Correcting errors and erasures via the syndrome variety

AbstractWe propose a new syndrome variety, which can be used to decode cyclic codes. We present also a generalization to erasure and error decoding. We can exhibit a polynomial whose roots give the error locations, once it has been specialized to a given syndrome. This polynomial has degree t in the variable corresponding to the error locations and its coefficients are polynomials in the syndromes

BlaSTorage: a fast package to parse, manage and store BLAST results

Background: Large-scale sequence studies requiring BLAST-based analysis produce huge amounts of data to be parsed. BLAST parsers are available, but they are often missing some important features, such as keeping all information from the raw BLAST output, allowing direct access to single results, and performing logical operations over them. Findings: We implemented BlaSTorage, a Python package that parses multi BLAST results and returns them in a purpose-built object-database format. Unlike other BLAST parsers, BlaSTorage retains and stores all parts of BLAST results, including alignments, without loss of information; a complete API allows access to all the data components. Conclusions: BlaSTorage shows comparable speed of more basic parser written in compiled languages as C++ and can be easily integrated into web applications or software pipelines.Pubblicat

How to drive passenger airport experience: A decision support system based on user profile

This work presents a decision support system for providing information and suggestions to airport users. The aim of the study is to design a system both to improve passengers\u2019 experience by reducing time spent queueing and waiting, and to raise airport revenues by increasing the time passengers spend in discretionary activities. Passengers\u2019 behaviour is modelled with an activity-choice model to be calibrated with their mobile phone traces. The model allows to predict activity sequences for passengers with given socio-demographic characteristics. In order to predict queue length at check-in desks and security control and congestion inside commercial areas, passengers\u2019 movements are simulated with a microscopic simulation tool. A system to generate suggestion has been designed: passengers are advised to perform mandatory activities when the predicted queue length is reasonable and specific discretionary activities according to time available, user profiles, location distance, location congestion and airport management preferences. A proof-of-concept case study has been developed: passengers\u2019 behaviour in both cases of receiving and not receiving suggestion has been simulated. In the first case, passengers experienced less queueing and waiting time; the time saved was spent in discretionary activities, improving passengers\u2019 airport experience and increasing airport revenues

Splice-mediated Variants of Proteins (SpliVaP) – data and characterization of changes in signatures among protein isoforms due to alternative splicing

<p>Abstract</p> <p>Background</p> <p>It is often the case that mammalian genes are alternatively spliced; the resulting alternate transcripts often encode protein isoforms that differ in amino acid sequences. Changes among the protein isoforms can alter the cellular properties of proteins. The effect can range from a subtle modulation to a complete loss of function.</p> <p>Results</p> <p>(i) We examined human splice-mediated protein isoforms (as extracted from a manually curated data set, and from a computationally predicted data set) for differences in the annotation for protein signatures (Pfam domains and PRINTS fingerprints) and we characterized the differences & their effects on protein functionalities. An important question addressed relates to the extent of protein isoforms that may lack any known function in the cell. (ii) We present a database that reports differences in protein signatures among human splice-mediated protein isoform sequences.</p> <p>Conclusion</p> <p>(i) Characterization: The work points to distinct sets of alternatively spliced genes with varying degrees of annotation for the splice-mediated protein isoforms. Protein molecular functions seen to be often affected are those that relate to: binding, catalytic, transcription regulation, structural molecule, transporter, motor, and antioxidant; and the processes that are often affected are nucleic acid binding, signal transduction, and protein-protein interactions. Signatures are often included/excluded and truncated in length among protein isoforms; truncation is seen as the predominant type of change. Analysis points to the following novel aspects: (a) Analysis using data from the manually curated Vega indicates that one in 8.9 genes can lead to a protein isoform of no "known" function; and one in 18 expressed protein isoforms can be such an "orphan" isoform; the corresponding numbers as seen with computationally predicted ASD data set are: one in 4.9 genes and one in 9.8 isoforms. (b) When swapping of signatures occurs, it is often between those of same functional classifications. (c) Pfam domains can occur in varying lengths, and PRINTS fingerprints can occur with varying number of constituent motifs among isoforms – since such a variation is seen in large number of genes, it could be a general mechanism to modulate protein function. (ii) Data: The reported resource (at <url>http://www.bioinformatica.crs4.org/tools/dbs/splivap/</url>) provides the community ability to access data on splice-mediated protein isoforms (with value-added annotation such as association with diseases) through changes in protein signatures.</p

On the Shape of the General Error Locator Polynomial for Cyclic Codes

General error locator polynomials were introduced in 2005 as an alternative decoding for cyclic codes. We now present a conjecture on their sparsity, which would imply polynomial-time decoding for all cyclic codes. A general result on the explicit form of the general error locator polynomial for all cyclic codes is given, along with several results for specific code families, providing evidence to our conjecture. From these, a theoretical justification of the sparsity of general error locator polynomials is obtained for all binary cyclic codes with t <= 2 and n < 105, as well as for t = 3 and n < 63, except for some cases where the conjectured sparsity is proved by a computer check. Moreover, we summarize all related results, previously published, and we show how they provide further evidence to our conjecture. Finally, we discuss the link between our conjecture and the complexity of bounded-distance decoding of the cyclic codes

Gap-acceptance behavior at roundabouts: validation of a driving simulator environment using field observations

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freeway rear end collision risk estimation with extreme value theory approach a case study

Abstract The current practice in crash-based safety analysis is hindered by some weaknesses: rarity of crashes, lack of timeliness, mistakes in crash reporting. Researchers are testing alternative approaches to safety estimation without the need of crash data. This paper presents an application of Extreme Value Theory in road safety analysis, using Time-To-Collision as a surrogate safety measure to estimate the risk to be involved in a freeway rear-end collision. The method was tested using data from an Italian toll-road with good results