From Sequential Layers to Distributed Processes, Deriving a minimum weight spanning tree algorithm

Analysis and design of distributed algorithms and protocols are difficult issues. An important cause for those difficulties is the fact that the logical structure of the solution is often invisible in the actual implementation. We introduce a framework that allows for a formal treatment of the design process, from an abstract initial design to an implementation tailored to specific architectures. A combination of algebraic and axiomatic techniques is used to verify correctness of the derivation steps. This is shown by deriving an implementation of a distributed minimum weight spanning tree algorithm in the style of [GHS]

Vision and Valuation of a Citizen-Centric Shared Information Portal

The administrative burden the government puts on citizens is substantial, whereas, generally speaking, service levels are low and a ‘customer’ orientation is lacking. There is a growing understanding that e-government can play an important role in tackling these issues by better exchange of information and electronic availability. This paper reports on the development and evaluation of an e-government vision as part of a strategic planning trajectory for the social security sector and other government agencies in the Netherlands. The vision approaches governmental service delivery from the citizen viewpoint and helps governmental organisations to take service- and citizen orientation to a higher level. The concepts used in the vision were tested by boardroom sessions as well as a survey, and has become the guiding principles for a number of e-government developments

Maak het waar(d) : elektronisch informatieverkeer voor kleinere spelers in de keten

Kleine partijen - MKB-ers en consumenten - spelen vaak een sleutelrol in het realiseren van nieuwe concepten voor\ud elektronische communicatie in ketens en netwerken. Juist bij deze kleinere, en vaak talrijke, partijen spelen echter allerlei\ud obstakels die adoptie bemoeilijken

Business model metrics: an open repository

Development of successful business models has become a necessity in turbulent business environments, but compared to research on business modeling tools, attention to the role of metrics in designing business models in literature is limited. Building on existing approaches to business models and performance measurement literature, we develop a generic open repository of metrics related to core business model concepts. We validate and assess the practical value of the repository based on four e-Business model cases. The repository can be utilized in designing business models, specifically for networked enterprises. It is neither complete nor universally applicable, but needs adjustment with each design. Ultimately, with this paper, we hope measurement will become an integral part of the business model innovation discussion.</p

A Procedure for Splitting Processes and its Application to Coordination

We present a procedure for splitting processes in a process algebra with multi-actions (a subset of the specification language mCRL2). This splitting procedure cuts a process into two processes along a set of actions A: roughly, one of these processes contains no actions from A, while the other process contains only actions from A. We state and prove a theorem asserting that the parallel composition of these two processes equals the original process under appropriate synchronization. We apply our splitting procedure to the process algebraic semantics of the coordination language Reo: using this procedure and its related theorem, we formally establish the soundness of splitting Reo connectors along the boundaries of their (a)synchronous regions in implementations of Reo. Such splitting can significantly improve the performance of connectors.Comment: In Proceedings FOCLASA 2012, arXiv:1208.432

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment