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.].

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.

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.

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.

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.

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.

Rethinking the Place of Qualitative Methods in Behavior Analysis.

Single-case design research is pervasive and dominant in the field of behavior analysis (BA). It allows for effective application of behavior change technologies in a wide variety of real-world settings. However, as the field has grown, behavioral scholars have suggested incorporating other methods into the investigator's toolbox to supplement single-case design. To date, the call to expand beyond using only variations of single-case design as the standard for behavior analytic research has gone largely unheard. Given the need for behavior analytic work to be more closely aligned with consumer and stakeholder needs and priorities, along with a proliferation of practitioners and researchers in the field, now is the time to consider the benefits of qualitative research methods for behavior analysts. In particular, in areas of social validity and in exploring diverse applied topics, qualitative methods may help the field of behavior analysis to achieve greater success with documenting the outcomes from behavior change interventions. The present article explores areas where behavior analysis may benefit from utilizing qualitative methods, namely social validity and breadth of topics for study, and provides examples of the value of qualitative research from other fields. A brief outline of qualitative research is provided alongside consideration of the seven dimensions of applied behavior analysis. In situations where single-case design does not offer behavior analysts sufficient methodological opportunity, qualitative research methods could form a powerful addition to the field of behavior analysis.

Bioavailability of potentially toxic elements influences antibiotic resistance gene and mobile genetic element abundances in urban and rural soils.

Antibiotic resistance genes (ARGs) that can encode resistance traits in bacteria are found across the environment. While it is often difficult to discern their origin, their prevalence and diversity depends on many factors, one of which is their exposure to potentially toxic elements (PTE, i.e., metals and metalloids) in soils. Here, we investigated how ambient ARGs and mobile genetic elements (MGEs) relate to the relative bioavailability of different PTEs (total versus exchangeable and carbonate-bound PTE) in rural and urban soils in northeast England. The average relative abundances of ARGs in rural sites varied over a 3-log range (7.24 × 10-7 to 1.0 × 10-4 genes/16S rRNA), and relative ARG abundances in urban sites varied by four orders of magnitude (1.75 × 10-6 to 2.85 × 10-2 genes/16S rRNA). While beta-lactam and aminoglycoside resistance genes dominated rural and urban sites, respectively, non-specific ARGs, also called multidrug-resistance genes, were significantly more abundant in urban sites (p < 0.05). Urban sites also had higher concentrations of total and exchangeable forms of PTE than rural sites, whereas rural sites were higher in carbonate-bound forms. Significant positive Spearman correlations between PTEs, ARGs and MGEs were apparent, especially with bioavailable PTE fractions and at urban sites. This study found significant positive correlations between ARGs and beryllium (Be), which has not previously been reported. Overall, our results show that PTE bioavailability is important in explaining the relative selection of ARGs in soil settings and must be considered in future co-selection and ARG exposure studies.

The electrophysiology of aphasia: A scoping review.

OBJECTIVE: To systematically assess the body of literature using N400 and P600 as they relate to people with aphasia. The primary aim was to reveal patterns in the literature which could be used to direct future research in the development of clinically relevant Event-Related Potentials (ERPs) for language assessment, while also identifying gaps in existing knowledge and highlight areas of further inquiry. METHODS: A literature search was performed on studies published before May 2021. Relevant studies on aphasia and the two ERPs of interest were assessed for quality, and the relationship between aphasia and these ERPs was explored. RESULTS: A total of 721 articles were identified, with 30 meeting inclusion criteria. Although there is significant variation in the literature, this scoping review revealed people with aphasia show reduced amplitude, delayed latency and different distribution compared to controls, and that ERPs are modulated by severity of aphasia. CONCLUSIONS: To develop a relevant clinical tool for the management of aphasia, future research must strive to improve consistency within ERP methodology, with a greater number of diverse aphasia subtypes included in research. SIGNIFICANCE: This scoping review reveals N400 and P600 represent promising potential biomarkers for the diagnosis and ongoing management of aphasia.

Organic complexation of U(VI) in reducing soils at a natural analogue site: Implications for uranium transport.

Understanding the long-term fate, stability, and bioavailability of uranium (U) in the environment is important for the management of nuclear legacy sites and radioactive wastes. Analysis of U behavior at natural analogue sites permits evaluation of U biogeochemistry under conditions more representative of long-term equilibrium. Here, we have used bulk geochemical and microbial community analysis of soils, coupled with X-ray absorption spectroscopy and µ-focus X-ray fluorescence mapping, to gain a mechanistic understanding of the fate of U transported into an organic-rich soil from a pitchblende vein at the UK Needle's Eye Natural Analogue site. U is highly enriched in the Needle's Eye soils (∼1600 mg kg-1). We show that this enrichment is largely controlled by U(VI) complexation with soil organic matter and not U(VI) bioreduction. Instead, organic-associated U(VI) seems to remain stable under microbially-mediated Fe(III)-reducing conditions. U(IV) (as non-crystalline U(IV)) was only observed at greater depths at the site (>25 cm); the soil here was comparatively mineral-rich, organic-poor, and sulfate-reducing/methanogenic. Furthermore, nanocrystalline UO2, an alternative product of U(VI) reduction in soils, was not observed at the site, and U did not appear to be associated with Fe-bearing minerals. Organic-rich soils appear to have the potential to impede U groundwater transport, irrespective of ambient redox conditions.

Beyond N and P: The impact of Ni on crude oil biodegradation.

N and P are the key limiting nutrients considered most important for the stimulation of crude oil degradation but other trace nutrients may also be important. Experimental soil microcosms were setup to investigate crude oil degradation in the context of Ni amendments. Amended Nickel as NiO, NiCl2, or, a porphyrin complex either inhibited, had no effect, or, enhanced aerobic hydrocarbon degradation in an oil-contaminated soil. Biodegradation was significantly (95% confidence) enhanced (70%) with low levels of Ni-Porph (12 mg/kg) relative to an oil-only control; whereas, NiO (200 and 350 mg/kg) significantly inhibited (36 and 87%) biodegradation consistent with oxide particle induced reactive oxygen stress. Microbial community compositions were also significantly affected by Ni. In 16S rRNA sequence libraries, the enriched hydrocarbon degrading genus, Rhodococcus, was partially replaced by a Nocardia sp. in the presence of low levels of NiO (12 and 50 mg/kg). In contrast, the highest relative and absolute Rhodococcus abundances were coincident with the maximal rates of oil degradation observed in the Ni-Porph-amended soils. Growth dependent constitutive requirements for Ni-dependent urease or perhaps Ni-dependent superoxide dismutase enzymes (found in Rhodococcus genomes) provided a mechanistic explanation for stimulation. These results suggest biostimulation technologies, in addition to N and P, should also consider trace nutrients such as Ni tacitly considered adequately supplied and available in a typical soil.

Understanding drivers of antibiotic resistance genes in High Arctic soil ecosystems.

Soils in tropical and temperate locations are known to be a sink for the genetic potential of anthropogenic-driven acquired antibiotic resistance (AR). In contrast, accumulation of acquired AR is less probable in most Polar soils, providing a platform for characterizing background resistance and establishing a benchmark for assessing AR spread. Here, high-throughput qPCR and geochemistry were used to quantify the abundance and diversity of both antibiotic resistance genes (ARGs) and selected mobile genetic elements (MGEs) across eight soil clusters in the Kongsfjorden region of Svalbard in the High Arctic. Relative ARG levels ranged by over two orders of magnitude (10-6 to 10-4 copies/16S rRNA gene copy), and showed a gradient of potential human and wildlife impacts across clusters as evidenced by altered geochemical conditions and increased "foreign" ARG abundances (i.e., allochthonous), including blaNDM-1. Impacted clusters exhibited 100× higher total ARGs and MGEs in tandem with elevated secondary nutrients, especially available P that is typically low and limiting in Arctic soils. In contrast, ARGs in less-impacted clusters correlated strongly to local soil lithology. The most plausible source of exogenous P and allochthonous ARGs in this region is bird and other wildlife guano, disseminated either by local human wastes or via direct carriage and deposition. Regardless of pathway, accumulation of apparent allochthonous ARGs and MGEs in High Arctic soils is concerning, highlighting the importance of characterizing Arctic sites now to establish benchmarks for tracking AR spread around the world.

In situ arsenic oxidation and sorption by a Fe-Mn binary oxide waste in soil.

The ability of a Fe-Mn binary oxide waste to adsorb arsenic (As) in a historically contaminated soil was investigated. Initial laboratory sorption experiments indicated that arsenite [As(III)] was oxidized to arsenate [As(V)] by the Mn oxide component, with concurrent As(V) sorption to the Fe oxide. The binary oxide waste had As(III) and As(V) adsorption capacities of 70mgg-1 and 32mgg-1 respectively. X-ray Absorption Near-Edge Structure and Extended X-ray Absorption Fine Structure at the As K-edge confirmed that all binary oxide waste surface complexes were As(V) sorbed by mononuclear bidentate corner-sharing, with 2 Fe at ∼3.27Ǻ. The ability of the waste to perform this coupled oxidation-sorption reaction in real soils was investigated with a 10% by weight addition of the waste to an industrially As contaminated soil. Electron probe microanalysis showed As accumulation onto the Fe oxide component of the binary oxide waste, which had no As innately. The bioaccessibility of As was also significantly reduced by 7.80% (p<0.01) with binary oxide waste addition. The results indicate that Fe-Mn binary oxide wastes could provide a potential in situ remediation strategy for As and Pb immobilization in contaminated soils.

Dissolved Mn(III) in water treatment works: Prevalence and significance.

Dissolved Mn(III) has been identified at all stages throughout a Water Treatment Works (WTW) receiving inflow from a peaty upland catchment in NE England. Ninety percent of the influent total manganese into the WTW is particulate Mn, in the form of Mn oxide (>0.2 µm). Approximately 9% (mean value, n = 22, range of 0-100%) of the dissolved (<0.2 µm) influent Mn is present as dissolved Mn(III). Mn(III) concentrations are highest (mean of 49% of total dissolved Mn; n = 26, range of 17-89%) within the WTW where water comes into contact with the organic-rich sludges which are produced as waste products in the WTW. These Mn(III)-containing wastewaters are recirculated to the head of the works and constitute a large input of Mn(III) into the WTW. This is the first report of Mn(III) being identified in a WTW. The ability of Mn(III) to act as both an oxidant and a reductant is of interest to the water industry. Understanding the formation and removal of Mn(III) within may help reduce Mn oxide deposits in pipe networks. Further understanding how the ratio of Mn(III) to Mn(II) can be used to optimise dissolved Mn removal would save the water industry significant money in reducing discoloration 'events' at the customers' tap.

Dynamic measures of voice stability in young and old adults.

This paper examines age-related differences in voice quality between 15 young and 15 old speakers, using electroglottographic (EGG) recordings of three elicitation types: sustained vowels, hVd word lists, and readings of the Rainbow Passage. For each elicitation type, fundamental frequency (F0), contact quotient (Qx), and their standard deviations are analysed. Results found, for all three elicitations, that Qx was significantly lower for older speakers. F0 was higher for the older speakers, but this was only significant for the hVd word lists. Sustained vowels were used to examine the effect of target pitch and loudness on F0 and Qx. Both Qx and F0 were raised with increased target loudness. The hVd word lists were used to examine the phonetic effects of different vowels. Lip rounded vowels had higher Qx than non-lip rounded vowels. Readings of the Rainbow Passage encompassed prosodic and phonetic variations in F0 and Qx, in addition to voice quality. F0 and Qx contours of the hVd word lists and the vowel/ei/taken from the Rainbow Passage were analysed using the discrete cosine transform. The hVd frame produced coarticulation effects on the Qx contour, but no such effects were evident for the vowel /ei/. The study concluded that using multiple elicitation types is beneficial in the study of the effect of age on the voice, and that analysing contour tracks for F0 and Qx will allow further examination of how prosodic and phonetic effects interact with age-related changes in voice quality.