BUGS Code for Item Response Theory

I present BUGS code to fit common models from item response theory (IRT), such as the two parameter logistic model, three parameter logisitic model, graded response model, generalized partial credit model, testlet model, and generalized testlet models. I demonstrate how the code in this article can easily be extended to fit more complicated IRT models, when the data at hand require a more sophisticated approach. Specifically, I describe modifications to the BUGS code that accommodate longitudinal item response data

The analytic structure of heavy quark propagators

The renormalised quark Dyson-Schwinger equation is studied in the limit of the renormalised current heavy quark mass m_R --> infinity. We are particularly interested in the analytic pole structure of the heavy quark propagator in the complex momentum plane. Approximations in which the quark-gluon vertex is modelled by either the bare vertex or the Ball-Chiu Ansatz, and the Landau gauge gluon propagator takes either a gaussian form or a gaussian form with an ultraviolet asymptotic tail are used.Comment: 21 pages Latex and 5 postscript figures. The original version of this paper has been considerably extended to include a formalism dealing with the renormalised heavy quark Dyson-Schwinger equation and uses a more realistic Ansatz for the gluon propagator

Dynamical chiral symmetry breaking and confinement with an infrared-vanishing gluon propagator?

We study a model Dyson-Schwinger equation for the quark propagator closed using an {\it Ansatz} for the gluon propagator of the form \mbox{$D(q) \sim q^2/[(q^2)^2 + b^4]$} and two {\it Ans\"{a}tze} for the quark-gluon vertex: the minimal Ball-Chiu and the modified form suggested by Curtis and Pennington. Using the quark condensate as an order parameter, we find that there is a critical value of $b=b_c$ such that the model does not support dynamical chiral symmetry breaking for $b>b_c$. We discuss and apply a confinement test which suggests that, for all values of $b$, the quark propagator in the model {\bf is not} confining. Together these results suggest that this Ansatz for the gluon propagator is inadequate as a model since it does not yield the expected behaviour of QCD.Comment: 21 Pages including 4 PostScript figures uuencoded at the end of the file. Replacement: slight changes of wording and emphasis. ADP-93-215/T133, ANL-PHY-7599-TH-93, FSU-SCRI-93-108, REVTEX 3.

Advancing PROMIS’s methodology: results of the Third Patient-Reported Outcomes Measurement Information System (PROMIS ® ) Psychometric Summit

In 2002, the NIH launched the ‘Roadmap for Medical Research’. The Patient-Reported Outcomes Measurement Information System (PROMIS®) is one of the Roadmap’s key aspects. To create the next generation of patient-reported outcome measures, PROMIS utilizes item response theory (IRT) and computerized adaptive testing. In 2009, the NIH funded the second wave of PROMIS studies (PROMIS II). PROMIS II studies continue PROMIS’s agenda, but also include new features, including longitudinal analyses and more sociodemographically diverse samples. PROMIS II also includes increased emphasis on pediatric populations and evaluation of PROMIS item banks for clinical research and population science. These aspects bring new psychometric challenges. To address this, investigators associated with PROMIS gathered at the Third Psychometric Summit in September 2010 to identify, describe and discuss pressing psychometric issues and new developments in the field, as well as make analytic recommendations for PROMIS. The summit addressed five general themes: linking, differential item functioning, dimensionality, IRT models for longitudinal applications and new IRT software. In this article, we review the discussions and presentations that occurred at the Third PROMIS Psychometric Summit

A missense variant in CST3 exerts a recessive effect on susceptibility to age-related macular degeneration resembling its association with Alzheimer’s disease

Age-related macular degeneration (AMD) and Alzheimer’s disease (AD) are degenerative, multifactorial diseases involving age-related accumulation of extracellular deposits linked to dysregulation of protein homeostasis. Here, we strengthen the evidence that an nsSNP (p.Ala25Thr) in the cysteine proteinase inhibitor cystatin C gene CST3, previously confirmed by meta-analysis to be associated with AD, is associated with exudative AMD. To our knowledge, this is the first report highlighting a genetic variant that increases the risk of developing both AD and AMD. Furthermore, we demonstrate that the risk associated with the mutant allele follows a recessive model for both diseases. We perform an AMD-CST3 case–control study genotyping 350 exudative AMD Caucasian individuals. Bringing together our data with the previously reported AMD-CST3 association study, the evidence of a recessive effect on AMD risk is strengthened (OR = 1.89, P = 0.005). This effect closely resembles the AD-CST3 recessive effect (OR = 1.73, P = 0.005) previously established by meta-analysis. This resemblance is substantiated by the high correlation between CST3 genotype and effect size across the two diseases (R2 = 0.978). A recessive effect is in line with the known function of cystatin C, a potent enzyme inhibitor. Its potency means that, in heterozygous individuals, a single functional allele is sufficient to maintain its inhibitory function; only homozygous individuals will lack this form of proteolytic regulation. Our findings support the hypothesis that recessively acting variants account for some of the missing heritability of multifactorial diseases. Replacement therapy represents a translational opportunity for individuals homozygous for the mutant allele

High-resolution haplotype block structure in the cattle genome

<p>Abstract</p> <p>Background</p> <p>The Bovine HapMap Consortium has generated assay panels to genotype ~30,000 single nucleotide polymorphisms (SNPs) from 501 animals sampled from 19 worldwide taurine and indicine breeds, plus two outgroup species (Anoa and Water Buffalo). Within the larger set of SNPs we targeted 101 high density regions spanning up to 7.6 Mb with an average density of approximately one SNP per 4 kb, and characterized the linkage disequilibrium (LD) and haplotype block structure within individual breeds and groups of breeds in relation to their geographic origin and use.</p> <p>Results</p> <p>From the 101 targeted high-density regions on bovine chromosomes 6, 14, and 25, between 57 and 95% of the SNPs were informative in the individual breeds. The regions of high LD extend up to ~100 kb and the size of haplotype blocks ranges between 30 bases and 75 kb (10.3 kb average). On the scale from 1–100 kb the extent of LD and haplotype block structure in cattle has high similarity to humans. The estimation of effective population sizes over the previous 10,000 generations conforms to two main events in cattle history: the initiation of cattle domestication (~12,000 years ago), and the intensification of population isolation and current population bottleneck that breeds have experienced worldwide within the last ~700 years. Haplotype block density correlation, block boundary discordances, and haplotype sharing analyses were consistent in revealing unexpected similarities between some beef and dairy breeds, making them non-differentiable. Clustering techniques permitted grouping of breeds into different clades given their similarities and dissimilarities in genetic structure.</p> <p>Conclusion</p> <p>This work presents the first high-resolution analysis of haplotype block structure in worldwide cattle samples. Several novel results were obtained. First, cattle and human share a high similarity in LD and haplotype block structure on the scale of 1–100 kb. Second, unexpected similarities in haplotype block structure between dairy and beef breeds make them non-differentiable. Finally, our findings suggest that ~30,000 uniformly distributed SNPs would be necessary to construct a complete genome LD map in <it>Bos taurus </it>breeds, and ~580,000 SNPs would be necessary to characterize the haplotype block structure across the complete cattle genome.</p

Sport and Society

Despite its economic and cultural centrality, sport is a relatively neglected and undertheorized area of sociological research. In this review, we examine sports\u27 articulation with stratification issues, especially race, class, and gender. In addition, we look at how the media and processes of globalization have affected sports.We suggest that sports and cultural sociologists need to attend more closely to how leisure products and practices are produced and distributed and how they intersect with educational, political, and cultural institutions. We propose the work of Bourdieu andthe new institutionalism to undergird future research

Model gluon propagator and pion and rho-meson observables

A one parameter, model confined-gluon propagator is employed in a phenomenological application of the Dyson-Schwinger and Bethe-Salpeter equations to the calculation of a range of $\pi$- and $\rho$-meson observables. Good agreement is obtained with the data. The calculated quark propagator does not have a singularity on the real-$p^2$ axis. A mass formula for the pion, involving only the vacuum, dressed quark propagator, is presented and shown to provide an accurate estimate of the mass obtained via a direct solution of the Bethe-Salpeter equation.Comment: 17 Pages, no figures, REVTE

Genome-wide Association Study of Borderline Personality Disorder Reveals Genetic Overlap with Bipolar Disorder, Major Depression and Schizophrenia

Borderline personality disorder (BOR) is determined by environmental and genetic factors, and characterized by affective instability and impulsivity, diagnostic symptoms also observed in manic phases of bipolar disorder (BIP). Up to 20% of BIP patients show comorbidity with BOR. This report describes the first case–control genome-wide association study (GWAS) of BOR, performed in one of the largest BOR patient samples worldwide. The focus of our analysis was (i) to detect genes and gene sets involved in BOR and (ii) to investigate the genetic overlap with BIP. As there is considerable genetic overlap between BIP, major depression (MDD) and schizophrenia (SCZ) and a high comorbidity of BOR and MDD, we also analyzed the genetic overlap of BOR with SCZ and MDD. GWAS, gene-based tests and gene-set analyses were performed in 998 BOR patients and 1545 controls. Linkage disequilibrium score regression was used to detect the genetic overlap between BOR and these disorders. Single marker analysis revealed no significant association after correction for multiple testing. Gene-based analysis yielded two significant genes: DPYD (P=4.42 × 10−7) and PKP4 (P=8.67 × 10−7); and gene-set analysis yielded a significant finding for exocytosis (GO:0006887, PFDR=0.019; FDR, false discovery rate). Prior studies have implicated DPYD, PKP4 and exocytosis in BIP and SCZ. The most notable finding of the present study was the genetic overlap of BOR with BIP (rg=0.28 [P=2.99 × 10−3]), SCZ (rg=0.34 [P=4.37 × 10−5]) and MDD (rg=0.57 [P=1.04 × 10−3]). We believe our study is the first to demonstrate that BOR overlaps with BIP, MDD and SCZ on the genetic level. Whether this is confined to transdiagnostic clinical symptoms should be examined in future studies