Modelling survival data to account for model uncertainty: a single model or model averaging?

This study considered the problem of predicting survival, based on three alternative models: a single Weibull, a mixture of Weibulls and a cure model. Instead of the common procedure of choosing a single “best” model, where “best” is defined in terms of goodness of fit to the data, a Bayesian model averaging (BMA) approach was adopted to account for model uncertainty. This was illustrated using a case study in which the aim was the description of lymphoma cancer survival with covariates given by phenotypes and gene expression. The results of this study indicate that if the sample size is sufficiently large, one of the three models emerge as having highest probability given the data, as indicated by the goodness of fit measure; the Bayesian information criterion (BIC). However, when the sample size was reduced, no single model was revealed as “best”, suggesting that a BMA approach would be appropriate. Although a BMA approach can compromise on goodness of fit to the data (when compared to the true model), it can provide robust predictions and facilitate more detailed investigation of the relationships between gene expression and patient survival. Keywords: Bayesian modelling; Bayesian model averaging; Cure model; Markov Chain Monte Carlo; Mixture model; Survival analysis; Weibull distribution

A demand-responsive decision support system for coal transportation

In this paper, a demand-responsive decision support system is proposed by integrating the operations of coal shipment, coal stockpiles and coal railing within a whole system. A generic and flexible scheduling optimisation methodology is developed to identify, represent, model, solve and analyse the coal transport problem in a standard and convenient way. As a result, the integrated train-stockpile-ship timetable is created and optimised for improving overall efficiency of coal transport system. A comprehensive sensitivity analysis based on extensive computational experiments is conducted to validate the proposed methodology. The mathematical proposition and proof are concluded as technical and insightful advices for industry practice. The proposed methodology provides better decision making on how to assign rail rolling-stocks and upgrade infrastructure in order to significantly improve capacity utilisation with the best resource-effectiveness ratio. The proposed decision support system with train-stockpile-ship scheduling optimisation techniques is promising to be applied in railway or mining industry, especially as a useful quantitative decision making tool on how to use more current rolling-stocks or whether to buy additional rolling-stocks for mining transportation.

Genomic resources notes accepted 1 December 2013 - 31 January 2014

This article documents the public availability of (i) transcriptome sequence data, assembled and annotated contigs and unigenes, and BLAST hits from the Queensland fruit fly, Bactrocera tryoni; (ii) 75 single-nucleotide variants (SNVs) from 454 sequencing of reduced representation libraries for Phalangiidae harvestmen, Megabunus armatus, Megabunus vignai, Megabunus lesserti, and Rilaena triangularis; and (iii) expressed sequence tags from 454 sequencing of the lepidopterans Lymantria dispar and Lymantria monacha.

Invasive and metastatic properties of MCF-7 cells and ras(H)-transfected MCF-7 cell lines

In vitro invasion and in vivo metastasis assays were performed with a panel of MCF-7 cells transfected with isogenic constructs of mutated ras(H) genes. Both increased levels of ras(H) expression and ras(H) oncogene activation increased activity of derivative cell lines in in vitro invasion assays. In vivo formation of spontaneous metastases was assessed after intradermal inoculation of MCF-7 cells in the vicinity of the mammary fat pads of ovariectomized nude mice. No metastases were seen in the absence of estradiol treatment of the mice. With estradiol supplementation of the mice both the ras(H)-transfected and control transfected cell lines gave a higher incidence of metastases than parental MCF-7 cells. Prolonged treatment of mice with exogenous estradiol (60 days vs. 21 days) resulted in more frequent metastases to liver and lung at the end of the 90-day observation period. In contrast to activated ras(H)-gene enhancement of metastatic capacity of rodent fibroblast and epithelial cell lines, there was no correlation of ras(H) expression with in vivo metastatic capacity of a human mammary carcinoma cell line.

The SEA-CALIPSO volcano imaging experiment at Montserrat : plans, campaigns at sea and on land, scientific results, and lessons learned

Since 1995 the eruption of the andesitic Soufrière Hills Volcano (SHV), Montserrat, has been studied in substantial detail. As an important contribution to this effort, the Seismic Experiment with Airgunsource-Caribbean Andesitic Lava Island Precision Seismo-geodetic Observatory (SEA-CALIPSO) experiment was devised to image the arc crust underlying Montserrat, and, if possible, the magma system at SHV using tomography and reflection seismology. Field operations were carried out in October–December 2007, with deployment of 238 seismometers on land supplementing seven volcano observatory stations, and with an array of 10 ocean-bottom seismometers deployed offshore. The RRS James Cook on NERC cruise JC19 towed a tuned airgun array plus a digital 48-channel streamer on encircling and radial tracks for 77 h about Montserrat during December 2007, firing 4414 airgun shots and yielding about 47 Gb of data. The main objecctives of the experiment were achieved. Preliminary analyses of these data published in 2010 generated images of heterogeneous high-velocity bodies representing the cores of volcanoes and subjacent intrusions, and shallow areas of low velocity on the flanks of the island that reflect volcaniclastic deposits and hydrothermal alteration. The resolution of this preliminary work did not extend beyond 5 km depth. An improved three-dimensional (3D) seismic velocity model was then obtained by inversion of 181 665 first-arrival travel times from a more-complete sampling of the dataset, yielding clear images to 7.5 km depth of a low-velocity volume that was interpreted as the magma chamber which feeds the current eruption, with an estimated volume 13 km3. Coupled thermal and seismic modelling revealed properties of the partly crystallized magma. Seismic reflection analyses aimed at imaging structures under southern Montserrat had limited success, and suggest subhorizontal layering interpreted as sills at a depth of between 6 and 19 km. Seismic reflection profiles collected offshore reveal deep fans of volcaniclastic debris and fault offsets, leading to new tectonic interpretations. This chapter presents the project goals and planning concepts, describes in detail the campaigns at sea and on land, summarizes the major results, and identifies the key lessons learned.

‘It's all scientific to me’ : focus group insights into why young people do not apply safe-sex knowledge

Despite rising levels of safe-sex knowledge in Australia, sexually transmitted infection notifications continue to increase. A culture-centred approach suggests it is useful in attempting to reach a target population first to understand their perspective on the issues. Twenty focus groups were conducted with 89 young people between the ages of 14 and 16 years. Key findings suggest that scientific information does not articulate closely with everyday practice, that young people get the message that sex is bad and they should not be preparing for it and that it is not appropriate to talk about sex. Understanding how young people think about these issues is particularly important because the focus groups also found that young people disengage from sources of information that do not match their own experiences.

Simulation study for analysis of online dielectric measurement problems on transformer insulation system

Determining the condition as well as the remaining life of an insulation system is essential for the reliable operation of large oil-filled power transformers. Frequency-domain spectroscopy (FDS) is one of the diagnostic techniques used to identify the dielectric status of a transformer. Currently, this technique can only be implemented on a de-energized transformer. This paper presents an initial investigation into a novel online monitoring method based on FDS dielectric measurements for transformers. The proposed technique specifically aims to address the real operational constraints of online testing. This is achieved by designing an online testing model extending the basic “extended Debye” linear dielectric model and taking unique noise issues only experienced during online measurements into account via simulations. Approaches to signal denoising and potential problems expected to be encountered during online measurements will also be discussed. Using fixed-frequency sinusoidal excitation waveforms will result in a long measurement times. The use of alternatives such as a chirp has been investigated using simulations. The results presented in the paper predict that reliable measurements should be possible during online testing.

What impact might the economic crisis have on HIV epidemics in Southeast Asia?

Objective: To evaluate the potential impact of the current global economic crisis (GEC) on the spread of HIV. Design: To evaluate the impact of the economic downturn we studied two distinct HIV epidemics in Southeast Asia: the generalized epidemic in Cambodia where incidence is declining and the epidemic in Papua New Guinea (PNG) which is in an expansion phase. Methods: Major HIV-related risk factors that may change due to the GEC were identified and a dynamic mathematical transmission model was developed and used to forecast HIV prevalence, diagnoses, and incidence in Cambodia and PNG over the next 3 years. Results: In Cambodia, the total numbers of HIV diagnoses are not expected to be largely affected. However, an estimated increase of up to 10% in incident cases of HIV, due to potential changes in behavior, may not be observed by the surveillance system. In PNG, HIV incidence and diagnoses could be more affected by the GEC, resulting in respective increases of up to 17% and 11% over the next 3 years. Decreases in VCT and education programs are the factors that may be of greatest concern in both settings. A reduction in the rollout of antiretroviral therapy could increase the number of AIDS-related deaths (by up to 7.5% after 3 years). Conclusions: The GEC is likely to have a modest impact on HIV epidemics. However, there are plausible conditions under which the economic downturns can noticeably influence epidemic trends. This study highlights the high importance of maintaining funding for HIV programs.

A description of neck motor performance, neck pain, fatigue, and mental effort while driving in a sample with chronic whiplash-associated disorders

Objective: Individuals with chronic whiplash-associated disorders (WADs) often note driving as a difficult task. This study’s aims were to (1) compare, while driving, neck motor performance, mental effort, and fatigue in individuals with chronic WAD against healthy controls and (2) investigate the relationships of these variables and neck pain to self-reported driving difficulty in the WAD group. Design: This study involved 14 participants in each group (WAD and control). Measures included self-reported driving difficulty and measures of neck pain intensity, overall fatigue, mental effort, and neck motor performance (head rotation and upper trapezius activity) while driving a simulator. Results: The WAD group had greater absolute path of head rotation in a simulated city area and used greater mental effort (P = 0.04), but there were no differences in other measures while driving compared with the controls (all P Q 0.05). Self-reported driving difficulty correlated moderately with neck pain intensity, fatigue level, and maximum velocity of head rotation while driving in the WAD group (all P G 0.05). Conclusions: Individuals with chronic WAD do not seem to have impaired neck motor performance while driving yet use greater mental effort. Neck pain, fatigue, and maximum head rotation velocity could be potential contributors to self-reported driving difficulty in this group.

Estimating the burden of disease attributable to high cholesterol in South Africa in 2000

Objectives To estimate the burden of disease attributable to high cholesterol in adults aged 30 years and older in South Africa in 2000. Design World Health Organization comparative risk assessment (CRA) methodology was followed. Small community studies were used to derive the prevalence by population group. Population-attributable fractions were calculated and applied to revised burden of disease estimates for the relevant disease categories for each population group. The total attributable burden for South Africa in 2000 was obtained by adding the burden attributed to high cholesterol for the four population groups. Monte Carlo simulation-modelling techniques were used for uncertainty analysis. Setting South Africa. Subjects Black African, coloured, white and Indian adults aged 30 years and older. Outcome measures Mortality and disability-adjusted life years (DALYs) from ischaemic heart disease (IHD) and ischaemic stroke. Results Overall, about 59% of IHD and 29% of ischaemic stroke burden in adult males and females (30+ years) were attributable to high cholesterol (≥ 3.8 mmol/l), with marked variation by population group. High cholesterol was estimated to have caused 24 144 deaths (95% uncertainty interval 22 404 - 25 286) or 4.6% (95% uncertainty interval 4.3 - 4.9%) of all deaths in South Africa in 2000. Since most cholesterol-related cardiovascular disease events occurred in middle or old age, the loss of life years comprised a smaller proportion of the total: 222 923 DALYs (95% uncertainty interval 206 712 - 233 460) or 1.4% of all DALYs (95% uncertainty interval 1.3 - 1.4%) in South Africa in 2000. Conclusions High cholesterol is an important cardiovascular risk factor in all population groups in South Africa.

Subpopulation triage: How to allocate conservation effort among populations

Threatened species often exist in a small number of isolated subpopulations. Given limitations on conservation spending, managers must choose from strategies that range from managing just one subpopulation and risking all other subpopulations to managing all subpopulations equally and poorly, thereby risking the loss of all subpopulations. We took an economic approach to this problem in an effort to discover a simple rule of thumb for optimally allocating conservation effort among subpopulations. This rule was derived by maximizing the expected number of extant subpopulations remaining given n subpopulations are actually managed. We also derived a spatiotemporally optimized strategy through stochastic dynamic programming. The rule of thumb suggested that more subpopulations should be managed if the budget increases or if the cost of reducing local extinction probabilities decreases. The rule performed well against the exact optimal strategy that was the result of the stochastic dynamic program and much better than other simple strategies (e.g., always manage one extant subpopulation or half of the remaining subpopulation). We applied our approach to the allocation of funds in 2 contrasting case studies: reduction of poaching of Sumatran tigers (Panthera tigris sumatrae) and habitat acquisition for San Joaquin kit foxes (Vulpes macrotis mutica). For our estimated annual budget for Sumatran tiger management, the mean time to extinction was about 32 years. For our estimated annual management budget for kit foxes in the San Joaquin Valley, the mean time to extinction was approximately 24 years. Our framework allows managers to deal with the important question of how to allocate scarce conservation resources among subpopulations of any threatened species. © 2008 Society for Conservation Biology.

A vibrational spectroscopic study of the silicate mineral plumbophyllite Pb2Si4O10⋅H2O

Raman spectroscopy complimented with infrared spectroscopy has been used to study the molecular structure of the mineral of plumbophyllite. The Raman spectrum is dominated by a very intense sharp peak at 1027 cm−1, assigned to the SiO stretching vibrations of (SiO3)n units. A very intense Raman band at 643 cm−1 is assigned to the bending mode of (SiO3)n units. Raman bands observed at 3215, 3443, 3470, 3494 and 3567 cm−1 are assigned to water stretching vibrations. Multiple water stretching and bending modes are observed showing that there is much variation in hydrogen bonding between water and the silicate surfaces. Because of the close similarity in the structure of plumbophyllite and apophyllite, a comparison of the spectra with that of apophyllites is made. By using vibrational spectroscopy an assessment of the molecular structure of plumbophyllite has been made.

Infinite Dimensional Slow Modulations In A Delayed Model For Orthogonal Cutting Vibrations

We apply the method of multiple scales (MMS) to a well known model of regenerative cutting vibrations in the large delay regime. By ``large'' we mean the delay is much larger than the time scale of typical cutting tool oscillations. The MMS upto second order for such systems has been developed recently, and is applied here to study tool dynamics in the large delay regime. The second order analysis is found to be much more accurate than first order analysis. Numerical integration of the MMS slow flow is much faster than for the original equation, yet shows excellent accuracy. The main advantage of the present analysis is that infinite dimensional dynamics is retained in the slow flow, while the more usual center manifold reduction gives a planar phase space. Lower-dimensional dynamical features, such as Hopf bifurcations and families of periodic solutions, are also captured by the MMS. Finally, the strong sensitivity of the dynamics to small changes in parameter values is seen clearly.

Determination of beta-turn conformation by laser Raman spectroscopy

To correlate the Raman frequencies of the amide I and III bands to beta-turn structures, three peptides shown to contain beta-turn structure by x-ray diffraction and NMR were examined. The compounds examined were tertiary (formula: see text). The amide I band of these compounds is seen at 1,668, 1,665, and 1,677 cm-1, and the amide III band appears at 1,267, 1,265, and 1,286 cm-1, respectively. Thus, it is concluded that the amide I band for type III beta-turn structure appears in the range between 1,665 and 1,677 cm-1 and the amide III band between 1,265 and 1,286 cm-1.