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PubMed1996

DNA-drug refinement: a comparison of the programs NUCLSQ, PROLSQ, SHELXL93 and X-PLOR, using the low-temperature d(TGATCA)-nogalamycin structure.

In an earlier study [Smith, Davies, Dodson & Moore (1995). Biochemistry, 34, 415-425] the crystal structure of the d(TGATCA)-nogalamycin complex was determined to 1.8 A and refined with PROLSQ to R = 19.5% against 4767 reflections with F> 1sigma(F). A low-temperature crystallographic study on this complex has now been performed. Native data collection at liquid-nitrogen temperature (120 K) improved the resolution to 1.4 A. The structure has now been refined against these new diffraction data in the resolution range 8-1.4 A using NUCLSQ, PROLSQ, SHELXL93 and X-PLOR, in order to determine to what extent the resulting DNA conformation and associated solvent structure would differ and to examine the suitability of these programs for the refinement of oligonucleotide structures. With the advent of more DNA-protein structure determinations, it is of interest to see how well the protein-refinement packages, PROLSQ and X-PLOR, and the small-molecule program, SHELXL93, are able to accommodate DNA. Comparisons are made between the dictionaries, weights and restraints used and the final models obtained from each program. Although the final R values, using all data in the resolution range 8.0-1.4 A, from PROLSQ (22.8%), SHELXL93 (R1 =21.7% after isotropic refinement) and X-PLOR (24.4%) are higher than the R value from the NUCLSQ refinement (21.2%), the root-mean-square deviations between the four final models are very small. Using this high-quality 8.0-1.4 A data set neither the dictionary nor the refinement program leave an imprint on the final fully refined complex. Likewise, the helical parameters and backbone conformation including sugar-puckering modes are not influenced by the refinement procedure used. Although a different number of water molecules is found in each refinement, varying from 62 (X-PLOR) to 86 (NUCLSQ), the first hydration sphere is well conserved in all four models.

Journal Article↗

PubMed1999

Remarks about protein structure precision.

Full-matrix least squares is taken as the basis for an examination of protein structure precision. A two-atom protein model is used to compare the precisions of unrestrained and restrained refinements. In this model, restrained refinement determines a bond length which is the weighted mean of the unrestrained diffraction-only length and the geometric dictionary length. Data of 0.94 A resolution for the 237-residue protein concanavalin A are used in unrestrained and restrained full-matrix inversions to provide standard uncertainties sigma(r) for positions and sigma(l) for bond lengths. sigma(r) is as small as 0.01 A for atoms with low Debye B values but increases strongly with B. The results emphasize the distinction between unrestrained and restrained refinements and between sigma(r) and sigma(l). Other full-matrix inversions are reported. Such inversions require massive calculations. Several approximate methods are examined and compared critically. These include a Fourier map formula [Cruickshank (1949). Acta Cryst. 2, 65-82], Luzzati plots [Luzzati (1952). Acta Cryst. 5, 802-810] and a new diffraction-component precision index (DPI). The DPI estimate of sigma(r, Bavg) is given by a simple formula. It uses R or Rfree and is based on a very rough approximation to the least-squares method. Many examples show its usefulness as a precision comparator for high- and low-resolution structures. The effect of restraints as resolution varies is examined. More regular use of full-matrix inversion is urged to establish positional precision and hence the precision of non-dictionary distances in both high- and low-resolution structures. Failing this, parameter blocks for representative residues and their neighbours should be inverted to gain a general idea of sigma(r) as a function of B. The whole discussion is subject to some caveats about the effects of disordered regions in the crystal.

Protein Conformation↗

PubMed2006

JPEG compression history estimation for color images.

We routinely encounter digital color images that were previously compressed using the Joint Photographic Experts Group (JPEG) standard. En route to the image's current representation, the previous JPEG compression's various settings-termed its JPEG compression history (CH)-are often discarded after the JPEG decompression step. Given a JPEG-decompressed color image, this paper aims to estimate its lost JPEG CH. We observe that the previous JPEG compression's quantization step introduces a lattice structure in the discrete cosine transform (DCT) domain. This paper proposes two approaches that exploit this structure to solve the JPEG Compression History Estimation (CHEst) problem. First, we design a statistical dictionary-based CHEst algorithm that tests the various CHs in a dictionary and selects the maximum a posteriori estimate. Second, for cases where the DCT coefficients closely conform to a 3-D parallelepiped lattice, we design a blind lattice-based CHEst algorithm. The blind algorithm exploits the fact that the JPEG CH is encoded in the nearly orthogonal bases for the 3-D lattice and employs novel lattice algorithms and recent results on nearly orthogonal lattice bases to estimate the CH. Both algorithms provide robust JPEG CHEst performance in practice. Simulations demonstrate that JPEG CHEst can be useful in JPEG recompression; the estimated CH allows us to recompress a JPEG-decompressed image with minimal distortion (large signal-to-noise-ratio) and simultaneously achieve a small file-size.

Algorithms↗

PubMed2004

Analysis and synthesis of textured motion: particles and waves.

Natural scenes contain a wide range of textured motion phenomena which are characterized by the movement of a large amount of particle and wave elements, such as falling snow, wavy water, and dancing grass. In this paper, we present a generative model for representing these motion patterns and study a Markov chain Monte Carlo algorithm for inferring the generative representation from observed video sequences. Our generative model consists of three components. The first is a photometric model which represents an image as a linear superposition of image bases selected from a generic and overcomplete dictionary. The dictionary contains Gabor and LoG bases for point/particle elements and Fourier bases for wave elements. These bases compete to explain the input images and transfer them to a token (base) representation with an O(10(2))-fold dimension reduction. The second component is a geometric model which groups spatially adjacent tokens (bases) and their motion trajectories into a number of moving elements--called "motons." A moton is a deformable template in time-space representing a moving element, such as a falling snowflake or a flying bird. The third component is a dynamic model which characterizes the motion of particles, waves, and their interactions. For example, the motion of particle objects floating in a river, such as leaves and balls, should be coupled with the motion of waves. The trajectories of these moving elements are represented by coupled Markov chains. The dynamic model also includes probabilistic representations for the birth/death (source/sink) of the motons. We adopt a stochastic gradient algorithm for learning and inference. Given an input video sequence, the algorithm iterates two steps: 1) computing the motons and their trajectories by a number of reversible Markov chain jumps, and 2) learning the parameters that govern the geometric deformations and motion dynamics. Novel video sequences are synthesized from the learned models and, by editing the model parameters, we demonstrate the controllability of the generative model.

Algorithms↗

PubMed1990

An exploratory study of selected female registered nurses: meaning and expression of nurturance.

The words 'nurse' and 'nursing' originate in the word 'nurture' which dates back to the 14th century. 'Nurturance' appeared for the first time in the 1976 Supplement to the Oxford English Dictionary and in a United States dictionary in 1983. Etymologically and semantically bound to nursing, little is known about the term nurturance. An exploratory design using phenomenological analysis was applied to understand the female registered nurses' experience of nurturing patients throughout the life-span and to uncover behaviours commonly believed nurturant. Interviews with 14 RNs practising in diverse settings revealed 39 nurturant behaviours that were intuited into four themes describing the subjects' perceived structure of nurturance as: (1) enabling maximum potential; (2) providing physical and emotional protection; (3) engaging in a supportive interaction; and (4) conveying shared humanity. Data were formulated into an exhaustive description of the phenomenon nurturance. Additionally, the results support Greenberg-Edelstein's theoretical model of the positive reciprocity of nurturance between nurse and patient.

Adult↗

PubMed1975

Topological formulation of finger-tip patterns: comparison of complete and incomplete 21 trisomics with normal subjects.

Description of the topological formulation of finger-print patterns is given and illustrated by examples. In particular, the way of setting up a dictionary of total finger pattern types for the two hands separately and combined is explained. Samples of 302 normal individuals, 225 complete 21-trisomics and 173 incomplete 21-trisomics are analysed here using this method. The frequencies of the commonest total finger pattern types are compared in the three groups, using dictionaries, in which all the formulae have been listed. The mean values of radial and ulnar components for each pair of homologous fingers separately are also compared. The method is recommended for comparisons of populations, particularly if the use of a computer is expected; it can also be helpful in evaluating the total finger pattern type of any individual, in terms of the probability of belonging to one population or another, particularly if the total palmar and sole pattern types can be compared as well. Some limitations of the method from a statistical point of view are also discussed.

Chromosomes, Human, 21-22 and Y↗

PubMed1983

Stress and vowel duration effects on syllable recognition.

Systems designed to recognize continuous speech must be able to adapt to many types of acoustic variation, including variations in stress. A speaker-dependent recognition study was conducted on a group of stressed and destressed syllables. These syllables, some containing the short vowel /I/ and others the long vowel /ae/, were excised from continuous speech and transformed into arrays of cepstral coefficients at two levels of precision. From these data, four types of template dictionaries varying in size and stress composition were formed by a time-warping procedure. Recognition performance data were gathered from listeners and from a computer recognition algorithm that also employed warping. It was found that for a significant portion of the data base, stressed and destressed versions of the same syllable are sufficiently different from one another as to justify the use of separate dictionary templates. Second, destressed syllables exhibit roughly the same acoustic variance as their stressed counterparts. Third, long vowels tend to be involved in proportionally fewer cross-vowel errors but tend to diminish the warping algorithm's ability to discriminate consonantal information. Finally, the pattern of consonant errors that listeners make as a function of vowel length shows significant differences from that produced by the computer.

Computers↗

PubMed1984

MRIDIR--a system for integrating research databases.

Lederle's Medical Research Integrated Database Information Retrieval (MRIDIR) system provides timely and facile access to a growing body of computerized, in-house data relating to pharmaceutical discovery and development. It was created in response to a proliferation of special-purpose programs, each dealing with a specific dataset and each with its own query syntax. Written in FORTRAN and interfacing to the System-1022 Database Management System, MRIDIR provides relational links between these datasets and, from the user's viewpoint, integrates them into a single database with a simple query language. A special dataset called the "data dictionary" describes these linkages, and alterations to the database structure (eg, addition of new datasets) are smoothly accomplished through changes to the data dictionary.

Drug Evaluation↗

PubMed2006

A graph-search framework for associating gene identifiers with documents.

BACKGROUND: One step in the model organism database curation process is to find, for each article, the identifier of every gene discussed in the article. We consider a relaxation of this problem suitable for semi-automated systems, in which each article is associated with a ranked list of possible gene identifiers, and experimentally compare methods for solving this geneId ranking problem. In addition to baseline approaches based on combining named entity recognition (NER) systems with a "soft dictionary" of gene synonyms, we evaluate a graph-based method which combines the outputs of multiple NER systems, as well as other sources of information, and a learning method for reranking the output of the graph-based method. RESULTS: We show that named entity recognition (NER) systems with similar F-measure performance can have significantly different performance when used with a soft dictionary for geneId-ranking. The graph-based approach can outperform any of its component NER systems, even without learning, and learning can further improve the performance of the graph-based ranking approach. CONCLUSION: The utility of a named entity recognition (NER) system for geneId-finding may not be accurately predicted by its entity-level F1 performance, the most common performance measure. GeneId-ranking systems are best implemented by combining several NER systems. With appropriate combination methods, usefully accurate geneId-ranking systems can be constructed based on easily-available resources, without resorting to problem-specific, engineered components.

Animals↗

PubMed1986

A methodological note on content analysis: estimates of reliability.

The reliability of measurements obtained from a dictionary-based form of content analysis was investigated in this experiment by tape-recording subjects as they spoke about a predetermined topic in two separate sessions 1 week apart. Subjects were randomly assigned to speak in one of two contexts. The content of transcripts of these sessions was analyzed using adaptations of the Harvard III Psychosociological Dictionary and the General Inquirer content analysis program (Stone, Dunphy, Smith, & Ogilvie, 1966). Reliability was high over time, both within and between sessions, and there were few differences observed between contexts. Results are discussed in terms of their implications for the use of content analysis in personality research.

Journal Article↗

PubMed2005

A seqlet-based maximum entropy Markov approach for protein secondary structure prediction.

A novel method for predicting the secondary structures of proteins from amino acid sequence has been presented. The protein secondary structure seqlets that are analogous to the words in natural language have been extracted. These seqlets will capture the relationship between amino acid sequence and the secondary structures of proteins and further form the protein secondary structure dictionary. To be elaborate, the dictionary is organism-specific. Protein secondary structure prediction is formulated as an integrated word segmentation and part of speech tagging problem. The word-lattice is used to represent the results of the word segmentation and the maximum entropy model is used to calculate the probability of a seqlet tagged as a certain secondary structure type. The method is markovian in the seqlets, permitting efficient exact calculation of the posterior probability distribution over all possible word segmentations and their tags by viterbi algorithm. The optimal segmentations and their tags are computed as the results of protein secondary structure prediction. The method is applied to predict the secondary structures of proteins of four organisms respectively and compared with the PHD method. The results show that the performance of this method is higher than that of PHD by about 3.9% Q3 accuracy and 4.6% SOV accuracy. Combining with the local similarity protein sequences that are obtained by BLAST can give better prediction. The method is also tested on the 50 CASP5 target proteins with Q3 accuracy 78.9% and SOV accuracy 77.1%. A web server for protein secondary structure prediction has been constructed which is available at http://www.insun.hit.edu.cn:81/demos/biology/index.html.

Algorithms↗

PubMed2002

Automated signal generation in prescription-event monitoring.

Signal generation is a method of highlighting potential safety issues in a drug that then need to be investigated further. Previously automated signal generation has mainly been applied to spontaneous reporting systems. The Drug Safety Research Unit (DSRU) performs observational postmarketing studies on selected newly marketed medicines in England using a method known as prescription-event monitoring (PEM). The DSRU has investigated automated procedures for the generation of signals using the event data from PEM studies. Proportional reporting ratios (PRRs) and incidence rate ratios (IRRs) were studied as possible tools for signal generation in PEM data. The PEM database contains 78 completed studies of drugs prescribed in primary care from a variety of therapeutic classes. Retrospective studies were carried out to identify the implications of changing the comparator group of drugs, along with analysing the results at different levels in the DSRU's hierarchical dictionary and performing signal generation after 30 and 180 days of observation since starting the drug. Automated signal generation is a useful hypothesis generating method that is likely to prove to be useful both in clinical trials and postmarketing studies. PRRs are simple to apply and do not require a denominator. IRRs take into account the time subjects were exposed to the drug prior to the event of interest, and offers a useful, and more in depth look into the data. However, with both methods it is important to perform signal generation at multiple levels in the dictionary and with careful selection of the comparator group.

Adverse Drug Reaction Reporting Systems↗

PubMed2001

BindingDB: a web-accessible molecular recognition database.

This paper presents an initial description of the BindingDB, a public web-accessible database of measured binding affinities for various molecular types (http://www.bindingdb.org). The BindingDB allows queries based upon a range of criteria, including chemical similarity or substructure, sequence homology, numerical criteria (e.g. delta G(o) < 5 kcal/mol) and reactant names (e.g. "lysozyme"). Principles of Human-Computer Interactions are being employed in creating the query interface and user-feedback is being solicited. The data specification includes significant experimental detail. A full dictionary has been created for isothermal titration calorimetry data in consultation with experimentalists and data dictionaries for enzyme-inhibition and other measurement techniques are being developed. Currently, the BindingDB contains several data sets of broad interest, such as antigen-antibody binding and cyclodextrin/small molecule binding. However, it is anticipated that online deposition by experimentalists will ultimately contribute to a larger flow of data. We are actively developing software and file specifications to facilitate such deposition.

Binding Sites↗

PubMed2000

The emotional importance of key: do Beatles songs written in different keys convey different emotional tones?

Lyrics from 155 songs written by the Lennon-McCartney team were scored using the Dictionary of Affect in Language. Resultant scores (pleasantness, activation, and imagery of words) were compared across key signatures using one way analyses of variance. Words from songs written in minor keys were less pleasant and less active than those from songs written in major keys. Words from songs written in the key of F scored extremely low on all three measures. Lyrics from the keys of C, D, and G were relatively active in tone. Results from Dictionary scoring were compared with assignments of character to keys made more than one century ago and with current musicians' opinions.

Emotions↗

PubMedDate not supplied

Design and implementation of a biomedical image database (BDIM).

We developed a biomedical image database (BDIM) which proposes a standardized representation of value arrays such as images and curves, and of their associated parameters, independently of their acquisition mode to make their transmission and processing easier. It includes three kinds of interactions, oriented to the users. The network concept was kept as a constraint to incorporate the BDIM in a distributed structure and we maintained compatibility with the ACR/NEMA communication protocol. The management of arrays and their associated parameters includes two distinct bases of objects, linked together via a gateway. The first one manages arrays according to their storage mode: long term storage on optionally on-line mass storage devices, and, for consultations, partial copies of long term stored arrays on hard disk. The second one manages the associated parameters and the gateway by means of the relational DBMS ORACLE. Parameters are grouped into relations. Some of them are in agreement with groups defined by the ACR/NEMA. The other relations describe objects resulting from processed initial objects. These new objects are not described by the ACR/NEMA but they can be inserted as shadow groups of ACR/NEMA description. The relations describing the storage and their pathname constitute the gateway. ORACLE distributed tools and the two-level storage technique will allow the integration of the BDIM into a distributed structure, Queries and array (alone or in sequences) retrieval module has access to the relations via a level in which a dictionary managed by ORACLE is included. This dictionary translates ACR/NEMA objects into objects that can be handled by the DBMS.(ABSTRACT TRUNCATED AT 250 WORDS)

Database Management Systems↗

PubMed1989

The effect of polysemy on lexical decision time: now you see it, now you don't.

Gernsbacher (1984) found that number of word meanings (polysemy) did not influence lexical decision time when it was operationalized as number of dictionary definitions. This finding supports her contention that subjects do not store all possible dictionary meanings for words in memory. The present experiments extended Gernsbacher's research by determining whether more psychologically valid measures of polysemy affect lexical decision time. Three metrics were used to represent the meanings that subjects actually access from memory (accessible polysemy): (1) the first meanings subjects think of when asked to define stimulus words, (2) all the meanings subjects generate for words, and (3) the average number of meanings subjects generate. The results showed that the second and third metrics of polysemy influenced lexical decision time, whereas the first metric (representing mostly the access to dominant meanings for words) only approached significance.

Adult↗

PubMed1989

The term preceptor: its interpretation in South African nursing colleges and international nursing literature.

The purpose of this study was two-fold, namely: 1) to obtain clarity on the meaning of the term preceptor, and 2) to establish how the term preceptor is interpreted in the nursing colleges of the RSA and to ascertain whether this interpretation is consistent with the general connotation of the term in contemporary nursing literature. Dictionaries and relevant contemporary nursing literature formed the unit of analysis for obtaining clarity on the meaning of the term preceptor, while the unit of analysis for the second section of the study comprised responses of nursing college principals to a questionnaire. The data obtained in the investigation indicate that the term has acquired a specific connotation within the international nursing context and that specific defined attributes distinguishes it from the broad and general definition found in standard dictionaries. Within the South African nursing context the term preceptor has not yet acquired a specific connotation, but appears to mean different things to different people.

Education, Nursing, Baccalaureate↗

PubMed1997

ADM-INDEX: an automated system for indexing and retrieval of medical texts.

ADM-INDEX is a system for indexing and retrieval of Patients Discharge Summaries (PDSs) by using linguistic methods (morphologic, syntaxic and semantic processing). The ADM-INDEX knowledge base is a restructuring of a diagnostic aid knowledge base (ADM) in order to allow the linguistic analysis of medical texts. The ADM system is a comprehensive medical knowledge base which has been developed since 1972 at the University Hospital of Rennes and which has been the first professional videotex medical diagnostic aid in France. After linguistic analysis, ADM-INDEX build the index table with thesaurus wording, medical words, concepts and phrases, unknown words contained in each PDS. The benefit of using those different elements is to improve information retrieval. Although our system is constructed with the ADM dictionary, it can be easily applied to other medical nomenclature or thesaurus. In this paper, we present on the one hand the ADM-INDEX knowledge base which is constituted by rules, a dictionary and a thesaurus, and on the other hand, the process of indexing and retrieval information.

Abstracting and Indexing↗