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JMIR Res Protoc ; 11(11): e36583, 2022 Nov 11.
Article in English | MEDLINE | ID: covidwho-2118109


BACKGROUND: Chronic tinnitus is an increasing worldwide health concern, causing a significant burden to the health care system each year. The COVID-19 pandemic has seen a further increase in reported cases. For people with tinnitus, symptoms are exacerbated because of social isolation and the elevated levels of anxiety and depression caused by quarantines and lockdowns. Although it has been reported that patients with tinnitus can experience changes in cognitive capabilities, changes in adaptive learning via decision-making tasks for people with tinnitus have not yet been investigated. OBJECTIVE: In this study, we aim to assess state- and trait-related impairments in adaptive learning ability on probabilistic learning tasks among people with tinnitus. Given that performance in such tasks can be quantified through computational modeling methods using a small set of neural-informed model parameters, such approaches are promising in terms of the assessment of tinnitus severity. We will first examine baseline differences in the characterization of decision-making under uncertainty between healthy individuals and people with tinnitus in terms of differences in the parameters of computational models in a cross-sectional experiment. We will also investigate whether these computational markers, which capture characteristics of decision-making, can be used to understand the cognitive impact of tinnitus symptom fluctuations through a longitudinal experimental design. METHODS: We have developed a mobile app, AthenaCX, to deliver e-consent and baseline tinnitus and psychological assessments as well as regular ecological momentary assessments (EMAs) of perceived tinnitus loudness and a web-based aversive version of a probabilistic decision-making task, which can be triggered based on the participants' responses to the EMA surveys. Computational models will be developed to fit participants' choice data in the task, and cognitive parameters will be estimated to characterize participants' current ability to adapt learning to the change of the simulated environment at each session when the task is triggered. Linear regression analysis will be conducted to evaluate the impacts of baseline tinnitus severity on adapting decision-making performance. Repeated measures linear regression analysis will be used to examine model-derived parameters of decision-making in measuring real-time perceived tinnitus loudness fluctuations. RESULTS: Ethics approval was received in December 2020 from Dublin City University (DCUREC/2021/070). The implementation of the experiments, including both the surveys and the web-based decision-making task, has been prepared. Recruitment flyers have been shared with audiologists, and a video instruction has been created to illustrate to the participants how to participate in the experiment. We expect to finish data collection over 12 months and complete data analysis 6 months after this. The results are expected to be published in December 2023. CONCLUSIONS: We believe that EMA with context-aware triggering can facilitate a deeper understanding of the effects of tinnitus symptom severity upon decision-making processes as measured outside of the laboratory. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): PRR1-10.2196/36583.

Wellcome Open Res ; 5: 184, 2020.
Article in English | MEDLINE | ID: covidwho-808195


Background: India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India. Methods: We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. Results: The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). The local transmission and persistence of genomes A4, A2a and A3 was also observed in the studied locations. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, and are here proposed as A4-clade based on its divergence within the A cluster. Conclusions: The viral haplotypes may link their persistence to geo-climatic conditions and host response. Multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.

J Proteins Proteom ; 11(3): 159-165, 2020.
Article in English | MEDLINE | ID: covidwho-747107


In the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel coronavirus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation are key to contain the rapid spread of the virus. Towards this goal, we report a simple, sensitive and rapid method to detect the virus using a targeted mass spectrometric approach, which can directly detect the presence of virus from naso-oropharyngeal swabs. Using a multiple reaction monitoring we can detect the presence of two peptides specific to SARS-CoV-2 in a 2.3 min gradient run with 100% specificity and 90.5% sensitivity when compared to RT-PCR. Importantly, we further show that these peptides could be detected even in the patients who have recovered from the symptoms and have tested negative for the virus by RT-PCR highlighting the sensitivity of the technique. This method has the translational potential of in terms of the rapid diagnostics of symptomatic and asymptomatic COVID-19 and can augment current methods available for diagnosis of SARS-CoV-2.