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Reduction in Greenhouse Gas Emissions Associated with Worm Control in Lambs
Fiona Kenyon,Jan M. Dick,Ron I. Smith,Drew G. Coulter,David McBean,Philip J. Skuce
Agriculture , 2013, DOI: 10.3390/agriculture3020271
Abstract: There are currently little or no data on the role of endemic disease control in reducing greenhouse gas (GHG) emissions from livestock. In the present study, we have used an Intergovernmental Panel on Climate Change (IPCC)-compliant model to calculate GHG emissions from naturally grazing lambs under four different anthelmintic drug treatment regimes over a 5-year study period. Treatments were either “monthly” (NST), “strategic” (SPT), “targeted” (TST) or based on “clinical signs” (MT). Commercial sheep farming practices were simulated, with lambs reaching a pre-selected target market weight (38 kg) removed from the analysis as they would no longer contribute to the GHG budget of the flock. Results showed there was a significant treatment effect over all years, with lambs in the MT group consistently taking longer to reach market weight, and an extra 10% emission of CO 2e per kg of weight gain over the other treatments. There were no significant differences between the other three treatment strategies (NST, SPT and TST) in terms of production efficiency or cumulated GHG emissions over the experimental period. This study has shown that endemic disease control can contribute to a reduction in GHG emissions from animal agriculture and help reduce the carbon footprint of livestock farming.
Polyclonal Spread and Outbreaks with ESBL Positive Gentamicin Resistant Klebsiella spp. in the Region Kennemerland, The Netherlands
Dennis Souverein, Stefan A. Boers, Dick Veenendaal, Sjoerd M. Euser, Jan Kluytmans, Jeroen W. Den Boer
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0101212
Abstract: Objective The objective of this study was to analyze the transmission dynamics of ESBL positive Klebsiella spp. with an additional resistance towards gentamicin (ESBL-G) in a Dutch region of 650,000 inhabitants in 2012. Methods All patient related ESBL-G isolates isolated in 2012 were genotyped using both Amplification Fragment Length Polymorphism (AFLP) and High-throughput MultiLocus Sequence Typing (HiMLST). HiMLST was used to analyze the presence of (unidentified) clusters of ESBL-G positive patients. Furthermore, all consecutive ESBL-G isolates within patients were studied in order to evaluate the intra-patient variation of antibiotic phenotypes. Results There were 38 ESBL-G isolates, which were classified into 18 different sequence types (STs) and into 21 different AFLP types. Within the STs, four clusters were detected from which two were unknown resulting in a transmission index of 0.27. An analysis of consecutive ESBL-G isolates (with similar STs) within patients showed that for 68.8% of the patients at least one isolate had a different consecutive antibiotic phenotype. Conclusion The transmission of ESBL-G in the region Kennemerland in 2012 was polyclonal with several outbreaks (with a high level of epidemiological linkage). Furthermore, clustering by antibiotic phenotype characterization seems to be an inadequate approach in this setting. The routine practice of molecular typing of collected ESBL-G isolates may help to detect transmission in an early stage, which opens the possibility of a rapid response.
A Construction of Polynomial Lattice Rules with Small Gain Coefficients
Jan Baldeaux,Josef Dick
Mathematics , 2010,
Abstract: In this paper we construct polynomial lattice rules which have, in some sense, small gain coefficients using a component-by-component approach. The gain coefficients, as introduced by Owen, indicate to what degree the method improves upon Monte Carlo. We show that the variance of an estimator based on a scrambled polynomial lattice rule constructed component-by-component decays at a rate of $N^{-(2\alpha + 1) +\delta}$, for all $\delta >0$, assuming that the function under consideration has bounded fractional variation of order $\alpha$ and where $N$ denotes the number of quadrature points. An analogous result is obtained for Korobov polynomial lattice rules. It is also established that these rules are almost optimal for the function space considered in this paper. Furthermore, we discuss the implementation of the component-by-component approach and show how to reduce the computational cost associated with it. Finally, we present numerical results comparing scrambled polynomial lattice rules and scrambled digital nets.
A population-based nested case control study on recurrent pneumonias in children with severe generalized cerebral palsy: ethical considerations of the design and representativeness of the study sample
Rebekka Veugelers, Elsbeth AC Calis, Corine Penning, Arianne Verhagen, Roos Bernsen, Jan Bouquet, Marc A Benninga, Peter JFM Merkus, Hubertus GM Arets, Dick Tibboel, Heleen M Evenhuis
BMC Pediatrics , 2005, DOI: 10.1186/1471-2431-5-25
Abstract: A nested case-control design with 18 months follow-up was chosen. Dysphagia, respiratory function and constipation will be assessed at baseline, malnutrition and gastro-oesophageal reflux at the end of the follow-up. The study population consists of a representative population sample of children with severe generalized cerebral palsy. Inclusion was done through care-centres in a predefined geographical area and not through hospitals. All measurements will be done on-site which sets high demands on all measurements. If these demands were not met in "gold standard" methods, other methods were chosen. Although the inclusion period was prolonged, the desired sample size of 300 children was not met. With a consent rate of 33%, nearly 10% of all eligible children in the Netherlands are included (n = 194). The study population is subtly different from the non-participants with regard to severity of dysphagia and prevalence rates of pneumonias and gastro-oesophageal reflux.Ethical issues complicated the study design. Assessment of malnutrition and gastro-oesophageal reflux at baseline was considered unethical, since these conditions can be easily treated. Therefore, we postponed these diagnostics until the end of the follow-up. In order to include a representative sample, all eligible children in a predefined geographical area had to be contacted. To increase the consent rate, on-site measurements are of first choice, but timely inclusion is jeopardised. The initiation of this first study among children with severe neurological impairment led to specific, unexpected problems. Despite small differences between participants and non-participating children, our sample is as representative as can be expected from any population-based study and will provide important, new information to bring us further towards effective interventions to prevent pneumonias in this population.Children with severe generalized cerebral palsy often have a combination of motor and intellectual disabil
Calculation of the relative metastabilities of proteins using the CHNOSZ software package
Jeffrey M Dick
Geochemical Transactions , 2008, DOI: 10.1186/1467-4866-9-10
Abstract: A software package called CHNOSZ implementing the revised Helgeson-Kirkham-Flowers (HKF) equations of state and group additivity for ionized unfolded aqueous proteins was developed. The program can be used to calculate standard molal Gibbs energies and other thermodynamic properties of reactions and to make chemical speciation and predominance diagrams that represent the metastable equilibrium distributions of proteins. The approach takes account of the chemical affinities of reactions in open systems characterized by the chemical potentials of basis species. The thermodynamic database included with the package permits application of the software to mineral and other inorganic systems as well as systems of proteins or other biomolecules.Metastable equilibrium activity diagrams were generated for model cell-surface proteins from archaea and bacteria adapted to growth in environments that differ in temperature and chemical conditions. The predicted metastable equilibrium distributions of the proteins can be compared with the optimal growth temperatures of the organisms and with geochemical variables. The results suggest that a thermodynamic assessment of protein metastability may be useful for integrating bio- and geochemical observations.Owing to the growing body of compositional data for microbial proteins and the exploration of environments that are extreme from the human standpoint, it has become possible in recent years to draw correlations between the compositions of proteins and environmental parameters such as temperature [1]. Accounting for the underlying causes of the observed correlations between environmental parameters and protein composition is an ongoing challenge. Biochemical approaches are based in part on the notion that proteins from thermophilic and hyperthermophilic organisms should have greater structural stabilities than their mesophilic counterparts [2]. Compositional features of thermophilic proteins that may enhance their structural stabiliti
Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae
Jeffrey M Dick
BMC Systems Biology , 2009, DOI: 10.1186/1752-0509-3-75
Abstract: I adopt the hypothesis that the state of yeast subcellular organization is in a local energy minimum. This hypothesis implies that equilibrium thermodynamic models can yield predictions about the interdependence between populations of proteins and their subcellular chemical environments.Three types of tests are proposed. First, there should be correlations between modeled and observed oxidation states for different compartments. Second, there should be a correspondence between the energy requirements of protein formation and the order the appearance of organelles during cellular development. Third, there should be correlations between the predicted and observed relative abundances of interacting proteins within compartments.The relative metastability fields of subcellular homologs of glutaredoxin and thioredoxin indicate a trend from less to more oxidizing as mitochondrion – cytoplasm – nucleus. Representing the overall amino acid compositions of proteins in 23 different compartments each with a single reference model protein suggests that the formation reactions for proteins in the vacuole (in relatively oxidizing conditions), ER and early Golgi (in relatively reducing conditions) are relatively highly favored, while that for the microtubule is the most costly. The relative abundances of model proteins for each compartment inferred from experimental data were found in some cases to correlate with the predicted abundances, and both positive and negative correlations were found for some assemblages of proteins in known complexes.The results of these calculations and tests suggest that a tendency toward a metastable energy minimum could underlie some organizational links between the the chemical thermodynamic properties of proteins and subcellular chemical environments. Future models of this kind will benefit from consideration of additional thermodynamic variables together with more detailed subcellular observations.A complex interplay of chemical and biological forc
Cosmological implications of a light dilaton
R. Dick,M. Gaul
Physics , 1998,
Abstract: Supersymmetric Peccei-Quinn symmetry and string theory predict a complex scalar field comprising a dilaton and an axion. These fields are massless at high energies, but it is known since long that the axion is stabilized in an instanton dominated vacuum. Instantons and axions together also provide a mechanism to stabilize a dilaton, thus accounting for a dilaton as a possible cold dark matter component accompanying the axion. We briefly review the prospects of this scenario and point out further implications.
Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae
Jeffrey M. Dick
Quantitative Biology , 2008,
Abstract: [abridged] Background: The distribution of chemical species in an open system at metastable equilibrium can be expressed as a function of environmental variables which can include temperature, oxidation-reduction potential and others. Calculations of metastable equilibrium for various model systems were used to characterize chemical transformations among proteins and groups of proteins found in different compartments of yeast cells. Results: With increasing oxygen fugacity, the relative metastability fields of model proteins for major subcellular compartments go as mitochondrion, endoplasmic reticulum, cytoplasm, nucleus. In a metastable equilibrium setting at relatively high oxygen fugacity, proteins making up actin are predominant, but those constituting the microtubule occur with a low chemical activity. A reaction sequence involving the microtubule and spindle pole proteins was predicted by combining the known intercompartmental interactions with a hypothetical program of oxygen fugacity changes in the local environment. In further calculations, the most-abundant proteins within compartments generally occur in relative abundances that only weakly correspond to a metastable equilibrium distribution. However, physiological populations of proteins that form complexes often show an overall positive or negative correlation with the relative abundances of proteins in metastable assemblages. Conclusions: This study explored the outlines of a thermodynamic description of chemical transformations among interacting proteins in yeast cells. The results suggest that these methods can be used to measure the degree of departure of a natural biochemical process or population from a local minimum in Gibbs energy.
A characterization of higher order nets using Weyl sums and its applications
Jan Baldeaux,Josef Dick,Friedrich Pillichshammer
Uniform Distribution Theory , 2010,
Abstract: Point sets referred to as $(t,\alpha,\beta,n,m,s)$-nets were recently introducedand shown to generalize both digital $(t,\alpha,\beta, n \times m,s)$-nets and classical $(t,m,s)$-nets. Their definition captures the geometrical properties of their digital analogue, which has recently been shown to yield quadrature points for quasi-Monte Carlo rules which can achieve arbitrary high convergence rates of the integration error for sufficiently smooth functions. In this paper, we characterize $(t,\alpha,\beta,n,m,s)$-nets using Weyl sums generalizing the analogous result for $(t,m,s)$-nets. As an application of this characterization we study numerical integration using such higher order nets. It is shown that for functions having square integrable mixed partial derivatives of order $\alpha$ in each variable, integration errors converge at a rate of $N^{-(\alpha-1)+ \delta}$ for any $\delta > 0$, establishing that $(t,\alpha,\beta, n, m, s)$-nets can exploit the smoothness of the function under consideration. The characterization is consequently employed to study the randomization of $(t,\alpha,\beta,n,m,s)$-nets and the application of randomized $(t,\alpha,\beta,n,m,s)$-nets to numerical integration. It is found that the root mean-square error converges at a rate of $N^{-(\alpha - \frac{1}{2}) + \delta }$ for any $\delta > 0$, improving on the result on integration errors associated with $(t,\alpha, \beta,n,m,s)$-nets. As a further application, it can be used for the construction of new $(t,\alpha, \beta,n,m,s)$-nets itself: We introduce an analogue of the $(u,u + v)$-construction for digital $(t,\alpha, \beta, n \times m,s)$-nets and $(t,m,s)$-nets.
Regulation of 11β-Hydroxysteroid Dehydrogenase Type 1 and 2 in Rheumatoid Arthritis  [PDF]
Christine Beyeler, Bernhard Dick, Howard A. Bird, Brigitte M. Frey
International Journal of Clinical Medicine (IJCM) , 2012, DOI: 10.4236/ijcm.2012.34051
Abstract: Objective. The sequential activities of the 11β-hydroxysteroid dehydrogenase enzymes type 1 and 2 have not been investigated so far in patients suffering from rheumatoid arthritis before and after starting treatment though the enzymes balancing cortisol and cortisone levels are involved in regulating various inflammatory diseases. Methods. In a retrospective study, a panel of 41 urinary steroid metabolites has been analysed in a group of 18 patients with active rheumatoid arthritis (RA) as they were brought under control with disease modifying drugs. Results. No major changes were found in a variety of androgen, oestrogen and progesterone metabolites, however the ratio of THF + 5αTHF/THE as an index of 11β-HSD1 oxidative activity demonstrated down-regulation with modification correlating significantly with change in acute phase reactants as the disease came under control. These findings were supported by a tendency of a reduced ratio of F/E, an index of 11β-HSD2 oxidative activity, resulting in a significant correlation of the two ratios (p < 0.001). This parallelism of the two enzymes with functions of clinical laboratory parameters during drug-induced improvement of the disease is novel. Conclusions. Urinary steroid metabolites, which alter with disease activity, may provide further insight into the mechanisms by which stress can modify arthritis through hormones.
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