scholarly journals Microstructural organizational patterns in the human corticostriatal system

2012 ◽  
Vol 107 (11) ◽  
pp. 2984-2995 ◽  
Author(s):  
Timothy D. Verstynen ◽  
David Badre ◽  
Kevin Jarbo ◽  
Walter Schneider
Keyword(s):  
Basal Ganglia ◽  
Computational Models ◽  
Ex Vivo ◽  
Local Level ◽  
Fiber Tractography ◽  
Asymmetry Of Information ◽  
Cortical Areas ◽  
Posterior Direction ◽  
Organizational Patterns

The axons that project into the striatum are known to segregate according to macroscopic cortical systems; however, the within-region organization of these fibers has yet to be described in humans. We used in vivo fiber tractography, in neurologically healthy adults, to map white matter bundles that originate in different neocortical areas, navigate complex fiber crossings, and project into the striatum. As expected, these fibers were generally segregated according to cortical origin. Within a subset of pathways, a patched pattern of inputs was observed, consistent with previous ex vivo histological studies. In projections from the prefrontal cortex, we detected a topography in which fibers from rostral prefrontal areas projected mostly to rostral parts of the striatum and vice versa for inputs originating in caudal cortical areas. Importantly, within this prefrontal system there was also an asymmetry in the subset of divergent projections, with more fibers projecting in a posterior direction than anterior. This asymmetry of information projecting into the basal ganglia was predicted by previous network-level computational models. A rostral-caudal topography was also present at the local level in otherwise somatotopically organized fibers projecting from the motor cortex. This provides clear evidence that the longitudinal organization of input fields, observed at the macroscopic level across cortical systems, is also found at the microstructural scale at which information is segregated as it enters the human basal ganglia.

A New Hypothesis for Human Atherosclerotic Plaque Progression Based on Serial In Vivo MRI and Computational Modeling Method

2007 ◽  
Author(s):  
Sayan Mondal ◽  
Chun Yang ◽  
Joseph D. Petruccelli ◽  
Chun Yuan ◽  
Fei Liu ◽  
...  
Keyword(s):  
Shear Stress ◽  
Wall Thickness ◽  
Computational Models ◽  
Ex Vivo ◽  
Maximum Principal Stress ◽  
Magnetic Resonance Images ◽  
Shear Stresses ◽  
Flow Shear ◽  
Flow Shear Stress

It has been well-accepted that atherosclerosis initiation and progression correlate positively with low and oscillating flow wall shear stresses. However, this shear stress mechanism cannot fully explain why advanced plaques continue to grow under elevated flow shear stress conditions. Our previous investigations using 3D computational models with fluid-structure interactions (FSI) based on in vivo/ex vivo magnetic resonance images (MRI) of human carotid atherosclerotic plaques indicated that there is a negative correlation between advanced plaque wall thickness and structural maximum principal stress (Stress-P1) in the plaque and a positive correlation between plaque wall thickness and flow shear stress [3].

scholarly journals Models of tendon development and injury

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Sophia K. Theodossiou ◽  
Nathan R. Schiele
Keyword(s):  
Computational Models ◽  
Ex Vivo ◽  
Current Model ◽  
Stem Cell Differentiation ◽  
Tendon Injury ◽  
Model Systems ◽  
Tendon Development ◽  
Key Aspects

AbstractTendons link muscle to bone and transfer forces necessary for normal movement. Tendon injuries can be debilitating and their intrinsic healing potential is limited. These challenges have motivated the development of model systems to study the factors that regulate tendon formation and tendon injury. Recent advances in understanding of embryonic and postnatal tendon formation have inspired approaches that aimed to mimic key aspects of tendon development. Model systems have also been developed to explore factors that regulate tendon injury and healing. We highlight current model systems that explore developmentally inspired cellular, mechanical, and biochemical factors in tendon formation and tenogenic stem cell differentiation. Next, we discuss in vivo, in vitro, ex vivo, and computational models of tendon injury that examine how mechanical loading and biochemical factors contribute to tendon pathologies and healing. These tendon development and injury models show promise for identifying the factors guiding tendon formation and tendon pathologies, and will ultimately improve regenerative tissue engineering strategies and clinical outcomes.

scholarly journals Mapping Short Association Fibers in the Early Cortical Visual Processing Stream Using In Vivo Diffusion Tractography

2020 ◽  
Vol 30 (8) ◽  
pp. 4496-4514 ◽  
Author(s):  
Fakhereh Movahedian Attar ◽  
Evgeniya Kirilina ◽  
Daniel Haenelt ◽  
Kerrin J Pine ◽  
Robert Trampel ◽  
...  
Keyword(s):  
Human Brain ◽  
Visual Processing ◽  
Repeated Measurements ◽  
Fiber Tractography ◽  
Cortical Areas ◽  
Brain Connectome ◽  
Cortical Visual Processing ◽  
Association Fibers ◽  
Fiber Connectivity

Abstract Short association fibers (U-fibers) connect proximal cortical areas and constitute the majority of white matter connections in the human brain. U-fibers play an important role in brain development, function, and pathology but are underrepresented in current descriptions of the human brain connectome, primarily due to methodological challenges in diffusion magnetic resonance imaging (dMRI) of these fibers. High spatial resolution and dedicated fiber and tractography models are required to reliably map the U-fibers. Moreover, limited quantitative knowledge of their geometry and distribution makes validation of U-fiber tractography challenging. Submillimeter resolution diffusion MRI—facilitated by a cutting-edge MRI scanner with 300 mT/m maximum gradient amplitude—was used to map U-fiber connectivity between primary and secondary visual cortical areas (V1 and V2, respectively) in vivo. V1 and V2 retinotopic maps were obtained using functional MRI at 7T. The mapped V1–V2 connectivity was retinotopically organized, demonstrating higher connectivity for retinotopically corresponding areas in V1 and V2 as expected. The results were highly reproducible, as demonstrated by repeated measurements in the same participants and by an independent replication group study. This study demonstrates a robust U-fiber connectivity mapping in vivo and is an important step toward construction of a more complete human brain connectome.

scholarly journals Fluid Structural Analysis of Urine Flow in a Stented Ureter

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
J. Carlos Gómez-Blanco ◽  
F. Javier Martínez-Reina ◽  
Domingo Cruz ◽  
J. Blas Pagador ◽  
Francisco M. Sánchez-Margallo ◽  
...  
Keyword(s):  
Computational Models ◽  
Mechanical Characterization ◽  
Ex Vivo ◽  
Biological Tissues ◽  
Urine Flow ◽  
Computational Environment ◽  
Computational Fluid Dynamics Cfd

Many urologists are currently studying new designs of ureteral stents to improve the quality of their operations and the subsequent recovery of the patient. In order to help during this design process, many computational models have been developed to simulate the behaviour of different biological tissues and provide a realistic computational environment to evaluate the stents. However, due to the high complexity of the involved tissues, they usually introduce simplifications to make these models less computationally demanding. In this study, the interaction between urine flow and a double-J stented ureter with a simplified geometry has been analysed. The Fluid-Structure Interaction (FSI) of urine and the ureteral wall was studied using three models for the solid domain: Mooney-Rivlin, Yeoh, and Ogden. The ureter was assumed to be quasi-incompressible and isotropic. Data obtained in previous studies from ex vivo and in vivo mechanical characterization of different ureters were used to fit the mentioned models. The results show that the interaction between the stented ureter and urine is negligible. Therefore, we can conclude that this type of models does not need to include the FSI and could be solved quite accurately assuming that the ureter is a rigid body and, thus, using the more simple Computational Fluid Dynamics (CFD) approach.

Determination of Real Time In-Vivo Cartilage Contact Deformation in the Ankle Joint

2007 ◽  
Author(s):  
Guoan Li ◽  
Lu Wan ◽  
Michal Kozanek
Keyword(s):  
Computational Models ◽  
Ex Vivo ◽  
Loading Conditions ◽  
Contact Deformation ◽  
Normal Cartilage ◽  
Physiological Loading ◽  
Contact Data ◽  
Biomechanical Responses

Knowledge of in-vivo articular cartilage contact deformation is critical for understanding normal cartilage function and the etiology of osteoarthritis (2,8). This knowledge is also instrumental for design of ex-vivo experiment to investigate the chondrocyte mechanotransductions under physiological loading conditions (7). Further, in-vivo cartilage contact data is necessary for validation of 3D computational models used to predict biomechanical responses of the articular joints (1,5). However, due to the complexity of in-vivo joint loading conditions as well as the complicated joint geometry, little information is available on in-vivo cartilage deformation in literature (9). In-vivo cartilage deformation as a function of loading history has not been delineated.

scholarly journals iAmideV-Deep: Valine Amidation Site Prediction in Proteins Using Deep Learning and Pseudo Amino Acid Compositions

Symmetry ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 560
Author(s):  
Sheraz Naseer ◽  
Rao Faizan Ali ◽  
Amgad Muneer ◽  
Suliman Mohamed Fati
Keyword(s):  
Amino Acid ◽  
Computational Models ◽  
Ex Vivo ◽  
Biologically Active ◽  
Peptide Sequence ◽  
Post Translational Modification ◽  
Amino Acid Compositions ◽  
Efficient Alternative

Amidation is an important post translational modification where a peptide ends with an amide group (–NH2) rather than carboxyl group (–COOH). These amidated peptides are less sensitive to proteolytic degradation with extended half-life in the bloodstream. Amides are used in different industries like pharmaceuticals, natural products, and biologically active compounds. The in-vivo, ex-vivo, and in-vitro identification of amidation sites is a costly and time-consuming but important task to study the physiochemical properties of amidated peptides. A less costly and efficient alternative is to supplement wet lab experiments with accurate computational models. Hence, an urgent need exists for efficient and accurate computational models to easily identify amidated sites in peptides. In this study, we present a new predictor, based on deep neural networks (DNN) and Pseudo Amino Acid Compositions (PseAAC), to learn efficient, task-specific, and effective representations for valine amidation site identification. Well-known DNN architectures are used in this contribution to learn peptide sequence representations and classify peptide chains. Of all the different DNN based predictors developed in this study, Convolutional neural network-based model showed the best performance surpassing all other DNN based models and reported literature contributions. The proposed model will supplement in-vivo methods and help scientists to determine valine amidation very efficiently and accurately, which in turn will enhance understanding of the valine amidation in different biological processes.

scholarly journals Nanoscale patterning of in vitro neuronal circuits

2021 ◽  
Author(s):  
János Vörös ◽  
Sean Weaver ◽  
Jose C. Mateus ◽  
Paulo Aguiar ◽  
Dirk van Swaay ◽  
...  
Keyword(s):  
Computational Models ◽  
Synapse Formation ◽  
Ex Vivo ◽  
Axon Growth ◽  
Neuronal Circuits ◽  
Calcium Indicator ◽  
The Difference ◽  
Pass Through

Methods for patterning neurons in vitro have gradually improved and are used to investigate questions difficult to address in or ex vivo. Though these techniques guide axons between groups of neurons, multiscale control of neuronal connectivity, from circuits to synapses, is yet to be achieved in vitro. As studying neuronal circuits with synaptic resolution in vivo poses significant challenges, an in vitro alternative could serve as a testbed for in vivo experiments or as a platform for validating biophysical and computational models. In this work we use a combination of electron beam and photolithography to create polydimethylsiloxane (PDMS) structures with features ranging from 150 nanometers to a few millimeters. Leveraging the difference between average axon and dendritic spine diameters, we restrict axon growth while allowing spines to pass through nanochannels to guide synapse formation between small groups of neurons (i.e. nodes). We show this technique can be used to generate large numbers of isolated feed-forward circuits where connections between nodes are restricted to regions connected by nanochannels. Using a genetically encoded calcium indicator in combination with fluorescently tagged post synaptic protein, PSD-95, we demonstrate functional synapses can form in this region. Although more work needs to be done to control connectivity in vitro, we believe this is a significant step in that direction.

scholarly journals Dysregulation of the basal ganglia indirect pathway prior to cell loss in the Q175 mouse model of Huntington's disease

2021 ◽  
Author(s):  
Joshua Callahan ◽  
David L Wokosin ◽  
Mark D Bevan
Keyword(s):  
Basal Ganglia ◽  
Huntington's Disease ◽  
Huntington’S Disease ◽  
Ex Vivo ◽  
Cell Loss ◽  
Projection Neurons ◽  
Indirect Pathway ◽  
Cortical Input ◽  
Psychomotor Symptoms

The psychomotor symptoms of Huntington's disease (HD) are linked to degeneration of the basal ganglia indirect pathway. To determine how this pathway is perturbed prior to cell loss, optogenetic- and reporter-guided electrophysiological interrogation approaches were applied to early symptomatic 6-month-old Q175 HD mice. Although cortical activity was unaffected, indirect pathway striatal projection neurons were hypoactive in vivo, consistent with reduced cortical input strength and dendritic excitability. Downstream parvalbumin-expressing prototypic external globus pallidus (GPe) neurons were hyperactive in vivo and exhibited elevated autonomous firing ex vivo. Optogenetic inhibition of prototypic GPe neurons ameliorated the abnormal hypoactivity of postsynaptic subthalamic nucleus (STN) and putative arkypallidal neurons in vivo. In contrast to STN neurons, autonomous arkypallidal activity was unimpaired ex vivo. Together with previous studies, these findings demonstrate that basal ganglia indirect pathway neurons are highly dysregulated in Q175 mice through changes in presynaptic activity and/or intrinsic properties 6-12 months before cell loss.

Sudden Death in Coronary Artery Disease are Associated With High 3D Critical Plaque Wall Stress: A 3D Multi-Patient FSI Study Based on Ex Vivo MRI of Coronary Plaques

2013 ◽  
Author(s):  
Xueying Huang ◽  
Chun Yang ◽  
Jie Zheng ◽  
Richard Bach ◽  
David Muccigrosso ◽  
...  
Keyword(s):  
Computational Models ◽  
Plaque Rupture ◽  
Ex Vivo ◽  
Carotid Artery Disease ◽  
Wall Stress ◽  
Carotid Plaques ◽  
Group 2 ◽  
Artery Disease ◽  
Atherosclerotic Plaque Rupture

Atherosclerotic plaque rupture is the primary cause of cardiovascular clinical events such as heart attack and stroke. It is commonly believed that plaque rupture may be linked to critical mechanical conditions. Image-based computational models of vulnerable plaques have been introduced seeking critical mechanical indicators which may be used to identify potential sites of rupture [1–5]. A recent study by Tang et al. [4] using in vivo MRI-based 3D fluid-structure interaction (FSI) models for human carotid plaques with and without rupture reported that higher critical plaque wall stress (CPWS) values were associated with plaques with rupture, compared to those without rupture. However, existing computational plaque models are mostly for carotid plaques based on MRI data. Comparable similar studies for coronary plaques are lacking in the current literature. In this study, 3D computational multi-component models with FSI were constructed to identified 3D critical plaque wall stress, critical flow shear stress (CFSS) based on ex vivo MRI data of coronary plaques acquired from 10 patients. The patients were split into 2 groups: patients died in carotid artery disease (CAD, Group 1, 6 patients) and non CAD (Group 2, 4 patients). The possible link between CPWS and death in CAD was investigated by comparing the CPWS values from the two groups.

scholarly journals In vivo 3D Reconstruction of the Human Pallidothalamic and Nigrothalamic Pathways With Super-Resolution 7T MR Track Density Imaging and Fiber Tractography

2021 ◽  
Vol 15 ◽  
Author(s):  
Dae-Hyuk Kwon ◽  
Sun Ha Paek ◽  
Young-Bo Kim ◽  
Haigun Lee ◽  
Zang-Hee Cho
Keyword(s):  
Basal Ganglia ◽  
3D Reconstruction ◽  
Human Brain ◽  
Super Resolution ◽  
Track Density ◽  
7 Tesla ◽  
Fiber Tractography ◽  
Resolution Limit ◽  
Magnetic Resonance Imaging Mri

The output network of the basal ganglia plays an important role in motor, associative, and limbic processing and is generally characterized by the pallidothalamic and nigrothalamic pathways. However, these connections in the human brain remain difficult to elucidate because of the resolution limit of current neuroimaging techniques. The present study aimed to investigate the mesoscopic nature of these connections between the thalamus, substantia nigra pars reticulata, and globus pallidus internal segment using 7 Tesla (7T) magnetic resonance imaging (MRI). In this study, track-density imaging (TDI) of the whole human brain was employed to overcome the limitations of observing the pallidothalamic and nigrothalamic tracts. Owing to the super-resolution of the TD images, the substructures of the SN, as well as the associated tracts, were identified. This study demonstrates that 7T MRI and MR tractography can be used to visualize anatomical details, as well as 3D reconstruction, of the output projections of the basal ganglia.

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