Greenhouse gas and ammonia emission mitigation priorities for UK policy targets

Acknowledgements Many thanks to the Association of Applied Biologist’s for organising and hosting the ‘Agricultural greenhouse gases and ammonia mitigation: Solutions, challenges, and opportunities’ workshop. This work was supported with funding from the Scottish Government’s Strategic Research Programme (2022-2027, C2-1 SRUC) and BBSRC (BBS/E/C/000I0320 and BBS/E/C/000I0330). We also acknowledge support from UKRI694 BBSRC (United Kingdom Research and Innovation-Biotechnology and Biological Sciences 695 Research Council; United Kingdom) via grants BBS/E/C/000I0320 and BBS/E/C/000I0330. and Rothamsted Research's Science Initiative Catalyst Award (SICA) supported by BBSRC.Peer reviewedPublisher PD

Priorities for mitigating greenhouse gas and ammonia emissions to meet UK policy targets

Agriculture is essential for providing food and maintaining food security while concurrently delivering multiple other ecosystem services. However, agricultural systems are generally a net source of greenhouse gases and ammonia. They, therefore, need to substantively contribute to climate change mitigation and net zero ambitions. It is widely acknowledged that there is a need to further reduce and mitigate emissions across sectors, including agriculture to address the climate emergency and emissions gap. This discussion paper outlines a collation of opinions from a range of experts within agricultural research and advisory roles following a greenhouse gas and ammonia emission mitigation workshop held in the UK in March 2022. The meeting identified the top mitigation priorities within the UK’s agricultural sector to achieve reductions in greenhouse gases and ammonia that are compatible with policy targets. In addition, experts provided an overview of what they believe are the key knowledge gaps, future opportunities and co-benefits to mitigation practices as well as indicating the potential barriers to uptake for mitigation scenarios discussed

Pregnancy-specific stress, fetoplacental haemodynamics, and neonatal outcomes in women with small for gestational age pregnancies: a secondary analysis of the multicentre Prospective Observational Trial to Optimise Paediatric Health in Intrauterine Growth Restriction

Objectives: To examine associations between maternal pregnancy-specific stress and umbilical (UA PI) and middle cerebral artery pulsatility indices (MCA PI), cerebroplacental ratio, absent end diastolic flow (AEDF), birthweight, prematurity, neonatal intensive care unit admission and adverse obstetric outcomes in women with small for gestational age pregnancies. It was hypothesised that maternal pregnancy-specific stress would be associated with fetoplacental haemodynamics and neonatal outcomes. Design: This is a secondary analysis of data collected for a large-scale prospective observational study. Setting: This study was conducted in the seven major obstetric hospitals in Ireland and Northern Ireland. Participants: Participants included 331 women who participated in the Prospective Observational Trial to Optimise Paediatric Health in Intrauterine Growth Restriction. Women with singleton pregnancies between 24 and 36 weeks gestation, estimated fetal weight <10th percentile and no major structural or chromosomal abnormalities were included. Primary and secondary outcome measures Serial Doppler ultrasound examinations of the umbilical and middle cerebral arteries between 20 and 42 weeks gestation, Pregnancy Distress Questionnaire (PDQ) scores between 23 and 40 weeks gestation and neonatal outcomes. Results: Concerns about physical symptoms and body image at 35–40 weeks were associated with lower odds of abnormal UAPI (OR 0.826, 95% CI 0.696 to 0.979, p=0.028). PDQ score (OR 1.073, 95% CI 1.012 to 1.137, p=0.017), concerns about birth and the baby (OR 1.143, 95% CI 1.037 to 1.260, p=0.007) and concerns about physical symptoms and body image (OR 1.283, 95% CI 1.070 to 1.538, p=0.007) at 29–34 weeks were associated with higher odds of abnormal MCA PI. Concerns about birth and the baby at 29–34 weeks (OR 1.202, 95% CI 1.018 to 1.421, p=0.030) were associated with higher odds of AEDF. Concerns about physical symptoms and body image at 35–40 weeks were associated with decreased odds of neonatal intensive care unit admission (OR 0.635, 95% CI 0.435 to 0.927, p=0.019). Conclusions: These findings suggest that fetoplacental haemodynamics may be a mechanistic link between maternal prenatal stress and fetal and neonatal well-being, but additional research is required

Probabilistic Phylogenetic Inference with Insertions and Deletions

A fundamental task in sequence analysis is to calculate the probability of a multiple alignment given a phylogenetic tree relating the sequences and an evolutionary model describing how sequences change over time. However, the most widely used phylogenetic models only account for residue substitution events. We describe a probabilistic model of a multiple sequence alignment that accounts for insertion and deletion events in addition to substitutions, given a phylogenetic tree, using a rate matrix augmented by the gap character. Starting from a continuous Markov process, we construct a non-reversible generative (birth–death) evolutionary model for insertions and deletions. The model assumes that insertion and deletion events occur one residue at a time. We apply this model to phylogenetic tree inference by extending the program dnaml in phylip. Using standard benchmarking methods on simulated data and a new “concordance test” benchmark on real ribosomal RNA alignments, we show that the extended program dnamlε improves accuracy relative to the usual approach of ignoring gaps, while retaining the computational efficiency of the Felsenstein peeling algorithm

10 Recommended core outcome domains for tendinopathy derived from a delphi of patients and health care professionals: the groningen ISTS2018 consensus

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Obesity in adults: a 2022 adapted clinical practice guideline for Ireland

This Clinical Practice Guideline (CPG) for the management of obesity in adults in Ireland, adapted from the Canadian CPG, defines obesity as a complex chronic disease characterised by excess or dysfunctional adiposity that impairs health. The guideline reflects substantial advances in the understanding of the determinants, pathophysiology, assessment, and treatment of obesity. It shifts the focus of obesity management toward improving patient-centred health outcomes, functional outcomes, and social and economic participation, rather than weight loss alone. It gives recommendations for care that are underpinned by evidence-based principles of chronic disease management; validate patients' lived experiences; move beyond simplistic approaches of "eat less, move more" and address the root drivers of obesity. People living with obesity face substantial bias and stigma, which contribute to increased morbidity and mortality independent of body weight. Education is needed for all healthcare professionals in Ireland to address the gap in skills, increase knowledge of evidence-based practice, and eliminate bias and stigma in healthcare settings. We call for people living with obesity in Ireland to have access to evidence-informed care, including medical, medical nutrition therapy, physical activity and physical rehabilitation interventions, psychological interventions, pharmacotherapy, and bariatric surgery. This can be best achieved by resourcing and fully implementing the Model of Care for the Management of Adult Overweight and Obesity. To address health inequalities, we also call for the inclusion of obesity in the Structured Chronic Disease Management Programme and for pharmacotherapy reimbursement, to ensure equal access to treatment based on health-need rather than ability to pay

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Commonly used clinical criteria following ACL reconstruction including time from surgery and isokinetic limb symmetry thresholds are not associated with between-limb loading deficits during running

Objectives We included objective measures of gait and functional assessments to examine their associations in athletes who had recently commenced running after ACL reconstruction. Design Cross-sectional. Setting Sports medicine. Participants 65 male athletes with a history of ACL reconstruction. Main outcome measures Time from surgery, isokinetic knee extension/flexion strength (60°/s), and peak vertical ground reaction force (pVGRF) measured during running using an instrumented treadmill. We also investigated if a range of recommended isokinetic thresholds (e.g. > 70% quadriceps limb symmetry index) affected the magnitude of pVGRF asymmetry during running. Results There were significant relationships between quadriceps (r = 0.50) and hamstrings (r = 0.46) peak torque and pVGRF. Quadriceps peak torque explained a quarter of the variance in pVGRF (R2 = 0.24; p < 0.001). There was no association was between running pVGRF and time from surgery. Between-group differences in running pVGRF LSI% were trivial (d < 0.20) for all quadriceps and hamstring peak torque LSI thresholds. Conclusions Current clinical criteria including time from surgery and isokinetic strength limb symmetry thresholds were not associated with lower pVGRF asymmetry measured during running. Quadriceps strength is important, but ‘minimum symmetry thresholds’ should be used with caution