79 variables that are all included in the imputation model. The proposed method is especially useful for such large data sets because standard methods for dealing with missing data in categorical variables break down when the number of variables is so large.},
year = {2008},
date-added = {2010-01-07 16:00:44 +0100},
date-modified = {2010-07-29 20:42:55 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Vermunt-2008

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib