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DIANA—algorithmic improvements for analysis of data-independent acquisition MS data

Johan Teleman, Hannes L Röst, George Rosenberger, Uwe Schmitt, Lars Malmström, Johan Malmström, Fredrik Levander
2014 Computer applications in the biosciences : CABIOS  
Importantly, we further demonstrate increased confidence gained by the use of two complementary data-independent acquisition targeted analysis algorithms, as well as increased numbers of quantified peptide  ...  Importantly, we further demonstrate increased confidence gained by the use of two complementary data-independent acquisition targeted analysis algorithms, as well as increased numbers of quantified peptide  ...  ACKNOWLEDGEMENTS The authors thank Ufuk Kirik for the helpful discussions on the algorithms. Conflict of interest: none declared.  ... 
doi:10.1093/bioinformatics/btu686 pmid:25348213 fatcat:gc3puzdt6vbc5gbrxm3el2rqo4

DIANA, a Process-Oriented Model of Human Auditory Word Recognition

Louis ten Bosch, Lou Boves, Mirjam Ernestus
2022 Brain Sciences  
The article also describes how DIANA could be improved in the future in order to even better resemble the behavior of human listeners.  ...  For instance, DIANA accounts for the effect of ambiguity in the acoustic signal on reaction times following the Hick–Hyman law and it interprets the acoustic signal in the form of spectro-temporal receptive  ...  Implementation The activation component in DIANA used in previous experiments (e.g., [2, 6] ) relied on speech analysis and decoding algorithms in the HTK software package, which can also be applied for  ... 
doi:10.3390/brainsci12050681 pmid:35625067 fatcat:iyjz7hidqbafnmspvm2mqkhqsu

Quantification Improvements of 1H MRS Signals [chapter]

Maria I., Anca R. Croitor Sava, Diana M., Flemming U., Uwe Himmelreich, Sabine Van
2012 Magnetic Resonance Spectroscopy  
See Fig. 1 for an example of a single and multi-voxel acquisition.  ...  Preprocessing 1 H MRS(I) signals Preprocessing of MRS signals aims at the improvement of signal quality in order to accurately extract relevant information about the metabolites via the technique called  ...  Improved algorithm for noniterative time-domain model fitting to exponentially damped magnetic resonance signals, Journal of Magnetic Resonance 73(3): 553 -557. Fig. 1.  ... 
doi:10.5772/31546 fatcat:zxzib7nkdrdw3pjp2j7bgmdoia

Within-subject template estimation for unbiased longitudinal image analysis

Martin Reuter, Nicholas J. Schmansky, H. Diana Rosas, Bruce Fischl
2012 NeuroImage  
Longitudinal image analysis has become increasingly important in clinical studies of normal aging and neurodegenerative disorders.  ...  In this paper we introduce a novel longitudinal image processing framework, based on unbiased, robust, withinsubject template creation, for automatic surface reconstruction and segmentation of brain MRI  ...  One of the major caveats in these studies is the use of tools that were originally designed for the analysis of data collected cross-sectionally.  ... 
doi:10.1016/j.neuroimage.2012.02.084 pmid:22430496 pmcid:PMC3389460 fatcat:gv4muaiizvfsxizgqkoi6ixupm

Relevance Vector Machines for Harmonization of MRI Brain Volumes Using Image Descriptors [chapter]

Maria Ines Meyer, Ezequiel de la Rosa, Koen Van Leemput, Diana M. Sima
2019 Lecture Notes in Computer Science  
Namely, current algorithms for brain volume quantification are unreliable for the longitudinal assessment of volume changes in this type of setting.  ...  We show that image descriptors can be used as input to a machine learning algorithm to improve the reliability of longitudinal volumetric studies.  ...  A data-driven approach based on independent component analysis was explored by [4] , where correction was performed by selecting independent components related to scanning parameters.  ... 
doi:10.1007/978-3-030-32695-1_9 fatcat:rfcdxbcwobggfdaoww432smqqy

Patch-Based Super-Resolution of MR Spectroscopic Images: Application to Multiple Sclerosis

Saurabh Jain, Diana M. Sima, Faezeh Sanaei Nezhad, Gilbert Hangel, Wolfgang Bogner, Stephen Williams, Sabine Van Huffel, Frederik Maes, Dirk Smeets
2017 Frontiers in Neuroscience  
Conclusions: These results suggest that the method has potential for clinically relevant neuroimaging applications.  ...  The accuracy of the method is validated against conventional interpolation techniques using a phantom, as well as simulated and in vivo acquired human brain images of multiple sclerosis subjects.  ...  AUTHOR CONTRIBUTIONS SJ, DMS, SV, FM, DS contributed to the design and analysis of the work; FS, GH, WB, SW contributed to the data acquisition; SJ and DMS wrote the paper; all authors revised the manuscript  ... 
doi:10.3389/fnins.2017.00013 pmid:28197066 pmcid:PMC5281632 fatcat:5rmb44mvz5anbefttmvp6mm3h4

Use Case I: Imaging Biomarkers in Neurological Disease. Focus on Multiple Sclerosis [chapter]

Diana M. Sima, Dirk Loeckx, Dirk Smeets, Saurabh Jain, Paul M. Parizel, Wim Van Hecke
2016 Imaging Biomarkers  
improve imaging and analysis of brain lesion load and atrophy in longitudinal MS studies [ 59 , 60 ] .  ...  Standardisation of MRI acquisition protocols and improvement of quantitative reporting tools will provide better understanding of the natural history of MS and allow accurate treatment monitoring, for  ... 
doi:10.1007/978-3-319-43504-6_15 fatcat:jjue6uryjba3vpnm3eblmlauge

Tissue Optimisation Strategies for High Quality Ex Vivo Diffusion Imaging [article]

Rachel L. C. Barrett, Diana Cash, Camilla Simmons, Eugene Kim, Tobias C. Wood, Richard Stones, Anthony C. Vernon, Marco Catani, Flavio Dell'Acqua
2021 bioRxiv   pre-print
A major challenge for the successful acquisition of ex vivo diffusion imaging data however are changes in the relaxivity and diffusivity of brain tissue following perfusion fixation.  ...  This enabled the acquisition of excellent quality high-resolution (78 μm isotropic voxel size) diffusion data in less than 4 days, with a b-value of 4000 s/mm2, 30 diffusion directions and a field of view  ...  Acknowledgements The authors thank Bernard Siow for contributing to our supply of Magnevist, Karen Randall for assisting with perfusion and tissue preparation, the members of the NatBrainLab for providing  ... 
doi:10.1101/2021.12.13.472113 fatcat:3erw3qzchfhbjdvp66ns62clyi

Bayesian segmentation of brainstem structures in MRI

Juan Eugenio Iglesias, Koen Van Leemput, Priyanka Bhatt, Christen Casillas, Shubir Dutt, Norbert Schuff, Diana Truran-Sacrey, Adam Boxer, Bruce Fischl
2015 NeuroImage  
As such, the investigators within the ADNI contributed to the design and implementation of ADNI and/or provided data but did not participate in analysis or writing of this report.  ...  with a protocol that was specifically designed for this study.  ...  Acknowledgments Support for this research was provided in part by the National Center for Research Resources (U24 RR021382, P41 RR14075, 1 K L2RR025757-  ... 
doi:10.1016/j.neuroimage.2015.02.065 pmid:25776214 pmcid:PMC4434226 fatcat:he46q5yiyffuhj4i5t3x2wcq7i

Action kinematics as an organising principle in the cortical control of human hand movement [article]

James Kolasinski, Diana C Dima, David M A Mehler, Alice Stevenson, Sara Valadan, Slawomir Kusmia, Holly E Rossiter
2019 bioRxiv   pre-print
Human imaging data concur: relative differences in movement kinematics are mirrored by differences in the associated patterns of M1 activity.  ...  Using a powerful combination of high-field fMRI and MEG, a spatial and temporal multivariate representational similarity analysis revealed that patterns of M1 activity mirrored kinematic, but not muscle-based  ...  Alignment was undertaken independently for data from the two MEG sessions.  ... 
doi:10.1101/613323 fatcat:nlm6xu55wndvjdld3m7mxuoh2i

A comparison of nLC-ESI-MS/MS and nLC-MALDI-MS/MS for GeLC-based protein identification and iTRAQ-based shotgun quantitative proteomics

Yong Yang, Sheng Zhang, Kevin Howe, David B Wilson, Felix Moser, Diana Irwin, Theodore W Thannhauser
2007 Journal of Biomolecular Techniques  
The use of nLC-ESI-MS/MS in shotgun proteomics experiments and GeLC-MS/MS analysis is well accepted and routinely available in most proteomics laboratories.  ...  As an illustration, in an analysis of moderately complex sample of E. coli proteins, the use MALDI in addition to ESI in GeLC-MS/MS resulted in a 16% average increase in protein identifications, while  ...  Xiaolong Yang for critical reviewing of this manuscript and helpful discussions.  ... 
pmid:17916795 pmcid:PMC2062563 fatcat:o54r525rqnhnlmiqmuj7rmwsk4

Cortical Power-Density Changes of Different Frequency Bands in Visually Guided Associative Learning: A Human EEG-Study

András Puszta, Xénia Katona, Balázs Bodosi, Ákos Pertich, Diána Nyujtó, Gábor Braunitzer, Attila Nagy
2018 Frontiers in Human Neuroscience  
The test consists of an acquisition (pair learning) and a test (rule transfer) phase, associated with the function of the basal ganglia and the hippocampi, respectively.  ...  The involvement of the frontal areas in the acquisition phase was remarkably weaker. No remarkable cortical power elevations were found in the test phase.  ...  Myers at Rutgers University for her generousity in allowing us to re-code and use the RAET test in Hungarian.  ... 
doi:10.3389/fnhum.2018.00188 pmid:29867412 pmcid:PMC5951962 fatcat:fx7afbfmsnczlgv24kaojqj47m

Power-spectra and cross-frequency coupling changes in visual and Audio-visual acquired equivalence learning

András Puszta, Ákos Pertich, Xénia Katona, Balázs Bodosi, Diána Nyujtó, Zsófia Giricz, Gabriella Eördegh, Attila Nagy
2019 Scientific Reports  
The three phases of the applied acquired equivalence learning test, i.e. acquisition, retrieval and generalization, investigate the capabilities of humans in associative learning, working memory load and  ...  Earlier findings denoted the role of different subcortical structures and cortical regions in the visual test.  ...  Acknowledgements The authors thank to Nóra Cserháti for her help during data collection and all the participants for engaging in the research.  ... 
doi:10.1038/s41598-019-45978-3 pmid:31263168 pmcid:PMC6603188 fatcat:xmoxodaj2jcv7kizik7vwle2gq

Spatially and temporally distinct encoding of muscle and kinematic information in rostral and caudal primary motor cortex

James Kolasinski, Diana C Dima, David M A Mehler, Alice Stephenson, Sara Valadan, Slawomir Kusmia, Holly E Rossiter
2020 Cerebral Cortex Communications  
, over 200 ms before movement onset.  ...  Here we provide evidence for spatially and temporally distinct encoding of kinematic and muscle information in human M1 during the production of a wide variety of naturalistic hand movements.  ...  Conflict of Interest: None declared.  ... 
doi:10.1093/texcom/tgaa009 pmid:32864612 pmcid:PMC7446240 fatcat:wkfcso3cezfghhxb4zole7pl24

High-Speed Video System for Micro-Expression Detection and Recognition

Diana Borza, Radu Danescu, Razvan Itu, Adrian Darabant
2017 Sensors  
We propose a fully micro-expression analysis system consisting of a high-speed image acquisition setup and a software framework which can detect the frames when the micro-expressions occurred as well as  ...  Recently, the SASE-FE [13] database was developed for the analysis of genuine vs. deceptive emotional displays from high resolution, high frame-rate video sequences.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/s17122913 pmid:29240700 pmcid:PMC5751645 fatcat:vyeaumpc2fdutmft57xihpxhgi
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