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

Strong stability in the Hospitals/Residents problem

We study a version of the well-known Hospitals/Residents problem in which participants' preferences may involve ties or other forms of indifference. In this context, we investigate the concept of strong stability, arguing that this may be the most appropriate and desirable form of stability in many practical situations. When the indifference is in the form of ties, we describe an O(a^2) algorithm to find a strongly stable matching, if one exists, where a is the number of mutually acceptable resident-hospital pairs. We also show a lower bound in this case in terms of the complexity of determining whether a bipartite graph contains a perfect matching. By way of contrast, we prove that it becomes NP-complete to determine whether a strongly stable matching exists if the preferences are allowed to be arbitrary partial orders

Bourn-normal monomorphisms in regular Mal'tsev categories

Normal monomorphisms in the sense of Bourn describe the equivalence classes of an internal equivalence relation. Although the definition is given in the fairly general setting of a category with finite limits, later investigations on this subject often focus on protomodular settings, where normality becomes a property. This paper clarifies the connections between internal equivalence relations and Bourn-normal monomorphisms in regular Mal'tesv categories with pushouts of split monomorphisms along arbitrary morphisms, whereas a full description is achieved for quasi-pointed regular Mal'tsev categories with pushouts of split monomorphisms along arbitrary morphisms.Comment: This vesion fixes one error present in the last section of the previous versio

Traces on ideals in pivotal categories

We extend the notion of an ambidextrous trace on an ideal (developed by the first two authors) to the setting of a pivotal category. We show that under some conditions, these traces lead to invariants of colored spherical graphs (and so to modified 6j-symbols)

A generic Hopf algebra for quantum statistical mechanics

In this paper, we present a Hopf algebra description of a bosonic quantum model, using the elementary combinatorial elements of Bell and Stirling numbers. Our objective in doing this is as follows. Recent studies have revealed that perturbative quantum field theory (pQFT) displays an astonishing interplay between analysis (Riemann zeta functions), topology (Knot theory), combinatorial graph theory (Feynman diagrams) and algebra (Hopf structure). Since pQFT is an inherently complicated study, so far not exactly solvable and replete with divergences, the essential simplicity of the relationships between these areas can be somewhat obscured. The intention here is to display some of the above-mentioned structures in the context of a simple bosonic quantum theory, i.e. a quantum theory of non-commuting operators that do not depend on space-time. The combinatorial properties of these boson creation and annihilation operators, which is our chosen example, may be described by graphs, analogous to the Feynman diagrams of pQFT, which we show possess a Hopf algebra structure. Our approach is based on the quantum canonical partition function for a boson gas.Comment: 8 pages/(4 pages published version), 1 Figure. arXiv admin note: text overlap with arXiv:1011.052

Novel actions of next-generation taxanes benefit advanced stages of prostate cancer.

PURPOSE: To improve the outcomes of patients with castration-resistant prostate cancer (CRPC), there is an urgent need for more effective therapies and approaches that individualize specific treatments for patients with CRPC. These studies compared the novel taxane cabazitaxel with the previous generation docetaxel, and aimed to determine which tumors are most likely to respond. EXPERIMENTAL DESIGN: Cabazitaxel and docetaxel were compared via in vitro modeling to determine the molecular mechanism, biochemical and cell biologic impact, and cell proliferation, which was further assessed ex vivo in human tumor explants. Isogenic pairs of RB knockdown and control cells were interrogated in vitro and in xenograft tumors for cabazitaxel response. RESULTS: The data herein show that (i) cabazitaxel exerts stronger cytostatic and cytotoxic response compared with docetaxel, especially in CRPC; (ii) cabazitaxel induces aberrant mitosis, leading to pyknotic and multinucleated cells; (iii) taxanes do not act through the androgen receptor (AR); (iv) gene-expression profiling reveals distinct molecular actions for cabazitaxel; and (v) tumors that have progressed to castration resistance via loss of RB show enhanced sensitivity to cabazitaxel. CONCLUSIONS: Cabazitaxel not only induces improved cytostatic and cytotoxic effects, but also affects distinct molecular pathways, compared with docetaxel, which could underlie its efficacy after docetaxel treatment has failed in patients with CRPC. Finally, RB is identified as the first potential biomarker that could define the therapeutic response to taxanes in metastatic CRPC. This would suggest that loss of RB function induces sensitization to taxanes, which could benefit up to 50% of CRPC cases