147 research outputs found
MR Spectra from rat hippocampus with LCModel quantification and the corresponding basis set
No full text<p>This folder contains the LCModel quantifications of spectra acquired in hippocampus from 7 rats. The spectra were quntified using six different DKNTMN (spline stiffness) values (0.1, 0.25, 0.4, 0.5, 1, 5). In the folder Control_files_Basis_set you can find all the control files used in this quantification along with the corresponding basis set (metabolites/simulated using NMRScopeB from jMRUI and <em>in vivo </em>parameters + full MM spectrum).</p>
<p>Please cite the following manuscript if you are using the data</p>
<p><a href="https://pubmed.ncbi.nlm.nih.gov/34268821/">In vivo macromolecule signals in rat brain 1 H-MR spectra at 9.4T: Parametrization, spline baseline estimation, and T2 relaxation times - PubMed (nih.gov)</a><br> </p>
Processing of MM signals acquired in vivo at 9.4T using 1H SVS
No full text<p>Processing of MM signals acquired in vivo at 9.4T using 1H SVS @ <a href="https://www.epfl.ch/labs/mrs4brain/">MRS4Brain research group</a>. </p>
<p>The video was recording during a presentation done by Dunja Simicic for the Virtual jMRUI Training Course @ <a href="https://inspire-med.eu/events">INSPiRE-MED EU project </a>H2020-MSCA-ITN-2018, no 813120. </p>
<p>Please use the VLC media player to view this video.</p>
<p>Please cite the following article if you are using the protocol described herein: <a href="https://pubmed.ncbi.nlm.nih.gov/34268821/">In vivo macromolecule signals in rat brain 1 H-MR spectra at 9.4T: Parametrization, spline baseline estimation, and T2 relaxation times - PubMed (nih.gov)</a></p>
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<div>Magn Reson Med</div>
. 2021 Nov;86(5):2384-2401.</div>
doi: 10.1002/mrm.28910. Epub 2021 Jul 15.</div>
<h1>In vivo macromolecule signals in rat brain <sup>1</sup> H-MR spectra at 9.4T: Parametrization, spline baseline estimation, and T<sub>2</sub> relaxation times</h1>
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<div><a href="https://pubmed.ncbi.nlm.nih.gov/?sort=pubdate&term=Simicic+D&cauthor_id=34268821">Dunja Simicic</a><sup> <a title="CIBM Center for Biomedical Imaging, Switzerland." href="https://pubmed.ncbi.nlm.nih.gov/34268821/#full-view-affiliation-1">1</a> <a title="Animal Imaging and Technology, EPFL, Lausanne, Switzerland." href="https://pubmed.ncbi.nlm.nih.gov/34268821/#full-view-affiliation-2">2</a> <a title="Laboratory for functional and metabolic imaging (LIFMET), EPFL, Lausanne, Switzerland." href="https://pubmed.ncbi.nlm.nih.gov/34268821/#full-view-affiliation-3">3</a></sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=pubdate&term=Rackayova+V&cauthor_id=34268821">Veronika Rackayova</a><sup> <a title="CIBM Center for Biomedical Imaging, Switzerland." href="https://pubmed.ncbi.nlm.nih.gov/34268821/#full-view-affiliation-1">1</a> <a title="Animal Imaging and Technology, EPFL, Lausanne, Switzerland." href="https://pubmed.ncbi.nlm.nih.gov/34268821/#full-view-affiliation-2">2</a></sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=pubdate&term=Xin+L&cauthor_id=34268821">Lijing Xin</a><sup> <a title="CIBM Center for Biomedical Imaging, Switzerland." href="https://pubmed.ncbi.nlm.nih.gov/34268821/#full-view-affiliation-1">1</a> <a title="Animal Imaging and Technology, EPFL, Lausanne, Switzerland." href="https://pubmed.ncbi.nlm.nih.gov/34268821/#full-view-affiliation-2">2</a></sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=pubdate&term=Tk%C3%A1%C4%8D+I&cauthor_id=34268821">Ivan Tkáč</a><sup> <a title="Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minnesota, USA." href="https://pubmed.ncbi.nlm.nih.gov/34268821/#full-view-affiliation-4">4</a></sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=pubdate&term=Borbath+T&cauthor_id=34268821">Tamas Borbath</a><sup> <a title="High-Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany." href="https://pubmed.ncbi.nlm.nih.gov/34268821/#full-view-affiliation-5">5</a> <a title="Faculty of Science, University of Tübingen, Tübingen, Germany." href="https://pubmed.ncbi.nlm.nih.gov/34268821/#full-view-affiliation-6">6</a></sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=pubdate&term=Starcuk+Z+Jr&cauthor_id=34268821">Zenon Starcuk Jr</a><sup> <a title="Institute of Scientific Instruments, Czech Academy of Sciences, Brno, Czech Republic." href="https://pubmed.ncbi.nlm.nih.gov/34268821/#full-view-affiliation-7">7</a></sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=pubdate&term=Starcukova+J&cauthor_id=34268821">Jana Starcukova</a><sup> <a title="Institute of Scientific Instruments, Czech Academy of Sciences, Brno, Czech Republic." href="https://pubmed.ncbi.nlm.nih.gov/34268821/#full-view-affiliation-7">7</a></sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=pubdate&term=Lanz+B&cauthor_id=34268821">Bernard Lanz</a><sup> <a title="Laboratory for functional and metabolic imaging (LIFMET), EPFL, Lausanne, Switzerland." href="https://pubmed.ncbi.nlm.nih.gov/34268821/#full-view-affiliation-3">3</a></sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=pubdate&term=Cudalbu+C&cauthor_id=34268821">Cristina Cudalbu</a><sup> <a title="CIBM Center for Biomedical Imaging, Switzerland." href="https://pubmed.ncbi.nlm.nih.gov/34268821/#full-view-affiliation-1">1</a> <a title="Animal Imaging and Technology, EPFL, Lausanne, Switzerland." href="https://pubmed.ncbi.nlm.nih.gov/34268821/#full-view-affiliation-2">2</a></sup></div>
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The story
No full textKratka, topla, često bolna, od srca ispričana ljudska priča iz pera Dunje Frankental (rođene Kovačević). Njena životna sudbina, vjerovatno i nenadano, nekim sudbonosnim nitima i vezama, dovodi je u Izrael. U toj priči jednostavnoj i po naslovu, a naizgled i realno nevelikog i obima, ispričana je životna sudbina njene porodice, tako lako prepoznatljiva i u mogućim životnim okolnostima mnogih od nas! Da li se porodični ’životni krug’ opisanih sudbina i događaja ’zatvorio’ ... ili ne ... neka o tome sude oni koje je pročitaju, a vjerujem da ni sama autorka ne može i neće na ovo dati ’konačni odgovor’.A short, warm, often painful, heartfelt human story from the pen of Dunja Frankental (née Kovačević). Her fate in life, probably unexpectedly, by some fateful threads and connections, brings her to Israel. In that story, which is simple in its title, and seemingly realistically small in scope, the life fate of her family is told, so easily recognizable even in the possible life circumstances of many of us! Whether the family 'circle of life' of the described destinies and events has 'closed' ... or not ... let those who read it judge that, and I believe that even the author herself cannot and will not give a 'final answer' to this
April fool
No full textCatalogue essay by Dunja Rmandic.
"Presenting photography, mixed media, video and installation."
Published to accompany the exhibition held at C3 Contemporary Art Space, Abbotsford, Vic., in 2009
Advanced metabolite mapping at ultra-high field using 1H-MRS, 1H-MRSI and macromolecules: applications in a rat model of type C hepatic encephalopathy
No full textMagnetic Resonance Spectroscopy (MRS) is the only technique capable of measuring a large number of metabolites simultaneously in vivo. Ultra-high magnetic fields (UHF) combined with ultra-short echo time (TE) sequences allow the detection of high-quality 1H MR spectra and the quantification of 20 different metabolites in the brain (markers of energy metabolism, osmoregulation etc.).
In vivo brain localized 1H MR spectra at short TEs contain the contribution of mobile macromolecules (MM). Reliable detection and fitting of MM are crucial for accurate quantification. Higher spectral resolution at UHF led to increased interest in using a parametrized MM spectrum and flexible spline baselines to address unpredicted spectroscopic components.
In this thesis the MM spectra (from the rat brain at 9.4T) were characterized using an improved methodological approach for their post-processing, fitting and quantification. This method provided an efficient tool for parametrization of the MM spectrum into individual components and estimation of their T2app relaxation times. An extensive assessment on how the MM spectrum and spline baseline stiffness affect the metabolite and MM quantification is also reported
Type C hepatic encephalopathy (HE) is a complication of chronic liver disease (CLD). Children and adults respond differently to CLD and its related toxic accumulation of molecules (i.e. ammonium (NH4+), glutamine (Gln)). Children with CLD may grow up with significant neurocognitive deficits even after liver transplantation. Despite considerable advances in understanding the pathogenesis of type C HE, the exact metabolic mechanisms and their regional variations are not fully understood.
The advantages of UHF short TE 1H MRS were used herein to describe the regional distribution of metabolites in the developing and adult brain using the bile duct ligated model (BDL) of type C HE (adult and postnatal day 21 rats). Three brain regions were assessed (hippocampus, cerebellum and striatum) pointing towards cerebellum as a region with the heaviest burden of Gln and unique metabolic response. Changes in cell morphology were followed longitudinally and related to the metabolic alterations. Elevated oxidative stress is reported using electron paramagnetic resonance, together with the decreased antioxidants (1H MRS) emphasizing its important role in HE. The brain regional measurements confirmed the higher susceptibility of developing brain to the disease and the increased vulnerability of cerebellum. Finally, the beneficial effect of Cr supplementation on the neurometabolic profile is described using 1H MRS and 31P MRS in CLD pups (BDL at postnatal day 15) suggesting that an appropriate treatment may have significant public health impact.
MRSI is a powerful tool to non-invasively and spatially map the brain regional distribution of metabolites in vivo. While MRSI in human brain is increasingly used, preclinical MRSI is not widely applied mainly due to the small rodent brain, long acquisition times and low signal to noise ratio.
The implementation of a novel approach: free induction decay (FID) MRSI on the 14.1T preclinical scanner is described herein. This method offers a fast and robust data acquisition with high spatial resolution resulting in high quality spectroscopic maps. Finally, preliminary assessment of the effect of two noise reduction techniques (MP-PCA and TGV reconstruction) on the spectra from preclinical MRSI datasets is briefly presented.LIFME
Model-based frequency-and-phase correction of 1H MRS data with 2D linear-combination modeling.
No full textNoise-reduction techniques for 1H-FID-MRSI at 14.1T: Monte-Carlo validation & in vivo application
No full textProton magnetic resonance spectroscopic imaging (1H-MRSI) is a powerful tool
that enables the multidimensional non-invasive mapping of the neurochemical
profile at high-resolution over the entire brain. The constant demand for
higher spatial resolution in 1H-MRSI led to increased interest in
post-processing-based denoising methods aimed at reducing noise variance. The
aim of the present study was to implement two noise-reduction techniques, the
Marchenko-Pastur principal component analysis (MP-PCA) based denoising and the
low-rank total generalized variation (LR-TGV) reconstruction, and to test their
potential and impact on preclinical 14.1T fast in vivo 1H-FID-MRSI datasets.
Since there is no known ground truth for in vivo metabolite maps, additional
evaluations of the performance of both noise-reduction strategies were
conducted using Monte-Carlo simulations. Results showed that both denoising
techniques increased the apparent signal-to-noise ratio SNR while preserving
noise properties in each spectrum for both in vivo and Monte-Carlo datasets.
Relative metabolite concentrations were not significantly altered by either
methods and brain regional differences were preserved in both synthetic and in
vivo datasets. Increased precision of metabolite estimates was observed for the
two methods, with inconsistencies noted on lower concentrated metabolites. Our
study provided a framework on how to evaluate the performance of MP-PCA and
LR-TGV methods for preclinical 1H-FID MRSI data at 14.1T. While gains in
apparent SNR and precision were observed, concentration estimations ought to be
treated with care especially for low-concentrated metabolites.Comment: Brayan Alves and Dunja Simicic are joint first authors. Currently in
revision for NMR in Biomedicin
Neurometabolic changes in a rat pup model of type C HE - 1H MRS dataset (hippocampus)
No full text1H MRS in hippocampus was used to study longitudinally the effect of chronic liver disease (bile duct ligated rat model) in the brain (type C hepatic encephalopathy) of animals having developed disease a post natal day 15 (p15) corresponding to ~4 months old human brain. The dataset contains MR spectra and LCModel Quanifications from 7 bile duct ligated and 8 control animals at week 2, 4 and 6 after surgery
MP-PCA denoising for diffusion MRS data: promises and pitfalls.
No full textDiffusion-weighted (DW) magnetic resonance spectroscopy (MRS) suffers from a lower signal to noise ratio (SNR) compared to conventional MRS owing to the addition of diffusion attenuation. This technique can therefore strongly benefit from noise reduction strategies. In the present work, Marchenko-Pastur principal component analysis (MP-PCA) denoising is tested on Monte Carlo simulations and on in vivo DW-MRS data acquired at 9.4T in rat brain and at 3T in human brain. We provide a descriptive study of the effects observed following different MP-PCA denoising strategies (denoising the entire matrix versus using a sliding window), in terms of apparent SNR, rank selection, noise correlation within and across b-values and quantification of metabolite concentrations and fitted diffusion coefficients. MP-PCA denoising yielded an increased apparent SNR, a more accurate B0 drift correction between shots, and similar estimates of metabolite concentrations and diffusivities compared to the raw data. No spectral residuals on individual shots were observed but correlations in the noise level across shells were introduced, an effect which was mitigated using a sliding window, but which should be carefully considered
Rituals of the enchanted world: Noh theater and religion in medieval Japan
No full textThis study explores of the religious underpinnings of medieval Noh theater and its operating as a form of ritual. As a multifaceted performance art and genre of literature, Noh is understood as having rich and diverse religious influences, but is often studied as a predominantly artistic and literary form that moved away from its religious/ritual origin. This study aims to recapture some of the Noh’s religious aura and reclaim its religious efficacy, by exploring the ways in which the art and performance of Noh contributed to broader religious contexts of medieval Japan.
Chapter One, the Introduction, provides the background necessary to establish the context for analyzing a selection of Noh plays which serve as case studies of Noh’s religious and ritual functioning. Historical and cultural context of Noh for this study is set up as a medieval Japanese world view, which is an enchanted world with blurred boundaries between the visible and invisible world, human and non-human, sentient and non-sentient, enlightened and conditioned. The introduction traces the religious and ritual origins of Noh theater, and establishes the characteristics of the genre that make it possible for Noh to be offered up as an alternative to the mainstream ritual, and proposes an analysis of this ritual through dynamic and evolving schemes of ritualization and mythmaking, rather than ritual as a superimposed structure.
Chapters Two through Five are analyses of four Noh plays, Kanawa, Dōjōji, Yamamba, and Hyakuman. This selection reflects my argument that a particularly efficacious form of Noh ritual is one that best responds to the liminal quality of the medieval worldview, and this is expressed through a specific way in which the main protagonist of each play is constructed as a ritualist and an object of ritual, and symbolically embodied in various incarnations of the character of demon - oni.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2018-12-01The student, Dunja Jelesijevic, accepted the attached license on 2016-08-11 at 12:00.The student, Dunja Jelesijevic, submitted this Dissertation for approval on 2016-08-11 at 12:13.This Dissertation was approved for publication on 2016-08-11 at 16:02.DSpace SAF Submission Ingestion Package generated from Vireo submission #10109 on 2017-02-28 at 14:40:43Made available in DSpace on 2017-03-01T17:00:49Z (GMT). No. of bitstreams: 2
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