A genomic map of the effects of linked selection in Drosophila

Natural selection at one site shapes patterns of genetic variation at linked sites. Quantifying the effects of 'linked selection' on levels of genetic diversity is key to making reliable inference about demography, building a null model in scans for targets of adaptation, and learning about the dynamics of natural selection. Here, we introduce the first method that jointly infers parameters of distinct modes of linked selection, notably background selection and selective sweeps, from genome-wide diversity data, functional annotations and genetic maps. The central idea is to calculate the probability that a neutral site is polymorphic given local annotations, substitution patterns, and recombination rates. Information is then combined across sites and samples using composite likelihood in order to estimate genome-wide parameters of distinct modes of selection. In addition to parameter estimation, this approach yields a map of the expected neutral diversity levels along the genome. To illustrate the utility of our approach, we apply it to genome-wide resequencing data from 125 lines in Drosophila melanogaster and reliably predict diversity levels at the 1Mb scale. Our results corroborate estimates of a high fraction of beneficial substitutions in proteins and untranslated regions (UTR). They allow us to distinguish between the contribution of sweeps and other modes of selection around amino acid substitutions and to uncover evidence for pervasive sweeps in untranslated regions (UTRs). Our inference further suggests a substantial effect of linked selection from non-classic sweeps. More generally, we demonstrate that linked selection has had a larger effect in reducing diversity levels and increasing their variance in D. melanogaster than previously appreciated

RPCs Considered Harmful

Scholars agree that amphibious configurations are an interesting new topic in the field of cryp- toanalysis, and mathematicians concur. After years of structured research into gigabit switches, we argue the improvement of forward-error correction, which embodies the private principles of cryptography. In our research, we use authenticated modalities to demonstrate that digital-to-analog converters and evolutionary programming can collude to address this question. Such a hypothesis at first glance seems unexpected but is derived from known results

Lecture recordings to support learning: a contested space between students and teachers

Universities, globally, are increasingly offering students a blended learning approach to support their campus-based education, through use of a wide range of educational technologies, tools and systems. Research has demonstrated that blended learning offers at least equivalent learning outcomes for students, and enhances flexibility, inclusivity, engagement and motivation. Many universities across the world (including Australia, the US, Canada, Singapore, Qatar, and across Europe) have adopted lecture capture as a means to support a blended learning approach, and students have strong positive perceptions about the value of lecture recordings to enhance their learning and support their education. However, research shows that teaching staff are generally less positive about the value of lecture capture, believing it to diminish the value of the live lecture experience, reduce learning, and encourage student absenteeism from lectures. In this study, we used mixed methods and repeated cross-sectional data collection to investigate the use and value of lecture recordings from the perspective of students and teaching staff in a large campus-based university, employing a blended learning approach. Our data show that students make significant use of lecture recordings, throughout the academic session, and place great value on recordings for note-taking, more in-depth understanding or clarification, and assessment preparation. As a result, students have high expectations about the availability and quality of recordings. Teaching staff reported a range of reservations about the value of lecture recordings, including its impact on teaching style, and strong concerns about the negative impact of lecture recordings on students learning and attendance. Our data show that over 80% of students attended recorded lectures, but lectures that weren’t recorded had significantly higher attendance. In conclusion, our research demonstrates a contested space between staff and students in relation to the use and value of lecture recordings, a contested space that will need to be debated and resolved as universities grow their use of blended learning. This study contributes significantly to this global debate by its use of a wide range of additional data sets to delve further and provide a more nuanced view of this space

Quantifying the evolution of soil fabric during shearing using directional parameters

Over the past 50 years, experimental studies have repeatedly demonstrated that the mechanical behaviour of sand is sensitive to the material fabric, that is, the arrangement of the grains. Up until now there have been relatively few attempts to describe this fabric quantitatively. Much of our understanding of the link between the particle movements and interactions and the macro-scale response of granular materials, including sand, comes from discrete-element modelling and experiments on ‘analogue’ sands with simple, idealised shapes. This paper investigates methods of quantifying the directional fabric of a real sand and its evolution under loading. Statistical analyses of the distribution of fabric directional data in terms of particle, contact normal, branch vector and void orientations were carried out at different stages of shearing deformation. The data show that the initial particle orientation fabric that develops during the deposition of the material tends to persist during shearing, while in the post-peak regime the contact normals seem to be reoriented along the direction of the major principal stress. Different patterns were observed within the shear band, as both the particles and the contact normal vectors appeared to rotate along the shear plane

Negotiating growth of online education in higher education

Universities are facing growing internal and external pressures to generate income, educate a widening continuum of learners, and make effective use of digital technologies. One response has been growth of online education, catalysed by Massive Open Online Courses, availability of digital devices and technologies, and notions of borderless global education. In growing online education, learning and teaching provision has become increasingly disaggregated, and universities are partnering with a range of private companies to reach new learners, and commercialise educational provision. In this paper, we explore the competing drivers which impact decision making within English universities and their strategies to grow online education provision, through interviews with senior managers, and interrogation of their views through the lens of a range of internal, external and organisational drivers. We show that pressures facing universities may be alleviated by growth of online education provision, but that negotiating an appropriate route to realise this ambition involves attempts to resolve these underlying tensions deriving from competing drivers. We use a modified form of the PEST model to demonstrate the complexities, inter-dependencies and processes associated with these drivers when negotiating delivery of unbundled online education through use of private company services, or in partnership with private companies

The behaviour of a low- to medium-density chalk under a wide range of pressure conditions

Experiments are described which provided the basis for advanced numerical modelling of large-scale axial and lateral pile tests undertaken chalk to assist the design of offshore wind and other projects in northern Europe. The research explored the mechanical behaviour of chalk from a UK research site under effective cell pressures up to 12.8 MPa. When sheared from low confining pressures the chalk’s interparticle bonds contribute a large proportion of the peak deviator stresses available to specimens that crack, bifurcate and dilate markedly after failing at relatively small strains. Progressively more ductile behaviour is seen as pressures are raised, with failures being delayed until increasingly large strains and stable critical states are attained. Loading invokes very stiff responses within the chalk’s (Y1) linear elastic limits and behaviour remains stiff, although non-linear, up to large-scale (Y3) yield points. Near-elliptical Y1 and Y3 yield loci can be defined in q-p′ stress space and a critical state v-p′ curve is identified. The chalk’s initially bonded, high porosity, structure is explored by normalising the shearing and compression state paths with reference to both critical state and intrinsic compression lines. The results have important implications for pile test analysis and practical design in this challenging geomaterial

Development and Evaluation of a Trapping System for Anoplophora glabripennis (Coleoptera: Cerambycidae) in the United States

Anoplophora glabripennis (Motschulsky) (Coleoptera: Cerambycidae), commonly known as the Asian longhorned beetle, is an invasive wood-boring pest that infests a number of hardwood species and causes considerable economic losses in North America, several countries in Europe, and in its native range in Asia. The success of eradication efforts may depend on early detection of introduced populations; however, detection has been limited to identification of tree damage (oviposition pits and exit holes), and the serendipitous collection of adults, often by members of the public. Here we describe the development, deployment, and evaluation of semiochemical-baited traps in the greater Worcester area in Massachusetts. Over 4 yr of trap evaluation (2009-2012), 1013 intercept panel traps were deployed, 876 of which were baited with three different families of lures. The families included lures exhibiting different rates of release of the male-produced A. glabripennis pheromone, lures with various combinations of plant volatiles, and lures with both the pheromone and plant volatiles combined. Overall, 45 individual beetles were captured in 40 different traps. Beetles were found only in traps with lures. In several cases, trap catches led to the more rapid discovery and management of previously unknown areas of infestation in the Worcester county regulated area. Analysis of the spatial distribution of traps and the known infested trees within the regulated area provides an estimate of the relationship between trap catch and beetle pressure exerted on the traps. Studies continue to optimize lure composition and trap placemen