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At least 307 records · Page 17Linked to original sources
PubMed2003

Identification of biological relationships from text documents using efficient computational methods.

The biological literature databases continue to grow rapidly with vital information that is important for conducting sound biomedical research and development. The current practices of manually searching for information and extracting pertinent knowledge are tedious, time-consuming tasks even for motivated biological researchers. Accurate and computationally efficient approaches in discovering relationships between biological objects from text documents are important for biologists to develop biological models. The term "object" refers to any biological entity such as a protein, gene, cell cycle, etc. and relationship refers to any dynamic action one object has on another, e.g. protein inhibiting another protein or one object belonging to another object such as, the cells composing an organ. This paper presents a novel approach to extract relationships between multiple biological objects that are present in a text document. The approach involves object identification, reference resolution, ontology and synonym discovery, and extracting object-object relationships. Hidden Markov Models (HMMs), dictionaries, and N-Gram models are used to set the framework to tackle the complex task of extracting object-object relationships. Experiments were carried out using a corpus of one thousand Medline abstracts. Intermediate results were obtained for the object identification process, synonym discovery, and finally the relationship extraction. For the thousand abstracts, 53 relationships were extracted of which 43 were correct, giving a specificity of 81 percent. These results are promising for multi-object identification and relationship finding from biological documents.

Algorithms↗
PubMed2006

Determining suitable lego-structures to estimate stability of larger peptide nanostructures using computational methods.

Nanofibers, nanofilms and nanotubes constructed of one to four strands of oligo-alpha- and oligo-beta-peptides were obtained by using carefully selected building units. Lego-type approaches based on thermoneutral isodesmic reactions can be used to reconstruct the total energies of both linear and tubular periodic nanostructures with acceptable accuracy. Total energies of several different nanostructures were accurately determined with errors typically falling in the subchemical range. Thus, attention will be focused on the description of suitable isodesmic reactions that have enabled the determination of the total energy of polypeptides and therefore offer a very fast, efficient and accurate method to obtain energetic information on large and even very large nanosystems.

Algorithms↗
PubMed1999

Computational methods for the identification of differential and coordinated gene expression.

With the first complete 'draft' of the human genome sequence expected for Spring 2000, the three basic challenges for today's bioinformatics are more than ever: (i) finding the genes; (ii) locating their coding regions; and (iii) predicting their functions. However, our capacity for interpreting vertebrate genomic and transcript (cDNA) sequences using experimental or computational means very much lags behind our raw sequencing power. If the performances of current programs in identifying internal coding exons are good, the precise 5'-->3' delineation of transcription units (and promoters) still requires additional experiments. Similarly, functional predictions made with reference to previously characterized homologues are leaving >50% of human genes unannotated or classified in uninformative categories ('kinase', 'ATP-binding', etc.). In the context of functional genomics, large-scale gene expression studies using massive cDNA tag sequencing, two-dimensional gel proteome analysis or microarray technologies are the only approaches providing genome-scale experimental information at a pace consistent with the progress of sequencing. Given the difficulty and cost of characterizing genes one by one, academic and industrial researchers are increasingly relying on those methods to prioritize their studies and choose their targets. The study of expression patterns can also provide some insight into the function, reveal regulatory pathways, indicate side effects of drugs or serve as a diagnostic tool. In this article, I review the theoretical and computational approaches used to: (i) identify genes differentially expressed (across cell types, developmental stages, pathological conditions, etc.); (ii) identify genes expressed in a coordinated manner across a set of conditions; and (iii) delineate clusters of genes sharing coherent expression features, eventually defining global biological pathways.

Animals↗
PubMed2004

Theoretical and computational methods for the noninvasive detection of gastric electrical source coupling.

The ability to study the pathology of the stomach noninvasively from magnetic field measurements is important due to the significant practical advantages offered by noninvasive methods over other techniques of investigation. The inverse biomagnetic problem can play a central role in this process due to the information that inverse solutions can yield concerning the characteristics of the gastric electrical activity (GEA). To analyze gastrointestinal (GI) magnetic fields noninvasively, we have developed a computer implementation of a least-squares minimization algorithm that obtains numerical solutions to the biomagnetic inverse problem for the stomach. In this paper, we show how electric current propagation and the mechanical coupling of gastric smooth muscle cells during electrical control activity can be studied using such solutions. To validate our model, two types of numerical simulations of the GEA were developed and successfully used to demonstrate the ability of our computer algorithm to detect and accurately analyze these two phenomena. We also describe our analysis of experimental, noninvasively acquired gastric biomagnetic data as well as the information of interest that our numerical method can yield in clinical studies. Most importantly, we present experimental evidence that the coupling of gastric electrical sources can be observed using noninvasive techniques of measurement, in our case with the use of a superconducting quantum interference device magnetometer. We discuss the relevance and implications of our achievement to the future of GI research.

Algorithms↗
PubMed2000

Identification of parasitic genes by computational methods.

A number of parasite genome projects are under way, and large amounts of nucleotide sequence data are becoming available for analysis. There is an urgent need for development of theoretical tools to analyze the genome data, including identification of protein-coding sequences. The majority of the methods developed to date require prior information about the genome before accurate predictions can be made. Because such information is not available for many parasites, these methods cannot be directly applied. In this article, Alok Bhattacharya and colleagues describe some of the gene-prediction methods commonly in use, and a new method, GeneScan, that they have developed for the analysis of parasite genomes.

Animals↗
PubMed2002

Combinatorial computational method gives new picomolar ligands for a known enzyme.

Combinatorial small molecule growth algorithm was used to design inhibitors for human carbonic anhydrase II. Two enantiomeric candidate molecules were predicted to bind with high potency (with R isomer binding stronger than S), but in two distinct conformations. The experiments verified that computational predictions concerning the binding affinities and the binding modes were correct for both isomers. The designed R isomer is the best-known inhibitor (K(d) approximately 30 pM) of human carbonic anhydrase II.

Algorithms↗
PubMed2005

A computer method for validating traditional Chinese medicine herbal prescriptions.

Traditional Chinese medicine (TCM) has been widely practiced and is considered as an alternative to conventional medicine. TCM herbal prescriptions contain a mixture of herbs that collectively exert therapeutic actions and modulating effects. Traditionally defined herbal properties, related to the pharmacodynamic, pharmacokinetic and toxicological, as well as physicochemical properties of their principal ingredients, have been used as the basis for formulating TCM multi-herb prescriptions. These properties are used in this work to develop a computer program for predicting whether a multi-herb recipe is a valid TCM prescription. This program is based on a statistical learning method, support vector machine (SVM), and it is trained by using 575 well-known TCM prescriptions and 1961 non-TCM recipes generated by random combination of TCM herbs. Testing results by using 72 well-known TCM prescriptions and 5039 non-TCM recipes showed that 73.6% of the TCM prescriptions and 99.9% of non-TCM recipes are correctly classified by this system. A further test by using 48 TCM prescriptions published in recent years found that 68.7% of these are correctly classified. These accuracies are comparable to those of SVM classification of other biological systems. Our study indicates the potential of SVM for facilitating the analysis of TCM prescriptions.

Chemistry, Pharmaceutical↗
PubMed2005

A comparison of skyshine computational methods.

A variety of methods employing radiation transport and point-kernel codes have been used to model two skyshine problems. The first problem is a 1 MeV point source of photons on the surface of the earth inside a 2 m tall and 1 m radius silo having black walls. The skyshine radiation downfield from the point source was estimated with and without a 30-cm-thick concrete lid on the silo. The second benchmark problem is to estimate the skyshine radiation downfield from 12 cylindrical canisters emplaced in a low-level radioactive waste trench. The canisters are filled with ion-exchange resin with a representative radionuclide loading, largely 60Co, 134Cs and 137Cs. The solution methods include use of the MCNP code to solve the problem by directly employing variance reduction techniques, the single-scatter point kernel code GGG-GP, the QADMOD-GP point kernel code, the COHORT Monte Carlo code, the NAC International version of the SKYSHINE-III code, the KSU hybrid method and the associated KSU skyshine codes.

Air↗
PubMed2000

Benzodiazepine-induced hyperphagia: development and assessment of a 3D pharmacophore by computational methods.

Benzodiazepine receptor (BDZR) ligands are structurally diverse compounds that bind to specific binding sites on GABA(A) receptors and allosterically modulate the effect of GABA on chloride ion flux. The binding of BDZR ligands to this receptor system results in activity at multiple behavioral endpoints, including anxiolytic, sedative, anticonvulsant, and hyperphagic effects. In the work presented here, a computational procedure developed in our laboratory has been used to obtain a 3D pharmacophore for ligand recognition of the GABA(A)/BDZRs initiating the hyperphagic response. To accomplish this goal, 17 structurally diverse compounds, previously assessed in our laboratory for activity at the hyperphagic endpoint, were used. The result is a four-component 3D pharmacophore. It consists of two proton acceptor atoms, the centroid of an aromatic ring and the centroid of a hydrophobic moiety in a common geometric arrangement in all compounds with activity at this endpoint. This 3D pharmacophore was then assessed and successfully validated using three different tests. First, two BDZR ligands, which were included as negative controls in the set of seventeen compounds used for the pharmacophore development, did not fit the pharmacophore. Second, some benzodiazepine ligands known to have activity at the hyperphagia endpoint, but not included in the pharmacophore development, were used as positive controls and were found to fit the pharmacophore. Finally, using the 3D pharmacophore developed in the present work to search 3D databases, over 50 classical benzodiazepines were found. Among them, were benzodiazepine ligands known to have an effect at the hyperphagic endpoint. In addition, the novel compounds also found in this search are promising therapeutic agents that could beneficially affect feeding behavior.

Benzodiazepines↗
PubMed1984

Testing a theory of brain function by computer methods. III. Detecting cerebral asymmetry in normal adults.

Pursuing a plan for overall testing of the timing and sequencing of brain processes, testing techniques are introduced for probing a normal adult's short-term central processes, especially those which are employed in reading a digit span of 6 numbers or less. The tests are administered by means of a personal computer and can provide information on the individual subject's characteristic sequencing and timing of particular central processes. In a subject whose first language is read from left to right, the presented tests reported in this paper reveal an asymmetry in normal adults wherein digits presented in the left visual field are processed more efficiently than those presented in the right visual field. It is suggested that the right hemisphere 'holds the image' while the left hemisphere 'transforms' the spatial image into a temporal sequence for use in speech. The 'right-positioned' or 'later' components must be held at least until a successful spoken response is completed.

Brain↗
PubMed1984

Testing a theory of brain function by computer methods. IV. Comparing spatial and temporal order in the two cerebral hemispheres.

Continuing with a plan for overall testing of the timing and sequencing of brain processes, further testing techniques are introduced for probing a normal adult's short-term central processes, especially those which are employed in reading a short digit span. The tests are administered by means of a personal computer and can provide information on the individual subject's characteristic sequencing and timing of particular central processes. In a subject whose first language is read from left to right, the presented tests reported in this paper can reveal an interesting asymmetry. A temporal display of digits in the right visual field is correctly perceived more readily than in the left. Conversely, a brief, spatial display of digits in the left visual field is correctly reported more often than in the right. It is suggested, therefore, that there are individuals whose left hemisphere is superior in handling a temporal sequence of digits while the right hemisphere is superior in handling a spatial display of digits.

Adult↗