Applying Prolog to Develop Distributed Systems

Development of distributed systems is a difficult task. Declarative programming techniques hold a promising potential for effectively supporting programmer in this challenge. While Datalog-based languages have been actively explored for programming distributed systems, Prolog received relatively little attention in this application area so far. In this paper we present a Prolog-based programming system, called DAHL, for the declarative development of distributed systems. DAHL extends Prolog with an event-driven control mechanism and built-in networking procedures. Our experimental evaluation using a distributed hash-table data structure, a protocol for achieving Byzantine fault tolerance, and a distributed software model checker - all implemented in DAHL - indicates the viability of the approach

Quantitative Detection of Schistosoma japonicum Cercariae in Water by Real-Time PCR

In China alone, an estimated 30 million people are at risk of schistosomiasis, caused by the Schistosoma japonicum parasite. Disease has re-emerged in several regions that had previously attained transmission control, reinforcing the need for active surveillance. The environmental stage of the parasite is known to exhibit high spatial and temporal variability, and current detection techniques rely on a sentinel mouse method which has serious limitations in obtaining data in both time and space. Here we describe a real-time PCR assay to quantitatively detect S. japonicum cercariae in laboratory samples and in natural water that has been spiked with known numbers of S. japonicum. Multiple primers were designed and assessed, and the best performing set, along with a TaqMan probe, was used to quantify S. japonicum. The resulting assay was selective, with no amplification detected for Schistosoma mansoni, Schistosoma haematobium, avian schistosomes nor organisms present in non-endemic surface water samples. Repeated samples containing various concentrations of S. japonicum cercariae showed that the real-time PCR method had a strong linear correlation (R2 = 0.921) with light microscopy counts, and the detection limit was below the DNA equivalent of half of one cercaria. Various cercarial concentrations spiked in 1 liter of natural water followed by a filtration process produced positive detection from 93% of samples analyzed. The real-time PCR method performed well quantifying the relative concentrations of various spiked samples, although the absolute concentration estimates exhibited high variance across replicated samples. Overall, the method has the potential to be applied to environmental water samples to produce a rapid, reliable assay for cercarial location in endemic areas

Whole genome analysis of a schistosomiasis-transmitting freshwater snail

Biomphalaria snails are instrumental in transmission of the human blood fluke Schistosoma mansoni. With the World Health Organization's goal to eliminate schistosomiasis as a global health problem by 2025, there is now renewed emphasis on snail control. Here, we characterize the genome of Biomphalaria glabrata, a lophotrochozoan protostome, and provide timely and important information on snail biology. We describe aspects of phero-perception, stress responses, immune function and regulation of gene expression that support the persistence of B. glabrata in the field and may define this species as a suitable snail host for S. mansoni. We identify several potential targets for developing novel control measures aimed at reducing snail-mediated transmission of schistosomiasis

Corrigendum: Whole genome analysis of a schistosomiasis-transmitting freshwater snail

This corrects the article DOI: 10.1038/ncomms15451

Storage management and caching in PAST, a large-scale, persistent peer-to-peer storage utility

This paper presents and evaluates the storage management and caching in PAST, a large-scale peer-to-peer persistent storage utility. PAST is based on a self-organizing, Internetbased overlay network of storage nodes that cooperatively route file queries, store multiple replicas of files, and cache additional copies of popular files. In the PAST system, storage nodes and files are each assigned uniformly distributed identifiers, and replicas of a file are stored at nodes whose identifier matches most closely the file’s identifier. This statistical assignment of files to storage nodes approximately balances the number of files stored on each node. However, non-uniform storage node capacities and file sizes require more explicit storage load balancing to permit graceful behavior under high global storage utilization; likewise, non-uniform popularity of files requires caching to minimize fetch distance and to balance the query load. We present and evaluate PAST, with an emphasis on its storage management and caching system. Extensive tracedriven experiments show that the system minimizes fetch distance, that it balances the query load for popular files, and that it displays graceful degradation of performance as the global storage utilization increases beyond 95%

In silico analysis and developmental expression of ubiquitin-conjugating enzymes in Schistosoma mansoni.

Ubiquitin-conjugating enzymes (Ub-E2) perform the second step of ubiquitination and, consequently, are essential for regulating proteolysis and for modulating protein function, interactions and trafficking. Previously, our group demonstrated the crucial role of ubiquitination and the Ubproteasome pathway during the Schistosoma mansoni life cycle. In the present investigation, we used a homology-based genome-wide bioinformatics approach to identify and molecularly characterise the Ub-E2 enzymes in S. mansoni. The putative functions were further investigated through molecular phylogenetic and expression profile analyses using cercariae, adult worms, eggs and mechanically transformed schistosomula (MTS) cultured in vitro for 3.5 h or 1 or 3 days. We identified, via in silico analysis, 17 Ub-E2 enzymes with conserved structural characteristics: the beta-sheet and the helix-2 form a central core bordered by helix-1 at one side and helix-3 and helix-4 at the other. The observed quantitative differences in the steady-state transcript levels between the cercariae and adult worms may contribute to the differential protein ubiquitination observed during the parasite?s life cycle. This study is the first to identify and characterise the E2 ubiquitin conjugation family in S. mansoni and provides fundamental information regarding their molecular phylogenetics and developmental expression during intra-mammalian stages