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PubMed2003

Cortical surface registration for image-guided neurosurgery using laser-range scanning.

In this paper, a method of acquiring intraoperative data using a laser range scanner (LRS) is presented within the context of model-updated image-guided surgery. Registering textured point clouds generated by the LRS to tomographic data is explored using established point-based and surface techniques as well as a novel method that incorporates geometry and intensity information via mutual information (SurfaceMI). Phantom registration studies were performed to examine accuracy and robustness for each framework. In addition, an in vivo registration is performed to demonstrate feasibility of the data acquisition system in the operating room. Results indicate that SurfaceMI performed better in many cases than point-based (PBR) and iterative closest point (ICP) methods for registration of textured point clouds. Mean target registration error (TRE) for simulated deep tissue targets in a phantom were 1.0 +/- 0.2, 2.0 +/- 0.3, and 1.2 +/- 0.3 mm for PBR, ICP, and SurfaceMI, respectively. With regard to in vivo registration, the mean TRE of vessel contour points for each framework was 1.9 +/- 1.0, 0.9 +/- 0.6, and 1.3 +/- 0.5 for PBR, ICP, and SurfaceMI, respectively. The methods discussed in this paper in conjunction with the quantitative data provide impetus for using LRS technology within the model-updated image-guided surgery framework.

Adult↗
PubMed2006

Accuracy of dental digitizers.

UNLABELLED: The need for proper validation and verification methodology for CAD/CAM systems is imminent. CAD/CAM systems consisting of an optical impression system, design software and a fabrication machine have to perform to a certain level, whereby manufacturers need to prove the effectiveness of the system as a whole. However, especially when dental surface digitization devices are used as open, stand-alone applications in dental outsourcing, a reliable standard test for comparison is necessary. PURPOSE: This study evaluates a proposed test method to be used to quantify "digitizing quality" with respect to accuracy and reproducibility of two dental surface digitization devices. Comparability of the characteristics should be ensured. METHOD: Two laser light section scanners: DentaScope II and D200 were evaluated by means of the 'Sphere Test', that involves repeated measurements of a precision ball (radius: 6mm) according to a pre-defined protocol. The surface information was received as unmatched, overlapping point clouds and statistically processed with a newly developed software package. The standard deviation of all points as well as a measure for undercutting the equator were determined. RESULTS: The standard deviation for the radius for D and S were 7.7 (+/-0.8) and 13.9 (+/-1.0) microm respectively. The equator undercut elevations were -2.0 degrees and -0.25 degrees for scanner D and S respectively. CONCLUSION: Scanner D had a significantly higher accuracy than S (p<0.05), corresponding with the smaller pixel distance of the sensor. Both devices show adequate accuracy and reproducibility and have an adequate ability to detect the equator. The test is also suitable for calibration purposes.

Computer-Aided Design↗
PubMed2005

Nodoids and toroids: comparison of two geometries for the meniscus profile of a wetting liquid between two touching isolated spheres and extensions to the model of a collection of packed spheres.

In the mid 1960s the present authors published two papers dealing with penetration of nonwetting liquids such as mercury into the interstitial void spaces using the model of uniform packed spheres. A circular arc was used to approximate the liquid-vapor interface in both papers. However, our circular arc-toroid values for the pressure-volume relationship in the pendular ring which exists between two touching spheres was criticized. The authors concluded that our approximation led to unacceptably large differences compared to the values calculated from the exact nodoid shape. This incorrect conclusion was never rebutted and has, in fact, been misinterpreted by subsequent workers to include values calculated for the shape of the access opening and the associated pressure for penetration into the void space of a collection of spheres. This leaves a cloud of uncertainty, not only over our original work on nonwetting fluids, but on the application of our procedures to the field of wetting fluids. The contrast in the geometrical shapes of the toroid and nodoid is depicted and the pressure values are compared at equal volumes. In contrast to the claim of excessive error, we show the toroid geometry, in conjunction with a pressure-volume work derivation, to have a maximum error of 0.06% as compared to the nodoid at all liquid-solid contact angles. The toroid also has the advantage of using a readily derived work versus surface free energy balance rather than requiring the use of incomplete elliptic integrals to evaluate the nodoid. Attempts to use radii of curvature to evaluate the toroid shape are shown to give extremely poor approximations of the exact values for the pressure. Values reported for access to the interior void space of a collection of spheres still need adjustment for the effect of contact angles between 0 degrees and 180 degrees for characterizing assemblies of real solids by computing "equivalent spherical" particle size from porosity and mercury penetration data. However, there is no anticipation that use of the circular arc will introduce large errors in the results. This gives confidence to us and others working with wetting media to test the potential applicability of the packed sphere model to various diverse fields.

Journal Article↗
PubMed2006

Photostability via sloped conical intersections: a computational study of the excited states of the naphthalene radical cation.

On the basis of an extensive ab initio electronic structure study of the ground and excited-state potential energy surfaces of the naphthalene radical cation (N*+), we propose a mechanism for its ultrafast nonradiative relaxation from the second excited state (D2) down to the ground state (D0), which could explain the experimentally observed photostability [Zhao, L.; Lian, R.; Shkrob I. A.; Crowell, R. A.; Pommeret, S.; Chronister, E. L.; Liu, A. D.; Trifunac, A. D. J. Phys. Chem. A., 2004, 108, 25]. The proposed photophysical relaxation pathway involves internal conversion from the D2 state down to the D0 state via two consecutive, accessible, sloped conical intersections (CIs). The two crossings, D0/D1 and D1/D2, are characterized at the complete active space self-consistent field (CASSCF) level. At this level of theory, the D0/D1 crossing is energetically readily accessible, while the D1/D2 CI appears too high in energy to be involved in internal conversion. However, the inclusion of dynamic correlation effects, via single point CASPT2 calculations including excitations out of the valence pi- and sigma-orbitals, lowers the D0 and D2 state energies with respect to D1. Extrapolations at the CASPT2 level predict that the D1/D2 crossing is then significantly lower in energy than with CASSCF indicating that with a higher-level treatment of dynamic correlation it may be energetically accessible following vertical excitation to D2. N*+ is proposed as one of the species contributing to a series of diffuse infrared absorption bands originating from interstellar clouds. Understanding the mechanism for photostability in the gas phase, therefore, has important consequences for astrophysics.

Journal Article↗
PubMed1992

[Chaos research, fractals, fuzzy logic. From stereotypes to reality--consequences for medicine].

Both language and conventional mathematics aim to describe reality. Although language is more flexible, it is usually also inaccurate, while mathematics permits accurate presentations and clear prognoses. However, it is burdened by the fact that it is not everywhere applicable. Such chaotic structures as clouds, or lang-term weather forecasting, for example, cannot be expressed in terms of mathematics. Chaos researchers are attempting, in a non-linear world, to understand mathematically dynamic, apparently unordered systems. In this connection, the fractal dimension also appears--which can be employed in the area of diagnosis to define tumor contours. Fuzzy logic comes closer to reality by replacing the inflexible yes/no by a more or less option and by introducing linguistic nuances into machine-controlled processes. Chaos research and fuzzy logic teach us that there is no such thing as certainty of action or prognosis. In the world as it is, whoever claims to possess it is either naive or guilty of self-deception.

Artificial Intelligence↗
PubMed2025

Target and biomarker exploration portal for drug discovery.

MOTIVATION: The discovery of novel drug targets and precision biomarkers remains a major challenge in drug development, with traditional differential expression analysis often overlooking key regulatory proteins. Here, we present a novel, web-based bioinformatics tool, the Target and Biomarker Exploration Portal (TBEP), designed to accelerate the drug discovery process by integrating large-scale biomedical data with network analysis techniques. RESULTS: TBEP harnesses machine-learning approaches to mine and combine multimodal datasets, including human genetics, functional genomics, and protein-protein interaction networks, to decode causal disease mechanisms and uncover novel therapeutic targets and precision biomarkers for specific phenotypes. A unique feature of the tool is its ability to process large-scale data in real-time, facilitated by an efficient cloud-based architecture. Additionally, the tool incorporates an integrated large language model (LLM), which assists researchers in exploring and interpreting complex biological relationships within the generated networks and multi-omics data using natural language (English). By offering an intuitive, interactive interface, the LLM enhances the exploration of biological insights, making it easier for scientists to derive actionable conclusions. This powerful integration of network analysis, multi-omics data, and LLM provides a robust framework for accelerating the identification of novel drug targets. AVAILABILITY AND IMPLEMENTATION: The tool is publicly available at https://tbep.missouri.edu. The source code, documentation and installation instructions are available at GitHub repository: https://github.com/mizzoudbl/tbep.

Drug Discovery↗
PubMed1980

Reconstruction of an arbitrary cross section from the serial drawings of a stereotaxic brain atlas.

A method is described for the reconstruction of arbitrary cross section from the serial line drawings of a stereotaxic brain atlas. Mathematically, the problem reduces to the intersection of a plane with a line pattern lying in another plane. However, the calculation yields a cloud of points, often confusing and unusable for the surgeon. Because it is impossible to link correctly all the calculated points in all cases [1,2], we propose a method where the number of points is drastically reduced: only regions of interest are depicted, i.e., the area where the electrode point is situated and the neighbouring regions. Instead of points, symbols are displayed, each symbol representing a different region. The efficiency of the method is shown using an atlas simulation of four intersecting spheres in the three dimensional space, Although the procedure is useful for all stereotaxic brain atlasses, a practical example is given where the poor quality of the reconstructed images does not allow good interpretation.

Analog-Digital Conversion↗
PubMed2006

Quantum mechanical modeling of self-assembly and photoinduced electron transfer in PNA-based artificial living organisms.

In order to support the creation of both artificial living organisms in the USA LANL "Protocell Assembly" project and programmable nano-biorobots in the EU "Programmable Artificial Cell Evolution" project, we used quantum mechanical (QM), density functional theory (DFT), the semiempirical PM3 method, and molecular mechanics (MM) software to investigate various complex photosynthetic systems based on peptide nucleic acid (PNA) in a water environment. Quantum mechanical DFT PBEPBE simulations, including electron correlations, confirm that water molecules that surround all the photosynthetic complex of the LANL protoorganism are main constructing factors and stabilize this system consisting of: PNA fragment attached by covalent bond sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule, lipid precursor molecule and fragment of lipid molecules mono layer. The absorption spectrum shift to the red wavelengths in the complex artificial protocell photosynthetic center might be used as the measure of the complexity of this system. The electron pi-pi* transitions in the first and third excited states are from HOMO and HOMO-1 located on the conjugated water molecules and sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule to the LUMO of the lipid precursor molecule as calculated using the time dependent (TD) PBEPBE/6-31G model. Electron charge tunneling in the first and third excited states should induce metabolic photodissociation of the lipid precursor molecule because of localization of the transferred electron cloud on the head (waste) of the lipid precursor molecule. TD electron correlation PBEPBE/6-31G calculations show that in the different energies of excitation, the charge transfer tunneling is from sensitizer to lipid precursor and cytosine molecules. One should note that in a water solvent, the electron charge transfer pi-pi* transition in the fifth and sixth excited state is from the HOMO and HOMO-1 located on the sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule to the LUMO+2 located on the cytosine-PNA fragment molecule. Investigation results indicate that strong back electron tunneling from the sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule to the cytosine molecule in the LANL artificial photosynthetic system exists.

Biomimetics↗
PubMed2003

Systematic errors in DFT calculations of haloalkane heats of formation.

The B3LYP and B3PW91 density functionals were employed with a large [BS1 = 6-311+G(3df,2p)] and small [BS2 = 6-311G(d,p)] basis set to compute enthalpies of formation (at optimized MP2/6-31G(d) geometries and with scaled HF/6-31G(d) frequencies) in the following series of haloalkanes: (1) the 15 fluoro-, chloro-, and chlorofluoromethanes, (2) the 18 fluorinated and chlorinated ethanes. Similar to earlier higher level calculations on haloalkanes, the computed enthalpies exhibited very large, systematic deviations from experiment. It was found that these errors could be largely eliminated using a very simple Bond Additivity Correction (BAC) formula, Delta(f)H degrees (BAC) = Delta(f)H degrees (calc) - n(CX). Delta(CX) [X = F, Cl], in which the BAC parameters, Delta(CF) and Delta(CCl) were determined by fitting the equation to experimental data on the four fluoroethanes and chloroethanes, respectively. The resultant BAC corrected enthalpies of formation are in excellent agreement with experiment, with RMS deviations in the same range as quoted RMS errors in measured enthalpies. Therefore, this simple BAC procedure may be utilized to provide reliable semiquantitative estimates of enthalpies of formation in larger haloalkanes, for which higher level ab initio calculations are not feasible.

Journal Article↗
PubMed1996

Septo-optic dysplasia associated with bilateral complex microphthalmos.

An 8-month-old girl was examined because of corneal clouding and microphthalmos. The fundi of both eyes could not be visualized because of corneal clouding. Orbital and cranial computerized tomographic scanning and magnetic resonance imaging demonstrated bilateral microphthalmos and presumed retinal dysplasia, hypoplasia of the optic nerves and chiasm, agenesis of the septum pellucidum, thinning of corpus callosum, and a normal pituitary infundibulum. Cerebral cortex and white matter were unremarkable. Other ocular malformations were anterior segment dysgenesis in the right eye and congenital cataract or lens abnormality in the left eye. Endocrine studies revealed normal serum hormone levels. There were no colobomatous lesions and systemic anomalies suggestive of a coloboma syndrome. This case represents the rare association of septo-optic dysplasia with complex microphthalmos.

Anterior Eye Segment↗
PubMed1997

[Prolonged antegrade amnesia due to left anterior thalamic infarct, and SPECT findings].

A 60-year-old right-handed man developed disorientation, antegrade amnesia and transient mild clouding of consciousness. The antegrade amnesia persisted for more than one year after its onset. T2-weighted MR images showed high signal intensity in the left anteromedial thalamus. 99mTc-HM-PAO SPECT revealed decreased uptake in the left frontal and temporal lobes. These SPECT findings were still observed a year later. These findings suggest that functional involvement of the frontal and temporal lobe connections with the dorsomedial nucleus, anterior nucleus, and the mamillothalamic tract in the anteromedial part of thalamus were responsible for the prolonged antegrade amnesia. We think that SPECT findings are important for evaluating the outcome of thalamic amnesia.

Amnesia↗
PubMed2002

CT manifestations and features of solid cystic tumors of the pancreas.

OBJECTIVE: To study retrospectively the manifestations and characteristics of solid cystic tumor of the pancreas(SCTP)on CT. METHODS: Nine patients with solid cystic tumor of the pancreas underwent resection with pathological and immunohistochemical confirmation. All the patients were female, aged 27.7 years on average at onset of the disease. CT scan was performed in patients with or without intravenous injection of contrast medium; it was also performed in the arterial phase in 4 patients. RESULTS: Solid and cystic structures were observed in tumors of the pancreas. Solid structure demonstrated low or iso-density on unenhanced CT, poor enhancement in the arterial phase and marked enhancement in the portal venous phase on contrast material-enhanced CT. Cystic structure showed low density on both pre- and pro-contrast views. The CT findings of tumors with predominantly cystic or equal proportion of solid and cystic structure: mural nodules for solid structure, "floating cloud" signs, or solid and cystic crossing distributions. Cystic structure of tumors predominately solid presenting as a beading appearance under capsule. In round, oval and completely encapsulated tumors in the pancreas, the greater vessel enhanced with well-defined margins on pro-contrast images. No dilatation was observed of the common bile and pancreatic ducts. CONCLUSION: The characteristics of solid cystic tumor of the pancreas revealed by CT could confirm the diagnosis of the disease in combination with onset age and sex of patients.

Adult↗
PubMed2005

Psychophysical study of the visual sun location in pictures of cloudy and twilight skies inspired by Viking navigation.

In the late 1960s it was hypothesized that Vikings had been able to navigate the open seas, even when the sun was occluded by clouds or below the sea horizon, by using the angle of polarization of skylight. To detect the direction of skylight polarization, they were thought to have made use of birefringent crystals, called "sun-stones," and a large part of the scientific community still firmly believe that Vikings were capable of polarimetric navigation. However, there are some critics who treat the usefulness of skylight polarization for orientation under partly cloudy or twilight conditions with extreme skepticism. One of their counterarguments has been the assumption that solar positions or solar azimuth directions could be estimated quite accurately by the naked eye, even if the sun was behind clouds or below the sea horizon. Thus under partly cloudy or twilight conditions there might have been no serious need for a polarimetric method to determine the position of the sun. The aim of our study was to test quantitatively the validity of this qualitative counterargument. In our psychophysical laboratory experiments, test subjects were confronted with numerous 180 degrees field-of-view color photographs of partly cloudy skies with the sun occluded by clouds or of twilight skies with the sun below the horizon. The task of the subjects was to guess the position or the azimuth direction of the invisible sun with the naked eye. We calculated means and standard deviations of the estimated solar positions and azimuth angles to characterize the accuracy of the visual sun location. Our data do not support the common belief that the invisible sun can be located quite accurately from the celestial brightness and/or color patterns under cloudy or twilight conditions. Although our results underestimate the accuracy of visual sun location by experienced Viking navigators, the mentioned counterargument cannot be taken seriously as a valid criticism of the theory of the alleged polarimetric Viking navigation. Our results, however, do not bear on the polarimetric theory itself.

Computer Graphics↗
PubMed1995

Galileo multispectral imaging of Earth.

Nearly 6000 multispectral images of Earth were acquired by the Galileo spacecraft during its two flybys. The Galileo images offer a unique perspective on our home planet through the spectral capability made possible by four narrowband near-infrared filters, intended for observations of methane in Jupiter's atmosphere, which are not incorporated in any of the currently operating Earth orbital remote sensing systems. Spectral variations due to mineralogy, vegetative cover, and condensed water are effectively mapped by the visible and near-infrared multispectral imagery, showing a wide variety of biological, meteorological, and geological phenomena. Global tectonic and volcanic processes are clearly illustrated by these images, providing a useful basis for comparative planetary geology. Differences between plant species are detected through the narrowband IR filters on Galileo, allowing regional measurements of variation in the "red edge" of chlorophyll and the depth of the 1-micrometer water band, which is diagnostic of leaf moisture content. Although evidence of life is widespread in the Galileo data set, only a single image (at approximately 2 km/pixel) shows geometrization plausibly attributable to our technical civilization. Water vapor can be uniquely imaged in the Galileo 0.73-micrometer band, permitting spectral discrimination of moist and dry clouds with otherwise similar albedo. Surface snow and ice can be readily distinguished from cloud cover by narrowband imaging within the sensitivity range of Galileo's silicon CCD camera. Ice grain size variations can be mapped using the weak H2O absorption at 1 micrometer, a technique which may find important applications in the exploration of the moons of Jupiter. The Galileo images have the potential to make unique contributions to Earth science in the areas of geological, meteorological and biological remote sensing, due to the inclusion of previously untried narrowband IR filters. The vast scale and near global coverage of the Galileo data set complements the higher-resolution data from Earth orbiting systems and may provide a valuable reference point for future studies of global change.

Africa↗
PubMed2007

A statistics-based approach to binary image registration with uncertainty analysis.

A new technique is described for the registration of edge-detected images. While an extensive literature exists on the problem of image registration, few of the current approaches include a well-defined measure of the statistical confidence associated with the solution. Such a measure is essential for many autonomous applications, where registration solutions that are dubious (involving poorly focused images or terrain that is obscured by clouds) must be distinguished from those that are reliable (based on clear images of highly structured scenes). The technique developed herein utilizes straightforward edge pixel matching to determine the "best" among a class of candidate translations. A well-established statistical procedure, the McNemar test, is then applied to identify which other candidate solutions are not significantly worse than the best solution. This allows for the construction of confidence regions in the space of the registration parameters. The approach is validated through a simulation study and examples are provided of its application in numerous challenging scenarios. While the algorithm is limited to solving for two-dimensional translations, its use in validating solutions to higher-order (rigid body, affine) transformation problems is demonstrated.

Algorithms↗
PubMed2005

Protein structure elucidation from minimal NMR data: the CLOUDS approach.

In this chapter we review automated methods of protein NMR data analysis and expand on the assignment-independent CLOUDS approach. As presented, given a set of reliable NOEs it is feasible to derive a spatial H-atom distribution that provides a low-resolution image of the protein structure. In order to generate such a list of unambiguous NOEs, a probabilistic assessment of the NOE identities (in terms of frequency-labeled H-atom sources) was developed on the basis of Bayesian inference. The methodology, encompassing programs SPI and BACUS, provides a list of "clean" NOEs that does not hinge on prior knowledge of sequence-specific resonance assignments or a preliminary structural model. As such, the combined SPI/BACUS approach, intrinsically adaptable to include 13C- and/or 15N-edited experiments, affords a useful tool for the analysis of NMR data irrespective of whether the adopted structure calculation protocol is assignment-dependent.

Bayes Theorem↗
PubMed2006

Accuracy of facial plaster casts.

OBJECTIVE: The aim of this study was to evaluate the accuracy of facial plaster casts and their suitability for 3-D mapping. MATERIALS AND METHODS: All measurements were carried out on 15 adult probands (seven female and eight male; age range 19-31 years, mean 24.7 years). A plaster cast of the facial surface was prepared for all probands using alginate impressions. The plaster casts and the probands faces were digitized using a three-dimensional laser-scanner operating with structured light. The resulting point clouds were matched in a virtual environment to analyze the deviations between the cast and the facial surfaces, both qualitatively and quantitatively. RESULTS: The average deviations depended on the facial area and lay between 0.95 and 3.55 mm. Marked differences between the plaster cast and the facial surface were found, particularly in the area of the lips, at the roof of the nose, at the cheeks, and in the entire lower facial area. CONCLUSIONS: The regionally exacerbated soft tissue deformations that occur during impression of the facial surface lead to inaccuracies in the resulting plaster cast that forbids any use for morphometric analysis. Documentation of pathological findings in cleft lip and palate using facial plaster casts does appear to be justifiable.

Adult↗
PubMed2004

Passive remote sensing of pollutant clouds by Fourier-transform infrared spectrometry: signal-to-noise ratio as a function of spectral resolution.

In a passive infrared remote sensing measurement, the spectral radiance difference caused by the presence of a pollutant cloud is proportional to the difference between the temperature of the cloud and the brightness temperature of the background (first-order approximation). In many cases, this difference is of the order of a few kelvins. Thus the measured signals are small, and the signal-to-noise ratio (SNR) is one of the most important quantities to be optimized in passive remote sensing. A model for the SNR resulting from passive remote sensing measurements with a Fourier-transform infrared spectrometer is presented. Analytical expressions for the SNR of a single Lorentzian line for the limiting cases of high and low spectral resolutions are derived. For constant measurement time the SNR increases with decreasing spectral resolution, i.e., low spectral resolutions yield the highest SNRs. For a single scan of the interferometer, a spectral resolution that maximizes the SNR exists. The calculated SNRs are in good agreement with the measured SNRs.

Air Pollutants↗