Novel Methods for Determining Effective Interactions for the Nuclear Shell Model

The Contractor Renormalization (CORE) method is applied in combination with modern effective-theory techniques to the nuclear many-body problem. A one-dimensional--yet ``realistic''--nucleon-nucleon potential is introduced to test these novel ideas. It is found that the magnitude of ``model-space'' (CORE) corrections diminishes considerably when an effective potential that eliminates the hard-momentum components of the potential is first introduced. As a result, accurate predictions for the ground-state energy of the there-body system are made with relatively little computational effort when both techniques are used in a complementary fashion.Comment: 14 pages, 5 figures and 2 tabl

Factors associated with changes of state of foot conformation and lameness in a flock of sheep

The aim of this research was to investigate transitions between foot conformation, lameness and footrot in sheep. Data came from one lowland flock of approximately 700 ewes studied for 18 months. Multilevel multistate analyses of transitions between good and poor foot conformation states in ewes, and lame and non-lame states in ewes and lambs were conducted. Key results were that the longer sheep had feet in good conformation, the more likely they were to stay in this state; similarly, the longer a ewe was not lame the more likely she was not to become lame. Ewes with poor foot conformation were more likely to become lame (OR: 1.83 (1.24-2.67)) and to be > 4 years (OR: 1.50(1.09-2.05)). Ewes with footrot were less likely to move to good foot conformation (OR: 0.48 (0.31-0.75)) and were more likely to become lame (OR: 3.81(2.60-5.59)). Ewes lame for > 4 days and not treated with parenteral antibacterials had a higher risk of developing (OR: 2.00 (1.08-3.61)), or remaining in (OR: 0.49 (0.29-0.95)) poor foot conformation compared with ewes never lame. Treatment of ewes lame with footrot with parenteral antibacterials increased the probability of transition from a lame to a non-lame state (OR: 1.46 (1.05-2.02)) and these ewes, even if lame for > 4 days, were not more likely to develop poor foot conformation. The risk of a ewe becoming lame increased when at least one of her offspring was lame (OR: 2.03 (1.42-2.92)) and when the prevalence of lameness in the group was ≥ 5% (OR: 1.42 (1.06-1.92)). Lambs were at increased risk of becoming lame when they were male (OR: 1.42 (1.01-2.01)), single (OR: 1.86 (1.34-2.59)) or had a lame dam or sibling (OR: 3.10 (1.81-5.32)). There were no explanatory variables associated with lambs recovering from lameness. We conclude that poor foot conformation in ewes increases the susceptibility of ewes to become lame and that this can arise from untreated footrot. Treatment of ewes lame with footrot with parenteral antibacterials leads to recovery from lameness and prevents or resolves poor foot conformation which then reduces the susceptibility to further lameness with footrot

Development of an integrated economic and ecological framework for ecosystem-based fisheries management in New England

Author Posting. © The Author(s), 2012. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Progress in Oceanography 102 (2012): 93-101, doi:10.1016/j.pocean.2012.03.007.We present an integrated economic-ecological framework designed to help assess the implementation of ecosystem-based fisheries management (EBFM) in New England. We develop the framework by linking a computable general equilibrium (CGE) model of a coastal economy to an end-to-end (E2E) model of a marine food web for Georges Bank. We focus on the New England region using coastal county economic data for a restricted set of industry sectors and marine ecological data for three top level trophic feeding guilds: planktivores, benthivores, and piscivores. We undertake numerical simulations to model the welfare effects of changes in alternative combinations of yields from feeding guilds and alternative manifestations of biological productivity. We estimate the economic and distributional effects of these alternative simulations across a range of consumer income levels. This framework could be used to extend existing methodologies for assessing the impacts on human communities of groundfish stock rebuilding strategies, such as those expected through the implementation of the sector management program in the US northeast fishery. We discuss other possible applications of and modifications and limitations to the framework.This work was supported by the NOAA Saltonstall-Kennedy Grant Program (Award No. NA09NMF4270097), the MIT Sea Grant College Program (NOAA Award No. NA10OAR4170086, Subaward No. 5710002974), and the Johnson Endowment of the WHOI Marine Policy Center

Herschel-ATLAS/GAMA: A difference between star formation rates in strong-line and weak-line radio galaxies

We have constructed a sample of radio-loud objects with optical spectroscopy from the Galaxy and Mass Assembly (GAMA) project over the Herschel Astrophysical Terahertz Large Area Survey (Herschel-ATLAS) Phase 1 fields. Classifying the radio sources in terms of their optical spectra, we find that strong-emission-line sources ('high-excitation radio galaxies') have, on average, a factor of ~4 higher 250-μm Herschel luminosity than weak-line ('lowexcitation') radio galaxies and are also more luminous than magnitude-matched radio-quiet galaxies at the same redshift. Using all five H-ATLAS bands, we show that this difference in luminosity between the emission-line classes arises mostly from a difference in the average dust temperature; strong-emission-line sources tend to have comparable dust masses to, but higher dust temperatures than, radio galaxies with weak emission lines. We interpret this as showing that radio galaxies with strong nuclear emission lines are much more likely to be associated with star formation in their host galaxy, although there is certainly not a one-to-one relationship between star formation and strong-line active galactic nuclei (AGN) activity. The strong-line sources are estimated to have star formation rates at least a factor of 3-4 higher than those in the weak-line objects. Our conclusion is consistent with earlier work, generally carried out using much smaller samples, and reinforces the general picture of high-excitation radio galaxies as being located in lower-mass, less evolved host galaxies than their low-excitation counterparts.Peer reviewe

Synchronisation in networks of delay-coupled type-I excitable systems

We use a generic model for type-I excitability (known as the SNIPER or SNIC model) to describe the local dynamics of nodes within a network in the presence of non-zero coupling delays. Utilising the method of the Master Stability Function, we investigate the stability of the zero-lag synchronised dynamics of the network nodes and its dependence on the two coupling parameters, namely the coupling strength and delay time. Unlike in the FitzHugh-Nagumo model (a model for type-II excitability), there are parameter ranges where the stability of synchronisation depends on the coupling strength and delay time. One important implication of these results is that there exist complex networks for which the adding of inhibitory links in a small-world fashion may not only lead to a loss of stable synchronisation, but may also restabilise synchronisation or introduce multiple transitions between synchronisation and desynchronisation. To underline the scope of our results, we show using the Stuart-Landau model that such multiple transitions do not only occur in excitable systems, but also in oscillatory ones.Comment: 10 pages, 9 figure

The smfBox is an open-source platform for single-molecule FRET

Single-molecule Förster Resonance Energy Transfer (smFRET) is a powerful technique capable of resolving both relative and absolute distances within and between structurally dynamic biomolecules. High instrument costs, and a lack of open-source hardware and acquisition software have limited smFRET’s broad application by non-specialists. Here, we present the smfBox, a cost-effective confocal smFRET platform, providing detailed build instructions, open-source acquisition software, and full validation, thereby democratising smFRET for the wider scientific community

Active Brownian Particles. From Individual to Collective Stochastic Dynamics

We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of such self-propelled entities in the framework of statistical mechanics. Examples of such active units in complex physico-chemical and biological systems are chemically powered nano-rods, localized patterns in reaction-diffusion system, motile cells or macroscopic animals. Based on the description of individual motion of point-like active particles by stochastic differential equations, we discuss different velocity-dependent friction functions, the impact of various types of fluctuations and calculate characteristic observables such as stationary velocity distributions or diffusion coefficients. Finally, we consider not only the free and confined individual active dynamics but also different types of interaction between active particles. The resulting collective dynamical behavior of large assemblies and aggregates of active units is discussed and an overview over some recent results on spatiotemporal pattern formation in such systems is given.Comment: 161 pages, Review, Eur Phys J Special-Topics, accepte

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Measurement of the p-pbar -> Wgamma + X cross section at sqrt(s) = 1.96 TeV and WWgamma anomalous coupling limits

The WWgamma triple gauge boson coupling parameters are studied using p-pbar -> l nu gamma + X (l = e,mu) events at sqrt(s) = 1.96 TeV. The data were collected with the DO detector from an integrated luminosity of 162 pb^{-1} delivered by the Fermilab Tevatron Collider. The cross section times branching fraction for p-pbar -> W(gamma) + X -> l nu gamma + X with E_T^{gamma} > 8 GeV and Delta R_{l gamma} > 0.7 is 14.8 +/- 1.6 (stat) +/- 1.0 (syst) +/- 1.0 (lum) pb. The one-dimensional 95% confidence level limits on anomalous couplings are -0.88 < Delta kappa_{gamma} < 0.96 and -0.20 < lambda_{gamma} < 0.20.Comment: Submitted to Phys. Rev. D Rapid Communication

Measurement of the ttbar Production Cross Section in ppbar Collisions at sqrt{s} = 1.96 TeV using Kinematic Characteristics of Lepton + Jets Events

We present a measurement of the top quark pair ttbar production cross section in ppbar collisions at a center-of-mass energy of 1.96 TeV using 230 pb**{-1} of data collected by the DO detector at the Fermilab Tevatron Collider. We select events with one charged lepton (electron or muon), large missing transverse energy, and at least four jets, and extract the ttbar content of the sample based on the kinematic characteristics of the events. For a top quark mass of 175 GeV, we measure sigma(ttbar) = 6.7 {+1.4-1.3} (stat) {+1.6- 1.1} (syst) +/-0.4 (lumi) pb, in good agreement with the standard model prediction.Comment: submitted to Phys.Rev.Let