Linear LL-positive sets and their polar subspaces

In this paper, we define a Banach SNL space to be a Banach space with a certain kind of linear map from it into its dual, and we develop the theory of linear $L$-positive subsets of Banach SNL spaces with Banach SNL dual spaces. We use this theory to give simplified proofs of some recent results of Bauschke, Borwein, Wang and Yao, and also of the classical Brezis-Browder theorem.Comment: 11 pages. Notational changes since version

Toxoplasma effectors targeting host signaling and transcription

Early electron microscopy studies revealed the elaborate cellular features that define the unique adaptations of apicomplexan parasites. Among these were bulbous rhoptry (ROP) organelles and small, dense granules (GRAs), both of which are secreted during invasion of host cells. These early morphological studies were followed by the exploration of the cellular contents of these secretory organelles, revealing them to be comprised of highly divergent protein families with few conserved domains or predicted functions. In parallel, studies on host-pathogen interactions identified many host signaling pathways that were mysteriously altered by infection. It was only with the advent of forward and reverse genetic strategies that the connections between individual parasite effectors and the specific host pathways that they targeted finally became clear. The current repertoire of parasite effectors includes ROP kinases and pseudokinases that are secreted during invasion and that block host immune pathways. Similarly, many secretory GRA proteins alter host gene expression by activating host transcription factors, through modification of chromatin, or by inducing small noncoding RNAs. These effectors highlight novel mechanisms by whichhas learned to harness host signaling to favor intracellular survival and will guide future studies designed to uncover the additional complexity of this intricate host-pathogen interaction

Aspects of Discrete Breathers and New Directions

We describe results concerning the existence proofs of Discrete Breathers (DBs) in the two classes of dynamical systems with optical linear phonons and with acoustic linear phonons. A standard approach is by continuation of DBs from an anticontinuous limit. A new approach, which is purely variational, is presented. We also review some numerical results on intraband DBs in random nonlinear systems. Some non-conventional physical applications of DBs are suggested. One of them is understanding slow relaxation properties of glassy materials. Another one concerns energy focusing and transport in biomolecules by targeted energy transfer of DBs. A similar theory could be used for describing targeted charge transfer of nonlinear electrons (polarons) and, more generally, for targeted transfer of several excitations (e.g. Davydov soliton).Comment: to appear in the Proceedings of NATO Advanced Research Workshop "Nonlinearity and Disorder: Theory and Applications", Tashkent,Uzbekistan,October 1-6, 200

SQG-Differential Evolution for difficult optimization problems under a tight function evaluation budget

In the context of industrial engineering, it is important to integrate efficient computational optimization methods in the product development process. Some of the most challenging simulation-based engineering design optimization problems are characterized by: a large number of design variables, the absence of analytical gradients, highly non-linear objectives and a limited function evaluation budget. Although a huge variety of different optimization algorithms is available, the development and selection of efficient algorithms for problems with these industrial relevant characteristics, remains a challenge. In this communication, a hybrid variant of Differential Evolution (DE) is introduced which combines aspects of Stochastic Quasi-Gradient (SQG) methods within the framework of DE, in order to improve optimization efficiency on problems with the previously mentioned characteristics. The performance of the resulting derivative-free algorithm is compared with other state-of-the-art DE variants on 25 commonly used benchmark functions, under tight function evaluation budget constraints of 1000 evaluations. The experimental results indicate that the new algorithm performs excellent on the 'difficult' (high dimensional, multi-modal, inseparable) test functions. The operations used in the proposed mutation scheme, are computationally inexpensive, and can be easily implemented in existing differential evolution variants or other population-based optimization algorithms by a few lines of program code as an non-invasive optional setting. Besides the applicability of the presented algorithm by itself, the described concepts can serve as a useful and interesting addition to the algorithmic operators in the frameworks of heuristics and evolutionary optimization and computing

Transforming and evaluating electronic health record disease phenotyping algorithms using the OMOP common data model: a case study in heart failure

Objective: The aim of the study was to transform a resource of linked electronic health records (EHR) to the OMOP common data model (CDM) and evaluate the process in terms of syntactic and semantic consistency and quality when implementing disease and risk factor phenotyping algorithms. Materials and Methods: Using heart failure (HF) as an exemplar, we represented three national EHR sources (Clinical Practice Research Datalink, Hospital Episode Statistics Admitted Patient Care, Office for National Statistics) into the OMOP CDM 5.2. We compared the original and CDM HF patient population by calculating and presenting descriptive statistics of demographics, related comorbidities, and relevant clinical biomarkers. Results: We identified a cohort of 502 536 patients with the incident and prevalent HF and converted 1 099 195 384 rows of data from 216 581 914 encounters across three EHR sources to the OMOP CDM. The largest percentage (65%) of unmapped events was related to medication prescriptions in primary care. The average coverage of source vocabularies was >98% with the exception of laboratory tests recorded in primary care. The raw and transformed data were similar in terms of demographics and comorbidities with the largest difference observed being 3.78% in the prevalence of chronic obstructive pulmonary disease (COPD). Conclusion: Our study demonstrated that the OMOP CDM can successfully be applied to convert EHR linked across multiple healthcare settings and represent phenotyping algorithms spanning multiple sources. Similar to previous research, challenges mapping primary care prescriptions and laboratory measurements still persist and require further work. The use of OMOP CDM in national UK EHR is a valuable research tool that can enable large-scale reproducible observational research

A Process Framework for Designing Software Reference Architectures for Providing Tools as a Service

Product-Focused Software Process ImprovementSoftware Reference Architecture (SRA), which is a generic architecture solution for a specific type of software systems, provides foundation for the design of concrete architectures in terms of architecture design guidelines and architecture elements. The complexity and size of certain types of software systems need customized and systematic SRA design and evaluation methods. In this paper, we present a software Reference Architecture Design process Framework (RADeF) that can be used for analysis, design and evaluation of the SRA for provisioning of Tools as a Service as part of a cloud-enabled workSPACE (TSPACE). The framework is based on the state of the art results from literature and our experiences with designing software architectures for cloud-based systems. We have applied RADeF SRA design two types of TSPACE: software architecting TSPACE and software implementation TSPACE. The presented framework emphasizes on keeping the conceptual meta-model of the domain under investigation at the core of SRA design strategy and use it as a guiding tool for design, evaluation, implementation and evolution of the SRA. The framework also emphasizes to consider the nature of the tools to be provisioned and underlying cloud platforms to be used while designing SRA. The framework recommends adoption of the multi-faceted approach for evaluation of SRA and quantifiable measurement scheme to evaluate quality of the SRA. We foresee that RADeF can facilitate software architects and researchers during design, application and evaluation of a SRA and its instantiations into concrete software systems.Muhammad Aufeef Chauhan, Muhammad Ali Babar, and Christian W. Probs

Guaranteed clustering and biclustering via semidefinite programming

Identifying clusters of similar objects in data plays a significant role in a wide range of applications. As a model problem for clustering, we consider the densest k-disjoint-clique problem, whose goal is to identify the collection of k disjoint cliques of a given weighted complete graph maximizing the sum of the densities of the complete subgraphs induced by these cliques. In this paper, we establish conditions ensuring exact recovery of the densest k cliques of a given graph from the optimal solution of a particular semidefinite program. In particular, the semidefinite relaxation is exact for input graphs corresponding to data consisting of k large, distinct clusters and a smaller number of outliers. This approach also yields a semidefinite relaxation for the biclustering problem with similar recovery guarantees. Given a set of objects and a set of features exhibited by these objects, biclustering seeks to simultaneously group the objects and features according to their expression levels. This problem may be posed as partitioning the nodes of a weighted bipartite complete graph such that the sum of the densities of the resulting bipartite complete subgraphs is maximized. As in our analysis of the densest k-disjoint-clique problem, we show that the correct partition of the objects and features can be recovered from the optimal solution of a semidefinite program in the case that the given data consists of several disjoint sets of objects exhibiting similar features. Empirical evidence from numerical experiments supporting these theoretical guarantees is also provided