Prevalence of persistent SARS-CoV-2 in a large community surveillance study.

Persistent SARS-CoV-2 infections may act as viral reservoirs that could seed future outbreaks1-5, give rise to highly divergent lineages6-8 and contribute to cases with post-acute COVID-19 sequelae (long COVID)9,10. However, the population prevalence of persistent infections, their viral load kinetics and evolutionary dynamics over the course of infections remain largely unknown. Here, using viral sequence data collected as part of a national infection survey, we identified 381 individuals with SARS-CoV-2 RNA at high titre persisting for at least 30 days, of which 54 had viral RNA persisting at least 60 days. We refer to these as 'persistent infections' as available evidence suggests that they represent ongoing viral replication, although the persistence of non-replicating RNA cannot be ruled out in all. Individuals with persistent infection had more than 50% higher odds of self-reporting long COVID than individuals with non-persistent infection. We estimate that 0.1-0.5% of infections may become persistent with typically rebounding high viral loads and last for at least 60 days. In some individuals, we identified many viral amino acid substitutions, indicating periods of strong positive selection, whereas others had no consensus change in the sequences for prolonged periods, consistent with weak selection. Substitutions included mutations that are lineage defining for SARS-CoV-2 variants, at target sites for monoclonal antibodies and/or are commonly found in immunocompromised people11-14. This work has profound implications for understanding and characterizing SARS-CoV-2 infection, epidemiology and evolution.

Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias.

In this study, we evaluated the impact of viral variant, in addition to other variables, on within-host viral burden, by analysing cycle threshold (Ct) values derived from nose and throat swabs, collected as part of the UK COVID-19 Infection Survey. Because viral burden distributions determined from community survey data can be biased due to the impact of variant epidemiology on the time-since-infection of samples, we developed a method to explicitly adjust observed Ct value distributions to account for the expected bias. By analysing the adjusted Ct values using partial least squares regression, we found that among unvaccinated individuals with no known prior exposure, viral burden was 44% lower among Alpha variant infections, compared to those with the predecessor strain, B.1.177. Vaccination reduced viral burden by 67%, and among vaccinated individuals, viral burden was 286% higher among Delta variant, compared to Alpha variant, infections. In addition, viral burden increased by 17% for every 10-year age increment of the infected individual. In summary, within-host viral burden increases with age, is reduced by vaccination, and is influenced by the interplay of vaccination status and viral variant.

Correction: Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias.

[This corrects the article DOI: 10.1371/journal.ppat.1011461.].

Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey.

The Office for National Statistics Coronavirus (COVID-19) Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each sweeping lineage having a distinct growth advantage compared to their predecessors, although this was also accompanied by a gradual fall in average viral burdens from June 2021 to March 2023. The sweeps also generated an alternating pattern in which most samples had either S-gene target failure (SGTF) or non-SGTF over time. Evolution was characterized by steadily increasing divergence and diversity within lineages, but with step increases in divergence associated with each sweeping major lineage. This led to a faster overall rate of evolution when measured at the between-lineage level compared to within lineages, and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens.

Investigating Variability in Microbial Fuel Cells.

In scientific studies, replicas should replicate, and identical conditions should produce very similar results which enable parameters to be tested. However, in microbial experiments which use real world mixed inocula to generate a new "adapted" community, this replication is very hard to achieve. The diversity within real-world microbial systems is huge, and when a subsample of this diversity is placed into a reactor vessel or onto a surface to create a biofilm, stochastic processes occur, meaning there is heterogeneity within these new communities. The smaller the subsample, the greater this heterogeneity is likely to be. Microbial fuel cells are typically operated at a very small laboratory scale and rely on specific communities which must include electrogenic bacteria, known to be of low abundance in most natural inocula. Microbial fuel cells (MFCs) offer a unique opportunity to investigate and quantify variability as they produce current when they metabolize, which can be measured in real time as the community develops. In this research, we built and tested 28 replica MFCs and ran them under identical conditions. The results showed high variability in terms of the rate and amount of current production. This variability perpetuated into subsequent feeding rounds, both with and without the presence of new inoculate. In an attempt to control this variability, reactors were reseeded using established "good" and "bad" reactors. However, this did not result in replica biofilms, suggesting there is a spatial as well as a compositional control over biofilm formation. IMPORTANCE The research presented, although carried out in the area of microbial fuel cells, reaches an important and broadly impacting conclusion that when using mixed inoculate in replica reactors under replicated conditions, different communities emerge capable of different levels of metabolism. To date there has been very little research focusing on this, or even reporting it, with most studies using duplicate or triplicate reactors, in which this phenomenon is not fully observed. Publishing data in which replicas do not replicate will be an important and brave first step in the research into understanding this fundamental microbial process.

The treatment journey of attention-related communication difficulties following traumatic brain injury: Perspectives of international health professionals.

Traumatic brain injuries (TBI) can result in long-lasting changes in cognition, communication, behavior, and physical abilities that require specialized rehabilitation by health professionals. Communication difficulties following TBI are driven by difficulties in all aspects of cognition and linguistic skills. This study focuses specifically on attention-related communication difficulties and how international health professionals are treating this frequently occurring difficulty following TBI. One hundred and sixty-four international health professionals (e.g., speech language therapists, occupational therapists, neuropsychologists, clinical psychologists, and medical doctors) from seven countries completed an online survey. A small portion from New Zealand then participated in a focus group reviewing the topic of attention-related communication difficulties following TBI. This mixed-methods study used reflexive thematic analysis to analyse the qualitative data from both survey and focus groups alongside quantitative survey results. Fourmain themes were identified that relate to how attention-related communication difficulties should be treated and a roadmap for this important area following TBI was outlined. The four themes include: (1) signposts for attention and communication recovery; (2) change agents of attention and communication; (3) core therapy components; and (4) collaborative teams allow for better and more efficient treatment related to the client's goals. Clinical implications are discussed.

Outcomes of attention-related communication deficits following traumatic brain injury: perspectives of international health professionals.

PRIMARY OBJECTIVE: Attention and communication difficulties are common yet often invisible following Traumatic Brain Injury (TBI). The focus of this paper is to use practice-based evidence from health professionals working with individuals following TBI to gain a deep and relevant understanding of the impact that attention and communication can have in the lives of individuals following TBI. RESEARCH DESIGN: This dataset comes from a larger mixed-methods study that includes a survey with both open and closed questions and focus group data sources. METHODS AND PROCEDURES: Thematic analysis was completed on a single open-ended question from the survey of health professionals. It asked health professionals about the outcomes they believe are directly related to attention difficulties that result in specific communication difficulties. MAIN OUTCOMES AND RESULTS: Responses from 73 health professionals who work in neurorehabilitation generated five themes: behavior, connections, self, purpose, and empowerment. The themes were pervasive across all aspects of the recovery journey for individuals post-TBI. CONCLUSIONS: The implications for clinical practice and future research indicate a need to focus on attention-related strategies for language deficits; treating communication difficulties related to relationships and friendships; and redefining a sense of self following TBI.

The experiences of young witnesses and caregivers in Aotearoa New Zealand's Sexual Violence Pilot Courts.

New Zealand's Sexual Violence Courts Pilot was established in late 2016, intended in part, to reduce the stress experienced by complainants. Young witnesses who testified in the specialist courts and their caregivers were interviewed about their experiences of court involvement. Interview transcripts were analysed using thematic analysis and the following themes were identified: The period between reporting an alleged offence and the trial is far too long and stressful; moving forward with life is difficult until the trial has concluded; cross-examination is distressing; feeling comfortable and supported when at court is important; safety and distance from the defendant when at court is important; separation of young witnesses from their caregivers at court is difficult; information is lacking throughout the process; and parenting young witnesses through the court process is challenging. Young witnesses typically experienced court involvement as very stressful and distressing, and further innovation within the courts is therefore needed.

Linguistic analysis in public speaking: evidence from a Gavel Club for people with aphasia.

Public speaking has been described as one of the most daunting tasks one can engage in, even more so for people with aphasia (PWA). Gavel Clubs (affiliated with Toastmasters International) were established over 20 years ago for those who want to engage in public speaking but do not meet the eligibility criteria for Toastmasters membership. This study is the first of its kind to systematically evaluate changes in the speeches of PWA attending a weekly Gavel Club. The aims were to compare Table Topics (TT) and Prepared Speeches (PS) which are two different tasks regularly performed in a Gavel Club; to measure linguistic change over time in the two speech types; and to determine the feasibility of a discourse measure for analysing public speeches. Thirty-six speeches (four each from nine PWA) were audio-recorded, transcribed and analysed using the Linguistic Communication Measure (LCM). The nine participants represented a wide range of aphasia severity. Analysis revealed that engaging in weekly speaking activities in the GC was associated with an improvement in conveying content and in grammaticality through an increase in total number of words and number of correct words produced. The LCM is a comprehensive analysis tool but proved to be challenging in its speed and utility when measuring linguistic change in public speeches of PWA. Regular GC participation appears to facilitate improved language abilities, but we have yet to find the best tool to demonstrate this.

Attention and Communication Following TBI: Making the Connection through a Meta-Narrative Systematic Review.

BACKGROUND AND AIM: Communication difficulties are one of the hallmark characteristics of adults following traumatic brain injury (TBI), a difficulty that incorporates multiple aspects of cognition and language. One aspect of cognition that impacts communication is attention. This review explores both attention and communication following moderate to severe TBI and aims to connect them through a narrative analysis of the discourse surrounding the terms and how they have evolved over time. This includes exploring and reviewing theories and specific constructs of these two aspects of cognition. METHOD: A meta-narrative systematic literature review was completed according to RAMESES methodology. RESULTS: A total of 37 articles were included in the review. The disciplines that populated the articles included, but were not limited to, speech language pathology (SLP) 36.5%, psychology 23.8%, and a collaboration of neuropsychology and SLP 7.9%. Of the papers that were included, 10% explored and supported theories of attention related to executive function affecting communication. Specific levels of attention were mapped onto specific communication skills with the corresponding year and authors to create a timeline and narrative of these concepts. CONCLUSIONS: The main communication behaviours that are related to attention in the context of post-TBI cognition include discourse, tangential communication, social communication, auditory comprehension, verbal reasoning, topic maintenance, interpretation of social cues and emotions, verbal expression, reading comprehension, verbal response speed, and subvocal rehearsal.

Recalibrating hope: A longitudinal study of the experiences of people with aphasia after stroke.

BACKGROUND: Hope is a critical resource for people with aphasia after stroke, sustaining people though times of distress and uncertainty and providing motivation. In the first months after stroke, hope is vulnerable to different influences, and people can struggle to identify and work towards hopes for the future. We have little knowledge about how people with aphasia experience hope in the longer term after stroke. OBJECTIVES: To identify how people with aphasia experience hope 1 year after stroke and how hope may change in the year after stroke. METHODS: The study used an Interpretive Description methodology. Interviews were conducted with four people with aphasia who had been interviewed 1 year previously. These were analysed using content analysis. RESULTS: All people reported a broad sense of hope for the future. They described an active process of recalibrating their early poststroke hopes through a process of reflecting on past progress, current function and what they considered might be possible and desirable in the future. People were able to develop 'new' hopes that were meaningful and seemingly achievable when they had a sense of a possible, desirable future. Those who struggled to see a possible future maintained a hope that things will be good. Social supports, a sense of progress, engagement in meaningful activities and interactions appeared crucial in helping people (re)develop hopes for their future. CONCLUSIONS: Hope and hopes for the future gradually changed after stroke. Hope, identity and social connectedness were closely entwined and could enable people to both dwell in the present and move towards desired futures. This research suggests clinicians should prioritise creating hope-fostering environments which support people to develop hope for their future.

What is communication assistance? Describing a new and emerging profession in the New Zealand youth justice system.

'Communication assistance' is a term that derives from section 80 of the Evidence Act 2006: a legislative provision that has given birth to a whole new profession in the New Zealand legal system. This legislative provision has been used to appoint a new role: that of the communication assistant to support complainants, witnesses and defendants of all ages with identified communication needs. This study focuses specifically on the provision of communication assistance for young people who offend in the New Zealand criminal justice system. It provides a qualitative analysis of professionals' descriptions (n = 28 participants) of communication assistance for this population in justice processes. The findings illustrate that communication assistance shares its core with a similar role in England and Wales, that of the intermediary, but that communication assistants in New Zealand have broader scope than their counterparts working in the area of youth justice.

Predictors of the time to attain full oral feeding in late preterm infants.

AIM: The aim of this study was to determine the factors that predict the timing and age at which preterm infants (born 32-36 weeks gestation) commenced and attained full oral feeding. METHODS: We conducted a retrospective review of medical records of 647 preterm infants born 2005-2011. Infants were from six neonatal intensive care units in New Zealand, all World Health Organisation Baby-friendly Hospital Initiative accredited. RESULTS: Median time to the first oral feed offered was one day, and median time to the time of full oral feeding was 12 days. No infants attained full oral feeding before 33(+3) weeks postmenstrual age. Gestational age, birthweight, medical conditions and location of the neonatal unit were significantly associated with the time taken to commence and attain full oral feeding. CONCLUSION: This study highlights the factors that are associated with the rate at which late preterm infants commence oral feeding and progress to full oral feeding. These findings offer important considerations not only for clinical practice but also discharge planning given the preference for preterm infants reaching full oral feeds before discharge from hospital. Prospective experimental research is required to confirm infant, maternal and environmental factors that influence feeding milestones in late preterm infants.

Stroke awareness and knowledge in an urban New Zealand population.

BACKGROUND: Stroke is the third most common cause of death and a major cause of chronic disability in New Zealand. Linked to risk factors that develop across the life-course, stroke is considered to be largely preventable. This study assessed the awareness of stroke risk, symptoms, detection, and prevention behaviors in an urban New Zealand population. METHODS: Demographics, stroke risk factors awareness, symptoms, responsiveness, and prevention behaviors were evaluated using a structured oral questionnaire. Binomial logistic regression analyses were used to identify predictors of stroke literacy. RESULTS: Although personal experience of stroke increased awareness of symptoms and their likeliness to indicate the need for urgent medical attention, only 42.7% of the respondents (n = 850) identified stroke as involving both blood and the brain. Educational attainment at or above a trade certificate, apprenticeship, or diploma increased the awareness of stroke symptoms compared with those with no formal educational attainment. Pacific Island respondents were less likely than New Zealand Europeans to identify a number of stroke risk factors. Maori, Pacific Island, and Asian respondents were less likely to identify symptoms of stroke and indicate the need for urgent medical attention. CONCLUSIONS: The variability in stroke awareness and knowledge may suggest the need to enhance stroke-related health literacy that facilitates understanding of risk and of factors that reduce morbidity and mortality after stroke in people of Maori and Pacific Island descent and in those with lower educational attainment or socioeconomic status. It is therefore important that stroke awareness campaigns include tailored components for target audiences.

The use of interpretive description within Kaupapa Maori research.

Kaupapa Maori research (KMR) is an Indigenous research approach that is decolonizing and transformative. Interpretive description (ID) is a qualitative methodology used to generate knowledge relevant to the applied health disciplines. In this article, we discuss how we combined KMR and ID to investigate the experiences of Maori (the Indigenous peoples of New Zealand) with aphasia and their whanau (extended family). This is novel because it is the first time these two approaches have been combined. In the context of aphasia research, we discuss how they work together in theory, and the synergies that became apparent in practice. We conclude that the combination of KMR and ID enables clinicians and Maori with aphasia to learn from each other and work together, thereby generating knowledge that makes a difference for Maori with aphasia and their whanau.

Examining the approaches used to assess decision-making capacity in healthcare practice.

AIM: To examine the approaches that are being used in New Zealand when conducting decision-making capacity (DMC) assessments among the healthcare professionals that commonly conduct DMC assessments and those that are involved in, but do not conduct, the assessments. METHOD: An online quantitative survey was conducted, lasting 10 minutes, including a mix of closed- and open-ended questions. The survey garnered responses from a total of n=78 participants. RESULTS: Bedside cognitive tests were found to be the most commonly reported tool used to assess DMC among those conducting and those contributing to DMC assessments. Nearly a third (31.9%) of participants conducting DMC assessments used a structured clinical interview as one of their most common approaches while 27.5% of this same group reported not being aware of this approach. It was reported by both those conducting and those contributing to DMC assessments that the current standards lack quality and consistency, with partial capacity being poorly understood and identified, and supported decision making often being overlooked for substitute decision making. CONCLUSIONS: Current approaches to DMC assessment lack standardisation and consistency, with assessment approaches being widely varied. This article serves as a call for the development of and adherence to nationally recognised standards for DMC assessments.

How Can Qualitative Methods Be Applied to Behavior Analytic Research: A Discussion and Suggestions for Implementation.

Behavior analysts in research and clinical practice are interested in an ever-expanding array of topics. They are compelled to explore the social validity of the interventions they propose and the findings they generate. As the field moves in these important directions, qualitative methods are becoming increasingly relevant. Representing a departure from small-n design favored by behavior analysts, qualitative approaches provide analysts a unique set of tools to answer questions that prioritize voice, experience, and understandings in context. Despite recognition of the value of qualitative approaches in other disciplines, application of qualitative methods in behavior analysis remains limited. One likely explanation is that behavior analysts are not yet fluent in applying qualitative approaches within their clinical and research investigations. To address this issue, exploration of qualitative research approaches in behavior analytic literature is needed, alongside practical advice for analysts who are interested in using qualitative methods. This article briefly outlines qualitative literature which pertains to behavior analysts wanting to incorporate qualitative methods into their inquiries. Attention is primarily drawn to the need for coherence in designing and implementing a robust qualitative study that aligns with the behavior analyst's aims and perspective on knowing. A set of guiding questions are provided to orient behavior analysts to considerations in qualitative research and outline how analysts can conceptualize a strong qualitative study. This article aims to support increased application of qualitative methods by behavior analysts, where these methods best address the function of the behavior analytic investigation.

Exploring training, involvement and confidence: a study of healthcare professionals in decision-making capacity assessments.

AIM: To explore the training, involvement and confidence of healthcare professionals involved in decision-making capacity (DMC) assessments, and to compare any differences between those conducting and those involved in, but not conducting DMC assessments. METHOD: A 10-minute anonymous, online survey was conducted with both closed and open questions. A total of 78 participants completed the survey. RESULTS: Training was lacking in quantity and adequacy. Only 14.1% received formal training during and post their qualification and only 38.5% reported the right amount of training. Just over 55% reported having the right amount of involvement, with 18% having too much and 27% having not enough involvement. A significantly higher response was given for having too much involvement by those conducting DMC assessments (p=0.006), while those not conducting felt they do not have enough involvement (p<0.001). Only 25.6% (n=20) were very confident in being able to explain DMC to a patient. CONCLUSIONS: Healthcare professionals working in this area urgently require support in the form of formal training and defined roles. Given what can be at stake for an individual undergoing a DMC assessment, it is imperative that improvements are made to upskill the workforce and utilise expertise of all healthcare professionals.

NowIKnowMyABCD: A global resource hub for researchers using data from the ABCD Study.

The Adolescent Brain and Cognitive Development (ABCD) Study, involving over 11,000 youth and their families, is a groundbreaking project examining various factors impacting brain and cognitive development. Despite yielding hundreds of publications and counting, the ABCD Study has lacked a centralized help platform to assist researchers in navigating and analyzing the extensive ABCD dataset. To support the ABCD research community, we created NowIKnowMyABCD, the first centralized documentation and communication resource publicly available to researchers using ABCD Study data. It consists of two core elements: a user-focused website and a moderated discussion board. The website serves as a repository for ABCD-related resources, tutorials, and a live feed of relevant updates and queries sourced from social media websites. The discussion board offers a platform for researchers to seek guidance, troubleshoot issues, and engage with peers. Our aim is for NowIKnowMyABCD to grow with participation from the ABCD research community, fostering transparency, collaboration, and adherence to open science principles.

Comparing the multivariate relationships of conceptual adversity models and structural brain development in adolescent girls: A registered report.

Adverse experiences throughout development confer risk for a multitude of negative long-term outcomes, but the processes via which these experiences are neurobiologically embedded are still unclear. Adolescence provides an opportunity to understand how these experiences impact the brain's rapidly changing structure. Two models are central to current adversity conceptualizations: a cumulative risk model, where all types of experiences are combined to represent accumulating stress, and a dimensional model, where certain features of experience (e.g., threat or deprivation) exert unique neurophysiological influence. In this registered report, we extended upon previous research by using a form of representational similarity analysis to examine whether the dimensional and cumulative risk models of adversity predict cortical thinning in frontoparietal and frontotemporal networks and volumetric changes in subcortical regions throughout adolescence. Drawing from a longitudinal sample of 179 adolescent girls (ages 10-13 years at the first wave) from Lane County, Oregon, United States, and up to four waves of follow-up data, we found that operationalizing adversity by similarity in threat and deprivation provided better prediction of brain development than similarity in overall adversity. However, these dimensions do not exhibit unique associations with developmental changes in the hypothesized brain changes. These results underscore the significance of carefully defining adversity and considering its impact on the entire brain. (PsycInfo Database Record (c) 2024 APA, all rights reserved).