Applications of omics approaches to the development of microbiological risk assessment using RNA virus dose-response models as a case study

T e in the amount of ‘omics’ data available and in our ability to interpret those data. The aim of this paper was to consider how omics techniques can be used to improve and refine microbiological risk assessment, using dose–response models for RNA viruses, with particular reference to norovirus through the oral route as the case study. The dose–response model for initial infection in the gastrointestinal tract is broken down into the component steps at the molecular level and the feasibility of assigning probabilities to each step assessed. The molecular mechanisms are not sufficiently well understood at present to enable quantitative estimation of probabilities on the basis of omics data. At present, the great strength of gene sequence data appears to be in giving information on the distribution and proportion of susceptible genotypes (for example due to the presence of the appropriate pathogen‐binding receptor) in the host population rather than in predicting specificities from the amino acid sequences concurrently obtained. The nature of the mutant spectrum in RNA viruses greatly complicates the application of omics approaches to the development of mechanistic dose–response models and prevents prediction of risks of disease progression (given infection has occurred) at the level of the individual host. However, molecular markers in the host and virus may enable more broad predictions to be made about the consequences of exposure in a population. In an alternative approach, comparing the results of deep sequencing of RNA viruses in the faeces/vomitus from donor humans with those from their infected recipients may enable direct estimates of the average probability of infection per virion to be made.

Potential-based methodology for active sound control in three dimensional settings

This paper extends a potential-based approach to active noise shielding with preservation of wanted sound in three-dimensional settings. The approach, which was described in a previous publication [Lim et al., J. Acoust. Soc. Am. 129(2), 717-725 (2011)], provides several significant advantages over conventional noise control methods. Most significantly, the methodology does not require any information including the characterization of sources, impedance boundary conditions and surrounding medium, and that the methodology automatically differentiates between the wanted and unwanted sound components. The previous publication proved the concept in one-dimensional conditions. In this paper, the approach for more realistic conditions is studied by numerical simulation and experimental validation in three-dimensional cases. The results provide a guideline to the implementation of the active shielding method with practical three-dimensional conditions. Through numerical simulation it is demonstrated that while leaving the wanted sound unchanged, the developed approach offers selective volumetric noise cancellation within a targeted domain. In addition, the method is implemented in a three-dimensional experiment with a white noise source in a semi-anechoic chamber. The experimental study identifies practical difficulties and limitations in the use of the approach for real applications.

Entry of H5N1 highly pathogenic avian influenza virus into Europe through migratory wild birds: a qualitative release assessment at the species level

AIMS

To estimate qualitatively the probabilities of release (or entry) of Eurasian lineage H5N1 highly pathogenic avian influenza (HPAI) virus into Great Britain (GB), the Netherlands and Italy through selected higher risk species of migratory water bird.

METHODS AND RESULTS

The probabilities of one or more release events of H5N1 HPAI per year (Pre(lease)) were estimated qualitatively for 15 avian species, including swans, geese, ducks and gulls, by assessing the prevalence of H5N1 HPAI in different regions of the world (weighted to 2009) and estimates of the total numbers of birds migrating from each of those regions. The release assessment accommodated the migration times for each species in relation to the probabilities of their surviving infection and shedding virus on arrival. Although the predicted probabilities of release of H5N1 per individual bird per year were low, very low or negligible, Pre(lease) was high for a few species reflecting the high numbers of birds migrating from some regions. Values of Pre(lease) were generally higher for the Netherlands than for GB, while ducks and gulls from Africa presented higher probabilities to Italy compared to the Netherlands and GB.

CONCLUSIONS

Bird species with high values of Pre(lease) in GB, the Netherlands and Italy generally originate from within Europe based on data for global prevalence of H5N1 between 2003 and 2009 weighted to 2009. Potential long-distance transfer of H5N1 HPAI from North Asia and Eurasia to GB, the Netherlands and Italy is limited to a few species and does not occur from South-East Asia, an area where H5N1 is endemic.

SIGNIFICANCE AND IMPACT OF THE STUDY

The approach accommodates biogeographical conditions and variability in the estimated worldwide prevalence of the virus. The outputs of this release assessment can be used to inform surveillance activities through focusing on certain species and migratory pathways.

A prospective study of risk factors for foot ulceration: the West of Ireland Diabetes Foot Study

BACKGROUND

This is the first study to examine risk factors for diabetic foot ulceration in Irish general practice.

AIM

To determine the prevalence of established risk factors for foot ulceration in a community-based cohort, and to explore the potential for estimated glomerular filtration rate (eGFR) to act as a novel risk factor.

DESIGN

A prospective observational study.

METHODS

Patients with diabetes attending 12 (of 17) invited general practices were invited for foot screening. Validated clinical tests were carried out at baseline to assess for vascular and sensory impairment and foot deformity. Ulcer incidence was ascertained by patient self-report and medical record. Patients were re-assessed 18 months later.

RESULTS

Of 828 invitees, 563 (68%) attended screening. On examination 23-25% had sensory dysfunction and 18-39% had evidence of vascular impairment. Using the Scottish Intercollegiate Guidelines Network risk stratification system we found the proportion at moderate and high risk of future ulceration to be 25% and 11%, respectively. At follow-up 16/383 patients (4.2%) developed a new foot ulcer (annual incidence rate of 2.6%). We observed an increasing probability of abnormal vascular and sensory test results (pedal pulse palpation, doppler waveform assessment, 10 g monofilament, vibration perception and neuropathy disability score) with declining eGFR levels. We were unable to show an independent association between new ulceration and reduced eGFR [Odds ratio 1.01; P = 0.64].

CONCLUSION

Our data show the extent of foot complications in a representative sample of diabetes patients in Ireland. Use of eGFR did not improve identification of patients at risk of foot ulceration.

Profiling of Glucose-Sensing Neurons Reveals that GHRH Neurons Are Activated by Hypoglycemia

Comprehensive transcriptional profiling of glucose-sensing neurons is challenging because of low expression levels of glucokinase (Gck) and other key proteins that transduce a glucose signal. To overcome this, we generated and validated transgenic mice with a neuronal/endocrine-specific Gck promoter driving cre expression and mated them to mice with cre-dependent expression of an EGFP-tagged ribosomal protein construct (EEF1A1-LSL.EGFPL10) that can be used to map and profile cells. We found significant Gck expression in hypothalamic and limbic regions in cells that are activated following administration of glucose or 2-deoxyglucose. Transcriptional profiling from Gck-cre/EEF1A1-LSL.EGFPL10 mice enriched known and previously unknown glucose-sensing populations including neurons expressing growth hormone releasing hormone (GHRH). Electrophysiological recordings show that hypoglycemia activates GHRH neurons, suggesting a mechanistic link between hypoglycemia and growth hormone release. These studies provide a means for mapping glucose-sensitive neurons and for generating transcriptional profiles from other cell types expressing cre in a cell-specific manner.

Prognosticating in patients with advanced cancer--observational study comparing the accuracy of clinicians' and patients' estimates of survival

BACKGROUND

Clinicians' prognoses in patients with advanced cancer are imprecise. The aim of this study was to compare doctors', nurses' and patients' survival predictions and to identify factors which influence accuracy.

PATIENTS AND METHODS

Some 1018 patients with advanced cancer were recruited. Survival estimates were obtained from the attending doctor, nurse, multidisciplinary team (MDT) and patient (n = 829, 954, 987 and 290 estimates, respectively) and were compared with actual survival. Clinician and patient characteristics were recorded.

RESULTS

MDTs', doctors' and nurses' predictions were accurate 57.5%, 56.3% and 55.5% of occasions, respectively. Nurses were less accurate than the MDT (P = 0.007) but were no worse than doctors (P = 0.284). Estimates of clinicians and patients were more optimistic (doctors: 31%; nurses: 34%; MDT: 31.1%; patients: 45.1%) than pessimistic (12.7%, 11%, 11.4% and 2.7%). Nurses' accuracy increased if they had reviewed the patient within 24 h. Most patients (61.4%) wanted to know their prognosis. Only 37.1% were willing to offer an estimate regarding their own survival. Patients' prognostic estimates were less accurate than health care professionals' (P < 0.001).

CONCLUSIONS

MDTs were better at predicting survival than doctors' or nurses' alone. Patients were substantially worse. Among nurses, recency of review was related to improved prognostic accuracy.

A rare case of chronic benign tracheo-oesophageal fistula, with Candida albicans cultured from a pleural effusion

We present a case of chronic benign tracheo-oesophageal fistula in an immunologically competent elderly female, cured with a period of nasogastric feeding.

Facilitating medical withdrawal from opiates in rural Ontario

CONTEXT

The abuse of oxycodone in Northwestern Ontario, Canada, has escalated at alarming rates raising concerns that opiate use has reached epidemic proportions, particularly among the First Nations communities. The authors were involved in establishing Ontario's first rural inpatient medical withdrawal unit to serve patients seeking abstinence.

ISSUES

The development of the medical withdrawal support services (MWSS) required creative and adaptive strategies to respond to the geographical, cultural and institutional circumstances.

LESSONS LEARNED

Key factors to support program efficacy and successful outcomes for clients during the inaugural eight months of operation are interprofessional and collaborative approaches with a cultural awareness.Key words: addiction, Canada, First Nation, medical withdrawal.

Epidemic threats to the European Union: expert views on six virus groups

In recent years, several animal disease epidemics have occurred within the European Union (EU). At the 4th Annual Meeting of the EPIZONE network (7-10 June 2010, St. Malo, France), an interactive session was run to elicit the opinions of delegates on a pre-defined list of epidemic threats to the EU. Responses from over 190 delegates, to questions relating to impact and likelihood, were used to rank six virus groups with respect to their perceived threat now (2010) and in 2020. The combined opinions of all delegates suggested that, from the pre-selected list of virus groups, foot-and-mouth disease and influenza are currently of most concern. Delegates thought that influenza would be less of a threat and zoonotic arboviruses would be more of a threat in 2020. Although the virus group rankings should not be taken as definitive, the results could be used in conjunction with experimental and field data, by scientists, policy-makers and stakeholders when assessing and managing risks associated with these virus groups.