Monte Carlo inference for semiparametric Bayesian regression

Data transformations are essential for broad applicability of parametric regression models. However, for Bayesian analysis, joint inference of the transformation and model parameters typically involves restrictive parametric transformations or nonparametric representations that are computationally inefficient and cumbersome for implementation and theoretical analysis, which limits their usability in practice. This paper introduces a simple, general, and efficient strategy for joint posterior inference of an unknown transformation and all regression model parameters. The proposed approach directly targets the posterior distribution of the transformation by linking it with the marginal distributions of the independent and dependent variables, and then deploys a Bayesian nonparametric model via the Bayesian bootstrap. Crucially, this approach delivers (1) joint posterior consistency under general conditions, including multiple model misspecifications, and (2) efficient Monte Carlo (not Markov chain Monte Carlo) inference for the transformation and all parameters for important special cases. These tools apply across a variety of data domains, including real-valued, integer-valued, compactly-supported, and positive data. Simulation studies and an empirical application demonstrate the effectiveness and efficiency of this strategy for semiparametric Bayesian analysis with linear models, quantile regression, and Gaussian processes

A national registry for juvenile dermatomyositis and other paediatric idiopathic inflammatory myopathies: 10 years' experience; the Juvenile Dermatomyositis National (UK and Ireland) Cohort Biomarker Study and Repository for Idiopathic Inflammatory Myopathies

Objectives: The paediatric idiopathic inflammatory myopathies (IIMs) are a group of rare chronic inflammatory disorders of childhood, affecting muscle, skin and other organs. There is a severe lack of evidence base for current treatment protocols in juvenile myositis. The rarity of these conditions means that multicentre collaboration is vital to facilitate studies of pathogenesis, treatment and disease outcomes. We have established a national registry and repository for childhood IIM, which aims to improve knowledge, facilitate research and clinical trials, and ultimately to improve outcomes for these patients. Methods: A UK-wide network of centres and research group was established to contribute to the study. Standardized patient assessment, data collection forms and sample protocols were agreed. The Biobank includes collection of peripheral blood mononuclear cells, serum, genomic DNA and biopsy material. An independent steering committee was established to oversee the use of data/samples. Centre training was provided for patient assessment, data collection and entry. Results: Ten years after inception, the study has recruited 285 children, of which 258 have JDM or juvenile PM; 86% of the cases have contributed the biological samples. Serial sampling linked directly to the clinical database makes this a highly valuable resource. The study has been a platform for 20 sub-studies and attracted considerable funding support. Assessment of children with myositis in contributing centres has changed through participation in this study. Conclusions: This establishment of a multicentre registry and Biobank has facilitated research and contributed to progress in the management of a complex group of rare muscloskeletal conditions

A categorification of Morelli's theorem

We prove a theorem relating torus-equivariant coherent sheaves on toric varieties to polyhedrally-constructible sheaves on a vector space. At the level of K-theory, the theorem recovers Morelli's description of the K-theory of a smooth projective toric variety. Specifically, let $X$ be a proper toric variety of dimension $n$ and let M_\bR = \mathrm{Lie}(T_\bR^\vee)\cong \bR^n be the Lie algebra of the compact dual (real) torus T_\bR^\vee\cong U(1)^n. Then there is a corresponding conical Lagrangian \Lambda \subset T^*M_\bR and an equivalence of triangulated dg categories \Perf_T(X) \cong \Sh_{cc}(M_\bR;\Lambda), where \Perf_T(X) is the triangulated dg category of perfect complexes of torus-equivariant coherent sheaves on $X$ and \Sh_{cc}(M_\bR;\Lambda) is the triangulated dg category of complex of sheaves on M_\bR with compactly supported, constructible cohomology whose singular support lies in $\Lambda$. This equivalence is monoidal---it intertwines the tensor product of coherent sheaves on $X$ with the convolution product of constructible sheaves on M_\bR.Comment: 20 pages. This is a strengthened version of the first half of arXiv:0811.1228v3, with new results; the second half becomes arXiv:0811.1228v

Social Studies Preservice Teachers’ Citizenship Knowledge and Perceptions of the U.S. Naturalization Test

Teacher educators from six states invited their social studies methodology students to complete an abbreviated version of the U.S. Citizenship and Immigration Services (USCIS) Naturalization Test. The preservice teachers were also asked to share their conceptions of citizenship and evaluate the naturalization test. The findings from this study indicated that although this sample of preservice teachers had limited conceptions of citizenship, most were able to get a satisfactory score on the test. The authors discuss the implications of these results and suggest ways to broaden citizenship education in teacher preparation programs

A Double-Blind, Placebo-Controlled Withdrawal Trial of Dexmethylphenidate Hydrochloride in Children with Attention Deficit Hyperactivity Disorder

Objectives: d,l-threo-methylphenidate HCl (d,l-MPH) is the most common treatment of attention deficit hyperactivity disorder (ADHD). A previous report showed placebo-controlled efficacy for the purified disomer (dexmethylphenidate hydrochloride, d-MPH, Focalin™) with a 2:1 potency compared to dl, and suggested a 6-hour duration of action. This study complements that report by studying the effect of placebo-controlled discontinuation and retesting the duration of action. Methods: A 6-week, open-label titration of d-MPH (2.5–10 mg twice-a-day) was followed by a doubleblind, placebo-controlled, 2-week withdrawal study of responders. Results: In the open titration, 82% of the 89 enrolled patients achieved a Clinical Global Impression— Improvement (CGI-I) rating of much or very much improved. Only 5 patients discontinued for adverse events. Seventy-five patients continued into the placebo-controlled discontinuation. For the randomly assigned d-MPH (n = 35) and placebo (n = 40) groups, mean ages, respectively, were 10.1 ± 2.9 and 9.9 ± 2.7 years, 86% and 78% were male, and 70.6% and 80.0% took the ceiling dose of 10 mg twice-daily, respectively. Each group had 80% combined-type ADHD and 20% inattentive type. By the end of the 2- week, placebo-masked withdrawal, significantly more placebo patients (24 of 39) than d-MPH continuers (6 of 35) relapsed (61.5% versus 17.1%, p = 0.001). Compared to d-MPH continuers, placebo patients deteriorated significantly more in the 2-week period on teacher ratings of the 18 ADHD symptoms rated 0– 3 (p = 0.028), the 3 p.m. and 6 p.m. parent ADHD symptom ratings (p = 0.0026 and p = 0.0381, respectively), and clinic (2–3 p.m.) and home (6 p.m.) Math Tests (p = 0.024 and p < 0.0001, respectively). The 6 p.m. scores replicated the significant effect at 6 hours reported in the previous study. Conclusions: d-MPH is safe, tolerable, and effective, with a 6-hour duration of effect suggested by the significant difference from placebo at 6 hours on a double-blind discontinuation

Potential landscape-scale pollinator networks across Great Britain: structure, stability and influence of agricultural land cover

Understanding spatial variation in the structure and stability of plant-pollinator networks, and their relationship with anthropogenic drivers, is key to maintaining pollination services and mitigating declines. Constructing sufficient networks to examine patterns over large spatial scales remains challenging. Using biological records (citizen science), we constructed potential plant-pollinator networks at 10km resolution across Great Britain, comprising all potential interactions inferred from recorded floral visitation and species co-occurrence. We calculated network metrics (species richness, connectance, pollinator and plant generality) and adapted existing methods to assess robustness to sequences of simulated plant extinctions across multiple networks. We found positive relationships between agricultural land cover and both pollinator generality and robustness to extinctions under several extinction scenarios. Increased robustness was attributable to changes in plant community composition (fewer extinction-prone species) and network structure (increased pollinator generality). Thus, traits enabling persistence in highly agricultural landscapes can confer robustness to potential future perturbations on plant-pollinator networks

The heart in sporadic inclusion body myositis: a study in 51 patients

The purpose of this study was to explore the prevalence and nature of cardiac abnormalities in sporadic inclusion body myositis (sIBM). Fifty-one sIBM patients were cross-sectionally studied using history-taking, physical examination, measurements of serum creatine kinase activity, the MB fraction (CK-MB), cardiac troponin T (cTnT) and I (cTnI), a 12-lead electrocardiogram (ECG) and 2-dimensional echocardiography. Present cardiac history was abnormal in 12 (24%) out of 51 patients, 12 (24%) patients had abnormalities on ECG, mostly aspecific, and in 12 (24%) patients the echocardiograph showed abnormalities. Elevated CK-MB was present in 42 (82%) patients and 40 (78%) had an elevated cTnT in the absence of acute cardiac pathology. In contrast, in one patient (2%) cTnI was elevated. There was no apparent association between elevated biomarkers, ECG or echocardiographic abnormalities. The prevalence of cardiac abnormalities in sIBM does not seem to be higher than would be expected in these elderly patients. Elevated CK-MB and cTnT levels are common, in contrast to cTnI, but do not reflect cardiac pathology

The environmental impacts of biomass crops: use by birds of miscanthus in summer and winter in southwestern England

We compared birds in a group of established and well-managed miscanthus (Miscanthus x giganteus) fields in Somerset and East Devon, southwestern England, with plots of short rotation coppice (SRC) willow, arable crops and grassland in two winters and one summer. Following early spring cutting, 19 miscanthus fields grew taller, initially produced greater cover and were less weedy than SRC. As stubble in May, the miscanthus contained broadly similar species at similar densities to arable and grassland comparison plots. By July, at 2-m-tall, miscanthus held higher densities of birds but of fewer species, most of them characteristic of woodland and scrub. SRC, previously identified as being a beneficial crop for many birds, always contained more species and individuals than miscanthus. Throughout each of two winters, 15 miscanthus plots remained unharvested and contained more wood/scrub species such as Blackbirds Turdus merula, tits, Reed Buntings Emberiza schoeniclus and Woodcock Scolopax rusticola than the comparison plots, which held more corvids and Skylarks Alauda arvensis amongst others. Similar overall mean densities of birds in the miscanthus and the comparison plots masked relatively low density variance in miscanthus and very high variance in the comparison plots. Unharvested miscanthus crops grown in place of habitat types supporting flocks of wintering birds would displace these flocks. Miscanthus plantations with open patches attracted more finches and waders in winter. The two previous studies of birds in miscanthus in the UK found more species and more individuals than we did in summer and winter. Both these studies documented high levels of weediness and patchy crop growth. In the context of this previous work our data suggest that bird use of miscanthus in summer and winter is likely to be variable, affected by region, weediness, crop structure and patchiness. While large-scale cropping of SRC in England is likely to have a positive overall impact on a suite of common farmland and woodland birds, our data suggest that miscanthus in the southwest of England may have an approximately neutral effect. However, some open farmland specialist species may be lost when planting either crop