Regular Rules Research Articles

RegExpBlasting (REB), a Regular Expression Blasting algorithm based on multiply aligned sequences

BackgroundOne of the most frequent uses of bioinformatics tools concerns functional characterization of a newly produced nucleotide sequence (a query sequence) by applying Blast or FASTA against a set of sequences (the subject sequences).However, in some specific contexts, it is useful to compare the query sequence against a cluster such as a MultiAlignment (MA). We present here the RegExpBlasting (REB) algorithm, which compares an unclassified sequence with a dataset of patterns defined by application of Regular Expression rules to a given-as-input MA datasets.The REB algorithm workflow consists ini. the definition of a dataset of multialignmentsii. the association of each MA to a pattern, defined by application of regular expression rules;iii. automatic characterization of a submitted biosequence according to the function of the sequences described by the pattern best matching the query sequence.ResultsAn application of this algorithm is used in the "characterize your sequence" tool available in the PPNEMA resource. PPNEMA is a resource of Ribosomal Cistron sequences from various species, grouped according to nematode genera. It allows the retrieval of plant nematode multialigned sequences or the classification of new nematode rDNA sequences by applying REB. The same algorithm also supports automatic updating of the PPNEMA database. The present paper gives examples of the use of REB within PPNEMA.ConclusionThe use of REB in PPNEMA updating, the PPNEMA "characterize your sequence" option clearly demonstrates the power of the method. Using REB can also rapidly solve any other bioinformatics problem, where the addition of a new sequence to a pre-existing cluster is required. The statistical tests carried out here show the powerful flexibility of the method.

Ternary butterfly subdivision

This paper presents an interpolating ternary butterfly subdivision scheme for triangular meshes based on a 1-9 splitting operator. The regular rules are derived from a C^2 interpolating subdivision curve, and the irregular rules are established through the Fourier analysis of the regular case. By analyzing the eigenstructures and characteristic maps, we show that the subdivision surfaces generated by this scheme is C^1 continuous up to valence 100. In addition, the curvature of regular region is bounded. Finally we demonstrate the visual quality of our subdivision scheme with several examples.

Brainstorming, Brainstorming Rules and Decision Making

This study investigated the effect of brainstorming experience on the ability of groups to subsequently select the best ideas for implementation. Participants generated ideas either alone or in interactive groups and with either the regular brainstorming rules or with additional rules designed to further increase the number of ideas generated. All participants subsequently were asked to select their top five ideas in a group evaluation phase.Groups of individuals generating ideas in isolation (nominal groups) generated more ideas and more original ideas and were more likely to select original ideas during the group decision phase than interactive group brainstormers. Additional rules increased idea generation but not idea originality or idea selection.

Word sense disambiguation using word ontology and concept distribution

This paper presents a method of word sense disambiguation that assigns a target word the sense that is most related to the senses of its neighbor words. We explore the use of measures of relatedness between word senses based on a novel hybrid approach. First, we investigate how to “literally” and “regularly” express a “concept”. We apply set algebra to Wordnet's synsets cooperating with Wordnet's word ontology. In this way we establish regular rules for constructing various representations (lexical notations) of a concept using Boolean operators and word forms in various synset(s) defined in Wordnet. Then we establish a formal mechanism for quantifying and estimating the semantic relatedness between concepts – we facilitate “concept distribution statistics” to determine the degree of semantic relatedness between two lexically expressed concepts. Human languages have words that can mean different things in different contexts, such words with multiple meanings are potentially “ambiguous”. The process of “deciding which of several meanings of a term is intended in a given context” is known as “Word Sense Disambiguation (WSD)”. The proposed method is not supervised, and does not require any manually created sense‐tagged training examples. The experimental results showed good performance on Semcor, a subset of the Brown corpus. We observe that measures of semantic relatedness are useful sources of information for word sense disambiguation.

The epidemiology of injuries in American Flag Football (AFF): Initial pilot study results

Background: Although AFF is considered a non-tackle sport, many serious contact-type injuries are reported annually worldwide. Neither previous studies have investigated the epidemiology nor the prevention of injuries in this sport. Objective: To examine the epidemiology of sports injuries in the AFF league (AFFL) in Israel. Design: Descriptive epidemiology study. Setting: Sports field, amateur AFFL. Participants: Seven hundred and forty-six amateur male players. Methodology: All time-loss injuries sustained in game sessions were recorded by the off-the-field medical personnel over a one-season period. Detailed phone questionnaires were carried out 7-14 days following the injury. Results: Three hundred and twenty-nine games were played in the 2006/7 season. The number of athlete-exposures was 245,434. Although 70 injuries were reported over this period, 50 detailed questionnaires were fully completed, representing 44 individual players in total. Six of the 70 injuries involved players with multiple injuries. Overall, this represents an injury rate of 0.29 per 1000 athlete-exposures (95% CI: 0.35, 0.22). The estimated incidence per season of a player sustaining an injury is 8.6% (95% CI: 6.5%, 10.5%). All the injuries were traumatic, caused directly by either contact with the ground (22 or 46%) or involving another player (15 or 30%). Fourteen (28%) of the injuries occurred to the hand, 11 (22%) to the knee and 10 (20%) to the head/face. Only 3 (6%) of the players wore any type of protective equipment. Thirty (61%) occurred in the second half of the game. Six (12%) occurred not in accordance with regular game rules. In terms of injury type, 6 (12%) involved concussion-type injuries, 16 (36%) were dislocations, whilst 22 (44%) resulted in haematoma/contusions. Thirty-one (62%) involved the defensive line and receiver player-positions. Thirty-seven (74%) were moderate to severe in nature whilst only 2 (4%) were recurrent in nature. Five (11%) of the players participated in a pre-season conditioning program. Conclusions: These initial pilot study results reflect both the high number of moderate to severe type-injuries in this so-called “non-tackle” sport. Despite the fact that most of the injuries resulted from either direct contact with the ground or another player, very few players used any form of protective equipment. These results have accentuated the urgent need for protective measures to reduce injuries in the AFFL, and have formed the basis of the consecutive 2-season epidemiological study which is currently underway. A randomised controlled injury prevention trial will thereafter be introduced.

Applying Suffix Rules to Organization Name Recognition

This paper presents a method for boosting the performance of the organization name recognition, which is a part of named entity recognition (NER). Although gazetteers (lists of the NEs) have been known as one of the effective features for supervised machine learning approaches on the NER task, the previous methods which have applied the gazetteers to the NER were very simple. The gazetteers have been used just for searching the exact matches between input text and NEs included in them. The proposed method generates regular expression rules from gazetteers, and, with these rules, it can realize a high-coverage searches based on looser matches between input text and NEs. To generate these rules, we focus on the two well-known characteristics of NE expressions; 1) most of NE expressions can be divided into two parts, class-reference part and instance-reference part, 2) for most of NE expressions the class-reference parts are located at the suffix position of them. A pattern mining algorithm runs on the set of NEs in the gazetteers, and some frequent word sequences from which NEs are constructed are found. Then, we employ only word sequences which have the class-reference part at the suffix position as suffix rules. Experimental results showed that our proposed method improved the performance of the organization name recognition, and achieved the 84.58 F-value for evaluation data.

Intrusion Prevention in Depth System Research Based on Data Mining

This article proposes a data mining based intrusion prevention in depth system model to manage the huge amounts of unreliable and uncontrollable security events, which are generated by the extensive utilization of heterogeneous security devices in computer networks. A method of combining online detection and offline data mining is made use of as the core of the model. On the other hand, the work process of the system can be compartmentalized into two phases: online examination through pattern matching and offline training through data mining. By the online real-time data examination, the data are captured through the protocol analyzer at first, and then passed through the processor of regular rule set and parameters based detection engine. After corresponding processing to the data, the system can decide if the data should be stored and forwarded or an alarm management operation should be stimulated. By the offline data mining, the data preprocess module pretreats the data from various kinds of invasion and appraisal, and combines the mined knowledge to data that come from the compound detection engine and the policy making engine. The regular rule set is then updated and optimized through the new knowledge acquired by the offline data mining phase. The phases of online examination and offline data mining are executed alternatively and/or synchronously according to requirements of achieving optimal performance of the system. In our UPNSM, we unify the rule and the policy together to form the policy by the classified rule set and the human-computer interface and distribute policy to examination engines. This method provides our platform a better assistance to carry on various kinds of nimble effective operation. In fact, the model is a united network security management platform used to analyze the network and host data from different layers: the kernel layer, the concentration layer, and the access layer. Through enhancing the capture speed of the network data package, the proposed model can evidently improve the efficiency of traditional IPS for detection network intrusion. This verity can be demonstrated by simulation and experiment results. Thus, the proposed intrusion prevention in depth system model can be used for defense in real-time and defense in depth.

Collective numeral constructions in Dutch

In this paper, we discuss some collective numeral constructions from Dutch, which display a remarkable plural morpheme -en: wij vieren “the four of us”, met ons vieren “with four” and met z’n vieren “with four”. We argue that these at first sight idiosyncratic constructs are formed in syntax by application of the regular syntactic rules: Merge and Move. A central claim we make is that these collective numeral constructions contain a silent noun PERSOON/PERSON (cf. Kayne 2002, 2003, 2007). Although the noun itself is silent, its plurality is realized as -en. The silent noun is licensed by a local (i.e., DP-internal) antecedent. Dialectal variation in the realization of these constructions is analyzed in terms of “externalization”. It is argued that the basic syntactic make-up is similar in all variants. It is the (morpho-) phonological realization of heads, which causes the differences at the surface.

Characterizations of majoritarianism: a unified approach

Defining regularity as the conjunction of unanimity, anonymity, neutrality and monotonicity, we show that every regular social choice rule can be expressed as a function of vote differences and the maximal number of canceling couples. This equivalence not only identifies the class of regular social choice rules but also allows a unified conception of various majority characterizations.

Frequency-time codes based on the decimation method

A regular rule for building uniform frequency-time codes, having length p and a large volume, over the Galois prime fields GF(p) based on the decimation method has been proposed. It was shown that the noise immunity coefficient of the decimation code proposed was higher than the uniform Reed-Solomon codes built over the corresponding fields GF(p).

Limitations on Reliability: Regularity Rules in the English Plural and Past Tense

Two studies investigated 3- to 5-year-olds' trust in a reliable informant when judging novel labels and novel plural and past tense forms. In Study 1, children (N = 24) endorsed the names of new objects given by an informant who had earlier labeled familiar objects correctly over the names given by an informant who had labeled the same objects incorrectly. In Study 2, children (N = 24) endorsed novel names given by an informant who had earlier expressed the plural of familiar nouns correctly over one who had expressed the plural incorrectly. But children overwhelmingly endorsed the regular plural and past tense forms of new words provided by the formerly unreliable labeler (Study 1) or morphologist (Study 2) rather than irregular forms of those words provided by the formerly reliable informant.

Simulation-based optimization of dispatching rules for semiconductor wafer fabrication system scheduling by the response surface methodology

Scheduling of a semiconductor wafer fabrication system (SWFS) is complicated due to its re-entrant product flow, high uncertainties in operations, and rapidly changing products and technologies; thus dispatching rules have been widely used for real-time scheduling because they can provide a very quick and pretty good solution. However, deciding how to select appropriate rules is very difficult and seldom tackled. This paper describes an approach into the evaluation and optimization of dispatching rules by integrating the simulation and response surface methodology (RSM). In order to implement the proposed approach, a dynamic bottleneck dispatching (DBD) policy is designed, in which bottlenecks are detected in a timely way and adaptive dispatching decisions are made according to the real-time conditions. In addition, two case studies are carried out to demonstrate the approach. One case compares DBD to regular rules, such as CR + FIFO, EDD, SRPT, SPT, SPNB and Justice, a bottleneck dispatching method. Simulation results show that the DBD policy is superior to the other six methods. In another case study, the parameters of DBD are optimized by RSM and desirability function, and the result proves that the optimized DBD method can get even better performance.

Symmetry in electron diffractions from helical structures

In this work, we elucidate the regular rule of the symmetry in electron diffraction patterns from helical structures. It is affected by the value of the dominating Bessel function orders for the layer lines and relative orientation of the samples with respect to the electron beam. For Single-Walled Carbon nanotubes (SWCNTs), we use analytic analysis and computer simulations to demonstrate that the 2 mm symmetry of the electron diffraction may break down not only from an achiral SWCNT, but also from a chiral SWCNT. Also, the simulation work for B-DNA is presented to corroborate the theoretical analysis.

RETRIEVING MUTATION-SPECIFIC INFORMATION FOR HUMAN PROTEINS IN UNIPROT/SWISS-PROT KNOWLEDGEBASE

The UniProt/Swiss-Prot Knowledgebase records about 30,500 variants in 5,664 proteins (Release 52.2). Most of these variants are manually curated single amino acid polymorphisms (SAPs) with references to the literature. In order to keep the list of published documents related to SAPs up to date, an automatic information retrieval method is developed to recover texts mentioning SAPs. The method is based on the use of regular expressions (patterns) and rules for the detection and validation of mutations. When evaluated using a corpus of 9,820 PubMed references, the precision of the retrieval was determined to be 89.5% over all variants. It was also found that the use of nonstandard mutation nomenclature and sequence positional correction is necessary to retrieve a significant number of relevant articles. The method was applied to the 5,664 proteins with variants. This was performed by first submitting a PubMed query to retrieve articles using gene or protein names and a list of mutation-related keywords; the SAP detection procedure was then used to recover relevant documents. The method was found to be efficient in retrieving new references on known polymorphisms. New references on known SAPs will be rendered accessible to the public via the Swiss-Prot variant pages.

Rules for constructing full classes of optimal and quasioptimal systems of discrete frequency signals over isomorphic Galois fields

Regular rules for building full classes of optimal DF signals systems are proposed with the property of not more than one coincidence (λ ≤ 1) and DF signals quasioptimal systems with the property of not more than two coincidences (λ ≤ 2) over extended (isomorphic) Galois fields GF(q).

Linked and Fused Tungstaborane Clusters: Synthesis, Characterization, and Electronic Structures ofbis-{(η5-C5Me5W)2B5H8}2and (η5-C5Me5W)2{Fe(CO)3}nB6-nH10-n,n= 0, 1

In addition to (η5-C5Me5W)2B5H9, (η5-C5Me5W)3(μ-H)B8H8, and (η5-C5Me5W)2B7H9 reported earlier, thermolysis of {η5-C5Me5W}H3B4H8 (1) with BH3·THF leads to the formation of bicapped closo-{η5-C5Me5W}2B6H10 (2) in parallel with a B−B linked dimer of {η5-C5Me5W}2B5H9 (4) and bis-{(η5-C5Me5W)2B5H8}2 (3). Reaction of 4 with a 3-fold excess of Fe2(CO)9 in hexane generates an iron analogue of 2, (η5-C5Me5W)2B5H9Fe(CO)3 (5) in 46% yield. All the metallaboranes, 2, 3, and 5, have been characterized by 1H, 11B NMR spectra and crystal structure determinations. The structures of 2 and 5 appear to follow the regular electron counting rules as they possess seven skeletal electron pairs (sep) appropriate for bicapped octahedral structures. However, their electronic structures revealed by a molecular orbital analysis is more closely related to that of [{η5-C5Me5Re}2B7H7], a cluster that does not obey the classical electron counting rules. Clusters 2 and 5 are notable examples of closo clusters containing four bridging hydrogens. 3 is a coupled-cage structure in which two bicapped trigonal bipyramidal frameworks, W2B5, are joined by an exopolyhedral boron−boron bond.

Psychoticism and attentional flexibility

In three separate experiments, we tested the hypothesis that a systematic relationship between psychoticism (P) and visual selective attention is infrequently observed because the tasks typically used to test individual differences in efficiency of attentional mechanisms do not entail attentional flexibility. We manipulated the selection rule of the computerized divided visual attention (DIVA) task to be either (a) a predictable, or (b) a random manner, and a secondary task was added to check the quality of high P scorers’ performance in an interference condition; and we also introduced breaks between DIVA tasks to allow for cue utilization. Results revealed that low P scorers outperformed high P scorers in the regular selection rule alternation condition (cue utilization possible), whereas high P scorers performed better in random alternation condition – high P scorers also showed performance superiority in the dual task condition unless stimuli presentation was speeded up. Thus, P does not necessarily impair attentional performance; indeed, our data point to performance advantages of high P, especially attentional efficiency in tasks requiring small demands of attentional control.

OReFiL: an online resource finder for life sciences

BackgroundMany online resources for the life sciences have been developed and introduced in peer-reviewed papers recently, ranging from databases and web applications to data-analysis software. Some have been introduced in special journal issues or websites with a search function, but others remain scattered throughout the Internet and in the published literature. The searchable resources on these sites are collected and maintained manually and are therefore of higher quality than automatically updated sites, but also require more time and effort.DescriptionWe developed an online resource search system called OReFiL to address these issues. We developed a crawler to gather all of the web pages whose URLs appear in MEDLINE abstracts and full-text papers on the BioMed Central open-access journals. The URLs were extracted using regular expressions and rules based on our heuristic knowledge. We then indexed the online resources to facilitate their retrieval and comparison by researchers. Because every online resource has at least one PubMed ID, we can easily acquire its summary with Medical Subject Headings (MeSH) terms and confirm its credibility through reference to the corresponding PubMed entry. In addition, because OReFiL automatically extracts URLs and updates the index, minimal time and effort is needed to maintain the system.ConclusionWe developed OReFiL, a search system for online life science resources, which is freely available. The system's distinctive features include the ability to return up-to-date query-relevant online resources introduced in peer-reviewed papers; the ability to search using free words, MeSH terms, or author names; easy verification of each hit following links to the corresponding PubMed entry or to papers citing the URL through the search systems of BioMed Central, Scirus, HighWire Press, or Google Scholar; and quick confirmation of the existence of an online resource web page.

RETRACTION: A New WSD approach using word ontology and concept distribution

This paper presents a method of word sense disambiguation that assigns a target word the sense that is most related to the senses of its neighbor words. Human languages have words that can mean different things in different contexts, and such words with multiple meanings are potentially `ambiguous'. `Word sense disambiguation' means the process of `deciding which of several meanings of a term is intended in a given context'. We explore the use of measures of relatedness between word senses based on a novel hybrid approach. First, we investigate how to express a `concept' literally and regularly. We apply set algebra to Wordnet's synsets, cooperating with Wordnet's word ontology. We establish regular rules for constructing various representations (lexical notations) of a concept using Boolean operators and word forms in various synset(s) defined in Wordnet. Thus, we establish a formal mechanism for quantifying and estimating the semantic relatedness between concepts—we facilitate `concept distribution statistics' to determine the semantic relatedness between two lexically expressed concepts. Our method does not require any training in advanced. The experimental results showed good performance on Semcor, a subset of the Brown corpus. We observe that measures of semantic relatedness are useful sources of information for word sense disambiguation.

Regular expression matching with input compression: a hardware design for use within network intrusion detection systems

This paper describes an optimised finite state automata based hardware design for implementing high speed regular expression matching. Automata based implementations of regular expression matching can become quite complex and if table driven can use large amounts of memory—this can be a problem for hardware based implementations, as the amount of memory available within standard Field Programmable Gate Array (FPGA) components can be quite small as compared with the amount of resources we expect to find within a software environment. This work uses an existing ‘packed array’ style of table based automata implementation, but then adds a form of input compression to group together characters that are treated identically by the automata. A hardware design for such a system has been created for use within a Xilinx Field Programmable Gate Array and tested by simulation. The design operates at a fixed scan rate of 2.0 Gbps independent of the regular expression used or the input data being scanned. The regular expression rules are first compiled by software and then loaded into the design at run time and may be updated dynamically without modification to the design.