Intercontinental transport of pollution manifested in the variability and seasonal trend of springtime O3 at northern middle and high latitudes

Observations (0–8 km) from the Tropospheric Ozone Production about the Spring Equinox (TOPSE) experiment are analyzed to examine air masses contributing to the observed variability of springtime O3 and its seasonal increase at 40°–85°N over North America. Factor analysis using the positive matrix factorization and principal component analysis methods is applied to the data set with 14 chemical tracers (O3, NOy, PAN, CO, CH4, C2H2, C3H8, CH3Cl, CH3Br, C2Cl4, CFC-11, HCFC-141B, Halon-1211, and 7Be) and one dynamic tracer (potential temperature). Our analysis results are biased by the measurements at 5–8 km (70% of the data) due to the availability of 7Be measurements. The identified tracer characteristics for seven factors are generally consistent with the geographical origins derived from their 10 day back trajectories. Stratospherically influenced air accounts for 14 ppbv (35–40%) of the observed O3 variability for data with O3concentrations \u3c100 ppbv at middle and high latitudes. It accounts for about 2.5 ppbv/month (40%) of the seasonal O3 trend at midlatitudes but for only 0.8 ppbv/month (\u3c20%) at high latitudes, likely reflecting more vigorous midlatitude dynamical systems in spring. At midlatitudes, reactive nitrogen-rich air masses transported through Asia are much more significant (11 ppbv in variability and 3.5 ppbv/month in trend) than other tropospheric contributors. At high latitudes the O3 variability is significantly influenced by air masses transported from lower latitudes (11 ppbv), which are poor in reactive nitrogen. The O3 trend, in contrast, is largely defined by air masses rich in reactive nitrogen transported through Asia and Europe across the Pacific or the Arctic (3 ppbv/month). The influence from the stratospheric source is more apparent at 6–8 km, while the effect of O3 production and transport within the troposphere is more apparent at lower altitudes. The overall effect of tropospheric photochemical production, through long-range transport, on the observed O3 variability and its seasonal trend is more important at high latitudes relative to more photochemically active midlatitudes

An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries

Advances in imaging methods such as electron microscopy, tomography and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for biophysical and mathematical modeling once these data can be represented as a geometric mesh, which, when carefully conditioned, enables the discretization and solution of partial differential equations. In this study, we outline the steps for a na\"ive user to approach GAMer 2, a mesh generation code written in C++ designed to convert structural datasets to realistic geometric meshes, while preserving the underlying shapes. We present two example cases, 1) mesh generation at the subcellular scale as informed by electron tomography, and 2) meshing a protein with structure from x-ray crystallography. We further demonstrate that the meshes generated by GAMer are suitable for use with numerical methods. Together, this collection of libraries and tools simplifies the process of constructing realistic geometric meshes from structural biology data.Comment: 6 pages and 4 figures. Supplemental Movie available upon reques

Clinical and Genetic Evaluation of People with or at Risk of Hereditary ATTR Amyloidosis: An Expert Opinion and Consensus on Best Practice in Ireland and the UK

Hereditary transthyretin-mediated amyloidosis (hATTR) is challenging to diagnose early owing to the heterogeneity of clinical presentation, which differs according to the TTR gene variant and its penetrance in each individual. The TTR variants seen most frequently in the UK and Ireland (T80A, V142I and V50M) differ to those commonly occurring in other geographic locations and warrant a specific consideration for diagnosis and genetic testing. In addition, recent availability of treatment for this condition has reinforced the need for a more consistent approach to the management of patients, including access to specialist services, genetic testing and counselling, and clinical investigation for families living in the UK and Ireland. A multidisciplinary panel of experts from the UK and Ireland was convened to identify the current challenges, provide recommendations, and develop a consensus for the diagnosis and screening of people with, or at risk of, hATTR. Over a series of meetings, experts shared their current practices and drafted, refined and approved a consensus statement. This consensus statement provides recommendations for three different groups: (1) people with symptoms raising a possibility of hATTR amyloidosis; (2) people with biopsy-confirmed hATTR amyloidosis; and (3) people without symptoms who may have hATTR amyloidosis (i.e. relatives of people with identified TTR variants). For each group, recommendations are made for the required steps for the diagnosis and follow-up of symptomatic patients, and for guidance on the specialist support for counselling and pre-symptomatic genetic testing of at-risk individuals. This guidance is intended to be practical and based on available evidence. The aim is for regional amyloid specialist centres to provide timely diagnosis, clinical screening, and treatment for individuals and their families with hATTR amyloidosis

Seven-membered ring scaffolds for drug discovery: access to functionalised azepanes and oxepanes through diazocarbonyl chemistry

Functionalised azepane and oxepane scaffolds were prepared using diazocarbonyl chemistry and elaborated to show their potential use in library synthesis. Key dicarbonyl containing seven-membered rings were functionalised via diastereoselective Luche reduction of the ketone followed by manipulation of the ester and amine groups. Further scaffolds could be accessed by C-alkylation of the dicarbonyl compounds. In addition, an oxepane containing amino acid could be prepared via a diastereoselective enamine reduction

Ozone depletion events observed in the high latitude surface layer during the TOPSE aircraft program

During the Tropospheric Ozone Production about the Spring Equinox (TOPSE) aircraft program, ozone depletion events (ODEs) in the high latitude surface layer were investigated using lidar and in situ instruments. Flight legs of 100 km or longer distance were flown 32 times at 30 m altitude over a variety of regions north of 58° between early February and late May 2000. ODEs were found on each flight over the Arctic Ocean but their occurrence was rare at more southern latitudes. However, large area events with depletion to over 2 km altitude in one case were found as far south as Baffin Bay and Hudson Bay and as late as 22 May. There is good evidence that these more southern events did not form in situ but were the result of export of ozone-depleted air from the surface layer of the Arctic Ocean. Surprisingly, relatively intact transport of ODEs occurred over distances of 900–2000 km and in some cases over rough terrain. Accumulation of constituents in the frozen surface over the dark winter period cannot be a strong prerequisite of ozone depletion since latitudes south of the Arctic Ocean would also experience a long dark period. Some process unique to the Arctic Ocean surface or its coastal regions remains unidentified for the release of ozone-depleting halogens. There was no correspondence between coarse surface features such as solid ice/snow, open leads, or polynyas with the occurrence of or intensity of ozone depletion over the Arctic or subarctic regions. Depletion events also occurred in the absence of long-range transport of relatively fresh “pollution” within the high latitude surface layer, at least in spring 2000. Direct measurements of halogen radicals were not made. However, the flights do provide detailed information on the vertical structure of the surface layer and, during the constant 30 m altitude legs, measurements of a variety of constituents including hydroxyl and peroxy radicals. A summary of the behavior of these constituents is made. The measurements were consistent with a source of formaldehyde from the snow/ice surface. Median NOx in the surface layer was 15 pptv or less, suggesting that surface emissions were substantially converted to reservoir constituents by 30 m altitude and that ozone production rates were small (0.15–1.5 ppbv/d) at this altitude. Peroxyacetylnitrate (PAN) was by far the major constituent of NOy in the surface layer independent of the ozone mixing ratio

Densely functionalised spirocyclic oxetane-piperidine scaffolds for drug discovery

A spirocyclic, sp3-atom rich oxetane-containing scaffold was synthesised in just two steps via a gold catalysed propargylic alcohol rearrangement. The key gold cyclisation can be undertaken on a 40 g scale allowing the preparation of 419 lead-like compounds based on the scaffold for the European Lead Factory

The Late Stage of COPI Vesicle Fission Requires Shorter Forms of Phosphatidic Acid and Diacylglycerol

Studies on vesicle formation by the Coat Protein I (COPI) complex have contributed to a basic understanding of how vesicular transport is initiated. Phosphatidic acid (PA) and diacylglycerol (DAG) have been found previously to be required for the fission stage of COPI vesicle formation. Here, we find that PA with varying lipid geometry can all promote early fission, but only PA with shortened acyl chains promotes late fission. Moreover, diacylglycerol (DAG) acts after PA in late fission, with this role of DAG also requiring shorter acyl chains. Further highlighting the importance of the short-chain lipid geometry for late fission, we find that shorter forms of PA and DAG promote the vesiculation ability of COPI fission factors. These findings advance a general understanding of how lipid geometry contributes to membrane deformation for vesicle fission, and also how proteins and lipids coordinate their actions in driving this process

The late stage of COPI vesicle fission requires shorter forms of phosphatidic acid and diacylglycerol

Studies on vesicle formation by the Coat Protein I (COPI) complex have contributed to a basic understanding of how vesicular transport is initiated. Phosphatidic acid (PA) and diacylglycerol (DAG) have been found previously to be required for the fission stage of COPI vesicle formation. Here, we find that PA with varying lipid geometry can all promote early fission, but only PA with shortened acyl chains promotes late fission. Moreover, diacylglycerol (DAG) acts after PA in late fission, with this role of DAG also requiring shorter acyl chains. Further highlighting the importance of the short-chain lipid geometry for late fission, we find that shorter forms of PA and DAG promote the vesiculation ability of COPI fission factors. These findings advance a general understanding of how lipid geometry contributes to membrane deformation for vesicle fission, and also how proteins and lipids coordinate their actions in driving this process

Making Big Data Useful for Health Care: A Summary of the Inaugural MIT Critical Data Conference

With growing concerns that big data will only augment the problem of unreliable research, the Laboratory of Computational Physiology at the Massachusetts Institute of Technology organized the Critical Data Conference in January 2014. Thought leaders from academia, government, and industry across disciplines--including clinical medicine, computer science, public health, informatics, biomedical research, health technology, statistics, and epidemiology--gathered and discussed the pitfalls and challenges of big data in health care. The key message from the conference is that the value of large amounts of data hinges on the ability of researchers to share data, methodologies, and findings in an open setting. If empirical value is to be from the analysis of retrospective data, groups must continuously work together on similar problems to create more effective peer review. This will lead to improvement in methodology and quality, with each iteration of analysis resulting in more reliability