The effect of dairy cow breed on milk production, cow traffic and milking characteristics in a pasture-based automatic milking system

peer-reviewedDespite the increasing frequency of integrated automatic milking (AM) and pasture-based systems, there is limited knowledge available on the suitability of different dairy cow breeds to these systems. Thus, the objective of this experiment was to establish the performance of three breeds in a pasture-based AM system with respect to milk production, cow traffic and milking characteristics. The breeds examined were Holstein Friesian (HF), Jersey x HF (JEX) and Norwegian Red x HF (NRX), all of which have been previously identified as being compatible with conventional milking pasture-based systems. The experiment was conducted in mid-lactation and variables measured included milking frequency, -interval, -outcome and -characteristics, milk yield/milking and per day, wait time/visit and per day, return time/visit and the daily distribution of milking events. Data were statistically analysed using least squares means mixed procedure models, while the proportion of different milking events were analysed using the logistics procedure. While there were no significant differences between breeds for milking frequency, or milk production, significant differences did exist for proportion of successful and failed milkings events, with NRX cows recording the highest and lowest proportions, respectively. JEX also recorded a significantly shorter dead time/quarter at 17.6 s/milking compared to the HF and NRX breeds at 28.5 and 27.7 s/milking, respectively. Significant differences also existed with regard to cow traffic, with the NRX breed returning from pasture more quickly and waiting a shorter time both per visit and per day in the pre-milking yard. The distribution of milking events differed between the breeds examined, with the JEX cows recording less milkings in the hour after the pre-selection gate changes of 0000 h and 1600 h. JEX also recorded a significantly greater proportion of milkings than the NRX and HF cows during the hours at which the lowest proportion of total milking events were recorded (0400–0600 h). For the optimisation of the AM system it is important to have an even distribution of milkings throughout the day. Based on the evidence from the current experiment, this may be best achieved by a mixed breed herd rather than a single breed herd. However, the performance of the examined breeds should also be analysed in the context of the whole AM farm system, over an entire lactation, taking into consideration the range of variables that contribute to a profitable farm system

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis

peer-reviewedRapid advancements in sequencing technologies along with falling costs present widespread opportunities for microbiome studies across a vast and diverse array of environments. These impressive technological developments have been accompanied by a considerable growth in the number ofmethodological variables, including sampling, storage, DNA extraction, primer pairs, sequencing technology, chemistry version, read length, insert size, and analysis pipelines, amongst others. This increase in variability threatens to compromise both the reproducibility and the comparability of studies conducted. Here we perform the first reported study comparing both amplicon and shotgun sequencing for the three leading next-generation sequencing technologies. These were applied to six human stool samples using Illumina HiSeq, MiSeq and Ion PGM shotgun sequencing, as well as amplicon sequencing across two variable 16S rRNA gene regions. Notably, we found that the factor responsible for the greatest variance inmicrobiota composition was the chosen methodology rather than the natural inter-individual variance, which is commonly one of the most significant drivers in microbiome studies. Amplicon sequencing suffered from this to a large extent, and this issue was particularly apparent when the 16S rRNA V1-V2 region amplicons were sequenced withMiSeq. Somewhat surprisingly, the choice of taxonomic binning software for shotgun sequences proved to be of crucial importance with even greater discriminatory power than sequencing technology and choice of amplicon. Optimal N50 assembly values for the HiSeq was obtained for 10million reads per sample, whereas the applied MiSeq and PGM sequencing depths proved less sufficient for shotgun sequencing of stool samples. The latter technologies, on the other hand, provide a better basis for functional gene categorisation, possibly due to their longer read lengths. Hence, in addition to highlighting methodological biases, this study demonstrates the risks associated with comparing data generated using different strategies. We also recommend that laboratories with particular interests in certain microbes should optimise their protocols to accurately detect these taxa using different techniques.This publication has emanated from research supported in part by a research grant from Science Foundation Ireland (SFI) under Grant Number SFI/12/RC/2273 and 11/PI/1137 and by FP7 funded CFMATTERS (Cystic Fibrosis Microbiome-determined Antibiotic Therapy Trial in Exacerbations: Results Stratified, Grant Agreement no. 603038)

A quantum-mechanical Maxwell's demon

A Maxwell's demon is a device that gets information and trades it in for thermodynamic advantage, in apparent (but not actual) contradiction to the second law of thermodynamics. Quantum-mechanical versions of Maxwell's demon exhibit features that classical versions do not: in particular, a device that gets information about a quantum system disturbs it in the process. In addition, the information produced by quantum measurement acts as an additional source of thermodynamic inefficiency. This paper investigates the properties of quantum-mechanical Maxwell's demons, and proposes experimentally realizable models of such devices.Comment: 13 pages, Te

Measurement of conditional phase shifts for quantum logic

Measurements of the birefringence of a single atom strongly coupled to a high-finesse optical resonator are reported, with nonlinear phase shifts observed for intracavity photon number much less than one. A proposal to utilize the measured conditional phase shifts for implementing quantum logic via a quantum-phase gate (QPG) is considered. Within the context of a simple model for the field transformation, the parameters of the "truth table" for the QPG are determined.Comment: 4 pages in Postscript format, including 4 figures (attached as uuencoded version of a gzip-file

Neighborhoods of trees in circular orderings

In phylogenetics, a common strategy used to construct an evolutionary tree for a set of species X is to search in the space of all such trees for one that optimizes some given score function (such as the minimum evolution, parsimony or likelihood score). As this can be computationally intensive, it was recently proposed to restrict such searches to the set of all those trees that are compatible with some circular ordering of the set X. To inform the design of efficient algorithms to perform such searches, it is therefore of interest to find bounds for the number of trees compatible with a fixed ordering in the neighborhood of a tree that is determined by certain tree operations commonly used to search for trees: the nearest neighbor interchange (nni), the subtree prune and regraft (spr) and the tree bisection and reconnection (tbr) operations. We show that the size of such a neighborhood of a binary tree associated with the nni operation is independent of the tree’s topology, but that this is not the case for the spr and tbr operations. We also give tight upper and lower bounds for the size of the neighborhood of a binary tree for the spr and tbr operations and characterize those trees for which these bounds are attained

KP line solitons and Tamari lattices

The KP-II equation possesses a class of line soliton solutions which can be qualitatively described via a tropical approximation as a chain of rooted binary trees, except at "critical" events where a transition to a different rooted binary tree takes place. We prove that these correspond to maximal chains in Tamari lattices (which are poset structures on associahedra). We further derive results that allow to compute details of the evolution, including the critical events. Moreover, we present some insights into the structure of the more general line soliton solutions. All this yields a characterization of possible evolutions of line soliton patterns on a shallow fluid surface (provided that the KP-II approximation applies).Comment: 49 pages, 36 figures, second version: section 4 expande

Approximate Quantum Fourier Transform and Decoherence

We discuss the advantages of using the approximate quantum Fourier transform (AQFT) in algorithms which involve periodicity estimations. We analyse quantum networks performing AQFT in the presence of decoherence and show that extensive approximations can be made before the accuracy of AQFT (as compared with regular quantum Fourier transform) is compromised. We show that for some computations an approximation may imply a better performance.Comment: 14 pages, 10 fig. (8 *.eps files). More information on http://eve.physics.ox.ac.uk/QChome.html http://www.physics.helsinki.fi/~kasuomin http://www.physics.helsinki.fi/~kira/group.htm

A geometric theory of non-local two-qubit operations

We study non-local two-qubit operations from a geometric perspective. By applying a Cartan decomposition to su(4), we find that the geometric structure of non-local gates is a 3-Torus. We derive the invariants for local transformations, and connect these local invariants to the coordinates of the 3-Torus. Since different points on the 3-Torus may correspond to the same local equivalence class, we use the Weyl group theory to reduce the symmetry. We show that the local equivalence classes of two-qubit gates are in one-to-one correspondence with the points in a tetrahedron except on the base. We then study the properties of perfect entanglers, that is, the two-qubit operations that can generate maximally entangled states from some initially separable states. We provide criteria to determine whether a given two-qubit gate is a perfect entangler and establish a geometric description of perfect entanglers by making use of the tetrahedral representation of non-local gates. We find that exactly half the non-local gates are perfect entanglers. We also investigate the non-local operations generated by a given Hamiltonian. We first study the gates that can be directly generated by a Hamiltonian. Then we explicitly construct a quantum circuit that contains at most three non-local gates generated by a two-body interaction Hamiltonian, together with at most four local gates generated by single qubit terms. We prove that such a quantum circuit can simulate any arbitrary two-qubit gate exactly, and hence it provides an efficient implementation of universal quantum computation and simulation.Comment: 22 pages, 6 figure

Polarization state of a biphoton: quantum ternary logic

Polarization state of biphoton light generated via collinear frequency-degenerate spontaneous parametric down-conversion is considered. A biphoton is described by a three-component polarization vector, its arbitrary transformations relating to the SU(3) group. A subset of such transformations, available with retardation plates, is realized experimentally. In particular, two independent orthogonally polarized beams of type-I biphotons are transformed into a beam of type-II biphotons. Polarized biphotons are suggested as ternary analogs of two-state quantum systems (qubits)