A multiple regression method for analysing stage-frequency data

A linear regression method that allows survival rates to vary from stage to stage is described for the analysis of stage-frequency data. It has advantages over previously suggested methods since the calculations are not iterative, and it is not necessary to have independent estimates of stage durations, numbers entering stages, or the rate of entry to stage 1. Simulation is proposed to determine standard errors for estimates of population parameters, and to assess the goodness of fit of models.     

Genetic Determinants of the Pre‐ and Post‐Azathioprine Therapy Thiopurine Methyltransferase Activity Phenotype

Thiopurine drug therapy has been reported to lead to a variable increase in red cell TPMT activity that may alter effective dose and therapeutic outcome. The aim of this study was to correlate Variable Number Tandem Repeat (VNTR) in the promoter region of the TPMT gene with induction of red cell TPMT activity in patients treated with azathioprine (AZA). In 58 patients, TPMT activity measured at 3 months was not significantly induced on average above pre‐therapy levels. Individual patients showed variation in TPMT activity pre‐ and post‐AZA therapy, however changes in TPMT activity were not predicted by VNTR configuration. In conclusion, TPMT promoter VNTRs are unlikely to play a significant role in changes in TPMT activity in response to AZA therapy.     

Genetic counselling for pulmonary arterial hypertension: a matter of variable variability

We report three cases which highlight the complex considerations surrounding genetic counselling for pulmonary arterial hypertension (PAH). The first counselee developed PAH symptoms shortly after his daughter’s death from PAH and was diagnosed with a delay of 1 year. An early diagnosis of familial PAH was established in the second counselee. Oral therapy was initiated immediately, and her functional status has since remained stable. The third counselee was a healthy woman who struggled to cope with her risk for familial PAH, having lost two siblings from the disease. These cases show that incomplete penetrance and variable expression need particular attention during clinical assessment and genetic counselling of heritable PAH patients and family members.     

Effects of AMPARs trafficking and glutamate-receptors binding probability on stochastic variability of EPSC

Mathematical models of the excitatory synapse are providing valuable information about the synaptic response. The effects of several synaptic components on EPSC variability have been tested by computer simulation. Our model, based on Brownian diffusion of glutamate in the synaptic cleft, is basically the same we have used in previous papers but parameters have been upgraded according to the new experimental findings. The presence of filaments into the synaptic cleft and the number and the ratio of AMPA and NMDA receptors have been the main parameters upgraded. A different way of computing the binding probability of glutamate molecules to receptors by means of geometrical considerations has been also used. The obtained results were more precise and they suggested that the new elements can play a significant role in the stochastic variability of the synaptic response. Nevertheless, new problems arise concerning the value of the lower limit of the binding probability.     

Diffusivity of CH4 In Model Silica Nanopores: Molecular Dynamics and Quasichemical Mean Field Theory

Equilibrium molecular dynamics and dual control volume grand canonical molecular dynamics experiments were carried out aiming at the investigation of the dependence of transport diffusivity upon the adsorbent pore size and sorbate concentration of CH₄ in cylindrical silica nanopores at 298?K, calibrated with respect to experimental data of zeolite VPI 5; the results of simulation were elaborated on the basis of the quasichemical mean field approximation via a theoretical model for surface diffusion. Our mapping procedure between simulation and quasichemical theory reveals that sorbate–sorbate energetics emerge as the physical reason for the variation of corrected (Darken) and hence transport diffusivity with respect to pore size and sorbed phase fractional occupancy.     

Penalized gaussian process regression and classification for high-dimensional nonlinear data

The model based on Gaussian process (GP) prior and a kernel covariance function can be used to fit nonlinear data with multidimensional covariates. It has been used as a flexible nonparametric approach for curve fitting, classification, clustering, and other statistical problems, and has been widely applied to deal with complex nonlinear systems in many different areas particularly in machine learning. However, it is a challenging problem when the model is used for the large-scale data sets and high-dimensional data, for example, for the meat data discussed in this article that have 100 highly correlated covariates. For such data, it suffers from large variance of parameter estimation and high predictive errors, and numerically, it suffers from unstable computation. In this article, penalized likelihood framework will be applied to the model based on GPs. Different penalties will be investigated, and their ability in application given to suit the characteristics of GP models will be discussed. The asymptotic properties will also be discussed with the relevant proofs. Several applications to real biomechanical and bioinformatics data sets will be reported.     

Structural features of cytochrome P450 1A associated with the absence of EROD activity in liver of the loricariid catfish Pterygoplichthys sp

The Amazon catfish genus Pterygoplichthys (Loricariidae, Siluriformes) is closely related to the loricariid genus Hypostomus, in which at least two species lack detectable ethoxyresorufin-O-deethylase (EROD) activity, typically catalyzed by cytochrome P450 1 (CYP1) enzymes. Pterygoplichthys sp. liver microsomes also lacked EROD, as well as activity with other substituted resorufins, but aryl hydrocarbon receptor agonists induced hepatic CYP1A mRNA and protein suggesting structural/functional differences in Pterygoplichthys CYP1s from those in other vertebrates. Comparing the sequences of CYP1As of Pterygoplichthys sp. and of two phylogenetically related siluriform species that do catalyze EROD (Ancistrus sp., Loricariidae and Corydoras sp., Callichthyidae) showed that these three proteins share amino acids at 17 positions that are not shared by any fish in a set of 24 other species. Pterygoplichthys and Ancistrus (the loricariids) have an additional 22 amino acid substitutions in common that are not shared by Corydoras or by other fish species. Pterygoplichthys has six exclusive amino acid substitutions. Molecular docking and dynamics simulations indicate that Pterygoplichthys CYP1A has a weak affinity for ER, which binds infrequently in a productive orientation, and in a less stable conformation than in CYP1As of species that catalyze EROD. ER also binds with the carbonyl moiety proximal to the heme iron. Pterygoplichthys CYP1A has amino acid substitutions that reduce the frequency of correctly oriented ER in the AS preventing the detection of EROD activity. The results indicate that loricariid CYP1As may have a peculiar substrate selectivity that differs from CYP1As of most vertebrate.     

Variation in the content of hypericins in four generations of seed progeny of <Emphasis Type="Italic">Hypericum perforatum</Emphasis> somaclones

The content of hypericins in in vitro regenerated Hypericum perforatum plants (R ₀) and four generations of their seed progeny (R ₁–R ₄) was compared. The mean content of hypericins in field-grown plants over the period 1992–2002 gradually increased under selection, and in the R ₄ generation it was almost seven-times higher than that in the R ₀ somaclones. Significant difference between hypericin content in diploids and tetraploids was detected in R ₀, R ₁ and R ₃ generations. Hypericin content in four diploid and tetraploid lineages originated from a single somaclone was genotype dependent. To eliminate the influence of environmental conditions during different growing seasons, we used seeds of selected R ₀–R ₃ plants to derive R′₁ to R′₄ generations cultivated during the same years. In this case no statistically significant difference in hypericin content was found between the R′₁–R′₄ generations. Apomictically and sexually derived plants were distinguished by PCR using variable numbers of tandem repeats (VNTR) primers. The content of hypericins in apomictically derived progenies was compared.     

Specific Amyloid β Clearance by a Catalytic Antibody Construct

Classical immunization methods do not generate catalytic antibodies (catabodies), but recent findings suggest that the innate antibody repertoire is a rich catabody source. We describe the specificity and amyloid β (Aβ)-clearing effect of a catabody construct engineered from innate immunity principles. The catabody recognized the Aβ C terminus noncovalently and hydrolyzed Aβ rapidly, with no reactivity to the Aβ precursor protein, transthyretin amyloid aggregates, or irrelevant proteins containing the catabody-sensitive Aβ dipeptide unit. The catabody dissolved preformed Aβ aggregates and inhibited Aβ aggregation more potently than an Aβ-binding IgG. Intravenous catabody treatment reduced brain Aβ deposits in a mouse Alzheimer disease model without inducing microgliosis or microhemorrhages. Specific Aβ hydrolysis appears to be an innate immune function that could be applied for therapeutic Aβ removal.