Methods and Applications of In Silico Aptamer Design and Modeling

Aptamers are nucleic acid analogues of antibodies with high affinity to different targets, such as cells, viruses, proteins, inorganic materials, and coenzymes. Empirical approaches allow the design of in vitro aptamers that bind particularly to a target molecule with high affinity and selectivity. Theoretical methods allow significant expansion of the possibilities of aptamer design. In this study, we review theoretical and joint theoretical-experimental studies dedicated to aptamer design and modeling. We consider aptamers with different targets, such as proteins, antibiotics, organophosphates, nucleobases, amino acids, and drugs. During nucleic acid modeling and in silico design, a full set of in silico methods can be applied, such as docking, molecular dynamics (MD), and statistical analysis. The typical modeling workflow starts with structure prediction. Then, docking of target and aptamer is performed. Next, MD simulations are performed, which allows for an evaluation of the stability of aptamer/ligand complexes and determination of the binding energies with higher accuracy. Then, aptamer/ligand interactions are analyzed, and mutations of studied aptamers made. Subsequently, the whole procedure of molecular modeling can be reiterated. Thus, the interactions between aptamers and their ligands are complex and difficult to understand using only experimental approaches. Docking and MD are irreplaceable when aptamers are studied in silico.     

An Acoustic Converter Used to Measure Ionizing Radiation Energy Loss

A monitor is proposed based on ultrasonic production when ionizing radiation passes through a medium. The recording element is a 0.2 mm aluminum plate mounted in a ceramic acoustic converter AC in the form of a wedge of thickness 2 mm. The low plate thickness minimizes the beam parameter distortion, while special technology used in the AC provides high sensitivity. The device has been calibrated in the proton beam from the ITEP accelerator at 200 MeV with 2·10⁹–6·10¹⁰ particles in a pulse and a pulse length of 70 nsec.     

The social consequences of expressive suppression.

At times, people keep their emotions from showing during social interactions. The authors' analysis suggests that such expressive suppression should disrupt communication and increase stress levels. To test this hypothesis, the authors conducted 2 studies in which unacquainted pairs of women discussed an upsetting topic. In Study 1, one member of each pair was randomly assigned to (a) suppress her emotional behavior, (b) respond naturally, or (c) cognitively reappraise in a way that reduced emotional responding. Suppression alone disrupted communication and magnified blood pressure responses in the suppressors' partners. In Study 2, suppression had a negative impact on the regulators' emotional experience and increased blood pressure in both regulators and their partners. Suppression also reduced rapport and inhibited relationship formation. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Effect of sampling density on the measurement of stream condition indicators in two lowland Australian streams

There is widespread application of indicators to the assessment of environmental condition of streams. These indicators are intended for use by managers in making various comparative and absolute assessments and often have a role in resource allocation and performance assessment. Therefore, the problem of formally defining confidence in the results is important but difficult because the sampling strategies used are commonly based on a compromise between the requirements of statistical rigour and the pragmatic issues of access and resources. It is rare to see this compromise explicitly considered and consequently there is seldom quantification of the uncertainty that could affect the confidence a manager has in an indicator. In this paper, we present a method for quantitatively assessing the tradeoffs between sampling density and uncertainty in meeting various monitoring objectives. Assessments using judgement‐based representative reaches are shown to be unreliable; instead a sampling approach is recommended based on the random selection of measuring sites. A detailed dataset was collected along two streams in Victoria, Australia, and the effect of sampling density was assessed by subsampling from this dataset with precision related to the number of sites assessed per reach length and the intensity of the sampling at each site. The sampling scheme to achieve a given precision is shown to depend on the monitoring objective. In particular, three objectives were considered: (1) making a baseline assessment of current condition; (2) change detection; and (3) detection of a critical threshold in condition. Change detection is shown to be more demanding than assessing baseline condition with additional sampling effort required to achieve the same precision. Sampling to detect a critical threshold depends on nominating acceptable values of Type I and II error and the size of the effect to be detected. Copyright © 2006 John Wiley & Sons, Ltd.     

Mathematical model of an industrial robot with articulated configuration and six degrees of freedom

This paper analyses the load influence on a d.c. drive motor servo system for all six degrees of freedom of industrial robots with an articulated configuration. Through the analyses, the analytical equations of total inertia and gravitation moments of an industrial robot servo system for external coordinate function were obtained. A mathematical model of an electro-mechanical industrial robot system was also developed.     

Semiconductor-insulator structures in the phototargets of vidicons sensitive in the middle infrared region of the spectrum

The kinetics of electronic processes in vidicon phototargets based on semiconductor-insulator structures with a narrow-gap semiconductor is considered taking into account charge drain in the insulator layer and relaxation of the nonequilibrium depletion region in the semiconductor layer. The integration time, threshold sensitivity, and resolution at various intensities of incident radiation are estimated.     

A note on the variance of rank-based selection strategies for genetic algorithms and genetic programming

This paper evaluates different forms of rank-based selection that are used with genetic algorithms and genetic programming. Many types of rank based selection have exactly the same expected value in terms of the sampling rate allocated to each member of the population. However, the variance associated with that sampling rate can vary depending on how selection is implemented. We examine two forms of tournament selection and compare these to linear rank-based selection using an explicit formula. Because selective pressure has a direct impact on population diversity, we also examine the interaction between selective pressure and different mutation strategies.     

Effect of repositioning of rhodium direct-charge detectors in a RBMK-1000 reactor on fuel and emitter-material burnup coefficients

Scientific-Technical Center “Atomtekhénergo.” Leningrad Nuclear Power Plant. N. V. Sultanov Institute of Nuclear Reactors, Russian Scientific Center “Kurchatovskii institut.” Translated from Atomnaya énergiya, Vol. 76, No. 6, pp. 470–473, June, 1994.