Dynamic Package Interfaces - Extended Version

A hallmark of object-oriented programming is the ability to perform computation through a set of interacting objects. A common manifestation of this style is the notion of a package, which groups a set of commonly used classes together. A challenge in using a package is to ensure that a client follows the implicit protocol of the package when calling its methods. Violations of the protocol can cause a runtime error or latent invariant violations. These protocols can extend across different, potentially unboundedly many, objects, and are specified informally in the documentation. As a result, ensuring that a client does not violate the protocol is hard. We introduce dynamic package interfaces (DPI), a formalism to explicitly capture the protocol of a package. The DPI of a package is a finite set of rules that together specify how any set of interacting objects of the package can evolve through method calls and under what conditions an error can happen. We have developed a dynamic tool that automatically computes an approximation of the DPI of a package, given a set of abstraction predicates. A key property of DPI is that the unbounded number of configurations of objects of a package are summarized finitely in an abstract domain. This uses the observation that many packages behave monotonically: the semantics of a method call over a configuration does not essentially change if more objects are added to the configuration. We have exploited monotonicity and have devised heuristics to obtain succinct yet general DPIs. We have used our tool to compute DPIs for several commonly used Java packages with complex protocols, such as JDBC, HashSet, and ArrayList.Comment: The only changes compared to v1 are improvements to the Abstract and Introductio

Constrained by managerialism : caring as participation in the voluntary social services

The data in this study show that care is a connective process, underlying and motivating participation and as a force that compels involvement in the lives of others, care is at least a micro-participative process. Care or affinity not only persisted in the face of opposition, but it was also used by workers as a counter discourse and set of practices with which to resist the erosion of worker participation and open up less autonomized practices and ways of connecting with fellow staff, clients and the communities they served. The data suggest that while managerialism and taylorised practice models may remove or reduce opportunities for worker participation, care is a theme or storyline that gave workers other ways to understand their work and why they did it, as well as ways they were prepared to resist managerial priorities and directives, including the erosion of various kinds of direct and indirect participation. The degree of resistance possible, even in the highly technocratic worksite in Australia, shows that cracks and fissures exist within managerialism

Parameterized Verification of Safety Properties in Ad Hoc Network Protocols

We summarize the main results proved in recent work on the parameterized verification of safety properties for ad hoc network protocols. We consider a model in which the communication topology of a network is represented as a graph. Nodes represent states of individual processes. Adjacent nodes represent single-hop neighbors. Processes are finite state automata that communicate via selective broadcast messages. Reception of a broadcast is restricted to single-hop neighbors. For this model we consider a decision problem that can be expressed as the verification of the existence of an initial topology in which the execution of the protocol can lead to a configuration with at least one node in a certain state. The decision problem is parametric both on the size and on the form of the communication topology of the initial configurations. We draw a complete picture of the decidability and complexity boundaries of this problem according to various assumptions on the possible topologies.Comment: In Proceedings PACO 2011, arXiv:1108.145

Power management and control strategies for off-grid hybrid power systems with renewable energies and storage

This document is the Accepted Manuscript of the following article: Belkacem Belabbas, Tayeb Allaoui, Mohamed Tadjine, and Mouloud Denai, 'Power management and control strategies for off-grid hybrid power systems with renewable energies and storage', Energy Systems, September 2017. Under embargo. Embargo end date: 19 September 2018. The final publication is available at Springer via https://doi.org/10.1007/s12667-017-0251-y.This paper presents a simulation study of standalone hybrid Distributed Generation Systems (DGS) with Battery Energy Storage System (BESS). The DGS consists of Photovoltaic (PV) panels as Renewable Power Source (RPS), a Diesel Generator (DG) for power buck-up and a BESS to accommodate the surplus of energy, which may be employed in times of poor PV generation. While off-grid DGS represent an efficient and cost-effective energy supply solution particularly to rural and remote areas, fluctuations in voltage and frequency due to load variations, weather conditions (temperature, irradiation) and transmission line short-circuits are major challenges. The paper suggests a hierarchical Power Management (PM) and controller structure to improve the reliability and efficiency of the hybrid DGS. The first layer of the overall control scheme includes a Fuzzy Logic Controller (FLC) to adjust the voltage and frequency at the Point of Common Coupling (PCC) and a Clamping Bridge Circuit (CBC) which regulates the DC bus voltage. A maximum power point tracking (MPPT) controller based on FLC is designed to extract the optimum power from the PV. The second control layer coordinates among PV, DG and BESS to ensure reliable and efficient power supply to the load. MATLAB Simulink is used to implement the overall model of the off-grid DGS and to test the performance of the proposed control scheme which is evaluated in a series of simulations scenarios. The results demonstrated the good performance of the proposed control scheme and effective coordination between the DGS for all the simulation scenarios considered.Peer reviewedFinal Accepted Versio

Longitudinal characteristics of T2-FLAIR mismatch in IDH-mutant astrocytomas: Relation to grade, histopathology, and overall survival in the GLASS-NL cohort.

BACKGROUND: The T2-FLAIR mismatch sign is defined by signal loss of the T2-weighted hyperintense area with Fluid-Attenuated Inversion Recovery (FLAIR) on magnetic resonance imaging, causing a hypointense region on FLAIR. It is a highly specific diagnostic marker for IDH-mutant astrocytoma and is postulated to be caused by intercellular microcystic change in the tumor tissue. However, not all IDH-mutant astrocytomas show this mismatch sign and some show the phenomenon in only part of the lesion. The aim of the study is to determine whether the T2-FLAIR mismatch phenomenon has any prognostic value beyond initial noninvasive molecular diagnosis. METHODS: Patients initially diagnosed with histologically lower-grade (2 or 3) IDH-mutant astrocytoma and with at least 2 surgical resections were included in the GLASS-NL cohort. T2-FLAIR mismatch was determined, and the growth pattern of the recurrent tumor immediately before the second resection was annotated as invasive or expansive. The relation between the T2-FLAIR mismatch sign and tumor grade, microcystic change, overall survival (OS), and other clinical parameters was investigated both at first and second resection. RESULTS: The T2-FLAIR mismatch sign was significantly related to Grade 2 (80% vs 51%), longer post-resection median OS (8.3 vs 5.2 years), expansive growth, and lower age at second resection. At first resection, no relation was found between the mismatch sign and OS. Microcystic change was associated with areas of T2-FLAIR mismatch. CONCLUSIONS: T2-FLAIR mismatch in IDH-mutant astrocytomas is correlated with microcystic change in the tumor tissue, favorable prognosis, and Grade 2 tumors at the time of second resection

On Sets with Cardinality Constraints in Satisfiability Modulo Theories

Boolean Algebra with Presburger Arithmetic (BAPA) is a decidable logic that can express constraints on sets of elements and their cardinalities. Problems from verification of complex properties of software often contain fragments that belong to quantifier-free BAPA (QFBAPA). Deciding the satisfiability of QFBAPA formulas has been shown to be NP-complete using an eager reduction to quantifier-free Presburger arithmetic that exploits a sparse-solution property. In contrast to many other NP-complete problems (such as quantifier-free first-order logic or linear arithmetic), the applications of QFBAPA to a broader set of problems has so far been hindered by the lack of an efficient implementation that can be used alongside other efficient decision procedures. We overcome these limitations by extending the efficient SMT solver Z3 with the ability to reason about cardinality constraints. Our implementation uses the DPLL(T) mechanism of Z3 to reason about the top-level propositional structure of a QFBAPA formula, improving the efficiency compared to previous implementations. Moreover, we present a new algorithm for automated decomposition of QFBAPA formulas. Our algorithm alleviates the exponential explosion of considering all Venn regions, significantly improving the tractability of formulas with many set variables. Because it is implemented as a theory plugin, our implementation enables Z3 to prove formulas that use QFBAPA constructs alongside constructs from other theories that Z3 supports (e.g. linear arithmetic, uninterpreted function symbols, algebraic data types), as well as in formulas with quantifiers. We have applied our implementation to verification of functional programs; we show it can automatically prove formulas that no automated approach was reported to be able to prove before

Human Herpesvirus 8 Interferon Regulatory Factor-Mediated BH3-Only Protein Inhibition via Bid BH3-B Mimicry

Viral replication efficiency is in large part governed by the ability of viruses to counteract pro-apoptotic signals induced by infection of host cells. For HHV-8, viral interferon regulatory factor-1 (vIRF-1) contributes to this process in part via inhibitory interactions with BH3-only protein (BOP) Bim, recently identified as an interaction partner of vIRF-1. Here we recognize that the Bim-binding domain (BBD) of vIRF-1 resembles a region (BH3-B) of Bid, another BOP, which interacts intramolecularly with the functional BH3 domain of Bid to inhibit it pro-apoptotic activity. Indeed, vIRF-1 was found to target Bid in addition to Bim and to interact, via its BBD region, with the BH3 domain of each. In functional assays, BBD could substitute for BH3-B in the context of Bid, to suppress Bid-induced apoptosis in a BH3-binding-dependent manner, and vIRF-1 was able to protect transfected cells from apoptosis induced by Bid. While vIRF-1 can mediate nuclear sequestration of Bim, this was not the case for Bid, and inhibition of Bid and Bim by vIRF-1 could occur independently of nuclear localization of the viral protein. Consistent with this finding, direct BBD-dependent inactivation by vIRF-1 of Bid-induced mitochondrial permeabilization was demonstrable in vitro and isolated BBD sequences were also active in this assay. In addition to Bim and Bid BH3 domains, BH3s of BOPs Bik, Bmf, Hrk, and Noxa also were found to bind BBD, while those of both pro- and anti-apoptotic multi-BH domain Bcl-2 proteins were not. Finally, the significance of Bid to virus replication was demonstrated via Bid-depletion in HHV-8 infected cells, which enhanced virus production. Together, our data demonstrate and characterize BH3 targeting and associated inhibition of BOP pro-apoptotic activity by vIRF-1 via Bid BH3-B mimicry, identifying a novel mechanism of viral evasion from host cell defenses

Molecular and Functional Characterization of Human Intestinal Organoids and Monolayers for Modeling Epithelial Barrier

BACKGROUND: Patient-derived organoid (PDO) models offer potential to transform drug discovery for inflammatory bowel disease (IBD) but are limited by inconsistencies with differentiation and functional characterization. We profiled molecular and cellular features across a range of intestinal organoid models and examined differentiation and establishment of a functional epithelial barrier. METHODS: Patient-derived organoids or monolayers were generated from control or IBD patient-derived colon or ileum and were molecularly or functionally profiled. Biological or technical replicates were examined for transcriptional responses under conditions of expansion or differentiation. Cell-type composition was determined by deconvolution of cell-associated gene signatures and histological features. Differentiated control or IBD-derived monolayers were examined for establishment of transepithelial electrical resistance (TEER), loss of barrier integrity in response to a cocktail of interferon (IFN)-γ and tumor necrosis factor (TNF)-α, and prevention of cytokine-induced barrier disruption by the JAK inhibitor, tofacitinib. RESULTS: In response to differentiation media, intestinal organoids and monolayers displayed gene expression patterns consistent with maturation of epithelial cell types found in the human gut. Upon differentiation, both colon- and ileum-derived monolayers formed functional barriers, with sustained TEER. Barrier integrity was compromised by inflammatory cytokines IFN-γ and TNF-α, and damage was inhibited in a dose-dependent manner by tofacitinib. CONCLUSIONS: We describe the generation and characterization of human colonic or ileal organoid models capable of functional differentiation to mature epithelial cell types. In monolayer culture, these cells formed a robust epithelial barrier with sustained TEER and responses to pharmacological modulation. Our findings demonstrate that control and IBD patient-derived organoids possess consistent transcriptional and functional profiles that can enable development of epithelial-targeted therapies