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PubMedDate not supplied

Computational haemodynamics analysis and comparison study of arterio-venous grafts.

Haemodialysis arterio-venous graft failure is related to the development of stenotic lesions most commonly located near the venous anastomosis, especially in the toe region. 'Disturbed flow' interaction with the vessel wall surface, characterized by haemodynamic parameters based on the local wall shear stress or the radial pressure gradient, have been widely recognized as the trigger mechanism of a cascade of abnormal biological events leading to occlusive developments. Assuming incompressible laminar flow and rigid, in-plane vessel walls, validated haemodynamics are numerically simulated for a constant-diameter end-to-side base case, the Venaflo graft, and an improved graft-end configuration. The geometric design of the new graft-end was based on the reduction of three time- and area-averaged haemodynamic parameters, i.e. the wall shear stress gradient, wall shear stress angle gradient, and radial pressure gradient. Considering the critical toe region, the Venaflo graft has demonstrated measurable improvements over the base case configuration in predictive computer simulations as well as in clinical trials. The performance improvement should be further enhanced with the modifications illustrated by the new design.

Arteriovenous Shunt, Surgical↗
PubMed2006

Functional and topological characterization of novel components of the comB DNA transformation competence system in Helicobacter pylori.

Helicobacter pylori is one of the most diverse bacterial species known. A rational basis for this genetic variation may be provided by its natural competence for genetic transformation and high-frequency recombination. Many bacterial competence systems have homology with proteins that are involved in the assembly of type IV pili and type II secretion systems. In H. pylori, DNA uptake relies on a transport system related to type IV secretion systems (T4SS) designated the comB system. The prototype of a T4SS in Agrobacterium tumefaciens consists of 11 VirB proteins and VirD4, which form the core unit necessary for the delivery of single proteins or large nucleoprotein complexes into target cells. In the past we identified proteins ComB4 and ComB7 through ComB10 as being involved in the process of DNA uptake in H. pylori. In this study we identified and functionally characterized further (T4SS-homologous) components of the comB transformation competence system. By combining computer prediction modeling, experimental topology determination, generation of knockout strains, and genetic complementation studies we identified ComB2, ComB3, and ComB6 as essential components of the transformation apparatus, structurally and functionally homologous to VirB2, VirB3, and VirB6, respectively. comB2, comB3, and comB4 are organized as a separate operon. Thus, for the H. pylori comB system, all T4SS core components have been identified except for homologues to VirB1, VirD4, VirB5, and VirB11.

Bacterial Proteins↗
PubMed2007

Mitoproteome: human heart mitochondrial protein sequence database.

The human mitochondrial proteome database has been developed by deriving data from a combination of public repositories and experimental and computational prediction methods. The experimental data is derived from highly purified mitochondria from human heart tissue, whereas predictions have been performed by MITOPRED, a genome-scale method for the prediction of nucleus-encoded mitochondrial proteins. Mitochondrial protein sequences from different sources have been clustered to generate a nonredundant dataset. Annotations related to the protein function, structure, disease association, pathways, and so on are collected from a number of public databases using commonly used UNIX and Perl scripts. This chapter provides a detailed description of various data sources and methods used to download, curate, parse, and generate meaningful annotations from primary as well as derived databases.

Computational Biology↗
PubMed1990

Computer simulation in the design of local exhaust hoods for shielded metal arc welding.

Computer simulations were used to examine competing exhaust hood configurations for shielded metal arc welding. The welder's breathing zone concentration appears to be an inverse linear function of the computer-predicted hood capture efficiency. Hood aspect ratio, hood flow, and the welder's position relative to the hood all have a significant effect on the breathing zone concentration. The height of the hood above the welding surface showed no significant effect in reducing breathing zone concentration. Further examination of breathing zone concentration as a function of capture efficiency is needed before reliable design methods can be developed using this parameter.

Air Movements↗
PubMed2006

Plant 5S rDNA has multiple alternative nucleosome positions.

In plants, 5S ribosomal DNA (5S rDNA) is typically found in hundreds of copies of tandemly arranged units. Nucleotide database searches revealed that the majority of 5S genes (>90%) have repeat lengths that are not simple multiples of a plant nucleosomal unit, ranging in plants from 175-185 bp. To get insight into the chromatin structure, we have determined positions of nucleosomes in the Nicotiana sylvestris and Nicotiana tomentosiformis 5S rDNA units with repeat lengths of about 430 and 645 bp, respectively. Mapping experiments carried out on isolated nucleo somal DNA revealed many (>50) micrococcal nuclease cleavage sites in each class of repeats. Permutation analysis and theoretical computer prediction showed multiple DNA bend sites, mostly located in the nontranscribed spacer region. The distance between bend sites, however, did not correspond to the average spacing of nucleosomes in 5S chromatin (approximately 180 bp). These data indicate that 5S rDNA does not have fixed nucleosomal positioning sites and that units can be wrapped in a number of alternative nucleosome frames. Consequently, accessibility of transcription factors to cognate motifs might vary across the tandem array, potentially influencing gene expression.

Chromatin↗
PubMed2005

Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database.

Based on comparative genomics, we created a bioinformatic package for computer prediction of small nucleolar RNA (snoRNA) genes in mammalian introns. The core of our approach was the use of the Mammalian Orthologous Intron Database (MOID), which contains all known introns within the human, mouse and rat genomes. Introns from orthologous genes from these three species, that have the same position relative to the reading frame, are grouped in a special orthologous intron table. Our program SNO.pl searches for conserved snoRNA motifs within MOID and reports all cases when characteristic snoRNA-like structures are present in all three orthologous introns of human, mouse and rat sequences. Here we report an example of the SNO.pl usage for searching a particular pattern of conserved C/D-box snoRNA motifs (canonical C- and D-boxes and the 6 nt long terminal stem). In this computer analysis, we detected 57 triplets of snoRNA-like structures in three mammals. Among them were 15 triplets that represented known C/D-box snoRNA genes. Six triplets represented snoRNA genes that had only been partially characterized in the mouse genome. One case represented a novel snoRNA gene, and another three cases, putative snoRNAs. Our programs are publicly available and can be easily adapted and/or modified for searching any conserved motifs within mammalian introns.

Algorithms↗
PubMed2000

EID: the Exon-Intron Database-an exhaustive database of protein-coding intron-containing genes.

To aid studies of molecular evolution and to assist in gene prediction research, we have constructed an Exon-Intron Database (EID) in FASTA format. Currently, the database is derived from GenBank release 112, and it contains 51 289 protein-coding genes (287 209 exons) that harbor introns, along with extensive descriptions of each gene and its DNA and protein sequences, as well as splice motif information. There is 17% redundancy inherited from GenBank-a purge at the 99% identity level reduced the database to 42 460 genes (243 589 exons). We have created subdatabases of genes whose intron positions have been experimentally determined. One such database, constructed by comparing genomic and mRNA sequences, contains 11 242 genes (62 474 exons). A larger database of 22 196 genes (105 595 exons) was constructed by selecting on keywords to eliminate computer-predicted genes. By examining the two nucleotides adjacent to the intron boundary, we infer that there is a 2% rate of errors or other deviations from the standard GTellipsisAG motif in nuclear genes. This criterion can be used to eliminate 4921 genes from the overall database. Various tools are provided to enable generation of user-specific subsets of the EID. The EID distribution can be obtained from http://mcb.harvard.edu/gilbert/EID

Base Sequence↗
PubMed2004

Frequency bandwidth limitation of external pulse electric field in microchannels. Applications to analyte velocity modulation detections.

Pulse field driven electro-separations have been used for different analytical advantages, such as signal quality improvement and separation performance improvement. We have studied the temporal electro-osmosis in microchannels due to viscous diffusivity under the external pulse electric fields. Theoretical studies derived from Navier-Stokes equations conclude the dependence of the time to steady state electro-osmosis on the channel sizes. Pulse field frequency should be limited by the electro-osmosis setting-in time. We also observed the unstable electro-osmosis as the external field frequency increases. As channel geometry characterization results are employed in the mathematical models, the threshold frequencies obtained in experimental data are consistent with the computational predictions. In previous studies, effective signal quality improvement of electro-separations has been demonstrated, when external pulse fields modulate analyte velocities with synchronous lock-in detection. The results indicate signal-to-noise ratio improvement would be more significant at the high frequency regime where flicker noise is not dominant. Since bandwidth limitation due to fluid viscosity constrains the pulse frequency, optimum analyte velocity modulation is in need of further investigation. Under the bandwidth constrains, we have investigated the theoretical optimum modulation frequencies.

Computer Simulation↗
PubMedDate not supplied

Phantom studies and preliminary clinical experience with the BSD 2000.

The BSD 2000 system is an array of microwave antennas operating in the 60-120 MHz range. It is a four-quadrant regional hyperthermia device with phase control permitting the operator to choose the point of constructive interference. A computer preplanning system is provided. We have compared the computer predictions with measured relative specific absorption rate (SAR) distributions in muscle equivalent phantoms and pig cadaver. The predicted SAR distribution is in qualitative agreement with observation, although differences of approximately 3-5 cm in the location of iso- SAR contours were noted. The longitudinal dependence of relative of distance cephalad to the central plane of the power distribution was measured, and it was found that a length of 15-20 cm was covered by the 50% iso-SAR. SAR measurements in the spinal canal of a pig cadaver showed that, even at resonance frequency, the measured SAR in the cervical spine was small (0.07 of central axis SAR). However, the spinal canal SAR as measured in the central plane of an evenly balanced configuration was 0.6 of the peak SAR. Marked reduction of the spinal canal SAR could be obtained with steering techniques and was in good agreement with the computer preplan. This paper reviews preliminary clinical experience with 17 patients. All but 2 patients were treated with steering techniques to permit partial sparing of normal tissues. The goal of maintaining central tumour temperature at or above 42 degrees C for at least 30 min was maintained in 41 of 67 sessions (61%) and in at least one session for all but 2 patients. Seventy-seven per cent of monitored tumor points attained at least 42 degrees C in patients for whom thermal mapping was performed. Significant cardiovascular stress developed during hyperthermia in two patients. There have been five complete responses and seven partial responses in the 17 patients.

Combined Modality Therapy↗
PubMed2005

Fluorotrimethylsilane affinities of anionic nucleophiles: a study of fluoride-induced desilylation.

In this study, preparation and decomposition of five novel pentavalent fluorosiliconates, RSi(CH3)3F- (R = CH3CH2O, CF3CH2O, (CH3)2CHO, (CH3)3SiO, and (CH3)3SiNH) is used to investigate the process of fluoride-induced desilylation. The siliconates were characterized by collision-induced dissociation and energy-resolved mass spectrometry. Decomposition of RSi(CH3)3F- leads to loss of the nucleophile R- and FSi(CH3)3, except in the case of (CH3)3SiNHSi(CH3)3F-, where HF loss is also observed. Ion affinities for FSi(CH3)3 have been measured for all five nucleophiles, and compare well with computational predictions. The observed trend of the bond dissociation energies resembles the trend of deltaH(acid) values for the corresponding conjugate acids, RH. Additionally, this data has been incorporated with existing thermochemistry to derive fluoride affinities for four of the silanes (R = CH3CH2O, (CH3)2CHO, (CH3)3SiO, and (CH3)3SiNH). We use the fluoride affinity of the silanes and the FSi(CH3)3 affinity of the departing nucleophilic anion to assess the feasibility of fluoride-induced desilylation of the silanes examined in this work.

Anions↗
PubMed2005

Why relevant chemical information cannot be exchanged without disclosing structures.

Both society and industry are interested in increasing the safety of pharmaceuticals. Potentially dangerous compounds could be filtered out at early stages of R&D by computer prediction of biological activity and ADMET characteristics. Accuracy of such predictions strongly depends on the quality & quantity of information contained in a training set. Suggestion that some relevant chemical information can be added to such training sets without disclosing chemical structures was generated at the recent ACS Symposium. We presented arguments that such safety exchange of relevant chemical information is impossible. Any relevant information about chemical structures can be used for search of either a particular compound itself or its close analogues. Risk of identifying such structures is enough to prevent pharma industry from relevant chemical information exchange.

Computer Simulation↗
PubMed1992

A computer model to predict empty body weight in cattle from diet and animal characteristics.

A computer model was developed to predict empty BW in cattle as a function of diet (forage NDF, physical form of forage [hay vs silage and pasture], proportion of dietary concentrates) and animal (full BW) characteristics. The model was empty BW = full BW * (1 - GFILL), where GFILL is gut fill expressed as a fraction of full BW. An equation obtained from published data (GFILL = .05354 + .329 * NDF) was used to provide a base prediction of GFILL from the fraction of NDF in the forage. Predicted GFILL was then corrected for full BW, physical form of forage, and fraction of concentrates using multiplicative factors obtained from published data. The model was evaluated with data from 11 published experiments. Several breeds of cattle, a wide range of forage types, and diets with 0 to 93% concentrates were represented in these data. Observed values for empty BW were compared to model-predicted values and to values predicted by systems published by the Agricultural Research Council (ARC) and National Research Council (NRC). Sums of squared deviations of predicted values from observed (n = 64) were 3,074, 37,327, and 25,920 for the model, ARC, and NRC systems, respectively. After fitting predicted empty BW values to observed values, proportion of concentrates and forage NDF accounted for a significant (P less than .01) amount of the residual variation with the ARC and NRC systems, but not for the model. This finding suggests that the model will predict empty BW more accurately than the ARC and NRC systems with diets similar to those used in the evaluation.

Animal Feed↗
PubMed1980

Restriction mapping of cDNA recombinants including the adult chicken and duck globin messenger sequences: a comparative study.

A comparison of the organization of six avian adult globin messenger sequences is based on previously reported recombinant duck adult globin cDNA plasmids (Therwath et al., 1980) and the actual construction and characterization of pBR322 recombinant plasmids including the beta and the normal alpha A and alpha D chicken adult globin mRNA sequences. Identification of the cloned DNA was performed using hybridization-selection under conditions permitting complete purification in one step of the three globin mRNAs, and translation of the corresponding mRNA. Orientation of the globin insert in the vector was determined, taking into account the computer prediction of the restriction sites based on the known amino acid sequences of the three globin chains (Roizès and Pelaquier, 1980) and those actually observed, and by identification of restriction fragments using 3'-specific probes. Identification, orientation and restriction mapping of these cloned DNAs reveals extensive homologies in organisation of beta sequences between duck and chicken, as well as among the alpha sequences in every two possible combinations.

Animals↗
PubMed2006

A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila.

BACKGROUND: Biological processes are mediated by networks of interacting genes and proteins. Efforts to map and understand these networks are resulting in the proliferation of interaction data derived from both experimental and computational techniques for a number of organisms. The volume of this data combined with the variety of specific forms it can take has created a need for comprehensive databases that include all of the available data sets, and for exploration tools to facilitate data integration and analysis. One powerful paradigm for the navigation and analysis of interaction data is an interaction graph or map that represents proteins or genes as nodes linked by interactions. Several programs have been developed for graphical representation and analysis of interaction data, yet there remains a need for alternative programs that can provide casual users with rapid easy access to many existing and emerging data sets. DESCRIPTION: Here we describe a comprehensive database of Drosophila gene and protein interactions collected from a variety of sources, including low and high throughput screens, genetic interactions, and computational predictions. We also present a program for exploring multiple interaction data sets and for combining data from different sources. The program, referred to as the Interaction Map (IM) Browser, is a web-based application for searching and visualizing interaction data stored in a relational database system. Use of the application requires no downloads and minimal user configuration or training, thereby enabling rapid initial access to interaction data. IM Browser was designed to readily accommodate and integrate new types of interaction data as it becomes available. Moreover, all information associated with interaction measurements or predictions and the genes or proteins involved are accessible to the user. This allows combined searches and analyses based on either common or technique-specific attributes. The data can be visualized as an editable graph and all or part of the data can be downloaded for further analysis with other tools for specific applications. The database is available at http://proteome.wayne.edu/PIMdb.html CONCLUSION: The Drosophila Interactions Database described here places a variety of disparate data into one easily accessible location. The database has a simple structure that maintains all relevant information about how each interaction was determined. The IM Browser provides easy, complete access to this database and could readily be used to publish other sets of interaction data. By providing access to all of the available information from a variety of data types, the program will also facilitate advanced computational analyses.

Database Management Systems↗
PubMed2000

A stable argon compound

The noble gases have a particularly stable electronic configuration, comprising fully filled s and p valence orbitals. This makes these elements relatively non-reactive, and they exist at room temperature as monatomic gases. Pauling predicted in 1933 that the heavier noble gases, whose valence electrons are screened by core electrons and thus less strongly bound, could form stable molecules. This prediction was verified in 1962 by the preparation of xenon hexafluoroplatinate, XePtF6, the first compound to contain a noble-gas atom. Since then, a range of different compounds containing radon, xenon and krypton have been theoretically anticipated and prepared. Although the lighter noble gases neon, helium and argon are also expected to be reactive under suitable conditions, they remain the last three long-lived elements of the periodic table for which no stable compound is known. Here we report that the photolysis of hydrogen fluoride in a solid argon matrix leads to the formation of argon fluorohydride (HArF), which we have identified by probing the shift in the position of vibrational bands on isotopic substitution using infrared spectroscopy. Extensive ab initio calculations indicate that HArF is intrinsically stable, owing to significant ionic and covalent contributions to its bonding, thus confirming computational predictions that argon should form a stable hydride species with properties similar to those of the analogous xenon and krypton compounds reported before.

Journal Article↗
PubMed2006

DRTF: a database of rice transcription factors.

SUMMARY: DRTF contains 2025 putative transcription factors (TFs) in Oryza sativa L. ssp. indica and 2384 in ssp. japonica, distributed in 63 families, identified by computational prediction and manual curation. It includes detailed annotations of each TF including sequence features, functional domains, Gene Ontology assignment, chromosomal localization, EST and microarray expression information, as well as multiple sequence alignment of the DNA-binding domains for each TF family. The database can be browsed and searched with a user-friendly web interface. AVAILABILITY: DRTF is available at http://drtf.cbi.pku.edu.cn

Database Management Systems↗
PubMed2006

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

Information about the genomic coordinates and the sequence of experimentally identified transcription factor binding sites is found scattered under a variety of diverse formats. The availability of standard collections of such high-quality data is important to design, evaluate and improve novel computational approaches to identify binding motifs on promoter sequences from related genes. ABS (http://genome.imim.es/datasets/abs2005/index.html) is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. A simple and easy-to-use web interface facilitates data retrieval allowing different views of the information. In addition, the release 1.0 of ABS includes a customizable generator of artificial datasets based on the known sites contained in the collection and an evaluation tool to aid during the training and the assessment of motif-finding programs.

Animals↗
PubMed2007

MicroRNA and cancer: Current status and prospective.

Gene expression in normal cells is highly regulated by complex gene regulatory networks. Disruption of these networks may lead to cancer. Recent studies have revealed the existence of an abundant class of small nonprotein-coding regulatory RNAs, known as microRNAs (miRNAs). MiRNAs may regulate diverse biological processes including development, cell proliferation, differentiation and apoptosis, through suppressing the expression of their target genes. Posttranscriptional silencing of target genes by miRNAs occurs either by cleavage of homologous target messenger RNAs (mRNAs), or by inhibition of target protein synthesis. Computational predictions indicate that 1 miRNA may target on hundreds of genes, and suggest that over 50% of human protein-coding genes might be regulated by miRNAs. MiRNAs are receiving increased attention in cancer genomic research. We are beginning to understand that miRNAs may act as oncogenes and/or tumor suppressor genes within the molecular architecture of gene regulatory networks, thereby contributing to the development of cancer. MiRNAs may provide useful diagnostic and prognostic markers for cancer diagnosis and treatment, as well as serving as potential therapeutic targets or tools.

Animals↗