A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata)

Background: Genetic linkage maps are essential tools when searching for quantitative trait loci (QTL). To maximize genome coverage and provide an evenly spaced marker distribution a combination of different types of genetic marker are sometimes used. In this study we created linkage maps of four zebra finch (Taeniopygia guttata) chromosomes (1, 1A, 2 and 9) using two types of marker, Single Nucleotide Polymorphisms (SNPs) and microsatellites. To assess the effectiveness and accuracy of each kind of marker we compared maps built with each marker type separately and with both types of marker combined. Linkage map marker order was validated by making comparisons to the assembled zebra finch genome sequence. Results: We showed that marker order was less reliable and linkage map lengths were inflated for microsatellite maps relative to SNP maps, apparently due to differing error rates between the two types of marker. Guidelines on how to minimise the effects of error are provided. In particular, we show that when combining both types of marker the conventional process of building linkage maps, whereby the most informative markers are added to the map first, has to be modified in order to improve map accuracy. Conclusions: When using multiple types and large numbers of markers to create dense linkage maps, the least error prone loci (SNPs) rather than the most informative should be used to create framework maps before the addition of other potentially more error prone markers (microsatellites). This raises questions about the accuracy of marker order and predicted recombination rates in previous microsatellite linkage maps which were created using the conventional building process, however, provided suitable error detection strategies are followed microsatellite-based maps can continue to be regarded as reasonably reliable

Development and application of 3D X-ray diffraction for the study of phase transformations in metallic materials

Many steel alloy types, both currently in use and under development, exploit a deformation-induced phase transformation to achieve a combined high strength and ductility. As deformation is applied to these alloys, a metastable retained austenite phase transforms to martensite. This process acts as a significant carrier of plasticity, increasing the work-hardening rate and therefore the ductility. The "stability", or resistance against martensitic transformation, of the austenite phase is the main parameter that governs the martensitic transformation rate and therefore the work-hardening behaviour of the steel. In the last few decades, the stability of an individual austenite grain has been shown to depend on a number of microstructural properties, such as the size of the grain, its orientation relative to the loading axis, the alloy chemistry, and the configuration of the grain's immediate crystallographic neighbourhood. A good understanding of how exactly these properties modify austenite grain stability is crucial to the development of accurate models of deformation-induced phenomena, which themselves directly contribute to the design of new and improved alloys that better exploit said phenomena. In the past, austenite grain stability has usually been evaluated for a steel sample either through phase-averaged behaviour, where the stability of the phase overall is characterised, or on an individual grain level, where typically only a few grains are considered. This is primarily due to the difficulties involved with measuring the martensitic transformation in situ at a per-grain level for a large number of grains simultaneously. The recent development of far-field Three-Dimensional X-Ray Diffraction (3DXRD) has enabled such measurements on a range of polycrystalline materials, capturing the grain-level position, orientation and strain tensor for many thousands of grains in situ. However, the 3DXRD technique poses a number of significant challenges related to data analysis and post-processing, both crucial steps that must be carefully implemented to enable detailed measurements of complicated polycrystal samples. In this study, 3DXRD was implemented at the I12 Joint Engineering, Environmental, and Processing (JEEP) Beamline at the Diamond Light Source X-ray synchrotron. Then, the capabilities of the technique were explored by examining how a microstructurally "simple" single phase ferritic steel responds to in-situ tensile deformation on a per-grain level. A number of micromechanical phenomena were investigated, including a small (but statistically significant) grain neighbourhood effect, where the stress state of a central grain was found to depend on the orientation of its immediate neighbourhood grains, a finding never before seen for large numbers of grains in a cubic polycrystal. During this 3DXRD implementation, a sophisticated automated data analysis and post-processing pipeline was developed, that enabled rapid exploration of such micromechanical effects. With 3DXRD implemented and a data analysis pipeline developed, a novel metastable stainless steel alloy system was devised that enabled the exploration of the martensitic transformation at very low applied strains, as 3DXRD is typically limited to ~2% maximum strain. This alloy system was extensively characterised non-destructively in three dimensions with laboratory electron-based and X-ray based techniques, and was used to evaluate both the performance of multi-phase laboratory-based Diffraction Contrast Tomography (DCT), as well as a novel registration algorithm that accurately located two-dimensional planes measured with Electron Back-Scatter Diffraction (EBSD) within the three-dimensional DCT dataset. Finally, the deformation response of the alloy was measured in-situ with 3DXRD at the ID11 beamline of the European Synchrotron Radiation Facility, coupled with in-situ EBSD scans using an in-chamber tensile stage. Substantial martensite transformations were found even within the ~2% maximum strain window, proving the alloy design was successful and enabling extensive in-situ analyses of austenite grain stability in the bulk material with 3DXRD. Austenite grain stability was found to be influenced by grain size, orientation, and local neighbourhood. Larger grains, grains oriented with {100} close to the loading axis, and grains with more ferrite/martensite-dense neighbourhoods were found to have reduced stability against deformation. The minimum strain work criterion model was also evaluated against the experimental data — it was found to correctly predict the orientation of martensite that formed in the majority of grains, given the parent orientation and macroscopic applied load. Grains where the model failed tended to have reduced levels of stress just before forming martensite, which was attributed to the use of the global stress state by the model as opposed to more granular measurements of the immediate stress field around a grain

Diesel engine fuel injection monitoring using acoustic measurements and independent component analysis

Air-borne acoustic based condition monitoring is a promising technique because of its intrusive nature and the rich information contained within the acoustic signals including all sources. However, the back ground noise contamination, interferences and the number of Internal Combustion Engine ICE vibro-acoustic sources preclude the extraction of condition information using this technique. Therefore, lower energy events; such as fuel injection, are buried within higher energy events and/or corrupted by background noise. This work firstly investigates diesel engine air-borne acoustic signals characteristics and the benefits of joint time-frequency domain analysis. Secondly, the air-borne acoustic signals in the vicinity of injector head were recorded using three microphones around the fuel injector (120° apart from each other) and an Independent Component Analysis (ICA) based scheme was developed to decompose these acoustic signals. The fuel injection process characteristics were thus revealed in the time-frequency domain using Wigner-Ville distribution (WVD) technique. Consequently the energy levels around the injection process period between 11 and 5 degrees before the top dead center and of frequency band 9 to 15 kHz are calculated. The developed technique was validated by simulated signals and empirical measurements at different injection pressure levels from 250 to 210 bars in steps of 10 bars. The recovered energy levels in the tested conditions were found to be affected by the injector pressure settings

BFKL predictions at small x from k_T and collinear factorization viewpoints

Hard scattering processes involving hadrons at small $x$ are described by a $k_T$-factorization formula driven by a BFKL gluon. We explore the equivalence of this description to a collinear-factorization approach in which the anomalous dimensions $\gamma_{gg}$ and $\gamma_{qg}/\alpha_S$ are expressed as power series in $\alpha_S \log (1/x)$, or to be precise $\alpha_S/\omega$ where $\omega$ is the moment index. In particular we confront the collinear-factorization expansion with that extracted from the BFKL approach with running coupling included.Comment: 11 LaTeX pages, 1 figure (uuencoded

Total variation approximation for quasi-equilibrium distributions

Quasi-stationary distributions, as discussed by Darroch & Seneta (1965), have been used in biology to describe the steady state behaviour of population models which, while eventually certain to become extinct, nevertheless maintain an apparent stochastic equilibrium for long periods. These distributions have some drawbacks: they need not exist, nor be unique, and their calculation can present problems. In this paper, we give biologically plausible conditions under which the quasi-stationary distribution is unique, and can be closely approximated by distributions that are simple to compute.Comment: 16 page

The small x gluon and b\bar{b} production at the LHC

We study open b\bar{b} production at large rapidity at the LHC in an attempt to pin down the gluon distribution at very low x. For the LHC energy of 7 TeV, at next-to-leading order (NLO), there is a large factorization scale uncertainty. We show that the uncertainty can be greatly reduced if events are selected in which the transverse momenta of the two B-mesons balance each other to some accuracy, that is |\vec p_{1T}+\vec p_{2T}| < k_0. This will fix the scale \mu_F \simeq k_0, and will allow the LHCb experiment, in particular, to study the x-behaviour of gluon distribution down to x ~ 10^{-5}, at rather low scales, \mu ~ 2 GeV. We evaluate the expected cross sections using, for illustrative purposes, various recent sets of Parton Distribution Functions.Comment: 13 pages, 5 figure

Pinning down the Glue in the Proton

The latest measurements of $F_2$ at HERA allow for a {\it combination} of gluon and sea quark distributions at small $x$ that is significantly different from those of existing parton sets. We perform a new global fit to deep-inelastic and related data. We find a gluon distribution which is larger for x \lapproxeq 0.01, and smaller for $x \sim 0.1$, and a flatter input sea quark distribution than those obtained in our most recent global analysis. The new fit also gives $\alpha_s(M_Z^2) = 0.114$. We study other experimental information available for the gluon including, in particular, the constraints coming from fixed-target and collider prompt $\gamma$ production data.Comment: 8 pages, LATEX, 6 figs available as .uu fil

Levels of extra-pair paternity are associated with parental care in penduline tits (Remizidae)

In most passerine birds, individuals attempt to maximise their fitness by providing parental care while also mating outside their pair bond. A sex-specific trade-off between these two behaviours is predicted to occur since the fitness benefits of extra-pair mating differs between the sexes. We use nest observations and parentage analysis to reveal a negative association between male care and the incidence of extra-pair paternity across three species of penduline tit (Remizidae)

Pion Content of the Nucleon as seen in the NA51 Drell-Yan experiment

In a recent CERN Drell-Yan experiment the NA51 group found a strong asymmetry of $\bar u$ and $\bar d$ densities in the proton at $x\simeq0.18$. We interpret this result as a decisive confirmation of the pion-induced sea in the nucleon.Comment: 10 pages + 3 figures, Preprint KFA-IKP(TH)-1994-14 .tex file. After \enddocument a uu-encodeded Postscript file comprising the figures is appende

Antibiotic treatment targeting gram negative bacteria prevents neratinib-induced diarrhea in rats

Background: Neratinib is a pan-ErbB tyrosine kinase inhibitor used for extended adjuvant treatment of HER2-positive breast cancer. Diarrhea is the main adverse event associated with neratinib treatment. We aimed here to determine whether antibiotic-induced gut microbial shifts altered development of neratinib-induced diarrhea. Methods: Female Albino Wistar rats (total n = 44) were given antibiotics (vancomycin, neomycin, or a cocktail of vancomycin, neomycin and ampicillin) in drinking water for four weeks, and then treated daily with neratinib (50 mg/kg) for 28 days. Diarrhea, along with markers of gastrointestinal damage and microbial alterations were measured by histopathology and 16S sequencing, respectively. Results: Rats treated with vancomycin or neomycin had significantly lower levels of diarrhea than rats treated with neratinib alone. In the distal ileum, neratinib was associated with a statistically significant increase in histological damage in all treatment groups expect the antibiotic cocktail. Key features included villous blunting and fusion and some inflammatory infiltrate. Differences in microbial composition at necropsy in vehicle control, neratinib and neratinib + neomycin groups, were characterized by a neratinib-induced increase in gram-negative bacteria that was reversed by neomycin. Neomycin shifted bacterial composition so that Blautia become the dominant genus. Conclusions: Narrow spectrum antibiotics reduced neratinib-induced diarrhea. This suggests that the microbiome may play a key role in the development and prolongation of diarrhea following neratinib treatment, although further research is required to understand the key bacteria and mechanisms by which they reduce diarrhea, as well as how this may impact presentation of diarrhea in clinical cohorts.Kate R. Secombe, Imogen A. Ball, Anthony D. Wignall, Emma Bateman, Dorothy M. Keefe, Joanne M. Bowe