Verification of Invariant Properties of Business Process based on Formal Approach

Abstract-Recently, the concept of business process management (BPM) is in the spotlight and it is getting popular to design, enact and monitor a business process from the viewpoint of BPM. It often happens, however, that designed business process models often do not satisfy correctness properties such as executability, satisfiability and so on. Therefore it is necessary to check those correctness properties of a business process at its design phase. Although most of BPM systems have a functionality of simulation, it is not based on rigorous mathematical background. In this paper, we propose an approach to use formal specification in order to verify invariant properties of a business process rigorously at the design phase. Toward this goal, firstly, we define the transformation from a business process model in XML Process Definition Language (XPDL), which is one of the standard description of a process in BPM, to the model in VDM specification language (VDM-SL), which is one of popular formal specification language for software. Then we verify the invariant properties of the transformed model with VDM development support tool called VDMTools

Estimation of broad-leaved canopy growth in the urban forested area using multi-temporal airborne LiDAR datasets

Inter-annual canopy growth is one of the key indicators for assessing forest conditions, but the measurements require laborious field surveys. Up-to-date LiDAR remote sensing provides sufficient three-dimensional morphological information of the ground to monitor canopy heights on a broad scale. Thus, we attempted to use multi-temporal airborne LiDAR datasets in the estimation of vertical canopy growth, across various types of broad-leaved trees in a large urban park. The growth of broad-leaved canopies in the EXPO '70 urban forest in Osaka, Japan was assessed with 19 plots at the stand level and 39 selected trees at the individual-tree level. Airborne LiDAR campaigns repeatedly observed the park in the summers of 2004, 2008, and 2010. We acquired canopy height models (CHMs) for each year from the height values of the uppermost laser returns at every 0.5 m grid. The annual canopy growth was calculated by the differences in CHMs and validated with the annual changes in field-measured basal areas and tree heights. LiDAR estimations revealed that the average annual canopy growth from 2004 to 2010 was 0.26 ± 0.11 m m−2 yr−1 at the plot level and 0.26 ± 0.10 m m−2 yr−1 at the individual-tree level. This result showed that growing trends were consistent at different scales through 2004 to 2010 despite uncertainty in estimating short-term growth for small crown areas at the individual-tree level. This LiDAR-estimated canopy growth shows a moderate relation to field-measured increase of basal areas and average heights. The estimation uncertainties seem to result from the complex canopy structure and irregular crown shape of broad-leaved trees. Challenges still remain on how to incorporate the growth of understory trees, growth in the lateral direction, and gap dynamics inside the canopy, particularly in applying multi-temporal LiDAR datasets to the large-scale growth assessment

Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of oligo-capped cDNAs

<p>Abstract</p> <p>Background</p> <p>Apicomplexan parasites are causative agents of various diseases including malaria and have been targets of extensive genomic sequencing. We generated 5'-EST collections for six apicomplexa parasites using our full-length oligo-capping cDNA library method. To improve upon the current genome annotations, as well as to validate the importance for physical cDNA clone resources, we generated a large-scale collection of full-length cDNAs for several apicomplexa parasites.</p> <p>Results</p> <p>In this study, we used a total of 61,056 5'-end-single-pass cDNA sequences from <it>Plasmodium falciparum</it>, <it>P. vivax</it>, <it>P. yoelii</it>, <it>P. berghei</it>, <it>Cryptosporidium parvum</it>, and <it>Toxoplasma gondii</it>. We compared these partially sequenced cDNA sequences with the currently annotated gene models and observed significant inconsistencies between the two datasets. In particular, we found that on average 14% of the exons in the current gene models were not supported by any cDNA evidence, and that 16% of the current gene models may contain at least one mis-annotation and should be re-evaluated. We also identified a large number of transcripts that had been previously unidentified. For 732 cDNAs in <it>T. gondii</it>, the entire sequences were determined in order to evaluate the annotated gene models at the complete full-length transcript level. We found that 41% of the <it>T. gondii </it>gene models contained at least one inconsistency. We also identified and confirmed by RT-PCR 140 previously unidentified transcripts found in the intergenic regions of the current gene annotations. We show that the majority of these discrepancies are due to questionable predictions of one or two extra exons in the upstream or downstream regions of the genes.</p> <p>Conclusion</p> <p>Our data indicates that the current gene models are likely to still be incomplete and have much room for improvement. Our unique full-length cDNA information is especially useful for further refinement of the annotations for the genomes of apicomplexa parasites.</p

Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs

Comparasite is a database for comparative studies of transcriptomes of parasites. In this database, each data is defined by the full-length cDNAs from various apicomplexan parasites. It integrates seven individual databases, Full-Parasites, consisting of numerous full-length cDNA clones that we have produced and sequenced: 12 484 cDNA sequences from Plasmodium falciparum, 11 262 from Plasmodium yoelii, 9633 from Plasmodium vivax, 1518 from Plasmodium berghei, 7400 from Toxoplasma gondii, 5921 from Cryptosporidium parvum and 10 966 from the tapeworm Echinococcus multilocularis. Putatively counterpart gene groups are clustered and comparative analysis of any combination of six apicomplexa species is implemented, such as interspecies comparisons regarding protein motifs (InterPro), predicted subcellular localization signals (PSORT), transmembrane regions (SOSUI) or upstream promoter elements. By specifying keywords and other search conditions, Comparasite retrieves putative counterpart gene groups containing a given feature in common or in a species-specific manner. By enabling multi-faceted comparative analyses of genes of apicomplexa protozoa, monophyletic organisms that have evolved to diversify to parasitize various hosts by adopting complex life cycles, Comparasite should help elucidate the mechanism behind parasitism. Our full-length cDNA databases and Comparasite are accessible from

Tricellulin constitutes a novel barrier at tricellular contacts of epithelial cells

For epithelia to function as barriers, the intercellular space must be sealed. Sealing two adjacent cells at bicellular tight junctions (bTJs) is well described with the discovery of the claudins. Yet, there are still barrier weak points at tricellular contacts, where three cells join together. In this study, we identify tricellulin, the first integral membrane protein that is concentrated at the vertically oriented TJ strands of tricellular contacts. When tricellulin expression was suppressed with RNA interference, the epithelial barrier was compromised, and tricellular contacts and bTJs were disorganized. These findings indicate the critical function of tricellulin for formation of the epithelial barrier

Colorectal Carcinoma with Extremely Low CA19-9

Aim. The aim of this study is to determine the significance of postoperative sequential measurements of serum CA19-9 in patients with extremely low serum level. Patients and Methods. Serum level of CA19-9 of 1096 patients who underwent surgery was measured preoperatively and every three months after surgery for 5 years. Patients with CA19-9 level of less than 2 U/mL at the time of diagnosis were defined as Extremely Low CA19-9 (ELCA). Results. One hundred and seven patients (9.8%) were ELCA. Of these, 86 underwent surgery with curative intent. Serum levels of CA19-9 in patients who did not undergo curative resection (N = 12) and who developed recurrence (N = 10) were less than 2.0 U/mL in all occasions during followup. In all patients without recurrence, serum level of CA19-9 also remained less than 2.0 U/mL. Conclusion. In patients with extremely low CA19-9, who consist of 9.8% of colorectal carcinoma cases, postoperative sequential measurement of serum level of CA19-9 contributed neither to assessment of curability of surgical resection nor to detection of recurrence