scholarly journals Three-Dimensional Computer Model of Brainstem Respiratory Neuronal Circuits - Application for Research in Respirology

2013 ◽  
Vol 13 (Supplement-1) ◽  
pp. 7-14
Author(s):  
S. Gavliakova ◽  
J. Plevkova ◽  
J. Jakus ◽  
I. Poliacek
Keyword(s):  
Programming Languages ◽  
Computer Model ◽  
Ex Vivo ◽  
Three Dimensional ◽  
Neuronal Circuits ◽  
Spatial Image ◽  
The Matrix ◽  
Computationally Intensive ◽  
High Level

Abstract Methods that had been applied to study central neuronal circuits regulating cough and respiratory reflexes so far rely on recording performed in vivo, ex vivo, micro injecting and lesion methods. Based on the available data it is clear that this network is complicated, multilevel, holarchical, undergoing reconfiguration under afferent inputs. For many students and researchers it is complicated to get a virtual spatial image of these cooperating neuronal populations. The project was aimed to create graphical three-dimensional computer model of the brainstem using environment MATLAB and the matrix algebra to visualize neuron localization within the brainstem. Relevant data for the model had been taken from recent and also former research papers published in particular areas. This model may help scientists to visualize groups of neurons, help them to find targets for microinjecting or lesion studies together with stereotaxic positioning. The model is upgradeable and highly flexible for future use, research and teaching applications in MATLAB environment. MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages

Abstract 2876: Early Retention and Subsequent Engraftment of Transplanted Progenitor Cells is Improved by Delivery within Collagen Matrix

Circulation ◽  
2008 ◽  
Vol 118 (suppl_18) ◽  
Author(s):  
Yan Zhang ◽  
Marc Lamoureux ◽  
Stephanie Thorn ◽  
Vincent Chan ◽  
Joel Price ◽  
...  
Keyword(s):  
Cell Therapy ◽  
Progenitor Cells ◽  
Pet Imaging ◽  
Ex Vivo ◽  
Collagen Matrix ◽  
Cell Labeling ◽  
Type I ◽  
The Matrix ◽  
Early Retention

Background: To investigate the mechanisms involved in the potentiation of cell therapy by delivery matrices, we evaluated the retention and engraftment of transplanted human circulating progenitor cells (CPCs) injected in a collagen matrix by using in vivo positron emission tomography (PET) imaging, ex vivo biodistribution, and immunohistochemistry. Methods: CPCs were labeled with 18 F-FDG and injected with or without a collagen type I-based matrix in the ischemic hindlimb muscle (IM) of rats (2x10 6 cells; n=15/group). Localization of cells was acquired by PET imaging (15 min) at 150 min post-injection. In addition, radionuclide biodistribution, immunofluorescence, and immunohistochemical examination of transplanted CPCs were performed at up to 14 days. Results: Cell labeling efficiency was CPC-concentration dependent (r=0.61, p <0.001), but not 18 F-FDG-dose dependent. Labeled CPCs exhibited excellent short-term stability and viability. Persistence of 18 F-FDG radioactivity in cells was markedly greater than non-specific retention in the matrix. Wholebody (WB) PET images revealed better CPC retention in the IM and less non-specific leakage to other tissues when CPCs were delivered within the matrix (IM/WB retention ratio of 43.9±8.2%), compared to cells injected alone (22.3±10.4%; p =0.040) and to 18 F-FDG injected with or without the matrix (9.7±5.5% and 11.0±5.5%, respectively; p <0.005). Radioactivity biodistribution confirmed that accumulation was increased (by 92.5%; p =0.024) in the IM and reduced (by 1.1 to 23.8%; p <0.05) in non-specific tissues when cells were injected within the matrix, compared to cells injected alone. Anti-human mitochondria staining showed increased cell retention in the IM with use of matrices (3.0±2.1%) versus cells only (1.9±0.8%; p =0.048). At 14 days the number of CD31 + transplanted human cells was greater (1.6±0.1%) when injected within the matrix than injected alone (0.7±0.1%; p =0.004). Conclusions: Collagen-based delivery matrices improve the early retention of transplanted CPCs, which in turn favors subsequent cell engraftment in the ischemic tissue. This mechanism conferred by the matrix has potential implications for the optimization of cell therapy at the early stages after cell delivery.

scholarly journals The NADPH Oxidase Nox4 Controls Macrophage Polarization in an NFκB-Dependent Manner

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
V. Helfinger ◽  
K. Palfi ◽  
A. Weigert ◽  
K. Schröder
Keyword(s):  
Ex Vivo ◽  
Macrophage Polarization ◽  
Dependent Manner ◽  
Oxygen Species ◽  
Superoxide Anions ◽  
Wild Type ◽  
Macrophage Population ◽  
The Family ◽  
High Level

The family of NADPH oxidases represents an important source of reactive oxygen species (ROS) within the cell. Nox4 is a special member of this family as it constitutively produces H2O2 and its loss promotes inflammation. A major cellular component of inflammation is the macrophage population, which can be divided into several subpopulations depending on their phenotype, with proinflammatory M(LPS+IFNγ) and wound-healing M(IL4+IL13) macrophages being extremes of the functional spectrum. Whether Nox4 is expressed in macrophages is discussed controversially. Here, we show that macrophages besides a high level of Nox2 indeed express Nox4. As Nox4 contributes to differentiation of many cells, we hypothesize that Nox4 plays a role in determining the polarization and the phenotype of macrophages. In bone marrow-derived monocytes, ex vivo treatment with LPS/IFNγ or IL4/IL13 results in polarization of the cells into M(LPS+IFNγ) or M(IL4+IL13) macrophages, respectively. In this ex vivo setting, Nox4 deficiency reduces M(IL4+IL13) polarization and forces M(LPS+IFNγ). Nox4-/- M(LPS+IFNγ)-polarized macrophages express more Nox2 and produce more superoxide anions than wild type M(LPS+IFNγ)-polarized macrophages. Mechanistically, Nox4 deficiency reduces STAT6 activation and promotes NFκB activity, with the latter being responsible for the higher level of Nox2 in Nox4-deficient M(LPS+IFNγ)-polarized macrophages. According to those findings, in vivo, in a murine inflammation-driven fibrosarcoma model, Nox4 deficiency forces the expression of proinflammatory genes and cytokines, accompanied by an increase in the number of proinflammatory Ly6C+ macrophages in the tumors. Collectively, the data obtained in this study suggest an anti-inflammatory role for Nox4 in macrophages. Nox4 deficiency results in less M(IL4+IL13) polarization and suppression of NFκB activity in monocytes.

An Exploratory Framework for Combining CFD Analysis and Evolutionary Optimization Into a Single Integrated Computational Environment

2011 ◽  
Author(s):  
Douglas S. McCorkle ◽  
Kenneth M. Bryden
Keyword(s):  
Programming Languages ◽  
Transport System ◽  
Flow Analysis ◽  
Three Dimensional ◽  
Software Framework ◽  
Computational Engineering ◽  
Geometric Models ◽  
Computational Environment ◽  
Computational Fluid Dynamics Cfd ◽  
High Level

Several recent reports and workshops have identified integrated computational engineering as an emerging technology with the potential to transform engineering design. The goal is to integrate geometric models, analyses, simulations, optimization and decision-making tools, and all other aspects of the engineering process into a shared, interactive computer-generated environment that facilitates multidisciplinary and collaborative engineering. While integrated computational engineering environments can be constructed from scratch with high-level programming languages, the complexity of these proposed environments makes this type of approach prohibitively slow and expensive. Rather, a high-level software framework is needed to provide the user with the capability to construct an application in an intuitive manner using existing models and engineering tools with minimal programming. In this paper, we present an exploratory open source software framework that can be used to integrate the geometric models, computational fluid dynamics (CFD), and optimization tools needed for shape optimization of complex systems. This framework is demonstrated using the multiphase flow analysis of a complete coal transport system for an 800 MW pulverized coal power station. The framework uses engineering objects and three-dimensional visualization to enable the user to interactively design and optimize the performance of the coal transport system.

scholarly journals Video-rate multimodal multiphoton imaging and three-dimensional characterization of cellular dynamics in wounded skin

2020 ◽  
Vol 13 (02) ◽  
pp. 2050007
Author(s):  
Joanne Li ◽  
Madison N. Wilson ◽  
Andrew J. Bower ◽  
Marina Marjanovic ◽  
Eric J. Chaney ◽  
...  
Keyword(s):  
Cell Tracking ◽  
Skin Diseases ◽  
Ex Vivo ◽  
Three Dimensional ◽  
Biological Information ◽  
Cellular Dynamics ◽  
Multiphoton Imaging ◽  
Cellular Events ◽  
Analysis Platform

To date, numerous studies have been performed to elucidate the complex cellular dynamics in skin diseases, but few have attempted to characterize these cellular events under conditions similar to the native environment. To address this challenge, a three-dimensional (3D) multimodal analysis platform was developed for characterizing in vivo cellular dynamics in skin, which was then utilized to process in vivo wound healing data to demonstrate its applicability. Special attention is focused on in vivo biological parameters that are difficult to study with ex vivo analysis, including 3D cell tracking and techniques to connect biological information obtained from different imaging modalities. These results here open new possibilities for evaluating 3D cellular dynamics in vivo, and can potentially provide new tools for characterizing the skin microenvironment and pathologies in the future.

scholarly journals Characterization of the Cellular Reaction to a Collagen-Based Matrix: An In Vivo Histological and Histomorphometrical Analysis

Materials ◽  
2020 ◽  
Vol 13 (12) ◽  
pp. 2730 ◽  
Author(s):  
Samuel Ebele Udeabor ◽  
Carlos Herrera-Vizcaíno ◽  
Robert Sader ◽  
C. James Kirkpatrick ◽  
Sarah Al-Maawi ◽  
...  
Keyword(s):  
Mononuclear Cells ◽  
Ex Vivo ◽  
Test Group ◽  
Tissue Reaction ◽  
Implantation Site ◽  
Control Group ◽  
The Matrix ◽  
Tissue Reactions ◽  
Post Implantation

The permeability and inflammatory tissue reaction to Mucomaix® matrix (MM), a non- cross-linked collagen-based matrix was evaluated in both ex vivo and in vivo settings. Liquid platelet rich fibrin (PRF), a blood concentrate system, was used to assess its capacity to absorb human proteins and interact with blood cells ex vivo. In the in vivo aspect, 12 Wister rats had MM implanted subcutaneously, whereas another 12 rats (control) were sham-operated without biomaterial implantation. On days 3, 15 and 30, explantation was completed (four rats per time-point) to evaluate the tissue reactions to the matrix. Data collected were statistically analyzed using analysis of variance (ANOVA) and Tukey multiple comparisons tests (GraphPad Prism 8). The matrix absorbed the liquid PRF in the ex vivo study. Day 3 post-implantation revealed mild tissue inflammatory reaction with presence of mononuclear cells in the implantation site and on the biomaterial surface (mostly CD68-positive macrophages). The control group at this stage had more mononuclear cells than the test group. From day 15, multinucleated giant cells (MNGCs) were seen in the implantation site and the outer third of the matrix with marked increase on day 30 and spread to the matrix core. The presence of these CD68-positive MNGCs was associated with significant matrix vascularization. The matrix degraded significantly over the study period, but its core was still visible as of day 30 post-implantation. The high permeability and fast degradation properties of MM were highlighted.

scholarly journals A Uniform Architecture Design for Accelerating 2D and 3D CNNs on FPGAs

Electronics ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 65 ◽  
Author(s):  
Zhiqiang Liu ◽  
Paul Chow ◽  
Jinwei Xu ◽  
Jingfei Jiang ◽  
Yong Dou ◽  
...  
Keyword(s):  
Design Space ◽  
State Of The Art ◽  
Three Dimensional ◽  
Architecture Design ◽  
Computer Vision Applications ◽  
Computationally Intensive ◽  
On Chip ◽  
3D Cnn ◽  
High Level ◽  
2D And 3D

Three-dimensional convolutional neural networks (3D CNNs) have gained popularity in many complicated computer vision applications. Many customized accelerators based on FPGAs are proposed for 2D CNNs, while very few are for 3D CNNs. Three-D CNNs are far more computationally intensive and the design space for 3D CNN acceleration has been further expanded since one more dimension is introduced, making it a big challenge to accelerate 3D CNNs on FPGAs. Motivated by the finding that the computation patterns of 2D and 3D CNNs are very similar, we propose a uniform architecture design for accelerating both 2D and 3D CNNs in this paper. The uniform architecture is based on the idea of mapping convolutions to matrix multiplications. A customized mapping module is developed to generate the feature matrix tilings with no need to store the entire enlarged feature matrix on-chip or off-chip, a splitting strategy is adopted to reconstruct a convolutional layer to adapt to the on-chip memory capacity, and a 2D multiply-and-accumulate (MAC) array is adopted to compute matrix multiplications efficiently. For demonstration, we implement an accelerator prototype with a high-level synthesis (HLS) methodology on a Xilinx VC709 board and test the accelerator on three typical CNN models: AlexNet, VGG16, and C3D. Experimental results show that the accelerator achieves state-of-the-art throughput performance on both 2D and 3D CNNs, with much better energy efficiency than the CPU and GPU.

α7β1-Integrin regulates mechanotransduction and prevents skeletal muscle injury

2006 ◽  
Vol 290 (6) ◽  
pp. C1660-C1665 ◽  
Author(s):  
Marni D. Boppart ◽  
Dean J. Burkin ◽  
Stephen J. Kaufman
Keyword(s):  
Skeletal Muscle ◽  
Muscle Damage ◽  
Intracellular Signaling ◽  
Ex Vivo ◽  
Negative Regulator ◽  
Blue Dye ◽  
The Matrix ◽  
Mitogen Activated Protein ◽  
Exercise Induced

α7β1-Integrin links laminin in the extracellular matrix with the cell cytoskeleton and therein mediates transduction of mechanical forces into chemical signals. Muscle contraction and stretching ex vivo result in activation of intracellular signaling molecules that are integral to postexercise injury responses. Because α7β1-integrin stabilizes muscle and provides communication between the matrix and cytoskeleton, the role of this integrin in exercise-induced cell signaling and skeletal muscle damage was assessed in wild-type and transgenic mice overexpressing the α7BX2 chain. We report here that increasing α7β1-integrin inhibits phosphorylation of molecules associated with muscle damage, including the mitogen-activated protein kinases (JNK, p38, and ERK), following downhill running. Likewise, activation of molecules associated with hypertrophy (AKT, mTOR, and p70S6k) was diminished in mice overexpressing integrin. While exercise resulted in Evans blue dye-positive fibers, an index of muscle damage, increased integrin protected mice from injury. Moreover, exercise leads to an increase in α7β1 protein. These experiments provide the first evidence that α7β1-integrin is a negative regulator of mechanotransduction in vivo and provides resistance to exercise-induced muscle damage.

Prolonged High-Level Detection of Retrovirally Marked Hematopoietic Cells in Nonhuman Primates after Transduction of CD34+ Progenitors Using Clinically Feasible Methods.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 1137-1137
Author(s):  
Tong Wu ◽  
Hyeoung Joon Kim ◽  
Stephanie E. Sellers ◽  
Kristin E. Meade ◽  
Brian A. Agricola ◽  
...  
Keyword(s):  
Stem Cell ◽  
Gene Transfer ◽  
Nonhuman Primates ◽  
Ex Vivo ◽  
Hematopoietic Stem ◽  
Retroviral Transduction ◽  
Colony Pcr ◽  
High Level

Abstract Low-level retroviral transduction and engraftment of hematopoietic long-term repopulating cells in large animals and humans remain primary obstacles to the successful application of hematopoietic stem cell(HSC) gene transfer in humans. Recent studies have reported improved efficiency by including stromal cells(STR), or the fibronectin fragment CH-296(FN), and various cytokines such as flt3 ligand(FLT) during ex vivo culture and transduction in nonhuman primates. In this work, we extend our studies using the rhesus competitive repopulation model to further explore optimal and transduction in the presence of either preformed autologous STR or immobilized FN. Long-term clinically relevant gene marking levels in multiple hematopoietic lineages from both conditions were demonstrated in vivo by semiquantitative PCR, colony PCR, and genomic Southern blotting, suggesting that FN could replace STR in ex vivo transduction protocols. Second, we compared transduction on FN in the presence of IL-3, IL-6, stem cell factor(SCF), and FLT(our best cytokine combination in prior studies)with a combination of megakaryocyte growth and development factor(MGDF), SCF, and FLT. Gene marking levels were equivalent in these animals, with no significant effect on retroviral gene transfer efficiency assessed in vivo by the replacement of IL-3 and IL-6 with MGDF. Our results indicate that SCF/G-CSF-mobilized PB CD34+ cells are transduced with equivalent efficiency in the presence of either STR or FN, with stable long-term marking of multiple lineages at levels of 10–15% and transient marking as high as 54%. These results represent an advance in the field of HSC gene transfer using methods easily applied in the clinical setting.

Newmouse models of melanoma metastasis and differences in brain tropism and metastatic growth pattern.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. e19015-e19015
Author(s):  
Amr M. Morsi ◽  
Avital Gazial-Sovran ◽  
Hana Baig ◽  
Robert S. Kerbel ◽  
John Golfinos ◽  
...  
Keyword(s):  
Brain Metastases ◽  
Ex Vivo ◽  
Three Dimensional ◽  
Melanoma Cells ◽  
Melanoma Metastasis ◽  
Optimal Method ◽  
In Vivo Models ◽  
Dismal Prognosis ◽  
Intracardiac Injection

e19015 Background: 75% of patients with metastatic melanoma develop brain metastases (B-mets). Such patients show dismal prognosis with a median survival of < 6 months. Scarcity of clinically relevant in vivo models has hindered melanoma B-met studies. We compared the in vivo dissemination upon ultrasound (u/s) guided intracardiac injection of B16F10 cells to 131/4-5B1 (hereafter 5B1), a WM239A subclone with enhanced brain tropism. We also implemented an ex vivo MRI protocol as a high throughput three dimensional approach for characterizing B-mets penetrance and growth. Methods: B16-F10 or 5B1 melanoma cells were injected in C57BL/6J mice (n=40) or athymic/nude mice (n=40) respectively using u/s-guided intracardiac injection. Upon weight loss, mice were euthanized, and heads prepared for ex vivo imaging. All µMRI experiments were performed with a 7T Bruker Avance II console. The protocol consisted of (110-mm)3 isotropic T1-, T2- and T2*-weighted sequences. Results: Our ex vivo MRI recapitulates the clinical radiological T1 and T2 brightening as well as susceptibility-induced T2* darkening effect of melanoma. The B16F10 model revealed exclusive ventricular and leptomeningeal spread while the 5B1 model showed parenchymal lesions. In addition, 90% of the 5B1 mice with brain tumors showed multiple lesions (3-16) vs. 18% in the B16F10 model (1- 3). Finally, 3D volume studies revealed a higher B-met penetrance (68% vs. 18%), delayed onset of tumor detection (earliest-day 27 vs. day 15) post-injection and a slower growth rate of 5B1 brain metastases compared to B16F10 tumors. Conclusions: Our results suggest that u/s-guided intracardiac injection of melanoma cells is an optimal method to capture the cells’ spontaneous dissemination pattern (or site-specific tropism) and that the 5B1 model is a more clinically relevant model of melanoma B-met for preclinical studies.

Sign in / Sign up

Export Citation Format

Share Document