Search results for "CONSTANT"
showing 10 items of 1718 documents
Warhead Reactivity Limits the Speed of Inhibition of the Cysteine Protease Rhodesain.
2021
Viral and parasitic pathogens rely critically on cysteine proteases for host invasion, replication, and infectivity. Their inhibition by synthetic inhibitors, such as vinyl sulfone compounds, has emerged as a promising treatment strategy. However, the individual reaction steps of protease inhibition are not fully understood. Using the trypanosomal cysteine protease rhodesain as a medically relevant target, we design photoinduced electron transfer (PET) fluorescence probes to detect kinetics of binding of reversible and irreversible vinyl sulfones directly in solution. Intriguingly, the irreversible inhibitor, apart from its unlimited residence time in the enzyme, reacts 5 times faster than …
Multiple steady states and the form of response functions to antigen in a model for the initiation of T cell activation
2017
The aim of this paper is to study the qualitative behaviour predicted by a mathematical model for the initial stage of T-cell activation. The state variables in the model are the concentrations of phosphorylation states of the T-cell receptor (TCR) complex and the phosphatase SHP-1 in the cell. It is shown that these quantities cannot approach zero and that the model possesses more than one positive steady state for certain values of the parameters. It can also exhibit damped oscillations. It is proved that the chemical concentration which represents the degree of activation of the cell, that of the maximally phosphorylated form of the TCR complex, is, in general, a non-monotone function of…
Partitioned learning of deep Boltzmann machines for SNP data.
2016
Abstract Motivation Learning the joint distributions of measurements, and in particular identification of an appropriate low-dimensional manifold, has been found to be a powerful ingredient of deep leaning approaches. Yet, such approaches have hardly been applied to single nucleotide polymorphism (SNP) data, probably due to the high number of features typically exceeding the number of studied individuals. Results After a brief overview of how deep Boltzmann machines (DBMs), a deep learning approach, can be adapted to SNP data in principle, we specifically present a way to alleviate the dimensionality problem by partitioned learning. We propose a sparse regression approach to coarsely screen…
A heuristic, iterative algorithm for change-point detection in abrupt change models
2017
Change-point detection in abrupt change models is a very challenging research topic in many fields of both methodological and applied Statistics. Due to strong irregularities, discontinuity and non-smootheness, likelihood based procedures are awkward; for instance, usual optimization methods do not work, and grid search algorithms represent the most used approach for estimation. In this paper a heuristic, iterative algorithm for approximate maximum likelihood estimation is introduced for change-point detection in piecewise constant regression models. The algorithm is based on iterative fitting of simple linear models, and appears to extend easily to more general frameworks, such as models i…
Inhibition of Formation of Rev-RRE Complex by Pyronin Y
1993
The interaction of pyronin Y, an RNA intercalating drug, with the binding of Rev protein from human immunodeficiency virus type 1 (HIV-1) to Rev-responsive element (RRE)-containing env RNA was studied. In gel retardation assays, recombinant Rev protein tightly bound to in vitro transcribed RRE RNA. Nitrocellulose-filter-binding studies revealed a dissociation constant of ≈(1–2) = 10−10M (Pfeifer et al., 1991). Pyronin Y efficiently suppressed formation of the Rev-RRE complex. At a concentration of 1 μg ml−1, complex formation was almost completely inhibited. Electron microscopy showed that Rev oligomerizes in the presence of RRE-containing RNA with the formation of short rod-like structures…
Adaptive Large Neighborhood Search with a Constant-Time Feasibility Test for the Dial-a-Ride Problem
2019
In the dial-a-ride problem, user-specified transport requests from origin to destination points have to be served by a fleet of homogeneous vehicles. The problem variant we consider aims at finding a set of minimum-cost routes satisfying constraints on vehicle capacity, time windows, maximum route duration, and maximum user ride times. We propose an adaptive large neighborhood search (ALNS) for its solution. The key novelty of the approach is an exact amortized constant-time algorithm for evaluating the feasibility of request insertions in the repair steps of the ALNS. In addition, we use two optional improvement techniques: a local-search-based intraroute improvement of routes of promisin…
The Chinese Postman Problem with Load-Dependent Costs
2018
[EN] We introduce an interesting variant of the well-known Chinese postman problem (CPP). While in the CPP the cost of traversing an edge is a constant (equal to its length), in the variant we present here the cost of traversing an edge depends on its length and on the weight of the vehicle at the moment it is traversed. This problem is inspired by the perspective of minimizing pollution in transportation, since the amount of pollution emitted by a vehicle not only depends on the travel distance but also on its load, among other factors. We define the problem, study its computational complexity, provide two mathematical programming formulations, and propose two metaheuristics for its soluti…
Rho resonance, timelike pion form factor, and implications for lattice studies of the hadronic vacuum polarization
2020
We study isospin-1 P-wave ππ scattering in lattice QCD with two flavors of O(a) improved Wilson fermions. For pion masses ranging from mπ=265 MeV to mπ=437 MeV, we determine the energy spectrum in the center-of-mass frame and in three moving frames. We obtain the scattering phase shifts using Lüscher’s finite-volume quantization condition. Fitting the dependence of the phase shifts on the scattering momentum to a Breit-Wigner form allows us to determine the corresponding ρ mass mρ and gρππ coupling. By combining the scattering phase shifts with the decay matrix element of the vector current, we calculate the timelike pion form factor, Fπ, and compare the results to the Gounaris-Sakurai repr…
Partition of Indicaxanthin in Membrane Biomimetic Systems. A Kinetic and Modeling Approach
2009
The solubilization site of indicaxanthin (Ind) in lipid bilayers was investigated by the kinetics of Ind oxidation by peroxyl radicals in water and in aqueous/L-alpha-dipalmitoyl-phosphatidylcholine (DPPC) vesicles, pH 7.4, and 37.0 and 48.0 degrees C, that is, in a gel-like and a crystal liquidlike bilayer state, respectively. The time-dependent Ind absorbance decay, matched with a successful simulation of the reaction kinetic mechanism by Gepasi software, supported a multistep pathway. Computer-assisted analysis allowed calculation of the rate constants associated with the reactions involved, the values of which decreased with increasing DPPC concentration. The binding constant calculated…