Characterization of Frost-Damaged Immature Soybeans for Alfalfa and Alfalfa-Brome Hay, Corn Silage or Corn Based Diets

One compositional study and three single stage in vitro rumen fermentation experiments were conducted to characterize the feeding profile of frost-damaged immature soybeans (FDIS). Dauson and Dassel soybean plants were harvested at 86, 93, 100, 107 days post-planting and frozen at -5 C to contrast with natural frozen soybeans of the same varieties that were serially planted and harvested after the first killing frost. No differences between soybean variety were detected for crude protein (CP), ether extract (EE) or dry matter content (DM). Crude protein and EE content differed (P\u3c.05) between maturities of artificially frozen (AF) soybeans. Only the EE content differed (P\u3c.01) with maturity of naturally frozen (NF) soybeans. Planting date had an effect (P\u3c.001) on composition of mature soybeans primarily due to increasing EE component. Exp. 1. Five levels of FDIS (0, 5,10, 15, 20%). three substrates (alfalfa hay, ALF), corn silage (CS), ground corn (WSC)) and two fermentation times (24 or 48 hours) were evaluated in single stage in vitro fermentations. FDIS supplementation had no effect on in vitro dry matter disappearance (IVDMD) of ALF or USC, indicating at the upper limit of FDIS supplementation had not been reached. IVDMD of corn silage was depressed (P\u3c.01) when FDIS exceeded 10%. Increasing levels of FDIS increased NH –N (P\u3c.01) but had no effect on VFA concentration in fermentation liquor. Exp. 2. Alfalfa-brome hay, ALF and CS were supplemented with FDlS for 48-hour IVDMD comparisons. IVDMD was not affected by substrate, but FDIS increased IVDMD of CS (P\u3c.001). Exp.3. Four treatments, soybean meal (SBM), heated mature raw soybeans (HMB), heated FDIS (HFDIS) and FDIS, were used to differentiate oil content and trypsin inhibitor effects on roughage fermentation. Only SBM increased IVDMD (P\u3c.05) of forages tested. FDIS included at 20% of the DM did not significantly decrease IVDMD of forages in most instances but may not stimulate digestion in the same manner as SBM

Long working distance objective lenses for single atom trapping and imaging

We present a pair of optimized objective lenses with long working distances of 117 mm and 65 mm respectively that offer diffraction limited performance for both Cs and Rb wavelengths when imaging through standard vacuum windows. The designs utilise standard catalog lens elements to provide a simple and cost-effective solution. Objective 1 provides NA = 0.175 offering 3 μm resolution whilst objective 2 is optimized for high collection efficiency with NA = 0.29 and 1.8 μm resolution. This flexible design can be further extended for use at shorter wavelengths by simply re-optimising the lens separations

Almost-Tight Distributed Minimum Cut Algorithms

We study the problem of computing the minimum cut in a weighted distributed message-passing networks (the CONGEST model). Let $\lambda$ be the minimum cut, $n$ be the number of nodes in the network, and $D$ be the network diameter. Our algorithm can compute $\lambda$ exactly in $O((\sqrt{n} \log^{*} n+D)\lambda^4 \log^2 n)$ time. To the best of our knowledge, this is the first paper that explicitly studies computing the exact minimum cut in the distributed setting. Previously, non-trivial sublinear time algorithms for this problem are known only for unweighted graphs when $\lambda\leq 3$ due to Pritchard and Thurimella's $O(D)$-time and $O(D+n^{1/2}\log^* n)$-time algorithms for computing $2$-edge-connected and $3$-edge-connected components. By using the edge sampling technique of Karger's, we can convert this algorithm into a $(1+\epsilon)$-approximation $O((\sqrt{n}\log^{*} n+D)\epsilon^{-5}\log^3 n)$-time algorithm for any $\epsilon>0$. This improves over the previous $(2+\epsilon)$-approximation $O((\sqrt{n}\log^{*} n+D)\epsilon^{-5}\log^2 n\log\log n)$-time algorithm and $O(\epsilon^{-1})$-approximation $O(D+n^{\frac{1}{2}+\epsilon} \mathrm{poly}\log n)$-time algorithm of Ghaffari and Kuhn. Due to the lower bound of $\Omega(D+n^{1/2}/\log n)$ by Das Sarma et al. which holds for any approximation algorithm, this running time is tight up to a $\mathrm{poly}\log n$ factor. To get the stated running time, we developed an approximation algorithm which combines the ideas of Thorup's algorithm and Matula's contraction algorithm. It saves an $\epsilon^{-9}\log^{7} n$ factor as compared to applying Thorup's tree packing theorem directly. Then, we combine Kutten and Peleg's tree partitioning algorithm and Karger's dynamic programming to achieve an efficient distributed algorithm that finds the minimum cut when we are given a spanning tree that crosses the minimum cut exactly once

Frost Damaged, Immature Soybeans for Ruminant Diets

The potential for including freeze damaged, immature soybeans (FDIS) into corn based diets for ruminant animals was evaluated in a series of experiments. No differences in feeding value were evident for FDlS and normal soybeans except due to oil content. Oil content of soybeans depressed dry matter and particularly fiber digestion of corn silage fed to lambs (Pe.05). Nitrogen digestion and retention were also reduced (Pe.10) by feeding raw soybeans. The effect on N utilization appeared to be due to trypsin inhibitor activity, since this did not occur when soybean meal + oil supplements were fed. Nitrogen, dry matter and gross energy utilization decreased dramatically (Pe.05) when FDlS increased from 14 to 21% of corn silage diets. Use of FDlS in corn silage diets should be restricted to no more than 15% of diet dry matter

Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of "effector" proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen's predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology. This collection includes novel tools, and widely-used third-party tools such as NCBI BLASTC wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browserbased form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting.Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols. The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu)

Phenazine cations as anticancer theranostics

The biological properties of two water-soluble organic cations based on polypyridyl structures commonly used as ligands for photoactive transition metal complexes designed to interact with biomolecules are investigated. A cytotoxicity screen employing a small panel of cell lines reveals that both cations show cytotoxicity toward cancer cells but show reduced cytotoxicity to noncancerous HEK293 cells with the more extended system being notably more active. Although it is not a singlet oxygen sensitizer, the more active cation also displayed enhanced potency on irradiation with visible light, making it active at nanomolar concentrations. Using the intrinsic luminescence of the cations, their cellular uptake was investigated in more detail, revealing that the active compound is more readily internalized than its less lipophilic analogue. Colocalization studies with established cell probes reveal that the active cation predominantly localizes within lysosomes and that irradiation leads to the disruption of mitochondrial structure and function. Stimulated emission depletion (STED) nanoscopy and transmission electron microscopy (TEM) imaging reveal that treatment results in distinct lysosomal swelling and extensive cellular vacuolization. Further imaging-based studies confirm that treatment with the active cation induces lysosomal membrane permeabilization, which triggers lysosome-dependent cell-death due to both necrosis and caspase-dependent apoptosis. A preliminary toxicity screen in the Galleria melonella animal model was carried out on both cations and revealed no detectable toxicity up to concentrations of 80 mg/kg. Taken together, these studies indicate that this class of synthetically easy-to-access photoactive compounds offers potential as novel therapeutic leads

BB flavour tagging using charm decays at the LHCb experiment

An algorithm is described for tagging the flavour content at production of neutral $B$ mesons in the LHCb experiment. The algorithm exploits the correlation of the flavour of a $B$ meson with the charge of a reconstructed secondary charm hadron from the decay of the other $b$ hadron produced in the proton-proton collision. Charm hadron candidates are identified in a number of fully or partially reconstructed Cabibbo-favoured decay modes. The algorithm is calibrated on the self-tagged decay modes $B^+ \to J/\psi \, K^+$ and $B^0 \to J/\psi \, K^{*0}$ using $3.0\mathrm{\,fb}^{-1}$ of data collected by the LHCb experiment at $pp$ centre-of-mass energies of $7\mathrm{\,TeV}$ and $8\mathrm{\,TeV}$. Its tagging power on these samples of $B \to J/\psi \, X$ decays is $(0.30 \pm 0.01 \pm 0.01) \%$.Comment: All figures and tables, along with any supplementary material and additional information, are available at http://lhcbproject.web.cern.ch/lhcbproject/Publications/LHCbProjectPublic/LHCb-PAPER-2015-027.htm

Measurements of long-range near-side angular correlations in sNN=5\sqrt{s_{\text{NN}}}=5TeV proton-lead collisions in the forward region

Two-particle angular correlations are studied in proton-lead collisions at a nucleon-nucleon centre-of-mass energy of $\sqrt{s_{\text{NN}}}=5$TeV, collected with the LHCb detector at the LHC. The analysis is based on data recorded in two beam configurations, in which either the direction of the proton or that of the lead ion is analysed. The correlations are measured in the laboratory system as a function of relative pseudorapidity, $\Delta\eta$, and relative azimuthal angle, $\Delta\phi$, for events in different classes of event activity and for different bins of particle transverse momentum. In high-activity events a long-range correlation on the near side, $\Delta\phi \approx 0$, is observed in the pseudorapidity range $2.0<\eta<4.9$. This measurement of long-range correlations on the near side in proton-lead collisions extends previous observations into the forward region up to $\eta=4.9$. The correlation increases with growing event activity and is found to be more pronounced in the direction of the lead beam. However, the correlation in the direction of the lead and proton beams are found to be compatible when comparing events with similar absolute activity in the direction analysed.Comment: All figures and tables, along with any supplementary material and additional information, are available at https://lhcbproject.web.cern.ch/lhcbproject/Publications/LHCbProjectPublic/LHCb-PAPER-2015-040.htm

Study of the production of Λb0\Lambda_b^0 and B‾0\overline{B}^0 hadrons in pppp collisions and first measurement of the Λb0→J/ψpK−\Lambda_b^0\rightarrow J/\psi pK^- branching fraction

The product of the $\Lambda_b^0$ ($\overline{B}^0$) differential production cross-section and the branching fraction of the decay $\Lambda_b^0\rightarrow J/\psi pK^-$ ($\overline{B}^0\rightarrow J/\psi\overline{K}^*(892)^0$) is measured as a function of the beauty hadron transverse momentum, $p_{\rm T}$, and rapidity, $y$. The kinematic region of the measurements is $p_{\rm T}<20~{\rm GeV}/c$ and $2.0<y<4.5$. The measurements use a data sample corresponding to an integrated luminosity of $3~{\rm fb}^{-1}$ collected by the LHCb detector in $pp$ collisions at centre-of-mass energies $\sqrt{s}=7~{\rm TeV}$ in 2011 and $\sqrt{s}=8~{\rm TeV}$ in 2012. Based on previous LHCb results of the fragmentation fraction ratio, $f_{\Lambda_B^0}/f_d$, the branching fraction of the decay $\Lambda_b^0\rightarrow J/\psi pK^-$ is measured to be \begin{equation*} \mathcal{B}(\Lambda_b^0\rightarrow J/\psi pK^-)= (3.17\pm0.04\pm0.07\pm0.34^{+0.45}_{-0.28})\times10^{-4}, \end{equation*} where the first uncertainty is statistical, the second is systematic, the third is due to the uncertainty on the branching fraction of the decay $\overline{B}^0\rightarrow J/\psi\overline{K}^*(892)^0$, and the fourth is due to the knowledge of $f_{\Lambda_b^0}/f_d$. The sum of the asymmetries in the production and decay between $\Lambda_b^0$ and $\overline{\Lambda}_b^0$ is also measured as a function of $p_{\rm T}$ and $y$. The previously published branching fraction of $\Lambda_b^0\rightarrow J/\psi p\pi^-$, relative to that of $\Lambda_b^0\rightarrow J/\psi pK^-$, is updated. The branching fractions of $\Lambda_b^0\rightarrow P_c^+(\rightarrow J/\psi p)K^-$ are determined.Comment: 29 pages, 19figures. All figures and tables, along with any supplementary material and additional information, are available at https://lhcbproject.web.cern.ch/lhcbproject/Publications/LHCbProjectPublic/LHCb-PAPER-2015-032.htm