A review of studies of ionizing radiation-induced double-strand break clustering

Underpinning current models of the mechanisms of the action of radiation is a central role for DNA damage and in particular double-strand breaks (DSBs). For radiations of different LET, there is a need to know the exact yields and distributions of DSBs in human cells. Most measurements of DSB yields within cells now rely on pulsed-field gel electrophoresis as the technique of choice. Previous measurements of DSB yields have suggested that the yields are remarkably similar for different types of radiation with RBE values less than or equal to1.0. More recent studies in mammalian cells, however, have suggested that both the yield and the spatial distribution of DSBs are influenced by radiation quality. RBE values for DSBs induced by high-LET radiations are greater than 1.0, and the distributions are nonrandom. Underlying this is the interaction of particle tracks with the higher-order chromosomal structures within cell nuclei. Further studies are needed to relate nonrandom distributions of DSBs to their rejoining kinetics. At the molecular level, we need to determine the involvement of clustering of damaged bases with strand breakage, and the relationship between higher-order clustering over sizes of kilobase pairs and above to localized clustering at the DNA level. Overall, these studies will allow us to elucidate whether the nonrandom distributions of breaks produced by high-LET particle tracks have any consequences for their repair and biological effectiveness. (C) 2001 by Radiation Research Society.

A Monte Carlo model of DNA double-strand break clustering and rejoining kinetics for the analysis of pulsed-field gel electrophoresis data

In studies of radiation-induced DNA fragmentation and repair, analytical models may provide rapid and easy-to-use methods to test simple hypotheses regarding the breakage and rejoining mechanisms involved. The random breakage model, according to which lesions are distributed uniformly and independently of each other along the DNA, has been the model most used to describe spatial distribution of radiation-induced DNA damage. Recently several mechanistic approaches have been proposed that model clustered damage to DNA. In general, such approaches focus on the study of initial radiation-induced DNA damage and repair, without considering the effects of additional (unwanted and unavoidable) fragmentation that may take place during the experimental procedures. While most approaches, including measurement of total DNA mass below a specified value, allow for the occurrence of background experimental damage by means of simple subtractive procedures, a more detailed analysis of DNA fragmentation necessitates a more accurate treatment. We have developed a new, relatively simple model of DNA breakage and the resulting rejoining kinetics of broken fragments. Initial radiation-induced DNA damage is simulated using a clustered breakage approach, with three free parameters: the number of independently located clusters, each containing several DNA double-strand breaks (DSBs), the average number of DSBs within a cluster (multiplicity of the cluster), and the maximum allowed radius within which DSBs belonging to the same cluster are distributed. Random breakage is simulated as a special case of the DSB clustering procedure. When the model is applied to the analysis of DNA fragmentation as measured with pulsed-field gel electrophoresis (PFGE), the hypothesis that DSBs in proximity rejoin at a different rate from that of sparse isolated breaks can be tested, since the kinetics of rejoining of fragments of varying size may be followed by means of computer simulations. The problem of how to account for background damage from experimental handling is also carefully considered. We have shown that the conventional procedure of subtracting the background damage from the experimental data may lead to erroneous conclusions during the analysis of both initial fragmentation and DSB rejoining. Despite its relative simplicity, the method presented allows both the quantitative and qualitative description of radiation-induced DNA fragmentation and subsequent rejoining of double-stranded DNA fragments. (C) 2004 by Radiation Research Society.

Behavior-Based branch prediction by dynamically clustering branch instructions

Conditional branches frequently exhibit similar behavior (bias, time-varying behavior,...), a property that can be used to improve branch prediction accuracy. Branch clustering constructs groups or clusters of branches with similar behavior and applies different branch prediction techniques to each branch cluster. We revisit the topic of branch clustering with the aim of generalizing branch clustering. We investigate several methods to measure cluster information, with the most effective the storage of information in the branch target buffer. Also, we investigate alternative methods of using the branch cluster identification in the branch predictor. By these improvements we arrive at a branch clustering technique that obtains higher accuracy than previous approaches presented in the literature for the gshare predictor. Furthermore, we evaluate our branch clustering technique in a wide range of predictors to show the general applicability of the method. Branch clustering improves the accuracy of the local history (PAg) predictor, the path-based perceptron and the PPM-like predictor, one of the 2004 CBP finalists.

Serviceability design of a cold-formed steel portal frame having semi-rigid joints

Details are given of a cold-formed steel portal framing system that uses simple bolted moment-connections for both the eaves and apex joints. However, such joints function as semi-rigid and, as a result, the design of the proposed system will be dominated by serviceability requirements. While serviceability is a mandatory design requirement, actual deflection limits for portal frames are not prescribed in many of the national standards. In this paper, a review of the design constraints that have an effect on deflection limits is discussed, and rational values appropriate for use with cold-formed steel portal frames are recommended. Adopting these deflection limits, it is shown through a design example how a cold-formed steel portal frame having semi-rigid eaves and apex joints can be a feasible alternative to rigid-jointed frames in appropriate circumstances.

Max separation clustering for feature extraction from Optical Emission Spectroscopy Data

This paper proposes max separation clustering (MSC), a new non-hierarchical clustering method used for feature extraction from optical emission spectroscopy (OES) data for plasma etch process control applications. OES data is high dimensional and inherently highly redundant with the result that it is difficult if not impossible to recognize useful features and key variables by direct visualization. MSC is developed for clustering variables with distinctive patterns and providing effective pattern representation by a small number of representative variables. The relationship between signal-to-noise ratio (SNR) and clustering performance is highlighted, leading to a requirement that low SNR signals be removed before applying MSC. Experimental results on industrial OES data show that MSC with low SNR signal removal produces effective summarization of the dominant patterns in the data.

Novel semi-interpenetrating hydrogel networks with enhanced mechanical properties and thermoresponsive engineered drug delivery, designed as bioactive endotracheal tube biomaterials

Thermoresponsive polymeric platforms are used to optimise drug delivery in pharmaceutical systems and bioactive medical devices. However, the practical application of these systems is compromised by their poor mechanical properties. This study describes the design of thermoresponsive semi-interpenetrating polymer networks (s-IPNs) based on cross-linked p(NIPAA) or p(NIPAA-co-HEMA) hydrogels containing poly(e-caprolactone) designed to address this issue. Using DSC, the lower critical solution temperature of the co-polymer and p(NIPAA) matrices were circa 34 °C and 32 °C, respectively. PCL was physically dispersed within the hydrogel matrices as confirmed using confocal scanning laser microscopy and DSC and resulted in marked changes in the mechanical properties (ultimate tensile strength, Young's modulus) without adversely compromising the elongation properties. P(NIPAA) networks containing dispersed PCL exhibited thermoresponsive swelling properties following immersion in buffer (pH 7), with the equilibrium-swelling ratio being greater at 20 °C than 37 °C and greatest for p(NIPAA)/PCL systems at 20 °C. The incorporation of PCL significantly lowered the equilibrium swelling ratio of the various networks but this was not deemed practically significant for s-IPNs based on p(NIPAA). Thermoresponsive release of metronidazole was observed from s-IPN composed of p(NIPAA)/PCL at 37 °C but not from p(NIPAA-co-HEMA)/PCL at this temperature. In all other platforms, drug release at 20 °C was significantly similar to that at 37 °C and was diffusion controlled. This study has uniquely described a strategy by which thermoresponsive drug release may be performed from polymeric platforms with highly elastic properties. It is proposed that these materials may be used clinically as bioactive endotracheal tubes, designed to offer enhanced resistance to ventilator associated pneumonia, a clinical condition associated with the use of endotracheal tubes where stimulus responsive drug release from biomaterials of significant mechanical properties would be advantageous. © 2012 Elsevier B.V. All rights reserved.

Automatic decomposition and efficient semi-structured meshing of complex solids

In this paper, a novel approach to automatically sub-divide a complex geometry and apply an efficient mesh is presented. Following the identification and removal of thin-sheet regions from an arbitrary solid using the thick/thin decomposition approach developed by Robinson et al. [1], the technique here employs shape metrics generated using local sizing measures to identify long-slender regions within the thick body. A series of algorithms automatically partition the thick region into a non-manifold assembly of long-slender and complex sub-regions. A structured anisotropic mesh is applied to the thin-sheet and long-slender bodies, and the remaining complex bodies are filled with unstructured isotropic tetrahedra. The resulting semi-structured mesh possesses significantly fewer degrees of freedom than the equivalent unstructured mesh, demonstrating the effectiveness of the approach. The accuracy of the efficient meshes generated for a complex geometry is verified via a study that compares the results of a modal analysis with the results of an equivalent analysis on a dense tetrahedral mesh.

Quantitative structure-toxicity relationships for chlorophenols to bioluminescent lux-marked bacteria using atom-based semi-empirical molecular-orbital descriptors

Literature data on the toxicity of chlorophenols for three luminescent bacteria (Vibrio fischeri, and the lux-marked Pseudomonas fluorescens 10586s pUCD607 and Burkholderia spp. RASC c2 (Tn4431)) have been analyzed in relation to a set of computed molecular physico-chemical properties. The quantitative structure-toxicity relationships of the compounds in each species showed marked differences when based upon semi-empirical molecular-orbital molecular and atom based properties. For mono-, di- and tri-chlorophenols multiple linear regression analysis of V. fischeri toxicity showed a good correlation with the solvent accessible surface area and the charge on the oxygen atom. This correlation successfully predicted the toxicity of the heavily chlorinated phenols, suggesting in V. fischeri only one overall mechanism is present for all chlorophenols. Good correlations were also found for RASC c2 with molecular properties, such as the surface area and the nucleophilic super-delocalizability of the oxygen. In contrast the best QSTR for P. fluorescens contained the 2nd order connectivity index and ELUMO suggesting a different, more reactive mechanism. Cross-species correlations were examined, and between V. fischeri and RASC c2 the inclusion of the minimum value of the nucleophilic susceptibility on the ring carbons produced good results. Poorer correlations were found with P. fluorescens highlighting the relative similarity of V. fischeri and RASC c2, in contrast to that of P. fluorescens.

Influence of the type of coarse lightweight aggregate on properties of Semi-Lightweight Self-Consolidating Concrete

This paper presents studies on the properties of fresh and hardened semilightweight self-consolidating concrete (SLWSCC) mixtures, produced with two types of manufactured coarse lightweight aggregates (LWA) and normal weight sand. The first type, a sintered pulverized fuel ash, was made from an industrial by-product, fly ash, whereas the second one, an expanded clay, was produced from a naturally sourced clay. For all mixtures, normal weight sand was used as a fine fraction of aggregates, and the portland cement was partially replaced with a limestone powder. The SLWSCC was produced with different water presaturation regimes of the LWAs. The desired initial slump-flow spread was set between 700 and 800 mm. The effect of three superplasticizers was evaluated by testing properties of SLWSCC, normal weight SCC, and paste mixtures. Three SCC fresh properties were measured: the slump-flow, the V-funnel flow time, and the J-ring blocking step. Moreover, the slump-flow loss was evaluated. The degree of segregation was assessed in both fresh and hardened states. Additionally, the hardened density and the compressive strengths were tested. All SLWSCC mixtures were produced with a desired range of slump-flow spread and with satisfactory passing ability assessed with the J-ring test. SLWSCCs prepared with the expanded clay LWA were less sensitive to the variation of water presaturation levels and showed lower viscosity than those made with the sintered pulverized fuel ash LWA. Only mixtures containing SP-3 superplasticizer showed acceptable workability loss resistance. The saturated surface-dry density of all of the mixtures varied in a range of 2,025–2,125??kg/m 3 . Mixtures containing 29% of coarse LWAs and 71% of sand (by mass) had 24-h and 28-day compressive strengths above 20 and 40 MPa, respectively, but the mixtures made with the expanded clay were slightly weaker.