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Mammalian carnivores can be particularly sensitive to human disturbance, even within protected areas (PAs). Our objective was to understand how human disturbance affects carnivore communities in southern Arizona, USA by studying habitat occupancy based on data collected using non-invasive methods in three PAs with different levels of human disturbance. Carnivore occupancy varied based on human disturbance variables (i.e., roads, trails, etc.). Common carnivore species (coyotes, gray foxes, and bobcats) had high occupancy probability in highly disturbed sites, while all other carnivore species had a higher probability of occupancy in low disturbance protected areas. Additionally, overall carnivore diversity was higher in PAs with low human disturbance. Edges of PAs appeared to negatively impact occupancy of nearly all carnivore species. We also found the presence of roads and trails, and not necessarily how much they are used, had a significant negative impact on the occupancy of most carnivore species. Furthermore, the overall level of disturbance within a PA influenced how sensitive carnivores were to human disturbance variables. Carnivores were more sensitive in PAs with higher levels of disturbance and were relatively unaffected by disturbance variables in a PA with low base levels of disturbance. Increased visitation to PAs, expected with the region's high level of population growth, is likely to cause shifts in the carnivore communities favoring species that are less sensitive to disturbance.

There are several known risks relating to poor nutrition during pregnancy, including the development of complications and poor birth outcomes. While food insecurity is associated with poorer nutrition, data on the prevalence and severity of food insecurity in pregnancy in the UK is lacking. This study aims to explore the prevalence, experiences and health impact of food insecurity in pregnancy in England to develop strategic recommendations for intervention strategies. Food, Pregnancy & Me is an observational, multi-method study. Questionnaires exploring diet quality, food security, mental health, and other health behaviours will be distributed to all women and pregnant people in their third trimester in two NHS Trusts in England (North East and West Midlands). Returned questionnaires (n=605) will be linked to routine maternal and birth outcome data and pseudo-anonymised. We will estimate the prevalence of food insecurity in pregnancy in these locations, associations with diet quality, maternal mental health, and pregnancy outcomes (e.g., pre-term birth, pre-eclampsia, gestational diabetes). Qualitative interviews (n=40) with participants identified as having experienced food insecurity will explore their lived experience, support received, and recommendations for additional support needs. Through a series of co-production workshops with local and national system shapers and experts by lived experience, we will use the data gathered to produce strategic recommendations for intervention with pregnant women and people facing food insecurity. We will then explore the potential costs and benefits of implementing the proposed recommendations. Ethical approval was obtained from Newcastle and North Tyneside 1 NHS Research Ethics Committee (24/NE/0027). Findings will be disseminated to key national and local system shapers and policy makers, advocacy groups, and the public through reports, presentations, the media and open access publications. ISRCTN16655955.

Large and effective reductions in emissions of long-lived ozone-depleting substance (ODS) are being achieved through the Montreal Protocol, the effectiveness of which can be seen in the declining atmospheric abundances of many ODSs. An important remaining uncertainty concerns the role of very short-lived substances (VSLSs) which, owing to their relatively short atmospheric lifetimes (less than 6 months), are not regulated under the Montreal Protocol. Recent studies have found an unexplained increase in the global tropospheric abundance of one VSLS, dichloromethane (CH2Cl2), which has increased by around 60% over the past decade. Here we report dramatic enhancements of several chlorine-containing VSLSs (Cl-VSLSs), including CH2Cl2 and CH2ClCH2Cl (1,2-dichloroethane), observed in surface and upper-tropospheric air in East and South East Asia. Surface observations were, on occasion, an order of magnitude higher than previously reported in the marine boundary layer, whilst upper-tropospheric data were up to 3 times higher than expected. In addition, we pro-vide further evidence of an atmospheric transport mechanism whereby substantial amounts of industrial pollution from East Asia, including these chlorinated VSLSs, can rapidly, and regularly, be transported to tropical regions of the western Pacific and subsequently uplifted to the tropical upper troposphere. This latter region is a major provider of air entering the stratosphere, and so this mechanism, in conjunction with increasing emissions of Cl-VSLSs from East Asia, could potentially slow the expected recovery of stratospheric ozone.

Friedreich's ataxia (FA) is a progressive, multisystem, degenerative disorder caused by a reduction in frataxin. Loss of frataxin results in mitochondrial dysfunction and oxidative damage in patients and model systems. Previous studies have indicated that the antioxidant idebenone (5 mg/kg daily) reduces cardiac hypertrophy, but definite improvement in neurological function has not been shown. 48 genetically confirmed FA patients, aged 9–17 years, were enrolled in a 6-month, randomised, double-blind, placebo-controlled study. The patients received placebo or one of three doses of idebenone (∼5 mg/kg, 15 mg/kg, and 45 mg/kg), stratified by body weight. The primary endpoint was change from baseline in urinary 8-hydroxy-2′-deoxyguanosine (8OH2′dG), a marker of oxidative DNA damage. Secondary endpoints included changes in the international cooperative ataxia rating scale (ICARS), the FA rating scale (FARS), and a survey of activities of daily living (ADL). This study is registered with ClinicalTrials.gov, number NCT00229632. Idebenone was generally well tolerated with similar numbers of adverse events in each group. One child receiving high-dose idebenone developed neutropenia after 6 months, which resolved after discontinuation of treatment. 8OH2′dG concentrations were not increased, and did not significantly change with idebenone treatment. Whereas an overall analysis did not show a significant difference in ICARS, FARS, or ADL total scores, there were indications of a dose-dependent response in the ICARS score. A second, pre-specified analysis, excluding patients who required wheelchair assistance, showed a significant improvement in ICARS (Bonferroni p=0·03) and suggested a dose-related response in ICARS, FARS, and ADL scores. Treatment with higher doses of idebenone was generally well tolerated and associated with improvement in neurological function and ADL in patients with FA. The degree of improvement correlated with the dose of idebenone, suggesting that higher doses may be necessary to have a beneficial effect on neurological function.

We compare in situ measurements of ozone (O3) and carbon monoxide (CO) profiles from the CARIBIC program with the results from the regional chemistry transport model (WRF-Chem) to investigate the role of local and regional emissions and long-range transport over southern India during the summer monsoon of 2008. WRF-Chem successfully reproduces the general features of O3 and CO distributions over the South Asian region. However, absolute CO concentrations in the lower troposphere are typically underestimated. Here we investigate the influence of local relative to remote emissions through sensitivity simulations. The influence of 50 % increased CO emissions over South Asia leads to a significant enhancement (upto 20 % in July) in upper tropospheric CO in the northern and central Indian regions. Over Chennai in southern India, this causes a 33 % increase in surface CO during June. However, the influence of enhanced local and regional emissions is found to be smaller (5 %) in the free troposphere over Chennai, except during September. Local to regional emissions are therefore suggested to play a minor role in the underestimation of CO by WRF-Chem during June–August. In the lower troposphere, a high pollution (O3: 146.4 ± 12.8, CO: 136.4 ± 12.2 nmol mol−1) event (15 July 2008), not reproduced by the model, is shown to be due to transport of photochemically processed air masses from the boundary layer in southern India. A sensitivity simulation combined with backward trajectories indicates that long-range transport of CO to southern India is significantly underestimated, particularly in air masses from the west, i.e., from Central Africa. This study highlights the need for more aircraft-based measurements over India and adjacent regions and the improvement of global emission inventories.

Olfactory neuroblastoma (ONB) is a rare cancer of the sinonasal tract with little molecular characterization. We performed whole genome sequencing (WGS) on paired normal and tumor DNA from a patient with metastatic-ONB to identify the somatic alterations that might be drivers of tumorigenesis and/or metastatic progression. Genomic DNA was isolated from fresh frozen tissue from a metastatic lesion and whole blood, followed by WGS at >30X depth, alignment and mapping, and mutation analyses. Sanger sequencing was used to confirm selected mutations. Sixty-two somatic short nucleotide variants (SNVs) and five deletions were identified inside coding regions, each causing a non-synonymous DNA sequence change. We selected seven SNVs and validated them by Sanger sequencing. In the metastatic ONB samples collected several months prior to WGS, all seven mutations were present. However, in the original surgical resection specimen (prior to evidence of metastatic disease), mutations in KDR, MYC, SIN3B, and NLRC4 genes were not present, suggesting that these were acquired with disease progression and/or as a result of post-treatment effects. This work provides insight into the evolution of ONB cancer cells and provides a window into the more complex factors, including tumor clonality and multiple driver mutations.

The chlorine radical is a potent atmospheric oxidant, capable of perturbing tropospheric oxidative cycles normally controlled by the hydroxyl radical. Significantly faster reaction rates allow chlorine radicals to expedite oxidation of hydrocarbons, including methane, and in polluted environments, to enhance ozone production. Here we present evidence, from the CARIBIC airborne dataset, for extensive chlorine radical chemistry associated with Asian pollution outflow, from airborne observations made over the Malaysian Peninsula in winter. This region is known for persistent convection that regularly delivers surface air to higher altitudes and serves as a major transport pathway into the stratosphere. Oxidant ratios inferred from hydrocarbon relationships show that chlorine radicals were regionally more important than hydroxyl radicals for alkane oxidation and were also important for methane and alkene oxidation (>10%). Our observations reveal pollution-related chlorine chemistry that is both widespread and recurrent, and has implications for tropospheric oxidizing capacity, stratospheric composition and ozone chemistry.

Large-scale multiplexed identification of somatic alterations in cancer has become feasible with next generation sequencing (NGS). However, calibration of NGS somatic analysis tools has been hampered by a lack of tumor/normal reference standards. We thus performed paired PCR-free whole genome sequencing of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. We generated mean mapped coverages of 99X for COLO829 and 103X for the paired normal across three institutions. Results were combined with previously generated data allowing for comparison to a fourth lineage on earlier NGS technology. Aggregate variant detection led to the identification of consensus variants, including key events that represent hallmark mutation types including amplified BRAF V600E, a CDK2NA small deletion, a 12 kb PTEN deletion, and a dinucleotide TERT promoter substitution. Overall, common events include >35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected by copy number changes. We present this reference to the community as an initial standard for enabling quantitative evaluation of somatic mutation pipelines across institutions.

IntroductionThe Australian population presenting with surgical pathology is becoming older, frailer and more comorbid. Shared decision-making is rapidly becoming the gold standard of care for patients considering high-risk surgery to ensure that appropriate, value-based healthcare decisions are made. Positive benefits around patient perception of decision-making in the immediacy of the decision are described in the literature. However, short-term and long-term holistic patient-centred outcomes and cost implications for the health service require further examination to better understand the full impact of shared decision-making in this population.MethodsWe propose a novel multidisciplinary shared decision-making model of care in the perioperative period for patients considering high-risk surgery in the fields of general, vascular and head and neck surgery. We assess it in a two arm prospective randomised controlled trial. Patients are randomised to either ‘standard’ perioperative care, or to a multidisciplinary (surgeon, anaesthetist and end-of-life care nurse practitioner or social worker) shared decision-making consultation. The primary outcome is decisional conflict prior to any surgical procedure occurring. Secondary outcomes include the patient’s treatment choice, how decisional conflict changes longitudinally over the subsequent year, patient-centred outcomes including life impact and quality of life metrics, as well as morbidity and mortality. Additionally, we will report on healthcare resource use including subsequent admissions or representations to a healthcare facility up to 1 year.Ethics and disseminationThis study has been approved by the Hunter New England Human Research Ethics Committee (2019/ETH13349). Study findings will be presented at local and national conferences and within scientific research journals.Trial registration numberACTRN12619001543178.

During the summer monsoon the upper troposphere over South Asia is characterized by the monsoon anticyclone centered above the Tibetan Plateau. Surface air that has been rapidly transported upwards through deep convection becomes trapped within the strong anticyclonic circulation. Observations of trace gases within this anticyclone by the CARIBIC flying observatory revealed large enhancements in the greenhouse gas methane (CH4), which increased over the course of the monsoon. Meteorological analysis indicated that these air masses originated primarily in India, for which relatively little is known about CH4 emissions. Using correlations between concentrations of CH4 and carbon monoxide (CO) we estimated total emissions of 30.8 Tg CH4during the 2008 monsoon season (June–September), 19.7 Tg of which were identified as additional, monsoon‐related biogenic methane using the relationship of CH4 to ethane (C2H6). After accounting for the ∼3.9 Tg attributed to rice agriculture in the current inventories, ∼15.8 Tg of additional CH4 remain. Underestimated rice emissions provide a partial explanation, with the remainder most likely attributable to microbial production in waterlogged areas such as landfills, polluted waterways and wetlands. Key Points Observed large increase in S. Asian methane emissions during the summer monsoon Sources identified as biogenic, releasing ~15.8 Tg of additional methane Accounts for ~50% of total June–Sept methane emissions