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At least 253 records · Page 14Linked to original sources
PubMed1996

Motion parallax is used to control postural sway during walking.

Three experiments tested the hypothesis that postural sway during locomotion is visually regulated by motion parallax as well as optical expansion. Oscillating displays of three-dimensional scenes were presented to participants walking on a treadmill, while postural sway was recorded. Displays simulated: (a) a cloud, in which parallax and expansion are congruent, (b) a hallway, (c) the side walls of the hallway, (d) a ground surface, (e) a wall, (f) the wall with a central hole, (g) a hall farther from the observer, and (h) a wall farther from the observer. In contrast to previous results with a hallway, responses with the cloud were isotropic and directionally specific. The other displays demonstrated that motion parallax was more effective than simple horizontal flow in eliciting lateral sway. These results are consistent with the hypothesis that adaptive control of sway during walking is based on congruent expansion and parallax in natural environments.

Adult↗
PubMed2026

pmultiqc: An Open-Source, Lightweight, and Metadata-Oriented QC Reporting Library for MS Proteomics.

The increasing scale and complexity of proteomics data demand robust, scalable, and interpretable quality control (QC) frameworks to ensure data reliability and reproducibility. Here, we present pmultiqc, an open-source Python package that standardizes and generates web-based QC reports across multiple proteomics data analysis platforms. Built on top of the widely adopted MultiQC framework, pmultiqc offers specialized modules tailored to mass spectrometry workflows, with full initial support for quantms, DIA-NN, MaxQuant/MaxDIA, FragPipe, and mzIdentML/mzML-based pipelines. The package computes a wide range of QC metrics, including raw intensity distributions, identification rates, retention time consistency, and missing value patterns, and presents them in interactive, publication-ready reports. By leveraging sample metadata in the Sample and Data Relationship Format format, pmultiqc enables metadata-aware QC and introduces, for the first time in proteomics, QC reports and metrics guided by standardized sample metadata. Its modular architecture allows easy extension to new workflows and formats. Alongside comprehensive documentation and examples for running pmultiqc locally or integrated into existing workflows, we offer a cloud-based service that enables users to generate QC reports from their own data or public PRIDE datasets.

Proteomics↗
PubMed2004

A particle-dynamics study of dissipation in colliding clouds of ultracold fermions.

We present a numerical study of the micro-dynamical roots of dissipation in two colliding mesoscopic clouds of point-like fermions as a function of the scattering length and of temperature approaching full quantum degeneracy. This study, which is motivated by current experiments on ultracold gaseous mixtures of fermionic atoms inside magnetic traps, combines the solution of the coupled Vlasov-Landau equations for the Wigner distribution functions with a locally adaptive importance-sampling technique for handling collisional interactions. The results illustrate the consequences of genuinely quantum collisional phenomena, and in particular the role of Pauli blocking in the transition to hydrodynamic behaviour. We also compare the computed quantum collision rate as a function of temperature in the weak-coupling case with theoretical results assuming that equilibrium distributions determine the quantum collision integral.

Journal Article↗
PubMed2006

Principal component-based radiative transfer model for hyperspectral sensors: theoretical concept.

Modern infrared satellite sensors such as the Atmospheric Infrared Sounder (AIRS), the Cross-Track Infrared Sounder (CrIS), the Tropospheric Emission Spectrometer (TES), the Geosynchronous Imaging Fourier Transform Spectrometer (GIFTS), and the Infrared Atmospheric Sounding Interferometer (IASI) are capable of providing high spatial and spectral resolution infrared spectra. To fully exploit the vast amount of spectral information from these instruments, superfast radiative transfer models are needed. We present a novel radiative transfer model based on principal component analysis. Instead of predicting channel radiance or transmittance spectra directly, the principal component-based radiative transfer model (PCRTM) predicts the principal component (PC) scores of these quantities. This prediction ability leads to significant savings in computational time. The parameterization of the PCRTM model is derived from the properties of PC scores and instrument line-shape functions. The PCRTM is accurate and flexible. Because of its high speed and compressed spectral information format, it has great potential for superfast one-dimensional physical retrieval and for numerical weather prediction large volume radiance data assimilation applications. The model has been successfully developed for the NAST-I and AIRS instruments. The PCRTM model performs monochromatic radiative transfer calculations and is able to include multiple scattering calculations to account for clouds and aerosols.

Journal Article↗
PubMed2004

Imaging density disturbances in water with a 41.3-attosecond time resolution.

We show that the momentum flexibility of inelastic x-ray scattering may be exploited to invert its loss function, allowing real time imaging of density disturbances in a medium. We show the disturbance arising from a point source in liquid water, with a resolution of 41.3 attoseconds (4.13 x 10(-17) s) and 1.27 A (1.27 x 10(-8) cm). This result is used to determine the structure of the electron cloud around a photoexcited chromophore in solution, as well as the wake generated in water by a 9 MeV gold ion. We draw an analogy with pump-probe techniques and suggest that energy-loss scattering may be applied more generally to the study of attosecond phenomena.

Elasticity↗
PubMed2004

The Rossby Centre Regional Atmospheric Climate Model part II: application to the Arctic climate.

The Rossby Centre regional climate model (RCA2) has been integrated over the Arctic Ocean as part of the international ARCMIP project. Results have been compared to observations derived from the SHEBA data set. The standard RCA2 model overpredicts cloud cover and downwelling longwave radiation, during the Arctic winter. This error was improved by introducing a new cloud parameterization, which significantly improves the annual cycle of cloud cover. Compensating biases between clear sky downwelling longwave radiation and longwave radiation emitted from cloud base were identified. Modifications have been introduced to the model radiation scheme that more accurately treat solar radiation interaction with ice crystals. This leads to a more realistic representation of cloud-solar radiation interaction. The clear sky portion of the model radiation code transmits too much solar radiation through the atmosphere, producing a positive bias at the top of the frequent boundary layer clouds. A realistic treatment of the temporally evolving albedo, of both sea-ice and snow, appears crucial for an accurate simulation of the net surface energy budget. Likewise, inclusion of a prognostic snow-surface temperature seems necessary, to accurately simulate near-surface thermodynamic processes in the Arctic.

Arctic Regions↗
PubMed1995

Methods for displaying macromolecular structural uncertainty: application to the globins.

Most molecular graphics programs ignore any uncertainty in the atomic coordinates being displayed. Structures are displayed in terms of perfect points, spheres, and lines with no uncertainty. However, all experimental methods for defining structures, and many methods for predicting and comparing structures, associate uncertainties with each atomic coordinate. We have developed graphical representations that highlight these uncertainties. These representations are encapsulated in a new interactive display program, PROTEAND. PROTEAND represents structural uncertainty in three ways: (1) The traditional way: The program shows a collection of structures as superposed and overlapped stick-figure models. (2) Ellipsoids: At each atom position, the program shows an ellipsoid derived from a three-dimensional Gaussian model of uncertainty. This probabilistic model provides additional information about the relationship between atoms that can be displayed as a correlation matrix. (3) Rigid-body volumes: Using clouds of dots, the program can show the range of rigid-body motion of selected substructures, such as individual alpha helices. We illustrate the utility of these display modalities by the applying PROTEAND to the globin family of proteins, and show that certain types of structural variation are best illustrated with different methods of display.

Animals↗
PubMed2026

PMBB Geno-Pheno Toolkit: A suite of scalable, reproducible pipelines for cross-biobank association analyses.

Electronic health record (EHR)-linked biobanks generate unprecedented genomic and phenotypic datasets, but their scientific utility is constrained by data fragmentation across institutional silos and incompatible computing infrastructures, forcing researchers to rewrite ad-hoc scripts for each new environment. We present the PMBB Geno-Pheno Toolkit, a suite of modular Nextflow pipelines for biobank-scale association analyses. This note focuses on the toolkit's SAIGE family of pipelines - supporting genome-wide (GWAS), exome-wide (ExWAS), and phenome-wide (PheWAS) association testing - together with the companion GWAMA and ExWAS meta-analysis pipelines that enable cross-biobank replication. All components are containerized (Docker/Apptainer) and orchestrated with Nextflow, allowing the same workflows to run unmodified on local HPC clusters, cloud platforms, and the All of Us Research Workbench. Complementary toolkit pipelines for PLINK-based GWAS, polygenic scoring, LD-based clumping, and phenotype harmonization are also available and briefly noted.

Journal Article↗
PubMedDate not supplied

Inclusion of ionic interactions in force field calculations of charged biomolecules--DNA structural transitions.

The potential of mean force (PMF) approach for treating polyion-diffuse ionic cloud interactions [D. M. Soumpasis (1984) Proceedings of the National Academy of Sciences USA 81, 5116-5120] has been combined with the AMBER force field describing intramolecular interactions. The resultant generalized AMBER-PMF force field enables one to treat the conformational stabilities and structural transitions of charged biomolecules in aqueous electrolytes more realistically. For example, we have used it to calculate the relative stabilities of the B and Z conformations of d(C-G)6, and the B and heteronomous (H) conformations of dA12.dT12, as a function of salt concentration. In the case of d(C-G)6, the predicted B-ZI transition occurs at 2.4M and is essentially driven by the phosphate-diffuse ionic cloud interactions alone as suggested by the results of earlier PMF calculations. The ZII conformer is less stable than the B form under all conditions. It is found that the helical parameters of the refined B and Z structures change with salt concentration. For example, the helical rise of B-DNA increases about 10% and the twist angle decreases by the same amount above 1M NaCl. In the range of 0.01-0.3M NaCl, the H form of dA12.dT12 is found to be more stable than the B form and its stability increases with increasing salt concentration. The computed greater relative stability of the H conformation is likely due to noninclusion of the free energy contribution from the spine of hydration, a feature presumed to stabilize the B form of this sequence.

Biopolymers↗
PubMedDate not supplied

Detecting the edge of the tongue: a tutorial.

The goal of this paper is to provide a tutorial introduction to the topic of edge detection of the tongue from ultrasound scans for researchers in speech science and phonetics. The method introduced here is Active Contours (also called snakes), a method for searching for an edge, assuming that it is a smooth curve in the image data. The advantage of this approach is that it is robust to the noisy speckle that clouds edges. This method has been implemented in several software packages currently used for detecting the edge of the tongue in ultrasound images. The tutorial concludes with an overview of the scale-space and Kalman filter approaches, state-of-the-art developments in image processing that will likely influence work on tongue edge detection in the coming years.

Humans↗
PubMed1999

Clouds and rainbows on the HIPAA horizon.

In the planning phase for several years, the administrative simplification provisions of the Health Insurance Portability and Accountability Act of 1996 (HIPAA) finally appear ready for implementation. The Health Care Financing Administration (HCFA) expects that the major HIPAA measures will be released in late 1999. For group practices, it is expected that implementation of these provisions will be complicated and consume significant amounts of time and money. Still, the end result should justify the effort.

Computer Security↗
PubMed2005

A novel 3D partitioned active shape model for segmentation of brain MR images.

A 3D Partitioned Active Shape Model (PASM) is proposed in this paper to address the problems of the 3D Active Shape Models (ASM). When training sets are small. It is usually the case in 3D segmentation, 3D ASMs tend to be restrictive. This is because the allowable region spanned by relatively few eigenvectors cannot capture the full range of shape variability. The 3D PASM overcomes this limitation by using a partitioned representation of the ASM. Given a Point Distribution Model (PDM), the mean mesh is partitioned into a group of small tiles. In order to constrain deformation of tiles, the statistical priors of tiles are estimated by applying Principal Component Analysis to each tile. To avoid the inconsistency of shapes between tiles, training samples are projected as curves in one hyperspace instead of point clouds in several hyperspaces. The deformed points are then fitted into the allowable region of the model by using a curve alignment scheme. The experiments on 3D human brain MRIs show that when the numbers of the training samples are limited, the 3D PASMs significantly improve the segmentation results as compared to 3D ASMs and 3D Hierarchical ASMs.

Algorithms↗
PubMed1997

Normal pressure hydrocephalus and deep white matter stroke: a case report.

The symptoms of urinary incontinence, ataxia, and mental confusion are an integral part of the clinical presentation of normal pressure hydrocephalus (NPH). They are also common presentations in the rehabilitation setting of patients who have had a cerebral vascular accident. The concurrence of these entities challenges the physiatrist to carefully diagnose and properly manage the patient to maximize the rehabilitation outcome. In the older population the clinical picture may be clouded by several overlapping conditions such as dementia, deconditioning, and age-related decline in bladder control. A case is presented in which the diagnosis of NPH was made after the patient showed a lack of progress in ambulation despite dramatic improvement in strength of the lower extremities.

Aged↗
PubMed2006

Resonance Raman spectrum of the solvated electron in methanol: simulation within a cluster model.

The microsolvation of the CH(3)OH(2) hypervalent radical in methanol clusters has been investigated by density functional theory. It is shown that the CH(3)OH(2) radical spontaneously decomposes within methanol clusters into protonated methanol and a localized solvated electron cloud. The geometric and electronic structures of these clusters as well as their vibrational frequencies have been characterized. Resonance Raman intensities, associated with the s --> p transition of the unpaired electron, have been estimated for CH(3)OH(2)M(n) (M = CH(3)OH, n = 1-3) clusters. It is shown that with increasing cluster size the simulated spectra converge toward the resonance Raman spectrum of the solvated electron in methanol measured recently by Tauber and Mathies (J. Am. Chem. Soc. 2004, 126, 3414). The results suggest that CH(3)OH(2)M(n) clusters are useful finite-size model systems for the computational investigation of the spectroscopic properties of the solvated electron in liquid methanol.

Computer Simulation↗
PubMed2002

Optical and physical properties of stratospheric aerosols from balloon measurements in the visible and near-infrared domains. 1. Analysis of aerosol extinction spectra from the AMON and SALOMON balloonborne spectrometers.

Aerosol extinction coefficients have been derived in the 375-700-nm spectral domain from measurement in the stratosphere since 1992, at night, at mid- and high latitudes from 15 to 40 km, by two balloonborne spectrometers, Absorption par les Minoritaires Ozone et NO(chi) (AMON) and Spectroscopie d'Absorption Lunaire pour l'Observation des Minoritaires Ozone et NO(chi) (SALOMON). Log-normal size distributions associated with the Mie-computed extinction spectra that best fit the measurements permit calculation of integrated properties of the distributions. Although measured extinction spectra that correspond to background aerosols can be reproduced by the Mie scattering model by use of monomodal log-normal size distributions, each flight reveals some large discrepancies between measurement and theory at several altitudes. The agreement between measured and Mie-calculated extinction spectra is significantly improved by use of bimodal log-normal distributions. Nevertheless, neither monomodal nor bimodal distributions permit correct reproduction of some of the measured extinction shapes, especially for the 26 February 1997 AMON flight, which exhibited spectral behavior attributed to particles from a polar stratospheric cloud event.

Journal Article↗
PubMed1999

Laser 3-D scanning for surface rendering in biomedical research and education.

A technique based on laser scanning is applied to body parts and organs. Laser light is projected onto the surface of objects and recorded by CCD sensors. This is a fast and flexible method for accurately scanning surface geometry. It also allows conversion to NURBS patches. We have, so far, made 'point-cloud' surface renderings from a head model, a plastic brain model, a human brain, moulds of bites and a cranium. The limits, quality, efforts and costs of employing the laser 3-D scanning technique are evaluated. The experiments are currently in progress and results give interesting 3D renderings and attempts to triangulated solid-models.

Brain↗
PubMed1986

Ethmoid sinus disease: CT evaluation in 400 cases. Part I. Nonsurgical patients.

The unique anatomy of the ethmoid sinuses makes it difficult to interpret "soft-tissue clouding," especially on plain films. The clinical significance of isolated or generalized soft-tissue disease within ethmoid cells is unclear, and the patterns of bone erosion or remodeling must be relied on in establishing a specific differential diagnosis. Of 400 patients studied, 186 had inflammatory disease and 214 had tumors. Squamous cell carcinomas, metastases, and a few aggressive sarcomas were found almost exclusively to have bone destruction, while 94% of the remaining neoplasms were characterized by cavity remodeling. Further differentiation was sometimes possible because of the pattern and degree of tumor enhancement. Of the neoplasms, only the minor salivary gland lesions and neuromas had nonhomogeneous enhancement. Malignant lesions cannot be diagnosed with computed tomography (CT) unless bone destruction is present. Similarly, although the significance of persistent, benign-appearing soft-tissue disease during chemotherapy is unclear, tumor must always be suspected, even after many months of a stable CT appearance.

Diagnosis, Differential↗
PubMedDate not supplied

Passive nighttime warming facility for forest ecosystem research.

A nighttime warming experiment is proposed. Over the last four decades a significant rise in nighttime minimum temperature has been determined from analysis of meteorological records from a global distribution of locations. The experiment involves nighttime deployment of infrared (IR) reflecting curtains around four sides of a forest canopy and across the top of the forest to mimic the top-down warming effect of cloud cover. The curtains are deployed with cable and pulley systems mounted on a tower and scaffolding structure built around the selected forest site. The trunk space is not enclosed except as an optional manipulation. The curtains reflect long-wave radiation emitted from the forest and ground back into the forest warming the trees, litter, and soil. Excellent infrared reflection can be obtained with commercially available fabrics that have aluminum foil bonded to one side. A canopy warming of 3 to 5 degrees C is expected on cloudless nights, and on cloudy nights, a warming of 1 to 3 degrees C is anticipated relative to a control plot. The curtains are withdrawn by computer control during the day and also at night during periods with precipitation or excessive wind. Examples of hypothesized ecosystem responses to nighttime warming include: (1) increase in tree maintenance respiration (decreasing carbon reserves and ultimately tree growth), (2) increase in the length of the growing season (increasing growth), (3) increase in soil respiration, (4) increase in litter decomposition, (5) increase in mineralization of N and other nutrients from soil organic matter, (6) increase in nutrient uptake (increasing growth), and (7) increase in N immobilization in litter. Hypothesis 1 has the opposite consequence for tree growth to Hypotheses 2 and 6, and thus opposite consequences for the feedback regulation that vegetation has on net greenhouse gas releases to the atmosphere. If Hypothesis 1 is dominant, warming could lead to more warming from the additional CO(2) emissions. Site-specific meteorological, ecophysiological, and phenological measurements are obtained in the warming treatment and in a carefully selected control plot to investigate site-specific hypotheses. Measurements made on both plots for a baseline period and during the period of curtain deployment provide data to test the hypotheses statistically by the "before-after-control-impact" method applicable to unreplicated experiments. The enclosure has a modular design that can be adapted and combined with other forest-scale manipulation experiments such as free air CO(2) enrichment and throughfall displacement.

Journal Article↗