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Results for “High-performance computing”

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At least 37 records · Page 2Linked to original sources

PubMed2026

An automated geometric modeling framework in GATE for the design and optimization of high-sensitivity converging-beam SPECT collimators.

Objective.The trade-off between detection sensitivity and spatial resolution is a fundamental challenge in designing organ-dedicated Single-photon emission computed tomography (SPECT) collimators. While converging-hole geometries offer a solution, their optimization is often hindered by the lack of flexible computational tools capable of modeling large-scale, non-parallel hole arrays. This study aims to develop an automated geometric modeling framework to facilitate the design and evaluation of complex converging- and diverging-hole collimators within standard Monte Carlo environments.Approach.We developed a specialized modeling framework by implementing custom C++ classes and a vector-based alignment algorithm within GATE. This platform enables automated, orientation-consistent construction of large-scale converging arrays not natively supported by standard implementations. A high-sensitivity pure cone-beam collimator (CBC) was designed using this framework. The evaluation used hot-rod, disc, and Jaszczak phantoms for physical characterization, while XCAT and dedicated brain models were employed for clinical tasks, including cardiac, brain perfusion, and DaTscan SPECT simulations.Main results.The CBC achieved a nearly fourfold sensitivity increase compared to a conventional low-energy high-resolution parallel-hole collimator at a 20 cm radius of rotation, while maintaining comparable spatial resolution. Despite a 52.3% field of view reduction, the CBC yielded a 2.2-fold noise reduction (CV: 11.7% vs 25.9%) and mitigated partial volume effects via geometric magnification. XCAT and brain phantom simulations confirmed enhanced anatomical definition and contrast recovery in cardiac, perfusion, and DaTscan tasks.Significance.This work provides an efficient computational tool for rapid design space exploration of advanced collimator geometries. The results demonstrate that the proposed CBC design offers a significant sensitivity advantage, making it highly suitable for high-performance, small-volume clinical applications such as brain and cardiac molecular imaging.

Tomography, Emission-Computed, Single-Photon↗

PubMed1979

Dual-detector-post-column reactor system for the detection of isoenzymes separated by high-performance liquid chromatography. I. Description and theory.

We describe a dual-detector-post-column chromatographic reaction detector system that corrects for substances present in biological samples that interfere with the measurement of isoenzymes separated on a chromatographic column. The response observed at the detector in front of the reaction coil is mathematically dispersed, time transformed and subtracted from the detector behind the coil to produce a blank corrected chromatogram. The same computer program calculates peak areas and other chromatographic parameters such as height equivalent to a theoretical plate and retention time. In addition, we have evaluated the dispersion effects caused by various changes in our experimental system.

Chromatography, High Pressure Liquid↗

PubMed2026

Odon: an ultra-fast viewer for spatial proteomics.

MOTIVATION: Multiplexed spatial proteomics and spatial transcriptomics generate large, high-dimensional imaging datasets that are challenging to visualize efficiently, particularly at whole-slide and cohort scale. Visualization is an essential step for rapid detection of staining artefacts, such as protein aggregates or non-specific staining. RESULTS: Here, we present Odon, a native Rust desktop viewer designed for rapid, interactive exploration of multiplex imaging data on a standard laptop. Odon is primarily built around the OME-Zarr imaging format, and supports annotations via GeoJSON and GeoParquet, with secondary support for SpatialData, Xenium containers, and TIFF. Data can be stored locally or streamed directly from HTTP or S3-compatible object storage using viewport-driven tile loading. Odon incorporates a highly optimized rendering engine designed for viewport-driven tile loading and GPU-based compositing. In scripted benchmarks using synthetic multiplex OME-Zarr datasets, Odon showed lower peak memory use, lower affine-derived zoom-step error, and faster warm-start image loading than napari and QuPath under the tested conditions. Its GPU-based compositing pipeline also enables smooth rendering and interaction with >1 000 000 segmented cells. Odon further supports integrated visual analytics, including live thresholding and cell selection, and a mosaic mode for simultaneous viewing of hundreds of regions of interest in cohort and tissue microarray studies. Together, these features establish Odon as a high-performance platform for scalable visualization of spatial proteomics data. AVAILABILITY AND IMPLEMENTATION: Source code and compiled installers are available at https://github.com/alexcoulton/odon.

Proteomics↗

PubMed2026

A study on the directed engineering and multiple transformations of cannabidiolic acid synthase to enhance the expression level of the recombinant enzyme.

To increase the activity of cannabidiolic acid synthase (CBDAS) and its expression levels in yeast, this study focused on the CBDASG183V-N482W mutant. Using computer-aided techniques and literature reviews, four mutation sites were further identified, resulting in the mutant CBDASH114E-S116A-C176Y-G183V-N328Q-N482W. The CBDAS gene was integrated into the Pichia pastoris genome via multiple transformation rounds, and relative enzyme activity was analyzed using high-performance liquid chromatography. The results of the molecular docking analysis revealed factors such as increased intermolecular forces, shorter bond lengths, and an increased number of amino acid-substrate interaction sites, which may have contributed to the enhanced catalytic activity of the mutant. The concentrations of CBDA and CBD produced by the CBDASH114E-S116A-C176Y-G183V-N328Q-N482W mutant were 71.543 ng/mL and 75.163 ng/mL, respectively, which were 11.87% and 11.53% greater than those produced by the CBDASG183V-N482W mutant. The recombinant CBDAS strain obtained after two consecutive transformations of the CBDASH114E-S116A-C176Y-G183V-N328Q-N482W vector presented the highest CBDAS expression levels and CBD and CBDA yields; compared with those obtained after a single transformation, the CBDA and CBD yields increased by 9.77% and 12.65%, respectively. In addition, the tolerance of the recombinant strain to induction culture conditions was analyzed, revealing that the strain could be induced to express the protein at temperatures ranging from 20 to 45 °C and at pH values ranging from 3 to 9, with optimal expression observed at 30 °C and pH 6. These findings provide theoretical and technical support for the production of enzyme preparations for the in vitro-directed biosynthesis of cannabidiol.

Molecular Docking Simulation↗

PubMed1979

High-performance liquid chromatographic assay for the anthelmintic agent mebendazole in human plasma.

A rapid and specific high-performance liquid chromatographic (HPLC) assay for quantitative plasma mebendazole determination is described. After a simple extraction, the compound was analyzed by HPLC using a reversed-phase column and a UV detector (313 nm). Quantitation was accomplished using an internal standard; peak area ratios were determined with an integrating computer. The average mebendazole recovery over a concentration range of 0.01-0.20 microgram/ml was 75.9 +/- 3.8% SD, and the maximum assay sensitivity was approximately 10 ng/ml.

Benzimidazoles↗

PubMed1978

High-performance liquid chromatographic assay for suprofen, a potent new analgesic, in plasma.

A simple, rapid, high-performance liquid chromatographic (HPLC) determination of therapeutic levels of suprofen, a potent new analgesic, in human plasma is described. After a simple extraction, the compound is analyzed by HPLC using a reversed-phase column and a UV detector. Quantitation is accomplished using an external standard; peak areas are determined by computer. An average recovery of 80.0 +/- 8.5% SD of the drug was obtained over the 0.2-20.0-microgram/ml range. Maximum sensitivity is approximately 0.1 microgram/ml. No interference is encountered from any known metabolite of suprofen.

Chromatography, High Pressure Liquid↗

PubMed1992

The way to adequate control of microbial processes passes via real-time knowledge-based supervision.

Knowledge-based supervision is viewed as a major tool for achieving high-performance control of microbial processes. By providing an adequate insight into the integral state of the cell culture, knowledge-based supervisory systems allow for monitoring and handling various important phenomena which usually remain outside the scope of the conventional control approach. The present paper focuses on the development of a computer system for knowledge-based supervision of bioprocesses. Its application to the control of fed-batch cultivation of recombinant Escherichia coli for phenylalanine production is also discussed.

Biotechnology↗

PubMed1979

High-performance liquid chromatographic assay for the antiprotozoal agent, tinidazole, in human plasma.

A rapid and specific high-performance liquid chromatographic (HPLC) assay for the quantitative determination of tinidazole in human plasma is described. After a simple extraction procedure, the compound is analyzed by HPLC using a reversed-phase column and a UV detector. Quantitation is accomplished using an external standard, and peak areas are determined with an integrating computer. The average recovery of tinidazole over a concentration range of 0.20-20.0 microgram/ml was 86.9 +/- 2.8% SD. The maximum sensitivity of the assay is approximately 0.10 microgram/ml; it is suitable for use in pharmacokinetic studies following administration of therapeutic levels of tinidazole to humans.

Chromatography, High Pressure Liquid↗

PubMed1977

Sampling and extra-column effects in high-performance liquid chromatography; influence of peak skew on plate count calculations.

Chromatographic resolution and analysis accuracy can be seriously affected by broadening of very sharp bands associated with both high-performance size-exclusion chromatography and other liquid chromatography methods using less than 5 micron particles. The effect on column plate count by extra-column band broadening from injection systems, detectors, connectors and "guard" columns is discussed and exemplified with experimental data. The special cases of tailing and doublet peaks for a single species are investigated. These effects are eliminated by a special sample injection technique. Computer simulation studies demonstrated that serious errors can result from calculating column plate count with non-Gaussian peaks. The maximum allowable peak tailing is suggested and a new method for quantitating peak skew is proposed.

Chromatography, High Pressure Liquid↗

PubMed1990

High-performance liquid chromatography.

Gas chromatography has developed over the past 25 years or so into one of the most extensively used on-line analytical techniques in industrial process control and optimization. Liquid chromatography, and its several individual techniques, is firmly established in the laboratory, but its on-line process use has not developed as rapidly as GC. At the present time, only three companies (Applied Automation Inc., Dionex Corp., and Millipore Corp.) are active in this area. Nevertheless, substantial growth in on-line process LC is predicted for the next few years. The techniques of HPLC (normal-phase and reversed-phase), IEC, and SEC have great potential in industry as on-line analytical techniques, including the new field of biotechnology. Computer-based, multistream, multicomponent systems should find extensive use in pilot-plant investigations, where their ability to gather large amounts of data (on-line rather than by laboratory testing) could have important implications. In bioprocess control, undoubtedly the greatest challenge will come in the area of sample-handling technique. On-line chromatography has traditionally involved the sampling and conditioning of fairly conventional process gases and liquids. One exception is in the plastics and elastomers areas, where on-line SEC has been used for polymer MWD measurement. Here the sample is more difficult to handle, and some specialized techniques have been used. In biotechnology, we are treading new ground; nevertheless, it is hoped that some of the experience in sample handling gained in industry over the past 25 years will be of use in this new field.

Chromatography, High Pressure Liquid↗

PubMed2025

CaXML: Chemistry-informed machine learning explains mutual changes between protein conformations and calcium ions in calcium-binding proteins using structural and topological features.

Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. When binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium-binding proteins and their versatile pool of partners depending on the circumstances they transmit. Accurately determining the ionic charges of those ions is essential for understanding their role in such processes. However, it is unclear whether the limited experimental data available can be effectively used to train models to accurately predict the charges of calcium-binding protein variants. Here, we developed a chemistry-informed, machine-learning algorithm that implements a game theoretic approach to explain the output of a machine-learning model without the prerequisite of an excessively large database for high-performance prediction of atomic charges. We used the ab initio electronic structure data representing calcium ions and the structures of the disordered segments of calcium-binding peptides with surrounding water molecules to train several explainable models. Network theory was used to extract the topological features of atomic interactions in the structurally complex data dictated by the coordination chemistry of a calcium ion, a potent indicator of its charge state in protein. Our design created a computational tool of CaXML, which provided a framework of explainable machine learning model to annotate ionic charges of calcium ions in calcium-binding proteins in response to the chemical changes in an environment. Our framework will provide new insights into protein design for engineering functionality based on the limited size of scientific data in a genome space.

Machine Learning↗

PubMed1979

Simultaneous microdetermination of capsaicin and its four analogues by using high-performance liquid chromatography and gas chromatography--mass spectrometry.

An improved method is described for the simultaneous determination of capsaicin and its analogues at levels from nanograms to micrograms using high-performance liquid chromatography (HPLC) and gas chromatography--mass spectrometry. This method consists of two steps: firstly, purification and determination of total capsaicinoid by HPLC, and secondly, the simultaneous determination of capsaicin and its analogues by mass chromatography (MC) or mass fragmentography (MF). Crude extracts of capsaicinoid were purified with a Zorbax SIL column. Total capsaicinoid was detected at 235 nm and measured automatically by a microcomputer. It was collected, evaporated, trimethylsilylated and subjected to MC or MF. After monitoring the molecular ions of trimethylsilyl derivatives of capsaicinoid and the internal standard, the absolute contents of each analogue were determined by computer. By using this method, capsaicin and all of its analogues can be determined simultaneously at levels from micrograms to nanograms without any interferences from other components.

Capsaicin↗

PubMed1977

High-performance liquid chromatographic determination of chlordiazepoxide and major related impurities in pharmaceuticals.

A rapid, precise, forward-phase (adsorption) high-performance liquid chromatographic procedure is presented for the determination of chlordiazepoxide and two common impurities, 7-chloro-1,3-dihydro-5-phenyl-2H-1,4-benzodiazepin-2-one 4-oxide and 2-amino-5-chlorobenzophenone, in commercial formulations and for the determination of the benzophenone in the chlordiazepoxide drug substance. The method involves simultaneous quantitation of chlordiazepoxide and the 1,3-dihhydro impurity, followed by quantitation of the benzophenone from a separate sample extract using a second mobile phase. A single microparticulate silica gel column is used throughout. Nitrazepam and o-dinitrobenzene are the internal standards, Quantitation is by peak area using a computing integrator, except that the peak due to the benzophenone is quantitated by peak height. The described procedure is of equivalent precision, but superior accuracy, to the BP 1973 spectrophotometric procedure for the analysis of chlordiazepoxide in chlordiazepoxide formulations. Quantitation of the 1,3-dihydro and the benzophenone impurities at levels as low as 6.3 and 0.9 ng, respectively, is demonstrated.

Benzodiazepinones↗

PubMed2025

Columba: fast approximate pattern matching with optimized search schemes.

MOTIVATION: Aligning sequencing reads to reference genomes is a fundamental task in bioinformatics. Aligners can be classified as lossy or lossless: lossy aligners prioritize speed by reporting only one or a few high-scoring alignments, whereas lossless aligners output all optimal alignments, ensuring completeness and sensitivity. RESULTS: This paper introduces Columba, a high-performance lossless aligner tailored for Illumina sequencing data. Columba processes single or paired-end reads in FASTQ format and outputs alignments in SAM format. By utilizing advanced search schemes and bit-parallel alignment techniques, Columba achieves exceptional speed. Columba is available in two variants. The first, based on the bidirectional FM-index, prioritizes speed. The second, Columba RLC, uses run-length compression using a bidirectional move structure, significantly reducing memory usage for large, repetitive datasets like pan-genomes. Benchmarks on the human genome, as well as bacterial and human pan-genome datasets, demonstrate that Columba is much faster than existing lossless aligners and even competitive with lossy tools. We integrated Columba into the OptiType HLA genotyping pipeline, where it substantially reduced computational time while maintaining accuracy. These results position Columba as a versatile, state-of-the-art tool for high-sensitivity genomic analyses. AVAILABILITY AND IMPLEMENTATION: The source code of Columba is available at https://github.com/biointec/columba under AGPL license. Scripts to reproduce the benchmarks and analyses are available at https://doi.org/10.5281/zenodo.15849246.

Software↗

PubMed1975

A mathematical model of the ventilatory control system to carbon dioxide with special reference to athletes and nonathletes.

The ventilatory response curve (VRC) as a function of alveolar and arterial pCO2 was recorded in 6 high-performance athletes and 6 nonathletes. The best fit to the data points could be found for an equation of the form (see article) showing that the results are strongly related to a Gaussian probability density function (PDF). After normalizing the equation to a form (see article) (M = mean value of PDF), sigma, A and M could be determined for both groups. Sigma and A are smaller in the athletic group, whereas M did not show any systematic difference. Regarding the respiratory center consisting of functional "elements" responding indirectly to variable pCO2 it can be concluded that the frequency distribution of the different active elements is greater and spread over a wider pCO2 range in the nonathletes with the same mean value in both groups. Using Loeschcke's model (1960), the open loop gain factor for different V CO2 as a function of p(A)CO2 was computed; the gain factor showed a maximum in the physiological range of pCO2.

Adult↗

PubMed1977

Development and use of analytical systems based on mass spectrometry.

Contemporary analytical systems based on mass spectrometry include as components a gas chromatograph, a mass spectrometer, and a computer. The form of operation is usually in electron impact ionization mode for identification and structural studies, and in chemical ionization mode for quantitative analyses. Important stages in the development of these systems included the design of "molecule separators" for the concentration of solutes in the gas phase, the use of mass spectrometers as specific ion detectors, the introduction of chemical ionization techniques, and the development of computer-based operation, data acquisition, and data analysis capabilities. A current line of investigation is concerned with the design and use of systems based on atmospheric pressure ionization. Samples are ionized in a small reaction chamber external to the low-pressure region of a quadrupole mass analyzer. The primary source of electrons is a 63Ni foil or a corona discharge. The ionization process leading to positive ions involves a sequence of ion molecule reactions, usually electrons leads to carrier gas ions leads to reagent ions leads to sample component ions. Negative ions may be formed by direct electron attachment, or by ion molecule reactions that include new types of elimination reactions. The source will accept a variety of gases and solvents. The sample may be introduced in the gas phase without solvents, by probe injection, or in the effluent stream from a gas chromatograph. Samples may be introduced in the liquid phase in solvents by injection after the fashion of gas chromatography or in the effluent stream from a high-performance liquid chromatograph. The novel aspects of atmospheric pressure ionization mass spectrometry lie in its versatility and high sensitivity of detection. Few clinical chemistry laboratories now use these systems. Significant future uses are likely to be in analytical work involving therapeutic drug monitoring and studies of drug metabolism, and in analyses for environmental biohazards including pesticides, herbicides, polyhalobiphenyls, dibenzodioxins, and other toxic compounds.

Anions↗

PubMed1978

Quantitative thin-layer and high-performance liquid chromatographic determination of the diuretic agent 2-chloro-5-[44-hydroxy-3-methyl-2-(methylimino)-4-thiazolidinyl]benzenesulphonamide hydrochloride in serum and urine.

Sensitive and specific thin-layer (TLC) and high-performance liquid chromatographic (HPLC) methods were developed for the determination of the diuretic agent 2-chloro-5-[4-hydroxy-3-methyl-2-(methylimino)-4-thiazolidinyl]benzenesulphonamide hydrochloride (HOE 740). HOE 740 can be determined in serum by HPLC. The detection is performed at a very short wavelength (202 nm), resulting in a detection limit of 10 ng/ml. By TLC only urine levels that are normally high can be determined directly (the detection limit is 70 ng/ml). For the determination of the lower serum levels it is necessary to convert the drug into its dehydration product, which has a higher absorbance and gives sufficient sensitivity (the detection limit is 10 ng/ml). Serum levels determined by the two methods correlate well. Some pharmacokinetic and excretion-kinetic data were computed using two-compartment open models.

Chromatography, High Pressure Liquid↗

PubMed2025

Vcfexpress: flexible, rapid user-expressions to filter and format VCFs.

MOTIVATION: Variant call format (VCF) files are the standard output format for various software tools that identify genetic variation from DNA sequencing experiments. Downstream analyses require the ability to query, filter, and modify them simply and efficiently. Several tools are available to perform these operations from the command line, including BCFTools, vembrane, slivar, and others. RESULTS: Here, we introduce vcfexpress, a new, high-performance toolset for the analysis of VCF files, written in the Rust programming language. It is nearly as fast as BCFTools, but adds functionality to execute user expressions in the lua programming language for precise filtering and reporting of variants from a VCF or BCF file. We demonstrate performance and flexibility by comparing vcfexpress to other tools using the vembrane benchmark. AVAILABILITY AND IMPLEMENTATION: vcfexpress is available under the MIT license at https://github.com/brentp/vcfexpress with code used for the manuscript deposited in https://doi.org/10.5281/zenodo.14756838.

Software↗