Electrons in feldspar II: a consideration of the influence of conduction band-tail states on luminescence processes

Poolton, Nigel; Ozanyan, K.B.; Wallinga, J.; Murray, A.S., (2002) 'Electrons in feldspar II: a consideration of the influence of conduction band-tail states on luminescence processes', Physics and Chemistry of Minerals 29(3) pp.217-225 RAE2008

Alignment of the genomes of brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization

Robert Hasterok, Agnieszka Marasek, Iain S. Donnison, Ian Armstead, Ann Thomas, Ian P. King, Elzbieta Wolny, Dominika Idziak, John Draper and Glyn Jenkins (2006). Alignment of the genomes of brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization.Genetics, 73 (1), 349-362. Sponsorship: Royal Society / BBSRC;BBSRC RAE2008

A Geometric Approach to Slot Alignment in Wireless Sensor Networks

Traditionally, slotted communication protocols have employed guard times to delineate and align slots. These guard times may expand the slot duration significantly, especially when clocks are allowed to drift for longer time to reduce clock synchronization overhead. Recently, a new class of lightweight protocols for statistical estimation in wireless sensor networks have been proposed. This new class requires very short transmission durations (jam signals), thus the traditional approach of using guard times would impose significant overhead. We propose a new, more efficient algorithm to align slots. Based on geometrical properties of space, we prove that our approach bounds the slot duration by only a constant factor of what is needed. Furthermore, we show by simulation that this bound is loose and an even smaller slot duration is required, making our approach even more efficient.

An alignment based similarity measure for hand detection in cluttered sign language video

Locating hands in sign language video is challenging due to a number of factors. Hand appearance varies widely across signers due to anthropometric variations and varying levels of signer proficiency. Video can be captured under varying illumination, camera resolutions, and levels of scene clutter, e.g., high-res video captured in a studio vs. low-res video gathered by a web cam in a user’s home. Moreover, the signers’ clothing varies, e.g., skin-toned clothing vs. contrasting clothing, short-sleeved vs. long-sleeved shirts, etc. In this work, the hand detection problem is addressed in an appearance matching framework. The Histogram of Oriented Gradient (HOG) based matching score function is reformulated to allow non-rigid alignment between pairs of images to account for hand shape variation. The resulting alignment score is used within a Support Vector Machine hand/not-hand classifier for hand detection. The new matching score function yields improved performance (in ROC area and hand detection rate) over the Vocabulary Guided Pyramid Match Kernel (VGPMK) and the traditional, rigid HOG distance on American Sign Language video gestured by expert signers. The proposed match score function is computationally less expensive (for training and testing), has fewer parameters and is less sensitive to parameter settings than VGPMK. The proposed detector works well on test sequences from an inexpert signer in a non-studio setting with cluttered background.

Online and Offline Character Recognition Using Alignment to Prototypes

Nearest neighbor classifiers are simple to implement, yet they can model complex non-parametric distributions, and provide state-of-the-art recognition accuracy in OCR databases. At the same time, they may be too slow for practical character recognition, especially when they rely on similarity measures that require computationally expensive pairwise alignments between characters. This paper proposes an efficient method for computing an approximate similarity score between two characters based on their exact alignment to a small number of prototypes. The proposed method is applied to both online and offline character recognition, where similarity is based on widely used and computationally expensive alignment methods, i.e., Dynamic Time Warping and the Hungarian method respectively. In both cases significant recognition speedup is obtained at the expense of only a minor increase in recognition error.

A dual-band antenna enabling improved quality of service in multi-radio wireless sensor applications in indoor environments

Science Foundation Ireland (CSET - Centre for Science, Engineering and Technology, Grant No. 07/CE/11147)

A novel and miniaturized 433/868MHz multi-band wireless sensor platform for body sensor network applications

Body Sensor Network (BSN) technology is seeing a rapid emergence in application areas such as health, fitness and sports monitoring. Current BSN wireless sensors typically operate on a single frequency band (e.g. utilizing the IEEE 802.15.4 standard that operates at 2.45GHz) employing a single radio transceiver for wireless communications. This allows a simple wireless architecture to be realized with low cost and power consumption. However, network congestion/failure can create potential issues in terms of reliability of data transfer, quality-of-service (QOS) and data throughput for the sensor. These issues can be especially critical in healthcare monitoring applications where data availability and integrity is crucial. The addition of more than one radio has the potential to address some of the above issues. For example, multi-radio implementations can allow access to more than one network, providing increased coverage and data processing as well as improved interoperability between networks. A small number of multi-radio wireless sensor solutions exist at present but require the use of more than one radio transceiver devices to achieve multi-band operation. This paper presents the design of a novel prototype multi-radio hardware platform that uses a single radio transceiver. The proposed design allows multi-band operation in the 433/868MHz ISM bands and this, together with its low complexity and small form factor, make it suitable for a wide range of BSN applications.

Hybrid integration and packaging of grating-coupled silicon photonics

This thesis covers both the packaging of silicon photonic devices with fiber inputs and outputs as well as the integration of laser light sources with these same devices. The principal challenge in both of these pursuits is coupling light into the submicrometer waveguides that are the hallmark of silicon-on-insulator (SOI) systems. Previous work on grating couplers is leveraged to design new approaches to bridge the gap between the highly-integrated domain of silicon, the Interconnected world of fiber and the active region of III-V materials. First, a novel process for the planar packaging of grating couplers with fibers is explored in detail. This technology allows the creation of easy-to-use test platforms for laser integration and also stands on its own merits as an enabling technology for next-generation silicon photonics systems. The alignment tolerances of this process are shown to be well-suited to a passive alignment process and for wafer-scale assembly. Furthermore, this technology has already been used to package demonstrators for research partners and is included in the offerings of the ePIXfab silicon photonics foundry and as a design kit for PhoeniX Software’s MaskEngineer product. After this, a process for hybridly integrating a discrete edge-emitting laser with a silicon photonic circuit using near-vertical coupling is developed and characterized. The details of the various steps of the design process are given, including mechanical, thermal, optical and electrical steps. The interrelation of these design domains is also discussed. The construction process for a demonstrator is outlined, and measurements are presented of a series of single-wavelength Fabry-Pérot lasers along with a two-section laser tunable in the telecommunications C-band. The suitability and potential of this technology for mass manufacture is demonstrated, with further opportunities for improvement detailed and discussed in the conclusion.

Dilute nitride semiconductors : band structure, scattering and high field transport

The substitution of a small fraction x of nitrogen atoms, for the group V elements in conventional III-V semiconductors such as GaAs and GaSb strongly perturbs the conduction band of the host semiconductor. In this thesis we investigate the effects of nitrogen states on the band dispersion, carrier scattering and mobility of dilute nitride alloys. In the supercell model we solve the single particle Hamiltonian for a very large supercell containing randomly placed nitrogen. This model predicts a gap in the density of states of GaNxAs1−x, where this gap is filled in the Green’s function model. Therefore we develop a self-consistent Green’s function (SCGF) approach, which provides excellent agreement with supercell calculations and reveals a gap in the DOS, in contrast with the results of previous non-self-consistent Green’s function calculations. However, including the distribution of N states destroys this gap, as seen in experiment. We then examine the high field transport of carriers by solving the steadystate Boltzmann transport equation and find that it is necessary to include the full distribution of N levels in order to account for the small, low-field mobility and the absence of a negative differential velocity regime observed experimentally with increasing x. Overall the results account well for a wide range of experimental data. We also investigate the band structure, scattering and mobility of carriers by finding the poles of the SCGF, which gives lower carrier mobility for GaNxAs1−x, compared to those already calculated, in better agreement with experiments. The calculated optical absorption spectra for InyGa1−yNxAs1−x and GaNxSb1−x using the SCGF agree well with the experimental data, confirming the validity of this approach to study the band structure of these materials.

Transformation optics with photonic band gap media.

We introduce a class of optical media based on adiabatically modulated, dielectric-only, and potentially extremely low-loss, photonic crystals (PC). The media we describe represent a generalization of the eikonal limit of transformation optics (TO). The basis of the concept is the possibility to fit some equal frequency surfaces of certain PCs with elliptic surfaces, allowing them to mimic the dispersion relation of light in anisotropic effective media. PC cloaks and other TO devices operating at visible wavelengths can be constructed from optically transparent substances such as glasses, whose attenuation coefficient can be as small as 10 dB/km, suggesting the TO design methodology can be applied to the development of optical devices not limited by the losses inherent to metal-based, passive metamaterials.

Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs.

The computational detection of regulatory elements in DNA is a difficult but important problem impacting our progress in understanding the complex nature of eukaryotic gene regulation. Attempts to utilize cross-species conservation for this task have been hampered both by evolutionary changes of functional sites and poor performance of general-purpose alignment programs when applied to non-coding sequence. We describe a new and flexible framework for modeling binding site evolution in multiple related genomes, based on phylogenetic pair hidden Markov models which explicitly model the gain and loss of binding sites along a phylogeny. We demonstrate the value of this framework for both the alignment of regulatory regions and the inference of precise binding-site locations within those regions. As the underlying formalism is a stochastic, generative model, it can also be used to simulate the evolution of regulatory elements. Our implementation is scalable in terms of numbers of species and sequence lengths and can produce alignments and binding-site predictions with accuracy rivaling or exceeding current systems that specialize in only alignment or only binding-site prediction. We demonstrate the validity and power of various model components on extensive simulations of realistic sequence data and apply a specific model to study Drosophila enhancers in as many as ten related genomes and in the presence of gain and loss of binding sites. Different models and modeling assumptions can be easily specified, thus providing an invaluable tool for the exploration of biological hypotheses that can drive improvements in our understanding of the mechanisms and evolution of gene regulation.

Comparison of extramedullary versus intramedullary referencing for tibial component alignment in total ankle arthroplasty.

BACKGROUND: The majority of total ankle arthroplasty (TAA) systems use extramedullary alignment guides for tibial component placement. However, at least 1 system offers intramedullary referencing. In total knee arthroplasty, studies suggest that tibial component placement is more accurate with intramedullary referencing. The purpose of this study was to compare the accuracy of extramedullary referencing with intramedullary referencing for tibial component placement in total ankle arthroplasty. METHODS: The coronal and sagittal tibial component alignment was evaluated on the postoperative weight-bearing anteroposterior (AP) and lateral radiographs of 236 consecutive fixed-bearing TAAs. Radiographs were measured blindly by 2 investigators. The postoperative alignment of the prosthesis was compared with the surgeon's intended alignment in both planes. The accuracy of tibial component alignment was compared between the extramedullary and intramedullary referencing techniques using unpaired t tests. Interrater and intrarater reliabilities were assessed with intraclass correlation coefficients (ICCs). RESULTS: Eighty-three tibial components placed with an extramedullary referencing technique were compared with 153 implants placed with an intramedullary referencing technique. The accuracy of the extramedullary referencing was within a mean of 1.5 ± 1.4 degrees and 4.1 ± 2.9 degrees in the coronal and sagittal planes, respectively. The accuracy of intramedullary referencing was within a mean of 1.4 ± 1.1 degrees and 2.5 ± 1.8 degrees in the coronal and sagittal planes, respectively. There was a significant difference (P < .001) between the 2 techniques with respect to the sagittal plane alignment. Interrater ICCs for coronal and sagittal alignment were high (0.81 and 0.94, respectively). Intrarater ICCs for coronal and sagittal alignment were high for both investigators. CONCLUSIONS: Initial sagittal plane tibial component alignment was notably more accurate when intramedullary referencing was used. Further studies are needed to determine the effect of this difference on clinical outcomes and long-term survivability of the implants. LEVEL OF EVIDENCE: Level III, retrospective comparative study.

The inoculum effect and band-pass bacterial response to periodic antibiotic treatment.

The inoculum effect (IE) refers to the decreasing efficacy of an antibiotic with increasing bacterial density. It represents a unique strategy of antibiotic tolerance and it can complicate design of effective antibiotic treatment of bacterial infections. To gain insight into this phenomenon, we have analyzed responses of a lab strain of Escherichia coli to antibiotics that target the ribosome. We show that the IE can be explained by bistable inhibition of bacterial growth. A critical requirement for this bistability is sufficiently fast degradation of ribosomes, which can result from antibiotic-induced heat-shock response. Furthermore, antibiotics that elicit the IE can lead to 'band-pass' response of bacterial growth to periodic antibiotic treatment: the treatment efficacy drastically diminishes at intermediate frequencies of treatment. Our proposed mechanism for the IE may be generally applicable to other bacterial species treated with antibiotics targeting the ribosomes.

TEACHING AMERICAN CIVIL WAR MUSIC IDSTORY WITH MODERN EDITIONS OF PERIOD MUSIC FOR FULL CONCERT BAND

This dissertation explores a method of teaching the history of Civil War music and musicians through modern full-band editions of original brass band music. In the study of music history the period of the Civil War is rarely discussed, or at best, mentioned only if a student takes a specific course on the history of bands and happens to look deeply into the background of some of the early band pioneers such as Patrick Gilmore, who served in the Union Army as a bandmaster. The history of the musicians, bands, and music performed during the Civil War deserves study to provide a way for students and audiences to learn this history. This project includes lesson plans that can be used with the arrangements of the period music as well as select published music that is also representative of the period. Included with the historical information are four arrangements of original brass band music now scored for full concert band. Each arrangement includes a section scored for brass only with optional brass band parts. Historical information is provided on the Civil War period bands and how each side used them, on the composers of the music, and also on the individual compositions. The historical information can be used to supplement the lesson plans to teach the history, as well as for program notes for audiences. The research involved locating information on both Union and Confederate bands available in books, other dissertations, articles, and interviews with Civil War music historians. The original brass band music is scored for full band. This method will allow teachers and conductors to highlight this period of wind band history and to share it with both students and audiences. Included with this project are photos and video footage taken during a visit with the 1st Brigade Band of Watertown, Wisconsin, an historical organization dedicated to recreating the music and performances of an actual Civil War era band.