PCA and K-Means decipher genome

In this paper, we aim to give a tutorial for undergraduate students studying statistical methods and/or bioinformatics. The students will learn how data visualization can help in genomic sequence analysis. Students start with a fragment of genetic text of a bacterial genome and analyze its structure. By means of principal component analysis they ``discover'' that the information in the genome is encoded by non-overlapping triplets. Next, they learn how to find gene positions. This exercise on PCA and K-Means clustering enables active study of the basic bioinformatics notions. Appendix 1 contains program listings that go along with this exercise. Appendix 2 includes 2D PCA plots of triplet usage in moving frame for a series of bacterial genomes from GC-poor to GC-rich ones. Animated 3D PCA plots are attached as separate gif files. Topology (cluster structure) and geometry (mutual positions of clusters) of these plots depends clearly on GC-content.Comment: 18 pages, with program listings for MatLab, PCA analysis of genomes and additional animated 3D PCA plot

Novel designs for Penning ion traps

We present a number of alternative designs for Penning ion traps suitable for quantum information processing (QIP) applications with atomic ions. The first trap design is a simple array of long straight wires which allows easy optical access. A prototype of this trap has been built to trap Ca+ and a simple electronic detection scheme has been employed to demonstrate the operation of the trap. Another trap design consists of a conducting plate with a hole in it situated above a continuous conducting plane. The final trap design is based on an array of pad electrodes. Although this trap design lacks the open geometry of the traps described above, the pad design may prove useful in a hybrid scheme in which information processing and qubit storage take place in different types of trap. The behaviour of the pad traps is simulated numerically and techniques for moving ions rapidly between traps are discussed. Future experiments with these various designs are discussed. All of the designs lend themselves to the construction of multiple trap arrays, as required for scalable ion trap QIP.Comment: 11 pages, 10 figure

Cladding strategies for building-integrated photovoltaics

Photovoltaic cladding on the surfaces of commercial buildings has the potential for considerable reductions in carbon emissions due to embedded renewable power generation displacing conventional power utilization. In this paper, a model is described for the optimization of photovoltaic cladding densities on commercial building surfaces. The model uses a modified form of the ‘fill factor’ method for photovoltaic power supply coupled to new regression-based procedures for power demand estimation. An optimization is included based on a defined ‘mean index of satisfaction’ for matched power supply and demand (i.e., zero power exportation to the grid). The mean index of satisfaction directly translates to the reduction in carbon emission that might be expected over conventional power use. On clear days throughout the year, reductions of conventional power use of at least 60% can be achieved with an optimum cladding pattern targeted to lighting and small power load demands

Dynamics of axialized laser-cooled ions in a Penning trap

We report the experimental characterization of axialization - a method of reducing the magnetron motion of a small number of ions stored in a Penning trap. This is an important step in the investigation of the suitability of Penning traps for quantum information processing. The magnetron motion was coupled to the laser-cooled modified cyclotron motion by the application of a near-resonant oscillating quadrupole potential (the "axialization drive"). Measurement of cooling rates of the radial motions of the ions showed an order-of-magnitude increase in the damping rate of the magnetron motion with the axialization drive applied. The experimental results are in good qualitative agreement with a recent theoretical study. In particular, a classical avoided crossing was observed in the motional frequencies as the axialization drive frequency was swept through the optimum value, proving that axialization is indeed a resonant effect.Comment: 8 pages, 9 figure

Human rights and public education

This article attempts a contrast to the contribution by Hugh Starkey. Rather than his account of the inexorable rise of human rights discourse, and of the implementation of human rights standards, human rights are here presented as always and necessarily scandalous and highly contested. First, I explain why the UK has lagged so far behind its European neighbours in implementing citizenship education. Second, a comparison with France shows that the latest UK reforms bring us up to 1789. Third, the twentieth-century second-generation social and economic rights are still anathema in the UK. Fourth, the failure to come to terms with Empire and especially the slave trade means that the UK’s attitude to third-generation rights, especially the right of peoples to self-determination, is heavily compromised. Taking into account the points I raise, citizenship education in the UK might look very different

A model for estimating mental health service needs in South Africa

Objective. To develop a model for estimating the services and human resources needed. to care for people with severe psychiatric conditions in a hypothetical population of 100 000 people in South Africa.Method. Annual mental health service needs were estimated. in terms of numbers of daily patient visits (DPV) in ambulatory care, the number of beds required, and staffing_ Developed within a spreadsheet format, the model allows for the adjustment of key service variables according.to estimated or existing service data.Results. At 100% coverage, 87 DPV, 28 acute beds, and 10 medium-long stay beds are necessary for a population of 100 000 people. This would require 352 full-time equivalent mental health staff: 21.3 for inpatient care, 12.0 for ambulatory care, and 1.9 for management.Conclusion. Because the model can produce a range of service recommendations, the assumptions that inform it should be clearly stated. and justified.. This method makes the assumptions on which services are planned. explicit and allows for a rational approach to decision making

Mental and substance use disorders in sub-saharan Africa: predictions of epidemiological changes and mental health workforce requirements for the next 40 years

The world is undergoing a rapid health transition, with an ageing population and disease burden increasingly defined by disability. In Sub-Saharan Africa the next 40 years are predicted to see reduced mortality, signalling a surge in the impact of chronic diseases. We modelled these epidemiological changes and associated mental health workforce requirements. Years lived with a disability (YLD) predictions for mental and substance use disorders for each decade from 2010 to 2050 for four Sub-Saharan African regions were calculated using Global Burden of Disease 2010 study (GBD 2010) data and UN population forecasts. Predicted mental health workforce requirements for 2010 and 2050, by region and for selected countries, were modelled using GBD 2010 prevalence estimates and recommended packages of care and staffing ratios for low- and middle-income countries, and compared to current staffing from the WHO Mental Health Atlas. Significant population growth and ageing will result in an estimated 130% increase in the burden of mental and substance use disorders in Sub-Saharan Africa by 2050, to 45 million YLDs. As a result, the required mental health workforce will increase by 216,600 full time equivalent staff from 2010 to 2050, and far more compared to the existing workforce. The growth in mental and substance use disorders by 2050 is likely to significantly affect health and productivity in Sub-Saharan Africa. To reduce this burden, packages of care for key mental disorders should be provided through increasing the mental health workforce towards targets outlined in this paper. This requires a shift from current practice in most African countries, involving substantial investment in the training of primary care practitioners, supported by district based mental health specialist teams using a task sharing model that mobilises local community resources, with the expansion of inpatient psychiatric units based in district and regional general hospitals

Dissociation in a polymerization model of homochirality

A fully self-contained model of homochirality is presented that contains the effects of both polymerization and dissociation. The dissociation fragments are assumed to replenish the substrate from which new monomers can grow and undergo new polymerization. The mean length of isotactic polymers is found to grow slowly with the normalized total number of corresponding building blocks. Alternatively, if one assumes that the dissociation fragments themselves can polymerize further, then this corresponds to a strong source of short polymers, and an unrealistically short average length of only 3. By contrast, without dissociation, isotactic polymers becomes infinitely long.Comment: 16 pages, 6 figures, submitted to Orig. Life Evol. Biosp

UK export performance research - review and implications

Previous research on export performance has been criticized for being a mosaic of autonomous endeavours and for a lack of theoretical development. Building upon extant models of export performance, and a review and analysis of research on export performance in the UK for the period 1990-2005, an integrated model of export performance is developed and theoretical explanations of export performance are put forward. It is suggested that a multi-theory approach to explaining export performance is viable. Management and policy implications for the UK emerging from the review and synthesis of the literature and the integrated model are discussed

Selective transmission through very deep zero-order metallic gratings at microwave frequencies

Copyright © 2000 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in Applied Physics Letters 77 (2000) and may be found at http://link.aip.org/link/?APPLAB/77/2789/1Zero-order metal grating structures are found to give extraordinary selective transmission at microwave frequencies through the resonant excitation of coupled surface waves. The metal slat structures with dielectric spacings as small as 250 µm strongly transmit wavelengths of several millimeters. A simple interpretation of these novel results which treats the deep grating structures as "filled" Fabry–Perot cavity systems gives model transmissivities which agree very well with the experimental data