motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences

Next-generation sequencing technology enables the identification of thousands of gene regulatory sequences in many cell types and organisms. We consider the problem of testing if two such sequences differ in their number of binding site motifs for a given transcription factor (TF) protein. Binding site motifs impart regulatory function by providing TFs the opportunity to bind to genomic elements and thereby affect the expression of nearby genes. Evolutionary changes to such functional DNA are hypothesized to be major contributors to phenotypic diversity within and between species; but despite the importance of TF motifs for gene expression, no method exists to test for motif loss or gain. Assuming that motif counts are Binomially distributed, and allowing for dependencies between motif instances in evolutionarily related sequences, we derive the probability mass function of the difference in motif counts between two nucleotide sequences. We provide a method to numerically estimate this distribution from genomic data and show through simulations that our estimator is accurate. Finally, we introduce the R package {\tt motifDiverge} that implements our methodology and illustrate its application to gene regulatory enhancers identified by a mouse developmental time course experiment. While this study was motivated by analysis of regulatory motifs, our results can be applied to any problem involving two correlated Bernoulli trials

Magnetic characterization of perpendicular recording media

In this paper, we describe techniques for the magnetic characterization of perpendicular recording media. Such measurements made using traditional techniques, such as the vibrating sample magnetometry (VSM) and alternating gradient force magnetometer (AGFM), have to be corrected for the sample shape demagnetizing factor, which is often found not to be equal to -4p. For measurements other than the simple hysteresis loop, such as remanence curves, this correction must be carried out in real time and we describe the method by which this can be achieved and the process for achieving the correct demagnetization of perpendicular films prior to measurements of the isothermal remanent magnetization curve. A further complication is that real perpendicular media have a soft underlayer beneath the recording layer, which swamps and confuses signals from instruments such as VSM or AGFM. Hence, we describe the construction and use of a magnetooptical Kerr effect magnetometer, which does not penetrate significantly into the soft layer and enables the perpendicular layer to be measured independently. We describe the properties of a traditional alloy perpendicular medium and a Co-Pd multilayer system, which in the latter case exhibits multiple switching behavior. We also address the issue of the effect of the soft underlayer on the coupling in similar longitudinal films and find that the presence of the underlayer induces significant additional coupling effects that may well give rise to an increase in noise in recorded signal

The Lore of Low Methane Livestock:Co-Producing Technology and Animals for Reduced Climate Change Impact

Methane emissions from sheep and cattle production have gained increasing profile in the context of climate change. Policy and scientific research communities have suggested a number of technological approaches to mitigate these emissions. This paper uses the concept of co-production as an analytical framework to understand farmers’ evaluation of a 'good animal’. It examines how technology and sheep and beef cattle are co-produced in the context of concerns about the climate change impact of methane. Drawing on 42 semi-structured interviews, this paper demonstrates that methane emissions are viewed as a natural and integral part of sheep and beef cattle by farmers, rather than as a pollutant. Sheep and beef cattle farmers in the UK are found to be an extremely heterogeneous group that need to be understood in their specific social, environmental and consumer contexts. Some are more amenable to appropriating methane reducing measures than others, but largely because animals are already co-constructed from the natural and the technical for reasons of increased production efficiency

'Open Marxism' against and beyond the 'Great Enclosure'? Reflections on How (Not) to Crack Capitalism

The main purpose of this article is to provide an in-depth discussion of John Holloway’s recent book, Crack Capitalism. To this end, the paper offers a detailed account of the key strengths and weaknesses of Holloway’s version of ‘open Marxism’. The analysis is divided into two parts. The first part focuses on six significant strengths of Crack Capitalism: (1) its insistence upon the importance of autonomous forms of agenda-setting for both individual and collective emancipation; (2) its emphasis on the ordinary constitution of social struggles; (3) its fine-grained interpretation of the socio-ontological conditions underlying human agency; (4) its processual conception of radical social transformation; (5) its recognition of the elastic, adaptable, and integrative power of capitalism; and (6) its proposal for an alternative critical theory, commonly known as ‘open Marxism’ or ‘autonomous Marxism’. The second part of the study examines the principal weaknesses of Crack Capitalism: (1) the counterproductive implications of the preponderance of negativity, owing to a one-sided concern with critique, cracks, and crises; (2) conceptual vagueness; (3) an overuse of poetic and metaphorical language; (4) the absence of a serious engagement with the question of normativity; (5) a lack of substantive evidence; (6) a residual economic reductionism; (7) a simplistic notion of gender; (8) the continuing presence of various problematic ‘isms’; (9) the misleading distinction between ‘doing’ and ‘labour’; (10) a reductive understanding of capitalism; (11) an unrealistic view of society; and (12) socio-ontological idealis

Gamma-ray Emission from an Outer-Gap Accelerator: Constraints on Magnetospheric Current, Magnetic Inclination, and Distance for PSR B1055-52

We investigate a stationary pair production cascade in the outer magnetosphere of a spinning neutron star. The charge depletion due to global flows of charged particles, causes a large electric field along the magnetic field lines. Migratory electrons and/or positrons are accelerated by this field to radiate curvature gamma-rays, some of which collide with the X-rays to materialize as pairs in the gap. The replenished charges partially screen the electric field, which is self-consistently solved, together with the distribution functions of particles and gamma-rays. By solving the Vlasov equations describing this pair production cascade, we demonstrate the existence of a stationary gap in the outer magnetosphere of PSR B1055-52 for a wide range of current densities flowing in the accelerator: From sub to super Goldreich-Julian values. However, we find that the expected GeV spectrum becomes very soft if the current density exceeds the Goldreich-Julian value. We also demonstrate that the GeV spectrum softens with decreasing magnetic inclination and with increasing distance to this pulsar. We thus conclude that a sub-Goldreich-Julian current, a large magnetic inclination, and a small distance (500 pc, say) are plausible to account for EGRET observations. Furthermore, it is found that the TeV flux due to inverse Compton scatterings of infrared photons whose spectrum is inferred from the Rayleigh-Jeans side of the soft blackbody spectrum is much less than the observational upper limit.Comment: 16 pages, 13 figures, ApJ in pres

UK Coal resource for new exploitation technologies. Final report

This focus of this report are the UK coal resources available for exploitation by the new technologies of Underground Coal Gasification, Coalbed Methane production and Carbon Dioxide Sequestration. It also briefly considers the potential for further underground and opencast mining and the extraction of methane from working and closed mines. The potential for mining was mainly considered because it has a bearing on the scope for the new exploitation technologies rather than to identify resources or potential mine development areas. The report covers the UK landward area and nearshore areas, although information on the extent of underground mining was not available for the nearshore areas. This work was carried out by the British Geological Survey, with the assistance of Wardell Armstrong and Imperial College, London. It represents a summary of the results of the Study of the UK Coal Resource for New Exploitation Technologies Project, carried out for the DTI Cleaner Coal Technology Programme (Contract No. C/01/00301/00/00) under the management of Future Energy Solutions (Agreement No. C/01/00301/00/00). Coalbed methane production can be subdivided into three categories: Methane drained from working mines, known as Coal Mine Methane (CMM), has been exploited in the UK since at least the 1950s. Currently all working mines except Daw Mill and Ellington drain methane. It is used to generate electricity at Harworth, Tower and Thoresby collieries and in boilers at Welbeck, Kellingley and Ricall/Whitemoor collieries. There is potential to increase the exploitation of CMM in the UK but this is mainly a question of economics. There is also an environmental case for further utilisation, as methane is an important greenhouse gas, 23 times more powerful than carbon dioxide on a mass basis. Methane drained from abandoned mines, known as Abandoned Mine Methane (AMM), is a methane-rich gas that is obtained from abandoned mines by applying suction to the workings. The fuel gas component consists primarily of methane desorbed from seams surrounding the mined seam(s). These unmined seams have been de-stressed and fractured by the collapse of overlying and underlying strata into the void left by the extracted seam(s). Currently AMM is being exploited at sites in North Staffordshire (Silverdale Colliery), the East Midlands (Bentinck, Shirebrook and Markham collieries) and Yorkshire (Hickleton, Monk Bretton and Wheldale collieries). The methane-rich gas is used for electricity generation or supplied to local industry for use in boilers and kilns. Over the last few years, the fledgling UK AMM industry has started to ascend a learning curve. However, it has suffered a major setback since the wholesale price of electricity fell under the New Electricity Trading Arrangements and AMM does not currently qualify as renewable energy in the UK. Coalbed methane produced via boreholes from virgin coal seams, known as Virgin Coalbed Methane (VCBM), has been the subject of significant exploration effort in Lancashire, North Wales, South Wales and Scotland. The best production of gas and water from a single well is understood to be from the project at Airth, north of Falkirk in Scotland. However, this is not economic at present. The main reason for the slow development of VCBM in the UK is perceived to be the widespread low permeability of UK coal seams, although little work has been carried out in the UK on coal permeability, or to truly identify the reasons for the lack of success. This must be overcome before the otherwise significant resource bases in the Clackmannan Syncline, Canonbie, Cumbria, South Lancashire, North Wales, North Staffordshire and South Wales coalfields can be exploited. A technological breakthrough is required to overcome the likely widespread low permeability in the UK Carboniferous coal seams. Otherwise, at best, production will probably be limited to niche opportunities in areas where high seam permeability exists. The criteria used to define and map the location of VCBM resources are as follows: • Coal seams greater than 0.4 m in thickness at depths >200 m • Seam gas content >1m3/tonne • 500 metres or more horizontal separation from underground coal workings • Vertical separation of 150m above and 40 m below a previously worked seam Vertical separation of >100 m from major unconformities of these areas is thought to be about ,900 x 109 m3 (about 29 years of UK natural gas consumption). he main criteria sed for the delineation and mapping of resource areas with potential for UCG were: eparation from underground coal workings and current omic and environmental grounds as described later in this report. he establishment of these criteria do not rule out UCG projects in shallower or thinner seams, if • Vertical separation of >100 m from major aquifers, and • Areas with a CMM resource (current underground coal mining licences) were excluded. Note that the presence of a CBM resource does not imply permeability in the coal seams or that the resource can be recovered economically now or at any time in the future. Using these criteria resource areas were defined and represented on the maps. The total VCBM resource 2 Underground coal gasification (UCG) is the process whereby the injection of oxygen and steam/water via a borehole results in the partial in-situ combustion of coal to produce a combustible gas mixture consisting of CO2, CH4, H2 and CO, the proportions depending on temperature, pressure conditions and the reactant gases injected. This product gas is then extracted via a producing well for use as an energy source. All previous trials of this technology in the UK took place in the 1950’s or before, e.g. Durham (1912), Newman Spinney (1949-1956) and Bayton (c.1955), although this country is well placed for UCG, with large reserves of indigenous coal both onshore and offshore. T u • Seams of 2 m thickness or greater • Seams at depths between 600 and 1200 m from the surface • 500 m or more horizontal and vertical scoal mining licences, and • Greater than 100 m from major aquifers While seams outside these depth and thicknesses criteria are known to support UCG, the criteria were chosen for this generic study on econ T local site specific factors support it. Mapping of the potential UCG resource has identified large areas suitable for UCG, particularly in Eastern England, Midland Valley of Scotland, North Wales, Cheshire Basin, South Lancashire, Canonbie, the Midlands and Warwickshire. Potential also exists in other coalfields but on a smaller scale; this is often limited by the extent of former underground coal mining activities. The total area where coals are suitable for gasification is approximately 2.8 x 109m2. Where the criteria for UCG are met, the minimum volume of coal available for gasification, calculated assuming only one 2 m thick seam meets the criteria across each area, is app63 roximately 5,698 x 10 m (~7 Btonnes). Using an verage of the total thickness of coals that meet the criteria across each area gives a more realistic source figure of 12,911 x 106m3 (~17 Btonnes). pass the expensive step of parating the CO2 from flue gases. If the main objective, however, is CO2 sequestration rather than ethane production then separation of the flue gases may be worthwhile. O2 on coal seams, is would render them unminable and ungasifiable (because the CO2 would be released). Any future ining of such coals would require re-capture and sequestration of the stored CO . ion, providing that other issues, such as low seam permeability, can be vercome. Large areas where coal is below 1,200 m occur in the UK, particularly in the Cheshire asin and Eastern England. In summary • and its potential application in the UK cannot be assessed. However, there are vast areas of coal at depths below 1,200 m that are possibly too deep for mining and in situ gasification

Robotic milking technologies and renegotiating situated ethical relationships on UK dairy farms

Robotic or automatic milking systems (AMS) are novel technologies that take over the labor of dairy farming and reduce the need for human-animal interactions. Because robotic milking involves the replacement of 'conventional' twice-a-day milking managed by people with a system that supposedly allows cows the freedom to be milked automatically whenever they choose, some claim robotic milking has health and welfare benefits for cows, increases productivity, and has lifestyle advantages for dairy farmers. This paper examines how established ethical relations on dairy farms are unsettled by the intervention of a radically different technology such as AMS. The renegotiation of ethical relationships is thus an important dimension of how the actors involved are re-assembled around a new technology. The paper draws on in-depth research on UK dairy farms comparing those using conventional milking technologies with those using AMS. We explore the situated ethical relations that are negotiated in practice, focusing on the contingent and complex nature of human-animal-technology interactions. We show that ethical relations are situated and emergent, and that as the identities, roles, and subjectivities of humans and animals are unsettled through the intervention of a new technology, the ethical relations also shift. © 2013 Springer Science+Business Media Dordrecht