High-coverage sequencing and annotated assemblies of the budgerigar genome.

BACKGROUND: Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds. They can imitate human speech, synchronize their body movements to a rhythmic beat, and understand complex concepts of referential meaning to sounds. However, little is known about the genetics of these traits. Elucidating the genetic bases would require whole genome sequencing and a robust assembly of a parrot genome. FINDINGS: We present a genomic resource for the budgerigar, an Australian Parakeet (Melopsittacus undulatus) -- the most widely studied parrot species in neuroscience and behavior. We present genomic sequence data that includes over 300× raw read coverage from multiple sequencing technologies and chromosome optical maps from a single male animal. The reads and optical maps were used to create three hybrid assemblies representing some of the largest genomic scaffolds to date for a bird; two of which were annotated based on similarities to reference sets of non-redundant human, zebra finch and chicken proteins, and budgerigar transcriptome sequence assemblies. The sequence reads for this project were in part generated and used for both the Assemblathon 2 competition and the first de novo assembly of a giga-scale vertebrate genome utilizing PacBio single-molecule sequencing. CONCLUSIONS: Across several quality metrics, these budgerigar assemblies are comparable to or better than the chicken and zebra finch genome assemblies built from traditional Sanger sequencing reads, and are sufficient to analyze regions that are difficult to sequence and assemble, including those not yet assembled in prior bird genomes, and promoter regions of genes differentially regulated in vocal learning brain regions. This work provides valuable data and material for genome technology development and for investigating the genomics of complex behavioral traits.

Two fluid approach to high speed impact interaction amongst solid structures

The issues surrounding collision of projectiles with structures has gained a high profile since the events of 11th September 2001. In such collision problems, the projectile penetrates the stucture so that tracking the interface between one material and another becomes very complex, especially if the projectile is essentially a vessel containing a fluid, e.g. fuel load. The subsequent combustion, heat transfer and melting and re-solidification process in the structure render this a very challenging computational modelling problem. The conventional approaches to the analysis of collision processes involves a Lagrangian-Lagrangian contact driven methodology. This approach suffers from a number of disadvantages in its implementation, most of which are associated with the challenges of the contact analysis component of the calculations. This paper describes a 'two fluid' approach to high speed impact between solid structures, where the objective is to overcome the problems of penetration and re-meshing. The work has been carried out using the finite volume, unstructured mesh multi-physics code PHYSICA+, where the three dimensional fluid flow, free surface, heat transfer, combustion, melting and re-solidification algorithms are approximated using cell-centred finite volume, unstructured mesh techniques on a collocated mesh. The basic procedure is illustrated for two cases of Newtonian and non-Newtonian flow to test various of its component capabilities in the analysis of problems of industrial interest.

Droplet oscillations in high gradient magnetic field

In high intensity and high gradient magnetic fields the volumetric force on diamagnetic material, such as water, leads to conditions very similar to microgravity in a terrestrial laboratory. In principle, this opens the possibility to determine material properties of liquid samples without wall contact, even for electrically non-conducting materials. In contrast, AC field levitation is used for conductors, but then terrestrial conditions lead to turbulent flow driven by Lorentz forces. DC field damping of the flow is feasible and indeed practiced to allow property measurements. However, the AC/DC field combination acts preferentially on certain oscillation modes and leads to a shift in the droplet oscillation spectrum.What is the cause? A nonlinear spectral numerical model is presented, to address these problems

Microwave curing for high density package

Summary form only given. Currently the vast majority of adhesive materials in electronic products are bonded using convection heating or infra-red as well as UV-curing. These thermal processing steps can take several hours to perform, slowing throughput and contributing a significant portion of the cost of manufacturing. With the demand for lighter, faster, and smaller electronic devices, there is a need for innovative material processing techniques and control methodologies. The increasing demand for smaller and cheaper devices pose engineering challenges in designing a curing systems that minimize the time required between the curing of devices in a production line, allowing access to the components during curing for alignment and testing. Microwave radiation exhibits several favorable characteristics and over the past few years has attracted increased academic and industrial attention as an alternative solution to curing of flip-chip underfills, bumps, glob top and potting cure, structural bonding, die attach, wafer processing, opto-electronics assembly as well as RF-ID tag bonding. Microwave energy fundamentally accelerates the cure kinetics of polymer adhesives. It provides a route to focus heat into the polymer materials penetrating the substrates that typically remain transparent. Therefore microwave energy can be used to minimise the temperature increase in the surrounding materials. The short path between the energy source and the cured material ensures a rapid heating rate and an overall low thermal budget. In this keynote talk, we will review the principles of microwave curing of materials for high density packing. Emphasis will be placed on recent advances within ongoing research in the UK on the realization of "open-oven" cavities, tailored to address existing challenges. Open-ovens do not require positioning of the device into the cavity through a movable door, hence being more suitable for fully automated processing. Further potential advantages of op- - en-oven curing include the possibility for simultaneous fine placement and curing of the device into a larger assembly. These capabilities promise productivity gains by combining assembly, placement and bonding into a single processing step. Moreover, the proposed design allows for selective heating within a large substrate, which can be useful particularly when the latter includes parts sensitive to increased temperatures.

Droplet oscillations in high gradient static magnetic field

In high intensity and high gradient magnetic fields the volumetric force on diamagnetic material, such as water, leads to conditions very similar to microgravity in a terrestrial laboratory. In principle, this opens the possibility to determine material properties of liquid samples without wall contact, even for electrically non-conducting materials. In contrast, AC field levitation is used for conductors, but then terrestrial conditions lead to turbulent flow driven by Lorentz forces. DC field damping of the flow is feasible and indeed practiced to allow property measurements. However, the AC/DC field combination acts preferentially on certain oscillation modes and leads to a shift in the droplet oscillation spectrum.What is the cause? A nonlinear spectral numerical model is presented, to address these problems.

Influence of megasonic agitation on the electrodeposition of high aspect ratio blind vias

This paper presents preliminary studies in electroplating using megasonic agitation to avoid the formation of voids within high aspect ratio microvias that are used for the redistribution of interconnects in high density interconnection technology in printed circuit boards. Through this technique, uniform deposition of metal on the side walls of the vias is possible. High frequency acoustic streaming at megasonic frequencies enables the decrease of the Nernst diffusion layer down to the sub-micron range, allowing thereby conformal electrodeposition in deep grooves. This effect enables the normally convection free liquid near the surface to be agitated. Higher throughput and better control of the material properties of the deposits can be achieved for the manufacturing of embedded interconnections and metal-based MEMS. For optimal filling performance of the microvias, a full design of experiments (DOE) and a multi-physics numerical simulation have been conducted to analyse the influence of megasonic agitation on the plating quality of the microvias. Megasonic based deposition has been found to increase the deposition rate as well as improving the quality of the metal deposits.

Evaluation of particle degradation due to high-speed impacts in a pneumatic handling system

Particle degradation can be a significant issue in particulate solids handling and processing, particularly in pneumatic conveying systems, in which high-speed impact is usually the main contributory factor leading to changes in particle size distribution (comparing the material to its virgin state). However, other factors may strongly influence particles breakage as well, such as particle concentrations, bend geometry,and hardness of pipe material. Because of such complex influences, it is often very difficult to predict particle degradation accurately and rapidly for industrial processes. In this article, a general method for evaluating particle degradation due to high-speed impacts is described, in which the breakage properties of particles are quantified using what are known as "breakage matrices". Rather than a pilot-size test facility, a bench-scale degradation tester has been used. Some advantages of using the bench-scale tester are briefly explored. Experimental determination of adipic acid has been carried out for a range of impact velocities in four particle size categories. Subsequently, particle breakage matrices of adipic acid have been established for these impact velocities. The experimental results show that the "breakage matrices" of particles is an effective and easy method for evaluation of particle degradation due to high-speed impacts. The possibility of the "breakage matrices" approach being applied to a pneumatic conveying system is also explored by a simulation example.

A comparison between ultraviolet disinfection and copper alginate beads within a vortex bioreactor for the deactivation of bacteria in simulated waste streams with high levels of colour, humic acid and suspended solids

We show in this study that the combination of a swirl flow reactor and an antimicrobial agent (in this case copper alginate beads) is a promising technique for the remediation of contaminated water in waste streams recalcitrant to UV-C treatment. This is demonstrated by comparing the viability of both common and UV-C resistant organisms in operating conditions where UV-C proves ineffective - notably high levels of solids and compounds which deflect UV-C. The swirl flow reactor is easy to construct from commonly available plumbing parts and may prove a versatile and powerful tool in waste water treatment in developing countries.

Predictors of therapy resistant asthma: outcome of a systematic evaluation protocol

Background: It has been suggested that asthmatic subjects with persisting symptoms despite adequate maintenance therapy should be systematically evaluated to identify factors contributing to poor control. The aims of this study were to examine the prevalence of these factors in a cohort of sequentially referred poorly controlled asthmatics, and to determine if any factor or combination of factors predicted true therapy resistant asthma (TRA).

Methods: Patients were evaluated using a systematic evaluation protocol including induced sputum analysis, psychiatric assessment, ear, nose and throat examination, pulmonary function testing, high resolution CT scan of the thorax, and 24 hour dual probe ambulatory oesophageal pH monitoring; any identified provoking factor was treated. Asthma was managed according to BTS guidelines.

Results: Of 73 subjects who completed the assessment, 39 responded to intervention and 34 had TRA. Subjects with TRA had a greater period of instability, a higher dose of inhaled steroids at referral, more rescue steroid use, and a lower best percentage forced expiratory volume in 1 second (FEV1%). Oesophageal reflux, upper airway disease, and psychiatric morbidity were common (57%, 95%, 49%, respectively) but were not more prevalent in either group. Using multivariate logistic regression analysis, inhaled steroid dose >2000 µg BDP, previous assessment by a respiratory specialist, and initial FEV1% of <70% at referral predicted a final diagnosis of TRA.

Conclusions: In poorly controlled asthmatics there is a high prevalence of co-morbidity, identified by detailed systematic assessment, but no difference in prevalence between those who respond to intervention and those with TRA. Targeted treatment of identified co-morbidities has minimal impact on asthma related quality of life in those with therapy resistant disease.

Optical Characterization of Indium Gallium Nitride for Application in High-Efficiency Solar Photovoltaic Cells

The semiconductor alloy indium gallium nitride (InxGa1-xN) offers substantial potential in the development of high-efficiency multi-junction photovoltaic devices due to its wide range of direct band gaps, strong absorption and other optoelectronic properties. This work uses a variety of characterization techniques to examine the properties of InxGa1-xN thin films deposited in a range of compositions by a novel plasma-enhanced evaporation deposition system. Due to the high vapour pressure and low dissociation temperature of indium, the indium incorporation and, ultimately, control of the InxGa1-xN composition was found to be influenced to a greater degree by deposition temperature than variations in the In:Ga source rates in the investigated region of deposition condition space. Under specific deposition conditions, crystalline films were grown in an advantageous nano-columnar microstructure with deposition temperature influencing column size and density. The InxGa1-xN films were determined to have very strong absorption coefficients with band gaps indirectly related to indium content. However, the films also suffer from compositional inhomogeneity and In-related defect complexes with strong phonon coupling that dominates the emission mechanism. This, in addition to the presence of metal impurities, harms the alloy’s electronic properties as no significant photoresponse was observed. This research has demonstrated the material properties that make the InxGa1-xN alloy attractive for multi-junction solar cells and the benefits/drawbacks of the plasma-enhanced evaporation deposition system. Future work is needed to overcome significant challenges relating to crystalline quality, compositional homogeneity and the optoelectronic properties of In-rich InxGa1-xN films in order to develop high-performance photovoltaic devices.

Material effects on stress-induced defect generation in trenched silicon-on-insulator structures

We have investigated the influence of the material properties of the silicon device layer on the generation of defects, and in particular slip dislocations, in trenched and refilled fusion-bonded silicon-on-insulator structures. A strong dependence of the ease of slip generation on the type of dopant species was observed, with the samples falling into three basic categories; heavily boron-doped silicon showed ready slip generation, arsenic and antimony-doped material was fairly resistant to slip, while silicon moderately or lightly doped with phosphorous or boron gave intermediate behavior. The observed behavior appears to be controlled by differences in the dislocation generation mechanism rather than by dislocation mobility. The introduction of an implanted buried layer at the bonding interface was found to result in an increase in slip generation in the silicon, again with a variation according to the dopant species. Here, the greatest slip occurred for both boron and antimony-implanted samples. The weakening of the implanted material may be related to the presence of a band of precipitates observed in the silicon near the bonding interface. (C) 2001 The Electrochemical Society.

A search for circumstellar material around B-type stars in the Galactic halo

19 B-type stars, selected from the Palomar-Green Survey, have been observed at infrared wavelengths to search for possible infrared excesses, as part of an ongoing programme to investigate the nature of early-type stars at high Galactic latitudes. The resulting infrared fluxes, along with Stromgren photometry, are compared with theoretical flux profiles to determine whether any of the targets show evidence of circumstellar material, which may be indicative of post-main- sequence evolution. Eighteen of the targets have flux distributions in good agreement with theoretical predictions. However, one star, PG 2120 + 062, shows a small near-infrared excess, which may be due either to a cool companion of spectral type F5-F7, or to circumstellar material, indicating that it may be an evolved object such as a post-asymptotic giant branch star, in the transition region between the asymptotic giant branch and planetary nebula phase, with the infrared excess due to recent mass loss during giant branch evolution.

Proton acceleration from high-intensity laser interactions with thin foil targets

Measurements of energetic proton production resulting from the interaction of high-intensity laser pulses with foil targets are described. Through the use of layered foil targets and heating of the target material we are able to distinguish three distinct populations of protons. One high energy population is associated with a proton source near the front surface of the target and is observed to be emitted with a characteristic ring structure. A source of typically lower energy, lower divergence protons originates from the rear surface of the target. Finally, a qualitatively separate source of even lower energy protons and ions is observed with a large divergence. Acceleration mechanisms for these separate sources are discussed.