Specifying and Verifying Concurrent Algorithms with Histories and Subjectivity

We present a lightweight approach to Hoare-style specifications for fine-grained concurrency, based on a notion of time-stamped histories that abstractly capture atomic changes in the program state. Our key observation is that histories form a partial commutative monoid, a structure fundamental for representation of concurrent resources. This insight provides us with a unifying mechanism that allows us to treat histories just like heaps in separation logic. For example, both are subject to the same assertion logic and inference rules (e.g., the frame rule). Moreover, the notion of ownership transfer, which usually applies to heaps, has an equivalent in histories. It can be used to formally represent helping---an important design pattern for concurrent algorithms whereby one thread can execute code on behalf of another. Specifications in terms of histories naturally abstract granularity, in the sense that sophisticated fine-grained algorithms can be given the same specifications as their simplified coarse-grained counterparts, making them equally convenient for client-side reasoning. We illustrate our approach on a number of examples and validate all of them in Coq.Comment: 17 page

Post Activation Potentiation of Back Squat and Trap Bar Deadlift on Acute Sprint Performance

Please refer to the pdf version of the abstract located adjacent to the title

On the Semantics of Snapshot Isolation

Snapshot isolation (SI) is a standard transactional consistency model used in databases, distributed systems and software transactional memory (STM). Its semantics is formally defined both declaratively as an acyclicity axiom, and operationally as a concurrent algorithm with memory bearing timestamps. We develop two simpler equivalent operational definitions of SI as lock-based reference implementations that do not use timestamps. Our first locking implementation is prescient in that requires a priori knowledge of the data accessed by a transaction and carries out transactional writes eagerly (in-place). Our second implementation is non-prescient and performs transactional writes lazily by recording them in a local log and propagating them to memory at commit time. Whilst our first implementation is simpler and may be better suited for developing a program logic for SI transactions, our second implementation is more practical due to its non-prescience. We show that both implementations are sound and complete against the declarative SI specification and thus yield equivalent operational definitions for SI. We further consider, for the first time formally, the use of SI in a context with racy non-transactional accesses, as can arise in STM implementations of SI. We introduce robust snapshot isolation (RSI), an adaptation of SI with similar semantics and guarantees in this mixed setting. We present a declarative specification of RSI as an acyclicity axiom and analogously develop two operational models as lock-based reference implementations (one eager, one lazy). We show that these operational models are both sound and complete against the declarative RSI model

The Agile Alert System For Gamma-Ray Transients

In recent years, a new generation of space missions offered great opportunities of discovery in high-energy astrophysics. In this article we focus on the scientific operations of the Gamma-Ray Imaging Detector (GRID) onboard the AGILE space mission. The AGILE-GRID, sensitive in the energy range of 30 MeV-30 GeV, has detected many gamma-ray transients of galactic and extragalactic origins. This work presents the AGILE innovative approach to fast gamma-ray transient detection, which is a challenging task and a crucial part of the AGILE scientific program. The goals are to describe: (1) the AGILE Gamma-Ray Alert System, (2) a new algorithm for blind search identification of transients within a short processing time, (3) the AGILE procedure for gamma-ray transient alert management, and (4) the likelihood of ratio tests that are necessary to evaluate the post-trial statistical significance of the results. Special algorithms and an optimized sequence of tasks are necessary to reach our goal. Data are automatically analyzed at every orbital downlink by an alert pipeline operating on different timescales. As proper flux thresholds are exceeded, alerts are automatically generated and sent as SMS messages to cellular telephones, e-mails, and push notifications of an application for smartphones and tablets. These alerts are crosschecked with the results of two pipelines, and a manual analysis is performed. Being a small scientific-class mission, AGILE is characterized by optimization of both scientific analysis and ground-segment resources. The system is capable of generating alerts within two to three hours of a data downlink, an unprecedented reaction time in gamma-ray astrophysics.Comment: 34 pages, 9 figures, 5 table

Formal Model Engineering for Embedded Systems Using Real-Time Maude

This paper motivates why Real-Time Maude should be well suited to provide a formal semantics and formal analysis capabilities to modeling languages for embedded systems. One can then use the code generation facilities of the tools for the modeling languages to automatically synthesize Real-Time Maude verification models from design models, enabling a formal model engineering process that combines the convenience of modeling using an informal but intuitive modeling language with formal verification. We give a brief overview six fairly different modeling formalisms for which Real-Time Maude has provided the formal semantics and (possibly) formal analysis. These models include behavioral subsets of the avionics modeling standard AADL, Ptolemy II discrete-event models, two EMF-based timed model transformation systems, and a modeling language for handset software.Comment: In Proceedings AMMSE 2011, arXiv:1106.596

Telomere lengths in human oocytes, cleavage stage embryos and blastocysts

Telomeres are repeated sequences that protect the ends of chromosomes and harbour DNA-repair proteins. Telomeres shorten during each cell division in the absence of telomerase. When telomere length becomes critically short, cell senescence occurs. Telomere length therefore reflects both cellular ageing and capacity for division. We have measured telomere length in human germinal vesicle (GV) oocytes and pre-implantation embryos, by quantitative fluorescence in-situ hybridisation (Q-FISH), providing baseline data towards our hypothesis that telomere length is a marker of embryo quality. The numbers of fluorescent foci suggest that extensive clustering of telomeres occurs in mature GV stage oocytes, and in pre-implantation embryos. When calculating average telomere length by assuming that each signal presents one telomere, the calculated telomere length decreased from the oocyte to the cleavage stages, and increased between the cleavage stages and the blastocyst (11.12 vs 8.43 vs 12.22kb respectively, p<0.001). Other methods of calculation, based upon expected maximum and minimum numbers of telomeres, confirm that telomere length in blastocysts is significantly longer than cleavage stages. Individual blastomeres within an embryo showed substantial variation in calculated average telomere length. This study implies that telomere length changes according to the stage of pre-implantation embryo development

DNA replication stress mediates APOBEC3 family mutagenesis in breast cancer

BACKGROUND: The APOBEC3 family of cytidine deaminases mutate the cancer genome in a range of cancer types. Although many studies have documented the downstream effects of APOBEC3 activity through next-generation sequencing, less is known about their upstream regulation. In this study, we sought to identify a molecular basis for APOBEC3 expression and activation. RESULTS: HER2 amplification and PTEN loss promote DNA replication stress and APOBEC3B activity in vitro and correlate with APOBEC3 mutagenesis in vivo. HER2-enriched breast carcinomas display evidence of elevated levels of replication stress-associated DNA damage in vivo. Chemical and cytotoxic induction of replication stress, through aphidicolin, gemcitabine, camptothecin or hydroxyurea exposure, activates transcription of APOBEC3B via an ATR/Chk1-dependent pathway in vitro. APOBEC3B activation can be attenuated through repression of oncogenic signalling, small molecule inhibition of receptor tyrosine kinase signalling and alleviation of replication stress through nucleoside supplementation. CONCLUSION: These data link oncogene, loss of tumour suppressor gene and drug-induced replication stress with APOBEC3B activity, providing new insights into how cytidine deaminase-induced mutagenesis might be activated in tumourigenesis and limited therapeutically

Desaturases : structural and mechanistic insights into the biosynthesis of unsaturated fatty acids

This review highlights the key role of fatty acid desaturases in the synthesis of naturally occurring, more common and not, unsaturated fatty acids. The three major classes of fatty acid desaturases, such as acyl-lipid, acyl-acyl carrier protein and acyl-coenzyme A (CoA), are described in details, with particular attention to the cellular localisation, the structure, the substrate and products specificity, and the expression and regulation of desaturases' genes. The review also gives an insight into the biocatalytic reaction of fatty acid desaturation by covering the general and the more class-specific mechanistic studies around the synthesis of unsaturated fatty acids Finally, we conclude the review looking at the numerous novel applications for desaturases in order to meet a very high demand for polyunsaturated fatty acids, taking into account the opportunity for the development of new, more efficient, easily reproducible, sustainable bioengineering advances in the field.Publisher PDFPeer reviewe

Enhancing low-rank solutions in semidefinite relaxations of Boolean quadratic problems

Boolean quadratic optimization problems occur in a number of applications. Their mixed integer-continuous nature is challenging, since it is inherently NP-hard. For this motivation, semidefinite programming relaxations (SDR's) are proposed in the literature to approximate the solution, which recasts the problem into convex optimization. Nevertheless, SDR's do not guarantee the extraction of the correct binary minimizer. In this paper, we present a novel approach to enhance the binary solution recovery. The key of the proposed method is the exploitation of known information on the eigenvalues of the desired solution. As the proposed approach yields a non-convex program, we develop and analyze an iterative descent strategy, whose practical effectiveness is shown via numerical results

Sparse linear regression from perturbed data

The problem of sparse linear regression is relevant in the context of linear system identification from large datasets. When data are collected from real-world experiments, measurements are always affected by perturbations or low-precision representations. However, the problem of sparse linear regression from fully-perturbed data is scarcely studied in the literature, due to its mathematical complexity. In this paper, we show that, by assuming bounded perturbations, this problem can be tackled by solving low-complex l2 and l1 minimization problems. Both theoretical guarantees and numerical results are illustrated in the paper