TABI-PB 2.0: An Improved Version of the Treecode-Accelerated Boundary Integral Poisson-Boltzmann Solver.

This work describes TABI-PB 2.0, an improved version of the treecode-accelerated boundary integral Poisson-Boltzmann solver. The code computes the electrostatic potential on the molecular surface of a solvated biomolecule, and further processing yields the electrostatic solvation energy.

Accelerating the 3D reference interaction site model theory of molecular solvation with treecode summation and cut-offs.

The 3D reference interaction site model (3D-RISM) of molecular solvation is a powerful tool for computing the equilibrium thermodynamics and density distributions of solvents, such as water and co-ions, around solute molecules. However, 3D-RISM solutions can be expensive to calculate, especially for proteins and other large molecules where calculating the potential energy between solute and solvent requires more than half the computation time. To address this problem, we have developed and implemented treecode summation for long-range interactions and analytically corrected cut-offs for short-range interactions to accelerate the potential energy and long-range asymptotics calculations in non-periodic 3D-RISM in the AmberTools molecular modeling suite.

Comparison of the MSMS and NanoShaper molecular surface triangulation codes in the TABI Poisson-Boltzmann solver.

The Poisson-Boltzmann (PB) implicit solvent model is a popular framework for studying the electrostatics of solvated biomolecules. In this model the dielectric interface between the biomolecule and solvent is often taken to be the molecular surface or solvent-excluded surface (SES), and the quality of the SES triangulation is critical in boundary element simulations of the model. This work compares the performance of the MSMS and NanoShaper surface triangulation codes for a set of 38 biomolecules.

Improvements to the APBS biomolecular solvation software suite.

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001.

Comparison of treecodes for computing electrostatic potentials in charged particle systems with disjoint targets and sources.

In molecular simulations, it is sometimes necessary to compute the electrostatic potential at M target sites due to a disjoint set of N charged source particles. Direct summation requires O(MN) operations, which is prohibitively expensive when M and N are large. Here, we consider two alternative tree-based methods that reduce the cost.

Percutaneous nephrostomy: placement under CT and fluoroscopy guidance.

Objective: The purpose of this paper is to present our experience with CT- and fluoroscopy-guided percutaneous nephrostomy tube (PNT) placement and to describe the technique of placement with patients in the supine-oblique position.

Materials And Methods: A CT scanner was coupled with a ceiling-mounted C-arm for fluoroscopy at the CT table, PNT was done with CT localization and fluoroscopic control. We attempted 148 placements in 129 patients, with most patients in the supine or the supine-oblique position.

Hepatic lesion characterization in cirrhosis: significance of arterial hypervascularity on dual-phase helical CT.

Objective: Our goal was to evaluate the diagnostic significance of the presence and pattern of arterial hypervascularity in lesions detected on dual-phase helical CT in cirrhotic patients.

Materials And Methods: Fifty-eight lesions greater than 1 cm in size were prospectively identified in 26 patients with end-stage liver disease who had undergone dual-phase helical CT for preoperative liver transplantation evaluation. All 26 patients had diagnoses proven by histologic evaluation or by clinical criteria.

Helical CT angiography for examination of living renal donors.

Objective: This prospective study was intended to determine if helical CT arteriography plus conventional radiography is sufficiently accurate to replace and less costly than excretory urography and conventional renal arteriography, the techniques currently used to examine living renal donors.

Subjects And Methods: Patients underwent CT arteriography with a helical CT scanner. Conventional radiographs were obtained during the pyelographic phase to evaluate the urothelium.

Local staging of pancreatic cancer: criteria for unresectability of major vessels as revealed by pancreatic-phase, thin-section helical CT.

Objective: This study was conducted to determine the criteria for unresectability of major peripancreatic vessels in patients with pancreatic carcinoma as revealed by optimally enhanced, pancreatic-phase thin-section helical CT.

Subjects And Methods: Twenty-five patients with pancreatic adenocarcinoma who underwent local dissection during curative or palliative surgery also underwent preoperative pancreatic-phase thin-section helical CT (40- to 70-sec delay, 2.5- to 3-mm collimation).

Two-phase helical CT for pancreatic tumors: pancreatic versus hepatic phase enhancement of tumor, pancreas, and vascular structures.

Purpose: To quantitatively evaluate and validate a two-phase helical computed tomographic (CT) protocol for evaluation of pancreatic tumors.

Materials And Methods: Twenty-seven patients with pathologically proved pancreatic adenocarcinomas prospectively underwent two-phase CT examination with helical acquisition during the pancreatic phase (40-70 seconds after infusion of intravenous contrast material at 3 mL/sec) and the hepatic phase (70-100 seconds after infusion). Mean CT attenuation values of tumor, bordering pancreas, and all major peripancreatic vessels were obtained for both time intervals.

Helical computed tomography for abdominal imaging.

Significant technologic advances have taken place in computed tomography (CT). Current-generation conventional CT scanners are able to image a slice of tissue in as little as 2 to 3 seconds and can acquire several consecutive images. Although it is a substantial improvement from the CT of 5 years ago, there remain practical limits to the utility of conventional CT imaging within the abdomen.

Proximal fetal cerebral ventricle: description of US technique and initial results.

Purpose: To establish adequacy and ease of visualization of the proximal ventricle, normal range of measurements of the proximal ventricle, and distance of the proximal choroid plexus from the lateral ventricular wall.

Materials And Methods: With use of an angled technique, ultrasound (US) evaluation of the proximal fetal ventricle was attempted in 439 fetuses during routine obstetric US examination. Ease of examination, additional time required, mean measurements, and standard deviation (SD) were calculated.

A new holder and surface MRI coil for the examination of the newborn infant hip.

A special holder was developed for examination of the infant hip joint using MRI. This holder allows the infant hip joint to be examined both in a neutral position and in various defined functional positions. A special integrated surface coil, also developed for this purpose, provides the high spatial resolution required for assessment of the fine joint structures.

[Stereolithographic model construction based on 3-dimensional reconstructed CT sectional image sequences].

Techniques for 3D reconstruction of medical objects and production of models by CAM have been markedly improved. Milling tools have limited abilities to reproduce complex anatomical structures. Even if 5-axis milling systems are used, the problem of collisions between tool and object is not yet under control.

Biomechanics of valvular plane displacement of the heart.

There has been no consensus concerning the particular movement of the valvular plane of the heart (VPM). As shown in this study involving a mathematical model based upon the momentum equation and experiments on a specially designed artificial heart pump, the VPM not only results from the shortening of the heart, but also from blood flow within the heart and large blood vessels, from the forces caused by the muscle movements, and from the elastic properties of the heart's suspension. The results of the calculations and the experiments confirm the effect of the so-called valve mechanism and its influence on the economic beating action of the heart.

[CO2 angiography: studies of gas filling of vessels and assessing the factors of influence on the injection process with a cardiovascular model].

Following the advent of digital subtraction angiography (DSA), carbon dioxide gas has become a useful contrast agent for arterial angiography. Former manual injection methods had precluded accurate dosing and reproducibility. An original gas injector was therefore developed and tested in a circulatory system model.

MR-anatomy of infants hip: comparison to anatomical preparations.

The correlation between anatomical preparations and MRI images of the most important structures of newborn hips in coronal and axial orientation was performed in 18 post mortem babies. T1-weighted images present a good differentiation between cartilage, bone, ligaments and surrounding soft tissues. Coronal images give the best opportunity to study the clinically important structures of the roof of acetabulum including the labrum and the ground of the acetabulum.

[Arterial DSA using CO2 as a contrast medium: improvement of picture quality using a novel gas injector in an animal experiment].

The use of CO2 as contrast medium for DSA requires accurate and reproducible doses of the gas. This cannot be achieved by manual injection or by using injectors designed for liquid contrast media. For this reason a new gas injector has been developed which meets these requirements despite the compressibility of gas.

[CO2 angiography: development and trial of an animal experimental gas dosage device].

Gas have long been used in radiological examinations, in particular for the diagnostic evaluation of gastrointestinal diseases. However, not until the introduction of digital subtraction angiography was carbon dioxide also used with success for angiography of arteries. In order to advice exact and reproducible dosage of the gas with freely selectable injection parameters, a carbon dioxide gas metering device was developed.

[Paget's disease of bone: MR characteristics at 1.5 T].

Thirteen patients with confirmed Paget's disease were examined using a 1.5 T MR tomograph. Five patients had polyostotic and eight patients monostotic forms of the disease.

[Hyaline articular cartilage in MR tomography of the knee joint at 1.5 T].

MRI is a new method for imaging the knee joint. There is still some uncertainty regarding the extent and the signal from hyaline articular cartilage. MRI images were therefore compared with anatomical and histological preparations of the knee joint and the difference between MRI and the anatomical sections have been determined.

[Initial experiences with CO2 as a gaseous contrast medium in digital subtraction angiography].

Electronic contrast enhancement allows the use of CO2 as a contrast material for studying the vascular system with DSA. Its use, safety and the information provided were studied in 40 patients and in 5 animal experiments and the results were compared with iodine-containing contrast media. The available results indicate that CO2 is a safe negative contrast medium for peripheral arteriography and that it provides angiograms with a picture quality comparable to those of iodinated contrast media in the extremities.