Segmentally Variable Genes: A New Perspective on Adaptation

Genomic sequence variation is the hallmark of life and is key to understanding diversity and adaptation among the numerous microorganisms on earth. Analysis of the sequenced microbial genomes suggests that genes are evolving at many different rates. We have attempted to derive a new classification of genes into three broad categories: lineage-specific genes that evolve rapidly and appear unique to individual species or strains; highly conserved genes that frequently perform housekeeping functions; and partially variable genes that contain highly variable regions, at least 70 amino acids long, interspersed among well-conserved regions. The latter we term segmentally variable genes (SVGs), and we suggest that they are especially interesting targets for biochemical studies. Among these genes are ones necessary to deal with the environment, including genes involved in host–pathogen interactions, defense mechanisms, and intracellular responses to internal and environmental changes. For the most part, the detailed function of these variable regions remains unknown. We propose that they are likely to perform important binding functions responsible for protein–protein, protein–nucleic acid, or protein–small molecule interactions. Discerning their function and identifying their binding partners may offer biologists new insights into the basic mechanisms of adaptation, context-dependent evolution, and the interaction between microbes and their environment. Segmentally variable genes show a mosaic pattern of one or more rapidly evolving, variable regions. Discerning their function may provide new insights into the forces that shape genome diversity and adaptationNational Science Foundation (998088, 0239435

ZAP -- Enhanced PCA Sky Subtraction for Integral Field Spectroscopy

We introduce Zurich Atmosphere Purge (ZAP), an approach to sky subtraction based on principal component analysis (PCA) that we have developed for the Multi Unit Spectrographic Explorer (MUSE) integral field spectrograph. ZAP employs filtering and data segmentation to enhance the inherent capabilities of PCA for sky subtraction. Extensive testing shows that ZAP reduces sky emission residuals while robustly preserving the flux and line shapes of astronomical sources. The method works in a variety of observational situations from sparse fields with a low density of sources to filled fields in which the target source fills the field of view. With the inclusion of both of these situations the method is generally applicable to many different science cases and should also be useful for other instrumentation. ZAP is available for download at http://muse-vlt.eu/science/tools.Comment: 12 pages, 7 figures, 1 table. Accepted to MNRA

The impact of regulation, ownership and business culture on managing corporate risk within the water industry

Although the specifics of water utility ownership, regulation and management culture have been explored in terms of their impact on economic and customer value, there has been little meaningful engagement with their influence on the risk environment and risk management. Using a literature review as the primary source of information, this paper maps the existing knowledge base onto two critical questions: what are the particular features of regulation, ownership and management culture which influence the risk dynamic, and what are the implications of these relationships in the context of ambitions for resilient organizations? In addressing these queries, the paper considers the mindful choices and adjustments a utility must make to its risk management strategy to manage strategic tensions between efficiency, risk and resilience. The conclusions note a gap in understanding of the drivers required for a paradigm shift within the water sector from a re-active to a pro-active risk management culture. A proposed model of the tensions between reactive risk management and pro-active, adaptive risk management provides a compelling case for measured risk management approaches which are informed by an appreciation of regulation, ownership and business culture. Such approaches will support water authorities in meeting corporate aspirations to become "high reliability" services while retaining the capacity to out-perform financial and service level targets

Making the Transition to Post-Quantum Cryptography

Without intervention, quantum computing could threaten the security of a large portion of our internet in the near future. However, solutions exist. This paper, which is intended for a general audience, provides a wider context for our current state of quantum-preparedness amid the transition from classical cryptosystems to post-quantum cryptosystems—cryptographic algorithms that can resist the attacks of quantum computers. It will also submit a possible way forward inspired by the actions taken around the globe to prevent the millennium (or Y2K) bug

Choosing a sophisticated, robust, and secure programming language

This paper explores which programming languages maximize the quality and efficiency of software development projects requiring high levels of sophistication, security, and stability. Of the four languages discussed in this paper—C, C++, Java, and Rust—we conclude that Rust is the best for this application

The evolution of binary populations in cool, clumpy star clusters

Observations and theory suggest that star clusters can form in a subvirial (cool) state and are highly substructured. Such initial conditions have been proposed to explain the level of mass segregation in clusters through dynamics, and have also been successful in explaining the origin of Trapezium-like systems. In this paper, we investigate, using N-body simulations, whether such a dynamical scenario is consistent with the observed binary properties in the Orion Nebula Cluster (ONC). We find that several different primordial binary populations are consistent with the overall fraction and separation distribution of visual binaries in the ONC (in the range 67-670 au), and that these binary systems are heavily processed. The substructured, cool-collapse scenario requires a primordial binary fraction approaching 100 per cent. We find that the most important factor in processing the primordial binaries is the initial level of substructure; a highly substructured cluster processes up to 20 per cent more systems than a less substructured cluster because of localized pockets of high stellar density in the substructure. Binaries are processed in the substructure before the cluster reaches its densest phase, suggesting that even clusters remaining in virial equilibrium or undergoing supervirial expansion would dynamically alter their primordial binary population. Therefore, even some expanding associations may not preserve their primordial binary populatio

Recent developments in the application of risk analysis to waste technologies.

The European waste sector is undergoing a period of unprecedented change driven by business consolidation, new legislation and heightened public and government scrutiny. One feature is the transition of the sector towards a process industry with increased pre-treatment of wastes prior to the disposal of residues and the co-location of technologies at single sites, often also for resource recovery and residuals management. Waste technologies such as in-vessel composting, the thermal treatment of clinical waste, the stabilisation of hazardous wastes, biomass gasification, sludge combustion and the use of wastes as fuel, present operators and regulators with new challenges as to their safe and environmentally responsible operation. A second feature of recent change is an increased regulatory emphasis on public and ecosystem health and the need for assessments of risk to and from waste installations. Public confidence in waste management, secured in part through enforcement of the planning and permitting regimes and sound operational performance, is central to establishing the infrastructure of new waste technologies. Well-informed risk management plays a critical role. We discuss recent developments in risk analysis within the sector and the future needs of risk analysis that are required to respond to the new waste and resource management agenda