Towards verification of computation orchestration

Recently, a promising programming model called Orc has been proposed to support a structured way of orchestrating distributed Web Services. Orc is intuitive because it offers concise constructors to manage concurrent communication, time-outs, priorities, failure of Web Services or communication and so forth. The semantics of Orc is precisely defined. However, there is no automatic verification tool available to verify critical properties against Orc programs. Our goal is to verify the orchestration programs (written in Orc language) which invoke web services to achieve certain goals. To investigate this problem and build useful tools, we explore in two directions. Firstly, we define a Timed Automata semantics for the Orc language, which we prove is semantically equivalent to the operational semantics of Orc. Consequently, Timed Automata models are systematically constructed from Orc programs. The practical implication is that existing tool supports for Timed Automata, e.g., Uppaal, can be used to simulate and model check Orc programs. An experimental tool has been implemented to automate this approach. Secondly, we start with encoding the operational semantics of Orc language in Constraint Logic Programming (CLP), which allows a systematic translation from Orc to CLP. Powerful constraint solvers like CLP(R) are then used to prove traditional safety properties and beyond, e.g., reachability, deadlock-freeness, lower or upper bound of a time interval, etc. Counterexamples are generated when properties are not satisfied. Furthermore, the stepwise execution traces can be automatically generated as the simulation steps. The two different approaches give an insight into the verification problem of Web Service orchestration. The Timed Automata approach has its merits in visualized simulation and efficient verification supported by the well developed tools. On the other hand, the CPL approach gives better expressiveness in both modeling and verification. The two approaches complement each other, which gives a complete solution for the simulation and verification of Computation Orchestration

Specifying and verifying sensor networks: An experiment of formal methods

10.1007/978-3-540-88194-0-20Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)5256 LNCS318-33

Reheating and Cosmic String Production

We compute the string production rate at the end of inflation, using the string spectrum obtained in \lss in a near-de Sitter space. Our result shows that highly excited strings are hardly produced, thus the simple slow-roll inflation alone does not offer a cosmic string production mechanism.Comment: 16 pages, harvmac, v2:minor change of the title v3: major change of the conclusio

Free-running 4H-SiC single-photon detector with ultralow afterpulse probability at 266 nm

Ultraviolet single-photon detector (UVSPD) provides a key tool for the applications requiring ultraweak light detection in the wavelength band. Here, we report a 4H-SiC single-photon avalanche diode (SPAD) based free-running UVSPD with ultralow afterpulse probability. We design and fabricate the 4H-SiC SPAD with a beveled mesa structure, which exhibits the characteristic of ultralow dark current. We further develop a readout circuit of passive quenching and active reset with tunable hold-off time setting to considerably suppress the afterpulsing effect. The nonuniformity of photon detection efficiency (PDE) across the SPAD active area with a diameter of $\sim$ 180 $\mu$m is investigated for performance optimization. The compact UVSPD is then characterized, exhibiting a typical performance of 10.3% PDE, 133 kcps dark count rate and 0.3% afterpulse probability at 266 nm. Such performance indicates that the compact UVSPD could be used for practical ultraviolet photon-counting applicationsComment: 5 pages, 5 figures, accepted for publication in Review of Scientific Instrument

A Hybrid Artificial Bee Colony Algorithm for Flexible Job Shop Scheduling Problems

In this paper, we propose a hybrid Pareto-based artificial bee colony (HABC) algorithm for solving the multi-objective flexible job shop scheduling problem. In the hybrid algorithm, each food sources is represented by two vectors, i.e., the machine assignment vector and the operation scheduling vector. The artificial bee is divided into three groups, namely, employed bees, onlookers, and scouts bees. Furthermore, an external Pareto archive set is introduced to record non-dominated solutions found so far. To balance the exploration and exploitation capability of the algorithm, the scout bees in the hybrid algorithm are divided into two parts. The scout bees in one part perform randomly search in the predefined region while each scout bee in another part randomly select one non-dominated solution from the Pareto archive set. Experimental results on the well-known benchmark instances and comparisons with other recently published algorithms show the efficiency and effectiveness of the proposed algorithm

Identification and characterization of microRNAs in Clonorchis sinensis of human health significance

<p>Abstract</p> <p>Background</p> <p><it>Clonorchis sinensis </it>is a zoonotic parasite causing clonorchiasis-associated human disease such as biliary calculi, cholecystitis, liver cirrhosis, and it is currently classified as carcinogenic to humans for cholangiocarcinoma. MicroRNAs (miRNAs) are non-coding, regulating small RNA molecules which are essential for the complex life cycles of parasites and are involved in parasitic infections. To identify and characterize miRNAs expressed in adult <it>C. sinensis </it>residing chronically in the biliary tract, we developed an integrative approach combining deep sequencing and bioinformatic predictions with stem-loop real-time PCR analysis.</p> <p>Results</p> <p>Here we report the use of this approach to identify and clone 6 new and 62,512 conserved <it>C. sinensis </it>miRNAs which belonged to 284 families. There was strong bias on families, family members and sequence nucleotides in <it>C. sinensis</it>. Uracil was the dominant nucleotide, particularly at positions 1, 14 and 22, which were located approximately at the beginning, middle and end of conserved miRNAs. There was no significant "seed region" at the first and ninth positions which were commonly found in human, animals and plants. Categorization of conserved miRNAs indicated that miRNAs of <it>C. sinensis </it>were still innovated and concentrated along three branches of the phylogenetic tree leading to bilaterians, insects and coelomates. There were two miRNA strategies in <it>C. sinensis </it>for its parasitic life: keeping a large category of miRNA families of different animals and keeping stringent conserved seed regions with high active innovation in other places of miRNAs mainly in the middle and the end, which were perfect for the parasite to perform its complex life style and for host changes.</p> <p>Conclusions</p> <p>The present study represented the first large scale characterization of <it>C. sinensis </it>miRNAs, which have implications for understanding the complex biology of this zoonotic parasite, as well as miRNA studies of other related species such as <it>Opisthorchis viverrini </it>and <it>Opisthorchis felineus </it>of human and animal health significance.</p

Negative thermal expansion in YbMn2Ge2 induced by the dual effect of magnetism and valence transition

AbstractNegative thermal expansion (NTE) is an intriguing property, which is generally triggered by a single NTE mechanism. In this work, an enhanced NTE (αv = −32.9 × 10−6 K−1, ΔT = 175 K) is achieved in YbMn2Ge2 intermetallic compound to be caused by a dual effect of magnetism and valence transition. In YbMn2Ge2, the Mn sublattice that forms the antiferromagnetic structure induces the magnetovolume effect, which contributes to the NTE below the Néel temperature (525 K). Concomitantly, the valence state of Yb increases from 2.40 to 2.82 in the temperature range of 300–700 K, which simultaneously causes the contraction of the unit cell volume due to smaller volume of Yb3+ than that of Yb2+. As a result, such combined effect gives rise to an enhanced NTE. The present study not only sheds light on the peculiar NTE mechanism of YbMn2Ge2, but also indicates the dual effect as a possible promising method to produce enhanced NTE materials

Kinase Suppressor of Ras 1 and Exo70 Promote Fatty Acid-Stimulated Neurotensin Secretion Through ERK1/2 Signaling

Neurotensin is a peptide hormone released from enteroendocrine cells in the small intestine in response to fat ingestion. Although the mechanisms regulating neurotensin secretion are still incompletely understood, our recent findings implicate a role for extracellular signal–regulated kinase 1 and 2 as positive regulators of free fatty acid-stimulated neurotensin secretion. Previous studies have shown that kinase suppressor of Ras 1 acts as a molecular scaffold of the Raf/MEK/extracellular signal–regulated kinase 1 and 2 kinase cascade and regulates intensity and duration of extracellular signal–regulated kinase 1 and 2 signaling. Here, we demonstrate that inhibition of kinase suppressor of Ras 1 attenuates neurotensin secretion and extracellular signal–regulated kinase 1 and 2 signaling in human endocrine cells. Conversely, we show that overexpression of kinase suppressor of Ras 1 enhances neurotensin secretion and extracellular signal–regulated kinase 1 and 2 signaling. We also show that inhibition of extracellular signal–regulated kinase 2 and exocyst complex component 70, a substrate of extracellular signal–regulated kinase 2 and mediator of secretory vesicle exocytosis, potently inhibits basal and docosahexaenoic acid-stimulated neurotensin secretion, whereas overexpression of exocyst complex component 70 enhances basal and docosahexaenoic acid-stimulated neurotensin secretion. Together, our findings demonstrate a role for kinase suppressor of Ras 1 as a positive regulator of neurotensin secretion from human endocrine cells and indicate that this effect is mediated by the extracellular signal–regulated kinase 1 and 2 signaling pathway. Moreover, we reveal a novel role for exocyst complex component 70 in regulation of neurotensin vesicle exocytosis through its interaction with the extracellular signal–regulated kinase 1 and 2 signaling pathway

Identification and Nearly Full-Length Genome Characterization of Novel Porcine Bocaviruses

The genus bocavirus includes bovine parvovirus (BPV), minute virus of canines (MVC), and a group of human bocaviruses (HBoV1-4). Using sequence-independent single primer amplification (SISPA), a novel bocavirus group was discovered with high prevalence (12.59%) in piglet stool samples. Two nearly full-length genome sequences were obtained, which were approximately 5,100 nucleotides in length. Multiple alignments revealed that they share 28.7–56.8% DNA sequence identity with other members of Parvovirinae. Phylogenetic analyses indicated their closest neighbors were members of the genus bocavirus. The new viruses had a putative non-structural NP1 protein, which was unique to bocaviruses. They were provisionally named porcine bocavirus 1 and 2 (PBoV1, PBoV2). PBoV1 and PBoV2 shared 94.2% nucleotide identity in NS1 gene sequence, suggesting that they represented two different bocavirus species. Two additional samples (6V, 7V) were amplified for 2,407 bp and 2,434 bp products, respectively, including a partial NP1 gene and the complete VP1 gene; Phylogenetic analysis indicated that 6Vand 7V grouped with PBoV1 and PBoV2 in the genus of bocavirus, but were in the separate clusters. Like other parvoviruses, PBoV1, PBoV2, 6Vand 7V also contained a putative secretory phospholipase A2 (sPLA2) motif in the VP1 unique region, with a conserved HDXXY motif in the catalytic center. The conserved motif YXGXF of the Ca2+-binding loop of sPLA2 identified in human bocavirus was also found in porcine bocavirus, which differs from the YXGXG motif carried by most other parvoviruses. The observation of PBoV and potentially other new bocavirus genus members may aid in molecular and functional characterization of the genus bocavirus