Comparison of Alternative Meat Inspection Regimes for Pigs From Non-Controlled Housing – Considering the Cost of Error

Denmark has not had cases of bovine tuberculosis (bovTB) for more than 30 years but is obliged by trade agreements to undertake traditional meat inspection (TMI) of finisher pigs from non-controlled housing to detect bovTB. TMI is associated with higher probability of detecting bovTB but is also more costly than visual-only inspection (VOI). To identify whether VOI should replace TMI of finisher pigs from non-controlled housing, the cost of error – defined here as probability of overlooking infection and associated economic costs - should be assessed and compared with surveillance costs. First, a scenario tree model was set up to assess the ability of detecting bovTB in an infected herd (HSe) calculated for three within-herd prevalences, WHP (1, 5 and 10%), for four different surveillance scenarios (TMI and VOI with or without serological test, respectively). HSe was calculated for six consecutive 4-week surveillance periods until predicted bovTB detection (considered high-risk periods HRP). 1-HSe was probability of missing all positives by each HRP. Next, probability of spread of infection, Pspread, and number of infected animals moved were calculated for each HRP. Costs caused by overlooking bovTB were calculated taking into account Pspread, 1-HSe, eradication costs, and trade impact. Finally, the average annual costs were calculated by adding surveillance costs and assuming one incursion of bovTB in either 1, 10 or 30 years. Input parameters were based on slaughterhouse statistics, literature and expert opinion. Herd sensitivity increased by high-risk period and within-herd prevalence. Assuming WHP=5%, HSe reached median 90% by 2nd HRP for TMI, whereas for VOI this would happen after 6th HRP. Serology had limited impact on HSe. The higher the probability of infection, the higher the probability of detection and spread. TMI resulted in lowest average annual costs, if one incursion of bovTB was expected every year. However, when assuming one introduction in 10 or 30 years, VOI resulted in lowest average costs. It may be more cost-effective to focus on imported high-risk animals coming into contact with Danish livestock, instead of using TMI as surveillance on all pigs from non-controlled housing

Pump-Enhanced Continuous-Wave Magnetometry using Nitrogen-Vacancy Ensembles

Ensembles of nitrogen-vacancy centers in diamond are a highly promising platform for high-sensitivity magnetometry, whose efficacy is often based on efficiently generating and monitoring magnetic-field dependent infrared fluorescence. Here we report on an increased sensing efficiency with the use of a 532-nm resonant confocal cavity and a microwave resonator antenna for measuring the local magnetic noise density using the intrinsic nitrogen-vacancy concentration of a chemical-vapor deposited single-crystal diamond. We measure a near-shot-noise-limited magnetic noise floor of 200 pT/$\sqrt{\text{Hz}}$ spanning a bandwidth up to 159 Hz, and an extracted sensitivity of approximately 3 nT/$\sqrt{\text{Hz}}$, with further enhancement limited by the noise floor of the lock-in amplifier and the laser damage threshold of the optical components. Exploration of the microwave and optical pump-rate parameter space demonstrates a linewidth-narrowing regime reached by virtue of using the optical cavity, allowing an enhanced sensitivity to be achieved, despite an unoptimized collection efficiency of <2 %, and a low nitrogen-vacancy concentration of about 0.2 ppb.Comment: 10 pages and 5 figure

Detection of Campylobacter concisus and other Campylobacter species in colonic biopsies from adults with ulcerative colitis

Peer reviewedPublisher PD

COCO: A Platform for Comparing Continuous Optimizers in a Black-Box Setting

We introduce COCO, an open source platform for Comparing Continuous Optimizers in a black-box setting. COCO aims at automatizing the tedious and repetitive task of benchmarking numerical optimization algorithms to the greatest possible extent. The platform and the underlying methodology allow to benchmark in the same framework deterministic and stochastic solvers for both single and multiobjective optimization. We present the rationales behind the (decade-long) development of the platform as a general proposition for guidelines towards better benchmarking. We detail underlying fundamental concepts of COCO such as the definition of a problem as a function instance, the underlying idea of instances, the use of target values, and runtime defined by the number of function calls as the central performance measure. Finally, we give a quick overview of the basic code structure and the currently available test suites.Comment: Optimization Methods and Software, Taylor & Francis, In press, pp.1-3

Extremal fullerene graphs with the maximum Clar number

A fullerene graph is a cubic 3-connected plane graph with (exactly 12) pentagonal faces and hexagonal faces. Let $F_n$ be a fullerene graph with $n$ vertices. A set $\mathcal H$ of mutually disjoint hexagons of $F_n$ is a sextet pattern if $F_n$ has a perfect matching which alternates on and off each hexagon in $\mathcal H$. The maximum cardinality of sextet patterns of $F_n$ is the Clar number of $F_n$. It was shown that the Clar number is no more than $\lfloor\frac {n-12} 6\rfloor$. Many fullerenes with experimental evidence attain the upper bound, for instance, $\text{C}_{60}$ and $\text{C}_{70}$. In this paper, we characterize extremal fullerene graphs whose Clar numbers equal $\frac{n-12} 6$. By the characterization, we show that there are precisely 18 fullerene graphs with 60 vertices, including $\text{C}_{60}$, achieving the maximum Clar number 8 and we construct all these extremal fullerene graphs.Comment: 35 pages, 43 figure

EGFR Activation and Ultraviolet Light-Induced Skin Carcinogenesis

The epidermal growth factor receptor (EGFR) regulates the proliferation of keratinocytes through multiple mechanisms that differ depending on the localization of the cell within the skin. Ultraviolet (UV) irradiation, the main etiologic factor in the development of skin cancer, also activates the receptor. In this review, we discuss how the UV-induced activation of EGFR regulates the response of the skin to UV. UV-induced EGFR activation increases keratinocyte proliferation, suppresses apoptosis, and augments and accelerates epidermal hyperplasia in response to UV. Pharmacological inhibition of the UV-induced activation of EGFR in a genetically initiated mouse skin tumorigenesis model suppresses tumorigenesis and the activation of mitogen-activated protein (MAP) kinases and phosphatidyl inositol-3-kinase (PI3K)/AKT signaling pathways. EGFR has pleiotropic, complex, and cell-type-specific functions in cutaneous keratinocytes; suggesting that the receptor is an appropriate target for the development of molecularly targeted therapies for skin cancer and other pathologies

Nitrogen-Vacancy Ensemble Magnetometry Based on Pump Absorption

We demonstrate magnetic field sensing using an ensemble of nitrogen-vacancy centers by recording the variation in the pump-light absorption due to the spin-polarization dependence of the total ground state population. Using a 532 nm pump laser, we measure the absorption of native nitrogen-vacancy centers in a chemical vapor deposited diamond placed in a resonant optical cavity. For a laser pump power of 0.4 W and a cavity finesse of 45, we obtain a noise floor of $\sim$ 100 nT/$\sqrt{\textrm{Hz}}$ spanning a bandwidth up to 125 Hz. We project a photon shot-noise-limited sensitivity of $\sim$ 1 pT/$\sqrt{\textrm{Hz}}$ by optimizing the nitrogen-vacancy concentration and the detection method.Comment: 7 pages and 5 figure

Nature and Nurture in Dark Matter Halos

Cosmological simulations consistently predict specific properties of dark matter halos, but these have not yet led to a physical understanding that is generally accepted. This is especially true for the central regions of these structures. Recently two major themes have emerged. In one, the dark matter halo is primarily a result of the sequential accretion of primordial structure (ie `Nature'); while in the other, dynamical relaxation (ie `Nurture') dominates at least in the central regions. Some relaxation is however required in either mechanism. In this paper we accept the recently established scale-free sub-structure of halos as an essential part of both mechanisms. Consequently; a simple model for the central relaxation based on a self-similar cascade of tidal interactions, is contrasted with a model based on the accretion of adiabatically self-similar, primordial structure. We conclude that a weak form of this relaxation is present in the simulations, but that is normally described as the radial orbit instability.Comment: 25 pages, 3 figures, fig with parts 1 to d, fig 3 with parts a to

Determination of protein binding affinities within hydrogel-based molecularly imprinted polymers (HydroMIPs)

Hydrogel-based molecularly imprinted polymers (HydroMIPs) were prepared for several proteins (haemoglobin, myoglobin and catalase) using a family of acrylamide-based monomers. Protein affinity towards the HydroMIPs was investigated under equilibrium conditions and over a range of concentrations using specific binding with Hill slope saturation profiles. We report HydroMIP binding affinities, in terms of equilibrium dissociation constants (Kd) within the micro-molar range (25 ± 4 mM, 44 ± 3 mM, 17 ± 2 mM for haemoglobin, myoglobin and catalase respectively within a polyacrylamide-based MIP). The extent of non-specific binding or cross-selectivity for non-target proteins has also been assessed. It is concluded that both selectivity and affinity for both cognate and non-cognate proteins towards the MIPs were dependent on the concentration and the complementarity of their structures and size. This is tentatively attributed to the formation of protein complexes during both the polymerisation and rebinding stages at high protein concentrations. We have used atomic force spectroscopy to characterize molecular interactions in the MIP cavities using protein-modified AFM tips. Attractive and repulsive force curves were obtained for the MIP and NIP (non-imprinted polymer) surfaces (under protein loaded or unloaded states). Our force data suggest that we have produced selective cavities for the template protein in the MIPs and we have been able to quantify the extent of non-specific protein binding on, for example, a non-imprinted polymer (NIP) control surface

Response of primiparous and multiparous buffaloes to yeast culture supplementation during early and mid-lactation

Strains of live Saccharomyces cerevisiae yeast have exhibited probiotic effects in ruminants. This study investigated the effects of the dietary yeast supplement, S. cerevisiae (Yea-Sacc1026), on primiparous (PP) and multiparous (MP) Egyptian buffaloes in early to mid-lactation. Lactating buffaloes were fed either a basal total mixed ration (TMR, control; 4 PP and 8 MP) or the basal TMR plus 10 g Yea-Sacc1026 per buffalo cow per day (yeast; 4 PP and 8 MP). The feeds were given from 15 days prepartum to 180 days postpartum. Feed intake, body weight, and milk yields (MY) were recorded, and milk and blood samples were collected for analyses. Feces were collected from days 45 to 47 during early lactation and from days 90 to 92 during mid-lactation to determine apparent digestibility of dry matter (DM), organic matter (OM), crude protein (CP) and crude fiber (CF). Energy corrected milk yield (ECM), feed conversion, and energy and nitrogen conversion efficiency were calculated. Yeast treated MP buffaloes consumed more DM (P ≤ 0.041) and CP than the untreated control group. Apparent digestibility of DM and OM were significantly greater at mid-lactation for treated versus control group (P = 0.001). Crude fiber digestibility was greater in MP than in PP buffaloes (P = 0.049), and yeast supplemented MP cows had a greater CF digestibility than control MP buffaloes at mid-lactation (P = 0.010). Total blood lipids decreased after yeast supplementation (P = 0.029). Milk yields, ECM, fat and protein yields increased for yeast treated MP buffaloes (P ≤ 0.039). The study concluded that the response to yeast supplementation in buffalo cows is parity dependent. Multiparous buffaloes respond to yeast supplementation with an increased DM intake and CF digestibility without significant weight gains, allowing a greater ECM yield with less fat mobilization. Supplementing buffaloes with yeast culture may increase milk production in early lactation and results in a more persistent milk production during mid-lactation. Feed conversion and energy and nitrogen conversion efficiency may be increased with the use of yeast supplementation in Egyptian buffaloes