Cruciform-extruding regulatory element controls cell-specific activity of the tyrosine hydroxylase gene promoter

Tyrosine hydroxylase (TH) is expressed specifically in catecholaminergic cells. We have identified a novel regulatory sequence in the upstream region of the bovine TH gene promoter formed by a dyad symmetry element (DSE1;-352/-307 bp). DSE1 supports TH promoter activity in TH-expressing bovine adrenal medulla chromaffin (BAMC) cells and inhibits promoter activity in non-expressing TE671 cells. DNase I footprinting of relaxed TH promoter DNA showed weak binding of nuclear BAMC cell proteins to a short sequence in the right DSE1 arm. In BAMC cells, deletion of the right arm markedly reduced the expression of luciferase from the TH promoter. However, deletion of the left DSE1 arm or its reversed orientation (RevL) also inactivated the TH promoter. In supercoiled TH promoter, DSE1 assumes a cruciform-like conformation i.e., it binds cruciform-specific 2D3 antibody, and S1 nuclease-cleavage and OsO4-modification assays have identified an imperfect cruciform extruded by the DSE1. DNase I footprinting of supercoiled plasmid showed that cruciformed DSE1 is targeted by nuclear proteins more efficiently than the linear duplex isomer and that the protected site encompasses the left arm and center of DSE1. Our results suggest that the disruption of intrastrand base-pairing preventing cruciform formation and protein binding to DSE1 is responsible for its inactivation in DSE1 mutants. DSE1 cruciform may act as a target site for activator (BAMC cells) and repressor (TE671) proteins. Its extrusion emerges as a novel mechanism that controls cell-specific promoter activity.     

Transcriptional regulation of fibroblast growth factor-2 expression in human astrocytes: implications for cell plasticity

Induction of the fibroblast growth factor-2 (FGF-2) gene and the consequent accumulation of FGF-2 in the nucleus are operative events in mitotic activation and hypertrophy of human astrocytes. In the brain, these events are associated with cellular degeneration and may reflect release of the FGF-2 gene from cell contact inhibition. We used cultures of human astrocytes to examine whether expression of FGF-2 is also controlled by soluble growth factors. Treatment of subconfluent astrocytes with interleukin-1beta, epidermal or platelet-derived growth factors, 18-kDa FGF-2, or serum or direct stimulation of protein kinase C (PKC) with phorbol 12-myristate 13-acetate or adenylate cyclase with forskolin increased the levels of 18-, 22-, and 24-kDa FGF-2 isoforms and FGF-2 mRNA. Transfection of FGF-2 promoter-luciferase constructs identified a unique -555/-513 bp growth factor-responsive element (GFRE) that confers high basal promoter activity and activation by growth factors to a downstream promoter region. It also identified a separate region (-624/-556 bp) essential for PKC and cAMP stimulation. DNA-protein binding assays indicated that novel cis-acting elements and trans-acting factors mediate activation of the FGF-2 gene. Southwestern analysis identified 40-, 50-, 60-, and 100-kDa GFRE-binding proteins and 165-, 112-, and 90-kDa proteins that interacted with the PKC/cAMP-responsive region. The GFRE and the element essential for PKC and cAMP stimulation overlap with the region that mediates cell contact inhibition of the FGF-2 promoter. The results show a two-stage regulation of the FGF-2 gene: 1) an initial induction by reduced cell contact, and 2) further activation by growth factors or the PKC-signaling pathway. The hierarchic regulation of the FGF-2 gene promoter by cell density and growth factors or PKC reflects a two-stage activation of protein binding to the GFRE and to the PKC/cAMP-responsive region, respectively.     

Evaluation of glass samples for forensic purposes — An application of likelihood ratios and an information-theoretical approach

This article presents an experimental study about the influence of the selection of an adequate database for evidence evaluation using chemical profiles. Evidence evaluation in the forensic sense can be seen as the comparison of two glass objects, one of known origin, denoted as control glass, and typically would be from the scene of a crime, and the other one of unknown origin, termed recovered glass, which might be found in association with a suspect. The aim is to obtain some estimate of the weight of evidence for the degree of support to any of the hypothesis in the case, typically these might be that the control and recovered glass come from the same source (θ_p), and control and recovered glass come from different sources (θ_d). A likelihood ratio is considered a suitable measure of the evidential weight for the competing propositions. The observations are of the elemental composition of glass, measured using a Scanning Electron Microscopy, coupled with an Energy Dispersive X-ray spectrometer technique. A number of glass objects have been analyzed and their chemical profiles form a database which represents several sources of variation. In this paper questions surrounding the choice of observations to make are addressed empirically by assessing the impact of building each model using a database different from the one using for comparison. The performance of each evidence evaluation method is assessed by classical methods such as Tippett plots, or more recent information-theoretical approaches such as empirical cross-entropy (ECE) plots.The results show that several of the compositional elements are very robust to the selection of the background database, namely; calcium, silicon and sodium observed in their oxide forms. We also show that the likelihood ratio computed with the combination of these variables show a remarkable discriminating power, and good calibration, allowing them to be employed for the calculation of the strength of evidence in forensic case work.     

A variable-size local domain approach for increased design confidence in simulation-based optimization

Simulation-based design optimization utilizes computational models that rely on assumptions and approximations. There is a need therefore, to ensure that the obtained designs will exhibit the desired behavior as anticipated given the model predictions. The common approach to accomplish that is to validate the utilized computational models prior to the design optimization process. However, this is practically an impossible task especially for design problems with high-dimensional design and parameter spaces. We have recently proposed a different approach for maximizing confidence in the designs generated during a sequential simulation-based optimization process based on calibrating the computational models when necessary and within local subdomains of the design space. In that work, the size of the local domains was held fixed and not linked to uncertainty, and the confidence in designs was quantified using Bayesian hypothesis testing. In this article, we present an improved methodology. Specifically, we use a statistical methodology to account for uncertainty and to determine the size of the local domains at each stage of the sequential design optimization process using parametric bootstrapping that involves maximum likelihood estimators of model parameters. The sequential process continues until the local domain does not change from stage to stage during the design optimization process, ensuring convergence to an optimal design. The proposed methodology is illustrated with the design of a thermal insulator using one-dimensional, linear heat conduction in a solid slab with heat flux boundary conditions.     

Modeling computational limitations in H-Phy and Overlay-NoC architectures

High performance computing demands constant growth in computational power and services that can be offered by modern supercomputers. It requires technological and designing advances in the multiprocessor internal structures as well as novel computing models considering the very high computing demands. One of the increasingly important requirements of computing platforms is a functionality that allows efficient managing computational resources, i.e., monitor them, restrict an access to some part of the resources, account for computational service, or ensure reliability and quality of service when some resources are broken or disabled. In this paper, we present a new model describing computational limitations for processing tasks on multiprocessor systems. The model is implemented in Hardware-Physical (H-Phy) and Overlay-Network-on-Chip (Overlay-NoC) architectures. Both architectures and the model are described and analyzed. Experimentation system is also presented, together with simulation assumptions, results of research and their study. The paper provides complete models of H-Phy and Overlay-NoC structures with an ability to restrict processing resources.     

Algebraic Constructions: A Simple Framework for Complex Dependencies and Parameterisation

We propose a simple framework of algebraic constructions for software specification, modular design and development. Algebraic constructions generalise (parameterised) modules by allowing on one hand a rather arbitrary collection of elements to form the parameter and on the other hand dependencies between the module elements to be spelled out explicitly. Algebraic constructions are specified in a very natural way by means of ordinary algebraic specifications. They are combined using a sum operation which captures as special cases various operations on (parameterised) modules offered by standard specification and development frameworks. We show the expected composability result for the sum of algebraic constructions and of their specifications.     

The influence of zinc ions discharged in a non-aqueous cell on a copper catalyst on the rate of cyclohexanol dehydrogenation reaction

Results of studies on the influence of a copper catalyst modification with zinc ions on the activity in the reaction of cyclohexanol dehydrogenation are presented. The modification has been performed by electrochemical discharging-insertion of zinc ions on a copper electrode in a non-aqueous cell. It has been demonstrated that the catalyst activity depends on the amount of discharged zinc ions as well as on the nature and concentration of the electrolyte. In the case of zinc ions discharged from a solution of ZnCl₂ in propylene carbonate, the yield of cyclohexanone increased up to five times and using Zn(BF₄)₂ in dimethylformamide almost twenty times. The activity of the system in the competing reaction of dehydration was low, hence the selectivity in the dehydrogenation reaction was high.     

Parallel implementation of background subtraction algorithms for real-time video processing on a supercomputer platform

Results of evaluation of the background subtraction algorithms implemented on a supercomputer platform in a parallel manner are presented in the article. The aim of the work is to chose an algorithm, a number of threads and a task scheduling method, that together provide satisfactory accuracy and efficiency of a real-time processing of high-resolution camera images, maintaining the cost of resources usage at a reasonable level. Two selected algorithms: the Gaussian mixture models and the Codebook, are presented and their computational complexity is discussed. Various approaches to the parallel implementation, including assigning the image pixels to threads, the task scheduling methods and the thread management systems, are presented. The experiments were performed on a supercomputer cluster, using a single machine with 12 physical cores. The accuracy and performance of the implemented algorithms were evaluated for varying image resolutions and numbers of concurrent processing threads. On a basis of the evaluation results, an optimal configuration for the parallel implementation of the system for real-time video content analysis on a supercomputer platform was proposed.