Biomedical subjects

Peter Kipfer

Publications and source records attributed to Peter Kipfer.

3 recordsLinked to original sources

PubMed2006

Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package.

BACKGROUND: Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal RNA (rRNA) for evaluating sequence alignments of rRNA genes. Furthermore, the secondary and tertiary structural features of rRNA are highly useful and successfully employed in designing rRNA targeted oligonucleotide probes intended for in situ hybridization experiments. RNA3D, a program to combine sequence alignment information with three-dimensional structure of rRNA was developed. Integration into ARB software package, which is used extensively by the scientific community for phylogenetic analysis and molecular probe designing, has substantially extended the functionality of ARB software suite with 3D environment. RESULTS: Three-dimensional structure of rRNA is visualized in OpenGL 3D environment with the abilities to change the display and overlay information onto the molecule, dynamically. Phylogenetic information derived from the multiple sequence alignments can be overlaid onto the molecule structure in a real time. Superimposition of both statistical and non-statistical sequence associated information onto the rRNA 3D structure can be done using customizable color scheme, which is also applied to a textual sequence alignment for reference. Oligonucleotide probes designed by ARB probe design tools can be mapped onto the 3D structure along with the probe accessibility models for evaluation with respect to secondary and tertiary structural conformations of rRNA. CONCLUSION: Visualization of three-dimensional structure of rRNA in an intuitive display provides the biologists with the greater possibilities to carry out structure based phylogenetic analysis. Coupled with secondary structure models of rRNA, RNA3D program aids in validating the sequence alignments of rRNA genes and evaluating probe target sites. Superimposition of the information derived from the multiple sequence alignment onto the molecule dynamically allows the researchers to observe any sequence inherited characteristics (phylogenetic information) in real-time environment. The extended ARB software package is made freely available for the scientific community via http://www.arb-home.de.

Algorithms↗

PubMedDate not supplied

A particle system for interactive visualization of 3D flows.

We present a particle system for interactive visualization of steady 3D flow fields on uniform grids. For the amount of particles we target, particle integration needs to be accelerated and the transfer of these sets for rendering must be avoided. To fulfill these requirements, we exploit features of recent graphics accelerators to advect particles in the graphics processing unit (GPU), saving particle positions in graphics memory, and then sending these positions through the GPU again to obtain images in the frame buffer. This approach allows for interactive streaming and rendering of millions of particles and it enables virtual exploration of high resolution fields in a way similar to real-world experiments. The ability to display the dynamics of large particle sets using visualization options like shaded points or oriented texture splats provides an effective means for visual flow analysis that is far beyond existing solutions. For each particle, flow quantities like vorticity magnitude and wavelength2 are computed and displayed. Built upon a previously published GPU implementation of a sorting network, visibility sorting of transparent particles is implemented. To provide additional visual cues, the GPU constructs and displays visualization geometry like particle lines and stream ribbons.

Algorithms↗

PubMedDate not supplied

Systolic dysfunction: correlation of acoustic cardiography with Doppler echocardiography.

For detection of left ventricular (LV) systolic dysfunction in the outpatient setting, simultaneous electrocardiographic and heart sound data have been shown to be helpful. In 161 patients with suspected or known cardiac disease, echocardiography and acoustic cardiography were performed. Acoustic cardiographic parameters correlated to echocardiography included: presence or absence of S3, electromechanical activation time (EMAT), LV systolic time (LVST), and EMAT/LVST. LV ejection fraction was >or=50% in 82 patients (S3 present in 9.8%) and <50% in 79 patients (S3 present in 30.4%; the <50% group also had a greater EMAT, EMAT/LVST, and lower mean LVST [p<0.05]). Patients with an S3 had a lower ejection fraction, larger mean left atrial and LV dimensions, and an increased proportion of diastolic dysfunction. Acoustic cardiography allows reliable detection of the S3, which correlates with echocardiographic evidence of impaired LV function, and the EMAT/LVST ratio reflects reduced ejection fraction, providing an affordable, accessible means to assess LV dysfunction in the outpatient setting.

Adult↗