The Experts below are selected from a list of 98934 Experts worldwide ranked by ideXlab platform
Annick Moing - One of the best experts on this subject based on the ideXlab platform.
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nmrprocflow a graphical and Interactive Tool dedicated to 1d spectra processing for nmr based metabolomics
Metabolomics, 2017Co-Authors: Daniel J Jacob, Catherine Deborde, Marie Lefebvre, Mickael Maucourt, Annick MoingAbstract:Introduction Concerning NMR-based metabolomics, 1D spectra processing often requires an expert eye for disentangling the intertwined peaks.
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nmrprocflow a graphical and Interactive Tool dedicated to 1d spectra processing for nmr based metabolomics
arXiv: Quantitative Methods, 2016Co-Authors: Daniel J Jacob, Catherine Deborde, Marie Lefebvre, Mickael Maucourt, Annick MoingAbstract:Concerning NMR-based metabolomics, 1D spectra processing often requires an expert eye for disentangling the intertwined peaks, and so far the best way is to proceed Interactively with a spectra viewer. NMRProcFlow is a graphical and Interactive 1D NMR (1H \& 13C) spectra processing Tool dedicated to metabolic fingerprinting and targeted metabolomic, covering all spectra processing steps including baseline correction, chemical shift calibration, alignment. It does not require programming skills. Biologists and NMR spectroscopists can easily interact and develop synergies by visualizing the NMR spectra along with their corresponding experimental-factor levels, thus setting a bridge between experimental design and subsequent statistical analyses.
Stefan Matile - One of the best experts on this subject based on the ideXlab platform.
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Pnictogen‐Bonding Catalysis: An Interactive Tool to Uncover Unorthodox Mechanisms in Polyether Cascade Cyclizations
Chemistry (Weinheim an der Bergstrasse Germany), 2020Co-Authors: Miguel Paraja, Naomi Sakai, Andrea Gini, Stefan MatileAbstract:Pnictogen-bonding catalysis and supramolecular σ-hole catalysis in general is currently being introduced as the non-covalent counterpart of covalent Lewis acid catalysis. With access to anti-Baldwin cyclizations identified as unique characteristic, pnictogen-bonding catalysis appeared promising to elucidate one of the hidden enigmas of brevetoxin-type epoxide opening polyether cascade cyclizations, that is the cyclization of certain trans epoxides into cis-fused rings. In principle, a shift from SN 2- to SN 1-type mechanisms could suffice to rationalize this inversion of configuration. However, the same inversion could be explained by a completely different mechanism: Ring opening with C-C bond cleavage into a branched hydroxy-5-enal and the corresponding cyclic hemiacetal, followed by cascade cyclization under conformational control, including stereoselective C-C bond formation. In this report, a pnictogen-bonding supramolecular SbV catalyst is used to demonstrate that this unorthodox polyether cascade cyclization mechanism occurs.
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pnictogen bonding catalysis an Interactive Tool to uncover unorthodox mechanisms in polyether cascade cyclizations
Chemistry: A European Journal, 2020Co-Authors: Miguel Paraja, Naomi Sakai, Andrea Gini, Stefan MatileAbstract:Pnictogen-bonding catalysis and supramolecular σ-hole catalysis in general is currently being introduced as the non-covalent counterpart of covalent Lewis acid catalysis. With access to anti-Baldwin cyclizations identified as unique characteristic, pnictogen-bonding catalysis appeared promising to elucidate one of the hidden enigmas of brevetoxin-type epoxide opening polyether cascade cyclizations, that is the cyclization of certain trans epoxides into cis-fused rings. In principle, a shift from SN 2- to SN 1-type mechanisms could suffice to rationalize this inversion of configuration. However, the same inversion could be explained by a completely different mechanism: Ring opening with C-C bond cleavage into a branched hydroxy-5-enal and the corresponding cyclic hemiacetal, followed by cascade cyclization under conformational control, including stereoselective C-C bond formation. In this report, a pnictogen-bonding supramolecular SbV catalyst is used to demonstrate that this unorthodox polyether cascade cyclization mechanism occurs.
Daniel J Jacob - One of the best experts on this subject based on the ideXlab platform.
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nmrprocflow a graphical and Interactive Tool dedicated to 1d spectra processing for nmr based metabolomics
Metabolomics, 2017Co-Authors: Daniel J Jacob, Catherine Deborde, Marie Lefebvre, Mickael Maucourt, Annick MoingAbstract:Introduction Concerning NMR-based metabolomics, 1D spectra processing often requires an expert eye for disentangling the intertwined peaks.
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nmrprocflow a graphical and Interactive Tool dedicated to 1d spectra processing for nmr based metabolomics
arXiv: Quantitative Methods, 2016Co-Authors: Daniel J Jacob, Catherine Deborde, Marie Lefebvre, Mickael Maucourt, Annick MoingAbstract:Concerning NMR-based metabolomics, 1D spectra processing often requires an expert eye for disentangling the intertwined peaks, and so far the best way is to proceed Interactively with a spectra viewer. NMRProcFlow is a graphical and Interactive 1D NMR (1H \& 13C) spectra processing Tool dedicated to metabolic fingerprinting and targeted metabolomic, covering all spectra processing steps including baseline correction, chemical shift calibration, alignment. It does not require programming skills. Biologists and NMR spectroscopists can easily interact and develop synergies by visualizing the NMR spectra along with their corresponding experimental-factor levels, thus setting a bridge between experimental design and subsequent statistical analyses.
Hannes L Rost - One of the best experts on this subject based on the ideXlab platform.
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drawalignr an Interactive Tool for across run chromatogram alignment visualization
Proteomics, 2020Co-Authors: Shubham Gupta, Justin Sing, Arshia Mahmoodi, Hannes L RostAbstract:Multi-run alignment is widely used in proteomics to establish analyte correspondence across runs. Generally alignment algorithms return a cumulative score, which may not be easily interpretable for each peptide. Here a novel and Interactive Tool for cross-run chromatogram alignment visualization (DrawAlignR) of data-independent acquisition (DIA) data is presented. Furthermore, a novel C++ based implementation of raw chromatogram alignment which is 35 times faster than the previously published algorithm is developed. This not only enables users to plot alignment Interactively by DrawAlignR, but also allows other software platforms to use the algorithm. DrawAlignR is an open-source web application using R Shiny that can be hosted using the source-code available at https://github.com/Roestlab/DrawAlignR.
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drawalignr an Interactive Tool for across run chromatogram alignment visualization
Proteomics, 2020Co-Authors: Shubham Gupta, Justin Sing, Arshia Mahmoodi, Hannes L RostAbstract:: Multi-run alignment is widely used in proteomics to establish analyte correspondence across runs. Generally alignment algorithms return a cumulative score, which may not be easily interpretable for each peptide. Here we present a novel Tool, DrawAlignR, to visualize each chromatographic alignment for DIA/SWATH data. Furthermore, we have developed a novel C++ based implementation of raw chromatogram alignment which is 35 times faster than the previously published algorithm. This not only enables users to plot alignment Interactively by DrawAlignR, but also allows other software platforms to use the algorithm. DrawAlignR is an open-source web application using R Shiny that can be hosted using the source-code available at https://github.com/Roestlab/DrawAlignR. This article is protected by copyright. All rights reserved.
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drawalignr an Interactive Tool for across run chromatogram alignment visualization
bioRxiv, 2020Co-Authors: Shubham Gupta, Justin Sing, Arshia Mahmoodi, Hannes L RostAbstract:Multi-run alignment is widely used in proteomics to establish analyte correspondence across runs. Generally alignment algorithms return a cumulative score, which may not be easily interpretable for each peptide. Here we present a novel Tool, DrawAlignR, to visualize each chromatographic alignment for DIA/SWATH data. Furthermore, we have developed a novel C++ based implementation of raw chromatogram alignment which is 35 times faster than the previously published algorithm. This not only enables users to plot alignment Interactively by DrawAlignR, but also allows other software platforms to use the algorithm. DrawAlignR is an open-source web application using R Shiny that can be hosted using the source-code available at https://github.com/Roestlab/DrawAlignR.
Paul Suetens - One of the best experts on this subject based on the ideXlab platform.
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an Interactive Tool to estimate achilles tendon local strain using high frequency ultrasound preliminary results
Orthopaedic Proceedings, 2018Co-Authors: Catarina De Brito Carvalho, Stijn Bogaerts, Pieter Slagmolen, Jan Dhooge, Lennart Scheys, Koen Peers, Paul SuetensAbstract:IntroductionTendinopathies are among the most common musculoskeletal injuries. Nowadays, part of its diagnosis is established through subjective qualitative evaluation of 2D ultrasound (US). This enables limited diagnostic differentiation or therapeutic optimization and has limited added value to diagnosis in an earlier stage. It is generally accepted that extra diagnostic information can be obtained via strain evaluation. The accurate validation of strain estimation is challenging due to the lack of a ground-truth. Therefore we evaluate the repeatability of displacement and strain estimations in the longitudinal direction, using an easy, fast and Interactive application to estimate local strain during dynamic loading of the tendon.Materials and MethodsOne healthy volunteer laid in a prone position with the foot fixed to an isokinetic device. Three sets of passive movement between −10° plantarflexion and +10° dorsiflexion were performed and repeated the following day. During this, US images with a spatial...
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an Interactive Tool to estimate achilles tendon local strain using high frequency ultrasound preliminary results
Journal of Bone and Joint Surgery-british Volume, 2015Co-Authors: Catarina De Brito Carvalho, Stijn Bogaerts, Pieter Slagmolen, Jan Dhooge, Lennart Scheys, Koen Peers, Paul SuetensAbstract:Introduction Tendinopathies are among the most common musculoskeletal injuries. Nowadays, part of its diagnosis is established through subjective qualitative evaluation of 2D ultrasound (US). This enables limited diagnostic differentiation or therapeutic optimization and has limited added value to diagnosis in an earlier stage. It is generally accepted that extra diagnostic information can be obtained via strain evaluation. The accurate validation of strain estimation is challenging due to the lack of a ground-truth. Therefore we evaluate the repeatability of displacement and strain estimations in the longitudinal direction, using an easy, fast and Interactive application to estimate local strain during dynamic loading of the tendon. Materials and Methods One healthy volunteer laid in a prone position with the foot fixed to an isokinetic device. Three sets of passive movement between −10° plantarflexion and +10° dorsiflexion were performed and repeated the following day. During this, US images with a spatial resolution of 0.02mm × 0.09mm were acquired at a frame-rate of 100Hz. The US system used was the Vevo2100 with a MS250 linear array transducer with a center frequency of 20MHz. After image collection, consecutive pairs of 2D images were registered in a multi-resolution scheme, using an affine and b-spline transformation optimized by the minimization of the sum-of-squared differences, to obtain deformation vector fields. Lastly the Interactive application allows local analysis of tissue displacement and strain within selected regions of interest. Mean and standard deviation of the intra- and inter-day relative differences were calculated. Results The results show a mean intra-day relative difference of 13.71%±4.76% in displacement and of 16.29%±5.17% in strain. For inter-day comparison, the relative difference was 16.98%±14.62% in displacement and was 16%±13.51% in strain. Results show physiologically meaningful and similar strain tendencies when grouping proximal and distal regions. Discussion This work shows promising preliminary data that suggest that with our method strain and deformation can be measured in a reproducible way using high-frequency US, with little effect of slight variations in acquisition conditions. This brings the application of US based strain estimation in clinical scenarios closer to reality. However, further tests are needed to confirm these conclusions.
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a spatially dense regression study of facial form and tissue depth towards an Interactive Tool for craniofacial reconstruction
Forensic Science International, 2014Co-Authors: Sarah Shrimpton, Katleen Daniels, Sven De Greef, Francoise Tilotta, Guy Willems, Dirk Vandermeulen, Paul Suetens, Peter ClaesAbstract:Forensic Craniofacial Reconstruction (CFR) is an investigative technique used to illicit recognition of a deceased person by reconstructing the most likely face starting from the skull. A key component in most CFR methods are estimates of facial soft tissue depths (TD) at particular points (landmarks) on the skull based on averages from databases of TD recordings. These databases vary in their method of extraction, number and position of landmarks (usually sparse <100), condition of the body, population studied, and sub-categorization of the data. In this work a new dataset is presented in a novel manner based on 156 CT scans using a spatially-dense set (∼7500) of TD recordings to allow for a complete understanding of TD variation interpolating between typical landmarks. Furthermore, to unravel the interplay between soft-tissue layers, skull and facial morphology, TD and Facial Form (FF) are investigated both separately and combined. Using a partial least squares regression (PLSR) analysis, which allows for working with multivariate and spatially-dense data, on metadata of Sex, Age and BMI, different significant patterns on TD and FF variation were found. A similar, but with TD and FF combined, PLSR generated a model useful to report on both, in function of Sex, Age and BMI. In contrast to other datasets and due to the continuous nature of the regression there is no need for data sub-categorization. In further contrast, previous datasets have been presented in tabulated form, which is impractical for spatially-dense data. Instead an Interactive Tool was built to visualize the regression model in an accessible way for CFR practitioners as well as anatomists. The Tool is free to the community and forms a base for data contributions to augment the model and its future use in practice.
