Soil carbon sequestration in rangelands: a critical review of the impacts of major management strategies

The agronomic benefits of soil organic matter have been studied for centuries, but contemporary focus has expanded to ask how increasing long-term storage of soil organic carbon (SOC) can contribute to mitigation of climate change. Understanding the potential for SOC sequestration in the vast rangelands is crucial for climate change policy, agricultural land management and carbon market opportunities. In this review, we evaluate the evidence from published field trials and modelling studies for sequestration in Australian rangeland soils managed for livestock grazing. We found few long-term studies with high quality SOC stock change data linked to new management, and our analysis was constrained by data limitations, conflicting results between studies, and highly variable climate, soil and landscape conditions across production systems. Rainfall and soil properties are dominant determinants of variation in SOC stocks in rangelands, and it was difficult to detect management impacts in these environments. However, there was consistent evidence that: (1) Sowing more productive grasses or legumes in existing grass pastures generally increases SOC stocks; (2) Prolonged high stocking is associated with net SOC loss; (3) Destocking or exclusion of grazing results in small SOC increases, especially in degraded soils; (4) Conversion from cropping to permanent pasture results in sequestration, influenced by management history; (5) Rotational grazing strategies show negligible impact on SOC stocks relative to continuous grazing; and (6) Waterponding increased SOC stocks initially but persistence has not been demonstrated. We discuss possible opportunities for SOC sequestration in rangelands in the context of uncertainties and associated benefits and trade-offs for livestock production, and make recommendations to improve the evidence-base for major management strategies

Dietary therapy to improve nutrition and gut health in paediatric Crohn’s disease; a feasibility study

Bovine colostrum (BC) has anti-inflammatory, anti-infective, growth and intestinal repair factors that may be beneficial in Crohn’s disease (CD). We assessed whether daily BC for up to 3 months was acceptable to children and young people (CYP) with CD in remission or of mild/moderate severity. CYP were randomised to receive either BC or matching placebo milk daily for 6 weeks (blinded phase); all received BC for the following 6 weeks (open phase). In 23 CYP, median (inter-quartile range) age was 15.2 (13.9–16.1) years and 9 (39.1%) were girls. A similar proportion of CYP in the BC and placebo arms completed the blinded phase (8/12, 75.0% and 9/11, 81.8% respectively). Twelve (70.6%) CYP completed the open phase with 7 (58.3%) tolerating BC for 3 months. Diaries in weeks 2, 6 and 12 revealed that most CYP took BC every day (5/7, 71.4%; 5/8, 62,5% and 6/11, 54.5% respectively). In interviews, opinions were divided as to preference of BC over the placebo milk and some preferred BC over other nutritional supplements. Symptoms, clinical and laboratory variables and quality of life were similar in the two arms. BC may be an acceptable nutritional supplement for daily, longer-term use in CYP with CD

Protocol for PRImary care Management of lower Urinary tract Symptoms in men:Protocol for development and validation of a diagnostic and clinical decision support tool (The PriMUS Study)

Introduction Lower urinary tract symptoms (LUTS) is a bothersome condition affecting older men which can lead to poor quality of life. General practitioners (GPs) currently have no easily available assessment tools to help effectively diagnose causes of LUTS and aid discussion of treatment with patients. Men are frequently referred to urology specialists who often recommend treatments that could have been initiated in primary care. GP access to simple, accurate tests and clinician decision tools are needed to facilitate accurate and effective patient management of LUTS in primary care. Methods and analysis PRImary care Management of lower Urinary tract Symptoms (PriMUS) is a prospective diagnostic accuracy study based in primary care. The study will determine which of a number of index tests used in combination best predict three urodynamic observations in men who present to their GP with LUTS. These are detrusor overactivity, bladder outlet obstruction and/or detrusor underactivity. Two cohorts of participants, one for development of the prototype diagnostic tool and other for validation, will undergo a series of simple index tests and the invasive reference standard (invasive urodynamics). We will develop and validate three diagnostic prediction models based on each condition and then combine them with management recommendations to form a clinical decision support tool. Ethics and dissemination Ethics approval is from the Wales Research Ethics Committee 6. Findings will be disseminated through peer-reviewed journals and conferences, and results will be of interest to professional and patient stakeholders

Managing LUTS in primary care: qualitative study of GPs’ and patients’ experiences

Background: Lower urinary tract symptoms (LUTS) are common in older men and impact considerably on their quality of life. Management can be complex, and although most LUTS could be treated effectively in primary care, referrals to urology outpatients are increasing. The experiences of General Practitioners (GPs) and patients relating to the management of LUTS have not yet been fully explored. Aim: To explore GPs’ experiences of managing LUTS, together with patients’ experiences of and preferences for treatment in primary care. Design and setting: Qualitative telephone interviews with GPs and male patients presenting to primary care with bothersome LUTS. Method: Eleven GPs and 25 male patients were purposively sampled from 20 GP practices in 3 UK regions. Interviews were conducted between May 2018 and January 2019 and analysed using a framework approach. Results: Difficulty establishing causes and differentiating between prostate and bladder symptoms were key challenges to the diagnosis of LUTS in primary care, making treatment often a process of trial and error. Pharmacological treatments were commonly ineffective and often caused side-effects. Despite this, patients were generally satisfied with GP consultations and expressed a preference for treatment in primary care. Conclusion: Managing LUTS in primary care is a more accessible option for patients. Given the challenges of LUTS diagnosis, an effective diagnostic tool for use by GPs would be beneficial. Ensuring bothersome LUTS are not dismissed as a normal part of ageing is essential in improving patients’ quality of life. Greater exploration of the role of non-pharmacological treatments is needed

Conducting invasive urodynamics in primary care: Qualitative interview study examining experiences of patients and healthcare professionals

Background Invasive urodynamics is used to investigate the causes of lower urinary tract symptoms; a procedure usually conducted in secondary care by specialist practitioners. No study has yet investigated the feasibility of carrying out this procedure in a non-specialist setting. Therefore, the aim of this study was to explore, using qualitative methodology, the feasibility and acceptability of conducting invasive urodynamic testing in primary care. Methods Semi-structured interviews were conducted during the pilot phase of the PriMUS study, in which men experiencing bothersome lower urinary tract symptoms underwent invasive urodynamic testing along with a series of simple index tests in a primary care setting. Interviewees were 25 patients invited to take part in the PriMUS study and 18 healthcare professionals involved in study delivery. Interviews were audio-recorded, transcribed verbatim and analysed using a framework approach. Results Patients generally found the urodynamic procedure acceptable and valued the primary care setting due to its increased accessibility and familiarity. Despite some logistical issues, facilitating invasive urodynamic testing in primary care was also a positive experience for urodynamic nurses. Initial issues with general practitioners receiving and utilising the results of urodynamic testing may have limited the potential benefit to some patients. Effective approaches to study recruitment included emphasising the benefits of the urodynamic test and maintaining contact with potential participants by telephone. Patients’ relationship with their general practitioner was an important influence on study participation. Conclusions Conducting invasive urodynamics in primary care is feasible and acceptable and has the potential to benefit patients. Facilitating study procedures in a familiar primary care setting can impact positively on research recruitment. However, it is vital that there is a support network for urodynamic nurses and expertise available to help interpret urodynamic results

1H-NMR metabolite profiles of different strains of Plasmodium falciparum

Although efforts to understand the basis for inter-strain phenotypic variation in the most virulent malaria species, Plasmodium falciparum, have benefited from advances in genomic technologies, there have to date been few metabolomic studies of this parasite. Using 1H-NMR spectroscopy, we have compared the metabolite profiles of red blood cells infected with different P. falciparum strains. These included both chloroquine-sensitive and chloroquine-resistant strains, as well as transfectant lines engineered to express different isoforms of the chloroquine-resistance-conferring pfcrt (P. falciparum chloroquine resistance transporter). Our analyses revealed strain-specific differences in a range of metabolites. There was marked variation in the levels of the membrane precursors choline and phosphocholine, with some strains having >30-fold higher choline levels and >5-fold higher phosphocholine levels than others. Chloroquineresistant strains showed elevated levels of a number of amino acids relative to chloroquine-sensitive strains, including an approximately 2-fold increase in aspartate levels. The elevation in amino acid levels was attributable to mutations in pfcrt. Pfcrt-linked differences in amino acid abundance were confirmed using alternate extraction and detection (HPLC) methods. Mutations acquired to withstand chloroquine exposure therefore give rise to significant biochemical alterations in the parasite

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Mapping genomic loci implicates genes and synaptic biology in schizophrenia

Schizophrenia has a heritability of 60-80%1, much of which is attributable to common risk alleles. Here, in a two-stage genome-wide association study of up to 76,755 individuals with schizophrenia and 243,649 control individuals, we report common variant associations at 287 distinct genomic loci. Associations were concentrated in genes that are expressed in excitatory and inhibitory neurons of the central nervous system, but not in other tissues or cell types. Using fine-mapping and functional genomic data, we identify 120 genes (106 protein-coding) that are likely to underpin associations at some of these loci, including 16 genes with credible causal non-synonymous or untranslated region variation. We also implicate fundamental processes related to neuronal function, including synaptic organization, differentiation and transmission. Fine-mapped candidates were enriched for genes associated with rare disruptive coding variants in people with schizophrenia, including the glutamate receptor subunit GRIN2A and transcription factor SP4, and were also enriched for genes implicated by such variants in neurodevelopmental disorders. We identify biological processes relevant to schizophrenia pathophysiology; show convergence of common and rare variant associations in schizophrenia and neurodevelopmental disorders; and provide a resource of prioritized genes and variants to advance mechanistic studies

Convalescent plasma in patients admitted to hospital with COVID-19 (RECOVERY): a randomised controlled, open-label, platform trial

SummaryBackground Azithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatoryactions. We aimed to evaluate the safety and efficacy of azithromycin in patients admitted to hospital with COVID-19.Methods In this randomised, controlled, open-label, adaptive platform trial (Randomised Evaluation of COVID-19Therapy [RECOVERY]), several possible treatments were compared with usual care in patients admitted to hospitalwith COVID-19 in the UK. The trial is underway at 176 hospitals in the UK. Eligible and consenting patients wererandomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once perday by mouth or intravenously for 10 days or until discharge (or allocation to one of the other RECOVERY treatmentgroups). Patients were assigned via web-based simple (unstratified) randomisation with allocation concealment andwere twice as likely to be randomly assigned to usual care than to any of the active treatment groups. Participants andlocal study staff were not masked to the allocated treatment, but all others involved in the trial were masked to theoutcome data during the trial. The primary outcome was 28-day all-cause mortality, assessed in the intention-to-treatpopulation. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.Findings Between April 7 and Nov 27, 2020, of 16 442 patients enrolled in the RECOVERY trial, 9433 (57%) wereeligible and 7763 were included in the assessment of azithromycin. The mean age of these study participants was65·3 years (SD 15·7) and approximately a third were women (2944 [38%] of 7763). 2582 patients were randomlyallocated to receive azithromycin and 5181 patients were randomly allocated to usual care alone. Overall,561 (22%) patients allocated to azithromycin and 1162 (22%) patients allocated to usual care died within 28 days(rate ratio 0·97, 95% CI 0·87–1·07; p=0·50). No significant difference was seen in duration of hospital stay (median10 days [IQR 5 to >28] vs 11 days [5 to >28]) or the proportion of patients discharged from hospital alive within 28 days(rate ratio 1·04, 95% CI 0·98–1·10; p=0·19). Among those not on invasive mechanical ventilation at baseline, nosignificant difference was seen in the proportion meeting the composite endpoint of invasive mechanical ventilationor death (risk ratio 0·95, 95% CI 0·87–1·03; p=0·24).Interpretation In patients admitted to hospital with COVID-19, azithromycin did not improve survival or otherprespecified clinical outcomes. Azithromycin use in patients admitted to hospital with COVID-19 should be restrictedto patients in whom there is a clear antimicrobial indication

Fast and robust association tests for untyped SNPs in case-control studies.

Genome-wide association studies (GWASs) aim to genotype enough single nucleotide polymorphisms (SNPs) to effectively capture common genetic variants across the genome. Even though the number of SNPs genotyped in such studies can exceed a million, there is still interest in testing association with SNPs that were not genotyped in the study sample. Analyses of such untyped SNPs can assist in signal localization, permit cross-platform integration of samples from separate studies, and can improve power - especially for rarer SNPs. External information on a larger collection of SNPs from an appropriate reference panel, comprising both SNPs typed in the sample and the untyped SNPs we wish to test for association, is necessary for an untyped variant analysis to proceed. Linkage disequilibrium patterns observed in the reference panel are then used to infer the likely genotype at the untyped SNPs in the study sample. We propose here a novel statistical approach for testing untyped SNPs in case-control GWAS, based on an efficient score function derived from a prospective likelihood, that automatically accounts for the variability in the process of estimating the untyped variant. Computationally efficient methods of phasing can be used without affecting the validity of the test, and simple measures of haplotype sharing can be used to infer genotypes at the untyped SNPs, making our approach computationally much faster than existing approaches for untyped analysis. At the same time, we show, using simulated data, that our approach often has performance nearly equivalent to hidden Markov methods of untyped analysis. The software package 'untyped' is available to implement our approach