Neonatal Seizure Detection using Convolutional Neural Networks

This study presents a novel end-to-end architecture that learns hierarchical representations from raw EEG data using fully convolutional deep neural networks for the task of neonatal seizure detection. The deep neural network acts as both feature extractor and classifier, allowing for end-to-end optimization of the seizure detector. The designed system is evaluated on a large dataset of continuous unedited multi-channel neonatal EEG totaling 835 hours and comprising of 1389 seizures. The proposed deep architecture, with sample-level filters, achieves an accuracy that is comparable to the state-of-the-art SVM-based neonatal seizure detector, which operates on a set of carefully designed hand-crafted features. The fully convolutional architecture allows for the localization of EEG waveforms and patterns that result in high seizure probabilities for further clinical examination.Comment: IEEE International Workshop on Machine Learning for Signal Processin

Whose voices? Patient and public involvement in clinical commissioning

AIM: This paper aims to explore patient and public representation in a NHS clinical commissioning group and how this is experienced by staff and lay members involved. BACKGROUND: Patient and public involvement is believed to foster greater public representativeness in the development and delivery of health care services. However, there is widespread debate about what representation is or what it should be. Questions arise about the different constructions of representation and the representativeness of patients and the public in decision-making structures and processes. DESIGN: Ethnographic, two-phase study involving twenty-four observations across two types of clinical commissioning group meetings with patient and public involvement, fourteen follow-up interviews with NHS staff and lay members, and a focus group with five lay members. RESULTS: Perceptions of what constitutes legitimate representativeness varied between respondents, ranging from representing an individual patient experience to reaching large numbers of people. Consistent with previous studies, there was a lack of clarity about the role of lay members in the work of the clinical commissioning group. CONCLUSIONS: Unlike previous studies, it was lay members, not staff, who raised concerns about their representativeness and legitimacy. Although the clinical commissioning group provides resources to support patient and public involvement, there continues to be a lack of clarity about roles and scope for impact. Lay members are still some way from constituting a powerful voice at the table

Protein-DNA charge transport: Redox activation of a DNA repair protein by guanine radical

DNA charge transport (CT) chemistry provides a route to carry out oxidative DNA damage from a distance in a reaction that is sensitive to DNA mismatches and lesions. Here, DNA-mediated CT also leads to oxidation of a DNA-bound base excision repair enzyme, MutY. DNA-bound Ru(III), generated through a flash/quench technique, is found to promote oxidation of the [4Fe-4S](2+) cluster of MutY to [4Fe-4S](3+) and its decomposition product [3Fe-4S](1+). Flash/quench experiments monitored by EPR spectroscopy reveal spectra with g = 2.08, 2.06, and 2.02, characteristic of the oxidized clusters. Transient absorption spectra of poly(dGC) and [Ru(phen)(2)dppz](3+) (dppz = dipyridophenazine), generated in situ, show an absorption characteristic of the guanine radical that is depleted in the presence of MutY with formation instead of a long-lived species with an absorption at 405 nm; we attribute this absorption also to formation of the oxidized [4Fe-4S](3+) and [3Fe4S](1+) clusters. In ruthenium-tethered DNA assemblies, oxidative damage to the 5'-G of a 5'-GG-3' doublet is generated from a distance but this irreversible damage is inhibited by MutY and instead EPR experiments reveal cluster oxidation. With ruthenium-tethered assemblies containing duplex versus single-stranded regions, MutY oxidation is found to be mediated by the DNA duplex, with guanine radical as an intermediate oxidant; guanine radical formation facilitates MutY oxidation. A model is proposed for the redox activation of DNA repair proteins through DNA CT, with guanine radicals, the first product under oxidative stress, in oxidizing the DNA-bound repair proteins, providing the signal to stimulate DNA repair

A hierarchy of power : the place of patient and public involvement in healthcare service development

Amidst statutory and non-statutory calls for effective patient and public involvement (PPI), questions continue to be raised about the impact of PPI in healthcare services. Stakeholders, policy makers, researchers, and members of the public ask in what ways and at what level PPI makes a difference. Patient experience is widely seen as an important and valuable resource to the development of healthcare services, yet there remain legitimacy issues concerning different forms of knowledge that members of the public and professionals bring to the table, and related power struggles. This paper draws on data from a qualitative study of PPI in a clinical commissioning group (CCG) in the UK. The study looked at some of the activities in which there was PPI; this involved researchers conducting observations of meetings, and interviews with staff and lay members who engaged in CCG PPI activities. This paper explores power imbalances when it comes to influencing the work of the CCG mainly between professionals and members of public, but also between different CCG staff members and between different groups of members of public. The authors conclude that a hierarchy of power exists, with some professionals and public and lay members afforded more scope for influencing healthcare service development than others—an approach which is reflected in the ways and extent to which different forms and holders of knowledge are viewed, managed, and utilized

Investigating the impact of CNN depth on neonatal seizure detection performance

This study presents a novel, deep, fully convolutional architecture which is optimized for the task of EEG-based neonatal seizure detection. Architectures of different depths were designed and tested; varying network depth impacts convolutional receptive fields and the corresponding learned feature complexity. Two deep convolutional networks are compared with a shallow SVMbased neonatal seizure detector, which relies on the extraction of hand-crafted features. On a large clinical dataset, of over 800 hours of multichannel unedited EEG, containing 1389 seizure events, the deep 11-layer architecture significantly outperforms the shallower architectures, improving the AUC90 from 82.6% to 86.8%. Combining the end-to-end deep architecture with the feature-based shallow SVM further improves the AUC90 to 87.6%. The fusion of classifiers of different depths gives greatly improved performance and reduced variability, making the combined classifier more clinically reliable

Direct Lysis RT-qPCR of SARS-CoV-2 in Cell Culture Supernatant Allows for Fast and Accurate Quantification

Studying the entire virus replication cycle of SARS-CoV-2 is essential to identify the host factors involved and treatments to combat infection. Quantification of released virions often requires lengthy procedures, whereas quantification of viral RNA in supernatant is faster and applicable to clinical isolates. Viral RNA purification is expensive in terms of time and resources, and is often unsuitable for high-throughput screening. Direct lysis protocols were explored for patient swab samples, but the lack of virus inactivation, cost, sensitivity, and accuracy is hampering their application and usefulness for in vitro studies. Here, we show a highly sensitive, accurate, fast, and cheap direct lysis RT-qPCR method for quantification of SARS-CoV-2 in culture supernatant. This method inactivates the virus and permits detection limits of 0.043 TCID(50) virus and <1.89 copy RNA template per reaction. Comparing direct lysis with RNA extraction, a mean difference of +0.69 ± 0.56 cycles was observed. Application of the method to established qPCR methods for RSV (-ve RNA), IAV (segmented -ve RNA), and BHV (dsDNA) showed wider applicability to other enveloped viruses, whereby IAV showed poorer sensitivity. This shows that accurate quantification of SARS-CoV-2 and other enveloped viruses can be achieved using direct lysis protocols, facilitating a wide range of high- and low-throughput applications

Dietary quality in a sample of adults with type 2 diabetes mellitus in Ireland; a cross-sectional case control study

BACKGROUND A number of dietary quality indices (DQIs) have been developed to assess the quality of dietary intake. Analysis of the intake of individual nutrients does not reflect the complexity of dietary behaviours and their association with health and disease. The aim of this study was to determine the dietary quality of individuals with type 2 diabetes mellitus (T2DM) using a variety of validated DQIs. METHODS In this cross-sectional analysis of 111 Caucasian adults, 65 cases with T2DM were recruited from the Diabetes Day Care Services of St. Columcille's and St. Vincent's Hospitals, Dublin, Ireland. Forty-six controls did not have T2DM and were recruited from the general population. Data from 3-day estimated diet diaries were used to calculate 4 DQIs. RESULTS Participants with T2DM had a significantly lower score for consumption of a Mediterranean dietary pattern compared to the control group, measured using the Mediterranean Diet Score (Range 0-9) and the Alternate Mediterranean Diet Score (Range 0-9) (mean ± SD) (3.4 ± 1.3 vs 4.8 ± 1.8, P < 0.001 and 3.3 ± 1.5 vs 4.2 ± 1.8, P = 0.02 respectively). Participants with T2DM also had lower dietary quality than the control population as assessed by the Healthy Diet Indicator (Range 0-9) (T2DM; 2.6 ± 2.3, control; 3.3 ± 1.1, P = 0.001). No differences between the two groups were found when dietary quality was assessed using the Alternate Healthy Eating Index. Micronutrient intake was assessed using the Micronutrient Adequacy Score (Range 0-8) and participants with T2DM had a significantly lower score than the control group (T2DM; 1.6 ± 1.4, control; 2.3 ± 1.4, P = 0.009). When individual nutrient intakes were assessed, no significant differences were observed in macronutrient intake. CONCLUSION Overall, these findings demonstrate that T2DM was associated with a lower score when dietary quality was assessed using a number of validated indices.This study was funded by Science Foundation Ireland (Grant number 08/RFP/BMT1342)

Expect the unexpected? Challenges of prospectively exploring stakeholder engagement in research

Abstract: Stakeholder engagement in research is increasingly viewed as making a major contribution to assisting impact. This paper draws on a longitudinal, prospective impact study exploring stakeholder engagement in a 3-year tobacco control research project which used stakeholder engagement in the development, testing and dissemination of its return on investment tool. The paper presents the challenges of data collection when undertaking prospective research on stakeholder engagement in health-related research. The impact study used mixed methods of data collection to explore stakeholder engagement in the target project, comprising surveys, interviews and observations of meetings and events involving stakeholders. Stakeholder engagement that actually occurred in the target project, and the data collection methods of stakeholder engagement that were actually used in the impact study, varied substantially from those intended in each case. Data collection for the impact study was dependent on the target project’s stakeholder engagement, which became substantially reduced. Modifications to data collection for the impact study were required. One of the reasons for the reduction of stakeholder engagement was linked to constraints on the target project to meet non-negotiable deadlines. Another factor was concerns about overburdening stakeholders. The knock-on effect of reduced stakeholder engagement highlighted the impact study’s lack of control over its data collection, which was related to the prospective nature of the study. The authors acknowledge that an advantage of a retrospective approach over a prospective one is researchers knowing about data availability and accessibility from the outset. However, the prospective approach of the impact study enabled insight into stakeholder engagement in real-time: how and when it occurred, the challenges, and the experiences of stakeholders and the target project researchers. While the quantity of data gathered was considerably less than anticipated, the quality of data was rich and enabled the impact study objectives to be achieved. With increasing emphasis on public engagement in research and calls for engagement to be evaluated for impact, this paper aims—by highlighting the challenges the impact study experienced—to provide some insight to future research that seeks to respond to those calls