Anti-microbial Use in Animals: How to Assess the Trade-offs

Antimicrobials are widely used in preventive and curative medicine in animals. Benefits from curative use are clear – it allows sick animals to be healthy with a gain in human welfare. The case for preventive use of antimicrobials is less clear cut with debates on the value of antimicrobials as growth promoters in the intensive livestock industries. The possible benefits from the use of antimicrobials need to be balanced against their cost and the increased risk of emergence of resistance due to their use in animals. The study examines the importance of animals in society and how the role and management of animals is changing including the use of antimicrobials. It proposes an economic framework to assess the trade-offs of anti-microbial use and examines the current level of data collection and analysis of these trade-offs. An exploratory review identifies a number of weaknesses. Rarely are we consistent in the frameworks applied to the economic assessment anti-microbial use in animals, which may well be due to gaps in data or the prejudices of the analysts. There is a need for more careful data collection that would allow information on (i) which species and production systems antimicrobials are used in, (ii) what active substance of antimicrobials and the application method and (iii) what dosage rates. The species need to include companion animals as well as the farmed animals as it is still not known how important direct versus indirect spread of resistance to humans is. In addition, research is needed on pricing antimicrobials used in animals to ensure that prices reflect production and marketing costs, the fixed costs of anti-microbial development and the externalities of resistance emergence. Overall, much work is needed to provide greater guidance to policy, and such work should be informed by rigorous data collection and analysis systems

The impact of freight transport capacity limitations on supply chain dynamics

We investigate how capacity limitations in the transportation system affect the dynamic behaviour of supply chains. We are interested in the more recently defined, 'backlash' effect. Using a system dynamics simulation approach, we replicate the well-known Beer Game supply chain for different transport capacity management scenarios. The results indicate that transport capacity limitations negatively impact on inventory and backlog costs, although there is a positive impact on the 'backlash' effect. We show that it is possible for both backlog and inventory to simultaneous occur, a situation which does not arise with the uncapacitated scenario. A vertical collaborative approach to transport provision is able to overcome such a trade-off. © 2013 Taylor & Francis

From solid solution to cluster formation of Fe and Cr in α\alpha-Zr

To understand the mechanisms by which Fe and Cr additions increase the corrosion rate of irradiated Zr alloys, a combination of experimental (atom probe tomography, x-ray diffraction and thermoelectric power measurements) and modelling (density functional theory) techniques are employed to investigate the non-equilibrium solubility and clustering of Fe and Cr in binary Zr alloys. Cr occupies both interstitial and substitutional sites in the {\alpha}-Zr lattice, Fe favours interstitial sites, and a low-symmetry site that was not previously modelled is found to be the most favourable for Fe. Lattice expansion as a function of alloying concentration (in the dilute regime) is strongly anisotropic for Fe additions, expanding the $c$-axis while contracting the $a$-axis. Defect clusters are observed at higher solution concentrations, which induce a smaller amount of lattice strain compared to the dilute defects. In the presence of a Zr vacancy, all two-atom clusters are more soluble than individual point defects and as many as four Fe or three Cr atoms could be accommodated in a single Zr vacancy. The Zr vacancy is critical for the increased solubility of defect clusters, the implications for irradiation induced microstructure changes in Zr alloys are discussed.Comment: 15 pages including figure, 9 figures, 2 tables. Submitted for publication in Acta Mater, Journal of Nuclear Materials (2015

CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences

<p>Abstract</p> <p>Background</p> <p>Cowpea [<it>Vigna unguiculata </it>(L.) Walp.] is one of the most important food and forage legumes in the semi-arid tropics because of its ability to tolerate drought and grow on poor soils. It is cultivated mostly by poor farmers in developing countries, with 80% of production taking place in the dry savannah of tropical West and Central Africa. Cowpea is largely an underexploited crop with relatively little genomic information available for use in applied plant breeding. The goal of the Cowpea Genomics Initiative (CGI), funded by the Kirkhouse Trust, a UK-based charitable organization, is to leverage modern molecular genetic tools for gene discovery and cowpea improvement. One aspect of the initiative is the sequencing of the gene-rich region of the cowpea genome (termed the genespace) recovered using methylation filtration technology and providing annotation and analysis of the sequence data.</p> <p>Description</p> <p>CGKB, Cowpea Genespace/Genomics Knowledge Base, is an annotation knowledge base developed under the CGI. The database is based on information derived from 298,848 cowpea genespace sequences (GSS) isolated by methylation filtering of genomic DNA. The CGKB consists of three knowledge bases: GSS annotation and comparative genomics knowledge base, GSS enzyme and metabolic pathway knowledge base, and GSS simple sequence repeats (SSRs) knowledge base for molecular marker discovery. A homology-based approach was applied for annotations of the GSS, mainly using BLASTX against four public FASTA formatted protein databases (NCBI GenBank Proteins, UniProtKB-Swiss-Prot, UniprotKB-PIR (Protein Information Resource), and UniProtKB-TrEMBL). Comparative genome analysis was done by BLASTX searches of the cowpea GSS against four plant proteomes from <it>Arabidopsis thaliana, Oryza sativa, Medicago truncatula</it>, and <it>Populus trichocarpa</it>. The possible exons and introns on each cowpea GSS were predicted using the HMM-based Genscan gene predication program and the potential domains on annotated GSS were analyzed using the HMMER package against the Pfam database. The annotated GSS were also assigned with Gene Ontology annotation terms and integrated with 228 curated plant metabolic pathways from the <it>Arabidopsis </it>Information Resource (TAIR) knowledge base. The UniProtKB-Swiss-Prot ENZYME database was used to assign putative enzymatic function to each GSS. Each GSS was also analyzed with the Tandem Repeat Finder (TRF) program in order to identify potential SSRs for molecular marker discovery. The raw sequence data, processed annotation, and SSR results were stored in relational tables designed in key-value pair fashion using a PostgreSQL relational database management system. The biological knowledge derived from the sequence data and processed results are represented as views or materialized views in the relational database management system. All materialized views are indexed for quick data access and retrieval. Data processing and analysis pipelines were implemented using the Perl programming language. The web interface was implemented in JavaScript and Perl CGI running on an Apache web server. The CPU intensive data processing and analysis pipelines were run on a computer cluster of more than 30 dual-processor Apple XServes. A job management system called Vela was created as a robust way to submit large numbers of jobs to the Portable Batch System (PBS).</p> <p>Conclusion</p> <p>CGKB is an integrated and annotated resource for cowpea GSS with features of homology-based and HMM-based annotations, enzyme and pathway annotations, GO term annotation, toolkits, and a large number of other facilities to perform complex queries. The cowpea GSS, chloroplast sequences, mitochondrial sequences, retroelements, and SSR sequences are available as FASTA formatted files and downloadable at CGKB. This database and web interface are publicly accessible at <url>http://cowpeagenomics.med.virginia.edu/CGKB/</url>.</p

Human osteoblasts obtained from distinct periarticular sites demonstrate differences in biological function in vitro.

AIMS: Accumulated evidence indicates that local cell origins may ingrain differences in the phenotypic activity of human osteoblasts. We hypothesized that these differences may also exist in osteoblasts harvested from the same bone type at periarticular sites, including those adjacent to the fixation sites for total joint implant components. METHODS: Human osteoblasts were obtained from the acetabulum and femoral neck of seven patients undergoing total hip arthroplasty (THA) and from the femoral and tibial cuts of six patients undergoing total knee arthroplasty (TKA). Osteoblasts were extracted from the usually discarded bone via enzyme digestion, characterized by flow cytometry, and cultured to passage three before measurement of metabolic activity, collagen production, alkaline phosphatase (ALP) expression, and mineralization. RESULTS: Osteoblasts from the acetabulum showed lower proliferation (p = 0.034), cumulative collagen release (p < 0.001), and ALP expression (p = 0.009), and produced less mineral (p = 0.006) than those from the femoral neck. Osteoblasts from the tibia produced significantly less collagen (p = 0.021) and showed lower ALP expression than those from the distal femur. CONCLUSION: We have demonstrated for the first time an anatomical regional variation in the biological behaviours of osteoblasts on either side of the hip and knee joint. The lower osteoblast proliferation, matrix production, and mineralization from the acetabulum compared to those from the proximal femur may be reflected in differences in bone formation and implant fixation at these sites. Cite this article: Bone Joint Res 2021;10(9):611-618

The properties of V838 Mon in 2002 November

We present the results of modelling the 0.45--1 micron spectral energy distribution of V838 Mon for 2002 November. Synthetic spectra were calculated using the NextGen model atmospheres of Hauschildt et al. (1999), which incorporate line lists for H2O, TiO, CrH, FeH, CO, and MgH, as well as the VALD atomic line list. Fits to the observed spectra show that, in 2002 November, the effective temperature of V838 Mon was approximately 2000 +/-100 K. Our theoretical spectra show a comparatively weak dependence on log g. Preliminary analysis of the hot star observed together with V838 Mon shows it to be a normal B3V dwarf.Comment: 7 pages, 4 figs, accepted by A&