Sample preparation for point of care molecular diagnostics of STIs

This paper was presented at the 4th Micro and Nano Flows Conference (MNF2014), which was held at University College, London, UK. The conference was organised by Brunel University and supported by the Italian Union of Thermofluiddynamics, IPEM, the Process Intensification Network, the Institution of Mechanical Engineers, the Heat Transfer Society, HEXAG - the Heat Exchange Action Group, and the Energy Institute, ASME Press, LCN London Centre for Nanotechnology, UCL University College London, UCL Engineering, the International NanoScience Community, www.nanopaprika.eu.Brunel DoCLab is part of the esti2 consortium developing electronic self-testing instruments for sexually transmitted infections using nucleic acid amplification testing (NAAT). A proprietary sample collection device has been designed to integrate directly with a microfluidic cartridge. Cell lysis was conducted using a chemical method and nucleic acid purification was done on an activated cellulose membrane. The microfluidic device incorporates passive mixing of the lysis-binding buffers and sample. Preliminary results have shown extraction efficiencies for this new membrane of 69% and 57% compared to the commercial Qiagen extraction method of 85% and 59.4% for 0.1ng/μL and 100ng/μL salmon sperm DNA spiked in phosphate buffered solution. Preliminary extraction experiments in the passive mixer cartridges with lysis and nucleic acid purification showed extraction efficiency around 80% of the commercial Qiagen kit. Isothermal amplification was conducted using thermophillic helicase dependant amplification. A low cost benchtop real-time isothermal amplification platform has been developed capable of running six amplifications simultaneously. Work to integrate sample collection, nucleic acid extraction and isothermal amplification is currently underway

Statistical Properties of Height of Japanese Schoolchildren

We study height distributions of Japanese schoolchildren based on the statictical data which are obtained from the school health survey by the ministry of education, culture, sports, science and technology, Japan . From our analysis, it has been clarified that the distribution of height changes from the lognormal distribution to the normal distribution in the periods of puberty.Comment: 2 pages, 2 figures, submitted to J. Phys. Soc. Jpn.; resubmitted to J. Phys. Soc. Jpn. after some revisio

Schwinger Boson Formulation and Solution of the Crow-Kimura and Eigen Models of Quasispecies Theory

We express the Crow-Kimura and Eigen models of quasispecies theory in a functional integral representation. We formulate the spin coherent state functional integrals using the Schwinger Boson method. In this formulation, we are able to deduce the long-time behavior of these models for arbitrary replication and degradation functions. We discuss the phase transitions that occur in these models as a function of mutation rate. We derive for these models the leading order corrections to the infinite genome length limit.Comment: 37 pages; 4 figures; to appear in J. Stat. Phy

Drivers of redistribution of fishing and non-fishing effort after the implementation of a marine protected area network

Marine spatial planning (MSP) is increasingly utilized to sustainably manage ocean uses. Marine protected areas (MPAs), a form of spatial management in which parts of the ocean are regulated to fishing, are now a common tool in MSP for conserving marine biodiversity and managing fisheries. However, the use of MPAs in MSP often neglects, or simplifies, the redistribution of fishing and non-fishing activities inside and outside of MPAs following their implementation. This redistribution of effort can have important implications for effective MSP. Using long-term (14 yr) aerial surveys of boats at the California Channel Islands, we examined the spatial redistribution of fishing and non-fishing activities and their drivers following MPA establishment. Our data represent 6 yr of information before the implementation of an MPA network and 8 yr after implementation. Different types of boats responded in different ways to the closures, ranging from behaviors by commercial dive boats that support the hypothesis of fishing-the-line, to behaviors by urchin, sport fishing, and recreational boats that support the theory of ideal free distribution. Additionally, we found that boats engaged in recreational activities targeted areas that are sheltered from large waves and located near their home ports, while boats engaged in fishing activities also avoided high wave areas but were not constrained by the distance to their home ports. We did not observe the expected pattern of effort concentration near MPA borders for some boat types; this can be explained by the habitat preference of certain activities (for some activities, the desired habitat attributes are not inside the MPAs), species’ biology (species such as urchins where the MPA benefit would likely come from larval export rather than adult spillover), or policy-infraction avoidance. The diversity of boat responses reveals variance from the usual simplified assumption that all extractive boats respond similarly to MPA establishment. Our work is the first empirical study to analyze the response of both commercial and recreational boats to closure. Our results will inform MSP in better accounting for effort redistribution by ocean users in response to the implementation of MPAs and other closures

Optimal discrete stopping times for reliability growth tests

Often, the duration of a reliability growth development test is specified in advance and the decision to terminate or continue testing is conducted at discrete time intervals. These features are normally not captured by reliability growth models. This paper adapts a standard reliability growth model to determine the optimal time for which to plan to terminate testing. The underlying stochastic process is developed from an Order Statistic argument with Bayesian inference used to estimate the number of faults within the design and classical inference procedures used to assess the rate of fault detection. Inference procedures within this framework are explored where it is shown the Maximum Likelihood Estimators possess a small bias and converges to the Minimum Variance Unbiased Estimator after few tests for designs with moderate number of faults. It is shown that the Likelihood function can be bimodal when there is conflict between the observed rate of fault detection and the prior distribution describing the number of faults in the design. An illustrative example is provided

Angiogenesis in Paget's Disease of the Vulva and the Breast: Correlation with Microvessel Density

Our understanding of the pathogenesis of Paget's disease of the vulva and the breast remains limited. Current evidence supports the fact that angiogenesis plays an important role in the pathogenesis of several diseases. Therefore, we sought to define its role, as correlated with microvessel density, in Paget's disease of the vulva and the breast. Microvessels were analysed using anti-von Willebrand factor antibody in 105 cases of Paget's disease of the vulva and the breast comprising 71 cases of Paget's disease of the vulva, including 8 cases with invasive disease, and 34 cases of Paget's disease of the breast. The latter included 12 cases with DCIS, 5 cases with both DCIS and invasive carcinoma, and 6 with carcinoma alone. Eleven cases had no underlying tumour identified. Increased microvessel density was demonstrated in Paget's disease of the breast with DCIS and with carcinoma alone compared to Paget's disease of the breast alone, P < 0.08 and P < 0.013, respectively. There were no significant differences in microvessel density in the vulval cases. Neovascularisation is an important process in the development of Paget's disease of the breast. Other biological and molecular processes are more involved in the pathogenesis of Paget's disease of the vulva

Finite population size effects in quasispecies models with single-peak fitness landscape

We consider finite population size effects for Crow-Kimura and Eigen quasispecies models with single-peak fitness landscape. We formulate accurately the iteration procedure for the finite population models, then derive the Hamilton-Jacobi equation (HJE) to describe the dynamic of the probability distribution. The steady-state solution of HJE gives the variance of the mean fitness. Our results are useful for understanding the population sizes of viruses in which the infinite population models can give reliable results for biological evolution problems