Reading spaced and unspaced Chinese text: Evidence from eye movements.

Native Chinese readers' eye movements were monitored as they read text that did or did not demark word boundary information. In Experiment 1, sentences had 4 types of spacing: normal unspaced text, text with spaces between words, text with spaces between characters that yielded nonwords, and finally text with spaces between every character. The authors investigated whether the introduction of spaces into unspaced Chinese text facilitates reading and whether the word or, alternatively, the character is a unit of information that is of primary importance in Chinese reading. Global and local measures indicated that sentences with unfamiliar word spaced format were as easy to read as visually familiar unspaced text. Nonword spacing and a space between every character produced longer reading times. In Experiment 2, highlighting was used to create analogous conditions: normal Chinese text, highlighting that marked words, highlighting that yielded nonwords, and highlighting that marked each character. The data from both experiments clearly indicated that words, and not individual characters, are the unit of primary importance in Chinese reading. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

A novel family of compression algorithms for ECG and other semiperiodical, one-dimensional, biomedical signals

In this paper, a novel family of compression algorithms is presented, which is designed to exploit the redundancy of one-dimensional (1-D) semiperiodical biomedical signals resulting from the cyclic nature of the underlying physical process. The basic idea is that a pool of past-seen cycles is maintained and cycles to be encoded can be stored as transformed versions of those residing in the pool. Conceptually, this approach is an extension of dictionary-based coding schemes used for text compression to signal patterns residing in an n-dimensional space. A cycle transformation method is introduced in order to render the pattern matching process practical and to enable cycle substitution. Based on the principles of the algorithmic family and this transformation method, an electrocardiogram (ECG)-oriented algorithm is implemented and thoroughly tested. The performance of this implementation is examined theoretically and deductions about the optimal algorithm settings are made. The ECG compression algorithm is superior to the average beat subtraction algorithm as proposed by Hamilton and Tompkins in cases where high compression ratios are required.     

MHCPEP, a database of MHC-binding peptides: update 1996

MHCPEP is a curated database comprising over 9000 peptide sequences known to bind MHC molecules. Entries are compiled from published reports as well as from direct submissions of experimental data. Each entry contains the peptide sequence, its MHC specificity and, when available, experimental method, observed activity, binding affinity, source protein, anchor positions and publication references. The present format of the database allows text string matching searches but can easily be converted for use in conjunction with sequence analysis packages. The database can be accessed via Internet using WWW, FTP or Gopher.     

利用数组和指针对字符串操作的比较应用

文中通过实例阐述了字符串指针变量与字符数组在处理字符串上的区别,利用指针数组比二维数组更适合于对若干个字符串的处理,使用更加方便灵活、效率更高。     

A comparison of three methods of analysis for age-period-cohort models with application to incidence data on non-Hodgkin''s lymphoma

Solution structures and hydrogen exchange characteristics of ligand-RNA aptamer and ligand-DNA aptamer complexes have been solved within the past year. The ligands range from cofactors to amino acids, nucleotides, aminoglycoside antibiotics and peptides that are targeted by the nucleic acid aptamers with high specificity and affinity. The structural and dynamics studies provide insights into the principles, patterns and diversity associated with nucleic acid architecture, molecular recognition and the adaptive binding that takes place upon complex formation. These new results provide opportunities for structure-based drug design strategies relevant to therapeutic intervention.     

Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment

A sequential assignment protocol for proteins was developed using heteronuclear 3D NMR. The protocol consists of an amino acid type recognition algorithm and a primary sequence mapping algorithm. The former measures the similarity between each detected spin pattern and 20 standard amino acid coupling patterns. Both chemical shift and topologically likeness are considered. The mapping algorithm uses the amino acid type information to direct detected polypeptides to proper position onto protein primary sequence. The assignment protocol can be applied to spin systems generated by many different approaches. We designed a few computer programs to derive a protein's backbone and side chain spin systems using heteronuclear 3D NMR. The results was then input to the sequential assignment protocol. All of the algorithms were tested on NMR data of a 90-residue N-domain of chicken skeletal troponin-C.     

Comparison of fixed-fee Grateful Med database use and searching success rates given the continued availability of MEDLINE in other formats

This study compared in-house Grateful Med database use and searching success rates for four-month periods at four sites of the Library of the Health Sciences of the University of Illinois at Chicago. Data were collected from Grateful Med workstation uselogs and analyzed. Database use patterns and searching success rates were fairly consistent across the four sites. Though MEDLINE was available in other formats and use in these other formats remained high, 65.48% of all Grateful Med searching was done by using MEDLINE, and an additional 21.34% was done by using the MEDLINE Backfiles. In-house use patterns were similar to the overall use pattern for the University of Illinois, with the exception of MEDLINE Backfiles. Overall, 54.30% of searches were successful.     

Revisiting play elements and self-handicapping in play: A comparative ethogram of five Old World monkey species.

Play behavior has been viewed as a mixture of elements drawn from “serious” behavior, interspersed by ritualized play signals. Two other types of play behaviors have been overlooked: patterns that are dissimilar from any serious behavior and patterns with self-handicapping character, that is, those that put the animal into unnecessary disadvantageous positions or situations. Here the authors show that these 2 types of patterns can constitute a major part of play repertoire. From our own videorecordings and observations, we constructed play ethograms of 5 monkey species (Semnopithecus entellus, Erythrocebus patas, Chlorocebus pygerythrus, Cercopithecus neglectus, and Cercopithecus diana). The authors evaluated the self-handicapping character of each pattern and in Hanuman langurs also the (dis)similarity to serious behavior. Of the 74 patterns in the 5 species, 33 (45%) were judged to have a self-handicapping character. Of 48 patterns observed in langurs, 16 (33%) were totally dissimilar to any serious langur behavior known to us. The authors discuss the possibility that the different types of play elements may have different functions in play. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Efficient discovery of conserved patterns using a pattern graph

MOTIVATION: We have previously reported an algorithm for discovering patterns conserved in sets of related unaligned protein sequences. The algorithm was implemented in a program called Pratt. Pratt allows the user to define a class of patterns (e.g. the degree of ambiguity allowed and the length and number of gaps), and is then guaranteed to find the conserved patterns in this class scoring highest according to a defined fitness measure. In many cases, this version of Pratt was very efficient, but in other cases it was too time consuming to be applied. Hence, a more efficient algorithm was needed. RESULTS: In this paper, we describe a new and improved searching strategy that has two main advantages over the old strategy. First, it allows for easier integration with programs for multiple sequence alignment and data base search. Secondly, it makes it possible to use branch-and-bound search, and heuristics, to speed up the search. The new search strategy has been implemented in a new version of the Pratt program.     

Mefloquine insusceptibility of malaria in Thailand not promoted by nonregulated drug-use

The program HBexplore is a new tool for identifying and analysing H-bonding patterns in biological macromolecules. It selects all potential H-bonds according to geometrical criteria. The H-bond table can then be subjected to further automatic or interactive analysis tools. These tools include the calculation of mean values and distributions of geometrical H-bond parameters for parts of a single structure, for complete single structures and for structure sets, the classification of each H-bond according to the participation of backbone, side chain or base, ligand and water parts of nucleic acids or proteins, identification of Watson-Crick nucleotide pairs and of H-bonded pairs of equal nucleotides, the calculation of the mean number of H-bonds per residue, and of the fraction of potential donor and acceptor atoms involved in H-bonds. HBexplore further generates automatically a H-bond residue interaction table. This table lists for all residues of the structure the other residues, ligands or water molecules directly connected via a H-bond. By means of a binary tree search algorithm, this table is then converted into a H-bond cluster table. Clusters are understood here as an uninterrupted network of H-bonded residues. For nucleic acids, secondary structures and tertiary interactions are automatically derived from the H-bonding pattern. HBexplore is applied to two example RNA structures: a pseudoknot and a hairpin. It provides a comprehensive listing of individual H-bonds and statistical information for larger structure sets. In addition, it can identify interesting new H-bond motifs. One example is a pentanucleotide base-base H-bond interaction motif in the RNA pseudoknot. HBexplore is intended to contribute both to the elucidation of general principles of the architecture of biological macromolecules, and to the prediction and refinement of single structures.     

Genotoxic modification of nucleic acid bases and biological consequences of it. Review and prospects of experimental and computational investigations

The review is presented of experimental and computational data on the influence of genotoxic modification of bases (deamination, alkylation, oxidation) on the structure and biological functioning of nucleic acids. Pathways are discussed for the influence of modification on coding properties of bases, on possible errors of nucleic acid biosynthesis, and on configurations of nucleotide mispairs. The atomic structure of nucleic acid fragments with modified bases and the role of base damages in mutagenesis and carcinogenesis are considered.     

Sequence database searches via de novo peptide sequencing by tandem mass spectrometry

A method is described for searching protein sequence databases using tandem mass spectra of tryptic peptides. The approach uses a de novo sequencing algorithm to derive a short list of possible sequence candidates which serve as query sequences in a subsequent homology-based database search routine. The sequencing algorithm employs a graph theory approach similar to previously described sequencing programs. In addition, amino acid composition, peptide sequence tags and incomplete or ambiguous Edman sequence data can be used to aid in the sequence determinations. Although sequencing of peptides from tandem mass spectra is possible, one of the frequently encountered difficulties is that several alternative sequences can be deduced from one spectrum. Most of the alternative sequences, however, are sufficiently similar for a homology-based sequence database search to be possible. Unfortunately, the available protein sequence database search algorithms (e.g. Blast or FASTA) require a single unambiguous sequence as input. Here we describe how the publicly available FASTA computer program was modified in order to search protein databases more effectively in spite of the ambiguities intrinsic in de novo peptide sequencing algorithms.     

Predicting quadriceps muscle activity during gait with an automatic rule determination method

It has been suggested that control using a skill-based expert system can be applicable to gait restoration. Rule-based systems have several advantages for this application: they generate a fast response (they are not computationally intensive) and they are easy to comprehend and implement. A major problem with using such systems is the inability of users to determine its rules. In this study, an automatic method for obtaining the production rules from a set of examples is described. The rule base was automatically induced from a model which used external sensor signals as inputs and electromyogram (EMG) patterns as outputs. The method is based on the minimization of entropy. A production rule estimated the muscle activity pattern using the sensor information. The algorithm was tested using data recorded from six able-bodied individuals during ground level walking, with and without ankle-foot orthoses. The data showed that gait variability will increase in able-bodied subjects when the motion of ankle joints is restricted, thus, providing a good test for generalization. The experimental results illustrate performance of the production rule that estimates quadriceps muscle group activity pattern for ground level walking in able-bodied subjects.     

Data mining in a behavioral test detects early symptoms in a model of amyotrophic lateral sclerosis.

"What's wrong with my genetically engineered animal?" is a common yet often difficult to answer question in behavioral phenotyping. We present here a method termed Pattern Array for mining movement patterns and isolating those that best capture an effect of a genetic manipulation. We demonstrate the method by searching for early motor symptoms in the open-field behavior of SOD1 mutant rats, an animal model of amyotrophic lateral sclerosis. Pattern Array was able to identify a unique motor pattern that differentiated the SOD1 mutants from the wild-type controls 2 months before disease onset. This pattern included heavy braking while moving near the arena wall but turning away from it. SOD1 mutants performed this pattern significantly less than wild-type controls in 2 independent data sets. At such early age the SOD1 mutants could not be differentiated from the controls by standard behavioral measures or by subjective observation. The early discovered symptom may enable investigators to test therapies aimed for intervention rather than remediation. Our results demonstrate the feasibility and potential of detecting subtle behavioral effects using data mining strategies. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Multiple repetitive DNA sequences in the paracentromeric regions of Arabidopsis thaliana L

An efficient purification protocol for infectivity causing a transmissible spongiform encephalopathy (TSE) is described. From fractions purified by this protocol about 3 x 10(8) LD50 but only 3 ng of nucleic acids per gram of brain material can be isolated from all TSE-affected brains (hamster, human, sheep, cattle). By PAGE such fractions from brains of infected and control hamsters contained only one distinct nucleic acid band of 1.5 kg together with some broader smear of nucleic acid material. Although distilled water was used for such purifications, quite often a similar nucleic acid band was isolated from blanks containing no brain material. In all instances this material proved to be DNA. The result challenges the potentially important claim that purified infectious preparations of TSE-specific amyloid are free of nucleic acids of viral size. Nucleic acids isolated by other groups from diseased brain were not detected in preparations isolated by the new protocol. The application of this purification protocol in future studies will be helpful to decide whether TSEs are caused by agents containing nucleic acid or by protein only.     

Scapholunate dissociation: a practical approach for the emergency physician

The development of new techniques in sequencing nuclei acids has produced a great amount of sequence data and has led to the discovery of new relationships. In this paper, we study a method for parallelizing the algorithm WORDUP, which detects the presence of statistically significant patterns in DNA sequences. WORDUP implements an efficient method to identify the presence of statistically significant oligomers in a non-homologous group of sequences. It is based on a modified version of the Boyer-Moore algorithm, which is one of the fastest algorithms for string matching available in the literature. The aim of the parallel version of WORDUP presented here is to speed up the computational time and allow the analysis of a greater set of longer nucleotide sequences, which is usually impractical with sequential algorithms.     

Representation of amino acid sequences as two-dimensional point patterns

An algorithm for the representation of amino acid sequences as two-dimensional point patterns (2-D plot) is described. The algorithm is based on chaos game representation (CGR) for DNA sequences and was extended for amino acid sequences. The 2-D plot depicts the sequentiality of amino acids and the amino acid composition of a protein. Changes in a protein sequence as insertion, deletion and repeats of amino acids are characterized by specific geometrical properties and changes in the 2-D plots. The 2-D plot may be considered as a two-dimensional "fingerprint" of a protein. The properties of the algorithm are explained by user-defined amino acid sequences. As an example the 2-D plots of two selected heart proteins are generated. The sequences of these proteins are obtained from the protein sequence database SWISS-PROT.     

SS3D-P2: a three dimensional substructure search program for protein motifs based on secondary structure elements

This paper discusses the implementation of a three-dimensional (3D) structure motif search of proteins. Each protein structure is represented by a set of secondary structure elements (SSEs) which involves alpha-helix segments and beta-strand segments. In describing it, every SSE is further reduced into a two-node graph that consists of the starting amino acid residue, the ending residue and a pseudo-bond between them. The searching algorithm is based on a graph theoretical clique-finding algorithm that has been used for 3D substructure searching in small organic molecules. The program SS3D-P2 was validated using proteins that have well-known 3D motifs, and it correctly found the Greek key motif within an eye lens protein, crystallin, that consists of four anti-parallel beta strands. The program was also successfully applied to searching for the more complex 3D motif, TIM-type beta-barrel motif, with a protein structure database from the Protein Data Bank.     

Use of GA to Determine Areas of Accretionto Semiconfined Aquifer

The goal of any groundwater inverse problem is to identify the distribution of an input function or certain other variables describing the unique flow dynamics of an aquifer system. A genetic algorithm (GA) combined with a numerical modeling technique is useful in determining both the spatial distribution and the flux represented by the accretion component of the groundwater flow equation. The GA technique was compared to a modified Gauss-Newton iterative technique. Binary and hexadecimal representations provided mapping of parameters from genetic operators to the numerical model. The technique used the patterns that developed in the string representations to determine probability regions. Two synthetic test cases were used to test the effectiveness of the technique. The stability of the technique was evaluated by introducing random error into the observation data. The technique was capable of locating the accretion area and tended to converge to a flux most representative of the flux entering the aquifer. However, the technique was susceptible to typical problems affecting the inverse problem, such as nonuniqueness.