Exploratory analysis of spatiotemporal patterns of cellular automata by clustering compressibility

In this paper we study the classification of spatiotemporal pattern of one-dimensional cellular automata (CA) whereas the classification comprises CA rules including their initial conditions. We propose an exploratory analysis method based on the normalized compression distance (NCD) of spatiotemporal patterns which is used as dissimilarity measure for a hierarchical clustering. Our approach is different with respect to the following points. First, the classification of spatiotemporal pattern is comparative because the NCD evaluates explicitly the difference of compressibility among two objects, e.g., strings corresponding to spatiotemporal patterns. This is in contrast to all other measures applied so far in a similar context because they are essentially univariate. Second, Kolmogorov complexity, which underlies the NCD, was used in the classification of CA with respect to their spatiotemporal pattern. Third, our method is semiautomatic allowing us to investigate hundreds or thousands of CA rules or initial conditions simultaneously to gain insights into their organizational structure. Our numerical results are not only plausible confirming previous classification attempts but also shed light on the intricate influence of random initial conditions on the classification results.

RNA polymerase I-specific subunits promote polymerase clustering to enhance the rRNA gene transcription cycle.

RNA polymerase I (Pol I) produces large ribosomal RNAs (rRNAs). In this study, we show that the Rpa49 and Rpa34 Pol I subunits, which do not have counterparts in Pol II and Pol III complexes, are functionally conserved using heterospecific complementation of the human and Schizosaccharomyces pombe orthologues in Saccharomyces cerevisiae. Deletion of RPA49 leads to the disappearance of nucleolar structure, but nucleolar assembly can be restored by decreasing ribosomal gene copy number from 190 to 25. Statistical analysis of Miller spreads in the absence of Rpa49 demonstrates a fourfold decrease in Pol I loading rate per gene and decreased contact between adjacent Pol I complexes. Therefore, the Rpa34 and Rpa49 Pol I–specific subunits are essential for nucleolar assembly and for the high polymerase loading rate associated with frequent contact between adjacent enzymes. Together our data suggest that localized rRNA production results in spatially constrained rRNA production, which is instrumental for nucleolar assembly.

Clustering and synchrony in laying hens: The effect of environmental resources on social dynamics

Laying hens generally choose to aggregate, but the extent to which the environments in which we house them impact on social group dynamics is not known. In this paper the effect of pen environment on spatial clustering is considered. Twelve groups of four laying hens were studied under three environmental conditions: wire floor (W), shavings (Sh) and perches, peat, nestbox and shavings (PPN). Groups experienced each environment twice, for five weeks each time, in a systematic order that varied from group to group. Video recordings were made one day per week for 30 weeks. To determine level of clustering, we recorded positional data from a randomly selected 20-min excerpt per video (a total of 20 min x 360 videos analysed). On screen, pens were divided into six equal areas. In addition, PPN pens were divided into an additional four (sub) areas, to account for the use of perches (one area per half perch). Every 5 s, we recorded the location of each bird and calculated location use over time, feeding synchrony and cluster scores for each environment. Feeding synchrony and cluster scores were compared against unweighted and weighted (according to observed proportional location use) Poisson distributions to distinguish between resource and social attraction.

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.