Utilization of Pyrosequencing to Monitor the Microbiome Dynamics of Probiotic Treated Poultry (Gallus gallus domesticus) during Downstream Poultry Processing

Antibiotic growth promoters that have been historically employed to control pathogens and increase the rate of animal development for human consumption are currently banned in many countries. Probiotics have been proposed as an alternative to control pathogenic bacteria. Traditional culture methods typically used to monitor probiotic effects on pathogens possess significant limitations such as a lack in sensitivity to detect fastidious and non-culturable bacteria, and are both time consuming and costly. Here, we tested next generation pyrosequencing technology as a streamline and economical method to monitor the effects of a probiotic on microbial communities in juvenile poultry (Gallus gallus domesticus) after exposure to several microbiological challenges and litter conditions. Seven days and repeated again at 39 days following hatching, chicks were challenged with either Salmonella enterica serovar Enteritidis, Campylobacter jejuni, or no bacteria in the presence of, or without a probiotic (i.e., Bacillus subtilis) added to the feed. Three days following each of two challenges (i.e., days 10 and 42, respectively) the microbiome distributions of the poultry caecum were characterized based on 16S rDNA analysis. Generated PCR products were analyzed by automated identification of the samples after pooling, multiplexing and sequencing. A bioinformatics pipeline was then employed to identify microbial distributions at the phylum and genus level for the treatments. In conclusion, our results demonstrated that pyrosequencing technology is a rapid, efficient and cost-effective method to monitor the effects of probiotics on the microbiome of poultry propagated in an agricultural setting

Robustness of multiple objective GP stock-picking in unstable financial markets: Real-world applications track

Multiple Objective Genetic Programming (MOGP) is a promising stock-picking technique for fund managers, because the Pareto front approximates the risk/reward Efficient Frontier and simplifies the choice of investment model for a given client's attitude to risk. Unfortunately GP solutions don't work well if used in an environment that is different from the training environment, and the financial markets are notoriously unstable, often lurching from one market context to another (e.g. "bull" to "bear"). This turns out to be a hard problem -- simple dynamic adaptation methods are insufficient and robust behaviour of solutions becomes extremely important. In this paper we provide the first known empirical results on the robustness of MOGP solutions in an unseen environment consisting of real-world financial data. We focus on two well-known mechanisms to determine which leads to the more robust solutions: Mating Restriction, and Diversity Preservation. We introduce novel metrics for Pareto front robustness, and a novel variation on Mating Restriction, both based on phenotypic cluster analysis

Multiobjective robustness for portfolio optimization in volatile environments

Multiobjective methods are ideal for evolving a set of portfolio optimisation solutions that span a range from high-return/high-risk to low-return/low-risk, and an investor can choose her preferred point on the risk-return frontier. However, there are no guarantees that a low-risk solution will remain low-risk . if the environment changes, the relative positions of previously identified solutions may alter. A low-risk solution may become high-risk and vice versa. The robustness of a Multiobjective Genetic Programming (MOGP) algorithm such as SPEA2 is vitally important in the context of the real-world problem of portfolio optimisation. We explore robustness in this context, providing new definitions and a statistical measure to quantify the robustness of solutions. A new robustness measure is incorporated into a MOGP fitness function to bias evolution towards more robust solutions. This new system ("R-SPEA2") is compared against the original SPEA2 and we present our results

Bulk Band Gaps in Divalent Hexaborides

Complementary angle-resolved photoemission and bulk-sensitive k-resolved resonant inelastic x-ray scattering of divalent hexaborides reveal a >1 eV X-point gap between the valence and conduction bands, in contradiction to the band overlap assumed in several models of their novel ferromagnetism. This semiconducting gap implies that carriers detected in transport measurements arise from defects, and the measured location of the bulk Fermi level at the bottom of the conduction band implicates boron vacancies as the origin of the excess electrons. The measured band structure and X-point gap in CaB_6 additionally provide a stringent test case for proper inclusion of many-body effects in quasi-particle band calculations.Comment: 4 pages, 3 figures; new RIXS analysis; accepted for publication in PR

Morphology of the earliest reconstructable tetrapod Parmastega aelidae.

The known diversity of tetrapods of the Devonian period has increased markedly in recent decades, but their fossil record consists mostly of tantalizing fragments1-15. The framework for interpreting the morphology and palaeobiology of Devonian tetrapods is dominated by the near complete fossils of Ichthyostega and Acanthostega; the less complete, but partly reconstructable, Ventastega and Tulerpeton have supporting roles2,4,16-34. All four of these genera date to the late Famennian age (about 365-359 million years ago)-they are 10 million years younger than the earliest known tetrapod fragments5,10, and nearly 30 million years younger than the oldest known tetrapod footprints35. Here we describe Parmastega aelidae gen. et sp. nov., a tetrapod from Russia dated to the earliest Famennian age (about 372 million years ago), represented by three-dimensional material that enables the reconstruction of the skull and shoulder girdle. The raised orbits, lateral line canals and weakly ossified postcranial skeleton of P. aelidae suggest a largely aquatic, surface-cruising animal. In Bayesian and parsimony-based phylogenetic analyses, the majority of trees place Parmastega as a sister group to all other tetrapods

Nonlinear effects in resonant layers in solar and space plasmas

The present paper reviews recent advances in the theory of nonlinear driven magnetohydrodynamic (MHD) waves in slow and Alfven resonant layers. Simple estimations show that in the vicinity of resonant positions the amplitude of variables can grow over the threshold where linear descriptions are valid. Using the method of matched asymptotic expansions, governing equations of dynamics inside the dissipative layer and jump conditions across the dissipative layers are derived. These relations are essential when studying the efficiency of resonant absorption. Nonlinearity in dissipative layers can generate new effects, such as mean flows, which can have serious implications on the stability and efficiency of the resonance

A platform for brain-wide imaging and reconstruction of individual neurons

The structure of axonal arbors controls how signals from individual neurons are routed within the mammalian brain. However, the arbors of very few long-range projection neurons have been reconstructed in their entirety, as axons with diameters as small as 100 nm arborize in target regions dispersed over many millimeters of tissue. We introduce a platform for high-resolution, three-dimensional fluorescence imaging of complete tissue volumes that enables the visualization and reconstruction of long-range axonal arbors. This platform relies on a high-speed two-photon microscope integrated with a tissue vibratome and a suite of computational tools for large-scale image data. We demonstrate the power of this approach by reconstructing the axonal arbors of multiple neurons in the motor cortex across a single mouse brain.Howard Hughes Medical InstitutePublished versio

Russia-UK collaboration in paleontology: past, present, and future

There is a long history of collaboration between Russia and the United Kingdom in paleontology. This began, arguably, in 1821, with the seminal work by William Fox-Strangways, who produced a geological map of the area around St Petersburg. Most famously, Roderick Murchison carried out extensive surveying and observations throughout European Russia in 1840 and 1841, and published a major monograph on geology and paleontology of European Russia in 1845. Since then, and continuing today, there have been many fruitful collaborations on Precambrian life, Paleozoic marine organisms, terrestrialization of plants and vertebrates, the Permian–Triassic mass extinction, fossil mammals, human evolution, and conservation paleobiology

Phylogenetic and environmental context of a Tournaisian tetrapod fauna

The end-Devonian to mid-Mississippian time interval has long been known for its depauperate palaeontological record, especially for tetrapods. This interval encapsulates the time of increasing terrestriality among tetrapods, but only two Tournaisian localities previously produced tetrapod fossils. Here we describe five new Tournaisian tetrapods ($\textit{Perittodus apsconditus}$, $\textit{Koilops herma}$, $\textit{Ossirarus kierani}$, $\textit{Diploradus austiumensis}$ and $\textit{Aytonerpeton microps}$) from two localities in their environmental context. A phylogenetic analysis retrieved three taxa as stem tetrapods, interspersed among Devonian and Carboniferous forms, and two as stem amphibians, suggesting a deep split among crown tetrapods. We also illustrate new tetrapod specimens from these and additional localities in the Scottish Borders region. The new taxa and specimens suggest that tetrapod diversification was well established by the Tournaisian. Sedimentary evidence indicates that the tetrapod fossils are usually associated with sandy siltstones overlying wetland palaeosols. Tetrapods were probably living on vegetated surfaces that were subsequently flooded. We show that atmospheric oxygen levels were stable across the Devonian/Carboniferous boundary, and did not inhibit the evolution of terrestriality. This wealth of tetrapods from Tournaisian localities highlights the potential for discoveries elsewhere.NERC consortium grants NE/J022713/1 (Cambridge), NE/J020729/1 (Leicester), NE/J021067/1 (BGS), NE/J020621/1 (NMS) and NE/J021091/1 (Southampton