Knowledge synthesis: Animal health and welfare in organic pig production - Final Report COREPIG

This report reviews the available information on the welfare of pigs when maintained according to organic standards in Europe. It begins by overviewing the populations of organic pigs in different countries at the time of writing (2007), the organic standards which govern their management and the systems in which they are typically kept. It then reviews for each stage in the production cycle (sows, suckling piglets, weaned pigs and fattening pigs) the available literature on health and welfare problems which might be experienced by the animals and the hazards which might give rise to these problems. Finally the report reviews the methods current available for the measurement of pig health and welfare and the extent to which monitoring systems currently exist in different countries, or might be developed. The information gathered in this review formed the basis for the subsequent development of tools for use in a HACCP based management and surveillance system for organic pig herds. These tools will assist the organic pig farmer to prevent selected pig diseases and welfare problems by monitoring and controlling the risk factors. Further details can be found on the COREPIG project website www.icrofs.org/coreorganic/corepig.htm

A Method for Simulating Chiral Fermions on the Lattice

A method for simulating chiral gauge theories on the lattice is proposed, involving zeromodes on a topological defect. Lattice doublers may be decoupled in a gauge invariant manner, and flavor anomalies can be directly observed on a finite lattice. (Requires harvmac)Comment: 10 pages, UCSD-PTH-92-1

Phenomenology with Wilson fermions using smeared sources

We investigate the use of two types of non-local (``smeared'') sources for quark propagators in quenched lattice QCD at $\beta=6.0$ using Wilson fermions at $\kappa=0.154$ and $0.155$. We present results for the hadron mass spectrum, meson decay constants, quark masses, the chiral condensate and the quark distribution amplitude of the pion. The use of smeared sources leads to a considerable improvement over previous results. We find a disturbing discrepancy between the baryon spectra obtained using Wuppertal and wall sources. We find good signals in the ratio of correlators used to calculate the quark mass and the chiral condensate and show that the extrapolation to the chiral limit is smooth.Comment: (revised), 57 pages (29 pages of PostScript in landscape mode, 765924 bytes

The Standard Model from a New Phase Transition on the Lattice

Several years ago it was conjectured in the so-called Roma Approach, that gauge fixing is an essential ingredient in the lattice formulation of chiral gauge theories. In this paper we discuss in detail how the gauge-fixing approach may be realized. As in the usual (gauge invariant) lattice formulation, the continuum limit corresponds to a gaussian fixed point, that now controls both the transversal and the longitudinal modes of the gauge field. A key role is played by a new phase transition separating a conventional Higgs or Higgs-confinement phase, from a phase with broken rotational invariance. In the continuum limit we expect to find a scaling region, where the lattice correlators reproduce the euclidean correlation functions of the target (chiral) gauge theory, in the corresponding continuum gauge.Comment: 16 pages, revtex, one figure. Clarifications made, mainly in sections 3 and 6 that deal with the fermion action, to appear in Phys Rev

Recent Developments in Lattice QCD

I review the current status of lattice QCD results. I concentrate on new analytical developments and on numerical results relevant to phenomenology.Comment: 35 pages, 4 figures (Figures are excerpted from others' work and are not included) Uses harvmac.te

ProPIG - Organic pig health, welfare and environmental impact across Europe

Organic production is perceived by consumers as being superior in animal welfare and sustainability and the demand for organic pork products is slowly increasing. Within the past ten years a variety of husbandry and management systems have been developed across the EU, ranging from farms with pigs outdoors all year round using local breeds to farms with housed pigs having concrete outside runs and using conventional breeds (CorePIG, Rousing et al, 2011). So far, mainly clinical parameters have been used to describe the health situation on organic pig farms, identifying some key problems, such as weaning diarrhoea and piglet mortality. Organic pig production is - amongst others - characterised through a holistic approach based on the EU Regulation (EC) No 834/2007 and the IFOAM principles: ‘health, ecology, fairness and care’. This clearly states that health is more than absence of clinical symptoms and, the relation between animals and their environment is identified: ‘Health’ is defined as ‘the wholeness and integrity of living systems. It is not simply the absence of illness, but the maintenance of physical, mental, social and ecological well-being’ (IFOAM; 2006). Concepts of animal welfare include physical and mental welfare as well as the concept of naturalness (Fraser 2003), which is often interpreted as the ability to perform natural behaviour. Verhoog et al (2003) describe three main approaches within organic agriculture’s concept of nature and naturalness: the no-chemicals approach, the agro-ecology approach and the integrity approach. Applying those concepts to organic pig production can highlight potential conflicts: outdoor systems are perceived as the optimal housing system for pigs, as they allow natural behaviour such as rooting. However, this behaviour can cause damage to the grass cover and furthermore the manure fate in outdoor areas needs to be considered. A few studies on outdoor pig production have shown a clear N and P surplus and a high degree of distribution heterogeneity in outdoor areas, increasing the risk of N and P losses (Watson et al. 2003). Robust and competitive organic pig production needs to encompass low environmental impacts and good animal health and welfare. So far few studies have quantified both aspects in different pig husbandry systems. In addition, the theory that improving animal health and welfare reduces environmental impacts through decreased medicine use, improved growth rate and feed conversion efficiency has still to be verified. The aim of the CoreOrganic2 project ProPIG (2011-2014; carried out in eight European countries) is to examine the relationship between health, welfare and environmental impact. On-farm assessment protocols will be carried out on 75 farms in three pig husbandry systems (outdoor, partly outdoor, indoor with concrete outside run). Environmental impact will be assessed using both Life Cycle Assessment and calculations of nutrient balances at farm and outdoor area level. Animal health and welfare will be evaluated from animal based parameters including clinical and selected behavioural parameters. Results will be fed back and used by the farmers to decide farm specific goals and strategies to achieve these goals. As an outcome, all farms will create their individual health, welfare and environmental plan, which will be reviewed after one year to allow continuous development. This will provide the opportunity not only to investigate, but also improve the influence of organic pig farming systems on animal welfare and environmental impact. This fulfils the fourth IFOAM principle of care: ‘Organic Agriculture should be managed in a precautionary and responsible manner to protect the health and well-being of current and future generations and the environment’ (IFOAM, 2006)

Theta dependence of SU(N) gauge theories in the presence of a topological term

We review results concerning the theta dependence of 4D SU(N) gauge theories and QCD, where theta is the coefficient of the CP-violating topological term in the Lagrangian. In particular, we discuss theta dependence in the large-N limit. Most results have been obtained within the lattice formulation of the theory via numerical simulations, which allow to investigate the theta dependence of the ground-state energy and the spectrum around theta=0 by determining the moments of the topological charge distribution, and their correlations with other observables. We discuss the various methods which have been employed to determine the topological susceptibility, and higher-order terms of the theta expansion. We review results at zero and finite temperature. We show that the results support the scenario obtained by general large-N scaling arguments, and in particular the Witten-Veneziano mechanism to explain the U(1)_A problem. We also compare with results obtained by other approaches, especially in the large-N limit, where the issue has been also addressed using, for example, the AdS/CFT correspondence. We discuss issues related to theta dependence in full QCD: the neutron electric dipole moment, the dependence of the topological susceptibility on the quark masses, the U(1)_A symmetry breaking at finite temperature. We also consider the 2D CP(N) model, which is an interesting theoretical laboratory to study issues related to topology. We review analytical results in the large-N limit, and numerical results within its lattice formulation. Finally, we discuss the main features of the two-point correlation function of the topological charge density.Comment: A typo in Eq. (3.9) has been corrected. An additional subsection (5.2) has been inserted to demonstrate the nonrenormalizability of the relevant theta parameter in the presence of massive fermions, which implies that the continuum (a -> 0) limit must be taken keeping theta fixe

Medulloblastoma Exome Sequencing Uncovers Subtype-Specific Somatic Mutations

Medulloblastomas are the most common malignant brain tumors in children1. Identifying and understanding the genetic events that drive these tumors is critical for the development of more effective diagnostic, prognostic and therapeutic strategies. Recently, our group and others described distinct molecular subtypes of medulloblastoma based on transcriptional and copy number profiles2–5. Here, we utilized whole exome hybrid capture and deep sequencing to identify somatic mutations across the coding regions of 92 primary medulloblastoma/normal pairs. Overall, medulloblastomas exhibit low mutation rates consistent with other pediatric tumors, with a median of 0.35 non-silent mutations per megabase. We identified twelve genes mutated at statistically significant frequencies, including previously known mutated genes in medulloblastoma such as CTNNB1, PTCH1, MLL2, SMARCA4 and TP53. Recurrent somatic mutations were identified in an RNA helicase gene, DDX3X, often concurrent with CTNNB1 mutations, and in the nuclear co-repressor (N-CoR) complex genes GPS2, BCOR, and LDB1, novel findings in medulloblastoma. We show that mutant DDX3X potentiates transactivation of a TCF promoter and enhances cell viability in combination with mutant but not wild type beta-catenin. Together, our study reveals the alteration of Wnt, Hedgehog, histone methyltransferase and now N-CoR pathways across medulloblastomas and within specific subtypes of this disease, and nominates the RNA helicase DDX3X as a component of pathogenic beta-catenin signaling in medulloblastoma

Large-order NSPT for lattice gauge theories with fermions:the plaquette in massless QCD

Numerical Stochastic Perturbation Theory (NSPT) allows for perturbative computations in quantum field theory. We present an implementation of NSPT that yields results for high orders in the perturbative expansion of lattice gauge theories coupled to fermions. The zero-momentum mode is removed by imposing twisted boundary conditions; in turn, twisted boundary conditions require us to introduce a smell degree of freedom in order to include fermions in the fundamental representation. As a first application, we compute the critical mass of two flavours of Wilson fermions up to order $O(\beta^{-7})$ in a ${\mathrm{SU}}(3)$ gauge theory. We also implement, for the first time, staggered fermions in NSPT. The residual chiral symmetry of staggered fermions protects the theory from an additive mass renormalisation. We compute the perturbative expansion of the plaquette with two flavours of massless staggered fermions up to order $O(\beta^{-35})$ in a ${\mathrm{SU}}(3)$ gauge theory, and investigate the renormalon behaviour of such series. We are able to subtract the power divergence in the Operator Product Expansion (OPE) for the plaquette and estimate the gluon condensate in massless QCD. Our results confirm that NSPT provides a viable way to probe systematically the asymptotic behaviour of perturbative series in QCD and, eventually, gauge theories with fermions in higher representations.Comment: 49 pages, 28 figures. Revised version, to be published in EPJC. Some references added, typos corrected, and improved discussion on finite-volume effect

Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone

The 2013-2015 Ebola virus disease (EVD) epidemic is caused by the Makona variant of Ebola virus (EBOV). Early in the epidemic, genome sequencing provided insights into virus evolution and transmission and offered important information for outbreak response. Here, we analyze sequences from 232 patients sampled over 7 months in Sierra Leone, along with 86 previously released genomes from earlier in the epidemic. We confirm sustained human-to-human transmission within Sierra Leone and find no evidence for import or export of EBOV across national borders after its initial introduction. Using high-depth replicate sequencing, we observe both host-to-host transmission and recurrent emergence of intrahost genetic variants. We trace the increasing impact of purifying selection in suppressing the accumulation of nonsynonymous mutations over time. Finally, we note changes in the mucin-like domain of EBOV glycoprotein that merit further investigation. These findings clarify the movement of EBOV within the region and describe viral evolution during prolonged human-to-human transmission