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.

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.

Resonant transmission near nonrobust periodic slab modes.

We present a precise theoretical explanation and prediction of certain resonant peaks and dips in the electromagnetic transmission coefficient of periodically structured slabs in the presence of nonrobust guided slab modes. We also derive the leading asymptotic behavior of the related phenomenon of resonant enhancement near the guided mode. The theory applies to structures in which losses are negligible and to very general geometries of the unit cell. It is based on boundary-integral representations of the electromagnetic fields. These depend on the frequency and on the Bloch wave vector and provide a complex-analytic connection in these parameters between generalized scattering states and guided slab modes. The perturbation of three coincident zeros-those of the dispersion relation for slab modes, the reflection constant, and the transmission constant-is central to calculating transmission anomalies both for lossless dielectric materials and for perfect metals.

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.

Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing.

A precise molecular identification of transmitted hepatitis C virus (HCV) genomes could illuminate key aspects of transmission biology, immunopathogenesis and natural history. We used single genome sequencing of 2,922 half or quarter genomes from plasma viral RNA to identify transmitted/founder (T/F) viruses in 17 subjects with acute community-acquired HCV infection. Sequences from 13 of 17 acute subjects, but none of 14 chronic controls, exhibited one or more discrete low diversity viral lineages. Sequences within each lineage generally revealed a star-like phylogeny of mutations that coalesced to unambiguous T/F viral genomes. Numbers of transmitted viruses leading to productive clinical infection were estimated to range from 1 to 37 or more (median = 4). Four acutely infected subjects showed a distinctly different pattern of virus diversity that deviated from a star-like phylogeny. In these cases, empirical analysis and mathematical modeling suggested high multiplicity virus transmission from individuals who themselves were acutely infected or had experienced a virus population bottleneck due to antiviral drug therapy. These results provide new quantitative and qualitative insights into HCV transmission, revealing for the first time virus-host interactions that successful vaccines or treatment interventions will need to overcome. Our findings further suggest a novel experimental strategy for identifying full-length T/F genomes for proteome-wide analyses of HCV biology and adaptation to antiviral drug or immune pressures.

Transmission electron microscopy of marine crustacean eggs

Ultrastructural investigations of eggs can be important in helping to understand embryonic development. There are few transmission electron microscope studies of marine arthropod eggs, however, as they have proved difficult to fix and infiltrate with resin. Here, we describe a modification of a standard method that allows the preparation of the quite different eggs of the marine copepod, Acartia tonsa and the lobster, Homarus gammarus, for transmission electron microscopy. By using double fixation and an extended resin infiltration time we obtained good preparations for electron microscopy. We anticipate that these modifications to the standard protocol will be widely applicable and useful for the study of the eggs and early developmental stages of many marine arthropod taxa. Les recherches sur l'ultrastructure des oeufs peuvent être importantes en aidant à comprendre le développement embryonnaire. Il existe cependant peu d'études en microscopie électronique à transmission sur les oeufs d'arthropodes marins, car il est difficile de les fixer et d'y infiltrer de la résine. Dans ce travail, nous décrivons une modification de la méthode standard, qui permet la préparation pour la microscopie électronique à transmission d'oeufs aussi différents que ceux du copépode marin Acartia tonsa et du homard Homarus gammarus. En utilisant une double fixation et un temps plus long d'infiltration de la résine, nous avons obtenu de bonnes préparations pour la microscopie électronique. Nous prévoyons que ces modifications du protocole standard seront largement applicables et utiles pour l'étude des oeufs et des premiers stades de développement de nombreux taxons d'arthropodes marins.