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At least 505 records · Page 28Linked to original sources
PubMed2001

Conditional optimization: a new formalism for protein structure refinement.

Conditional optimization allows unlabelled loose-atom refinement to be combined with extensive application of geometrical restraints. It offers an N-particle solution for the assignment of topology to loose atoms, with weighted gradients applied to all possibilities. For a simplified test structure consisting of a polyalanine four-helical bundle, this method shows a large radius of convergence using calculated diffraction data to at least 3.5 A resolution. It is shown that with a new multiple-model protocol to estimate sigma(A) values, this structure can be successfully optimized against 2.0 A resolution diffraction data starting from a random atom distribution. Conditional optimization has potentials for map improvement and automated model building at low or medium resolution limits. Future experiments will have to be performed to explore the possibilities of this method for ab initio phasing of real protein diffraction data.

Crystallization↗
PubMed2003

Ab initio protein phasing at 1.4 A resolution.

All the techniques today available for the ab initio crystal structure solution of proteins require that the atomicity condition is satisfied. Accordingly, diffraction data at resolution equal or better than 1.2 A are necessary. This condition reduces the role of the ab initio techniques in macromolecular crystallography. The computer program SIR2002 has been modified in such a way that it may succeed also with 1.4 A resolution diffraction data. The modifications concern all the modules of the program: the modified program also benefits by the efficiency of a figure of merit.

Collagen↗
PubMed2005

Flow-based fiber tracking with diffusion tensor and q-ball data: validation and comparison to principal diffusion direction techniques.

In this study, we evaluate the performance of a flow-based surface evolution fiber tracking algorithm by means of a physical anisotropic diffusion phantom with known connectivity. We introduce a novel speed function for surface evolution that is derived from either diffusion tensor (DT) data, high angular resolution diffusion (HARD) data, or a combined DT-HARD hybrid approach. We use the model-free q-ball imaging (QBI) approach for HARD reconstruction. The anisotropic diffusion phantom allows us to compare and evaluate the performance of different fiber tracking approaches in the presence of real imaging artifacts, noise, and subvoxel partial volume averaging of fiber directions. The surface evolution approach, using the full diffusion tensor as opposed to the principal diffusion direction (PDD) only, is compared to PDD-based line propagation fiber tracking. Additionally, DT reconstruction is compared to HARD reconstruction for fiber tracking, both using surface evolution. We show the potential for surface evolution using the full diffusion tensor to map connections in regions of subvoxel partial volume averaging of fiber directions, which can be difficult to map with PDD-based methods. We then show that the fiber tracking results can be improved by using high angular resolution reconstruction of the diffusion orientation distribution function in cases where the diffusion tensor model fits the data poorly.

Algorithms↗
PubMed2005

Estimation of the cortical functional connectivity with the multimodal integration of high-resolution EEG and fMRI data by directed transfer function.

Nowadays, several types of brain imaging device are available to provide images of the functional activity of the cerebral cortex based on hemodynamic, metabolic, or electromagnetic measurements. However, static images of brain regions activated during particular tasks do not convey the information of how these regions communicate with each other. In this study, advanced methods for the estimation of cortical connectivity from combined high-resolution electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) data are presented. These methods include a subject's multicompartment head model (scalp, skull, dura mater, cortex) constructed from individual magnetic resonance images, multidipole source model, and regularized linear inverse source estimates of cortical current density. Determination of the priors in the resolution of the linear inverse problem was performed with the use of information from the hemodynamic responses of the cortical areas as revealed by block-designed (strength of activated voxels) fMRI. We estimate functional cortical connectivity by computing the directed transfer function (DTF) on the estimated cortical current density waveforms in regions of interest (ROIs) on the modeled cortical mantle. The proposed method was able to unveil the direction of the information flow between the cortical regions of interest, as it is directional in nature. Furthermore, this method allows to detect changes in the time course of information flow between cortical regions in different frequency bands. The reliability of these techniques was further demonstrated by elaboration of high-resolution EEG and fMRI signals collected during visually triggered finger movements in four healthy subjects. Connectivity patterns estimated for this task reveal an involvement of right parietal and bilateral premotor and prefrontal cortical areas. This cortical region involvement resembles that revealed in previous studies where visually triggered finger movements were analyzed with the use of separate EEG or fMRI measurements.

Adult↗
PubMed1998

Electronic States of Lanthanum Monoiodide: Preliminary Data from High-Resolution LIF Spectroscopy.

Fluorescence spectra of lanthanum monoiodide excited by the Ar+ 501.7-nm laser line have been observed and analyzed. Seven (sub)states are characterized. Preliminary rovibrational data are obtained for the four low-lying states (I-IV). The first two can be ascribed as X1Sigma and a3Delta: III does have Omega = 1, and IV is possibly 1Delta. The 11 laser-excited levels are tentatively grouped into three entities. Copyright 1998 Academic Press.

Journal Article↗
PubMed2005

Assessment of MODIS-EVI, MODIS-NDVI and VEGETATION-NDVI composite data using agricultural measurements: an example at corn fields in western Mexico.

Although several types of satellite data provide temporal information of the land use at no cost, digital satellite data applications for agricultural studies are limited compared to applications for forest management. This study assessed the suitability of vegetation indices derived from the TERRA-Moderate Resolution Imaging Spectroradiometer (MODIS) sensor and SPOT-VEGETATION (VGT) sensor for identifying corn growth in western Mexico. Overall, the Normalized Difference Vegetation Index (NDVI) composites from the VGT sensor based on bi-directional compositing method produced vegetation information most closely resembling actual crop conditions. The NDVI composites from the MODIS sensor exhibited saturated signals starting 30 days after planting, but corresponded to green leaf senescence in April. The temporal NDVI composites from the VGT sensor based on the maximum value method had a maximum plateau for 80 days, which masked the important crop transformation from vegetative stage to reproductive stage. The Enhanced Vegetation Index (EVI) composites from the MODIS sensor reached a maximum plateau 40 days earlier than the occurrence of maximum leaf area index (LAI) and maximum intercepted fraction of photosynthetic active radiation (fPAR) derived from in-situ measurements. The results of this study showed that the 250-m resolution MODIS data did not provide more accurate vegetation information for corn growth description than the 500-m and 1000-m resolution MODIS data.

Crops, Agricultural↗
PubMed1994

Structure of the ADP complex of the 3-phosphoglycerate kinase from Bacillus stearothermophilus at 1.65 A.

The structure of the ADP complex of the enzyme 3-phosphoglycerate kinase (PGK, E.C. 2.7.2.3) from Bacillus stearothermophilus NCA-1503 has been determined by the method of molecular replacement. The structure has been refined to an R factor of 0.16 for all data between 10.0 and 1.65 A resolution, using data collected on the Hendrix-Lentfer imaging plate at the EMBL outstation in Hamburg. The r.m.s. deviations from stereochemical ideality are 0.010 and 0.011 A for bonds and planes, respectively. Although crystallized in the presence of the nucleotide product MgATP, the high-resolution structure reveals the bound nucleotide to be MgADP reflecting the low intrinsic ATPase activity of PGK. Although the two domains of this enzyme are found to be some 4.5 degrees closer together than is found in the yeast and horse-muscle apo-enzyme structures, this structure represents the 'open' rather than the 'closed', catalytically competent form, of the enzyme.

Journal Article↗
PubMed2006

Multivariate analysis of integrated and full-resolution 1H-NMR spectral data from complex pharmaceutical preparations: St. John's wort.

Commercial herbal preparations are typically very complex mixtures and the relationship between content of various constituents and pharmacological action of the formulation is usually unclear. Such formulations are nevertheless standardized using a single marker constituent or a group of closely related constituents, which provides no information about other abundant constituents present in the extract. In this study, principal component analysis of 600 MHz 1H-NMR spectra of extracts of commercial formulations of St. John's wort (Hypericum perforatum), acquired in methanol-d4 and DMSO-d6, was shown to be able to discriminate between various preparations according to their global composition, including differentiation between various batches from the same supplier, while no clustering into classes of tablets and capsules was observed. This suggests that the plant extract variability rather than the manufacturing process accounts for the data clustering. Major variations in the content of flavonoids, recently linked to the antidepressant activity of St. John's wort extracts, were detected. Use of two NMR solvents provided complementary data sets, allowing assessment of various aspects of sample composition from separate PCA models. Both integrated (about 200 variables) and full-resolution NMR data (about 30,000 variables) have been used. The latter approach, applied for the first time in analysis of a herbal preparation, provided via loading plots more precise information about constituents responsible for data clustering, and may be generally preferable for PCA analysis of NMR data of plant extracts and herbal medicines.

Humans↗
PubMed2025

Unicorn: enhancing single-cell Hi-C data with blind super-resolution for 3D genome structure reconstruction.

MOTIVATION: Single-cell Hi-C (scHi-C) data provide critical insights into chromatin interactions at individual cell levels, uncovering unique genomic 3D structures. However, scHi-C datasets are characterized by sparsity and noise, complicating efforts to accurately reconstruct high-resolution chromosomal structures. In this study, we present ScUnicorn, a novel blind super-resolution framework for scHi-C data enhancement. ScUnicorn uses an iterative degradation kernel optimization process, unlike traditional super-resolution approaches, which rely on downsampling, predefined degradation ratios, or constant assumptions about the input data to reconstruct high-resolution interaction matrices. Hence, our approach more reliably preserves critical biological patterns and minimizes noise. Additionally, we propose 3DUnicorn, a maximum likelihood algorithm that leverages the enhanced scHi-C data to infer precise 3D chromosomal structures. RESULTS: Our evaluation demonstrates that ScUnicorn achieves superior performance over the state-of-the-art methods in terms of Peak Signal-to-Noise Ratio, Structural Similarity Index Measure, and GenomeDisco scores. Moreover, 3DUnicorn's reconstructed structures align closely with experimental 3D-FISH data, underscoring its biological relevance. Together, ScUnicorn and 3DUnicorn provide a robust framework for advancing genomic research by enhancing scHi-C data fidelity and enabling accurate 3D genome structure reconstruction. AVAILABILITY AND IMPLEMENTATION: Unicorn implementation is publicly accessible at https://github.com/OluwadareLab/Unicorn.

Single-Cell Analysis↗
PubMed1999

Shope fibroma virus DNA topoisomerase catalyses holliday junction resolution and hairpin formation in vitro.

The telomeres of poxviral chromosomes comprise covalently closed hairpin structures bearing mismatched bases. These hairpins are formed as concatemeric replication intermediates and are processed into mature, unit-length genomes. The structural transitions and enzymes involved in telomere resolution are poorly understood. Here we show that the type I topoisomerase of Shope fibroma virus (SFV) can promote a recombination reaction which converts cloned SFV replication intermediates into hairpin-ended molecules resembling mature poxviral telomeres. Recombinant SFV topoisomerase linearised a palindromic plasmid bearing 1.5 kb of DNA encoding the SFV concatemer junction, at a site near the centre of inverted-repeat symmetry. Most of these linear reaction products bore hairpin tips as judged by denaturing gel electrophoresis. The resolution reaction required palindromic SFV DNA sequences and was inhibited by compounds which block branch migration (MgCl2) or poxviral topoisomerases. The resolution reaction was also slow, needed substantial quantities of topoisomerase, and required that the palindrome be extruded in a cruciform configuration. DNA cleavage experiments identified a pair of suitably oriented topoisomerase recognition sites, 90 bases from the centre of the cloned SFV terminal inverted repeat, which may mark the resolution site. These data suggest a resolution scheme in which branch migration of a Holliday junction through a site occupied by covalently bound topoisomerase molecules, could lead to telomere resolution.

DNA Topoisomerases, Type I↗
PubMed2004

Semia: semi-automatic interactive graphic editing tool to annotate ambulatory ECG records.

We designed and developed a special purpose interactive graphic editing tool semi-automatic (Semia) to annotate transient ischaemic ST segment episodes and other non-ischaemic ST segment events in 24h ambulatory electrocardiogram (ECG) records. The tool allows representation and viewing of the data, interaction with the data globally and locally at different resolutions, examining data at any point, manual adjustment of heart-beat fiducial points, and manual and automatic editing of annotations. Efficient and fast display of ambulatory ECG signal waveforms, display of diagnostic and morphology feature-vector time-series, dynamic interface controls, and automated procedures to help annotate, made the tool efficient, user friendly and usable. Human expert annotators used the Semia tool to successfully annotate the Long-Term ST database (LTST DB), a result of a multinational effort. The tool supported paperless editing of annotations at dislocated geographical sites. We present design, characteristic "look and feel", functionality, and development of Semia annotating tool.

Ambulatory Care Information Systems↗
PubMed2002

History and timing of human impact on Lake Victoria, East Africa.

Lake Victoria, the largest tropical lake in the world, suffers from severe eutrophication and the probable extinction of up to half of its 500+ species of endemic cichlid fishes. The continuing degradation of Lake Victoria's ecological functions has serious long-term consequences for the ecosystem services it provides, and may threaten social welfare in the countries bordering its shores. Evaluation of recent ecological changes in the context of aquatic food-web alterations, catchment disturbance and natural ecosystem variability has been hampered by the scarcity of historical monitoring data. Here, we present high-resolution palaeolimnological data, which show that increases in phytoplankton production developed from the 1930s onwards, which parallels human-population growth and agricultural activity in the Lake Victoria drainage basin. Dominance of bloom-forming cyanobacteria since the late 1980s coincided with a relative decline in diatom growth, which can be attributed to the seasonal depletion of dissolved silica resulting from 50 years of enhanced diatom growth and burial. Eutrophication-induced loss of deep-water oxygen started in the early 1960s, and may have contributed to the 1980s collapse of indigenous fish stocks by eliminating suitable habitat for certain deep-water cichlids. Conservation of Lake Victoria as a functioning ecosystem is contingent upon large-scale implementation of improved land-use practices.

Africa, Eastern↗
PubMed1999

Isolation, purification, crystallization and preliminary X-ray analysis of beta 1-bungarotoxin from Bungarus caeruleus (Indian common krait).

Beta-Bungarotoxin is a heterodimeric neurotoxin consisting of a phospholipase A2 subunit linked by a disulfide bond to a K+ channel binding subunit, which is a member of of the Kunitz protease-inhibitor subfamily. Purified beta1-bungarotoxin was crystallized using microdialysis techniques. The rectangular-shaped crystals are orthorhombic, space group C2221, with unit-cell dimensions a = 80.7, b = 82.5, c = 56.9 A. The crystals have a calculated Vm of 2.35 A3 Da-1 for one molecule in the asymmetric unit. This corresponds to a solvent content of 48%. X-ray intensity data were collected to 2.6 A resolution. The data set is 97.4% complete.

Animals↗
PubMed1988

Crystallization and preliminary X-ray analysis of a quadruple mutant of staphylococcal nuclease.

A quadruple mutant of staphylococcal nuclease, nuclease (V66L/G79S/G88V/L108V), has been crystallized in a form well suited to moderate-to-high resolution x-ray diffraction analysis. This mutant is highly unstable; only about 20% of the protein in solution at room temperature is in its folded form. Under the crystallization conditions, the protein exhibits circular dichroism properties similar to, but not identical with, those of native wild type protein. The crystals belong to the space group P6(1)22 or P6(5)22 with unit cell dimensions of a = b = 61.1 A, c = 170.1 A and diffract to at least 2.5 A resolution. A data set complete to 3.7 A resolution has been collected and processed; attempts to determine the structure using molecular replacement techniques are under way.

Circular Dichroism↗
PubMedDate not supplied

Use of personal digital assistants for retrieval of medical images and data on high-resolution flat panel displays.

For its new acute care hospital, the University of California at Los Angeles is evaluating innovative technology involving high-resolution flat panel display devices configured as "network appliances" that can be wall mounted for use in the retrieval and display of medical images and data. Physicians and healthcare providers can log on with wireless handheld computers, which can serve as an identification device as well as a navigational tool for selecting patient records and data. These data are displayed and manipulated on the flat panel display without the need for a keyboard or mouse. A prototype was developed with commercially available image display software, which was modified to allow the remote control of software functions from a handheld device through an infrared communication port. The system also allows navigation through the patient data in a World Wide Web-based electronic patient record. This prototype illustrates the evolution of radiologic facilities toward "shareable" high-quality display devices that allow more convenient and cost-effective access to medical images and related data in complex clinical environments, resulting in a paradigm shift in data navigation and accessibility.

Computers, Handheld↗
PubMed2006

Predictive metabolite profiling applying hierarchical multivariate curve resolution to GC-MS data--a potential tool for multi-parametric diagnosis.

A method for predictive metabolite profiling based on resolution of GC-MS data followed by multivariate data analysis is presented and applied to three different biofluid data sets (rat urine, aspen leaf extracts, and human blood plasma). Hierarchical multivariate curve resolution (H-MCR) was used to simultaneously resolve the GC-MS data into pure profiles, describing the relative metabolite concentrations between samples, for multivariate analysis. Here, we present an extension of the H-MCR method allowing treatment of independent samples according to processing parameters estimated from a set of training samples. Predictions or inclusion of the new samples, based on their metabolite profiles, into an existing model could then be carried out, which is a requirement for a working application within, e.g., clinical diagnosis. Apart from allowing treatment and prediction of independent samples the proposed method also reduces the time for the curve resolution process since only a subset of representative samples have to be processed while the remaining samples can be treated according to the obtained processing parameters. The time required for resolving the 30 training samples in the rat urine example was approximately 13 h, while the treatment of the 30 test samples according to the training parameters required only approximately 30 s per sample (approximately 15 min in total). In addition, the presented results show that the suggested approach works for describing metabolic changes in different biofluids, indicating that this is a general approach for high-throughput predictive metabolite profiling, which could have important applications in areas such as plant functional genomics, drug toxicity, treatment efficacy and early disease diagnosis.

Animals↗
PubMed2003

The BrainIT group: concept and core dataset definition.

INTRODUCTION: An open collaborative international network has been established which aims to improve inter-centre standards for collection of high-resolution, neurointensive care data on patients with traumatic brain injury. The group is also working towards the creation of an open access, detailed and validated database that will be useful for post-hoc hypothesis testing. In Part A, the underlying concept, the group coordination structure, membership guidelines and database access and publication criteria are described. Secondly, in part B, we describe a set of meetings funded by the EEC that allowed us to define a "Core Dataset" and we present the results of a feasibility exercise for collection of this core dataset. METHODS: Four group meetings funded by the EEC have enabled definition of a "Core Dataset" to be collected from all centres regardless of specific project aim. A paper based pilot collection of data was conducted to determine the feasibility for collection of the core dataset. Specially designed forms to collect the core dataset demographic and clinical information as well as sample the time-series data elements were distributed by both email and standard mail to 22 BrainIT centres. A deadline of two months was set to receive completed forms back from centres. A pilot data collection of minute by minute physiological monitoring data was also performed. FINDINGS: A core-dataset was defined and can be downloaded from the BrainIT web-site (go to "Core dataset" link at: www.brainit.org). Eighteen centres (82%) returned completed forms by the set deadline. Overall the feasibility for collection of the core data elements was high with only 10 of the 64 questions (16%) showing missing data. Of those 10 fields with missing data, the average number of centres not responding was 12% and the median 6%. An SQL database to hold the data has been designed and is being tested. Software tools for collection of the core dataset have been developed. Ethics approval has been granted for collection of multi-centre data as part of a pilot data collection study. INTERPRETATION: The BrainIT network provides a more standardised and higher resolution data collection mechanism for research groups, organisations and the device industry to conduct multi-centre trials of new health care technology in patients with traumatic brain injury.

Brain Injuries↗