751 results match your criteria deconvolution software

Simultaneous Intelligent Imaging of Nanoscale Reactivity and Topography by Scanning Electrochemical Microscopy.

Anal Chem 2021 Jun 15. Epub 2021 Jun 15.

Center for Environmentally Beneficial Catalysis, Department of Chemical and Petroleum Engineering, University of Kansas, 1501 Wakarusa Drive, Lawrence, Kansas 66047, United States.

Scanning electrochemical microscopy (SECM) enables reactivity and topography imaging of single nanostructures in the electrolyte solution. The in situ reactivity and topography, however, are convoluted in the real-time image, thus requiring another imaging method for subsequent deconvolution. Herein, we develop an intelligent mode of nanoscale SECM to simultaneously obtain separate reactivity and topography images of non-flat substrates with reactive and inert regions. Read More

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Iliski, a software for robust calculation of transfer functions.

PLoS Comput Biol 2021 Jun 14;17(6):e1008614. Epub 2021 Jun 14.

INSERM U1128, Laboratory of Neurophysiology and New Microscopy, Université de Paris, Paris, France.

Understanding the relationships between biological processes is paramount to unravel pathophysiological mechanisms. These relationships can be modeled with Transfer Functions (TFs), with no need of a priori hypotheses as to the shape of the transfer function. Here we present Iliski, a software dedicated to TFs computation between two signals. Read More

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Untargeted metabolomics analysis by gas chromatography/time-of-flight mass spectrometry of human serum from methamphetamine abusers.

Addict Biol 2021 Jun 10:e13062. Epub 2021 Jun 10.

School of Food Science, State Key Laboratory of Food Science and Technology, National Engineering Research Center for Functional Foods, School of Food Science Synergetic Innovation Center of Food Safety and Nutrition, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, China.

Methamphetamine (METH) abuse has become a global public health problem. However, the potential mechanisms involving METH-induced metabolic disorders have thus far remained poorly understood. Metabolomics can provide a clue for the cause of apparent changes and consequently be used to investigate the METH-induced dysregulation of metabolite expression and the mechanism of metabolic disorder mechanism. Read More

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CDSeqR: fast complete deconvolution for gene expression data from bulk tissues.

BMC Bioinformatics 2021 May 24;22(1):262. Epub 2021 May 24.

Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, 27709, USA.

Background: Biological tissues consist of heterogenous populations of cells. Because gene expression patterns from bulk tissue samples reflect the contributions from all cells in the tissue, understanding the contribution of individual cell types to the overall gene expression in the tissue is fundamentally important. We recently developed a computational method, CDSeq, that can simultaneously estimate both sample-specific cell-type proportions and cell-type-specific gene expression profiles using only bulk RNA-Seq counts from multiple samples. Read More

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A Step-by-Step Guide to Instant Structured Illumination Microscopy (iSIM).

Methods Mol Biol 2021 ;2304:347-359

NHLBI Light Microscopy Facility, National Institutes of Health, Bethesda, MD, USA.

Instant structured illumination microscopy (iSIM) allows for rapid multicolor three-dimensional fluorescence imaging at levels of resolution approaching twice the diffraction limit. Here we briefly describe the theory of iSIM and outline a typical hardware setup. We also provide step-by-step guides for generating a cellular-based fluorescent standard, obtaining a multicolor image with iSIM, and the post-processing steps of de-striping and deconvolution using freely distributed software to minimize time and expense. Read More

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January 2021

Novel acquisition strategies for metabolomics using drift tube ion mobility-quadrupole resolved all ions time-of-flight mass spectrometry (IM-QRAI-TOFMS).

Anal Chim Acta 2021 Jun 12;1163:338508. Epub 2021 Apr 12.

Institute of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria. Electronic address:

The focus of this work was the implementation of ion mobility (IM) and a prototype quadrupole driver within data independent acquisition (DIA) using a drift tube IM-QTOFMS aiming to improve the level of confidence in identity confirmation workflows for non-targeted metabolomics. In addition to conventional all ions (IM-AI) acquisition, quadrupole resolved all ions (IM-QRAI) acquisition allows a drift time-directed precursor ion isolation in DIA using sequential isolation of precursor ions using mass windows of up to 100 Da which can be rapidly ramped across single ion mobility transients (i.e. Read More

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Screening and Risk Evaluation of Organic Contaminants in an Urban Wetland Fed with Wastewater Effluents.

Bull Environ Contam Toxicol 2021 Apr 28. Epub 2021 Apr 28.

Biología, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.

Wastewater release in an urban wetland in Mexico City entails discharging complex mixtures of hundreds of chemical substances into the aquatic system. Therefore, in order to identify the most important contaminants, a GC-MS screening method coupled with deconvolution software was used. LC values from ECOSAR and Toxic Units were obtained to identify the organic pollutants-of-concern and to pinpoint the most ecotoxic sites. Read More

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Protocol for live enhanced resolution confocal imaging of dendritic spinule dynamics in primary mouse cortical neuron culture.

STAR Protoc 2021 Jun 5;2(2):100427. Epub 2021 Apr 5.

Department of Physiology, Northwestern University, Chicago, IL 60611, USA.

Dendritic spinules are fine membranous protrusions of neuronal spines that play a role in synaptic plasticity, but their nanoscale requires resolution beyond conventional confocal microscopy, hindering live studies. Here, we describe how to track individual spinules in live dissociated cortical pyramidal neurons utilizing fluorescence labeling, optimized confocal imaging parameters, and post-acquisition iterative 3D deconvolution, employing NIS Elements software. This approach enables investigations of spinule structural dynamics and function without using super-resolution microscopy, which involves special fluorophores and/or high laser power. Read More

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Denaturing and Native Mass Spectrometric Analytics for Biotherapeutic Drug Discovery Research: Historical, Current, and Future Personal Perspectives.

J Am Soc Mass Spectrom 2021 Apr 22. Epub 2021 Apr 22.

Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States.

Mass spectrometry (MS) plays a key role throughout all stages of drug development and is now as ubiquitous as other analytical techniques such as surface plasmon resonance, nuclear magnetic resonance, and supercritical fluid chromatography, among others. Herein, we aim to discuss the history of MS, both electrospray and matrix-assisted laser desorption ionization, specifically for the analysis of antibodies, evolving through to denaturing and native-MS analysis of newer biologic moieties such as antibody-drug conjugates, multispecific antibodies, and interfering nucleic acid-based therapies. We discuss challenging therapeutic target characterization such as membrane protein receptors. Read More

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Development of an In Vivo Predictive Dissolution Methodology of Topiroxostat Immediate-Release Tablet Using In Silico Simulation.

AAPS PharmSciTech 2021 Apr 13;22(3):132. Epub 2021 Apr 13.

Zhongcai Health (Beijing) Biological Technology Development Co., Ltd., Beijing, 101500, People's Republic of China.

The main objective of this study was to develop an in vivo predictive dissolution (IVPD) model for topiroxostat immediate-release (IR) formulation by the combination of mechanistic absorption model (MAM) deconvolution method with time shifting factor (TSF) adjustment. The in vitro dissolution profiles in different biorelevant dissolution media containing different concentrations of sodium lauryl sulfate (SLS) were obtained from dissolution testing with the paddle method of the US Pharmacopeia, while the human pharmacokinetic profile was taken from the published experimental results. The GastroPlus™ software was used to observe the linear relationship between in vitro drug dissolution and in vivo absorption. Read More

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Spotting isomer mixtures in forensic illicit drug casework with GC-VUV using automated coelution detection and spectral deconvolution.

J Chromatogr B Analyt Technol Biomed Life Sci 2021 Mar 29;1173:122675. Epub 2021 Mar 29.

Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, PO Box 94157, Amsterdam 1090 GD, the Netherlands; Co van Ledden Hulsebosch Center (CLHC), Amsterdam Center for Forensic Science and Medicine, PO Box 94157, Amsterdam 1090 GD, the Netherlands.

Analysis of isomeric mixtures is a significant analytical challenge. In the forensic field, for example, over 1000 new psychoactive substances (NPSs), comprising of many closely related and often isomeric varieties, entered the drugs-of-abuse market within the last decade. Unambiguous identification of the isomeric form requires advanced spectroscopic techniques, such as GC-Vacuum Ultraviolet Spectroscopy (GC-VUV). Read More

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Analysis of patchclamp recordings: model-free multiscale methods and software.

Eur Biophys J 2021 Mar 9;50(2):187-209. Epub 2021 Apr 9.

Institute for Mathematical Stochastics, Georg-August-University of Goettingen, Göttingen, Germany.

Analysis of patchclamp recordings is often a challenging issue. We give practical guidance how such recordings can be analyzed using the model-free multiscale idealization methodology JSMURF, JULES, and HILDE. We provide an operational manual how to use the accompanying software available as an R-package and as a graphical user interface. Read More

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Improving deconvolution methods in biology through open innovation competitions: an application to the connectivity map.

Bioinformatics 2021 Apr 6. Epub 2021 Apr 6.

Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.

Motivation: Do machine learning methods improve standard deconvolution techniques for gene expression data? This article uses a unique new dataset combined with an open innovation competition to evaluate a wide range of approaches developed by 294 competitors from 20 countries. The competition's objective was to address a deconvolution problem critical to analyzing genetic perturbations from the Connectivity Map. The issue consists of separating gene expression of individual genes from raw measurements obtained from gene pairs. Read More

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HPAStainR: a Bioconductor and Shiny app to query protein expression patterns in the Human Protein Atlas.

F1000Res 2020 8;9:1210. Epub 2020 Oct 8.

Department of Pathology, Johns Hopkins University School of Medicine Baltimore, Baltimore, MD, 21205, USA.

The Human Protein Atlas is a website of protein expression in human tissues. It is an excellent resource of tissue and cell type protein localization, but only allows the query of a single protein at a time. We introduce HPAStainR as a new Shiny app and Bioconductor/R package used to query the scored staining patterns in the Human Protein Atlas with multiple proteins/genes of interest. Read More

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TopMSV: A Web-Based Tool for Top-Down Mass Spectrometry Data Visualization.

J Am Soc Mass Spectrom 2021 Jun 29;32(6):1312-1318. Epub 2021 Mar 29.

Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States.

Top-down mass spectrometry (MS) investigates intact proteoforms for proteoform identification, characterization, and quantification. Data visualization plays an essential role in top-down MS data analysis because proteoform identification and characterization often involve manual data inspection to determine the molecular masses of highly charged ions and validate unexpected alterations in identified proteoforms. While many software tools have been developed for MS data visualization, there is still a lack of web-based visualization software designed for top-down MS. Read More

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Experiments and Monte Carlo simulations on multiple Coulomb scattering of protons.

Med Phys 2021 Mar 27. Epub 2021 Mar 27.

West German Proton Therapy Centre Essen WPE, Essen, Germany.

Background And Purpose: Monte Carlo simulations as well as analytical computations of proton transport in material media require accurate values of multiple Coulomb scattering (MCS) angles. High-quality experimental data on MCS angles in the energy range for proton therapy are, however, sparse. In this work, MCS modeling in proton transport was evaluated employing an experimental method to measure these angles on a medical proton beamline in clinically relevant materials. Read More

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Mesh Fragmentation Improves Dissociation Efficiency in Top-down Proteomics.

J Am Soc Mass Spectrom 2021 Jun 23;32(6):1319-1325. Epub 2021 Mar 23.

Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States.

Top-down proteomics is a key mass spectrometry-based technology for comprehensive analysis of proteoforms. Proteoforms exhibit multiple high charge states and isotopic forms in full MS scans. The dissociation behavior of proteoforms in different charge states and subjected to different collision energies is highly variable. Read More

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Normalized Mass Maps in Three-Dimensional Space Combining Kendrick-like Values with Chromatographic Separation for Enhanced Data Deconvolution.

J Am Soc Mass Spectrom 2021 Apr 18;32(4):989-995. Epub 2021 Mar 18.

Mass Spectrometry Laboratory, Corporate Functions-Analytical, The Procter & Gamble Co., 8700 Mason-Montgomery Road, Mason, Ohio 45040, United States.

The incorporation of retention-time information into a fully rotatable and interactive three-dimensional (3D), "Kendrick-like" normalized mass map (NMM) using a single software platform is reported. Surprising discoveries were made about the elution pattern of block ethoxylate-propoxylate oligomers (ca. 2800 Da) in the supercritical fluid after combined SFC-Orbitrap FTMS analysis. Read More

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: a general method to deconvolve X-ray scattering data from evolving mixtures.

IUCrJ 2021 Mar 6;8(Pt 2):225-237. Epub 2021 Feb 6.

Department of Chemistry and Chemical Biology, Cornell University, 259 East Avenue, Ithaca, NY 14853, USA.

Mixtures of biological macromolecules are inherently difficult to study using structural methods, as increasing complexity presents new challenges for data analysis. Recently, there has been growing interest in studying evolving mixtures using small-angle X-ray scattering (SAXS) in conjunction with time-resolved, high-throughput or chromatography-coupled setups. Deconvolution and interpretation of the resulting datasets, however, are nontrivial when neither the scattering components nor the way in which they evolve are known . Read More

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Using the Gouy phase anomaly to localize and track bacteria in digital holographic microscopy 4D images.

J Opt Soc Am A Opt Image Sci Vis 2021 Feb;38(2):A11-A18

Described over 100 years ago, the Gouy phase anomaly refers to the additional phase shift that is accumulated as a wave passes through focus. It is potentially useful in analyzing any type of phase-sensitive imaging; in light microscopy, digital holographic microscopy (DHM) provides phase information in the encoded hologram. One limitation of DHM is the weak contrast generated by many biological cells, especially unpigmented bacteria. Read More

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February 2021

Automated estimation of ischemic core prior to thrombectomy: comparison of two current algorithms.

Neuroradiology 2021 Feb 12. Epub 2021 Feb 12.

Melbourne Brain Centre at Royal Melbourne Hospital, University of Melbourne, Grattan St, Parkville, Victoria, 3050, Australia.

Purpose: Endovascular thrombectomy (EVT) improves clinical outcomes in ischemic stroke with large vessel occlusion. Clinical benefits are inversely proportional to size of the pre-treatment ischemic core. This study compared estimated ischemic core volumes by two different CT perfusion (CTP) automated algorithms to the gold standard follow-up infarct volume using diffusion-weighted imaging (DWI) to assess for congruence, and thus eligibility for EVT. Read More

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February 2021

Deconvolution of Complex DNA Repair (DECODR): Establishing a Novel Deconvolution Algorithm for Comprehensive Analysis of CRISPR-Edited Sanger Sequencing Data.

CRISPR J 2021 Feb 10;4(1):120-131. Epub 2021 Feb 10.

Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA.

During CRISPR-directed gene editing, multiple gene repair mechanisms interact to produce a wide and largely unpredictable variety of sequence changes across an edited population of cells. Shortcomings inherent to previously available proposal-based insertion and deletion (indel) analysis software necessitated the development of a more comprehensive tool that could detect a larger range and variety of indels while maintaining the ease of use of tools currently available. To that end, we developed convolution of mplex NA epair (DECODR). Read More

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February 2021

DSTG: deconvoluting spatial transcriptomics data through graph-based artificial intelligence.

Brief Bioinform 2021 Jan 22. Epub 2021 Jan 22.

Department of Biostatistics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.

Recent development of spatial transcriptomics (ST) is capable of associating spatial information at different spots in the tissue section with RNA abundance of cells within each spot, which is particularly important to understand tissue cytoarchitectures and functions. However, for such ST data, since a spot is usually larger than an individual cell, gene expressions measured at each spot are from a mixture of cells with heterogenous cell types. Therefore, ST data at each spot needs to be disentangled so as to reveal the cell compositions at that spatial spot. Read More

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January 2021

Clutter-Masked Waveform Design for LPI/LPD Radarcom Signal Encoding.

Sensors (Basel) 2021 Jan 18;21(2). Epub 2021 Jan 18.

U.S. Air Force Research Laboratory, Wright-Patterson AFB, Fairborn, OH 45433, USA.

In this work we propose a method of in situ clutter deconvolution and modeling using experimentally obtained UWB radar data. The obtained clutter models are then used for random sequence encoding of radar-communication (radarcom) signals to achieve clutter-masked transmissions and improve communication security. We present the results of clutter modeling from the laboratory data obtained with the software-defined radar system. Read More

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January 2021

Analysis Protocol for Dynamic Contrast Enhanced (DCE) MRI of Renal Perfusion and Filtration.

Methods Mol Biol 2021 ;2216:637-653

Washington University School of Medicine, St. Louis, MO, USA.

Here we present an analysis protocol for dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data of the kidneys. It covers comprehensive steps to facilitate signal to contrast agent concentration mapping via T mapping and the calculation of renal perfusion and filtration parametric maps using model-free approaches, model free analysis using deconvolution, the Toft's model and a Bayesian approach.This chapter is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers. Read More

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Regression-based analysis of combined EEG and eye-tracking data: Theory and applications.

J Vis 2021 01;21(1)

Institute of Cognitive Science, Universität Osnabrück, Osnabrück, Germany.

Fixation-related potentials (FRPs), neural responses aligned to the end of saccades, are a promising tool for studying the dynamics of attention and cognition under natural viewing conditions. In the past, four methodological problems have complicated the analysis of such combined eye-tracking/electroencephalogram experiments: (1) the synchronization of data streams, (2) the removal of ocular artifacts, (3) the condition-specific temporal overlap between the brain responses evoked by consecutive fixations, and (4) the fact that numerous low-level stimulus and saccade properties also influence the postsaccadic neural responses. Although effective solutions exist for the first two problems, the latter two are only beginning to be addressed. Read More

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January 2021

Novel Method for Accurately Assessing Pull-up Artifacts in STR Analysis.

Forensic Sci Int Genet 2021 Mar 2;51:102410. Epub 2020 Nov 2.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. Electronic address:

OSIRIS is a mathematically-based software tool for Short Tandem Repeat (STR) and DNA fragment analysis (https://www.ncbi.nlm. Read More

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PyClone-VI: scalable inference of clonal population structures using whole genome data.

BMC Bioinformatics 2020 Dec 10;21(1):571. Epub 2020 Dec 10.

Department of Molecular Oncology, BC Cancer Research Institute, 675 W 10th Ave, Vancouver, V5Z 1L3, Canada.

Background: At diagnosis tumours are typically composed of a mixture of genomically distinct malignant cell populations. Bulk sequencing of tumour samples coupled with computational deconvolution can be used to identify these populations and study cancer evolution. Existing computational methods for populations deconvolution are slow and/or potentially inaccurate when applied to large datasets generated by whole genome sequencing data. Read More

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December 2020

Doubling the resolution of a confocal spinning-disk microscope using image scanning microscopy.

Nat Protoc 2021 01 27;16(1):164-181. Epub 2020 Nov 27.

Department of Physics, Third Institute of Physics-Biophysics, Georg August University, Friedrich-Hund-Platz 1, Göttingen, Germany.

Fluorescence microscopy has become an indispensable tool for cell biology. Recently, super-resolution methods have been developed to overcome the diffraction limit of light and have shown living cells in unprecedented detail. Often, these methods come at a high cost and with complexity in terms of instrumentation and sample preparation, thus calling for the development of low-cost, more accessible methods. Read More

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January 2021

Optimisation of the use of sliding window deconvolution for comprehensive characterisation of trastuzumab and adalimumab charge variants by native high resolution mass spectrometry.

Eur J Pharm Biopharm 2021 Jan 16;158:83-95. Epub 2020 Nov 16.

Characterisation and Comparability Laboratory, NIBRT - The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co., Dublin, Ireland; School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4 D04 V1W8, Ireland. Electronic address:

The biopharmaceutical industry continues to develop mAb-based biotherapeutics in increasing numbers. Due to their complexity, there are several critical quality attributes (CQAs) that need to be measured and controlled to guarantee product safety and efficacy. Charge variant analysis is a widely used method to monitor changes in product quality during the manufacturing process of monoclonal antibodies (mAbs) and, together with a bottom-up peptide centred approach, acts as a key analytical platform to fulfil regulatory requirements. Read More

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January 2021