Metagenomic assembled plasmids of the human microbiome vary across disease cohorts.

We compiled a human metagenome assembled plasmid (MAP) database and interrogated differences across multiple studies that were originally designed to investigate the composition of the human microbiome across various lifestyles, life stages and events. This was performed as plasmids enable bacteria to rapidly expand their functional capacity through mobilisation, yet their contribution to human health and disease is poorly understood. We observed that inter-sample ß-diversity differences of plasmid content (plasmidome) could distinguish cohorts across a multitude of conditions. We also show that reduced intra-sample plasmidome α-diversity is consistent amongst patients with inflammatory bowel disease (IBD) and Clostridioides difficile infections. We also show that faecal microbiota transplants can restore plasmidome diversity. Overall plasmidome diversity, specific plasmids, and plasmid-encoded functions can all potentially act as biomarkers of IBD or its severity. The human plasmidome is an overlooked facet of the microbiome and should be integrated into investigations regarding the role of the microbiome in promoting health or disease. Including MAP databases in analyses will enable a greater understanding of the roles of plasmid-encoded functions within the gut microbiome and will inform future human metagenome analyses.

Application of 15N tracing for estimating nitrogen cycle processes in soils of a constructed wetland.

Integrated Constructed Wetlands (ICW) area technology for the attenuation of contaminants such as organic carbon (C), nitrogen (N), phosphorous (P) and sulphur (S) in water coming from point or diffuse sources. Currently there is a lack of knowledge on the rates of gross N transformations in soils of the ICW bed leading to losses of reactive N to the environment. In addition, the kinetics of these processes need to be studied thoroughly for the sustainable use of ICW for removal of excessive N in the treatment of waste waters. Gross N transformation processes were quantified at two soil depths (0-15 and 30-45 cm) in the bed of a surface flow ICW using a 15N tracing approach. The ICW, located in Dunhill village at Waterford in Southeastern Ireland, receives 500 person equivalent waste waters containing large quantities of organic pollutants (ca. mean annual C, N, P and S contents of 240, 60, 5 and 73 mg L-1). Soil was removed from these depths in December 2014 and incubated anaerobically in the laboratory, with either 15N labeled ammonium (NH4+) or nitrate (NO3-), differentially labeled with 14NH415NO3 and 15NH414NO3 in parallel setups, enriched to 50 atm% 15N. Results showed that at both soil depths, NO3- production rates were small, which may have resulted in lower NO3- reduction by either denitrification or dissimilatory NO3- reduction to ammonium (DNRA). However, despite being low, the DNRA rates were greater than denitrification rates. Direct transformation of organic N to NO3-, without mineralization to NH4+, was a prevalent pathway of NO3- production accounting for 28-33% of the total NO3- production. Relative contribution of this process to the total N mineralization was negligible at depth 1 (0.01%) but dominant at depth 2 (99.7%). Total NO3-production to total immobilization of NH4+ and NO3- was very small (<0.50%) suggesting that ICW soils are not a source of NO3-. Despite a large potential of N immobilization existed at both the layers, relative N immobilization to the total N conversion was higher at depth 2 (ca. 2.2) than at depth 1 (ca. 1.5). The NH4+ desorption rate at 30-45 cm was high. However, immobilization in the recalcitrant and labile organic N pools was higher. Mineralization and immobilization of NH4+ processes showed that recalcitrant organic N was the predominant source in ICW soils whereas the labile organic N was comparatively small. Source apportionment of N2O production showed that the majority of the N2O produced through denitrification (ca. 92.5%) followed by heterotrophic nitrification (ca. 5.5%), co-denitrification (ca. 1.90%) and nitrification (0.20%). These results revealed that application of a detailed 15N tracing method can provide insights on the underlying processes of ecosystem based abundances of reactive N. A key finding of this study was that both investigated ICW layers were characterised by large N immobilization which restricts production of NO3- and further gaseous N losses.

Reductions in sugar sales from soft drinks in the UK from 2015 to 2018.

BACKGROUND: The consumption of free sugars in the UK is more than double the guideline intake for adults and close to triple for children, with soft drinks representing a significant proportion. The aim of this study was to assess how individual soft drink companies and consumers have responded to calls to reduce sugar consumption, including the soft drink industry levy (SDIL), between 2015 and 2018. METHODS: This was an annual cross-sectional study using nutrient composition data of 7377 products collected online, paired with volume sales data for 195 brands offered by 57 companies. The main outcome measures were sales volume, sugar content and volume of sugars sold by company and category, expressed in total and per capita per day terms. RESULTS: Between 2015 and 2018, the volume of sugars sold per capita per day from soft drinks declined by 30%, equivalent to a reduction of 4.6 g per capita per day. The sales-weighted mean sugar content of soft drinks fell from 4.4 g/100 ml in 2015 to 2.9 g/100 ml in 2018. The total volume sales of soft drinks that are subject to the SDIL (i.e. contain more than 5 g/100 ml of sugar) fell by 50%, while volume sales of low- and zero-sugar (< 5 g/100 ml) drinks rose by 40%. CONCLUSION: Action by the soft drinks industry to reduce sugar in products and change their product portfolios, coupled with changes in consumer purchasing, has led to a significant reduction in the total volume and per capita sales of sugars sold in soft drinks in the UK. The rate of change accelerated between 2017 and 2018, which also implies that the implementation of the SDIL acted as an extra incentive for companies to reformulate above and beyond what was already being done as part of voluntary commitments to reformulation, or changes in sales driven by consumer preferences.

Effect of extended-duration thromboprophylaxis on venous thromboembolism and major bleeding among acutely ill hospitalized medical patients: a bivariate analysis.

Essentials Anticoagulants prevent venous thromboembolism but may be associated with greater bleeding risks. Bivariate analysis assumes a non-linear relationship between efficacy and safety outcomes. Extended full-dose betrixaban is favorable over standard enoxaparin in bivariate endpoint. Clinicians must weigh efficacy and safety outcomes in decision-making on thromboprophylaxis. SUMMARY: Background Among acutely ill hospitalized medical patients, extended-duration thromboprophylaxis reduces the risk of venous thromboembolism (VTE), but some pharmacologic strategies have been associated with greater risks of major bleeding, thereby offsetting the net clinical benefit (NCB). Methods To assess the risk-benefit profile of anticoagulation regimens, a previously described bivariate method that does not assume a linear risk-benefit tradeoff and can accommodate different margins for efficacy and safety was performed to simultaneously assess efficacy (symptomatic VTE) and safety (major bleeding) on the basis of data from four randomized controlled trials of extended-duration (30-46 days) versus standard-duration (6-14 days) thromboprophylaxis among 28 227 patients (EXCLAIM, ADOPT, MAGELLAN and APEX trials). Results Extended thromboprophylaxis with full-dose betrixaban (80 mg once daily) was superior in efficacy and non-inferior in safety to standard-duration enoxaparin, and showed a significantly favorable NCB, with a risk difference of - 0.51% (- 0.89% to - 0.10%) in the bivariate outcome. Extended enoxaparin was superior in efficacy and inferior in safety (bivariate outcome: 0.03% [- 0.37% to 0.43%]), whereas apixaban and rivaroxaban were non-inferior in efficacy and inferior in safety (- 0.20% [- 0.49% to 0.17%] and 0.23% [- 0.16% to 0.69%], respectively). Reduced-dose betrixaban did not show a significant difference in either efficacy or safety (0.41% [- 0.85% to 1.94%]). Conclusions In a bivariate analysis that assumes non-linear risk-benefit tradeoffs, extended prophylaxis with full-dose betrixaban was superior to standard-duration enoxaparin, whereas other regimens failed to simultaneously achieve both superiority and non-inferiority with respect to symptomatic VTE and major bleeding in the management of acutely ill hospitalized medical patients.

In situ denitrification and DNRA rates in groundwater beneath an integrated constructed wetland.

Evaluation of the environmental benefits of constructed wetlands (CWs) requires an understanding of their impacts on the groundwater quality under the wetlands. Empirical mass-balance (nitrogen in/nitrogen out) approaches for estimating nitrogen (N) removal in CWs do not characterise the final fate of N; where nitrate (NO3--N) could be reduced to either ammonium (NH4+-N) or N2 with the potential for significant production of N2O. Herein, in situ denitrification and DNRA (dissimilatory nitrate reduction to ammonium) rates were measured in groundwater beneath cells of an earthen lined integrated constructed wetland (ICW, used to remove the nutrients from municipal wastewater) using the 15N-enriched NO3--N push-pull method. Experiments were conducted utilising replicated (n = 3) shallow (1 m depth) and deep (4 m depth) piezometers installed along two control planes. These control planes allowed for the assessment of groundwater underlying high (Cell 2, septic tank waste) and low (Cell 3) load cells of the ICW. Background piezometers were also installed off-site. Results showed that denitrification (N2O-N + N2-N) and DNRA were major NO3--N consumption processes accounting together for 54-79% of the total biochemical consumption of the applied NO3--N. Of which 14-16% and 40-63% were consumed by denitrification and DNRA, respectively. Both processes differed significantly across ICW cells indicating that N transformation depends on nutrient loading rates and were significantly higher in shallow compared to the deep groundwater. In such a reduced environment (low dissolved oxygen and low redox potential), higher DNRA over the denitrification rate can be attributed to the high C concentration and high TC/NO3--N ratio. Low pH (6.5-7.1) in this system might have limited denitrification to some extent to an incomplete state, evidenced by a high N2O-N/(N2O-N+N2-N) ratio (0.35 ± 0.17, SE). A relatively higher N2O-N/(N2O-N+N2-N) ratio and higher DNRA rate over denitrification, suggest that the end products of N transformations are reactive. This N2O can be consumed to N2 and/or emitted to the atmosphere. The DNRA rate and accumulation of NH4+-N indicated that the ICW created a suitable groundwater biogeochemical environment that enhanced NO3--N reduction to NH4+-N. This study showed that CWs significantly influence NO3--N attenuation to reactive forms of N in the groundwater beneath them and that solely focusing on within wetland NO3--N attenuation can underestimate the environmental benefits of wetlands.

A Comparison of Adherence Timeframes Using Missed Dose Items and Their Associations with Viral Load in Routine Clinical Care: Is Longer Better?

Questions remain regarding optimal timeframes for asking about adherence in clinical care. We compared 4-, 7-, 14-, 30-, and 60-day timeframe missed dose items with viral load levels among 1099 patients on antiretroviral therapy in routine care. We conducted logistic and linear regression analyses examining associations between different timeframes and viral load using Bayesian model averaging (BMA). We conducted sensitivity analyses with subgroups at increased risk for suboptimal adherence (e.g. patients with depression, substance use). The 14-day timeframe had the largest mean difference in adherence levels among those with detectable and undetectable viral loads. BMA estimates suggested the 14-day timeframe was strongest overall and for most subgroups although findings differed somewhat for hazardous alcohol users and those with current depression. Adherence measured by all missed dose timeframes correlated with viral load. Adherence calculated from intermediate timeframes (e.g. 14-day) appeared best able to capture adherence behavior as measured by viral load.

Unannounced telephone-based pill counts: a valid and feasible method for monitoring adherence.

Phone-based unannounced pill counts to measure medication adherence are much more practical and less expensive than home-based unannounced pill counts, but their validity has not been widely assessed. We examined the validity of phone versus home-based pill counts using a simplified protocol streamlined for studies embedded in clinical care settings. A total of 100 paired counts were used to compare concordance between unannounced phone and home-based pill counts using interclass correlations. Discrepancy analyses using χ(2) tests compared demographic and clinical characteristics across patients who were concordant between phone and home-based pill counts and patients who were not concordant. Concordance was high for phone-based and home-based unannounced total pill counts, as well as individual medication counts and calculated adherence. This study demonstrates that a simplified phone-based pill count protocol can be implemented among patients from a routine clinical care setting and is a feasible means of monitoring medication adherence.

Preparation and properties of a calcium(II)-based molecular chain decorated with manganese(II) butterfly-like complexes.

The room temperature reaction of [Mn2O2(bipy)4](ClO4)3 (bipy = 2,2'-bipyridine) with Ca(CHCl2COO)2 in methanol produced a yellow crystalline material. The X-ray determined structure comprises of a multiple calcium(II) carboxylate bridged chain-like structure which is decorated with [Mn(bipy)2(OH2)](2+) subunits. The redox behaviour for the complex in H2O and MeCN is reported. In the latter solvent the oxidation of the manganese ions appears to be facilitated by the presence of the calcium ions. Magnetic susceptibility and low temperature magnetization measurements show that the Mn moment is isotropic, with g = 1.99(1) and S = 5/2, confirming it is in the 2+ oxidation state. A very weak antiferromagnetic interaction is also detected. Frequency-dependent ac measurements evidence slow magnetic relaxation of the Mn(bipy)2 units. Two relaxation mechanisms are identified: a very slow direct process and a faster one caused by the Resonant Phonon Trapping mechanism. This is the first example of field-induced single ion magnet (SIM) behavior in a mononuclear Mn(II) complex.

Pentacoordinate silicon complexes with dynamic motion resembling a pendulum on the S(N)2 reaction pathway.

A series of glutarimide derivatives which has two carbonyl coordination sites for intramolecular pentacoordination at silicon with a X(1+n)SiC(3-n)O moiety have been synthesised and characterized. The substituent (leaving group) effects on the Si-O bond exchange between the two coordination sites (resembling a pendulum) have been studied by comparison of the differently substituted (X = F, Cl, OTf, Br and I) structures. The activation parameters for the Si-O bond exchange process were measured by NMR and separately computed and are consistent with the strength of Si-O bond coordination and the nature of the leaving group, X. The temperature-dependent (29)Si NMR spectroscopy is supported by X-ray crystallography and shows that the tetrahedral reactant is converted into pentacoordinate intermediates by intramolecular O-Si association followed by reversion to a tetrahedral geometry by Si-X dissociation. The two association/dissociation patterns offer a model for nucleophilic substitution at a silicon atom. A continuum of structures on the S(N)2 reaction profile from the glutarimide derivatives correlates reasonably well with the structural data obtained from derivatives of lactams, diketopiperazines and quinolones.

Disease-associated prion protein in neural and lymphoid tissues of mink (Mustela vison) inoculated with transmissible mink encephalopathy.

Transmissible spongiform encephalopathies (TSEs) are diagnosed by immunodetection of disease-associated prion protein (PrP(d)). The distribution of PrP(d) within the body varies with the time-course of infection and between species, during interspecies transmission, as well as with prion strain. Mink are susceptible to a form of TSE known as transmissible mink encephalopathy (TME), presumed to arise due to consumption of feed contaminated with a single prion strain of ruminant origin. After extended passage of TME isolates in hamsters, two strains emerge, HY and DY, each of which is associated with unique structural isoforms of PrP(TME) and of which only the HY strain is associated with accumulation of PrP(TME) in lymphoid tissues. Information on the structural nature and lymphoid accumulation of PrP(TME) in mink is limited. In this study, 13 mink were challenged by intracerebral inoculation using late passage TME inoculum, after which brain and lymphoid tissues were collected at preclinical and clinical time points. The distribution and molecular nature of PrP(TME) was investigated by techniques including blotting of paraffin wax-embedded tissue and epitope mapping by western blotting. PrP(TME) was detected readily in the brain and retropharyngeal lymph node during preclinical infection, with delayed progression of accumulation within other lymphoid tissues. For comparison, three mink were inoculated by the oral route and examined during clinical disease. Accumulation of PrP(TME) in these mink was greater and more widespread, including follicles of rectoanal mucosa-associated lymphoid tissue. Western blot analyses revealed that PrP(TME) accumulating in the brain of mink is structurally most similar to that accumulating in the brain of hamsters infected with the DY strain. Collectively, the results of extended passage in mink are consistent with the presence of only a single strain of TME, the DY strain, capable of inducing accumulation of PrP(TME) in the lymphoid tissues of mink but not in hamsters. Thus, mink are a relevant animal model for further study of this unique strain, which ultimately may have been introduced through consumption of a TSE of ruminant origin.

Integrating a web-based, patient-administered assessment into primary care for HIV-infected adults.

Providers routinely under diagnose at risk behaviors and outcomes, including depression, suicidal ideation, substance abuse, and poor medication adherence. To address this, we developed a web-based, self-administered patient-reported assessment tool and integrated it into routine primary care for HIV-infected adults. Printed results were delivered to providers and social workers immediately prior to patient appointments. The assessment included brief, validated instruments measuring clinically relevant domains including depression, substance use, medication adherence, and HIV transmission risk behaviors. Utilizing the Institute for Healthcare Improvement's Plan-Do-Study-Act (PDSA) approach to quality improvement, we addressed issues with clinic flow, technology, scheduling, and delivery of assessment results with the support of all levels of clinic staff. We found web-based patient-reported assessments to be a feasible tool that can be integrated into a busy multi-provider HIV primary care clinic. These assessments may improve provider recognition of key patient behaviors and outcomes. Critical factors for successful integration of such assessments into clinical care include: strong top-level /ort from clinic management, provider understanding of patient-reported assessments as a valuable clinical tool, tailoring the assessment to meet provider needs, communication among clinic staff to address flow issues, timeliness of delivery, and sound technological resources.

Integrated constructed wetlands: water management as a land-use issue, implementing the 'Ecosystem Approach'.

Awareness of the need for social, economic and environmental coherence in the management of water is becoming evermore apparent. Water supply as well as treatment is becoming more costly; a challenge that is not only limited to developing countries. The use of wetlands, natural and constructed, is now more widely accepted as a means of tackling a range of problems in water management to deliver this coherence. The use of 16 Integrated Constructed Wetlands that mimic shallow, emergent-vegetated, palustrine wetlands in a 2,500 ha catchment in County Waterford, Southeast Ireland, has shown a number of distinct advantages in implementing the all encompassing 'Ecosystem Approach', addressing the key elements for sustainable water management in an intensively used agricultural area. The significant increase in water quality, biodiversity, social amenities and acceptance by the local rural community provided by this 'real' field-scale demonstration show the benefits that such a joined-up approach can have on catchment management in the widest sense.

Dose selection for a direct and selective factor IXa inhibitor and its complementary reversal agent: translating pharmacokinetic and pharmacodynamic properties of the REG1 system to clinical trial design.

We performed detailed pharmacokinetic and pharmacodynamic modeling of REG1, an anticoagulation system composed of the direct factor IXa (FIXa) inhibitor pegnivacogin (RB006) and its matched active control agent anivamersen (RB007), with a focus on level of target inhibition to translate phase 1 results to phase 2 dose selection. We modeled early-phase clinical data relating weight-adjusted pegnivacogin dose and plasma concentration to prolongation of the activated partial thromboplastin time (aPTT). Using an in vitro calibration curve, percent FIXa inhibition was determined and related to aPTT prolongation and pegnivacogin dose and concentration. Similar methods were applied to relate anivamersen dose and level of reversal of pegnivacogin anticoagulation. Combined early-phase data suggested that ≥0.75 mg/kg pegnivacogin was associated with >99% inhibition of FIX activity and prolongation of plasma aPTT values ≈2.5 times above baseline, leading to selection of a 1 mg/kg dose for a phase 2a elective percutaneous coronary intervention study to achieve a high intensity of anticoagulation and minimize intersubject variability. Phase 2 validated our predictions, demonstrating 1 mg/kg pegnivacogin yielded plasma concentrations ≈25 µg/ml and >99% inhibition of FIX activity. The relationship between the anivamersen to pegnivacogin dose ratio and degree of pegnivacogin reversal was also validated. Our approach decreased the need for extensive dose-response studies, reducing the duration, complexity and cost of clinical development. The 1 mg/kg pegnivacogin dose and a range of anivamersen dose ratios are being tested in the phase 2b RADAR study (NCT00932100).

Group therapy for adolescents with repeated self harm: randomised controlled trial with economic evaluation.

OBJECTIVE: To examine the effectiveness and cost-effectiveness of group therapy for self harm in young people. DESIGN: Two arm, single (assessor) blinded parallel randomised allocation trial of a group therapy intervention in addition to routine care, compared with routine care alone. Randomisation was by minimisation controlling for baseline frequency of self harm, presence of conduct disorder, depressive disorder, and severity of psychosocial stress. PARTICIPANTS: Adolescents aged 12-17 years with at least two past episodes of self harm within the previous 12 months. Exclusion criteria were: not speaking English, low weight anorexia nervosa, acute psychosis, substantial learning difficulties (defined by need for specialist school), current containment in secure care. Setting Eight child and adolescent mental health services in the northwest UK. INTERVENTIONS: Manual based developmental group therapy programme specifically designed for adolescents who harm themselves, with an acute phase over six weekly sessions followed by a booster phase of weekly groups as long as needed. Details of routine care were gathered from participating centres. MAIN OUTCOME MEASURES: Primary outcome was frequency of subsequent repeated episodes of self harm. Secondary outcomes were severity of subsequent self harm, mood disorder, suicidal ideation, and global functioning. Total costs of health, social care, education, and criminal justice sector services, plus family related costs and productivity losses, were recorded. RESULTS: 183 adolescents were allocated to each arm (total n = 366). Loss to follow-up was low (<4%). On all outcomes the trial cohort as a whole showed significant improvement from baseline to follow-up. On the primary outcome of frequency of self harm, proportional odds ratio of group therapy versus routine care adjusting for relevant baseline variables was 0.99 (95% confidence interval 0.68 to 1.44, P = 0.95) at 6 months and 0.88 (0.59 to 1.33, P = 0.52) at 1 year. For severity of subsequent self harm the equivalent odds ratios were 0.81 (0.54 to 1.20, P = 0.29) at 6 months and 0.94 (0.63 to 1.40, P = 0.75) at 1 year. Total 1 year costs were higher in the group therapy arm (£21,781) than for routine care (£15,372) but the difference was not significant (95% CI -1416 to 10782, P = 0.132). CONCLUSIONS: The addition of this targeted group therapy programme did not improve self harm outcomes for adolescents who repeatedly self harmed, nor was there evidence of cost effectiveness. The outcomes to end point for the cohort as a whole were better than current clinical expectations. Trial registration ISRCTN 20496110.