Cutting-Edge Advances in Brain Tumor Imaging (2-hydroxyglutarate, IDH mutation Magnetic Resonance Spectroscopy Imaging) at 3 Tesla (3T) and 7 Tesla (7T)
Noninvasive assessment of isocitrate dehydrogenase mutation
2-Hydroxyglutarate MR spectroscopy for prediction of isocitrate dehydrogenase mutant glioma
2-Hydroxyglutarate as a Magnetic Resonance Biomarker for Glioma
Detection of oncogenic IDH mutations using magnetic resonance spectroscopy of 2-hydroxyglutarate
metabolomic analysis
RSNA
Wellcome Centre for Integrative Neuroimaging
FMRIB
Purdue
2-HG IDH1 IDH2 MRS MRSI MRI ultra-high field
CLINICAL ROLE OF MRS QUANTIFICATION OF 2HG IN DIAGNOSIS OF GLIOMAS
Ultra-high-field MRI – Precision Medicine
the clinical application of 7-Tesla imaging
UHF 7T 7Tesla
Semi-LASER, semilaser Slaser
Time-Resolved fMRI-fMRS measures simultaneous Neurotransmitters and BOLD-fMRI...Uzay Emir
Time-Resolved fMRI-fMRS measures simultaneous Neurotransmitters and BOLD-fMRI signals in the human brain at 7T
2021 Minnesota Workshop on High and Ultra-high Field Imaging
https://bit.ly/3kE66qk
GABA spectroscopy
edited GABA 1H MEGA-PRESS spectra
GABA-edited
In this study, we have developed and demonstrated a non-water suppressed GABA editing Magnetic Resonance Spectroscopic Imaging technique using density-weighted concentric rings k-space trajectory that performs robustly within a clinically feasible acquisition time at 3T. The method has been validated in a series of phantom experiments and its feasibility assessed in a healthy volunteer with a high in-plane resolution of 7.5 × 7.5 mm. Experiments qualitatively demonstrate the advantage of the proposed method in terms of its improved resolution and reduced contamination of spectra from neighboring voxels.
CMRR workshop in vivo GABA Glutamate and fMRI BOLD imaging Event-Related fMRSUzay Emir
CMRR workshop
Time-Resolved fMRI-fMRS measures simultaneous Neurotransmitters and BOLD-fMRI signals in the human brain at 7T
GABA Glutamate UHF Semi-laser
Advanced Magnetic Resonance Spectroscopy Protocol at 7T
7T hardware (Siemens Scanner and Nova Medical head coil), BaTiO3 dielectric padding
Ip et al., 2017 NeuroImage
Event-Related fMRS A transient break in excitatory-inhibitory balance
An untargeted metabolomics approach to MRS in the human brain: a comparison b...Uzay Emir
An untargeted metabolomics approach to MRS in the human brain: a comparison between LCModel and MRS-based classifier development system
The pattern recognition process successfully caught changes where glucose concertation increase was around 1% estimated by LCModel.
High spectral quality and reliable data acquisition techniques resulted in similar estimates of the glucose signal for LCModel and SpectralClassifier.
Effect of naringenin on 3 np induced huntington’s disease like symptoms by es...IJARIIT
The main aim of this study was to investigate the effect of Naringenin, a flavonoid on 3-Nitropropionic acid (3-NP)-
induced Huntington’s disease like symptoms by estimations of motor co-ordination and behavioral parameters. 3-NP is an
irreversible inhibitor of complex II in the mitochondria. 3-NP-induced neurodegeneration has been widely used as an animal
model of Huntington’s disease (HD). It replicates the pathology of HD by causing oxidative stress. Naringenin is a polyphenolic
compound, a bioflavonoid, known to have a neuroprotective effect in a rat model of Alzheimer’s disease. In the present study,
the neuroprotective effect of Naringenin on 3-NP induced oxidative stress in the rat was determined by behavioral parameters.
Rats were induced with 3-NP (15 mg/kg) intraperitoneally for 21 days and rats induced with 3-NP were treated with Naringenin
(25mg/kg and 75mg/kg) for 21 days. 3-NP caused a decline in motor function in the neurological score, locomotor activity, and
impaired rotarod activity. Naringenin treatment significantly improved grip strength indicating an improvement in motor
performance, alterations in % spontaneous alternations. These findings suggest the antioxidant potential of Naringenin
flavonoid against 3-Nitropionic acid induced neurotoxicity. However, more investigations are required to elucidate the cellular
mechanisms of Naringenin against 3-Nitropropionic acid induced Huntington’s disease like symptoms.
Time-Resolved fMRI-fMRS measures simultaneous Neurotransmitters and BOLD-fMRI...Uzay Emir
Time-Resolved fMRI-fMRS measures simultaneous Neurotransmitters and BOLD-fMRI signals in the human brain at 7T
2021 Minnesota Workshop on High and Ultra-high Field Imaging
https://bit.ly/3kE66qk
GABA spectroscopy
edited GABA 1H MEGA-PRESS spectra
GABA-edited
In this study, we have developed and demonstrated a non-water suppressed GABA editing Magnetic Resonance Spectroscopic Imaging technique using density-weighted concentric rings k-space trajectory that performs robustly within a clinically feasible acquisition time at 3T. The method has been validated in a series of phantom experiments and its feasibility assessed in a healthy volunteer with a high in-plane resolution of 7.5 × 7.5 mm. Experiments qualitatively demonstrate the advantage of the proposed method in terms of its improved resolution and reduced contamination of spectra from neighboring voxels.
CMRR workshop in vivo GABA Glutamate and fMRI BOLD imaging Event-Related fMRSUzay Emir
CMRR workshop
Time-Resolved fMRI-fMRS measures simultaneous Neurotransmitters and BOLD-fMRI signals in the human brain at 7T
GABA Glutamate UHF Semi-laser
Advanced Magnetic Resonance Spectroscopy Protocol at 7T
7T hardware (Siemens Scanner and Nova Medical head coil), BaTiO3 dielectric padding
Ip et al., 2017 NeuroImage
Event-Related fMRS A transient break in excitatory-inhibitory balance
An untargeted metabolomics approach to MRS in the human brain: a comparison b...Uzay Emir
An untargeted metabolomics approach to MRS in the human brain: a comparison between LCModel and MRS-based classifier development system
The pattern recognition process successfully caught changes where glucose concertation increase was around 1% estimated by LCModel.
High spectral quality and reliable data acquisition techniques resulted in similar estimates of the glucose signal for LCModel and SpectralClassifier.
Effect of naringenin on 3 np induced huntington’s disease like symptoms by es...IJARIIT
The main aim of this study was to investigate the effect of Naringenin, a flavonoid on 3-Nitropropionic acid (3-NP)-
induced Huntington’s disease like symptoms by estimations of motor co-ordination and behavioral parameters. 3-NP is an
irreversible inhibitor of complex II in the mitochondria. 3-NP-induced neurodegeneration has been widely used as an animal
model of Huntington’s disease (HD). It replicates the pathology of HD by causing oxidative stress. Naringenin is a polyphenolic
compound, a bioflavonoid, known to have a neuroprotective effect in a rat model of Alzheimer’s disease. In the present study,
the neuroprotective effect of Naringenin on 3-NP induced oxidative stress in the rat was determined by behavioral parameters.
Rats were induced with 3-NP (15 mg/kg) intraperitoneally for 21 days and rats induced with 3-NP were treated with Naringenin
(25mg/kg and 75mg/kg) for 21 days. 3-NP caused a decline in motor function in the neurological score, locomotor activity, and
impaired rotarod activity. Naringenin treatment significantly improved grip strength indicating an improvement in motor
performance, alterations in % spontaneous alternations. These findings suggest the antioxidant potential of Naringenin
flavonoid against 3-Nitropionic acid induced neurotoxicity. However, more investigations are required to elucidate the cellular
mechanisms of Naringenin against 3-Nitropropionic acid induced Huntington’s disease like symptoms.
Green Synthesis of Nano-Particles and its Application in Treatment of Rheumat...ijcoa
This paper presents an overview of silver nanoparticles (Ag NPs) preparation by green synthesis approaches that have advantages over conventional methods involving chemical agents associated with environmental toxicity and also explains its application in the cure of Rheumatoid arthritis. We have used Night Jasmine (Nyctanthes arbor-tristis), one of the best medicinal plants to synthesis Ag NPs. The plant extract contain some biomolecules like proteins carbohydrates etc., which act as both reducing and capping agents forming stable and shape-controlled Ag NPs. The basic principle behind the synthesis is that the silver (Ag+) of AgNO3 is reduced to Ag0 by the bio-molecules present in the extract. Rather than applying the conventional method of using micro waves to induce the reduction reaction, we have used direct sunlight as the inducer by which the reduction is faster than the former. The synthesized silver nanoparticles were characterized with UV-Visible spectroscopy, X-ray Diffraction (XRD), scanning electron microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR). The results of all these analysis were shown. Our work mainly concerns about the cure for Rheumatoid arthritis so, we have checked the Nano-particles for the Anti-Arthritic activity and the results were positive. The procedure for Invitro analysis of anti-arthritic activity and its result are clearly shown.
The Wonderful World of Scanning Electrochemical Microscopy (SECM)InsideScientific
To watch the webinar, go to:
https://insidescientific.com/webinar/the-wonderful-world-of-scanning-electrochemical-microscopy-secm/
In this webinar, Dr. Janine Mauzeroll discusses the fundamentals, critical experimental parameters and recent applications for scanning electrochemical Microscopy (SECM).
In its simplest form, SECM is a scanning probe technique in which a small-scale electrode is scanned across an immersed substrate while recording the current response. This response is dependent on both the surface topography and the electrochemical activity of the substrate. Consequently, using an array of operational modes, a wide variety of substrates and experimental systems can be characterized. The strength of SECM lies in its ability to quantify material flux from a surface with a high spatial and temporal resolution. It has been used in a variety of applications fields.
Dr. Janine Mauzeroll describes the fundamentals of SECM, including the required instrumentation and the principles of the most frequently used operational modes. Following this basic understanding of SECM principles, she then moves towards a comprehensive summary of the critical parameters for any SECM experiment. Specifically, she discusses in detail redox mediators, probes, and solvent systems that are used in SECM experiments. Finally, she presents recent applications of SECM with an emphasis on her work in the last five years related to material characterization, corrosion and batteries.
Comparative Study of Metabolites in the Imago of Silkworm, Philosamia Ricinipaperpublications3
Abstract: Acetylcholine is present in higher concentration in insects when compared with most other invertebrates & vertebrates & functions as a chemical mediator of nervous activity. In the present study, biochemical analysis of acetylcholine alongwith protein, trehalose and glucose on male and female adult moths of Philosamia ricini have been made during their 5 day life span. The results demonstrated that head of female adults contains quite higher concentration of acetylcholine than the male head and shows sexual dimorphism. On the converse, the pattern of protein content of heads reveals a slight increase in males over that in females. This sexual dimorphic study on P.ricini adult moths suggests that the cholinergic system of females is more active than that of males.
Bio-field Treatment: An Effective Strategy to Improve the Quality of Beef Ext...Mahendra Kumar Trivedi
The present research work investigated the influence of bio-field treatment on two common flavoring agents used in food industries namely beef extract powder (BEP) and meat infusion powder (MIP)
Exploring Neural Circuitry of Predatory Pursuit, Capture and Kill in MiceAshleyWilliamson29
Informational Powerpoint presented with oral presentation to Neurobiology class outlining the use of optogenetics, chemogenetics and behavioral analysis in mapping neural circuits.
An Effective Strategy to Improve the Quality of Beef Extract and Meat Infusio...rachelsalk
The present research work investigated the influence of bio-field treatment on two common flavoring agents used in food industries namely beef extract powder (BEP) and meat infusion powder (MIP). The treated powders were characterized by Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), particle size analysis, surface area analysis, differential scanning calorimetry (DSC), and thermogravimetric analysis (TGA). The FT-IR results showed disappearance of triglycerides peaks in both the treated powders as compared to control. XRD results corroborated the amorphous nature of both control and treated samples. The BEP showed enhanced average particle size (d50) and d99 (size exhibited by 99% of powder particles) by 5.7% and 16.1%, respectively as compared to control. Contrarily, the MIP showed a decreased particle size (d50;0.4% and d99; 18.1%) as compared to control.It was assumed that enormous energy was stored in MIP after bio-field treatment that led to fracture into smaller particles. The surface area was increased in both the treated powders. DSC result showed significant increase in melting temperature, in BEP and MIP, which indicated the higher thermal stability of the samples. However, the specific heat capacity (∆H) was decreased in both samples, which was probably due to high energy state of the powders.
Expanding Surface Plasmon Resonance Capabilities with ReichertReichertSPR
Surface Plasmon Resonance (SPR) is a widely-used label-free technique to characterize a variety of molecular interactions. SPR is an optical phenomenon that is sensitive to changes in the dielectric properties of the medium close to a metal surface. Specifically, the resonance condition is affected by changes in refractive index occurring up to 300 nm above the metal surface (Au) and thus by the material absorbed onto the metal film. Therefore, the SPR signal is a measure of the total mass concentration at the gold sensor chip surface.
Typically, a mobile molecule (analyte) is injected across an immobilized binding partner (ligand) and as the analyte binds, this mass accumulation on the sensor surface leads to an increase in refractive index, and the result is plotted as response versus time. SPR is commonly utilized by researchers to determine association/dissociation rates, affinities and thermodynamics of biomolecular interactions.
Traditionally, the interactions under study with SPR include those occurring with and between the major classes of biological macromolecules along with those involving small molecules and drugs. These classic experiments have been primarily carried with just purified samples. Reichert’s SPR systems implement a very robust fluidics arrangement that can accommodate a wide variety of sample compositions including crude samples such as lysates, whole cells and serum. In addition, Reichert’s systems are housed in an open architecture that easily allows coupling to other analytical techniques and instruments. Along with excelling at traditional biomolecular interactions, Reichert’s systems pave the way for new avenues of investigation involving crude samples and whole cells along with the ability to couple SPR to other techniques. This presentation will focus on the SPR technique and provide examples of unique applications with cells along with the possibility of interfacing SPR with other analytical methods.
http://www.reichertspr.com/webinars/general/expanding-surface-plasmon-resonance-capabilities-with-reichert/
Detection of Cystathionine, 2-Hydroxyglutarate and Citrate in Oligodendroglio...Uzay Emir
The semi-LASER sequence optimized for 2-HG detection with a TE of 110 ms successfullydemonstrated distinct cystathionine peaks in glioma patients with molecularly definedoligodendroglioma (IDH-mutant and 1p/19q codeleted) at 7T. While a prospective, betterpowered study is needed to confirm our observations, we propose that our method has thepotential to allow presurgical stratification of patients with IDH-mutant glioma into those witholigodendrogliomas and astrocytomas; which is of important prognostic significance.
(PDF) Detection of Cystathionine, 2-Hydroxyglutarate and Citrate in Oligodendrogliomas at 7T using Long-TE Semi-LASER. Available from: https://www.researchgate.net/publication/349575306_Detection_of_Cystathionine_2-Hydroxyglutarate_and_Citrate_in_Oligodendrogliomas_at_7T_using_Long-TE_Semi-LASER [accessed Mar 03 2021].
Green Synthesis of Nano-Particles and its Application in Treatment of Rheumat...ijcoa
This paper presents an overview of silver nanoparticles (Ag NPs) preparation by green synthesis approaches that have advantages over conventional methods involving chemical agents associated with environmental toxicity and also explains its application in the cure of Rheumatoid arthritis. We have used Night Jasmine (Nyctanthes arbor-tristis), one of the best medicinal plants to synthesis Ag NPs. The plant extract contain some biomolecules like proteins carbohydrates etc., which act as both reducing and capping agents forming stable and shape-controlled Ag NPs. The basic principle behind the synthesis is that the silver (Ag+) of AgNO3 is reduced to Ag0 by the bio-molecules present in the extract. Rather than applying the conventional method of using micro waves to induce the reduction reaction, we have used direct sunlight as the inducer by which the reduction is faster than the former. The synthesized silver nanoparticles were characterized with UV-Visible spectroscopy, X-ray Diffraction (XRD), scanning electron microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR). The results of all these analysis were shown. Our work mainly concerns about the cure for Rheumatoid arthritis so, we have checked the Nano-particles for the Anti-Arthritic activity and the results were positive. The procedure for Invitro analysis of anti-arthritic activity and its result are clearly shown.
The Wonderful World of Scanning Electrochemical Microscopy (SECM)InsideScientific
To watch the webinar, go to:
https://insidescientific.com/webinar/the-wonderful-world-of-scanning-electrochemical-microscopy-secm/
In this webinar, Dr. Janine Mauzeroll discusses the fundamentals, critical experimental parameters and recent applications for scanning electrochemical Microscopy (SECM).
In its simplest form, SECM is a scanning probe technique in which a small-scale electrode is scanned across an immersed substrate while recording the current response. This response is dependent on both the surface topography and the electrochemical activity of the substrate. Consequently, using an array of operational modes, a wide variety of substrates and experimental systems can be characterized. The strength of SECM lies in its ability to quantify material flux from a surface with a high spatial and temporal resolution. It has been used in a variety of applications fields.
Dr. Janine Mauzeroll describes the fundamentals of SECM, including the required instrumentation and the principles of the most frequently used operational modes. Following this basic understanding of SECM principles, she then moves towards a comprehensive summary of the critical parameters for any SECM experiment. Specifically, she discusses in detail redox mediators, probes, and solvent systems that are used in SECM experiments. Finally, she presents recent applications of SECM with an emphasis on her work in the last five years related to material characterization, corrosion and batteries.
Comparative Study of Metabolites in the Imago of Silkworm, Philosamia Ricinipaperpublications3
Abstract: Acetylcholine is present in higher concentration in insects when compared with most other invertebrates & vertebrates & functions as a chemical mediator of nervous activity. In the present study, biochemical analysis of acetylcholine alongwith protein, trehalose and glucose on male and female adult moths of Philosamia ricini have been made during their 5 day life span. The results demonstrated that head of female adults contains quite higher concentration of acetylcholine than the male head and shows sexual dimorphism. On the converse, the pattern of protein content of heads reveals a slight increase in males over that in females. This sexual dimorphic study on P.ricini adult moths suggests that the cholinergic system of females is more active than that of males.
Bio-field Treatment: An Effective Strategy to Improve the Quality of Beef Ext...Mahendra Kumar Trivedi
The present research work investigated the influence of bio-field treatment on two common flavoring agents used in food industries namely beef extract powder (BEP) and meat infusion powder (MIP)
Exploring Neural Circuitry of Predatory Pursuit, Capture and Kill in MiceAshleyWilliamson29
Informational Powerpoint presented with oral presentation to Neurobiology class outlining the use of optogenetics, chemogenetics and behavioral analysis in mapping neural circuits.
An Effective Strategy to Improve the Quality of Beef Extract and Meat Infusio...rachelsalk
The present research work investigated the influence of bio-field treatment on two common flavoring agents used in food industries namely beef extract powder (BEP) and meat infusion powder (MIP). The treated powders were characterized by Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), particle size analysis, surface area analysis, differential scanning calorimetry (DSC), and thermogravimetric analysis (TGA). The FT-IR results showed disappearance of triglycerides peaks in both the treated powders as compared to control. XRD results corroborated the amorphous nature of both control and treated samples. The BEP showed enhanced average particle size (d50) and d99 (size exhibited by 99% of powder particles) by 5.7% and 16.1%, respectively as compared to control. Contrarily, the MIP showed a decreased particle size (d50;0.4% and d99; 18.1%) as compared to control.It was assumed that enormous energy was stored in MIP after bio-field treatment that led to fracture into smaller particles. The surface area was increased in both the treated powders. DSC result showed significant increase in melting temperature, in BEP and MIP, which indicated the higher thermal stability of the samples. However, the specific heat capacity (∆H) was decreased in both samples, which was probably due to high energy state of the powders.
Expanding Surface Plasmon Resonance Capabilities with ReichertReichertSPR
Surface Plasmon Resonance (SPR) is a widely-used label-free technique to characterize a variety of molecular interactions. SPR is an optical phenomenon that is sensitive to changes in the dielectric properties of the medium close to a metal surface. Specifically, the resonance condition is affected by changes in refractive index occurring up to 300 nm above the metal surface (Au) and thus by the material absorbed onto the metal film. Therefore, the SPR signal is a measure of the total mass concentration at the gold sensor chip surface.
Typically, a mobile molecule (analyte) is injected across an immobilized binding partner (ligand) and as the analyte binds, this mass accumulation on the sensor surface leads to an increase in refractive index, and the result is plotted as response versus time. SPR is commonly utilized by researchers to determine association/dissociation rates, affinities and thermodynamics of biomolecular interactions.
Traditionally, the interactions under study with SPR include those occurring with and between the major classes of biological macromolecules along with those involving small molecules and drugs. These classic experiments have been primarily carried with just purified samples. Reichert’s SPR systems implement a very robust fluidics arrangement that can accommodate a wide variety of sample compositions including crude samples such as lysates, whole cells and serum. In addition, Reichert’s systems are housed in an open architecture that easily allows coupling to other analytical techniques and instruments. Along with excelling at traditional biomolecular interactions, Reichert’s systems pave the way for new avenues of investigation involving crude samples and whole cells along with the ability to couple SPR to other techniques. This presentation will focus on the SPR technique and provide examples of unique applications with cells along with the possibility of interfacing SPR with other analytical methods.
http://www.reichertspr.com/webinars/general/expanding-surface-plasmon-resonance-capabilities-with-reichert/
Detection of Cystathionine, 2-Hydroxyglutarate and Citrate in Oligodendroglio...Uzay Emir
The semi-LASER sequence optimized for 2-HG detection with a TE of 110 ms successfullydemonstrated distinct cystathionine peaks in glioma patients with molecularly definedoligodendroglioma (IDH-mutant and 1p/19q codeleted) at 7T. While a prospective, betterpowered study is needed to confirm our observations, we propose that our method has thepotential to allow presurgical stratification of patients with IDH-mutant glioma into those witholigodendrogliomas and astrocytomas; which is of important prognostic significance.
(PDF) Detection of Cystathionine, 2-Hydroxyglutarate and Citrate in Oligodendrogliomas at 7T using Long-TE Semi-LASER. Available from: https://www.researchgate.net/publication/349575306_Detection_of_Cystathionine_2-Hydroxyglutarate_and_Citrate_in_Oligodendrogliomas_at_7T_using_Long-TE_Semi-LASER [accessed Mar 03 2021].
Diagnostic Efficacy of Ultra-High-Field MRS in Glioma PatientsUzay Emir
Synopsis: We have recently initiated a 7T MRS glioma consortium, intending to bring together experts in the field to discuss pitfalls, promises, and potential research avenues of MRS in gliomas. During the "GlioMaRS-NET Workshop" in 2020, we tested the efficacy of UHF MRS for predicting the molecular characteristics by visual inspection by conducting a survey with a set of previously acquired UHF spectra from glioma patients. In the post-genomics era, the World Health Organization (WHO) classification of gliomas has become even more tightly integrated with molecular parameters in addition to histology. Integrated diagnoses offer prospects for precision medicine strategies tailoring therapies for each individual. The International Society of Neuropathology-Haarlem Consensus has proposed the personalized layered diagnosis for gliomas that merge all of the distinct but related information. For the final diagnosis, the concept of integrated diagnosis (Layer 1) relies on all available data, which include the histological classification (Layer 2, e.g., astrocytoma vs. oligodendroglioma), the grading (Layer 3, e.g., WHO grade II vs. III), and molecular characteristics (Layer 4, e.g., isocitrate dehydrogenase (IDH)-mutant, 1p/19q-codeletion) (1). Thus, the personalized layered diagnosis approach has emphasized to tailor the diagnostic imaging to contribute to the integrated diagnosis by discovering reliable imaging biomarkers and tools capable of differential diagnosis according to genetic subtypes. It has recently been shown that definitional features of glioma, such as IDH mutation and 1p/19q codeletion (Layer 4), can be identified with non-invasive MRS at 3T, opening up exciting new opportunities for diagnostics, clinical trials, and assessment of treatments (2,3). Ultra-high-field (UHF, >=7T) MRI scanners offer enhanced detection relative to routine 3T MRI of 2-HG peaks in the MRS spectra of IDH mutated patients (4,5). This is due to increased SNR at the higher field strength and increased spectral dispersion, which can improve the delineation of 2HG from neighboring metabolites such as glutamate and glutamine. Furthermore, at 7T, the 2-HG peak is not only to contribute to layer 4 of the integrated diagnosis by identifying molecular features but also to detect subtle changes due to the reprogramming of cellular metabolism during the disease progression or treatment. With the recent successes of 2-HG and increased use of UHF MRI in clinical settings as a basis, we have recently initiated a 7T MRS glioma consortium, intending to bring together experts in the field to discuss pitfalls, promises, and potential research avenues of MRS in gliomas. During the "Multi-center 7T Glioma Consortium (GlioMaRS-NET) Workshop" held on 16-20 Novembe
Integrative bioinformatics analysis of Parkinson's disease related omics dataEnrico Glaab
Presentation on statistical meta analysis of omics data from Parkinson's disease case-control studies. The results are used for a comparative analysis against aging-related omics alterations in the brain and a prioritization of new candidate disease genes using the phenologs approach.
Nanotechnology implementation in photodynamic therapy ghada moneerghada altoukhy
Photo dynamic therapy is old modality using up tel now.e
this presentation will give lights on the PDT from the beginning up to date and overcome the disadvantages by using new modality of treatment by nanotechnology.
Next Generation Sequencing and its Applications in Medical Research - Frances...Sri Ambati
The so-called “next-generation” sequencing (NGS) technologies allows us, in a short time and in parallel, to sequence massive amounts of DNA, overcoming the limitations of the original Sanger sequencing methods used to sequence the first human genome. NGS technologies have had an enormous impact on biomedical research within a short time frame. This talk will give an overview of these applications with specific examples from Mendelian genomics and cancer research. #h2ony
dkNET Webinar: Illuminating The Druggable Genome With Pharos 10/23/2020dkNET
Abstract
Pharos (https://pharos.nih.gov/) is an integrated web-based informatics platform for the analysis of data aggregated by the Illuminating the Druggable Genome (IDG) Knowledge Management Center, an NIH Common Fund initiative. The current version of Pharos (as of October 2019) spans 20,244 proteins in the human proteome, 19,880 disease and phenotype associations, and 226,829 ChEMBL compounds. This resource not only collates and analyzes data from over 60 high-quality resources to generate these types, but also uses text indexing to find less apparent connections between targets, and has recently begun to collaborate with institutions that generate data and resources. Proteins are ranked according to a knowledge-based classification system, which can help researchers to identify less studied “dark” targets that could be potentially further illuminated. This is an important process for both drug discovery and target validation, as more knowledge can accelerate target identification, and previously understudied proteins can serve as novel targets in drug discovery. In this webinar, Dr. Tudor Oprea will introduce how to use Pharos to find targets of interest for drug discovery.
The top 3 key questions that Pharos can answer:
1. What are the novel drug targets that may play a role in a specific disease?
2. What are the diseases that are related directly or indirectly to a drug target?
3. Find researchers that are related directly or indirectly to a drug target.
Presenter: Tudor Oprea, MD, PhD, Professor of Medicine, Chief of Translational Informatics Division & Internal Medicine, University of New Mexico
dkNET Webinar Information: https://dknet.org/about/webinar
Illuminating the Druggable Genome with Knowledge Engineering and Machine Lear...Jeremy Yang
Talk given at 14th Annual New Mexico BioInformatics, Science and Technology (NMBIST) Symposium, entitled Integrative Omics, on March 14-15, 2019. Most slides c/o IDG KMC PI Tudor Oprea, MD, PhD.
In this work, we demonstrate the sodium magnetic resonance imaging (MRI) capabilities of a three-dimensional (3D) dual-echo ultrashort echo time (UTE) sequence with a novel rosette petal trajectory (PETALUTE), in comparison to the 3D density-adapted (DA) radial spokes UTE sequence. #mri #ismrm #msk
3D UTE 31P-MRSI with modified rosette k-space (PETALUTE): Comparison with con...Uzay Emir
Phosphorus-31 magnetic resonance spectroscopic imaging (31P-MRSI) provides valuable non-invasive in vivo information on tissue metabolism but is burdened by poor sensitivity and prolonged scan duration. Ultra-short echo time (UTE) acquisitions minimize signal loss when probing signals with relatively short spin-spin relaxation time (T2), while also preventing first-order dephasing. Here, a three-dimensional (3D) UTE sequence with a rosette k-space trajectory is applied to 31P-MRSI at 3T. Conventional chemical shift imaging (CSI) employs highly regular Cartesian k-space sampling, susceptible to substantial artifacts when accelerated via undersampling. In contrast, this novel sequence’s “petal-like” pattern offers incoherent sampling more suitable for compressed sensing (CS). These results showcase the competitive performance of UTE rosette 31P-MRSI against conventional weighted CSI with simulation, phantom, and in vivo leg muscle comparisons.
Modified Rosette PETALUTE for preclinical imagingUzay Emir
We have demonstrated a sequence, PETALUTE, for clinical and preclinical high (3T) and ultra-high fields (>7T) scanners.
The modified Rosette kspace dual-echo Acquisition/ PETALUTE strategy could further enhance integrated and translational research studies to understand human and non-human complex structures and physiologies better.
While Phosphorous (31P) MRS (I) has been promising in experimental and clinical settings since the early 70s, it has been beset by prohibitively lower sensitivity, limited spectral-spatial resolution, and prolonged acquisition. This manuscript and proceedings of the annual scientific meeting of ISMRM in 2022 (REF1) and 2023 (REF2) demonstrate that our novel acquisition strategy, the novel Rosette Trajectory for fast and flexible MR(S)I contrast (Shen et al. 2023 (REF3), later we renamed it as PETALUTE after the translation to the preclinical scanners of 7T and 9.4T), enables operator-independent (1) rapid acquisition (~7 minutes), (2) reconstruction, and (3) processing pipeline, resulting in phosphorous metabolite ratio maps (10 x 10 x 10 mm3) of the whole brain.
In response to the “Repeat it with Me” challenge organized by the Reproducible Research study group of ISMRM, we demonstrated the power of this technique in 5 healthy volunteers at three different institutions with different experimental setups (2nd Place: UTE 31P 3D Rosette MRSI Reproducibility Team, REF4). Since the proposed acquisition/reconstruction/processing pipeline was operator/scanner/coil-independent, the Reproducer sub-teams successfully replicated the findings of the original proceeding in 2022 (REF1). As part of this challenge, we provided some MATLAB scripts and k-space data to reproduce some of the results described in this manuscript. The software and data can be downloaded from https://purr.purdue.edu/projects/ismrm31pmrsi.
These results will likely be of broad interest across clinical settings since the proposed acquisition strategy is not specific to any region, nuclei, or magnetic field and is operator-independent. This study's resolution and signal-to-noise ratios permit the metabolite maps in an experimentally and clinically feasible timeframe at 3 Tesla and 7T.
REF1 Bozymski B, Shen X, Ozen AC, Ibey S, Chiew M, Thomas A, Dydak U, Emir UE. Ultra-Short Echo Time 31P 3D MRSI at 3T with Novel Rosette k-space Trajectory. Proceedings 30th Scientific Meeting, International Society for Magnetic Resonance in Medicine, 2022.
REF2 Farley N, Bozymski B, Dydak U, Emir UE*. Fast 3D 31P MRSI Using Novel Rosette Petal Trajectory at 3T with x4 Accelerated Compressed Sensing. Proceedings 31st Scientific Meeting, International Society for Magnetic Resonance in Medicine, 2023.
REF3 Shen X, Özen AC, Sunjar A, Ilbey S, Sawiak S, Shi R, Chiew M, Emir UE. Ultrashort T2 components imaging of the whole brain using 3D dual-echo UTE MRI with rosette k-space pattern. Magnetic Resonance in Medicine. 2023;89(2):508–521.
REF4 https://challenge.ismrm.org/2023-24-reproducibility-challenge/results-22-23/
Rosette Applications (MRI and MRSI) at UHF human (7T) and animal scanners (9....Uzay Emir
MRI
MRSI
LEAF
PETAL
EGG
ROSETTE
MRI
siemens
bruker
his study aimed to develop a new 3D dual-echo rosette k-space trajectory, specifically for applications of ultra-short echo time (UTE) magnetic resonance imaging (MRI). The direct imaging of the myelin bilayer, which has ultra-short transverse relaxation time (uT2), was acquired to test the performance of the proposed UTE sequence.
Theory and Methods The rosette trajectory was developed based on rotations of a ‘petal-like’ pattern in the kx-ky plane, with oscillated extensions in kz-direction for 3D coverage. Five healthy volunteers were recruited and underwent ten dual-echo rosette UTE scans with varied echo times (TEs). Dual-exponential model fitting was performed to separate uT2 signals, with the output of uT2 fraction, uT2 value and long T2 value.
Results The reconstructed images’ signal contrast between white matter (WM) and grey matter (GM) increased with longer TEs. The WM regions had higher uT2 fraction values than GM (10.9%±1.9% vs. 5.7%±2.4%). The uT2 value was about 0.12 milliseconds in WM.
Conclusion The higher uT2 fraction value in WM compared to GM demonstrated the ability of the proposed sequence to capture rapidly decaying signals.
UTE 31P 3D Rosette MRSI reproducibility Team has demonstrated the Reproducibility of the method. The method has been challenged on #siemenshealthineers PET-MRI (mMR) and Prisma 3T scanners.ISMRM #spectroscopy ISMRM ChallengeISMRM RAPID Biomedical
https://lnkd.in/gnjCHtu2
Submillimeter fMRI Acquisition using a dual-echo Rosette kspace trajectory at 3TUzay Emir
n this study, we overcome the technological barrier against acquiring submillimeter resolution (~ 0.5 mm) fMRI data at 3T via a novel dual-echo Rosette k-space design. This design results in the fine representation of activation maps in two different functional tasks and might be a springboard in neuroimaging by providing very high-resolution spatiotemporal dynamics of neural networks. The method will be further evolved with the feedback from the MRI community via the GitHub platform as such for further acceleration, inflow saturation, and 3D coverage via 3D sampling and/or multiband approaches.
3D-UTE Rosette MRI and MRSI at UHF human (7T) and animal scanners (9.4T) usin...Uzay Emir
#ismrm #ISMRM2022 #ISMRM22
3D-UTE Rosette Applications (MRI and MRSI) at UHF human (7T) and animal scanners (9.4T) using The Berkeley Advanced Reconstruction Toolbox (BART) toolbox
Uzay Emir
Afternoon Tea with BART
Time: 15:45-16:45
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
2-Hydroxyglutarate MR spectroscopy for prediction of isocitrate dehydrogenase mutant glioma 2-HG MRS IDH UHF
1. See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/333189636
A Noninvasive Comparison Study between Human Gliomas with IDH1
and IDH2 Mutations by MR Spectroscopy
Conference Paper · May 2019
CITATIONS
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4
13 authors, including:
Some of the authors of this publication are also working on these related projects:
FAST MRSI View project
2-HG Detection View project
Sarah Jane Larkin
University of Oxford
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2. A Noninvasive Comparison Study
between Human Gliomas with
IDH1 and IDH2 Mutations by MR
Spectroscopy
Xin Shen1, Natalie Voets2, Sarah Larkin2, Nick de
Pennington2, Puneet Plaha3, Richard Stacey3, James
Mccullagh2, Christopher Schofield2, Stuart Clare2, Peter
Jezzard2, Tom Cadoux-Hudson3, Olaf Ansorge2, and Uzay
Emir1,2,4
1Weldon School of Biomedical Engineering, Purdue University,
West Lafayette, IN, United States,
2University of Oxford, Oxford, United Kingdom,
3Oxford University Hospitals NHS Trust, Oxford, United
Kingdom,
4School of Health Sciences, Purdue University, West Lafayette,
IN, United States
4. Cancer Metabolism
(Post-Genome)
IDH-mutant
80% of grade II-III gliomas + secondary
glioblastomas
(Dang et al. 2009)
q Linked to prognosis
q Sensitivity to targeted therapy
q IDH inhibitors are being developed
5. simulated 2-HG spectral pattern at 3T
5 - 35
mM
2-HG
Pope et al., Neurooncol., 2011
Choi et al., Nat Med., 2012
Andronesi et al., Sci Transl Med. ,2012
Berrington A. et al. Tomography (2016)
2-Hydroxyglutarate (2-HG) Detection at 3T
6. 2-HG detection with semi-LASER Echo
Time=110 ms (Double Spin-Echo Adiabatic
Localization)
Emir UE. et al. Cancer Research (2016)
Berrington A. et al.Tomography (2016)
Berrington A. et al. NMR Biomed (2018)
3T
7T
7. 3 Tesla
Increase in sensitivity
allows the highest
resolution 2-HG
mapping at 3T
Semi-LASER
TE = 110 ms
VOI = 5 x 5 x 10 mm3
IDH2 patient, Steel at al., Scientific Reports, volume 8, Article number: 7792 (2018)
10. • Aim: To determine whether metabolic reprogramming
associated with IDH mutant gliomas at 7T.
• A total of 21 patients (age = 37 ± 11, 13 males)
• IDH1 (n = 15) and IDH2 (n = 5) and
• No histopathological diagnosis could be established for one
glioma patient
• Nova Medical single-channel transmit and 32 channel
receive array head-coil.
• Spectra were fitted with LCModel using simulated basis
sets
• The mutation subtype (IDH1 or IDH2) was assessed by
IHC and DNA sequencing from a surgical tissue biopsy
12. IDH1 vs IDH2
Mitochondria vs Cytoplasm
Shen et al., Metabolites 2019, 9, 35.
Hypermethylation
ISYNA1
Oxidative
phosphorylation
Oxidative
phosphorylation
Oxidative
phosphorylation
13. Metabolomics of IDH1 and IDH2 using MRS
at 7 Tesla
Shen et al., Metabolites 2019, 9, 35.
14. IDH –ve (GBMs), IDH1 and IDH2
7T, semi-LASER (Double Spin-Echo Adiabatic Localization, TE = 110 ms)
15. Conclusion
The high-quality spectra of semi-
LASER (TE = 110 ms)
q Enabled the quantification of neurochemical profiles
in both IDH1 and IDH2 mutations at 7T and 3T
q Enabled the noninvasive measurement of metabolic
reprogramming associated IDH mutant brain tumors.
q Enabled the highest resolution 2-HG mapping at 3T
q Adiabatic spin-echo localization has less false
positive 2HG detection than the PRESS97 and the
MEGA68 sequence, as shown in volunteers (Abstract
#2532)
Prognostic precision medicine biomarker detection system at 3T and 7T for
identifying,
stratifying,
monitoring
IDH1 and IDH2 mutant glioma patients and beyond.
Steel at al., Scientific Reports, volume 8,
Article number: 7792 (2018)
16. Acknowledgement
• Irene Tracey, Nuffield Department of Clinical Neurosciences, University of
Oxford
• Heidi Johansen-Berg, The Wellcome Centre for Integrative Neuroimaging,
University of Oxford
• The work was supported by the NIHR Oxford Biomedical Research Centre. The Wellcome Centre for Integrative
Neuroimaging is supported by core funding from the Wellcome Trust (203139/Z/16/Z).
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