SNPmplexViewer--toward a cost-effective traceability system

<p>Abstract</p> <p>Background</p> <p>Beef traceability has become mandatory in many regions of the world and is typically achieved through the use of unique numerical codes on ear tags and animal passports. DNA-based traceability uses the animal's own DNA code to identify it and the products derived from it. Using <it>SNaPshot</it>, a primer-extension-based method, a multiplex of 25 SNPs in a single reaction has been practiced for reducing the expense of genotyping a panel of SNPs useful for identity control.</p> <p>Findings</p> <p>To further decrease <it>SNaPshot</it>'s cost, we introduced the Perl script <it>SNPmplexViewer</it>, which facilitates the analysis of trace files for reactions performed without the use of fluorescent size standards. <it>SNPmplexViewer </it>automatically aligns reference and target trace electropherograms, run with and without fluorescent size standards, respectively. <it>SNPmplexViewer </it>produces a modified target trace file containing a normalised trace in which the reference size standards are embedded. <it>SNPmplexViewer </it>also outputs aligned images of the two electropherograms together with a difference profile.</p> <p>Conclusions</p> <p>Modified trace files generated by <it>SNPmplexViewer </it>enable genotyping of <it>SnaPshot </it>reactions performed without fluorescent size standards, using common fragment-sizing software packages. <it>SNPmplexViewer</it>'s normalised output may also improve the genotyping software's performance. Thus, <it>SNPmplexViewer </it>is a general free tool enabling the reduction of <it>SNaPshot</it>'s cost as well as the fast viewing and comparing of trace electropherograms for fragment analysis. <it>SNPmplexViewer </it>is available at <url>http://cowry.agri.huji.ac.il/cgi-bin/SNPmplexViewer.cgi</url>.</p

Particle emission characteristics of a gas turbine with a double annular combustor

The total climate, air quality and health impact of aircraft black carbon (BC) emissions depends on quantity (mass and number concentration), as well as morphology (fractal dimension and surface area) of emitted BC aggregates. This study examines multiple BC emission metrics from a gas turbine with a double annular combustor, CFM56-5B4-2P. As a part of the SAMPLE III.2 campaign, concurrent measurements of particle mobility, particle mass, particle number concentration and mass concentration, as well as collection of transmission electron microscopy (TEM) samples, allowed for characterization of the BC emissions. Mass- and number-based emission indices were strongly influenced by thrust setting during pilot combustion and ranged from <1 to 208 mg/kg-fuel and 3×1012 to 3×1016 particles/kg-fuel, respectively. Mobility measurements indicated that mean diameters ranged from 7-44 nm with a strong dependence on thrust during pilot-only combustion. Using aggregation and sintering theory with empirical effective density relationships, a power law relationship between primary particle diameter and mobility diameter is presented. Mean primary particle diameter ranged from 6-19 nm, however, laser induced incandescence (LII) and mass-mobility calculated primary particle diameters demonstrated opposite trends with thrust setting. Similarly, mass-mobility-calculated aggregate mass specific surface area and LII-measured surface area were not in agreement, indicating both methods need further development and validation before use as quantitative indicators of primary particle diameter and mass-specific surface area.The authors express their gratitude to a number of people and organizations in helping to plan, conduct, finance and provide instruments for this measurement campaign. The 537 European Aviation Safety Agency (EASA) funded the SAMPLE III SC02 campaign (EASA.2010.FC.10, Specific Contract No: SC02). The Federal Office of Civil Aviation, Switzerland (FOCA) was critical in for providing additional financial support and arranging facilities which made this study possible. We also thank the SR Technics test bed staff, including Frithjof Siegerist, for operating the engines and enabling access to the test facility. We thank AVL, Cambustion, Grimm & TSI supplying both instruments and expertise.This is the author accepted manuscript. The final version is available from Taylor & Francis via http://dx.doi.org/10.1080/02786826.2015.107845

The importance of post-translocation monitoring of habitat use and population growth: insights from a Seychelles Warbler (Acrocephalus sechellensis) translocation

Translocations are a valuable tool within conservation, and when performed successfully can rescue species from extinction. However, to label a translocation a success, extensive post-translocation monitoring is required, ensuring the population is growing at the expected rate. In 2011, a habitat assessment identified Frégate Island as a suitable island to host a Seychelles Warbler (Acrocephalus sechellensis) population. Later that year, 59 birds were translocated from Cousin Island to Frégate Island. Here, we determine Seychelles Warbler habitat use and population growth on Frégate Island, assessing the status of the translocation and identifying any interventions that may be required. We found that territory quality, an important predictor of fledgling production on Cousin Island, was a poor predictor of bird presence on Frégate Island. Instead, tree diversity, middle-storey vegetation density, and broad-leafed vegetation density all predicted bird presence positively. A habitat suitability map based on these results suggests most of Frégate Island contains either a suitable or a moderately suitable habitat, with patches of unsuitable overgrown coconut plantation. To achieve the maximum potential Seychelles Warbler population size on Frégate Island, we recommend habitat regeneration, such that the highly diverse subset of broad-leafed trees and a dense middle storey should be protected and replace the unsuitable coconut. Frégate Island’s Seychelles Warbler population has grown to 141 birds since the release, the slowest growth rate of all Seychelles Warbler translocations; the cause of this is unclear. This study highlights the value of post-translocation monitoring, identifying habitat use and areas requiring restoration, and ultimately ensuring that the population is growing

Exercise and manual auricular acupuncture: a pilot assessor-blind randomised controlled trial. (The acupuncture and personalised exercise programme (APEP) Trial)

<p>Abstract</p> <p>Background</p> <p>Evidence supports the use of exercise for chronic low back pain (CLBP); however, adherence is often poor due to ongoing pain. Auricular acupuncture is a form of pain relief involving the stimulation of points on the outer ear corresponding with specific body parts. It may be a useful adjunct to exercise in managing CLBP; however, there is only limited evidence to support its use with this patient group.</p> <p>Methods/Design</p> <p>This study was designed to test the feasibility of an assessor-blind randomised controlled trial which assess the effects on clinical outcomes and exercise adherence of adding manual auricular acupuncture to a personalised and supervised exercise programme (PEP) for CLBP. No sample size calculation has been carried out as this study aims to identify CLBP referral rates within the catchment area of the study site. The researchers aim to recruit four cohorts of n = 20 participants to facilitate a power analysis for a future randomised controlled trial. A computer generated random allocation sequence will be prepared centrally and used to allocate participants by cohort to one of the following interventions: 1) six weeks of PEP <it>plus </it>manual auricular acupuncture; 2) six weeks of PEP alone. Both groups will also complete a further six weeks of self-paced exercise with telephone follow-up support. In addition to a baseline and exit questionnaire at the beginning and end of the study, the following outcomes will be collected at baseline, and after 7, 13 and 25 weeks: pain frequency and bothersomeness, back-specific function, objective assessment and recall of physical activity, use of analgesia, perceived self-efficacy, fear avoidance beliefs, and beliefs about the consequences of back pain. Since this is a feasibility study, significance tests will not be presented, and treatment effects will be represented by point estimates and confidence intervals. For each outcome variable, analysis of covariance will be performed on the data, conditioning on the baseline value.</p> <p>Discussion</p> <p>The results of this study investigating the adjuvant effects of auricular acupuncture to exercise in managing CLBP will be used to inform the design of a future multi-centre randomised controlled trial.</p> <p>Trial Registration</p> <p>Current Controlled Trials ISRCTN94142364.</p

A Deep Learning Approach Validates Genetic Risk Factors for Late Toxicity After Prostate Cancer Radiotherapy in a REQUITE Multi-National Cohort.

Background: REQUITE (validating pREdictive models and biomarkers of radiotherapy toxicity to reduce side effects and improve QUalITy of lifE in cancer survivors) is an international prospective cohort study. The purpose of this project was to analyse a cohort of patients recruited into REQUITE using a deep learning algorithm to identify patient-specific features associated with the development of toxicity, and test the approach by attempting to validate previously published genetic risk factors. Methods: The study involved REQUITE prostate cancer patients treated with external beam radiotherapy who had complete 2-year follow-up. We used five separate late toxicity endpoints: ≥grade 1 late rectal bleeding, ≥grade 2 urinary frequency, ≥grade 1 haematuria, ≥ grade 2 nocturia, ≥ grade 1 decreased urinary stream. Forty-three single nucleotide polymorphisms (SNPs) already reported in the literature to be associated with the toxicity endpoints were included in the analysis. No SNP had been studied before in the REQUITE cohort. Deep Sparse AutoEncoders (DSAE) were trained to recognize features (SNPs) identifying patients with no toxicity and tested on a different independent mixed population including patients without and with toxicity. Results: One thousand, four hundred and one patients were included, and toxicity rates were: rectal bleeding 11.7%, urinary frequency 4%, haematuria 5.5%, nocturia 7.8%, decreased urinary stream 17.1%. Twenty-four of the 43 SNPs that were associated with the toxicity endpoints were validated as identifying patients with toxicity. Twenty of the 24 SNPs were associated with the same toxicity endpoint as reported in the literature: 9 SNPs for urinary symptoms and 11 SNPs for overall toxicity. The other 4 SNPs were associated with a different endpoint. Conclusion: Deep learning algorithms can validate SNPs associated with toxicity after radiotherapy for prostate cancer. The method should be studied further to identify polygenic SNP risk signatures for radiotherapy toxicity. The signatures could then be included in integrated normal tissue complication probability models and tested for their ability to personalize radiotherapy treatment planning

Potential role of p53 on metallothionein induction in human epithelial breast cancer cells

The expression and induction of metallothionein has been associated with protection against oxidative stress and apoptosis. This study examines the effect of tumour suppressor protein p53 on metallothionein expression following CdCl2 treatment in eight human epithelial breast cancer cell lines differing in p53 and oestrogen-receptor status. Cells were treated with 10 μM CdCl2 for 24 h and metallothionein protein levels were measured by cadmium binding assay. MCF7 cells which are p53-positive (p53+) and oestrogen-receptor-positive showed a large induction in metallothionein synthesis by 10.79±1.36-fold. Other breast cancer cell lines which are p53-negative (p53−) and oestrogen-receptor-negative or weakly oestrogen-receptor-positive showed a small induction ranging from 1.40±0.10 to 3.65±0.30-fold. RT–PCR analysis showed an induction of metallothionein mRNA in MCF7 cells by about 1.61±0.08-fold, while in HCC1806 cells (p53−, oestrogen-receptor-negative) by 1.11±0.13-fold, and in MDA-MB-231 (p53−, oestrogen-receptor-negative) by 1.25±0.06-fold. Metallothionein localisation was determined by immunohistochemical staining. Prior to metal treatment, metallothionein was localised mainly in the cytoplasm of MCF7 and MDA-MB-231 cells. After treatment with 10 μM CdCl2 for 24 h, MCF7 cells showed intense nuclear and cytoplasmic staining for metallothionein, while MDA-MB-231 cells showed staining in the cytoplasm with weak nuclear staining. Apoptosis induced by 10–40 μM CdCl2 at time points between 4 and 48 h was examined with TUNEL assay. In MCF7 cells, apoptosis increased with higher concentrations of CdCl2, it peaked at 6–8 h and appeared again at 48 h for all concentrations of CdCl2 tested. In MDA-MB-231 cells, apoptosis remained at low levels for 10–40 μM CdCl2 at all time points. Studies on cadmium uptake showed similar uptake and accumulation of cadmium at 8 and 24 h in all the cell lines. The data demonstrate that treatment of epithelial breast cancer cells with 10 μM CdCl2 for 24 h caused a greater induction of metallothionein protein and mRNA expression in p53+ and oestrogen-receptor-positive cells as compared to p53− and oestrogen-receptor-negative or weakly oestrogen-receptor-positive cells. This effect may be associated with the occurrence of apoptosis and suggests a role for p53 and oestrogen-receptor on the expression and induction of metallothionein in epithelial cells

Mathematical Model of Plasmid-Mediated Resistance to Ceftiofur in Commensal Enteric Escherichia coli of Cattle

Antimicrobial use in food animals may contribute to antimicrobial resistance in bacteria of animals and humans. Commensal bacteria of animal intestine may serve as a reservoir of resistance-genes. To understand the dynamics of plasmid-mediated resistance to cephalosporin ceftiofur in enteric commensals of cattle, we developed a deterministic mathematical model of the dynamics of ceftiofur-sensitive and resistant commensal enteric Escherichia coli (E. coli) in the absence of and during parenteral therapy with ceftiofur. The most common treatment scenarios including those using a sustained-release drug formulation were simulated; the model outputs were in agreement with the available experimental data. The model indicated that a low but stable fraction of resistant enteric E. coli could persist in the absence of immediate ceftiofur pressure, being sustained by horizontal and vertical transfers of plasmids carrying resistance-genes, and ingestion of resistant E. coli. During parenteral therapy with ceftiofur, resistant enteric E. coli expanded in absolute number and relative frequency. This expansion was most influenced by parameters of antimicrobial action of ceftiofur against E. coli. After treatment (>5 weeks from start of therapy) the fraction of ceftiofur-resistant cells among enteric E. coli, similar to that in the absence of treatment, was most influenced by the parameters of ecology of enteric E. coli, such as the frequency of transfer of plasmids carrying resistance-genes, the rate of replacement of enteric E. coli by ingested E. coli, and the frequency of ceftiofur resistance in the latter