Physical Sciences and Mathematics Commons^™

Investigating The Use Of Ultraviolet Light Emitting Diodes (Uv-Leds) For The Inactivation Of Bacteria In Powdered Food Ingredients, Laura Nyhan, Milosz Przyjalgowski, Liam O'Faolain, Máire Begley, Michael Callanan

Cappa Publications

The addition of contaminated powdered spices and seasonings to finished products which do not undergo further processing represents a significant concern for food manufacturers. To reduce the incidence of bacterial contamination, seasoning ingredients should be subjected to a decontamination process. Ultraviolet light emitting diodes (UV-LEDs) have been suggested as an alternative to UV lamps for reducing the microbial load of foods, due to their increasing efficiency, robustness and decreasing cost. In this study, we investigated the efficacy of UV-LED devices for the inactivation of four bacteria (Listeria monocytogenes, Escherichia coli, Bacillus subtilis and Salmonella Typhimurium) on a plastic surface and …

The Role Of Software Engineering In Bioinformatics, Brendan Sean Lawlor

Theses

This thesis proposes that by applying state-of-the-art software engineering tools, techniques and frameworks to currently recognised challenges in bioinformatics, improved outcomes can be attained in that field. It begins by decomposing software engineering into two categories, namely process and architecture, and choosing two key challenges in the practice of bioinformatics: reproducibility and scalability. The body of the thesis is an exploration of the intersection between these two software engineering categories and these two bioinformatics challenges. The question is asked: Can best practices in professional software engineering be applied to address key issues in the bioinformatics domain, creating positive outcomes? And …

Predicting Carcass Cut Yields In Cattle From Digitalimages Using Artificial Intelligence, Darragh Matthews

Theses

Beef carcass classification in Europe is predicated on the EUROP grid for both fatness and conformation. Although this system performs well for grouping visually similar carcasses, it cannot be used to accurately predict meat yields from these groups, especially when considered on an individual cut level. Deep Learning (DL) has proven to be a successful tool for many image classification problems but has yet to be fully proven in a regression scenario using carcass images. Here we have trained DL models to predict carcass cut yields and compared predictions to more standard machine learning (ML) methods. Three approaches were undertaken …

Covid-19: In The Absence Of Vaccination – ‘Mask-The-Nation’, Roy D. Sleator, Steven Darby, Alan Giltinan, Niall Smith

Department of Biological Sciences Publications

“In the absence of a vaccine, or effective antiviral, one of our only remaining strategies for controlling COVID-19 is to physically block the spread of SARS-CoV-2 in the community”

Odx: A Fitness Tracker-Based Device For Continuous Bacterial Growth Monitoring, Venkata V.B. Yallapragada, Uday Gowda, David Wong, Liam O'Faolain, Mark Tangney, Ganga C.R. Devarapu

Cappa Publications

Continuous monitoring of bacterial growth in aqueous media is a crucial process in academic research as well as in the biotechnology industry. Bacterial growth is usually monitored by measuring the optical density of bacteria in liquid media, using benchtop spectrophotometers. Due to the large form factor of the existing spectrophotometers, they cannot be used for live monitoring of the bacteria inside bacterial incubation chambers. Additionally, the use of benchtop spectrometers for continuous monitoring requires multiple samplings and is labour intensive. To overcome these challenges, we have developed an optical density measuring device (ODX) by modifying a generic fitness tracker. The …

Simplicity Diffexpress: A Bespoke Cloud-Based Interface For Rna-Seq Differential Expression Modeling And Analysis, Cintia C. Palu, Marcelo Ribeiro-Alves, Yanxin Wu, Brendan Lawlor, Pavel V. Baranov, Brian Kelly, Paul Walsh

Department of Computer Science Publications

One of the key challenges for transcriptomics-based research is not only the processing of large data but also modeling the complexity of features that are sources of variation across samples, which is required for an accurate statistical analysis. Therefore, our goal is to foster access for wet lab researchers to bioinformatics tools, in order to enhance their ability to explore biological aspects and validate hypotheses with robust analysis. In this context, user-friendly interfaces can enable researchers to apply computational biology methods without requiring bioinformatics expertise. Such bespoke platforms can improve the quality of the findings by allowing the researcher to …

Development Of Multi-Class Analytical Methods For Agrochemical Contaminants, Sarah Tuck

Theses

In this project, cost-effective multi-class analytical methods were developed to detect a range of antiparasitic, feed additive and pesticide substances in foodstuffs of animal origin. These substances have the potential to enter the food chain through their occurrence as residues either through the animals themselves or other routes e.g. contamination. To ensure the continued safety of food destined for human consumption regulatory control limits have been established for permitted levels of these residues in foods of animal origin. Despite these controls the continued monitoring of foodstuffs is necessary to ensure these limits are not breached and that substances are not …

Predicting Energy And Water Consumption On Dairy Farms Through Statistical Analysis And Machine-Learning Methods, Philip Shine

Theses

With the abolishment of milking quotas across all European Union member states in April 2015, dairy farmers must adjust their farming practises to minimise milk production costs to adequately prepare for potential periods of reduced revenue. Milk production is an intense energy and water consuming process. Coupled with challenging European greenhouse gas reduction targets and legislation regarding the prevention of groundwater pollution and deterioration, increasing the production of milk in Ireland must be met with the sustainable consumption of on-farm energy and direct water resources, to ensure the future monetary and environmental sustainability of Ireland’s dairy industry. Thus, this body …

The Use Of Machine Learning To Detect Suckling In Pre-Weaned Calves, Sukumar Katamreddy

Theses

The weaning of cattle is a process which is known to be labour intensive and to have stressful effects on both cow and calf Common methods used in the weaning process include the temporary removal of a mother from the calf and manual observation and intervention. Early and speedy weaning is known to have a number of benefits, including health benefits for both cow and calf, additional weight gains for the calves as well as reduced labour and feed requirements. The process known as Two-Stage Weaning is recognised to be an effective low-stress approach to weaning in which the calf …

Novel Neuroevolution Techniques For The Life Science Domain, Timothy Manning

Theses

The life science domain is a high value research area, both in terms of the benefits in increased knowledge and in societal impact. Much of the research funding has focused on wet lab based approaches to increase visibility into biological processes and producing maximal relevant information on which to make decisions. Given the complexity of biological functions, in many cases this has led to an information overload. Researchers are now able to routinely generate and access petabytes of data as a result of high throughput experiments, and this capability is growing. This data can be difficult to interpret and intractable …

An Application Of Time Series Methods To Investigate Eu Dairy Commodity Price Dynamics, Dennis Bergmann

Theses

Fundamental changes to the common agricultural policy (CAP) have led to greater market orientation which in turn has resulted in significantly changed price dynamics of EU dairy prices. These changed dynamics include sharply increased price variability of EU farm gate milk prices as well EU dairy commodity prices such as butter and Skimmed Milk Powder (SMP). In addition it was expected that EU dairy prices will align to Word dairy prices. This alignment of prices would also see an alignment of volatility levels which were significantly higher for World dairy prices than EU dairy prices. The aim of this thesis …

Exploration And Implementation Of Innovative Efficiencies/Devices In Beet Processing For Energy Production, Patrick Mcinerney

Theses

The imminent depletion of fossil fuels, as well as concerns for energy security and the obligation to respond to climate change has led to expanding worldwide popularity of Anaerobic Digestion (AD) of energy crops. Sugar beet is a popular AD feedstock due to its favourable characteristics; however it can be quite labour intensive requiring a range of specialist equipment to process the crop prior to undergoing AD. A crucial stage of this process involves the size reduction of beet by a mechanical chopper unit; this pretreatment breaks open the cellulose structure of the crop and increases the surface area available …

The Definitions Of Three-Dimensional Landmarks On The Human Face: An Interdisciplinary View, Stanislav Katina, Kathryn Mcneil, Ashraf Ayoub, Brendan Guilfoyle, Balvinder Khambay, Paul Siebert, Federico Sukno, Mario Rojas, Liberty Vittert, John Waddington, Paul F. Whelan, Adrian W. Bowman

Publications

The analysis of shape is a key part of anatomical research and in the large majority of cases landmarks provide a standard starting point. However, while the technology of image capture has developed rapidly and in particular three-dimensional imaging is widely available, the definitions of anatomical landmarks remain rooted in their two-dimensional origins. In the important case of the human face, standard definitions often require careful orientation of the subject. This paper considers the definitions of facial landmarks from an interdisciplinary perspective, including biological and clinical motivations, issues associated with imaging and subsequent analysis, and the mathematical definition of surface …

The Development Of Liquid Chromatography Mass Spectrometry Methods For The Analysis Of Cyanobacterial Toxins In Environmental Freshwaters, Brian Anthony Dineen

Theses

Cyanobacteria, also known as blue-green algae, are a common component of many freshwater and marine ecosystems and have a potential to produce several different classes of biotoxins. The most common class of cyanobacterial toxins are the microcystins (MCs) and cylindrospermopsins (CYLs). MCs are cyclic heptapeptides that display potent hepatotoxicity and are tumour promoters. CYLs are alkaloids that are cytotoxic and can cause illness and display hepatotoxic effects in animals and humans. Worldwide, these toxins have caused fatal poisonings to animals, birds and fish. Several incidents of human intoxications have been reported and the presence of these toxins in environmental waters …

Investigation Of Pyrrolizidine Alkaloids In Foods Using Liquid Chromatography Mass Spectrometry, Caroline Griffin

Theses

Pyrrolizidine Alkaloids (PAs) are known plant toxins which can cause hepatic veno-occlusive disease (HVOD) in both humans and livestock when ingested. Although PAs are primarily known for their hepatotoxicity they also induce genotoxicity, carcinogenicity and pneumotoxicity. PAs are consumed through plants as food, for medicinal purposes, or as contaminants of agricultural crops. Aside from ingesting the plants directly PA exposure may occur through the consumption of honey produced by bees that visit PA-containing plants or by drinking milk produced by animals that have consumed PA-containing plants. Possible PA contamination in our food chain is a potential health risk.

To assess …

Investigation Of Pyrrolizidine Alkaloids In Foods Using Liquid Chromatography Mass Spectrometry, Caroline Griffin

PhDs

Pyrrolizidine Alkaloids (PAs) are known plant toxins which can cause hepatic veno-occlusive disease (HVOD) in both humans and livestock when ingested. Although PAs are primarily known for their hepatotoxicity they also induce genotoxicity, carcinogenicity and pneumotoxicity. PAs are consumed through plants as food, for medicinal purposes, or as contaminants of agricultural crops. Aside from ingesting the plants directly PA exposure may occur through the consumption of honey produced by bees that visit PA-containing plants or by drinking milk produced by animals that have consumed PA-containing plants. Possible PA contamination in our food chain is a potential health risk.

To assess …

Evaluation, Adaptation And Validation Of A Model To Predict Grass Growth In Ireland, Christina Hurtado Uria

Theses

Budgeting grass supply allows producers to minimise the quantity of purchased feed required in the diet of grazing livestock. One tool for managing grass supply could be a mathematical model that can simulate grass growth. The development of such a model would allow better management around the variability of feed supply and help identify feed surpluses and deficits, and therefore increase the accuracy of management decisions. This would be a key feature of profitable milk and meat production systems in the future which will be hugely important as global food demand increases due to population growth. It is forecasted that …

Novel Liquid Chromatography - Fourier Transform Mass Spectrometry (Ms) And Triple Quadrupole Ms Methods For The Determination Of Diarrhetic Shellfish Poisoning (Dsp) Toxins., Bébhine Carey

Theses

Harmful algal blooms (HABs) appear to be on the rise globally, which not only has a negative impact on the shellfish industry but can also cause human and animal intoxications. In order to advance our knowledge of HABs, specific and sensitive analytical methods are required to aid in monitoring shellfish and algal samples for biotoxins, harmful to consumers.

Development Of Mass Spectrometric Methods For The Analysis Of Serotonin And Related Compounds In Biological Matrices, Merisa Moriarty

Theses

Serotonin is a major neurotransmitter in the brain and affects various functions both in the brain and in the rest of the body. It has been linked to depression, migraines, and aggression, as well as many psychiatric disorders including schizophrenia, dementia and anorexia nervosa. It also has been associated with conditions like Alzheimer’s disease along with other neurotransmitters such as dopamine.

The aim of this research project is to develop various mass spectrometric methods for the analysis of serotonin, dopamine and similar indoles in both urine and serum matrices. This thesis provides extensive reviews detailing a general overview of serotonin …

The Effects Of Climate On The Growth Of Winter Wheat And Spring Barley In An Irish Context, Adrian Kennedy

Theses

The climate of earth is always changing due to natural events, however it is thought that the rapid warming period currently taking place is primarily due human activity to (environmental protection agency 2012). Climate change is altering the environment and this will have consequences for agriculture (Teagasc publications 2012). In this study we examine the relationship between weather and the yield of winter wheat and spring barley in an Irish context using data gathered from 2004-2010 at the Teagasc Oak Park research centre in Carlow. The data was analysed using a mixed effect model to test which if any weather …

Investigation Of Factors Influencing Trichloromethane Levels In Milk And Its Control., Siobhan Ryan

Theses

Trichloromethane (TCM) is an undesirable chemical residue that can develop in milk. While TCM levels in milk are not within ranges of public health concern, it is important that minimal levels are maintained in order to promote the marketing of Irish dairy products abroad. Germany has enacted strict regulations on TCM concentrations in foodstuffs with a recommended level of0.002 mg/kg and re-analyse those milks, subsequent to cause identification and provision of advice on reducing TCM levels in milk. Milk samples were analysed using Gas chromatography (GC) with electron capture detection. The GC method was adapted and a standard curve was …

High Resolution Hybrid Mass Spectrometry For The Determination Of Marine Biotoxins, Azaspiracids, And Their Biotransformation Products., Zuzana Skrabakova

Theses

Azaspiracids (AZAs), polyether marine toxins, are produced by marine microalgae and accumulate in filter-feeding bivalve molluscs, such as mussels, clams, oysters and scallops, while grazing on phytoplankton, from which they derive nutrition. Although being discovered quite recently, AZAs have caused several human intoxication events and thus became a problem for health authorities and shellfish industries. The rapid development of highly sensitive liquid chromatography multiple tandem mass spectrometry (LC-MS/MS, LC-MS") methods enabled the identification of numerous AZA analogues and added to the control of shellfish contamination. Tandem mass spectrometry techniques, while being highly selective and sensitive for determination of AZAs in …

Automated Interpretation Of The Tandem Mass Spectra Of Peptides Using Artificial Neural Networks, Timothy Patrick Manning

Theses

The manual interpretation of mass spectra is a complex and time consuming task. The problem of manually interpreting this data is further exacerbated by the large numbers of mass spectra which can potentially be produced in a single proteoniics experiment. This shows the need for high throughput approaches to the interpretation of mass spectra. Existing automated approaches are however error prone due to the complexity of the task. Accordingly, this thesis discusses and evaluates the application of neural networks to improving the sensitivity, specificity and robustness of current approaches to the automated interpretation of such mass spectral data.

Several neural …

Toxicodynamics And Biotransformation Of Azaspiracids Incorporating Liquid Chromatography-Tandem-Mass Spectrometry (Lc-Ms/Ms) Techniques., Daniel O'Driscoll

Theses

Azaspiracids (AZAs) are a family of lipophilic polyether marine biotoxins, that have caused a number of human intoxication incidents in Europe since 1995, which was the first incident reported following the consumption by consumers of intoxicated shellfish {Mytilus edulis). This class of phycotoxins has been responsible for extended closures of shellfisheries in various locations around Europe, where levels of AZAl-3 are regulated in shellfish. Since their discovery in 1995, AZAs have become the focus of extensive research, resulting in the discovery of numerous analogues. Only AZAl and AZA2 have been found in phytoplankton and all the other analogues are believed …

Application Of Multiple Mass Spectrometric Techniques In The Isolation, Determination And Characterisation Of The Marine Toxins; Azaspiracid, Keith O'Callaghan

Theses

The Azaspiracids are a class of polyether marine biotoxins that present a significant health risk to consumers of shellfish. Since their discovery in the late 1990s several human intoxications have been reported, and traced to Irish shellfish farms resulting in closures or harvest rejections. As such incidents involving azaspiracid shellfish poisoning have a major socio-economic impact on communities that rely on shellfish farming revenues.

Recent evidence suggests that azaspiracid poisoning events may become more commonplace. With this increased risk the understanding of azaspiracids mode of action and biological targets becomes crucial. To support these endeavours effective analytical methods need to …

Accumulation Of Phycotoxins In The Mussel Mytilus Galloprovincialis From The Central Adriatic Sea, Maja Pavela-Vrančić, Ivana Ujević, Živana Ninčević Gladan, Ambrose Furey

Physical Sciences Publications

Surveys of DSP (Diarrheic Shellfish Poisoning) toxin profiles in the mussel Mytilus galloprovincialis from coastal waters of the central Adriatic Sea, over the years 1995 to 2001, demonstrate that incidents of shellfish toxicity in this area are dominated by the occurrence of okadaic acid (OA) and a PTX derivative, 7-epi-pectenotoxin-2-seco acid (7-epi-PTX-2SA). Toxin composition and the relative ratio of toxic components in shellfish is in correlation with the occurrence of DSP producing organisms from the Dinophysis species along with Prorocentrum micans and Lingulodinium polyedrum. The occurrence of D. sacculus shortly before the appearance of OA in shellfish implicates its possible …

Exploring Marine Biotoxins Using Analytical Techniques Based On Mass Spectrometry, Mónica Fernández Amandi

Theses

The impact of phycotoxins on human and animal health is of important concern for worldwide authorities and the scientific community. Domoic acid (DA) is a neurotoxin produced by phytoplankton {Pseudonitzchia spp.). It enters the food chain through the consumption of shellfish that feed on toxic diatoms. DA has been responsible for several outbreaks affecting humans and animals all around the world. Yessotoxin (YTX) is produced by dinoflagellate species {Protoceratiuni reticulatum) which are globally distributed. Its toxicity is low when ingested orally. However, the co-extraction of YTX with diarrhetic shellfish poisoning (DSP) toxins, derives false positives when the mouse bioassay is …

Analytical And Synthetic Methods For Anatoxins., Janet Crowley

Theses

This thesis is focused on the potent cyanobacterial neurotoxins anatoxin-a (AN), its methyl analogue homoanatoxin-a (HMAN) and their non-toxic dihydro- and epoxydegradation products. In commencing the investigation into this area a literature review was performed in order to identify areas where more research and method development was required (Chapter 1). The review highlighted the fact that although a number of analytical methods had been developed for the analysis of AN, there were few methods for the determination of its potent homologue HMAN and their non-toxic degradation products. As these neurotoxins degrade quickly it is important to monitor their degradation products, …

Analysis Of Phycotoxin And Mycotoxin, Contaminants In Foods, Using Liquid Chromatography - Mass Spectrometry Techniques, Ana Brana Magdalena

Theses

The impact of phycotoxins and mycotoxins on human and animal health are of important concern for worldwide authorities and the scientific community. Liquid chromatography-mass spectrometry (LC-MS) techniques have been developed, optimised and validated for the analysis of these toxins.

Phycotoxins are potentially toxic substances, which are produced by marine phytoplankton and which may accumulate in shellfish or finfish. Azaspiracid poisoning (AZP) is a recently discovered syndrome that has been implicated in several incidents of human intoxications. A study was undertaken to examine the distribution of azaspiracids (AZA) in scallops {Pecten maximiis) and mussels {Mytiliis edulis). Domoic acid (DA) is an …

Applications Of The Atomic Force Microscope Within The Fields Of Haematology And Cytogenetics, Margaret O'Reilly-Crowley

Theses

Atomic force microscopy [AFM] has become a rapidly developing interdisciplinary field of research in recent years. The technique, including instrumentation and specimen preparation methods, is now more sophisticated and its application has increased dramatically. The key advantage of AFM is in providing three-dimensional images of samples imaged. Both size and shape of samples imaged can be obtained allowing their subsequent quantification. Red blood cells [RBCs] and chromosomes were imaged in this work. A brief overview of the current status of biomedical AFM, has been presented in the review.

Measurement of mean cell volume [MCV] of immobilised red blood cells with …