Uncovering the expression patterns of chimeric transcripts using surveys of affymetrix GeneChips.

BACKGROUND: A chimeric transcript is a single RNA sequence which results from the transcription of two adjacent genes. Recent studies estimate that at least 4% of tandem human gene pairs may form chimeric transcripts. Affymetrix GeneChip data are used to study the expression patterns of tens of thousands of genes and the probe sequences used in these microarrays can potentially map to exotic RNA sequences such as chimeras. RESULTS: We have studied human chimeras and investigated their expression patterns using large surveys of Affymetrix microarray data obtained from the Gene Expression Omnibus. We show that for six probe sets, a unique probe mapping to a transcript produced by one of the adjacent genes can be used to identify the expression patterns of readthrough transcripts. Furthermore, unique probes mapping to an intergenic exon present only in the MASK-BP3 chimera can be used directly to study the expression levels of this transcript. CONCLUSIONS: We have attempted to implement a new method for identifying tandem chimerism. In this analysis unambiguous probes are needed to measure run-off transcription and probes that map to intergenic exons are particularly valuable for identifying the expression of chimeras

Simulating Pathogen Transport within a Naturally Ventilated Hospital Ward

Understanding how airborne pathogens are transported through hospital wards is essential for determining the infection risk to patients and healthcare workers. This study utilizes Computational Fluid Dynamics (CFD) simulations to explore pathogen transport within a six-bed Nightingale hospital ward. Grid independence of a ward model was addressed using the Grid Convergence Index (GCI) from solutions obtained using three fully-structured grids. Pathogens were simulated using source terms in conjunction with a scalar transport equation and a RANS turbulence model. Errors were found to be less than 4% in the prediction of air velocities but an average of 13% was seen in the scalar field. A parametric study into the pathogen release point illustrated that its distribution is strongly influenced by the local velocity field and the degree of mixing present

Electrochemical behaviour of gamma hydroxybutyric acid at a platinum electrode in acidic medium

The electrooxidation of Gamma Hydroxybutyric Acid (GHB) on a polycrystalline platinum electrode is studied by cyclic voltammetry in acidic medium. Two oxidation peaks, A and B, are obtained in the positive scan within the potential range of the double layer region and of the platinum oxide region, respectively. In the negative going potential sweep an inverted oxidation peak with an onset partially overlapping with the tail of the cathodic peak for the reduction of the platinum oxide formed during the anodic scan is obtained (peak C). This inverted peak can be observed at a potential close to +0.2 V (vs Ag/AgCl at pH 2) and separated 0.4 and 0.8 V from the two other oxidation peaks obtained during the anodic scan and in such conditions that the surface is particularly activated to favour this electrochemical process. The response obtained in the electronic current for the different peaks when GHB concentration and scan rate were changed to allows inferring that these are the result of a potential dependent mechanism. The behaviour observed is according with the oxidation of the alcohol group to the corresponding aldehyde and carboxylic acid (succinic acid) as main products

VeSV- Value at the end of the Sanitation Value Chain: Final Report

Bangladesh is no stranger to composting projects using both green waste and faecal sludge (FS). There have been many initiatives over the years with varying degrees of success. Similarly there have been hundreds, if not thousands of projects to improve access to latrines, latrine use and latrine management. Again there has been a great deal of success, especially in increasing the number of latrines being built. However, a key gap regarding the safe collection and processing of the waste from the pit still remains. In cases where projects have attempted addressing this, the solution has rarely been viable on a large scale. That is where this project—VeSV—is different. The aim of this project is to provide scientific evidence to support the commercial viability of collecting and composting faecal sludge for use in agriculture and horticulture. The gap between a good idea and commercial success is bridged on this project by producing primary scientific data based on qualitative and quantitative research methods and by engaging a number of stakeholders across sectors. A rigorous research was conducted to characterize raw faecal sludge material from single pit latrines in rural Bangladesh, as the starting point to develop value across the sanitation chain from processing FS material, through adding value by recovering nutrient and finally by assessing the potential commercialization of the final product in the fertilizer market. Crucially academics, NGOs, business groups and existing fertilizer, composting and latrine management companies were involved as part of our Reference Group, which helped to develop practical engineering solutions in harmony with the right and relevant context in rural Bangladesh. Our research outcomes include the development of safe methodologies for pit emptying; the assessment of people's intentions to change current operation and maintenance practices of pit latrines at household level and their willingness to participate in commercially viable and sustainable methods for FS management; the assessment of optimised engineering process for FS stabilisation and the production of a safe, high quality fertilizer that is desirable to farmers; and the identification of potential hurdles that may obstruct the widespread adoption of business models for FS fertiliser

An Effective Surrogate Tracer Technique for S. aureus Bioaerosols in a Mechanically Ventilated Hospital Room Replica Using Dilute Aqueous Lithium Chloride

Finding a non-pathogenic surrogate aerosol that represents the deposition of typical bioaerosols in healthcare settings is beneficial from the perspective of hospital facility testing, general infection control and outbreak analysis. This study considers aerosolization of dilute aqueous lithium chloride (LiCl) and sodium chloride (NaCl) solutions as surrogate tracers capable of representing Staphylococcus aureus bioaerosol deposition on surfaces in mechanically ventilated rooms. Tests were conducted in a biological test chamber set up as a replica hospital single patient room. Petri dishes on surfaces were used to collect the Li, Na and S. aureus aerosols separately after release. Biological samples were analyzed using cultivation techniques on solid media, and flame atomic absorption spectroscopy was used to measure Li and Na atom concentrations. Spatial deposition distribution of Li tracer correlated well with S. aureus aerosols (96% of pairs within a 95% confidence interval). In the patient hospital room replica, results show that the most contaminated areas were on surfaces 2 m away from the source. This indicates that the room’s airflow patterns play a significant role in bioaerosol transport. NaCl proved not to be sensitive to spatial deposition patterns. LiCl as a surrogate tracer for bioaerosol deposition was most reliable as it was robust to outliers, sensitive to spatial heterogeneity and found to require less replicates than the S. aureus counterpart to be in good spatial agreement with biological results

The Large Quasar Reference Frame (LQRF) - an optical representation of the ICRS

The large number and all-sky distribution of quasars from different surveys, along with their presence in large, deep astrometric catalogs,enables the building of an optical materialization of the ICRS following its defining principles. Namely: that it is kinematically non-rotating with respect to the ensemble of distant extragalactic objects; aligned with the mean equator and dynamical equinox of J2000; and realized by a list of adopted coordinates of extragalatic sources. Starting from the updated and presumably complete LQAC list of QSOs, the initial optical positions of those quasars are found in the USNO B1.0 and GSC2.3 catalogs, and from the SDSS DR5. The initial positions are next placed onto UCAC2-based reference frames, following by an alignment with the ICRF, to which were added the most precise sources from the VLBA calibrator list and the VLA calibrator list - when reliable optical counterparts exist. Finally, the LQRF axes are inspected through spherical harmonics, contemplating to define right ascension, declination and magnitude terms. The LQRF contains J2000 referred equatorial coordinates for 100,165 quasars, well represented across the sky, from -83.5 to +88.5 degrees in declination, and with 10 arcmin being the average distance between adjacent elements. The global alignment with the ICRF is 1.5 mas, and the individual position accuracies are represented by a Poisson distribution that peaks at 139 mas in right ascension and 130 mas in declination. It is complemented by redshift and photometry information from the LQAC. The LQRF is designed to be an astrometric frame, but it is also the basis for the GAIA mission initial quasars' list, and can be used as a test bench for quasars' space distribution and luminosity function studies.Comment: 23 pages, 23 figures, 6 tables Accepted for publication by Astronomy & Astrophysics, on 25 May 200

Towards sustainable sanitation management: Establishing the costs and willingness to pay for emptying and transporting sludge in rural districts with high rates of access to latrines

MOTIVATION: Proper management of fecal sludge has significant positive health and environmental externalities. Most research on managing onsite sanitation so far either simulates the costs of, or the welfare effects from, managing sludge in situ in pit latrines. Thus, designing management strategies for onsite rural sanitation is challenging, because the actual costs of transporting sludge for treatment, and sources for financing these transport costs, are not well understood. METHODS: In this paper we calculate the actual cost of sludge management from onsite latrines, and identify the contributions that latrine owners are willing to make to finance the costs. A spreadsheet-based model is used to identify a cost-effective transport option, and to calculate the cost per household. Then a double-bound contingent valuation method is used to elicit from pit-latrine owners their willingness-to-pay to have sludge transported away. This methodology is employed for the case of a rural subdistrict in Bangladesh called Bhaluka, a unit of administration at which sludge management services are being piloted by the Government of Bangladesh. RESULTS: The typical sludge accumulation rate in Bhaluka is calculated at 0.11 liters/person/day and a typical latrine will need to be emptied approximately once every 3 to 4 years. The costs of emptying and transport are high; approximately USD 13 per emptying event (circa 14% of average monthly income); household contributions could cover around 47% of this cost. However, if costs were spread over time, the service would cost USD 4 per year per household, or USD 0.31 per month per household-comparable to current expenditures of rural households on telecommunications. CONCLUSION: This is one of few research papers that brings the costs of waste management together with financing of that cost, to provide evidence for an implementable solution. This framework can be used to identify cost effective sludge management options and private contributions towards that cost in other (context-specific) administrative areas where onsite sanitation is widespread

Calibrating Lattice Boltzmann Flow Simulations and Estimating Uncertainty in the Permeability of Complex Porous Media:Lattice Boltzmann Flow Simulations and Estimating Uncertainty

A common way to simulate fluid flow in porous media is to use Lattice Boltzmann (LB) methods. Permeability predictions from such flow simulations arecontrolled by parameters whose settings must be calibrated in order to producerealistic modelling results. Herein we focus on the simplest and most commonlyused implementation of the LB method: the single-relaxation-time BGK model.A key parameter in the BGK model is the relaxation time which controls flowvelocity and has a substantial influence on the permeability calculation. Currentlythere is no rigorous scheme to calibrate its value for models of real media.We show that the standard method of calibration, by matching the flow profileof the analytic Hagen-Poiseuille pipe-flow model, results in a BGK-LB modelthat is unable to accurately predict permeability even in simple realistic porousmedia (herein, Fontainebleau sandstone). In order to reconcile the differencesbetween predicted permeability and experimental data, we propose a method tocalibrate using an enhanced Transitional Markov Chain Monte Carlo method,which is suitable for parallel computer architectures. We also propose a porosity dependent calibration that provides an excellent fit to experimental data andwhich creates an empirical model that can be used to choose for new samplesof known porosity. Our Bayesian framework thus provides robust predictions of permeability of realistic porous media, herein demonstrated on the BGK-LBmodel, and should therefore replace the standard pipe-flow based methods ofcalibration for more complex media. The calibration methodology can also beextended to more advanced LB methods

A precision study of the fine tuning in the DiracNMSSM

Recently the DiracNMSSM has been proposed as a possible solution to reduce the fine tuning in supersymmetry. We determine the degree of fine tuning needed in the DiracNMSSM with and without non-universal gaugino masses and compare it with the fine tuning in the GNMSSM. To apply reasonable cuts on the allowed parameter regions we perform a precise calculation of the Higgs mass. In addition, we include the limits from direct SUSY searches and dark matter abundance. We find that both models are comparable in terms of fine tuning, with the minimal fine tuning in the GNMSSM slightly smaller.Comment: 20 pages + appendices, 10 figure

Inactivation of viable Ascaris eggs during faecal sludge co-composting with chicken feathers and market waste

Faecal Sludge (FS) contains high concentrations of pathogenic microorganisms that are 10–100 times higher than those in domestic wastewater. Proper and sustainable treatment is required to inactivate these pathogens if FS is to be recycled in agriculture, so as to minimise public health and environmental risks. Composting is one of the common low-cost technologies of sanitising FS in Urban Africa; however, it is associated with longer pathogen inactivation periods that make it commercially uneconomical. This study investigated the effect of different organic wastes types and their mixing ratios with FS on the inactivation efficiency of viable Ascaris eggs (suum and lumbricoides) during composting. Dewatered FS was mixed with market waste (MW), chicken feathers (CF) and sawdust (SD) in different ratios. Compost piles of FS:MW:SD and FS:CF:SD both in volumetric ratios of 1:2:1 and 1:3:1 were set-up in duplicate (3m3 each), composted and monitored weekly for viable Ascaris eggs presence for a period of 15 weeks. The results suggest that the organic waste types have a significant effect on the temperature evolution and pathogen inactivation efficiency while their mixing ratios do not. Piles containing CF achieved the shortest pathogen survival period of 4 weeks compared with 6–8 weeks for those with MW. The temperature–time factor was found to be the most important variable responsible for viable Ascaris eggs inactivation. However, other mechanisms such as microbial antagonism or antibiotic action induced by indigenous microorganisms and toxic by-products such as free ammonia were found to have also played an important role in Ascaris eggs inactivation. All piles attained 100% Ascaris eggs inactivation from FS, and therefore, the compost was safe for use in agriculture. The study findings suggest that composting of FS with CF can reduce Ascaris eggs inactivation periods by 42%, which may thus reduce the operational costs of FS treatment facilities