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Computing the distance distribution of systematic non-linear codes [article]

Eleonora Guerrini, Emmanuela Orsini, Massimiliano Sala
2009 arXiv   pre-print
The most important families of non-linear codes are systematic. A brute-force check is the only known method to compute their weight distribution and distance distribution. On the other hand, it outputs also all closest word pairs in the code. In the black-box complexity model, the check is optimal among closest-pair algorithms. In this paper we provide a Groebner basis technique to compute the weight/distance distribution of any systematic non-linear code. Also our technique outputs all
more » ... pairs. Unlike the check, our method can be extended to work on code families.
arXiv:0909.1626v1 fatcat:tiqm5xzc35dexn4tn2wjyhjziy

Putative human sperm Interactome: a networks study

Alessandra Ordinelli, Nicola Bernabò, Massimiliano Orsini, Mauro Mattioli, Barbara Barboni
2018 BMC Systems Biology  
For over sixty years, it has been known that mammalian spermatozoa immediately after ejaculation are virtually infertile. They became able to fertilize only after they reside for long time (hours to days) within female genital tract where they complete their functional maturation, the capacitation. This process is finely regulated by the interaction with the female environment and involves, in spermatozoa, a myriad of molecules as messengers and target of signals. Since, to date, a model able
more » ... represent the molecular interaction that characterize sperm physiology does not exist, we realized the Human Sperm Interactme Network3.0 (HSIN3.0) and its main component (HSNI3.0_MC), starting from the pathway active in male germ cells. Results: HSIN3.0 and HSIN3.0_MC are scale free networks, adherent to the Barabasi-Albert model, and are characterised by an ultra-small world topology. We found that they are resistant to random attacks and that are designed to respond quickly and specifically to external inputs. In addition, it has been possible to identify the most connected nodes (the hubs) and the bottlenecks nodes. This result allowed us to explore the control mechanisms active in driving sperm biochemical machinery and to verify the different levels of controls: party vs. date hubs and hubs vs. bottlenecks, thanks the availability of data from KO mice. Finally, we found that several key nodes represent molecules specifically involved in function that are thought to be not present or not active in sperm cells, such as control of cell cycle, proteins synthesis, nuclear trafficking, and immune response, thus potentially open new perspectives on the study of sperm biology. Conclusions: For the first time we present a network representing putative human sperm interactome. This result gives very intriguing biological information and could contribute to the knowledge of spermatozoa, either in physiological or pathological conditions.
doi:10.1186/s12918-018-0578-6 pmid:29642908 pmcid:PMC5896140 fatcat:cnr7r27bybdurjllnbye2msewq

Advanced Research Infrastructure for Experimentation in genomicS (ARIES): a lustrum of Galaxy experience [article]

Arnold Knijn, Valeria Michelacci, Massimiliano Orsini, Stefano Morabito
2020 bioRxiv   pre-print
With the introduction of Next Generation Sequencing (NGS) and Whole-Genome Sequencing (WGS) in microbiology and molecular epidemiology, the development of an information system for the collection of genomic and epidemiological data and subsequent transparent and reproducible data analysis became indispensable. Further requirements for the system included accessibility and ease of use by bioinformatics as well as command line profane scientists. Findings: The ARIES (Advanced Research
more » ... re for Experimentation in genomicS, https://aries.iss.it) platform has been implemented in 2015 as an instance of the Galaxy framework specific for use of WGS in molecular epidemiology. Here, the experience with ARIES is reported. Conclusions: During its five years existence, ARIES has grown into a well-established reality not only as a web service but as well as a workflow engine for the Integrated Rapid Infectious Disease Analysis (IRIDA) platform. In fact, an environment has been created with the implementation of complex bioinformatic tools in an easy-to-use context allowing scientists to concentrate on what to do instead of how to do it.
doi:10.1101/2020.05.14.095901 fatcat:o7omjbqi5vdtrfgfmpk6wcupfi

An automatic method for identifying surface proteins in bacteria: SLEP

Emanuela Giombini, Massimiliano Orsini, Danilo Carrabino, Anna Tramontano
2010 BMC Bioinformatics  
Bacterial infections represent a global health challenge. The identification of novel antibacterial targets for both therapy and vaccination is needed on a constant basis because resistance continues to spread worldwide at an alarming rate. Even infections that were once easy to treat are becoming difficult or, in some cases, impossible to cure. Ideal targets for both therapy and vaccination are bacterial proteins exposed on the surface of the organism, which are often involved in host-pathogen
more » ... interaction. Their identification can greatly benefit from technologies such as bioinformatics, proteomics and DNA microarrays. Results: Here we describe a pipeline named SLEP (Surface Localization Extracellular Proteins), based on an automated optimal combination and sequence of usage of reliable available tools for the computational identification of the surfome, i.e. of the subset of proteins exposed on the surface of a bacterial cell. Conclusions: The tool not only simplifies the usage of these methods, but it also improves the results by selecting the specifying order and combination of the instruments. The tool is freely available at
doi:10.1186/1471-2105-11-39 pmid:20089159 pmcid:PMC2832898 fatcat:5v2bcxbn3fdxfjlcaxqqfvbkma

Correcting errors and erasures via the syndrome variety

Emmanuela Orsini, Massimiliano Sala
2005 Journal of Pure and Applied Algebra  
We 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. Observe that I = I X I XW I XW Z I XW ZU I XW ZU Y and that G = G X G XW G XW Z G XW ZU G XW ZU Y (
more » ... s disjoint union). Remark 2.6. We extend our notation to the case = 0, meaning that the variable sets W and U are void, e.g. P XW Z = P XZ = F q [X, Z]\F q [X]. When convenient, we enclose the ideal name within brackets, e.g. (I ) X = I X . Assume G is a Gröbner basis for an ideal I ⊂ K[S, Z, T ], S = (s 1 , . . . , s H ), Z = (z 1 , . . . , z L ), T = (t 1 , . . . , t M ) w.r.t. a block order with S < Z < T and with the Z-variables
doi:10.1016/j.jpaa.2004.12.027 fatcat:rqwepmil2vafdopuxxxlw24tva

COMPUTING THE DISTANCE DISTRIBUTION OF SYSTEMATIC NONLINEAR CODES

ELEONORA GUERRINI, EMMANUELA ORSINI, MASSIMILIANO SALA
2010 Journal of Algebra and its Applications  
The most important families of non-linear codes are systematic. We provide a Gröbner bases technique to compute the distance distribution of systematic nonlinear codes.
doi:10.1142/s0219498810003884 fatcat:ubcecjeuhfggzfvll7gvefludm

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

Massimiliano Orsini, Simone Carcangiu
2013 Source Code for Biology and Medicine  
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
more » ... rs, 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.
doi:10.1186/1751-0473-8-4 pmid:23363699 pmcid:PMC3571973 fatcat:dcjqrawan5cltejfmldi4bsldu

Complete Genome Sequence of a Myoviridae Bacteriophage Infecting Salmonella enterica Serovar Typhimurium

Rubina Paradiso, Massimiliano Orsini, Sergio Bolletti Censi, Giorgia Borriello, Giorgio Galiero
2016 Genome Announcements  
Orsini, unpublished data). Genome annotation was manually curated after a preliminary annotation performed by Prokka (4). The 118970_sal3 genome consisted of 39,464 bp, with a GϩC content of 50.7%.  ... 
doi:10.1128/genomea.00940-16 pmid:27688333 pmcid:PMC5043551 fatcat:2wltxih5rndg5ccjggrqy7wi7u

Highway Deceleration Lane Safety: Effects of Real-Time Coaching Programs on Driving Behavior

Federico Orsini, Mariaelena Tagliabue, Giulia De Cet, Massimiliano Gastaldi, Riccardo Rossi
2021 Sustainability  
Real-time coaching programs are designed to give feedback on driving behavior to usage-based motor insurance users; they are often general purpose programs that aim to promote smooth driving. Here, we investigated the effect of different on-board real-time coaching programs on the driving behavior on highway deceleration lanes with a driving simulator experiment. The experiment was organized into two trials. The first was a baseline trial, in which participants drove without receiving any
more » ... ck; a cluster analysis was then performed to divide participants into two groups, based on their observed driving style. One month later, a second trial was carried out, with participants driving on the same path as the first trial, this time receiving contingent feedback related to their braking/acceleration behavior. Four feedback systems were tested; overall, there were eight experimental groups, depending on the clustered driving style (aggressive and defensive), feedback modality (visual and auditory), and feedback valence (positive and negative). Speed, deceleration, trajectory, and lateral control variables, collected before and onto the deceleration lane, were investigated with mixed ANOVAs, which showed that the real-time coaching programs significantly reduced speeds and maximum deceleration values, while improving lateral control. A change toward a safer exit strategy (i.e., entering the lane before starting to decelerate) was also observed in defensive drivers.
doi:10.3390/su13169089 fatcat:svsy7rqrujbpxpda664juhllsm

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

Riccardo Rossi, Claudio Meneguzzer, Federico Orsini, Massimiliano Gastaldi
2020 Transportation Research Procedia  
A general procedure for the validation of a driving simulation environment for the analysis of gap-acceptance behavior was developed in this study. It allows to test whether a synthetic indicator of gap-acceptance behavior (the mean critical gap) shows significant differences when computed on the basis of field observations versus observations collected in the simulated environment. If such differences are not significant, driver behavior can be considered similar in the two contexts, thus
more » ... rting validation of the driving simulation environment. In order to demonstrate its effectiveness, the proposed procedure is applied to the case of a three-leg roundabout located in the Veneto region (Italy). The results show that the mean critical gap estimated in the field and the mean critical gap estimated in the virtual environment are not significantly different. The proposed procedure can be applied in various contexts in which gap-acceptance behavior is a central element in terms of safety and operational performance of the traffic system under analysis. Abstract A general procedure for the validation of a driving simulation environment for the analysis of gap-acceptance behavior was developed in this study. It allows to test whether a synthetic indicator of gap-acceptance behavior (the mean critical gap) shows significant differences when computed on the basis of field observations versus observations collected in the simulated environment. If such differences are not significant, driver behavior can be considered similar in the two contexts, thus supporting validation of the driving simulation environment. In order to demonstrate its effectiveness, the proposed procedure is applied to the case of a three-leg roundabout located in the Veneto region (Italy). The results show that the mean critical gap estimated in the field and the mean critical gap estimated in the virtual environment are not significantly different. The proposed procedure can be applied in various contexts in which gap-acceptance behavior is a central element in terms of safety and operational performance of the traffic system under analysis.
doi:10.1016/j.trpro.2020.03.069 fatcat:onbd3mta7jearaddz2vpcnjubm

Duplication of the dystroglycan gene in most branches of teleost fish

Ernesto Pavoni, Davide Cacchiarelli, Roberta Tittarelli, Massimiliano Orsini, Antonio Galtieri, Bruno Giardina, Andrea Brancaccio
2007 BMC Molecular Biology  
The dystroglycan (DG) complex is a major non-integrin cell adhesion system whose multiple biological roles involve, among others, skeletal muscle stability, embryonic development and synapse maturation. DG is composed of two subunits: α-DG, extracellular and highly glycosylated, and the transmembrane β-DG, linking the cytoskeleton to the surrounding basement membrane in a wide variety of tissues. A single copy of the DG gene (DAG1) has been identified so far in humans and other mammals,
more » ... for a precursor protein which is post-translationally cleaved to liberate the two DG subunits. Similarly, D. rerio (zebrafish) seems to have a single copy of DAG1, whose removal was shown to cause a severe dystrophic phenotype in adult animals, although it is known that during evolution, due to a whole genome duplication (WGD) event, many teleost fish acquired multiple copies of several genes (paralogues). Results: Data mining of pufferfish (T. nigroviridis and T. rubripes) and other teleost fish (O. latipes and G. aculeatus) available nucleotide sequences revealed the presence of two functional paralogous DG sequences. RT-PCR analysis proved that both the DG sequences are transcribed in T. nigroviridis. One of the two DG sequences harbours an additional mini-intronic sequence, 137 bp long, interrupting the uncomplicated exon-intron-exon pattern displayed by DAG1 in mammals and D. rerio. A similar scenario emerged also in D. labrax (sea bass), from whose genome we have cloned and sequenced a new DG sequence that also harbours a shorter additional intronic sequence of 116 bp. Western blot analysis confirmed the presence of DG protein products in all the species analysed including two teleost Antarctic species (T. bernacchii and C. hamatus). Conclusion: Our evolutionary analysis has shown that the whole-genome duplication event in the Class Actinopterygii (ray-finned fish) involved also DAG1. We unravelled new important molecular genetic details about fish orthologous DGs, which might help to increase the current knowledge on DG expression, maturation and targeting and on its physiopathological role in higher organisms.
doi:10.1186/1471-2199-8-34 pmid:17509131 pmcid:PMC1885269 fatcat:65qhjhv6tvdfrgrxbvenklo4oe

The PARIGA Server for Real Time Filtering and Analysis of Reciprocal BLAST Results

Massimiliano Orsini, Simone Carcangiu, Gianmauro Cuccuru, Paolo Uva, Anna Tramontano, Niall James Haslam
2013 PLoS ONE  
BLAST-based similarity searches are commonly used in several applications involving both nucleotide and protein sequences. These applications span from simple tasks such as mapping sequences over a database to more complex procedures as clustering or annotation processes. When the amount of analysed data increases, manual inspection of BLAST results become a tedious procedure. Tools for parsing or filtering BLAST results for different purposes are then required. We describe here PARIGA
more » ... esources.bioinformatica.crs4.it/pariga/), a server that enables users to perform all-against-all BLAST searches on two sets of sequences selected by the user. Moreover, since it stores the two BLAST output in a pythonserialized-objects database, results can be filtered according to several parameters in real-time fashion, without re-running the process and avoiding additional programming efforts. Results can be interrogated by the user using logical operations, for example to retrieve cases where two queries match same targets, or when sequences from the two datasets are reciprocal best hits, or when a query matches a target in multiple regions. The Pariga web server is designed to be a helpful tool for managing the results of sequence similarity searches. The design and implementation of the server renders all operations very fast and easy to use.
doi:10.1371/journal.pone.0062224 pmid:23667459 pmcid:PMC3646873 fatcat:cdlhmpvr6jfsfg37fbbfo2vhpu

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

Fabrizio Caruso, Emmanuela Orsini, Massimiliano Sala, Claudia Tinnirello
2017 IEEE Transactions on Information Theory  
Orsini and Sala [12] introduced the general error locator polynomials and presented an algebraic decoder which permits to determine the correctable error patterns of a cyclic code in one step.  ...  The decoding procedure developed by Orsini and Sala in [13] consists of five steps: 1) Computation of the r syndromes s 1 , . . . , s r corresponding to the received vector. 2) Evaluation of L C (x 1  ... 
doi:10.1109/tit.2017.2692213 fatcat:ieqpfa35qzayfpf2vc4kgwbpnm

Visual Feedback Effectiveness in Reducing Over Speeding of Moped-Riders

Mariaelena Tagliabue, Riccardo Rossi, Massimiliano Gastaldi, Giulia De Cet, Francesca Freuli, Federico Orsini, Leandro L. Di Stasi, Giulio Vidotto
2021 Frontiers in Psychology  
The authors would like to thank Alberto Sarto and Massimiliano Martinelli for their support in designing the experiment and in data extraction, and Marta Lodi and Cristian Fronea for helping in data collection  ... 
doi:10.3389/fpsyg.2021.611603 pmid:33776838 pmcid:PMC7990878 fatcat:ud6at5bykbhwvioxxtbzw4lvbm

Complete Genome Sequences of Three Siphoviridae Bacteriophages Infecting Salmonella enterica Serovar Enteritidis

Rubina Paradiso, Serena Lombardi, Maria Grazia Iodice, Marita Georgia Riccardi, Massimiliano Orsini, Sergio Bolletti Censi, Giorgio Galiero, Giorgia Borriello
2016 Genome Announcements  
Orsini, unpublished data). Genome annotation was manually curated after a preliminary annotation performed by Prokka (4) .  ... 
doi:10.1128/genomea.00939-16 pmid:27856572 pmcid:PMC5114364 fatcat:vynbrnfwfbc5pf2edvl4xlcvxi
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