Screening the human exome: a comparison of whole genome and whole transcriptome sequencing.

BACKGROUND: There is considerable interest in the development of methods to efficiently identify all coding variants present in large sample sets of humans. There are three approaches possible: whole-genome sequencing, whole-exome sequencing using exon capture methods, and RNA-Seq. While whole-genome sequencing is the most complete, it remains sufficiently expensive that cost effective alternatives are important. RESULTS: Here we provide a systematic exploration of how well RNA-Seq can identify human coding variants by comparing variants identified through high coverage whole-genome sequencing to those identified by high coverage RNA-Seq in the same individual. This comparison allowed us to directly evaluate the sensitivity and specificity of RNA-Seq in identifying coding variants, and to evaluate how key parameters such as the degree of coverage and the expression levels of genes interact to influence performance. We find that although only 40% of exonic variants identified by whole genome sequencing were captured using RNA-Seq; this number rose to 81% when concentrating on genes known to be well-expressed in the source tissue. We also find that a high false positive rate can be problematic when working with RNA-Seq data, especially at higher levels of coverage. CONCLUSIONS: We conclude that as long as a tissue relevant to the trait under study is available and suitable quality control screens are implemented, RNA-Seq is a fast and inexpensive alternative approach for finding coding variants in genes with sufficiently high expression levels.

Spatial distribution of bednet coverage under routine distribution through the public health sector in a rural district in Kenya.

Insecticide-treated nets (ITNs) are one of the most important and cost-effective tools for malaria control. Maximizing individual and community benefit from ITNs requires high population-based coverage. Several mechanisms are used to distribute ITNs, including health facility-based targeted distribution to high-risk groups; community-based mass distribution; social marketing with or without private sector subsidies; and integrating ITN delivery with other public health interventions. The objective of this analysis is to describe bednet coverage in a district in western Kenya where the primary mechanism for distribution is to pregnant women and infants who attend antenatal and immunization clinics. We use data from a population-based census to examine the extent of, and factors correlated with, ownership of bednets. We use both multivariable logistic regression and spatial techniques to explore the relationship between household bednet ownership and sociodemographic and geographic variables. We show that only 21% of households own any bednets, far lower than the national average, and that ownership is not significantly higher amongst pregnant women attending antenatal clinic. We also show that coverage is spatially heterogeneous with less than 2% of the population residing in zones with adequate coverage to experience indirect effects of ITN protection.

Designing Climate Mitigation Policy

This paper provides an exhaustive review of critical issues in the design of climate mitigation policy by pulling together key findings and controversies from diverse literatures on mitigation costs, damage valuation, policy instrument choice, technological innovation, and international climate policy. We begin with the broadest issue of how high assessments suggest the near and medium term price on greenhouse gases would need to be, both under cost-effective stabilization of global climate and under net benefit maximization or Pigouvian emissions pricing. The remainder of the paper focuses on the appropriate scope of regulation, issues in policy instrument choice, complementary technology policy, and international policy architectures.

Chronic opioid therapy and opioid tolerance: a new hypothesis.

Opioids are efficacious and cost-effective analgesics, but tolerance limits their effectiveness. This paper does not present any new clinical or experimental data but demonstrates that there exist ascending sensory pathways that contain few opioid receptors. These pathways are located by brain PET scans and spinal cord autoradiography. These nonopioid ascending pathways include portions of the ventral spinal thalamic tract originating in Rexed layers VI-VIII, thalamocortical fibers that project to the primary somatosensory cortex (S1), and possibly a midline dorsal column visceral pathway. One hypothesis is that opioid tolerance and opioid-induced hyperalgesia may be caused by homeostatic upregulation during opioid exposure of nonopioid-dependent ascending pain pathways. Upregulation of sensory pathways is not a new concept and has been demonstrated in individuals impaired with deafness or blindness. A second hypothesis is that adjuvant nonopioid therapies may inhibit ascending nonopioid-dependent pathways and support the clinical observations that monotherapy with opioids usually fails. The uniqueness of opioid tolerance compared to tolerance associated with other central nervous system medications and lack of tolerance from excess hormone production is discussed. Experimental work that could prove or disprove the concepts as well as flaws in the concepts is discussed.

In vivo small animal micro-CT using nanoparticle contrast agents.

Computed tomography (CT) is one of the most valuable modalities for in vivo imaging because it is fast, high-resolution, cost-effective, and non-invasive. Moreover, CT is heavily used not only in the clinic (for both diagnostics and treatment planning) but also in preclinical research as micro-CT. Although CT is inherently effective for lung and bone imaging, soft tissue imaging requires the use of contrast agents. For small animal micro-CT, nanoparticle contrast agents are used in order to avoid rapid renal clearance. A variety of nanoparticles have been used for micro-CT imaging, but the majority of research has focused on the use of iodine-containing nanoparticles and gold nanoparticles. Both nanoparticle types can act as highly effective blood pool contrast agents or can be targeted using a wide variety of targeting mechanisms. CT imaging can be further enhanced by adding spectral capabilities to separate multiple co-injected nanoparticles in vivo. Spectral CT, using both energy-integrating and energy-resolving detectors, has been used with multiple contrast agents to enable functional and molecular imaging. This review focuses on new developments for in vivo small animal micro-CT using novel nanoparticle probes applied in preclinical research.

The Application of an Exogenous Linear and Radial Electrical Field to an In Vitro Chronic Diabetic Ulcer Model for Evaluation as a Potential Treatment

Chronic diabetic ulcers affect approximately 15% of patients with diabetes worldwide. Currently, applied electric fields are being investigated as a reliable and cost-effective treatment. This in vitro study aimed to determine the effects of a constant and spatially variable electric field on three factors: endothelial cell migration, proliferation, and angiogenic gene expression. Results for a constant electric field of 0.01 V demonstrated that migration at short time points increased 20-fold and proliferation at long time points increased by a factor of 1.40. Results for a spatially variable electric field did not increase directional migration, but increased proliferation by a factor of 1.39 and by a factor of 1.55 after application of 1.00 V and 0.01 V, respectively. Both constant and spatially variable applied fields increased angiogenic gene expression. Future research that explores a narrower range of intensity levels may more clearly identify the optimal design specifications of a spatially variable electric field.

In situ chemical modification of peptide microarrays: application to the study of the antibody responses to methylated antigens.

Peptide microarrays are useful tools for characterizing the humoral response against methylated antigens. They are usually prepared by printing unmodified and methylated peptides on substrates such as functionalized microscope glass slides. The preferential capture of antibodies by methylated peptides suggests the specific recognition of methylated epitopes. However, unmodified peptide epitopes can be masked due to their interaction with the substrate. The accessibility of unmodified peptides and thus the specificity of the recognition of methylated peptide epitopes can be probed using the in situ methylation procedure described here. Alternately, the in situ methylation of peptide microarrays allows probing the presence of antibodies directed toward methylated epitopes starting from easy-to-make and cost-effective unmodified peptide libraries. In situ methylation was performed using formaldehyde in the presence of sodium cyanoborohydride and nickel chloride. This chemical procedure converts lysine residues into mono- or dimethyl lysines.

Bulk synchronous parallelization of industrial electromagentic software

The parallelization of existing/industrial electromagnetic software using the bulk synchronous parallel (BSP) computation model is presented. The software employs the finite element method with a preconditioned conjugate gradient-type solution for the resulting linear systems of equations. A geometric mesh-partitioning approach is applied within the BSP framework for the assembly and solution phases of the finite element computation. This is combined with a nongeometric, data-driven parallel quadrature procedure for the evaluation of right-hand-side terms in applications involving coil fields. A similar parallel decomposition is applied to the parallel calculation of electron beam trajectories required for the design of tube devices. The BSP parallelization approach adopted is fully portable, conceptually simple, and cost-effective, and it can be applied to a wide range of finite element applications not necessarily related to electromagnetics.

The recovery mechanism of platinum group metals from catalytic converters in spent automotive exhaust systems

The recovery of platinum group metals (PGMs) from catalytic converters of spent exhaust systems is considered in this paper. To be cost-effective, recovery processes must be well over 90% efficient and so the optimisation of their operation is vital. Effective optimisation requires a sound understanding of the operation and the underlying process mechanisms. This paper focuses on pyrometallurgical recovery operations used and typified by the Johnson–Matthey process. Analysis of this process reveals that it cannot be simply explained by the gravity model that is normally assumed. The analysis reveals that the affinity of PGM particles for the melted collector metal is a key factor in the behaviour of the process. A rational explanation of the key issues that govern the process behaviour is proposed and shown to be consistent with available operational data. The results generated would be applicable to other similar processes.

Obtaining data to validate a model of an induction skull melting furnace

A casting route is often the most cost-effective means of producing engineering components. However, certain materials, particularly those based on Ti, TiAl and Zr alloy systems, are very reactive in the molten condition and must be melted in special furnaces. Induction Skull Melting (ISM) is the most widely-used process for melting these alloys prior to casting components such as turbine blades, engine valves, turbocharger rotors and medical prostheses. A major research project is underway with the specific target of developing robust techniques for casting TiAl components. The aims include increasing the superheat in the molten metal to allow thin section components to be cast, improving the quality of the cast components and increasing the energy efficiency of the process. As part of this, the University of Greenwich (UK) is developing a computer model of the ISM process in close collaboration with the University of Birmingham (UK) where extensive melting trials are being undertaken. This paper describes the experimental measurements to obtain data to feed into and to validate the model. These include measurements of the true RMS current applied to the induction coil, the heat transfer from the molten metal to the crucible cooling water, and the shape of the column of semi-levitated molten metal. Data are presented for Al, Ni and TiAl.

Impact of assembly process technologies on electronic packaging materials

Assembly processes used to bond components to printed circuit boards can have a significant impact on these boards and the final packaged component. Traditional approaches to bonding components to printed circuit boards results in heat being applied across the whole board assembly. This can lead to board warpage and possibly high residual stresses. Another approach discussed in this paper is to use Variable Frequency Microwave (VFM) heating to cure adhesives and underfills and bond components to printed circuit boards. In terms of energy considerations the use of VFM technology is much more cost effective compared to convection/radiation heating. This paper will discuss the impact of traditional reflow based processes on flexible substrates and it will demonstrate the possible advantages of using localised variable frequency microwave heating to cure materials in an electronic package.

Hypertension - a contemporary approach to nursing care

The incidence of hypertension is increasing as the number of patients with obesity and diabetes mellitus increases. Hypertension results when the peripheral vascular resistance is increased, the blood viscosity is elevated and/or the flow of blood through the main arteries is impeded. Chronic hypertension results in enlarged heart, myocardial damage and lung and renal abnormalities. While some causative factors such as obesity can be controlled, others for example genetics are more difficult to treat because often there is more than one factor involved. This paper explores how essential and secondary factors contribute to the incidence of hypertension and the physiological changes resulting from raised blood pressure. It proposes that although traditional treatment has some success, nurse-led clinics are having better success not only in controlling raised blood pressure but also in reducing cardiac, pulmonary and renal morbidity. It is more cost-effective, staff is more productive and clients are more compliant with treatment.

The benefits of a health impact assessment in relation to fuel poverty: assessing Luton's affordable warmth strategy and the need for a national strategy

The links between fuel poverty and poor health are well documented, yet there is no statutory requirement on local authorities to develop fuel poverty strategies, which tend to be patchy nationally and differ substantially in quality. Fuel poverty starts from the perspective of income, even though interventions can improve health. The current public health agenda calls for more partnership-based, cost-effective strategies based on sound evidence. Fuel poverty represents a key area where there is currently little local evidence quantifying and qualifying health gain arising from strategic interventions. As a result, this initial study sought to apply the principles of a health impact assessment to Luton’s Affordable Warmth Strategy, exploring the potential to identify health impact arising – as a baseline for future research – in the context of the public health agenda. A national strategy would help ensure the promotion of targeted fuel poverty strategies.

Finance for water and sanitation as a public service

Drawing on empirical evidence gathered through the PSIRU database, this contribution aims at addressing the potential of public finance to enhance the provision of water supply and sanitation as a public service. It highlights the problems associated with (and the disappointing results obtained from) resort to Private Sector Participation and private finance, both historically and in the last 15-20 years, in developed and developing countries. It also addresses the advantages of using public finance as a more cost-effective and equitable instrument to achieve developmental objectives such as the expansion of service coverage and development of water and sanitation infrastructure. The potential of public operations in maximising developmental impact from the social, economic and environmental points of view is then explored referring to specific examples from a variety of countries and regions. These include the in-house restructuring of public operations to enhance transparency, accountability and effectiveness, as well as the use of Public-Public Partnerships (PUPs) to build capacity. Attention is devoted to the specific financial requirements of expanding sewerage services at global level to achieve MDGs or broader developmental goals. These requirements are revisited in light of a regional breakdown of coverage gaps, available resources and development aid flows. These findings challenge the established view among international and bilateral agencies that expanding sewerage services in developing countries is excessively costly and should be abandoned as a priority because unaffordable. This contribution draws on a number of PSIRU Reports, and particularly the following. - http://www.psiru.org/reports/2008-03-W-sewers.pdf - http://boell-latinoamerica.org/download_es/agua08_privatizacion_LA_2007.pdf - http://boell-latinoamerica.org/download_es/agua08_agua_un_servicio_publico.pdf - http://www.psiru.org/reports/2006-03-W-investment.pdf All PSIRU Reports are accessible at http://www.psiru.org/publicationsindex.asp.

The CPR: Antique technology observing today's oceans

First designed in the 1920s and in routine use in the Atlantic since the 1930s, the Continuous Plankton Recorder (CPR) is an ocean observing tool that has been used in the north Pacific since 2000 and still retains its relevance. It was the sampler of choice in 2000 because it is reliable, cost-effective, samples on the scale of an entire ocean and, while not a perfect sampler, its limitations are mostly well-known. Earlier this year, the GOOS Scientific Steering Committee endorsed the north Pacific CPR survey as an ocean observing tool. Data from the seven years of sampling in the North Pacific have already shown responses in open ocean plankton to changes from cool to warm ocean conditions, from which we can start to make predictions on responses to future climate changes. This presentation describes and presents results from the survey, and ends with some thoughts on development of the north Pacific CPR survey.