Normal, Abby Normal, Prefix Normal

A prefix normal word is a binary word with the property that no substring has more 1s than the prefix of the same length. This class of words is important in the context of binary jumbled pattern matching. In this paper we present results about the number $pnw(n)$ of prefix normal words of length $n$, showing that $pnw(n) =\Omega\left(2^{n - c\sqrt{n\ln n}}\right)$ for some $c$ and $pnw(n) = O \left(\frac{2^n (\ln n)^2}{n}\right)$. We introduce efficient algorithms for testing the prefix normal property and a "mechanical algorithm" for computing prefix normal forms. We also include games which can be played with prefix normal words. In these games Alice wishes to stay normal but Bob wants to drive her "abnormal" -- we discuss which parameter settings allow Alice to succeed.Comment: Accepted at FUN '1

Event-related desynchronization related to the anticipation of a stimulus providing knowledge of results

In the present paper, event-related desynchronization (ERD) in the alpha and beta frequency bands is quantified in order to investigate the processes related to the anticipation of a knowledge of results (KR) stimulus. In a time estimation task, 10 subjects were instructed to press a button 4 s after the presentation of an auditory stimulus. Two seconds after the response they received auditory or visual feedback on the timing of their response. Preceding the button press, a centrally maximal ERD is found. Preceding the visual KR stimulus, an ERD is present that has an occipital maximum. Contrary to expectation, preceding the auditory KR stimulus there are no signs of a modalityspecific ERD. Results are related to a thalamo-cortical gating model which predicts a correspondence between negative slow potentials and ERD during motor preparation and stimulus anticipation

Rassendiscriminatie... tenslotte is het verboden bij de wet

Contains fulltext : 3767.pdf (publisher's version ) (Open Access

Desynchronization during anticipatory attention for an upcoming stimulus: A comparative EEG/MEG study

Objectives: Our neurophysiological model of anticipatory behaviour (e.g. Acta Psychol 101 (1999) 213; Bastiaansen et al., 1999a) predicts an activation of (primary) sensory cortex during anticipatory attention for an upcoming stimulus. In this paper we attempt to demonstrate this by means of event-related desynchronization (ERD). Methods: Five subjects performed a time estimation task, and were informed about the quality of their time estimation by either visual or auditory stimuli providing Knowledge of Results (KR). EEG and MEG were recorded in separate sessions, and ERD was computed in the 8± 10 and 10±12 Hz frequency bands for both datasets. Results: Both in the EEG and the MEG we found an occipitally maximal ERD preceding the visual KR for all subjects. Preceding the auditory KR, no ERD was present in the EEG, whereas in the MEG we found an ERD over the temporal cortex in two of the 5 subjects. These subjects were also found to have higher levels of absolute power over temporal recording sites in the MEG than the other subjects, which we consider to be an indication of the presence of a `tau' rhythm (e.g. Neurosci Lett 222 (1997) 111). Conclusions: It is concluded that the results are in line with the predictions of our neurophysiological model

Exploring the limits of the geometric copolymerization model

The geometric copolymerization model is a recently introduced statistical Markov chain model. Here, we investigate its practicality. First, several approaches to identify the optimal model parameters from observed copolymer fingerprints are evaluated using Monte Carlo simulated data. Directly optimizing the parameters is robust against noise but has impractically long running times. A compromise between robustness and running time is found by exploiting the relationship between monomer concentrations calculated by ordinary differential equations and the geometric model. Second, we investigate the applicability of the model to copolymerizations beyond living polymerization and show that the model is useful for copolymerizations involving termination and depropagation reactions

Partial Homology Relations - Satisfiability in terms of Di-Cographs

Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A variety of methods based on pairwise sequence comparisons can be used to infer such homology relations (e.g.\ orthology, paralogy, xenology). They are \emph{satisfiable} if the relations can be explained by an event-labeled gene tree, i.e., they can simultaneously co-exist in an evolutionary history of the underlying genes. Every gene tree is equivalently interpreted as a so-called cotree that entirely encodes the structure of a di-cograph. Thus, satisfiable homology relations must necessarily form a di-cograph. The inferred homology relations might not cover each pair of genes and thus, provide only partial knowledge on the full set of homology relations. Moreover, for particular pairs of genes, it might be known with a high degree of certainty that they are not orthologs (resp.\ paralogs, xenologs) which yields forbidden pairs of genes. Motivated by this observation, we characterize (partial) satisfiable homology relations with or without forbidden gene pairs, provide a quadratic-time algorithm for their recognition and for the computation of a cotree that explains the given relations

The development of a knowledge base for basic active structures: an example case of dopamine agonists

<p>Abstract</p> <p>Background</p> <p>Chemical compounds affecting a bioactivity can usually be classified into several groups, each of which shares a characteristic substructure. We call these substructures "basic active structures" or BASs. The extraction of BASs is challenging when the database of compounds contains a variety of skeletons. Data mining technology, associated with the work of chemists, has enabled the systematic elaboration of BASs.</p> <p>Results</p> <p>This paper presents a BAS knowledge base, BASiC, which currently covers 46 activities and is available on the Internet. We use the dopamine agonists D1, D2, and Dauto as examples and illustrate the process of BAS extraction. The resulting BASs were reasonably interpreted after proposing a few template structures.</p> <p>Conclusions</p> <p>The knowledge base is useful for drug design. Proposed BASs and their supporting structures in the knowledge base will facilitate the development of new template structures for other activities, and will be useful in the design of new lead compounds via reasonable interpretations of active structures.</p