Analysis of Canadian and Irish forage, oats and commercially available equine concentrate feed for pathogenic fungi and mycotoxins

Respiratory infections, recurrent airway obstruction (RAO) and exercise induced pulmonary haemorrhage (EIPH) are major causes of poor performance in horses. Fungi and mycotoxins are now recognised as a major cause of these conditions. The most notable fungi are Aspergillus and Fusarium. Fungal spores can originate from forage, bedding and feed and, in turn, these fungal spores can produce a series of mycotoxins as secondary metabolites

Mycotoxin occurrence in commodities, feeds and feed ingredients sourced in the Middle East and Africa

Between February and October 2009, 324 grain, feed and feed commodity samples were sourced directly at animal farms or feed production sites in Middle East and Africa and tested for the presence of A- and B-trichothecenes, zearalenone, fumonisins, aflatoxins and ochratoxin A, or for selected groups of mycotoxins only. Samples were analyzed after clean-up by immunoaffinity or solid-phase extraction followed by HPLC with derivatization where appropriate and fluorescence, UV or mass spectrometric detection. The percentage of positive samples of B-trichothecenes ranged from 0 to 87% of tested samples. The prevalence of fumonisins in the different countries was >50% in most cases. Zearalenone was present in tested commodities from all countries except three. The presence of aflatoxin in analyzed samples varied from 0 to 94%. Ochratoxin A was present in 67% of samples in Sudan and in 100% of Nigerian samples. No A-trichothecenes were found in this survey

A Determination of the Charm Content of the Proton

We present an unbiased determination of the charm content of the proton, in which the charm parton distribution function (PDF) is parametrized on the same footing as the light quarks and the gluon in a global PDF analysis. This determination relies on the calculation of deep-inelastic structure functions in the FONLL scheme, generalized to account for massive charm-initiated contributions. In contrast to the usual situation in which the charm PDF is assumed to be generated perturbatively by pair radiation off gluons and light quarks, vanishing at a scale set by the value of the charm mass m_c, we find that the fitted charm PDF vanishes within uncertainties at a scale Q~1.5 GeV for all x~0.1 and low scales does not vanish, but rather has an "intrinsic" component, very weakly scale dependent and almost independent of the value of m_c, carrying about 1% of the total momentum of the proton. The uncertainties in all other PDFs are only slightly increased by the inclusion of fitted charm, while the dependence of these PDFs on m_c is significantly reduced. When the EMC charm structure function dataset is included, it is well described by the fit, and PDF uncertainties in the fitted charm PDF are significantly reduced, though we verify that excluding the EMC data does not qualitatively modify any of our findings. The increased stability with respect to m_c persists at high scales and is the main implication of our results for LHC phenomenology. Fitting the charm PDF modifies the predictions for processes such as high p_T and large rapidity charm pair production and Z+c production, and thus we expect that future LHC data will further constrain the charm content of the proton

Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock

<p>Abstract</p> <p>Background</p> <p>Molecular docking methods are commonly used for predicting binding modes and energies of ligands to proteins. For accurate complex geometry and binding energy estimation, an appropriate method for calculating partial charges is essential. AutoDockTools software, the interface for preparing input files for one of the most widely used docking programs AutoDock 4, utilizes the Gasteiger partial charge calculation method for both protein and ligand charge calculation. However, it has already been shown that more accurate partial charge calculation - and as a consequence, more accurate docking- can be achieved by using quantum chemical methods. For docking calculations quantum chemical partial charge calculation as a routine was only used for ligands so far. The newly developed Mozyme function of MOPAC2009 allows fast partial charge calculation of proteins by quantum mechanical semi-empirical methods. Thus, in the current study, the effect of semi-empirical quantum-mechanical partial charge calculation on docking accuracy could be investigated.</p> <p>Results</p> <p>The docking accuracy of AutoDock 4 using the original AutoDock scoring function was investigated on a set of 53 protein ligand complexes using Gasteiger and PM6 partial charge calculation methods. This has enabled us to compare the effect of the partial charge calculation method on docking accuracy utilizing AutoDock 4 software. Our results showed that the docking accuracy in regard to complex geometry (docking result defined as accurate when the RMSD of the first rank docking result complex is within 2 Å of the experimentally determined X-ray structure) significantly increased when partial charges of the ligands and proteins were calculated with the semi-empirical PM6 method.</p> <p>Out of the 53 complexes analyzed in the course of our study, the geometry of 42 complexes were accurately calculated using PM6 partial charges, while the use of Gasteiger charges resulted in only 28 accurate geometries. The binding affinity estimation was not influenced by the partial charge calculation method - for more accurate binding affinity prediction development of a new scoring function for AutoDock is needed.</p> <p>Conclusion</p> <p>Our results demonstrate that the accuracy of determination of complex geometry using AutoDock 4 for docking calculation greatly increases with the use of quantum chemical partial charge calculation on both the ligands and proteins.</p

PDF dependence of Higgs cross sections at the Tevatron and LHC: response to recent criticism

We respond to some criticism questioning the validity of the current Standard Model Higgs exclusion limits at the Tevatron, due to the significant dependence of the dominant production cross section from gluon-gluon fusion on the choice of parton distribution functions (PDFs) and the strong coupling (alpha_S). We demonstrate the ability of the Tevatron jet data to discriminate between different high-x gluon distributions, performing a detailed quantitative comparison to show that fits not explicitly including these data fail to give a good description. In this context we emphasise the importance of the consistent treatment of luminosity uncertainties. We comment on the values of alpha_S obtained from fitting deep-inelastic scattering data, particularly the fixed-target NMC data, and we show that jet data are needed for stability. We conclude that the Higgs cross-section uncertainties due to PDFs and alpha_S currently used by the Tevatron and LHC experiments are not significantly underestimated, contrary to some recent claims.Comment: 44 pages, 19 figures. v2: version published in JHEP (paragraph added at bottom of p.15

Parton distributions with small-x resummation:evidence for BFKL dynamics in HERA data

We present a determination of the parton distribution functions of the proton in which NLO and NNLO fixed-order calculations are supplemented by NLLx small-x resummation. Deep inelastic structure functions are computed consistently at NLO+NLLx or NNLO+NLLx, while for hadronic processes small-x resummation is included only in the PDF evolution, with kinematic cuts introduced to ensure the fitted data lie in a region where the fixed-order calculation of the hard cross-sections is reliable. In all other respects, the fits use the same methodology and are based on the same global dataset as the recent NNPDF3.1 analysis. We demonstrate that the inclusion of small-x resummation leads to a quantitative improvement in the perturbative description of the HERA inclusive and charm-production reduced cross-sections in the small x region. The impact of the resummation in our fits is greater at NNLO than at NLO, because fixed-order calculations have a perturbative instability at small x due to large logarithms that can be cured by resummation. We explore the phenomenological implications of PDF sets with small-x resummation for the longitudinal structure function $F_L$ at HERA, for parton luminosities and LHC benchmark cross-sections, for ultra-high energy neutrino-nucleus cross-sections, and for future high-energy lepton-proton colliders such as the LHeC.Comment: 70 pages, many figures. Discussion on uncertainties due to subleading logarithmic contributions. Discussion on fits with pseudodata from future high-energy lepton-proton colliders. Updated references. Version to be published in EPJ

Parton distributions for the LHC run II

We present NNPDF3.0, the first set of parton distribution functions (PDFs) determined with a methodology validated by a closure test. NNPDF3.0 uses a global dataset including HERA-II deep-inelastic inclusive cross-sections, the combined HERA charm data, jet production from ATLAS and CMS, vector boson rapidity and transverse momentum distributions from ATLAS, CMS and LHCb, W+c data from CMS and top quark pair production total cross sections from ATLAS and CMS. Results are based on LO, NLO and NNLO QCD theory and also include electroweak corrections. To validate our methodology, we show that PDFs determined from pseudo-data generated from a known underlying law correctly reproduce the statistical distributions expected on the basis of the assumed experimental uncertainties. This closure test ensures that our methodological uncertainties are negligible in comparison to the generic theoretical and experimental uncertainties of PDF determination. This enables us to determine with confidence PDFs at different perturbative orders and using a variety of experimental datasets ranging from HERA-only up to a global set including the latest LHC results, all using precisely the same validated methodology. We explore some of the phenomenological implications of our results for the upcoming 13 TeV Run of the LHC, in particular for Higgs production cross-sections.Comment: 151 pages, 69 figures. More typos corrected: published versio