Qualitative Modelling of Linear Networks in ECAD Applications

Lee M.H., Qualitative Modelling of Linear Networks in ECAD Applications, Expert Update, Vol. 3, Num. 2, pp23-32, BCS SGES, Summer 2000. Qualitative modeling of linear networks in ecad applications (1999) by M Lee Venue: Pages 146?152 of: Proceedings 13th international workshop on qualitative reasoning, QR ?99

Characteristics of preferred gait patterns: considerations for exercise prescription

Gait patterns have been widely studied in different fields of science for their particular characteristics. A dynamic approach of human locomotion considers walking and running as two stable behaviors adopted spontaneously under certain levels and natures of constraints. When no constraints are imposed, people naturally prefer to walk at the typical speed (i.e., around 4.5 km.h-1) that minimizes metabolic energy cost. The preferred walking speed (PWS) is also known to be an indicator of mobility and an important clinical factor in tracking impairements in motor behaviors. When constrained to move at higher speeds (e.g., being late), people naturally switch their preference to running for similar optimization reasons (e.g., physiological, biomechanical, perceptual, attentionnal costs). Indeed, the preferred transition speed (PTS) marks the natural seperation between walking and running and consistently falls within a speed range around 7.5 km.h-1. This chapter describes the constraint-dependant spontaneous organisation of the locomotor system, specifically on the walk-to-run speed continuum. We provide examples of the possibility of long-term adaptations of preferred behaviors to specific constraints such as factors related to traditional clothing or practice. We use knowledge from studies on preferred behaviors and on the relationship between affect and exercise adherence as a backdrop to prescribing a walk exercise program with an emphasis on populations with overweight or obesity.

Exponential sensitivity of noise-driven switching in genetic networks

Cells are known to utilize biochemical noise to probabilistically switch between distinct gene expression states. We demonstrate that such noise-driven switching is dominated by tails of probability distributions and is therefore exponentially sensitive to changes in physiological parameters such as transcription and translation rates. However, provided mRNA lifetimes are short, switching can still be accurately simulated using protein-only models of gene expression. Exponential sensitivity limits the robustness of noise-driven switching, suggesting cells may use other mechanisms in order to switch reliably.

TCP Boston: A Fragmentation-tolerant TCP Protocol for ATM Networks

The popularity of TCP/IP coupled with the premise of high speed communication using Asynchronous Transfer Mode (ATM) technology have prompted the network research community to propose a number of techniques to adapt TCP/IP to ATM network environments. ATM offers Available Bit Rate (ABR) and Unspecified Bit Rate (UBR) services for best-effort traffic, such as conventional file transfer. However, recent studies have shown that TCP/IP, when implemented using ABR or UBR, leads to serious performance degradations, especially when the utilization of network resources (such as switch buffers) is high. Proposed techniques-switch-level enhancements, for example-that attempt to patch up TCP/IP over ATMs have had limited success in alleviating this problem. The major reason for TCP/IP's poor performance over ATMs has been consistently attributed to packet fragmentation, which is the result of ATM's 53-byte cell-oriented switching architecture. In this paper, we present a new transport protocol, TCP Boston, that turns ATM's 53-byte cell-oriented switching architecture into an advantage for TCP/IP. At the core of TCP Boston is the Adaptive Information Dispersal Algorithm (AIDA), an efficient encoding technique that allows for dynamic redundancy control. AIDA makes TCP/IP's performance less sensitive to cell losses, thus ensuring a graceful degradation of TCP/IP's performance when faced with congested resources. In this paper, we introduce AIDA and overview the main features of TCP Boston. We present detailed simulation results that show the superiority of our protocol when compared to other adaptations of TCP/IP over ATMs. In particular, we show that TCP Boston improves TCP/IP's performance over ATMs for both network-centric metrics (e.g., effective throughput) and application-centric metrics (e.g., response time).

Preserving Bandwidth Using A Lazy Packet Discard Policy in ATM Networks

A number of recent studies have pointed out that TCP's performance over ATM networks tends to suffer, especially under congestion and switch buffer limitations. Switch-level enhancements and link-level flow control have been proposed to improve TCP's performance in ATM networks. Selective Cell Discard (SCD) and Early Packet Discard (EPD) ensure that partial packets are discarded from the network "as early as possible", thus reducing wasted bandwidth. While such techniques improve the achievable throughput, their effectiveness tends to degrade in multi-hop networks. In this paper, we introduce Lazy Packet Discard (LPD), an AAL-level enhancement that improves effective throughput, reduces response time, and minimizes wasted bandwidth for TCP/IP over ATM. In contrast to the SCD and EPD policies, LPD delays as much as possible the removal from the network of cells belonging to a partially communicated packet. We outline the implementation of LPD and show the performance advantage of TCP/LPD, compared to plain TCP and TCP/EPD through analysis and simulations.

Neural Control of Interlimb Coordination and Gait Timing in Bipeds and Quadrupeds

1) A large body of behavioral data conceming animal and human gaits and gait transitions is simulated as emergent properties of a central pattern generator (CPG) model. The CPG model incorporates neurons obeying Hodgkin-Huxley type dynamics that interact via an on-center off-surround anatomy whose excitatory signals operate on a faster time scale than their inhibitory signals. A descending cornmand or arousal signal called a GO signal activates the gaits and controL their transitions. The GO signal and the CPG model are compared with neural data from globus pallidus and spinal cord, among other brain structures. 2) Data from human bimanual finger coordination tasks are simulated in which anti-phase oscillations at low frequencies spontaneously switch to in-phase oscillations at high frequencies, in-phase oscillations can be performed both at low and high frequencies, phase fluctuations occur at the anti-phase in-phase transition, and a "seagull effect" of larger errors occurs at intermediate phases. When driven by environmental patterns with intermediate phase relationships, the model's output exhibits a tendency to slip toward purely in-phase and anti-phase relationships as observed in humans subjects. 3) Quadruped vertebrate gaits, including the amble, the walk, all three pairwise gaits (trot, pace, and gallop) and the pronk are simulated. Rapid gait transitions are simulated in the order--walk, trot, pace, and gallop--that occurs in the cat, along with the observed increase in oscillation frequency. 4) Precise control of quadruped gait switching is achieved in the model by using GO-dependent modulation of the model's inhibitory interactions. This generates a different functional connectivity in a single CPG at different arousal levels. Such task-specific modulation of functional connectivity in neural pattern generators has been experimentally reported in invertebrates. Phase-dependent modulation of reflex gain has been observed in cats. A role for state-dependent modulation is herein predicted to occur in vertebrates for precise control of phase transitions from one gait to another. 5) The primary human gaits (the walk and the run) and elephant gaits (the amble and the walk) are sirnulated. Although these two gaits are qualitatively different, they both have the same limb order and may exhibit oscillation frequencies that overlap. The CPG model simulates the walk and the run by generating oscillations which exhibit the same phase relationships. but qualitatively different waveform shapes, at different GO signal levels. The fraction of each cycle that activity is above threshold quantitatively distinguishes the two gaits, much as the duty cycles of the feet are longer in the walk than in the run. 6) A key model properly concerns the ability of a single model CPG, that obeys a fixed set of opponent processing equations to generate both in-phase and anti-phase oscillations at different arousal levels. Phase transitions from either in-phase to anti-phase oscillations, or from anti-phase to in-phase oscillations, can occur in different parameter ranges, as the GO signal increases.

Frequency-Dependent Phase Transitions in the Coordination of Human Bimanual Tasks

The 2-channel Ellias-Grossberg neural pattern generator of Cohen, Grossberg, and Pribe [1] is shown to simulate data from human bimanual coordination tasks in which anti-phase oscillations at low frequencies spontaneously switch to in-phase oscillations at high frequencies, in-phase oscillations can be performed at both low and high frequencies, phase fluctuations occur at the anti-phase to in-phase transition, and a "seagull effect" of larger errors occurs at intermediate phases.

Wearable wireless inertial measurement for sports applications

A wearable WIMU (Wireless Inertial Measurement Unit) [1] system for sports applications based on Tyndall's 25mm mote technology [2] has been developed to identify tennis performance determining factors, giving coaches & players improved feedback [3, 4]. Multiple WIMUs transmit player motion data to a PC/laptop via a receiver unit. Internally the WIMUs consist of: an IMU layer with MEMS based sensors; a microcontroller/transceiver layer; and an interconnect layer with supplemental 70g accelerometers and a lithium-ion battery. Packaging consists of a robust ABS plastic case with internal padding, a power switch, battery charging port and status LED with Velcro-elastic straps that are used to attach the device to the player. This offers protection from impact, sweat, and movement of sensors which could cause degradation in device performance. In addition, an important requirement for this device is that it needs to be lightweight and comfortable to wear. Calibration ensures that misalignment of the accelerometer and magnetometer axes are accounted for, allowing more accurate measurements to be made.

A miniaturised arrow ballistic measurement system

A novel miniaturised system for measurement of the in-flight characteristics of an arrow is introduced in this paper. The system allows the user to measure in-flight parameters such as the arrow’s speed, kinetic energy and momentum, arrow drag and vibrations of the arrow shaft. The system consists of electronics, namely a three axis accelerometer, shock switch, microcontroller and EEPROM memory embedded in the arrow tip. The system also includes a docking station for download and processing of in-flight ballistic data from the tip to provide the measured values. With this system, a user can evaluate and optimize their archery equipment setup based on measured ballistic values. Recent test results taken at NIST show the accuracy of the launch velocities to be within +/- 0.59%, when compared with NIST’s most accurate ballistic chronograph.

Planning the deployment of fault-tolerant wireless sensor networks

Since Wireless Sensor Networks (WSNs) are subject to failures, fault-tolerance becomes an important requirement for many WSN applications. Fault-tolerance can be enabled in different areas of WSN design and operation, including the Medium Access Control (MAC) layer and the initial topology design. To be robust to failures, a MAC protocol must be able to adapt to traffic fluctuations and topology dynamics. We design ER-MAC that can switch from energy-efficient operation in normal monitoring to reliable and fast delivery for emergency monitoring, and vice versa. It also can prioritise high priority packets and guarantee fair packet deliveries from all sensor nodes. Topology design supports fault-tolerance by ensuring that there are alternative acceptable routes to data sinks when failures occur. We provide solutions for four topology planning problems: Additional Relay Placement (ARP), Additional Backup Placement (ABP), Multiple Sink Placement (MSP), and Multiple Sink and Relay Placement (MSRP). Our solutions use a local search technique based on Greedy Randomized Adaptive Search Procedures (GRASP). GRASP-ARP deploys relays for (k,l)-sink-connectivity, where each sensor node must have k vertex-disjoint paths of length ≤ l. To count how many disjoint paths a node has, we propose Counting-Paths. GRASP-ABP deploys fewer relays than GRASP-ARP by focusing only on the most important nodes – those whose failure has the worst effect. To identify such nodes, we define Length-constrained Connectivity and Rerouting Centrality (l-CRC). Greedy-MSP and GRASP-MSP place minimal cost sinks to ensure that each sensor node in the network is double-covered, i.e. has two length-bounded paths to two sinks. Greedy-MSRP and GRASP-MSRP deploy sinks and relays with minimal cost to make the network double-covered and non-critical, i.e. all sensor nodes must have length-bounded alternative paths to sinks when an arbitrary sensor node fails. We then evaluate the fault-tolerance of each topology in data gathering simulations using ER-MAC.

Novel smart modules for imaging, communications, and displays

This dissertation proposes and demonstrates novel smart modules to solve challenging problems in the areas of imaging, communications, and displays. The smartness of the modules is due to their ability to be able to adapt to changes in operating environment and application using programmable devices, specifically, electronically variable focus lenses (ECVFLs) and digital micromirror devices (DMD). The proposed modules include imagers for laser characterization and general purpose imaging which smartly adapt to changes in irradiance, optical wireless communication systems which can adapt to the number of users and to changes in link length, and a smart laser projection display that smartly adjust the pixel size to achieve a high resolution projected image at each screen distance. The first part of the dissertation starts with the proposal of using an ECVFL to create a novel multimode laser beam characterizer for coherent light. This laser beam characterizer uses the ECVFL and a DMD so that no mechanical motion of optical components along the optical axis is required. This reduces the mechanical motion overhead that traditional laser beam characterizers have, making this laser beam characterizer more accurate and reliable. The smart laser beam characterizer is able to account for irradiance fluctuations in the source. Using image processing, the important parameters that describe multimode laser beam propagation have been successfully extracted for a multi-mode laser test source. Specifically, the laser beam analysis parameters measured are the M2 parameter, w0 the minimum beam waist, and zR the Rayleigh range. Next a general purpose incoherent light imager that has a high dynamic range (>100 dB) and automatically adjusts for variations in irradiance in the scene is proposed. Then a data efficient image sensor is demonstrated. The idea of this smart image sensor is to reduce the bandwidth needed for transmitting data from the sensor by only sending the information which is required for the specific application while discarding the unnecessary data. In this case, the imager demonstrated sends only information regarding the boundaries of objects in the image so that after transmission to a remote image viewing location, these boundaries can be used to map out objects in the original image. The second part of the dissertation proposes and demonstrates smart optical communications systems using ECVFLs. This starts with the proposal and demonstration of a zero propagation loss optical wireless link using visible light with experiments covering a 1 to 4 m range. By adjusting the focal length of the ECVFLs for this directed line-of-sight link (LOS) the laser beam propagation parameters are adjusted such that the maximum amount of transmitted optical power is captured by the receiver for each link length. This power budget saving enables a longer achievable link range, a better SNR/BER, or higher power efficiency since more received power means the transmitted power can be reduced. Afterwards, a smart dual mode optical wireless link is proposed and demonstrated using a laser and LED coupled to the ECVFL to provide for the first time features of high bandwidths and wide beam coverage. This optical wireless link combines the capabilities of smart directed LOS link from the previous section with a diffuse optical wireless link, thus achieving high data rates and robustness to blocking. The proposed smart system can switch from LOS mode to Diffuse mode when blocking occurs or operate in both modes simultaneously to accommodate multiple users and operate a high speed link if one of the users requires extra bandwidth. The last part of this section presents the design of fibre optic and free-space optical switches which use ECVFLs to deflect the beams to achieve switching operation. These switching modules can be used in the proposed optical wireless indoor network. The final section of the thesis presents a novel smart laser scanning display. The ECVFL is used to create the smallest beam spot size possible for the system designed at the distance of the screen. The smart laser scanning display increases the spatial resoluti on of the display for any given distance. A basic smart display operation has been tested for red light and a 4X improvement in pixel resolution for the image has been demonstrated.

Crystal engineering: exploiting variation of sulfur oxidation for the control of the solid state structure of organosulfur compounds

This thesis is focused on the design and synthesis of a diverse range of novel organosulfur compounds (sulfides, sulfoxides and sulfones), with the objective of studying their solid state properties and thereby developing an understanding of how the molecular structure of the compounds impacts upon their solid state crystalline structure. In particular, robust intermolecular interactions which determine the overall structure were investigated. These synthons were then exploited in the development of a molecular switch. Chapter One provides a brief overview of crystal engineering, the key hydrogen bonding interactions utilized in this work and also a general insight into “molecular machines” reported in the literature of relevance to this work. Chapter Two outlines the design and synthetic strategies for the development of two scaffolds suitable for incorporation of terminal alkynes, organosulfur and ether functionalities, in order to investigate the robustness and predictability of the S=O•••H-C≡C- and S=O•••H-C(α) supramolecular synthons. Crystal structures and a detailed analysis of the hydrogen bond interactions observed in these compounds are included in this chapter. Also the biological activities of four novel tertiary amines are discussed. Chapter Three focuses on the design and synthesis of diphenylacetylene compounds bearing amide and sulfur functionalities, and the exploitation of the N-H•••O=S interactions to develop a “molecular switch”. The crystal structures, hydrogen bonding patterns observed, NMR variable temperature studies and computer modelling studies are discussed in detail. Chapter Four provides the overall conclusions from chapter two and chapter three and also gives an indication of how the results of this work may be developed in the future. Chapter Five contains the full experimental details and spectral characterisation of all novel compounds synthesised in this project, while details of the NCI (National Cancer Institute) biological test results are included in the appendix.

Investigation of polyhydroxyalkanoate production by an activated sludge microbial consortium treating artificial dairy wastewater

Petrochemical plastics/polymers are a common feature of day to day living as they occur in packaging, furniture, mobile phones, computers, construction equipment etc. However, these materials are produced from non-renewable materials and are resistant to microbial degradation in the environment. Considerable research has therefore been carried out into the production of sustainable, biodegradable polymers, amenable to microbial catabolism to CO2 and H2O. A key group of microbial polyesters, widely considered as optimal replacement polymers, are the Polyhydroxyalkaonates (PHAs). Primary research in this area has focused on using recombinant pure cultures to optimise PHA yields, however, despite considerable success, the high costs of pure culture fermentation have thus far hindered the commercial viability of PHAs thus produced. In more recent years work has begun to focus on mixed cultures for the optimisation of PHA production, with waste incorporations offering optimal production cost reductions. The scale of dairy processing in Ireland, and the high organic load wastewaters generated, represent an excellent potential substrate for bioconversion to PHAs in a mixed culture system. The current study sought to investigate the potential for such bioconversion in a laboratory scale biological system and to establish key operational and microbial characteristics of same. Two sequencing batch reactors were set up and operated along the lines of an enhanced biological phosphate removal (EBPR) system, which has PHA accumulation as a key step within repeated rounds of anaerobic/aerobic cycling. Influents to the reactors varied only in the carbon sources provided. Reactor 1 received artificial wastewater with acetate alone, which is known to be readily converted to PHA in the anaerobic step of EBPR. Reactor 2 wastewater influent contained acetate and skim milk to imitate a dairy processing effluent. Chemical monitoring of nutrient remediation within the reactors as continuously applied and EBPR consistent performances observed. Qualitative analysis of the sludge was carried out using fluorescence microscopy with Nile Blue A lipophillic stain and PHA production was confirmed in both reactors. Quantitative analysis via HPLC detection of crotonic acid derivatives revealed the fluorescence to be short chain length Polyhydroxybutyrate, with biomass dry weight accumulations of 11% and 13% being observed in reactors 1 and 2, respectively. Gas Chromatography-Mass Spectrometry for medium chain length methyl ester derivatives revealed the presence of hydroxyoctanoic, -decanoic and -dodecanoic acids in reactor 1. Similar analyses in reactor 2 revealed monomers of 3-hydroxydodecenoic and 3-hydroxytetradecanoic acids. Investigation of the microbial ecology of both reactors as conducted in an attempt to identify key species potentially contributing to reactor performance. Culture dependent investigations indicated that quite different communities were present in both reactors. Reactor 1 isolates demonstrated the following species distributions Pseudomonas (82%), Delftia acidovorans (3%), Acinetobacter sp. (5%) Aminobacter sp., (3%) Bacillus sp. (3%), Thauera sp., (3%) and Cytophaga sp. (3%). Relative species distributions among reactor 2 profiled isolates were more evenly distributed between Pseudoxanthomonas (32%), Thauera sp (24%), Acinetobacter (24%), Citrobacter sp (8%), Lactococcus lactis (5%), Lysinibacillus (5%) and Elizabethkingia (2%). In both reactors Gammaproteobacteria dominated the cultured isolates. Culture independent 16S rRNA gene analyses revealed differing profiles for both reactors. Reactor 1 clone distribution was as follows; Zooglea resiniphila (83%), Zooglea oryzae (2%), Pedobacter composti (5%), Neissericeae sp. (2%) Rhodobacter sp. (2%), Runella defluvii (3%) and Streptococcus sp. (3%). RFLP based species distribution among the reactor 2 clones was as follows; Runella defluvii (50%), Zoogloea oryzae (20%), Flavobacterium sp. (9%), Simplicispira sp. (6%), Uncultured Sphingobacteria sp. (6%), Arcicella (6%) and Leadbetterella bysophila (3%). Betaproteobacteria dominated the 16S rRNA gene clones identified in both reactors. FISH analysis with Nile Blue dual staining resolved these divergent findings, identifying the Betaproteobacteria as dominant PHA accumulators within the reactor sludges, although species/strain specific allocations could not be made. GC analysis of the sludge had indicated the presence of both medium chain length as well short chain length PHAs accumulating in both reactors. In addition the cultured isolates from the reactors had been identified previously as mcl and scl PHA producers, respectively. Characterisations of the PHA monomer profiles of the individual isolates were therefore performed to screen for potential novel scl-mcl PHAs. Nitrogen limitation driven PHA accumulation in E2 minimal media revealed a greater propensity among isoates for mcl-pHA production. HPLC analysis indicated that PHB production was not a major feature of the reactor isolates and this was supported by the low presence of scl phaC1 genes among PCR screened isolates. A high percentage distribution of phaC2 mcl-PHA synthase genes was recorded, with the majority sharing high percentage homology with class II synthases from Pseudomonas sp. The common presence of a phaC2 homologue was not reflected in the production of a common polymer. Considerable variation was noted in both the monomer composition and ratios following GC analysis. While co-polymer production could not be demonstrated, potentially novel synthase substrate specificities were noted which could be exploited further in the future.

X-ray and optical studies of soft x-ray transients in M31

Soft X-ray transients (SXTs) are a subgroup of low-mass X-ray binaries consisting of a neutron star or a black hole and a companion low-mass star. SXTs exhibit a sudden outburst by increasing the luminosity from ∼ 1033 to ∼ 1036−38ergs1. After spending a few months in outburst, SXTs switch back to quiescence. Optical study of the binary system during the quiescence state of SXTs provides an opportunity to discriminate between BH binaries and neutron star binaries. The first part ot this research is composed of result of 10 years joint project between Hubble space telescope and Chandra, to study SXTs in M31. The other part of this thesis focused on the light curve of bright SXTs in M31. Disc irradiation is thought to be capable of explaining the global behaviour of the light curves of SXTs. Depending on the strength of the central X-ray emission in irradiating the disc, the light curve may exhibit an exponential or a linear decay. The model predicts that in brighter transients a transition from exponential decline to a linear one may be detectable. In this study, having excluded super-soft sources and hard X-ray transients, a sample of bright SXTs in M31 (Lpeak > 1038ergs1) has been studied. The expected change in the shape of the decay function is only observed in two of the light curves from the six light curves in the sample. Also, a systematic correlation between the shape of the light curve and the X-ray luminosity has not been seen.

A novel activation mechanism for Clostridial bacteriophage endolysins

Bacteriophage-encoded endolysins are produced at the end of the phage lytic cycle for the degradation of the host bacterial cell. Endolysins offer the potential as alternatives to antibiotics as biocontrol agents or therapeutics. The lytic mechanisms of three bacteriophage endolysins that target Clostridium species living under different conditions were investigated. For these endolysins a trigger and release mechanism is proposed for their activation. During host lysis, holin lesion formation suddenly permeabilises the membrane which exposes the cytosol-sequestered endolysins to a sudden environmental shock. This shock is suggested to trigger a conformational switch of the endolysins between two distinct dimer states. The switch between dimer states is proposed to activate a novel autocleavage mechanism that cleaves the linker connecting the N-terminal catalytic domain and the C-terminal domain to release the catalytic domain for more efficient digestion of the bacterial cell wall. Crystal structures of cleaved fragments of CD27L and CTP1L were previously obtained. In these structures cleavage occurs at the stem of the linker connected to the C-terminal domain. Despite a sequence identity of only 22% between 81 residues of the C-terminal domains of CD27L and CTP1L, they represent a novel fold that is identified in a number of different lysins. Within the crystal structures the two distinct dimerization modes are represented: the elongated head‐on dimer and the side-by‐side dimer. Introducing mutations that inhibit either of the dimerization states caused a decrease in the efficiency of both the autocleavage mechanism and the lytic activity of the endolysins. The two dimer states were validated for the full-length endolysins in solution by using right angle light scattering, small angle X‐ray scattering and cross-linking experiments. Overall, the data represents a new type of regulation governed by the C-terminal domains that is used to activate these endolysins once they enter the bacterial cell wall.