NUI Maynooth Eprint Archive
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Automated Raman Micro-Spectroscopy of Epithelial Cell Nuclei for High-Throughput Classification
No full textRaman micro-spectroscopy is a powerful technique for the identification and classification
of cancer cells and tissues. In recent years, the application of Raman spectroscopy to detect bladder,
cervical, and oral cytological samples has been reported to have an accuracy greater than that of
standard pathology. However, despite being entirely non-invasive and relatively inexpensive, the
slow recording time, and lack of reproducibility have prevented the clinical adoption of the technology.
Here, we present an automated Raman cytology system that can facilitate high-throughput screening
and improve reproducibility. The proposed system is designed to be integrated directly into the
standard pathology clinic, taking into account their methodologies and consumables. The system
employs image processing algorithms and integrated hardware/software architectures in order to
achieve automation and is tested using the ThinPrep standard, including the use of glass slides, and
a number of bladder cancer cell lines. The entire automation process is implemented, using the open
source Micro-Manager platform and is made freely available. We believe that this code can be readily
integrated into existing commercial Raman micro-spectrometers
Genome sequence of the English grain aphid, Sitobion avenae and its endosymbiont Buchnera aphidicola
No full textThe English grain aphid, Sitobion avenae, is a major agricultural pest of wheat, barley and oats, and one of the principal vectors of barley yellow dwarf virus leading to significant reductions in grain yield, annually. Emerging resistance to and increasing regulation of insecticides has resulted in limited options for their control. Using PacBio HiFi data, we have produced a high-quality draft assembly of the S. avenae genome; generating a primary assembly with a total assembly size of 475.7 Mb, and an alternate assembly with a total assembly size of 430.8 Mb. Our primary assembly was highly contiguous with only 326 contigs and a contig N50 of 15.95 Mb. Assembly completeness was estimated at 97.7% using BUSCO analysis and 31,007 and 29,037 protein-coding genes were predicted from the primary and alternate assemblies, respectively. This assembly, which is to our knowledge the first for an insecticide resistant clonal lineage of English grain aphid, will provide novel insight into the molecular and mechanistic determinants of resistance and will facilitate future research into mechanisms of viral transmission and aphid behavior
A post-processing technique for addressing ‘irregular frequencies’ and other issues in the results from BEM solvers
No full textWithin the wave energy community, hydrodynamic coefficients obtained from boundary element methods (BEMs) are commonly used to predict the behaviour
of wave energy converters (WECs) in response to incident
waves. A number of commercially-available BEM solvers
exist, with a number of open-source alternatives also
available. While open-source solvers have an obvious cost
advantage compared to their commercial counterparts, the
results from such solvers are often susceptible to so-called
‘irregular frequencies’, which arise from ill-conditioning
in boundary integral problems, and result in large under or over-estimation of hydrodynamic parameters at certain excitation frequencies. Furthermore, while commercial
solvers may employ techniques to suppress the effects
of irregular frequencies, such solvers may, under certain
circumstances, exhibit other problems in the hydrodynamic
results produced. For example, the results obtained for the
added mass at high frequencies, and the infinite frequency
added mass for a water column, may be incorrect. The
current work first focusses on an approach to remove the
effects of irregular frequencies from the results obtained
for the radiation damping of a particular WEC geometry.
The use of radiation damping results to obtain values for
the added mass, through the use of the Ogilvie relations,
is then considered. The technique described herein has
been implemented in BEMRosetta, an open-source tool
which allows a user to view the results from various BEM
solvers, as well as converting input files between solvers.
The results presented in this paper have been obtained
using the BEMRosetta implementation
A realistic nonlinear benchmark problem for wave energy controllers - COERbuoy1
No full textThis paper presents a realistic, nonlinear numerical open-source benchmark model for Wave Energy
Converters (WECs) to facilitate the effective comparison
of WEC control strategies. The model represents a point absorber WEC, and was developed in cooperation with
CorPower Ocean to obtain a realistic control problem
(COERbuoy1), constituting real device characteristics. At
the same time, the model is sufficiently representative
of the broad class of point absorbers to allow universal
findings.
The hydrodynamic forces are calculated using instantaneous linearisation of the hydrodynamic parameters for
body-exact wave-body interactions in two degrees of freedom. Additionally, the model includes nonlinear effects
such as viscous drag, static and dynamic friction, a power take-off using an electric generator with saturation effects,
and a nonlinear spring opposing the hydrostatic stiffness.
The benchmark problem consists of three stages: Testing
the control performance in (1) regular and (2) irregular
waves and by (3) using small modifications in the model
to challenge the controller’s ability to handle modelling
errors. The benchmark scoring system evaluates the controller on the basis of the absorbed power and adherence
to motion and power constraints.
The system is tested with an illustrative constant damping
power-take-off, showing reasonably good results in power
absorption for low period cases, but poor results for long
wave periods
Open Geodemographics: Classification of Small Areas, Ireland 2016
No full textGeodemographics is a tool to summarize the characteristics of spatial units based on
socio-economic data. It has been used over several decades to classify the characteristics of areas based on the similarities in such data, generally working by identifying
groups or clusters of similar areas. It has seen use in the academic and private sectors
but mostly became popular by 1980s for market research purposes – this rise in use
drew attention to many issues that needed to be addressed in the literature. The
purpose of this paper is to provide a geodemographic classification for the
smallest scale administrative units in Ireland (Small Areas) based on the latest
2016 census population data. A further aim is to support reproducible research
by following the methodology of an earlier study for the 2011 Census and to
bring up the opportunity to compare the cluster results between the 2011 and
2016 census data. The comparison output provides useful insights for policy
discussions in the Irish context. One of the other focal points of this study is to
bring some clarity regarding some criticisms of geodemographics from an
academic perspective. The paper also argues for the use of open data, open
source software and supports open analysis
An embodied distress: African asylum seekers' experiences of mental health difficulties while awaiting an asylum outcome in Ireland.
No full textThe mental health of asylum seekers has attracted significant interest and examination. Quantitative studies have consistently
indicated that asylum seekers experience mental distress at a higher rate than both host populations and their
refugee counterparts. Qualitative insight into asylum seekers’ embodied experience of mental distress is limited. This
qualitative narrative study aimed to explore African asylum seekers’ everyday embodied experiences of mental distress.
Sixteen semi-structured one-to-one interviews were conducted with African asylum seekers who had experienced
mental distress and were receiving mental health care services in Ireland. Narrative data were analysed using a holistic
analysis framework of narrative form and content. Participants described their everyday endurance of relentless rumination,
shame, self-loathing, anger, and mistrust, and of becoming demoralised and hopeless. Study findings indicate that
asylum seekers’ mental distress interweaves the physical, psychological, emotional, and social realms, thus impacting
on the whole of their being. Consequences for asylum seekers include feeling anaesthetised, having a severely
diminished capacity to connect and interact with their external surroundings and other people, and, for some, efforts
to end their life.
Examinations of, and responses to, asylum seekers’ mental distress must delve beyond the confines of diagnostic
categorisations and codifications of symptomology. To achieve heightened understanding and efficacious interventions,
we must empathetically listen and engage with asylum seekers’ narratives of distress and the socio-cultural and sociopolitical
context they inhabit
Pathways between types of crime and criminal social identity: A network approach
No full textCriminal social identity (CSI) is a factor for criminal behaviour. CSI should therefore be a target of interventive
strategies aiming to reduce the risk of re-offending. To date, there is limited knowledge on how CSI is expressed
among individuals with different criminal histories, undermining the efforts to develop and target appropriate
rehabilitative strategies. In the present investigation, network analysis was applied to model the pattern of relationships between different crime types and CSI. In total, eight networks were estimated among prisoners from
the USA (n = 772), UK (n = 638), and Poland (n = 1591).
Results show different pathways between CSI scores and crime types across samples. CSI formed positive links
with acquisitive crime among U.S. and Polish male prisoners. Homicide formed negative associations with CSI
among male prisoners from the USA and Poland as well as U.S. female prisoners. Crimes for which an individual
is likely to face social stigmatization were positively associated with CSI in U.S. females and UK males. It is
anticipated that from these results, we will be able to build a better understanding of the structural relationships
between different types of criminal activity and CSI, subsequently leading to more effective rehabilitation
strategies
A Qualitative Study of Child and Adolescent Mental Health during the COVID-19 Pandemic in Ireland
No full textMitigating the adverse physical health risks associated with COVID-19 has been a priority of public health incentives. Less attention has been placed on understanding the psychological factors related to the global pandemic, especially among vulnerable populations. This qualitative study sought to understand the experiences of children and adolescents during COVID-19. This study interviewed 48 families during the COVID-19 pandemic restrictions, and a national lockdown, to understand its impacts. The study used an Interpretative Phenomenological Analysis (IPA) methodology. Parents and children discussed the negative impact of the restrictions on young people’s wellbeing. Children and adolescents experienced adverse mental health effects, including feelings of social isolation, depression, anxiety, and increases in maladaptive behaviour. Families with children with Autism Spectrum Disorders reported increased mental health difficulties during this period mostly due to changes to routine. The findings highlight the impact of severe restrictions on vulnerable populations’ wellbeing and mental health outcomes, including children, adolescents, and those with Autism spectrum disorder (ASD)
Draíocht Dara - This is an Irish language publication for teachers to use to aid them with teaching children between 10 and 14 the Irish language.
No full textThis is an Irish language publication for teachers to use to aid them with teaching children between 10 and 14 the Irish language. It uses outdoor learning activities and nature-based activities to help children to learn Irish in a fun and easy way. Activities are ready to use. Funded by An Chomhairle um Oideachas Gaeltachta agus Gaelscolaíochta. This publication highlights the intrinsic link between the Irish language and nature. SDGs embedded in publication
Brand Royal: Meghan Markle, feuding families, and disruptive duchessing in Brexit era Britain
No full textFocusing on mainstream and tabloid news reporting and ancillary texts, this article analyses the media presentation of Meghan Markle’s intersectional identities through a rhetoric of the feuding famous family. We argue that the media discourse centred on family conflict and domestic drama used to characterise Markle’s position as a royal during the Brexit era both surfaces and suppresses the significance of her existential challenge to the normative racial, class, national and gendered attributes associated with British royalty. That discourse also obfuscates and trivializes the power struggle over the significant economic capital and political “soft power” associated with the British Royal Family bran