Enhancing Qualitative Coding with Large Language Models: Potential and Challenges
Qualitative coding is the process of categorizing and labeling raw data to identify themes, patterns, and concepts within qualitative research. This process requires significant time, reflection, and discussion, often characterized by inherent subjectivity and uncertainty. Here, we explore the possibility to leverage large language models (LLM) to enhance the process and assist researchers with qualitative coding. LLMs, trained on extensive human-generated text, possess an architecture that renders them capable of understanding the broader context of a conversation or text. This allows them to extract patterns and meaning effectively, making them particularly useful for the accurate extraction and coding of relevant themes. In our current approach, we employed the chatGPT 3.5 Turbo API, integrating it into the qualitative coding process for data from the SWISS100 study, specifically focusing on data derived from centenarians' experiences during the Covid-19 pandemic, as well as a systematic centenarian literature review. We provide several instances illustrating how our approach can assist researchers with extracting and coding relevant themes. With data from human coders on hand, we highlight points of convergence and divergence between AI and human thematic coding in the context of these data. Moving forward, our goal is to enhance the prototype and integrate it within an LLM designed for local storage and operation (LLaMa). Our initial findings highlight the potential of AI-enhanced qualitative coding, yet they also pinpoint areas requiring attention. Based on these observations, we formulate tentative recommendations for the optimal integration of LLMs in qualitative coding research. Further evaluations using varied datasets and comparisons among different LLMs will shed more light on the question of whether and how to integrate these models into this domain.
Family Planning in Academia
PROGRAM: 16:00 - 16:30 Rebuild the Academy: Supporting academic mothers during COVID-19 and beyond with Robinson W. Fulweiler & Sarah W. Davies --- 16:30 - 17:00 Experiences with academia and family life by Siri Leknes (Norway-based) and Rachel Buckley (USA-based)--- 17:00 - 17:30 Questions and discussion
Apathy and Anhedonia in Adult and Adolescent Cannabis Users and Controls Before and During the COVID-19 Pandemic Lockdown
COVID-19 lockdown measures have caused severe disruptions to work and education and prevented people from engaging in many rewarding activities. Cannabis users may be especially vulnerable, having been previously shown to have higher levels of apathy and anhedonia than non-users. In this survey study, we measured apathy and anhedonia, before and after lockdown measures were implemented, in n = 256 adult and n = 200 adolescent cannabis users and n = 170 adult and n = 172 adolescent controls. Scores on the Apathy Evaluation Scale (AES) and Snaith-Hamilton Pleasure Scale (SHAPS) were investigated with mixed-measures ANCOVA, with factors user group, age group, and time, controlling for depression, anxiety, and other drug use. Adolescent cannabis users had significantly higher SHAPS scores before lockdown, indicative of greater anhedonia, compared with adolescent controls (P = .03, η p2 = .013). Contrastingly, adult users had significantly lower scores on both the SHAPS (P < .001, η p2 = .030) and AES (P < .001, η p2 = .048) after lockdown compared with adult controls. Scores on both scales increased during lockdown across groups, and this increase was significantly smaller for cannabis users (AES: P = .001, η p2 = .014; SHAPS: P = .01, η p2 = .008). Exploratory analyses revealed that dependent cannabis users had significantly higher scores overall (AES: P < .001, η p2 = .037; SHAPS: P < .001, η p2 = .029) and a larger increase in scores (AES: P = .04, η p2 =.010; SHAPS: P = .04, η p2 = .010), compared with non-dependent users. Our results suggest that adolescents and adults have differential associations between cannabis use as well as apathy and anhedonia. Within users, dependence may be associated with higher levels of apathy and anhedonia regardless of age and a greater increase in levels during the COVID-19 lockdown.
Monash Biomedical Imaging highlights from 2021 and looking ahead to 2022
Despite the challenges COVID-19 has continued to present, Monash Biomedical Imaging (MBI) has had another outstanding year in terms of publications and scientific output. In this webinar, Professor Gary Egan, Director of MBI, will present an overview of MBI’s achievements during 2021 and outline the biomedical imaging research programs and partnerships in 2022. His presentation will cover: • MBI operational and research achievements during 2021 • Biomedical imaging technology developments and research outcomes during 2021 • Linked laboratories and research teams at MBI • Progress on the development of a cyclotron and precision radiopharmaceutical facility at Clayton • Emerging research opportunities at the Monash Heart Hospital in cardiology and cardiovascular disease. Professor Gary Egan is Director of Monash Biomedical Imaging, Director of the ARC Centre of Excellence for Integrative Brain Function and a Distinguished Professor at the Turner Institute for Brain and Mental Health, Monash University. He is also lead investigator of the Victorian Biomedical Imaging Capability, and Deputy Director of the Australian National Imaging Facility. His substantive body of published work has made a significant impact on the neuroimaging and neuroscience fields. He has sustained success in obtaining significant grants to support his own research and the development of facilities to advance biomedical imaging.
Mutation induced infection waves in diseases like COVID-19
After more than 4 million deaths worldwide, the ongoing vaccination to conquer the COVID-19 disease is now competing with the emergence of increasingly contagious mutations, repeatedly supplanting earlier strains. Following the near-absence of historical examples of the long-time evolution of infectious diseases under similar circumstances, models are crucial to exemplify possible scenarios. Accordingly, in the present work we systematically generalize the popular susceptible-infected-recovered model to account for mutations leading to repeatedly occurring new strains, which we coarse grain based on tools from statistical mechanics to derive a model predicting the most likely outcomes. The model predicts that mutations can induce a super exponential growth of infection numbers at early times, which self-amplify to giant infection waves which are caused by a positive feedback loop between infection numbers and mutations and lead to a simultaneous infection of the majority of the population. At later stages -- if vaccination progresses too slowly -- mutations can interrupt an ongoing decrease of infection numbers and can cause infection revivals which occur as single waves or even as whole wave trains featuring alternative periods of decreasing and increasing infection numbers. Our results might be useful for discussions regarding the importance of a release of vaccine-patents to reduce the risk of mutation-induced infection revivals but also to coordinate the release of measures following a downwards trend of infection numbers.
Impact evaluation for COVID-19 non-pharmaceutical interventions: what is (un)knowable?
COVID-19 non-pharmaceutical intervention (NPI) policies have been one of the most important and contentious decisions of our time. Beyond even the "normal" inherent difficulties in impact evaluation with observational data, COVID-19 NPI policy evaluation is complicated by additional challenges related to infectious disease dynamics and lags, lack of direct observation of key outcomes, and a multiplicity of interventions occurring on an accelerated time scale. Randomized controlled trials also suffer from what is feasible and ethical to randomize as well as the sheer scale, scope, time, and resources required for an NPI trial to be informative (or at least not misinformative). In this talk, Dr. Haber will discuss the challenges in generating useful evidence for COVID-19 NPIs, the landscape of the literature, and highlight key controversies in several high profile studies over the course of the pandemic. Chasing after unknowables poses major problems for the metascience/replicability movement, institutional research science, and decision makers. If the only choices for informing an important topic are "weak study design" vs "do nothing," when is "do nothing" the best choice?
The life of a mucosalivary droplet: Lessons from synthetic breaths and sneezes
The main transmission mode of the COVID-19 disease is through virus-laden aerosols and droplets generated by expiratory events, such as breathing and sneezing. Patients with respiratory diseases are typically treated with oxygenation devices in hospitals, homes, and other settings where they increase the risk of spreading the disease to caregivers and first responders. Here, I will discuss a systematic study of aerosol and droplet dispersal through the air and their final deposition on surfaces. Through laser and fluorescent imaging techniques, we measure the volumetric spatial-temporal dynamics of droplet dispersal while varying rheological properties of the mucosaliva. We then demonstrate that a standard nose and mouth mask reduces the amount of mucosaliva dispersed by a factor of at least a hundred. Our ongoing collaborations with doctors and respiratory therapists from the Baystate Medical Hospital are developing new guidelines to help mitigate disease spread in a hospital setting.
Covid And Cognition
ONS figures suggest that at least 10% of individuals suffering COVID -19 Infection continue to experience several weeks after testing positive, and other studies report the proportions as even higher (e.g. Logue et al., 2021). One of the most prevalent reported symptoms among these “Long Covid” sufferers is cognitive dysfunction (Davis et al., 2020). However, to date the cognitive sequelae of COVID -19 are little understood. There are a number of reasons why COVID -19 infection might be associated with cognitive impairment and mental illness (e.g. Bougakov et al., 2020). In particular, increasing evidence indicates inflammation (e.g. Huang et al., 2020) and dysfunctional clotting (e.g. Taquet et al., 2021) as issues of major concern, both of which have been previously linked to a range of cognitive deficits (e.g. Vintimilla et al., 2019; Cumming et al., 2013). Indeed, evidence is beginning to emerge that cognitive issues may be widespread in the post-infection period, particularly among hospitalised and ventilated patients (e.g. Hampshire et al., 2020; Alemanno et al,. 2020). Here I shall present “Hot off the [SPSS]Press” results from a study on memory and cognition following COVID infection in a non-hospitalized cohort.
Mobilefuge: A low-cost, portable, open source, 3D-printed centrifuge that can be used for purification of saliva samples for SARS-CoV2 detection
We made a low-cost centrifuge that can be useful for carrying out low-cost LAMP based detection of SARS-Cov2 virus in saliva. The 3D printed centrifuge (Mobilefuge) is portable, robust, stable, safe, easy to build and operate. The Mobilefuge doesn’t require soldering or programming skills and can be built without any specialised equipment, yet practical enough for high throughput use. More importantly, Mobilefuge can be powered from widely available USB ports, including mobile phones and associated power supplies. This allows the Mobilefuge to be used even in off-grid and resource limited settings. Website: https://www.cappa.ie/chinna-devarapu/
British Neuroscience Association (BNA) Festival - 2021
In April 2021, in partnership with the UK Dementia Research Institute, the British Neuroscience Association will host its fifth Festival of Neuroscience. Due to the ongoing uncertainty around COVID19, our 2021 event will be the first ever online Festival of Neuroscience. Although we are sorry to miss meeting in person, we're excited to create a whole new Festival experience! The ambition and scope of the BNA Festivals make them unparalleled across neuroscience. Being online will not change how the BNA2021 event will: - bring together multiple organisations with an interest in brain research at a single, shared event, creating a novel, multi-organisation forum featuring all areas of fundamental research in neuroscience and psychology, from both academia and the commercial sector, plus clinical expertise in neurology and psychiatry. - include a programme of public events as well. Past Festivals have seen a rap performance about consciousness, lunchtime talks, sessions in schools, and much more.
Hyperbaric Oxygen and the Brain: Concussions to COVID
Hyperbaric oxygen [HBO] treatments are an underappreciated way to get oxygen to injured tissue. Concussions, and now post-COVID neuropsychiatric issues have become a major cause of disability. Data from objective testing will be presented to discuss our clinic experience TREATING these conditions.
“PSYCHISCHE AUSWIRKUNGEN DER COVID19 PANDEMIE IN DER SCHWEIZ”
Die Covid-19-Pandemie hat viele Menschen in der Schweiz unter grossen psychischen Druck gesetzt. Wie waren die unterschiedlichen Reaktionen auf diese Einschränkungen? Wie haben sich die Veränderungen im Alltag auf den Stresspegel ausgewirkt und die Psyche beeinflusst? Am Freitag, 19. März werden wir durch die Ergebnisse der Analyse aus der «Swiss Corona Stress Study» der Universität Basel mehr erfahren.
SARC-CoV-2 modeling: What have we learned from this pandemic about how (not) to model disease spread?
The SARS-CoV-2 pandemic is awash in data, including daily, spatially-resolved COVID case data, virus sequence data, patients `omics data, and mobility data. Journals are now also awash in studies that make use of quantitative modeling approaches to gain insight into the geographic spread of SARS-CoV-2 and its temporal dynamics, as well as studies that predict the impact of control strategies on SARS-CoV-2 circulation. Some, but by no means all, of these studies are informed by the massive amounts of available data. Some, but by no means all, of these studies have been useful — in that their predictions revealed something beyond simple back of the envelope calculations. To summarize some of these findings, in this symposium, we will address questions such as: What do we want from models of disease spread? What can and should be predicted? Which data are the most useful for predictions? When do we need mechanistic models? What have we learned about how to model disease spread from unmet and/or conflicting predictions? The workshop speakers will explore these questions from different perspectives on what data need to be considered and how models can be evaluated. As at other TMLS workshops, each speaker will deliver a 10-minute talk with ample time set aside for moderated questions/discussion. We expect the talks to be provocative and bold, while respecting different perspectives.
Soft matter physics and the COVID-19 pandemic
Much of the science underpinning the global response to the COVID-19 pandemic lies in the soft matter domain. Coronaviruses are composite particles with a core of nucleic acids complexed to proteins surrounded by a protein-studded lipid bilayer shell. A dominant route for transmission is via air-borne aerosols and droplets. Viral interaction with polymeric body fluids, particularly mucus, and cell membranes controls their infectivity, while their interaction with skin and artificial surfaces underpins cleaning and disinfection and the efficacy of masks and other personal protective equipment. The global response to COVID-19 has highlighted gaps in the soft matter knowledge base. I will survey these gaps, especially as pertaining to the transmission of the disease, and suggest questions that can (and need to) be tackled, both in response to COVID-19 and to better prepare for future viral pandemics.
Social deprivation, coping and drugs: a bad cocktail in the COVID-19 era: evidence from preclinical studies
The factors that underlie an individual’s vulnerability to switch from controlled, recreational drug use to addiction are not well understood. I will discuss the evidence in rats that in individuals housed in enriched conditions, the experience of drugs in the relative social and sensory impoverishment of the drug taking context, and the associated change in behavioural traits of resilience to addiction, exacerbate the vulnerability to develop compulsive drug intake. I will further discuss the importance of the acquisition of alcohol drinking as a mechanism to cope with distress as a factor of exacerbated vulnerability to develop compulsive alcohol intake. Together these results demonstrate that experiential factors in the drug taking context, which can be substantially driven by social isolation, shape the vulnerability to addiction.
Generation Covid-19: Should the fetus be worried?
Historically pregnant women and their unborn baby have been amongst those with the poorest outcomes in previous epidemics, most notably the Zika virus. For much of 2020, with the emergence of the novel coronavirus, the effect on the fetus remains unclear. While initial reports suggest that vertical transmission with SARS-CoV2 is reassuringly rare, the complex socioeconomic, domestic and broader maternal lifestyle factors which can influence a child’s lifelong well-being have been modulated during the experience of this pandemic. The developing brain is particularly susceptible to maternal stress, resulting in permanent structural changes and increased incidence of behavioural and mental health illness later in childhood. A large international longitudinal survey is being undertaken by the Department of Psychology to better understand the impact of the pandemic on those yet to be born.
Blursday again! What Covid-19 might tell us about real-world time experience
Global responses to the Covid-19 pandemic have resulted in various forms of “lockdown” being imposed on citizens. These lockdown measures have resulted in significant changes to all aspects of daily life for all those who live under them. Lockdowns have however, also provided a unique opportunity for psychologists to examine how changes in the structure of daily life influence our experience of time. This talk will review recent research examining the impact on covid-19 on real-world time experience. It will look to discuss whether the factors which influence “normal” time experience also influenced time experience during lockdown. Finally, it will try to highlight some potential future directions for enhancing our understanding of real-life time distortion.
Development of the social brain in adolescence and effects of social distancing
Adolescence is a period of life characterised by heightened sensitivity to social stimuli, an increased need for peer interaction and peer acceptance, and development of the social brain. Lockdown and social distancing measures intended to mitigate the spread of COVID-19 are reducing the opportunity to engage in face-to-face social interaction with peers. The consequences of social distancing on human social brain and social cognitive development are unknown, but animal research has shown that social deprivation and isolation have unique effects on brain and behaviour in adolescence compared with other stages of life. It is possible that social distancing might have a disproportionate effect on an age group for whom peer interaction is a vital aspect of development.
The early impact of COVID-19 on mental health and community physical health services and their patients’ mortality in Cambridgeshire and Peterborough, UK
COVID -19 has affected social interaction and healthcare worldwide. This talk will focus on the impact of the pandemic and “lockdown” on mental health services, community physical health services, and patient mortality in Cambridgeshire and Peterborough, based on the analysis of de-identified data from the primary NHS provider of secondary care mental health services to this population (~0.86 million)
Investigating the impact of the pandemic on adolescent anxiety and cognitive function
Meg was awarded funding to look into how the coronavirus pandemic has affected children's mental health and wellbeing.
Population studies and ageing brains, in a time of COVID
This presentation will include a brief resume of research in older populations led from Cambridge that have informed current clinical understanding and policy regarding services and prevention for and of dementia. These population studies have more recently been ‘re-purposed’ with enthusiasm from participants into a trial platform, and this also has enabled ongoing follow-up by telephone during the COVID pandemic. Although there are no formal outputs from these latter developments general impressions will be shared.
Lab-on-a-chip and diagnostic tools for COVID-19
The SARS-CoV-2 virus has rapidly evolved into a pandemic that is threatening public health, economics, and quality of life worldwide. The gold-standard for testing individuals for COVID-19 is using traditional RT-qPCR, which is expensive and can take up to several hours. Expanding surveillance across a global scale will call for new strategies and tests that are inexpensive, require minimal reagents, decrease assay time, and allow for simple point-of-care (POC) monitoring without need of trained personnel and with quick turnaround time. To expand the speed of COVID-19 surveillance, we are working on a point-of-care microfluidic chip to enable significantly faster and easier testing. This is based upon digital drop loop-mediated isothermal amplification that will allow for rapid testing of large populations at a reasonable cost. The device will employ a nucleic-acid based test called reverse transcriptase LAMP (RT- LAMP) that operates at a temperature of 60-65°C. RT-LAMP removes the bottleneck of thermal cycling and high temperatures required by traditional RT-qPCR thermocycling. The simplicity, speed, and sensitivity will enable early treatment and response to infection.
The impact of Covid-19 on the mental health of children and young people
The recent pandemic arrived at a time when mental health of children and young people was deteriorating, particular among teenage girls and young women. Lockdown produced a plethora of mental health surveys, but very few of these had pre-pandemic data. This talk will summarise the current evidence of how covid-19 seems to have affected the mental health of children and young people from various studies in the UK.
NeuroCOVID: Epidemiology, biomarkers, and pathophysiology
Neurological consequences of COVID-19
The speakers will outline how neurologists in Bristol have been research-active during the COVID-19 pandemic including our contribution to national and international surveillance programmes as well as initiating research studies such as an evaluation of the impact of COVID anxiety on sleep and neurodegeneration and determining whether vascular changes in the eye predict COVID-19 severity.
Is the COVID-19 pandemic really causing mental illness?
“Super Spreaders in the Corona Epidemics”
Recently a powerful example of a replicating nano-machine entered our society. In principle, it’s just a normal disease, that one attempts to model with 3 or 4 simple coupled equations with 2 important parameters: a timescale, and a replication factor (the famous R0). Then one tries to guess how changes in society change R0 and perhaps adopt some more or less strong lock-down measures. However, this virus has more “personality” than that. It behaves differently in different persons, and persons behave differently. Presumably, only a few of us infect a lot, while most do not infect so much. This assumption is supported by the observation that couples living together only infect each other with about 15 percent probability, indicating that most infected people are not really infectious. I will discuss this and other aspects of Covid-19 in the perspective of models that describe heterogeneous individuals in a society. In particular, we suggest that limiting superspreading opportunities is a cost-effective strategy to mitigate Covid-19.