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Abstract PhD students are particularly vulnerable to experiencing poor mental health. Mental health concerns that arise during their studies can not only affect their study progress but also have long-lasting impacts on their mental health after their studies. Extensive research has been conducted on the mental health of university students, but few studies have focused on PhD students and even fewer on PhD students in Australia. The present study investigated demographic, occupational, psychological, social, and relational determinants of mental health symptoms (depression, anxiety, and suicidality) in PhD students in Australia. PhD students enrolled in Australian universities were invited to complete an online survey. Results from regression analyses identified key determinants of mental health symptoms in our sample of PhD students (N = 302). In particular, higher levels of imposter thoughts, perfectionism discrepancy, and loneliness were strong predictors of depression, anxiety, and suicidality. These findings contribute to our understanding of the mental health of PhD students in Australia. Importantly, these findings inform areas of focus where potential strategies can be implemented to better protect the mental health of this population. For example, strategies that mitigate loneliness or foster effective, collaborative student-supervisor relationships.

BACKGROUND: Colombia has experienced decades of conflict between the government and non-state actors. Attacks on healthcare have been a grave but regular facet of that violence. In response, the Misión Médica (MM) program was developed to support, protect, and defend healthcare. Sporadic violence continues, with many recent attacks perpetrated not by armed actors but by residents. Given the history of conflict and ongoing violence, we sought to capture the perspectives of both healthcare workers (HCWs) and community members (CMs) regarding the characteristics and impacts of attacks on health in Colombia to gain insight into how to better prevent violence and mitigate its impacts. METHODS: A cross-sectional survey was conducted from January to March 2021 in seven departments in Colombia in regions that witnessed attacks on healthcare. Questionnaires were administered to HCWs and CMs via purposive sampling, probing their experiences with attacks on health with both closed and open-ended questions. The categorical responses were stratified by health worker vs. non-health worker and descriptively analyzed. Narrative responses were analyzed via a hybrid deductive/inductive thematic approach. RESULTS: Seventy-three individuals participated in the study (36 HCWs and 37 cm). Approximately 77% of HCWs believed that attacks on healthcare impacted health outcomes while 68% of CMs did not see a direct connection between violence against healthcare and poor health outcomes. Awareness of the MM program was significantly different between HCWs (83.3%) and CMs (37.8%). The survey responses explored the characteristics of attacks on health, compounded impacts of violence on the health system, personal impacts, and perspectives on mitigation efforts. CONCLUSIONS: The study demonstrates that: (1) attacks on healthcare are context-dependent and require a local lens for mitigation and management; (2) both HCWs and CMs have critical perspectives that must be considered, (3) the impacts of violence against healthcare are complex and compounded and (4) that awareness of the legal protections of the Geneva Conventions must be combined with education on the health impacts for robust protection strategies. Critically, Both CMs and HCWs experience fear and psychosocial ramifications of these attacks, suggesting the need for stronger protections and resources to support the health workforce and the local community.

Light exerts multiple non-image-forming biological effects on physiology including the stimulation of alertness and cognition. However, the subcortical circuitry underlying the stimulating impact of light is not established in humans. We used 7 Tesla functional magnetic resonance imaging to assess the impact of variations in light illuminance on the regional activity of the hypothalamus while healthy young adults (N=26; 16 women; 24.3±2.9 y) were completing two auditory cognitive tasks. We find that, during both the executive and emotional tasks, higher illuminance triggered an activity increase over the posterior part of the hypothalamus, which includes part of the tuberomamillary nucleus and the posterior part of the lateral hypothalamus. In contrast, increasing illuminance evoked a decrease in activity over the anterior and ventral parts of the hypothalamus, encompassing notably the suprachiasmatic nucleus and another part of the tuberomammillary nucleus. Critically, the performance of the executive task was improved under higher illuminance and was negatively correlated with the activity of the posterior hypothalamus area. These findings reveal the distinct local dynamics of different hypothalamus regions that underlie the impact of light on cognition.

Objective To predict birth weight at various potential gestational ages of delivery based on data routinely available at the first antenatal visit.Design Individual participant data meta-analysis.Data sources Individual participant data of four cohorts (237 228 pregnancies) from the International Prediction of Pregnancy Complications (IPPIC) network dataset.Eligibility criteria for selecting studies Studies in the IPPIC network were identified by searching major databases for studies reporting risk factors for adverse pregnancy outcomes, such as pre-eclampsia, fetal growth restriction, and stillbirth, from database inception to August 2019. Data of four IPPIC cohorts (237 228 pregnancies) from the US (National Institute of Child Health and Human Development, 2018; 233 483 pregnancies), UK (Allen et al, 2017; 1045 pregnancies), Norway (STORK Groruddalen research programme, 2010; 823 pregnancies), and Australia (Rumbold et al, 2006; 1877 pregnancies) were included in the development of the model.Results The IPPIC birth weight model was developed with random intercept regression models with backward elimination for variable selection. Internal-external cross validation was performed to assess the study specific and pooled performance of the model, reported as calibration slope, calibration-in-the-large, and observed versus expected average birth weight ratio. Meta-analysis showed that the apparent performance of the model had good calibration (calibration slope 0.99, 95% confidence interval (CI) 0.88 to 1.10; calibration-in-the-large 44.5 g, −18.4 to 107.3) with an observed versus expected average birth weight ratio of 1.02 (95% CI 0.97 to 1.07). The proportion of variation in birth weight explained by the model (R2) was 46.9% (range 32.7-56.1% in each cohort). On internal-external cross validation, the model showed good calibration and predictive performance when validated in three cohorts with a calibration slope of 0.90 (Allen cohort), 1.04 (STORK Groruddalen cohort), and 1.07 (Rumbold cohort), calibration-in-the-large of −22.3 g (Allen cohort), −33.42 (Rumbold cohort), and 86.4 g (STORK Groruddalen cohort), and observed versus expected ratio of 0.99 (Rumbold cohort), 1.00 (Allen cohort), and 1.03 (STORK Groruddalen cohort); respective pooled estimates were 1.00 (95% CI 0.78 to 1.23; calibration slope), 9.7 g (−154.3 to 173.8; calibration-in-the-large), and 1.00 (0.94 to 1.07; observed v expected ratio). The model predictions were more accurate (smaller mean square error) in the lower end of predicted birth weight, which is important in informing clinical decision making.Conclusions The IPPIC birth weight model allowed birth weight predictions for a range of possible gestational ages. The model explained about 50% of individual variation in birth weights, was well calibrated (especially in babies at high risk of fetal growth restriction and its complications), and showed promising performance in four different populations included in the individual participant data meta-analysis. Further research to examine the generalisability of performance in other countries, settings, and subgroups is required.Trial registration PROSPERO CRD42019135045

Background Tracking the spread of antibiotic resistant bacteria is critical to reduce global morbidity and mortality associated with human and animal infections. There is a need to understand the role that wild animals in maintenance and transfer of antibiotic resistance genes (ARGs). Methods This study used metagenomics to identify and compare the abundance of bacterial species and ARGs detected in the gut microbiomes from sympatric humans and wild mouse lemurs in a forest-dominated, roadless region of Madagascar near Ranomafana National Park. We examined the contribution of human geographic location toward differences in ARG abundance and compared the genomic similarity of ARGs between host source microbiomes. Results Alpha and beta diversity of species and ARGs between host sources were distinct but maintained a similar number of detectable ARG alleles. Humans were differentially more abundant for four distinct tetracycline resistance-associated genes compared to lemurs. There was no significant difference in human ARG diversity from different locations. Human and lemur microbiomes shared 14 distinct ARGs with highly conserved in nucleotide identity. Synteny of ARG-associated assemblies revealed a distinct multidrug-resistant gene cassette carrying dfrA1 and aadA1 present in human and lemur microbiomes without evidence of geographic overlap, suggesting that these resistance genes could be widespread in this ecosystem. Further investigation into intermediary processes that maintain drug-resistant bacteria in wildlife settings is needed.

BackgroundThe lack of regular physical activity (PA) in individuals with spinal cord injury (SCI) in the United States is an ongoing health crisis. Regular PA and exercise-based interventions have been linked with improved outcomes and healthier lifestyles among those with SCI. Providing people with an accurate estimate of their everyday PA level can promote PA. Furthermore, PA tracking can be combined with mobile health technology such as smartphones and smartwatches to provide a just-in-time adaptive intervention (JITAI) for individuals with SCI as they go about everyday life. A JITAI can prompt an individual to set a PA goal or provide feedback about their PA levels. ObjectiveThe primary aim of this study is to investigate whether minutes of moderate-intensity PA among individuals with SCI can be increased by integrating a JITAI with a web-based PA intervention (WI) program. The WI program is a 14-week web-based PA program widely recommended for individuals with disabilities. A secondary aim is to investigate the benefit of a JITAI on proximal PA, defined as minutes of moderate-intensity PA within 120 minutes of a PA feedback prompt. MethodsIndividuals with SCI (N=196) will be randomized to a WI arm or a WI+JITAI arm. Within the WI+JITAI arm, a microrandomized trial will be used to randomize participants several times a day to different tailored feedback and PA recommendations. Participants will take part in the 24-week study from their home environment in the community. The study has three phases: (1) baseline, (2) WI program with or without JITAI, and (3) PA sustainability. Participants will provide survey-based information at the initial meeting and at the end of weeks 2, 8, 16, and 24. Participants will be asked to wear a smartwatch every day for ≥12 hours for the duration of the study. ResultsRecruitment and enrollment began in May 2023. Data analysis is expected to be completed within 6 months of finishing participant data collection. ConclusionsThe JITAI has the potential to achieve long-term PA performance by delivering tailored, just-in-time feedback based on the person’s actual PA behavior rather than a generic PA recommendation. New insights from this study may guide intervention designers to develop engaging PA interventions for individuals with disability. Trial RegistrationClinicalTrials.gov NCT05317832; https://clinicaltrials.gov/study/NCT05317832 International Registered Report Identifier (IRRID)DERR1-10.2196/57699

BackgroundThe COVID-19 pandemic acted as a catalyst for the use of information and communication technology (ICT) in inpatient and outpatient health care settings. Digital tools were used to connect patients, families, and providers amid visitor restrictions, while web-based platforms were used to continue care amid COVID-19 lockdowns. What we have yet to learn is the experiences of health care providers (HCPs) regarding the use of ICT that supported changes to clinical care during the COVID-19 pandemic. ObjectiveThe aim of this paper was to describe the experiences of HCPs in using ICT to support clinical care changes during the COVID-19 pandemic. This paper is reporting on a subset of a larger body of data that examined changes to models of care during the pandemic. MethodsThis study used a qualitative, descriptive study design. In total, 30 HCPs were recruited from 3 hospitals in Canada. One-on-one semistructured interviews were conducted between December 2022 and June 2023. Qualitative data were analyzed using an inductive thematic approach to identify themes across participants. ResultsA total of 30 interviews with HCPs revealed 3 themes related to their experiences using ICT to support changes to clinical care during the COVID-19 pandemic. These included the use of ICT (1) to support in-person communication with patients, (2) to facilitate connection between provider to patient and patient to family, and (3) to provide continuity of care. ConclusionsHCP narratives revealed the benefits of digital tools to support in-person communication between patient and provider, the need for thoughtful consideration for the use of ICT at end-of-life care, and the decision-making that is needed when choosing service delivery modality (eg, web based or in person). Moving forward, organizations are encouraged to provide education and training on how to support patient-provider communication, find ways to meet patient and family wishes at end-of-life care, and continue to give autonomy to HCPs in their clinical decision-making regarding service delivery modality.

Objective To determine and identify distance patterns in the movements of medical students and junior doctors between their training locations.Design A retrospective cohort study of UK medical students from 2002 to 2015 (UKMED data).Setting All UK medical schools, foundations and specialty training organisation.Participants All UK medical students from 2002 to 2015, for a total of 97 932 participants.Outcome measures Individual movements and number of movements by county of students from family home to medical school training, from medical school to foundation training and from foundation to specialty training.Methods Leslie matrix, principal components analysis, Gini coefficient, χ2 test, generalised linear models and variable selection methods were employed to explore the different facets of students’ and junior doctors’ movements from the family home to medical school and for the full pathway (from family home to specialty training).Results The majority of the movements between the different stages of the full pathway were restricted to a distance of up to 50 km; although the proportion of movements changed from year-to-year, with longer movements during 2007–2008. At the individual level, ethnicity, socioeconomic class of the parent(s) and the deprivation score of the family home region were found to be the most important factors associated with the length of the movements from the family home to medical school. Similar results were found when movements were aggregated at the county level, with the addition of factors such as gender and qualification at entry (to medical school) being statistically associated with the number of new entrant students moving between counties.Conclusion Our findings show that while future doctors do not move far from their family home or training location, this pattern is not homogeneous over time. Distances are influenced by demographics, socioeconomic status and deprivation. These results may contribute in designing interventions aimed at solving the chronic problems of maldistribution and underdoctoring in the UK.

Abstract Monitoring the presence of commensal and pathogenic respiratory microorganisms is of critical global importance. However, community-based surveillance is difficult because nasopharyngeal swabs are uncomfortable and painful for a wide age range of participants. We designed a methodology for minimally invasive self-sampling at home and assessed its use for longitudinal monitoring of the oral, nasal and hand microbiota of adults and children within families. Healthy families with two adults and up to three children, living in and near Liverpool, United Kingdom, self-collected saliva, nasal lining fluid using synthetic absorptive matrices and hand swabs at home every two weeks for six months. Questionnaires were used to collect demographic and epidemiological data and assess feasibility and acceptability. Participants were invited to take part in an exit interview. Thirty-three families completed the study. Sampling using our approach was acceptable to 25/33 (76%) families, as sampling was fast (76%), easy (76%) and painless (60%). Saliva and hand sampling was acceptable to all participants of any age, whereas nasal sampling was accepted mostly by adults and children older than 5 years. Multi-niche self-sampling at home can be used by adults and children for longitudinal surveillance of respiratory microorganisms, providing key data for design of future studies.

Abstract Background Significant disparity in gender distribution exists among medical specialties. Residency program websites are a main source of preliminary program information for candidates, and website content may influence a prospective applicant’s sense of belongingness within a particular program. Given the importance of the residency program website as a recruiting tool, this study sought to examine and compare the presence of gendered language and imagery on residency program websites across various specialties. Methods A list of words considered masculine or feminine was used to evaluate residency program websites of the two most male-dominated specialties (orthopedic and thoracic surgery), female-dominated specialties (pediatrics and obstetrics and gynecology), and gender-balanced specialties (dermatology and family medicine) in the United States in 2022. Forty-five residency programs were randomly selected from each specialty across different regions of the US, with the exception of thoracic surgery of which there are only 33 programs. Masculine and feminine words were evaluated using a parsing and scraping program. Representation of female and male-presenting team members in photos on program websites was also evaluated. Results Masculine wording occurred more frequently in male-dominated specialties compared to gender-balanced (p = 0.0030), but not female-dominated specialties (p = 0.2199). Feminine language was used more frequently in female-dominated compared to male dominated fields (p = 0.0022), but not gender balanced (p = 0.0909). The ratio of masculine-to-feminine words used was significantly higher in male-dominated specialties compared to both gender-balanced (p

BackgroundAttacks on health care in armed conflict, including those on health workers, facilities, patients and transports, represent serious violations of human rights and international humanitarian law. Information about these incidents and their characteristics are available in myriad forms: as published research or commentary, investigative reports, and within online data collection initiatives. We review the research on attacks on health to understand what data they rely on, what subjects they cover and what gaps exist in order to develop a research agenda going forward.Methods and findingsThis study utilizes a systematic review of peer-reviewed to identify and understand relevant data about attacks on health in situations of conflict. We identified 1479 papers published before January 1, 2020 using systematic and hand-searching and chose 45 articles for review that matched our inclusion criteria. We extracted data on geographical and conflict foci, methodology, objectives and major themes. Among the included articles, 26 focused on assessment of evidence of attacks, 15 on analyzing their impacts, three on the legal and human rights principles and one on the methods of documentation. We analyzed article data to answer questions about where and when attacks occur and are investigated, what types of attacks occur, who is perpetrating them, and how and why they are studied. We synthesized cross-cutting themes on the impacts of these attacks, mitigation efforts, and gaps in existing data.ConclusionRecognizing limitations in the review, we find there have been comparatively few studies over the past four decades but the literature is growing. To deepen the discussions of the scope of attacks and to enable cross-context comparisons, documentation of attacks on health must be enhanced to make the data more consistent, more thorough, more accessible, include diverse perspectives, and clarify taxonomy. As the research on attacks on health expands, practical questions on how the data is utilized for advocacy, protection and accountability must be prioritized.

ObjectivesTo identify the engagement of health sciences librarians (HSLs) in open science (OS) through the delivery of library services, support, and programs for researchers.MethodsWe performed a scoping review guided by Arksey and O'Malley's framework and Joanna Briggs' Manual for Scoping Reviews. Our search methods consisted of searching five bibliographic databases (MEDLINE, Embase, CINAHL, LISTA, and Web of Science Core Collection), reference harvesting, and targeted website and journal searching. To determine study eligibility, we applied predetermined inclusion and exclusion criteria and reached consensus when there was disagreement. We extracted data in duplicate and performed qualitative analysis to map key themes.ResultsWe included fifty-four studies. Research methods included descriptive or narrative approaches (76%); surveys, questionnaires, and interviews (15%); or mixed methods (9%). We labeled studies with one or more of FOSTER's six OS themes: open access (54%), open data (43%), open science (24%), open education (6%), open source (6%), and citizen science (6%). Key drivers in OS were scientific integrity and transparency, openness as a guiding principle in research, and funder mandates making research publicly accessible.ConclusionsHSLs play key roles in advancing OS worldwide. Formal studies are needed to assess the impact of HSLs' engagement in OS. HSLs should promote adoption of OS within their research communities and develop strategic plans aligned with institutional partners. HSLs can promote OS by adopting more rigorous and transparent research practices of their own. Future research should examine HSLs' engagement in OS through social justice and equity perspectives.

The aim was to investigate the cohort trends of the experienced social connectedness in secondary school students between 2017 and 2021 and whether these trends vary by gender, school level and sociodemographic background. We used nationally representative Finnish data of 450,864 students in lower and upper secondary education. Social connectedness was measured by number of close friends, feelings of loneliness and sense of belonging at school. Adjusted regression analyses included year, gender, school level and sociodemographic factors (parental education, immigrant status of the student and urban-rural area of the school). The results showed that social connectedness declined from 2017 to 2021: 11% decline in having 3+ close friends, 15% increase in loneliness and 8% decline in belonging at school. The decline was especially large in girls and upper secondary school. Although some socio-demographically disadvantaged groups showed lower levels of social connectedness, there were differences by gender, school level and year. Many differences diminished because the more advantaged groups declined faster, i.e. moved towards the less advantaged groups. Declining social connectedness in young people is a worrying trend that requires a public health focus on the whole cohort while accommodating the variation by the individual and environmental context.

The Accelerating COVID-19 Therapeutic Interventions and Vaccines Therapeutic-Clinical Working Group members gathered critical recommendations in follow-up to lessons learned manuscripts released earlier in the COVID-19 pandemic. Lessons around agent prioritization, preclinical therapeutics testing, master protocol design and implementation, drug manufacturing and supply, data sharing, and public–private partnership value are shared to inform responses to future pandemics.

Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) was an extraordinary example of a public-private partnership (PPP) that brought together over thirty organizations and hundreds of individuals to address one of the most pressing global health needs in recent decades. In particular, ACTIV provided a key avenue for testing numerous therapeutics for their potential benefit in treating the SARS-CoV-2 virus or the resulting symptoms of acute COVID-19 infection. Given the speed and scale at which ACTIV designed and implemented master protocols across global networks that it was simultaneously working to create, the PPP can provide valuable lessons for best practices and avoiding pitfalls the next time the world is faced with a global pandemic of a novel pathogen. This report provides a general overview of the ACTIV partnership to set the stage and context for the subsequent articles in this issue that will relay these lessons learned.

IntroductionEpidemiological transition to NCDs is a challenge for fragile health systems in the Caribbean. The Congregations Taking Action against NCDs (CONTACT) Study intervention proposes that trained health advocates (HAs) from places of worship (PoWs), supervised by nurses at nearby primary healthcare centres (PHCs), could facilitate access to primary care among vulnerable communities. Drawing on participatory and systems thinking, we explored the capacity of local PHCs in three Caribbean countries to support this intervention.MethodsCommunities in Jamaica (rural, urban), Guyana (rural) and Dominica (Indigenous Kalinago Territory) were selected for CONTACT because of their differing socio-economic, cultural, religious and health system contexts. Through mixed-method concept mapping, we co-developed a list of perceived actionable priorities (possible intervention points ranked highly for feasibility and importance) with 48 policy actors, healthcare practitioners and civic society representatives. Guided in part by the concept mapping findings, we assessed the readiness of 12 purposefully selected PHCs for the intervention, using a staff questionnaire and an observation checklist to identify enablers and constrainers.ResultsConcept mapping illustrated stakeholder optimism for the intervention, but revealed perceptions of inadequate primary healthcare service capacity, resources and staff training to support implementation. Readiness assessments of PHCs identified potential enablers and constrainers that were consistent with concept mapping results. Staff support was evident. Constraints included under-staffing, which could hinder supervision of HAs; and inadequate essential NCD medicines, training in NCDs and financial and policy support for embedding community interventions. Despite a history of socio-political disadvantage, the most enabling context was found in the Kalinago Territory, where ongoing community engagement activities could support joint development of programmes between churches and PHCs.ConclusionMulti-sectoral stakeholder consultation and direct PHC assessments revealed viability of the proposed POW-PHC partnership for NCD prevention and control. However, structural and policy support will be key for implementing change.

Insecticidal Bacillus thuringiensis Berliner (Bt) toxins produced by transgenic cotton (Gossypium hirsutum L.) plants have become an essential component of cotton pest management. Bt toxins are the primary management tool in transgenic cotton for lepidopteran pests, the most important of which is the bollworm (Helicoverpa zea Boddie) (Lepidoptera: Noctuidae) in the United States (U.S.). However, bollworm larvae that survive after consuming Bt toxins may experience sublethal effects, which could alter interactions with other organisms, such as natural enemies. Experiments were conducted to evaluate how sublethal effects of a commercial Bt product (Dipel) incorporated into artificial diet and from Bt cotton flowers impact predation from the convergent lady beetle (Hippodamia convergens Guérin-Méneville) (Coleoptera: Coccinellidae), common in cotton fields of the mid-southern U.S. Sublethal effects were detected through reduced weight and slower development in bollworm larvae which fed on Dipel incorporated into artificial diet, Bollgard II, and Bollgard 3 cotton flowers. Sublethal effects from proteins incorporated into artificial diet were found to significantly alter predation from third instar lady beetle larvae. Predation of bollworm larvae also increased significantly after feeding for three days on a diet incorporated with Bt proteins. These results suggest that the changes in larval weight and development induced by Bt can be used to help predict consumption of bollworm larvae by the convergent lady beetle. These findings are essential to understanding the potential level of biological control in Bt cotton where lepidopteran larvae experience sublethal effects.

In Trypanosoma brucei, gene expression is primarily regulated posttranscriptionally making RNA metabolism critical. T. brucei has an epitranscriptome containing modified RNA bases. Yet, the identity of the enzymes catalyzing modified RNA base addition and the functions of the enzymes and modifications remain unclear. Homology searches indicate the presence of numerous T. brucei cytosine RNA methyltransferase homologs. One such homolog, TbNop2 was studied in detail. TbNop2 contains the six highly conserved motifs found in cytosine RNA methyltransferases and is evolutionarily related to the Nop2 protein family required for rRNA modification and processing. RNAi experiments targeting TbNop2 resulted in reduced levels of TbNop2 RNA and protein, and a cessation of parasite growth. Next generation sequencing of bisulfite-treated RNA (BS-seq) detected the presence of two methylation sites in the large rRNA; yet TbNop2 RNAi did not result in a significant reduction of methylation. However, TbNop2 RNAi resulted in the retention of 28S internal transcribed spacer RNAs, indicating a role for TbNop2 in rRNA processing.

Male contraceptive options and infertility treatments are limited, and almost all innovation has been limited to updates to medically assisted reproduction protocols and methods. To accelerate the development of drugs that can either improve or inhibit fertility, we established a small molecule library as a toolbox for assay development and screening campaigns using human spermatozoa. We have profiled all compounds in the Sperm Toolbox in several automated high-throughput assays that measure stimulation or inhibition of sperm motility or the acrosome reaction. We have assayed motility under non-capacitating and capacitating conditions to distinguish between pathways operating under these different physiological states. We also assayed cell viability to ensure any effects on sperm function are specific. A key advantage of our studies is that all compounds are assayed together in the same experimental conditions, which allows quantitative comparisons of their effects in complementary functional assays. We have combined the resulting datasets to generate fingerprints of the Sperm Toolbox compounds on sperm function. The data are included in an on-line R-based app for convenient querying.

Introduction Human papillomavirus-related (HPV + ) oropharyngeal squamous cell carcinoma (OPSCC) is increasing in incidence and presents diagnostic challenges given its unique clinical presentation.

When wild honey bee colonies (Apis mellifera) nest in hollow tree cavities, they coat the rough cavity walls with a continuous layer of propolis, a substance comprised primarily of plant resins. Studies have shown that the resulting "propolis envelope" leads to both individual- and colony-level health benefits. Unfortunately, the smooth wooden boxes most commonly used in beekeeping do little to stimulate propolis collection. As a result, most managed bees live in hives that are propolis-poor. In this study, we assessed different surface texture treatments (rough wood boxes, boxes outfitted with propolis traps, and standard, smooth wood boxes) in terms of their ability to stimulate propolis collection, and we examined the effect of propolis on colony health, pathogen loads, immune gene expression, bacterial gene expression, survivorship, and honey production in both stationary and migratory beekeeping contexts. We found that rough wood boxes are the most effective box type for stimulating propolis deposition. Although the use of rough wood boxes did not improve colony survivorship overall, Melissococcus plutonius detections via gene expression were significantly lower in rough wood boxes, and viral loads for multiple viruses tended to decrease as propolis deposition increased. By the end of year one, honey bee populations in migratory rough box colonies were also significantly larger than those in migratory control colonies. The use of rough wood boxes did correspond with decreased honey production in year one migratory colonies but had no effect during year two. Finally, in both stationary and migratory operations, propolis deposition was correlated with a seasonal decrease and/or stabilization in the expression of multiple immune and bacterial genes, suggesting that propolis-rich environments contribute to hive homeostasis. These findings provide support for the practical implementation of rough box hives as a means to enhance propolis collection and colony health in multiple beekeeping contexts.

Introduction Pregnant women have been historically excluded from interventional research. While recent efforts have been made to improve their involvement, there remains a disparity in the evidence base for treatments available to pregnant women compared with the non-pregnant population. A significant barrier to the enrolment of pregnant women within research is risk perception and a poor understanding of decision-making in this population.Objective Assess the risk perception and influences on decision-making in pregnant women, when considering whether to enrol in a hypothetical interventional research study.Design Semistructured interviews were undertaken, and thematic analysis was undertaken of participant responses.Participants Twelve pregnant women were enrolled from an antenatal outpatient clinic.Results Participants were unanimously positive about enrolling in the proposed hypothetical interventional study. Risk perception was influenced by potential risks to their fetus and their previous experiences of healthcare and research. Participants found the uncertainty in quantifying risk for new research interventions challenging. They were motivated to enrol in research by altruism and found less invasive research interventions more tolerable.Conclusion It is vital to understand how pregnant women balance the perceived risks and benefits of interventional research. This may help clinicians and scientists better communicate risk to pregnant women and address the ongoing under-representation of pregnant women in interventional research.

Abstract Nuclear pore proteins (Nups) prominently are among the few genes linked to speciation from hybrid incompatibility in Drosophila. These studies have focused on coding sequence evolution of Nup96 and Nup160 and shown evidence of positive selection driving nucleoporin evolution. Intriguingly, channel Nup54 functionality is required for neuronal wiring underlying the female post-mating response induced by male-derived sex-peptide. A region of rapid evolution in the core promoter of Nup54 suggests a critical role for general transcriptional regulatory elements at the onset of speciation, but whether this is a general feature of Nup genes has not been determined. Consistent with findings for Nup54, additional channel Nup58 and Nup62 promoters also rapidly accumulate insertions/deletions (indels). Comprehensive examination of Nup upstream regions reveals that core Nup complex gene promoters accumulate indels rapidly. Since changes in promoters can drive changes in expression, these results indicate an evolutionary mechanism driven by indel accumulation in core Nup promoters. Compensation of such gene expression changes could lead to altered neuronal wiring, rapid fixation of traits caused by promoter changes and subsequently the rise of new species. Hence, the nuclear pore complex may act as a nexus for species-specific changes via nucleo-cytoplasmic transport regulated gene expression.

Abstract This prospective study investigated the magnitude and pattern of variation in choroidal optical coherence tomography angiography (OCT-A) indices every 4 h over 24 h in healthy young myopic (n = 24) and non-myopic (n = 20) adults. Choriocapillaris and deep choroid en-face images from macular OCT-A scans were analysed from each session to extract magnification-corrected vascular indices including choriocapillaris flow deficit number, size and density and deep choroid perfusion density in the sub-foveal, sub-parafoveal, and sub-perifoveal regions. Choroidal thickness was also obtained from structural OCT scans. Significant variations over 24 h (P

Objective To determine current UK medical students’ career intentions after graduation and on completing the Foundation Programme (FP), and to ascertain the motivations behind these intentions.Design Cross-sectional, mixed-methods survey of UK medical students, using a non-random sampling method.Setting All 44 UK medical schools recognised by the General Medical Council.Participants All UK medical students were eligible to participate. The study sample consisted of 10 486 participants, approximately 25.50% of the medical student population.Outcome measures Career intentions of medical students postgraduation and post-FP, motivations behind these career intentions, characterising the medical student population and correlating demographic factors and propensity to leave the National Health Service (NHS).Results The majority of participating students (8806/10 486, 83.98%) planned to complete both years of the FP after graduation, with under half of these students (4294/8806, 48.76%) intending to pursue specialty training thereafter. A subanalysis of career intentions after the FP by year of study revealed a significant decrease in students’ intentions to enter specialty training as they advanced through medical school. Approximately a third of surveyed students (3392/10 486, 32.35%) intended to emigrate to practise medicine, with 42.57% (n=1444) of those students not planning to return. In total, 2.89% of students intended to leave medicine altogether (n=303). Remuneration, work-life balance and working conditions were identified as important factors in decision-making regarding emigration and leaving the profession. Subgroup analyses based on gender, type of schooling, fee type and educational background were performed. Only 17.26% of surveyed students were satisfied or very satisfied with the overall prospect of working in the NHS.Conclusions The Ascertaining the career Intentions of UK Medical Students study highlights UK students’ views and career intentions, revealing a concerning proportion of those surveyed considering alternative careers or emigration. Addressing factors such as remuneration, work-life balance and working conditions may increase retention of doctors and improve workforce planning efforts.

Abstract Deep learning methods have enabled a fast, accurate and automated approach for retinal layer segmentation in posterior segment OCT images. Due to the success of semantic segmentation methods adopting the U-Net, a wide range of variants and improvements have been developed and applied to OCT segmentation. Unfortunately, the relative performance of these methods is difficult to ascertain for OCT retinal layer segmentation due to a lack of comprehensive comparative studies, and a lack of proper matching between networks in previous comparisons, as well as the use of different OCT datasets between studies. In this paper, a detailed and unbiased comparison is performed between eight U-Net architecture variants across four different OCT datasets from a range of different populations, ocular pathologies, acquisition parameters, instruments and segmentation tasks. The U-Net architecture variants evaluated include some which have not been previously explored for OCT segmentation. Using the Dice coefficient to evaluate segmentation performance, minimal differences were noted between most of the tested architectures across the four datasets. Using an extra convolutional layer per pooling block gave a small improvement in segmentation performance for all architectures across all four datasets. This finding highlights the importance of careful architecture comparison (e.g. ensuring networks are matched using an equivalent number of layers) to obtain a true and unbiased performance assessment of fully semantic models. Overall, this study demonstrates that the vanilla U-Net is sufficient for OCT retinal layer segmentation and that state-of-the-art methods and other architectural changes are potentially unnecessary for this particular task, especially given the associated increased complexity and slower speed for the marginal performance gains observed. Given the U-Net model and its variants represent one of the most commonly applied image segmentation methods, the consistent findings across several datasets here are likely to translate to many other OCT datasets and studies. This will provide significant value by saving time and cost in experimentation and model development as well as reduced inference time in practice by selecting simpler models.

Biguanides, including the world’s most prescribed drug for type 2 diabetes, metformin, not only lower blood sugar, but also promote longevity in preclinical models. Epidemiologic studies in humans parallel these findings, indicating favorable effects of metformin on longevity and on reducing the incidence and morbidity associated with aging-related diseases. Despite this promise, the full spectrum of molecular effectors responsible for these health benefits remains elusive. Through unbiased screening in Caenorhabditis elegans, we uncovered a role for genes necessary for ether lipid biosynthesis in the favorable effects of biguanides. We demonstrate that biguanides prompt lifespan extension by stimulating ether lipid biogenesis. Loss of the ether lipid biosynthetic machinery also mitigates lifespan extension attributable to dietary restriction, target of rapamycin (TOR) inhibition, and mitochondrial electron transport chain inhibition. A possible mechanistic explanation for this finding is that ether lipids are required for activation of longevity-promoting, metabolic stress defenses downstream of the conserved transcription factor skn-1/Nrf. In alignment with these findings, overexpression of a single, key, ether lipid biosynthetic enzyme, fard-1/FAR1, is sufficient to promote lifespan extension. These findings illuminate the ether lipid biosynthetic machinery as a novel therapeutic target to promote healthy aging.

Introduction A substantial proportion of COVID-19 survivors continue to have symptoms more than 3 months after infection, especially of those who required medical intervention. Lasting symptoms are wide-ranging, and presentation varies between individuals and fluctuates within an individual. Improved understanding of undulation in symptoms and triggers may improve efficacy of healthcare providers and enable individuals to better self-manage their Long Covid. We present a protocol where we aim to develop and examine the feasibility and usability of digital home monitoring for capturing daily fluctuation of symptoms in individuals with Long Covid and provide data to facilitate a personalised approach to the classification and management of Long Covid symptoms.Methods and analysis This study is a longitudinal prospective cohort study of adults with Long Covid accessing 10 National Health Service (NHS) rehabilitation services in the UK. We aim to recruit 400 people from participating NHS sites. At referral to study, 6 weeks and 12 weeks, participants will complete demographic data (referral to study) and clinical outcome measures, including ecological momentary assessment (EMA) using personal mobile devices. EMA items are adapted from the COVID-19 Yorkshire Rehabilitation Scale items and include self-reported activities, symptoms and psychological factors. Passive activity data will be collected through wrist-worn sensors. We will use latent class growth models to identify trajectories of experience, potential phenotypes defined by co-occurrence of symptoms and inter-relationships between stressors, symptoms and participation in daily activities. We anticipate that n=300 participants provide 80% power to detect a 20% improvement in fatigue over 12 weeks in one class of patients relative to another.Ethics and dissemination The study was approved by the Yorkshire & The Humber—Bradford Leeds Research Ethics Committee (ref: 21/YH/0276). Findings will be disseminated in peer-reviewed publications and presented at conferences.Trial registration number ISRCTN15022307.

Abstract We use a national citizen science monitoring scheme to quantify how agricultural intensification affects honeybee diet breadth (number of plant species). To do this we used DNA metabarcoding to identify the plants present in 527 honey samples collected in 2019 across Great Britain. The species richness of forage plants was negatively correlated with arable cropping area, although this was only found early in the year when the abundance of flowering plants was more limited. Within intensively farmed areas, honeybee diets were dominated by Brassica crops (including oilseed rape). We demonstrate how the structure and complexity of honeybee foraging relationships with plants is negatively affected by the area of arable crops surrounding hives. Using information collected from the beekeepers on the incidence of an economically damaging bee disease (Deformed Wing Virus) we found that the occurrence of this disease increased where bees foraged in agricultural land where there was a high use of foliar insecticides. Understanding impacts of land use on resource availability is fundamental to assessing long-term viability of pollinator populations. These findings highlight the importance of supporting temporally timed resources as mitigation strategies to support wider pollinator population viability.

Calder, Tong et al. discuss how the rapid development of COVID-19 vaccines benefited from HIV/AIDS research. They highlight lessons learned from the COVID-19 vaccine development experience that could accelerate and re-energize the development of a safe and efficacious HIV vaccine.

Objectives Kenya has long and porous borders with its neighbouring countries. These regions, predominantly inhabited by highly mobile rural communities with strong cross-border cultural ties, present major challenges in managing movement of people and COVID-19 preventive measures. Our study sought to assess knowledge of COVID-19 prevention behaviours, how these varied by socioeconomic (SEC) factors and the challenges of engagement and implementation, in two border counties of Kenya.Methods We conducted a mixed methods study using a household e-survey (Busia, N=294; Mandera, N=288; 57% females, 43% males), and qualitative telephone interviews (N=73: Busia 55; Mandera 18) with policy actors, healthcare workers, truckers and traders, and community members. Interviews were transcribed, English translated and analysed using the framework method. Associations between SEC (wealth quintiles, educational level) and knowledge of COVID-19 preventive behaviours were explored using Poisson regression.Results Participants were mostly educated to primary school level (54.4% Busia, 61.6% Mandera). Knowledge of COVID-19 prevention varied by behaviour: hand washing-86.5%, use of hand sanitiser-74.8%, wearing a face mask-63.1%, covering the mouth when sneezing or coughing-56.3% and social distancing-40.1%. Differences in knowledge by area, educational level and the wealth index were marked, greatest for Mandera, the less educated and the poor. Interviews with stakeholders revealed challenges in health messaging, psychosocial and socioeconomic factors, lack of preparedness for truck border crossings, language barrier, denial and livelihood insecurity as key challenges to engagement with and implementation of COVID-19 prevention behaviours in the border regions.Conclusion The influence of SEC disparities and border dynamics on knowledge and engagement with COVID-19 prevention behaviours calls for contextually appropriate risk communication strategies that are cognisant of community needs and local patterns of information flow. Coordinating response measures across border points is crucial in winning communities’ trust and maintaining essential economic and social activities.

Background. Rheumatic heart disease (RHD) is a preventable chronic cardiac condition that causes over 350 000 deaths annually, largely in low and middle-income countries, as a direct result of structural inequalities and inadequate access to comprehensive healthcare. People living with and affected by this disease are a key stakeholder group and need to be directing research priorities. Objective. To improve care and provide direction for future research, a group of qualitative researchers and pe living with RHD from six countries convened in Cape Town in 2016. Methods. People with RHD shared their lived experiences while RHD researchers, clinicians and advocates presented a spectrum of qualitative research methods to explore these experiences. The Continuum of Care© (CoC, developed by the Medtronic Foundation) was used as a framework to guide participant discussions. Thematic summaries of the discussions were undertaken in an iterative process throughout the workshop. Results. Three themes emerged in the summaries: there is no ‘typical’ patient journey; a biomedical focus on RHD does not reflect people’s lived experiences; and a diversity of research methods is required to investigate experiences of people living with RHD. Practice implications. Qualitative research methods are invaluable for allowing patient ‘voices’ to be heard. To this end, qualitative approaches should be incorporated in all RHD research to ensure maximum benefit for patients. Conclusion. Greater understanding of the patient journey was gained for strengthening and expanding the global RHD research agenda. Future research should reflect on and incorporate the realities of patients’ lived experiences, and these experiences should be integrated into healthcare models for chronic conditions.

Plasmids enable the dissemination of antimicrobial resistance (AMR) in common Enterobacterales pathogens, representing a major public health challenge. However, the extent of plasmid sharing and evolution between Enterobacterales causing human infections and other niches remains unclear, including the emergence of resistance plasmids. Dense, unselected sampling is essential to developing our understanding of plasmid epidemiology and designing appropriate interventions to limit the emergence and dissemination of plasmid-associated AMR. We established a geographically and temporally restricted collection of human bloodstream infection (BSI)-associated, livestock-associated (cattle, pig, poultry, and sheep faeces, farm soils) and wastewater treatment work (WwTW)-associated (influent, effluent, waterways upstream/downstream of effluent outlets) Enterobacterales. Isolates were collected between 2008 and 2020 from sites

BACKGROUND To date, only limited data are available on the mechanisms of protection against colonization with Bordetella pertussis in humans.METHODS In this study, the cellular responses to B. pertussis challenge were monitored longitudinally using high-dimensional EuroFlow-based flow cytometry, allowing quantitative detection of more than 250 different immune cell subsets in the blood of 15 healthy donors.RESULTS Participants who were protected against colonization showed different early cellular responses compared with colonized participants. Especially prominent for colonization-protected participants were the early expansion of CD36– nonclassical monocytes on day 1 (D1), natural killer cells (D3), follicular T helper cells (D1–D3), and plasma cells (D3). Plasma cell expansion on D3 correlated negatively with the CFU load on D7 and D9 after challenge. Increased plasma cell maturation on D11–D14 was found in participants with seroconversion.CONCLUSION These early cellular immune responses following experimental infection can now be further characterized and potentially linked to an efficient mucosal immune response, preventing colonization. Ultimately, their presence may be used to evaluate whether new B. pertussis vaccine candidates are protective against B. pertussis colonization, e.g., by bacterial challenge after vaccination.TRIAL REGISTRATION ClinicalTrials.gov NCT03751514.FUNDING Innovative Medicines Initiative 2 Joint Undertaking and the EuroFlow Consortium.

Objective: Open science (OS) is a global movement focused on improving research equity, reproducibility, and transparency of research outputs in publicly funded research. This paper describes how a librarian collaborated with teaching faculty and a research program coordinator to integrate an OS curriculum into an undergraduate professional practice course and assess students’ perceptions of OS after participating. Methods: A librarian developed an OS-specific curriculum for an undergraduate professional practice course in Nutrition. This course is part of the First Year Research Experience (FYRE) program, which is integrated into 13-week undergraduate courses to introduce students to core elements of the research process in their first year of study by carrying out a research project. The OS curriculum included an Introduction to OS class, a requirement that students share their research outputs in the Open Science Framework, and an assignment asking students to reflect on their experience learning about and practicing OS. Twenty-one of 30 students consented to having their reflection assignment undergo thematic analysis. Results: Students indicated transparency, accountability, accessibility to research outputs, and increased efficiency as positive attributes of OS. The time commitment, fear of being scooped, and concerns over having research be misinterpreted were considered negative attributes. 90% (n=19) of students indicated that they intend to practice OS in the future. Conclusion: Based on strong engagement from the students, we believe that this OS curriculum could be adapted to other undergraduate or graduate student contexts where a research project is required.

Abstract Returning university students represent large-scale, transient demographic shifts and a potential source of transmission to adjacent communities during the COVID-19 pandemic. In this prospective longitudinal cohort study, we tested for IgG antibodies against SARS-CoV-2 in a non-random cohort of residents living in Centre County prior to the Fall 2020 term at the Pennsylvania State University and following the conclusion of the Fall 2020 term. We also report the seroprevalence in a non-random cohort of students collected at the end of the Fall 2020 term. Of 1313 community participants, 42 (3.2%) were positive for SARS-CoV-2 IgG antibodies at their first visit between 07 August and 02 October 2020. Of 684 student participants who returned to campus for fall instruction, 208 (30.4%) were positive for SARS-CoV-2 antibodies between 26 October and 21 December. 96 (7.3%) community participants returned a positive IgG antibody result by 19 February. Only contact with known SARS-CoV-2-positive individuals and attendance at small gatherings (20–50 individuals) were significant predictors of detecting IgG antibodies among returning students (aOR, 95% CI 3.1, 2.07–4.64; 1.52, 1.03–2.24; respectively). Despite high seroprevalence observed within the student population, seroprevalence in a longitudinal cohort of community residents was low and stable from before student arrival for the Fall 2020 term to after student departure. The study implies that heterogeneity in SARS-CoV-2 transmission can occur in geographically coincident populations.

Abstract Common alphacoronaviruses and human rhinoviruses (HRV) induce type I and III interferon (IFN) responses important to limiting viral replication in the airway epithelium. In contrast, highly pathogenic betacoronaviruses including SARS-CoV-2 may evade or antagonize RNA-induced IFN I/III responses. In airway epithelial cells (AECs) from children and older adults we compared IFN I/III responses to SARS-CoV-2 and HRV-16, and assessed whether pre-infection with HRV-16, or pretreatment with recombinant IFN-β or IFN-λ, modified SARS-CoV-2 replication. Bronchial AECs from children (ages 6–18 years) and older adults (ages 60–75 years) were differentiated ex vivo to generate organotypic cultures. In a biosafety level 3 (BSL-3) facility, cultures were infected with SARS-CoV-2 or HRV-16, and RNA and protein was harvested from cell lysates 96 h. following infection and supernatant was collected 48 and 96 h. following infection. In additional experiments cultures were pre-infected with HRV-16, or pre-treated with recombinant IFN-β1 or IFN-λ2 before SARS-CoV-2 infection. In a subset of experiments a range of infectious concentrations of HRV-16, SARS-CoV-2 WA-01, SARS-CoV-2 Delta variant, and SARS-CoV-2 Omicron variant were studied. Despite significant between-donor heterogeneity SARS-CoV-2 replicated 100 times more efficiently than HRV-16. IFNB1, INFL2, and CXCL10 gene expression and protein production following HRV-16 infection was significantly greater than following SARS-CoV-2. IFN gene expression and protein production were inversely correlated with SARS-CoV-2 replication. Treatment of cultures with recombinant IFNβ1 or IFNλ2, or pre-infection of cultures with HRV-16, markedly reduced SARS-CoV-2 replication. In addition to marked between-donor heterogeneity in IFN responses and viral replication, SARS-CoV-2 (WA-01, Delta, and Omicron variants) elicits a less robust IFN response in primary AEC cultures than does rhinovirus, and heterologous rhinovirus infection, or treatment with recombinant IFN-β1 or IFN-λ2, reduces SARS-CoV-2 replication, although to a lesser degree for the Delta and Omicron variants.

We report an outbreak of severe acute respiratory syndrome coronavirus 2 involving 3 Malayan tigers (Panthera tigris jacksoni) at a zoo in Tennessee, USA. Investigation identified naturally occurring tiger-to-tiger transmission; genetic sequence change occurred with viral passage. We provide epidemiologic, environmental, and genomic sequencing data for animal and human infections.

Abstract Vocal expression of emotions has been observed across species and could provide a non-invasive and reliable means to assess animal emotions. We investigated if pig vocal indicators of emotions revealed in previous studies are valid across call types and contexts, and could potentially be used to develop an automated emotion monitoring tool. We performed an analysis of an extensive and unique dataset of low (LF) and high frequency (HF) calls emitted by pigs across numerous commercial contexts from birth to slaughter (7414 calls from 411 pigs). Our results revealed that the valence attributed to the contexts of production (positive versus negative) affected all investigated parameters in both LF and HF. Similarly, the context category affected all parameters. We then tested two different automated methods for call classification; a neural network revealed much higher classification accuracy compared to a permuted discriminant function analysis (pDFA), both for the valence (neural network: 91.5%; pDFA analysis weighted average across LF and HF (cross-classified): 61.7% with a chance level at 50.5%) and context (neural network: 81.5%; pDFA analysis weighted average across LF and HF (cross-classified): 19.4% with a chance level at 14.3%). These results suggest that an automated recognition system can be developed to monitor pig welfare on-farm.

Abstract Pandemics have the potential to incur significant health and economic impacts, and can reach a large number of countries from their origin within weeks. Early identification and containment of a newly emerged pandemic within the source country is key for minimising global impact. To identify a country’s potential to control and contain a pathogen with pandemic potential, we compared the quality of a country’s healthcare system against its global airline connectivity. Healthcare development was determined using three multi-factorial indices, while detailed airline passenger data was used to identify the global connectivity of all countries. Proximities of countries to a putative ‘Worst Case Scenario’ (extreme high-connectivity and low-healthcare development) were calculated. We found a positive relationship between a country’s connectivity and healthcare metrics. We also identified countries that potentially pose the greatest risk for pandemic dissemination, notably Dominican Republic, India and Pakistan. China and Mexico, both sources of recent influenza and coronavirus pandemics were also identified as among the highest risk countries. Collectively, lower-middle and upper-middle income countries represented the greatest risk, while high income countries represented the lowest risk. Our analysis represents an alternative approach to identify countries where increased within-country disease surveillance and pandemic preparedness may benefit global health.

Longitudinal, community-based sampling is important for understanding prevalence and transmission of respiratory pathogens. Using a minimally invasive sampling method, the FAMILY Micro study monitored the oral, nasal and hand microbiota of families for 6 months. Here, we explore participant experiences and opinions. A mixed methods approach was utilised. A quantitative questionnaire was completed after every sampling timepoint to report levels of discomfort and pain, as well as time taken to collect samples. Participants were also invited to discuss their experiences in a qualitative structured exit interview. We received questionnaires from 36 families. Most adults and children >5y experienced no pain (94% and 70%) and little discomfort (73% and 47% no discomfort) regardless of sample type, whereas children ≤5y experienced variable levels of pain and discomfort (48% no pain but 14% hurts even more, whole lot or worst; 38% no discomfort but 33% moderate, severe, or extreme discomfort). The time taken for saliva and hand sampling decreased over the study. We conducted interviews with 24 families. Families found the sampling method straightforward, and adults and children >5y preferred nasal sampling using a synthetic absorptive matrix over nasopharyngeal swabs. It remained challenging for families to fit sampling into their busy schedules. Adequate fridge/freezer space and regular sample pick-ups were found to be important factors for feasibility. Messaging apps proved extremely effective for engaging with participants. Our findings provide key information to inform the design of future studies, specifically that self-sampling at home using minimally invasive procedures is feasible in a family context.

Background: Over a life course, human adaptive immunity to antigenically mutable pathogens exhibits competitive and facilitative interactions. We hypothesize that such interactions may lead to cyclic dynamics in immune responses over a lifetime. Methods: To investigate the cyclic behavior, we analyzed hemagglutination inhibition titers against 21 historical influenza A(H3N2) strains spanning 47 years from a cohort in Guangzhou, China, and applied Fourier spectrum analysis. To investigate possible biological mechanisms, we simulated individual antibody profiles encompassing known feedbacks and interactions due to generally recognized immunological mechanisms. Results: We demonstrated a long-term periodicity (about 24 years) in individual antibody responses. The reported cycles were robust to analytic and sampling approaches. Simulations suggested that individual-level cross-reaction between antigenically similar strains likely explains the reported cycle. We showed that the reported cycles are predictable at both individual and birth cohort level and that cohorts show a diversity of phases of these cycles. Phase of cycle was associated with the risk of seroconversion to circulating strains, after accounting for age and pre-existing titers of the circulating strains. Conclusions: Our findings reveal the existence of long-term periodicities in individual antibody responses to A(H3N2). We hypothesize that these cycles are driven by preexisting antibody responses blunting responses to antigenically similar pathogens (by preventing infection and/or robust antibody responses upon infection), leading to reductions in antigen-specific responses over time until individual’s increasing risk leads to an infection with an antigenically distant enough virus to generate a robust immune response. These findings could help disentangle cohort effects from individual-level exposure histories, improve our understanding of observed heterogeneous antibody responses to immunizations, and inform targeted vaccine strategy. Funding: This study was supported by grants from the NIH R56AG048075 (DATC, JL), NIH R01AI114703 (DATC, BY), the Wellcome Trust 200861/Z/16/Z (SR), and 200187/Z/15/Z (SR). This work was also supported by research grants from Guangdong Government HZQB-KCZYZ-2021014 and 2019B121205009 (YG and HZ). DATC, JMR and SR acknowledge support from the National Institutes of Health Fogarty Institute (R01TW0008246). JMR acknowledges support from the Medical Research Council (MR/S004793/1) and the Engineering and Physical Sciences Research Council (EP/N014499/1). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Objectives To quantify and characterise non-household contact and to identify the effect of shielding and isolating on contact patterns.Design Cross-sectional study.Setting and participants Anyone living in the UK was eligible to take part in the study. We recorded 5143 responses to the online questionnaire between 28 July 2020 and 14 August 2020.Outcome measures Our primary outcome was the daily non-household contact rate of participants. Secondary outcomes were propensity to leave home over a 7 day period, whether contacts had occurred indoors or outdoors locations visited, the furthest distance travelled from home, ability to socially distance and membership of support bubble.Results The mean rate of non-household contacts per person was 2.9 d-1. Participants attending a workplace (adjusted incidence rate ratio (aIRR) 3.33, 95% CI 3.02 to 3.66), self-employed (aIRR 1.63, 95% CI 1.43 to 1.87) or working in healthcare (aIRR 5.10, 95% CI 4.29 to 6.10) reported significantly higher non-household contact rates than those working from home. Participants self-isolating as a precaution or following Test and Trace instructions had a lower non-household contact rate than those not self-isolating (aIRR 0.58, 95% CI 0.43 to 0.79). We found limited evidence that those shielding had reduced non-household contacts compared with non-shielders.Conclusion The daily rate of non-household interactions remained lower than prepandemic levels measured by other studies, suggesting continued adherence to social distancing guidelines. Individuals attending a workplace in-person or employed as healthcare professionals were less likely to maintain social distance and had a higher non-household contact rate, possibly increasing their infection risk. Shielding and self-isolating individuals required greater support to enable them to follow the government guidelines and reduce non-household contact and therefore their risk of infection.

Abstract Bacterial antibiotic resistance is an important global health threat and the interfaces of antibiotic resistance between humans, animals and the environment are complex. We aimed to determine the associations and overtime trends of antibiotic resistance between humans, animals and water sources from the same area and time and estimate attribution of the other sources to cases of human antibiotic resistance. A total of 125 children (aged 1–3 years old) had stool samples analysed for antibiotic-resistant bacteria at seven time points over two years, with simultaneous collection of samples of animal stools and water sources in a rural Indian community. Newey–West regression models were used to calculate temporal associations, the source with the most statistically significant relationships was household drinking water. This is supported by use of SourceR attribution modelling, that estimated the mean attribution of cases of antibiotic resistance in the children from animals, household drinking water and wastewater, at each time point and location, to be 12.6% (95% CI 4.4–20.9%), 12.1% (CI 3.4–20.7%) and 10.3% (CI 3.2–17.3%) respectively. This underlines the importance of the ‘one health’ concept and requires further research. Also, most of the significant trends over time were negative, suggesting a possible generalised improvement locally.

We characterized common exposures reported by a convenience sample of 202 US patients with coronavirus disease during January–April 2020 and identified factors associated with presumed household transmission. The most commonly reported settings of known exposure were households and healthcare facilities; among case-patients who had known contact with a confirmed case-patient compared with those who did not, healthcare occupations were more common. Among case-patients without known contact, use of public transportation was more common. Within the household, presumed transmission was highest from older (>65 years) index case-patients and from children to parents, independent of index case-patient age. These findings may inform guidance for limiting transmission and emphasize the value of testing to identify community-acquired infections.

Abstract Background and Aims In moving towards the elimination of hepatitis C virus (HCV) infection among people living with HIV, understanding HCV transmission patterns may provide insights to guide and evaluate interventions. In this study, we evaluated patterns of, and factors associated with HCV phylogenetic clustering among people living with HIV/HCV co‐infection in Australia in the direct‐acting antiviral era. Methods HCV RNA was extracted from dried blood spot (DBS) samples collected between 2014 and 2018 in the CEASE cohort study. The HCV Core‐E2 region was amplified by a polymerase chain reaction and Sanger sequenced. Maximum likelihood phylogenetic trees (1000 bootstrap replicates) were used to identify patterns of clustering (3% genetic distance threshold). Mixed‐effects logistic regression was used to determine correlates of phylogenetic clustering. Factors assessed were sexual risk behavior, education, injecting drug use, housing, employment, HIV viral load, age, sex, and sexuality. Results Phylogenetic trees were reconstructed for HCV subtype 1a (n = 139) and 3a (n = 63) sequences, with 29% (58/202) in a pair or cluster. Overall (n = 202), phylogenetic clustering was positively associated with younger age (under 40; adjusted odds ratio [aOR] 2.52, 95% confidence interval [CI] 1.20–5.29), and among gay and bisexual men (n = 168), was positively associated with younger age (aOR 2.61, 95% CI 1.10–6.19), higher education (aOR 2.58, 95% CI 1.09–6.13), and reporting high‐risk sexual behavior (aOR 3.94, 95% CI 1.31–11.84). During follow‐up, five reinfections were observed, but none were in phylogenetic clusters. Conclusion This study found a high proportion of phylogenetic relatedness, predominantly among younger people and gay and bisexual men reporting high‐risk sexual behavior. Despite this, few reinfections were observed, and reinfections demonstrated little relationship with known clusters. These findings highlight the importance of rapid HCV treatment initiation, together with monitoring of the phylogeny.