Fragmentative and stereochemical isomerization probes for homolytic carbon to phosphorus bond scission catalyzed by bacterial carbon-phosphorus lyase

Three bacterial strains, Agrobacterium radiobacter, Klebsiella oxytoca, and Kluyvera ascorbata, isolated by enrichment culture for carbon to phosphorus bond cleavage ability, were analyzed for the mode of C---P bond fission. The cleavage of alkyl phosphonic acids to alkanes and inorganic phosphates proceeded both aerobically and anaerobically, and growth on trideuteromethylphosphonic acid yielded trideuteromethane as product. These data indicate that functionalization of the organic moiety does not precede carbon to phosphorus bond cleavage. As probes for radical intermediates, cyclopropylmethylphosphonic acid and cis-1,2-dideutero-1-propenylphosphonic acid were used in growth experiments and the gaseous hydrocarbon products were examined. With the cyclopropylmethylphosphonic acid probe, all three bacteria produced methylcyclopropane, but only K. oxytoca and K. ascorbata also generated the acyclic olefin 1-butene, and then only in very low quantity (0.6 and 0.3% versus methylcyclopropane, respectively). With the propenylphosphonic acid probe, cis-1,2-dideuteropropene was formed with greater than 98% retention of configuration with each bacterial strain. Only for K. oxytoca was the alternate product, in this case trans-1,2-dideuteropropene, clearly detected at 1.5%. Thus, C---P bond fission may yield radical intermediates that are trapped efficiently at the enzyme active site or, alternatively, homolysis of the C---P bond may occur as a minor reaction pathway.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/26489/1/0000025.pd

Quantifying erosion rates and weathering pathways that maximize soil organic carbon storage

Primary minerals that enter soils through bedrock weathering and atmospheric deposition can generate poorly crystalline minerals (PCM) that preferentially associate with soil organic carbon (SOC). These associations hinder microbial decomposition and the release of CO₂ from soils to the atmosphere, making them a critical geochemical control on terrestrial carbon abundance and persistence. Studies that explore these relationships are typically derived from soil chronosequences that experience negligible erosion and thus do not readily translate to eroding landscapes. Here, we propose a theoretical framework to estimate steady-state PCM density and stocks for hilly and mountainous settings by coupling geochemical and geomorphic mass balance equations that account for soil production from bedrock and dust, soil erosion, PCM formation from weathering, and the transformation of PCMs into crystalline phases. We calculate an optimal erosion rate for maximum PCM abundance that arises because PCMs are limited by insufficient weathering at faster erosion rates and loss via “ripening” into more crystalline forms at slower erosion rates. The optimal erosion rate for modeled hilltop soil is modulated by reaction rate constants that govern the efficiency of primary mineral weathering and PCM ripening. By comparing our analysis with global compilations of erosion and soil production rates derived from cosmogenic nuclides, we show that landscapes with slow-to-moderate erosion rates may be optimal for harboring abundant PCM stocks that can facilitate SOC sequestration and limit turnover. Given the growing array of erosion-topography metrics and the widespread availability of high-resolution topographic data, our framework demonstrates how weathering and critical zone processes can be coupled to inform landscape prioritization for persistent SOC storage potential across a broad range of spatial and temporal scales

Acute day units in non-residential settings for people in mental health crisis: the AD-CARE mixed-methods study

BACKGROUND: For people in mental health crisis, acute day units provide daily structured sessions and peer support in non-residential settings as an alternative to crisis resolution teams. OBJECTIVES: To investigate the provision, effectiveness, intervention acceptability and re-admission rates of acute day units. DESIGN: Work package 1 – mapping and national questionnaire survey of acute day units. Work package 2.1 – cohort study comparing outcomes during a 6-month period between acute day unit and crisis resolution team participants. Work package 2.2 – qualitative interviews with staff and service users of acute day units. Work package 3 – a cohort study within the Mental Health Minimum Data Set exploring re-admissions to acute care over 6 months. A patient and public involvement group supported the study throughout. SETTING AND PARTICIPANTS: Work package 1 – all non-residential acute day units (NHS and voluntary sector) in England. Work packages 2.1 and 2.2 – four NHS trusts with staff, service users and carers in acute day units and crisis resolution teams. Work package 3 – all individuals using mental health NHS trusts in England. RESULTS: Work package 1 – we identified 27 acute day units in 17 out of 58 trusts. Acute day units are typically available on weekdays from 10 a.m. to 4 p.m., providing a wide range of interventions and a multidisciplinary team, including clinicians, and having an average attendance of 5 weeks. Work package 2.1 – we recruited 744 participants (acute day units, n = 431; crisis resolution teams, n = 312). In the primary analysis, 21% of acute day unit participants (vs. 23% of crisis resolution team participants) were re-admitted to acute mental health services over 6 months. There was no statistically significant difference in the fully adjusted model (acute day unit hazard ratio 0.78, 95% confidence interval 0.54 to 1.14; p = 0.20), with highly heterogeneous results between trusts. Acute day unit participants had higher satisfaction and well-being scores and lower depression scores than crisis resolution team participants. The health economics analysis found no difference in resource use or cost between the acute day unit and crisis resolution team groups in the fully adjusted analysis. Work package 2.2 – 36 people were interviewed (acute day unit staff, n = 12; service users, n = 21; carers, n = 3). There was an overwhelming consensus that acute day units are highly valued. Service users found the high amount of contact time and staff continuity, peer support and structure provided by acute day units particularly beneficial. Staff also valued providing continuity, building strong therapeutic relationships and providing a variety of flexible, personalised support. Work package 3 – of 231,998 individuals discharged from acute care (crisis resolution team, acute day unit or inpatient ward), 21.4% were re-admitted for acute treatment within 6 months, with women, single people, people of mixed or black ethnicity, those living in more deprived areas and those in the severe psychosis care cluster being more likely to be re-admitted. Little variation in re-admissions was explained at the trust level, or between trusts with and trusts without acute day units (adjusted odds ratio 0.96, 95% confidence interval 0.80 to 1.15). LIMITATIONS: In work package 1, some of the information is likely to be incomplete as a result of trusts’ self-reporting. There may have been recruitment bias in work packages 2.1 and 2.2. Part of the health economics analysis relied on clinical Health of the Nations Outcome Scale ratings. The Mental Health Minimum Data Set did not contain a variable identifying acute day units, and some covariates had a considerable number of missing data. CONCLUSIONS: Acute day units are not provided routinely in the NHS but are highly valued by staff and service users, giving better outcomes in terms of satisfaction, well-being and depression than, and no significant differences in risk of re-admission or increased costs from, crisis resolution teams. Future work should investigate wider health and care system structures and the place of acute day units within them; the development of a model of best practice for acute day units; and staff turnover and well-being (including the impacts of these on care). FUNDING: This project was funded by the National Institute for Health Research (NIHR) Health Services and Delivery Research programme and will be published in full in Health Services and Delivery Research; Vol. 9, No. 18. See the NIHR Journals Library website for further project information

High-sensitivity troponin in the evaluation of patients with suspected acute coronary syndrome: a stepped-wedge, cluster-randomised controlled trial.

BACKGROUND: High-sensitivity cardiac troponin assays permit use of lower thresholds for the diagnosis of myocardial infarction, but whether this improves clinical outcomes is unknown. We aimed to determine whether the introduction of a high-sensitivity cardiac troponin I (hs-cTnI) assay with a sex-specific 99th centile diagnostic threshold would reduce subsequent myocardial infarction or cardiovascular death in patients with suspected acute coronary syndrome. METHODS: In this stepped-wedge, cluster-randomised controlled trial across ten secondary or tertiary care hospitals in Scotland, we evaluated the implementation of an hs-cTnI assay in consecutive patients who had been admitted to the hospitals' emergency departments with suspected acute coronary syndrome. Patients were eligible for inclusion if they presented with suspected acute coronary syndrome and had paired cardiac troponin measurements from the standard care and trial assays. During a validation phase of 6-12 months, results from the hs-cTnI assay were concealed from the attending clinician, and a contemporary cardiac troponin I (cTnI) assay was used to guide care. Hospitals were randomly allocated to early (n=5 hospitals) or late (n=5 hospitals) implementation, in which the high-sensitivity assay and sex-specific 99th centile diagnostic threshold was introduced immediately after the 6-month validation phase or was deferred for a further 6 months. Patients reclassified by the high-sensitivity assay were defined as those with an increased hs-cTnI concentration in whom cTnI concentrations were below the diagnostic threshold on the contemporary assay. The primary outcome was subsequent myocardial infarction or death from cardiovascular causes at 1 year after initial presentation. Outcomes were compared in patients reclassified by the high-sensitivity assay before and after its implementation by use of an adjusted generalised linear mixed model. This trial is registered with ClinicalTrials.gov, number NCT01852123. FINDINGS: Between June 10, 2013, and March 3, 2016, we enrolled 48 282 consecutive patients (61 [SD 17] years, 47% women) of whom 10 360 (21%) patients had cTnI concentrations greater than those of the 99th centile of the normal range of values, who were identified by the contemporary assay or the high-sensitivity assay. The high-sensitivity assay reclassified 1771 (17%) of 10 360 patients with myocardial injury or infarction who were not identified by the contemporary assay. In those reclassified, subsequent myocardial infarction or cardiovascular death within 1 year occurred in 105 (15%) of 720 patients in the validation phase and 131 (12%) of 1051 patients in the implementation phase (adjusted odds ratio for implementation vs validation phase 1·10, 95% CI 0·75 to 1·61; p=0·620). INTERPRETATION: Use of a high-sensitivity assay prompted reclassification of 1771 (17%) of 10 360 patients with myocardial injury or infarction, but was not associated with a lower subsequent incidence of myocardial infarction or cardiovascular death at 1 year. Our findings question whether the diagnostic threshold for myocardial infarction should be based on the 99th centile derived from a normal reference population. FUNDING: The British Heart Foundation

Acute day units in non-residential settings for people in mental health crisis: the AD-CARE mixed-methods study

Background For people in mental health crisis, acute day units provide daily structured sessions and peer support in non-residential settings as an alternative to crisis resolution teams. Objectives To investigate the provision, effectiveness, intervention acceptability and re-admission rates of acute day units. Design Work package 1 – mapping and national questionnaire survey of acute day units. Work package 2.1 – cohort study comparing outcomes during a 6-month period between acute day unit and crisis resolution team participants. Work package 2.2 – qualitative interviews with staff and service users of acute day units. Work package 3 – a cohort study within the Mental Health Minimum Data Set exploring re-admissions to acute care over 6 months. A patient and public involvement group supported the study throughout. Setting and participants Work package 1 – all non-residential acute day units (NHS and voluntary sector) in England. Work packages 2.1 and 2.2 – four NHS trusts with staff, service users and carers in acute day units and crisis resolution teams. Work package 3 – all individuals using mental health NHS trusts in England. Results Work package 1 – we identified 27 acute day units in 17 out of 58 trusts. Acute day units are typically available on weekdays from 10 a.m. to 4 p.m., providing a wide range of interventions and a multidisciplinary team, including clinicians, and having an average attendance of 5 weeks. Work package 2.1 – we recruited 744 participants (acute day units, n = 431; crisis resolution teams, n = 312). In the primary analysis, 21% of acute day unit participants (vs. 23% of crisis resolution team participants) were re-admitted to acute mental health services over 6 months. There was no statistically significant difference in the fully adjusted model (acute day unit hazard ratio 0.78, 95% confidence interval 0.54 to 1.14; p = 0.20), with highly heterogeneous results between trusts. Acute day unit participants had higher satisfaction and well-being scores and lower depression scores than crisis resolution team participants. The health economics analysis found no difference in resource use or cost between the acute day unit and crisis resolution team groups in the fully adjusted analysis. Work package 2.2 – 36 people were interviewed (acute day unit staff, n = 12; service users, n = 21; carers, n = 3). There was an overwhelming consensus that acute day units are highly valued. Service users found the high amount of contact time and staff continuity, peer support and structure provided by acute day units particularly beneficial. Staff also valued providing continuity, building strong therapeutic relationships and providing a variety of flexible, personalised support. Work package 3 – of 231,998 individuals discharged from acute care (crisis resolution team, acute day unit or inpatient ward), 21.4% were re-admitted for acute treatment within 6 months, with women, single people, people of mixed or black ethnicity, those living in more deprived areas and those in the severe psychosis care cluster being more likely to be re-admitted. Little variation in re-admissions was explained at the trust level, or between trusts with and trusts without acute day units (adjusted odds ratio 0.96, 95% confidence interval 0.80 to 1.15). Limitations In work package 1, some of the information is likely to be incomplete as a result of trusts’ self-reporting. There may have been recruitment bias in work packages 2.1 and 2.2. Part of the health economics analysis relied on clinical Health of the Nations Outcome Scale ratings. The Mental Health Minimum Data Set did not contain a variable identifying acute day units, and some covariates had a considerable number of missing data. Conclusions Acute day units are not provided routinely in the NHS but are highly valued by staff and service users, giving better outcomes in terms of satisfaction, well-being and depression than, and no significant differences in risk of re-admission or increased costs from, crisis resolution teams. Future work should investigate wider health and care system structures and the place of acute day units within them; the development of a model of best practice for acute day units; and staff turnover and well-being (including the impacts of these on care). Funding This project was funded by the National Institute for Health Research (NIHR) Health Services and Delivery Research programme and will be published in full in Health Services and Delivery Research; Vol. 9, No. 18. See the NIHR Journals Library website for further project information

Bootstrapping the energy flow in the beginning of life.

This paper suggests that the energy flow on which all living structures depend only started up slowly, the low-energy, initial phase starting up a second, slightly more energetic phase, and so on. In this way, the build up of the energy flow follows a bootstrapping process similar to that found in the development of computers, the first generation making possible the calculations necessary for constructing the second one, etc. In the biogenetic upstart of an energy flow, non-metals in the lower periods of the Periodic Table of Elements would have constituted the most primitive systems, their operation being enhanced and later supplanted by elements in the higher periods that demand more energy. This bootstrapping process would put the development of the metabolisms based on the second period elements carbon, nitrogen and oxygen at the end of the evolutionary process rather than at, or even before, the biogenetic even

Transcriptional Analysis of Lactobacillus brevis to N-Butanol and Ferulic Acid Stress Responses

The presence of anti-microbial phenolic compounds, such as the model compound ferulic acid, in biomass hydrolysates pose significant challenges to the widespread use of biomass in conjunction with whole cell biocatalysis or fermentation. Currently, these inhibitory compounds must be removed through additional downstream processing or sufficiently diluted to create environments suitable for most industrially important microbial strains. Simultaneously, product toxicity must also be overcome to allow for efficient production of next generation biofuels such as n-butanol, isopropanol, and others from these low cost feedstocks.This study explores the high ferulic acid and n-butanol tolerance in Lactobacillus brevis, a lactic acid bacterium often found in fermentation processes, by global transcriptional response analysis. The transcriptional profile of L. brevis reveals that the presence of ferulic acid triggers the expression of currently uncharacterized membrane proteins, possibly in an effort to counteract ferulic acid induced changes in membrane fluidity and ion leakage. In contrast to the ferulic acid stress response, n-butanol challenges to growing cultures primarily induce genes within the fatty acid synthesis pathway and reduced the proportion of 19:1 cyclopropane fatty acid within the L. brevis membrane. Both inhibitors also triggered generalized stress responses. Separate attempts to alter flux through the Escherichia coli fatty acid synthesis by overexpressing acetyl-CoA carboxylase subunits and deleting cyclopropane fatty acid synthase (cfa) both failed to improve n-butanol tolerance in E. coli, indicating that additional components of the stress response are required to confer n-butanol resistance.Several promising routes for understanding both ferulic acid and n-butanol tolerance have been identified from L. brevis gene expression data. These insights may be used to guide further engineering of model industrial organisms to better tolerate both classes of inhibitors to enable facile production of biofuels from lignocellulosic biomass

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Global data on earthworm abundance, biomass, diversity and corresponding environmental properties

Earthworms are an important soil taxon as ecosystem engineers, providing a variety of crucial ecosystem functions and services. Little is known about their diversity and distribution at large spatial scales, despite the availability of considerable amounts of local-scale data. Earthworm diversity data, obtained from the primary literature or provided directly by authors, were collated with information on site locations, including coordinates, habitat cover, and soil properties. Datasets were required, at a minimum, to include abundance or biomass of earthworms at a site. Where possible, site-level species lists were included, as well as the abundance and biomass of individual species and ecological groups. This global dataset contains 10,840 sites, with 184 species, from 60 countries and all continents except Antarctica. The data were obtained from 182 published articles, published between 1973 and 2017, and 17 unpublished datasets. Amalgamating data into a single global database will assist researchers in investigating and answering a wide variety of pressing questions, for example, jointly assessing aboveground and belowground biodiversity distributions and drivers of biodiversity change