Genome analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared t

The co-occurrence of intimate partner violence and violence against children:A systematic review on associated factors in low- and middle-income countries

Violence against women (VAW) and violence against children (VAC) are public health issues of global concern. Intimate partner violence (IPV) is a commonly occurring form of VAW and there is evidence to suggest that IPV and VAC frequently co-occur within the same families. This systematic literature review searched for studies published in any language between 1st January 2000 to 16th February 2021 and identified 33 studies that provided findings for co-occurring IPV and VAC in 24 low- and middle-income countries (PROSPERO: CRD42020180179). These studies were split into subgroups based on the types of co-occurring violence they present and meta-analyses were conducted to calculate pooled odds ratios (ORs) within these subgroups. Our results indicate a significant association between IPV and VAC, with all pooled ORs showing a significant positive association between the two. Almost half of the studies focused exclusively on co-occurrence between male-to-female IPV and female caregiver-to-child VAC; few authors reported on male caregiver-to-child violence. Only three studies identified risk factors for co-occurring IPV and VAC, and those that did suggested conflicting findings on the risks associated with maternal age, alcohol and drug use, and parental education level. We also found incongruity in the violence definitions and measurements used across studies. Future research should aim to develop more consistent definitions and measurements for co-occurrence and move beyond solely examining dyadic and unidirectional violence occurrence in families; this will allow us to better understand the interrelationships between these different forms of abuse

Speleothem growth intervals reflect New Zealand montane vegetation response to temperature change over the last glacial cycle

Flowstone speleothem growth beneath Mount Arthur, New Zealand shows a clear relationship to vegetation density and soil development on the surface above. Flowstone does not currently form beneath sub-alpine Nothofagus forest above ca. 1000–1100 m altitude but U-Th dating shows it has formed there during past intervals of warmer-than-present conditions including an early–mid Holocene optimum and the last interglacial from ca. 131–119 ka. Some flowstones growing beneath ca. 600 m surface altitude, currently mantled with dense broadleaf-podocarp forest, grew during full glacial conditions, indicating that local tree line was never below this altitude. This implies that Last Glacial Maximum annual temperature was no more than ca. 4 °C cooler than today. Flowstone growth appears to be a robust indicator of dense surface vegetation and well-developed soil cover in this setting, and indicates that past interglacial climates of MIS 7e, 5e, the early–mid Holocene and possibly MIS 5a were more conducive to growth of trees than was the late Holocene, reflecting regional temperature changes similar in timing to Antarctic temperature changes. Here, flowstone speleothem growth is a sensitive indicator of vegetation density at high altitude, but may respond to other factors at lower altitudes

Measurement and prevalence of sexual harassment in low- and middle-income countries: a systematic review and meta-analysis.

OBJECTIVES: We synthesise evidence on sexual harassment from studies in low-income and middle-income countries (LMICs) to estimate its prevalence and conduct a meta-analysis of the association between sexual harassment and depressive symptoms. METHODS: We searched eight databases. We included peer-reviewed studies published in English from 1990 until April 2020 if they measured sexual harassment prevalence in LMICs, included female or male participants aged 14 and over and conceptualised sexual harassment as an independent or dependant variable. We appraised the quality of evidence, used a narrative syntheses approach to synthesise data and conducted a random effects meta-analysis. RESULTS: From 49 included studies, 38 focused on workplaces and educational institutions and 11 on public places. Many studies used an unclear definition of sexual harassment and did not deploy a validated measurement tool. Studies either used a direct question or a series of behavioural questions to elicit information on acts considered offensive or defined as sexual harassment. Prevalence was higher in educational institutions than in workplaces although there was high heterogeneity in prevalence estimates across studies with no international comparability. This posed a challenge for calculating an overall estimate or measuring a range. Our meta-analysis showed some evidence of an association between sexual harassment and depressive symptoms (OR: 1.75; 95% CI: 1.11 to 2.76; p=0.016) although there were only three studies with a high risk of bias. CONCLUSION: To our knowledge, this is the first systematic review to assess measurement approaches and estimate the prevalence of sexual harassment across settings in LMICs. We also contribute a pooled estimate of the association between sexual harassment and depressive symptoms in LMICs. There is limited definitional clarity, and rigorously designed prevalence studies that use validated measures for sexual harassment in LMICs. Improved measurement will enable us to obtain more accurate prevalence estimates across different settings to design effective interventions and policies

Reconstruction of primary vertices at the ATLAS experiment in Run 1 proton–proton collisions at the LHC

This paper presents the method and performance of primary vertex reconstruction in proton–proton collision data recorded by the ATLAS experiment during Run 1 of the LHC. The studies presented focus on data taken during 2012 at a centre-of-mass energy of √s=8 TeV. The performance has been measured as a function of the number of interactions per bunch crossing over a wide range, from one to seventy. The measurement of the position and size of the luminous region and its use as a constraint to improve the primary vertex resolution are discussed. A longitudinal vertex position resolution of about 30μm is achieved for events with high multiplicity of reconstructed tracks. The transverse position resolution is better than 20μm and is dominated by the precision on the size of the luminous region. An analytical model is proposed to describe the primary vertex reconstruction efficiency as a function of the number of interactions per bunch crossing and of the longitudinal size of the luminous region. Agreement between the data and the predictions of this model is better than 3% up to seventy interactions per bunch crossing

Effectiveness of Influenza Vaccination in Preventing Hospitalization Due to Influenza in Children: A Systematic Review and Meta-analysis.

This systematic review assesses the literature for estimates of influenza vaccine effectiveness (IVE) against laboratory-confirmed influenza-associated hospitalization in children. Studies of any design to June 8, 2020, were included if the outcome was hospitalization, participants were 17 years or younger and influenza infection was laboratory-confirmed. A random-effects meta-analysis of 37 studies that used a test-negative design gave a pooled seasonal IVE against hospitalization of 53.3% (47.2-58.8) for any influenza. IVE was higher against influenza A/H1N1pdm09 (68.7%, 56.9-77.2) and lowest against influenza A/H3N2 (35.8%, 23.4-46.3). Estimates by vaccine type ranged from 44.3% (30.1-55.7) for live-attenuated influenza vaccines to 68.9% (53.6-79.2) for inactivated vaccines. IVE estimates were higher in seasons when the circulating influenza strains were antigenically matched to vaccine strains (59.3%, 48.3-68.0). Influenza vaccination gives moderate overall protection against influenza-associated hospitalization in children supporting annual vaccination. IVE varies by influenza subtype and vaccine type

The use of Qualitative Comparative Analysis (QCA) in child well-being research: a scoping review of research on child well-being research and interventions.

BACKGROUND: Qualitative Comparative Analysis (QCA) is a method for examining configurational causality by identifying pathways that lead to an outcome of interest. There is a growing body of literature that uses QCA to measure child well-being due to its ability to generate evidence of causality for complex social phenomena. This scoping review examines how QCA studies are being employed to investigate child well-being and assesses the potential of QCA as a method to produce intervention-focused evidence and to contribute to future methodological development to address the complexity of child well-being. METHOD: We systematically searched Embase, PsyINFO, MEDLINE, Social Policy and Practice, Global Health, Econlit, Scopus and Web of Science for peer-reviewed studies that had used QCA methods in child well-being studies. We searched studies published in English up until 2023. Systematic reviews and meta-analyses using QCA were excluded due to insufficient methodological detail for inclusion in our analysis. We followed the PRISMA-ScR flowchart and guidelines for study screening to ensure a systematic selection process. Data extraction was undertaken to capture information of most relevance to QCA best practice. Data were analysed using a basic qualitative content analysis approach. RESULTS: The search identified 626 papers, of which 28 met our inclusion criteria. Dimensions of well-being included: psychological/mental health (n = 9); physical health (n = 2); language development under education (n = 1); socio-emotional health (n = 7); physical and psychological/mental health (n = 3), psychological/mental health and education (n = 1); and multi-dimensional health (n = 3). Two studies stated explicitly that they used well-being concepts-subjective well-being and psychological well-being. Most studies (n = 23) were predominantly in high income countries (HIC). Commonly reported strengths of QCA were the capacity to a) describe various pathways or combinations of pathways to the same outcome (equifinality); and b) examine conjunctural causation (combination of absent/present conditions), known as 'causal complexity'. Weaknesses related to a) generalisability of the data; and b) the number of causal conditions that can be included in the analysis. Our findings suggest that QCA can be effectively used alongside traditional analyses to provide a more nuanced understanding. CONCLUSION: QCA is a promising method with potential to address complexity when assessing the different dimensions of child well-being. More comprehensive guidelines are now available that offer good practices to enhance the quality of the QCA research. To build greater confidence using this method, scholars are recommended to adhere to these good practices to establish the highest levels of transparency of the analysis

Interventions that prevent or respond to intimate partner violence against women and violence against children: a systematic review.

Efforts to prevent or respond to intimate partner violence (IPV) and violence against children (VAC) are still disparate worldwide, despite increasing evidence of intersections across these forms of violence. We conducted a systematic review to explore interventions that prevent or respond to IPV and VAC by parents or caregivers, aiming to identify common intervention components and mechanisms that lead to a reduction in IPV and VAC. 30 unique interventions from 16 countries were identified, with 20 targeting both IPV and VAC. Key mechanisms for reducing IPV and VAC in primary prevention interventions included improved communication, conflict resolution, reflection on harmful gender norms, and awareness of the adverse consequences of IPV and VAC on children. Therapeutic programmes for women and children who were exposed to IPV facilitated engagement with IPV-related trauma, increased awareness of the effects of IPV, and promoted avoidance of unhealthy relationships. Evidence gaps in low-income and middle-income countries involved adolescent interventions, post-abuse interventions for women and children, and interventions addressing both prevention and response to IPV and VAC. Our findings strengthen evidence in support of efforts to address IPV and VAC through coordinated prevention and response programmes. However, response interventions for both IPV and VAC are rare and predominantly implemented in high-income countries. Although therapeutic programmes for parents, caregivers, and children in high-income countries are promising, their feasibility in low-income and middle-income countries remains uncertain. Despite this uncertainty, there is potential to improve the use of health services to address IPV and VAC together

Anthropogenic pressures and life history predict trajectories of seagrass meadow extent at a global scale

Seagrass meadows are threatened by multiple pressures, jeopardizing the many benefits they provide to humanity and biodiversity, including climate regulation and food provision through fisheries production. Conservation of seagrass requires identification of the main pressures contributing to loss and the regions most at risk of ongoing loss. Here, we model trajectories of seagrass change at the global scale and show they are related to multiple anthropogenic pressures but that trajectories vary widely with seagrass life-history strategies. Rapidly declining trajectories of seagrass meadow extent (>25% loss from 2000 to 2010) were most strongly associated with high pressures from destructive demersal fishing and poor water quality. Conversely, seagrass meadow extent was more likely to be increasing when these two pressures were low. Meadows dominated by seagrasses with persistent life-history strategies tended to have slowly changing or stable trajectories, while those with opportunistic species were more variable, with a higher probability of either rapidly declining or rapidly increasing. Global predictions of regions most at risk for decline show high-risk areas in Europe, North America, Japan, and southeast Asia, including places where comprehensive long-term monitoring data are lacking. Our results highlight where seagrass loss may be occurring unnoticed and where urgent conservation interventions are required to reverse loss and sustain their essential services

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements