Synaptic weighting in single flux quantum neuromorphic computing.

Josephson junctions act as a natural spiking neuron-like device for neuromorphic computing. By leveraging the advances recently demonstrated in digital single flux quantum (SFQ) circuits and using recently demonstrated magnetic Josephson junction (MJJ) synaptic circuits, there is potential to make rapid progress in SFQ-based neuromorphic computing. Here we demonstrate the basic functionality of a synaptic circuit design that takes advantage of the adjustable critical current demonstrated in MJJs and implement a synaptic weighting element. The devices were fabricated with a restively shunted Nb/AlOx-Al/Nb process that did not include MJJs. Instead, the MJJ functionality was tested by making multiple circuits and varying the critical current, but not the external shunt resistance, of the oxide Josephson junction that represents the MJJ. Experimental measurements and simulations of the fabricated circuits are in good agreement.

Refined efficacy estimates of the Sanofi Pasteur dengue vaccine CYD-TDV using machine learning.

CYD-TDV is the first licensed dengue vaccine for individuals 9-45 (or 60) years of age. Using 12% of the subjects enroled in phase-2b and phase-3 trials for which baseline serostatus was measured, the vaccine-induced protection against virologically confirmed dengue during active surveillance (0-25 months) was found to vary with prior exposure to dengue. Because age and dengue exposure are highly correlated in endemic settings, refined insight into how efficacy varies by serostatus and age is essential to understand the increased risk of hospitalisation observed among vaccinated individuals during the long-term follow-up and to develop safe and effective vaccination strategies. Here we apply machine learning to impute the baseline serostatus for subjects with post-dose 3 titres but missing baseline serostatus. We find evidence for age dependence in efficacy independent of serostatus and estimate that among 9-16 year olds, CYD-TDV is protective against serotypes 1, 3 and 4 regardless of baseline serostatus.

Early warning of footpad dermatitis and hockburn in broiler chicken flocks using optical flow, bodyweight and water consumption.

Footpad dermatitis and hockburn are serious welfare and economic issues for the production of broiler (meat) chickens. The authors here describe the use of an inexpensive camera system that monitors the movements of broiler flocks throughout their lives and suggest that it is possible to predict, even in young birds, the cross-sectional prevalence at slaughter of footpad dermatitis and hockburn before external signs are visible. The skew and kurtosis calculated from the authors' camera-based optical flow system had considerably more power to predict these outcomes in the 50 flocks reported here than water consumption, bodyweight or mortality and therefore have the potential to inform improved flock management through giving farmers early warning of welfare issues. Further trials are underway to establish the generality of the results.

Quantum superposition at the half-metre scale.

The quantum superposition principle allows massive particles to be delocalized over distant positions. Though quantum mechanics has proved adept at describing the microscopic world, quantum superposition runs counter to intuitive conceptions of reality and locality when extended to the macroscopic scale, as exemplified by the thought experiment of Schrödinger's cat. Matter-wave interferometers, which split and recombine wave packets in order to observe interference, provide a way to probe the superposition principle on macroscopic scales and explore the transition to classical physics. In such experiments, large wave-packet separation is impeded by the need for long interaction times and large momentum beam splitters, which cause susceptibility to dephasing and decoherence. Here we use light-pulse atom interferometry to realize quantum interference with wave packets separated by up to 54 centimetres on a timescale of 1 second. These results push quantum superposition into a new macroscopic regime, demonstrating that quantum superposition remains possible at the distances and timescales of everyday life. The sub-nanokelvin temperatures of the atoms and a compensation of transverse optical forces enable a large separation while maintaining an interference contrast of 28 per cent. In addition to testing the superposition principle in a new regime, large quantum superposition states are vital to exploring gravity with atom interferometers in greater detail. We anticipate that these states could be used to increase sensitivity in tests of the equivalence principle, measure the gravitational Aharonov-Bohm effect, and eventually detect gravitational waves and phase shifts associated with general relativity.

Exploration of the power of routine surveillance data to assess the impacts of industry-led badger culling on bovine tuberculosis incidence in cattle herds.

In the UK, badgers (Meles meles) are a well-known reservoir of infection, and there has been lively debate about whether badger culling should play a role within the British Government's strategy to control and eventually eradicate tuberculosis (TB) in cattle. The key source of information on the potential for badger culling to reduce cattle TB in high-cattle-TB-incidence areas remains the Randomised Badger Culling Trial (RBCT). In late 2013, two pilot areas were subjected to industry-led badger culls. These culls differed importantly from RBCT culling in that free-ranging as well as cage-trapped badgers were shot, and culling took place over a longer time period. Their impacts will be harder to evaluate because culling was not randomised between comparable areas for subsequent comparisons of culling versus no culling. However, the authors present calculations that explore the power of routine surveillance data to assess the impacts of industry-led badger culling on cattle TB incidence. The rollout of industry-led culling as a component of a national cattle TB control policy would be controversial. The best possible estimates of the effects of such culling on confirmed cattle TB incidence should be made available to inform all stakeholders and policy-makers.

Bovine Tuberculosis Risk Factors for British Herds Before and After the 2001 Foot-and-Mouth Epidemic: What have we Learned from the TB99 and CCS2005 Studies?

Over the last couple of decades, the UK experienced a substantial increase in the incidence and geographical spread of bovine tuberculosis (TB), in particular since the epidemic of foot-and-mouth disease (FMD) in 2001. The initiation of the Randomized Badger Culling Trial (RBCT) in 1998 in south-west England provided an opportunity for an in-depth collection of questionnaire data (covering farming practices, herd management and husbandry, trading and wildlife activity) from herds having experienced a TB breakdown between 1998 and early 2006 and randomly selected control herds, both within and outside the RBCT (the so-called TB99 and CCS2005 case-control studies). The data collated were split into four separate and comparable substudies related to either the pre-FMD or post-FMD period, which are brought together and discussed here for the first time. The findings suggest that the risk factors associated with TB breakdowns may have changed. Higher Mycobacterium bovis prevalence in badgers following the FMD epidemic may have contributed to the identification of the presence of badgers on a farm as a prominent TB risk factor only post-FMD. The strong emergence of contact/trading TB risk factors post-FMD suggests that the purchasing and movement of cattle, which took place to restock FMD-affected areas after 2001, may have exacerbated the TB problem. Post-FMD analyses also highlighted the potential impact of environmental factors on TB risk. Although no unique and universal solution exists to reduce the transmission of TB to and among British cattle, there is an evidence to suggest that applying the broad principles of biosecurity on farms reduces the risk of infection. However, with trading remaining as an important route of local and long-distance TB transmission, improvements in the detection of infected animals during pre- and post-movement testing should further reduce the geographical spread of the disease.

Transmission scenarios for Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and how to tell them apart.

Detection of human cases of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection internationally is a global public health concern. Rigorous risk assessment is particularly challenging in a context where surveillance may be subject to under-ascertainment and a selection bias towards more severe cases. We would like to assess whether the virus is capable of causing widespread human epidemics, and whether self-sustaining transmission is already under way. Here we review possible transmission scenarios for MERS-CoV and their implications for risk assessment and control. We discuss how existing data, future investigations and analyses may help in reducing uncertainty and refining the public health risk assessment and present analytical approaches that allow robust assessment of epidemiological characteristics, even from partial and biased surveillance data. Finally, we urge that adequate data be collected on future cases to permit rigorous assessment of the transmission characteristics and severity of MERS-CoV, and the public health threat it may pose. Going beyond minimal case reporting, open international collaboration, under the guidance of the World Health Organization and the International Health Regulations, will impact on how this potential epidemic unfolds and prospects for control.

Herd-level risk factors of bovine tuberculosis in England and Wales after the 2001 foot-and-mouth disease epidemic.

OBJECTIVES: We present the results of a 2005 case-control study of bovine tuberculosis (bTB) breakdowns in English and Welsh herds. The herd management, farming practices, and environmental factors of 401 matched pairs of case and control herds were investigated to provide a picture of herd-level risk factors in areas of varying bTB incidence. METHODS: A global conditional logistic regression model, with region-specific variants, was used to compare case herds that had experienced a confirmed bTB breakdown to contemporaneous control herds matched on region, herd type, herd size, and parish testing interval. RESULTS: Contacts with cattle from contiguous herds and sourcing cattle from herds with a recent history of bTB were associated with an increased risk in both the global and regional analyses. Operating a farm over several premises, providing cattle feed inside the housing, and the presence of badgers were also identified as significantly associated with an increased bTB risk. CONCLUSIONS: Steps taken to minimize cattle contacts with neighboring herds and altering trading practices could have the potential to reduce the size of the bTB epidemic. In principle, limiting the interactions between cattle and wildlife may also be useful; however this study did not highlight any specific measures to implement.

Recurrence of bovine tuberculosis breakdowns in Great Britain: risk factors and prediction.

Bovine tuberculosis (bTB) is an important economic disease worldwide with implications for both animal and human health. In Great Britain the number of herds that test positive for bTB, termed "breakdowns", has increased over the last two decades. Despite more intensive testing during a breakdown, around 23% of breakdowns recur within 12 months of the previous breakdown ending, and around 38% within 24 months. These "recurrent" breakdowns may be important for onward transmission of infection. Detailed case-control data were analysed to identify factors associated with recurrence within 12 months. The model predicted 83% of all recurrent breakdowns, with a positive predictive value (PPV) of 44%. A further model, restricted to data currently available nationally, was not sufficient to predict recurrence reliably; at a sensitivity of 72-76%, the PPV was 33-36%, when validated on independent data. Factors identified to be associated with recurrence are consistent with previous studies; namely, the number of reactors, a recent bTB history in the herd and a lack of association with the confirmation status of the initial breakdown. These variables are indicative of a higher level of infection or residual infection, and could be useful in the future development of predictive models for bTB recurrence.

Influence of rearing and lay risk factors on propensity for feather damage in laying hens.

1. Feather pecking is one of the major problems facing the egg industry in non-cage systems and is set to become even more of an issue with the European Union ban on the keeping of laying hens in barren battery cages which comes into force in 2012 and the prospect of a ban on beak-trimming. Reducing feather pecking without resorting to beak treatment is an important goal for the poultry industry. 2. We report here a longitudinal study that included over 335,500 birds from 22 free range and organic laying farms. Accelerated failure time models and proportional hazards models were used to examine the effects of a wide range of factors (management, environment and bird) on development of substantial feather damage in lay. Particular emphasis was placed on risk factors during rear and on practices that could feasibly be changed or implemented. 3. The age at which a flock exhibits substantial feather damage could be predicted both by factors in the environment and by early symptoms in the birds themselves. Factors that were associated with earlier onset of severe feather damage included the presence of chain feeders, raised levels of carbon dioxide and ammonia, higher sound and light levels, particularly in younger birds. Increased feather damage (even very slight) in birds at 17-20 weeks of age was also highly predictive of the time of onset of severe feather damage during lay. Increased feed intake also indicated that a flock was at risk of early severe feather damage. 4. Birds that stayed on the same farm for rearing and lay showed later onset of serious feather damage than those that experienced a change in farm from rearing to lay. However, an increased number of changes between rearing and lay (feeder type, drinker type, light intensity etc) was not associated with earlier onset of serious feather damage. Further research needs to be done on the role of the transition from rearing to lay as a risk factor for FP in lay.

Predicting prolonged bovine tuberculosis breakdowns in Great Britain as an aid to control.

Bovine tuberculosis (bTB) is an important notifiable disease in cattle in Great Britain (GB), and is subject to statutory control measures. Despite this, disease incidence has increased since the mid-1980s, and around 30% of herd breakdowns continue for more than 240 days. This is twice the shortest possible time for confirmed breakdowns to test clear from infection (≈120 days), and four times the shortest possible time for unconfirmed breakdowns (≈60 days). These "prolonged" breakdowns consume substantial resources and may act as an ongoing source of infection. It is not clear why some breakdowns become prolonged. Existing detailed case-control data have been re-analysed to determine risk factors for breakdowns lasting longer than 240 days, the strongest of which was the confirmation status of the breakdown: OR 12.6 (95%CI: 6.7-25.4). A further model restricted to data available early on in a breakdown for all breakdowns nationally, can predict 82-84% of prolonged breakdowns with a positive predictive value of 44-49% when validated using existing national datasets over a 4-year period. Identification of prolonged breakdowns at an earlier stage could help to target bTB controls in GB.

Specificity of the Toxoplasma gondii-altered behaviour to definitive versus non-definitive host predation risk.

The hypothesis that the parasite Toxoplasma gondii manipulates the behaviour of its intermediate rat host in order to increase its chance of being predated specifically by its feline definitive host, rather than a non-definitive host predator species, was tested. The impact of a range of therapeutic drugs, previously demonstrated to be effective in preventing the development of T. gondii-associated behavioural and cognitive alterations in rats, on definitive-host predator specificity was also tested. Using a Y-shaped maze design, we demonstrated that T. gondii-associated behavioural changes, apparently aimed to increase predation rate, do appear to be specific to that of the feline definitive host--there were significant and consistent differences between the (untreated) infected and uninfected rats groups where T. gondii-infected rats tended to choose the definitive host feline-predator-associated maze arm and nest-box significantly more often than a maze arm or nest-box treated with non-definitive host predator (mink) odour. Drug treatment of infected rats prevented any such host-specificity from being displayed. We discuss our results in terms of their potential implications both for T. gondii epidemiology and the evolution of parasite-altered behaviour.

The prevalence, distribution and severity of detectable pathological lesions in badgers naturally infected with Mycobacterium bovis.

The Randomized Badger Culling Trial (RBCT) began in 1998 to determine the impact of badger culling in controlling bovine tuberculosis in cattle. A total of 1166 badgers (14% of total) proactively culled during the RBCT were found to be tuberculous, offering a unique opportunity to study the pathology caused by Mycobacterium bovis in a large sample of badgers. Of these, 39% of adults (approximately 6% of all adults culled) had visible lesions (detectable at necropsy) of bovine tuberculosis; cubs had a lower prevalence of infection (9%) but a higher percentage of tuberculous cubs (55.5%) had visible lesions. Only approximately 1% of adult badgers had extensive, severe pathology. Tuberculous badgers with recorded bite wounds (approximately 5%) had a higher prevalence of visible lesions and a different distribution of lesions, suggesting transmission via bite wounds. However, the predominance of lesions in the respiratory tract indicates that most transmission occurs by the respiratory route.

Parasites as causative agents of human affective disorders? The impact of anti-psychotic, mood-stabilizer and anti-parasite medication on Toxoplasma gondii's ability to alter host behaviour.

With increasing pressure to understand transmissible agents, renewed recognition of infectious causation of both acute and chronic diseases is occurring. Epidemiological and neuropathological studies indicate that some cases of schizophrenia may be associated with environmental factors, such as exposure to the ubiquitous protozoan Toxoplasma gondii. Reasons for this include T. gondii's ability to establish persistent infection within the central nervous system, its ability to manipulate intermediate host behaviour, the occurrence of neurological and psychiatric symptoms in some infected individuals, and an association between infection with increased incidence of schizophrenia. Moreover, several of the medications used to treat schizophrenia and other psychiatric disease have recently been demonstrated in vitro to possess anti-parasitic, and in particular anti-T. gondii, properties. Our aim here was thus to test the hypothesis that the anti-psychotic and mood stabilizing activity of some medications may be achieved, or at least augmented, through their in vivo inhibition of T. gondii replication and invasion in infected individuals. In particular we predicted, using the epidemiologically and clinically applicable rat-T. gondii model system, and following a previously described and neurologically characterized 'feline attraction' protocol that haloperidol (an anti-psychotic used in the treatment of mental illnesses including schizophrenia) and/or valproic acid (a mood stabilizer used in the treatment of mental illnesses including schizophrenia), would be, at least, as effective in preventing the development of T. gondii-associated behavioural and cognitive alterations as the standard anti-T. gondii chemotherapeutics pyrimethamine with Dapsone. We demonstrate that, while T. gondii appears to alter the rats' perception of predation risk turning their innate aversion into a 'suicidal' feline attraction, anti-psychotic drugs prove as efficient as anti-T. gondii drugs in preventing such behavioural alterations. Our results have important implications regarding the aetiology and treatment of such disorders.

Seroprevalence of IgG antibodies to SARS-coronavirus in asymptomatic or subclinical population groups.

We systematically reviewed the current understanding of human population immunity against SARS-CoV in different groups, settings and geography. Our meta-analysis, which included all identified studies except those on wild animal handlers, yielded an overall seroprevalence of 0.10% [95% confidence interval (CI) 0.02-0.18]. Health-care workers and others who had close contact with SARS patients had a slightly higher degree of seroconversion (0.23%, 95% CI 0.02-0.45) compared to healthy blood donors, others from the general community or non-SARS patients recruited from the health-care setting (0.16%, 95% CI 0-0.37). When analysed by the two broad classes of testing procedures, it is clear that serial confirmatory test protocols resulted in a much lower estimate (0.050%, 95% CI 0-0.15) than single test protocols (0.20%, 95% CI 0.06-0.34). Potential epidemiological and laboratory pitfalls are also discussed as they may give rise to false or inconsistent results in measuring the seroprevalence of IgG antibodies to SARS-CoV.

Epidemiological analysis of data for scrapie in Great Britain.

In recent years, the control or eradication of scrapie and any other transmissible spongiform encephalopathies (TSEs) possibly circulating in the sheep population has become a priority in Britain and elsewhere in Europe. A better understanding of the epidemiology of scrapie would greatly aid the development and evaluation of control and eradication strategies. Here we bound the range of key epidemiological parameters using a combination of relatively detailed pathogenesis and demography data, more limited data on susceptibility and incubation times, and recent survey data on scrapie incidence in Great Britain. These data are simultaneously analysed using mathematical models describing scrapie transmission between sheep and between flocks. Our analysis suggests that occurrence of scrapie in a flock typically provokes changes in flock management that promote termination of the outbreak, such as the adoption of selective breeding, and that a large fraction of cases (possibly over 80%) goes undetected. We show that the data analysed are consistent with the within-flock reproduction number of scrapie lying in the range 1.5-6, consistent with previous epidemiological studies.