Using birth-death processes to infer tumor subpopulation structure from live-cell imaging drug screening data.

Tumor heterogeneity is a complex and widely recognized trait that poses significant challenges in developing effective cancer therapies. In particular, many tumors harbor a variety of subpopulations with distinct therapeutic response characteristics. Characterizing this heterogeneity by determining the subpopulation structure within a tumor enables more precise and successful treatment strategies. In our prior work, we developed PhenoPop, a computational framework for unravelling the drug-response subpopulation structure within a tumor from bulk high-throughput drug screening data. However, the deterministic nature of the underlying models driving PhenoPop restricts the model fit and the information it can extract from the data. As an advancement, we propose a stochastic model based on the linear birth-death process to address this limitation. Our model can formulate a dynamic variance along the horizon of the experiment so that the model uses more information from the data to provide a more robust estimation. In addition, the newly proposed model can be readily adapted to situations where the experimental data exhibits a positive time correlation. We test our model on simulated data (in silico) and experimental data (in vitro), which supports our argument about its advantages.

Prior exposure to immunogenic peptides found in human influenza A viruses may influence the age distribution of cases with avian influenza H5N1 and H7N9 virus infections.

The epidemiology of H5N1 and H7N9 avian viruses of humans infected in China differs despite both viruses being avian reassortants that have inherited six internal genes from a common ancestor, H9N2. The median age of infected populations is substantially younger for H5N1 virus (26 years) compared with H7N9 virus (63 years). Population susceptibility to infection with seasonal influenza is understood to be influenced by cross-reactive CD8+ T cells directed towards immunogenic peptides derived from internal viral proteins which may provide some level of protection against further influenza infection. Prior exposure to seasonal influenza peptides may influence the age-related infection patterns observed for H5N1 and H7N9 viruses. A comparison of relatedness of immunogenic peptides between historical human strains and the two avian emerged viruses was undertaken for a possible explanation in the differences in age incidence observed. There appeared to be some relationship between past exposure to related peptides and the lower number of H5N1 virus cases in older populations, however the relationship between prior exposure and older populations among H7N9 virus patients was less clear.

Australia's National Notifiable Diseases Surveillance System 1991-2011: expanding, adapting and improving.

We reviewed key attributes (flexibility, data quality and timeliness) of Australia's National Notifiable Diseases Surveillance System (NNDSS) over its first 21 years. Cases notified to NNDSS from 1991 to 2011 were examined by jurisdiction (six states and two territories) and sub-period to describe changes in the number of notifiable diseases, proportion of cases diagnosed using PCR tests, data quality (focusing on data completeness), and notification delays. The number of notifiable diseases increased from 37 to 65. The proportion of cases diagnosed by PCR increased from 1% (1991-1997) to 49% (2005-2011). Indigenous status was complete for only 44% notifications (jurisdictional range 19-87%). Vaccination status was complete for 62% (jurisdictional range 32-100%) and country of acquisition for 24% of relevant cases. Data completeness improved over the study period with the exception of onset date. Median time to notification was 8 days (interquartile range 4-17 days, jurisdictional range 5-15 days); this decreased from 11 days (1991-1997) to 5 days (2005-2011). NNDSS expanded during the study period. Data completeness and timeliness improved, likely related to mandatory laboratory reporting and electronic data transfer. A nationally integrated electronic surveillance system, including electronic laboratory reporting, would further improve infectious disease surveillance in Australia.

Spatial Measures of Genetic Heterogeneity During Carcinogenesis.

In this work we explore the temporal dynamics of spatial heterogeneity during the process of tumorigenesis from healthy tissue. We utilize a spatial stochastic model of mutation accumulation and clonal expansion in a structured tissue to describe this process. Under a two-step tumorigenesis model, we first derive estimates of a non-spatial measure of diversity: Simpson's Index, which is the probability that two individuals sampled at random from the population are identical, in the premalignant population. We next analyze two new measures of spatial population heterogeneity. In particular we study the typical length scale of genetic heterogeneity during the carcinogenesis process and estimate the extent of a surrounding premalignant clone given a clinical observation of a premalignant point biopsy. This evolutionary framework contributes to a growing literature focused on developing a better understanding of the spatial population dynamics of cancer initiation and progression.

Overwhelming post-splenectomy sepsis in patients with asplenia and hyposplenia: a retrospective cohort study.

Overwhelming post-splenectomy infection (OPSI) is a serious complication of asplenia and is associated with encapsulated organisms, most commonly Streptococcus pneumoniae, but also Haemophilus influenzae and Neisseria meningitidis. We aimed to estimate the risk of infection in this patient group. We reviewed data collected by the Victorian Spleen Registry in Australia. On registration, all patients are asked about significant infections requiring admission to hospital for intravenous antibiotics; those requiring admission to ICU were defined as OPSI. In the 3274 asplenic patients registered 492 patients reported at least one episode of infection. There were 47 episodes of OPSI requiring intensive care (incidence rate 1·11/1000 patient-years). The risk of OPSI was highest in older patients, and there were no statistically significant differences in incidence by reason for splenectomy except for a higher rate in patients with medical hyposplenia. This study reinforces that post-splenectomy infection is a clinically significant but uncommon complication, and that fulminant infection requiring intensive care is a minority of all infections.

An overview of the epidemiology of notifiable infectious diseases in Australia, 1991-2011.

We reviewed the first 21 years (1991-2011) of Australia's National Notifiable Diseases Surveillance System (NNDSS). All nationally notified diseases (except HIV/AIDS and Creutzfeldt-Jakob disease) were analysed by disease group (n = 8), jurisdiction (six states and two territories), Indigenous status, age group and notification year. In total, 2 421 134 cases were analysed. The 10 diseases with highest notification incidence (chlamydial infection, campylobacteriosis, varicella zoster, hepatitis C, influenza, pertussis, salmonellosis, hepatitis B, gonococcal infection, and Ross River virus infection) comprised 88% of all notifications. Annual notification incidence was 591 cases/100 000, highest in the Northern Territory (2598/100 000) and in children aged <5 years (698/100 000). A total of 8·4% of cases were Indigenous Australians. Notification incidence increased by 6·4% per year (12% for sexually transmissible infections and 15% for vaccine-preventable diseases). The number of notifiable diseases also increased from 37 to 65. The number and incidence of notifications increased throughout the study period, partly due to addition of diseases to the NNDSS and increasing availability of sensitive diagnostic tests. The most commonly notified diseases require a range of public health responses addressing high-risk sexual and drug-use behaviours, food safety and immunization. Our results highlight populations with higher notification incidence that might require tailored public health interventions.

Associations of hospital characteristics with nosocomial pneumonia after cardiac surgery can impact on standardized infection rates.

To identify hospital-level factors associated with post-cardiac surgical pneumonia for assessing their impact on standardized infection rates (SIRs), we studied 43 691 patients in a cardiac surgery registry (2001-2011) in 16 hospitals. In a logistic regression model for pneumonia following cardiac surgery, associations with hospital characteristics were quantified with adjustment for patient characteristics while allowing for clustering of patients by hospital. Pneumonia rates varied from 0·7% to 12·4% across hospitals. Seventy percent of variability in the pneumonia rate was attributable to differences in hospitals in their long-term rates with the remainder attributable to within-hospital differences in rates over time. After adjusting for patient characteristics, the pneumonia rate was found to be higher in hospitals with more registered nurses (RNs)/100 intensive-care unit (ICU) admissions [adjusted odds ratio (aOR) 1·2, P = 0·006] and more RNs/available ICU beds (aOR 1·4, P < 0·001). Other hospital characteristics had no significant association with pneumonia. SIRs calculated on the basis of patient characteristics alone differed substantially from the same rates calculated on the basis of patient characteristics and the hospital characteristic of RNs/100 ICU admissions. Since SIRs using patient case-mix information are important for comparing rates between hospitals, the additional allowance for hospital characteristics can impact significantly on how hospitals compare.

Optimization of radiation dosing schedules for proneural glioblastoma.

Glioblastomas are the most aggressive primary brain tumor. Despite treatment with surgery, radiation and chemotherapy, these tumors remain uncurable and few significant increases in survival have been observed over the last half-century. We recently employed a combined theoretical and experimental approach to predict the effectiveness of radiation administration schedules, identifying two schedules that led to superior survival in a mouse model of the disease (Leder et al., Cell 156(3):603-616, 2014). Here we extended this approach to consider fractionated schedules to best minimize toxicity arising in early- and late-responding tissues. To this end, we decomposed the problem into two separate solvable optimization tasks: (i) optimization of the amount of radiation per dose, and (ii) optimization of the amount of time that passes between radiation doses. To ensure clinical applicability, we then considered the impact of clinical operating hours by incorporating time constraints consistent with operational schedules of the radiology clinic. We found that there was no significant loss incurred by restricting dosage to an 8:00 a.m. to 5:00 p.m. window. Our flexible approach is also applicable to other tumor types treated with radiotherapy.

Spatial Moran models, II: cancer initiation in spatially structured tissue.

We study the accumulation and spread of advantageous mutations in a spatial stochastic model of cancer initiation on a lattice. The parameters of this general model can be tuned to study a variety of cancer types and genetic progression pathways. This investigation contributes to an understanding of how the selective advantage of cancer cells together with the rates of mutations driving cancer, impact the process and timing of carcinogenesis. These results can be used to give insights into tumor heterogeneity and the "cancer field effect," the observation that a malignancy is often surrounded by cells that have undergone premalignant transformation.

Leprosy: diagnosis and management in a developed setting.

Leprosy remains an important global health concern, but little has been published about its diagnosis and management in developed settings. It has been postulated that delay in diagnosis is common in developed settings. We reviewed all the cases of leprosy seen at a major tertiary referral centre between 1999 and 2013 and demonstrated that delay in diagnosis is common, especially when patients present with symptoms of leprosy reactions rather than classical symptoms, such as hypo-pigmented hypo-aesthetic skin lesions and neuropathy.

The microbiological and sustainability effects of washing anaesthesia breathing circuits less frequently.

In the presence of single-use airway filters, we quantified anaesthetic circuit aerobic microbial contamination rates when changed every 24 h, 48 h and 7 days. Microbiological samples were taken from the interior of 305 anaesthetic breathing circuits over a 15-month period (3197 operations). There was no significant difference in the proportion of contaminated circuits when changed every 24 h (57/105 (54%, 95% CI 45-64%)) compared with 48 h (43/100 (43%, 95% CI 33-53%, p = 0.12)) and up to 7 days (46/100 (46%, 95% CI 36-56%, p = 0.26)). Median bacterial counts were not increased at 48 h or 7 days provided circuits were routinely emptied of condensate. Annual savings for one hospital (six operating theatres) were $AU 5219 (£3079, €3654, $US 4846) and a 57% decrease in anaesthesia circuit steriliser loads associated with a yearly saving of 2760 kWh of electricity and 48 000 l of water. Our findings suggest that extended circuit use from 24 h up to 7 days does not significantly increase bacterial contamination, and is associated with labour, energy, water and financial savings.

External validation and updating of a prediction model for nosocomial pneumonia after coronary artery bypass graft surgery.

The generalizability of a prediction model from North America for incident nosocomial pneumonia following coronary artery bypass graft surgery was assessed for 23247 patients on the Australian and New Zealand Society of Cardiac and Thoracic Surgeons (ANZSCTS) registry. The performance of the North American model was evaluated using measures of calibration and discrimination. The model had reasonable discrimination (area under the receiver-operating characteristic curve, AUC=0·69), but unsatisfactory calibration (Hosmer-Lemeshow test, P<0·001) in the ANZSCTS patients. An update of the model coefficients yielded a model with AUC=0·71 and good calibration (P=0·46).

Aggregate travel vs. single trip assessment: arguments for cumulative risk analysis.

Vaccine recommendations for travellers are based on individual risk assessments of multiple factors, most importantly the destination and duration of the impending trip. Many people undertake frequent trips, but existing WHO, CDC and national advisory board recommendations do not explicitly consider cumulative travel-associated risks. Given the period of protection provided by many vaccines, in particular rabies, hepatitis A, hepatitis B and yellow fever vaccines, an aggregate multi-trip risk assessment which views vaccines as an investment for future travel health may be more appropriate than separately evaluating the risks for each trip.

Incidence and seroprevalence of dengue virus infections in Australian travellers to Asia.

The purpose of this study was to estimate the incidence density and prevalence of dengue virus infection in Australian travellers to Asia. We conducted a multi-centre prospective cohort study of Australian travellers over a 32-month period. We recruited 467 travellers (≥ 16 years of age) from three travel clinics who intended to travel Asia, and 387 (82.9%) of those travellers completed questionnaires and provide samples pre- and post-travel for serological testing for dengue virus infection. Demographic data, destination countries and history of vaccinations and flavivirus infections were obtained. Serological testing for dengue IgG and IgM by enzyme-linked immunosorbent assay (ELISA) (PanBio assay) was performed. Acute seroconversion for dengue infection was demonstrated in 1.0% of travellers, representing an incidence of 3.4 infections per 10,000 days of travel (95% confidence interval [CI]: 0.9-8.7). The seroprevalence of dengue infection was 4.4% and a greater number of prior trips to Asia was a predictor for dengue seroprevalence (p = 0.019). All travellers experienced subclinical dengue infections and had travelled to India (n = 3) and China (n = 1). This significant attack rate of dengue infection can be used to advise prospective travellers to dengue-endemic countries.

Innovative community-based initiatives to engage VFR travelers.

This report describes novel initiatives to inform ethnic groups contributing high numbers of VFRs about potential travel risks. Multilingual and culturally appropriate information was distributed to the media (newspaper, radio, web-based, and television), via printed materials (posters, tear sheets and z-cards) and at community festivals to convey simple travel health messages.

Rabies post-exposure prophylaxis in travellers returning from Bali, Indonesia, November 2008 to March 2010.

Since 2008, when the outbreak of rabies in Bali began, 45 patients have attended GeoSentinel or EuroTravNet sites for rabies post-exposure prophylaxis (PEP), representing 12.6% of all travellers seen for PEP in all network clinics during the same time period. This suggests that Bali is emerging as a commonly visited destination among travellers presenting for rabies PEP. The data demonstrate that the majority of animal-related injuries in travellers returning from Bali are associated with exposure to monkeys, and not dog bites/scratches. The clinical implications of this are discussed.

Risk factors for gastroenteritis: a nested case-control study.

This nested case-control study investigated the risk factors for gastroenteritis in a cohort using rainwater as their primary domestic water source. Consumption of beef [odds ratio (OR) 2·74, 95% confidence interval (CI) 1·56-4·80], handling of raw fresh chicken in the household (OR 1·52, 95% CI 1·02-2·29) and animal contact (OR 1·83, 95% CI 1·20-2·83) were found to be significant risk factors (P>0·05). Significant protective effects were observed with raw salad prepared at home (OR 0·33, 95% CI 0·18-0·58), consumption of salami (OR 0·60, 95% CI 0·36-0·98), and shellfish (OR 0·31, 95% CI 0·14-0·67). This study provides novel insight into community-based endemic gastroenteritis showing that consumption of beef was associated with increased odds of illness and with a population attributable fraction (PAF) of 57·6%. Detecting such a high PAF for beef in a non-outbreak setting was unexpected.

A survey of the characteristics and maintenance of rainwater tanks in urban areas of South Australia.

Households resident in metropolitan Adelaide and surrounding areas in South Australia were recruited into a randomised controlled trial. A total of 630 rainwater tanks with a total tank capacity of 14.5 ML were installed at the 325 households surveyed. The majority of the tanks were plumbed into the kitchen (64.6%), over 10 years in age (45.5%), over 15,000 L in capacity (42.5%) and composed of galvanised steel (36.9%). Over 90% of the households undertook one or more prevention and maintenance strategies for reducing contamination of collected rainwater. The use of first flush diverters was reported by 30.8% households, the presence of leaf control devices on the tank by 57.2%, and the presence of leaf control screens on gutters by 25.5% households. Most households reported that the rainwater tank was cleaned at some time, with 50.4% of these households stating that tank cleaning occurred 1 to 5 years previously, and 31.9% more than 5 years prior to enrolment Rainwater from the main drinking tank was sampled from a subset of households for turbidity and metals (Al, Ca, Cu, Fe, Mg, Pb, Zn). This information regarding tank characteristics and degree of adherence to recommended maintenance procedures may assist understanding of variability in rainwater quality data and may help determine whether untreated rainwater can be considered a safe water supply for household purposes including drinking.

Risk in the mist? Deriving data to quantify microbial health risks associated with aerosol generation by water-efficient devices during typical domestic water-using activities.

The aim of this study was to address existing data gaps and to determine the size distribution of aerosols associated with water-efficient devices during typical domestic activities. This information is important to assist in understanding infection spread during water-using activities and in designing water regulations. Three water-using scenarios were evaluated: i) showering using a water-efficient showerhead; ii) use of a high pressure spray unit for cleaning cars and iii) toilet flushing using a dual flush low volume flush device. For each scenario a control condition (conventional lower efficiency device) was selected for benchmarking purposes. Shower module results highlighted the complexity of particle generation and removal processes and showed that more than 90% of total particle mass in the breathing zone was attributed to particle diameters greater than 6 mum. Conversely, results for car washing experiments showed that particle diameters up to 6 mum constituted the major part of the total mass generated by both water-efficient and conventional devices. Even under worse case scenario conditions for toilet flushing, particle measurements were at or below the level of detection of the measuring instrumentation. The data provide information that assists in health risk assessment and in determining future research directions, including methodological aspects.

Influence of sample preservation on endotoxin measurement in water.

Appropriate preservation of a range of water types prior to analysis for endotoxin was investigated, including sample storage and addition of sodium thiosulphate. Biologically active endotoxin in water samples was assayed using a chromogenic Limulus Amoebocyte Lysate (LAL) assay. Statistical analysis of measured mean endotoxin levels obtained for samples with and without sodium thiosulphate showed no significant difference in results. There was a 44% mean decline in the concentration of detectable endotoxin in water samples stored at -80 degrees C for 4 weeks compared with samples stored at 4 degrees C and analysed within 24 hours. Freezing of water samples at -80 degrees C in pyrogen-free containers for 4 weeks or longer, then thawing may lead to considerable endotoxin loss; however the addition of sodium thiosulphate to water samples interferes minimally with the LAL assay. These results provide methodological information that can be used to assist researchers in future water endotoxin monitoring studies. The validation and standardisation of water sample preservation protocols are necessary, given the likely increase in the quantification of endotoxin levels in a variety of water sources and the use of such results for health effect determinations.