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  1. Article ; Online: Machine Learning for 3D Kinematic Analysis of Movements in Neurorehabilitation.

    Arac, Ahmet

    Current neurology and neuroscience reports

    2020  Volume 20, Issue 8, Page(s) 29

    Abstract: Purpose of review: Recent advances in the machine learning field, especially in deep learning, provide the opportunity for automated, detailed, and unbiased analysis of motor behavior. Although there has not yet been wide use of these techniques in the ... ...

    Abstract Purpose of review: Recent advances in the machine learning field, especially in deep learning, provide the opportunity for automated, detailed, and unbiased analysis of motor behavior. Although there has not yet been wide use of these techniques in the motor rehabilitation field, they have great potential. In this review, I describe how the current state of machine learning can be applied to 3D kinematic analysis, and how this will have an impact on neurorehabilitation.
    Recent findings: Applications of deep learning methods, in the form of convolutional neural networks, have been revolutionary for image analysis such as face recognition and object detection in images, exceeding human level performance. Recent studies have shown applicability of these deep learning approaches to human posture and movement classification. It is to be expected that portable stereo-camera systems will bring 3D pose estimation into the clinical setting and allow the assessment of movement quality in response to interventions. Advances in machine learning can help automate the process of obtaining 3D kinematics of human movements and to identify/classify patterns of movement.
    MeSH term(s) Biomechanical Phenomena ; Humans ; Machine Learning ; Movement ; Neural Networks, Computer ; Neurological Rehabilitation
    Language English
    Publishing date 2020-06-15
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2057363-7
    ISSN 1534-6293 ; 1528-4042
    ISSN (online) 1534-6293
    ISSN 1528-4042
    DOI 10.1007/s11910-020-01049-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A Step-by-Step Implementation of DeepBehavior, Deep Learning Toolbox for Automated Behavior Analysis.

    Shukla, Sanjay / Arac, Ahmet

    Journal of visualized experiments : JoVE

    2020  , Issue 156

    Abstract: Understanding behavior is the first step to truly understanding neural mechanisms in the brain that drive it. Traditional behavioral analysis methods often do not capture the richness inherent to the natural behavior. Here, we provide detailed step-by- ... ...

    Abstract Understanding behavior is the first step to truly understanding neural mechanisms in the brain that drive it. Traditional behavioral analysis methods often do not capture the richness inherent to the natural behavior. Here, we provide detailed step-by-step instructions with visualizations of our recent methodology, DeepBehavior. The DeepBehavior toolbox uses deep learning frameworks built with convolutional neural networks to rapidly process and analyze behavioral videos. This protocol demonstrates three different frameworks for single object detection, multiple object detection, and three-dimensional (3D) human joint pose tracking. These frameworks return cartesian coordinates of the object of interest for each frame of the behavior video. Data collected from the DeepBehavior toolbox contain much more detail than traditional behavior analysis methods and provides detailed insights to the behavior dynamics. DeepBehavior quantifies behavior tasks in a robust, automated, and precise way. Following the identification of behavior, post-processing code is provided to extract information and visualizations from the behavioral videos.
    MeSH term(s) Animals ; Automation ; Behavior ; Behavior, Animal/physiology ; Computer Graphics ; Deep Learning ; Humans ; Imaging, Three-Dimensional ; Interpersonal Relations ; Mice ; Neural Networks, Computer ; User-Computer Interface ; Video Recording
    Language English
    Publishing date 2020-02-06
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Video-Audio Media
    ZDB-ID 2259946-0
    ISSN 1940-087X ; 1940-087X
    ISSN (online) 1940-087X
    ISSN 1940-087X
    DOI 10.3791/60763
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Rab7a activation promotes degradation of select tight junction proteins at the blood-brain barrier after ischemic stroke.

    Cottarelli, Azzurra / Shahriar, Sanjid / Arac, Ahmet / Glendinning, Michael / Tuohy, Mary Claire / Prochilo, Grace / Neal, Jason B / Edinger, Aimee L / Agalliu, Dritan

    bioRxiv : the preprint server for biology

    2023  

    Abstract: The stability of tight junctions (TJs) between endothelial cells (ECs) is essential to maintain blood-brain barrier (BBB) function in the healthy brain. Following ischemic stroke, TJ strand dismantlement due to protein degradation leads to BBB ... ...

    Abstract The stability of tight junctions (TJs) between endothelial cells (ECs) is essential to maintain blood-brain barrier (BBB) function in the healthy brain. Following ischemic stroke, TJ strand dismantlement due to protein degradation leads to BBB dysfunction, yet the mechanisms driving this process are poorly understood. Here, we show that endothelial-specific ablation of Rab7a, a small GTPase that regulates endolysosomal protein degradation, reduces stroke-induced TJ strand disassembly resulting in decreased paracellular BBB permeability and improved neuronal outcomes. Two pro-inflammatory cytokines, TNFα and IL1β, but not glucose and oxygen deprivation, induce Rab7a activation via Ccz1 in brain ECs
    Language English
    Publishing date 2023-08-30
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.08.29.555373
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Vim-Thalamic Deep Brain Stimulation for Cervical Dystonia and Upper-Limb Tremor: Quantification by Markerless-3D Kinematics and Accelerometry.

    Mason, Xenos L / Cross, Katy A / Arac, Ahmet / Bordelon, Yvette / Wu, Allan D

    Tremor and other hyperkinetic movements (New York, N.Y.)

    2022  Volume 12, Page(s) 5

    Abstract: Background: Deep Brain Stimulation (DBS) for dystonia is usually targeted to the globus pallidus internus (GPi), though stimulation of the ventral-intermediate nucleus of the thalamus (Vim) can be an effective treatment for phasic components of dystonia ...

    Abstract Background: Deep Brain Stimulation (DBS) for dystonia is usually targeted to the globus pallidus internus (GPi), though stimulation of the ventral-intermediate nucleus of the thalamus (Vim) can be an effective treatment for phasic components of dystonia including tremor. We report on a patient who developed a syndrome of bilateral upper limb postural and action tremor and progressive cervical dystonia with both phasic and tonic components which were responsive to Vim DBS. We characterize and quantify this effect using markerless-3D-kinematics combined with accelerometry.
    Methods: Stereo videography was used to record our subject in 3D. The DeepBehavior toolbox was applied to obtain timeseries of joint position for kinematic analysis [1]. Accelerometry was performed simultaneously for comparison with prior literature.
    Results: Bilateral Vim DBS improved both dystonic tremor magnitude and tonic posturing. DBS of the hemisphere contralateral to the direction of dystonic head rotation (left Vim) had greater efficacy. Assessment of tremor magnitude by 3D-kinematics was concordant with accelerometry and was able to quantify tonic dystonic posturing.
    Discussion: In this case, Vim DBS treated both cervical dystonic tremor and dystonic posturing. Markerless-3D-kinematics should be further studied as a method of quantifying and characterizing tremor and dystonia.
    MeSH term(s) Accelerometry ; Biomechanical Phenomena ; Deep Brain Stimulation/methods ; Dystonic Disorders/therapy ; Humans ; Thalamus ; Torticollis/therapy ; Tremor/therapy ; Ventral Thalamic Nuclei/physiology
    Language English
    Publishing date 2022-03-10
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
    ZDB-ID 2674453-3
    ISSN 2160-8288 ; 2160-8288
    ISSN (online) 2160-8288
    ISSN 2160-8288
    DOI 10.5334/tohm.673
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: A step-by-step implementation of deepbehavior, deep learning toolbox for automated behavior analysis

    Shukla, Sanjay / Arac, Ahmet

    Journal of visualized experiments. 2020 Feb. 06, , no. 156

    2020  

    Abstract: Understanding behavior is the first step to truly understanding neural mechanisms in the brain that drive it. Traditional behavioral analysis methods often do not capture the richness inherent to the natural behavior. Here, we provide detailed step-by- ... ...

    Abstract Understanding behavior is the first step to truly understanding neural mechanisms in the brain that drive it. Traditional behavioral analysis methods often do not capture the richness inherent to the natural behavior. Here, we provide detailed step-by-step instructions with visualizations of our recent methodology, DeepBehavior. The DeepBehavior toolbox uses deep learning frameworks built with convolutional neural networks to rapidly process and analyze behavioral videos. This protocol demonstrates three different frameworks for single object detection, multiple object detection, and three-dimensional (3D) human joint pose tracking. These frameworks return cartesian coordinates of the object of interest for each frame of the behavior video. Data collected from the DeepBehavior toolbox contain much more detail than traditional behavior analysis methods and provides detailed insights to the behavior dynamics. DeepBehavior quantifies behavior tasks in a robust, automated, and precise way. Following the identification of behavior, post-processing code is provided to extract information and visualizations from the behavioral videos.
    Keywords automation ; brain ; data collection ; humans ; neural networks
    Language English
    Dates of publication 2020-0206
    Size p. e60763.
    Publishing place Journal of Visualized Experiments
    Document type Article
    ZDB-ID 2259946-0
    ISSN 1940-087X
    ISSN 1940-087X
    DOI 10.3791/60763
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Hearing and Vision Loss in an Older Man.

    Ho, Victoria M / Arac, Ahmet / Shieh, Perry B

    JAMA neurology

    2018  Volume 75, Issue 11, Page(s) 1439–1440

    MeSH term(s) Arthroplasty, Replacement, Hip/adverse effects ; Cardiomyopathies/diagnosis ; Cardiomyopathies/etiology ; Cobalt/toxicity ; Fatal Outcome ; Hearing Loss/diagnosis ; Hearing Loss/etiology ; Heavy Metal Poisoning/complications ; Heavy Metal Poisoning/diagnosis ; Humans ; Magnetic Resonance Imaging ; Male ; Middle Aged ; Vision Disorders/diagnosis ; Vision Disorders/etiology
    Chemical Substances Cobalt (3G0H8C9362)
    Language English
    Publishing date 2018-07-23
    Publishing country United States
    Document type Case Reports ; Journal Article
    ZDB-ID 2702023-X
    ISSN 2168-6157 ; 2168-6149
    ISSN (online) 2168-6157
    ISSN 2168-6149
    DOI 10.1001/jamaneurol.2018.1868
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  7. Article: Meningeal Mast Cells as Key Effectors of Stroke Pathology.

    Arac, Ahmet / Grimbaldeston, Michele A / Galli, Stephen J / Bliss, Tonya M / Steinberg, Gary K

    Frontiers in cellular neuroscience

    2019  Volume 13, Page(s) 126

    Abstract: Stroke is the leading cause of adult disability in the United States. Because post-stroke inflammation is a critical determinant of damage and recovery after stroke, understanding the interplay between the immune system and the brain after stroke holds ... ...

    Abstract Stroke is the leading cause of adult disability in the United States. Because post-stroke inflammation is a critical determinant of damage and recovery after stroke, understanding the interplay between the immune system and the brain after stroke holds much promise for therapeutic intervention. An understudied, but important aspect of this interplay is the role of meninges that surround the brain. All blood vessels travel through the meningeal space before entering the brain parenchyma, making the meninges ideally located to act as an immune gatekeeper for the underlying parenchyma. Emerging evidence suggests that the actions of immune cells resident in the meninges are essential for executing this gatekeeper function. Mast cells (MCs), best known as proinflammatory effector cells, are one of the long-term resident immune cells in the meninges. Here, we discuss recent findings in the literature regarding the role of MCs located in the meningeal space and stroke pathology. We review the latest advances in mouse models to investigate the roles of MCs and MC-derived products
    Language English
    Publishing date 2019-04-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2452963-1
    ISSN 1662-5102
    ISSN 1662-5102
    DOI 10.3389/fncel.2019.00126
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  8. Article: DeepBehavior: A Deep Learning Toolbox for Automated Analysis of Animal and Human Behavior Imaging Data.

    Arac, Ahmet / Zhao, Pingping / Dobkin, Bruce H / Carmichael, S Thomas / Golshani, Peyman

    Frontiers in systems neuroscience

    2019  Volume 13, Page(s) 20

    Abstract: Detailed behavioral analysis is key to understanding the brain-behavior relationship. Here, we present deep learning-based methods for analysis of behavior imaging data in mice and humans. Specifically, we use three different convolutional neural network ...

    Abstract Detailed behavioral analysis is key to understanding the brain-behavior relationship. Here, we present deep learning-based methods for analysis of behavior imaging data in mice and humans. Specifically, we use three different convolutional neural network architectures and five different behavior tasks in mice and humans and provide detailed instructions for rapid implementation of these methods for the neuroscience community. We provide examples of three dimensional (3D) kinematic analysis in the food pellet reaching task in mice, three-chamber test in mice, social interaction test in freely moving mice with simultaneous miniscope calcium imaging, and 3D kinematic analysis of two upper extremity movements in humans (reaching and alternating pronation/supination). We demonstrate that the transfer learning approach accelerates the training of the network when using images from these types of behavior video recordings. We also provide code for post-processing of the data after initial analysis with deep learning. Our methods expand the repertoire of available tools using deep learning for behavior analysis by providing detailed instructions on implementation, applications in several behavior tests, and post-processing methods and annotated code for detailed behavior analysis. Moreover, our methods in human motor behavior can be used in the clinic to assess motor function during recovery after an injury such as stroke.
    Language English
    Publishing date 2019-05-07
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2453005-0
    ISSN 1662-5137
    ISSN 1662-5137
    DOI 10.3389/fnsys.2019.00020
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  9. Article ; Online: Effect of Euthyroid Nodular Goiter on Anxiety and Depression

    Ferit Akıl / Ahmet Üzer / Akif Deniz / Muhammed Ayral / Serkan Dedeoğlu / Eşref Araç / Mehmet Güven / Ayhan Kaydu

    Van Tip Dergisi, Vol 24, Iss 3, Pp 146-

    2017  Volume 149

    Abstract: INTRODUCTION: The aim of this study was to evaluate the effect of the euthyroid nodular gouiter on the anxiety and depression. METHODS: 50 male and 50 female patients between ages of 18-50 who diagnosed euthyroid nodular gouiter at least 6 months were ... ...

    Abstract INTRODUCTION: The aim of this study was to evaluate the effect of the euthyroid nodular gouiter on the anxiety and depression. METHODS: 50 male and 50 female patients between ages of 18-50 who diagnosed euthyroid nodular gouiter at least 6 months were included in our study (group 2). 20 male and 20 female healthy patients were included as control group (group 1). The patients who had psychiatric problems and chronic comorbidities were excluded. The BDS ( Beck Depression scale) and BAS (Beck anxiety scale) tests were used as compasion of two groups. Student's T-test was performed for parametric data A p level of <0,05 was taken as statistically significant. RESULTS: Comparing between unhealthy and control groups: BDS test and BAS test were significantly higher in group 2 male patients than group 1 male patients, p <0.019 and p <0.005 respectively. Group 2 female patients showed significantly higher results in BDS and BAS tests than group 1 female patients, p <0.001 and p <0.001 respectively. DISCUSSION AND CONCLUSION: The result of this study showed that euthyroid nodular gouiter had negative effects on anxiety and depression and our article is the first article in literature on this issue.
    Keywords euthyroid nodular goiter ; anxiety ; depression ; Medicine ; R
    Subject code 150
    Language English
    Publishing date 2017-07-01T00:00:00Z
    Publisher Van Yuzuncu Yil University, School of Medicine
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Lymphangiomatosis in a child: eight years' follow-up without treatment.

    Küpeli, Serhan / Araç, Ahmet / Yalçin, Bilgehan / Sökmensüer, Cenk / Büyükpamukçu, Münevver

    Pediatric hematology and oncology

    2008  Volume 25, Issue 6, Page(s) 614–619

    Abstract: Lymphangiomatosis of the spleen with diffuse lymphangiomatosis of the bone is extremely rare and there is no consensus about management at present. Here, the authors report a child presenting initially with back pain and diagnosed as lymphangiomatosis on ...

    Abstract Lymphangiomatosis of the spleen with diffuse lymphangiomatosis of the bone is extremely rare and there is no consensus about management at present. Here, the authors report a child presenting initially with back pain and diagnosed as lymphangiomatosis on several sites throughout the bony structures and the spleen. The patient is in a stable state at the end of 8 years without any treatment. The authors also discuss the follow-up option that may be considered as a strategy for management.
    MeSH term(s) Bone Neoplasms/pathology ; Child ; Female ; Humans ; Lymphangioleiomyomatosis/pathology ; Lymphangioma/pathology ; Splenic Neoplasms/pathology
    Language English
    Publishing date 2008-09
    Publishing country England
    Document type Case Reports ; Journal Article
    ZDB-ID 632914-7
    ISSN 1521-0669 ; 0888-0018
    ISSN (online) 1521-0669
    ISSN 0888-0018
    DOI 10.1080/08880010802234879
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