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At least 937 records · Page 52Linked to original sources
PubMed2003

2HAPI: a microarray data analysis system.

SUMMARY: 2HAPI (version 2 of High density Array Pattern Interpreter) is a web-based, publicly-available analytical tool designed to aid researchers in microarray data analysis. 2HAPI includes tools for searching, manipulating, visualizing, and clustering the large sets of data generated by microarray experiments. Other features include association of genes with NCBI information and linkage to external data resources. Unique to 2HAPI is the ability to retrieve upstream sequences of co-regulated genes for promoter analysis using MEME (Multiple Expectation-maximization for Motif Elicitation) AVAILABILITY: 2HAPI is freely available at http://array.sdsc.edu. Users can try 2HAPI anonymously with pre-loaded data or they can register as a 2HAPI user and upload their data.

Algorithms↗
PubMedDate not supplied

Evaluation of Hamilton-Thorn automated semen analysis system.

Sperm concentration and percentage motility values generated by the HT M-2030 system (CASA) were compared with those obtained by subjective semen analysis (SSA). Three calibrations arbitrarily designated as A, M, and D for gates and discriminators and three calibrations arbitrarily designated LI, MI, and HI for default pixel count (DPC) and default intensity (DI) were evaluated. The best correlation between CASA and SSA was observed utilizing M calibration (n = 114) with which sperm concentration was +0.3 x 10(6)/mL (r = .96) and motility was -6.3% (r = .89) compared to the values obtained by SSA. It was found that 35.9% of sperm concentration values and 34.2% of sperm motility values were within 10% of the values obtained by SSA. When sperm concentration was between 50 and 100 x 10(6)/mL the difference in motility was reduced (-3.2%) while the difference in sperm concentration was reversed (-2.6 x 10(6)/mL). LI calibration (DPC = 4, DI = 86) gave acceptable results with M calibration for sperm concentration (+2.1 x 10(6)/mL) and motility (-6.9%) compared to the values obtained by SSA. In the presence of sperm clumping, the difference between CASA and SSA was reversed for sperm concentration (+0.56 x 10(6)/mL for normal samples vs. -2.2 x 10(6)/mL for samples with clumping) and was reduced for sperm motility (-7.14% vs. -4.55%, respectively). HT M-2030 under proper calibration can be used as a rapid, objective, and reliable alternative to conventional semen analysis in routine and for research purposes.

Calibration↗
PubMed1999

System analysis of the flow/pressure response of rotodynamic blood pumps.

Design of a rotodynamic blood pumping system to have a suitable, controllable output is a key configuration issue. This study evaluates the benefits of selecting the impeller running specific speed, motor speed-torque line, and pump operating logic to jointly combine into a suitable characteristic. In this study, a "constant" flow for a given choice of control parameter value was the selected objective. The operating condition selected for analysis was chosen to be typical of an implanted, chronic support pump. Open-loop operation, fixed torque, fixed power, and fixed power/rpm2 ratio were combined with choices of impeller diameter and speed and motor speed-torque line. It was found that setting the running specific speed at a higher value than that associated with the best efficiency point resulted in a much more controllable pump. Overall efficiency was only slightly penalized for the model impeller chosen. Power/rpm2 control followed by torque control were most effective. With these control modes, motor characteristics were not critical.

Algorithms↗
PubMed2005

Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system.

BACKGROUND: Sequencing of EST and BAC end datasets is no longer limited to large research groups. Drops in per-base pricing have made high throughput sequencing accessible to individual investigators. However, there are few options available which provide a free and user-friendly solution to the BLAST result storage and data mining needs of biologists. RESULTS: Here we describe NuclearBLAST, a batch BLAST analysis, storage and management system designed for the biologist. It is a wrapper for NCBI BLAST which provides a user-friendly web interface which includes a request wizard and the ability to view and mine the results. All BLAST results are stored in a MySQL database which allows for more advanced data-mining through supplied command-line utilities or direct database access. NuclearBLAST can be installed on a single machine or clustered amongst a number of machines to improve analysis throughput. NuclearBLAST provides a platform which eases data-mining of multiple BLAST results. With the supplied scripts, the program can export data into a spreadsheet-friendly format, automatically assign Gene Ontology terms to sequences and provide bi-directional best hits between two datasets. Users with SQL experience can use the database to ask even more complex questions and extract any subset of data they require. CONCLUSION: This tool provides a user-friendly interface for requesting, viewing and mining of BLAST results which makes the management and data-mining of large sets of BLAST analyses tractable to biologists.

Algorithms↗
PubMedDate not supplied

Transient stirred-tank reactors operating with immobilized enzyme systems: analysis and simulation models and their experimental checking.

A mathematical model applicable to the analysis, design, and simulation of heterogeneous enzymatic processes reacting in a stirred-tank reactor has been formulated. The model develops the unsteady-state design equations for such reactors and also the diffusion reaction equation in the spherical catalyst particles for reversible Michaelis-Menten kinetics. This structured general model provides an overview of almost all of the processes occurring in an immobilized enzyme reactor system. Although the analysis presented here is limited to certain situations, it can be extended to other support geometries, enzyme kinetics, and reactor configurations. To check the model, the experimental data obtained with immobilized beta-galactosidase were compared to those theoretically predicted.

Biotechnology↗
PubMed2000

Integration of an immunosorbent assay system: analysis of secretory human immunoglobulin A on polystyrene beads in a microchip.

An immunosorbent assay system was integrated into a glass microchip. Polystyrene beads were introduced into a microchannel, and then human secretory immunoglobulin A (s-IgA) adsorbed on the bead surface was reacted with colloidal gold conjugated anti-s-IgA antibody and detected by a thermal lens microscope. The scale merits of liquid microspace on the molecular behavior remarkably contributed to reduced assay time. The integration cut the time necessary for the antigen-antibody reaction by 1/90, thus shortening the overall analysis time from 24 h to less than 1 h. Moreover, troublesome operations required for conventional immunosorbent assays could be replaced by simple operations.

Antigen-Antibody Reactions↗
PubMed1997

A medication capture and analysis system for use in epidemiology.

Epidemiological studies of elderly people have tended to avoid estimations of medication prevalence and adverse effects, partly because of the practical difficulties of capturing medication data and then rendering them analysable. This article describes a versatile coding system for medication data entry that greatly simplifies the process of medication analysis in epidemiological field studies. Five-digit numerical codes are used to identify individual preparations, and the system's hierarchical nature allows aggregation to a number of levels. To date, the MedCap (Medication Capture) system has been used successfully in 3 different ways in 2 major longitudinal studies of elderly people in Australia, and offers a possible solution to the practical difficulties of field pharmacoepidemiology.

Aging↗
PubMed1996

Genotyping of the ABO blood group system: analysis of nucleotide position 802 by PCR-RFLP and the distribution of ABO genotypes in a German population.

Genotypes of the ABO blood group system were studied by PCR-RFLP analysis of the eight polymorphic nucleotide positions (nps) 261, 467, 526, 646, 703, 796, 802 and 803 of the cDNA from A transferase. In 169 unrelated German individuals, 17 genotypes were found and the calculated allele frequencies of A(Pro), A(Leu), B, O(T), O(A) and O2 were 0.2130, 0.0770, 0.0473, 0.4260, 0.2160 and 0.0207, respectively. These frequency data may provide useful additional information for disputed paternity and stain testing. A variant O allele, O2, was fout at a polymorphic frequency. As the nucleotide (np 261) of the O2 allele is the same as that of A and B alleles, the analysis of at least three nucleotide positions, i.e. nps 261, 526 and 802, is necessary to avoid mistyping of the ABO genotype.

ABO Blood-Group System↗
PubMed1995

Postshock sensing performance in transvenous defibrillation lead systems: analysis of detection and redetection of ventricular fibrillation.

INTRODUCTION: The sensing performance of transvenous lead systems may be adversely affected by the delivery of high-energy shocks. This may be due to the proximity of the sensing and energy-delivery electrodes on transvenous leads. METHODS AND RESULTS: The time required for detection of ventricular fibrillation and redetection after a failed first shock was compared in 93 patients with five different lead system-pulse generator combinations: Cadence--Endotak 60 series, Ventak P--Endotak 60 series, Jewel--Transvene, Cadence--TVL, and Cadence--Transvene. A total of 418 successful and 204 failed first shocks were delivered during induced ventricular fibrillation. Redetection times (RED) were consistently shorter than detection times (DET) in the Jewel-Transvene (RED minus DET: -1.9 +/- 0.8 sec, P < 0.0001), the Cadence-TVL (-1.6 +/- 1.0 sec, P < 0.0001), and the Cadence-Transvene combinations (-2.0 +/- 0.9 sec, P < 0.0004). Redetection times were not significantly different than detection times in the Cadence-Endotak combination (0.9 +/- 3.1 sec; P = 0.09). Redetection times were significantly longer than detection times in the Ventak-Endotak combination (1.2 +/- 2.3 sec; P = 0.034). Prolonged individual redetection episodes (> 8.2 sec) were observed in the Cadence-Endotak (7 [10%] of 73 episodes) and the Ventak-Endotak (4 [10%] of 39 episodes), but not in the Jewel-Transvene, the Cadence-TVL, and the Cadence-Transvene combinations. CONCLUSIONS: Redetection of ventricular fibrillation may be delayed in some transvenous lead-pulse generator combinations. Successful redetection of ventricular fibrillation following a failed first shock should be demonstrated prior to hospital discharge of patients with implantable defibrillators.

Adolescent↗
PubMed2006

Class of basis functions for use in optical systems analysis.

A method is described for modeling the effects of spatial apertures on optical sensor systems. The method consists of defining a set of basis functions that is obtained by partitioning the aperture image plane into a series of rectangular regions and replacing the field in each rectangular subregion with an orthogonal function series approximation. Each orthogonal function has a finite extent that is matched to the aperture image. The individual functions are propagated by application of the Fresnel approximation of the Rayleigh-Sommerfeld diffraction formula to other ranges, and the resultant functions are shown to be valid basis functions for defining a field at any other range. The technique is applied to a scattering problem using complex Fourier series.

Journal Article↗
PubMed2003

A four-wavelength channel absorbance detector with a light emitting diode-fiber optics assembly for simplifying the flow-injection analysis system.

A four-channel absorbance detector was developed for simplifying the flow-injection analysis (FIA). This detector used four light-emitting-diodes (LEDs) as light sources; their wavelengths were 470, 495, 590 and 635 nm, respectively. Their amplitudes were modulated electronically with different frequencies. The light emissions from them were merged by plastic-core fiber optics, and were detected by a photo-diode (PD). The mixed signal was then sent to and discriminated by a four-channel lock-in amplifier corresponding to each modulation frequency. Neither a monochromator nor an optical filter was used. This detector was conveniently applied to the determination of iron in river water by FIA using 1,10-phenanthroline. Though a noisy peristaltic pump was used to propel the solutions, practical precision and accuracy were obtained by means of on-line dual-wavelength measurements and off-line moving average calculations.

Journal Article↗
PubMed1980

Skeletal muscle tissue preparation for image analysis systems.

A procedure for making histological sections of whole skeletal muscles suitable for automated image analysis of fiber size and number is described. Briefly the procedure involves the fixation/embedding technique of Schmitt and Dumont (1969) followed by section staining using phosphomolybdic acid and aniline blue. This procedure overcomes many of problems encountered with the more usual muscle section techniques in that it suppresses muscle fiber staining and stains only the intramuscular connective tissue.

Aniline Compounds↗
PubMed2006

A biomechanical study of activities of daily living using neck and upper limbs with an optical three-dimensional motion analysis system.

In activities of daily living such as eating meals, the neck and upper limbs move in coordination. However, no methods have been established to analytically and quantitatively capture motion of the neck and limbs during these activities. We used a Vicon 512 system to simultaneously measure ranges of motion (ROMs) for the cervical spine, shoulders, elbows, and forearms. Correlations between the motion analyzer and the universal goniometer were >0.76. Repeatability of measurements using this analyzer were <or=3 degrees for all values. This system is thus highly accurate and can be useful for motion analysis of the neck and upper limbs. The sum of flexion angles for the cervical spine, shoulders and elbows were almost constant for each activity, at 261 degrees for shampooing, 207 degrees for washing the face, and 185 degrees for eating a meal.

Activities of Daily Living↗
PubMed1997

CAMDAS: an automated conformational analysis system using molecular dynamics. Conformational Analyzer with Molecular Dynamics And Sampling.

We present an automated conformational analysis program, CAMDAS (Conformational Analyzer with Molecular Dynamics And Sampling). CAMDAS performs molecular dynamics (MD) calculations for a target molecule and samples conformers from the trajectory of the MD. The program then evaluates the similarities between each of the sampled conformers in terms of the root-mean-square deviations of the atomic positions, clusters similar conformers, and finally prints out the clustered conformers. This MD-based conformational analysis is a broadly used method, and CAMDAS is intended to provide a convenient framework for the method. CAMDAS has the ability to find the representative conformers automatically from an arbitrarily given structure of the molecule. The accuracy of the program was examined using N-acetylalanine-N'-methylamide, and the obtained result was consistent with that of the systematic search method. In the test calculation of cyclodecane, CAMDAS could identify most of the known conformers and their conformational enantiomers by examining only 5000 conformers. In addition, the potential-scaled method, which we have developed previously as an accelerating technique for MD, could find two additional conformers of cyclodecane that have not been reported. CAMDAS presents a convenient way to find the energetically possible conformers of a molecule, which is needed especially in the early stage of drug design.

Alanine↗