Representations of Circular Words

In this article we give two different ways of representations of circular words. Representations with tuples are intended as a compact notation, while representations with trees give a way to easily process all conjugates of a word. The latter form can also be used as a graphical representation of periodic properties of finite (in some cases, infinite) words. We also define iterative representations which can be seen as an encoding utilizing the flexible properties of circular words. Every word over the two letter alphabet can be constructed starting from ab by applying the fractional power and the cyclic shift operators one after the other, iteratively.Comment: In Proceedings AFL 2014, arXiv:1405.527

MisPred: a resource for identification of erroneous protein sequences in public databases

Correct prediction of the structure of protein-coding genes of higher eukaryotes is still a difficult task; therefore, public databases are heavily contaminated with mispredicted sequences. The high rate of misprediction has serious consequences because it significantly affects the conclusions that may be drawn from genome-scale sequence analyses of eukaryotic genomes. Here we present the MisPred database and computational pipeline that provide efficient means for the identification of erroneous sequences in public databases. The MisPred database contains a collection of abnormal, incomplete and mispredicted protein sequences from 19 metazoan species identified as erroneous by MisPred quality control tools in the UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, NCBI/RefSeq and EnsEMBL databases. Major releases of the database are automatically generated and updated regularly. The database (http://www.mispred.com) is easily accessible through a simple web interface coupled to a powerful query engine and a standard web service. The content is completely or partially downloadable in a variety of formats

Selection criteria for preoperative endoscopic retrograde cholangiopancreatography before laparoscopic cholecystectomy and endoscopic treatment of bile duct stones. Results of a retrospective; single center study between 1996-2002

AIM: The optimal treatment for bile duct stones (in terms of cost, complications and accuracy) is unclear. The aim of our study was to determine the predictive factors for preoperative endoscopic retrograde cholangiopancreatography (ERCP). METHODS: Patients undergoing preoperative ERCP (= 8 mm) and/or stone at US examination, coexisting acute pancreatitis and/or acute pancreatitis or jaundice in patient's history. Suspected prognostic factors and the combination of factors were compared to the result of ERCP. RESULTS: Two hundred and six preoperative ERCPs were performed during the observed period. The rate of successful cannulation for ERC was (97.1%). Bile duct stones were detected in 81 patients (39.3%), and successfully removed in 79 (97.5%). The number of prognostic factors correlated with the presence of bile duct stones. The positive predictive value for one prognostic factor was 1.2%, for two 43%, for three 72.5%, for four or more 91.4%. CONCLUSION: Based on our data preoperative ERCP is highly recommended in patients with three or more positive factors (high risk patients). In contrast, ERCP is not indicated in patients with zero or one factor (low risk patients). Preoperative ERCP should be offered to patients with two positive factors (moderate risk patients), however the practice should also be based on the local conditions (e.g. skill of the endoscopist, other diagnostic tools)

Estimating Dike Breach Length from Historical Data

Flood fighting activity in preceding centuries and systematic research conducted since 1995 have produced a collection of more than 2200 historical data regarding dike failures in the Carpathian Basin. Despite the gaps in and the frequent errors of historical data, the high number of dike breaches facilitates statistical processing and the evaluation of the results allows us to draw interesting conclusions and lessons for future generations, for instance regarding the length of levee breaches. The effect of human intervention is easy to trace in the system of flood control on the basis of the changing number and length of levee breaches