scholarly journals Exposure Optimization Trial for Patients With Medical Implants During MRI Exposure: Balance Between the Completeness and Efficiency

2021 ◽  
Vol 9 ◽  
Author(s):  
Aiping Yao ◽  
Pengfei Yang ◽  
Mingjuan Ma ◽  
Yunfeng Pei
Keyword(s):  
Complex Function ◽  
Exposure Condition ◽  
Clinical Factors ◽  
Data Set ◽  
Power Deposition ◽  
Tissue Heating ◽  
Redundant Data ◽  
Rf Exposure ◽  
Pacemaker Leads

Elongated conductors, such as pacemaker leads, can couple to the MRI radio-frequency (RF) field during MRI scan and cause dangerous tissue heating. By selecting proper RF exposure conditions, the RF-induced power deposition can be suppressed. As the RF-induced power deposition is a complex function of multiple clinical factors, the problem remains how to perform the exposure selection in a comprehensive and efficient way. The purpose of this work is to demonstrate an exposure optimization trail that allows a comprehensive optimization in an efficient and traceable manner. The proposed workflow is demonstrated with a generic 40 cm long cardio pacemaker, major components of the clinical factors are decoupled from the redundant data set using principle component analysis, the optimized exposure condition can not only reduce the in vivo power deposition but also maintain good image quality.

scholarly journals Stereoelectroencephalography

Neurosurgery ◽  
2012 ◽  
Vol 72 (3) ◽  
pp. 353-366 ◽  
Author(s):  
Francesco Cardinale ◽  
Massimo Cossu ◽  
Laura Castana ◽  
Giuseppe Casaceli ◽  
Marco Paolo Schiariti ◽  
...  
Keyword(s):  
Interquartile Range ◽  
Entry Point ◽  
Target Point ◽  
Epileptogenic Zone ◽  
Localization Error ◽  
Drug Resistant ◽  
Robot Assisted ◽  
Data Set ◽  
Essential Information

Abstract BACKGROUND: Stereoelectroencephalography (SEEG) methodology, originally developed by Talairach and Bancaud, is progressively gaining popularity for the presurgical invasive evaluation of drug-resistant epilepsies. OBJECTIVE: To describe recent SEEG methodological implementations carried out in our center, to evaluate safety, and to analyze in vivo application accuracy in a consecutive series of 500 procedures with a total of 6496 implanted electrodes. METHODS: Four hundred nineteen procedures were performed with the traditional 2-step surgical workflow, which was modified for the subsequent 81 procedures. The new workflow entailed acquisition of brain 3-dimensional angiography and magnetic resonance imaging in frameless and markerless conditions, advanced multimodal planning, and robot-assisted implantation. Quantitative analysis for in vivo entry point and target point localization error was performed on a sub-data set of 118 procedures (1567 electrodes). RESULTS: The methodology allowed successful implantation in all cases. Major complication rate was 12 of 500 (2.4%), including 1 death for indirect morbidity. Median entry point localization error was 1.43 mm (interquartile range, 0.91-2.21 mm) with the traditional workflow and 0.78 mm (interquartile range, 0.49-1.08 mm) with the new one (P < 2.2 × 10−16). Median target point localization errors were 2.69 mm (interquartile range, 1.89-3.67 mm) and 1.77 mm (interquartile range, 1.25-2.51 mm; P < 2.2 × 10−16), respectively. CONCLUSION: SEEG is a safe and accurate procedure for the invasive assessment of the epileptogenic zone. Traditional Talairach methodology, implemented by multimodal planning and robot-assisted surgery, allows direct electrical recording from superficial and deep-seated brain structures, providing essential information in the most complex cases of drug-resistant epilepsy.

scholarly journals On the correspondence of electrical and optical physiology in in vivo population-scale two-photon calcium imaging

2019 ◽  
Author(s):  
Peter Ledochowitsch ◽  
Lawrence Huang ◽  
Ulf Knoblich ◽  
Michael Oliver ◽  
Jerome Lecoq ◽  
...  
Keyword(s):  
Calcium Imaging ◽  
Biophysical Model ◽  
Data Set ◽  
Two Photon ◽  
Simultaneous Imaging ◽  
Fluorescence Measurements ◽  
Large Populations ◽  
Intractable Problem ◽  
Mouse Lines

AbstractMultiphoton calcium imaging is commonly used to monitor the spiking of large populations of neurons. Recovering action potentials from fluorescence necessitates calibration experiments, often with simultaneous imaging and cell-attached recording. Here we performed calibration for imaging conditions matching those of the Allen Brain Observatory. We developed a novel crowd-sourced, algorithmic approach to quality control. Our final data set was 50 recordings from 35 neurons in 3 mouse lines. Our calibration indicated that 3 or more spikes were required to produce consistent changes in fluorescence. Moreover, neither a simple linear model nor a more complex biophysical model accurately predicted fluorescence for small numbers of spikes (1-3). We observed increases in fluorescence corresponding to prolonged depolarizations, particularly in Emx1-IRES-Cre mouse line crosses. Our results indicate that deriving spike times from fluorescence measurements may be an intractable problem in some mouse lines.

scholarly journals Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2322 ◽  
Author(s):  
Saw Simeon ◽  
Nuttapat Anuwongcharoen ◽  
Watshara Shoombuatong ◽  
Aijaz Ahmad Malik ◽  
Virapong Prachayasittikul ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Molecular Docking ◽  
Binding Pocket ◽  
Binding Energies ◽  
Acetylcholinesterase Inhibition ◽  
Qsar Modeling ◽  
Qsar Study ◽  
Data Set ◽  
Ache Inhibitors ◽  
Redundant Data

Alzheimer’s disease (AD) is a chronic neurodegenerative disease which leads to the gradual loss of neuronal cells. Several hypotheses for AD exists (e.g., cholinergic, amyloid, tau hypotheses, etc.). As per the cholinergic hypothesis, the deficiency of choline is responsible for AD; therefore, the inhibition of AChE is a lucrative therapeutic strategy for the treatment of AD. Acetylcholinesterase (AChE) is an enzyme that catalyzes the breakdown of the neurotransmitter acetylcholine that is essential for cognition and memory. A large non-redundant data set of 2,570 compounds with reported IC50values against AChE was obtained from ChEMBL and employed in quantitative structure-activity relationship (QSAR) study so as to gain insights on their origin of bioactivity. AChE inhibitors were described by a set of 12 fingerprint descriptors and predictive models were constructed from 100 different data splits using random forest. Generated models affordedR2, ${Q}_{\mathrm{CV }}^{2}$ and ${Q}_{\mathrm{Ext}}^{2}$ values in ranges of 0.66–0.93, 0.55–0.79 and 0.56–0.81 for the training set, 10-fold cross-validated set and external set, respectively. The best model built using the substructure count was selected according to the OECD guidelines and it affordedR2, ${Q}_{\mathrm{CV }}^{2}$ and ${Q}_{\mathrm{Ext}}^{2}$ values of 0.92 ± 0.01, 0.78 ± 0.06 and 0.78 ± 0.05, respectively. Furthermore, Y-scrambling was applied to evaluate the possibility of chance correlation of the predictive model. Subsequently, a thorough analysis of the substructure fingerprint count was conducted to provide informative insights on the inhibitory activity of AChE inhibitors. Moreover, Kennard–Stone sampling of the actives were applied to select 30 diverse compounds for further molecular docking studies in order to gain structural insights on the origin of AChE inhibition. Site-moiety mapping of compounds from the diversity set revealed three binding anchors encompassing both hydrogen bonding and van der Waals interaction. Molecular docking revealed that compounds13,5and28exhibited the lowest binding energies of −12.2, −12.0 and −12.0 kcal/mol, respectively, against human AChE, which is modulated by hydrogen bonding,π–πstacking and hydrophobic interaction inside the binding pocket. These information may be used as guidelines for the design of novel and robust AChE inhibitors.

scholarly journals DCEMRI.jl: A fast, validated, open source toolkit for dynamic contrast enhanced MRI analysis

2014 ◽  
Author(s):  
David S Smith ◽  
Xia Li ◽  
Lori R Arlinghaus ◽  
Thomas E Yankeelov ◽  
E. Brian Welch
Keyword(s):  
Open Source ◽  
Tissue Concentration ◽  
Quantitative Imaging ◽  
Imaging Biomarkers ◽  
Problem Size ◽  
Data Set ◽  
Dynamic Contrast Enhanced ◽  
Contrast Enhanced ◽  
Run Time

We present a fast, validated, open-source toolkit for processing dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data. We validate it against the Quantitative Imaging Biomarkers Alliance (QIBA) Standard and Extended Tofts-Kety phantoms and find near perfect recovery in the absence of noise, with an estimated 10-20x speedup in run time compared to existing tools. To explain the observed trends in the fitting errors, we present an argument about the conditioning of the Jacobian in the limit of small and large parameter values. We also demonstrate its use on an in vivo data set to measure performance on a realistic application. For a 192 x 192 breast image, we achieved run times of < 1 s. Finally, we analyze run times scaling with problem size and find that the run time per voxel scales as O(N1.9), where N is the number of time points in the tissue concentration curve. DCEMRI.jl was much faster than any other analysis package tested and produced comparable accuracy, even in the presence of noise.

scholarly journals Biochemical Characterization of Individual Components of the Allochromatium vinosum DsrMKJOP Transmembrane Complex Aids Understanding of Complex Function In Vivo

2010 ◽  
Vol 192 (24) ◽  
pp. 6369-6377 ◽  
Author(s):  
Fabian Grein ◽  
Inês A. C. Pereira ◽  
Christiane Dahl
Keyword(s):  
Biochemical Characterization ◽  
Sulfur Metabolism ◽  
Complex Function ◽  
Redox Potentials ◽  
Allochromatium Vinosum ◽  
Purple Sulfur Bacterium ◽  
Membrane Anchoring ◽  
Integral Proteins ◽  
First Time

ABSTRACT The DsrMKJOP transmembrane complex has a most important function in dissimilatory sulfur metabolism and consists of cytoplasmic, periplasmic, and membrane integral proteins carrying FeS centers and b- and c-type cytochromes as cofactors. In this study, the complex was isolated from the purple sulfur bacterium Allochromatium vinosum and individual components were characterized as recombinant proteins. The two integral membrane proteins DsrM and DsrP were successfully produced in Escherichia coli C43(DE3) and C41(DE3), respectively. DsrM was identified as a diheme cytochrome b, and the two hemes were found to be in low-spin state. Their midpoint redox potentials were determined to be +60 and +110 mV. Although no hemes were predicted for DsrP, it was also clearly identified as a b-type cytochrome. To the best of our knowledge, this is the first time that heme binding has been experimentally proven for a member of the NrfD protein family. Both cytochromes were partly reduced after addition of a menaquinol analogue, suggesting interaction with quinones in vivo. DsrO and DsrK were both experimentally proven to be FeS-containing proteins. In addition, DsrK was shown to be membrane associated, and we propose a monotopic membrane anchoring for this protein. Coelution assays provide support for the proposed interaction of DsrK with the soluble cytoplasmic protein DsrC, which might be its substrate. A model for the function of DsrMKJOP in the purple sulfur bacterium A. vinosum is presented.

scholarly journals Multiclass Classification of Hepatic Anomalies with Dielectric Properties: From Phantom Materials to Rat Hepatic Tissues

Sensors ◽  
2020 ◽  
Vol 20 (2) ◽  
pp. 530 ◽  
Author(s):  
Tuba Yilmaz
Keyword(s):  
Logistic Regression ◽  
Dielectric Property ◽  
Measurement Error ◽  
Tissue Characterization ◽  
Linear Models ◽  
Hepatic Tissue ◽  
Data Set ◽  
Property Data

Open-ended coaxial probes can be used as tissue characterization devices. However, the technique suffers from a high error rate. To improve this technology, there is a need to decrease the measurement error which is reported to be more than 30% for an in vivo measurement setting. This work investigates the machine learning (ML) algorithms’ ability to decrease the measurement error of open-ended coaxial probe techniques to enable tissue characterization devices. To explore the potential of this technique as a tissue characterization device, performances of multiclass ML algorithms on collected in vivo rat hepatic tissue and phantom dielectric property data were evaluated. Phantoms were used for investigating the potential of proliferating the data set due to difficulty of in vivo data collection from tissues. The dielectric property measurements were collected from 16 rats with hepatic anomalies, 8 rats with healthy hepatic tissues, and in house phantoms. Three ML algorithms, k-nearest neighbors (kNN), logistic regression (LR), and random forests (RF) were used to classify the collected data. The best performance for the classification of hepatic tissues was obtained with 76% accuracy using the LR algorithm. The LR algorithm performed classification with over 98% accuracy within the phantom data and the model generalized to in vivo dielectric property data with 48% accuracy. These findings indicate first, linear models, such as logistic regression, perform better on dielectric property data sets. Second, ML models fitted to the data collected from phantom materials can partly generalize to in vivo dielectric property data due to the discrepancy between dielectric property variability.

scholarly journals Pharmacological curve fitting to analyze cutaneous adrenergic responses

2011 ◽  
Vol 111 (6) ◽  
pp. 1703-1709 ◽  
Author(s):  
Megan M. Wenner ◽  
Thad E. Wilson ◽  
Scott L. Davis ◽  
Nina S. Stachenfeld
Keyword(s):  
Dose Response ◽  
Curve Fitting ◽  
Repeated Measures ◽  
Nonlinear Modeling ◽  
Response Curves ◽  
Data Set ◽  
Sigmoidal Model ◽  
Dose Response Curves ◽  
Cutaneous Vasoconstriction

Although dose-response curves are commonly used to describe in vivo cutaneous α-adrenergic responses, modeling parameters and analyses methods are not consistent across studies. The goal of the present investigation was to compare three analysis methods for in vivo cutaneous vasoconstriction studies using one reference data set. Eight women (22 ± 1 yr, 24 ± 1 kg/m2) were instrumented with three cutaneous microdialysis probes for progressive norepinephrine (NE) infusions (1 × 10−8, 1 × 10−6, 1 × 10−5, 1 × 10−4, and 1 × 10−3 logM). NE was infused alone, co-infused with NG-monomethyl-l-arginine (l-NMMA, 10 mM) or Ketorolac tromethamine (KETO, 10 mM). For each probe, dose-response curves were generated using three commonly reported analyses methods: 1) nonlinear modeling without data manipulation, 2) nonlinear modeling with data normalization and constraints, and 3) percent change from baseline without modeling. Not all data conformed to sigmoidal dose-response curves using analysis 1, whereas all subjects' curves were modeled using analysis 2. When analyzing only curves that fit the sigmoidal model, NE + KETO induced a leftward shift in ED50 compared with NE alone with analyses 1 and 2 ( F test, P < 0.05) but only tended to shift the response leftward with analysis 3 (repeated-measures ANOVA, P = 0.08). Neither maximal vasoconstrictor capacity (Emax) in analysis 1 nor %change CVC change from baseline in analysis 3 were altered by blocking agents. In conclusion, although the overall detection of curve shifts and interpretation was similar between the two modeling methods of curve fitting, analysis 2 produced more sigmoidal curves.

130 A CATALOG OF REFERENCE GENES WITH HIGH, MEDIUM, AND LOW LEVELS OF EXPRESSION DURING BOVINE IN VIVO PRE-IMPLANTATION DEVELOPMENT

2017 ◽  
Vol 29 (1) ◽  
pp. 173
Author(s):  
Z. Jiang ◽  
J. Sun ◽  
S. Marjani ◽  
H. Dong ◽  
X. Zheng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
Target Genes ◽  
Stable Expression ◽  
Bovine Embryo ◽  
Rna Seq ◽  
Rt Pcr ◽  
Data Set ◽  
Low Expression

Appropriate reference genes for accurate normalization in RT-PCR are essential for the study of gene expression. Ideal reference genes should not only have stable expression across stages of embryo development, but also be expressed at comparable levels to the target genes. Using RNA-seq data from in vivo-produced bovine oocytes and embryos from the 2-cell to blastocyst stage (Jiang et al., 2014 BMC Genomics 15, 756), we tried to establish a catalogue of all reference genes for RT-PCR analysis. One-way ANOVA generated 4055 genes that did not differ across stages. To reduce this list, we used the entire RNA-seq data set and first removed genes with a FPKM (fragments per kilobase of transcript per million mapped reads) of <1, and then rescaled each gene’s expression values within a range of 0 to 1. We subsequently calculated the expression variance for each gene across all stages. By assuming that the calculated variances follow a Gaussian distribution and that the majority of the genes do not have a stable expression level, a gene was classified as a reference if its variance significantly deviated (P < 0.05) from these assumptions. We identified 346 potential reference genes, all of which were among the candidates from the ANOVA analysis. We arbitrarily assigned genes in this list to high (FPKM ≥ 100), medium (10 < FPKM < 100), and low expression levels (FPKM ≤ 10), and 37, 154, and 155 genes, respectively, fell into these groups. Surprisingly, none of the commonly used reference genes, such as GAPDH, PPIA, ACTB, PRL15, GUSB, and H3F2A, were identified as being stably expressed across in vivo development. This is consistent with findings of prior RT-PCR studies (Robert et al. 2002 Biol. Reprod. 67, 1465–1472; Ross et al. 2010 Cell Reprogram. 12, 709–717). The following gene ontology terms were significantly enriched for the 346 genes: cell cycle, translation, transport, chromatin, cell division, and metabolic process, indicating that the early embryos maintained constant levels of genes involved in fundamental biological functions. Finally, we performed RT-PCR to validate the RNA-seq results using different bovine in vivo-derived oocytes and embryos (n = 3/stage). We successfully validated 10 selected genes, including those in the high (CS, PGD, and ACTR3), medium (CCT5, MRPL47, COG2, CRT9, and HELLS), and low expression groups (CDC23 and TTF1). In conclusion, we recommend the use of reference genes that are expressed at comparable levels to target genes. This study offers a useful resource to aid in the appropriate selection of reference genes, which will improve the accuracy of quantitative gene expression analyses across bovine embryo pre-implantation development.

An Elaborate Data Set for Mechanical Characterization of the Foot

2008 ◽  
Author(s):  
Pavana Sirimamilla ◽  
Ahmet Erdemir ◽  
Antonie J. van den Bogert ◽  
Jason P. Halloran
Keyword(s):  
Mechanical Response ◽  
Experimental Testing ◽  
Experimental Tests ◽  
Shear Loading ◽  
Data Set ◽  
Material Response ◽  
Heel Pad ◽  
Biaxial Tests

Experimental testing of cadaver specimens is a useful means to quantify structural and material response of tissue and passive joint properties against applied loading[1,4]. Very often, specific material response (i.e., stress-strain behavior of a ligament or plantar tissue) has been the goal of experimental testing and is accomplished with uniaxial and/or biaxial tests of prepared tissue specimens with uniform geometries[2,5]. Material properties can then be calculated directly and if testing data involves individual sets of multiple loading modes (e.g. compression only, shear only, volumetric) an accurate representation of the global response of the specimen may be possible. In foot biomechanics, however, it is practically impossible to perform isolated mechanical testing in this manner. The structural response, therefore the stiffness characteristics, of the foot have been quantified, usually using a dominant loading mode: e.g., whole foot compression [6], heel pad indentation [3]. This approach ignores the complexity of most in vivo loading conditions, in which whole foot deformation involves interactions between compression, shear (e.g. heel pad) and tension (e.g. ligaments). Therefore, the purpose of this study was to quantify the mechanical response of a cadaver foot specimen subjected to compression and anterior-posterior (AP) shear loading of isolated heel and forefoot regions as well as whole foot compression. Results from the experimental tests represent a novel methodology to quantify a complete structural biomechanical response. Combined with medical imaging, followed by inverse finite element (FE) analysis, the data may also serve for material characterization of foot tissue.

WE-C-217BCD-03: Restricted Data Set Reconstruction Based on Respiration Quality to Improve Prospectively Gated in Vivo Micro-CT of Mice

2012 ◽  
Vol 39 (6Part27) ◽  
pp. 3949-3950
Author(s):  
L Burk ◽  
Y Lee ◽  
J Lu ◽  
O Zhou
Keyword(s):  
Micro Ct ◽  
Data Set
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