AtChem (version 1), an open-source box model for the Master Chemical Mechanism

AtChem is an open-source zero-dimensional box model for atmospheric chemistry. Any general set of chemical reactions can be used with AtChem, but the model was designed specifically for use with the Master Chemical Mechanism (MCM, http://mcm.york.ac.uk/, last access: 16 January 2020). AtChem was initially developed within the EUROCHAMP project as a web application (AtChem-online, https://atchem.leeds.ac.uk/webapp/, last access: 16 January 2020) for modelling environmental chamber experiments; it was recently upgraded and further developed into a stand-alone offline version (AtChem2), which allows the user to run complex and long simulations, such as those needed for modelling of intensive field campaigns, as well as to perform batch model runs for sensitivity studies. AtChem is installed, set up and configured using semi-automated scripts and simple text configuration files, making it easy to use even for inexperienced users. A key feature of AtChem is that it can easily be constrained to observational data which may have different timescales, thus retaining all the information contained in the observations. Implementation of a continuous integration workflow, coupled with a comprehensive suite of tests and version control software, makes the AtChem code base robust, reliable and traceable. The AtChem2 code and documentation are available at https://github.com/AtChem/ (last access: 16 January 2020) under the open-source MIT License

Low-NO atmospheric oxidation pathways in a polluted megacity

The impact of emissions of volatile organic compounds (VOCs) to the atmosphere on the production of secondary pollutants, such as ozone and secondary organic aerosol (SOA), is mediated by the concentration of nitric oxide (NO). Polluted urban atmospheres are typically considered to be “high-NO” environments, while remote regions such as rainforests, with minimal anthropogenic influences, are considered to be “low NO”. However, our observations from central Beijing show that this simplistic separation of regimes is flawed. Despite being in one of the largest megacities in the world, we observe formation of gas- and aerosol-phase oxidation products usually associated with low-NO “rainforest-like” atmospheric oxidation pathways during the afternoon, caused by extreme suppression of NO concentrations at this time. Box model calculations suggest that during the morning high-NO chemistry predominates (95 %) but in the afternoon low-NO chemistry plays a greater role (30 %). Current emissions inventories are applied in the GEOS-Chem model which shows that such models, when run at the regional scale, fail to accurately predict such an extreme diurnal cycle in the NO concentration. With increasing global emphasis on reducing air pollution, it is crucial for the modelling tools used to develop urban air quality policy to be able to accurately represent such extreme diurnal variations in NO to accurately predict the formation of pollutants such as SOA and ozone

Understanding the role of molecular diffusion and catalytic selectivity in liquid-phase Beckmann rearrangement

ABSTRACT: Understanding the role of diffusion in catalysis is essential in the design of highly active, selective, and stable industrial heterogeneous catalysts. By using a combination of advanced in situ spectroscopic characterization tools, particularly quasi-elastic and inelastic neutron scattering, we outline the crucial differences in diffusion modes and molecular interactions of active sites within solid-acid catalysts. This, coupled with 2D solid-state NMR and probe-based FTIR spectroscopy, reveals the nature of the active site in our SAPO- 37 catalyst and affords detailed information on the evolution of solid-acid catalysts that can operate at temperatures as low as 130 °C, for the Beckmann rearrangement of cyclohexanone oxime to ε-caprolactam (precursor for Nylon-6). The versatility of this approach leads to structure−property correlations that contrast the dynamics of the diffusion process in the different materials studied. Our results illustrate the power of these techniques in unravelling the interplay between active site and molecular diffusion in single-site heterogeneous catalysts, which can play a vital role in designing low-temperature, sustainable catalytic processes

Regulation of type 1 diabetes development and B-cell activation in nonobese diabetic mice by early life exposure to a diabetogenic environment

Microbes, including viruses, influence type 1 diabetes (T1D) development, but many such influences remain undefined. Previous work on underlying immune mechanisms has focussed on cytokines and T cells. Here, we compared two nonobese diabetic (NOD) mouse colonies, NODlow and NODhigh, differing markedly in their cumulative T1D incidence (22% vs. 90% by 30 weeks in females). NODhigh mice harbored more complex intestinal microbiota, including several pathobionts; both colonies harbored segmented filamentous bacteria (SFB), thought to suppress T1D. Young NODhigh females had increased B-cell activation in their mesenteric lymph nodes. These phenotypes were transmissible. Co-housing of NODlow with NODhigh mice after weaning did not change T1D development, but T1D incidence was increased in female offspring of co-housed NODlow mice, which were exposed to the NODhigh environment both before and after weaning. These offspring also acquired microbiota and B-cell activation approaching those of NODhigh mice. In NODlow females, the low rate of T1D was unaffected by cyclophosphamide but increased by PD-L1 blockade. Thus, environmental exposures that are innocuous later in life may promote T1D progression if acquired early during immune development, possibly by altering B-cell activation and/or PD-L1 function. Moreover, T1D suppression in NOD mice by SFB may depend on the presence of other microbial influences. The complexity of microbial immune regulation revealed in this murine model may also be relevant to the environmental regulation of human T1D

100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care — Preliminary Report

BACKGROUND: The U.K. 100,000 Genomes Project is in the process of investigating the role of genome sequencing in patients with undiagnosed rare diseases after usual care and the alignment of this research with health care implementation in the U.K. National Health Service. Other parts of this project focus on patients with cancer and infection. METHODS: We conducted a pilot study involving 4660 participants from 2183 families, among whom 161 disorders covering a broad spectrum of rare diseases were present. We collected data on clinical features with the use of Human Phenotype Ontology terms, undertook genome sequencing, applied automated variant prioritization on the basis of applied virtual gene panels and phenotypes, and identified novel pathogenic variants through research analysis. RESULTS: Diagnostic yields varied among family structures and were highest in family trios (both parents and a proband) and families with larger pedigrees. Diagnostic yields were much higher for disorders likely to have a monogenic cause (35%) than for disorders likely to have a complex cause (11%). Diagnostic yields for intellectual disability, hearing disorders, and vision disorders ranged from 40 to 55%. We made genetic diagnoses in 25% of the probands. A total of 14% of the diagnoses were made by means of the combination of research and automated approaches, which was critical for cases in which we found etiologic noncoding, structural, and mitochondrial genome variants and coding variants poorly covered by exome sequencing. Cohortwide burden testing across 57,000 genomes enabled the discovery of three new disease genes and 19 new associations. Of the genetic diagnoses that we made, 25% had immediate ramifications for clinical decision making for the patients or their relatives. CONCLUSIONS: Our pilot study of genome sequencing in a national health care system showed an increase in diagnostic yield across a range of rare diseases. (Funded by the National Institute for Health Research and others.)

Cardiovascular risk profile before coronary artery bypass graft surgery in relation to depression and anxiety disorders: An age and sex propensity matched study

Objective: The cardiovascular risk profile and postoperative morbidity outcomes of anxiety disorder patients undergoing coronary artery bypass surgery is not known. Methods: In a cross-sectional design, 114 consecutive coronary artery bypass graft surgery patients were evaluated to create four matched groups (30 with anxiety disorder, 27 with depression disorder and 57 age-sex matched coronary artery bypass surgery control patients with no depression or anxiety disorder). Results: By comparison to non-depression disorder age-sex matched controls, depressed patients pre-sented for coronary artery bypass surgery with significantly greater myocardial inflammatory markers (Troponin T > 02, 33.3% vs. 11.1%, 02, 33.3% vs. 11.1%, p = .03), metabolic risk (body surface area > 35 (22.2% vs. 0%, 35 (22.2% vs. 0%, p = .03), comorbid cardiovascular risk (peripheral vascular disease 18.5% vs. 0%, p = .05). Depressed patients also recorded longer intraoperative time at higher temperatures >37 °C on cardiopulmonary bypass (11.1 ± 9.0 vs. 6.0 ± 4.9, 37 °C on cardiopulmonary bypass (11.1 ± 9.0 vs. 6.0 ± 4.9, p p = .03). Patients with anxiety disorder on the other hand presented with significantly higher Creatinine Kinase-Muscle Brain (5 IQR 4–5 ng/ml vs. 4 IQR 3–4 ng/ml, p = .04), higher intraoperative glucose levels (7.8 ± 2.5 mmol/l vs. 7.0 ± 1.2 mmol/l, p = .05), and received fewer grafts (2.1 ± .9 vs. 2.5 ± .9 p = .04). Conclusions: A differential cardiovascular risk profile and postoperative outcome was observed dependent on anxiety and depression disorder status. There were few modifiable cardiovascular risk factors at the time of surgery other than psychiatric status, perioperative management of depression and anxiety may have promise to reduce further cardiac morbidity after coronary artery bypass surgery

Accuracy of Temperature Measurement in the Cardiopulmonary Bypass Circuit

Oxygenator arterial outlet blood temperature is routinely measured in the cardiopulmonary bypass (CPB) circuit as a surrogate for the temperature of the arterial blood delivered to sensitive organs such as the brain. The aim of this study was to evaluate the accuracy of the temperature thermistors used in the Terumo Capiox® SX25 oxygenator and to compare the temperature measured at the outlet of the oxygenator using the Capiox® CX*TL Luer Thermistor with temperatures measured at distal sites. Five experimental stages were performed in vitro to achieve this aim. Under our experimental conditions, the luer thermistors accurately measured the temperature as referenced by a precision thermometer. In the CPB circuit, the difference between arterial outlet and reference thermometer temperature varied with outlet temperature over-reading at low temperatures and under reading at high temperatures. There was negligible heat loss (−0.4 ± 0.1°C) measured at 4.5 m from the arterial outlet. The Terumo Capiox® CX*TL Luer Thermistor is an accurate and reliable instrument for measuring temperature when incorporated into the Capiox Oxygenator. The accuracy in the measurement of temperature using these thermistors is affected by the thermistor immersion depth. Under reading of the arterial blood temperature by approximately 0.5°C should be considered at normothermic temperatures, to avoid exceeding the maximum arterial blood temperature as described by institutional protocols. The accuracy of blood temperature measurements should be considered for all oxygenator arterial outlet temperature probes

Reactivity Studies of Phosphinines: The Selenation of Diphenyl-Phosphine Substituents and Formation of a Chelating Bis(Phosphinine) Palladium(II) Complex

Phosphinines and donor-substituted phosphinines are of recent interest due to their use in homogeneous catalysis. In this article, a Pd(II) bis(phosphinine) complex was characterised and phosphorus–selenium coupling constants were used to assess the donor properties of the diphenylphosphine substituents of phosphinine ligands to promote their further use in catalysis. The selenation of 2,5-bis(diphenylphosphino)-3,6-dimethylphosphinine (5) and 2-diphenylphosphino-3-methyl-6-trimethylsilylphosphinine (6) gave the corresponding phosphine selenides 8 and 9, respectively, leaving the phosphinine ring intact. Multinuclear NMR spectroscopy, mass spectrometry and single crystal X-ray diffraction confirmed the oxidation of all the diphenylphosphine substituents with 1JP-Se coupling constants determined to be similar to SePPh3, indicating that the phosphinine rings were electronically similar to phenyl substituents. Solutions of 6 were found to react with oxygen slowly to produce the phosphine oxide 10 along with other by-products. The reaction of [bis{3-methyl-6-(trimethylsilyl)phosphinine-2-yl}dimethylsilane] (4) with [PdCl2(COD)] gave the chelating dichloropalladium(II) complex, as determined by multinuclear NMR spectroscopy, mass spectrometry and an elemental analysis. The molecular structure of the intermediate 2 in the formation of 4,6-di(tert-butyl)-1,3,2-diazaphosphinine (3) was also determined, which confirmed the structure of the diazaphosphacycle P(Cl){N=C(tBu)CH=C(tBu)-N(H)}