A Comparison of Alfalfa, Sweet Clover, and Sudan Grass as Pasture Crops for Dairy Cows

Dairying is recognized as one of the major farm enterprises in the Northwest. Over much of this area conditions for producing winter feeds are very favorable but moisture conditions are such that it is difficult to maintain satisfactory pastures for dairy cows during the summer months. Native pastures, where available, will carry the herd in a satisfactory manner for a short time in the spring but these pastures soon dry up and are unsatisfactory during a large part of the pasture season. These conditions make it necessary for dairymen in this region to rely on cultivated crops for summer pasture. Information concerning the relative productivity, dependability, length of grazing season and other factors having to do with pasture crops is needed. With a view of supplying information on these points the experiment was started in 1927

The generalized Robinson-Foulds metric

The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to the original one; but the two trees are identical if we remove the single taxon. To this end, we propose a natural extension of the RF metric that does not simply count identical clades but instead, also takes similar clades into consideration. In contrast to previous approaches, our model requires the matching between clades to respect the structure of the two trees, a property that the classical RF metric exhibits, too. We show that computing this generalized RF metric is, unfortunately, NP-hard. We then present a simple Integer Linear Program for its computation, and evaluate it by an all-against-all comparison of 100 trees from a benchmark data set. We find that matchings that respect the tree structure differ significantly from those that do not, underlining the importance of this natural condition.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Mechanical ventilation alters airway nucleotides and purinoceptors in lung and extrapulmonary organs

Extracellular nucleotides are stress-responsive ligands that mediate a variety of cellular processes via purinoceptors. We hypothesized that mechanical ventilation (MV) would alter the extracellular adenyl-nucleotide profile and purinoceptor expression in lung and extrapulmonary tissues. Twenty-eight rats were randomized to: (i) unventilated control animals; (ii) tidal volume (V T; 6 ml/kg); (iii) VT (6 ml/kg) and positive end-expiratory pressure (PEEP; 5 cm H2O); (iv) VT (12 ml/kg); or (v) VT (12 ml/kg) and PEEP (5 cm H2O). Bronchoalveolar lavage (BAL) was analyzed for adenyl-nucleotides. Pulmonary, hepatic, and renal tissues were assessed for P2Y4, P 2Y6, P2X7, A3, and A 2b receptor expression by real-time reverse transcriptase-polymerase chain reaction and Fas/Fas ligand mRNA was quantified in the lung. MV produced volume-dependent changes in BAL nucleotides; AMP and adenosine increased, whereas ATP and ADP proportions decreased. Large-volume MV increased A 2b mRNA and decreased P2X7 in the lung; mRNA changes in lung Fas ligand paralleled P2X7. PEEP normalized BAL nucleotide profiles and A2b expression. Injurious MV reduced hepatic and renal P2X7 mRNA; PEEP normalized these levels in both tissues. Large-volume MV also decreased renal A2b mRNA. MV alters the BAL adenyl-nucleotide profile and purinoceptor patterns in lung, liver, and kidney. PEEP normalizes the BAL nucleotide profile and receptor patterns in lung and extrapulmonary tissues

Production and processing studies on calpain-system gene markers for tenderness in Brahman cattle: 2. Objective meat quality

Effects and interactions of calpain-system tenderness gene markers on objective meat quality traits of Brahman (Bos indicus) cattle were quantified within 2 concurrent experiments at different locations. Cattle were selected for study from commercial and research herds at weaning based on their genotype for cal-pastatin (CAST) and calpain 3 (GAPN3) gene markers for beef tenderness. Gene marker status for i-calpain (CAPN1-4751 and CAPN1-316) was also determined for inclusion in statistical analyses. Eighty-two heifer and 82 castrated male cattle with 0 or 2 favorable alleles for CAST and CAPN3 were studied in New South Wales (NSW), and 143 castrated male cattle with 0, 1, or 2 favorable alleles for CAST and CAPN3 were studied in Western Australia (WA). The cattle were backgrounded for 6 to 8 mo and grain-fed for 117 d (NSW) or 80 d (WA) before slaughter. One-half the cattle in each experiment were implanted with a hormonal growth promotant during feedlotting. One side of each carcass was suspended from the Achilles tendon (AT) and the other from the pelvis (tenderstretch). The M. longissimus lumborum from both sides and the M. semitendinosus from the AT side were collected; then samples of each were aged at 1°C for 1 or 7 d. Favorable alleles for one or more markers reduced shear force, with little effect on other meat quality traits. The size of effects of individual markers varied with site, muscle, method of carcass suspension, and aging period. Individual marker effects were additive as evident in cattle with 4 favorable alleles for CAST and CAPN3 markers, which had shear force reductions of 12.2 N (P 0.05) of interactions between the gene markers, or between the hormonal growth promotant and gene markers for any meat quality traits. This study provides further evidence that selection based on the CAST or CAPN3 gene markers improves meat tenderness in Brahman cattle, with little if any detrimental effects on other meat quality traits. The CAPN1-4751 gene marker also improved beef tenderness without affecting other objective meat quality traits in heterozygous cattle compared with homozygotes for the unfavorable allele

The induction of behavioural sensitization is associated with cocaine-induced structural plasticity in the core (but not shell) of the nucleus accumbens

Repeated exposure to cocaine increases the density of dendritic spines on medium spiny neurons in the nucleus accumbens (Acb) and pyramidal cells in the medial prefrontal cortex (mPFC). To determine if this is associated with the development of psychomotor sensitization, rats were given daily i.p. injections of 15 mg/kg of cocaine (or saline) for 8 days, either in their home cage (which failed to induce significant psychomotor sensitization) or in a distinct and relatively novel test cage (which induced robust psychomotor sensitization). Their brains were obtained 2 weeks after the last injection and processed for Golgi–Cox staining. In the Acb core (AcbC) cocaine treatment increased spine density only in the group that developed psychomotor sensitization (i.e. in the Novel but not Home group), and there was a significant positive correlation between the degree of psychomotor sensitization and spine density. In the Acb shell (AcbS) cocaine increased spine density to the same extent in both groups; i.e. independent of psychomotor sensitization. In the mPFC cocaine increased spine density in both groups, but to a significantly greater extent in the Novel group. Furthermore, when rats were treated at Home with a higher dose of cocaine (30 mg/kg), cocaine now induced psychomotor sensitization in this context, and also increased spine density in the AcbC. Thus, the context in which cocaine is experienced influences its ability to reorganize patterns of synaptic connectivity in the Acb and mPFC, and the induction of psychomotor sensitization is associated with structural plasticity in the AcbC and mPFC, but not the AcbS.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73532/1/j.1460-9568.2004.03612.x.pd

Dissipation and noise in adiabatic quantum pumps

We investigate the distribution function, the heat flow and the noise properties of an adiabatic quantum pump for an arbitrary relation of pump frequency $\omega$ and temperature. To achieve this we start with the scattering matrix approach for ac-transport. This approach leads to expressions for the quantities of interest in terms of the side bands of particles exiting the pump. The side bands correspond to particles which have gained or lost a modulation quantum $\hbar \omega$. We find that our results for the pump current, the heat flow and the noise can all be expressed in terms of a parametric emissivity matrix. In particular we find that the current cross-correlations of a multiterminal pump are directly related a to a non-diagonal element of the parametric emissivity matrix. The approach allows a description of the quantum statistical correlation properties (noise) of an adiabatic quantum pump

A Conformally Invariant Holographic Two-Point Function on the Berger Sphere

We apply our previous work on Green's functions for the four-dimensional quaternionic Taub-NUT manifold to obtain a scalar two-point function on the homogeneously squashed three-sphere (otherwise known as the Berger sphere), which lies at its conformal infinity. Using basic notions from conformal geometry and the theory of boundary value problems, in particular the Dirichlet-to-Robin operator, we establish that our two-point correlation function is conformally invariant and corresponds to a boundary operator of conformal dimension one. It is plausible that the methods we use could have more general applications in an AdS/CFT context.Comment: 1+49 pages, no figures. v2: Several typos correcte

A diversity of diversities: do complex environmental effects underpin associations between below‐ and above‐ground taxa?

•1. To predict how biodiversity will respond to global change, it is crucial to understand the relative roles of abiotic drivers and biotic interactions in driving associations between the biodiversity of disparate taxa. It is particularly challenging to understand diversity–diversity links across domains and habitats, because data are rarely available for multiple above- and below-ground taxa across multiple sites. •2. Here, we analyse data from a unique biodiversity data set gathered across a variety of oceanic temperate terrestrial habitats in Wales, comprising 300 sites with co-located soil microbial, plant, bird and pollinator surveys along with climate and soil physicochemical information. Soil groups are analysed using metabarcoding of the 16S, ITS1 and 18S DNA regions, allowing in-depth characterisation of microbial and soil animal biodiversity. •3. We explore biodiversity relationships along three aspects of community composition: First, we assess correlation between the alpha diversity of different groups. Second, we assess whether biotic turnover between sites is correlated across different groups. Finally, we investigate the co-occurrence of individual taxa across sites. In each analysis, we assess the contribution of linear or nonlinear environmental effects. •4. We find that a positive correlation between alpha diversity of plants, soil bacteria, soil fungi, soil heterotrophic protists, bees and butterflies is in fact driven by complex nonlinear responses to abiotic drivers. In contrast, environmental variation did not account for positive associations between the diversity of plants and both birds and AM fungi, suggesting a role for biotic interactions. •5. Both the diversity and taxon-level associations between the differing soil groups remained even after accounting for nonlinear environmental gradients. Above-ground, spatial factors played larger roles in driving biotic communities, while linear environmental gradients were sufficient to explain many group- and taxon-level relationships. •6. Synthesis. Our results show how nonlinear responses to environmental gradients drive many of the relationships between plant biodiversity and the biodiversity of above- and below-ground biological communities. Our work shows how different aspects of biodiversity might respond nonlinearly to changing environments and identifies cases where management-induced changes in one community could either influence other taxa or lead to loss of apparent biological associations

A Burgessian critique of nominalistic tendencies in contemporary mathematics and its historiography

We analyze the developments in mathematical rigor from the viewpoint of a Burgessian critique of nominalistic reconstructions. We apply such a critique to the reconstruction of infinitesimal analysis accomplished through the efforts of Cantor, Dedekind, and Weierstrass; to the reconstruction of Cauchy's foundational work associated with the work of Boyer and Grabiner; and to Bishop's constructivist reconstruction of classical analysis. We examine the effects of a nominalist disposition on historiography, teaching, and research.Comment: 57 pages; 3 figures. Corrected misprint