Distributed Packet Rewriting and its Application to Scalable Server Architectures

To construct high performance Web servers, system builders are increasingly turning to distributed designs. An important challenge that arises in distributed Web servers is the need to direct incoming connections to individual hosts. Previous methods for connection routing have employed a centralized node which handles all incoming requests. In contrast, we propose a distributed approach, called Distributed Packet Rewriting (DPR), in which all hosts of the distributed system participate in connection routing. We argue that this approach promises better scalability and fault-tolerance than the centralized approach. We describe our implementation of four variants of DPR and compare their performance. We show that DPR provides performance comparable to centralized alternatives, measured in terms of throughput and delay under the SPECweb96 benchmark. Finally, we argue that DPR is particularly attractive both for small scale systems and for systems following the emerging trend toward increasingly intelligent I/O subsystems.

Load Balancing a Cluster of Web Servers using Distributed Packet Rewriting

In this paper, we propose and evaluate an implementation of a prototype scalable web server. The prototype consists of a load-balanced cluster of hosts that collectively accept and service TCP connections. The host IP addresses are advertised using the Round Robin DNS technique, allowing any host to receive requests from any client. Once a client attempts to establish a TCP connection with one of the hosts, a decision is made as to whether or not the connection should be redirected to a different host---namely, the host with the lowest number of established connections. We use the low-overhead Distributed Packet Rewriting (DPR) technique to redirect TCP connections. In our prototype, each host keeps information about connections in hash tables and linked lists. Every time a packet arrives, it is examined to see if it has to be redirected or not. Load information is maintained using periodic broadcasts amongst the cluster hosts.

Comparison of K-ary N-cube and de Bruijn Overlays in QoS-Constrained Multicast Applications

Research on the construction of logical overlay networks has gained significance in recent times. This is partly due to work on peer-to-peer (P2P) systems for locating and retrieving distributed data objects, and also scalable content distribution using end-system multicast techniques. However, there are emerging applications that require the real-time transport of data from various sources to potentially many thousands of subscribers, each having their own quality-of-service (QoS) constraints. This paper primarily focuses on the properties of two popular topologies found in interconnection networks, namely k-ary n-cubes and de Bruijn graphs. The regular structure of these graph topologies makes them easier to analyze and determine possible routes for real-time data than complete or irregular graphs. We show how these overlay topologies compare in their ability to deliver data according to the QoS constraints of many subscribers, each receiving data from specific publishing hosts. Comparisons are drawn on the ability of each topology to route data in the presence of dynamic system effects, due to end-hosts joining and departing the system. Finally, experimental results show the service guarantees and physical link stress resulting from efficient multicast trees constructed over both kinds of overlay networks.

Distributed Placement of Service Facilities in Large-Scale Networks

The effectiveness of service provisioning in largescale networks is highly dependent on the number and location of service facilities deployed at various hosts. The classical, centralized approach to determining the latter would amount to formulating and solving the uncapacitated k-median (UKM) problem (if the requested number of facilities is fixed), or the uncapacitated facility location (UFL) problem (if the number of facilities is also to be optimized). Clearly, such centralized approaches require knowledge of global topological and demand information, and thus do not scale and are not practical for large networks. The key question posed and answered in this paper is the following: "How can we determine in a distributed and scalable manner the number and location of service facilities?" We propose an innovative approach in which topology and demand information is limited to neighborhoods, or balls of small radius around selected facilities, whereas demand information is captured implicitly for the remaining (remote) clients outside these neighborhoods, by mapping them to clients on the edge of the neighborhood; the ball radius regulates the trade-off between scalability and performance. We develop a scalable, distributed approach that answers our key question through an iterative reoptimization of the location and the number of facilities within such balls. We show that even for small values of the radius (1 or 2), our distributed approach achieves performance under various synthetic and real Internet topologies that is comparable to that of optimal, centralized approaches requiring full topology and demand information.

Scalable Overlay Multicast Tree Construction for QoS-Constrained Media Streaming

Overlay networks have become popular in recent times for content distribution and end-system multicasting of media streams. In the latter case, the motivation is based on the lack of widespread deployment of IP multicast and the ability to perform end-host processing. However, constructing routes between various end-hosts, so that data can be streamed from content publishers to many thousands of subscribers, each having their own QoS constraints, is still a challenging problem. First, any routes between end-hosts using trees built on top of overlay networks can increase stress on the underlying physical network, due to multiple instances of the same data traversing a given physical link. Second, because overlay routes between end-hosts may traverse physical network links more than once, they increase the end-to-end latency compared to IP-level routing. Third, algorithms for constructing efficient, large-scale trees that reduce link stress and latency are typically more complex. This paper therefore compares various methods to construct multicast trees between end-systems, that vary in terms of implementation costs and their ability to support per-subscriber QoS constraints. We describe several algorithms that make trade-offs between algorithmic complexity, physical link stress and latency. While no algorithm is best in all three cases we show how it is possible to efficiently build trees for several thousand subscribers with latencies within a factor of two of the optimal, and link stresses comparable to, or better than, existing technologies.

Plasmid biology of natural Lactococcus lactis strains and molecular mechanisms of bacteriophage-host interaction

Lacticin 3147, enterocin AS-48, lacticin 481, variacin, and sakacin P are bacteriocins offering promising perspectives in terms of preservation and shelf-life extension of food products and should find commercial application in the near future. The studies detailing their characterization and bio-preservative applications are reviewed. Transcriptomic analyses showed a cell wall-targeted response of Lactococcus lactis IL1403 during the early stages of infection with the lytic bacteriophage c2, which is probably orchestrated by a number of membrane stress proteins and involves D-alanylation of membrane lipoteichoic acids, restoration of the physiological proton motive force disrupted following bacteriophage infection, and energy conservation. Sequencing of the eight plasmids of L. lactis subsp. cremoris DPC3758 from raw milk cheese revealed three anti-phage restriction/modification (R/M) systems, immunity/resistance to nisin, lacticin 481, cadmium and copper, and six conjugative/mobilization regions. A food-grade derivative strain with enhanced bacteriophage resistance was generated via stacking of R/M plasmids. Sequencing and functional analysis of the four plasmids of L. lactis subsp. lactis biovar. diacetylactis DPC3901 from raw milk cheese revealed genes novel to Lactococcus and typical of bacteria associated with plants, in addition to genes associated with plant-derived lactococcal strains. The functionality of a novel high-affinity regulated system for cobalt uptake was demonstrated. The bacteriophage resistant and bacteriocin-producing plasmid pMRC01 places a metabolic burden on lactococcal hosts resulting in lowered growth rates and increased cell permeability and autolysis. The magnitude of these effects is strain dependent but not related to bacteriocin production. Starters’ acidification capacity is not significantly affected. Transcriptomic analyses showed that pMRC01 abortive infection (Abi) system is probably subjected to a complex regulatory control by Rgg-like ORF51 and CopG-like ORF58 proteins. These regulators are suggested to modulate the activity of the putative Abi effectors ORF50 and ORF49 exhibiting topology and functional similarities to the Rex system aborting bacteriophage λ lytic growth.

The impact of conifer plantation forestry on the ecology of peatland lakes

Blanket bog lakes are a characteristic feature of blanket bog habitats and harbour many rare and threatened invertebrate species. Despite their potential conservation value, however, very little is known about their physico-chemical or biological characteristics in western Europe, and their reference conditions are still unknown in Ireland. Furthermore, they are under considerable threat in Ireland from a number of sources, particularly afforestation of their catchments by exotic conifers. Plantation forestry can potentially lead to the increased input of substances including hydrogen ions (H+), plants nutrients, dissolved organic carbon (DOC), heavy metals and sediment. The aims of this study were to investigate the effect of conifer plantation forestry on the hydrochemistry and ecology of blanket bog lakes in western Ireland. Lake hydrochemistry, littoral Chydoridae (Cladocera) and littoral macroinvertebrate communities were compared among replicate lakes selected from three distinct catchment land use categories: i) unplanted blanket bog only present in the catchment, ii) mature (closed-canopy) conifer plantation forests only present in the catchment and iii) catchments containing mature conifer plantation forests with recently clearfelled areas. All three catchment land uses were replicated across two geologies: sandstone and granite. Lakes with afforested catchments across both geologies had elevated concentrations of phosphorus (P), nitrogen (N), total dissolved organic carbon (TDOC), aluminium (Al) and iron (Fe), with the highest concentrations of each parameter recorded from lakes with catchment clearfelling. Dissolved oxygen concentrations were also significantly reduced in the afforested lakes, particularly the clearfell lakes. This change in lake hydrochemistry was associated with profound changes in lake invertebrate communities. Within the chydorid communities, the dominance of Alonopsis elongata in the unplanted blanket bog lakes shifted to dominance by the smaller bodied Chydorus sphaericus, along with Alonella nana, Alonella excisa and Alonella exigua, in the plantation forestry-affected lakes, consistent with a shift in lake trophy. Similarly, there was marked changes in the macroinvertebrate communities, especially for the Coleoptera and Heteroptera assemblages which revealed increased taxon richness and abundance in the nutrient-enriched lakes. In terms of conservation status, despite having the greatest species-quality scores (SQS) and species richness, three of the four International Union for the Conservation of Nature (IUCN) red-listed species of Coleoptera and Odonata recorded during the study were absent from lakes subject to catchment clearfelling. The relative strengths of bottom-up (forestry-mediated nutrient enrichment) and top-down (fish) forces in structuring littoral macroinvertebrate communities was investigated in a separate study. Nutrient enrichment was shown to be the dominant force acting on communities, with fish having a lesser influence. These results confirmed that plantation forestry poses the single greatest threat to the conservation status of blanket bog lakes in western Ireland. The findings of this study have major implications for the management of afforested peatlands. Further research is required on blanket bog lakes to prevent any further plantation forestry-mediated habitat deterioration of this rare and protected habitat.

Quantum behavior in mesoscopic systems

In this thesis I present the work done during my PhD. The Thesis is divided into two parts; in the first one I present the study of mesoscopic quantum systems whereas in the second one I address the problem of the definition of Markov regime for quantum system dynamics. The first work presented is the study of vortex patterns in (quasi) two dimensional rotating Bose Einstein condensates (BECs). I consider the case of an anisotropy trapping potential and I shall show that the ground state of the system hosts vortex patterns that are unstable. In a second work I designed an experimental scheme to transfer entanglement from two entangled photons to two BECs. This work is meant to propose a feasible experimental set up to bring entanglement from microscopic to macroscopic systems for both the study of fundamental questions (quantum to classical transition) and technological applications. In the last work of the first part another experimental scheme is presented in order to detect coherences of a mechanical oscillator which is assumed to have been previously cooled down to the quantum regime. In this regime in fact the system can rapidly undergo decoherence so that new techniques have to be employed in order to detect and manipulate their states. In the scheme I propose a micro-mechanical oscillator is coupled to a BEC and the detection is performed by monitoring the BEC with a negligible back-action on the cantilever. In the second part of the thesis I give a definition of Markov regime for open quantum dynamics. The importance of such definition comes from both the mathematical description of the system dynamics and from the understanding of the role played by the environment in the evolution of an open system. In the Markov regime the mathematical description can be simplified and the role of the environment is a passive one.

Environmental and biological characteristics of lagoons on the southwest coast of Ireland

Coastal lagoons are defined as shallow coastal water bodies partially separated from the adjacent sea by a restrictive barrier. Coastal lagoons are protected under Annex I of the European Habitats Directive (92/43/EEC). Lagoons are also considered to be “transitional water bodies” and are therefore included in the “register of protected areas” under the Water Framework Directive (2000/60/EC). Consequently, EU member states are required to establish monitoring plans and to regularly report on lagoon condition and conservation status. Irish lagoons are considered relatively rare and unusual because of their North Atlantic, macrotidal location on high energy coastlines and have received little attention. This work aimed to assess the physicochemical and ecological status of three lagoons, Cuskinny, Farranamanagh and Toormore, on the southwest coast of Ireland. Baseline salinity, nutrient and biological conditions were determined in order to provide reference conditions to detect perturbations, and to inform future maintenance of ecosystem health. Accumulation of organic matter is an increasing pressure in coastal lagoon habitats worldwide, often compounding existing eutrophication problems. This research also aimed to investigate the in situ decomposition process in a lagoon habitat together with exploring the associated invertebrate assemblages. Re-classification of the lagoons, under the guidelines of the Venice system for the classifications of marine waters according to salinity, was completed by taking spatial and temporal changes in salinity regimes into consideration. Based on the results of this study, Cuskinny, Farranamanagh and Toormore lagoons are now classified as mesohaline (5 ppt – 18 ppt), oligohaline (0.5 ppt – 5 ppt) and polyhaline (18 ppt – 30 ppt), respectively. Varying vertical, longitudinal and transverse salinity patterns were observed in the three lagoons. Strong correlations between salinity and cumulative rainfall highlighted the important role of precipitation in controlling the lagoon environment. Maximum effect of precipitation on the salinity of the lagoon was observed between four and fourteen days later depending on catchment area geology, indicating the uniqueness of each lagoon system. Seasonal nutrient patterns were evident in the lagoons. Nutrient concentrations were found to be reflective of the catchment area and the magnitude of the freshwater inflow. Assessment based on the Redfield molar ratio indicated a trend towards phosphorus, rather than nitrogen, limitation in Irish lagoons. Investigation of the decomposition process in Cuskinny Lagoon revealed that greatest biomass loss occurred in the winter season. Lowest biomass loss occurred in spring, possibly due to the high density of invertebrates feeding on the thick microbial layer rather than the decomposing litter. It has been reported that the decomposition of plant biomass is highest in the preferential distribution area of the plant species; however, no similar trend was observed in this study with the most active zones of decomposition varying spatially throughout the seasons. Macroinvertebrate analysis revealed low species diversity but high abundance, indicating the dominance of a small number of species. Invertebrate assemblages within the lagoon varied significantly from communities in the adjacent freshwater or marine environments. Although carried out in coastal lagoons on the southwest coast of Ireland, it is envisaged that the overall findings of this study have relevance throughout the entire island of Ireland and possibly to many North Atlantic coastal lagoon ecosystems elsewhere.

A health status survey of clams, Mya arenaria and Ensis siliqua, in the Irish Sea

The soft shell clam, Mya arenaria, and the razor clam, Ensis siliqua, are widely distributed in Irish waters. Though the reproductive biology and other aspects of the physiology of these species has been previously investigated, little or no data are currently available on their health status. As this knowledge is essential for correct management of a species, M. arenaria and E. siliqua were examined to assess their current health status using histological and molecular methods, over a period of sixteen months. No pathogens or disease were observed in M. arenaria, and low incidences of Prokaryote inclusions, trematode parasites, Nematopsis spp. and eosinophilic bodies were recorded in razor clams for the first time in Northern European waters.

CD4+ CD25+ regulatory T cells control T helper cell type 1 responses to foreign antigens induced by mature dendritic cells in vivo.

Recent evidence suggests that in addition to their well known stimulatory properties, dendritic cells (DCs) may play a major role in peripheral tolerance. It is still unclear whether a distinct subtype or activation status of DC exists that promotes the differentiation of suppressor rather than effector T cells from naive precursors. In this work, we tested whether the naturally occurring CD4+ CD25+ regulatory T cells (Treg) may control immune responses induced by DCs in vivo. We characterized the immune response induced by adoptive transfer of antigen-pulsed mature DCs into mice depleted or not of CD25+ cells. We found that the development of major histocompatibility complex class I and II-restricted interferon gamma-producing cells was consistently enhanced in the absence of Treg. By contrast, T helper cell (Th)2 priming was down-regulated in the same conditions. This regulation was independent of interleukin 10 production by DCs. Of note, splenic DCs incubated in vitro with Toll-like receptor ligands (lipopolysaccharide or CpG) activated immune responses that remained sensitive to Treg function. Our data further show that mature DCs induced higher cytotoxic activity in CD25-depleted recipients as compared with untreated hosts. We conclude that Treg naturally exert a negative feedback mechanism on Th1-type responses induced by mature DCs in vivo.

Afro-Cuban Bata Drum Aesthetics: Developing Individual and Group Technique, Sound and Identity

The Lucumi religion (also Santeria and Regla de Ocha) developed in 19th-century colonial Cuba, by syncretizing elements of Catholicism with the Yoruba worship of orisha. When fully initiated, santeros (priests) actively participate in religious ceremonies by periodically being possessed or "mounted" by a patron saint or orisha, usually within the context of a drumming ritual, known as a toque de santo, bembe, or tambor. Within these rituals, there is a clearly defined goal of trance possession, though its manifestation is not the sole measure of success or failure. Rather than focusing on the fleeting, exciting moments that immediately precede the arrival of an orisha in the form of a possession trance, this thesis investigates the entire four- to six-hour musical performance that is central to the ceremony. It examines the brief pauses, the moments of reduced intensity, the slow but deliberate build-ups of energy and excitement, and even the periods when novices are invited to perform the sacred bata drums, and places these moments on an equal footing with the more dynamic periods where possession is imminent or in progress. This document approaches Lucumi ritual from the viewpoint of bata drummers, ritual specialists who, during the course of a toque de santo, exercise wide latitude in determining the shape of the event. Known as omo Ana (children of the orisha Ana who is manifest in drums and rhythms), bata drummers comprise a fraternity that is accessible only through ritual initiation. Though they are sensitive to the desires of the many participants during a toque de santo, and indeed make their living by satisfying the expectations of their hosts, many of the drummers' activities are inwardly focused on the cultivation and preservation of this fraternity. Occasionally interfering with spirit possession, and other expectations of the participants, these aberrant activities include teaching and learning, developing group identity or signature sound, and achieving a state of intimacy among the musicians known as "communitas."

Barnacle cement: a polymerization model based on evolutionary concepts.

Enzymes and biochemical mechanisms essential to survival are under extreme selective pressure and are highly conserved through evolutionary time. We applied this evolutionary concept to barnacle cement polymerization, a process critical to barnacle fitness that involves aggregation and cross-linking of proteins. The biochemical mechanisms of cement polymerization remain largely unknown. We hypothesized that this process is biochemically similar to blood clotting, a critical physiological response that is also based on aggregation and cross-linking of proteins. Like key elements of vertebrate and invertebrate blood clotting, barnacle cement polymerization was shown to involve proteolytic activation of enzymes and structural precursors, transglutaminase cross-linking and assembly of fibrous proteins. Proteolytic activation of structural proteins maximizes the potential for bonding interactions with other proteins and with the surface. Transglutaminase cross-linking reinforces cement integrity. Remarkably, epitopes and sequences homologous to bovine trypsin and human transglutaminase were identified in barnacle cement with tandem mass spectrometry and/or western blotting. Akin to blood clotting, the peptides generated during proteolytic activation functioned as signal molecules, linking a molecular level event (protein aggregation) to a behavioral response (barnacle larval settlement). Our results draw attention to a highly conserved protein polymerization mechanism and shed light on a long-standing biochemical puzzle. We suggest that barnacle cement polymerization is a specialized form of wound healing. The polymerization mechanism common between barnacle cement and blood may be a theme for many marine animal glues.

Clinical practice guidelines for the management of cryptococcal disease: 2010 update by the infectious diseases society of america.

Cryptococcosis is a global invasive mycosis associated with significant morbidity and mortality. These guidelines for its management have been built on the previous Infectious Diseases Society of America guidelines from 2000 and include new sections. There is a discussion of the management of cryptococcal meningoencephalitis in 3 risk groups: (1) human immunodeficiency virus (HIV)-infected individuals, (2) organ transplant recipients, and (3) non-HIV-infected and nontransplant hosts. There are specific recommendations for other unique risk populations, such as children, pregnant women, persons in resource-limited environments, and those with Cryptococcus gattii infection. Recommendations for management also include other sites of infection, including strategies for pulmonary cryptococcosis. Emphasis has been placed on potential complications in management of cryptococcal infection, including increased intracranial pressure, immune reconstitution inflammatory syndrome (IRIS), drug resistance, and cryptococcomas. Three key management principles have been articulated: (1) induction therapy for meningoencephalitis using fungicidal regimens, such as a polyene and flucytosine, followed by suppressive regimens using fluconazole; (2) importance of early recognition and treatment of increased intracranial pressure and/or IRIS; and (3) the use of lipid formulations of amphotericin B regimens in patients with renal impairment. Cryptococcosis remains a challenging management issue, with little new drug development or recent definitive studies. However, if the diagnosis is made early, if clinicians adhere to the basic principles of these guidelines, and if the underlying disease is controlled, then cryptococcosis can be managed successfully in the vast majority of patients.

Emerging Infectious Disease: Host and Parasite Perspectives

Avian malaria and related haematozoa are nearly ubiquitous parasites that can impose fitness costs of variable severity and may, in some cases, cause substantial mortality in their host populations. One example of the latter, the emergence of avian malaria in the endemic avifauna of Hawaii, has become a model for understanding the consequences of human-mediated disease introduction. The drastic declines of native Hawaiian birds due to avian malaria provided the impetus for examining more closely several aspects of host-parasite interactions in this system. Host-specificity is an important character determining the extent to which a parasite may emerge. Traditional parasite classification, however, has used host information as a character in taxonomical identification, potentially obscuring the true host range of many parasites. To improve upon previous methods, I first developed molecular tools to identify parasites infecting a particular host. I then used these molecular techniques to characterize host-specificity of parasites in the genera Plasmodium and Haemoproteus. I show that parasites in the genus Plasmodium exhibit low specificity and are therefore most likely to emerge in new hosts in the future. Subsequently, I characterized the global distribution of the single lineage of P. relictum that has emerged in Hawaii. I demonstrate that this parasite has a broad host distribution worldwide, that it is likely of Old World origin and that it has been introduced to numerous islands around the world, where it may have been overlooked as a cause of decline in native birds. I also demonstrate that morphological classification of P. relictum does not capture differences among groups of parasites that appear to be reproductively isolated based on molecular evidence. Finally, I examined whether reduced immunological capacity, which has been proposed to explain the susceptibility of Hawaiian endemics, is a general feature of an "island syndrome" in isolated avifauna of the remote Pacific. I show that, over multiple time scales, changes in immune response are not uniform and that observed changes probably reflect differences in genetic diversity, parasite exposure and life history that are unique to each species.