A practical approach for minimising inbreeding and maximising genetic gain in dairy cattle

A method that predicts the genetic composition and inbreeding (F) of the future dairy cow population using information on the current cow population, semen use and progeny test bulls is described. This is combined with information on genetic merit of bulls to compare bull selection methods that minimise F and maximise breeding value for profit (called APR in Australia). The genetic composition of the future cow population of Australian Holstein-Friesian (HF) and Jersey up to 6 years into the future was predicted. F in Australian HF and Jersey breeds is likely to increase by about 0.002 and 0.003 per year between 2002 and 2008, respectively. A comparison of bull selection methods showed that a method that selects the best bull from all available bulls for each current or future cow, based on its calf's APR minus F depression, is better than bull selection methods based on APR alone, APR adjusted for mean F of prospective progeny after random mating and mean APR adjusted for the relationship between the selected bulls. This method reduced F of prospective progeny by about a third to a half compared to the other methods when bulls are mated to current and future cows that will be available 5 to 6 years from now. The method also reduced the relationship between the bulls selected to nearly the same extent as the method that is aimed at maximising genetic gain adjusted for the relationship between bulls. The method achieves this because cows with different pedigree exist in the population and the method selects relatively unrelated bulls to mate to these different cows. Selecting the best bull for each current or future cow so that the calf's genetic merit minus F depression is maximised can slow the rate of increase in F in the population

Writing by numbers: case studies in digital art history

While art history claims to be among the most interdisciplinary of fields, the use of digital resources and methods to create new knowledge or rethink its traditional questions is less developed than other disciplines. My thesis contributes to narrowing that gap and promotes a kind of art writing where the numerical stands alongside the verbal and the visual as an essential part of the interpretations being offered. The approach I use is the case study. Each draws on different kinds of textual and numerical data, and statistical methods for processing that data, to address some of the areas where digital art history is underdeveloped. In the first I use statistical methods to analyse the structure and content of the catalogues and criticism of the nineteenth-century Paris Salon. The readings I develop show how that language was involved in practical, conceptual and institutional change in the nineteenth-century French art world. My readings shed new light on that art world, and extend or challenge existing scholarship. In the second I use linear regression to model auction sales with twelve contemporary artists. My models give an understanding of collectors' preferences with different characteristics of the artworks sold, and of some of the ways in which the contemporary art market has been changing. With traditional art historical methods, it is not possible to develop the kind of disaggregated perspective on collectors’ preferences I present in this case study. For my third case study I created a data set of the metadata for 59,000 artworks in the online collections of 35 modern and contemporary art museums. I use several techniques individually and in combination to identify trends in that metadata, to which I give art historical interpretations. These include correspondence analysis, topic modelling and parts-of-speech parsing. I set out a way of thinking about the history of modern and contemporary art in terms of ongoing concerns and interests which rise and fall in importance, and which cuts across conventional narratives of artist, period or movement. My case studies are illustrations of the art historical value of using statistical methods to address textual and numerical data. They serve as examples for other art historians interested in developing that approach within their own work. There are also lessons for those working across the digital humanities from my work. My readings show how drawing together different data sources or statistical methods can support richer interpretations than comes from using them in isolation

Analysis of the role of PCNA-DNA contacts during clamp loading

<p>Abstract</p> <p>Background</p> <p>Sliding clamps, such as Proliferating Cell Nuclear Antigen (PCNA) in eukaryotes, are ring-shaped protein complexes that encircle DNA and enable highly processive DNA replication by serving as docking sites for DNA polymerases. In an ATP-dependent reaction, clamp loader complexes, such as the Replication Factor-C (RFC) complex in eukaryotes, open the clamp and load it around primer-template DNA.</p> <p>Results</p> <p>We built a model of RFC bound to PCNA and DNA based on existing crystal structures of clamp loaders. This model suggests that DNA would enter the clamp at an angle during clamp loading, thereby interacting with positively charged residues in the center of PCNA. We show that simultaneous mutation of Lys 20, Lys 77, Arg 80, and Arg 149, which interact with DNA in the RFC-PCNA-DNA model, compromises the ability of yeast PCNA to stimulate the DNA-dependent ATPase activity of RFC when the DNA is long enough to extend through the clamp. Fluorescence anisotropy binding experiments show that the inability of the mutant clamp proteins to stimulate RFC ATPase activity is likely caused by reduction in the affinity of the RFC-PCNA complex for DNA. We obtained several crystal forms of yeast PCNA-DNA complexes, measuring X-ray diffraction data to 3.0 Å resolution for one such complex. The resulting electron density maps show that DNA is bound in a tilted orientation relative to PCNA, but makes different contacts than those implicated in clamp loading. Because of apparent partial disorder in the DNA, we restricted refinement of the DNA to a rigid body model. This result contrasts with previous analysis of a bacterial clamp bound to DNA, where the DNA was well resolved.</p> <p>Conclusion</p> <p>Mutational analysis of PCNA suggests that positively charged residues in the center of the clamp create a binding surface that makes contact with DNA. Disruption of this positive surface, which had not previously been implicated in clamp loading function, reduces RFC ATPase activity in the presence of DNA, most likely by reducing the affinity of RFC and PCNA for DNA. The interaction of DNA is not, however, restricted to one orientation, as indicated by analysis of the PCNA-DNA co-crystals.</p

Introduction : Subsurface sand remobilization and injection

Acknowledgement Thanks are due for informal information provided on the Nanaimo, Tierra del Fuego and Neoquen basins (David Hodgson), the East Carpathian Fold Belt (Alexandra Tamas) and the Paraná Basin (Gus- tavo Zvirtes). Funding This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.Peer reviewedPublisher PD

The Distributed Space Exploration Simulation (DSES)

The paper describes the Distributed Space Exploration Simulation (DSES) Project, a research and development collaboration between NASA centers which focuses on the investigation and development of technologies, processes and integrated simulations related to the collaborative distributed simulation of complex space systems in support of NASA's Exploration Initiative. This paper describes the three major components of DSES: network infrastructure, software infrastructure and simulation development. In the network work area, DSES is developing a Distributed Simulation Network that will provide agency wide support for distributed simulation between all NASA centers. In the software work area, DSES is developing a collection of software models, tool and procedures that ease the burden of developing distributed simulations and provides a consistent interoperability infrastructure for agency wide participation in integrated simulation. Finally, for simulation development, DSES is developing an integrated end-to-end simulation capability to support NASA development of new exploration spacecraft and missions. This paper will present current status and plans for each of these work areas with specific examples of simulations that support NASA's exploration initiatives

Exile Vol. I No. 2

SHORT STORIES Summer of the Anatolian Cyclops by Nil Muldur 7-13 El Patron by Jim Bowman 19-26 The Finishing Stroke by Sally Falch 39-47 ESSAYS The Fight for Free Will by Dottie Cartland 14-18 D. H. Lawrence and Classic American Literature by Betty Logcher 29-32 D. H. Lawrence by Diane Hostetler 33-37 POETRY Winter Forest by Mike Cook 18 Three Poems by John Miller: Security 27 Kitten, When I Fold You 28 Fable of Two Ages 28 Subway by Jane Erb 38 Four Dances by Midge Greenlee: The Mikado 48 Cirque de Deux 49 Madronos 50 Gaite Parisienne 5

The Hydrogen Epoch of Reionization Array Dish II: Characterization of Spectral Structure with Electromagnetic Simulations and its science Implications

We use time-domain electromagnetic simulations to determine the spectral characteristics of the Hydrogen Epoch of Reionization Arrays (HERA) antenna. These simulations are part of a multi-faceted campaign to determine the effectiveness of the dish's design for obtaining a detection of redshifted 21 cm emission from the epoch of reionization. Our simulations show the existence of reflections between HERA's suspended feed and its parabolic dish reflector that fall below -40 dB at 150 ns and, for reasonable impedance matches, have a negligible impact on HERA's ability to constrain EoR parameters. It follows that despite the reflections they introduce, dishes are effective for increasing the sensitivity of EoR experiments at relatively low cost. We find that electromagnetic resonances in the HERA feed's cylindrical skirt, which is intended to reduce cross coupling and beam ellipticity, introduces significant power at large delays ($-40$ dB at 200 ns) which can lead to some loss of measurable Fourier modes and a modest reduction in sensitivity. Even in the presence of this structure, we find that the spectral response of the antenna is sufficiently smooth for delay filtering to contain foreground emission at line-of-sight wave numbers below $k_\parallel \lesssim 0.2$ $h$Mpc$^{-1}$, in the region where the current PAPER experiment operates. Incorporating these results into a Fisher Matrix analysis, we find that the spectral structure observed in our simulations has only a small effect on the tight constraints HERA can achieve on parameters associated with the astrophysics of reionization.Comment: Accepted to ApJ, 18 pages, 17 Figures. Replacement matches accepted manuscrip