Scaffolder - Software for Reproducible Genome Scaffolding.

Background: Assembly of short-read sequencing data can result in a fragmented non-contiguous series of genomic sequences. Therefore a common step in a genome project is to join neighboring sequence regions together and fill gaps in the assembly using additional sequences. This scaffolding step, however, is non-trivial and requires manually editing large blocks of nucleotide sequence. Joining these sequences together also hides the source of each region in the final genome sequence. Taken together, these considerations may make reproducing or editing an existing genome build difficult.

Methods: The software outlined here, “Scaffolder,” is implemented in the Ruby programming language and can be installed via the RubyGems software management system. Genome scaffolds are defined using YAML - a data format, which is both human and machine-readable. Command line binaries and extensive documentation are available.

Results: This software allows a genome build to be defined in terms of the constituent sequences using a relatively simple syntax to define the scaffold. This syntax further allows unknown regions to be defined, and adds additional sequences to fill gaps in the scaffold. Defining the genome construction in a file makes the scaffolding process reproducible and easier to edit compared with FASTA nucleotide sequence.

Conclusions: Scaffolder is easy-to-use genome scaffolding software. This tool promotes reproducibility and continuous development in a genome project. Scaffolder can be found at http://next.gs

Low-Energy Heavy-Ion Reactions and the Skyrme Effective Interaction

The Skyrme effective interaction, with its multitude of parameterisations, along with its implemen- tation using the static and time-dependent density functional (TDHF) formalism have allowed for a range of microscopic calculations of low-energy heavy-ion collisions. These calculations allow variation of the effective interaction along with an interpretation of the results of this variation informed by a comparison to experimental data. Initial progress in implementing TDHF for heavy-ion collisions necessarily used many approximations in the geometry or the interaction. Over the last decade or so, the implementations have overcome all restrictions, and studies have begun to be made where details of the effective interaction are being probed. This review surveys these studies in low energy heavy-ion reactions, finding significant effects on observables from the form of the spin-orbit interaction, the use of the tensor force, and the inclusion of time-odd terms in the density functional.Comment: submitted to Prog. Part. Nucl. Phy

Rising Inequality and the Financial Crises of 1929 and 2008

Inequality increased dramatically in the decades leading up to the financial crises of both 1929 and 2008. Yet students of both crises have largely ignored any role that rising inequality might have played in rendering the financial sector more vulnerable to systemic dysfunction. This study draws upon the work of Thorstein Veblen, Michal Kalecki, and Karl Marx to clarify the manner in which growing inequality prior to both crises made U.S. financial markets more prone to systemic dysfunction. Greater inequality generated three dynamics that heightened conditions in which these financial crises might occur. The first is that greater inequality meant that individuals were forced to struggle harder to find ways to consume more to maintain their relative social status, thereby reducing their savings and increasing their indebtedness. The second is that holding ever greater income and wealth, the elite flooded financial markets with credit, helping keep interest rates low and encouraging the creation of new credit instruments. The third dynamic is that, as the rich took larger shares of income and wealth, they gained more command over ideology and hence politics. Reducing the size of government, tax cuts for the rich, deregulating the economy, and failing to regulate newly evolving credit instruments flowed out of this ideology.

Increasing Inequality, Status Insecurity, Ideology, and the Financial Crisis of 2008

The current financial crisis has been blamed on inadequate regulation stemming from laissez-faire ideology, combined with low interest rates. But beneath these widely-acknowledged causal factors lies a deeper underlying determining cause that has received less notice: the dramatic increase in inequality in the U.S. over the preceding 35 years. This rise in inequality generated three phenomena that heightened conditions in which this crisis could occur. The first is that greater inequality meant that individuals were forced to struggle harder to find ways to consume more to maintain their relative social status. The consequence was that over the preceding three decades household saving rates plummeted, workers worked longer hours, and households took on ever-greater debt. The second phenomenon is that, flush with ever greater income and wealth, the elite were able to flood financial markets with credit, helping keep interest rates low and encouraging the creation of new credit instruments. The third phenomenon is that, as the rich took larger shares of income and wealth, they gained relatively more command over everything, including ideology. Reducing the size of government, deregulating the economy, and failing to regulate newly evolving credit instruments flowed out of this ideology.deregulation, real estate boom, credit, conspicuous consumption, social respectability

Rising Inequality and the Financial Crises of 1929 and 2008

The most widely embraced explanations of the financial crisis of 2008 have centered upon inadequate regulation stemming from laissez-faire ideology, combined with low interest rates. Although these widely-acknowledged causal factors are true, beneath them lies a deeper determining force that has received less notice: the dramatic increase in inequality in the U.S. over the preceding 35 years. Heightened inequality generated three dynamics that made the economy vulnerable to systemic dysfunction. The first is that inequality constrained consumption, reducing profitable investment potential in the real economy, and thereby encouraging an every wealthier elite to flood financial markets with credit, helping keep interest rates low, encouraging the creation of new credit instruments, and fueling speculation. The second dynamic is that greater inequality meant that individuals were forced to struggle harder to find ways to consume more to maintain their relative social status. The consequence was that over the preceding three decades household saving rates plummeted, households took on evergreater debt, and workers worked longer hours. The third dynamic is that, as the rich took larger shares of income and wealth, they gained more command over ideology and hence politics. Reducing the size of government, cutting taxes on the rich and reducing welfare for the poor, deregulating the economy, and failing to regulate newly evolving credit instruments flowed out of this ideology.Underconsumption, deregulation, speculation, real estate boom, credit, conspicuous consumption, social respectability

The great outdoors: how a green exercise environment can benefit all

The studies of human and environment interactions usually consider the extremes of environment on individuals or how humans affect the environment. It is well known that physical activity improves both physiological and psychological well-being, but further evidence is required to ascertain how different environments influence and shape health. This review considers the declining levels of physical activity, particularly in the Western world, and how the environment may help motivate and facilitate physical activity. It also addresses the additional physiological and mental health benefits that appear to occur when exercise is performed in an outdoor environment. However, people's connectedness to nature appears to be changing and this has important implications as to how humans are now interacting with nature. Barriers exist, and it is important that these are considered when discussing how to make exercise in the outdoors accessible and beneficial for all. The synergistic combination of exercise and exposure to nature and thus the 'great outdoors' could be used as a powerful tool to help fight the growing incidence of both physical inactivity and non-communicable disease. © 2013 Gladwell et al.; licensee BioMed Central Ltd

Multipole expansion of Bessel and Gaussian beams for Mie scattering calculations

Multipole expansions of Bessel and Gaussian beams, suitable for use in Mie scattering calculations, are derived. These results allow Mie scattering calculations to be carried out considerably faster than existing methods, something that is of particular interest for time evolution simulations where large numbers of scattering calculations must be performed. An analytic result is derived for the Bessel beam that improves on a previously published expression requiring the evaluation of an integral. An analogous expression containing a single integral, similar to existing results quoted, but not derived, in literature, is derived for a Gaussian beam,valid from the paraxial limit all the way to arbitrarily high numerical apertures

Indigenous agroforestry in Latin America: A blueprint for sustainable agriculture?

Large-scale rainforest destruction in Latin America has occurred partly as a result of government policy incentives to colonize and clear forest for agriculture and ranching, in order to alleviate poor economic and social conditions in other regions. Inappropriate agricultural techniques have been used which are not sustainable, and the new colonist farmers are forced to clear ever more virgin forest for agriculture in order to survive. The objectives of this literature review are to assess the value of the traditional subsistence agroforestry (swidden) systems practised over centuries by the indigenous people of Latin America (Amerindians), and to suggest ways of incorporating these methods into a sustainable (non-destructive) and productive system for the new colonist farmers. In the past, researchers perceived these swidden methods as an exploitative and destructive form of agriculture, because they involved cutting and burning of the forest. However, clearings are small, and planting and protection of trees after the initial cultivation of annual crops aids the forest regrowth in the fallow phase. Specific examples of swidden agroforestry systems are described, and their contribution to sustainability, biodiversity, productivity for market, soil conservation, flexibility and population density support are discussed. Overall, they are found to be less destructive and more productive than the new colonist agriculture, and should form a basis for a sustainable system. The review then outlines the possibilities for and limits (often labour intensive, location-specific and socioeconomic constraints) to the adoption of these methods by new colonist farmers. Suggestions are made for research priorities to enable their effective transfer, including thorough documentation of existing systems and their capacity, participatory field research, the marketing potential for crops and forest products and the changes in government policy required to implement these methods. The review concludes that indigenous agroforestry systems are both ecologically and economically beneficial, but are not without some limitations. From the wealth of indigenous knowledge available and proposed new research, it should be possible to adapt these systems to produce a model or blueprint for sustainable and productive agriculture for the new colonist. Indigenous Agroforestry in Latin America: A Blueprint for Sustainable Agriculture? will not only be of interest to policy makers and donor agencies, but also to those interested in the preservation of the rainforests