Semiparametric estimation in copula models for bivariate sequential survival times

Sequentially observed survival times are of interest in many studies but there are difficulties in analyzing such data using nonparametric or semiparametric methods. First, when the duration of followup is limited and the times for a given individual are not independent, induced dependent censoring arises for the second and subsequent survival times. Non-identifiability of the marginal survival distributions for second and later times is another issue, since they are observable only if preceding survival times for an individual are uncensored. In addition, in some studies a significant proportion of individuals may never have the first event. Fully parametric models can deal with these features, but robustness is a concern. We introduce a new approach to address these issues. We model the joint distribution of the successive survival times by using copula functions, and provide semiparametric estimation procedures in which copula parameters are estimated without parametric assumptions on the marginal distributions. This provides more robust estimates and checks on the fit of parametric models. The methodology is applied to a motivating example involving relapse and survival following colon cancer treatment.     

Binding of small molecules to cavity forming mutants of a de novo designed protein

A central goal of protein design is to devise novel proteins for applications in biotechnology and medicine. Many applications, including those focused on sensing and catalysis will require proteins that recognize and bind to small molecules. Here, we show that stably folded α-helical proteins isolated from a binary patterned library of designed sequences can be mutated to produce binding sites capable of binding a range of small aromatic compounds. Specifically, we mutated two phenylalanine side chains to alanine in the known structure of de novo protein S-824 to create buried cavities in the core of this four-helix bundle. The parental protein and the Phe→Ala variants were exposed to mixtures of compounds, and selective binding was assessed by saturation transfer difference NMR. The affinities of benzene and a number of its derivatives were determined by pulse field gradient spin echo NMR, and several of the compounds were shown to bind the mutated protein with micromolar dissociation constants. These studies suggest that stably folded de novo proteins from binary patterned libraries are well-suited as scaffolds for the design of binding sites.     

Morphometric analyses reveal synonymy of two monotypic genera, Huangiella and Tumoris (Acari, Eriophyoidea, Eriophyidae)

Morphological variation of Huangiella lanyuensis (Huang, 2001) and Tumoris sanasaii Huang, 2001 from Taiwan was analyzed using multivariate statistical methods. We show that these species are the same and propose to use the name Tumoris sanasaii. No significant differences between populations from Lanyu and Green Island (type localities for Huangiella lanyuensis and Tumoris sanasaii, respectively) were found; however, mites from Yangmingshan (northern Taiwan) differed substantially from these two groups. Synonymy resulted from our study is as follows: Huangiella Kammerer, 2006 is a junior synonym of Tumoris Huang, 2001; Absentia lanyuensis Huang, 2001 is a junior synonym of Tumoris sanasaii Huang, 2001. We also study the sexual variation of populations from Green Island. The result showed the females significantly larger than the males at 17 variables.     

Monte Carlo Simulation of Binary Gas Adsorption in Zeolite Cavities

Abstract

Grand canonical Monte Carlo simulations have been performed for binary adsorption of Lennard-Jones molecules with point multipole moments in zeolite cavities of type X. Fluid-solid electrostatic interactions were taken into account. Phase diagrams and total coverage were calculated for three binaries and compared with experimental measurements. MC simulations gave good agreement with experiment for two mixtures (C₂H₄-CO₂ and CO₂-CH₄) but there were discrepancies between simulation and experiment for the system i-C₄H₁₀-C₂H₄. The dependence of excess Gibbs free energy on the composition and pressure was studied. Negative deviations from ideality are due to energetic heterogeneity and size effects. Unlike liquid-vapor equilibrium, deviations from the Lorentz-Berthelot mixing rules for the adsorbates have little effect upon the phase behavior. Density distributions show that the components compete for the high energy sites inside the cavity; depending on its relative strength of adsorption, one component may be excluded from such positions (CH₄ in CO₂-CH₄), or the two species may share sites inside the cavity (C₂H₄-CO₂).     

A density functional theory study on the Ti/P binary cluster ions

Under the framework of density functional theory, an all-electron calculation on the geometrical structures and dissociation channels of Ti/P binary cluster ions has been carried out. The P₂, P₃ and P₄ structures are found to be the relatively stable units in these cluster ions. The lowest energy geometries of these Ti/P binary cluster ions may be constructed by bonding Ti, Ti₂, Ti₃ or Ti₄ unit with one or two relatively stable P₂, P₃ and P₄ units. The most possible dissociation channels of these Ti/P binary cluster ions are the detachment of P₂, P₃ or P₄ fragment. It is well consistent with the photodissociation experimental results.     

Development of Gateway Binary Vectors,R4L1pGWBs,for Promoter Analysis in Higher Plants

We developed a new series of Gateway binary vectors for plant transformation, R4L1pGWBs, which allow easy construction of promoter:reporter clones. R4L1pGWBs contain a recombination attR4-attL1-reporter cassette, and thus an attL4-promoter-attR1 entry clone was efficiently incorporated by the Gateway LR reaction, resulting in the generation of an attB4-promoter-attB1-reporter construct. The reporters employed in R4L1pGWBs were β-glucuronidase (GUS), luciferase (LUC), enhanced yellow fluorescent protein (EYFP), enhanced cyan fluorescent protein (ECFP), G3 green fluorescent protein (G3GFP), G3GFP-GUS, and tag red fluorescent protein (TagRFP).     

Seasonal pattern of zooplankton communities and their environmental response in subtropical maritime channels systems in the Bay of Bengal,Bangladesh

Zooplankton are a primary component of aquatic food chain and play an important role in the functioning of aquatic food webs. Seasonal variation in community structures of zooplankton and potential environmental drivers were studied, during a 1-year cycle (summer 2015 – spring 2016) in subtropical maritime channels systems in the Bay of Bengal, coastal waters in Bangladesh. A total of 32 species representing 25 families, 13 orders and 15 taxonomic groups were identified. Of these species, 23 distributed in all four season of which 8 were dominant species with high contributions of the total communities. Species number was peaked in autumn and fell in summer while maximum abundance was in the winter and minimum in summer. Multivariate analyses showed that there was a clear seasonal shift in zooplankton community structures in relation with environmental conditions. Species diversity and evenness peaked in summer while the high value of species richness was found in autumn. Multivariate correlation (RELATE) and BIO-ENV analysis demonstrated that seasonal variation in community patterns was significantly correlated with temporal shift of environmental conditions and that variation mainly driven by water transparency, salinity, DO, TSS and nutrients. Thus, this finding implies that the zooplankton community represented a clear seasonal shift shaped by environmental drivers in subtropical channels systems.     

Hydrogeochemical characterization of Yercaud lake southern India: Implications on lake water chemistry through multivariate statistics

In this paper, a study on the surface and deeper waters of the Yercaud Lake, Tamil Nadu, South India, was carried out to understand the geochemistry of the lake waters and also to determine its utility for agricultural purposes. Totally, 50 surface and deep water samples were collected from Yercaud Lake. Major ion and heavy metals were measured. The data obtained were interpreted using the lake water composition. The mean concentration of physicochemical parameters and heavy metals for the surface and deep waters have the following values, pH (7.6), EC (263.4), Ca^2 +(16.3), Mg^2 +(7.4), Na⁺(19.2), K⁺(1.5), Cl^?(18.2), NO₃^?(1.5), SO₄^2 ?(1.5), HCO₃^– (97.9), Fe (1.3), Mn (0.1), Cr (0.4), Cu (0.005), Pb (0.31), Zn (0.01), Co (0.095) and Ni (0.075). The data generated reflects that the water samples are dominated by recharge process, especially due to the monsoonal rains and natural springs within the lake. The geochemical data reveals that the lake water is suitable for the agricultural purpose and the chemistry of water is mainly influenced by the weathering of bedrock, especially the charnockites bedrock. The sodium adsorption ratio and sodium percentage (%Na) values indicate that the lake water is suitable for irrigation. Dominant heavy metals in the lake waters are mainly because of the lithogenic as well as through minor anthropogenic inputs. Based on our data it is noted that proper management plans are required to monitor the pollution source in the lake, with strict policy measures.     

Estimation of the Parameters of two Parallel Regression Lines Under Uncertain Prior Information

The problem of parallelism for bi‐linear regression lines arises in many real life investigations. For two linear regression models with normal errors, the estimation of the slope as well as the intercept parameters is considered when it is apriori suspected that the two lines are parallel. Three different estimators are defined by using both the sample data and the non‐sample uncertain prior information. The relative performances of the unrestricted, restricted and preliminary test estimators are investigated based on the analysis of the bias, and risk functions under quadratic loss. An example based on a medical study is used to illustrate the method.