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PubMed2005

Effects of x-ray and CT image enhancements on the robustness and accuracy of a rigid 3D/2D image registration.

A rigid body three-dimensional/two-dimensional (3D/2D) registration method has been implemented using mutual information, gradient ascent, and 3D texturemap-based digitally reconstructed radiographs. Nine combinations of commonly used x-ray and computed tomography (CT) image enhancement methods, including window leveling, histogram equalization, and adaptive histogram equalization, were examined to assess their effects on accuracy and robustness of the registration method. From a set of experiments using an anthropomorphic chest phantom, we were able to draw several conclusions. First, the CT and x-ray preprocessing combination with the widest attraction range was the one that linearly stretched the histograms onto the entire display range on both CT and x-ray images. The average attraction ranges of this combination were 71.3 mm and 61.3 deg in the translation and rotation dimensions, respectively, and the average errors were 0.12 deg and 0.47 mm. Second, the combination of the CT image with tissue and bone information and the x-ray images with adaptive histogram equalization also showed subvoxel accuracy, especially the best in the translation dimensions. However, its attraction ranges were the smallest among the examined combinations (on average 36 mm and 19 deg). Last the bone-only information on the CT image did not show convergency property to the correct registration.

Algorithms↗
PubMed2005

Robust x-ray tubes for use within magnetic fields of MR scanners.

A hybrid system that combines an x-ray fluoroscopic system and a magnetic resonance (MR) system can provide physicians with the synergy of exquisite soft tissue contrast (from MR) and high temporal and spatial resolutions (from x ray), which may significantly benefit a number of image-guided interventional procedures. However, the system configuration may require the x-ray tube to be placed in a magnetic field, which can hinder the proper functioning of the x-ray tube by deflecting its electron beam. From knowledge of how the magnetic field affects the electron trajectories, we propose creating another magnetic field along the cathode-anode axis using either solenoids or permanent magnets to reduce the deflection of the electron beam for two cases: a strong and slightly misaligned field or a weak field that is arbitrary in direction. Theoretical analysis is presented and the electron beam is simulated in various external magnetic fields with a finite element modeling program. Results show that both correction schemes enhance the robustness of the x-ray tube operation in an externally applied magnetic field.

Computer-Aided Design↗
PubMed2005

FTRAC--a robust fluoroscope tracking fiducial.

C-arm fluoroscopy is ubiquitous in contemporary surgery, but it lacks the ability to accurately reconstruct three-dimensional (3D) information. A major obstacle in fluoroscopic reconstruction is discerning the pose of the x-ray image, in 3D space. Optical/magnetic trackers tend to be prohibitively expensive, intrusive and cumbersome in many applications. We present single-image-based fluoroscope tracking (FTRAC) with the use of an external radiographic fiducial consisting of a mathematically optimized set of ellipses, lines, and points. This is an improvement over contemporary fiducials, which use only points. The fiducial encodes six degrees of freedom in a single image by creating a unique view from any direction. A nonlinear optimizer can rapidly compute the pose of the fiducial using this image. The current embodiment has salient attributes: small dimensions (3 x 3 x 5 cm); need not be close to the anatomy of interest; and accurately segmentable. We tested the fiducial and the pose recovery method on synthetic data and also experimentally on a precisely machined mechanical phantom. Pose recovery in phantom experiments had an accuracy of 0.56 mm in translation and 0.33 degrees in orientation. Object reconstruction had a mean error of 0.53 mm with 0.16 mm STD. The method offers accuracies similar to commercial tracking systems, and appears to be sufficiently robust for intraoperative quantitative C-arm fluoroscopy. Simulation experiments indicate that the size can be further reduced to 1 x 1 X 2 cm, with only a marginal drop in accuracy.

Algorithms↗
PubMed2006

Robust frameless stereotactic localization in extra-cranial radiotherapy.

In the field of extra-cranial radiotherapy, several inaccuracies can make the application of frameless stereotactic localization techniques error-prone. When optical tracking systems based on surface fiducials are used, inter- and intra-fractional uncertainties in marker three-dimensional (3D) detection may lead to inexact tumor position estimation, resulting in erroneous patient setup. This is due to the fact that external fiducials misdetection results in deformation effects that are poorly handled in a rigid-body approach. In this work, the performance of two frameless stereotactic localization algorithms for 3D tumor position reconstruction in extra-cranial radiotherapy has been specifically tested. Two strategies, unweighted versus weighted, for stereotactic tumor localization were examined by exploiting data coming from 46 patients treated for extra-cranial lesions. Measured isocenter displacements and rotations were combined to define isocentric procedures, featuring 6 degrees of freedom, for correcting patient alignment (isocentric positioning correction). The sensitivity of the algorithms to uncertainties in the 3D localization of fiducials was investigated by means of 184 numerical simulations. The performance of the implemented isocentric positioning correction was compared to conventional point-based registration. The isocentric positioning correction algorithm was tested on a clinical dataset of inter-fractional and intra-fractional setup errors, which was collected by means of an optical tracker on the same group of patients. The weighted strategy exhibited a lower sensitivity to fiducial localization errors in simulated misalignments than those of the unweighted strategy. Isocenter 3D displacements provided by the weighted strategy were consistently smaller than those featured by the unweighted strategy. The peak decrease in median and quartile values of isocenter 3D displacements were 1.4 and 2.7 mm, respectively. Concerning clinical data, the weighted strategy isocentric positioning correction provided the reduction of fiducial registration errors, featuring up to 61.7% decrease in median values (versus 46.8% for the unweighted strategy) of initial displacements. The weighted strategy proved high performance in minimizing the effects of fiducial localization errors, showing a great potential in improving patient setup. The clinical data analysis revealed that the application of a robust reconstruction algorithm may provide high-quality results in patient setup verification, by properly managing external fiducials localization errors.

Algorithms↗
PubMed1994

Pseudocorrelation: a fast, robust, absolute, grey-level image alignment algorithm.

A new image alignment algorithm--pseudocorrelation--has been developed based on the application of Monte Carlo techniques to the calculation of a cross-correlation integral for grey-scale images. It has many advantages over cross-correlation: it is at least a factor of 10 faster than fast-Fourier-transform-based cross-correlation, and requires 8 times less memory. Its high speed allows for the search space of geometric transformations between images to include magnification and rotation as well as translations without the search time becoming too long. It allows noise to be taken into account, making calculation of a robust, absolute probability of good alignment possible. It is relatively insensitive to differences in quality between images. This article describes the pseudocorrelation algorithm in detail and presents the results of tests of the effects of contrast enhancement, resolution differences, and noise on the algorithm's performance. These tests show that the algorithm is well suited to the task of automated alignment of very low contrast images from video electronic portal imaging devices.

Algorithms↗
PubMed2001

A robust method to study stress "deafness".

Previous research by Dupoux et al. [J. Memory Lang. 36, 406-421 (1997)] has shown that French participants, as opposed to Spanish participants, have difficulties in distinguishing nonwords that differ only in the location of stress. Contrary to Spanish, French does not have contrastive stress, and French participants are "deaf" to stress contrasts. The experimental paradigm used by Dupoux et al. (speeded ABX) yielded significant group differences, but did not allow for a sorting of individuals according to their stress "deafness." Individual assessment is crucial to study special populations, such as bilinguals or trained monolinguals. In this paper, a more robust paradigm based on a short-term memory sequence repetition task is proposed. In five French-Spanish cross-linguistic experiments, stress "deafness" is shown to crucially depend upon a combination of memory load and phonetic variability in F0. In experiments 3 and 4, nonoverlapping distribution of individual results for French and Spanish participants is observed. The paradigm is thus appropriate for assessing stress deafness in individual participants.

Adult↗
PubMed2003

Robust time reversal focusing in the ocean.

Recent time-reversal experiments with high-frequency transmissions (3.5 kHz) show that stable focusing is severely limited by the time-dependent ocean environments. The vertical focal structure displays dynamic variations associated with focal splitting and remerging resulting in large changes in focal intensity. Numerical simulations verify that the intensity variation is linked to the focal shift induced by phase changes in acoustic waves resulting from sound speed fluctuations due to internal waves. A relationship between focal range shift, frequency shift, or channel depth changes is illustrated using waveguide-invariant theory. Based on the analysis of experimental data and numerical simulations, methods for robust time-reversal focusing are developed to extend the period of stable focusing.

Journal Article↗
PubMed2003

Robustness of multichannel equalization in an acoustic reverberant environment.

A theoretical framework is established, for the robustness of multichannel sound equalization in reverberant environments. Using results from statistical room acoustics, a closed-form expression is derived that predicts the degradation in performance of an equalization system as the sound source moves from its nominal position inside the enclosure. The presented analysis also provides means of identifying the performance bounds that can be expected when using such a system in an actual room. Using extensive computer simulations, the effect of physical parameters such as the relative positions of the source and the receivers, as well as effects of different design parameters are investigated. Based on the conditions imposed by these parameters, it is shown that, depending on the array geometry and the exact form of the equalizers, slight performance gains can be expected as the number of receivers is increased.

Acoustics↗
PubMed2004

Robust and accurate fundamental frequency estimation based on dominant harmonic components.

This paper presents a new method for robust and accurate fundamental frequency (F0) estimation in the presence of background noise and spectral distortion. Degree of dominance and dominance spectrum are defined based on instantaneous frequencies. The degree of dominance allows one to evaluate the magnitude of individual harmonic components of the speech signals relative to background noise while reducing the influence of spectral distortion. The fundamental frequency is more accurately estimated from reliable harmonic components which are easy to select given the dominance spectra. Experiments are performed using white and babble background noise with and without spectral distortion as produced by a SRAEN filter. The results show that the present method is better than previously reported methods in terms of both gross and fine F0 errors.

Adult↗
PubMed2006

Multiple ping sonar accuracy improvement using robust motion estimation and ping fusion.

Noise degrades the accuracy of sonar systems. We demonstrate a practical method for increasing the effective signal-to-noise ratio (SNR) by fusing time delay information from a burst of multiple sonar pings. This approach can be useful when there is no relative motion between the sonar and the target during the burst of sonar pinging. Otherwise, the relative motion degrades the fusion and therefore, has to be addressed before fusion can be used. In this paper, we present a robust motion estimation algorithm which uses information from multiple receivers to estimate the relative motion between pings in the burst. We then compensate for motion, and show that the fusion of information from the burst of motion compensated pings improves both the resilience to noise and sonar accuracy, consequently increasing the operating range of the sonar system.

Journal Article↗
PubMed2006

An effective cluster-based model for robust speech detection and speech recognition in noisy environments.

This paper shows an accurate speech detection algorithm for improving the performance of speech recognition systems working in noisy environments. The proposed method is based on a hard decision clustering approach where a set of prototypes is used to characterize the noisy channel. Detecting the presence of speech is enabled by a decision rule formulated in terms of an averaged distance between the observation vector and a cluster-based noise model. The algorithm benefits from using contextual information, a strategy that considers not only a single speech frame but also a neighborhood of data in order to smooth the decision function and improve speech detection robustness. The proposed scheme exhibits reduced computational cost making it adequate for real time applications, i.e., automated speech recognition systems. An exhaustive analysis is conducted on the AURORA 2 and AURORA 3 databases in order to assess the performance of the algorithm and to compare it to existing standard voice activity detection (VAD) methods. The results show significant improvements in detection accuracy and speech recognition rate over standard VADs such as ITU-T G.729, ETSI GSM AMR, and ETSI AFE for distributed speech recognition and a representative set of recently reported VAD algorithms.

Algorithms↗
PubMed2003

Robust normal mode constraints on inner-core anisotropy from model space search.

A technique for searching full model space that was applied to measurements of anomalously split normal modes showed a robust pattern of P-wave and S-wave anisotropy in the inner core. The parameter describing P-wave anisotropy changes sign around a radius of 400 kilometers, whereas S-wave anisotropy is small in the upper two-thirds of the inner core and becomes negative at greater depths. Our results agree with observed travel-time anomalies of rays traveling at epicentral distances varying from 150 degrees to 180 degrees. The models may be explained by progressively tilted hexagonal close-packed iron in the upper half of the inner core and could suggest a different iron phase in the center.

Journal Article↗
PubMed2004

Robust temporal coding in the trigeminal system.

The ability of rats to use their whiskers for fine tactile discrimination rivals that of humans using their fingertips. Rats perform discriminations rapidly and accurately while palpating the environment with their whiskers. This suggests that whisker deflections produce a robust and reliable neural code. Whisker primary afferents respond with highly reproducible temporal spike patterns to transient stimuli. Here we show that, with the use of a linear kernel, any of these reproducible response trains recorded from an individual neuron can reliably predict complex whisker deflections. These predictions are significantly improved by integrating responses from neurons with opposite angular preferences.

Acoustic Stimulation↗
PubMed1999

The robust australopithecine face: a morphogenetic perspective.

The robust australopithecines were a side branch of human evolution. They share a number of unique craniodental features that suggest their monophyletic origin. However, virtually all of these traits appear to reflect a singular pattern of nasomaxillary modeling derived from their unusual dental proportions. Therefore, recent cladistic analyses have not resolved the phylogenetic history of these early hominids. Efforts to increase cladistic resolution by defining traits at greater levels of anatomical detail have instead introduced substantial phyletic error.

Africa↗
PubMed2025

Robust and highly efficient transformation method for a minimal mycoplasma cell.

UNLABELLED: Mycoplasmas have been widely investigated for their pathogenicity, as well as for genomics and synthetic biology. Conventionally, transformation of mycoplasmas was not highly efficient, and due to the low transformation efficiency, large amounts of DNA and recipient cells were required for that purpose. Here, we report a robust and highly efficient transformation method for the minimal cell JCVI-syn3B, which was created through streamlining the genome of Mycoplasma mycoides. When the growth states of JCVI-syn3B were examined in detail by focusing on such factors as pH, color, absorbance, colony forming unit, and transformation efficiency, it was found that the growth phase after the lag phase can be divided into three distinct phases, of which the highest transformation efficiency was observed during the early exponential growth phase. Notably, the transformation efficiency of up to 4.4 × 10-2 transformants per cell per microgram of plasmid DNA was obtained. A method to obtain several hundred to several thousand transformants with less than 0.2 mL of culture with approximately 1 × 107-108 cells and 10 ng of plasmid DNA was developed. Moreover, a transformation method using a frozen stock of transformation-ready cells was established. These procedures and information could simplify and enhance the transformation process of minimal cells, facilitating advanced genetic engineering and biological research using minimal cells. IMPORTANCE: Mycoplasmas are parasitic and pathogenic bacteria for many animals. They are also useful bacteria to understand the cellular process of life and for bioengineering because of their simple metabolism, small genomes, and cultivability. Genetic manipulation is crucial for these purposes, but transformation efficiency in mycoplasmas is typically quite low. Here, we report a highly efficient transformation method for the minimal genome mycoplasma JCVI-syn3B. Using this method, transformants can be obtained with only 10 ng of plasmid DNA, which is around one-thousandth of the amount required for traditional mycoplasma transformations. Moreover, a convenient method using frozen stocks of transformation-ready cells was established. These improved methods play a crucial role in further studies using minimal cells.

Transformation, Bacterial↗
PubMed2001

Quintuple deglycosylation mutant of simian immunodeficiency virus SIVmac239 in rhesus macaques: robust primary replication, tightly contained chronic infection, and elicitation of potent immunity against the parental wild-type strain.

We previously generated a mutant of simian immunodeficiency virus (SIV) lacking 5 of a total of 22 N-glycans in its external envelope protein gp120 with no impairment in viral replication capability and infectivity in tissue culture cells. Here, we infected rhesus macaques with this mutant and found that it also replicated robustly in the acute phase but was tightly, though not completely, contained in the chronic phase. Thus, a critical requirement for the N-glycans for the full extent of chronic infection was demonstrated. No evidence indicating reversion to a wild type was obtained during the observation period of more than 40 weeks. Monkeys infected with the mutant were found to tolerate a challenge infection with wild-type SIV very well. Analyses of host responses following challenge revealed no neutralizing antibodies against the challenge virus but strong secondary responses of cytotoxic T lymphocytes against multiple antigens, including Gag-Pol, Nef, and Env. Thus, the quintuple deglycosylation mutant appeared to represent a novel class of SIV live attenuated vaccine.

Animals↗
PubMed2003

nef gene is required for robust productive infection by simian immunodeficiency virus of T-cell-rich paracortex in lymph nodes.

The pathogenesis of AIDS virus infection in a nonhuman primate AIDS model was studied by comparing plasma viral loads, CD4(+) T-cell subpopulations in peripheral blood mononuclear cells, and simian immunodeficiency virus (SIV) infection in lymph nodes for rhesus macaques infected with a pathogenic molecularly cloned SIVmac239 strain and those infected with its nef deletion mutant (Deltanef). In agreement with many reports, whereas SIVmac239 infection induced AIDS and depletion of memory CD4(+) T cells in 2 to 3 years postinfection (p.i.), Deltanef infection did not induce any manifestation associated with AIDS up to 6.5 years p.i. To explore the difference in SIV infection in lymphoid tissues, we biopsied lymph nodes at 2, 8, 72, and 82 weeks p.i. and analyzed them by pathological techniques. Maximal numbers of SIV-infected cells (SIV Gag(+), Env(+), and RNA(+)) were detected at 2 weeks p.i. in both the SIVmac239-infected animals and the Deltanef-infected animals. In the SIVmac239-infected animals, most of the infected cells were localized in the T-cell-rich paracortex, whereas in the Deltanef-infected animals, most were localized in B-cell-rich follicles and in the border region between the paracortex and the follicles. Analyses by double staining of CD68(+) macrophages and SIV Gag(+) cells and by double staining of CD3(+) T cells and SIV Env(+) cells revealed that SIV-infected cells were identified as CD4(+) T cells in either the SIVmac239 or the Deltanef infection. Whereas the many functions of Nef protein were reported from in vitro studies, our finding of SIVmac239 replication in the T-cell-rich paracortex in the lymph nodes supports the reported roles of Nef protein in T-cell activation and enhancement of viral infectivity. Furthermore, the abundance of SIVmac239 infection and the paucity of Deltanef infection in the T-cell-rich paracortex accounted for the differences in viral replication and pathogenicity between SIVmac239 and the Deltanef mutant. Thus, our in vivo study indicated that the nef gene enhances SIV replication by robust productive infection in memory CD4(+) T cells in the T-cell-rich region in lymphoid tissues.

Animals↗
PubMed2026

ZILA-SRM: a probabilistic framework with zero-inflated latent models for robust strain reconstruction from metagenomes.

UNLABELLED: Resolving bacterial strain diversity from shotgun metagenomic data is fundamental to understanding intra-host evolution, transmission dynamics, and phenotypic heterogeneity. However, current probabilistic approaches face a severe "identifiability limit" when disentangling highly similar genomes. Under high-noise conditions, sequencing errors, coverage overdispersion, and collinearity confound standard expectation-maximization algorithms, resulting in overfitting and spurious "ghost" strains. Here, we introduce zero-inflated latent allocation for strain reconstruction from metagenomes with adaptive sparsity regularization (ZILA-SRM) to overcome this barrier through three innovations. First, we integrate a zero-inflated Poisson mixture model to decouple "structural zeros" (true strain absence) from "sampling zeros" (stochastic dropout), addressing overdispersion in standard Poisson-based tools. Second, we impose a convex adaptive sparsity regularization penalty that leverages biological sparsity priors to shrink noise artifacts dynamically. Third, we implement a graph-theoretic refinement step using maximal clique enumeration to resolve haplotype collinearity. Benchmarking against StrainFinder and MixtureS on 702 synthetic data sets shows that ZILA-SRM achieves a 20% improvement in precision in high-complexity scenarios while maintaining over 80% recall for minor variants at 0.5% abundance. Re-analysis of deep-sequencing data from 195 Mycobacterium tuberculosis clinical samples reveals cryptic low-abundance drug-resistant variants in 12% of patients, including a minor clone carrying the rpoB S450L mutation. Furthermore, application to skin microbiome data sets further reveals a strong negative correlation between dominant Staphylococcus aureus and Staphylococcus epidermidis strains, providing genomic evidence for competitive exclusion. These findings establish ZILA-SRM as a robust tool for resolving strain-level diversity in complex metagenomes. IMPORTANCE: Understanding microbial communities at the strain level is critical because closely related strains can differ dramatically in traits such as drug resistance, virulence, and ecological interactions. However, resolving individual strains from metagenomic sequencing data remains difficult, especially when strains are highly similar or present at low abundance. As a result, biologically meaningful diversity is often obscured or misinterpreted as noise. In this study, we introduce a new framework that improves the reliability of strain reconstruction from complex metagenomic data. By reducing false-positive strain detection while preserving sensitivity to rare variants, our approach enables more accurate characterization of microbial populations. This improved resolution reveals previously hidden subpopulations in clinical and microbiome datasets, providing clearer insights into microbial evolution, competition, and the emergence of clinically relevant traits such as antibiotic resistance.

Metagenomics↗