A novel hybrid approach for estimating total deposition in the United States

Atmospheric deposition of nitrogen and sulfur causes many deleterious effects on ecosystems including acidification and excess eutrophication. Assessments to support development of strategies to mitigate these effects require spatially and temporally continuous values of nitrogen and sulfur deposition. In the U.S., national monitoring networks exist that provide values of wet and dry deposition at discrete locations. While wet deposition can be interpolated between the monitoring locations, dry deposition cannot. Additionally, monitoring networks do not measure the complete suite of chemicals that contribute to total sulfur and nitrogen deposition. Regional air quality models provide spatially continuous values of deposition of monitored species as well as important unmeasured species. However, air quality modeling values are not generally available for an extended continuous time period. Air quality modeling results may also be biased for some chemical species. We developed a novel approach for estimating dry deposition using data from monitoring networks such as the Clean Air Status and Trends Network (CASTNET), the National Atmospheric Deposition Program (NADP) Ammonia Monitoring Network (AMoN), and the Southeastern Aerosol Research and Characterization (SEARCH) network and modeled data from the Community Multiscale Air Quality (CMAQ) model. These dry deposition values estimates are then combined with wet deposition values from the NADP National Trends Network (NTN) to develop values of total deposition of sulfur and nitrogen. Data developed using this method are made available via the CASTNET website

The Intrinsic Fundamental Group of a Linear Category

We provide an intrinsic definition of the fundamental group of a linear category over a ring as the automorphism group of the fibre functor on Galois coverings. If the universal covering exists, we prove that this group is isomorphic to the Galois group of the universal covering. The grading deduced from a Galois covering enables us to describe the canonical monomorphism from its automorphism group to the first Hochschild-Mitchell cohomology vector space.Comment: Final version, to appear in Algebras and Representation Theor

Assembly maps with coefficients in topological algebras and the integral K-theoretic Novikov conjecture

We prove that any countable discrete and torsion free subgroup of a general linear group over an arbitrary field or a similar subgroup of an almost connected Lie group satisfies the integral algebraic K-theoretic (split) Novikov conjecture over \cpt and \S, where \cpt denotes the C^*-algebra of compact operators and \S denotes the algebra of Schatten class operators. We introduce assembly maps with finite coefficients and under an additional hypothesis, we prove that such a group also satisfies the algebraic K-theoretic Novikov conjecture over \bar{\mathbb{Q}} and \mathbb{C} with finite coefficients. For all torsion free Gromov hyperbolic groups G, we demonstrate that the canonical algebra homomorphism \cpt[G]\map C^*_r(G)\hat{\otimes}\cpt induces an isomorphism between their algebraic K-theory groups.Comment: v2 Exposition improved; one lemma and grant acknowledgement added; v3 some terminology changed and details added, Theorems 4.5 and 4.7 in v3 need an extra hypothesis; v4 abridged version accepted for publication in JHR

The Waldschmidt constant for squarefree monomial ideals

Given a squarefree monomial ideal $I \subseteq R =k[x_1,\ldots,x_n]$, we show that $\widehat\alpha(I)$, the Waldschmidt constant of $I$, can be expressed as the optimal solution to a linear program constructed from the primary decomposition of $I$. By applying results from fractional graph theory, we can then express $\widehat\alpha(I)$ in terms of the fractional chromatic number of a hypergraph also constructed from the primary decomposition of $I$. Moreover, expressing $\widehat\alpha(I)$ as the solution to a linear program enables us to prove a Chudnovsky-like lower bound on $\widehat\alpha(I)$, thus verifying a conjecture of Cooper-Embree-H\`a-Hoefel for monomial ideals in the squarefree case. As an application, we compute the Waldschmidt constant and the resurgence for some families of squarefree monomial ideals. For example, we determine both constants for unions of general linear subspaces of $\mathbb{P}^n$ with few components compared to $n$, and we find the Waldschmidt constant for the Stanley-Reisner ideal of a uniform matroid.Comment: 26 pages. This project was started at the Mathematisches Forschungsinstitut Oberwolfach (MFO) as part of the mini-workshop "Ideals of Linear Subspaces, Their Symbolic Powers and Waring Problems" held in February 2015. Comments are welcome. Revised version corrects some typos, updates the references, and clarifies some hypotheses. To appear in the Journal of Algebraic Combinatoric

The protein structure initiative structural genomics knowledgebase

The Protein Structure Initiative Structural Genomics Knowledgebase (PSI SGKB, http://kb.psi-structuralgenomics.org) has been created to turn the products of the PSI structural genomics effort into knowledge that can be used by the biological research community to understand living systems and disease. This resource provides central access to structures in the Protein Data Bank (PDB), along with functional annotations, associated homology models, worldwide protein target tracking information, available protocols and the potential to obtain DNA materials for many of the targets. It also offers the ability to search all of the structural and methodological publications and the innovative technologies that were catalyzed by the PSI's high-throughput research efforts. In collaboration with the Nature Publishing Group, the PSI SGKB provides a research library, editorials about new research advances, news and an events calendar to present a broader view of structural biology and structural genomics. By making these resources freely available, the PSI SGKB serves as a bridge to connect the structural biology and the greater biomedical communitie

ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models

ModelCIF (github.com/ihmwg/ModelCIF) is a data information framework developed for and by computational structural biologists to enable delivery of Findable, Accessible, Interoperable, and Reusable (FAIR) data to users worldwide. ModelCIF describes the specific set of attributes and metadata associated with macromolecular structures modeled by solely computational methods and provides an extensible data representation for deposition, archiving, and public dissemination of predicted three-dimensional (3D) models of macromolecules. It is an extension of the Protein Data Bank Exchange / macromolecular Crystallographic Information Framework (PDBx/mmCIF), which is the global data standard for representing experimentally-determined 3D structures of macromolecules and associated metadata. The PDBx/mmCIF framework and its extensions (e.g., ModelCIF) are managed by the Worldwide Protein Data Bank partnership (wwPDB, wwpdb.org) in collaboration with relevant community stakeholders such as the wwPDB ModelCIF Working Group (wwpdb.org/task/modelcif). This semantically rich and extensible data framework for representing computed structure models (CSMs) accelerates the pace of scientific discovery. Herein, we describe the architecture, contents, and governance of ModelCIF, and tools and processes for maintaining and extending the data standard. Community tools and software libraries that support ModelCIF are also described

Quantification of cAMP and cGMP analogs in intact cells: pitfalls in enzyme immunoassays for cyclic nucleotides

Immunoassays are routinely used as research tools to measure intracellular cAMP and cGMP concentrations. Ideally, this application requires antibodies with high sensitivity and specificity. The present work evaluates the cross-reactivity of commercially available cyclic nucleotide analogs with two non-radioactive and one radioactive cAMP and cGMP immunoassay. Most of the tested cyclic nucleotide analogs showed low degree competition with the antibodies; however, with Rp-cAMPS, 8-Br-cGMP and 8-pCPT-cGMP, a strong cross-reactivity with the corresponding cAMP and cGMP, respectively, immunoassays was observed. The determined EIA-binding constants enabled the measurement of the intracellular cyclic nucleotide concentrations and revealed a time- and lipophilicity-dependent cell membrane permeability of the compounds in the range of 10–30% of the extracellular applied concentration, thus allowing a more accurate prediction of the intracellular analog levels in a given experiment

Noncommutative Geometry in the Framework of Differential Graded Categories

In this survey article we discuss a framework of noncommutative geometry with differential graded categories as models for spaces. We outline a construction of the category of noncommutative spaces and also include a discussion on noncommutative motives. We propose a motivic measure with values in a motivic ring. This enables us to introduce certain zeta functions of noncommutative spaces.Comment: 19 pages. Minor corrections and one reference added; to appear in the proceedings volume of AGAQ Istanbul, 200