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At least 649 records · Page 36Linked to original sources
PubMed2006

PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

BACKGROUND: Here we describe PathogenMIPer, a software program for designing molecular inversion probe (MIP) oligonucleotides for use in pathogen identification and detection. The software designs unique and specific oligonucleotide probes targeting microbial or other genomes. The tool tailors all probe sequence components (including target-specific sequences, barcode sequences, universal primers and restriction sites) and combines these components into ready-to-order probes for use in a MIP assay. The system can harness the genetic variability available in an entire genome in designing specific probes for the detection of multiple co-infections in a single tube using a MIP assay. RESULTS: PathogenMIPer can accept sequence data in FASTA file format, and other parameter inputs from the user through a graphical user interface. It can design MIPs not only for pathogens, but for any genome for use in parallel genomic analyses. The software was validated experimentally by applying it to the detection of human papilloma virus (HPV) as a model system, which is associated with various human malignancies including cervical and skin cancers. Initial tests of laboratory samples using the MIPs developed by the PathogenMIPer to recognize 24 different types of HPVs gave very promising results, detecting even a small viral load of single as well as multiple infections (Akhras et al, personal communication). CONCLUSION: PathogenMIPer is a software for designing molecular inversion probes for detection of multiple target DNAs in a sample using MIP assays. It enables broader use of MIP technology in the detection through genotyping of pathogens that are complex, difficult-to-amplify, or present in multiple subtypes in a sample.

Computational Biology↗
PubMed2006

Oligonucleotide microarray with RD-PCR labeling technique for detection and typing of human papillomavirus.

Currently, screening for high-risk human papillomavirus (HPV) infection remains an important health concern throughout the world, because of the close association between certain types of HPV and cervical cancer. In this study, we explore the possibility of using approximately 70mer oligonucleotide microarray for detection and genotyping of HPV. The approximately 70mer type-specific oligonucleotide probes of four different types HPV were designed by using biological software Array designer 2.0, which analyzed the whole genome sequences of HPV and selected optimal probes. These probes were synthesized and printed onto the surface of glass slides in order to prepare a low-density microarray. HPV samples were labeled with fluorescence dyes Cy3 using a method of restriction display polymerase chain reaction (RD-PCR). HPV plasmid DNA was restricted with Sau3A I to produce multiple fragments that were ligated to adaptors subsequently and used as PCR template. PCR labeling was performed with the fluorescently labeled universal primer (Cy3-UP) whose sequence is designed according to the adaptor of the RD-PCR approaches. The labeled samples were hybridized with the oligonucleotide microarray. The scanning results showed that HPV DNA hybridized specifically with multiple spots correspondingly to show positive signals, whereas no signals were detected of all the negative and blank controls. These results demonstrated that approximately 70mer oligonucleotide microarray can be applied to HPV detection and genotyping. The application of RD-PCR in the sample labeling can increase significantly the sensitivity of the assay and will be especially useful for the discriminate diagnosis of multiple pathogens.

Carbocyanines↗
PubMed2005

The de novo design of median molecules within a property range of interest.

In this paper an application is presented of the median molecule workflow to the de novo design of novel molecular entities with a property profile of interest. Median molecules are structures that are optimised to be similar to a set of existing molecules of interest as an approach for lead exploration and hopping. An overview of this workflow is provided together with an example of an instance using the similarity to camphor and menthol as objectives. The methodology of the experiments is defined and the workflow is applied to designing novel molecules for two physical property datasets: mean molecular polarisability and aqueous solubility. This paper concludes with a discussion of the characteristics of this method.

Camphor↗
PubMed2005

Concurrent sorption of Zn(II), Cu(II) and Co(II) by Oscillatoria angustissima as a function of pH in binary and ternary metal solutions.

This paper reports biosorption of Zn(II), Cu(II) and Co(II) onto O. angustissima biomass from single, binary and ternary metal solutions, as a function of pH and metal concentrations via Central Composite Design generated by statistical software package Design Expert 6.0. The experimental design revealed that metal interactions could be best studied at lower pH range i.e. 4.0-5.0, which facilitates adequate availability of all the metal ions. The sorption capacities for single metal decreased in the order Zn(II)>Co(II)>Cu(II). In absence of any interfering metals, at pH 4.0 and an initial metal concentration of 0.5 mM in the solution, the adsorption capacities were 0.33 mmol/g Zn(II), 0.26 mmol/g Co(II) and 0.12 mmol/g Cu(II). In a binary system, copper inhibited both Zn(II) and Co(II) sorption but the extent of inhibition of former was greater than the latter; sorption values being 0.14 mmol/g Zn(II) and 0.27 mmol/g Co(II) at initial Zn(II) and Co(II) concentration of 1.5 mM each, pH 4.0 and 1mM Cu(II) as the interfering metal. Zn(II) and Co(II) were equally antagonistic to each others sorption; Zn(II) and Co(II) sorption being 0.23 and 0.24 mmol/g, respectively, at initial metal concentration of 1.5 mM each, pH 4.0 and 1mM interfering metal concentration. In contrast, Cu(II) sorption remained almost unaffected at lower concentrations of the competing metals. Thus, in binary system inhibition dominance observed was Cu(II)>Zn(II), Cu(II)>Co(II) and Zn(II) approximately Co(II), due to this the biosorbent exhibited net preference/affinity for Cu(II) sorption over Zn(II) or Co(II). Hence, the affinity series showed a trend of Cu(II)>Co(II)>Zn(II). In a ternary system, increasing Co(II) concentration exhibited protection against the inhibitory effect of Cu(II) on Zn(II) sorption. On the other hand, the inhibitory effect of Zn(II) and Cu(II) on Co(II) sorption was additive. The model equation for metal interactions was found to be valid within the design space.

Algorithms↗
PubMed2002

PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database.

We describe PRIMROSE, a computer program for identifying 16S rRNA probes and PCR primers for use as phylogenetic and ecological tools in the identification and enumeration of bacteria. PRIMROSE is designed to use data from the Ribosomal Database Project (RDP) to find potentially useful oligonucleotides with up to two degenerate positions. The taxonomic range of these, and other existing oligonucleotides, can then be explored, allowing for the rapid identification of suitable oligonucleotides. PRIMROSE includes features to allow user-defined sequence databases to be used. An in silico trial of the program using the RDP database identified oligonucleotides that described their target taxa with a degree of accuracy far greater than that of equivalent currently used oligonucleotides. We identify oligonucleotides for subdivisions of the Proteobacteria and for the Cytophaga-Flexibacter-Bacteroides (CFB) division. These oligonucleotides describe up to 94.7% of their target taxon with fewer than 50 non-target hits, and the authors recommend that they be investigated further. A comparison with PROBE DESIGN within the ARB software package shows that PRIMROSE is capable of identifying oligonucleotides with a higher specificity. PRIMROSE has an intuitive graphical user interface and runs on the Microsoft Windows 95/NT/2000 operating systems. It is open source and is freely available from the authors.

Algorithms↗
PubMed2003

CDS annotation in full-length cDNA sequence.

The identification of coding sequences (CDS) is an important step in the functional annotation of genes. CDS prediction for mammalian genes from genomic sequence is complicated by the vast abundance of intergenic sequence in the genome, and provides little information about how different parts of potential CDS regions are expressed. In contrast, mammalian gene CDS prediction from cDNA sequence offers obvious advantages, yet encounters a different set of complexities when performed on high-throughput cDNA (HTC) sequences, such as the set of 60,770 cDNAs isolated from full-length enriched libraries of the FANTOM2 project. We developed a CDS annotation strategy that uses a variety of different CDS prediction programs to annotate the CDS regions of FANTOM2 cDNAs. These include rsCDS, which uses sequence similarity to known proteins; ProCrest; Longest-ORF and Truncated-ORF, which are ab initio based predictors; and finally, DECODER and NCBI CDS predictor, which use a combination of both principles. Aided by graphical displays of these CDS prediction results in the context of other sequence similarity results for each cDNA, FANTOM2 CDS inspection by curators and follow-up quality control procedures resulted in high quality CDS predictions for a total of 14,345 FANTOM2 clones.

Animals↗
PubMed1998

[Study of portable synchronous ECG recorder and its long-distance communication system].

This paper presents a convenient long-distance ECG communication system. It is made up of portable ECG recorder, hospital work station and public telephone network. This paper also introduces a kind of modulation and demodulation method in sound coupling communication-pulse edge modulation and demodulation. This system has rational structure, convenient operation and strong management power. A Philips 80C552 used as CPU in the recoder which is portable, cheap and reliable.

Electrocardiography, Ambulatory↗
PubMed1998

[The development of a computerized acidimeter].

A instrument combining advanced computer technology with tradition acidimeter in order to overcome the inconvenience of operating and the subjectivity of result is introduced. The instrument realizes, automatic adjust of Standard and automatic complement of temperature and improve the precision to 0.01 grade. It has a good performance.

Acids↗
PubMed2003

Modeling and implementing a health information provider on the Internet.

OBJECTIVES: To model and implement a medical web portal providing access to well qualified and high-quality information. MATERIAL AND METHODS: The Unified Medical Language System (UMLS) knowledge sources of the U.S. National Library of Medicine and an Information Sources Catalog (ISC) resulting from the ARIANE project are described. The XML technology that allows files transformations by the means of XSLT is briefly presented. RESULTS: The design and implementation of software modules that exploit knowledge sources, operate the translation of a user's query to selected information sources, and wrap obtained results are detailed. DISCUSSION: Current implementation and wrapping perspectives are discussed in terms of integration and interoperability of health information resources.

Humans↗
PubMed2000

Design and evaluation of a software prototype for participatory planning of environmental adaptations.

A software prototype to support the planning process for adapting home and work environments for people with physical disabilities was designed and later evaluated. The prototype exploits low-cost three-dimensional (3-D) graphics products in the home computer market. The essential features of the prototype are: interactive rendering with optional hardware acceleration, interactive walk-throughs, direct manipulation tools for moving objects and measuring distances, and import of 3-D-objects from a library. A usability study was conducted, consisting of two test sessions (three weeks apart) and a final interview. The prototype was then tested and evaluated by representatives of future users: five occupational therapist students, and four persons with physical disability, with no previous experience of the prototype. Emphasis in the usability study was placed on the prototype's efficiency and learnability. We found that it is possible to realise a planning tool for environmental adaptations, both regarding usability and technical efficiency. The usability evaluation confirms our findings from previous case studies, regarding the relevance and positive attitude towards this kind of planning tool. Although the prototype was found to be satisfactorily efficient for the basic tasks, the paper presents several suggestions for improvement of future prototype versions.

Activities of Daily Living↗
PubMed2006

[Design and implementation of aphasia rehabilitation software based on speech recognition].

A new software therapy instrument is proposed for the rehabilitation of aphasia caused by cerebral disorder, which is different from general drug therapy or physical therapy and is, based on modern speech and biofeedback principles. Aphasia rehabilitation software package on the therapy instrument were designed and implement. The features of the software and its future application were discussed.

Aphasia↗
PubMed1987

Strategic approaches to drug design. I. An integrated software framework for molecular modelling.

An integrated molecular graphics and computational chemistry framework is described which has been designed primarily to handle small molecules of up to 300 atoms. The system provides a means of integrating software from any source into a single framework. It is split into two functional subsystems. The first subsystem, called COSMIC, runs on low-cost, serial-linked colour graphics terminals and allows the user to prepare and examine structural data and to submit them for extensive computational chemistry. Links also allow access to databases, other modelling systems and user-written modules. Much of the output from COSMIC cannot be examined with low level graphics. A second subsystem, called ASTRAL, has been developed for the high-resolution Evans & Sutherland PS300 colour graphics terminal and is designed to manipulate complex display structures. The COSMIC minimisers, geometry investigators, molecular orbital displays, electrostatic isopotential generators and various interfaces and utilities are described.

Computer Graphics↗
PubMed2000

RegRand: statistical software for the multiple-baseline design.

RegRand (Version 1.0) is Macintosh-based software that enables a researcher to conduct a non-parametric statistical analysis of the data from Koehler and Levin's (1998) recently described regulated randomization single-case multiple-baseline design. Regulated randomization design and analysis principles are reviewed in relation to an educational research application and a step-by-step illustration of them in relation to the RegRand program is presented.

Education↗
PubMed2006

OligoSpawn: a software tool for the design of overgo probes from large unigene datasets.

BACKGROUND: Expressed sequence tag (EST) datasets represent perhaps the largest collection of genetic information. ESTs can be exploited in a variety of biological experiments and analysis. Here we are interested in the design of overlapping oligonucleotide (overgo) probes from large unigene (EST-contigs) datasets. RESULTS: OLIGOSPAWN is a suite of software tools that offers two complementary services, namely (1) the selection of "unique" oligos each of which appears in one unigene but does not occur (exactly or approximately) in any other and (2) the selection of "popular" oligos each of which occurs (exactly or approximately) in as many unigenes as possible. In this paper, we describe the functionalities of OLIGOSPAWN and the computational methods it employs, and we report on experimental results for the overgo probes designed with it. CONCLUSION: The algorithms we designed are highly efficient and capable of processing unigene datasets of sizes on the order of several tens of Mb in a few hours on a regular PC. The software has been used to design overgo probes employed to screen a barley BAC library (Hordeum vulgare). OLIGOSPAWN is freely available at http://oligospawn.ucr.edu/.

Base Sequence↗
PubMedDate not supplied

[Computer-assisted design in removable partial dentures. Expert system and software for framework tracing].

Stelligraph, a software program for designing the removable partial denture offers many possibilities in computer assisted technology. The design can be realized on any particular case, based on three different concepts. This software program can also provide on individual, manual and personalized design this offening complete freedom in the conception. This software program is an expert system in removable partial denture by providing the general practitioner with a rational design as well as clinical guidance for oral rehabilitation.

Denture Design↗
PubMed2003

[The research of noninvasive cardiovascular diagnosis and test instrument].

The study of pulse wave, including its quantitative analysis and propagation, is one of the hot topics in the fields of clinical medicine, such as how to detect cardiovascular diseases and make early diagnosis without harm. In this paper are discussed a new type of automatic cardiovascular diagnosis method and the corresponding test instrument. The cardiovascular system parameters can be achieved through the wave changes, related data processing and analyzing. This system includes piezo-film transducer, signal amplifier, data collecting and data analyzing equipment. Various pulse diagrams can be shown in omnidirectional and multifunctional ways. The measurement error can be reduced effectively by introducing Mini-wave analysis in the design of software. The research indicates that combination of this equipment with the traditional Chinese medicine will provide wide practical application.

Algorithms↗