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Abstract A crucial mechanism for controlling the actions of proteins is allostery. Allosteric modulators have the potential to provide many benefits compared to orthosteric ligands, such as increased selectivity and saturability of their effect. The identification of new allosteric sites presents prospects for the creation of innovative medications and enhances our comprehension of fundamental biological mechanisms. Allosteric sites are increasingly found in different protein families through various techniques, such as machine learning applications, which opens up possibilities for creating completely novel medications with a diverse variety of chemical structures. Machine learning methods, such as PASSer, exhibit limited efficacy in accurately finding allosteric binding sites when relying solely on 3D structural information. Scientific Contribution Prior to conducting feature selection for allosteric binding site identification, integration of supporting amino-acid–based information to 3D structural knowledge is advantageous. This approach can enhance performance by ensuring accuracy and robustness. Therefore, we have developed an accurate and robust model called Multimodel Ensemble Feature Selection for Allosteric Site Identification (MEF-AlloSite) after collecting 9460 relevant and diverse features from the literature to characterise pockets. The model employs an accurate and robust multimodal feature selection technique for the small training set size of only 90 proteins to improve predictive performance. This state-of-the-art technique increased the performance in allosteric binding site identification by selecting promising features from 9460 features. Also, the relationship between selected features and allosteric binding sites enlightened the understanding of complex allostery for proteins by analysing selected features. MEF-AlloSite and state-of-the-art allosteric site identification methods such as PASSer2.0 and PASSerRank have been tested on three test cases 51 times with a different split of the training set. The Student’s t test and Cohen’s D value have been used to evaluate the average precision and ROC AUC score distribution. On three test cases, most of the p-values ( $$< 0.05$$ < 0.05 ) and the majority of Cohen’s D values ( $$> 0.5$$ > 0.5 ) showed that MEF-AlloSite’s 1–6% higher mean of average precision and ROC AUC than state-of-the-art allosteric site identification methods are statistically significant.

Summary: Leukemia niche impacts quiescence; however, culturing patient-derived samples ex vivo is technically challenging. Here, we present a protocol for in vitro co-culture of patient-derived xenograft acute lymphoblastic leukemia (PDX-ALL) cells with human mesenchymal stem cells (MSCs). We describe steps for labeling PDX-ALL cells with CellTrace Violet dye to demonstrate MSC-primed PDX-ALL cycling. We then detail procedures to identify MSC-primed G0/quiescent PDX-ALL cells via Hoechst-33342/Pyronin Y live cell cycle analysis.For complete details on the use and execution of this protocol, please refer to Pal et al.1,2 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Abstract Becker muscular dystrophy (BMD) is characterised by fiber loss and expansion of fibrotic and adipose tissue. Several cells interact locally in what is known as the degenerative niche. We analysed muscle biopsies of controls and BMD patients at early, moderate and advanced stages of progression using Hyperion imaging mass cytometry (IMC) by labelling single sections with 17 markers identifying different components of the muscle. We developed a software for analysing IMC images and studied changes in the muscle composition and spatial correlations between markers across disease progression. We found a strong correlation between collagen-I and the area of stroma, collagen-VI, adipose tissue, and M2-macrophages number. There was a negative correlation between the area of collagen-I and the number of satellite cells (SCs), fibres and blood vessels. The comparison between fibrotic and non-fibrotic areas allowed to study the disease process in detail. We found structural differences among non-fibrotic areas from control and patients, being these latter characterized by increase in CTGF and in M2-macrophages and decrease in fibers and blood vessels. IMC enables to study of changes in tissue structure along disease progression, spatio-temporal correlations and opening the door to better understand new potential pathogenic pathways in human samples.

Abstract Immune-mediated inflammatory diseases (IMIDs) are typically characterised by relapsing and remitting flares of inflammation. However, the unpredictability of disease flares impedes their study. Addressing this critical knowledge gap, we use the experimental medicine approach of immunomodulatory drug withdrawal in rheumatoid arthritis (RA) remission to synchronise flare processes allowing detailed characterisation. Exploratory mass cytometry analyses reveal three circulating cellular subsets heralding the onset of arthritis flare – CD45RO+PD1hi CD4+ and CD8+ T cells, and CD27+CD86+CD21- B cells – further characterised by single-cell sequencing. Distinct lymphocyte subsets including cytotoxic and exhausted CD4+ memory T cells, memory CD8+CXCR5+ T cells, and IGHA1+ plasma cells are primed for activation in flare patients. Regulatory memory CD4+ T cells (Treg cells) increase at flare onset, but with dysfunctional regulatory marker expression compared to drug-free remission. Significant clonal expansion is observed in T cells, but not B cells, after drug cessation; this is widespread throughout memory CD8+ T cell subsets but limited to the granzyme-expressing cytotoxic subset within CD4+ memory T cells. Based on our observations, we suggest a model of immune dysregulation for understanding RA flare, with potential for further translational research towards novel avenues for its treatment and prevention.

Abstract Probing the surface of proteins to predict the binding site and binding affinity for a given small molecule is a critical but challenging task in drug discovery. Blind docking addresses this issue by performing docking on binding regions randomly sampled from the entire protein surface. However, compared with local docking, blind docking is less accurate and reliable because the docking space is too largetly sampled. Cavity detection-guided blind docking methods improved the accuracy by using cavity detection (also known as binding site detection) tools to guide the docking procedure. However, it is worth noting that the performance of these methods heavily relies on the quality of the cavity detection tool. This constraint, namely the dependence on a single cavity detection tool, significantly impacts the overall performance of cavity detection-guided methods. To overcome this limitation, we proposed Consensus Blind Dock (CoBDock), a novel blind, parallel docking method that uses machine learning algorithms to integrate docking and cavity detection results to improve not only binding site identification but also pose prediction accuracy. Our experiments on several datasets, including PDBBind 2020, ADS, MTi, DUD-E, and CASF-2016, showed that CoBDock has better binding site and binding mode performance than other state-of-the-art cavity detector tools and blind docking methods.

Abstract Mitochondrial dysfunction has been suggested to contribute to Parkinson’s disease pathogenesis, though an understanding of the extent or exact mechanism of this contribution remains elusive. This has been complicated by challenging nature of pathway-based analysis and an inability simultaneously study multiple related proteins within human brain tissue. We used imaging mass cytometry (IMC) to overcome these challenges, measuring multiple protein targets, whilst retaining the spatial relationship between targets in post-mortem midbrain sections. We used IMC to simultaneously interrogate subunits of the mitochondrial oxidative phosphorylation complexes, and several key signalling pathways important for mitochondrial homoeostasis, in a large cohort of PD patient and control cases. We revealed a generalised and synergistic reduction in mitochondrial quality control proteins in dopaminergic neurons from Parkinson’s patients. Further, protein-protein abundance relationships appeared significantly different between PD and disease control tissue. Our data showed a significant reduction in the abundance of PINK1, Parkin and phosphorylated ubiquitinSer65, integral to the mitophagy machinery; two mitochondrial chaperones, HSP60 and PHB1; and regulators of mitochondrial protein synthesis and the unfolded protein response, SIRT3 and TFAM. Further, SIRT3 and PINK1 did not show an adaptive response to an ATP synthase defect in the Parkinson’s neurons. We also observed intraneuronal aggregates of phosphorylated ubiquitinSer65, alongside increased abundance of mitochondrial proteases, LONP1 and HTRA2, within the Parkinson’s neurons with Lewy body pathology, compared to those without. Taken together, these findings suggest an inability to turnover mitochondria and maintain mitochondrial proteostasis in Parkinson’s neurons. This may exacerbate the impact of oxidative phosphorylation defects and ageing related oxidative stress, leading to neuronal degeneration. Our data also suggest that that Lewy pathology may affect mitochondrial quality control regulation through the disturbance of mitophagy and intramitochondrial proteostasis.

Summary: Background: Simian immunodeficiency viruses (SIV) have been jumping between non-human primates in West/Central Africa for thousands of years and yet, the HIV-1 epidemic only originated from a primate lentivirus over 100 years ago. Methods: This study examined the replicative fitness, transmission, restriction, and cytopathogenicity of 22 primate lentiviruses in primary human lymphoid tissue and both primary human and chimpanzee peripheral blood mononuclear cells. Findings: Pairwise competitions revealed that SIV from chimpanzees (cpz) had the highest replicative fitness in human or chimpanzee peripheral blood mononuclear cells, even higher fitness than HIV-1 group M strains responsible for worldwide epidemic. The SIV strains belonging to the “HIV-2 lineage” (including SIVsmm, SIVmac, SIVagm) had the lowest replicative fitness. SIVcpz strains were less inhibited by human restriction factors than the “HIV-2 lineage” strains. SIVcpz efficiently replicated in human tonsillar tissue but did not deplete CD4+ T-cells, consistent with the slow or nonpathogenic disease observed in most chimpanzees. In contrast, HIV-1 isolates and SIV of the HIV-2 lineage were pathogenic to the human tonsillar tissue, almost independent of the level of virus replication. Interpretation: Of all primate lentiviruses, SIV from chimpanzees appears most capable of infecting and replicating in humans, establishing HIV-1. SIV from other Old World monkeys, e.g. the progenitor of HIV-2, replicate slowly in humans due in part to restriction factors. Nonetheless, many of these SIV strains were more pathogenic than SIVcpz. Either SIVcpz evolved into a more pathogenic virus while in humans or a rare SIVcpz, possibly extinct in chimpanzees, was pathogenic immediately following the jump into human. Funding: Support for this study to E.J.A. was provided by the NIH/NIAID R01 AI49170 and CIHR project grant 385787. Infrastructure support was provided by the NIH CFAR AI36219 and Canadian CFI/Ontario ORF 36287. Efforts of J.A.B. and N.J.H. was provided by NIH AI099473 and for D.H.C., by VA and NIH AI AI080313.

Abstract Objective: To measure SARS-CoV-2 anti-nucleocapsid (anti-N) antibody seropositivity among healthcare personnel (HCP) without a history of COVID-19 and to identify HCP characteristics associated with seropositivity. Design: Prospective cohort study from September 22, 2020, to March 3, 2022. Setting: A tertiary care academic medical center. Participants: 727 HCP without prior positive SARS-CoV-2 PCR testing were enrolled; 559 HCP successfully completed follow-up. Methods: At enrollment and follow-up 1–6 months later, HCP underwent SARS-CoV-2 anti-N testing and were surveyed on demographics, employment information, vaccination status, and COVID-19 symptoms and exposures. Results: Of 727 HCP enrolled, 27 (3.7%) had a positive SARS-CoV-2 anti-N test at enrollment. Seropositive HCPs were more likely to have a household exposure to COVID-19 in the past 30 days (OR 7.92, 95% CI 2.44–25.73), to have had an illness thought to be COVID-19 (4.31, 1.94–9.57), or to work with COVID-19 patients more than half the time (2.09, 0.94–4.77). Among 559 HCP who followed-up, 52 (9.3%) had a positive SARS-CoV-2 anti-N antibody test result. Seropositivity at follow-up was associated with community/household exposures to COVID-19 within the past 30 days (9.50, 5.02–17.96; 2.90, 1.31–6.44), having an illness thought to be COVID-19 (8.24, 4.44–15.29), and working with COVID-19 patients more than half the time (1.50, 0.80–2.78). Conclusions: Among HCP without prior positive SARS-CoV-2 testing, SARS-CoV-2 anti-N seropositivity was comparable to that of the general population and was associated with COVID-19 symptomatology and both occupational and non-occupational exposures to COVID-19.

Summary: Background: Lung damage in severe COVID-19 is highly heterogeneous however studies with dedicated spatial distinction of discrete temporal phases of diffuse alveolar damage (DAD) and alternate lung injury patterns are lacking. Existing studies have also not accounted for progressive airspace obliteration in cellularity estimates. We used an imaging mass cytometry (IMC) analysis with an airspace correction step to more accurately identify the cellular immune response that underpins the heterogeneity of severe COVID-19 lung disease. Methods: Lung tissue was obtained at post-mortem from severe COVID-19 deaths. Pathologist-selected regions of interest (ROIs) were chosen by light microscopy representing the patho-evolutionary spectrum of DAD and alternate disease phenotypes were selected for comparison. Architecturally normal SARS-CoV-2-positive lung tissue and tissue from SARS-CoV-2-negative donors served as controls. ROIs were stained for 40 cellular protein markers and ablated using IMC before segmented cells were classified. Cell populations corrected by ROI airspace and their spatial relationships were compared across lung injury patterns. Findings: Forty patients (32M:8F, age: 22–98), 345 ROIs and >900k single cells were analysed. DAD progression was marked by airspace obliteration and significant increases in mononuclear phagocytes (MnPs), T and B lymphocytes and significant decreases in alveolar epithelial and endothelial cells. Neutrophil populations proved stable overall although several interferon-responding subsets demonstrated expansion. Spatial analysis revealed immune cell interactions occur prior to microscopically appreciable tissue injury. Interpretation: The immunopathogenesis of severe DAD in COVID-19 lung disease is characterised by sustained increases in MnPs and lymphocytes with key interactions occurring even prior to lung injury is established. Funding: UK Research and Innovation/Medical Research Council through the UK Coronavirus Immunology Consortium, Barbour Foundation, General Sir John Monash Foundation, Newcastle University, JGW Patterson Foundation, Wellcome Trust.

Between May and June 2021, healthcare personnel at two long-term care facilities underwent SARS-CoV-2 anti-nucleocapsid immunoglobulin G testing and completed a survey on COVID-19 exposures and symptoms. Antibody positivity rate was 8.9%. Similar rates of COVID-19 exposure occurred in non-occupational and occupational settings, with high self-reported adherence to workplace infection prevention practices.

Abstract Background This paper explores the feasibility of delivering a music festival-based drug checking service in Australia, evaluating service design and stakeholder acceptability. Methods Questionnaire and interview data were collected from adult service users and key stakeholders. A mixed methods approach was used to analyse the data on implementation, impact and acceptability. Results The trial service tested 170 substances with more than 230 patrons (including individuals who attended in groups). Adult service users had an average age of 21 years. Voluntary participation in the evaluation resulted in 158 participants completing the pre-service questionnaire, most of whom also completed the post-service (147 participants). Eleven in-depth qualitative interviews were conducted with patrons in the weeks following the drug checking. Concordance between what the patron expected the drug to be and drug checking results occurred in 88 per cent (n = 139) of the sample. Evaluation results show that the experience of testing and the accompanying harm reduction brief interventions positively impacted on patrons’ self-reported drug harm reduction knowledge, trust of health providers and stated drug use intentions. The service was received positively by service users. Conclusion This is the first independent evaluation of a pilot drug checking service in Australia. Consideration of operational feasibility and self-reported behavioural change suggests that the program was successful, although communication about the interpretation of drug checking results could be improved. Future studies should develop strategies for follow-up and consider the applicability of behavioural change theory.

Background: Healthcare personnel (HCP) working in non–acute-care facilities are at high risk of COVID-19. We sought to determine SARS-CoV-2 seroprevalence, and analyzed behaviors and activities related to COVID-19 acquisition in this cohort. Methods: Between May and June 2021, HCP were enrolled at a skilled nursing facility and a memory care facility in St. Louis, Missouri. Data regarding demographics, prior SARS-CoV-2 testing, symptoms consistent with COVID-19 in the previous 6 months, COVID-19 vaccination, personal protective equipment (PPE) use, and COVID-19 exposures were collected via survey. Blood specimens were obtained to determine SARS-CoV-2 nucleocapsid IgG antibody seroprevalence (Abbott Laboratories). Study protocol was approved by the Washington University Institutional Review Board. Results: The survey was completed by 74 HCP. 82% of participants were female, and 31% reported >10 years of healthcare experience. The overall SARS-CoV-2 seropositivity rate was 8.9% (5 HCP). Of the surveyed HCP, 50% reported symptoms concerning for COVID-19 in the prior 6 months. Headache (38%), fatigue (35%) and fever (27%) were the most common self-reported symptoms. Among symptomatic HCP, only 35% sought medical care for these symptoms. All HCP reported having taken at least 1 COVID-19 test prior to study enrollment. Of note, 18.9% (14 HCP) had a self-reported prior positive SARS-CoV-2 PCR test, of whom 9 HCP were seronegative. All seronegative HCP with a self-reported history of COVID-19 reported infection >3 months before study participation. Completion of a primary COVID-19 vaccination series was reported by 86% of HCP. Known exposure to COVID-19 at work was reported by 28% of HCP. When asked about PPE at the time of workplace exposure, N95 mask use was reported by 81%, gloves by 57%, gowns by 33%, face shields by 29% and surgical masks by 14%. Known specific exposure to COVID-19 outside work was reported by 31% of HCP. Conclusions: One year after the initial COVID-19 pandemic impacted the St. Louis region, HCP at non–acute-care facilities had a SARS-CoV-2 seroprevalence of 8.9%. Similar frequency of exposures were reported from both the workplace and community, with high rates of PPE use at the workplace. HCP in such settings remain at high risk of COVID-19 exposure from workplace and community exposures. Ongoing efforts are needed to maintain PPE use to prevent SARS-CoV-2 transmission within non–acute-care facilities, and continue access to timely COVID-19 screening for HCP.

Introduction Sepsis is characterised by a dysregulated immune response to infection, with exaggerated pro-inflammatory and anti-inflammatory responses. A predominant immunosuppressive profile affecting both innate and adaptive immune responses is associated with increased hospital-acquired infection and reduced infection-free survival. While hospital-acquired infection leads to additional antibiotic use, the role of the immunosuppressive phenotype in guiding complex decisions, such as those affecting antibiotic stewardship, is uncertain. This study is a mechanistic substudy embedded within a multicentre clinical and cost-effectiveness trial of biomarker-guided antibiotic stewardship. This mechanistic study aims to determine the effect of sepsis-associated immunosuppression on the trial outcome measures.Methods and analysis RISC-sepsis is a prospective, multicentre, exploratory, observational study embedded within the ADAPT-sepsis trial. A subgroup of 180 participants with antibiotics commenced for suspected sepsis, enrolled in the ADAPT-sepsis trial, will be recruited. Blood samples will be collected on alternate days until day 7. At each time point, blood will be collected for flow cytometric analysis into cell preservation tubes. Immunophenotyping will be performed at a central testing hub by flow cytometry. The primary outcome measures are monocyte human leucocyte antigen-DR; neutrophil CD88; programmed cell death-1 on monocytes, neutrophils and T lymphocytes and the percentage of regulatory T cells. Secondary outcome measures will link to trial outcomes from the ADAPT-sepsis trial including antibiotic days; occurrence of hospital-acquired infection and length of ICU-stay and hospital-stay.Ethics and dissemination Ethical approval has been granted (IRAS 209815) and RISC-sepsis is registered with the ISRCTN (86837685). Study results will be disseminated by peer-reviewed publications, presentations at scientific meetings and via patient and public participation groups and social media.

Persistence of residual disease in acute lymphoblastic leukemia (ALL) during the initial stages of chemotherapy is associated with inferior survival. To better understand clonal evolution and mechanisms of chemoresistance, we used multiparameter mass cytometry, at single-cell resolution, to functionally characterize pediatric B-ALL cells at disease presentation and those persisting during induction therapy. Analysis of ALL cells from presentation samples (n=42) showed that the most abundant phosphosignals were pCREB, pH2AX and pHH3 and we identified JAK-STAT and RAS pathway activation in five of six patients with JAK or RAS genetic aberrations. The clonal composition of ALL was heterogeneous and dynamic during treatment but all viable cell clusters showed pCREB activation. Levels of pCREB in ALL cells were increased or maintained during therapy and high dimensional analysis revealed a subpopulation of ALL cells at presentation that was positive for pCREB/pHH3/pS6 which increased during treatment in some patients, implicating this signaling node in conferring a survival advantage to multi-agent induction therapy. The small molecule CREB inhibitor, 666-15, was shown to reduce CREB transcriptional activity and induce apoptosis in ALL patient-derived xenograft cells of varying cytogenetic subtypes in vitro, both in the presence and absence of stromal support. Together, these data suggest that the cAMP signaling pathway may provide an opportunity for minimal residual disease-directed therapy for many patients at high risk of relapse.

Abstract Here we report the application of a mass spectrometry-based technology, imaging mass cytometry, to perform in-depth proteomic profiling of mitochondrial complexes in single neurons, using metal-conjugated antibodies to label post-mortem human midbrain sections. Mitochondrial dysfunction, particularly deficiency in complex I has previously been associated with the degeneration of dopaminergic neurons in Parkinson’s disease. To further our understanding of the nature of this dysfunction, and to identify Parkinson’s disease specific changes, we validated a panel of antibodies targeting subunits of all five mitochondrial oxidative phosphorylation complexes in dopaminergic neurons from Parkinson’s disease, mitochondrial disease, and control cases. Detailed analysis of the expression profile of these proteins, highlighted heterogeneity between individuals. There is a widespread decrease in expression of all complexes in Parkinson’s neurons, although more severe in mitochondrial disease neurons, however, the combination of affected complexes varies between the two groups. We also provide evidence of a potential neuronal response to mitochondrial dysfunction through a compensatory increase in mitochondrial mass. This study highlights the use of imaging mass cytometry in the assessment and analysis of expression of oxidative phosphorylation proteins, revealing the complexity of deficiencies of these proteins within individual neurons which may contribute to and drive neurodegeneration in Parkinson’s disease.

ABSTRACT Dental caries is caused by the buildup of acidic end products that result from the metabolism of dental plaque microbes. Natural products that are widely available could be used as an alternative or adjunctive anti-caries therapy. Sometimes, when two products are used together, they yield a more powerful antimicrobial effect than the anticipated additive effect. These synergistic combinations are often better treatment options because individual agents may not have sufficient antimicrobial action to be effective when used alone. Cranberries contain phenolic compounds like proanthocyanidins (PAC) that disrupt biofilm formation. Manuka honey has high concentrations of the agent methylglyoxal (MGO), which is cariostatic. Because these agents have varied modes of antimicrobial action, they show potential for possible synergistic effects when paired. Various cranberry extracts were tested pairwise with manuka honey or MGO by well-diffusion assays and 96-well checkerboard assays in the presence of Streptococcus mutans to test for synergy. Synergy was demonstrated in cranberry extracts Type R and RE when paired with manuka honey and MGO. The synergistic combinations found in this research thus can be considered candidates for the formulation of a dentifrice that could be used to inhibit the formation of dental plaque and thereby avoid the development of caries. IMPORTANCE The emergence of bacteria resistant to antimicrobial agents has led to a shortage of options when choosing effective treatment agents. Further, some antibiotics used at therapeutic doses can produce undesired side effects. An alternative to traditional antibiotics, natural antimicrobial agents can be used in combination to obtain synergistic outcomes without subjecting the patient to toxic or irritating doses of individual agents. Streptococcus mutans growth and biofilm formation are major contributors to the formation of dental caries. In this study, a synergistic combination of Manuka honey and cranberry extracts gives evidence that it can be used as an alternative or adjunctive anti-caries therapy.

BackgroundIn a rapidly aging population, new and efficient ways of providing health and social support to older adults are required that not only preserve independence but also maintain quality of life and safety. ObjectiveThe NEX project aims to develop an integrated Internet of Things system coupled with artificial intelligence to offer unobtrusive health and wellness monitoring to support older adults living independently in their home environment. The primary objective of this study is to develop and evaluate the technical performance and user acceptability of the NEX system. The secondary objective is to apply machine learning algorithms to the data collected via the NEX system to identify and eventually predict changes in the routines of older adults in their own home environment. MethodsThe NEX project commenced in December 2019 and is expected to be completed by August 2022. Mixed methods research (web-based surveys and focus groups) was conducted with 426 participants, including older adults (aged ≥60 years), family caregivers, health care professionals, and home care workers, to inform the development of the NEX system (phase 1). The primary outcome will be evaluated in 2 successive trials (the Friendly trial [phase 2] and the Action Research Cycle trial [phase 3]). The secondary objective will be explored in the Action Research Cycle trial (phase 3). For the Friendly trial, 7 older adult participants aged ≥60 years and living alone in their own homes for a 10-week period were enrolled. A total of 30 older adult participants aged ≥60 years and living alone in their own homes will be recruited for a 10-week data collection period (phase 3). ResultsPhase 1 of the project (n=426) was completed in December 2020, and phase 2 (n=7 participants for a 10-week pilot study) was completed in September 2021. The expected completion date for the third project phase (30 participants for the 10-week usability study) is June 2022. ConclusionsThe NEX project has considered the specific everyday needs of older adults and other stakeholders, which have contributed to the design of the integrated system. The innovation of the NEX system lies in the use of Internet of Things technologies and artificial intelligence to identify and predict changes in the routines of older adults. The findings of this project will contribute to the eHealth research agenda, focusing on the improvement of health care provision and patient support in home and community environments. International Registered Report Identifier (IRRID)DERR1-10.2196/35277

Immunocompromised adults can have prolonged acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive RT-PCR results, long after the initial diagnosis of coronavirus disease 2019 (COVID-19). This study aimed to determine if SARS-CoV-2 virus can be recovered in viral cell culture from immunocompromised adults with persistently positive SARS-CoV-2 RT-PCR tests. We obtained 20 remnant SARS-CoV-2 PCR positive nasopharyngeal swabs from 20 immunocompromised adults with a positive RT-PCR test ≥14 days after the initial positive test. The patients’ 2nd test samples underwent SARS-CoV-2 antigen testing, and culture with Vero-hACE2-TMPRSS2 cells. Viral RNA and cultivable virus were recovered from the cultured cells after qRT-PCR and plaque assays. Of 20 patients, 10 (50%) had a solid organ transplant and 5 (25%) had a hematologic malignancy. For most patients, RT-PCR Ct values increased over time. There were 2 patients with positive viral cell cultures; one patient had chronic lymphocytic leukemia treated with venetoclax and obinutuzumab who had a low viral titer of 27 PFU/mL. The second patient had marginal zone lymphoma treated with bendamustine and rituximab who had a high viral titer of 2 x 106 PFU/mL. Most samples collected ≥7 days after an initial positive SARS-CoV-2 RT-PCR had negative viral cell cultures. The 2 patients with positive viral cell cultures had hematologic malignancies treated with chemotherapy and B cell depleting therapy. One patient had a high concentration titer of cultivable virus. Further data are needed to determine risk factors for persistent viral shedding and methods to prevent SARS-CoV-2 transmission from immunocompromised hosts.

The diversity of human mononuclear phagocyte subsets remains to be characterized in many tissue-specific and functional contexts, including pulmonary inflammation. Here the authors characterize dendritic cell and monocyte subset recruitment to the bronchoalveolar space in a human LPS inhalation model.

The National Institute of Allergy and Infectious Diseases (NIAID) organised the Strategies for an HIV Cure 2018 meeting focused on research to develop innovative strategies for eradicating or achieving long-term remission of HIV infection. The purpose was to bring together researchers studying HIV persistence and cure strategies, including the six National Institutes of Health (NIH)-funded Martin Delaney Collaboratories for HIV Cure Research (MDCs), as well as industry and community partners, to share scientific results and stimulate active discussion among all stakeholders about the merits of various approaches under investigation. These discussions were intended to stimulate new collaborations and ideas for future research. The meeting covered a comprehensive range of topics spanning basic and translational research, drug discovery and development, and clinical research. Aside from the oral presentations described here, the meeting also included 130 poster presentations. Each of the three days of presentations is available for viewing via the NIH VideoCast website at: https://videocast.nih.gov/PastEvents.asp.

Objective To obtain consensus on the content and delivery of an occupational advice intervention for patients undergoing primary hip and knee replacement surgery. The primary targets for the intervention were (1) patients, carers and employers through the provision of individualised support and information about returning to work and (2) hospital orthopaedic teams through the development of a framework and materials to enable this support and information to be delivered.Design Modified Delphi study as part of a wider intervention development study (The Occupational advice for Patients undergoing Arthroplasty of the Lower limb (OPAL) study: Health Technology Assessment Reference 15/28/02) (ISRCTN27426982).Setting Five stakeholder groups (patients, employers, orthopaedic surgeons, general practitioners, allied health professionals and nurses) recruited from across the UK.Participants Sixty-six participants.Methods Statements for the Delphi process were developed relating to the content, format, delivery, timing and measurement of an occupational advice intervention. The statements were based on evidence gathered through the OPAL study that was processed using an intervention mapping framework. Intervention content was examined in round 1 and intervention format, delivery, timing and measurement were examined in round 2. In round 3, the developed intervention was presented to the stakeholder groups for comment.Consensus For rounds 1 and 2, consensus was defined as 70% agreement or disagreement on a 4-point scale. Statements reaching consensus were ranked according to the distribution of responses to create a hierarchy of agreement. Round 3 comments were used to revise the final version of the developed occupational advice intervention.Results Consensus was reached for 36 of 64 round 1 content statements (all agreement). In round 2, 13 questions were carried forward and an additional 81 statements were presented. Of these, 49 reached consensus (44 agreement/5 disagreement). Eleven respondents provided an appraisal of the intervention in round 3.Conclusions The Delphi process informed the development of an occupational advice intervention as part of a wider intervention development study. Stakeholder agreement was achieved for a large number of intervention elements encompassing the content, format, delivery and timing of the intervention. The effectiveness and cost-effectiveness of the developed intervention will require evaluation in a randomised controlled trial.Trial registration number International Standard Randomised Controlled Trials Number Trial ID: ISRCTN27426982

Abstract Background There are an increasing number of patients of working age undergoing hip and knee replacements. Currently there is variation in the advice and support given about sickness absence, recovery to usual activities and return to work after these procedures. Earlier, sustainable, return to work improves the health of patients and benefits their employers and society. An intervention that encourages and supports early recovery to usual activities, including work, has the potential to reduce the health and socioeconomic burden of hip and knee replacements. Methods/design A two-phase research programme delivered over 27 months will be used to develop and subsequently test the feasibility of an occupational advice intervention to facilitate return to work and usual activities in patients undergoing lower limb arthroplasty. The 2 phases will incorporate a six-stage intervention mapping process: Phase 1: Intervention mapping stages 1–3:1Needs assessment (including rapid evidence synthesis, prospective cohort analysis and structured stakeholder interviews)2Identification of intended outcomes and performance objectives3Selection of theory-based methods and practical strategies Phase 2: Intervention mapping stages 4–6:4Development of components and materials for the occupational advice intervention using a modified Delphi process5Adoption and implementation of the intervention6Evaluation and feasibility testing The study will be undertaken in four National Health Service (NHS) hospitals in the United Kingdom and two Higher Education Institutions. Discussion OPAL (Occupational advice for Patients undergoing Arthroplasty of the Lower limb) aims to develop an occupational advice intervention to support early recovery to usual activities including work, which is tailored to the requirements of patients undergoing hip and knee replacements. The developed intervention will then be assessed with a specific focus on evaluating its feasibility as a potential trial intervention to improve speed of recovery to usual activities including work. Trial registration The study was registered retrospectively with the International Standard Randomised Controlled Trials Number (ISRCTN): 27426982 (Date 20/12/2016) and the International prospective register of systematic reviews (PROSPERO): CRD42016045235 (Date 04/08/2016).

This article examines vigilantism and the question of hate crime. Broader shifts in penology have occurred in tandem with changes in the ways in which child sexual abuse has come to be understood. Using these shifts as a contextual backdrop, the article examines vigilance against the fear of crime where it manifests into vigilantism against real or perceived paedophiles. In doing so, the article attends to the politics of hate crime: namely, whether these actions belong within the confines of hate crime provisions or, alternatively, whether such provisions should expressly exclude the category of paedophilia. In its entirety, the article interrogates the dimensions of disgust associated with paedophilia, and explores issues arising from an alignment between paedophilia and hate crime.

Dendritic cells initiate and sustain immune responses by migrating to sites of pathogenic insult, transporting antigens to lymphoid tissues and signaling immune specific activation of T cells through the formation of the immunological synapse. Dendritic cells can also transfer intact, infectious HIV-1 to CD4 T cells through an analogous structure, the infectious synapse. This replication independent mode of HIV-1 transmission, known as trans-infection, greatly increases T cell infection in vitro and is thought to contribute to viral dissemination in vivo. This review outlines the recent data defining the mechanisms of trans-infection and provides a context for the potential contribution of trans-infection in HIV-1 disease.

Mycobacterium tuberculosis (Mtb) virulence is decreased by genetic deletion of the lipoprotein LprG, but the function of LprG remains unclear. We report that LprG expressed in Mtb binds to lipoglycans, such as lipoarabinomannan (LAM), that mediate Mtb immune evasion. Lipoglycan binding to LprG was dependent on both insertion of lipoglycan acyl chains into a hydrophobic pocket on LprG and a novel contribution of lipoglycan polysaccharide components outside of this pocket. An lprG null mutant (Mtb ΔlprG) had lower levels of surface-exposed LAM, revealing a novel role for LprG in determining the distribution of components in the Mtb cell envelope. Furthermore, this mutant failed to inhibit phagosome-lysosome fusion, an immune evasion strategy mediated by LAM. We propose that LprG binding to LAM facilitates its transfer from the plasma membrane into the cell envelope, increasing surface-exposed LAM, enhancing cell envelope integrity, allowing inhibition of phagosome-lysosome fusion and enhancing Mtb survival in macrophages.

With an increasing number of primary hip replacements being performed every year, the burden of revision hip arthroplasty, for septic and aseptic loosening, recurrent dislocation or periprosthetic fracture, is also increasing. In recent years, different approaches to revising the femoral prosthesis have emerged; including both cemented and cementless techniques. With a stable cement mantle and good bone quality, or through the use of impaction bone grafting when bone stock is lacking, it is possible to re-cement a femoral prosthesis. Alternatively, a cementless modular femoral prosthesis may be used, providing the surgeon with further options for restoring leg length, hip offset, anteversion and stability. Studies evaluating the use of modular cementless prostheses have so far been limited to mid-term studies, with results comparable to primary hip arthroplasty. There are some concerns, however, regarding tribological complications such as stem fracture, corrosion, and failure, and long-term studies are required to further evaluate these concerns. This review outlines the current evidence for the use of both cemented and cementless modular femoral prostheses in the setting of revision hip arthroplasty. Results of prospective and retrospective studies will be outlined, along with results obtained from national joint registries.

Several studies have found evidence of motor deficits in poor readers. There is no obvious reason for motor and literacy skills to go together, and it has been suggested that both deficits could be indicative of an underlying problem with cerebellar function and/or procedural learning. However, the picture is complicated by the fact that reading problems often co-occur with oral language impairments, which have also been linked with motor deficits. This raises the question of whether motor deficits characterise poor readers when language impairment has been accounted for – and vice versa. We considered these questions by assessing motor deficits associated with reading disability (RD) and language impairment (LI). A large community sample provided a subset of 9- to 10-year-olds, selected to oversample children with reading and/or language difficulties, to give 37 children with comorbid LI + RD, 67 children with RD only, 32 children with LI only, and 117 typically-developing (TD) children with neither type of difficulty. These children were given four motor tasks that taxed speed, sequence, and imitation abilities to differing extents. Different patterns of results were found for the four motor tasks. There was no effect of RD or LI on two speeded fingertip tapping tasks, one of which involved sequencing of movements. LI, but not RD, was associated with problems in imitating hand positions and slowed performance on a speeded peg-moving task that required a precision grip. Fine motor deficits in poor readers may be more a function of language impairment than literacy problems.

Roadside testing of oral fluids for a suite of illegal drugs has been taking place in Victoria since late 2004, is now operating in some form in all of Australia’s States and the Northern Territory. I suggest that the current roadside drug testing regimes have been introduced with insufficient rigour in the underlying policy analysis. The authorities state that it is a road safety initiative and not about punishing drivers for using illegal drugs, but this assertion can be challenged. The research evidence linking particular levels of drugs in the body and driving impairment is limited, no convincing evidence exists demonstrating that roadside drug testing improves traffic safety at the population level, the initiative fails to target some of the drugs the use of which has been demonstrated to be a traffic safety risk, the opportunity costs seem to have been ignored, and it may well fail the human rights test of proportionality.

In vitro, dendritic cells (DCs) bind and transfer intact, infectious HIV to CD4 T cells without first becoming infected, a process known as trans-infection. trans-infection is accomplished by recruitment of HIV and its receptors to the site of DC-T cell contact and transfer of virions at a structure known as the infectious synapse. In this study, we used fluorescent microscopy to track individual HIV particles trafficking in DCs during virus uptake and trans-infection. Mature DCs rapidly concentrated HIV into an apparently intracellular compartment that lacked markers characteristic of early endosomes, lysosomes, or antigen-processing vesicles. Live cell microscopy demonstrated that the HIV-containing compartment was rapidly polarized toward the infectious synapse after contact with a T cell; however, the bulk of the concentrated virus remained in the DCs after T cell engagement. Individual virions were observed emerging from the compartment and fusing with the T cell membrane at the infectious synapse. The compartmentalized HIV, although engulfed by the cytoplasm, was fully accessible to HIV envelope-specific inhibitors and other membrane-impermeable probes that were delivered to the cell surface. These results demonstrate that HIV resides in an invaginated domain within DCs that is both contiguous with the plasma membrane and distinct from endocytic vesicles. We conclude that HIV virions are routed through this specialized compartment, which allows individual particles to be delivered to T cells during trans-infection.