Shape restricted regression with random Bernstein polynomials

Shape restricted regressions, including isotonic regression and concave regression as special cases, are studied using priors on Bernstein polynomials and Markov chain Monte Carlo methods. These priors have large supports, select only smooth functions, can easily incorporate geometric information into the prior, and can be generated without computational difficulty. Algorithms generating priors and posteriors are proposed, and simulation studies are conducted to illustrate the performance of this approach. Comparisons with the density-regression method of Dette et al. (2006) are included.Comment: Published at http://dx.doi.org/10.1214/074921707000000157 in the IMS Lecture Notes Monograph Series (http://www.imstat.org/publications/lecnotes.htm) by the Institute of Mathematical Statistics (http://www.imstat.org

Profiling time course expression of virus genes---an illustration of Bayesian inference under shape restrictions

There have been several studies of the genome-wide temporal transcriptional program of viruses, based on microarray experiments, which are generally useful in the construction of gene regulation network. It seems that biological interpretations in these studies are directly based on the normalized data and some crude statistics, which provide rough estimates of limited features of the profile and may incur biases. This paper introduces a hierarchical Bayesian shape restricted regression method for making inference on the time course expression of virus genes. Estimates of many salient features of the expression profile like onset time, inflection point, maximum value, time to maximum value, area under curve, etc. can be obtained immediately by this method. Applying this method to a baculovirus microarray time course expression data set, we indicate that many biological questions can be formulated quantitatively and we are able to offer insights into the baculovirus biology.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS258 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

The epidemiology of patients with pterygium in southern Taiwanese adults: The Chiayi survey

AbstractPurposeTo investigate patients with pterygium in different geographic regions and the associated risk factors in southern Taiwan.MethodsA clinical observation survey was conducted in Chiayi County, a rural area in southern Taiwan. The subjects aged 40 years and above underwent complete ocular examinations. Associated risks factors were evaluated, including gender, age, occupations, smoking, and geographical living regions by univariant and multivariant logistic regression analysis.ResultsA total of 2197 participants (790 male, 36.0%) from 44 different villages were evaluated. In these, 554 participants (25.2%) have either unilateral or bilateral pterygium. Age is associated with the percentage of pterygium, and those aged between 60 and 69 had the highest percentage of 30.1% (p < 0.0001). The gender effect was higher among men than women (OR = 1.31, 95% CI: 1.08–1.60, p = 0.006). The percentage of pterygium lived in plain, seaside, and mountainous areas were 22.6%, 32.6%, and 14.5% respectively. Geographical regions also showed that seaside area had the highest percentage of pterygium (seaside area OR = 1.65, 95% CI: 1.35-2.03, and mountainous area OR = 0.58, 95% CI: 0.35-0.95 compared with plain areas). Primary outdoor workers and residents with smoking history had relative higher risk for pterygium (OR = 1.47, 95% CI: 1.17-1.86; OR = 1.36, 95% CI: 1.02-1.83).ConclusionsThe percentage of pterygium in southern Taiwan is about 25.2% among adults aged over 40 years in this survey. It is significantly higher in the age of 50 or more and in residents living in villages along the seaside than those living in the mountainous and the plain areas

Microbiota signatures associated with invasive Candida albicans infection in the gastrointestinal tract of immunodeficient mice

Candida albicans is a commensal microorganism in the human gut but occasionally causes invasive C. albicans infection (ICA), especially in immunocompromised individuals. Early initiation of antifungal therapy is associated with reduced mortality of ICA, but rapid diagnosis remains a challenge. The ICA-associated changes in the gut microbiota can be used as diagnostic and therapeutic targets but have been poorly investigated. In this study, we utilized an immunodeficient Rag2γc (Rag2-/-il2γc-/-) mouse model to investigate the gut microbiota alterations caused by C. albicans throughout its cycle, from its introduction into the gastrointestinal tract to invasion, in the absence of antibiotics. We observed a significant increase in the abundance of Firmicutes, particularly Lachnospiraceae and Ruminococcaceae, as well as a significant decrease in the abundance of Candidatus Arthromitus in mice exposed to either the wild-type SC5314 strain or the filamentation-defective mutant (cph1/cph1 efg1/efg1) HLC54 strain of C. albicans. However, only the SC5314-infected mice developed ICA. A linear discriminate analysis of the temporal changes in the gut bacterial composition revealed Bacteroides vulgatus as a discriminative biomarker associated with SC5314-infected mice with ICA. Additionally, a positive correlation between the B. vulgatus abundance and fungal load was found, and the negative correlation between the Candidatus Arthromitus abundance and fungal load after exposure to C. albicans suggested that C. albicans might affect the differentiation of intestinal Th17 cells. Our findings reveal the influence of pathogenic C. albicans on the gut microbiota and identify the abundance of B. vulgatus as a microbiota signature associated with ICA in an immunodeficient mouse model

Plasmonic Structure Enhanced Exciton Generation at the Interface between the Perovskite Absorber and Copper Nanoparticles

The refractive index and extinction coefficient of a triiodide perovskite absorber (TPA) were obtained by fitting the transmittance spectra of TPA/PEDOT:PSS/ITO/glass using the transfer matrix method. Cu nanoplasmonic structures were designed to enhance the exciton generation in the TPA and to simultaneously reduce the film thickness of the TPA. Excitons were effectively generated at the interface between TPA and Cu nanoparticles, as observed through the 3D finite-difference time-domain method. The exciton distribution is advantageous for the exciton dissociation and carrier transport

Role of pirenoxine in the effects of catalin on in vitro ultraviolet-induced lens protein turbidity and selenite-induced cataractogenesis in vivo

Purpose: In this study, we investigated the biochemical pharmacology of pirenoxine (PRX) and catalin under in vitro selenite/calcium- and ultraviolet (UV)-induced lens protein turbidity challenges. The systemic effects of catalin were determined using a selenite-induced cataractogenesis rat model. Methods: In vitro cataractogenesis assay systems (including UVB/C photo-oxidation of lens crystallins, calpain-induced proteolysis, and selenite/calcium-induced turbidity of lens crystallin solutions) were used to screen the activity of PRX and catalin eye drop solutions. Turbidity was identified as the optical density measured using spectroscopy at 405 nm. We also determined the in vivo effects of catalin on cataract severity in a selenite-induced cataract rat model. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS–PAGE) was applied to analyze the integrity of crystallin samples. Results: PRX at 1,000 μM significantly delayed UVC-induced turbidity formation compared to controls after 4 h of UVC exposure (p<0.05), but not in groups incubated with PRX concentrations of <1,000 μM. Results were further confirmed by SDS–PAGE. The absolute γ-crystallin turbidity induced by 4 h of UVC exposure was ameliorated in the presence of catalin equivalent to 1~100 μM PRX in a concentration-dependent manner. Samples with catalin-formulated vehicle only (CataV) and those containing PRX equivalent to 100 μM had a similar protective effect after 4 h of UVC exposure compared to the controls (p<0.05). PRX at 0.03, 0.1, and 0.3 μM significantly delayed 10 mM selenite- and calcium-induced turbidity formation compared to controls on days 0~4 (p<0.05). Catalin (equivalent to 32, 80, and 100 μM PRX) had an initial protective effect against selenite-induced lens protein turbidity on day 1 (p<0.05). Subcutaneous pretreatment with catalin (5 mg/kg) also statistically decreased the mean cataract scores in selenite-induced cataract rats on post-induction day 3 compared to the controls (1.3±0.2 versus 2.4±0.4; p<0.05). However, catalin (equivalent to up to 100 μM PRX) did not inhibit calpain-induced proteolysis activated by calcium, and neither did 100 μM PRX. Conclusions: PRX at micromolar levels ameliorated selenite- and calcium-induced lens protein turbidity but required millimolar levels to protect against UVC irradiation. The observed inhibition of UVC-induced turbidity of lens crystallins by catalin at micromolar concentrations may have been a result of the catalin-formulated vehicle. Transient protection by catalin against selenite-induced turbidity of crystallin solutions in vitro was supported by the ameliorated cataract scores in the early stage of cataractogenesis in vivo by subcutaneously administered catalin. PRX could not inhibit calpain-induced proteolysis activated by calcium or catalin itself, and may be detrimental to crystallins under UVB exposure. Further studies on formulation modifications of catalin and recommended doses of PRX to optimize clinical efficacy by cataract type are warranted

Design and Analysis of Impedance Pumps Utilizing Electromagnetic Actuation

This study designs and analyzes an impedance pump utilizing an electromagnetic actuator. The pump is designed to have three major components, namely a lower glass substrate patterned with a copper micro-coil, a microchannel, and an upper glass cover plate attached a magnetic PDMS diaphragm. When a current is passed through the micro-coil, an electromagnetic force is established between the coil and the magnetic diaphragm. The resulting deflection of the PDMS diaphragm creates an acoustic impedance mismatch within the microchannel, which results in a net flow. In performing the analysis, simulated models of the magnetic field, the diaphragm displacement and the flow rate are developed using Ansoft/Maxwell3D, ANSYS FEA and FLUENT 6.3 CFD software, respectively. Overall, the simulated results reveal that a net flow rate of 52.8 μL/min can be obtained using a diaphragm displacement of 31.5 μm induced by a micro-coil input current of 0.5 A. The impedance pump proposed in this study provides a valuable contribution to the ongoing development of Lab-on-Chips (LoCs) systems