Simulation-based fully Bayesian experimental design for mixed effects models

In this paper, we present fully Bayesian experimental designs for nonlinear mixed effects models, in which we develop simulation-based optimal design methods to search over both continuous and discrete design spaces. Although Bayesian inference has commonly been performed on nonlinear mixed effects models, there is a lack of research into performing Bayesian optimal design for nonlinear mixed effects models that require searches to be performed over several design variables. This is likely due to the fact that it is much more computationally intensive to perform optimal experimental design for nonlinear mixed effects models than it is to perform inference in the Bayesian framework. In this paper, the design problem is to determine the optimal number of subjects and samples per subject, as well as the (near) optimal urine sampling times for a population pharmacokinetic study in horses, so that the population pharmacokinetic parameters can be precisely estimated, subject to cost constraints. The optimal sampling strategies, in terms of the number of subjects and the number of samples per subject, were found to be substantially different between the examples considered in this work, which highlights the fact that the designs are rather problem-dependent and require optimisation using the methods presented in this paper.

Objectively measured physical activity behavior in children attending a half day preschool program

Obesity rates are increasing in children of all ages, and reduced physical activity (PA) is a likely contributor to this trend. Little is known about the physical activity behavior of preschool-age children, or about the influence of preschool attendance on physical activity. Purpose The purpose of this study was to quantify the physical activity levels of children attending a center-based half-day preschool program. Methods Forty-two 3-to-5-year old children (Mean age = 4.0 ± 0.7, 54.8% Male, Mean BMI = 16.5 ± 5.5, Mean BMI %tile = 52.1 ± 33.5) from four class groups (two morning and two afternoon), wore an Actigraph 7164 accelerometer for the entire halfday program (including classroom learning experiences, snack and recess time) 2 times per week, for 10 weeks (20 activity monitoring records in total). Activity counts for each 5-sec interval were uploaded to a customized data reduction program to determine total counts, minutes of moderate PA (MPA) (3–5.9 METs), and minutes of vigorous PA (VPA) (> = 6 METs) per session. Counts were categorized as either MPA or VPA using the cutpoints developed by Sirard and colleagues (2001). Results Across the four 2.5 hour programs, the average MPA, VPA and total counts (× 103) were 12.4 ± 3.1 minutes, 18.3 ± 4.6 minutes, and 171.1 ± 29.7 counts, respectively. Thus, on average, children accumulated just over 12 minutes of moderateto-vigorous PA per hour of program attendance. The PA variables did not differ significantly by gender, weight status, or time of day. There were, however, significant age differences, with 3-year-olds exhibiting significantly less PA than their 4- and 5-year-old counterparts. Conclusions These results suggest that young children are relatively lowactive while attending preschool. Accordingly, interventions to increase movement opportunities during the preschool day are warranted.

See to believe : the Center for Tactical Magic’s sleight of hand

The Bay Area’s Center for Tactical Magic has been performing ‘‘magical’’ art interventions since 2000. The Center’s work augments traditional activist techniques by offering new conceptions of what art and activism can entail in a contemporary urban context. This article explores how Jacques Rancie`re’s reconfigured relationship between art and politics can be applied to the Center’s work, providing new distributions of the sensible for participants.

Si quantum dots embedded in an amorphous SiC matrix : nanophase control by non-equilibrium plasma hydrogenation

Nanophase nc-Si/a-SiC films that contain Si quantum dots (QDs) embedded in an amorphous SiC matrix were deposited on single-crystal silicon substrates using inductively coupled plasma-assisted chemical vapor deposition from the reactive silane and methane precursor gases diluted with hydrogen at a substrate temperature of 200 °C. The effect of the hydrogen dilution ratio X (X is defined as the flow rate ratio of hydrogen-to-silane plus methane gases), ranging from 0 to 10.0, on the morphological, structural, and compositional properties of the deposited films, is extensively and systematically studied by scanning electron microscopy, high-resolution transmission electron microscopy, X-ray diffraction, Raman spectroscopy, Fourier-transform infrared absorption spectroscopy, and X-ray photoelectron spectroscopy. Effective nanophase segregation at a low hydrogen dilution ratio of 4.0 leads to the formation of highly uniform Si QDs embedded in the amorphous SiC matrix. It is also shown that with the increase of X, the crystallinity degree and the crystallite size increase while the carbon content and the growth rate decrease. The obtained experimental results are explained in terms of the effect of hydrogen dilution on the nucleation and growth processes of the Si QDs in the high-density plasmas. These results are highly relevant to the development of next-generation photovoltaic solar cells, light-emitting diodes, thin-film transistors, and other applications.

Silicon on silicon : self-organized nanotip arrays formed in reactive Ar+H2 plasmas

The formation of arrays of vertically aligned nanotips on a moderately heated (up to 500 degrees C) Si surface exposed to reactive low-temperature radio frequency (RF) Ar+H(2) plasmas is studied. It is demonstrated that the nanotip surface density, aspect ratio and height dispersion strongly depend on the substrate temperature, discharge power, and gas composition. It is shown that nanotips with aspect ratios from 2.0 to 4.0 can only be produced at a higher RF power density (41.7 mW cm(-3)) and a hydrogen content of about 60%, and that larger aspect ratios can be achieved at substrate temperatures of about 300 degrees C. The use of higher (up to 500 degrees C) temperatures leads to a decrease of the aspect ratio but promotes the formation of more uniform arrays with the height dispersion decreasing to 1.5. At lower (approximately 20 mW cm(-3)) RF power density, only semispherical nanodots can be produced. Based on these experimental results, a nanotip formation scenario is proposed suggesting that sputtering, etching, hydrogen termination, and atom/radical re-deposition are the main concurrent mechanisms for the nanostructure formation. Numerical calculations of the ion flux distribution and hydrogen termination profiles can be used to predict the nanotip shapes and are in a good agreement with the experimental results. This approach can be applied to describe the kinetics of low-temperature formation of other nanoscale materials by plasma treatment.

Correlates of foot pain severity in adults with hallux valgus : a cross-sectional study

Background Hallux valgus (HV) is highly prevalent and associated with progressive first metatarsophalangeal joint subluxation and osteoarthritis. The link between structural HV deformity and foot pain is unclear. This study investigated possible explanatory factors surrounding foot pain in HV, including radiographic HV angle and signs of joint degeneration. Methods Participants were 60 adults (53 female) with HV aged 20 to 75 years. Participant demographics and a range of radiographic, clinical and functional measures were considered potential correlates of foot pain. Self-reported foot pain (visual analogue scales and a dichotomous definition) was considered the dependent variable. Multivariate modelling was used to determine which characteristics and measures explained pain, with univariate analyses first used to screen potential variables. Results Approximately 20 to 30% of the variance in foot pain associated with HV could be explained by patient characteristics such as poorer general health status, lower educational attainment and increased occupational physical activity levels, in combination with some dynamic physical characteristics such as hallux plantarflexion weakness and reduced force-time integral under the second metatarsal during gait. Neither increasing lateral deviation of the hallux (HV angle) nor presence of first metatarsophalangeal joint osteoarthritis was associated with foot pain. Conclusions This study shows that passive structural factors, including HV angle, do not appear to be significant correlates of foot pain intensity in HV. Our data demonstrate the importance of considering patient characteristics such as general health and physical activity levels when assessing foot pain associated with HV.

Comparison of block and event-related experimental designs in diffusion-weighted functional MRI

PURPOSE To compare diffusion-weighted functional magnetic resonance imaging (DfMRI), a novel alternative to the blood oxygenation level-dependent (BOLD) contrast, in a functional MRI experiment. MATERIALS AND METHODS Nine participants viewed contrast reversing (7.5 Hz) black-and-white checkerboard stimuli using block and event-related paradigms. DfMRI (b = 1800 mm/s2 ) and BOLD sequences were acquired. Four parameters describing the observed signal were assessed: percent signal change, spatial extent of the activation, the Euclidean distance between peak voxel locations, and the time-to-peak of the best fitting impulse response for different paradigms and sequences. RESULTS The BOLD conditions showed a higher percent signal change relative to DfMRI; however, event-related DfMRI showed the strongest group activation (t = 21.23, P < 0.0005). Activation was more diffuse and spatially closer to the BOLD response for DfMRI when the block design was used. DfMRIevent showed the shortest TTP (4.4 +/- 0.88 sec). CONCLUSION The hemodynamic contribution to DfMRI may increase with the use of block designs.

Assessment of the temperature effect on childhood diarrhea using satellite imagery

A quasi-Poisson generalized linear model combined with a distributed lag non-linear model was used to quantify the main effect of temperature on emergency department visits (EDVs) for childhood diarrhea in Brisbane from 2001 to 2010. Residual of the model was checked to examine whether there was an added effect due to heat waves. The change over time in temperature-diarrhea relation was also assessed. Both low and high temperatures had significant impact on childhood diarrhea. Heat waves had an added effect on childhood diarrhea, and this effect increased with intensity and duration of heat waves. There was a decreasing trend in the main effect of heat on childhood diarrhea in Brisbane across the study period. Brisbane children appeared to have gradually adapted to mild heat, but they are still very sensitive to persistent extreme heat. Development of future heat alert systems should take the change in temperature-diarrhea relation over time into account.

Defining the spatiotemporal surveillance space for alien species’ invasions using approximate Bayesian computation

The spatiotemporal dynamics of an alien species invasion across a real landscape are typically complex. While surveillance is an essential part of a management response, planning surveillance in space and time present a difficult challenge due to this complexity. We show here a method for determining the highest probability sites for occupancy across a landscape at an arbitrary point in the future, based on occupancy data from a single slice in time. We apply to the method to the invasion of Giant Hogweed, a serious weed in the Czech republic and throughout Europe.

Plasmodium falciparum parasites lacking histidine-rich protein 2 and 3 : a review and recommendations for accurate reporting

Malaria rapid diagnostic tests (RDTs) play a critical role in malaria case management, surveillance and case investigations. Test performance is largely determined by design and quality characteristics, such as detection sensitivity, specificity, and thermal stability. However, parasite characteristics such as variable or absent expression of antigens targeted by RDTs can also affect RDT performance. Plasmodium falciparum parasites lacking the PfHRP2 protein, the most common target antigen for detection of P. falciparum, have been reported in some regions. Therefore, accurately mapping the presence and prevalence of P. falciparum parasites lacking pfhrp2 would be an important step so that RDTs targeting alternative antigens, or microscopy, can be preferentially selected for use in such regions. Herein the available evidence and molecular basis for identifying malaria parasites lacking PfHRP2 is reviewed, and a set of recommended procedures to apply for future investigations for parasites lacking PfHRP2, is proposed.

Building the youth sector from the bottom up : case studies from the Queensland CPLAN Initiative 2012-2013

As part of YANQ's decentralisation across the state, YANQ have set up 10 Networks across Queensland, with Facilitators based in each of the regions. We encourage you to get in contact with your local Facilitator if you would like to have input on Workforce Development or youth policy issues. CPLANs aim to create an ongoing and sustainable structure across ten regions in Queensland to support a consistent focus on: ⋅ Policy issues relevant to young people; and ⋅ Workforce development strategies for the youth sector from a local, regional and state perspective. The ten CPLANs fall under the existing structure of YANQ and utlise and lever off the comprehensive network of youth inter-­‐agencies and networks across the state. The ten CPLANs are made up of representatives from the youth sector in each region who have an interest in contributing to policy development and workforce issues.

Health education and the control of intestinal worm infections in China : a new vision

Background: The transmission of soil-transmitted helminths (STHs) is associated with poverty, poor hygiene behaviour, lack of clean water and inadequate waste disposal and sanitation. Periodic administration of benzimidazole drugs is the mainstay for global STH control but it does not prevent re-infection, and is unlikely to interrupt transmission as a stand-alone intervention. Findings: We reported recently on the development and successful testing in Hunan province, PR China, of a health education package to prevent STH infections in Han Chinese primary school students. We have recently commenced a new trial of the package in the ethnically diverse Xishuangbanna autonomous prefecture in Yunnan province and the approach is also being tested in West Africa, with further expansion into the Philippines in 2015. Conclusions: The work in China illustrates well the direct impact that health education can have in improving knowledge and awareness, and in changing hygiene behaviour. Further, it can provide insight into the public health outcomes of a multi-component integrated control program, where health education prevents re-infection and periodic drug treatment reduces prevalence and morbidity.

Predicting sense convergence with distributional semantics : an application to the CogALex-IV 2014 shared task

This paper presents our system to address the CogALex-IV 2014 shared task of identifying a single word most semantically related to a group of 5 words (queries). Our system uses an implementation of a neural language model and identifies the answer word by finding the most semantically similar word representation to the sum of the query representations. It is a fully unsupervised system which learns on around 20% of the UkWaC corpus. It correctly identifies 85 exact correct targets out of 2,000 queries, 285 approximate targets in lists of 5 suggestions.

Promoting law student well-being through the curriculum

The Australian tertiary sector is becoming increasingly concerned about the psychological well-being of its students.Empirical research in Australia indicates that more than one-third of law students suffer from psychological distress, and the competitive, isolated, adversarial learning environment at law school has been suggested as partly responsible (Brain and Mind Research Institute, 2009). This fellowship program has mobilised strategic change to improve the psychological health of law students. It has lead and stimulated advancement in the legal curriculum, its pedagogy, and assessment practice to better engage, motivate and support student learning of law, focussing on the potential of non-adversarial legal practice. A new conceptual framework for legal education has been developed, demonstrating the pursuit of excellence in the teaching of law, and raising the profile of learning and teaching in Australian law schools. In addition the fellowship has created a national community of practice around this issue through the Wellness Network for Law, and made significant contributions to research and scholarship in the field.

miRPlant : an integrated tool for identification of plant miRNA from RNA sequencing data

Background Small RNA sequencing is commonly used to identify novel miRNAs and to determine their expression levels in plants. There are several miRNA identification tools for animals such as miRDeep, miRDeep2 and miRDeep*. miRDeep-P was developed to identify plant miRNA using miRDeep’s probabilistic model of miRNA biogenesis, but it depends on several third party tools and lacks a user-friendly interface. The objective of our miRPlant program is to predict novel plant miRNA, while providing a user-friendly interface with improved accuracy of prediction. Result We have developed a user-friendly plant miRNA prediction tool called miRPlant. We show using 16 plant miRNA datasets from four different plant species that miRPlant has at least a 10% improvement in accuracy compared to miRDeep-P, which is the most popular plant miRNA prediction tool. Furthermore, miRPlant uses a Graphical User Interface for data input and output, and identified miRNA are shown with all RNAseq reads in a hairpin diagram. Conclusions We have developed miRPlant which extends miRDeep* to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants. miRPlant does not require any third party tools such as mapping or RNA secondary structure prediction tools. miRPlant is also the first plant miRNA prediction tool that dynamically plots miRNA hairpin structure with small reads for identified novel miRNAs. This feature will enable biologists to visualize novel pre-miRNA structure and the location of small RNA reads relative to the hairpin. Moreover, miRPlant can be easily used by biologists with limited bioinformatics skills.