Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans

Peer reviewedPublisher PD

Incorporating habitat distribution in wildlife disease models: conservation implications for the threat of squirrelpox on the Isle of Arran

Emerging infectious diseases are a substantial threat to native populations. The spread of disease through naive native populations will depend on both demographic and disease parameters, as well as on habitat suitability and connectivity. Using the potential spread of squirrelpox virus (SQPV) on the Isle of Arran as a case study, we develop mathematical models to examine the impact of an emerging disease on a population in a complex landscape of different habitat types. Furthermore, by considering a range of disease parameters, we infer more generally how complex landscapes interact with disease characteristics to determine the spread and persistence of disease. Specific findings indicate that a SQPV outbreak on Arran is likely to be short lived and localized to the point of introduction allowing recovery of red squirrels to pre-infection densities; this has important consequences for the conservation of red squirrels. More generally, we find that the extent of disease spread is dependent on the rare passage of infection through poor quality corridors connecting good quality habitats. Acute, highly transmissible infectious diseases are predicted to spread rapidly causing high mortality. Nonetheless, the disease typically fades out following local epidemics and is not supported in the long term. A chronic infectious disease is predicted to spread more slowly but can remain endemic in the population. This allows the disease to spread more extensively in the long term as it increases the chance of spread between poorly connected populations. Our results highlight how a detailed understanding of landscape connectivity is crucial when considering conservation strategies to protect native species from disease threats

Graphical Reasoning in Compact Closed Categories for Quantum Computation

Compact closed categories provide a foundational formalism for a variety of important domains, including quantum computation. These categories have a natural visualisation as a form of graphs. We present a formalism for equational reasoning about such graphs and develop this into a generic proof system with a fixed logical kernel for equational reasoning about compact closed categories. Automating this reasoning process is motivated by the slow and error prone nature of manual graph manipulation. A salient feature of our system is that it provides a formal and declarative account of derived results that can include `ellipses'-style notation. We illustrate the framework by instantiating it for a graphical language of quantum computation and show how this can be used to perform symbolic computation.Comment: 21 pages, 9 figures. This is the journal version of the paper published at AIS

Modulating attentional load affects numerosity estimation: evidence against a pre-attentive subitizing mechanism

Traditionally, the visual enumeration of a small number of items (1 to about 4), referred to as subitizing, has been thought of as a parallel and pre-attentive process and functionally different from the serial attentive enumeration of larger numerosities. We tested this hypothesis by employing a dual task paradigm that systematically manipulated the attentional resources available to an enumeration task. Enumeration accuracy for small numerosities was severely decreased as more attentional resources were taken away from the numerical task, challenging the traditionally held notion of subitizing as a pre-attentive, capacity-independent process. Judgement of larger numerosities was also affected by dual task conditions and attentional load. These results challenge the proposal that small numerosities are enumerated by a mechanism separate from large numerosities and support the idea of a single, attention-demanding enumeration mechanism

Children and older adults exhibit distinct sub-optimal cost-benefit functions when preparing to move their eyes and hands

"© 2015 Gonzalez et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited"Numerous activities require an individual to respond quickly to the correct stimulus. The provision of advance information allows response priming but heightened responses can cause errors (responding too early or reacting to the wrong stimulus). Thus, a balance is required between the online cognitive mechanisms (inhibitory and anticipatory) used to prepare and execute a motor response at the appropriate time. We investigated the use of advance information in 71 participants across four different age groups: (i) children, (ii) young adults, (iii) middle-aged adults, and (iv) older adults. We implemented 'cued' and 'non-cued' conditions to assess age-related changes in saccadic and touch responses to targets in three movement conditions: (a) Eyes only; (b) Hands only; (c) Eyes and Hand. Children made less saccade errors compared to young adults, but they also exhibited longer response times in cued versus non-cued conditions. In contrast, older adults showed faster responses in cued conditions but exhibited more errors. The results indicate that young adults (18 -25 years) achieve an optimal balance between anticipation and execution. In contrast, children show benefits (few errors) and costs (slow responses) of good inhibition when preparing a motor response based on advance information; whilst older adults show the benefits and costs associated with a prospective response strategy (i.e., good anticipation)

Recruitment of young women to a trial of chlamydia screening – as easy as it sounds?

BACKGROUND: Recruiting to trials is complex and difficult. The Prevention of Pelvic Infection (POPI) trial aims to see if screening women for chlamydia and treating those found to be infected reduces the incidence of pelvic inflammatory disease in the following twelve months. It focuses on young, sexually active, multiethnic, mainly inner city, female students. The main aim of this paper is to describe our recruitment methods. Secondary aims in two small subgroups, are to compare characteristics of women recruited with those not recruited, and to explore participants' understanding of when their samples would be tested for chlamydia. METHODS: Women students attending lectures or in common rooms at 22 universities and further education colleges were recruited by female research assistants working in pairs. Participants were asked to complete a questionnaire on sexual health and to provide self-taken vaginal swabs. In addition, during 3 recruitment sessions, a female medical student asked non-participants to complete a brief anonymous questionnaire on reasons for not taking part. Finally another female medical student contacted 40 consecutive participants within a month of recruitment and asked if they understood that their samples might not be tested for a year. RESULTS: With enormous effort over 2 years we recruited 2526 women. A survey of 61 non-responders showed only 18 (30%) were eligible to take part (age <28, been sexually active and not been tested for chlamydia in the past 3 months). Eligible non-responders were of similar age to the 35 responders in the same recruitment sessions, but more likely to be from ethnic minority groups (67% 12/18 versus 29% 10/35 p < 0.01). Email and telephone contact with 35/40 (88%) of consecutive participants showed only two (6%) did not understand that their specimen might not be tested for chlamydia for a year. Thirty participants (85%) could name one or more possible consequences of untreated chlamydia infection. CONCLUSION: As in other studies, a key to attaining recruitment targets was the enthusiasm of the research team. Minority ethnic groups were probably under-represented, but understanding of participants was good

R parity violating contribution to e+e−(μ+μ−)→tcˉe^+e^-(\mu^+\mu^-)\to t{\bar c}

In this article we consider the contribution of $R_p$ violating couplings to the process $e^+e^-(\mu^+\mu^-)\to t{\bar c}$ at high energy lepton collider. We show that the present upper bound on the relevant $R_p$ violating coulpings obtained from low energy measurements would produce a few hundred to a thousand top-charm events at the next linear $e^+e^-(\mu^+\mu^-)$ collider. Hence, it should be possible to observe the rare process at future lepton collider.Comment: LaTEX, 13 pages, one figure is removed. A brief discussion on possible backgrounds is added. To appear in Phys. Rev.

Further developments towards a genome-scale metabolic model of yeast

BACKGROUND: To date, several genome-scale network reconstructions have been used to describe the metabolism of the yeast Saccharomyces cerevisiae, each differing in scope and content. The recent community-driven reconstruction, while rigorously evidenced and well annotated, under-represented metabolite transport, lipid metabolism and other pathways, and was not amenable to constraint-based analyses because of lack of pathway connectivity. RESULTS: We have expanded the yeast network reconstruction to incorporate many new reactions from the literature and represented these in a well-annotated and standards-compliant manner. The new reconstruction comprises 1102 unique metabolic reactions involving 924 unique metabolites - significantly larger in scope than any previous reconstruction. The representation of lipid metabolism in particular has improved, with 234 out of 268 enzymes linked to lipid metabolism now present in at least one reaction. Connectivity is emphatically improved, with more than 90% of metabolites now reachable from the growth medium constituents. The present updates allow constraint-based analyses to be performed; viability predictions of single knockouts are comparable to results from in vivo experiments and to those of previous reconstructions. CONCLUSIONS: We report the development of the most complete reconstruction of yeast metabolism to date that is based upon reliable literature evidence and richly annotated according to MIRIAM standards. The reconstruction is available in the Systems Biology Markup Language (SBML) and via a publicly accessible database http://www.comp-sys-bio.org/yeastnet/

Economic evaluation of diagnosing and excluding ectopic pregnancy

BACKGROUND: The diagnosis of ectopic pregnancy in women presenting in early pregnancy is often protracted, relying on costly investigations that are psychologically burdensome to the patient. The aim of this study was to evaluate the financial costs to the health services in Scotland of the current methods used to diagnose and exclude ectopic pregnancy, and compare these with that of a theoretical single diagnostic serum biomarker. METHODS: We conducted a retrospective cost description analysis (with and without costs of diagnostic laparoscopy) of the healthcare costs incurred by all patients presenting to a large Scottish teaching hospital between June and September 2006 with pain and bleeding in early pregnancy, where ectopic pregnancy was not excluded. Additionally, a cost minimisation analysis was performed of the costs of current ectopic pregnancy investigations versus those of a theoretical single diagnostic serum biomarker. This included sensitivity analyses where the biomarker was priced at increasing values and assumed to have less than 100% diagnostic sensitivity and specificity. RESULTS: 175 patients were eligible to be included in the analysis. 47% of patients required more than 3 visits to diagnose or exclude ectopic pregnancy. The total yearly cost for diagnosing and excluding ectopic pregnancy was £197K for the hospital stated, and was estimated to be £1,364K for Scotland overall. Using a theoretical diagnostic serum biomarker we calculated that we could save health services up to £976K (lowest saving £251K after subanalyses) every year in Scotland. CONCLUSIONS: Ectopic pregnancy is expensive to diagnose and exclude, and the investigation process is often long and might involve significant psychological morbidity. The development of a single diagnostic serum biomarker would minimise this morbidity and lead to significant savings of up to £1 million pounds per year in Scotland