NUI Maynooth Eprint Archive
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Convolution Network with Custom Loss Function for the Denoising of Low SNR Raman Spectra
No full textRaman spectroscopy is a powerful diagnostic tool in biomedical science, whereby different disease groups can be classified based on subtle differences in the cell or tissue spectra. A key component in the classification of Raman spectra is the application of multi-variate statistical models. However, Raman scattering is a weak process, resulting in a trade-off between acquisition times and
signal-to-noise ratios, which has limited its more widespread adoption as a clinical tool. Typically
denoising is applied to the Raman spectrum from a biological sample to improve the signal-to noise ratio before application of statistical modeling. A popular method for performing this is Savitsky–Golay filtering. Such an algorithm is difficult to tailor so that it can strike a balance between denoising and excessive smoothing of spectral peaks, the characteristics of which are critically
important for classification purposes. In this paper, we demonstrate how Convolutional Neural Networks may be enhanced with a non-standard loss function in order to improve the overall signal to-noise ratio of spectra while limiting corruption of the spectral peaks. Simulated Raman spectra and experimental data are used to train and evaluate the performance of the algorithm in terms of the signal to noise ratio and peak fidelity. The proposed method is demonstrated to effectively smooth noise while preserving spectral features in low intensity spectra which is advantageous when compared with Savitzky–Golay filtering. For low intensity spectra the proposed algorithm was
shown to improve the signal to noise ratios by up to 100% in terms of both local and overall signal to noise ratios, indicating that this method would be most suitable for low light or high throughput applications
An Inexpensive Portable Self-Reference Module for Digital Holographic Microscopy
No full textThis paper describes a novel optical system that can be integrated to the image port of an existing brightfield microscope in order to enhance the microscope with the features of digital holographic microscopy. The proposed system is modular and portable. It is relatively inexpensive and robust to vibrations due to its compact design. An additional benefit is that the system does not need to undergo path-length realignment if the sample is changed, unlike several other architectures. The module is based on a square in-line Mach–Zender architecture but achieves the off-axis condition using two sets of wedge prism pairs. This design offers a significant advantage over competing Mach–Zender nearly common-path modules in terms of path length matching of object and reference wavefields for the case of low-temporal coherence sources, which are preferable for low noise phase imaging. An additional advantage that the proposed system has when compared with similar modules is the facility to continuously vary the tilt angles of the object and reference wavefields that are incident on the sensor, which enables the module to be readily adapted to any given microscope and camera. We provide a detailed overview of the module design and construction. Experimental results are demonstrated on a micro-lens array as well as buccal epithelial cells. We also provide a detailed discussion on the relationship between the proposed self-reference module and related common-path and nearly common-path holographic modules that have previously been proposed in the literature
Stochastic Geometry-Based Analysis of LEO Satellite Communication Systems
No full text— This letter studies the performance of a low-earth-orbit (LEO) satellite communication system where the locations of the LEO satellites are modeled as a binomial point
process (BPP) on a spherical surface. In particular, we study the user coverage probability for a scenario where satellite gateways (GWs) are deployed on the ground to act as a relay between the users and the LEO satellites. We use tools from stochastic geometry to derive the coverage probability for the described setup assuming that LEO satellites are placed at n different altitudes, given that the number of satellites at each altitude ak is Nk where 1 ≤ k ≤ n. To resemble practical scenarios where satellite communication can play an important role in coverage enhancement, we compare the performance of the considered setup with a scenario where the users are solely covered by a fiber-connected base station (referred to as anchored base station or ABS in the rest of the letter) at a relatively far distance, which is a common challenge in rural and remote areas. Using numerical results, we show the
performance gain, in terms of coverage probability, at rural
and remote areas when LEO satellite communication systems
are adopted. Finally, we draw multiple system-level insights
regarding the density of GWs required to outperform the ABS,
as well as the number of LEO satellites and their altitudes
How Volunteerism Enhances Workplace Skills
No full textThe idea of fostering learning through service is surprisingly
controversial. Employers should plan carefull
Covid-19 and Families With Parental Mental Illness: Crisis and Opportunity
No full textThe COVID-19 emergency has affected us all, but not equally. Families where parents have mental illness (PMI) are potentially at increased risk, but little is known about how
they or their support services managed under lockdown/restrictions. We harnessed our existing partnerships with adult and child mental health services in the Republic of Ireland (RoI) and Northern Ireland (NI) to investigate the qualitative experiences of service users and families in coping during the first COVID-19 lockdown (March–May 2020), and how services were supporting them. Semi-structured phone/online interviews were conducted with 22 clinicians/managers (12 from RoI; 10 from NI) who provided information from their caseloads (∼155 families with PMI). Sixteen family members (10 from RoI, 6 from NI) were also interviewed. Data were analysed using standard
thematic analysis. Sixty percent of families reported improved mental health, primarily due to respite from daily stresses and the “normalisation” of mental distress in the
general population. Approximately 30%, typically with more severe/enduring mental illness, reported additional challenges, and mental distress including: unmanageable
child behaviours; fear of relapse/hospitalisation; financial difficulties; absence of child care; and a lack of routines. Service provision varied considerably across regions. The
experiences within this case study highlight unique opportunities to address the multiple stresses of pre-emergency daily living. We also highlight how mental health services and governments might become more “pandemic ready” to more effectively support vulnerable families, including addressing service overload issues, optimising the use of
digital technologies, and providing in-person contact and social supports where require
Proteomic profiling of the interface between the stomach wall and the pancreas in dystrophinopathy
No full textThe neuromuscular disorder Duchenne muscular dystrophy is a multi-systemic disease that is caused by a primary abnormality in the X-chromosomal Dmd gene. Although progressive skeletal muscle wasting and cardio-respiratory complications are the most serious symptoms that
are directly linked to the almost complete loss of the membrane cytoskeletal protein dystrophin,
dystrophic patients also suffer from gastrointestinal dysfunction. In order to determine whether proteome-wide changes potentially occur in the gastrointestinal system due to dystrophin deficiency, total tissue extracts from the interface between the stomach wall and the pancreas of
the mdx-4cv model of dystrophinopathy were analysed by mass spectrometry. Following the proteomic establishment of both smooth muscle markers of the gastrointestinal system and key
enzymes of the pancreas, core members of the dystrophin-glycoprotein complex, including dystrophin, dystroglycans, sarcoglycans, dystrobrevins and syntrophins were identified in this tissue preparation. Comparative proteomics revealed a drastic reduction in dystrophin, sarcoglycan, dystroglycan, laminin, titin and filamin suggesting loss of cytoskeletal integrity in mdx-4cv smooth muscles. A concomitant increase in various mitochondrial enzymesisindicative of metabolic disturbances. These findings agree with abnormal gastrointestinal function in
dystrophinopath
Characterisation of the complete mitochondrial genome of the insect-parasitic nematode Heterorhabditis bacteriophora: an idiosyncratic gene order and the presence of multiple long non-coding regions
No full textWe present here the complete mtDNA genome (mitogenome) of Heterorhabditis bacteriophora, an important biological
control agent of soil-dwelling insect pests in agriculture and horticulture. This is the first description of a mitogenome for a member of the family Heterorhabditidae. The genome contains the typical chromadorean complement of 12 protein-coding genes, 22 tRNA genes and two rRNA genes. All genes are transcribed in the same direction and have a nucleotide composition high in A and T. For the entire
genome, the nucleotide contents are 47.02% (T), 28.81% (A), 16.10% (G), 8.08% (C) and 75.83% (AT). Heterorhabditis bacteriophora has a unique, idiosyncratic gene arrangement. It differs from that of Caenorhabditis elegans in having a block of seven genes: trnQtrnF-cytb-trnL1-cox3-trnT-nad4 translocated to a position between nad3 and nad5, as well as having a change in the position of the four tRNA block gene cluster, trnC-trnM-trnD-trnG, where trnC and trnM have switched places and trnD and trnG have translocated
between nad4 and nad5 genes. The H. bacteriophora mitogenome is 18 128 bp long, and thus is ca 4 kb larger than the mitogenomes of most chromadoreans. This relatively large genome is due to the presence of five non-coding regions (NCR): NCR1 (114 bp), NCR2 (159 bp), NCR3 (498 bp), NCR4 (1917 bp) and NCR5 (2154 bp), which make up 26.7% of the genome. The NCR5 had the highest A + T content of 83.47% indicating that this region is the likely AT-rich control region. The complete 498 bp NCR3 sequence is
duplicated in NCR4 and in NCR5 (the putative AT-rich control region). Such an organisation has not been reported previously in nematode mtDNA
Proteomic profiling of bacterial and fungal induced immune priming in Galleria mellonella larvae
No full textSome insects display immunological priming as a result of elevated humoral and cellular responses which give
enhanced survival against subsequent infection. The humoral immune response of Galleria mellonella larvae
following pre-exposure to heat killed Staphylococcus aureus or Candida albicans cells was determined by quantitative mass spectrometry in order to assess the relationship between the humoral immune response and
resistance to subsequent bacterial or fungal infection. Larvae pre-exposed to heat killed S. aureus showed
increased resistance to subsequent bacterial and fungal infection. Larvae displayed an increased hemocyte
density (14.08 ± 2.14 × 106 larva− 1 (p < 0.05) compared to the PBS injected control [10.41 ± 1.67 × 106
larva− 1
]) and increased abundance of antimicrobial proteins (cecropin-D-like peptide (+22.23 fold), hdd11
(+12.61 fold) and prophenol oxidase activating enzyme 3 (+5.96 fold) in response to heat killed S. aureus.
Larvae pre-exposed to heat killed C. albicans cells were resistant to subsequent fungal infection but not bacterial
infection and showed a reduced hemocyte density (6.01 ± 1.63 × 106 larva− 1 (p < 0.01) and increased abundance of hdd11 (+32.73 fold) and moricin-like peptide C1 (+16.76 fold). While immune priming is well recognised in G. mellonella larvae the results presented here indicate distinct differences in the response of larvae
following exposure to heat killed bacterial and fungal cells
statSuma: automated selection and performance of statistical comparisons for microbiome studies
No full textThere is a reproducibility crisis in scientific studies. Some of these crises arise from incorrect application of statistical tests to data that follow inappropriate distributions, have inconsistent equivariance, or have very small sample sizes. As determining which test is most appropriate for all data in a multi-categorical study (such as comparing taxa between sites in microbiome studies), we present statsSuma, an interactive Python notebook (which can be run from any desktop computer using the Google Colaboratory web service) and does not require a user to have any programming experience. This software assesses underlying data structures in a given dataset to advise what pairwise or listwise statistical procedure would be best suited for all data. As some users may be interested in further mining specific trends, statSuma performs 5 different two-tailed pairwise tests (Student’s t-test, Welch’s t-test, Mann-Whitney U-test, Brunner-Munzel test, and a pairwise Kruskal-Wallis H-test) and advises the best test for each comparison. This software also advises whether ANOVA or a multi-categorical Kruskal-Wallis H-test is most appropriate for a given dataset and performs both procedures. A data distribution-vs-Gaussian distribution plot is produced for each taxon at each site and a variance plot between all combinations of 2 taxa at each site are produced so Gaussian tests and variance tests can be visually confirmed alongside associated statistical determinants
Synthesis and Characterization of Pyrochlore-Type Praseodymium Stannate Nanoparticles: An Effective Electrocatalyst for Detection of Nitrofurazone Drug in Biological Samples
No full textApart from perovskites, the development of different
types of pyrochlore oxides is highly focused on various electrochemical applications in recent times. Based on this, we have synthesized pyrochlore-type praseodymium stannate nanoparticles (Pr2Sn2O7 NPs) by using a coprecipitation method and further investigated by different analytical and spectroscopic techniques such as X-ray diffraction, Raman spectroscopy, field emission-scanning electron
microscopy, high resolution-transmission electron microscopy, and X-ray photoelectron spectroscopy analysis. Followed by this, we have designed a unique and novel electrochemical sensor for nitrofurazone detection, by modifying the glassy carbon electrode (GCE) with the
prepared Pr2Sn2O7 NPs. For that, the electrochemical experiments were performed by using cyclic voltammetry and differential pulse voltammetry techniques. The Pr2Sn2O7 NPs modified GCE exhibits high sensitivity (2.11 μA μM−1 cm−2
), selectivity, dynamic linear ranges (0.01−24 μM and 32−332 μM), and lower detection limit (4 nM). Furthermore, the Pr2Sn2O7 NPs demonstrated promising real sample analysis with good recovery results in biological samples (human urine and blood serum) which showed better results than the noble metal catalysts. Based on these results, the present work gives clear evidence that the pyrochlore oxides are
highly suitable electrode materials for performing outstanding catalytic activity toward electrochemical sensors