Irish Universities
Not a member yet
78452 research outputs found
Sort by
Conserved redox-dependent DNA binding of ROXY glutaredoxins with TGA transcription factors
No full textThe Arabidopsis thaliana CC‐type glutaredoxin (GRX) ROXY1 and the bZIP TGA transcription factor (TF) PERIANTHIA (PAN) interact in the nucleus and together regulate petal development. The CC‐type GRXs exist exclusively in land plants, and in contrast to the ubiquitously occurring CPYC and CGFS GRX classes, only the CC‐type GRXs expanded strongly during land plant evolution. Phylogenetic analyses show that TGA TFs evolved before the CC‐type GRXs in charophycean algae. MpROXY1/2 and MpTGA were isolated from the liverwort Marchantia polymorpha to analyze regulatory ROXY/TGA interactions in a basal land plant. Homologous and heterologous protein interaction studies demonstrate that nuclear ROXY/TGA interactions are conserved since the occurrence of CC‐type GRXs in bryophytes and mediated by a conserved ROXY C‐terminus. Redox EMSA analyses show a redox‐sensitive binding of MpTGA to the cis‐regulatory as‐1‐like element. Furthermore, we demonstrate that MpTGA binds together with MpROXY1/2 to this motif under reducing conditions, whereas this interaction is not observed under oxidizing conditions. Remarkably, heterologous complementation studies reveal a strongly conserved land plant ROXY activity, suggesting an ancestral role for CC‐type GRXs in modulating the activities of TGA TFs. Super‐resolution microscopy experiments detected a strong colocalization of ROXY1 with the active form of the RNA polymerase II in the nucleus. Together, these data shed new light on the function of ROXYs and TGA TFs and the evolution of redox‐sensitive transcription regulation processes, which likely contributed to adapt land plants to novel terrestrial habitats
Safety of exercise training in multiple sclerosis: a protocol for an updated systematic review and meta-analysis
No full textBackground: There has been an exponential growth in the number of clinical research studies regarding exercise training in multiple sclerosis, and literature reviews and meta-analyses have documented the many benefits of exercise training. This research further requires careful review for documenting the safety of exercise training in multiple sclerosis, as clarity on safety represents a major hurdle in the clinical prescription of exercise behaviour. Objectives: To enhance understanding of the feasibility of exercise in multiple sclerosis, we (1) provide a protocol of a systematic review and meta-analysis that summarises rates and risks of clinical relapse, adverse events (i.e., an unfavourable outcome that occurs during the intervention delivery time period), and serious adverse events (i.e., an untoward occurrence that results in death or is life threatening, requires hospitalisation, or results in disability during the intervention delivery time period), as well as retention, adherence, and compliance, from randomised controlled trials of exercise training in persons with multiple sclerosis; and (2) identify moderators of relapse, adverse events, and serious adverse event rates. Methods: Eight field-relevant databases will be searched electronically. Studies that involve a randomised controlled trial of exercise training (with non-exercise, non-pharmacological, comparator), report on safety outcomes, and include adults with multiple sclerosis will be included. Rates and relative risks of the three primary outcomes (relapse, adverse event, and serious adverse event) will be calculated and reported each with standard error and 95% confidence interval. Random-effects meta-analysis will estimate mean population relative risk for outcomes. Potential sources of variability, including participant characteristics, features of the exercise stimulus, and comparison condition, will be examined with random-effects meta regression with maximum likelihood estimation. Discussion: The results from this systematic review and meta-analysis will inform and guide healthcare practitioners, researchers, and policymakers on the safety of exercise training in persons with multiple sclerosis. Where possible, we will identify the impact of exercise type, exercise delivery style, participant disability level, and the prescription of exercise guidelines, on the safety of exercise training. The result will identify critical information on the safety of exercise in persons with multiple sclerosis, while also identifying gaps in research and setting priorities for future enquirie
The role of Eya1 in otic neurogenesis in Xenopus laevis
No full textCranial placodes are specialized areas of thickening of the early embryonic ectoderm at the head and give rise to sensory organs and ganglia. In vertebrates, the inner ear is derived from one of these placodes, the otic placode. All cranial placodes arise from a common region of origin, the preplacodal ectoderm (PPE), determined by the expression of Eya1 and Six1 genes. Eya1 and Six1 were previously shown to play a crucial role both for the maintenance of proliferating progenitors and for neuronal differentiation in cranial placodes including the otic placode, but the mechanisms are still obscure.
The main aim of this study is to elucidate the role of Eya1 during neurogenesis in the developing inner ear (otic vesicle) of Xenopus laevis with a particular focus on the role of Eya1 for cell proliferation, the formation of progenitors and differentiating neurons as well as for the distribution of cell polarity proteins during otic vesicle development.
Since otic neurogenesis in Xenopus has not yet been studied in any detail, the first part of this study uses immunostaining and confocal microscopy to provide a detailed description of otic neurogenesis in Xenopus. It is shown that the otic vesicle of Xenopus comprises a pseudostratified epithelium with apicobasal polarity (apical enrichment of Par3, aPKC, phosphorylated Myosin light chain, N-cadherin) and interkinetic nuclear migration (apical localization of mitotic, pH3-positive cells). A Sox3-immunopositive neurosensory area in the ventromedial otic vesicle gives rise to neuroblasts, which delaminate through breaches in the basal lamina between stages 27 and 39. Delaminated cells congregate to form the vestibulocochlear ganglion, whose peripheral cells continue to proliferate (incorporate EdU), while central cells differentiate into Islet1/2-immunopositive neurons (stage 29) and send out neurites (stage 31). The central part of the neurosensory area retains Sox3 but stops proliferating from stage 33, forming the first sensory areas (utricular/saccular maculae).
Since only the expression of Eya1 mRNA but not of Eya1 protein has been previously analysed, the second part of the study then provides a detailed analysis of the subcellular distribution of Eya1 protein during development of the otic vesicle and its distribution in relation to markers of proliferation, progenitors and differentiating neurons using a Xenopus-specific Eya1 antibody, double-immunostaining with other antibodies and confocal microscopy. Eya1 protein localizes to both nuclei and cytoplasm in the otic epithelium, with levels of nuclear Eya1 declining in differentiating (Islet1/2+) ganglion neurons and in the developing sensory areas. The distribution of Eya1 in other cranial placodes throughout embryonic development is also characterized.
Finally, in the third part of the study Eya1 and Six1 gain and loss of function experiments demonstrated that Eya1 and Six1 are essential for cell proliferation, progenitor maintenance and neuronal differentiation in the epithelium of the developing otic vesicle. Eya1 is also required to establish a proper apical distribution of cell polarity proteins and of N-cadherin in the otic epithelium. This suggests that Eya1 plays an important role for maintenance of epithelial cells with apicobasal polarity during otic neurogenesis. Further studies are needed to elucidate whether and how this role is linked to Eya1’s function in progenitor proliferation and neuronal differentiation
Okra in translation: Asylum seekers, food, and integration
No full textThis article explores the theme of food translation, based on research conducted in Italy in 2018 with a group of asylum seekers from different West African countries. It concentrates on a community gardening project revolving around the cultivation of okra: a vegetable that is a staple in many African cuisines, but not very popular in Italy, which provided the occasion for the participants to communicate their home foodways.As something that is linked to the most basic human needs, and yet bears high cultural significance, food can be used as a lens to explore the shifting relationship between language and other embodied forms of meaning. Translating food means engaging with a complex interplay of language, sensory experiences, and socio-cultural norms. Drawing from recent semiotically-oriented developments in translation studies as well as applied linguistics, and the semiotics of food, I analyze key participants involvement with the project.This project has received funding from the Irish Research Council and from the European
Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
grant agreement No. 713279. This publication reflects only the author’s views, and the IRC
or the REA are not responsible for any use that may be made of the information it contains
Toward distributed, global, deep learning using IoT devices
No full textDeep learning (DL) using large scale, high-quality IoT datasets can be computationally expensive. Utilizing such datasets to produce a problem-solving model within a reasonable time frame requires a scalable distributed training platform/system. We present a novel approach where to train one DL model on the hardware of thousands of mid-sized IoT devices across the world, rather than the use of GPU cluster available within a data center. We analyze the scalability and model convergence of the subsequently generated model, identify three bottlenecks that are: high computational operations, time consuming dataset loading I/O, and the slow exchange of model gradients. To highlight research challenges for globally distributed DL training and classification, we consider a case study from the video data processing domain. A need for a two-step deep compression method, which increases the training speed and scalability of DL training processing, is also outlined. Our initial experimental validation shows that the proposed method is able to improve the tolerance of the distributed training process to varying internet bandwidth, latency, and Quality of Service metrics.This publication has emanated from research supported by grants from the European Union\u27s Horizon 2020 research and innovation program under grant agreement number 847577 (SMART 4.0 Marie Sklodowska-Curie actions COFUND) and from Science Foundation Ireland (SFI) under Grants SFI/16/RC/3918 and SFI/12/RC/2289_P2 cofunded by the European Regional Development Fund.Peer reviewe
Environmental performance of bioplastic packaging on fresh food produce: A consequential life cycle assessment
No full textPolylactic acid (PLA) is a compostable bio-based plastic that can be used for food packaging, potentially increasing separation of (packaged) food waste for targeted, more circular organic waste management via anaerobic digestion, industrial composting, or (in the future) insect protein meal feed production. Consequential life cycle assessment (LCA) was undertaken to rigorously assess the environmental impact of displacing petro-chemical plastic packaging of fresh fruit and vegetables with PLA. Eight end-of-life scenarios of bioplastic packaging were evaluated against a business-as-usual petrochemical packaging scenario, expanding LCA boundaries to include end-of-life impacts of fruit and vegetable food waste within a UK context. PLA production has a higher impact compared with petrochemical plastic production across many impact categories, but diversion of PLA-packaged food waste to organic recycling can compensate for this, improving the overall environmental performance of bioplastic packaging scenarios. Future diversion of organic waste streams to insect feed (following regulatory change) would lead to the best environmental outcomes, followed by anaerobic
digestion. Impact categories ameliorated in bioplastic scenarios include human health effects, climate change, freshwater eutrophication, ionising radiation, photochemical ozone formation, resource use energy carriers, and respiratory inorganics. On the other hand, petrochemical plastic scenarios generate smaller burdens for acidification, marine and terrestrial eutrophication, ozone depletion, and water scarcity. Sensitivity analyses indicate high improvement potential for bioplastic scenarios if the energy efficiency of PLA production can be increased, or if globalised production shifts to industrialised countries with cleaner energy mixes (that currently import most of their plastics). Whilst end-of-life management of the fruit and vegetable food waste has a considerable influence on environmental outcomes, plastic packaging represents a surprisingly large share of the dry matter material flow (about 25%) in fresh produce waste streams. Therefore, it is imperative that future LCA studies of food packaging account for both packaging and (diverted) food waste end-of-life flows
Sentence-Level Event Classification in Unstructured Texts
No full textThe ability to correctly classify sentences that describe events is an important task for many natural language applications such as Question Answering (QA) and Text Summarisation. In this paper, we treat event detection as a sentence level text classification problem. We compare the performance of two approaches to this task: a Support Vector Machine (SVM) classifier and a Language Modeling (LM) approach. We also investigate a rule-based method that uses hand-crafted lists of ‘trigger’ terms derived from WordNet. We use two datasets in our experiments and test each approach using six different event types, i.e, Die, Attack, Injure, Meet, Transport and Charge-Indict. Our experimental results indicate that although the trained SVM classifier consistently outperforms the language modeling approach, our rule-based system marginally outperforms the trained SVM classifier on three of our six event types. We also observe that overall performance is greatly affected by the type of corpus used to train the algorithms. Specifically, we have found that a homogeneous training corpus that contains many instances of a specific event type (i.e., Die events in the recent Iraqi war) produces a poorer performing classifier than one trained on a heterogeneous dataset containing more diverse instances of the event (i.e.,Die events in many different settings, for example, traffic accidents, natural disasters etc.). Our heterogeneous dataset is provided by the ACE (Automatic Content Extraction) initiative, while our novel homogeneous dataset consists of news articles and annotated Die events from the Iraq Body Count (IBC) database. Overall, our results show that the techniques presented here are effective solutions to the event classification task described in this paper, where F1 scores of over 90% are achieved.Irish Research Council for Science, Engineering and TechnologyTechnical report numbers ucd-csi-2008-06 and ucd-csi-2008-07 are identical; only one copy has been retained
GEVA - Grammatical Evolution in Java (v1.0)
No full textGEVA is an open source implementation of Grammatical Evolution in Java developed at UCD’s Natural Computing Research & Applications group. As well as providing the characteristic genotype-phenotype mapper of GE a search algorithm engine and a simple GUI are also provided. A number of sample problems and tutorials on how to use and adapt GEVA have been developed.Science Foundation IrelandUniversity College Dubli
What are the drivers of beef sensory quality using metadata of intramuscular connective tissue, fatty acids and muscle fiber characteristics?
No full textThe aim of this integrative study was to investigate the relationships between biochemical traits (total, insoluble and soluble collagens (TCol, ICol, SCol), cross-links (CLs), proteoglycans (TPGs), proportion of fiber types, total lipids (TLips), main fatty acids (FAs) families, the n-6/n-3 polyunsaturated FA (n-6/n-3PUFA) ratio and the sensory attributes scores (tenderness, juiciness, flavor) of two muscles from beef: Rectus abdominis (RA) and Longissimus thoracis (LT). For robust analysis, a database was prepared using samples from three studies from animals raised under different production systems. The analyses were performed either on each study separately or on pooled data per muscle after removing as many experimental effects as possible in each study. The CLs (across the muscles and studies) and, to a lower extent, type IIA muscle fibers (mainly for RA muscles), saturated FAs (SFAs), monounsaturated FAs (MUFAs) (for the LT muscles) were the components the most frequently associated with tenderness. The CLs, type IIA muscle fibers (mainly for the RA muscles), TLips, SFAs, MUFAs, conjugated linoleic acids (CLAs) and n-6/n-3 PUFA ratio (mainly for the LT muscles) were the components the most associated with juiciness. The TLips and CLAs (across the muscles and studies), SFAs, MUFAs (mainly for the LT muscles), CLs (mainly for the RA muscles) and TPGs (mainly for the LT muscles) were the components the most associated with flavor liking. The CLs, CLAs, TLips, SFAs, MUFAs, n-6/n-3 PUFA ratio, type IIA and I muscle fibers were the components the most frequently associated with the 3 sensory scores taken together. The SCol, TPGs and type IIX+B muscle fibers were little associated with the sensory scores taken together. The TCol, ICol and PUFAs were components the least associated with sensory scores. The data of this integrative study highlighted for the first time that the CLs were negatively involved in the determination of the three sensory traits mainly in the RA muscle. The muscle fibers in this integrative study had a weak impact on the variations in beef sensory traits. The type IIA and IIX+B muscle fibers were respectively negatively and positively associated with tenderness, negatively associated with juiciness and flavor. The type I muscle fibers were overall positively associated with juiciness and flavor and negatively or positively with tenderness and these associations were muscle and study-dependent. Overall, the TLips and FAs were positively associated with the sensory scores and the n-6/n-3 PUFA ratio was negatively associated with them.ADEM
Solubility of carbon dioxide in renneted casein matrices: Effect of pH, salt, temperature, partial pressure, and moisture to protein ratio
No full textThe solubility of carbon dioxide (CO2) in the moisture and protein components of cheese matrices and the influence of changing pH, salt and temperature levels remains unclear. In this study, model casein matrices were prepared, by renneting of micellar casein concentrate (MCC), with modulation of salt and pH levels by adding salt and glucono delta-lactone, respectively, to the MCC solutions prior to renneting. Different moisture-to-protein levels were achieved by freeze-drying, incubation of samples at different relative humidities, or by applying varying pressures during gel manufacture. The CO2 solubility of samples decreased linearly with both increasing temperature and salt-in-moisture content, whereas solubility of CO2 increased with increasing pH. A non-linear relationship was observed between CO2 solubility and the moisture-to-protein ratio of experimental samples. Overall, such knowledge may be applied to improve the quality and consistency of eye-type cheese, and in particular to avoid development of undesirable slits and cracks