Can we avoid high coupling?

It is considered good software design practice to organize source code into modules and to favour within-module connections (cohesion) over between-module connections (coupling), leading to the oft-repeated maxim "low coupling/high cohesion". Prior research into network theory and its application to software systems has found evidence that many important properties in real software systems exhibit approximately scale-free structure, including coupling; researchers have claimed that such scale-free structures are ubiquitous. This implies that high coupling must be unavoidable, statistically speaking, apparently contradicting standard ideas about software structure. We present a model that leads to the simple predictions that approximately scale-free structures ought to arise both for between-module connectivity and overall connectivity, and not as the result of poor design or optimization shortcuts. These predictions are borne out by our large-scale empirical study. Hence we conclude that high coupling is not avoidable--and that this is in fact quite reasonable

Why does fertilization reduce plant species diversity? Testing three competition-based hypotheses

1 Plant species diversity drops when fertilizer is added or productivity increases. To explain this, the total competition hypothesis predicts that competition above ground and below ground both become more important, leading to more competitive exclusion, whereas the light competition hypothesis predicts that a shift from below-ground to above-ground competition has a similar effect. The density hypothesis predicts that more above-ground competition leads to mortality of small individuals of all species, and thus a random loss of species from plots. 2 Fertilizer was added to old field plots to manipulate both below-ground and above-ground resources, while shadecloth was used to manipulate above-ground resources alone in tests of these hypotheses. 3 Fertilizer decreased both ramet density and species diversity, and the effect remained significant when density was added as a covariate. Density effects explained only a small part of the drop in diversity with fertilizer. 4 Shadecloth and fertilizer reduced light by the same amount, but only fertilizer reduced diversity. Light alone did not control diversity, as the light competition hypothesis would have predicted, but the combination of above-ground and below-ground competition caused competitive exclusion, consistent with the total competition hypothesis.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75695/1/j.1365-2745.2001.00662.x.pd

The Pervasiveness of Global Data in Evolving Software Systems

Abstract. In this research, we investigate the role of common coupling in evolving software systems. It can be argued that most software de-velopers understand that the use of global data has many harmful side-effects, and thus should be avoided. We are therefore interested in the answer to the following question: if global data does exist within a soft-ware project, how does global data usage evolve over a software project’s lifetime? Perhaps the constant refactoring and perfective maintenance eliminates global data usage, or conversely, perhaps the constant addi-tion of features and rapid development introduce an increasing reliance on global data? We are also interested in identifying if global data usage patterns are useful as a software metric that is indicative of an interesting or significant event in the software’s lifetime. The focus of this research is twofold: first to develop an effective and automatic technique for studying global data usage over the lifetime of large software systems and secondly, to leverage this technique in a case-study of global data usage for several large and evolving software systems in an effort to reach answers to these questions.

Can COBE see the shape of the universe?

In recent years, the large angle COBE--DMR data have been used to place constraints on the size and shape of certain topologically compact models of the universe. Here we show that this approach does not work for generic compact models. In particular, we show that compact hyperbolic models do not suffer the same loss of large angle power seen in flat or spherical models. This follows from applying a topological theorem to show that generic hyperbolic three manifolds support long wavelength fluctuations, and by taking into account the dominant role played by the integrated Sachs-Wolfe effect in a hyperbolic universe.Comment: 16 Pages, 5 Figures. Version published in Phys. Rev.

Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome

To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events42Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases

Detectable clonal mosaicism and its relationship to aging and cancer

In an analysis of 31,717 cancer cases and 26,136 cancer-free controls from 13 genome-wide association studies, we observed large chromosomal abnormalities in a subset of clones in DNA obtained from blood or buccal samples. We observed mosaic abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of >2 Mb in size in autosomes of 517 individuals (0.89%), with abnormal cell proportions of between 7% and 95%. In cancer-free individuals, frequency increased with age, from 0.23% under 50 years to 1.91% between 75 and 79 years (P = 4.8 × 10(-8)). Mosaic abnormalities were more frequent in individuals with solid tumors (0.97% versus 0.74% in cancer-free individuals; odds ratio (OR) = 1.25; P = 0.016), with stronger association with cases who had DNA collected before diagnosis or treatment (OR = 1.45; P = 0.0005). Detectable mosaicism was also more common in individuals for whom DNA was collected at least 1 year before diagnosis with leukemia compared to cancer-free individuals (OR = 35.4; P = 3.8 × 10(-11)). These findings underscore the time-dependent nature of somatic events in the etiology of cancer and potentially other late-onset diseases

FIRST SEARCHES FOR OPTICAL COUNTERPARTS TO GRAVITATIONAL-WAVE CANDIDATE EVENTS

During the LIGO and Virgo joint science runs in 2009-2010, gravitational wave (GW) data from three interferometer detectors were analyzed within minutes to select GW candidate events and infer their apparent sky positions. Target coordinates were transmitted to several telescopes for follow-up observations aimed at the detection of an associated optical transient. Images were obtained for eight such GW candidates. We present the methods used to analyze the image data as well as the transient search results. No optical transient was identified with a convincing association with any of these candidates, and none of the GW triggers showed strong evidence for being astrophysical in nature. We compare the sensitivities of these observations to several model light curves from possible sources of interest, and discuss prospects for future joint GW-optical observations of this type

Evolution of the Torso activation cassette, a pathway required for terminal patterning and moulting

Embryonic terminal patterning and moulting are critical developmental processes in insects. In Drosophila and Tribolium both of these processes are regulated by the Torso‐activation cassette (TAC). The TAC consists of a common receptor, Torso, ligands Trunk and prothoracicotropic hormone (PTTH), and the spatially restricted protein Torso‐like, with combinations of these elements acting mechanistically to activate the receptor in different developmental contexts. In order to trace the evolutionary history of the TAC we determined the presence or absence of TAC components in the genomes of arthropods. Our analyses reveal that Torso, Trunk and PTTH are evolutionarily labile components of the TAC with multiple individual or combined losses occurring in the arthropod lineages leading to and within the insects. These losses are often correlated, with both ligands and receptor missing from the genome of the same species. We determine that the PTTH gene evolved in the common ancestor of Hemiptera and Holometabola, and is missing from the genomes of a number of species with experimentally demonstrated PTTH activity, implying another molecule may be involved in ecdysis in these species. In contrast, the torso‐like gene is a common component of pancrustacean genomes