Nitrogen management is essential to prevent tropical oil palm plantations from causing ground-level ozone pollution.

More than half the world's rainforest has been lost to agriculture since the Industrial Revolution. Among the most widespread tropical crops is oil palm (Elaeis guineensis): global production now exceeds 35 million tonnes per year. In Malaysia, for example, 13% of land area is now oil palm plantation, compared with 1% in 1974. There are enormous pressures to increase palm oil production for food, domestic products, and, especially, biofuels. Greater use of palm oil for biofuel production is predicated on the assumption that palm oil is an "environmentally friendly" fuel feedstock. Here we show, using measurements and models, that oil palm plantations in Malaysia directly emit more oxides of nitrogen and volatile organic compounds than rainforest. These compounds lead to the production of ground-level ozone (O(3)), an air pollutant that damages human health, plants, and materials, reduces crop productivity, and has effects on the Earth's climate. Our measurements show that, at present, O(3) concentrations do not differ significantly over rainforest and adjacent oil palm plantation landscapes. However, our model calculations predict that if concentrations of oxides of nitrogen in Borneo are allowed to reach those currently seen over rural North America and Europe, ground-level O(3) concentrations will reach 100 parts per billion (10(9)) volume (ppbv) and exceed levels known to be harmful to human health. Our study provides an early warning of the urgent need to develop policies that manage nitrogen emissions if the detrimental effects of palm oil production on air quality and climate are to be avoided.

Methylation profiling of rectal cancer identifies novel markers of early-stage disease.

BACKGROUND: Radical surgery is the de facto treatment for early rectal cancer. Conservative surgery with transanal endoscopic microsurgery can achieve high rates of cure but the histopathological measures of outcome used to select local treatment lack precision. Biomarkers associated with disease progression, particularly mesorectal nodal metastasis, are urgently required. The aim was to compare patterns of gene-specific hypermethylation in radically excised rectal cancers with histopathological stage. METHODS: Locus-specific hypermethylation of 24 tumour suppressor genes was measured in 105 rectal specimens (51 radically excised adenocarcinomas, 35 tissues adjacent to tumour and 19 normal controls) using the methylation-specific multiplex ligation-dependent probe assay (MS-MLPA). Methylation values were correlated with histopathological indices of disease progression and validated using bisulphite pyrosequencing. RESULTS: Five sites (ESR1, CDH13, CHFR, APC and RARB) were significantly hypermethylated in cancer compared with adjacent tissue and normal controls (P < 0·050). Methylation at these sites was higher in Dukes' A than Dukes' 'D' cancers (P = 0·013). Methylation at two sites (GSTP1 and RARB) was individually associated with localized disease (N0 and M0 respectively; P = 0·006 and P = 0·008). Hypermethylation of at least two of APC, RARB, TIMP3, CASP8 and GSTP1 was associated with early (N0 M0) disease (N0, P = 0·002; M0, P = 0·044). Methylation levels detected by MS-MLPA and pyrosequencing were concordant. CONCLUSION: Locus-specific hypermethylation was more prevalent in early- than late-stage disease. Hypermethylation of two or more of a panel of five tumour suppressor genes was associated with localized disease.

Survey of fungi and yeast in polymicrobial infections in chronic wounds.

OBJECTIVE: To assess the incidence, abundance and species diversity of fungi in chronic wounds, as well as to describe the associations of major fungi populations. METHOD: Comprehensive molecular diagnostic reports were evaluated from a total of 915 chronic wounds in a retrospective study. RESULTS: Of the 915 clinical specimens, 208 (23%) were positive for fungal species. These samples were further compared in a compiled dataset, and sub-classified among the four major chronic wound types (decubitus ulcer, diabetic foot ulcer, non-healing surgical wound, and venous leg ulcer). The most abundant fungi were yeasts in the genus Candida; however, Curvularia, Malessezia, Aureobasidium, Cladosporium, Ulocladium, Engodontium and Trichtophyton were also found to be prevalent components of these polymicrobial infections. A notable bacterial/fungal negative correlation was found to be apparent between Staphylococcus and Candida. There were also significant relationships between both bacterial and fungal genera and patient metadata including gender, diabetes status and cardiovascular comorbidities. CONCLUSION: This microbial survey shows that fungi are more important wound pathogens and opportunistic pathogens than previously reported, exemplifying the impact of these under-reported pathogens. With the application of modern cost-effective and comprehensive molecular diagnostics, clinicians can now identify and address this significant component of chronic wound bioburden with targeted therapies, thereby improving healing trajectories.

Wnt signalling in adenomas of familial adenomatous polyposis patients.

BACKGROUND: Epigenetic silencing of Wnt antagonists and expression changes in genes associated with Wnt response pathways occur in early sporadic colorectal tumourigenesis, indicating that tumour cells are more sensitive to Wnt growth factors and respond differently. In this study, we have investigated whether similar changes occur in key markers of the Wnt response pathways in the genetic form of the disease, familial adenomatous polyposis (FAP). METHODS: We investigated epigenetic and expression changes using pyrosequencing and real-time RT-PCR in samples from seven patients without neoplasia, and matched normal and tumour tissues from 22 sporadic adenoma and 14 FAP patients. RESULTS: We found that 17 out of 24 (71%) FAP adenomas were hypermethylated at sFRP1, compared with 20 out of 22 (91%) of sporadic cases. This was reflected at the level of sFRP1 transcription, where 73% of FAP and 100% of sporadic cases were down-regulated. Increased expression levels of c-myc and FZD3 were less common in FAP (35 and 46% respectively) than sporadic tumours (78 and 67% respectively). CONCLUSION: Overall, the changes in expression and methylation were comparable, although the degree of change was generally lower in the FAP adenomas. Molecular heterogeneity between multiple adenomas from individual FAP patients may reflect different developmental fates for these premalignant tumours.

Repair of oesophageal atresia by consultants and supervised trainees results in similar outcomes.

INTRODUCTION: Consultants and trainees require exposure to complex cases for maintaining and gaining operative experience. Oesophageal atresia (OA) repair is a neonatal surgical procedure with indicative numbers for completion of training. A conflict of interest may exist between adequate training, maintaining consultant experience and achieving good outcomes. We aimed to review outcomes of procedures performed primarily by trainees and those performed by consultants. METHODS: We carried out a retrospective case note review of all consecutive infants who underwent surgical repair of OA with distal tracheooesophageal fistula (TOF) between January 1994 and December 2014 at our institution. Only cases that underwent primary oesophageal anastomosis were included. Surgical outcomes were compared between cases that had a trainee and those that had a consultant listed as the primary operator. RESULTS: One hundred and twenty-two cases were included. A total of 52 procedures were performed by trainees, and 68 by consultants. Two cases were undeterminable and excluded. Infant demographics, clinical characteristics and duration of follow-up were similar between groups. All infants survived to discharge. Procedures performed by trainees and those performed by consultants as primary operators had a similar incidence of postoperative pneumothorax (trainees 4, consultants 3; p=0.46), anastomotic leak (trainees 5, consultants 3; p=0.29) and recurrent TOF (trainees 0, consultants 2; p=0.5). Overall 52% of cases had an anastomotic dilatation during follow-up, with no difference between the trainee and consultant groups (50% vs 53%; p=0.85). CONCLUSIONS: Surgical outcomes for repair of OA/TOF are not adversely affected by trainee operating. Trainees with appropriate skills should perform supervised OA/TOF repair. These data are important for understanding the interrelationship between provision of training and surgical outcomes.

The effectiveness of influenza vaccination in pregnancy in relation to child health outcomes: Systematic review and meta-analysis.

OBJECTIVES: To determine the effectiveness of influenza vaccination during pregnancy on child health outcomes. DESIGN: Systematic review/meta-analysis. DATA SOURCES: Clinical Trials.gov, Cochrane Library, EMBASE, Medline, Medline in process, PubMed and Web of Science, from 1st January 1996 to 29th June 2018. An updated Medline search was performed 30th June 2018 to 31st October 2019. METHODS: Randomised controlled trials (RCTs) and observational studies reporting health outcomes of infants and children born to women who received inactivated influenza vaccine during pregnancy. The primary outcome was infant laboratory confirmed influenza (LCI). Secondary outcomes included influenza-like illness (ILI), other respiratory illnesses, primary care, clinic visit or hospitalisations due to influenza illness and long-term respiratory childhood outcomes. RESULTS: 19 studies were included; 15 observational studies and 4 primary RCTs with an additional 3 papers reporting secondary outcomes of these RCTs. In a random effects meta-analysis of 2 RCTs including 5742 participants, maternal influenza vaccination was associated with an overall reduction of LCI in infants of 34% (95% confidence interval 15-50%). However, there was no effect of maternal influenza vaccination on ILI in infants ≤6 months old. Two RCTs were excluded from the meta-analysis for the outcome of LCI in infants (different controls used). Both of these studies showed a protective effect for infants from LCI, with a vaccine efficacy of up to 70%. Overall observational studies showed an inverse (protective) association between maternal influenza vaccination and infant LCI, hospitalisation and clinic visits due to LCI or ILI in infants and other respiratory illness in infants ≤6 months old. CONCLUSIONS: This systematic review supports maternal influenza vaccination as a strategy to reduce LCI and influenza-related hospitalisations in young infants. Communicating these benefits to pregnant women may support their decision to accept influenza vaccination in pregnancy and increase vaccine coverage in pregnant women. REGISTRATION: PROSPERO CRD42018102776.

Improving paediatric antimicrobial stewardship in hospital-based settings: why, where and how?

BACKGROUND: Antimicrobial resistance (AMR) is being recognized as a priority by healthcare organizations across the world. However, many children are managed on IV antimicrobials in hospital with very little consideration of antimicrobial stewardship issues. OBJECTIVES: A nurse-led paediatric ambulatory outpatient parenteral antimicrobial therapy (OPAT) service, managing children with common infections being ambulated on short courses of IV antimicrobials, was introduced within Southampton Children's Hospital in January 2018. We evaluated the impact of this service in terms of the quality of antimicrobial prescribing and timing of ambulation in children presenting with common infections. METHODS: All cases managed within the service were reviewed in two separate 2 month time periods: prior to introduction of the service (September-October 2016) and then prospectively after its introduction (September-October 2018). RESULTS: A total of 96% of IV antibiotic management decisions at 48 h were deemed appropriate in 2018, compared with 75% in 2016. A total of 64% of patients were ambulated on IV antibiotics at some point during their treatment course in 2018, compared with 19% in 2016. However, a significant proportion of antimicrobial decisions made at the point of presentation to hospital remained suboptimal in 2018. CONCLUSIONS: Children are commonly managed with IV antibiotics in hospital. We demonstrate marked improvements in appropriate antimicrobial use through the introduction of a nurse-led ambulatory OPAT service. In addition, such a service can promote a greater proportion of children being ambulated from hospital, freeing up valuable inpatient beds and potentially delivering cost savings that can be used to fund such services.

Strange magnetism and the anapole structure of the proton.

The violation of mirror symmetry in the weak force provides a powerful tool to study the internal structure of the proton. Experimental results have been obtained that address the role of strange quarks in generating nuclear magnetism. The measurement reported here provides an unambiguous constraint on strange quark contributions to the proton's magnetic moment through the electron-proton weak interaction. We also report evidence for the existence of a parity-violating electromagnetic effect known as the anapole moment of the proton. The proton's anapole moment is not yet well understood theoretically, but it could have important implications for precision weak interaction studies in atomic systems such as cesium.

Effects of biofilm treatments on the multi-species Lubbock chronic wound biofilm model.

OBJECTIVE: To evaluate the efficacy of several biofilm effectors in inhibiting biofilm formation in an in vitro multi-species chronic wound biofilm model. METHOD: The Lubbock Chronic Wound Biofilm (LCWB) model has been described in detail elsewhere. Pathogens used in the model are Pseudomonas aeruginosa, Enterococcus faecalis and Staphylococcus aureus. These are three of the most important species associated with biofilms. Here, the model was exposed to the following biofilm effectors: xylitol, salicylic acid, farnesol, erythritol and two proprietary, semi-solid, wound-dressing formulations currently under development (Sanguitec gels). RESULTS: Biofilm formation was completely inhibited in the LCWB model following treatment with 20% xylitol, 10% erythritol, 1,000 microg/ml farnesol, 20mM salicylic acid or 0.1% of either of the two Sanguitec gel formulations. Salicylic acid specifically inhibited S. aureus (p<0.01) at 10mM and 20mM, consequently increasing the ratios of P. aeruginosa and E. faecalis within the biofilm. Xylitol had an increasing inhibitory effect on P. aeruginosa (p<0.01) at all concentrations evaluated. Erythritol had an inhibitory effect on P. aeruginosa and S. aureus growth (p<0.01) at over 5% concentrations. The inhibitory effect of both Sanguitec gel formulations was more broadly effective, with an increasingly inhibitory effect on all LCWB species (p<0.01). CONCLUSION: The LCWB model provides a multi-species format with which to evaluate the effect of biofilm effectors on wound flora in a biofilm phenotype. These results suggest that different treatments can target specific populations within a biofilm. Salicylic acid preferentially targeted S. aureus, xylitol preferentially targeted P. aeruginosa, while erythritol preferentially targeted both P. aeruginosa and S. aureus. In contrast, the two Sanguitec gel formulations provided a broad, less preferential, inhibition of biofilm development. DECLARATION OF INTEREST: Research and Testing Laboratory is a for-profit enterprise that develops molecular methods and performs service research work on biofilms. Sanguitec gel was developed by JPK and CEJ.

Intracellular copper routing: the role of copper chaperones.

Copper is required by all living systems. Cells have a variety of mechanisms to deal with this essential, yet toxic trace element. A recently discovered facet of homeostatic mechanisms is the protein-mediated, intracellular delivery of copper to target proteins. This routing is accomplished by a novel class of proteins, the 'copper chaperones'. They are a family of conserved proteins present in prokaryotes and eukaryotes, which suggests that copper chaperones are used throughout nature for intracellular copper routing.

Integral small field output factor measurements using a transmission ionisation chamber.

Previous studies describe the use of a large area parallel-plate chamber, the PTW Bragg Peak chamber, for measuring dose-area product (DAP) and output factors in small megavoltage photon fields. However, in radiotherapy departments without protons, this detector would have to be purchased separately for this purpose. This work investigated the feasibility of alternatively using a large transmission ionisation chamber, the IBA round Stealth chamber (SC), for output factor measurements of stereotactic fields. This type of detector is more commonly found in radiotherapy departments as a reference chamber for water tank scanning of small fields, and hence DAP could be performed without an additional purchase. The SC's large sensitive area (diameter of 94 mm) measures the integral dose, also known as DAP, over the whole two-dimensional (2D) dose distribution of the small field. The measurements were performed using a 6 MV beam from an Elekta Infinity linear accelerator. Conversion of DAP to central axis point dose was performed using 2D dose maps from Gafchromic EBT3 films. The field sizes measured ranged from side length of 5 mm to 50 mm (all square). The resultant output factors were compared against measurements with a stereotactic diode. The small field output factors measured using SC + film were in good agreement with the stereotactic diode (within 2% for field sizes as small as 6 mm; 3% difference at 5 mm). The new proposed method showed that a transmission chamber like SC is a good alternative large-area parallel plate chamber to measure DAP and derive small field OFs. Furthermore, the feasibility of using 2D reconstructed dose maps from water tank profiles and hence filmless approach was investigated. Results showed that filmless conversion of DAP to central axis point dose is feasible using profiles. However, a large number of profiles are required (i.e. 15° increments (star pattern) are required for accurate 2D dose reconstruction), and hence the water tank scanning for this approach may be prohibitively time-consuming.

Reorganisation of Wnt-response pathways in colorectal tumorigenesis.

In most colorectal tumours, APC mutation stabilises beta-catenin and mimics elements of Wnt growth factor signalling, but the high frequency of epigenetic loss of Wnt antagonists indicates an additional role for ligand-mediated Wnt signalling. Here, we have investigated the expression of key components of beta-catenin-independent Wnt response pathways to determine whether their profiles change during the transition from normal mucosa to colorectal adenomas. Transcription of the Wnt/planar cell polarity pathway determinant NKD1 (naked cuticle homologue 1) was induced in adenomas by a median 135-fold and in cancers by 7.4-fold. While some Frizzleds (FZDs) were downregulated in adenomas, the Wnt/Ca(2+) receptors FZD3 and FZD6 were induced by a median factor of 6.5 and 4.6, respectively. Naked cuticle homologue 1, FZD3 and FZD6 expression were coordinated in pre-malignant disease, but this relationship was lost in invasive cancers, where FZD induction was seen less frequently. Naked cuticle homologue 1 expression was associated with nuclear localisation of phospho-c-Jun in adenomas. In cultured cells, NKD1 transcription was induced by lithium chloride but FZD3 expression required Wnt growth factor treatment. These data show that Wnt responses are consistently directed towards both beta-catenin-independent routes in early colorectal tumorigenesis and elements of this are retained in more advanced cancers. These beta-catenin-independent Wnt signalling pathways may provide novel targets for chemoprevention of early colorectal tumours.

Binding of quinine- and quinidine-dependent drug antibodies to platelets is mediated by the Fab domain of the immunoglobulin G and is not Fc dependent.

The antibody domain controlling reactions between platelet membranes and drug-dependent (dd) antibodies from patients with thrombocytopenia induced by cinchona alkaloids was studied using F(ab')2, Fab, and Fc fragments made from purified dd-IgG. By direct binding radioimmunoassay (RIA) measurements, 20,000 to 50,000 antibody molecules bound per platelet equivalent of purified platelet membranes at apparent saturation with three different antibodies. F(ab')2 and Fab fragments bound to platelet membranes drug dependently but Fc fragments did not. The ability of dd-IgG fragments to compete with intact IgG was quantitatively measured by RIA and by complement fixation. F(ab')2 and Fab competed with intact IgG at an 8:1 and greater than 50:1 molar ratio, respectively, in RIA, and at a 1.6-3:1 and 44-75:1 ratio, respectively, by complement fixation assays. Fc did not compete with IgG in either assay. We conclude that the Fab domain supports attachment of dd antibody to the platelet surface.

Conversion of vitamin B 6 compounds to active forms in the red blood cell.

In studies with pyridoxine and other B(6) compounds in blood, the active forms pyridoxal and pyridoxal phosphate were measured by differential assays using Lactobacillus casei. Red cell uptake of tritiated pyridoxine was also measured. A new metabolic pathway for conversion of pyridoxine to active forms was demonstrated in red cells. In vivo studies in normal subjects suggested that pyridoxine was taken up by red cells where it was converted to pyridoxal phosphate and then pyridoxal, followed by gradual release of a proportion of pyridoxal into plasma. In vitro incubation of pyridoxine with blood confirmed this observation. Increasing amounts of pyridoxine were taken up and converted as the amount added to blood was increased, and only very small numbers of red cells were needed to convert appreciable amounts. Conversion was markedly inhibited at temperatures lower than 37 degrees C, and stopped altogether at - 20 degrees C.Release of pyridoxal into plasma was always directly proportional to the amount of pyridoxal formed and to the volume of plasma present. That pyridoxal phosphate was not released into plasma was demonstrated in stored blood, for pyridoxine was converted mainly only as far as pyridoxal phosphate, probably due to inactivation of the phosphatase. Pyridoxal phosphate remained in the red cells. Pyridoxine was converted when incubated with washed red cells in saline or phosphate buffer suspension (0.08 M). In saline suspension, pyridoxal formed but was not released in the absence of plasma. In phosphate buffer suspension, pyridoxal phosphate was formed but was not changed to pyridoxal, probably due to inactivation of phosphatase by excess phosphate. Pyridoxamine was converted to active forms in red cells less efficiently. Pyridoxal entered red cells rapidly, equilibrating between plasma and cells within 1 min in the same ratio as pyridoxal formed inside red cells. Pyridoxal phosphate did not enter red cells in whole blood but did so readily in washed cells in saline.

Spaceborne Synthetic Aperture Radar Survey of Subsidence in Hampton Roads, Virginia (USA).

Over the past century, the Hampton Roads area of the Chesapeake Bay region has experienced one of the highest rates of relative sea level rise on the Atlantic coast of the United States. This rate of relative sea level rise results from a combination of land subsidence, which has long been known to be present in the region, and rising seas associated with global warming on long timescales and exacerbated by shifts in ocean dynamics on shorter timescales. An understanding of the current-day magnitude of each component is needed to create accurate projections of future relative sea level rise upon which to base planning efforts. The objective of this study is to estimate the land component of relative sea level rise using interferometric synthetic aperture radar (InSAR) analysis applied to ALOS-1 synthetic aperture radar data acquired during 2007-2011 to generate high-spatial resolution (20-30 m) estimates of vertical land motion. Although these results are limited by the uncertainty associated with the small set of available historical SAR data, they highlight both localized rates of high subsidence and a significant spatial variability in subsidence, emphasizing the need for further measurement, which could be done with Sentinel-1 and NASA's upcoming NISAR mission.

Simple method for quantifying pulmonary metastases in a murine fibrosarcoma.

A simple method is described for quantitating pulmonary metastases in C57BL/6J mice implanted with the Lewis T241 fibrosarcoma. Lungs were removed from tumor-bearing mice, homogenized, and diluted to 14 ml with supplemented Roswell Park Memorial Institute Tissue Culture Medium 1640 (+5% fetal calf serum). Twenty-five microliters of lung suspension from individual mice were added to a flat-bottomed microtiter plate containing 175 microliters of supplemented media, pulsed with [3H]thymidine, and incubated for 20 hr at 37 degrees. The cells were processed with a multiple automated sample harvester and counted in a liquid scintillator. Total lung burden was extrapolated from measured radioactivity (as cpm) through the use of a standard curve. This method is reasonably accurate and precise and provides more quantitative information on the pulmonary metastatic process than most conventional assays.

Sequence of a phosphorylation site in nucleolar protein B23.

The sites of phosphorylation in protein B23, a silver-staining preribosomal ribonucleoprotein particle protein, were analyzed by tryptic peptide mapping. Three 32P peptides were found using in vitro labeling of nucleoli. An additional unlabeled phosphopeptide was identified by amino acid analysis. The sequence of the latter was Asp-Thr(P)-Pro-Ala-Lys. These results suggest that protein B23 contains one class of site labeled rapidly in vitro and another type of site phosphorylated only in vivo.

Bacteriophage T4 gene 59 helicase assembly protein binds replication fork DNA. The 1.45 A resolution crystal structure reveals a novel alpha-helical two-domain fold.

The bacteriophage T4 gene 59 helicase assembly protein is required for recombination-dependent DNA replication, which is the predominant mode of DNA replication in the late stage of T4 infection. T4 gene 59 helicase assembly protein accelerates the loading of the T4 gene 41 helicase during DNA synthesis by the T4 replication system in vitro. T4 gene 59 helicase assembly protein binds to both T4 gene 41 helicase and T4 gene 32 single-stranded DNA binding protein, and to single and double-stranded DNA. We show here that T4 gene 59 helicase assembly protein binds most tightly to fork DNA substrates, with either single or almost entirely double-stranded arms. Our studies suggest that the helicase assembly protein is responsible for loading T4 gene 41 helicase specifically at replication forks, and that its binding sites for each arm must hold more than six, but not more than 12 nucleotides. The 1.45 A resolution crystal structure of the full-length 217-residue monomeric T4 gene 59 helicase assembly protein reveals a novel alpha-helical bundle fold with two domains of similar size. Surface residues are predominantly basic (pI 9.37) with clusters of acidic residues but exposed hydrophobic residues suggest sites for potential contact with DNA and with other protein molecules. The N-terminal domain has structural similarity to the double-stranded DNA binding domain of rat HMG1A. We propose a speculative model of how the T4 gene 59 helicase assembly protein might bind to fork DNA based on the similarity to HMG1, the location of the basic and hydrophobic regions, and the site size of the fork arms needed for tight fork DNA binding. The fork-binding model suggests putative binding sites for the T4 gene 32 single-stranded DNA binding protein and for the hexameric T4 gene 41 helicase assembly.

Refractive index distribution and optical properties of the isolated human lens measured using magnetic resonance imaging (MRI).

Using a non-invasive MRI technique for measuring the refractive index distribution through the crystalline lens, refractive index maps were obtained through 20 intact isolated human lenses (7-82years). Focal length measurements, obtained by simulated light ray propagation through each index map were found to be in agreement with direct measurements performed on a scanning laser apparatus. With increasing age, the refractive index profiles became flatter in the central region, accompanied by steepening of the profile in the periphery. This appears to be an important mechanism underlying the observed changes in power and longitudinal aberration of the human lens.