BarraCUDA – a Fast Sequence Mapping Software using Graphics Processing Units

High-throughput DNA sequencing (HTS) instruments today are capable of generating millions of sequencing reads in a short period of time, and this represents a serious challenge to current bioinformatics pipeline in processing such an enormous amount of data in a fast and economical fashion. Modern graphics cards are powerful processing units that consist of hundreds of scalar processors in parallel in order to handle the rendering of high-definition graphics in real-time. It is this computational capability that we propose to harness in order to accelerate some of the time-consuming steps in analyzing data generated by the HTS instruments. We have developed BarraCUDA, a novel sequence mapping software that utilizes the parallelism of NVIDIA CUDA graphics cards to map sequencing reads to a particular location on a reference genome. While delivering a similar mapping fidelity as other mainstream programs , BarraCUDA is a magnitude faster in mapping throughput compared to its CPU counterparts. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the mapping throughput. BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the mapping of millions of sequencing reads generated by HTS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available at http://seqbarracuda.sf.net

Designing Accessible Technology

The key to this is maintaining a healthy population that is able and willing to work longer before retirement and can remain independent for as long as possible afterwards as well as bringing disabled people into mainstream life and ...

Influence of film cooling hole angles and geometries on aerodynamic loss and net heat flux reduction

Turbine design engineers have to ensure that film cooling can provide sufficient protection to turbine blades from the hot mainstream gas, while keeping the losses low. Film cooling hole design parameters include inclination angle (α), compound angle (β ), hole inlet geometry and hole exit geometry. The influence of these parameters on aerodynamic loss and net heat flux reduction is investigated, with loss being the primary focus. Low-speed flat plate experiments have been conducted at momentum flux ratios of IR = 0.16, 0.64 and 1.44. The film cooling aerodynamic mixing loss, generated by the mixing of mainstream and coolant, can be quantified using a three-dimensional analytical model that has been previously reported by the authors. The model suggests that for the same flow conditions, the aerodynamic mixing loss is the same for holes with different α and β but with the same angle between the mainstream and coolant flow directions (angle κ). This relationship is assessed through experiments by testing two sets of cylindrical holes with different α and β : one set with κ = 35°, another set with κ = 60°. The data confirm the stated relationship between α, β, κ and the aerodynamic mixing loss. The results show that the designer should minimise κ to obtain the lowest loss, but maximise β to achieve the best heat transfer performance. A suggestion on improving the loss model is also given. Five different hole geometries (α =35.0°, β =0°) were also tested: cylindrical hole, trenched hole, fan-shaped hole, D-Fan and SD-Fan. The D-Fan and the SD-Fan have similar hole exits to the fan-shaped hole but their hole inlets are laterally expanded. The external mixing loss and the loss generated inside the hole are compared. It was found that the D-Fan and the SD-Fan have the lowest loss. This is attributed to their laterally expanded hole inlets, which lead to significant reduction in the loss generated inside the holes. As a result, the loss of these geometries is ≈ 50 % of the loss of the fan-shaped hole at IR = 0.64 and 1.44. Copyright © 2011 by ASME.

Beyond niche thinking: Market selection in science-based ventures

Matching a new technology to an appropriate market is a major challenge for new technology-based firms (NTBF). Such firms are often advised to target niche-markets where the firms and their technologies can establish themselves relatively free of incumbent competition. However, technologies are diverse in nature and do not benefit from identical strategies. In contrast to many Information and Communication Technology (ICT) innovations which build on an established knowledge base for fairly specific applications, technologies based on emerging science are often generic and so have a number of markets and applications open to them, each carrying considerable technological and market uncertainty. Each of these potential markets is part of a complex and evolving ecosystem from which the venture may have to access significant complementary assets in order to create and sustain commercial value. Based on dataset and case study research on UK advanced material university spin-outs (USO), we find that, contrary to conventional wisdom, the more commercially successful ventures were targeting mainstream markets by working closely with large, established competitors during early development. While niche markets promise protection from incumbent firms, science-based innovations, such as new materials, often require the presence, and participation, of established companies in order to create value. © 2012 IEEE.

Classical plume theory: 1937-2010 and beyond

Developing a theoretical description of turbulent plumes, the likes of which may be seen rising above industrial chimneys, is a daunting thought. Plumes are ubiquitous on a wide range of scales in both the natural and the man-made environments. Examples that immediately come to mind are the vapour plumes above industrial smoke stacks or the ash plumes forming particle-laden clouds above an erupting volcano. However, plumes also occur where they are less visually apparent, such as the rising stream of warmair above a domestic radiator, of oil from a subsea blowout or, at a larger scale, of air above the so-called urban heat island. In many instances, not only the plume itself is of interest but also its influence on the environment as a whole through the process of entrainment. Zeldovich (1937, The asymptotic laws of freely-ascending convective flows. Zh. Eksp. Teor. Fiz., 7, 1463-1465 (in Russian)), Batchelor (1954, Heat convection and buoyancy effects in fluids. Q. J. R. Meteor. Soc., 80, 339-358) and Morton et al. (1956, Turbulent gravitational convection from maintained and instantaneous sources. Proc. R. Soc. Lond. A, 234, 1-23) laid the foundations for classical plume theory, a theoretical description that is elegant in its simplicity and yet encapsulates the complex turbulent engulfment of ambient fluid into the plume. Testament to the insight and approach developed in these early models of plumes is that the essential theory remains unchanged and is widely applied today. We describe the foundations of plume theory and link the theoretical developments with the measurements made in experiments necessary to close these models before discussing some recent developments in plume theory, including an approach which generalizes results obtained separately for the Boussinesq and the non-Boussinesq plume cases. The theory presented - despite its simplicity - has been very successful at describing and explaining the behaviour of plumes across the wide range of scales they are observed. We present solutions to the coupled set of ordinary differential equations (the plume conservation equations) that Morton et al. (1956) derived from the Navier-Stokes equations which govern fluid motion. In order to describe and contrast the bulk behaviour of rising plumes from general area sources, we present closed-form solutions to the plume conservation equations that were achieved by solving for the variation with height of Morton's non-dimensional flux parameter Γ - this single flux parameter gives a unique representation of the behaviour of steady plumes and enables a characterization of the different types of plume. We discuss advantages of solutions in this form before describing extensions to plume theory and suggesting directions for new research. © 2010 The Author. Published by Oxford University Press on behalf of the Institute of Mathematics and its Applications. All rights reserved.

Gasoline fuelled partially premixed compression ignition in a light duty multi cylinder engine: A study of low load and low speed operation

The objective of this study was to examine the operating characteristics of a light duty multi cylinder compression ignition engine with regular gasoline fuel at low engine speed and load. The effects of fuel stratification by means of multiple injections as well as the sensitivity of auto-ignition and burn rate to intake pressure and temperature are presented. The measurements used in this study included gaseous emissions, filter smoke opacity and in-cylinder indicated information. It was found that stable, low emission operation was possible with raised intake manifold pressure and temperature, and that fuel stratification can lead to an increase in stability and a reduced reliance on increased temperature and pressure. It was also found that the auto-ignition delay sensitivity of gasoline to intake temperature and pressure was low within the operating window considered in this study. Nevertheless, the requirement for an increase of pressure, temperature and stratification in order to achieve auto-ignition time scales small enough for combustion in the engine was clear, using pump gasoline. Copyright © 2009 SAE International.

Study of steady state and transient EGR behaviour of a medium duty diesel engine

It is well known that accurate EGR control is paramount to controlling engine out emissions during steady state and transient operation of a diesel engine. The direct measurement of EGR is however non-trivial and especially difficult in engines with no external EGR control where the intake manifold CO2 levels can be measured more readily. This work studies the EGR behaviour in a medium duty diesel engine with a passive EGR rebreathing strategy for steady state and transient operation. High speed (response time ∼1ms) in-cylinder sampling using modified GDI valves is coupled with high frequency response analysers to measure the cyclic in-cylinder CO2, from which the EGR rate is deduced. It was found that controlling the EGR using the passive rebreathing strategy during certain combined speed and load transients is challenging, causing high smoke and NO emissions. The in-cylinder sampling method coupled with fast CO2 measurement (time constant ∼8ms) in the exhaust port gave insights about the EGR rate during these transients. The complex interaction of the manifold pressures, turbo-charger operation and trapped charge composition from the previous cycle simply can cause high dilution and therefore high smoke levels. The steady state variation of NO emissions with respect to EGR is also studied using a fast NO analyzer (time constant ∼2ms) in the exhaust port. Cyclic variation was found to be up to ±5% at some load conditions. © 2008 SAE International.

Investigation into partially premixed combustion in a light-duty multi-cylinder diesel engine fuelled gasoline and diesel with a mixture of

Partially premixed compression ignition (PPCI) engines operating with a low temperature highly homogeneous charge have been demonstrated previously using conventional diesel fuel. The short ignition delay of conventional diesel fuel requires high fuel injection pressures to achieve adequate premixing along with high levels of EGR (exhaust gas recirculation) to achieve low NOx emissions. Low load operating regions are typified by substantial emissions of CO and HC and there exists an upper operating load limitation due to very high rates of in-cylinder gas pressure rise. In this study mixtures of gasoline and diesel fuel were investigated using a multi-cylinder light duty diesel engine. It was found that an increased proportion of gasoline fuel reduced smoke emissions at higher operating loads through an increase in charge premixing resulting from an increase in ignition delay and higher fuel volatility. The results of this investigation confirm that a combination of fuel properties, exhibiting higher volatility and increased ignition delay, would enable a widening of the low emission operating regime, but that consideration must be given to combustion stability at low operating loads. Copyright © 2007 SAE International.

A simple diesel engine air-path model to predict the cylinder charge during transients: Strategies for reducing transient emissions spikes

Simple air-path models for modern (VGT/EGR equipped) diesel engines are in common use, and have been reported in the literature. This paper addresses some of the shortcomings of control-oriented models to allow better prediction of the cylinder charge properties. A fast response CO2 analyzer is used to validate the model by comparing the recorded and predicted CO2 concentrations in both the intake port and exhaust manifold of one of the cylinders. Data showing the recorded NOx emissions and exhaust gas opacity during a step change in engine load illustrate the spikes in both NOx and smoke seen during transient conditions. The predicted cylinder charge properties from the model are examined and compared with the measured NOx and opacity. Together, the emissions data and charge properties paint a consistent picture of the phenomena occurring during the transient. Alternative strategies for the fueling and cylinder charge during these load transients are investigated and discussed. Experimental results are presented showing that spikes in both NOx and smoke can be avoided at the expense of some loss in torque response. Even if the torque response must be maintained, it is demonstrated that it is still possible to eliminate spikes in NOx emissions for the transient situation being examined. Copyright © 2006 SAE International.

Global civil aviation black carbon emissions.

Aircraft black carbon (BC) emissions contribute to climate forcing, but few estimates of BC emitted by aircraft at cruise exist. For the majority of aircraft engines the only BC-related measurement available is smoke number (SN)-a filter based optical method designed to measure near-ground plume visibility, not mass. While the first order approximation (FOA3) technique has been developed to estimate BC mass emissions normalized by fuel burn [EI(BC)] from SN, it is shown that it underestimates EI(BC) by >90% in 35% of directly measured cases (R(2) = -0.10). As there are no plans to measure BC emissions from all existing certified engines-which will be in service for several decades-it is necessary to estimate EI(BC) for existing aircraft on the ground and at cruise. An alternative method, called FOX, that is independent of the SN is developed to estimate BC emissions. Estimates of EI(BC) at ground level are significantly improved (R(2) = 0.68), whereas estimates at cruise are within 30% of measurements. Implementing this approach for global civil aviation estimated aircraft BC emissions are revised upward by a factor of ~3. Direct radiative forcing (RF) due to aviation BC emissions is estimated to be ~9.5 mW/m(2), equivalent to ~1/3 of the current RF due to aviation CO2 emissions.

Future, opportunities and challenges of inkjet technologies

Inkjet printing relies on the formation of small liquid droplets to deliver precise amounts of material to a substrate under digital control. Inkjet technology is becoming relatively mature and is of great industrial interest thanks to its flexibility for graphical printing and its potential use in less conventional applications such as additive manufacturing and the production of printed electronics and other functional devices. Its advantages over traditional methods of printing include the following: it produces little or no waste, it is versatile because several different methods exist, it is noncontact, and it does not require a master template so that printed patterns can be readily modified on demand. However, the technology is in need of further development to become mainstream in emerging applications such as additive manufacturing (3D printing). This review contains a description of conventional and less common inkjet methods and surveys the current applications of inkjet in industry. This is followed by specific examples of the barriers, limitations, and challenges faced by inkjet technology in both graphical printing and manufacturing. © 2013 by Begell House, Inc.

Influence of film cooling hole angles and geometries on aerodynamic loss and net heat flux reduction

Turbine design engineers have to ensure that film cooling can provide sufficient protection to turbine blades from the hot mainstream gas, while keeping the losses low. Film cooling hole design parameters include inclination angle (a), compound angle (b), hole inlet geometry, and hole exit geometry. The influence of these parameters on aerodynamic loss and net heat flux reduction is investigated, with loss being the primary focus. Low-speed flat plate experiments have been conducted at momentum flux ratios of IR=0.16, 0.64, and 1.44. The film cooling aerodynamic mixing loss, generated by the mixing of mainstream and coolant, can be quantified using a three-dimensional analytical model that has been previously reported by the authors. The model suggests that for the same flow conditions, the aerodynamic mixing loss is the same for holes with different a and b but with the same angle between the mainstream and coolant flow directions (angle k). This relationship is assessed through experiments by testing two sets of cylindrical holes with different a and b: one set with k=35 deg, and another set with k=60 deg. The data confirm the stated relationship between α, β, k and the aerodynamic mixing loss. The results show that the designer should minimize k to obtain the lowest loss, but maximize b to achieve the best heat transfer performance. A suggestion on improving the loss model is also given. Five different hole geometries (α=35.0 deg, β=0 deg) were also tested: cylindrical hole, trenched hole, fan-shaped hole, D-Fan, and SD-Fan. The D-Fan and the SD-Fan have similar hole exits to the fan-shaped hole but their hole inlets are laterally expanded. The external mixing loss and the loss generated inside the hole are compared. It was found that the D-Fan and the SD-Fan have the lowest loss. This is attributed to their laterally expanded hole inlets, which lead to significant reduction in the loss generated inside the holes. As a result, the loss of these geometries is≈50% of the loss of the fan-shaped hole at IR=0.64 and 1.44. © 2013 by ASME.

ALGAL GROWTH POTENTIAL AND NUTRIENT LIMITATION IN SPRING IN THREE-GORGES RESERVOIR, CHINA

In China, especially in Three-Gorges Reservoir, our knowledge of the algal growth potential and nutrient limitation was still limited. In the spring of 2006, the water column ratios of total nitrogen/total phosphorus were investigated and algal bioassays performed to determine algal growth potential of waters and nutrient limitation of mainstream and Xiangxi Bay of Three-Gorges Reservoir. The results showed sampling sites in mainstream were co-limited by N and P or P-limited alone, and sites in Xiangxi Bay were N-limited alone. Fe likely played an important role in determining the appearance and disappearance of algal blooms of Three-Gorges Reservoir. Native algae, Pseudokirchneriella subcapitata and Cyclotella meneghiniana, had high growth potential in Three-Gorges Reservoir.

A comparison of methods currently used in inclusive design.

Inclusive design has unique challenges because it aims to improve usability for a wide range of users. This typically includes people with lower levels of ability, as well as mainstream users. This paper examines the effectiveness of two methods that are used in inclusive design: user trials and exclusion calculations (an inclusive design inspection method). A study examined three autoinjectors using both methods (n=30 for the user trials). The usability issues identified by each method are compared and the effectiveness of the methods is discussed. The study found that each method identified different kinds of issues, all of which are important for inclusive design. We therefore conclude that a combination of methods should be used in inclusive design rather than relying on a single method. Recommendations are also given for how the individual methods can be used more effectively in this context.

Macrozoobenthic community of Poyang Lake, the largest freshwater lake of China, in the Yangtze floodplain

Poyang Lake (Poyang Hu) is located at the junction of the middle and lower reaches of the Yangtze (Changjiang) River, covering an area of 3283 km(2). As one of the few lakes that are still freely connected with the river, it plays an important role in the maintenance of the unique biota of the Yangtze floodplain ecosystem. To promote the conservation of Poyang Lake, an investigation of the macrobenthos in the lake itself and adjoining Yangtze mainstream was conducted in 1997-1999. Altogether 58 benthic taxa, including, 22 annelids, 8 mollusks, 26 arthropods, and 2 miscellaneous animals, were identified from quantitative samples. The benthic fauna shows a high diversity and a marine affinity. The standing crops of benthos in the lake were much higher than those in the river, being 659 individuals/m(2) and 187.3g/m(2) (wet mass) in the main lake, and 549 individuals/m(2) and 116.6 g/m(2) in the lake outlet, but only 129 individuals/m(2) and 0.4g/m(2) in the river. The dominant roup in the lake was Mollusca, comprising 63.4% of the total in density and 99.5% in biomass. An analysis of the functional feeding structure indicated that collector-filterers and scrapers were predominant in the lake, up to 42.2% and 24.7% in density and 70.2% and 29.2% in biomass, respectively, while shredders and collector-gatherers were relatively common in the river. The present study was restricted to the northern outlet and the northeast part of Poyang Lake. A scrutiny is required for the remaining areas.