Sciunits: Reusable Research Objects

Science is conducted collaboratively, often requiring knowledge sharing about computational experiments. When experiments include only datasets, they can be shared using Uniform Resource Identifiers (URIs) or Digital Object Identifiers (DOIs). An experiment, however, seldom includes only datasets, but more often includes software, its past execution, provenance, and associated documentation. The Research Object has recently emerged as a comprehensive and systematic method for aggregation and identification of diverse elements of computational experiments. While a necessary method, mere aggregation is not sufficient for the sharing of computational experiments. Other users must be able to easily recompute on these shared research objects. In this paper, we present the sciunit, a reusable research object in which aggregated content is recomputable. We describe a Git-like client that efficiently creates, stores, and repeats sciunits. We show through analysis that sciunits repeat computational experiments with minimal storage and processing overhead. Finally, we provide an overview of sharing and reproducible cyberinfrastructure based on sciunits gaining adoption in the domain of geosciences

B-urns

The fringe of a B-tree with parameter $m$ is considered as a particular P\'olya urn with $m$ colors. More precisely, the asymptotic behaviour of this fringe, when the number of stored keys tends to infinity, is studied through the composition vector of the fringe nodes. We establish its typical behaviour together with the fluctuations around it. The well known phase transition in P\'olya urns has the following effect on B-trees: for $m\leq 59$, the fluctuations are asymptotically Gaussian, though for $m\geq 60$, the composition vector is oscillating; after scaling, the fluctuations of such an urn strongly converge to a random variable $W$. This limit is $\mathbb C$-valued and it does not seem to follow any classical law. Several properties of $W$ are shown: existence of exponential moments, characterization of its distribution as the solution of a smoothing equation, existence of a density relatively to the Lebesgue measure on $\mathbb C$, support of $W$. Moreover, a few representations of the composition vector for various values of $m$ illustrate the different kinds of convergence

Anchoring of Surface Proteins to the Cell Wall of Staphylococcus aureus. III. Lipid II is an in vivo peptidoglycan substrate for sortase-catalyzed surface protein anchoring

Surface proteins of Staphylococcus aureus are anchored to the cell wall peptidoglycan by a mechanism requiring a C-terminal sorting signal with an LPXTG motif. Surface proteins are first synthesized in the bacterial cytoplasm and then transported across the cytoplasmic membrane. Cleavage of the N-terminal signal peptide of the cytoplasmic surface protein P1 precursor generates the extracellular P2 species, which is the substrate for the cell wall anchoring reaction. Sortase, a membrane-anchored transpeptidase, cleaves P2 between the threonine (T) and the glycine (G) of the LPXTG motif and catalyzes the formation of an amide bond between the carboxyl group of threonine and the amino group of cell wall cross-bridges. We have used metabolic labeling of staphylococcal cultures with [32P]phosphoric acid to reveal a P3 intermediate. The 32P-label of immunoprecipitated surface protein is removed by treatment with lysostaphin, a glycyl-glycine endopeptidase that separates the cell wall anchor structure. Furthermore, the appearance of P3 is prevented in the absence of sortase or by the inhibition of cell wall synthesis. 32P-Labeled cell wall anchor species bind to nisin, an antibiotic that is known to form a complex with lipid II. Thus, it appears that the P3 intermediate represents surface protein linked to the lipid II peptidoglycan precursor. The data support a model whereby lipid II-linked polypeptides are incorporated into the growing peptidoglycan via the transpeptidation and transglycosylation reactions of cell wall synthesis, generating mature cell wall-linked surface protein

The Zero-Undetected-Error Capacity Approaches the Sperner Capacity

Ahlswede, Cai, and Zhang proved that, in the noise-free limit, the zero-undetected-error capacity is lower bounded by the Sperner capacity of the channel graph, and they conjectured equality. Here we derive an upper bound that proves the conjecture.Comment: 8 Pages; added a section on the definition of Sperner capacity; accepted for publication in the IEEE Transactions on Information Theor

A qualitative description of graphs of discontinuous polynomial functions

We prove that, if f:R^n\to R satisfies Fr\'echet's functional equation and f(x_1,...,x_n) is not an ordinary algebraic polynomial in the variables x_1,...,x_n, then f is unbounded on all non-empty open set U of R^n. Furthermore, the closure of its graph contains an unbounded open set.Comment: 9 pages, submitted to a journa

Anchoring of Surface Proteins to the Cell Wall of Staphylococcus aureus: sortase catalyzed in vitro transpeptidation reaction using LPXTG peptide and NH2-Gly3 substrates

Staphylococcus aureus sortase anchors surface proteins to the cell wall envelope by cleaving polypeptides at the LPXTG motif. Surface proteins are linked to the peptidoglycan by an amide bond between the C-terminal carboxyl and the amino group of the pentaglycine cross-bridge. We find that purified recombinant sortase hydrolyzed peptides bearing an LPXTG motif at the peptide bond between threonine and glycine. In the presence of NH2-Gly3, sortase catalyzed exclusively a transpeptidation reaction, linking the carboxyl group of threonine to the amino group of NH2-Gly3. In the presence of amino group donors the rate of sortase mediated cleavage at the LPXTG motif was increased. Hydrolysis and transpeptidation required the sulfhydryl of cysteine 184, suggesting that sortase catalyzed the transpeptidation reaction of surface protein anchoring via the formation of a thioester acyl-enzyme intermediate