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

Estimation of advective methane flux in gas hydrate potential area offshore SW Taiwan and its tectonic implications

With the discoveries of Bottom Simulating Reflectors (BSRs), large and dense chemosynthetic communities and rapid sulfate reductions in pore space sediments, gas hydrates may exist in offshore southwestern Taiwan. Methane concentrations in pore space sediments have been measured to investigate if fluids and gases are derived from dissociation of gas hydrates. Very high methane concentrations and very shallow depths of sulfate methane interface (SMI) imply the high methane flux underneath the seafloor. Linear sulfate gradients, low total organic carbon (TOC) have been combined to describe the process of anaerobic methane oxidation (AMO) and calculate the iffusive methane flux in Chuang et al. (2010). However, the appearance of concave (or non-linear) profiles of sulfate in some cores might indicate advective fluid flows. Hence, the methane flux may be much greater under advective conditions. In this study, numerical transport-reaction models were applied to calculate the methane flux including diffusion and advection of dissolved sulfate and methane and the anaerobic methane oxidation of methane. According to the modeled results of three giant piston cores (MD05-2911, MD05-2912 and MD05-2913) collected during the r/v Marion Dufresne cruise in 2005, gas bubbling or bioirrigation may occur in these site. Values of the methane flux ranging from 1.91 to 5.17 mmol m-2yr-1 and upward fluid flow velocities around 0.05-0.13 cm yr-1 are related to different geologic structures in the active continental margin. Site MD05-2912 is located on the Tainan Ridge where anticlines and blind thrusts are the dominate structures. Site MD052911 is on the Yung-An Ridge characterized by emergent and imbricate thrusts

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

Nonhomogeneous seawater Sr isotopic composition in the coastal oceans : a novel tool for tracing water masses and submarine groundwater discharge

Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 12 (2011): Q05002, doi:10.1029/2010GC003372.Here we present high-precision (2σ = ±3 ppm) 87Sr/86Sr measurements in coastal waters, together with salinity, to evaluate water mass mixing and the influence of submarine groundwater discharge (SGD) in coastal waters and marginal seas. Nonhomogeneous Sr isotopic variations in water columns were documented in the Southern Okinawa Trough (SOT), South China Sea, and Kao-ping Canyon (KPC), where seawater 87Sr/86Sr varied up to 70 ppm. Seawater Sr isotopic composition changes only slightly in the upper 200 m of the SOT but was detectable and highly correlated with salinity, indicating a mixing between radiogenic North Pacific Tropical Water (high 87Sr/86Sr and high salinity) at 100–150 m and a less radiogenic component with low 87Sr/86Sr and low salinity at ∼200 m. Vertical profiles of seawater 87Sr/86Sr along the KPC show significant variations, suggesting dynamic mixing affected by continental inputs (i.e., river runoff and SGD) in this region. These results highlight the potential use of seawater Sr isotopes as a powerful tracer for determining mixing ratios and the dynamic mixing of oceanic water masses, especially in coastal and marginal seas.This research was supported by a postdoctoral fellowship from Top University (NCKU), Taiwan, to K.‐F. Huang and funds from NSC and MOE, Taiwan, to C.‐F. You

Predictors of psychiatric readmissions in the short- and long-term: a population-based study in taiwan

OBJECTIVES: To explore the risks and rates of readmission and their predictors 14 days, one year, and five years after discharge for the psychiatric population in Taiwan. METHODS: This was a prospective study based on claims from 44,237 first-time hospitalized psychiatric patients discharged in 2000, who were followed for up to five years after discharge. The cumulative incidence and incidence density of readmission were calculated for various follow-up periods after discharge, and Cox proportional hazard models were generated to identify the significant predictors for psychiatric readmission. RESULTS: The less than 14-day, one-year, and five-year cumulative incidences were estimated at 6.1%, 22.3%, and 37.8%, respectively. The corresponding figures for incidence density were 4.58, 1.04, and 0.69 per 1,000 person-days, respectively. Certain factors were significantly associated with increased risk of readmission irrespective of the length of follow-up, including male gender, length of hospital stay >15 days, economic poverty, a leading discharge diagnosis of schizophrenia/affective disorders, and residence in less-urbanized regions. Compared to children/adolescents, young adults (20-39 years) were significantly associated with increased risks of <one-year and <five-year readmissions, but not <14-day readmission. Additionally, hospital characteristics were significantly associated with increased risk of <14-day and <one-year readmission, but not with risk of <five-year readmission. CONCLUSIONS: This study found that the significant predictors for psychiatric readmission 14 days to five years after discharge were essentially the same except for patient's age and hospital accreditation level. This study also highlighted the importance of socioeconomic factors in the prediction of readmission

A Bayesian measurement error model for two-channel cell-based RNAi data with replicates

RNA interference (RNAi) is an endogenous cellular process in which small double-stranded RNAs lead to the destruction of mRNAs with complementary nucleoside sequence. With the production of RNAi libraries, large-scale RNAi screening in human cells can be conducted to identify unknown genes involved in a biological pathway. One challenge researchers face is how to deal with the multiple testing issue and the related false positive rate (FDR) and false negative rate (FNR). This paper proposes a Bayesian hierarchical measurement error model for the analysis of data from a two-channel RNAi high-throughput experiment with replicates, in which both the activity of a particular biological pathway and cell viability are monitored and the goal is to identify short hair-pin RNAs (shRNAs) that affect the pathway activity without affecting cell activity. Simulation studies demonstrate the flexibility and robustness of the Bayesian method and the benefits of having replicates in the experiment. This method is illustrated through analyzing the data from a RNAi high-throughput screening that searches for cellular factors affecting HCV replication without affecting cell viability; comparisons of the results from this HCV study and some of those reported in the literature are included.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS496 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Determination of Nucleopolyhedrovirus’ Taxonomic Position

To date , over 78 genomes of nucleopolyhedroviruses (NPVs) have been sequenced and deposited in NCBI. How to define a new virus from the infected larvae in the field is usually the first question. Two NPV strains, which were isolated from casuarina moth (L. xylina) and golden birdwing larvae (Troides aeacus), respectively, displayed the same question. Due to the identity of polyhedrin (polh) sequences of these two isolates to that of Lymantria dispar MNPV and Bombyx mori NPV, they are named LdMNPV-like virus and TraeNPV, provisionally. To further clarify the relationships of LdMNPV-like virus and TraeNPV to closely related NPVs, Kimura 2-parameter (K-2-P) analysis was performed. Apparently, the results of K-2-P analysis that showed LdMNPV-like virus is an LdMNPV isolate, while TraeNPV had an ambiguous relationship to BmNPV. Otherwise, MaviNPV, which is a mini-AcMNPV, also exhibited a different story by K-2-P analysis. Since K-2-P analysis could not cover all species determination issues, therefore, TraeNPV needs to be sequenced for defining its taxonomic position. For this purpose, different genomic sequencing technologies and bioinformatic analysis approaches will be discussed. We anticipated that these applications will help to exam nucleotide information of unknown species and give an insight and facilitate to this issue