The detection of 'soft' materials by selective energy xray transmission imaging and computer tomography

R. Zwiggelaar, C.R. Bull, M.J. Mooney and S. Czarnes, 'The detection of 'soft' materials by selective energy xray transmission imaging and computer tomography', Journal of Agricultural Engineering Research 66 (3), 203-212 (1997)

Information sets and partial permutation decoding for codes from finite geometries

Mavron, Vassili; McDonough, T.P.; Key, J.D., (2006) 'Information sets and partial permutation decoding for codes from finite geometries', Finite Fields and their applications 12(2) pp.232-247 RAE2008

Experimental and numerical simulation of dough kneading in filled geometries

Binding, David; Couch, M.A.; Sujatha, K.S.; Webster, M.F., (2003) 'Experimental and numerical simulation of dough kneading in filled geometries', Journal of Food Engineering 58 pp.111-123 RAE2008

Vertical transmission efficiency and insecticidal properties of Spodoptera exigua Nucleopolyhedrovirus (SeMNPV) genotypes for their use in biological control

El nucleopoliedrovirus de Spodoptera exigua (SeMNPV) es un patógeno natural de las poblaciones larvarias de S. exigua que constituye la base de un bioinsecticida comercializado en España para el control biológico de esta plaga en pimiento. Recientes estudios han demostrado que la transmisión del virus a la descendencia (transmisión vertical) se da con frecuencia y podría ser una característica deseable para su uso en aplicaciones de campo. En el presente trabajo se discute la conveniencia de utilizar una mezcla de dos genotipos SeAl1 (transmisión vertical) y SeG25 (transmisión horizontal) en determinadas proporciones para mejorar las características que cada uno de ellos presenta por separado y así explotar cada una de las vías de transmisión. La patogenicidad (CL50) del genotipo SeG25, y de cualquiera de las mezclas que contienen un 25, 50 o 75 % del mismo, fue más alta que la del aislado SeAl1. Sin embargo, en términos de virulencia (TMM) y productividad (OBs/larva) no se observaron diferencias significativas entre genotipos ni entre sus mezclas. Además se evaluó la capacidad de producir infecciones encubiertas de cada genotipo y sus mezclas sometiendo larvas de S. exigua a infecciones subletales del virus. Se encontraron transcritos del virus para el gen temprano ie0 mediante RT-PCR en los adultos supervivientes a infecciones provocadas por el genotipo SeG25 y todas las mezclas. También se testaron otros dos genes virales que se expresan de manera temprana y tardía en la infección de baculovirus (DNA-polimerasa y polihedrina) para los que en ningún caso se detectaron transcritos.

Long-Range Fiber Transmission of Optical Vortices

We use specialty fiber (“vortex fiber”), to create and propagate orbital angular momentum states over ~kilometer lengths in telecom band (~1550nm). The spiral phase structure of the vortex beams was confirmed by interference with a Gaussian reference. This result is an important step toward achieving long-range classical and quantum communication links using orbital angular momentum of light.

On the Efficiency and Fairness of Transmission Control Loops: A Case for Exogenous Losses

We postulate that exogenous losses-which are typically regarded as introducing undesirable "noise" that needs to be filtered out or hidden from end points-can be surprisingly beneficial. In this paper we evaluate the effects of exogenous losses on transmission control loops, focusing primarily on efficiency and convergence to fairness properties. By analytically capturing the effects of exogenous losses, we are able to characterize the transient behavior of TCP. Our numerical results suggest that "noise" resulting from exogenous losses should not be filtered out blindly, and that a careful examination of the parameter space leads to better strategies regarding the treatment of exogenous losses inside the network. Specifically, we show that while low levels of exogenous losses do help connections converge to their fair share, higher levels of losses lead to inefficient network utilization. We draw the line between these two cases by determining whether or not it is advantageous to hide, or more interestingly introduce, exogenous losses. Our proposed approach is based on classifying the effects of exogenous losses into long-term and short-term effects. Such classification informs the extent to which we control exogenous losses, so as to operate in an efficient and fair region. We validate our results through simulations.

TCP Optimization through FEC, ARQ and Transmission Power Tradeoffs

TCP performance degrades when end-to-end connections extend over wireless connections-links which are characterized by high bit error rate and intermittent connectivity. Such link characteristics can significantly degrade TCP performance as the TCP sender assumes wireless losses to be congestion losses resulting in unnecessary congestion control actions. Link errors can be reduced by increasing transmission power, code redundancy (FEC) or number of retransmissions (ARQ). But increasing power costs resources, increasing code redundancy reduces available channel bandwidth and increasing persistency increases end-to-end delay. The paper proposes a TCP optimization through proper tuning of power management, FEC and ARQ in wireless environments (WLAN and WWAN). In particular, we conduct analytical and numerical analysis taking into "wireless-aware" TCP) performance under different settings. Our results show that increasing power, redundancy and/or retransmission levels always improves TCP performance by reducing link-layer losses. However, such improvements are often associated with cost and arbitrary improvement cannot be realized without paying a lot in return. It is therefore important to consider some kind of net utility function that should be optimized, thus maximizing throughput at the least possible cost.

Spatial Pattern Learning, Catastophic Forgetting and Optimal Rules of Synaptic Transmission

It is a neural network truth universally acknowledged, that the signal transmitted to a target node must be equal to the product of the path signal times a weight. Analysis of catastrophic forgetting by distributed codes leads to the unexpected conclusion that this universal synaptic transmission rule may not be optimal in certain neural networks. The distributed outstar, a network designed to support stable codes with fast or slow learning, generalizes the outstar network for spatial pattern learning. In the outstar, signals from a source node cause weights to learn and recall arbitrary patterns across a target field of nodes. The distributed outstar replaces the outstar source node with a source field, of arbitrarily many nodes, where the activity pattern may be arbitrarily distributed or compressed. Learning proceeds according to a principle of atrophy due to disuse whereby a path weight decreases in joint proportion to the transmittcd path signal and the degree of disuse of the target node. During learning, the total signal to a target node converges toward that node's activity level. Weight changes at a node are apportioned according to the distributed pattern of converging signals three types of synaptic transmission, a product rule, a capacity rule, and a threshold rule, are examined for this system. The three rules are computationally equivalent when source field activity is maximally compressed, or winner-take-all when source field activity is distributed, catastrophic forgetting may occur. Only the threshold rule solves this problem. Analysis of spatial pattern learning by distributed codes thereby leads to the conjecture that the optimal unit of long-term memory in such a system is a subtractive threshold, rather than a multiplicative weight.

Performance, transmission and devotion: understanding the Anglo-Saxon prayer books, c.800-1050

Through an investigation of the Anglo-Saxon prayer books and selected psalters, this thesis corrects standard histories of medieval devotion that circumvent the Anglo-Saxon contribution to medieval piety. In the first half of the thesis, I establish a theoretical framework for Anglo-Saxon piety in which to explore the prayers. Current theoretical frameworks dealing with the medieval devotional material are flawed as scholars use terms such as ‘affective piety’, ‘private’ and even ‘devotion’ vaguely. After an introduction which defines some of the core terminology, Chapter 2 introduces the principal witnesses to the Anglo-Saxon prayer tradition. These include the prodigal eighth- and early ninth- century Mercian Group, comprising the Book of Nunnaminster (London, British Library, Harley 2965, s. viii ex/ix1), the Harleian Prayer Book (London, British Library, Harley 7653, s. viii ex/ix1), the Royal Prayer Book (London, British Library, Royal 2 A. xx, s. viii2/ix1/4), and the Book of Cerne (Cambridge, University Library, Ll. 1. 10). These prayer books are the earliest of their kind in Europe. This chapter challenges some established views concerning the prayer books, including purported Irish influence on their composition and the probability of female ownership. Chapter 3 explores the performance of prayer. The chapter demonstrates that Anglo-Saxon prayers, for example, the Royal Abecedarian Prayer, were transmitted fluidly. The complex relationship between this abecedarian prayer and its reflex in the Book of Nunnaminster reveals the complexity of prayer composition and transmission in the early medieval world but more importantly, it helps scholars theorise how the prayers may have been used, whether recited verbatim or used for extemporalisation. Changes made by later readers to earlier texts are also vital to this study, since they help answer questions of usage and show the evolution and subsequent influence of Anglo-Saxon religiosity. The second half of the thesis makes a special study of prayers to the Cross, the wounded Christ, and the Virgin, three important themes in later medieval spirituality. These focus on the Royal Abecedarian Prayer, which explores Christ’s life (Chapter 5), especially his Passion; the ‘Domine Ihesu Christe, adoro te cruce’ which celebrates the Cross (Chapter 4); and the Oratio Alchfriðo ad sanctam Mariam, which invokes the Virgin Mary (Chapter 6). These prayers occur in multiple, temporally-diverse witnesses and have complex transmission histories, involving both oral and written dissemination. The concluding chapter (7) highlights some of the avenues for future research opened by the thesis.

Coherent wavelength division multiplexing: a novel transmission format for high spectral density optical communication networks

In this thesis a novel transmission format, named Coherent Wavelength Division Multiplexing (CoWDM) for use in high information spectral density optical communication networks is proposed and studied. In chapter I a historical view of fibre optic communication systems as well as an overview of state of the art technology is presented to provide an introduction to the subject area. We see that, in general the aim of modern optical communication system designers is to provide high bandwidth services while reducing the overall cost per transmitted bit of information. In the remainder of the thesis a range of investigations, both of a theoretical and experimental nature are carried out using the CoWDM transmission format. These investigations are designed to consider features of CoWDM such as its dispersion tolerance, compatibility with forward error correction and suitability for use in currently installed long haul networks amongst others. A high bit rate optical test bed constructed at the Tyndall National Institute facilitated most of the experimental work outlined in this thesis and a collaboration with France Telecom enabled long haul transmission experiments using the CoWDM format to be carried out. An amount of research was also carried out on ancillary topics such as optical comb generation, forward error correction and phase stabilisation techniques. The aim of these investigations is to verify the suitability of CoWDM as a cost effective solution for use in both current and future high bit rate optical communication networks

Research and design of high-speed advanced analogue front-ends for fibre-optic transmission systems

In the last decade, we have witnessed the emergence of large, warehouse-scale data centres which have enabled new internet-based software applications such as cloud computing, search engines, social media, e-government etc. Such data centres consist of large collections of servers interconnected using short-reach (reach up to a few hundred meters) optical interconnect. Today, transceivers for these applications achieve up to 100Gb/s by multiplexing 10x 10Gb/s or 4x 25Gb/s channels. In the near future however, data centre operators have expressed a need for optical links which can support 400Gb/s up to 1Tb/s. The crucial challenge is to achieve this in the same footprint (same transceiver module) and with similar power consumption as today’s technology. Straightforward scaling of the currently used space or wavelength division multiplexing may be difficult to achieve: indeed a 1Tb/s transceiver would require integration of 40 VCSELs (vertical cavity surface emitting laser diode, widely used for short‐reach optical interconnect), 40 photodiodes and the electronics operating at 25Gb/s in the same module as today’s 100Gb/s transceiver. Pushing the bit rate on such links beyond today’s commercially available 100Gb/s/fibre will require new generations of VCSELs and their driver and receiver electronics. This work looks into a number of state‐of-the-art technologies and investigates their performance restraints and recommends different set of designs, specifically targeting multilevel modulation formats. Several methods to extend the bandwidth using deep submicron (65nm and 28nm) CMOS technology are explored in this work, while also maintaining a focus upon reducing power consumption and chip area. The techniques used were pre-emphasis in rising and falling edges of the signal and bandwidth extensions by inductive peaking and different local feedback techniques. These techniques have been applied to a transmitter and receiver developed for advanced modulation formats such as PAM-4 (4 level pulse amplitude modulation). Such modulation format can increase the throughput per individual channel, which helps to overcome the challenges mentioned above to realize 400Gb/s to 1Tb/s transceivers.

Optical micro- and nanofibres: Higher mode generation and particle manipulation studies

This thesis is centred on two experimental fields of optical micro- and nanofibre research; higher mode generation/excitation and evanescent field optical manipulation. Standard, commercial, single-mode silica fibre is used throughout most of the experiments; this generally produces high-quality, single-mode, micro- or nanofibres when tapered in a flame-heated, pulling rig in the laboratory. Single mode fibre can also support higher transverse modes, when transmitting wavelengths below that of their defined single-mode regime cut-off. To investigate this, a first-order Laguerre-Gaussian beam, LG01 of 1064 nm wavelength and doughnut-shaped intensity profile is generated free space via spatial light modulation. This technique facilitates coupling to the LP11 fibre mode in two-mode fibre, and convenient, fast switching to the fundamental mode via computer-generated hologram modulation. Following LP11 mode loss when exponentially tapering 125μm diameter fibre, two mode fibre with a cladding diameter of 80μm is selected fir testing since it is more suitable for satisfying the adiabatic criteria for fibre tapering. Proving a fruitful endeavour, experiments show a transmission of 55% of the original LP11 mode set (comprising TE01, TM01, HE21e,o true modes) in submicron fibres. Furthermore, by observing pulling dynamics and progressive mode-lass behaviour, it is possible to produce a nanofibre which supports only the TE01 and TM01 modes, while suppressing the HE21e,o elements of the LP11 group. This result provides a basis for experimental studies of atom trapping via mode-interference, and offers a new set of evanescent field geometries for sensing and particle manipulation applications. The thesis highlights the experimental results of the research unit’s Cold Atom subgroup, who successfully integrated one such higher-mode nanofibre into a cloud of cold Rubidium atoms. This led to the detection of stronger signals of resonance fluorescence coupling into the nanofibre and for light absorption by the atoms due to the presence of higher guided modes within the fibre. Theoretical work on the impact of the curved nanofibre surface on the atomic-surface van der Waals interaction is also presented, showing a clear deviation of the potential from the commonly-used flat-surface approximation. Optical micro- and nanofibres are also useful tools for evanescent-field mediated optical manipulation – this includes propulsion, defect-induced trapping, mass migration and size-sorting of micron-scale particles in dispersion. Similar early trapping experiments are described in this thesis, and resulting motivations for developing a targeted, site-specific particle induction method are given. The integration of optical nanofibres into an optical tweezers is presented, facilitating individual and group isolation of selected particles, and their controlled positioning and conveyance in the evanescent field. The effects of particle size and nanofibre diameter on pronounced scattering is experimentally investigated in this systems, as are optical binding effects between adjacent particles in the evanescent field. Such inter-particle interactions lead to regulated self-positioning and particle-chain speed enhancements.

Simultaneous two-wavelength transmission quantitative phase microscopy with a color camera.

We present a quantitative phase microscopy method that uses a Bayer mosaic color camera to simultaneously acquire off-axis interferograms in transmission mode at two distinct wavelengths. Wrapped phase information is processed using a two-wavelength algorithm to extend the range of the optical path delay measurements that can be detected using a single temporal acquisition. We experimentally demonstrate this technique by acquiring the phase profiles of optically clear microstructures without 2pi ambiguities. In addition, the phase noise contribution arising from spectral channel crosstalk on the color camera is quantified.

Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing.

We used ultra-deep sequencing to obtain tens of thousands of HIV-1 sequences from regions targeted by CD8+ T lymphocytes from longitudinal samples from three acutely infected subjects, and modeled viral evolution during the critical first weeks of infection. Previous studies suggested that a single virus established productive infection, but these conclusions were tempered because of limited sampling; now, we have greatly increased our confidence in this observation through modeling the observed earliest sample diversity based on vastly more extensive sampling. Conventional sequencing of HIV-1 from acute/early infection has shown different patterns of escape at different epitopes; we investigated the earliest escapes in exquisite detail. Over 3-6 weeks, ultradeep sequencing revealed that the virus explored an extraordinary array of potential escape routes in the process of evading the earliest CD8 T-lymphocyte responses--using 454 sequencing, we identified over 50 variant forms of each targeted epitope during early immune escape, while only 2-7 variants were detected in the same samples via conventional sequencing. In contrast to the diversity seen within epitopes, non-epitope regions, including the Envelope V3 region, which was sequenced as a control in each subject, displayed very low levels of variation. In early infection, in the regions sequenced, the consensus forms did not have a fitness advantage large enough to trigger reversion to consensus amino acids in the absence of immune pressure. In one subject, a genetic bottleneck was observed, with extensive diversity at the second time point narrowing to two dominant escape forms by the third time point, all within two months of infection. Traces of immune escape were observed in the earliest samples, suggesting that immune pressure is present and effective earlier than previously reported; quantifying the loss rate of the founder virus suggests a direct role for CD8 T-lymphocyte responses in viral containment after peak viremia. Dramatic shifts in the frequencies of epitope variants during the first weeks of infection revealed a complex interplay between viral fitness and immune escape.

WHO guidelines for antimicrobial treatment in children admitted to hospital in an area of intense Plasmodium falciparum transmission: prospective study.

OBJECTIVES: To assess the performance of WHO's "Guidelines for care at the first-referral level in developing countries" in an area of intense malaria transmission and identify bacterial infections in children with and without malaria. DESIGN: Prospective study. SETTING: District hospital in Muheza, northeast Tanzania. PARTICIPANTS: Children aged 2 months to 13 years admitted to hospital for febrile illness. MAIN OUTCOME MEASURES: Sensitivity and specificity of WHO guidelines in diagnosing invasive bacterial disease; susceptibility of isolated organisms to recommended antimicrobials. RESULTS: Over one year, 3639 children were enrolled and 184 (5.1%) died; 2195 (60.3%) were blood slide positive for Plasmodium falciparum, 341 (9.4%) had invasive bacterial disease, and 142 (3.9%) were seropositive for HIV. The prevalence of invasive bacterial disease was lower in slide positive children (100/2195, 4.6%) than in slide negative children (241/1444, 16.7%). Non-typhi Salmonella was the most frequently isolated organism (52/100 (52%) of organisms in slide positive children and 108/241 (45%) in slide negative children). Mortality among children with invasive bacterial disease was significantly higher (58/341, 17%) than in children without invasive bacterial disease (126/3298, 3.8%) (P<0.001), and this was true regardless of the presence of P falciparum parasitaemia. The sensitivity and specificity of WHO criteria in identifying invasive bacterial disease in slide positive children were 60.0% (95% confidence interval 58.0% to 62.1%) and 53.5% (51.4% to 55.6%), compared with 70.5% (68.2% to 72.9%) and 48.1% (45.6% to 50.7%) in slide negative children. In children with WHO criteria for invasive bacterial disease, only 99/211(47%) of isolated organisms were susceptible to the first recommended antimicrobial agent. CONCLUSIONS: In an area exposed to high transmission of malaria, current WHO guidelines failed to identify almost a third of children with invasive bacterial disease, and more than half of the organisms isolated were not susceptible to currently recommended antimicrobials. Improved diagnosis and treatment of invasive bacterial disease are needed to reduce childhood mortality.