Physical Sciences and Mathematics Commons^™

Solvent Stable Microbial Lipases: Current Understanding And Biotechnological Applications, Barry Ryan, Priyanka Priyanka, Yeqi Tan, Gemma K Kinsella, Gary T. Henehan

Articles

Objective: This review examines on our current understanding of microbial lipase solvent tolerance, with a specific focus on the molecular strategies employed to improve lipase stability in a non-aqueous environment.

Results: It provides an overview of known solvent tolerant lipases and of approaches to improving solvent stability such as; enhancing stabilising interactions, modification of residue flexibility and surface charge alteration. It shows that judicious selection of lipase source supplemented by appropriate enzyme stabilisation, can lead to a wide application spectrum for lipases.

Conclusion: Organic solvent stable lipases are, and will continue to be, versatile and adaptable biocatalytic workhorses commonly employed …

On The Exactitude Of Big Data: La Bêtise And Artificial Intelligence, Noel Fitzpatrick, John D. Kelleher

Articles

This article revisits the question of ‘la bêtise’ or stupidity in the era of Artificial Intelligence driven by Big Data, it extends on the questions posed by Gille Deleuze and more recently by Bernard Stiegler. However, the framework for revisiting the question of la bêtise will be through the lens of contemporary computer science, in particular the development of data science as a mode of analysis, sometimes, misinterpreted as a mode of intelligence. In particular, this article will argue that with the advent of forms of hype (sometimes referred to as the hype cycle) in relation to big data and …

Regeneration Of Aged Dmf For Use In Solid-Phase Peptide Synthesis, Jordan K. Magtaan, Marc Devocelle, Fintan Kelleher

Articles

DMF, which is still the most commonly used solvent for Fmoc-SPPS, has the potential for degradation over time on exposure to air (and water vapour) and storage, to give dimethylamine and formic acid impurities. In particular, dimethylamine can lead to unwanted deprotection of the Fmoc group during for example the initial loading of Fmoc amino acids in SPPS, which leads reduced calculated loading values. We have found that treatment of such aged DMF by simple sparging with an inert gas (N₂), or vacuum sonication, can regenerate the DMF in order to restore loading levels back to those found …

Exchanging Personal Health Data With Electronic Health Records: A Standardized Information Model For Patient Generated Health Data And Observations Of Daily Living, Panagiotis Plastiras, Dympna O'Sullivan

Articles

Objective: The development of a middleware information model to facilitate better interoperability between Personal and Electronic Health Record systems in order to allow exchange of Patient Generated Health Data and Observations of Daily Leaving between patients and providers in order to encourage patient self-management.

Materials and methods: An information model based on HL7 standards for interoperability has been extended to support PGHD and ODL data types. The new information models uses HL7 CDA to represent data, is instantiated as a Protégé ontology and uses a set of mapping rules to transfer data between Personal and Electronic Health Record …

Exploring Online Novelty Detection Using First Story Detection Models, Fei Wang, Robert J. Ross, John D. Kelleher

Conference papers

Online novelty detection is an important technology in understanding and exploiting streaming data. One application of online novelty detection is First Story Detection (FSD) which attempts to find the very first story about a new topic, e.g. the first news report discussing the “Beast from the East” hitting Ireland. Although hundreds of FSD models have been developed, the vast majority of these only aim at improving the performance of the detection for some specific dataset, and very few focus on the insight of novelty itself. We believe that online novelty detection, framed as an unsupervised learning problem, always requires a …

A Multi-Task Approach To Incremental Dialogue State Tracking, Anh Duong Trinh, Robert J. Ross, John D. Kelleher

Conference papers

Incrementality is a fundamental feature of language in real world use. To this point, however, the vast majority of work in automated dialogue processing has focused on language as turn based. In this paper we explore the challenge of incremental dialogue state tracking through the development and analysis of a multi-task approach to incremental dialogue state tracking. We present the design of our incremental dialogue state tracker in detail and provide evaluation against the well known Dialogue State Tracking Challenge 2 (DSTC2) dataset. In addition to a standard evaluation of the tracker, we also provide an analysis of the Incrementality …

Non-Manual Articulators In Irish Sign Language Verbs: An Analysis With Data Mining Association Rules, Robert G. Smith, Markus Hofmann

Conference Papers

The Signs of Ireland (SOI) corpus (Leeson et al., 2006) deploys a complex multi-tiered temporal data structure. The process of manually analyzing such data is laborious, cannot eliminate bias and often, important patterns can go completely unnoticed. In addition to this, as a result of the complex nature of grammatical structures contained in the corpus, identifying complex linguistic associations or patterns across tiers is simply too intricate a task for a human to carry out in an acceptable timeframe. This work explores the application of data mining techniques on a set of multi-tiered temporal data from the SOI corpus. Building …

Raman Spectroscopy Detects Biochemical Changes Due To Different Cell Culture Environments In Live Cells In Vitro, Mahmoud Gargotti, Esen Efeoglu, Hugh Byrne, Alan Casey

Articles

The in vitro cell culture environment can impact on cell biochemistry and cell cycle. The manifestation of such substrate-induced changes in cell cycle in the Raman microspectroscopic profiles of cell cultures is investigated at the level of nucleolus, nucleus and cytoplasm. HeLa immortalised human cervical cells and HaCaT dermal cells were cultured on three different substrates, conventional polystyrene cell culture dishes, CaF2 slides as a commonly used Raman substrate, and glass slides coated with Collagen Rat Tail, as a mimic of the extra cellular matrix (ECM) environment. A cell cycle study, based on percentage DNA content, as determined using Propidium …

The Goldilocks Approach: A Review Of Employing Design Of Experiments In Prokaryotic Recombinant Protein Production, Albert Uhoraningoga, Gemma K. Kinsella, Gary T. Henehan, Barry Ryan

Articles

The production of high yields of soluble recombinant protein is one of the main objectives of protein biotechnology. Several factors, such as expression system, vector, host, media composition and induction conditions can influence recombinant protein yield. Identifying the most important factors for optimum protein expression may involve significant investment of time and considerable cost. To address this problem, statistical models such as Design of Experiments (DoE) have been used to optimise recombinant protein production. This review examines the application of DoE in the production of recombinant proteins in prokaryotic expression systems with specific emphasis on media composition and culture conditions. …

Significance Of A Non-Thermal Plasma Treatment On Ldpe Biodegradation With Pseudomonas Aeruginosa, Laurence Scally, Miroslav Gulan, Lars Weigang, Patrick Cullen, Vladimir Milosavljevic

Articles

The use of plastics has spanned across almost all aspects of day to day life. Although their uses are invaluable, they contribute to the generation of a lot of waste products that end up in the environment and end up polluting natural habitats such as forests and the ocean. By treating low-density polyethylene (LDPE) samples with non-thermal plasma in ambient air and with an addition of 4% CO2, the biodegradation of the samples can be increased due to an increase in oxidative species causing better cell adhesion and acceptance on the polymer sample surface. It was, however, found that the …

From Rankings To Ratings: Rank Scoring Via Active Learning, Jack O'Neill, Sarah Jane Delany, Brian Mac Namee

Conference papers

In this paper we present RaScAL, an active learning approach to predicting real-valued scores for items given access to an oracle and knowledge of the overall item-ranking. In an experiment on six different datasets, we find that RaScAL consistently outperforms the state-of-the-art. The RaScAL algorithm represents one step within a proposed overall system of preference elicitations of scores via pairwise comparisons.

Scoped: Evaluating A Composite Visualisation Of The Scope Chain Hierarchy Within Source Code, Ivan Bacher, Brian Mac Namee, John D. Kelleher

Conference papers

This paper presents two studies that evaluate the effectiveness of a software visualisation tool which uses a com- posite visualisation to encode the scope chain and information related to the scope chain within source code. The first study evaluates the effectiveness of adding the composite visualisation to a source code editor to help programmers understand scope relationships within source code. The second study evaluates the effectiveness of each individual component within the composite visualisation. The composite visualisation is composed of a packed circle tree diagram (overview component) and a list view (detail view component). The packed circle tree functions as …

The Code Mini-Map Visualisation: Encoding Conceptual Structures Within Source Code, Ivan Bacher, Brian Mac Namee, John D. Kelleher

Conference papers

Modern source code editors typically include a code mini-map visualisation, which provides programmers with an overview of the currently open source code document. This paper proposes to add a layering mechanism to the code mini- map visualisation in order to provide programmers with visual answers to questions related to conceptual structures that are not manifested directly in the code. Details regarding the design and implementation of this scope information layer, which displays additional encodings that correspond to the scope chain and information related to the scope chain within a source code document, is presented. The scope information layer can be …

Ideating Mobile Health Behavioral Support For Compliance To Therapy For Patients With Chronic Disease: A Case Study Of Atrial Fibrillation Management, Mor Peleg, Wojtek Michalowski, Szymon Wilk, Enea Parimbelli, Silvia Bonaccio, Dympna O'Sullivan, Martin Michalowski, Silvana Quaglini, Marc Carrier

Articles

Poor patient compliance to therapy results in a worsening condition that often increases healthcare costs. In the MobiGuide project, we developed an evidence-based clinical decision-support system that delivered personalized reminders and recommendations to patients, helping to achieve higher therapy compliance. Yet compliance could still be improved and therefore building on the MobiGuide project experience, we designed a new component called the Motivational Patient Assistant (MPA) that is integrated within the MobiGuide architecture to further improve compliance. This component draws from psychological theories to provide behavioral support to improve patient engagement and thereby increasing patients' compliance. Behavior modification interventions are delivered …

Sure 2018 Undergraduate Science Conference Booklet, Sure Network

Group Reports

The SURE Network hosted the First Annual Science Undergraduate Research Experience (SURE) Conferences (SURE 2018) on 28th September 2018 in Athlone Institute of Technology, Dublin Institute of Technology and Waterford Institute of Technology. The simultaneous conferences had a total of 27 oral presentations and 67 poster presentations, and were attended by over 500 students, academic staff, professional body and industry representatives.

The aims of the conference were to:

1. Provide current students with an opportunity to gain an understanding of the work which has been undertaken by recent graduates, and the career opportunities that exist for graduates in Scientific disciplines.
2. Provide …

Building Classifiers With Gmdh For Health Social Networks (Bd Askapatient), John Cardiff, Liliya Akhtyamova, Mikhail Alexandrov

Conference Papers

Health social media offer useful data for patients and doctors concerning both various medicines and treatments. Usually, these data are accompanied by their assessments in 5- star scale. But such a detail classification has small usefulness because patients and doctors, first of all, want to know about negative cases and to study in detail the extreme ones. In the paper we build classifiers of texts just for these cases using combined classes as negative, all others and worst, satisfactory, best. For this, we study possibilities of different GMDH-based algorithms and compare them with the results of other methods. The selection …

Entity-Grounded Image Captioning, Annika Lindh, Robert J. Ross, John D. Kelleher

Conference papers

An urgent limitation in current Image Captioning models is their tendency to produce generic captions that avoid the interesting detail which makes each image unique. To address this limitation, we propose an approach that enforces a stronger alignment between image regions and specific segments of text. The model architecture is composed of a visual region proposer, a region-order planner and a region-guided caption generator. The region-guided caption generator incorporates a novel information gate which allows visual and textual input of different frequencies and dimensionalities in a Recurrent Neural Network.

The Influence Of Soft Contact Lens Materials On The Central, Para-Central And Peripheral Corneal Endothelium, Aoife Lloyd Mckernan, Luisa Simo Mannion, Veronica O'Dwyer

Other Resources

Title: The influence of soft contact lens materials on the central, para-central and peripheral corneal endothelium prior to and following two weeks cessation of soft contact lens wear.

Purpose: To examine the influence of a variety of soft contact lens (SCL) materials on the central, para-central and peripheral corneal endothelium measurements, prior to and following two weeks cessation of SCL wear.

Methods: Endothelial measurements were taken using the CEM-530 (Nidek, Japan) specular microscope. Full-time SCL wearers (n = 31 eyes) were compared to a non-contact lens (NCL) control group (n = 28 eyes) of a similar age. Seven areas of …

Serialised Holography For Brand Protection And Authentication, Dinesh Vather, Izabela Naydenova, Dervil Cody, Monika Zawadzka, Suzanne Martin, Emilia Mihaylova, Stephen Curran, Paul Duffy, Josune Portillo, Daniel Connell, Stephen Mcdonnell, Vincent Toal

Articles

The problems presented by counterfeit products and documentation are discussed. Limitations of existing holograms for anti-counterfeit applications are described. We describe the advantages of full holographic serialisation and the requirements in terms of materials and techniques for mass production of true serialised holograms. These requirements having been met, we report for the first time the mass production of fully serialised holograms. The novelty of approach consists of the direct use of product manufacturer’s information as the object in a holographic recording system along with a self-processing photopolymer and modular optical system to facilitate mass production of truly serialised volume holograms. …

Performance Comparison Of Support Vector Machine, Random Forest, And Extreme Learning Machine For Intrusion Detection, Iftikhar Ahmad, Muhammad Javed Iqbal, Mohammad Basheri, Aneel Rahim

Articles

Intrusion detection is a fundamental part of security tools, such as adaptive security appliances, intrusion detection systems, intrusion prevention systems, and firewalls. Various intrusion detection techniques are used, but their performance is an issue. Intrusion detection performance depends on accuracy, which needs to improve to decrease false alarms and to increase the detection rate. To resolve concerns on performance, multilayer perceptron, support vector machine (SVM), and other techniques have been used in recent work. Such techniques indicate limitations and are not efficient for use in large data sets, such as system and network data. The intrusion detection system is used …

Safety Implications Of Plasma-Induced Effects In Living Cells – A Review Of In Vitro And In Vivo Findings, Daniela Boehm, Paula Bourke

Articles

Cold atmospheric plasma is a versatile new tool in the biomedical field with applications ranging from disinfection, wound healing and tissue regeneration to blood coagulation, and cancer treatment. Along with improved insights into the underlying physical, chemical and biological principles, plasma medicine has also made important advances in the introduction into the clinic. However, in the absence of a standard plasma ‘dose’ definition, the diversity of the field poses certain difficulties in terms of comparability of plasma devices, treatment parameters and resulting biological effects, particularly with regards to the question of what constitutes a safe plasma application. Data from various …

Perception & Perspective: An Analysis Of Discourse And Situational Factors In Reference Frame Selection, Robert J. Ross, Kavita E. Thomas

Conference papers

To integrate perception into dialogue, it is necessary to bind spatial language descriptions to reference frame use. To this end, we present an analysis of discourse and situational factors that may influence reference frame choice in dialogues. We show that factors including spatial orientation, task, self and other alignment, and dyad have an influence on reference frame use. We further show that a computational model to estimate reference frame based on these features provides results greater than both random and greedy reference frame selection strategies.

Mind The Gap: Situated Spatial Language A Case-Study In Connecting Perception And Language, John D. Kelleher

Other

This abstract reviews the literature on computational models of spatial semantics and the potential of deep learning models as an useful approach to this challenge.

Advancing Raman Microspectroscopy For Cellular And Subcellular Analysis: Towards In Vitro High Content Spectralomic Analysis, Hugh Byrne, Franck Bonnier, Alan Casey, Marcus Maher, Jennifer Mcintyre, Esen Efeoglu, Zeineb Farhane

Articles

In the confocal mode, Raman microspectroscopy can profile the biochemical content of biological cells at a subcellular level, and any changes to it by exogenous agents, such as therapeutic drugs or toxicants. As an exploration of the potential of the technique as a high content, label free analysis technique, this report reviews work to monitor the spectroscopic signatures associated with the uptake and response pathways of commercial chemotherapeutic agents and polymeric nanoparticles by human lung cells. It is demonstrated that the signatures are reproducible and characteristic of the cellular event, and can be used, for example, to identify the mode …

Multicomponent Analysis Using A Confocal Raman Microscope, Zhengyuan Tang, Sinead J. Barton, Thomas E. Ward, John P. Lowry, Michelle M. Doran, Hugh Byrne, Bryan M. Hennelly

Articles

Measuring the concentration of multiple chemical components in a low volume aqueous mixture by Raman spectroscopy has received significant interest in the literature. All of the contributions to date focus on the design of optical systems that facilitate the recording of spectra with high signal-to-noise ratio, by collecting as many Raman scattered photons as possible. In this study, the confocal Raman microscope set-up is investigated for multicomponent analysis. Partial Least Squares Regression is used to quantify physiologically relevant aqueous mixtures of glucose, lactic acid, and urea. The predicted error is 17.81 mg/dL for glucose, 10.6 mg/dL for lactic acid and …

An Investigation Into The Effects Of Multiple Kernel Combinations On Solutions Spaces In Support Vector Machines, Paul Kelly, Luca Longo

Conference papers

The use of Multiple Kernel Learning (MKL) for Support Vector Machines (SVM) in Machine Learning tasks is a growing field of study. MKL kernels expand on traditional base kernels that are used to improve performance on non-linearly separable datasets. Multiple kernels use combinations of those base kernels to develop novel kernel shapes that allow for more diversity in the generated solution spaces. Customising these kernels to the dataset is still mostly a process of trial and error. Guidelines around what combinations to implement are lacking and usually they requires domain specific knowledge and understanding of the data. Through a brute …

Raman Spectral Analysis For Rapid Screening Of Dengue Infection, Tahir Mahmood, Haq Nawaz, A. Ditta, M.I. Majeed, M.A. Hanif, N. Rashid, H.N. Bhatti, H.F. Nargis, M. Saleem, Franck Bonnier, Hugh Byrne

Articles

Infection with the dengue virus is currently clinically detected according to different biomarkers in human blood plasma, commonly measured by enzyme linked immunosorbent assays, including non-structural proteins (Ns1), immunoglobulin M (IgM) and immunoglobulin G (IgG). However, there is little or no mutual correlation between the biomarkers, as demonstrated in this study by a comparison of their levels in samples from 17 patients. As an alternative, the label free, rapid screening technique, Raman spectroscopy has been used for the characterisation/diagnosis of healthy and dengue infected human blood plasma samples. In dengue positive samples, changes in specific Raman spectral bands associated with …

Evaluating Sequence Discovery Systems In An Abstraction-Aware Manner, Eoin Rogers, Robert J. Ross, John D. Kelleher

Conference papers

Activity discovery is a challenging machine learning problem where we seek to uncover new or altered behavioural patterns in sensor data. In this paper we motivate and introduce a novel approach to evaluating activity discovery systems. Pre-annotated ground truths, often used to evaluate the performance of such systems on existing datasets, may exist at different levels of abstraction to the output of the output produced by the system. We propose a method for detecting and dealing with this situation, allowing for useful ground truth comparisons. This work has applications for activity discovery, and also for related fields. For example, it …

Endoscopic Ultrasound Features Of Multiple Endocrine Neoplasia Type 1-Related Versus Sporadic Pancreatic Neuroendocrine Tumors: A Single-Center Retrospective Study, Gianluca Tamagno, Vanessa Scherer, Alberto Caimo, Simona Bergmann, Peter Kann

Articles

Pancreatic neuroendocrine tumors (pNETs) can occur in patients with a familial syndrome either as multiple endocrine neoplasia type 1 (MEN-1) or as sporadic tumors. Endoscopic ultrasound (EUS) has become one of the first-line investigations for pNET characterization. The ultrasonographic features of pNETs may differ depending on the familial versus sporadic pathogenesis of the tumor. Therefore, the EUS findings could help and direct the definition of a pNET with an impact on the most appropriate diagnostic and ther- apeutic patient management. Methods: In this single-center retrospective study, we reviewed the EUS features of 94 pNETs from 37 MEN-1 patients and 15 …

Conformational Studies Of Gram-Negative Bacterial Quorum Sensing Acyl Homoserine Lactone (Ahl) Molecules: The Importance Of The N→* Interaction, Fintan Kelleher, Goar Sánchez-Sanz, Darren Crowe, Alan Nicholson, Adrienne Fleming

Articles

A ¹H NMR study shows the presence of intermolecular hydrogen bonds for AHLs in CDCl₃ solution. A detailed computational study of the structure of AHLs and the relative stability between the extended conformations (X) and those showing n→p* interactions (np) have been carried out by means of DFT calculations. Solvent effects have been shown to be very important when stabilising np conformations, particularly with polar solvents. This was shown by the shortening of C···O intramolecular distances and the increase in the relative energies favouring the np conformation with the dielectric constant of the solvent. …