Diagnosis of human leptospirosis: systematic review and meta-analysis of the diagnostic accuracy of the Leptospira microscopic agglutination test, PCR targeting Lfb1, and IgM ELISA to Leptospira fainei serovar Hurstbridge.

BACKGROUND: Leptospirosis is an underdiagnosed infectious disease with non-specific clinical presentation that requires laboratory confirmation for diagnosis. The serologic reference standard remains the microscopic agglutination test (MAT) on paired serum samples. However, reported estimates of MAT's sensitivity vary. We evaluated the accuracy of four index tests, MAT on paired samples as well as alternative standards for leptospirosis diagnosis: MAT on single acute-phase samples, polymerase chain reaction (PCR) with the target gene Lfb1, and ELISA IgM with Leptospira fainei serovar Hurstbridge as an antigen. METHODS: We performed a systematic review of studies reporting results of leptospirosis diagnostic tests. We searched eight electronic databases and selected studies that tested human blood samples and compared index tests with blood culture and/or PCR and/or MAT (comparator tests). For MAT selection criteria we defined a threshold for single acute-phase samples according to a national classification of leptospirosis endemicity. We used a Bayesian random-effect meta-analysis to estimate the sensitivity and specificity of MAT in single acute-phase and paired samples separately, and assessed risk of bias using the Quality Assessment of Studies of Diagnostic Accuracy Approach- 2 (QUADAS-2) tool. RESULTS: For the MAT accuracy evaluation, 15 studies were included, 11 with single acute-phase serum, and 12 with paired sera. Two included studies used PCR targeting the Lfb1 gene, and one included study used IgM ELISA with Leptospira fainei serovar Hurstbridge as antigen. For MAT in single acute-phase samples, the pooled sensitivity and specificity were 14% (95% credible interval [CrI] 3-38%) and 86% (95% CrI 59-96%), respectively, and the predicted sensitivity and specificity were 14% (95% CrI 0-90%) and 86% (95% CrI 9-100%). Among paired MAT samples, the pooled sensitivity and specificity were 68% (95% CrI 32-92%) and 75% (95% CrI 45-93%) respectively, and the predicted sensitivity and specificity were 69% (95% CrI 2-100%) and 75% (2-100%). CONCLUSIONS: Based on our analysis, the accuracy of MAT in paired samples was not high, but it remains the reference standard until a more accurate diagnostic test is developed. Future studies that include larger numbers of participants with paired samples will improve the certainty of accuracy estimates.

Diagnostic performance of the IMMY cryptococcal antigen lateral flow assay on serum and cerebrospinal fluid for diagnosis of cryptococcosis in HIV-negative patients: a systematic review.

BACKGROUND: The incidence of cryptococcosis amongst HIV-negative persons is increasing. Whilst the excellent performance of the CrAg testing in people living with HIV is well described, the diagnostic performance of the CrAg LFA has not been systematically evaluated in HIV-negative cohorts on serum or cerebrospinal fluid. METHODS: We performed a systematic review to characterise the diagnostic performance of IMMY CrAg® LFA in HIV-negative populations on serum and cerebrospinal fluid. A systematic electronic search was performed using Medline, Embase, Global Health, CENTRAL, WoS Science Citation Index, SCOPUS, Africa-Wide Information, LILACS and WHO Global Health Library. Studies were screened and data extracted from eligible studies by two independent reviewers. A fixed effect meta-analysis was used to estimate the diagnostic sensitivity and specificity. RESULTS: Of 447 records assessed for eligibility, nine studies met our inclusion criteria, including 528 participants overall. Amongst eight studies that evaluated the diagnostic performance of the IMMY CrAg® LFA on serum, the pooled median sensitivity was 96% (95% Credible Interval (CrI) 68-100%) with a pooled specificity estimate of 96% (95%CrI 84-100%). Amongst six studies which evaluated the diagnostic performance of IMMY CrAg® LFA on CSF, the pooled median sensitivity was 99% (95%CrI 95-100%) with a pooled specificity median of 99% (95%CrI 95-100%). CONCLUSIONS: This review demonstrates a high pooled sensitivity and specificity for the IMMY CrAg® LFA in HIV-negative populations, in keeping with findings in HIV-positive individuals. The review was limited by the small number of studies. Further studies using IMMY CrAg® LFA in HIV-negative populations would help to better determine the diagnostic value of this test.

Accuracy of the direct agglutination test for diagnosis of visceral leishmaniasis: a systematic review and meta-analysis.

BACKGROUND: Parasitological investigation of bone marrow, splenic or lymph node aspirations is the gold standard for the diagnosis of visceral leishmaniasis (VL). However, this invasive test requires skilled clinical and laboratory staff and adequate facilities, and sensitivity varies depending on the tissue used. The direct agglutination test (DAT) is a serological test that does not need specialised staff, with just minimal training required. While previous meta-analysis has shown DAT to have high sensitivity and specificity when using parasitology as the reference test for diagnosis, meta-analysis of DAT compared to other diagnostic techniques, such as PCR and ELISA, that are increasingly used in clinical and research settings, has not been done. METHODS: We conducted a systematic review to determine the diagnostic performance of DAT compared to all available tests for the laboratory diagnosis of human VL. We searched electronic databases including Medline, Embase, Global Health, Scopus, WoS Science Citation Index, Wiley Cochrane Central Register of Controlled Trials, Africa-Wide Information, LILACS and WHO Global Index. Three independent reviewers screened reports and extracted data from eligible studies. A meta-analysis estimated the diagnostic sensitivity and specificity of DAT. RESULTS: Of 987 titles screened, 358 were selected for full data extraction and 78 were included in the analysis, reporting on 32,822 participants from 19 countries. Studies included were conducted between 1987-2020. Meta-analysis of studies using serum and DAT compared to any other test showed pooled sensitivity of 95% (95%CrI 90-98%) and pooled specificity of 95% (95%CrI 88-98%). Results were similar for freeze-dried DAT and liquid DAT when analysed separately. Sensitivity was lower for HIV-positive patients (90%, CrI 59-98%) and specificity was lower for symptomatic patients (70%, CrI 43-89%). When comparing different geographical regions, the lowest median sensitivity (89%, CrI 67-97%) was in Western Asia (five studies). CONCLUSIONS: This systematic review and meta-analysis demonstrates high estimated pooled sensitivity and specificity of DAT for diagnosis of VL, although sensitivity and specificity were lower for different patient groups and geographical locations. This review highlights the lack of standardisation of DAT methods and preparations, and the lack of data from some important geographical locations. Future well-reported studies could provide better evidence to inform test implementation for different patient populations and use cases. PROSPERO REGISTRATION: CRD42021240830.

Diagnostic accuracy of multiplex respiratory pathogen panels for influenza or respiratory syncytial virus infections: systematic review and meta-analysis.

Respiratory syncytial virus (RSV) and influenza viruses are important global causes of morbidity and mortality. We evaluated the diagnostic accuracy of the Luminex NxTAG respiratory pathogen panels (RPPs)™ (index) against other RPPs (comparator) for detection of RSV and influenza viruses. Studies comparing human clinical respiratory samples tested with the index and at least one comparator test were included. A random-effect latent class meta-analysis was performed to assess the specificity and sensitivity of the index test for RSV and influenza. Risk of bias was assessed using the QUADAS-2 tool and certainty of evidence using GRADE. Ten studies were included. For RSV, predicted sensitivity was 99% (95% credible interval [CrI] 96-100%) and specificity 100% (95% CrI 98-100%). For influenza A and B, predicted sensitivity was 97% (95% CrI 89-100) and 98% (95% CrI 88-100) respectively; specificity 100% (95% CrI 99-100) and 100% (95% CrI 99-100), respectively. Evidence was low certainty. Although index sensitivity and specificity were excellent, comparators' performance varied. Further research with clear patient recruitment strategies could ascertain performance across different populations.Protocol Registration: Prospero CRD42021272062.

What factors influence implementation of whole-school interventions aiming to promote student commitment to school to prevent substance use and violence? Systematic review and synthesis of process evaluations.

BACKGROUND: Whole-school interventions go beyond classroom health education to modify the school environment to promote health. A sub-set aim to promote student commitment to school to reduce substance use and violence (outcomes associated with low commitment). It is unclear what factors influence implementation of such interventions. METHODS: We conducted a systematic review including synthesis of evidence from process evaluations examining what factors affect implementation. Meta-ethnographic synthesis was informed by May's General Theory of Implementation. RESULTS: Sixteen reports, covering 13 studies and 10 interventions were included in our synthesis. In terms of May's concept of 'sense-making', we found that school staff were more likely to understand what was required in implementing an intervention when provided with good-quality materials and support. Staff could sometimes wilfully or unintentionally misinterpret interventions. In terms of May's concept of 'cognitive participation', whereby staff commit to implementation, we found that lack of intervention adaptability could in particular undermine implementation of whole-school elements. Interventions providing local data were reported as helping build staff commitment. School leaders were more likely to commit to an intervention addressing an issue they already intended to tackle. Collaborative planning groups were reported as useful in ensuring staff 'collective action' (May's term for working together) to enact interventions. Collective action was also promoted by the presence of sufficient time, leadership and relationships. Implementation of whole-school interventions took time to build. Considering May's concept of 'reflexive monitoring' (formal or informal review of progress), this was important in assessing and enhancing implementation. 'Quick wins' could help maintain collective impetus to implement further intervention activities. CONCLUSION: We identified novel factors influencing implementation of whole-school elements such as: local adaptability of interventions; providing local data to build commitment; interventions addressing an issue already on school leaders' agenda; collaborative planning groups; and 'reflexive monitoring' as an explicit intervention component.

Evidence for the Use of Triage, Respiratory Isolation, and Effective Treatment to Reduce the Transmission of Mycobacterium Tuberculosis in Healthcare Settings: A Systematic Review.

Evidence is limited for infection prevention and control (IPC) measures reducing Mycobacterium tuberculosis (MTB) transmission in health facilities. This systematic review, 1 of 7 commissioned by the World Health Organization to inform the 2019 update of global tuberculosis (TB) IPC guidelines, asked: do triage and/or isolation and/or effective treatment of TB disease reduce MTB transmission in healthcare settings? Of 25 included articles, 19 reported latent TB infection (LTBI) incidence in healthcare workers (HCWs; absolute risk reductions 1%-21%); 5 reported TB disease incidence in HCWs (no/slight [high TB burden] or moderate [low burden] reduction) and 2 in human immunodeficiency virus-positive in-patients (6%-29% reduction). In total, 23/25 studies implemented multiple IPC measures; effects of individual measures could not be disaggregated. Packages of IPC measures appeared to reduce MTB transmission, but evidence for effectiveness of triage, isolation, or effective treatment, alone or in combination, was indirect and low quality. Harmonizing study designs and reporting frameworks will permit formal data syntheses and facilitate policy making.

Dynamics of sputum conversion during effective tuberculosis treatment: A systematic review and meta-analysis.

BACKGROUND: Two weeks' isolation is widely recommended for people commencing treatment for pulmonary tuberculosis (TB). The evidence that this corresponds to clearance of potentially infectious tuberculous mycobacteria in sputum is not well established. This World Health Organization-commissioned review investigated sputum sterilisation dynamics during TB treatment. METHODS AND FINDINGS: For the main analysis, 2 systematic literature searches of OvidSP MEDLINE, Embase, and Global Health, and EBSCO CINAHL Plus were conducted to identify studies with data on TB infectiousness (all studies to search date, 1 December 2017) and all randomised controlled trials (RCTs) for drug-susceptible TB (from 1 January 1990 to search date, 20 February 2018). Included articles reported on patients receiving effective treatment for culture-confirmed drug-susceptible pulmonary TB. The outcome of interest was sputum bacteriological conversion: the proportion of patients having converted by a defined time point or a summary measure of time to conversion, assessed by smear or culture. Any study design with 10 or more particpants was considered. Record sifting and data extraction were performed in duplicate. Random effects meta-analyses were performed. A narrative summary additionally describes the results of a systematic search for data evaluating infectiousness from humans to experimental animals (PubMed, all studies to 27 March 2018). Other evidence on duration of infectiousness-including studies reporting on cough dynamics, human tuberculin skin test conversion, or early bactericidal activity of TB treatments-was outside the scope of this review. The literature search was repeated on 22 November 2020, at the request of the editors, to identify studies published after the previous censor date. Four small studies reporting 3 different outcome measures were identified, which included no data that would alter the findings of the review; they are not included in the meta-analyses. Of 5,290 identified records, 44 were included. Twenty-seven (61%) were RCTs and 17 (39%) were cohort studies. Thirteen studies (30%) reported data from Africa, 12 (27%) from Asia, 6 (14%) from South America, 5 (11%) from North America, and 4 (9%) from Europe. Four studies reported data from multiple continents. Summary estimates suggested smear conversion in 9% of patients at 2 weeks (95% CI 3%-24%, 1 single study [N = 1]), and 82% of patients at 2 months of treatment (95% CI 78%-86%, N = 10). Among baseline smear-positive patients, solid culture conversion occurred by 2 weeks in 5% (95% CI 0%-14%, N = 2), increasing to 88% at 2 months (95% CI 84%-92%, N = 20). At equivalent time points, liquid culture conversion was achieved in 3% (95% CI 1%-16%, N = 1) and 59% (95% CI 47%-70%, N = 8). Significant heterogeneity was observed. Further interrogation of the data to explain this heterogeneity was limited by the lack of disaggregation of results, including by factors such as HIV status, baseline smear status, and the presence or absence of lung cavitation. CONCLUSIONS: This systematic review found that most patients remained culture positive at 2 weeks of TB treatment, challenging the view that individuals are not infectious after this interval. Culture positivity is, however, only 1 component of infectiousness, with reduced cough frequency and aerosol generation after TB treatment initiation likely to also be important. Studies that integrate our findings with data on cough dynamics could provide a more complete perspective on potential transmission of Mycobacterium tuberculosis by individuals on treatment. TRIAL REGISTRATION: Systematic review registration: PROSPERO 85226.

eHealth Interventions to Address Sexual Health, Substance Use, and Mental Health Among Men Who Have Sex With Men: Systematic Review and Synthesis of Process Evaluations.

BACKGROUND: Men who have sex with men (MSM) face disproportionate risks concerning HIV and other sexually transmitted infections, substance use, and mental health. These outcomes constitute an interacting syndemic among MSM; interventions addressing all 3 together could have multiplicative effects. eHealth interventions can be accessed privately, and evidence from general populations suggests these can effectively address all 3 health outcomes. However, it is unclear how useable, accessible, or acceptable eHealth interventions are for MSM and what factors affect this. OBJECTIVE: We undertook a systematic review of eHealth interventions addressing sexual risk, substance use, and common mental illnesses among MSM and synthesized evidence from process evaluations. METHODS: We searched 19 databases, 3 trials registers, OpenGrey, and Google, and supplemented this by reference checks and requests to experts. Eligible reports were those that discussed eHealth interventions offering ongoing support to MSM aiming to prevent sexual risk, substance use, anxiety or depression; and assessed how intervention delivery or receipt varied with characteristics of interventions, providers, participants, or context. Reviewers screened citations on titles, abstracts, and then full text. Reviewers assessed quality of eligible studies, and extracted data on intervention, study characteristics, and process evaluation findings. The analysis used thematic synthesis. RESULTS: A total of 12 reports, addressing 10 studies of 8 interventions, were eligible for process synthesis. Most addressed sexual risk alone or with other outcomes. Studies were assessed as medium and high reliability (reflecting the trustworthiness of overall findings) but tended to lack depth and breadth in terms of the process issues explored. Intervention acceptability was enhanced by ease of use; privacy protection; use of diverse media; opportunities for self-reflection and to gain knowledge and skills; and content that was clear, interactive, tailored, reflective of MSM's experiences, and affirming of sexual-minority identity. Technical issues and interventions that were too long detracted from acceptability. Some evidence suggested that acceptability varied by race or ethnicity and educational level; findings on variation by socioeconomic status were mixed. No studies explored how intervention delivery or receipt varied by provider characteristics. CONCLUSIONS: Findings suggest that eHealth interventions targeting sexual risk, substance use, and mental health are acceptable for MSM across sociodemographic groups. We identified the factors shaping MSM's receipt of such interventions, highlighting the importance of tailored content reflecting MSM's experiences and of language affirming sexual-minority identities. Intervention developers can draw on these findings to increase the usability and acceptability of integrated eHealth interventions to address the syndemic of sexual risk, substance use, and mental ill health among MSM. Evaluators of these interventions can draw on our findings to plan evaluations that explore the factors shaping usability and acceptability.

Reduced TCR-dependent activation through citrullination of a T-cell epitope enhances Th17 development by disruption of the STAT3/5 balance.

Citrullination is a post-translational modification of arginine that commonly occurs in inflammatory tissues. Because T-cell receptor (TCR) signal quantity and quality can regulate T-cell differentiation, citrullination within a T-cell epitope has potential implications for T-cell effector function. Here, we investigated how citrullination of an immunedominant T-cell epitope affected Th17 development. Murine naïve CD4(+) T cells with a transgenic TCR recognising p89-103 of the G1 domain of aggrecan (agg) were co-cultured with syngeneic bone marrow-derived dendritic cells (BMDC) presenting the native or citrullinated peptides. In the presence of pro-Th17 cytokines, the peptide citrullinated on residue 93 (R93Cit) significantly enhanced Th17 development whilst impairing the Th2 response, compared to the native peptide. T cells responding to R93Cit produced less IL-2, expressed lower levels of the IL-2 receptor subunit CD25, and showed reduced STAT5 phosphorylation, whilst STAT3 activation was unaltered. IL-2 blockade in native p89-103-primed T cells enhanced the phosphorylated STAT3/STAT5 ratio, and concomitantly enhanced Th17 development. Our data illustrate how a post-translational modification of a TCR contact point may promote Th17 development by altering the balance between STAT5 and STAT3 activation in responding T cells, and provide new insight into how protein citrullination may influence effector Th-cell development in inflammatory disorders.

Diagnostic accuracy of tests to detect Hepatitis C antibody: a meta-analysis and review of the literature.

BACKGROUND: Although direct-acting antivirals can achieve sustained virological response rates greater than 90% in Hepatitis C Virus (HCV) infected persons, at present the majority of HCV-infected individuals remain undiagnosed and therefore untreated. While there are a wide range of HCV serological tests available, there is a lack of formal assessment of their diagnostic performance. We undertook a systematic review and meta-analysis to evaluate he diagnostic accuracy of available rapid diagnostic tests (RDT) and laboratory based EIA assays in detecting antibodies to HCV. METHODS: We used the PRISMA checklist and Cochrane guidance to develop our search protocol. The search strategy was registered in PROSPERO (CRD42015023567). The search focused on hepatitis C, diagnostic tests, and diagnostic accuracy within eight databases (MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials, Science Citation Index Expanded, Conference Proceedings Citation Index-Science, SCOPUS, Literatura Latino-Americana e do Caribe em Ciências da Saúde and WHO Global Index Medicus. Studies were included if they evaluated an assay to determine the sensitivity and specificity of HCV antibody (HCV Ab) in humans. Two reviewers independently extracted data and performed a quality assessment of the studies using the QUADAS tool. We pooled test estimates using the DerSimonian-Laird method, by using the software R and RevMan. 5.3. RESULTS: A total of 52 studies were identified that included 52,673 unique test measurements. Based on five studies, the pooled sensitivity and specificity of HCV Ab rapid diagnostic tests (RDTs) were 98% (95% CI 98-100%) and 100% (95% CI 100-100%) compared to an enzyme immunoassay (EIA) reference standard. High HCV Ab RDTs sensitivity and specificity were observed across screening populations (general population, high risk populations, and hospital patients) using different reference standards (EIA, nucleic acid testing, immunoblot). There were insufficient studies to undertake subanalyses based on HIV co-infection. Oral HCV Ab RDTs also had excellent sensitivity and specificity compared to blood reference tests, respectively at 94% (95% CI 93-96%) and 100% (95% CI 100-100%). Among studies that assessed individual oral RDTs, the eight studies revealed that OraQuick ADVANCE® had a slightly higher sensitivity (98%, 95% CI 97-98%) compared to the other oral brands (pooled sensitivity: 88%, 95% CI 84-92%). CONCLUSIONS: RDTs, including oral tests, have excellent sensitivity and specificity compared to laboratory-based methods for HCV antibody detection across a wide range of settings. Oral HCV Ab RDTs had good sensitivity and specificity compared to blood reference standards.

Diagnostic accuracy of tests to detect hepatitis B surface antigen: a systematic review of the literature and meta-analysis.

BACKGROUND: Chronic Hepatitis B Virus (HBV) infection is characterised by the persistence of hepatitis B surface antigen (HBsAg). Expanding HBV diagnosis and treatment programmes into low resource settings will require high quality but inexpensive rapid diagnostic tests (RDTs) in addition to laboratory-based enzyme immunoassays (EIAs) to detect HBsAg. The purpose of this review is to assess the clinical accuracy of available diagnostic tests to detect HBsAg to inform recommendations on testing strategies in 2017 WHO hepatitis testing guidelines. METHODS: The systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines using 9 databases. Two reviewers independently extracted data according to a pre-specified plan and evaluated study quality. Meta-analysis was performed. HBsAg diagnostic accuracy of rapid diagnostic tests (RDTs) was compared to enzyme immunoassay (EIA) and nucleic-acid test (NAT) reference standards. Subanalyses were performed to determine accuracy among brands, HIV-status and specimen type. RESULTS: Of the 40 studies that met the inclusion criteria, 33 compared RDTs and/or EIAs against EIAs and 7 against NATs as reference standards. Thirty studies assessed diagnostic accuracy of 33 brands of RDTs in 23,716 individuals from 23 countries using EIA as the reference standard. The pooled sensitivity and specificity were 90.0% (95% CI: 89.1, 90.8) and 99.5% (95% CI: 99.4, 99.5) respectively, but accuracy varied widely among brands. Accuracy did not differ significantly whether serum, plasma, venous or capillary whole blood was used. Pooled sensitivity of RDTs in 5 studies of HIV-positive persons was lower at 72.3% (95% CI: 67.9, 76.4) compared to that in HIV-negative persons, but specificity remained high. Five studies evaluated 8 EIAs against a chemiluminescence immunoassay reference standard with a pooled sensitivity and specificity of 88.9% (95% CI: 87.0, 90.6) and 98.4% (95% CI: 97.8, 98.8), respectively. Accuracy of both RDTs and EIAs using a NAT reference were generally lower, especially amongst HIV-positive cohorts. CONCLUSIONS: HBsAg RDTs have good sensitivity and excellent specificity compared to laboratory immunoassays as a reference standard. Sensitivity of HBsAg RDTs may be lower in HIV infected individuals.

Unconventional T-cell recognition of an arthritogenic epitope of proteoglycan aggrecan released from degrading cartilage.

It has been proposed that peptide epitopes bind to MHC class II molecules to form distinct structural conformers of the same MHC II-peptide complex termed type A and type B, and that the two conformers of the same peptide-MHC II complex are recognized by distinct CD4 T cells, termed type A and type B T cells. Both types recognize short synthetic peptides but only type A recognize endosomally processed intact antigen. Type B T cells that recognize self peptides from exogenously degraded proteins have been shown to escape negative selection during thymic development and so have the potential to contribute to the pathogenesis of autoimmunity. We generated and characterized mouse CD4 T cells specific for an arthritogenic epitope of the candidate joint autoantigen proteoglycan aggrecan. Cloned T-cell hybridomas specific for a synthetic peptide containing the aggrecan epitope showed two distinct response patterns based on whether they could recognize processed intact aggrecan. Fine mapping demonstrated that both types of T-cell recognized the same core epitope. The results are consistent with the generation of aggrecan-specific type A and type B T cells. Type B T cells were activated by supernatants released from degrading cartilage, indicating the presence of antigenic extracellular peptides or fragments of aggrecan. Type B T cells could play a role in the pathogenesis of proteoglycan-induced arthritis in mice, a model for rheumatoid arthritis, by recognizing extracellular peptides or protein fragments of joint autoantigens released by inflamed cartilage.

Contribution of natural antisense transcription to an endogenous siRNA signature in human cells.

BACKGROUND: Eukaryotic cells express a complex layer of noncoding RNAs. An intriguing family of regulatory RNAs includes transcripts from the opposite strand of protein coding genes, so called natural antisense transcripts (NATs). Here, we test the hypothesis that antisense transcription triggers RNA interference and gives rise to endogenous short RNAs (endo-siRNAs). RESULTS: We used cloned human embryonic kidney cells (HEK293) followed by short RNAseq to investigate the small genic RNA transcriptome. 378 genes gave rise to short RNA reads that mapped to exons of RefSeq genes. The length profile of short RNAs showed a broad peak of 20-24 nucleotides, indicative of endo-siRNAs. Collapsed reads mapped predominantly to the first and the last exon of genes (74%). RNAs reads were intersected with sequences occupied by RNAPII or bound to Argonaute (AGO1 by crosslinking, ligation, and sequencing of hybrids, CLASH). In the first exon, 94% of the reads correlated with RNAPII occupancy with an average density of 130 (relative units); this decreased to 65%/20 in middle exons and 54%/12 in the last exon. CLASH reads mapping to multi-exon genes showed little distribution bias with an average of about 5 CLASH reads overlapping with 60% of the endo-siRNA reads. However, endo-siRNAs (21-25 nt) intersecting with CLASH reads were enriched at the 5'end and decreased towards the 3'end.We then investigated the 378 genes with particular focus on features indicative for short RNA production; however, found that endo-siRNA numbers did not correlate with gene structures that favor convergent transcription. In contrast, our gene set was found notably over-represented in the NATsDB sense/antisense group as compared to non-overlapping and non-bidirectional groups. Moreover, read counts showed no correlation with the steady-state levels of the related mRNAs and the pattern of endo-siRNAs proved reproducible after an induced mutagenic insult. CONCLUSIONS: Our results suggest that antisense transcripts contribute to low levels of endo-siRNAs in fully differentiated human cells. A characteristic endo-siRNA footprint is being produced at sites of RNAPII transcription which is also related to AGO1. This endo-siRNA signature represents an intriguing finding and its reproducibility suggests that the production of endo-siRNAs is a regulated process with potential homoeostatic impact.

Intramolecular polyspecificity in CD4 T-cell recognition of Ad-restricted epitopes of proteoglycan aggrecan.

T-cell recognition of MHC­peptide complexes shows a high degree of polyspecificity extending to recognition of a large number of structurally unrelated peptides. Examples of polyspecificity reported to date are confined to recognition of epitopes from distinct proteins or synthetic peptide libraries. Here we describe intramolecular polyspecificity of CD4 T cells specific for several epitopes within proteoglycan aggrecan, a structural glycoprotein of cartilage and candidate autoantigen in rheumatoid arthritis. T-cell hybridomas from aggrecan-immunized mice recognized four structurally unrelated epitopes from the G1 domain of aggrecan, but not other aggrecan epitopes or a variety of other peptide epitopes restricted by the same MHC class II allele. We also showed that the hierarchy of cross-reactivity broadly correlated with the strength of peptide binding to MHC class II. Similar polyspecificity was observed in responses of lymph node cells from peptide-immunized mice, suggesting polyspecificity of a significant proportion of the in vivo aggrecan specific T-cell repertoire. Polyspecific recognition of several epitopes within the same autoantigen may provide a novel mechanism to reach the activation threshold of low-affinity autoreactive T cells in the initiation of autoimmune diseases.

Whole-school interventions promoting student commitment to school to prevent substance use and violence, and improve educational attainment: a systematic review.

Background: Whole-school interventions modify the school environment to promote health. A subset of these interventions promotes student commitment to school to prevent substance (tobacco, alcohol, other drugs) use and/or violence. A previous review identified the theory of human functioning and school organisation as a comprehensive theory of such interventions, and found evidence that these interventions reduce substance use and/or violence. Objectives: The objectives were to search for, appraise and synthesise evidence to address the following questions: (1) What whole-school interventions promoting student commitment to school to prevent substance use and/or violence have been evaluated, what intervention subtypes are apparent and how closely do these align with the theory of human functioning and school organisation? (2) What factors relating to setting, population and intervention affect implementation? (3) What are the effects on student substance use, violence and educational attainment? (4) What is the cost-effectiveness of such interventions? (5) Are intervention effects mediated by student commitment to school or moderated by setting or population? Data sources: A total of 56 information sources were searched (in January 2020), then an updated search of 48 of these was carried out (in May 2021). Reference lists were also searched and experts were contacted. Review methods: Eligible studies were process/outcome evaluations of whole-school interventions to reduce student violence or substance use among students aged 5-18 years attending schools, via actions aligning with the theory of human functioning and school organisation: modifying teaching to increase engagement, enhancing student-staff relationships, revising school policies, encouraging volunteering or increasing parental involvement. Data extraction and quality assessments used existing tools. Theory and process reports were synthesised qualitatively. Outcome and economic data were synthesised narratively; outcome data were meta-analysed. Results: Searches retrieved 63 eligible reports on 27 studies of 22 interventions. We identified four intervention subtypes focused on student participation in school-wide decisions, improving staff-student relationships, increasing engagement in learning and involving parents. The theories of change of most intervention subtypes aligned closely with the theory of human functioning and school organisation, and informed refinement of an intervention theory of change. Theories of change for interventions increasing learning engagement did not align with this theory, aiming instead to increase school commitment primarily via social skills curricula. Factors influencing the implementation included whether or not interventions were tailorable, workable and well explained. Interventions with action groups comprising staff/students, etc. and providing local data were well implemented. Implementation was also affected by whether or not schools accepted the need for change and staff had the resources for delivery. Meta-analyses suggest small, but significant, intervention effects in preventing violence victimisation and perpetration, and substance use. There was sparse and inconsistent evidence of moderation and some evidence of mediation by student commitment to school. Two economic evaluations suggested that there is the potential for the interventions to be cost-effective. Limitations: The quality of the studies was variable and the economic synthesis was limited to two studies. Conclusions: Whole-school interventions aiming to promote student commitment to school share similar theories of change and factors affecting implementation. They have the potential to contribute to preventing violence and substance use among young people. Future trials should aim to optimise intervention effectiveness by better theorisation, and assess implementation and effect moderators and mediators. Study registration: This study is registered as PROSPERO CRD42019154334. Funding: This award was funded by the National Institute for Health and Care Research (NIHR) Public Health Research programme (NIHR award ref: 17/151/05) and is published in full in Public Health Research; Vol. 12, No. 2. See the NIHR Funding and Awards website for further award information.

Whole-school health interventions aim to modify how schools are run, to promote students' health. Some aim to promote student commitment to school to prevent the important interlinked outcomes of substance (tobacco, alcohol, other drugs) use and violence. We searched for all evaluations of such interventions. We summarised what this research said about the sorts of interventions used, how they are meant to work, what factors affect delivery, whether or not they reduce violence and substance use and whether or not they are worth the money. We found 63 reports on 27 studies of 22 interventions. We identified four subtypes of interventions. These aimed to involve students in school decisions, improve staff­student relationships, increase engagement in learning or involve parents. Most of these interventions were intended to work by making sure schools focused on student needs, or by improving relationships between staff and students, between different areas of learning or between schools and communities. This aimed to make students feel committed to school and therefore avoid violence or substance use. A few aimed to work mostly by teaching students how to avoid violence and substance use. We found that interventions were well implemented if they were tailored for each school and had good materials and support. Interventions were well delivered if they were led by action groups (comprising staff, students, etc.) or provided schools with information on students' needs. Implementation was affected by whether or not schools accepted the need for change and whether or not staff had the necessary time and money to do the work. These interventions appear to have small, but significant, intervention impacts in preventing violence and substance use among young people. There was not consistent evidence of different effects for different students. A small number of studies suggest that such interventions might show economic benefit, but this would need further research. Future research should focus on interventions that are refined to make sure that they can be well delivered.

eHealth Interventions to Address HIV and Other Sexually Transmitted Infections, Sexual Risk Behavior, Substance Use, and Mental Ill-health in Men Who Have Sex With Men: Systematic Review and Meta-analysis.

BACKGROUND: Men who have sex with men experience disproportionately high levels of HIV and other sexually transmitted infections (STIs), sexual risk behavior, substance use, and mental ill-health. These experiences are interrelated, and these interrelations are potentiated by structural conditions of discrimination, stigma, and unequal access to appropriate health services, and they magnify each other and have intersecting causal pathways, worsening both risk for each condition and risk for the negative sequelae of each condition. eHealth interventions could address these issues simultaneously and thus have wide-ranging and greater effects than would be for any 1 outcome alone. OBJECTIVE: We systematically reviewed the evidence for the effectiveness of eHealth interventions in addressing these outcomes separately or together. METHODS: We searched 19 databases for randomized trials of interactive or noninteractive eHealth interventions delivered via mobile phone apps, internet, or other electronic media to populations consisting entirely or principally of men who have sex with men to prevent HIV, STIs, sexual risk behavior, alcohol and drug use, or common mental illnesses. We extracted data and appraised each study, estimated meta-analyses where possible by using random effects and robust variance estimation, and assessed the certainty of our findings (closeness of the estimated effect to the true effect) by using GRADE (Grading of Recommendations, Assessment, Development and Evaluations). RESULTS: We included 14 trials, of which 13 included active versus control comparisons; none reported mental health outcomes, and all drew from 12 months or less of follow-up postintervention. Findings for STIs drew on low numbers of studies and did not suggest consistent short-term (<3 months postintervention; d=0.17, 95% CI -0.18 to 0.52; I2=0%; 2 studies) or midterm (3-12 months postintervention, no meta-analysis, 1 study) evidence of effectiveness. Eight studies considering sexual risk behavior outcomes suggested a short-term, nonsignificant reduction (d=-0.14, 95% CI -0.30 to 0.03) with very low certainty, but 6 studies reporting midterm follow-ups suggested a significant impact on reducing sexual risk behavior (d=-0.12, 95% CI -0.19 to -0.05) with low certainty. Meta-analyses could not be undertaken for alcohol and drug use (2 heterogeneous studies) or for HIV infections (1 study for each of short-term or midterm follow-up), and alcohol outcomes alone were not captured in the included studies. Certainty was graded as low to very low for most outcomes, including all meta-analyses. CONCLUSIONS: To create a comprehensive eHealth intervention that targets multiple outcomes, intervention evaluations should seek to generalize both mechanisms and components that are successfully used to achieve change in 1 outcome over multiple outcomes. However, additional evaluations of interventions seeking to address outcomes other than sexual risk behavior are needed before development and evaluation of a joined-up intervention.

Quantifying the effectiveness and health co-benefits of climate change mitigation actions across sectors: a protocol for an umbrella review.

BACKGROUND: Effective and rapid actions are required to achieve global goals for climate change mitigation, and there is an opportunity to ensure that the actions taken are also positive for human health. However, little is known about the relative magnitude of the health co-benefits that can be achieved from mitigation actions, so robust and comprehensive syntheses of the evidence on the nature and effects of relevant actions are required. This paper presents a protocol for an interdisciplinary and cross-sectoral umbrella review of systematic reviews, synthesising modelled and empirical evidence on such actions. METHODS: Nine bibliographic databases will be searched, capturing literature across a wide range of disciplines and sectors. Unique records retrieved by the searches will be screened by two independent reviewers. The quality of all the included systematic reviews will be assessed using A MeaSurement Tool to Assess Systematic Reviews (AMSTAR) 2 critical appraisal tool. Data will be extracted on methodological and thematic characteristics of the reviews, nature of the actions, and their effects on greenhouse gas emission reduction, health, and its determinants, as well as any other reported effects and interactions across different actions. RESULTS: Narrative and quantitative synthesis methods will be used to create a typology of relevant actions, map pathways to their impacts on health, compare the magnitude of health and greenhouse gas (GHG) emission reduction impacts by selected characteristics of the actions and the nature of the evidence, as well as to identify gaps in evidence syntheses. CONCLUSION: This review will identify the most effective actions for global climate change mitigation and health based on the best available scientific evidence.   This protocol has been registered in PROSPERO, Reg No.: CRD42021239292.

Theories of change for e-health interventions targeting HIV/STIs and sexual risk, substance use and mental ill health amongst men who have sex with men: systematic review and synthesis.

BACKGROUND: Sexual risk, substance use, and mental ill health constitute a syndemic of co-occurring, mutually reinforcing epidemics amongst men who have sex with men (MSM). Developed since 1995, e-health interventions offer accessible, anonymous support and can be effective in addressing these outcomes, suggesting the potential value of developing e-health interventions that address these simultaneously amongst MSM. We conducted a systematic review of e-health interventions addressing one or more of these outcomes amongst MSM and in this paper describe the theories of change underpinning relevant interventions, what these offer and how they might complement each other. METHODS: We identified eligible reports via expert requests, reference-checking and database and Google searches. Results were screened for reports published in 1995 or later; focused on MSM; reporting on e-health interventions providing ongoing support to prevent HIV/STIs, sexual risk behaviour, substance use, anxiety or depression; and describing intervention theories of change. Reviewers assessed report quality, extracted intervention and theory of change data, and developed a novel method of synthesis using diagrammatic representations of theories of change. RESULTS: Thirty-three reports on 22 intervention theories of change were included, largely of low/medium-quality. Inductively grouping these theories according to their core constructs, we identified three distinct groupings of theorised pathways. In the largest, the 'cognitive/skills' grouping, interventions provide information and activities which are theorised to influence behaviour via motivation/intention and self-efficacy/perceived control. In the 'self-monitoring' grouping, interventions are theorised to trigger reflection, self-reward/critique and self-regulation. In the 'cognitive therapy' grouping, the theory of change is rooted in cognitive therapy techniques, aiming to reframe negative emotions to improve mental health. CONCLUSIONS: The synthesised theories of change provide a framework for developing e-health interventions that might holistically address syndemic health problems amongst MSM. Improving reporting on theories of change in primary studies of e-health interventions would enable a better understanding of how they are intended to work and the evidence supporting this. The novel diagrammatic method of theory of change synthesis used here could be used for future reviews where interventions are driven by existing well-defined behaviour and behaviour change theories. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42018110317.