A nutrient balance model for typical Irish farming systems

The twin objectives of the work described were to construct nutrient balance models (NBM) for a range of Irish animal production systems and to evaluate their potential as a means of estimating the nutrient composition of farm wastes. The NBM has three components. The first is the intake of nutrients in the animal's diet. The second is retention or the nutrients the animal retains for the production of milk, meat or eggs. The third is the balance or the difference between the nutrient intake and retention. Data on the intake levels and their nutrient value for dairy cows, beef cattle, pigs and poultry systems were assembled. Literature searches and interviews with National experts were the primary sources of information. NBMs were then constructed for each production system. Summary tables of the nutrient values for the common diet constituents used in Irish animal production systems, the nutrient composition of the animal products and the NBMs (nutrient intake, retention and excretion) for a range of production systems were assembled. These represent the first comprehensive data set of this type for Irish animal production systems. There was generally good agreement between the derived NBMs values and those published in the literature. The NBMs were validated on a number of farms. Data on animal numbers, fertiliser use, concentrates inputs and production output were recorded on seven farms. Using the data a nutrient input/output balance was constructed for each farm. This was compared with the NBM estimate of the farm nutrient balance. The results showed good agreement between the measured balance and the NBM estimate particularly for the pig and poultry farms. However, the validation emphasised the inherent risks associated with NBMs. The average values used for feed intake and production parameters in the NEMs may result in the under or over estimate of actual nutrient balances on individual farms where these variables are substantially different. On the grassland farms there was a poor correlation between the input/output estimate and the NBM. This possibly results from the omission of the soil's contribution to the nutrient balance. However, the results indicate that the NBMs developed are a potentially useful tool for estimating nutrient balances. They also will serve to highlight the significant fraction of the nutrient inputs into farming systems that are retained on the farm. The potential of the NBM as a means of estimating the nutrient composition of farm wastes was evaluated on two farms. Feed intake and composition, animal production, slurry production was monitored during the indoor winter feeding period. Slurry samples were taken for analysis. The appropriates NBMs were used to estimate the nutrient balance for each farm. The nutrient content of the slurry produced was calculated. There was a good agreement between the NBM estimate and the measured values. This preliminary evaluation suggests that the NBM has a potential to provide the farmer with a simple means of estimating the nutrient value of his slurry.

Evaluation of the determinism of the actuator sensor interface (ASI) on programmable logic controllers (PLC), personal computers (PC) and real-time operating systems (RTOS)

The purpose of this study was to evaluate the determinism of the AS-lnterface network and the 3 main families of control systems, which may use it, namely PLC, PC and RTOS. During the course of this study the PROFIBUS and Ethernet field level networks were also considered in order to ensure that they would not introduce unacceptable latencies into the overall control system. This research demonstrated that an incorrectly configured Ethernet network introduces unacceptable variable duration latencies into the control system, thus care must be exercised if the determinism of a control system is not to be compromised. This study introduces a new concept of using statistics and process capability metrics in the form of CPk values, to specify how suitable a control system is for a given control task. The PLC systems, which were tested, demonstrated extremely deterministic responses, but when a large number of iterations were introduced in the user program, the mean control system latency was much too great for an AS-I network. Thus the PLC was found to be unsuitable for an AS-I network if a large, complex user program Is required. The PC systems, which were tested were non-deterministic and had latencies of variable duration. These latencies became extremely exaggerated when a graphing ActiveX was included in the control application. These PC systems also exhibited a non-normal frequency distribution of control system latencies, and as such are unsuitable for implementation with an AS-I network. The RTOS system, which was tested, overcame the problems identified with the PLC systems and produced an extremely deterministic response, even when a large number of iterations were introduced in the user program. The RTOS system, which was tested, is capable of providing a suitable deterministic control system response, even when an extremely large, complex user program is required.

Development of an inspection regime for on-site domestic wastewater treatment systems

The overall purpose of this study was to develop a thorough inspection regime for onsite wastewater treatment systems, which is practical and could be implemented on all site conditions across the country. With approximately 450,000 onsite wastewater treatment systems in Ireland a risk based methodology is required for site selection. This type of approach will identify the areas with the highest potential risk to human health and the environment and these sites should be inspected first. In order to gain the required knowledge to develop an inspection regime in-depth and extensive research was earned out. The following areas of pertinent interest were examined and reviewed, history of domestic wastewater treatment, relevant wastewater legislation and guidance documents and potential detrimental impacts. Analysis of a questionnaire from a prior study, which assessed the resources available and the types of inspections currently undertaken by Local authorities was carried out. In addition to the analysis of the questionnaire results, interviews were carried out with several experts involved in the area of domestic wastewater treatment. The interview focussed on twelve key questions which were directed towards the expert’s opinions on the vital aspects of developing an inspection regime. The background research, combined with the questionnaire analysis and information from the interviews provided a solid foundation for the development of an inspection regime. Chapter 8 outlines the inspection regime which has been developed for this study. The inspection regime includes a desktop study, consultation with the homeowners, visual site inspection, non-invasive site tests, and inspection of the treatment systems. The general opinion from the interviews carried out, was that a standardised approach for the inspections was necessary. For this reason an inspection form was produced which provides a standard systematic approach for inspectors to follow. This form is displayed in Appendix 3. The development of a risk based methodology for site selection was discussed and a procedure similar in approach to the Geological Survey of Irelands Groundwater Protection Schemes was proposed. The EPA is currently developing a risk based methodology, but it is not available to the general public yet. However, the EPA provided a copy of a paper outlining the key aspects of their methodology. The methodology will use risk maps which take account of the following parameters: housing density, areas with inadequate soil conditions, risk of water pollution through surface and subsurface pathways. Sites identified with having the highest potential risk to human health and the environment shall be inspected first. Based on the research carried out a number of recommendations were made which are outlined in Chapter 10. The principle conclusion was that, if these systems fail to operate satisfactorily, home owners need to understand that these systems dispose of the effluent to the 'ground' and the effluent becomes part of the hydrological cycle; therefore, they are a potential hazard to the environment and human health. It is the owners, their families and their neighbours who will be at most immediate risk.

Experimental investigation of transient natural convection cooling of high prandtl number fluid with variable viscosity

Report for the scientific sojourn at the James Cook University, Australia, between June to December 2007. Free convection in enclosed spaces is found widely in natural and industrial systems. It is a topic of primary interest because in many systems it provides the largest resistance to the heat transfer in comparison with other heat transfer modes. In such systems the convection is driven by a density gradient within the fluid, which, usually, is produced by a temperature difference between the fluid and surrounding walls. In the oil industry, the oil, which has High Prandtl, usually is stored and transported in large tanks at temperatures high enough to keep its viscosity and, thus the pumping requirements, to a reasonable level. A temperature difference between the fluid and the walls of the container may give rise to the unsteady buoyancy force and hence the unsteady natural convection. In the initial period of cooling the natural convection regime dominates over the conduction contribution. As the oil cools down it typically becomes more viscous and this increase of viscosity inhibits the convection. At this point the oil viscosity becomes very large and unloading of the tank becomes very difficult. For this reason it is of primary interest to be able to predict the cooling rate of the oil. The general objective of this work is to develop and validate a simulation tool able to predict the cooling rates of high Prandtl fluid considering the variable viscosity effects.

Point-occurrence self-similarity in crackling-noise systems and in other complex systems

It has been recently found that a number of systems displaying crackling noise also show a remarkable behavior regarding the temporal occurrence of successive events versus their size: a scaling law for the probability distributions of waiting times as a function of a minimum size is fulfilled, signaling the existence on those systems of self-similarity in time-size. This property is also present in some non-crackling systems. Here, the uncommon character of the scaling law is illustrated with simple marked renewal processes, built by definition with no correlations. Whereas processes with a finite mean waiting time do not fulfill a scaling law in general and tend towards a Poisson process in the limit of very high sizes, processes without a finite mean tend to another class of distributions, characterized by double power-law waiting-time densities. This is somehow reminiscent of the generalized central limit theorem. A model with short-range correlations is not able to escape from the attraction of those limit distributions. A discussion on open problems in the modeling of these properties is provided.

Switching between apparently redundant iron-uptake mechanisms benefits bacteria in changeable environments.

Bacteria often possess multiple siderophore-based iron uptake systems for scavenging this vital resource from their environment. However, some siderophores seem redundant, because they have limited iron-binding efficiency and are seldom expressed under iron limitation. Here, we investigate the conundrum of why selection does not eliminate this apparent redundancy. We focus on Pseudomonas aeruginosa, a bacterium that can produce two siderophores-the highly efficient but metabolically expensive pyoverdine, and the inefficient but metabolically cheap pyochelin. We found that the bacteria possess molecular mechanisms to phenotypically switch from mainly producing pyoverdine under severe iron limitation to mainly producing pyochelin when iron is only moderately limited. We further show that strains exclusively producing pyochelin grew significantly better than strains exclusively producing pyoverdine under moderate iron limitation, whereas the inverse was seen under severe iron limitation. This suggests that pyochelin is not redundant, but that switching between siderophore strategies might be beneficial to trade off efficiencies versus costs of siderophores. Indeed, simulations parameterized from our data confirmed that strains retaining the capacity to switch between siderophores significantly outcompeted strains defective for one or the other siderophore under fluctuating iron availabilities. Finally, we discuss how siderophore switching can be viewed as a form of collective decision-making, whereby a coordinated shift in behaviour at the group level emerges as a result of positive and negative feedback loops operating among individuals at the local scale.

Molecular Epidemiologic Typing Systems of Bacterial Pathogens: Current Issues and Perpectives

The epidemiologic typing of bacterial pathogens can be applied to answer a number of different questions: in case of outbreak, what is the extent and mode of transmission of epidemic clone(s )? In case of long-term surveillance, what is the prevalence over time and the geographic spread of epidemic and endemic clones in the population? A number of molecular typing methods can be used to classify bacteria based on genomic diversity into groups of closely-related isolates (presumed to arise from a common ancestor in the same chain of transmission) and divergent, epidemiologically-unrelated isolates (arising from independent sources of infection). Ribotyping, IS-RFLP fingerprinting, macrorestriction analysis of chromosomal DNA and PCR-fingerprinting using arbitrary sequence or repeat element primers are useful methods for outbreak investigations and regional surveillance. Library typing systems based on multilocus sequence-based analysis and strain-specific probe hybridization schemes are in development for the international surveillance of major pathogens like Mycobacterium tuberculosis. Accurate epidemiological interpretation of data obtained with molecular typing systems still requires additional research on the evolution rate of polymorphic loci in bacterial pathogens.

Transitions from reproductive systems governed by two self-incompatible Loci to one in fungi.

Self-incompatibility (SI), a reproductive system broadly present in plants, chordates, fungi, and protists, might be controlled by one or several multiallelic loci. How a transition in the number of SI loci can occur and the consequences of such events for the population's genetics and dynamics have not been studied theoretically. Here, we provide analytical descriptions of two transition mechanisms: linkage of the two SI loci (scenario 1) and the loss of function of one incompatibility gene within a mating type of a population with two SI loci (scenario 2). We show that invasion of populations by the new mating type form depends on whether the fitness of the new type is lowered, and on the allelic diversity of the SI loci and the recombination between the two SI loci in the starting population. Moreover, under scenario 1, it also depends on the frequency of the SI alleles that became linked. We demonstrate that, following invasion, complete transitions in the reproductive system occurs under scenario 2 and is predicted only for small populations under scenario 1. Interestingly, such events are associated with a drastic reduction in mating type number.

Conceptual models for designing information systems supporting the strategic analysis of technology environments

1 6 STRUCTURE OF THIS THESIS -Chapter I presents the motivations of this dissertation by illustrating two gaps in the current body of knowledge that are worth filling, describes the research problem addressed by this thesis and presents the research methodology used to achieve this goal. -Chapter 2 shows a review of the existing literature showing that environment analysis is a vital strategic task, that it shall be supported by adapted information systems, and that there is thus a need for developing a conceptual model of the environment that provides a reference framework for better integrating the various existing methods and a more formal definition of the various aspect to support the development of suitable tools. -Chapter 3 proposes a conceptual model that specifies the various enviromnental aspects that are relevant for strategic decision making, how they relate to each other, and ,defines them in a more formal way that is more suited for information systems development. -Chapter 4 is dedicated to the evaluation of the proposed model on the basis of its application to a concrete environment to evaluate its suitability to describe the current conditions and potential evolution of a real environment and get an idea of its usefulness. -Chapter 5 goes a step further by assembling a toolbox describing a set of methods that can be used to analyze the various environmental aspects put forward by the model and by providing more detailed specifications for a number of them to show how our model can be used to facilitate their implementation as software tools. -Chapter 6 describes a prototype of a strategic decision support tool that allow the analysis of some of the aspects of the environment that are not well supported by existing tools and namely to analyze the relationship between multiple actors and issues. The usefulness of this prototype is evaluated on the basis of its application to a concrete environment. -Chapter 7 finally concludes this thesis by making a summary of its various contributions and by proposing further interesting research directions.

A Study of the Number, Profile and Progression Routes of Homeless Persons before the Court and in Custody

This study aimed to obtain information on homeless people appearing before the courts and in custody in the Dublin Metropolitan area and to track and to determine how homeless persons progress through the court and prison systems. The overall objective was to provide information the Probation and Welfare Service's processes of policy formation, service development and planning. Findings on the number of homeless offenders, their profile, their progression routes into the criminal justice system and prisoner reintegration are presented. Recommendations are made regarding sentencing policy, agency responsibility for ex-prisoners and appropriate issues for discussion by the Cross Departmental Committee on Homelessness. It is also recommended that drug free units be available across all closed regime prison establishments.This resource was contributed by The National Documentation Centre on Drug Use.

Geographic patterns in the distribution of social systems in terrestrial arthropods.

The role of ecology in the evolution and maintenance of arthropod sociality has received increasing research attention in recent years. In some organisms, such as halictine bees, polistine wasps, and social spiders, researchers are investigating the environmental factors that may contribute to high levels of variation in the degree of sociality exhibited both among and within species. Within lineages that include only eusocial members, such as ants and termites, studies focus more on identifying extrinsic factors that may contribute to the dramatic variation in colony size, number of queens, and division of labour that is evident across these species. In this review, I propose a comparative approach that seeks to identify environmental factors that may have a common influence across such divergent social arthropod groups. I suggest that seeking common biogeographic patterns in the distribution of social systems or key social traits may help us to identify ecological factors that play a common role in shaping the evolution of sociality across different organisms. I first review previous studies of social gradients that form along latitudinal and altitudinal axes. Within families and within species, many organisms show an increasing degree of sociality at lower latitudes and altitudes. In a smaller number of cases, organisms form larger groups or found nests cooperatively at higher latitudes and altitudes. I then describe several environmental factors that vary consistently along such gradients, including climate variables and abundance of predators, and outline their proposed role in the social systems of terrestrial arthropods. Finally, I map distributions of a social trait against several climatic factors in five case studies to demonstrate how future comparative studies could inform empirical research.

Evidence evaluation in fingerprint comparison and automated fingerprint identification systems: modeling between finger variability

In the context of the investigation of the use of automated fingerprint identification systems (AFIS) for the evaluation of fingerprint evidence, the current study presents investigations into the variability of scores from an AFIS system when fingermarks from a known donor are compared to fingerprints that are not from the same source. The ultimate goal is to propose a model, based on likelihood ratios, which allows the evaluation of mark-to-print comparisons. In particular, this model, through its use of AFIS technology, benefits from the possibility of using a large amount of data, as well as from an already built-in proximity measure, the AFIS score. More precisely, the numerator of the LR is obtained from scores issued from comparisons between impressions from the same source and showing the same minutia configuration. The denominator of the LR is obtained by extracting scores from comparisons of the questioned mark with a database of non-matching sources. This paper focuses solely on the assignment of the denominator of the LR. We refer to it by the generic term of between-finger variability. The issues addressed in this paper in relation to between-finger variability are the required sample size, the influence of the finger number and general pattern, as well as that of the number of minutiae included and their configuration on a given finger. Results show that reliable estimation of between-finger variability is feasible with 10,000 scores. These scores should come from the appropriate finger number/general pattern combination as defined by the mark. Furthermore, strategies of obtaining between-finger variability when these elements cannot be conclusively seen on the mark (and its position with respect to other marks for finger number) have been presented. These results immediately allow case-by-case estimation of the between-finger variability in an operational setting.

I-SS: integrated supervision systems approach based on interactive components

Process supervision is the activity focused on monitoring the process operation in order to deduce conditions to maintain the normality including when faults are present Depending on the number/distribution/heterogeneity of variables, behaviour situations, sub-processes, etc. from processes, human operators and engineers do not easily manipulate the information. This leads to the necessity of automation of supervision activities. Nevertheless, the difficulty to deal with the information complicates the design and development of software applications. We present an approach called "integrated supervision systems". It proposes multiple supervisors coordination to supervise multiple sub-processes whose interactions permit one to supervise the global process

Interacting software-agents to support a kind of expert supervision systems

Expert supervision systems are software applications specially designed to automate process monitoring. The goal is to reduce the dependency on human operators to assure the correct operation of a process including faulty situations. Construction of this kind of application involves an important task of design and development in order to represent and to manipulate process data and behaviour at different degrees of abstraction for interfacing with data acquisition systems connected to the process. This is an open problem that becomes more complex with the number of variables, parameters and relations to account for the complexity of the process. Multiple specialised modules tuned to solve simpler tasks that operate under a co-ordination provide a solution. A modular architecture based on concepts of software agents, taking advantage of the integration of diverse knowledge-based techniques, is proposed for this purpose. The components (software agents, communication mechanisms and perception/action mechanisms) are based on ICa (Intelligent Control architecture), software middleware supporting the build-up of applications with software agent features

Relationship of mating systems and metabolic rate with cycle length of spermatogenesis and sperm production rate in shrews

SUMMARY : The shrews are among the most ancient of living eutherian mammals. They represent an interesting comparative model because of their extreme divergent species. The two shrew subfamilies, Soricinae and Crocidurinae are characterized by fundamental differences concerning their metabolic rates, litter size, period of gestation and different mating pattern. In this study we established and compared the sperm characteristics in four species of different genera of shrews (Sorex araneus, Neomys fodiens, Crocidura russula and Suncus murinus) in the context of the sperm competition hypothesis. The sperm competition concerns the competition between ejaculates of different males for fertilization of ova of a female within a single estrus period. As expected, a greater relative testis size (indicating the importance of polyandry) was associated with a higher number of cauda epididymal spermatozoa, higher level of circulating testosterone and a higher percentage of progressive sperm motility. In addition, we investigated if the basal metabolic rate (BMR) and relative testis size (RTS) may be correlated with the cycle length of spermatogenesis. In this purpose, we determined and compared the cycle length of spermatogenesis in six species of shrews belonging to two subfamilies: Soiricinae (Sorex araneus, Sorex coronatus, Sorex minutus, Neomys fodiens) and Crocidurinae (Crocidura russula, Sunctes murinus). Our results indicate that sperm competition and metabolic rate may act independently or together reducing cycle length of spermatogenesis and thus increase sperm production. We finally investigated this correlation across 32 mammalian species. After testing the data for phylogenetic independence, our results showed that BMR explained only 21 % of the variation, while the RTS explained 44% of the variation of the cycle length of spermatogenesis. The level of the sperm competition, indicated by RTS, is thus to our knowledge the most important factor influencing the speed of spermatogenesis in mammals. RESUME : Les musaraignes sont parmi les plus anciens mammifères vivants. Grâce à leurs extrêmes divergences, ils sont souvent utilisés comme modèles dans des études comparatives. Les deux sous-familles Soricinae et Crocidurinae sont caractérisées par des différences fondamentales, notamment en termes d'intensité du métabolisme, des stratégies de reproduction et du comportement social. Dans la première partie de cette étude, nous avons établi et comparé certaines "caractéristiques des spermatozoïdes chez quatre espèces de musaraignes appartenant à des genres différents (Sorex araneus, Neomys fodiens, Crocidura russula et Suncus murinus). Les résultats ont été interprétés dans le contexte de la théorie de la compétition spermatique, c'est-à-dire la compétition entre le sperme de deux ou plusieurs mâles pour féconder un maximum d'ovules de la même femelle. Cette compétition spermatique peut amener à certaines adaptations biologiques afin de produire plus de sperme. Comme attendu, une grande taille relative des testicules est associée à un nombre élevé de spermatozoïdes, dont la majorité présente une mobilité progressive. Un taux élévé de testostérone a également été observé. De plus, nous avons étudié l'influence du métabolisme basal ainsi que l'intensité de la compétition spermatique sur la durée du cycle de la spermatogenèse. Dans ce but, nous avons déterminé et comparé les durées de la spermatogenèse chez six espèces de musaraignes appartenant à deux sous-familles : Soricinae (Sorex araneus, Sorex coronatus, Sorex minutus, Neomys fodiens) et Crocidurinae (Crocidura russula, Suncus murinus). Les résultats obtenus indiquent que ces deux facteurs (l'intensité du métabolisme basal et de la compétition spermatique) agissent d'une manière dépendante ou indépendante dans le même sens. La conséquence de ces actions est une diminution de la durée de la spermatogenèse entraînant une augmentation de la production de spermatozoïdes. Nous avons finalement étudié ce phénomène dans l'ensemble des mammifères. Après avoir testé l'indépendance phylogénétique, nos résultats montrent que l'intensité de la compétition spermatique indiquée par le RTS est mieux corrélée avec la régulation de la durée de la spermatogenèse qu'avec l'intensité du métabolisme.