Safe Composition of Web Communication Protocols for Extensible Edge Services

As new multi-party edge services are deployed on the Internet, application-layer protocols with complex communication models and event dependencies are increasingly being specified and adopted. To ensure that such protocols (and compositions thereof with existing protocols) do not result in undesirable behaviors (e.g., livelocks) there needs to be a methodology for the automated checking of the "safety" of these protocols. In this paper, we present ingredients of such a methodology. Specifically, we show how SPIN, a tool from the formal systems verification community, can be used to quickly identify problematic behaviors of application-layer protocols with non-trivial communication models—such as HTTP with the addition of the "100 Continue" mechanism. As a case study, we examine several versions of the specification for the Continue mechanism; our experiments mechanically uncovered multi-version interoperability problems, including some which motivated revisions of HTTP/1.1 and some which persist even with the current version of the protocol. One such problem resembles a classic degradation-of-service attack, but can arise between well-meaning peers. We also discuss how the methods we employ can be used to make explicit the requirements for hardening a protocol's implementation against potentially malicious peers, and for verifying an implementation's interoperability with the full range of allowable peer behaviors.

The formulation, testing and stability of 16% fat cream liqueurs

Cream liqueurs manufactured by a one-step process, where alcohol was added before homogenisation, were more stable than those processed by a two -step process which involved addition of alcohol after homogenisation. Using the one-step process, it was possible to produce creaming-stable liqueurs by using one pass through a homogeniser (27.6 MPa) equipped with "liquid whirl" valves. Test procedures to characterise cream liqueurs and to predict shelf life were studied in detail. A turbidity test proved simple, rapid and sensitive for characterising particle size and homogenisation efficiency. Prediction of age thickening/gelation in cream liqueurs during incubation at 45 °C depended on the age of the sample when incubated. Samples that gelled at 45 °C may not do so at ambient temperature. Commercial cream liqueurs were similar in gross chemical composition, and unlike experimentally produced liqueurs, these did not exhibit either age-gelation at ambient or elevated temperatures. Solutions of commercial sodium caseinates from different sources varied in their calcium sensitivity. When incorporated into cream liqueurs, caseinates influenced the rate of viscosity increase, coalescence and, possibly, gelation during incubated storage. Mild heat and alcohol treatment modified the properties of caseinate used to stabilise non-alcoholic emulsions, while the presence of alcohol in emulsions was important in preventing clustering of globules. The response to added trisodium citrate varied. In many cases, addition of the recommended level (0.18%) did not prevent gelation. Addition of small amounts of NaOH with 0.18 % trisodium citrate before homogenisation was beneficial. The stage at which citrate was added during processing was critical to the degree of viscosity increase (as opposed to gelation) in the product during 45 °C incubation. The component responsible for age-gelation was present in the milk-solids non fat portion of the cream and variations in the creams used were important in the age-gelation phenomenon Results indicated that, in addition to possibly Ca++, the micellar casein portion of serum may play a role in gelation. The role of the low molecular weight surfactants, sodium stearoyl lactylate and monodiglycerides in preventing gelation, was influenced by the presence of trisodium citrate. Clustering of fat globules and age-gelation were inhibited when 0.18 % citrate was included. Inclusion of sodium stearoyl lactylate, but not monodiglycerides, reduced the extent of viscosity increase at 45 °C in citrate containing liqueurs.

Sugar matrices in stabilization of bioactives by dehydration

Development of functional foods with bioactive components requires component stability in foods and ingredients. Stabilization of sensitive bioactive components can be achieved by entrapment or encapsulation of these components in solid food matrices. Lactose or trehalose was used as the structure-forming material for the entrapment of hydrophilic ascorbic acid and thiamine hydrochloride or the encapsulation of oil particles containing hydrophobic α-tocopherol. In the delivery of hydrophobic components, milk protein isolate, soy protein isolate, or whey protein isolate were used as emulsifiers and, in some cases, applied in excess amount to form matrices together with sugars. Dehydrated amorphous structures with bioactives were produced by freezing and freeze-drying. Experimental results indicated that: (i) lactose and trehalose showed similar water sorption and glass transition but very different crystallization behavior as pure sugars; (ii) the glass transition of sugar-based systems was slightly affected by the presence of other components in anhydrous systems but followed closely that of sugar after water plasticization; (iii) sugar crystallization in mixture systems was composition-dependent; (iv) the stability of bioactives was better retained in the amorphous matrices, although small losses of stability were observed for hydrophilic components above glass transition and for hydrophobic components as a function of water activity; (v) sugar crystallization caused significant loss of hydrophilic bioactives as a result of the exclusion from the continuous crystalline phase; (vi) loss of hydrophobic bioactives upon sugar crystallization was a result of dramatic change of emulsion properties and the exclusion of oil particles from the protecting structure; (vii) the double layers at the hydrophilic-hydrophobic interfaces improved the stability of hydrophobic bioactives in dehydrated systems. The present study provides information on the physical and chemical stability of sugar-based dehydrated delivery systems, which could be helpful in designing foods and ingredients containing bioactive components with improved storage stability.

Micronutrient intakes and the role of nutritional supplements in the diets of Irish adults and pre-school children

To investigate micronutrient intakes and the role of nutritional supplements in the diets of Irish adults aged 18-64 years and pre-school children aged 1-4 years. Analysis is based on data from the National Adult Nutrition Survey (NANS) (n=1274) and the National Pre-School Nutrition Survey (NPNS) (n=500). Food and beverage intakes and nutritional supplement use were recorded using 4-day food records. Nutrients were estimated using WISP© which is based on McCance and Widdowson’s The Composition of Foods, 6thEd and the Irish Food Composition Database. “Meats”, “milk/yoghurt”, “breads”, “fruit/fruit juices” and “breakfast cereals” made important contributions to the intakes of a number of micronutrients. Micronutrient intakes were generally adequate, with the exception of iron (in adult females and 1 year olds) and vitamin D (in all population groups). For iron, zinc, copper and vitamin B6, up to 2% of adults had intakes that exceeded the upper limit (UL). Small proportions of children had intakes of zinc (11%), copper (2%), retinol (4%) and folic acid (5%) exceeding the UL. Nutritional supplements (predominantly multivitamin and/or mineral preparations) were consumed by 28% of adults and 20% of pre-school children. Among users, supplements were effective in reducing the % with inadequate intakes for vitamins A and D (both population groups) and iron (adult females only). Supplement users had a lower prevalence of inadequate intakes for vitamin A and iron compared to non-users. In adults only, users had a lower prevalence of inadequate intakes for magnesium, calcium and zinc, and displayed better compliance with dietary recommendations and lifestyle characteristics compared with non-users. There is poor compliance among women of childbearing age for the recommendation to take a supplement containing 400µg/day of folic acid. These findings are important for the development of nutrition policies and future recommendations for adults and pre-school children in Ireland and the EU.

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.

Exploring processes of indeterminate determinism in music composition, programming and improvisation

This portfolio consists of 15 original musical works. Taking the form of electronic and acousmatic music, multimedia, and scores, these chamber works serve as a result of experimentation and improvisation with individually built computer interfaces. The accompanying commentary provides discourse on the conceptual practice of these interfaces becoming a compositional entity that present a multi-interpretative opportunity to explore, engage, and personalise. Following this, the commentary examines the path of creative decisions and musical choices that formed both these interfaces and the resulting musical and visual works. This portfolio is accompanied by interfaces used, transcoded interfacing behavioural information, and documented improvisational findings.

National food consumption surveys: micronutrient intakes and the role of fortified foods in the diets of Irish pre-school children and adults

This research investigated the micronutrient intakes of Irish pre-school children (1-4 years) and adults (18-64 years) and the role that fortified foods (FFs) play in the diets of these population groups. Dietary intake data were collected as part of the National Pre-school Nutrition Survey (NPNS) (2010-2011) and the National Adult Nutrition Survey (NANS) (2008-2010) using 4-day food and beverage records. Nutrient intakes were estimated using WISP©, which encompasses McCance and Widdowson’s The Composition of Foods and the Irish Food Composition Database. A FF is one in which one or more micronutrients are added. Key dietary sources of micronutrients in NPNS and NANS were “milk”, “meat & meat products”, “breakfast cereals”, “fruit & fruit juices” and “breads”. In general, intakes of most micronutrients were adequate with the exception of iron (1 year old children and adult women) and vitamin D (in all population groups). Small proportions of the pre-school population had intakes which exceeded the upper level (UL) (zinc: 11%, folic acid: 5%, retinol: 4%, copper: 2%). Less than 2% of adults had intakes of iron, copper, zinc and vitamin B6 which exceeded the UL. FFs were consumed by 97% of pre-school children and 82% of adults, representing 17% and 9% of mean daily energy intake respectively. Relative to energy intake, FFs contributed substantially greater proportions to intakes of key micronutrients, such as iron and vitamin D. FFs were effective in reducing the prevalence of inadequate micronutrient intakes in these population groups, particularly for iron in women and 1 year old children. FFs made a significant contribution to folate intake in women of childbearing age (72µg). FFs contributed greater proportions of carbohydrate and lower proportions of fat to the diets of consumers. Voluntary addition of nutrients to foods did not contribute appreciably to intakes exceeding the UL in these population groups.

Molecular composition of biogenic secondary organic aerosols using ultrahigh resolution mass spectrometry: comparing laboratory and field studies

Numerous laboratory experiments have been performed in an attempt to mimic atmospheric secondary organic aerosol (SOA) formation. However, it is still unclear how close the aerosol particles generated in laboratory experiments resemble atmospheric SOA with respect to their detailed chemical composition. In this study, we generated SOA in a simulation chamber from the ozonolysis of α-pinene and a biogenic volatile organic compound (BVOC) mixture containing α- and β-pinene, Δ3-carene, and isoprene. The detailed molecular composition of laboratory-generated SOA was compared with that of background ambient aerosol collected at a boreal forest site (Hyytiälä, Finland) and an urban location (Cork, Ireland) using direct infusion nanoelectrospray ultrahigh resolution mass spectrometry. Kendrick Mass Defect and Van Krevelen approaches were used to identify and compare compound classes and distributions of the detected species. The laboratory-generated SOA contained a distinguishable group of dimers that was not observed in the ambient samples. The presence of dimers was found to be less pronounced in the SOA from the VOC mixtures when compared to the one component precursor system. The elemental composition of the compounds identified in the monomeric region from the ozonolysis of both α-pinene and VOC mixtures represented the ambient organic composition of particles collected at the boreal forest site reasonably well, with about 70% of common molecular formulae. In contrast, large differences were found between the laboratory-generated BVOC samples and the ambient urban sample. To our knowledge this is the first direct comparison of molecular composition of laboratory-generated SOA from BVOC mixtures and ambient samples.

Dairy-Met: compositional metagenomic analysis of milk and cheeses

Unpasteurised milk and many cheeses contain a diverse microbiological population. These microorganisms play important roles in dairy foods and can, for example, contribute to the development of flavours and aromas, determine safety, cause spoilage or enhance the health of the consumer. It is thus important to understand thoroughly the microorganisms present in these food types. Traditional culture dependent and culture-independent methods have provided much detail regarding the microbial content of dairy foods. However, the development of next-generation DNA sequencing technologies has revolutionised our knowledge of complex microbial environments. Throughout this thesis we observe the benefits of applying these technologies to provide a detailed understanding of the bacterial content of dairy foods, including those present in milk pre- and post-pasteurisation, Irish farmhouse cheeses and commercially produced cheeses which encounter a discolouration defect, as well as to study genomic changes in microbes associated with dairy foods. Through the application of these state-of-the-art technologies we identified the presence of microorganisms not previously associated with dairy foods.

Composition portfolio and commentaries

In an attempt to provide an analytical entry point into my compositional practice, I have identified eight themes which are significantly recurrent: reduction – the selection of a small number of elements; imperfection – a damaged or warped characteristic of sound; hierarchy – a concern with the roles of instruments with regard to their relative prominence; motion – apparently static sound masses consist of fine internal movement; listener perception – expectations for change influence the experience of affect; translation – the transitioning of electronic sounds to the acoustic realm, and vice versa; immersion – the creation of an accommodating soundscape; blurring – smearing and overlapping sounds or genres. Each of these eight factors is associated with relevant precedents in the history and theory of music that have been influential on my work. These include the minimalist compositions of Steve Reich and Arvo Pärt; the lo-fi aesthetic of Boards of Canada and My Bloody Valentine; concerns with political hierarchy in the work of Louis Andriessen; the variations of dynamics and microtonal shifts of Giacinto Scelsi; Leonard B. Meyer's account of expectation in music; cross-fertilisation of the acoustic and electronic in pieces by Gérard Grisey and Gyorgy Ligeti; the immersive technique of Brian Eno's ambient music; and the overlapping sounds of Aphex Twin. These eight factors are variously applicable to the eleven submitted pieces, which are individually analysed with reference to the most significant of the categories. Together they form a musical language that sustains the interaction of a variety of techniques, concepts and genres.

Nutrition, growth and body composition in preterm infants

The goal of neonatal nutrition in the preterm infant is to achieve postnatal growth and body composition approximating that of a normal fetus of the same postmenstrual age and to obtain a functional outcome comparable to infants born at term. However, in clinical practice such a pattern is seldom achieved, with growth failure and altered body composition being extensively reported. The BabyGrow preterm nutrition study was a longitudinal, prospective, observational study designed to investigate nutrition and growth in 59 preterm infants following the implementation of evidence-based nutrition guidelines in the neonatal unit at Cork University Maternity Hospital. Nutrient delivery was precisely measured during the entire hospital stay and intakes were compared with current international recommendations. Barriers to nutrient delivery were identified across the phases of nutritional support i.e. exclusive parenteral nutrition and transition (establishment of enteral feeds) phases of nutrition and nutritional strategies to optimise nutrient delivery were proposed according to these phases. Growth was measured from birth up to 2 months corrected age and body composition was assessed in terms of fat mass and lean body mass by air displacement plethysmography (PEA POD) at 34 weeks gestation, term corrected age and 2 months corrected age. Anthropometric and body composition data in the preterm cohort were compared with a term reference group from the Cork BASELINE Birth Cohort Study (n=1070) at similar time intervals. The clinical and nutritional determinants of growth and body composition during the neonatal period were reported for the first time. These data have international relevance, informing authoritative agencies developing evidence-based practice guidelines for neonatal nutritional support. In the future, the nutritional management of preterm infants may need to be individualised to consider gestational age, birth weight as well as preterm morbidity.

Nutrition, growth and body composition in infancy

This thesis is presented in two parts. Data for this research is from the Cork BASELINE (Babies after SCOPE, Evaluating Longitudinal Impact using Neurological and Nutritional Endpoints) Birth Cohort Study (n = 2137). In this prospective birth cohort study, pediatric follow-up with in-person appointments were repeated from the time of birth through to 2, 6 and 12 months, and at 2 years. Body composition was measured by air displacement plethysmography at birth and at 2 months using the PEA POD Infant Body Composition Tracking System. This thesis provides the first extensive report on the study’s 2 year assessment. In part one, the aims were to investigate potential early-life risk factors for childhood overweight and obesity, including rapid growth and body composition in infancy and umbilical cord concentrations of leptin and high molecular weight (HMW) adiponectin. This research is the first to describe rapid growth in early infancy in terms of changes in direct measures of body composition. These are also the first data to examine associations between umbilical cord leptin and HMW adiponectin concentrations and changes in fat and lean mass in early infancy. These data provide additional insight into characterising the growth trajectory in infancy and into the role of perinatal factors in determining infant growth and subsequent overweight/obesity risk. In part two of this thesis, the aims were to quantify vitamin D intake and status at 2 years and to investigate whether 25-hydroxyvitamin D [25(OH)D] concentrations in early pregnancy and in umbilical cord blood are associated with infant growth and body composition. There was a low prevalence of vitamin D deficiency among Irish 2 year olds (n = 742) despite a high prevalence of inadequate intakes and high latitude (51°N). Maternal 25(OH)D concentrations at 15 weeks gestation and cord 25(OH)D concentrations at delivery were not associated with infant growth or adiposity.

Effect of biodiesel oil composition on droplet size distribution

Droplet size distribution of biodiesel oil with various compositions was investigated in this work. The droplets generated by a two-fluid atomizer were measured by a commercial PDA. It was found that viscosity of the fuel has a strong effect on the drop size distribution. Additionally, effect of air injection pressures applied to atomize the spray was taken into account. Shear force induced by flow field exerts an effect on distribution of biodiesel droplets in atomized spray.

Mixed self-assembled monolayers of 2-mercaptobenzimidazole and 2-mercaptobenzimidazole-5-sulfonate: determination and control of the surface composition

The behaviour towards electron transfer of self-assembled monolayers of 2-mercaptobenzimidazole (MBI) and 2-mercaptobenzimidazole-5-sulfonate (MBIS) on Au(1 1 1) was examined by cyclic voltammetry. The influence of the monolayers was drastically dependent on the charge of the redox probe used. When [Ru(NH3)6]3+ is used, a post-adsorption peak characteristic of the adsorption of the redox probe is detected only at the MBIS modified electrode. Taking advantage of this difference, ac voltammetry has been used to determine the surface composition when mixed monolayers are formed by immersion of the gold substrate in mixtures of different molar fractions of MBI and MBIS. Results clearly indicate that the ionic strength of the immersion solution plays a key role in the surface composition when a charged surfactant is mixed with non-charged surfactant. © 2006 Elsevier B.V. All rights reserved.

Polymeric and monomeric IgA response in serum and milk after parenteral cholera and oral typhoid vaccination

SCOPUS: ar.j