Session-Based Programming for Parallel Algorithms: Expressiveness and Performance

This paper investigates session programming and typing of benchmark examples to compare productivity, safety and performance with other communications programming languages. Parallel algorithms are used to examine the above aspects due to their extensive use of message passing for interaction, and their increasing prominence in algorithmic research with the rising availability of hardware resources such as multicore machines and clusters. We contribute new benchmark results for SJ, an extension of Java for type-safe, binary session programming, against MPJ Express, a Java messaging system based on the MPI standard. In conclusion, we observe that (1) despite rich libraries and functionality, MPI remains a low-level API, and can suffer from commonly perceived disadvantages of explicit message passing such as deadlocks and unexpected message types, and (2) the benefits of high-level session abstraction, which has significant impact on program structure to improve readability and reliability, and session type-safety can greatly facilitate the task of communications programming whilst retaining competitive performance

Choreographies with Secure Boxes and Compromised Principals

We equip choreography-level session descriptions with a simple abstraction of a security infrastructure. Message components may be enclosed within (possibly nested) "boxes" annotated with the intended source and destination of those components. The boxes are to be implemented with cryptography. Strand spaces provide a semantics for these choreographies, in which some roles may be played by compromised principals. A skeleton is a partially ordered structure containing local behaviors (strands) executed by regular (non-compromised) principals. A skeleton is realized if it contains enough regular strands so that it could actually occur, in combination with any possible activity of compromised principals. It is delivery guaranteed (DG) realized if, in addition, every message transmitted to a regular participant is also delivered. We define a novel transition system on skeletons, in which the steps add regular strands. These steps solve tests, i.e. parts of the skeleton that could not occur without additional regular behavior. We prove three main results about the transition system. First, each minimal DG realized skeleton is reachable, using the transition system, from any skeleton it embeds. Second, if no step is possible from a skeleton A, then A is DG realized. Finally, if a DG realized B is accessible from A, then B is minimal. Thus, the transition system provides a systematic way to construct the possible behaviors of the choreography, in the presence of compromised principals

Asian Theatre as Method: The Toki Experimental Project and Sino-Japanese Transnationalism in Performance

In 2012, Zuni Icosahedron (Hong Kong), Za-Koenji (Tokyo), and the Jiangsu Kun Opera Theatre (Nanjing) initiated the Toki Experimental Project, an intercultural platform devoted to the transmission of kunqu and noh through contemporary performance. Originating from a Shanghai Expo 2010 commission, Toki presents strategic interpenetration of national discourse and “minor” transnational dynamics. Most significantly, it provides a theatrical application of Chen Kuan-hsing’s influential notion of “Asia as method”. As epitomized by the yearly One Table, Two Chairs performances at Nanjing’s Toki International Arts Festival, Toki partakes in Asia as method’s effort toward “decolonization, deimperialization, and de-cold war” through aesthetic and epistemological deconstruction, endorsing a dialogic model of intercultural performance as inter-Asian relation

Clinical and molecular epidemiological features of tuberculosis after the 2011 Japan earthquake and tsunami

OBJECTIVE : To investigate clinical characteristics and prognosis in tuberculosis (TB) patients and the transmission dynamics of TB after the 2011 Japan earthquake and tsunami. METHOD: This was a retrospective observational cohort study. Data were analyzed among 93 pulmonary TB patients (tsunami-Affected areas 25, non-Tsunami areas 68) hospitalized during March 2011-March 2012 with 1-year follow-up since treatment commencement. Variable number of tandem repeats (VNTR) typing was conducted for 38 TB strains (tsunami-Affected areas 21, non-Tsunami areas 17). RESULT S : Patients from tsunami-Affected areas were significantly more likely to be refugees (OR 12.8, 95%CI 2.45-67.20), receive oxygenation (OR 5.0, 95%CI 1.68-14.85), and have a unique VNTR (OR 4.6, 95%CI 1.14-18.41). Patients who died within 1 year were significantly more likely to be older (OR 9.8, 95%CI 1.85-180.26), partially dependent or dependent (OR 11.9, 95%CI 4.28-37.62), and to require oxygenation (OR 4.3, 95%CI 1.47-12.89), and had lower serum albumin levels (OR 11.1, 95%CI 2.97-72.32). CONCLUS ION: Risk factors for prognosis of TB after the earthquake were associated with advanced age, low serum albumin level, functional status at admission, and oxygen requirement. The VNTR results suggest that most of the cases with pulmonary TB experienced reactivation of latent tuberculous infection, likely due to the impact of the earthquake and tsunami

Identification of glycosylation genes and glycosylated amino acids of flagellin in Pseudomonas syringae pv. tabaci

A glycosylation island is a genetic region required for glycosylation. The glycosylation island of flagellin in Pseudomonas syringae pv. tabaci 6605 consists of three orfs: orf1, orf2 and orf3. Orf1 and orf2 encode putative glycosyltransferases, and their deletion mutants, Delta orf1 and Delta orf2, exhibit deficient flagellin glycosylation or produce partially glycosylated flagellin respectively. Digestion of glycosylated flagellin from wild-type bacteria and non-glycosylated flagellin from Delta orf1 mutant using aspartic N-peptidase and subsequent HPLC analysis revealed candidate glycosylated amino acids. By generation of site-directed Ser/Ala-substituted mutants, all glycosylated amino acid residues were identified at positions 143, 164, 176, 183, 193 and 201. Matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (MS) analysis revealed that each glycan was about 540 Da. While all glycosylation-defective mutants retained swimming ability, swarming ability was reduced in the Delta orf1, Delta orf2 and Ser/Ala-substituted mutants. All glycosylation mutants were also found to be impaired in the ability to adhere to a polystyrene surface and in the ability to cause disease in tobacco. Based on the predicted tertiary structure of flagellin, S176 and S183 are expected to be located on most external surface of the flagellum. Thus the effect of Ala-substitution of these serines is stronger than that of other serines. These results suggest that glycosylation of flagellin in P. syringae pv. tabaci 6605 is required for bacterial virulence. It is also possible that glycosylation of flagellin may mask elicitor function of flagellin molecule

Channels as Objects in Concurrent Object-Oriented Programming

There is often a sort of a protocol associated to each class, stating when and how certain methods should be called. Given that this protocol is, if at all, described in the documentation accompanying the class, current mainstream object-oriented languages cannot provide for the verification of client code adherence against the sought class behaviour. We have defined a class-based concurrent object-oriented language that formalises such protocols in the form of usage types. Usage types are attached to class definitions, allowing for the specification of (1) the available methods, (2) the tests clients must perform on the result of methods, and (3) the object status - linear or shared - all of which depend on the object's state. Our work extends the recent approach on modular session types by eliminating channel operations, and defining the method call as the single communication primitive in both sequential and concurrent settings. In contrast to previous works, we define a single category for objects, instead of distinct categories for linear and for shared objects, and let linear objects evolve into shared ones. We introduce a standard sync qualifier to prevent thread interference in certain operations on shared objects. We formalise the language syntax, the operational semantics, and a type system that enforces by static typing that methods are called only when available, and by a single client if so specified in the usage type. We illustrate the language via a complete example.Comment: In Proceedings PLACES 2010, arXiv:1110.385

Nationwide surveillance of bacterial respiratory pathogens conducted by the surveillance committee of Japanese Society of Chemotherapy, the Japanese Association for Infectious Diseases, and the Japanese Society for Clinical Microbiology in 2010: General view of the pathogens\u27 antibacterial susceptibility

The nationwide surveillance on antimicrobial susceptibility of bacterial respiratory pathogens from patients in Japan, was conducted by Japanese Society of Chemotherapy, Japanese Association for Infectious Diseases and Japanese Society for Clinical Microbiology in 2010.The isolates were collected from clinical specimens obtained from well-diagnosed adult patients with respiratory tract infections during the period from January and April 2010 by three societies. Antimicrobial susceptibility testing was conducted at the central reference laboratory according to the method recommended by Clinical and Laboratory Standard Institutes using maximum 45 antibacterial agents.Susceptibility testing was evaluable with 954 strains (206 Staphylococcus aureus, 189 Streptococcus pneumoniae, 4 Streptococcus pyogenes, 182 Haemophilus influenzae, 74 Moraxella catarrhalis, 139 Klebsiella pneumoniae and 160 Pseudomonas aeruginosa). Ratio of methicillin-resistant S.aureus was as high as 50.5%, and those of penicillin-intermediate and -resistant S.pneumoniae were 1.1% and 0.0%, respectively. Among H.influenzae, 17.6% of them were found to be β-lactamase-non-producing ampicillin (ABPC)-intermediately resistant, 33.5% to be β-lactamase-non-producing ABPC-resistant and 11.0% to be β-lactamase-producing ABPC-resistant strains. Extended spectrum β-lactamase-producing K.pneumoniae and multi-drug resistant P.aeruginosa with metallo β-lactamase were 2.9% and 0.6%, respectively.Continuous national surveillance of antimicrobial susceptibility of respiratory pathogens is crucial in order to monitor changing patterns of susceptibility and to be able to update treatment recommendations on a regular basis

An Interaction-based Language and its Typing System

We present a small language L and its typing system based on the idea of interaction, one of the important notions in parallel and distributed computing. L is based on, apart from such constructs as parallel composition and process creation, three pairs of communication primitives which use the notion of a session, a semantically atomic chain of communication actions which can interleave with other such chains freely, for high-level abstraction of interaction-based computing. Three primitives enable programmers to elegantly describe complex interactions among processes with a rigorous type discipline similar to ML [4]. The language is given formal operational semantics and a type inference system, regarding which we prove that if a program is well-typed in the typing system, it never causes run-time error due to type inconsistent communication patterns, offering a new foundation for type discipline in parallel programming languages. 1 Introduction The idea of interaction, that is, rec..