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Abstract Plant genebanks contain large numbers of germplasm accessions that likely harbor useful alleles or genes absent in commercial plant breeding programs. Broadening the genetic base of commercial alfalfa germplasm with these valuable genetic variations can be achieved by screening the extensive genetic diversity in germplasm collections and enabling maximal recombination among selected genotypes. In this study, we assessed the genetic diversity and differentiation of germplasm pools selected in northern U.S. latitudes (USDA Plant Hardiness Zone 7 or below) originating from Eurasian germplasm. The germplasm evaluated included four BASE populations (C0) from different geographical origins (Central Asia, Northeastern Europe, Balkans-Turkey-Black Sea, and Siberia/Mongolia), 20 cycle-one populations (C1) derived from each of the four BASE populations selected across five locations in the U.S. and Canada, and four commercial cultivars. Using a panel of 3,000 Diversity Array Technologies (DArTag) marker loci, we retrieved 2,994 target SNPs and approximately 12,000 microhaplotypes. Microhaplotypes exhibited higher genetic diversity values than target SNPs. Principal component analysis and discriminant analysis of principal components revealed significant population structure among the alfalfa populations based on geographical origin, while the check cultivars formed a central cluster. Inbreeding coefficients (FIS) ranged from − 0.1 to 0.006, with 27 out of 28 populations showing negative FIS values, indicating an excess of heterozygotes. Interpopulation genetic distances were calculated using Rho pairwise distances (FST adapted for autotetraploid species) and analysis of molecular variance (AMOVA) parameters. All BASE populations showed lower Rho values compared to C1 populations and check cultivars. AMOVA revealed that most of the genetic diversity was among individuals within populations, especially in BASE populations (92.7%). This study demonstrates that individual plants in BASE populations possess high genetic diversity, low interpopulation distances, and minimal inbreeding, characteristics that are essential for base-broadening selection. The populations developed in this project serve as valuable sources of novel alleles for North American alfalfa breeding programs, offering breeders access to diverse, regionally adapted pools for improving various alfalfa traits.

Abstract* The swift parrot (Lathamus discolor) is a Critically Endangered migratory parrot that breeds in Tasmania and winters on the Australian mainland. Here we provide a reference genome assembly for the swift parrot. We sequence PacBio HiFi reads to create a high-quality reference assembly and identify a complete mitochondrial sequence. We also generate a reference transcriptome from five organs to inform genome annotation. The genome was 1.24 Gb in length and consisted of 847 contigs with a contig N50 of 18.97 Gb and L50 of 20 contigs. This study provides an annotated reference assembly and transcriptomic resources for the swift parrot to assist in future conservation genomic research.

Introduction Critically ill patients are at risk of suboptimal beta-lactam antibiotic (beta-lactam) exposure due to the impact of altered physiology on pharmacokinetics. Suboptimal concentrations can lead to treatment failure or toxicity. Therapeutic drug monitoring (TDM) involves adjusting doses based on measured plasma concentrations and individualising dosing to improve the likelihood of improving exposure. Despite its potential benefits, its adoption has been slow, and data on implementation, dose adaptation and safety are sparse. The aim of this trial is to assess the feasibility and fidelity of implementing beta-lactam TDM-guided dosing in the intensive care unit setting.Methods and analysis A beta-lactam antibiotic Dose AdaPtation feasibility randomised controlled Trial using Therapeutic Drug Monitoring (ADAPT-TDM) is a single-centre, unblinded, feasibility randomised controlled trial aiming to enroll up to 60 critically ill adult participants (≥18 years). TDM and dose adjustment will be performed daily in the intervention group; the standard of care group will undergo plasma sampling, but no dose adjustment. The main outcomes include: (1) feasibility of recruitment, defined as the number of participants who are recruited from a pool of eligible participants, and (2) fidelity of TDM, defined as the degree to which TDM as a test is delivered as intended, from accurate sample collection, sample processing to result availability. Secondary outcomes include target attainment, uptake of TDM-guided dosing and incidence of neurotoxicity, hepatotoxicity and nephrotoxicity.Ethics and dissemination This study has been approved by the Alfred Hospital human research ethics committee, Office of Ethics and Research Governance (reference: Project No. 565/22; date of approval: 22/11/2022). Prospective consent will be obtained and the study will be conducted in accordance with the Declaration of Helsinki. The finalised manuscript, including aggregate data, will be submitted for publication in a peer reviewed journal. ADAPT-TDM will determine whether beta-lactam TDM-guided dose adaptation is reproducible and feasible and provide important information required to implement this intervention in a phase III trial.Trial registration number Australian New Zealand Clinical Trials Registry, ACTRN12623000032651.

Abstract The number of genome-level resources for non-model species continues to rapidly expand. However, frog species remain underrepresented, with up to 90% of frog genera having no genomic or transcriptomic data. Here, we assemble the first genomic and transcriptomic resources for the recently described southern stuttering frog (Mixophyes australis). The southern stuttering frog is ground-dwelling, inhabiting naturally vegetated riverbanks in south-eastern Australia. Using PacBio HiFi long-read sequencing and Hi-C scaffolding, we generated a high-quality genome assembly, with a scaffold N50 of 369.3 Mb and 95.1% of the genome contained in twelve scaffolds. Using this assembly, we identified the mitochondrial genome, and assembled six tissue-specific transcriptomes. We also bioinformatically characterised novel sequences of two families of antimicrobial peptides (AMPs) in the southern stuttering frog, the cathelicidins and β-defensins. While traditional peptidomic approaches to peptide discovery have typically identified one or two AMPs in a frog species from skin secretions, our bioinformatic approach discovered 12 cathelicidins and two β-defensins that were expressed in a range of tissues. We investigated the novelty of the peptides and found diverse predicted activities. Our bioinformatic approach highlights the benefits of multi-omics resources in peptide discovery and contributes valuable genomic resources in an under-represented taxon.

Abstract The Tasmanian devil (Sarcophilus harrisii) is endangered due to the spread of Devil Facial Tumour Disease (DFTD), a contagious cancer with no current treatment options. Here we test whether seven recently characterized Tasmanian devil cathelicidins are involved in cancer regulation. We measured DFTD cell viability in vitro following incubation with each of the seven peptides and describe the effect of each on gene expression in treated cells. Four cathelicidins (Saha-CATH3, 4, 5 and 6) were toxic to DFTD cells and caused general signs of cellular stress. The most toxic peptide (Saha-CATH5) also suppressed the ERBB and YAP1/TAZ signaling pathways, both of which have been identified as important drivers of cancer proliferation. Three cathelicidins induced inflammatory pathways in DFTD cells that may potentially recruit immune cells in vivo. This study suggests that devil cathelicidins have some anti-cancer and inflammatory functions and should be explored further to determine whether they have potential as treatment leads.

Background/Aims Some sessile serrated lesions (SSLs) progress into dysplasia and colorectal cancer, however, the clinical and endoscopic characteristics of SSLs with dysplasia remain to be determined. In this study, we elucidated these characteristics in SSLs with dysplasia/carcinoma, compared with those of SSLs without dysplasia. Methods We retrospectively collected the clinical, endoscopic, and pathological data of 254 SSLs from 216 patients endoscopically resected between January 2009 and December 2020. Results All SSLs included 179 without dysplasia and 75 with dysplasia/carcinoma, including 55 with low-grade dysplasia, 10 with high-grade dysplasia, and 10 with submucosal cancer. In clinical characteristics, SSLs with dysplasia/carcinoma were significantly associated with advanced age, metabolic diseases, and high-risk adenomas. In endoscopic characteristics, SSLs with dysplasia/carcinoma were significantly associated with the distal colon, large size, polypoid morphology, surface-changes, no mucus cap, and narrow-band imaging international colorectal endoscopic classification (NICE) type 2/3. In the multivariate analysis, high-risk adenomas (odds ratio [OR], 2.98; p = 0.01), large size (OR, 1.18; p < 0.01), depression (OR, 11.74; p = 0.03), and NICE type 2/3 (OR, 14.97; p < 0.01) were significantly associated with SSLs with dysplasia/carcinoma. Conclusions SSLs had a higher risk of dysplasia in the distal colon than in the proximal colon. SSLs with large size, depression, and adenomatous surface-patterns, as well as those in patients with high-risk adenomas, increased the risk of dysplasia/carcinoma. This suggests that the clinical and endoscopic characteristics can aid in the diagnosis and management of SSLs with dysplasia/carcinoma.

Abstract Background The need to belong is a fundamental human desire that provides the basis for relationships and community; it provides a sense of security that enables growth and development. This sense of belonging is pivotal to new University students, indeed, without it, students are at greater risk of failing or withdrawing from their studies. Yet developing a sense of belonging within a new cohort is complex and multi-faceted and further complicated by a sudden shift away from in-person to online learning. Using the situated-learning framework, our study explores first year clinical health students’ sense of belonging in the context of the rapid transition to online learning because of the COVID-19 pandemic. Methods We utilised a current mixed-method approach including a survey incorporating previously validated tools, demographic and open-ended qualitative questions. Data was also gathered from three focus groups: two dedicated student groups and one academic focus group. Qualitative data was subjected to thematic analysis whilst descriptive statistics were used to describe the quantitative data. Results 179 first year students complete the survey and four students, and five academics were involved in the focus groups. All participants were from clinical health science courses at an Australian university. Our qualitative results indicated a global theme of: Navigating belonging during the COVID-19 crisis: a shared responsibility; with four organising themes describing (1) dimensions of belonging, (2) individual experiences and challenges, (3) reconceptualising teaching and learning, and (4) relationships are central to belonging. Conclusion While the rapid transition to online learning did not greatly impact knowledge acquisition of first-year students in this cohort, the lack of sense of belonging highlights the need for further research into development of this essential aspect of learning in the online domain. Although contextualised in the COVID-19 pandemic, it became clear that the findings will remain relevant beyond the current situation, as a student’s need to belong will always be present in the face of challenges or change.

There are many advantages to transitioning from conducting marine wildlife surveys via human observers onboard light-aircraft, to capturing aerial imagery using drones. However, it is important to maintain the validity of long-term data series whilst transitioning from observer to imagery surveys. We need to understand how the detection rates of target species in images compare to those collected from observers in piloted aircraft, and the factors influencing detection rates from each platform. We conducted trial ScanEagle drone surveys of dugongs in Shark Bay, Western Australia, covering the full extent of the drone’s range (∼100 km), concurrently with observer surveys, with the drone flying above or just behind the piloted aircraft. We aimed to test the assumption that drone imagery could provide comparable detection rates of dugongs to human observers when influenced by same environmental conditions. Overall, the dugong sighting rate (i.e., count of individual dugongs) was 1.3 (95% CI [0.98–1.84]) times higher from the drone images than from the observers. The group sighting rate was similar for the two platforms, however the group sizes detected within the drone images were significantly larger than those recorded by the observers, which explained the overall difference in sighting rates. Cloud cover appeared to be the only covariate affecting the two platforms differently; the incidence of cloud cover resulted in smaller group sizes being detected by both platforms, but the observer group sizes dropped much more dramatically (by 71% (95% CI [31–88]) compared to no cloud) than the group sizes detected in the drone images (14% (95% CI [−28–57])). Water visibility and the Beaufort sea state also affected dugong counts and group sizes, but in the same way for both platforms. This is the first direct simultaneous comparison between sightings from observers in piloted aircraft and a drone and demonstrates the potential for drone surveys over a large spatial-scale.

Summary: Background: COVID-19 vaccines have been critical for protection against severe disease following infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) but gaps remain in our understanding of the immune responses that contribute to controlling subclinical and mild infections. Methods: Vaccinated, active-duty US military service members were enrolled in a non-interventional, minimal-risk, observational study starting in May, 2021. Clinical data, serum, and saliva samples were collected from study participants and were used to characterise the humoral immune responses to vaccination and to assess its impact on clinical and subclinical infections, as well as virologic outcomes of breakthrough infections (BTI) including viral load and infection duration. Findings: The majority of VIRAMP participants had received the Pfizer COVID-19 vaccine and by January, 2022, N = 149 had a BTI. The median BTI duration (PCR+ days) was 4 days and the interquartile range was 1–8 days. Participants that were nucleocapsid seropositive prior to their BTI had significantly higher levels of binding and functional antibodies to the spike protein, shorter median duration of infections, and lower median peak viral loads compared to seronegative participants. Furthermore, levels of neutralising antibody, ACE2 blocking activity, and spike-specific IgA measured prior to BTI also correlated with the duration of infection. Interpretation: We extended previous findings and demonstrate that a subset of vaccine-induced humoral immune responses, along with nucleocapsid serostatus are associated with control of SARS-CoV-2 breakthrough infections in the upper airways. Funding: This work was funded by the DoD Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND) in collaboration with the Defense Health Agency (DHA) COVID-19 funding initiative for the VIRAMP study.

A novel Hendra virus variant, genotype 2, was recently discovered in a horse that died after acute illness and in Pteropus flying fox tissues in Australia. We detected the variant in flying fox urine, the pathway relevant for spillover, supporting an expanded geographic range of Hendra virus risk to horses and humans.

We identified and isolated a novel Hendra virus (HeV) variant not detected by routine testing from a horse in Queensland, Australia, that died from acute illness with signs consistent with HeV infection. Using whole-genome sequencing and phylogenetic analysis, we determined the variant had ≈83% nt identity with prototypic HeV. In silico and in vitro comparisons of the receptor-binding protein with prototypic HeV support that the human monoclonal antibody m102.4 used for postexposure prophylaxis and current equine vaccine will be effective against this variant. An updated quantitative PCR developed for routine surveillance resulted in subsequent case detection. Genetic sequence consistency with virus detected in grey-headed flying foxes suggests the variant circulates at least among this species. Studies are needed to determine infection kinetics, pathogenicity, reservoir-species associations, viral-host coevolution, and spillover dynamics for this virus. Surveillance and biosecurity practices should be updated to acknowledge HeV spillover risk across all regions frequented by flying foxes.

Introduction Patient-reported antibiotic allergy labels (AALs) are common. These labels have been demonstrated to have a negative impact on use of appropriate antibiotics and patient-related health outcomes. These patients are more likely to receive suboptimal antibiotics, have increased rates of surgical site infections and are more likely to be colonised with multidrug-resistant organisms. Increasing recognition that antibiotic allergy forms a key part of good antimicrobial stewardship has led to calls for greater access to antibiotic allergy assessment.PREPARE is a pilot randomised controlled trial of beta-lactam allergy assessment and point of care delabelling in perioperative patients utilising a validated antibiotic allergy assessment tool that has been repurposed into a smartphone application. The aim of the study is to assess the feasibility and safety of this approach in the perioperative outpatient setting.Methods and analysis Adult participants requiring elective surgery and are likely to require prophylactic intravenous antibiotics will be recruited. During the intervention phase, participants will be randomised to the intervention or control arm, with control patients receiving usual standard of care. Those randomised to intervention undertake a risk assessment via the smartphone application, with those deemed low risk proceeding to direct oral provocation with either a penicillin or cephalosporin. Study outcomes will be evaluated in the postintervention phase, 30 and 90 days after surgery.Feasibility of intervention delivery and recruitment will be reported as proportions with respective 95% CIs. Participants who experience an antibiotic adverse event will be reported by group with respective 95% CIs and compared using modified Poisson regression model with robust SE estimation.Ethics and dissemination This protocol has received approval from the Austin Health human research and ethics committee, Heidelberg, Victoria, Australia (HREC/17/Austin/575). Results will be disseminated via publication in peer-reviewed journals as well as presentation at international conferences.Trial registration number ACTRN12620001295932.

BackgroundChlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are the most common bacterial causes of sexually transmitted infection (STI) in the United States (US). The purpose of this study was to determine the frequency of reinfection during a six-month study period and to evaluate the retesting interval for those infected with CT or NG.MethodsWe conducted a prospective, six-month follow-up study among US military personnel with new onset, laboratory-confirmed CT or NG, recruited from an STI clinic at a large military base from January 2018 to January 2020. Each participant was randomly assigned to one of four groups, which differed only by the timing of the first study-associated follow-up visit after CT or NG diagnosis.ResultsOf the 347 initially recruited into the study, 267 participants completed a follow-up visit prior to their scheduled, final visit 6 months after initial infection. The median age at enrollment was 22 years and 41.0% were female. There were 32 (12.0%) reinfections (30 CT and 2 NG) after treatment of an index diagnosis of CT or NG within the six-month study period. Six of the CT reinfections were only detected at the final visit. A review of medical records revealed additional CT and NG reinfections. The probability of detecting a reinfection did not vary significantly by timing of follow-up.ConclusionsThe likelihood of detecting CT or NG reinfection did not differ according to time of follow up visit among study participants, thus supporting CDC guidance to retest three months post treatment. Efforts should continue to focus on STI prevention and risk reduction.

ObjectiveValidate the performance characteristics of two analyte specific, laboratory developed tests (LDTs) for the quantification of SARS-CoV-2 subgenomic RNA (sgRNA) and viral load on the Hologic Panther Fusion® using the Open Access functionality.MethodsCustom-designed primers/probe sets targeting the SARS-CoV-2 Envelope gene (E) and subgenomic E were optimized. A 20-day performance validation following laboratory developed test requirements was conducted to assess assay precision, accuracy, analytical sensitivity/specificity, lower limit of detection and reportable range.ResultsQuantitative SARS-CoV-2 sgRNA (LDT-Quant sgRNA) assay, which measures intermediates of replication, and viral load (LDT-Quant VLCoV) assay demonstrated acceptable performance. Both assays were linear with an R2 and slope equal to 0.99 and 1.00, respectively. Assay precision was evaluated between 4-6 Log10 with a maximum CV of 2.6% and 2.5% for LDT-Quant sgRNA and LDT-Quant VLCoV respectively. Using negative or positive SARS-CoV-2 human nasopharyngeal swab samples, both assays were accurate (kappa coefficient of 1.00 and 0.92). Common respiratory flora and other viral pathogens were not detected and did not interfere with the detection or quantification by either assay. Based on 95% detection, the assay LLODs were 729 and 1206 Copies/mL for the sgRNA and VL load LDTs, respectively.ConclusionThe LDT-Quant sgRNA and LDT-Quant VLCoV demonstrated good analytical performance. These assays could be further investigated as alternative monitoring assays for viral replication; and thus, medical management in clinical settings which could inform isolation/quarantine requirements.

BackgroundThe evidence for an increased incidence of sexually transmitted infections (STIs) among patients utilizing HIV pre-exposure prophylaxis (PrEP) has been inconsistent. We assessed the risk of incident STI while on PrEP compared to periods off PrEP among military service members starting PrEP.MethodsIncidence rates of chlamydia, gonorrhea, syphilis, hepatitis C virus, and HIV were determined among military service members without HIV prescribed daily oral tenofovir disoproxil fumarate and emtricitabine for HIV PrEP from February 1, 2014 through June 10, 2016. Hazard ratios for incident STIs were calculated using an Anderson-Gill recurrent event proportional hazard regression model.ResultsAmong 755 male service members, 477 (63%) were diagnosed with incident STIs (overall incidence 21.4 per 100 person-years). Male service members had a significantly lower risk of any STIs (adjusted hazard ratio (aHR) 0.21, 95% CI 0.11-0.40) while using PrEP compared to periods off PrEP after adjustment for socio-demographic characteristics, reasons for initiating PrEP, surveillance period prior to PrEP initiation, and the effect of PrEP on site and type of infection in multivariate analysis. However, when stratifying for anatomical site and type of infection, the risk of extragenital gonorrhea infection (pharyngeal NG: aHR 1.84, 95% CI 0.82-4.13, p = 0.30; rectal NG: aHR 1.23, 95% CI 0.60-2.51, p = 1.00) and extragenital CT infection (pharyngeal CT: aHR 2.30, 95% CI 0.46-11.46, p = 0.81; rectal CT: aHR 1.36, 95% CI 0.81-2.31, p = 0.66) was greater on PrEP compared to off PrEP although these values did not reach statistical significance.ConclusionsThe data suggest entry into PrEP care reduced the overall risk of STIs following adjustment for anatomical site of STI and treatment. Service members engaged in PrEP services also receive more STI prevention counseling, which might contribute to decreases in STI risk while on PrEP.

Background: Although biological therapies have transformed the outlook for those with rheumatoid arthritis, there is a lack of any meaningful response in approximately 40% of patients. The role of B cells in rheumatoid arthritis pathogenesis is well recognised and is supported by the clinical efficacy of the B-cell-depleting agent rituximab (MabThera, F. Hoffman La-Roche Ltd, Basel, Switzerland). Rituximab is licensed for use in rheumatoid arthritis following failure of conventional synthetic disease-modifying antirheumatic drugs and tumour necrosis factor inhibitor therapy. However, over 50% of patients show low/absent synovial B-cell infiltration, suggesting that, in these patients, inflammation is driven by alternative cell types. This prompted us to test the hypothesis that, in synovial biopsy B-cell-poor patients, tocilizumab (RoActemra, F. Hoffman La-Roche Ltd, Basel, Switzerland) (targeting interleukin 6) is superior to rituximab (targeting CD20+/B cells). Design: The R4–RA (A Randomised, open-labelled study in anti-TNFalpha inadequate responders to investigate the mechanisms for Response, Resistance to Rituximab versus Tocilizumab in Rheumatoid Arthritis patients) trial is a 48-week Phase IV, open-label, randomised controlled trial conducted in 19 European centres that recruited patients failing on or intolerant to conventional synthetic disease-modifying antirheumatic drug therapy and at least one tumour necrosis factor inhibitor. Participants: Synovial tissue was obtained at trial entry and classified histologically as B-cell rich or B-cell poor to inform balanced stratification. Patients were randomised on a 1 : 1 basis to receive standard therapy with rituximab or tocilizumab. B-cell-poor/-rich molecular classification was also carried out. The study was powered to test the superiority of tocilizumab over rituximab at 16 weeks in the B-cell-poor population. Main outcome measures: The primary end point was defined as an improvement in the Clinical Disease Activity Index (CDAI) score of ≥ 50% from baseline. In addition, patients were considered to be non-responders if they did not reach an improvement in CDAI score of ≥ 50% and a CDAI score of

Fascin is an important regulator of F-actin bundling leading to enhanced filopodia assembly. Fascin is also overexpressed in most solid tumours where it supports invasion through control of F-actin structures at the periphery and nuclear envelope. Recently, fascin has been identified in the nucleus of a broad range of cell types but the contributions of nuclear fascin to cancer cell behaviour remain unknown. Here, we demonstrate that fascin bundles F-actin within the nucleus to support chromatin organisation and efficient DDR. Fascin associates directly with phosphorylated Histone H3 leading to regulated levels of nuclear fascin to support these phenotypes. Forcing nuclear fascin accumulation through the expression of nuclear-targeted fascin-specific nanobodies or inhibition of Histone H3 kinases results in enhanced and sustained nuclear F-actin bundling leading to reduced invasion, viability, and nuclear fascin-specific/driven apoptosis. These findings represent an additional important route through which fascin can support tumourigenesis and provide insight into potential pathways for targeted fascin-dependent cancer cell killing.

Abstract Margins of wide local excisions in breast conserving surgery are tested through histology, which can delay results by days and lead to second operations. Detection of margin involvement intraoperatively would allow the removal of additional tissue during the same intervention. X-ray phase contrast imaging (XPCI) provides soft tissue sensitivity superior to conventional X-rays: we propose its use to detect margin involvement intraoperatively. We have developed a system that can perform phase-based computed tomography (CT) scans in minutes, used it to image 101 specimens approximately half of which contained neoplastic lesions, and compared results against those of a commercial system. Histological analysis was carried out on all specimens and used as the gold standard. XPCI-CT showed higher sensitivity (83%, 95% CI 69–92%) than conventional specimen imaging (32%, 95% CI 20–49%) for detection of lesions at margin, and comparable specificity (83%, 95% CI 70–92% vs 86%, 95% CI 73–93%). Within the limits of this study, in particular that specimens obtained from surplus tissue typically contain small lesions which makes detection more difficult for both methods, we believe it likely that the observed increase in sensitivity will lead to a comparable reduction in the number of re-operations.

Abstract Background The diverse rural medical education initiatives that have been developed in Australia to address the medical workforce maldistribution have been less successful in many smaller and remote communities. This study explored the factors that attract and retain GP registrars and supervisors and the impact that localised training (i.e., rural and remote workplace-based training and support) has on both GP registrars and supervisors, and the GP workforce in rural and remote underserved areas. Methods A purposive sample of 79 GP registrars, supervisors, practice managers, health services staff and community representatives living and working in areas of low GP workforce in rural and remote Australia were invited to participate in semi-structured interviews and one focus group divided over two phases. Thematic analysis was used to explore themes within the data. Findings Attractors and barriers to rural and remote practice were identified as the main themes. Attractors include family and community lifestyle factors, individual intrinsic motivators, and remote medicine experiences. In contrast, barriers include work related, location, or family factors. Further, localised GP training was reported to specifically influence GP registrars and supervisors through education, social and financial factors. Conclusion The current study has provided a contemporary overview of the issues encountered in expanding GP training capacity in rural and remote communities to improve the alignment of training opportunities with community and workforce needs. Strategies including matching scope of practice to registrar interests have been implemented to promote the attractors and lessen the barriers associated with rural and remote practice.

Introduction Antimicrobial resistance is a growing global health threat, driven by increasing inappropriate use of antimicrobials. High prevalence of unnecessary use of antimicrobials in residential aged care facilities (RACFs) has driven demand for the development and implementation of antimicrobial stewardship (AMS) programmes. The Stepped-wedge Trial to increase antibiotic Appropriateness in Residential aged care facilities and model Transmission of antimicrobial resistance (START) will implement and evaluate the impact of a nurse-led AMS programme on antimicrobial use in 12 RACFs.Methods and analysis The START trial will implement and evaluate a nurse-led AMS programme via a stepped-wedge cluster randomised controlled trial design in 12 RACFs over 16 months. The AMS programme will incorporate education, aged care-specific treatment guidelines, documentation forms, and audit and feedback strategies that will target aged care staff, general practitioners, pharmacists, and residents and their families. The intervention will primarily focus on urinary tract infections, lower respiratory tract infections, and skin and soft tissue infections. RACFs will transition from control to intervention phases in random order, two at a time, every 2 months, with a 2-month transition, wash-in period. The primary outcome is the cumulative proportion of residents within each facility prescribed an antibiotic during each month and total days of antibiotic use per 1000 occupied bed days. Secondary outcomes include the number of courses of systemic antimicrobial therapy, antimicrobial appropriateness, antimicrobial resistant organisms, Clostridioides difficile infection, change in antimicrobial susceptibility profiles, hospitalisations and all-cause mortality. Analyses will be conducted according to the intention-to-treat principle.Ethics and dissemination Ethics approval has been granted by the Alfred Hospital Human Research Ethics Committee (HREC/18/Alfred/591). Research findings will be disseminated through peer-reviewed publications, conferences and summarised reports provided to participating RACFs.Trial registration number NCT03941509.

ObjectivesThe development of frailty tools from electronically recorded healthcare data allows frailty assessments to be routinely generated, potentially beneficial for individuals and healthcare providers. We wished to assess the predictive validity of a frailty index (FI) derived from interRAI Community Health Assessment (CHA) for outcomes in older adults residing in retirement villages (RVs), elsewhere called continuing care retirement communities.DesignProspective cohort study.Setting and participants34 RVs across two district health boards in Auckland, Aotearoa New Zealand (NZ). 577 participants, mean age 81 years; 419 (73%) female; 410 (71%) NZ European, 147 (25%) other European, 8 Asian (1%), 7 Māori (1%), 1 Pasifika (MethodsinterRAI-CHA FI tool was used to stratify participants into fit (0-0.12), mild (>0.12-0.24), moderate (>0.24-0.36) and severe (>0.36) frail groups at baseline (the latter two grouped due to low numbers of severely frail). Primary outcome was acute hospitalization; secondary outcomes included long-term care (LTC) entry and mortality. The relationship between frailty and outcomes were explored with multivariable Cox regression, estimating hazard ratios (HRs) and 95% confidence intervals (95%CIs).ResultsOver mean follow-up of 2.5 years, 33% (69/209) of fit, 58% (152/260) mildly frail and 79% (85/108) moderate-severely frail participants at baseline had at least one acute hospitalization. Compared to the fit group, significantly increased risk of acute hospitalization were identified in mildly frail (adjusted HR = 1.88, 95%CI = 1.41-2.51, pConclusions and implicationsThe FI derived from interRAI-CHA has robust predictive validity for acute hospitalization, LTC entry and mortality. This adds to the growing literature of use of interRAI tools in this way and may assist healthcare providers with rapid identification of frailty.

The black flying fox (Pteropus alecto) is a natural reservoir for Hendra virus, a paramyxovirus that causes fatal infections in humans and horses in Australia. Increased excretion of Hendra virus by flying foxes has been hypothesized to be associated with physiological or energetic stress in the reservoir hosts. The objective of this study was to explore the leukocyte profiles of wild-caught P. alecto, with a focus on describing the morphology of each cell type to facilitate identification for clinical purposes and future virus spillover research. To this end, we have created an atlas of images displaying the commonly observed morphological variations across each cell type. We provide quantitative and morphological information regarding the leukocyte profiles in bats captured at two roost sites located in Redcliffe and Toowoomba, Queensland, Australia, over the course of two years. We examined the morphology of leukocytes, platelets, and erythrocytes of P. alecto using cytochemical staining and characterization of blood films through light microscopy. Leukocyte profiles were broadly consistent with previous studies of P. alecto and other Pteropus species. A small proportion of individual samples presented evidence of hemoparasitic infection or leukocyte morphological traits that are relevant for future research on bat health, including unique large granular lymphocytes. Considering hematology is done by visual inspection of blood smears, examples of the varied cell morphologies are included as a visual guide. To the best of our knowledge, this study provides the first qualitative assessment of P. alecto leukocytes, as well as the first set of published hematology reference images for this species.

Combining diagnostic specimens into pools has been considered as a strategy to augment throughput, decrease turnaround time, and leverage resources. This study utilized a multi-parametric approach to assess optimum pool size, impact of automation, and effect of nucleic acid amplification chemistries on the detection of SARS-CoV-2 RNA in pooled samples for surveillance testing on the Hologic Panther Fusion® System. Dorfman pooled testing was conducted with previously tested SARS-CoV-2 nasopharyngeal samples using Hologic's Aptima® and Panther Fusion® SARS-CoV-2 Emergency Use Authorization assays. A manual workflow was used to generate pool sizes of 5:1 (five samples: one positive, four negative) and 10:1. An automated workflow was used to generate pool sizes of 3:1, 4:1, 5:1, 8:1 and 10:1. The impact of pool size, pooling method, and assay chemistry on sensitivity, specificity, and lower limit of detection (LLOD) was evaluated. Both the Hologic Aptima® and Panther Fusion® SARS-CoV-2 assays demonstrated >85% positive percent agreement between neat testing and pool sizes ≤5:1, satisfying FDA recommendation. Discordant results between neat and pooled testing were more frequent for positive samples with CT>35. Fusion® CT (cycle threshold) values for pooled samples increased as expected for pool sizes of 5:1 (CT increase of 1.92-2.41) and 10:1 (CT increase of 3.03-3.29). The Fusion® assay demonstrated lower LLOD than the Aptima® assay for pooled testing (956 vs 1503 cp/mL, pool size of 5:1). Lowering the cut-off threshold of the Aptima® assay from 560 kRLU (manufacturer's setting) to 350 kRLU improved the assay sensitivity to that of the Fusion® assay for pooled testing. Both Hologic's SARS-CoV-2 assays met the FDA recommended guidelines for percent positive agreement (>85%) for pool sizes ≤5:1. Automated pooling increased test throughput and enabled automated sample tracking while requiring less labor. The Fusion® SARS-CoV-2 assay, which demonstrated a lower LLOD, may be more appropriate for surveillance testing.

Objective Inter-day reliability of sweat measurements, including the absorbent patch and modified iodine-paper techniques, at rest and exercise were evaluated. We further evaluated the effect of iodine paper size and the method of establishing sweat gland activation (sweat gland counting or surface area covered) on reliability. Furthermore, the relationships between all measurement techniques and metabolic heat production [Ḣprod] and evaporative requirement for heat balance [Ėreq] were determined. Method Twelve participants were assessed for whole-body sweat loss (WBSL), local sweat rate (LSR; absorbent patch) and sweat gland activation (SGA; iodine-paper) during rest and sub-maximal cycling at ~200, ~250 and ~300 W/m2 Ḣprod in the heat. Variations in iodine paper (1 x 1 cm-9 x 9 cm) were used to quantify SGA by counting sweat glands or surface area covered. The ‘optimal’ area of SGA was also determined based on the highest density of recruited glands. Results All measures of the sweating response were positively related with Ḣprod and Ėreq (r = 0.53–0.84), with the 9 x 9 cm and 6 x 6 cm iodine paper sizes being the strongest (r = 0.66–0.84) for SGA. Superior inter-day reliability was found for all measures during exercise (CV% = 6–33.2) compared to rest (CV% = 33.5–77.9). The iodine-paper technique was most reliable at 9 x 9 cm (CV% = 15.9) or when the 1 x 1 cm (CV% = 17.6) and 3 x 3 cm (CV% = 15.5) optimal SGA was determined, particularly when measuring the sweat gland number. Significance WBSL, LSR and SGA measurement techniques are sufficiently reliable to detect changes in thermal sweating typically reported. We recommend 9 x 9 cm paper sizes or 1 x 1 cm-3 x 3 cm optimal areas, using either gland counting or surface area to determine SGA.

Measures of lung function are heritable, and thus, we sought to utilise genetics to propose drug-repurposing candidates that could improve respiratory outcomes. Lung function measures were found to be genetically correlated with seven druggable biochemical traits, with further evidence of a causal relationship between increased fasting glucose and diminished lung function. Moreover, we developed polygenic scores for lung function specifically within pathways with known drug targets and investigated their relationship with pulmonary phenotypes and gene expression in independent cohorts to prioritise individuals who may benefit from particular drug-repurposing opportunities. A transcriptome-wide association study (TWAS) of lung function was then performed which identified several drug–gene interactions with predicted lung function increasing modes of action. Drugs that regulate blood glucose were uncovered through both polygenic scoring and TWAS methodologies. In summary, we provided genetic justification for a number of novel drug-repurposing opportunities that could improve lung function.

Devastating fires in Australia over 2019-20 decimated native fauna and flora, including koalas. The resulting population bottleneck, combined with significant loss of habitat, increases the vulnerability of remaining koala populations to threats which include disease. Chlamydia is one disease which causes significant morbidity and mortality in koalas. The predominant pathogenic species, Chlamydia pecorum, causes severe ocular, urogenital and reproductive tract disease. In marsupials, including the koala, gene expansions of an antimicrobial peptide family known as cathelicidins have enabled protection of immunologically naïve pouch young during early development. We propose that koala cathelicidins are active against Chlamydia and other bacteria and fungi. Here we describe ten koala cathelicidins, five of which contained full length coding sequences that were widely expressed in tissues throughout the body. Focusing on these five, we investigate their antimicrobial activity against two koala C. pecorum isolates from distinct serovars; MarsBar and IPTaLE, as well as other bacteria and fungi. One cathelicidin, PhciCath5, inactivated C. pecorum IPTaLE and MarsBar elementary bodies and significantly reduced the number of inclusions compared to the control (p

Serological assessment of SARS-CoV-2 specific responses are an essential tool for determining the prevalence of past SARS-CoV-2 infections in the population especially when testing occurs after symptoms have developed and limited contact tracing is in place. The goal of our study was to test a new 10-plex electro-chemiluminescence-based assay to measure IgM and IgG responses to the spike proteins from multiple human coronaviruses including SARS-CoV-2, assess the epitope specificity of the SARS-CoV-2 antibody response against full-length spike protein, receptor-binding domain and N-terminal domain of the spike protein, and the nucleocapsid protein. We carried out the assay on samples collected from three sample groups: subjects diagnosed with COVID-19 from the U.S. Army hospital at Camp Humphreys in Pyeongtaek, South Korea; healthcare administrators from the same hospital but with no reported diagnosis of COVID-19; and pre-pandemic samples. We found that the new CoV-specific multiplex assay was highly sensitive allowing plasma samples to be diluted 1:30,000 with a robust signal. The reactivity of IgG responses to SARS-CoV-2 nucleocapsid protein and IgM responses to SARS-CoV-2 spike protein could distinguish COVID-19 samples from non-COVID-19 and pre-pandemic samples. The data from the three sample groups also revealed a unique pattern of cross-reactivity between SARS-CoV-2 and SARS-CoV-1, MERS-CoV, and seasonal coronaviruses HKU1 and OC43. Our findings show that the CoV-2 IgM response is highly specific while the CoV-2 IgG response is more cross-reactive across a range of human CoVs and also showed that IgM and IgG responses show distinct patterns of epitope specificity. In summary, this multiplex assay was able to distinguish samples by COVID-19 status and characterize distinct trends in terms of cross-reactivity and fine-specificity in antibody responses, underscoring its potential value in diagnostic or serosurveillance efforts.

Introduction Increasing use of cleaner fuels, such as liquefied petroleum gas (LPG), and abandonment of solid fuels is key to reducing household air pollution and realising potential health improvements in low-income countries. However, achieving exclusive LPG use in households unaccustomed to this type of fuel, used in combination with a new stove technology, requires substantial behaviour change. We conducted theory-grounded formative research to identify contextual factors influencing cooking fuel choice to guide the development of behavioural strategies for the Household Air Pollution Intervention Network (HAPIN) trial. The HAPIN trial will assess the impact of exclusive LPG use on air pollution exposure and health of pregnant women, older adult women, and infants under 1 year of age in Guatemala, India, Peru, and Rwanda.Methods Using the Capability, Opportunity, Motivation–Behaviour (COM–B) framework and Behaviour Change Wheel (BCW) to guide formative research, we conducted in-depth interviews, focus group discussions, observations, key informant interviews and pilot studies to identify key influencers of cooking behaviours in the four countries. We used these findings to develop behavioural strategies likely to achieve exclusive LPG use in the HAPIN trial.Results We identified nine potential influencers of exclusive LPG use, including perceived disadvantages of solid fuels, family preferences, cookware, traditional foods, non-food-related cooking, heating needs, LPG awareness, safety and cost and availability of fuel. Mapping formative findings onto the theoretical frameworks, behavioural strategies for achieving exclusive LPG use in each research site included free fuel deliveries, locally acceptable stoves and equipment, hands-on training and printed materials and videos emphasising relevant messages. In the HAPIN trial, we will monitor and reinforce exclusive LPG use through temperature data loggers, LPG fuel delivery tracking, in-home observations and behavioural reinforcement visits.Conclusion Our formative research and behavioural strategies can inform the development, implementation, monitoring and evaluation of theory-informed strategies to promote exclusive LPG use in future stove programmes and research studies.Trial registration number NCT02944682, Pre-results.

Dr. Lysanne Campeau (M.D., C.M., Ph.D., F.R.C.S.C.) is an Assistant Professor of Urology at McGill University’s Jewish General Hospital. Through her flamboyant career in medicine, her research accomplishments and her advocacy work for gender equality in medicine, she is a model of ambition, dedication and passion. Dr. Campeau completed medical school as well as her urology residency at McGill University. She is the first woman to complete her entire residency at McGill University in this specific field. Dr. Campeau then went on to complete a clinical fellowship in Female Pelvic Medicine and Reconstructive Surgery at New York University, as well as a Ph.D. in Physiology and Pharmacology at Wake Forest Institute for Regenerative Medicine. She then came back to work as a urologist at the Jewish General Hospital and a clinical researcher at the Lady Davis Institute. Her research interests lie in female pelvic medicine, voiding dysfunction and urogenital reconstruction. In addition to her clinical and academic duties, Dr. Campeau is involved in teaching urology residents as well as in some volunteer endeavours in the community. A resilient person, Dr. Campeau builds on her experience of gender discrimination in medicine to advocate for equality in her field. She also aims to raise awareness on the topic of incontinence, which is often taboo among the public. Through awareness campaigns as well as her innovative research in the field, Dr. Campeau works to develop new treatments and improve outcomes for patients who suffer from this condition. Dr. Campeau is a positive leader and role model for aspiring female physicians, to whom she advises to cultivate adaptiveness, integrity and honesty in order to navigate the challenging journey that is medicine.

Pneumonia is both a treatable and preventable disease but remains a leading cause of death in children worldwide. Household air pollution caused by burning biomass fuels for cooking has been identified as a potentially preventable risk factor for pneumonia in low- and middle-income countries. We are conducting a randomised controlled trial of a clean energy intervention in 3200 households with pregnant women living in Guatemala, India, Peru and Rwanda. Here, we describe the protocol to ascertain the incidence of severe pneumonia in infants born to participants during the first year of the study period using three independent algorithms: the presence of cough or difficulty breathing and hypoxaemia (≤92% in Guatemala, India and Rwanda and ≤86% in Peru); presence of cough or difficulty breathing along with at least one World Health Organization-defined general danger sign and consolidation on chest radiography or lung ultrasound; and pneumonia confirmed to be the cause of death by verbal autopsy. Prior to the study launch, we identified health facilities in the study areas where cases of severe pneumonia would be referred. After participant enrolment, we posted staff at each of these facilities to identify children enrolled in the trial seeking care for severe pneumonia. To ensure severe pneumonia cases are not missed, we are also conducting home visits to all households and providing education on pneumonia to the mother. Severe pneumonia reduction due to mitigation of household air pollution could be a key piece of evidence that sways policymakers to invest in liquefied petroleum gas distribution programmes.

The COVID-19 pandemic has had a staggering impact on social, economic, and public health systems worldwide. Vaccine development and mobilization against SARS-CoV-2 (the etiologic agent of COVID-19) has been rapid. However, novel strategies are still necessary to slow the pandemic, and this includes new approaches to vaccine development and/or delivery that will improve vaccination compliance and demonstrate efficacy against emerging variants. Here, we report on the immunogenicity and efficacy of a SARS-CoV-2 vaccine comprising stabilized, pre-fusion spike protein trimers displayed on a ferritin nanoparticle (SpFN) adjuvanted with either conventional aluminum hydroxide or the Army Liposomal Formulation QS-21 (ALFQ) in a cynomolgus macaque COVID-19 model. Vaccination resulted in robust cell-mediated and humoral responses and a significant reduction in lung lesions following SARS-CoV-2 infection. The strength of the immune response suggests that dose sparing through reduced or single dosing in primates may be possible with this vaccine. Overall, the data support further evaluation of SpFN as a SARS-CoV-2 protein-based vaccine candidate with attention to fractional dosing and schedule optimization.

Abstract The terrestrial phase of the water cycle can be seriously impacted by water management and human water use behavior (e.g., reservoir operation, and irrigation withdrawals). Here we outline a method for assessing water availability in a changing climate, while explicitly considering anthropogenic water demand scenarios and water supply infrastructure designed to cope with climatic extremes. The framework brings a top-down and bottom-up approach to provide localized water assessment based on local water supply infrastructure and projected water demands. When our framework is applied to southeastern Australia we find that, for some combinations of climatic change and water demand, the region could experience water stress similar or worse than the epic Millennium Drought. We show considering only the influence of future climate on water supply, and neglecting future changes in water demand and water storage augmentation might lead to opposing perspectives on future water availability. While human water use can significantly exacerbate climate change impacts on water availability, if managed well, it allows societies to react and adapt to a changing climate. The methodology we present offers a unique avenue for linking climatic and hydrologic processes to water resource supply and demand management and other human interactions.

Objective: To determine the protective role of Pomegranate Juice (PJ) and Pomegranate Peel Extract (PPE) on steroid induced serum creatinine level in mice. Study Design: Randomized control trial. Place and Duration of Study: Department of Anatomy, Army Medical College Rawalpindi, in collaboration with the National Institute of Health (NIH), Islamabad, from May 1st to June 30th , 2015. Materials and Methods: Forty healthy mice (BALB/c strain), weighing 25-30 gms on average were randomly divided into four groups, each group having five male and female mice. Group A was control group and groups B, C and D were experimental groups. Mice in experimental groups were injected Nandrolone decanoate, 1 mg/100 gm body weight, intramuscularly in the hind limb once a week for 8 weeks. Mice in experimental group C were also given pomegranate Juice daily, 3ml/kg body weight by oral gavage tube for 8 weeks. Mice in experimental group D were given Pomegranate Peel Extract daily, 200mg/kg bodyweight through oral gavage tube for 8 weeks. After eight weeks 5ml blood was drawn from mice through cardiac puncture just before the sacrifice of animals. Data were entered and analyzed by using SPSS version 21. ANOVA test was applied for intergroup comparison of quantitative variables. P-value of

BackgroundCompared with those without dementia, older patients with dementia admitted to acute care settings are at higher risk for triad combination of polypharmacy (PP), potentially inappropriate medication (PIM), and drug-drug interaction (DDI), which may consequently result in detrimental health. The aims of this research were to assess risk factors associated with triad combination of PP, PIM and DDI among hospitalized older patients with dementia, and to assess prevalence and characteristics of PP, PIM and DDI in this population.MethodsIn this retrospective cross-sectional study, 416 older inpatients diagnosed with dementia and referred for specialist geriatric consultation at a tertiary hospital in Brisbane, Australia during 2006-2016 were enrolled. Patients were categorized into two groups according to their exposure to the combination of PP, PIM and DDI: 'triad combination' and 'non-triad combination'. Data were collected using the interRAI Acute Care (AC) assessment instrument. Independent risk factors of exposure to the triad combination were evaluated using bivariate and multivariate logistic regression analyses.ResultsOverall, 181 (43.5%) were classified as triad combination group. The majority of the population took at least 1 PIM (56%) or experienced at least one potential DDI (76%). Over 75% of the participants were exposed to polypharmacy. The most common prescribed PIMs were antipsychotics, followed by benzodiazepines. The independent risk factors of the triad combination were the presence of atrial fibrillation diagnosis and higher medications use in cardiac therapy, psycholeptics and psychoanaleptics.ConclusionsThe exposure to triad combination of PP, PIM and DDI are common among people with dementia as a result of their vulnerable conditions and the greater risks of adverse events from medications use. This study identified the use of cardiac therapy, psycholeptics and psychoanaleptics as predictors of exposure to PP, PIM and DDI. Therefore, use of these medications should be carefully considered and closely monitored. Furthermore, comprehensive medication reviews to optimize medication prescribing should be initiated and continually implemented for this vulnerable population.

BackgroundMen who have sex with men (MSM) and transgender women (TGW) are at risk for sexually transmitted infections (STIs), including those of the oropharynx. We estimated the prevalence and factors associated with oral sex practices and characterized oropharyngeal STIs among a cohort of MSM and TGW in Nigeria.MethodsFrom 2013 to 2018, TRUST/RV368 recruited MSM and TGW into HIV/STI diagnosis and treatment at community-based clinics in Nigeria. Participants who completed HIV testing and oral sex questions at enrollment were selected. Cross-sectional analyses with bivariate and multivariable logistic regression models estimated odds ratios (ORs) and 95% confidence intervals (CIs). Oropharyngeal swab testing for Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT) began in 2014 and for those with diagnostic results at enrollment, the unadjusted association of oral sex practices with oropharyngeal STIs was conducted.ResultsA total of 1342 participants had a median age of 25 years (interquartile range: 22-29), 58% were living with HIV, and 69% reported oral sex practices. Factors associated with increased odds of engaging in oral sex included living with HIV (adjusted [a]OR: 1.4, 95% CI: 1.1-1.8), self-identifying as a woman (aOR:1.8, 95% CI: 1.1-2.8), mobile phone ownership (aOR:2.3, 95% CI: 1.3-3.9), receptive anal sex (aOR:1.7, 95% CI:1.3-2.3) and multiple male sexual partners (2 to 4 vs. ≤1, aOR:1.5, 95% CI: 1.0-2.2; 5+ vs ≤1, aOR:2.9, 95% CI:1.9-4.3). Oropharyngeal STI prevalence was 7% (52/752) and higher among those who engaged in oral sex compared to those who did not (unadjusted OR: 2.5, 95% CI:1.2-5.3).ConclusionsOral sex was common and associated with an increased odds of oropharyngeal STIs among MSM and TGW from Nigeria. In the absence of screening and treatment guidelines, condoms continue to be the mainstay for oral STI prevention. A pre-exposure prophylaxis for bacterial STIs would complement current prevention strategies to curb transmission.

Management of Human Immunodeficiency Virus Type 2 (HIV-2) infections present unique challenges due to low viral titers, slow disease progression, and poor response to standard antiviral therapies. The need for a nucleic acid assay to detect and quantify HIV-2 virus has led to the development of a number of molecular-based assays for detection and/or quantification of HIV-2 viral RNA in plasma in order to provide laboratory evidence of HIV-2 infection and viral loads for use in treatment decisions. As HIV-2 is less pathogenic and transmissible than HIV-1 and has resistance to several of the antiretroviral drugs, delay of treatment is common. Cross sero-reactivity between HIV-1 and HIV-2 makes it difficult to distinguish between the two viruses based upon serological tests. As such we developed a quantitative reverse transcription PCR (qRT-PCR) assay targeting the 5' long terminal repeat of HIV-2 for detection and quantification of HIV-2 viral RNA in plasma to identify HIV-2 infection and for use in viral load monitoring. Serial dilutions of cultured HIV-2 virus demonstrated a wide dynamic range (10 to 100,000 copies/ml) with excellent reproducibility (standard deviation from 0.12-0.19), linearity (R2 = 0.9994), and a lower limit of detection at 79 copies/ml (NIH-Z). The assay is highly specific for HIV-2 Groups A and B and exhibits no cross reactivity to HIV-1, HBV or HCV. Precision of the assay was demonstrated for the High (Mean = 6.41; SD = 0.12) and Medium (Mean = 4.46; SD = 0.13) HIV-2 positive controls. Replicate testing of clinical specimens showed good reproducibility above 1,000 copies/ml, with higher variability under 1,000 copies/ml. Analysis of 220 plasma samples from HIV-2 infected West African individuals demonstrated significantly lower viral loads than those observed in HIV-1 infections, consistent with results of previous studies. Slightly more than seven percent of clinical samples (7.3%) demonstrated viral loads above 100,000 copies/ml, while 37.3% of samples were undetectable. The high sensitivity, specificity, precision, and linearity of the WRAIR qRT-PCR assay makes it well suited for detection and monitoring of HIV-2 RNA levels in plasma of infected individuals.

In general survival analysis, multiple studies have considered a single failure time corresponding to the time to the event of interest or to the occurrence of multiple events under the assumption that each event is independent. However, in real-world events, one event may impact others. Essentially, the potential structure of the occurrence of multiple events can be observed in several survival datasets. The interrelations between the times to the occurrences of events are immensely challenging to analyze because of the presence of censoring. Censoring commonly arises in longitudinal studies in which some events are often not observed for some of the subjects within the duration of research. Although this problem presents the obstacle of distortion caused by censoring, the advanced multivariate survival analysis methods that handle multiple events with censoring make it possible to measure a bivariate probability density function for a pair of events. Considering this improvement, this paper proposes a method called censored network estimation to discover partially correlated relationships and construct the corresponding network composed of edges representing non-zero partial correlations on multiple censored events. To demonstrate its superior performance compared to conventional methods, the selecting power for the partially correlated events was evaluated in two types of networks with iterative simulation experiments. Additionally, the correlation structure was investigated on the electronic health records dataset of the times to the first diagnosis for newborn babies in South Korea. The results show significantly improved performance as compared to edge measurement with competitive methods and reliability in terms of the interrelations of real-life diseases.

Introduction Resistant Gram-positive organisms, such as methicillin-resistant staphylococci, account for a significant proportion of infections following joint replacement surgery. Current surgical antimicrobial prophylaxis guidelines recommend the use of first-generation or second-generation cephalosporin antibiotics, such as cefazolin. Cefazolin, however, does not prevent infections due to these resistant organisms; therefore, new prevention strategies need to be examined. One proposed strategy is to combine a glycopeptide antibiotic with cefazolin for prophylaxis. The clinical benefit and cost-effectiveness of this combination therapy compared with usual therapy, however, have not been established.Methods and analysis This randomised, double-blind, parallel, superiority, placebo-controlled, phase 4 trial will compare the incidence of all surgical site infections (SSIs) including superficial, deep and organ/space (prosthetic joint) infections, safety and cost-effectiveness of surgical prophylaxis with cefazolin plus vancomycin to that with cefazolin plus placebo. The study will be performed in patients undergoing joint replacement surgery. In the microbiological sub-studies, we will examine the incidence of SSIs in participants with preoperative staphylococci colonisation (Sub-Study 1) and incidence of VRE acquisition (Sub-Study 2). The trial will recruit 4450 participants over a 4-year period across 13 orthopaedic centres in Australia. The primary outcome is the incidence of SSI at 90 days post index surgery. Secondary outcomes include the incidence of SSI according to joint and microorganism and other healthcare associated infections. Safety endpoints include the incidence of acute kidney injury, hypersensitivity reactions and all-cause mortality. The primary and secondary analysis will be a modified intention-to-treat analysis consisting of all randomised participants who undergo eligible surgery. We will also perform a per-protocol analysis.Ethics and dissemination The study protocol was reviewed and approved by The Alfred Hospital Human Research Ethics Committee (HREC/18/Alfred/102) on 9 July 2018. Study findings will be disseminated in the printed media, and learnt forums.Trial registration number ACTRN12618000642280

BackgroundImproving oxygen systems may improve clinical outcomes for hospitalised children with acute lower respiratory infection (ALRI). This paper reports the effects of an improved oxygen system on mortality and clinical practices in 12 general, paediatric, and maternity hospitals in southwest Nigeria.Methods and findingsWe conducted an unblinded stepped-wedge cluster-randomised trial comparing three study periods: baseline (usual care), pulse oximetry introduction, and stepped introduction of a multifaceted oxygen system. We collected data from clinical records of all admitted neonates (ConclusionsWe observed no mortality benefit for children and a possible higher risk of neonatal death following the introduction of a multifaceted oxygen system compared to introducing pulse oximetry alone. Where some oxygen is available, pulse oximetry may improve oxygen usage and clinical outcomes for children with ALRI.Trial registrationAustralian New Zealand Clinical Trials Registry: ACTRN12617000341325.

Objectives To survey the reported content, frequency and duration of upper limb treatment provided by occupational and physiotherapists for people after stroke in the UK.Design A cross-sectional online survey was used. Description and analysis of the data were based on items from the Template for Intervention Description and Replication (Who, Where, What and How much).Setting The online survey was distributed via professional and social networks to UK-based therapists.Participants Respondents were occupational or physiotherapists currently working clinically in the UK with people after stroke. Over the 6 week data collection period, 156 respondents opened the survey, and 154 completed it. Respondents comprised 85 physiotherapists and 69 occupational therapists.Results Respondents reported treating the upper limb a median of three times a week (range: 1 to 7) for a mean of 29 min (SD: 18). Most (n=110) stated this was supplemented by rehabilitation assistants, family and/or carers providing additional therapy a median of three times a week (range 1 to 7). Functional training was the most commonly reported treatment for people with mild and moderate upper limb deficits (>40%). There was much less consistency in treatments reported for people with severe upper limb deficits with less than 20% (n=28) reporting the same treatments.Conclusions This study provides a contemporaneous description of reported therapy in the UK for people with upper limb deficits after stroke and a detailed template to inform standard therapy interventions in future research. Several evidence-based therapies were reported to be used by respondents (eg, constraint induced movement therapy), but others were not (eg, mental imagery). The findings also highlight that the current reported provision of upper limb therapy is markedly less than what is likely to be effective. This underlines an urgent need to configure and fund services to empower therapists to deliver greater amounts of evidence-based treatment for people with upper limb deficits after stroke.

Chlamydia psittaci is traditionally regarded as a globally distributed avian pathogen that can cause zoonotic spill-over. Molecular research has identified an extended global host range and significant genetic diversity. However, Australia has reported a reduced host range (avian, horse, and human) with a dominance of clonal strains, denoted ST24. To better understand the widespread of this strain type in Australia, multilocus sequence typing (MLST) and ompA genotyping were applied on samples from a range of hosts (avian, equine, marsupial, and bovine) from Australia. MLST confirms that clonal ST24 strains dominate infections of Australian psittacine and equine hosts (82/88; 93.18%). However, this study also found novel hosts (Australian white ibis, King parrots, racing pigeon, bovine, and a wallaby) and demonstrated that strain diversity does exist in Australia. The discovery of a C. psittaci novel strain (ST306) in a novel host, the Western brush wallaby, is the first detection in a marsupial. Analysis of the results of this study applied a multidisciplinary approach regarding Chlamydia infections, equine infectious disease, ecology, and One Health. Recommendations include an update for the descriptive framework of C. psittaci disease and cell biology work to inform pathogenicity and complement molecular epidemiology.

The coronavirus disease 2019 (COVID-19) pandemic has highlighted the urgent need for effective prophylactic vaccination to prevent the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Intranasal vaccination is an attractive strategy to prevent COVID-19 as the nasal mucosa represents the first-line barrier to SARS-CoV-2 entry. The current intramuscular vaccines elicit systemic immunity but not necessarily high-level mucosal immunity. Here, we tested a single intranasal dose of our candidate adenovirus type 5-vectored vaccine encoding the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein (AdCOVID) in inbred, outbred, and transgenic mice. A single intranasal vaccination with AdCOVID elicited a strong and focused immune response against RBD through the induction of mucosal IgA in the respiratory tract, serum neutralizing antibodies, and CD4+ and CD8+ T cells with a Th1-like cytokine expression profile. A single AdCOVID dose resulted in immunity that was sustained for over six months. Moreover, a single intranasal dose completely protected K18-hACE2 mice from lethal SARS-CoV-2 challenge, preventing weight loss and mortality. These data show that AdCOVID promotes concomitant systemic and mucosal immunity and represents a promising vaccine candidate.

The use of antibiotics is a vital means of treating infections caused by the bacteria Bacillus (B.) anthracis. Importantly, with the potential future use of multidrug-resistant strains of B. anthracis as bioweapons, new antibiotics are needed as alternative therapeutics. In this blinded study, we assessed the protective efficacy of teixobactin, a recently discovered antibiotic, against inhalation anthrax infection in the adult rabbit model. New Zealand White rabbits were infected with a lethal dose of B. anthracis Ames spores via the inhalation route, and blood samples were collected at various times to assess antigenemia, bacteremia, tissue bacterial load, and antibody production. Treatments were administered upon detection of B. anthracis protective antigen in the animals’ sera. For comparison, a fully protective dose of levofloxacin was used as a positive control. Rabbits treated with teixobactin showed 100% survival following infection, and the bacteremia was completely resolved by 24–48 h post-treatment. In addition, the bacterial/spore loads in tissues of the animals treated with teixobactin were either zero or dramatically less relative to that of the negative control animals. Moreover, microscopic evaluation of the tissues revealed decreased pathology following treatment with teixobactin. Overall, these results show that teixobactin was protective against inhalation anthrax infection in the rabbit model, and they indicate the potential of teixobactin as a therapeutic for the disease.

BACKGROUND:Surgical antimicrobial prophylaxis (SAP) is a leading indication for antibiotic use in the hospital setting, with demonstrated high rates of inappropriateness. Decision-making for SAP is complex and multifactorial. A greater understanding of these factors is needed to inform the design of targeted antimicrobial stewardship interventions and strategies to support the optimization of SAP and its impacts on patient care. METHODS:A qualitative case study exploring the phenomenon of SAP decision-making. Focus groups were conducted with surgeons, anaesthetists, theatre nurses and pharmacists across one private and two public hospitals in Australia. Thematic analysis was guided by the Theoretical Domains Framework (TDF) and the Capabilities, Opportunities, Motivators-Behaviour (COM-B) model. RESULTS:Fourteen focus groups and one paired interview were completed. Ten of the fourteen TDF domains were identified as relevant. Thematic analysis revealed six significant themes mapped to the COM-B model, and subthemes mapped to the relevant TDF domains in a combined framework. Key themes identified were: 1) Low priority for surgical antimicrobial prophylaxis prescribing skills; 2) Prescriber autonomy takes precedence over guideline compliance; 3) Social codes of prescribing reinforce established practices; 4) Need for improved communication, documentation and collection of data for action; 5) Fears and perceptions of risk hinder appropriate SAP prescribing; and 6) Lack of clarity regarding roles and accountability. CONCLUSIONS:SAP prescribing is a complex process that involves multiple professions across the pre-, intra- and post-operative surgical settings. The utilisation of behaviour change frameworks to identify barriers and enablers to optimal SAP prescribing supports future development of theory-informed antimicrobial stewardship interventions. Interventions should aim to increase surgeon engagement, enhance the prioritisation of and accountability for SAP, and address the underlying social factors involved in SAP decision-making, such as professional hierarchy and varied perceptions or risks and fears.

Understanding the circuit mechanisms behind motion detection is a long-standing question in visual neuroscience. In Drosophila melanogaster, recently discovered synapse-level connectomes in the optic lobe, particularly in ON-pathway (T4) receptive-field circuits, in concert with physiological studies, suggest a motion model that is increasingly intricate when compared with the ubiquitous Hassenstein-Reichardt model. By contrast, our knowledge of OFF-pathway (T5) has been incomplete. Here, we present a conclusive and comprehensive connectome that, for the first time, integrates detailed connectivity information for inputs to both the T4 and T5 pathways in a single EM dataset covering the entire optic lobe. With novel reconstruction methods using automated synapse prediction suited to such a large connectome, we successfully corroborate previous findings in the T4 pathway and comprehensively identify inputs and receptive fields for T5. Although the two pathways are probably evolutionarily linked and exhibit many similarities, we uncover interesting differences and interactions that may underlie their distinct functional properties.

How do large-mammal communities reassemble after being pushed to the brink of extinction? Few data are available to answer this question, as it is rarely possible to document both the decline and recovery of wildlife populations. Here we present the first in-depth quantitative account of war-induced collapse and postwar recovery in a diverse assemblage of large herbivores. In Mozambique's Gorongosa National Park, we assembled data from 15 aerial wildlife counts conducted before (1968-1972) and after (1994-2018) the Mozambican Civil War (1977-1992). Pre-war total biomass density exceeded 9,000 kg km-2, but populations declined by >90% during the war. Since 1994, total biomass has substantially recovered, but species composition has shifted dramatically. Formerly dominant large herbivores-including elephant (Loxodonta africana), hippo (Hippopotamus amphibius), buffalo (Syncerus caffer), zebra (Equus quagga), and wildebeest (Connochaetes taurinus)-are now outnumbered by waterbuck (Kobus ellipsiprymnus) and other small to mid-sized antelopes. Waterbuck abundance has increased by an order of magnitude, with >55,000 individuals accounting for >74% of large-herbivore biomass in 2018. By contrast, elephant, hippo, and buffalo, which totaled 89% of pre-war biomass, now comprise just 23%. These trends mostly reflect natural population growth following the resumption of protection under the Gorongosa Restoration Project; reintroductions (465 animals of 7 species) accounted for a comparatively small fraction of the total numerical increase. Waterbuck are growing logistically, apparently as-yet unchecked by interspecific competition or predation (apex-carnivore abundance has been low throughout the post-war interval), suggesting a community still in flux. Most other herbivore populations have increased post-war, albeit at differing rates. Armed conflict remains a poorly understood driver of ecological change; our results demonstrate the potential for rapid post-war recovery of large-herbivore biomass, given sound protected-area management, but also suggest that restoration of community structure takes longer and may require active intervention.