Effects of memory on the shapes of simple outbreak trees

Genomic tools, including phylogenetic trees derived from sequence data, are increasingly used to understand outbreaks of infectious diseases. One challenge is to link phylogenetic trees to patterns of transmission. Particularly in bacteria that cause chronic infections, this inference is affected by variable infectious periods and infectivity over time. It is known that non-exponential infectious periods can have substantial effects on pathogens’ transmission dynamics. Here we ask how this non-Markovian nature of an outbreak process affects the branching trees describing that process, with particular focus on tree shapes. We simulate Crump-Mode-Jagers branching processes and compare different patterns of infectivity over time. We find that memory (non-Markovian-ness) in the process can have a pronounced effect on the shapes of the outbreak’s branching pattern. However, memory also has a pronounced effect on the sizes of the trees, even when the duration of the simulation is fixed. When the sizes of the trees are constrained to a constant value, memory in our processes has little direct effect on tree shapes, but can bias inference of the birth rate from trees. We compare simulated branching trees to phylogenetic trees from an outbreak of tuberculosis in Canada, and discuss the relevance of memory to this dataset

Audit of Antenatal Testing of Sexually Transmissible Infections and Blood Borne Viruses at Western Australian Hospitals

In August 2007, the Western Australian Department of Health (DOH) released updated recommendations for testing of sexually transmissible infections (STI) and blood-borne viruses (BBV) in antenates. Prior to this, the Royal Australian & New Zealand College of Obstetricians & Gynaecologists (RANZCOG) antenatal testing recommendations had been accepted practice in most antenatal settings. The RANZCOG recommends that testing for HIV, syphilis, hepatitis B and C be offered at the first antenatal visit. The DOH recommends that in addition, chlamydia testing be offered. We conducted a baseline audit of antenatal STI/BBV testing in women who delivered at selected public hospitals before the DOH recommendations. We examined the medical records of 200 women who had delivered before 1st July 2007 from each of the sevenWAhospitals included in the audit. STI and BBV testing information and demographic data were collected. Of the 1,409 women included, 1,205 (86%) were non-Aboriginal and 200 (14%) were Aboriginal. High proportions of women had been tested for HIV (76%), syphilis (86%), hepatitis C (87%) and hepatitis B (88%). Overall, 72% of women had undergone STI/BBV testing in accordance with RANZCOG recommendations. However, chlamydia testing was evident in only 18% of records. STI/BBV prevalence ranged from 3.9% (CI 1.5– 6.3%) for chlamydia, to 1.7% (CI 1–2.4%) for hepatitis C, 0.7% (CI 0.3–1.2) for hepatitis B and 0.6% (CI 0.2–1) for syphilis. Prior to the DOH recommendations, nearly three-quarters of antenates had undergone STI/BBV testing in accordance with RANZCOG recommendations, but less than one fifth had been tested for chlamydia. The DOH recommendations will be further promoted with the assistance of hospitals and other stakeholders. A future audit will be conducted to determine the proportion of women tested according to the DOH recommendations. The hand book from this conference is available for download Published in 2008 by the Australasian Society for HIV Medicine Inc © Australasian Society for HIV Medicine Inc 2008 ISBN: 978-1-920773-59-

Insecurity of position-based quantum cryptography protocols against entanglement attacks

Recently, position-based quantum cryptography has been claimed to be unconditionally secure. In contrary, here we show that the existing proposals for position-based quantum cryptography are, in fact, insecure if entanglement is shared among two adversaries. Specifically, we demonstrate how the adversaries can incorporate ideas of quantum teleportation and quantum secret sharing to compromise the security with certainty. The common flaw to all current protocols is that the Pauli operators always map a codeword to a codeword (up to an irrelevant overall phase). We propose a modified scheme lacking this property in which the same cheating strategy used to undermine the previous protocols can succeed with a rate at most 85%. We conjecture that the modified protocol is unconditionally secure and prove this to be true when the shared quantum resource between the adversaries is a two- or three- level system

The average number of spanning trees in sparse graphs with given degrees

We give an asymptotic expression for the expected number of spanning trees in a random graph with a given degree sequence d=(d1,…,dn), provided that the number of edges is at least n+12dmax4, where dmax is the maximum degree. A key part of our argument involves establishing a concentration result for a certain family of functions over random trees with given degrees, using Prüfer codes

The Radon Monitoring System in Daya Bay Reactor Neutrino Experiment

We developed a highly sensitive, reliable and portable automatic system (H$^{3}$) to monitor the radon concentration of the underground experimental halls of the Daya Bay Reactor Neutrino Experiment. H$^{3}$ is able to measure radon concentration with a statistical error less than 10\% in a 1-hour measurement of dehumidified air (R.H. 5\% at 25$^{\circ}$C) with radon concentration as low as 50 Bq/m$^{3}$. This is achieved by using a large radon progeny collection chamber, semiconductor $\alpha$-particle detector with high energy resolution, improved electronics and software. The integrated radon monitoring system is highly customizable to operate in different run modes at scheduled times and can be controlled remotely to sample radon in ambient air or in water from the water pools where the antineutrino detectors are being housed. The radon monitoring system has been running in the three experimental halls of the Daya Bay Reactor Neutrino Experiment since November 2013

IgA antibodies to Epstein-Barr viral capsid antigens in saliva of nasopharyngeal carcinoma patients.

THE majority of sera from naso-pharyngeal carcinoma (NPC) patients studied to date was shown to have a titre of IgA antibodies to the Epstein-Barr viral capsid antigen (VCA) of 1/10, while the same reactivity was seldom detectable in the sera of controls consisting of patients with other cancers and healthy subjects (Henle and Henle, 1976; Ho et al., 1976 and in preparation). In all these sera, the detection of IgA reactivity to VCA was concomitant with high titres of IgG anti-bodies to VCA. This led to the conclusion that both serum reactivities might reflect the intensity of systemic stimulation by EBV-specific antigens (Ho et al., 1976). However, these findings did not exclude a concurrent production of local antibodies. Indeed, in view of the fact that discharge from NPC readily finds its way to the oral cavity and the saliva, and the close association known to exist between the neoplastic disease and EBV (Klein, 1973; Ho, 1975; de-The, et al., 1975), production of local antibodies to VCA may well be anticipated. We therefore tested the saliva obtained from NPC patients and controls for the presence of IgA antibodies to EBV VCA. Parallel specimens of saliva and sera were obtained from 30 histologically confirmed NPC patients before treatmen