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PubMed2004

Paramagnetism-based restraints for Xplor-NIH.

Modules that use paramagnetism-based NMR restraints have been developed and integrated in the well known program for solution structure determination Xplor-NIH; the complete set of such modules is called PARArestraints for Xplor-NIH. Paramagnetism-based restraints are paramagnetic relaxation enhancements, pseudocontact shifts, residual dipolar couplings due to metal and overall magnetic anisotropy, and cross correlation between Curie relaxation and nuclear-nuclear dipolar relaxation. The complete program has been tested by back-calculating NOEs and paramagnetism-based restraints from the X-ray structure of cytochrome c (553) from B. pasteurii. Furthermore, the same experimental restraints previously used to determine the solution structure of cytochrome c (553) itself, of cytochrome b (5), and of calbindin D(9k) with the program PARAMAGNETIC DYANA, have been used for structure calculations by using PARArestraints for Xplor-NIH. The agreement between the two programs is quite satisfactory and validates both protocols.

Calbindins↗

PubMed2002

Identification of six novel genes by experimental validation of GeneMachine predicted genes.

In silico gene identification from finished and unfinished human genome sequence has become critically important in many projects seeking to gain insights into the gene content of genomic regions implicated in diseases. To establish limitations and criteria for in silico gene identification, and to identify novel genes of potential relevance to human prostate cancer and melanoma, 3 Mb of chromosome 1 sequence have been analyzed using GeneMachine. This program is a software suite comprising of sequence similarity programs and four gene identification programs. A total of 49 potential transcripts were selected and 37 of them were selected for experimental validation. We verified 16 of the predicted genes by experimental analysis. The comparison of the predicted transcripts with their cloned forms helped to refine predicted gene models as well as to identify splice variants for several of them. Although sequences matching with ten of our verified genes have been recently deposited in the GenBank, six of them remain novel. Our studies support the feasibility of identifying novel genes from regions of interest using draft human genome sequence.

Chromosomes, Human, Pair 1↗

PubMed1999

Face and contents validity, and feasibility of Healthometer: a Delphi study.

Our recent descriptive report in this journal of "Healthometer", an interactive instrument for self-mediated health counseling, was well received in the medical systems research and development community. Suitable for paper as well as electronic mediation and covering both screening, processing/storage, and advisory tasks in a positively reinforcing and confidential way, it has on the whole been considered to be an interesting model in the advancing "information society technologies" perspective; however, a closer scientific and operative evaluation is warranted. Because the power of the instrument in addition to the hardware is critically dependent upon the wet- and software quality, the present study aims at examining in the same forefront forum some basic aspects of all these modalities, with emphasis on face and content validity, feasibility, and users' attitudes and opinions. It can be summarized, quite briefly, that all of them were satisfactory.

Attitude to Health↗

PubMed2005

Analysis of glioma cell platinum response by metacomparison of two-dimensional chromatographic proteome profiles.

Successful clinical development of cancer treatments is aided by the development of molecular markers that allow the identification of patients likely to respond. In the case of broadly cytotoxic drugs, such as the multinuclear series of platinum chemotherapeutic agents that we are evaluating for the treatment of glioma, one route to marker identification is proteomic profiling. We are using the two-dimensional chromatography system, the ProteomeLab PF2D, to compare proteomic profiles of glioma cells in culture before and after drug treatment. The existing software tools allowed the rapid identification of peaks increased by treatment of a given drug as compared with control untreated cells. To compare across these pairs, we developed new software, called the MetaComparison Tool (MCT). The MCT uses the chromatographic characteristics of peaks as identifiers, an approach that was validated by mass spectrometry of two independent isolations of a peak, from cells that were treated with two different platinum compounds. The MCT made it possible to rapidly query whether a given peak responded to more than one treatment and so allowed the identification of peaks that were specific to a given drug. As a result, this analysis greatly reduced the list of peaks whose isolation and downstream analysis by mass spectrometry is warranted, accelerating the search for protein markers of response.

Antineoplastic Agents↗

PubMed2003

NOREC, a Monte Carlo code for simulating electron tracks in liquid water.

The work reported here was originally motivated by a discussion of Monte Carlo computer codes for electron transport in water given in Report No. 130 by the National Council on Radiation Protection and Measurements (NCRP). It was pointed out (correctly) that a published depth-dose distribution calculated by the Oak Ridge electron transport code, OREC, for 800 keV electrons normally incident on a water slab was apparently in error, possibly due to inadequate treatment of elastic scattering. In this paper we describe the replacement of the original OREC elastic cross sections by current ones from the National Institute of Standards and Technology (NIST). This investigation led also to the critical examination and revision of some other parts of the program, as described here. The revised code, which we have renamed NOREC, represents the first substantial review and modification of the Oak Ridge code in a number of years. We also present some comparisons of results calculated with the old and new versions and discuss their implications with respect to earlier studies. We have also written a version of NOREC in C++ language, which is available to other investigators. This paper provides a record of a response to the NCRP published statement and documentation for the revised code, NOREC.

Algorithms↗

PubMed1990

A BASIC software program to estimate cardiac output and alveolar ventilation.

This software program adds two very interesting data to the usual results of exercise testing: an estimation of cardiac output according to the most recent validations and a reliable estimation of alveolar ventilation. The main advantage of this additional ventilatory and cardiovascular information using the same data: end-tidal PCO2.

Carbon Dioxide↗

PubMedDate not supplied

A computer-assisted direct-imaging system to obtain numerical densities of neurons in human cortex.

Studies of the numerical density of microscopic items in brain tissue is a time-consuming endeavor. However, such information is important for numerous issues such as the relationship between structure and function in the normal brain, individual differences, and studies of brains of neuropsychiatric patients. A computer-assisted imaging system specifically devised to obtain estimates of numerical densities in human cortex is described here. Its main advantage is that the microscopist can analyze the original image directly under the microscope, and most aspects of data acquisition and quantitative analysis are accomplished by the computer. The key features of the system are a Microvid (an electronic camera lucida) and the use of X, Y, and Z stage encoders in conjunction with three-dimensional computer software. The complete system is relatively inexpensive and is simple to set up and use. The reliability and validity of the numerical densities obtained using this system are documented.

Cell Differentiation↗

PubMedDate not supplied

Metrological characterization of the ADONIS system used in gamma-ray spectrometry.

In gamma-ray spectrometry, new acquisition systems based on digital signal processing are now commercially available. In order to determine their performance at high count rates, the Commissariat à l'Energie Atomique (CEA), Laboratoire National Henri Becquerel has tested several of these systems. These tests have clearly shown that the performance levels announced by the manufacturers were generally not met. It was therefore a logical step to include the Atelier de DévelOppement Numérique pour l'Instrumentation en Spectrométrie (ADONIS) system in these tests. ADONIS is the new numerical system for gamma-ray spectrometry, developed by the CEA Service d'Instrumentation et d'Application des Rayonnements.

Algorithms↗

PubMed2005

Chlamydomonas reinhardtii proteomics.

Proteomics, based on the expanding genomic resources, has begun to reveal new details of Chlamydomonas reinhardtii biology. In particular, analyses focusing on subproteomes have already provided new insight into the dynamics and composition of the photosynthetic apparatus, the chloroplast ribosome, the oxidative phosphorylation machinery of the mitochondria, and the flagellum. It assisted to discovered putative new components of the circadian clockwork as well as shed a light on thioredoxin protein-protein interactions. In the future, quantitative techniques may allow large scale comparison of protein expression levels. Advances in software algorithms will likely improve the use of genomic databases for mass spectrometry (MS) based protein identification and validation of gene models that have been predicted from the genomic DNA sequences. Although proteomics has only been recently applied for exploring C. reinhardtii biology, it will likely be utilized extensively in the near future due to the already existing genetic, genomic, and biochemical tools.

Animals↗

PubMed2003

Software objects in distributed flow measurements.

Increasing complexity of the contemporary industrial measurement systems is a common characteristic. Partitioning of the measurement process into software components that can be realized as separate objects facilitates the development of the measurement system. Using a client/server approach, the measurement system components become shareable and accessible across the network. The components can be deployed anywhere on the network and shared by a considerable number of applications. The paper describes a realization of the flow measurement system with distributed software components, i.e., measurement procedures, which include the concurrent calculation of the measurement results and the corresponding uncertainties.

Computer Communication Networks↗

PubMed2003

Laser Doppler flux-metry in laryngeal squamous cell carcinoma.

Tumour angiogenesis has recently attracted a great deal of attention as a critical part of oncogenesis and a necessary prerequisite for a malignant phenotype. Novel antiangiogenic therapy for solid tumours including laryngeal cancer is entering clinical trials. Quantifying microvessel density is considered the gold standard for measuring baseline angiogenesis and indeed 'the response to intervention'. We hypothesize that laser Doppler flux-metry could provide a non-invasive reliable method of quantifying blood flux within tumours. The aims were to determine whether a laser Doppler flux meter could be used as a reliable and reproducible method of estimating blood flux in the human larynx and to establish baseline Doppler flux recordings for the human larynx. The method used was a validation study in patients with laryngeal squamous cell cancer and normal controls. Statistical analysis was performed using SPSS software. We have demonstrated good reproducibility of laser Doppler measurements in human laryngeal mucosa (correlation coefficient 0.956 @P = 0.01). We have also derived arbitrary means of laser Doppler flux-metry in normal laryngeal mucosa and in squamous cell carcinoma of the larynx. Comparisons between normal and tumour laser Doppler flux-metry (LDF) readings showed no significant difference. We suggest that Laser Doppler flux-metry is a potentially useful tool with which to study blood flow in the larynx and propose arbitrary LDF levels for the normal and diseased human larynx.

Carcinoma, Squamous Cell↗

PubMed2001

A refined prediction method for gel retardation of DNA oligonucleotides from dinucleotide step parameters: reconciliation of DNA bending models with crystal structure data.

The development and assessment of a prediction method for gel retardation and sequence dependent curvature of DNA based on dinulcleotide step parameters are described. The method is formulated using the Babcock-Olson equations for base pair step geometry (1) and employs Monte Carlo simulated annealing for parameter optimization against experimental data. The refined base pair step parameters define a stuctural construct which, when the width of observed parameter distributions is taken into account, is consistent with the results of DNA oligonucleotide crystal structures. The predictive power of the method is demonstrated and tested via comparisons with DNA bending data on sets of sequences not included in the training set, including A-tracts with and without periodic helix phasing, phased A4T4 and T4A4 motifs, a sequence with a phased GGGCCC motif, some "unconventional" helix phasing sequences, and three short fragments of kinetoplast DNA from Crithidia fasiculata that exhibit significantly different behavior on non-denaturing polyacrylamide gels. The nature of the structural construct produced by the methodology is discussed with respect to static and dynamic models of structure and representations of bending and bendability. An independent theoretical account of sequence dependent chemical footprinting results is provided. Detailed analysis of sequences with A-tract induced axis bending forms the basis for a critical discussion of the applicability of wedge models,junction models and non A-tract, general sequence models for understanding the origin of DNA curvature at the molecular level.

Base Sequence↗

PubMed2025

Comprehensive circRNA expression profile and hub genes screening during human liver development.

BACKGROUND: Understanding the expression of non-coding RNA in the liver during embryonic development provides important insights into liver diseases. Therefore, we investigated circular RNA (circRNA) roles in human liver development, an unexplored research domain. METHODS: Using high-throughput sequencing and bioinformatics, we analysed foetal liver samples across developmental stages (7-20 weeks post-conception). Differentially expressed (DE) genes were identified and subjected to enrichment analysis using Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG), and Disease Ontology (DO). Modular analysis was performed using the Search Tool for Retrieval of Interacting Genes (STRING), followed by construction of a protein-protein interaction (PPI) network using Cytoscape software. The key genes were screened using Molecular Complex Detection (MCODE). The mRNA levels of hub genes were validated using quantitative reverse transcription polymerase chain reaction (qRT-PCR). RESULTS: There were 645 DE circRNAs and 5,145 DE mRNAs between human livers at the three growth stages (HB, EH, and LH). It was found that the activity of circRNAs was boosted remarkably in the hepatoblastic stage. Enrichment analysis found they mainly involved in nervous system regulation of liver function, embryonic organ development and digestive system development. In addition, DE circRNAs were primarily involved in the PI3K-AKT, MAPK and calcium pathways, potentially contributing to adult liver diseases. Notably, only hsa_circ_001471 and novel_circ_017382 were simultaneously identified at all stages and were persistently downregulated. A co-expression regulatory network involving these circRNAs was established. Three hub genes (LGR5, FOXL1 and RSPO3) were identified from the PPI network of 167 genes and may play key roles in human liver development. The RT-qPCR validation results were in agreement with the sequencing data. CONCLUSIONS: Our findings provide the first insights into the roles and regulatory networks of circRNAs in human liver development, laying the groundwork for further investigations of molecular and signalling networks.

Humans↗

PubMed1998

Assembling genes from predicted exons in linear time with dynamic programming.

In a number of programs for gene structure prediction in higher eukaryotic genomic sequences, exon prediction is decoupled from gene assembly: a large pool of candidate exons is predicted and scored from features located in the query DNA sequence, and candidate genes are assembled from such a pool as sequences of nonoverlapping frame-compatible exons. Genes are scored as a function of the scores of the assembled exons, and the highest scoring candidate gene is assumed to be the most likely gene encoded by the query DNA sequence. Considering additive gene scoring functions, currently available algorithms to determine such a highest scoring candidate gene run in time proportional to the square of the number of predicted exons. Here, we present an algorithm whose running time grows only linearly with the size of the set of predicted exons. Polynomial algorithms rely on the fact that, while scanning the set of predicted exons, the highest scoring gene ending in a given exon can be obtained by appending the exon to the highest scoring among the highest scoring genes ending at each compatible preceding exon. The algorithm here relies on the simple fact that such highest scoring gene can be stored and updated. This requires scanning the set of predicted exons simultaneously by increasing acceptor and donor position. On the other hand, the algorithm described here does not assume an underlying gene structure model. Indeed, the definition of valid gene structures is externally defined in the so-called Gene Model. The Gene Model specifies simply which gene features are allowed immediately upstream which other gene features in valid gene structures. This allows for great flexibility in formulating the gene identification problem. In particular it allows for multiple-gene two-strand predictions and for considering gene features other than coding exons (such as promoter elements) in valid gene structures.

Algorithms↗

PubMed2002

Threading using neural nEtwork (TUNE): the measure of protein sequence-structure compatibility.

MOTIVATION: Fold recognition programs align a probe protein sequence onto protein three-dimensional (3D) structure templates. The alignment between the probe sequence and the most suitable template can be used to predict the 3D structure and often biological function of the probe. Here we present a new threading scoring function of protein sequence-structure compatibility. An artificial neural network model is trained to predict compatibility of amino acid side-chains with structural environments. Log-odds scores of predicted probabilities from this model can then be used to construct protein sequence-structure alignments. RESULTS: Our model is tested on discrimination of native and decoy protein 3D structures. With a residue level structural description, its performance is comparable to those of pseudo-energy functions with atom level structural descriptions, better than the two functions with residue level structural descriptions. AVAILABILITY: The C++ source code of our neural network model is available at http://mathbio.nimr.mrc.ac.uk/~kxlin.

Amino Acid Sequence↗

PubMed2002

Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA.

MOTIVATION: The Monte Carlo fragment insertion method for protein tertiary structure prediction (ROSETTA) of Baker and others, has been merged with the I-SITES library of sequence structure motifs and the HMMSTR model for local structure in proteins, to form a new public server for the ab initio prediction of protein structure. The server performs several tasks in addition to tertiary structure prediction, including a database search, amino acid profile generation, fragment structure prediction, and backbone angle and secondary structure prediction. Meeting reasonable service goals required improvements in the efficiency, in particular for the ROSETTA algorithm. RESULTS: The new server was used for blind predictions of 40 protein sequences as part of the CASP4 blind structure prediction experiment. The results for 31 of those predictions are presented here. 61% of the residues overall were found in topologically correct predictions, which are defined as fragments of 30 residues or more with a root-mean-square deviation in superimposed alpha carbons of less than 6A. HMMSTR 3-state secondary structure predictions were 73% correct overall. Tertiary structure predictions did not improve the accuracy of secondary structure prediction.

Algorithms↗

PubMed2003

ProPred1: prediction of promiscuous MHC Class-I binding sites.

SUMMARY: ProPred1 is an on-line web tool for the prediction of peptide binding to MHC class-I alleles. This is a matrix-based method that allows the prediction of MHC binding sites in an antigenic sequence for 47 MHC class-I alleles. The server represents MHC binding regions within an antigenic sequence in user-friendly formats. These formats assist user in the identification of promiscuous MHC binders in an antigen sequence that can bind to large number of alleles. ProPred1 also allows the prediction of the standard proteasome and immunoproteasome cleavage sites in an antigenic sequence. This server allows identification of MHC binders, who have the cleavage site at the C terminus. The simultaneous prediction of MHC binders and proteasome cleavage sites in an antigenic sequence leads to the identification of potential T-cell epitopes. AVAILABILITY: Server is available at http://www.imtech.res.in/raghava/propred1/. Mirror site of this server is available at http://bioinformatics.uams.edu/mirror/propred1/ SUPPLEMENTARY INFORMATION: Matrices and document on server are available at http://www.imtech.res.in/raghava/propred1/page2.html

Antigen Presentation↗

PubMed2003

BLAST++: BLASTing queries in batches.

UNLABELLED: BLAST++ is a tool that is integrated with NCBI BLAST, allowing multiple, say K, queries to be searched against a database concurrently. The results obtained by BLAST++ are identical to that obtained by executing BLAST on each of the K queries, but BLAST++ completes the processing in a much shorter time. AVAILABILITY: http://xena1.ddns.comp.nus.edu.sg/~genesis/blast++ SUPPLEMENTARY INFORMATION: http://xena1.ddns.comp.nus.edu.sg/~genesis/blast++

Algorithms↗