Physical Sciences and Mathematics Commons^™

An Exploratory Study On Refactoring Documentation In Issues Handling, Eman Abdullah Alomar, Anthony Peruma, Mohamed Wiem Mkaouer, Christian D. Newman, Ali Ouni

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Understanding the practice of refactoring documentation is of paramount importance in academia and industry. Issue tracking systems are used by most software projects enabling developers, quality assurance, managers, and users to submit feature requests and other tasks such as bug fixing and code review. Although recent studies explored how to document refactoring in commit messages, little is known about how developers describe their refactoring needs in issues. In this study, we aim at exploring developer-reported refactoring changes in issues to better understand what developers consider to be problematic in their code and how they handle it. Our approach relies on …

Code Review Practices For Refactoring Changes: An Empirical Study On Openstack, Mohamed Wiem Mkaouer, Eman Abdullah Alomar, Moatz Chouchen, Ali Ouni

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Modern code review is a widely used technique employed in both industrial and open-source projects to improve software quality, share knowledge, and ensure adherence to coding standards and guidelines. During code review, developers may discuss refactoring activities before merging code changes in the code base. To date, code review has been extensively studied to explore its general challenges, best practices and outcomes, and socio-technical aspects. However, little is known about how refactoring is being reviewed and what developers care about when they review refactored code. Hence, in this work, we present a quantitative and qualitative study to understand what are …

Estimating The Analytical Performance Of Raman Spectroscopy For Quantification Of Active Ingredients In Human Stratum Corneum, Hichem Kichou, Emilie Munnier, Yuri Dancik, Kamilia Kemel, Hugh Byrne, Ali Tfayli, Dominique Bertrand, Martin Soucé, Igor Chourpa, Franck Bonnier

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Confocal Raman microscopy (CRM) has become a versatile technique that can be applied routinely to monitor skin penetration of active molecules. In the present study, CRM coupled to multivariate analysis (namely PLSR—partial least squares regression) is used for the quantitative measurement of an active ingredient (AI) applied to isolated (ex vivo) human stratum corneum (SC), using systematically varied doses of resorcinol, as model compound, and the performance is quantified according to key figures of merit defined by regulatory bodies (ICH, FDA, and EMA). A methodology is thus demonstrated to establish the limit of detection (LOD), precision, accuracy, sensitivity (SEN), and …

Controlling Unequal Surface Energy Results Caused By Test Liquids: The Case Of Uv/O3 Treated Pet, Bilge N. Altay, Paul D. Fleming, Md Arifur Rahman, Alexandra Pekarovicova, Bruce Myers, Cem Aydemir, Arif Karademir

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Ultraviolet/ozone (UV/O3) treatment has been reported to be an effective method to modify properties such as wettability, adhesion or adsorption of plastic surfaces. The change in the surface is measured by contact angle analysis, which employs liquids and their surface tensions (ST) to estimate the surface energy (SE). We found two different practices in the scientific community: (1) the majority of researchers adopted the ST value of liquids from the literature, while (2) other researchers conducted real-time measurements in the lab under ambient conditions prior to SE estimation. To the best of our knowledge, there is no study that compares …

The World Is Our Classroom: Developing A Model For International Virtual Internships - The Global Innovations Project, Paul Doyle, Brian Keegan, Damian Gordon, Anna Becevel, Paul J. Gibson, Zhiying Jiang Phd, Dympna O'Sullivan

Articles

In the aftermath of COVID-19, remote working has become the norm, and graduates now need an even wider range of skills, which traditional classrooms and internships do not always provide. Working in multiple time zones, within global multi-cultural teams, and only ever meeting colleagues through online technology are just some of the challenges, which require a new type of global graduate. Transversal skills including leadership, collaboration, innovation, digital, green, organization and communication skills are critical. The disruption from COVID-19 also presents unprecedented opportunities to develop more inclusive approaches to internships and international experiences, to level the playing field for students …

Limits Of Detection Of Mycotoxins By Laminar Flow Strips: A Review, Xinyi Zhao, Hugh Byrne, Christine M. O’Connor, James Curtin, Furong Tian

Articles

Mycotoxins are secondary metabolic products of fungi. They are poisonous, carcinogenic, and mutagenic in nature and pose a serious health threat to both humans and animals, causing severe illnesses and even death. Rapid, simple and low-cost methods of detection of mycotoxins are of immense importance and in great demand in the food and beverage industry, as well as in agriculture and environmental monitoring, and, for this purpose, lateral flow immunochromatographic strips (ICSTs) have been widely used in food safety and environmental monitoring. The literature to date describing the development of ICSTs for the detection of different types of mycotoxins using …

Ai Insurance: How Liability Insurance Can Drive The Responsible Adoption Of Artificial Intelligence In Health Care, Ariel Dora Stern, Avi Goldfarb, Timo Minssen, W. Nicholson Price Ii

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Despite enthusiasm about the potential to apply artificial intelligence (AI) to medicine and health care delivery, adoption remains tepid, even for the most compelling technologies. In this article, the authors focus on one set of challenges to AI adoption: those related to liability. Well-designed AI liability insurance can mitigate predictable liability risks and uncertainties in a way that is aligned with the interests of health care’s main stakeholders, including patients, physicians, and health care organization leadership. A market for AI insurance will encourage the use of high-quality AI, because insurers will be most keen to underwrite those products that are …

Advancing Ubiquitous Collaboration For Telehealth - A Framework To Evaluate Technology-Mediated Collaborative Workflow For Telehealth, Hypertension Exam Workflow Study, Christopher Bondy Ph.D., Linlin Chen Ph.D, Pamela Grover Md, Pengcheng Shi Ph.D

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Healthcare systems are under siege globally regarding technology adoption; the recent pandemic has only magnified the issues. Providers and patients alike look to new enabling technologies to establish real-time connectivity and capability for a growing range of remote telehealth solutions. The migration to new technology is not as seamless as clinicians and patients would like since the new workflows pose new responsibilities and barriers to adoption across the telehealth ecosystem. Technology-mediated workflows (integrated software and personal medical devices) are increasingly important in patient-centered healthcare; software-intense systems will become integral in prescribed treatment plans [1]. My research explored the path to …

Towards An Ethical Framework For The Design And Development Of Inclusive Home-Based Smart Technology For Smart Spaces For Older Adults And People With Disabilities, Emma Murphy, Julie Doyle, Ioannis Stavrakakis, Damian Gordon, Brian Keegan, Dympna O'Sullivan

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Unique ethical, privacy and safety implications arise for people who are reliant on home-based smart technology due to health conditions or disabilities. As a result we need to carefully reflect on our approaches to ethical issues over the life cycle of smart home technology design and the wider living context for end users and relevant stakeholders. In this position paper we highlight a need for a reflective, inclusive ethical framework for the design of inclusive smart spaces. We present key ethical considerations in the design, development and deployment of smart home-based technology for older adults and people with disabilities. We …

A Microfluidic Approach For Synthesis And Kinetic Profiling Of Branched Gold Nanostructures, Qi Cai, Valentina Castagnola, Luca Boselli, Alirio Moura, Hender Lopez, Wei Zhang, João M. De Araújo, Kenneth A. Dawson

Articles

Automatized approaches for nanoparticle synthesis and characterization represent a great asset to their applicability in the biomedical field by improving reproducibility and standardization, which help to meet the selection criteria of regulatory authorities. The scaled-up production of nanoparticles with carefully defined characteristics, including intrinsic morphological features, and minimal intra-batch, batch-to-batch, and operator variability, is an urgent requirement to elevate nanotechnology towards more trustable biological and technological applications. In this work, microfluidic approaches were employed to achieve fast mixing and good reproducibility in synthesizing a variety of gold nanostructures. The microfluidic setup allowed exploiting spatial resolution to investigate the growth evolution …

Probability Models With Discrete And Continuous Parts, James E. Marengo, David L. Farnsworth

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In mathematical statistics courses, students learn that the quadratic function E ((X – x )-squared) is minimized when x is the mean of the random variable X, and that the graphs of this function for any two distributions of X are simply translates of each other. We focus on the problem of minimizing the function defined by y ( x) = E ( IX – xI-squared ) in the context of mixtures of probability distributions of the discrete, absolutely continuous, and singular continuous types. This problem is important, for example, in Bayesian statistics, when one attempts to compute the decision …

Detecting Patches On Road Pavement Images Acquired With 3d Laser Sensors Using Object Detection And Deep Learning, Syed Ibrahim Hassan, Dympna O'Sullivan, Susan Mckeever, Kieran Feighan, David Power, Ray Mcgowan

Articles

Regular pavement inspections are key to good road maintenance and road defect corrections. Advanced pavement inspection systems such as LCMS (Laser Crack Measurement System) can automatically detect the presence of different defects using 3D lasers. However, such systems still require manual involvement to complete the detection of pavement defects. This paper proposes an automatic patch detection system using object detection technique. To our knowledge, this is the first time state-of-the-art object detection models Faster RCNN, and SSD MobileNet-V2 have been used to detect patches inside images acquired by LCMS. Results show that the object detection model can successfully detect patches …

Assessing Feature Representations For Instance-Based Cross-Domain Anomaly Detection In Cloud Services Univariate Time Series Data, Rahul Agrahari, Matthew Nicholson, Clare Conran, Haythem Assem, John D. Kelleher

Articles

In this paper, we compare and assess the efficacy of a number of time-series instance feature representations for anomaly detection. To assess whether there are statistically significant differences between different feature representations for anomaly detection in a time series, we calculate and compare confidence intervals on the average performance of different feature sets across a number of different model types and cross-domain time-series datasets. Our results indicate that the catch22 time-series feature set augmented with features based on rolling mean and variance performs best on average, and that the difference in performance between this feature set and the next best …

Assessing Feature Representations For Instance-Based Cross-Domain Anomaly Detection In Cloud Services Univariate Time Series Data, Rahul Agrahari, Matthew Nicholson, Clare Conran, Haytham Assem, John D. Kelleher

Articles

In this paper, we compare and assess the efficacy of a number of time-series instance feature representations for anomaly detection. To assess whether there are statistically significant differences between different feature representations for anomaly detection in a time series, we calculate and compare confidence intervals on the average performance of different feature sets across a number of different model types and cross-domain time-series datasets. Our results indicate that the catch22 time-series feature set augmented with features based on rolling mean and variance performs best on average, and that the difference in performance between this feature set and the next best …

Bodipy–Pyrene Donor–Acceptor Sensitizers For Triplet–Triplet Annihilation Upconversion: The Impact Of The Bodipy-Core On Upconversion Efficiency, Natalia Kiseleva, Mikhail Filatov, Jan C. Fischer, Milian Kaiser, Marius Jakoby, Dimitry Busko, Ian A. Howard, Bryce Richards, Andrey Turshatov

Articles

Triplet–triplet annihilation upconversion (TTA-UC) is an important type of optical process with applications in biophotonics, solar energy harvesting and photochemistry. In most of the TTA-UC systems, the formation of triplet excited states takes place via spin–orbital interactions promoted by heavy atoms. Given the crucial role of heavy atoms (especially noble metals, such as Pd and Pt) in promoting intersystem crossing (ISC) and, therefore, in production of UC luminescence, the feasibility of using more readily available and inexpensive sensitizers without heavy atoms remains a challenge. Here, we investigated sensitization of TTA-UC using BODIPY–pyrene heavy-atom-free donor–acceptor dyads with different numbers of alkyl …

Mapping The Dna Damaging Effects Of Polypyridyl Copper Complexes With Dna Electrochemical Biosensors, Anna Banasiak, Nicolò Zuin Fantoni, Andrew Kellett, John Colleran

Articles

Several classes of copper complexes are known to induce oxidative DNA damage that mediates cell death. These compounds are potentially useful anticancer agents and detailed investigation can reveal the mode of DNA interaction, binding strength, and type of oxidative lesion formed. We recently reported the development of a DNA electrochemical biosensor employed to quantify the DNA cleavage activity of the well-studied [Cu(phen)₂]²⁺ chemical nuclease. However, to validate the broader compatibility of this sensor for use with more diverse—and biologically compatible—copper complexes, and to probe its use from a drug discovery perspective, analysis involving new compound libraries is …

Synthesis Of Fast Curing, Water-Resistant And Photopolymerizable Glass For Recording Of Holographic Structures By One- And Two-Photon Lithography, Tatsiana Mikulchyk, Mohamed Oubaha, Alicja Kaworek, Brendan Duffy, Markus Lunzer, Aleksandr Ovsianikov, Sabad-E Gul, Izabela Naydenova, Dervil Cody

Articles

Advancements in hybrid sol-gel technology have provided a new class of holographic materials as photopolymerizable glasses. Recently, a number of photosensitive glass compositions with high dynamic range and high spatial resolution have been reported and their excellent capability for volume holography has been demonstrated. Nevertheless, challenges remain, particularly in relation to the processing time and environmental stability of these materials, that strongly affect the performance and durability of the fabricated holograms. State-of-the-art photopolymerizable glasses possess long curing times (few days) required to achieve thick films, thus limiting the industrial implementation of this technology and its commercial viability. This article presents …

All Things Merge Into One, And A River Runs Through It: Exploring The Dimensions Of Blended Learning By Developing A Case Study Template For Blended Activities, Damian Gordon, Paul Doyle, Anna Becevel, Tina Baloh

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The BLITT (Blended Learning International Train the Trainer) Project is focused on developing a training programme to equip teachers to become proficient in championing the use of Blended Learning in the classroom. The training programme will be developed in two phases, in the first phase involves the development of a series of case studies relevant to Blended Learning, followed by a second phase where the BLITT training programme will be designed and developed, using input from these cases. In developing the blended learning case studies, two key documents were identified as being essential, first, a case study tracking template to …

Development And Validation Of A Raman Spectroscopic Classification Model For Cervical Intraepithelial Neoplasia (Cin), Damien Traynor, Shiyamala Duraipandian, Ramya Bhatia, Kate Cuschieri, Prerna Tewari, Padraig Kearney, Tom D'Arcy, John J. O'Leary, Cara M. Martin, Fiona Lyng

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The mortality associated with cervical cancer can be reduced if detected at the precancer stage, but current methods are limited in terms of subjectivity, cost and time. Optical spectroscopic methods such as Raman spectroscopy can provide a rapid, label-free and nondestructive measurement of the biochemical fingerprint of a cell, tissue or biofluid. Previous studies have shown the potential of Raman spectroscopy for cervical cancer diagnosis, but most were pilot studies with small sample sizes. The aim of this study is to show the clinical utility of Raman spectroscopy for identifying cervical precancer in a large sample set with validation in …

Micro-Rna And Proteomic Profiles Of Plasma-Derived Exosomes From Irradiated Mice Reveal Molecular Changes Preventing Apoptosis In Neonatal Cerebellum, Simonetta Pazzaglia, Barbara Tanno, Ilaria De Stefano, Paola Giardullo, Simona Leonardi, Caterina Merla, Gabriele Babini, Seda Tuncay Cagatay, Ammar Mayah, Munira Kadhim, Fiona Lyng, Christine Von Toerne, Zohaib N. Khan, Prabal Subedi, Soile Tapio, Anna Saran, Mariateresa Mancuso

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Cell communication via exosomes is capable of influencing cell fate in stress situations such as exposure to ionizing radiation. In vitro and in vivo studies have shown that exosomes might play a role in out-of-target radiation effects by carrying molecular signaling mediators of radiation damage, as well as opposite protective functions resulting in resistance to radiotherapy. However, a global understanding of exosomes and their radiation-induced regulation, especially within the context of an intact mammalian organism, has been lacking. In this in vivo study, we demonstrate that, compared to sham-irradiated (SI) mice, a distinct pattern of proteins and miRNAs is found …

First Long-Time Airborne Fungal Spores Study In Dublin, Ireland (1978–1980), Moisés Martínez-Bracero, Emma Markey, Jerry Hourihane Clancy, John Sodeau, David J. O'Connor

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Ambient fungal spores within the atmosphere can contribute to a range of negative human, animal and plant health conditions and diseases. However, trends in fungal spore seasonality, species prevalence, and geographical origin have been significantly understudied in Ireland. Previously unpublished data from the late 1970s have recently been collected and analysed to establish historical fungal spore trends/characteristics for Dublin. Historical spore concentrations were largely dominated by Alternaria, Ascospores, Basidiospores, Botrytis, Cladosporium, Erysiphe and Rusts. The main fungal spore season for Dublin commenced in April with the fructification of Scopulariopsis and Ganoderma. However, the vast majority of other spore types did …

Trends In Biomedical Analysis Of Red Blood Cells – Raman Spectroscopy Against Other Spectroscopic, Microscopic And Classical Techniques, Jakub Dybas, Fatih Celal Alcicek, Aleksandra Wajda, Magdalena Kaczmarska, Anna Zimna, Katarzyna Bulat, Aneta Blat, Tetiana Stepanenko, Tasnim Mohaissen, Ewa Szczesny-Malysiak, David Perez-Guaita, Bayden R. Wood, Katarzyna Maria Marzec

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Application of modern and innovative spectroscopic and microscopic approaches to biomedical analysis opens new horizons and sheds new light on many unexplored scientific territories. In this review, we critically summarize up-to-date Raman-based methodologies for red blood cells (RBCs) analysis used in biology and medicine, and compare them with both classical, as well as other spectroscopic and microscopic approaches. The main emphasis is placed on the advantages, disadvantages and capabilities of each technique for detection of RBC deteriorations and RBC-related diseases. Although currently used classical techniques of medical analysts serve as a gold standard for clinicians in diagnosis of erythropathies, they …

Monitoring And Modelling The Dynamics Of The Cellular Glycolysis Pathway: A Review And Future Perspectives, Nitin Patil, Hugh Byrne, Orla L. Howe, Paul A. Cahill

Articles

Background

The dynamics of the cellular glycolysis pathway underpin cellular function and dysfunction, and therefore ultimately health, disease, diagnostic and therapeutic strategies. Evolving our understanding of this fundamental process and its dynamics remains critical.

Scope of review

This paper reviews the medical relevance of glycolytic pathway in depth and explores the current state of the art for monitoring and modelling the dynamics of the process. The future perspectives of label free, vibrational microspectroscopic techniques to overcome the limitations of the current approaches are considered.

Major conclusions

Vibrational microspectroscopic techniques can potentially operate in the niche area of limitations of other …

Biofabrication Of Magnetic Nanoparticles And Their Use As Carriers For Pectinase And Xylanase, Shady S. Hassan, Brendan Duffy, Gwilym A. Williams, Amit Jaiswal

Articles

In this study, superparamagnetic iron oxide nanoparticles (MNPs) were synthesized via exposure of fungal cell filtrate from Aspergillus flavus to aqueous iron ions. The extracellular synthesis of MNPs was monitored by UV–Vis spectrophotometry and showed an absorption peak at 310 nm. The morphology of MNPs was found to be flake-like, as confirmed by Field Emission Scanning Electron Microscopy (FESEM), while the average crystallite size was ∼16 nm, as determined by X-ray diffraction (XRD). Energy dispersive X-ray (EDX) analysis was performed to confirm the presence of elemental Fe in the sample. Pectinase and xylanase were covalently immobilized on MNPs with efficiencies …

Evaluation Of The Potential Of Nanofluids Containing Different Ag Nanoparticle Size Distributions For Enhanced Solar Energy Conversion In Hybrid Photovoltaic-Thermal (Pvt) Applications, James Walshe, John Doran, George Amarandei

Articles

Hybridising photovoltaic and photothermal technologies into a single system that can simultaneously deliver heat and power represents one of the leading strategies for generating clean energy at more affordable prices. In a hybrid photovoltaic-thermal (PVT) system, the capability to modulate the thermal and electrical power output is significantly influenced by the spectral properties of the heat transfer fluid utilised. In this study, we report on one of the first experimental evaluations of the capability of a multimodal silver nanofluid containing various particle shapes and particle sizes to selectively modulate the solar energy for PVT applications. The diverse set of particle …

Satdbailiff- Mining And Tracking Self-Admitted Technical Debt, Mohamed Wiem Mkaouer, Eman Abdullah Alomar, Ben Christians, Mihal Busho, Ahmed Hamad Alkhalid, Christian D. Newman

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Self-Admitted Technical Debt (SATD) is a metaphorical concept to describe the self-documented addition of technical debt to a software project in the form of source code comments. SATD can linger in projects and degrade source-code quality, but it can also be more visible than unintentionally added or undocumented technical debt. Understanding the implications of adding SATD to a software project is important because developers can benefit from a better understanding of the quality trade-offs they are making. However, empirical studies, analyzing the survivability and removal of SATD comments, are challenged by potential code changes or SATD comment updates that may …

Fluctuating Temperature Modifies Heat-Mortality Association Around The Globe, Yao Wu, Bo Wen, Shanshan Li, Antonio Gasparrini, Shilu Tong, Ala Overcenco, Aleš Urban, Alexandra Schneider, Alireza Entezari, Ana Maria Vicedo-Cabrera, Antonella Zanobetti, Antonis Analitis, Ariana Zeka, Aurelio Tobias, Barrack Alahmad, Ben Armstrong, Bertil Forsberg, Carmen Íñiguez, Caroline Ameling, César De La Cruz Valencia, Chrisofer Åström, Danny Houthuijs, Do Van Dung, Dominic Royé, Ene Indermitte, Eric Lavigne, Fatemeh Mayvaneh, Fiorella Acquaotta, Francesca De’Donato, Francesco Sera, Gabriel Carrasco-Escobar, Haidong Kan, Hans Orru, Ho Kim, Iulian-Horia Holobaca, Jan Kyselý, Joana Madureira, Joel Schwartz, Klea Katsouyanni, Magali Hurtado-Diaz, Martina S. Ragettli, Masahiro Hashizume, Mathilde Pascal, Micheline De Sousa Zanotti Stagliorio Coélho, Noah Scovronick, Paola Michelozzi, Patrick J. Goodman, Paulo Hilario Nascimento Saldiva, Rosana Abrutzky, Samuel Osorio, Tran Ngoc Dang, Valentina Colistro, Veronika Huber, Whanhee Lee, Xerxes Seposo, Yasushi Honda, Michelle L. Bell, Yuming Guo

Articles

Studies have investigated the effects of heat and temperature variability (TV) on mortality. However, few assessed whether TV modifies the heat-mortality association. Data on daily temperature and mortality in the warm season were collected from 717 locations across 36 countries. TV was calculated as the standard deviation of the average of the same and previous days’ minimum and maximum temperatures. We used location-specific quasi-Poisson regression models with an interaction term between the cross-basis term for mean temperature and quartiles of TV to obtain heat-mortality associations under each quartile of TV, and then pooled estimates at the country, regional, and global …

Towards Plasmon Mapping Of Sers-Active Ag Dewetted Nanostructures Using Spels, Mohamed Beshr, E. Dexter, Paul E. Tierney, Aidan Meade, Shane Murphy, George Amarandei

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Thermal dewetting of silver thin flm can lead to SERS-active Ag nanoparticles. Here, we report our progress towards using scanning probe energy loss spectroscopy (SPELS) to map the plasmonic behaviour of SERS-active Ag nanoparticles (NP) by investigating NPs produced through the dewetting study of Ag thin flms on SiO2/Si and Ti/SiO2/Si substrates. The nanoparticles size and spatial distribution were controlled by the deposition and thermal annealing parameters. The results of preliminary SPELS measurements of these structures, alongside SERS data show that there is a correlation between the Raman enhancement and the nanoparticle size and interparticle spacing.

Biomolecular Corona Stability In Association With Plasma Cholesterol Level, Duong N. Trinh, Meda Radlinskaite, Jack Cheeseman, Gunther Kuhnle, Helen M.I. Osborn, Paula Meleady, Daniel I.R. Spencer, Marco P. Monopoli

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Biomolecular corona is spontaneously formed on the surface of nanoparticles (NPs) when they are in contact with biological fluids. It plays an important role in the colloidal stability of NPs, which is of importance for most of their medical applications and toxicity assessment. While typical studies use either blood plasma or serum from a pooled biobank, it is unclear whether differences in the media, such as cholesterol level or protein concentration, might affect the NP colloidal stability and corona composition. In this study, the silica corona was prepared at particularly low plasma concentrations (3%, v/v–1.98 mg/mL) to identify the critical …

Data Driven Bayesian Network To Predict Critical Alarm, Joseph Mietkiewicz, Anders Madsen

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Modern industrial plants rely on alarm systems to ensure their safe and effective functioning. Alarms give the operator knowledge about the current state of the industrial plants. Trip alarms indicating a trip event indicate the shutdown of systems. Trip events in power plants can be costly and critical for the running of the operation.This paper demonstrates how trips events based on an alarm log from an offshore gas production can be reliably predicted using a Bayesian network. If a trip event is reliably predicted and the main cause of it is identified, it will allow the operator to prevent it. …