Fast solution of Cahn-Hilliard variational inequalities using implicit time discretization and finite elements

We consider the e�cient solution of the Cahn-Hilliard variational inequality using an implicit time discretization, which is formulated as an optimal control problem with pointwise constraints on the control. By applying a semi-smooth Newton method combined with a Moreau-Yosida regularization technique for handling the control constraints we show superlinear convergence in function space. At the heart of this method lies the solution of large and sparse linear systems for which we propose the use of preconditioned Krylov subspace solvers using an e�ective Schur complement approximation. Numerical results illustrate the competitiveness of this approach

Arctic system on trajectory to new state

The Arctic system is moving toward a new state that falls outside the envelope of glacial-interglacial fluctuations that prevailed during recent Earth history. This future Arctic is likely to have dramatically less permanent ice than exists at present. At the present rate of change, a summer ice-free Arctic Ocean within a century is a real possibility, a state not witnessed for at least a million years. The change appears to be driven largely by feedback-enhanced global climate warming, and there seem to be few, if any processes or feedbacks within the Arctic system that are capable of altering the trajectory toward this “super interglacial” state

Linkages among runoff, dissolved organic carbon, and the stable oxygen isotope composition of seawater and other water mass indicators in the Arctic Ocean

Author Posting. © American Geophysical Union, 2005. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 110 (2005): G02013, doi:10.1029/2005JG000031.Concentrations of dissolved organic carbon (DOC) and δ18O values have been determined following sampling of runoff from a number of major arctic rivers, including the Ob, Yenisey, Lena, Kolyma, Mackenzie and Yukon in 2003-2004. These data are considered in conjunction with marine data for DOC, δ18O values, nutrients, salinity, and fluorometric indicators of DOC that were obtained as part of the Shelf-Basin Interactions program at the continental shelf-basin boundary of the Chukchi and Beaufort Seas. These marine data indicate that the freshwater component is most likely derived from regional sources, such as the Mackenzie, the Bering Strait inflow and possibly eastern Siberian rivers, including the Kolyma, or the Lena but not rivers further west in the Eurasian arctic. Contributions of freshwater from melted sea ice to marine surface waters appeared to be insignificant over annual cycles compared to runoff, although on a seasonal basis, freshwater from melted sea ice was locally dominant following a major sea-ice retreat into the Canada Basin in 2002. DOC concentrations were correlated with the runoff fraction, with an apparent meteoric water DOC concentration of 174 ± 1 μM (standard error). This concentration is lower than the flow-weighted concentrations measured at river mouths of the five largest Arctic rivers (358 to 917 μM), indicating that removal of terrigenous DOC during transport through estuaries, shelves and in the deep basin. DOC data indicate that flow-weighted concentrations in the two largest North American arctic rivers, the Yukon (625μM) and the Mackenzie (382 μM), are lower than in the three largest Eurasian arctic rivers, the Ob (825 μM), the Yenesey (858 μM) and the Lena (917 μM). A fluorometric indicator of chromophoric dissolved organic matter (CDOM) that has provided estimates of terrigenous DOC concentrations in the Eurasian Arctic was not correlated with DOC concentrations in the Amerasian marine waters studied, except below the upper Arctic Ocean halocline. Nutrient distributions and concentrations as well as derived nutrient ratios suggest the CDOM fluorometer may be responding to the release of chromophoric materials from continental shelf sediments. Shipboard incubation experiments with undisturbed sediment cores indicate that continental shelf sediments on the Bering and Chukchi Sea shelves are likely to be a net source of DOC to the Arctic Ocean.The PARTNERS and SBI projects have been supported by the Office of Polar Programs of the U.S. National Science Foundation

The HITRAN 2008 Molecular Spectroscopic Database

This paper describes the status of the 2008 edition of the HITRAN molecular spectroscopic database. The new edition is the first official public release since the 2004 edition, although a number of crucial updates had been made available online since 2004. The HITRAN compilation consists of several components that serve as input for radiative-transfer calculation codes: individual line parameters for the microwave through visible spectra of molecules in the gas phase; absorption cross-sections for molecules having dense spectral features, i.e., spectra in which the individual lines are not resolved; individual line parameters and absorption cross sections for bands in the ultra-violet; refractive indices of aerosols, tables and files of general properties associated with the database; and database management software. The line-by-line portion of the database contains spectroscopic parameters for forty-two molecules including many of their isotopologues

Antibody attributes that predict the neutralization and effector function of polyclonal responses to SARS-CoV-2

BACKGROUND: While antibodies can provide significant protection from SARS-CoV-2 infection and disease sequelae, the specific attributes of the humoral response that contribute to immunity are incompletely defined. METHODS: We employ machine learning to relate characteristics of the polyclonal antibody response raised by natural infection to diverse antibody effector functions and neutralization potency with the goal of generating both accurate predictions of each activity based on antibody response profiles as well as insights into antibody mechanisms of action. RESULTS: To this end, antibody-mediated phagocytosis, cytotoxicity, complement deposition, and neutralization were accurately predicted from biophysical antibody profiles in both discovery and validation cohorts. These models identified SARS-CoV-2-specific IgM as a key predictor of neutralization activity whose mechanistic relevance was supported experimentally by depletion. CONCLUSIONS: Validated models of how different aspects of the humoral response relate to antiviral antibody activities suggest desirable attributes to recapitulate by vaccination or other antibody-based interventions

Decomposition of Juncus seeds in a valley mire (Faroe Islands) over a 900 year period.

The influence of past depositional environments on the chemistry of sub-fossil Juncus seed coats (testa) from the top 1 m (corresponding to ca. 900 years of peat accumulation) of a peat bog in the Faroe Islands was examined. The chemistry of the testa of fresh Juncus seeds were characterised using thermally assisted pyrolysis and methylation (THM) in the presence of tetramethyl ammonium hydroxide (TMAH) and ‘type’ compounds were identified, representative of the major chemical groups in the testa (cellulose-related sugars, lignin-related phenolics, fatty acids). The abundance of the ‘type’ compounds in the products from sub-fossil testae (the internal tissues of the seeds do not survive beyond the very early stages of decomposition) was then quantified at contiguous 1 cm depth intervals. Major losses of C18 unsaturated fatty acid methyl esters and sugars were associated with the fresh to sub-fossil transition at ca. 7 cm depth. The preservation of the phenolic ferulic acid in the seed testa appears to be favoured by the input of small basaltic particles from the nearby stream channel. The mechanism by which inwash of inorganic material may be responsible for the improved chemical preservation of the Juncus seed testa is, however, unclear. The sugars were easily metabolised by microorganisms under aerobic conditions of low water table and preserved under anoxic conditions with high water table, suggesting that a drier mire surface may result in the more efficient depletion of polysaccharides and cellulose during the initial stage of decomposition in the acrotelm

Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life

Aminoacyl-tRNA synthetases (aaRS) consist of several families of functionally conserved proteins essential for translation and protein synthesis. Like nearly all components of the translation machinery, most aaRS families are universally distributed across cellular life, being inherited from the time of the Last Universal Common Ancestor (LUCA). However, unlike the rest of the translation machinery, aaRS have undergone numerous ancient horizontal gene transfers, with several independent events detected between domains, and some possibly involving lineages diverging before the time of LUCA. These transfers reveal the complexity of molecular evolution at this early time, and the chimeric nature of genomes within cells that gave rise to the major domains. Additionally, given the role of these protein families in defining the amino acids used for protein synthesis, sequence reconstruction of their pre-LUCA ancestors can reveal the evolutionary processes at work in the origin of the genetic code. In particular, sequence reconstructions of the paralog ancestors of isoleucyl- and valyl- RS provide strong empirical evidence that at least for this divergence, the genetic code did not co-evolve with the aaRSs; rather, both amino acids were already part of the genetic code before their cognate aaRSs diverged from their common ancestor. The implications of this observation for the early evolution of RNA-directed protein biosynthesis are discussed.National Science Foundation (U.S.) (Grant DEB 0830024)National Science Foundation (U.S.) (Grant DEB 0936234)United States. National Aeronautics and Space Administration (NASA Postdoctoral Fellowship

Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma

Despite the histological similarity of ependymomas from throughout the neuroaxis, the disease likely comprises multiple independent entities, each with a distinct molecular pathogenesis. Transcriptional profiling of two large independent cohorts of ependymoma reveals the existence of two demographically, transcriptionally, genetically, and clinically distinct groups of posterior fossa (PF) ependymomas. Group A patients are younger, have laterally located tumors with a balanced genome, and are much more likely to exhibit recurrence, metastasis at recurrence, and death compared with Group B patients. Identification and optimization of immunohistochemical (IHC) markers for PF ependymoma subgroups allowed validation of our findings on a third independent cohort, using a human ependymoma tissue microarray, and provides a tool for prospective prognostication and stratification of PF ependymoma patients

Evolution of Wenger's concept of community of practice

<p>Abstract</p> <p>Background</p> <p>In the experience of health professionals, it appears that interacting with peers in the workplace fosters learning and information sharing. Informal groups and networks present good opportunities for information exchange. Communities of practice (CoPs), which have been described by Wenger and others as a type of informal learning organization, have received increasing attention in the health care sector; however, the lack of uniform operating definitions of CoPs has resulted in considerable variation in the structure and function of these groups, making it difficult to evaluate their effectiveness.</p> <p>Objective</p> <p>To critique the evolution of the CoP concept as based on the germinal work by Wenger and colleagues published between 1991 and 2002.</p> <p>Discussion</p> <p>CoP was originally developed to provide a template for examining the learning that happens among practitioners in a social environment, but over the years there have been important divergences in the focus of the concept. Lave and Wenger's earliest publication (1991) centred on the interactions between novices and experts, and the process by which newcomers create a professional identity. In the 1998 book, the focus had shifted to personal growth and the trajectory of individuals' participation within a group (i.e., peripheral versus core participation). The focus then changed again in 2002 when CoP was applied as a managerial tool for improving an organization's competitiveness.</p> <p>Summary</p> <p>The different interpretations of CoP make it challenging to apply the concept or to take full advantage of the benefits that CoP groups may offer. The tension between satisfying individuals' needs for personal growth and empowerment versus an organization's bottom line is perhaps the most contentious of the issues that make CoPs difficult to cultivate. Since CoP is still an evolving concept, we recommend focusing on optimizing specific characteristics of the concept, such as support for members interacting with each other, sharing knowledge, and building a sense of belonging within networks/teams/groups. Interventions that facilitate relationship building among members and that promote knowledge exchange may be useful for optimizing the function of these groups.</p