Genome assembly comparison identifies structural variants in the human genome

Numerous types of DNA variation exist, ranging from SNPs to larger structural alterations such as copy number variants (CNVs) and inversions. Alignment of DNA sequence from different sources has been used to identify SNPs and intermediate-sized variants (ISVs). However, only a small proportion of total heterogeneity is characterized, and little is known of the characteristics of most smaller-sized (<50 kb) variants. Here we show that genome assembly comparison is a robust approach for identification of all classes of genetic variation. Through comparison of two human assemblies (Celera's R27c compilation and the Build 35 reference sequence), we identified megabases of sequence (in the form of 13,534 putative non-SNP events) that were absent, inverted or polymorphic in one assembly. Database comparison and laboratory experimentation further demonstrated overlap or validation for 240 variable regions and confirmed >1.5 million SNPs. Some differences were simple insertions and deletions, but in regions containing CNVs, segmental duplication and repetitive DNA, they were more complex. Our results uncover substantial undescribed variation in humans, highlighting the need for comprehensive annotation strategies to fully interpret genome scanning and personalized sequencing projects.     

Revertant mosaicism in genodermatoses

Inherited monogenic skin disorders include blistering disorders, inflammatory disorders, and disorders of differentiation or development. In most cases, the skin is broadly involved throughout the affected individual’s lifetime, but rarely, appearance of normal skin clones has been described. In these cases of revertant mosaicism, cells undergo spontaneous correction to ameliorate the effects of genetic mutation. While targeted reversion of genetic mutation would have tremendous therapeutic value, the mechanisms of reversion in the skin are poorly understood. In this review, we provide an overview of genodermatoses that demonstrate widespread reversion and their corrective mechanisms, as well as the current research aimed to understand this “natural gene therapy”.     

Records of the yellow-nosed cotton rat ( Sigmodon ochrognathus ) in southwestern New Mexico

The yellow-nosed cotton rat ( Sigmodon ochrognathus ) previously was known only from extreme southwestern New Mexico in the Peloncillo and Animas mountains. Here I document S. ochrognathus at 3 localities from the Big Burro and Mogollon mountains in southwestern New Mexico. My northernmost capture represents an extra-limital record of 160 km north of prior records in southern New Mexico and represents the northernmost occurrence in North America. Lack of intensive mammalian surveys in the region render it difficult to interpret my recent captures, but the most parsimonious explanation is that captures likely represent overlooked populations. I captured S. ochrognathus in grassy areas ungrazed by domestic livestock along the Gila River. Understanding the use of limited grassland habitats along arid rivers by terrestrial vertebrates in the region is important because many of these grasslands have been converted to agricultural lands or are grazed by livestock.     

Occurrence of Ord's kangaroo rat ( Dipodomys ordii ) along its eastern distributional limit in Nebraska

Changes in land use continue to alter habitats throughout Nebraska, and few studies have examined how such changes affect distributional limits of mammals. The distribution of Ord&rsquo;s kangaroo rat ( Dipodomys ordii ) was last examined in eastern Nebraska about 4 decades ago. We examined the current eastern distributional limits of D. ordii to see whether its range had expanded, contracted, or remained constant in the state since the 1960s. Based on our study, kangaroo rats have experienced little change in distribution during recent decades. Herein, we report on data for 8 counties without prior records and a marginal range extension, as well as comment on habitat, reproduction, and taxonomic status of kangaroo rats in eastern Nebraska. Los cambios en el uso del suelo siguen modificando los h&aacute;bitats a lo largo del estado de Nebraska, y pocos estudios han examinado c&oacute;mo estos cambios afectan los l&iacute;mites de distribuci&oacute;n de los mam&iacute;feros. La &uacute;ltima evaluaci&oacute;n de la distribuci&oacute;n de la rata canguro de Ord ( Dipodomys ordii ) en el este de Nebraska se llev&oacute; a cabo hace 4 d&eacute;cadas. Examinamos los l&iacute;mites orientales actuales de la distribuci&oacute;n de D. ordii para ver si su &aacute;rea de distribuci&oacute;n se ha expandido, contra&iacute;do o permanecido igual en el estado desde los a&ntilde;os 1960. Con base en nuestra investigaci&oacute;n, es posible decir que la distribuci&oacute;n de las ratas canguro ha cambiado poco en d&eacute;cadas recientes. Aqu&iacute; reportamos datos para 8 condados para los cuales no exist&iacute;an registros anteriores e informamos sobre una peque&ntilde;a expansi&oacute;n de su &aacute;rea de distribuci&oacute;n. Tambi&eacute;n comentamos sobre el h&aacute;bitat, la reproducci&oacute;n y la situaci&oacute;n taxon&oacute;mica de las ratas canguro en el este de Nebraska.     

Fuzzy preferences in conflicts

A systematic fuzzy approach is developed to model fuzziness and uncertainties in the preferences of decision makers involved in a conflict. This unique fuzzy preference formulation is used within the paradigm of the Graph Model for Conflict Resolution in which a given dispute is modeled in terms of decision makers, each decision maker＇s courses of actions or options, and each decision maker＇s preferences concerning the states or outcomes which could take place. In order to be able to determine the stability of each state for each decision maker and the possible equilibria or resolutions, a range of solution concepts describing potential human behavior under conflict are defined for use with fuzzy preferences. More specifically, strong and weak definitions of stability are provided for the solution concepts called Nash, general metarational, symmetric metarational, and sequential stability. To illustrate how these solution concepts can be conveniently used in practice, they are applied to a dispute over the contamination of an aquifer by a chemical company located in Elmira, Ontario, Canada.     

Reproduction and seasonal activity of silver-haired bats ( Lasionycteris noctivagans ) in western Nebraska

Silver-haired bats ( Lasionycteris noctivagans ) were thought only to migrate through Nebraska; however, recent surveys in eastern Nebraska report summer records of females and their young. Our study in western Nebraska also shows that silver-haired bats are summer residents. We discovered the 1st reproductively active L. noctivagans in this part of the state. We caught lactating females and volant young in riparian forests along the North Platte River and in forested areas of the Pine Ridge. Previously, adult males were not known from Nebraska in summer, and only 4 records of L. noctivagans were known from western Nebraska during migration. On 28 July we captured an adult male in a coniferous forest of the Wildcat Hills, and we have more than 100 records of migrating individuals. Lastly, an obese L. noctivagans captured on 4 November may represent an individual preparing to hibernate in the state.     

Spotted bats ( Euderma maculatum ) from Mt. Taylor, New Mexico

The spotted bat ( Euderma maculatum ) is an elusive and rarely captured species in western North America. In the United States, it is known from 12 western states. In New Mexico, few individuals have been reported in recent years, and multiple individuals are known from 9 of 12 capture sites. This study reports on additional captures of E. maculatum from Mt. Taylor (Cibola County) for 2 consecutive summers and includes evidence of a reproducing population in the area. On 30 June/1 July 2006, I captured 4 individuals of E. maculatum , including a lactating female, and on 5 June 2007, I captured a nonreproductive female. The flight of this species was directional and deliberate; I captured 5 of 6 spotted bats that came low over the earthen pond. This study demonstrates how human-made sources of water in an arid region provide opportunities for many species of bats to drink.     

Risk premia and long rates in Ireland

Using a number of long‐term maturities and monthly data, 1989–1997, we provide a number of tests of the expectations hypothesis (EH) of the term structure. The main insight in this paper is the use of the excess holding period return to provide a proxy for a possible time‐varying term premium. Nearly all previous studies using the VAR methodology have used only the spread and the change in (short) rates and they have ignored the excess holding period return. We find that we cannot reject the EH, but we do reject the presence of time‐varying risk premia. Copyright © 2001 John Wiley & Sons, Ltd.     

Enhancing Emancipatory Systems Methodologies for Sustainable Development

Our interest lies in applying the principles of critical systems thinking to human activity systems in developing countries in situations where issues of natural resource sustainability constrain the feasible set of long-term strategies. The concept of sustainable development provides an expanded domain for critical systems thinking. The fundamental values underpinning sustainable development are that both intragenerational and intergenerational equity are important. As a consequence, key stakeholders are often excluded from power-sharing within current social systems. Addressing these issues requires renewed focus on emancipatory commitment and methodologies. To date, Ulrich's critical systems heuristics is the only critical systems methodology that offers practicable tools for emancipation. A case study analysis in Tigray, northern Ethiopia, provides insights in relation to the application of critical system heuristics to issues of sustainable development and highlights the need to extend the use of critical systems heuristics beyond the design and monitoring of structured interventions.     

Capturing complex, non-linear team behaviours during competitive football performance

This study investigated changes in the complexity (magnitude and structure of variability) of the collective behaviours of association football teams during competitive performance. Raw positional data from an entire competitive match between two professional teams were obtained with the ProZone® tracking system. Five compound positional variables were used to investigate the collective patterns of performance of each team including: surface area, stretch index, team length, team width, and geometrical centre. Analyses involve the coefficient of variation (%CV) and approximate entropy (ApEn), as well as the linear association between both parameters. Collective measures successfully captured the idiosyncratic behaviours of each team and their variations across the six time periods of the match. Key events such as goals scored and game breaks (such as half time and full time) seemed to influence the collective patterns of performance. While ApEn values significantly decreased during each half, the %CV increased. Teams seem to become more regular and predictable, but with increased magnitudes of variation in their organisational shape over the natural course of a match.