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  1. Article ; Online: OmicNavigator: open-source software for the exploration, visualization, and archival of omic studies.

    Ernst, Terrence R / Blischak, John D / Nordlund, Paul / Dalen, Joe / Moore, Justin / Bhamidipati, Akshay / Dwivedi, Pankaj / LoGrasso, Joe / Curado, Marco Rocha / Engelmann, Brett Warren

    BMC bioinformatics

    2024  Volume 25, Issue 1, Page(s) 162

    Abstract: Background: The results of high-throughput biology ('omic') experiments provide insight into biological mechanisms but can be challenging to explore, archive and share. The scale of these challenges continues to grow as omic research volume expands and ... ...

    Abstract Background: The results of high-throughput biology ('omic') experiments provide insight into biological mechanisms but can be challenging to explore, archive and share. The scale of these challenges continues to grow as omic research volume expands and multiple analytical technologies, bioinformatic pipelines, and visualization preferences have emerged. Multiple software applications exist that support omic study exploration and/or archival. However, an opportunity remains for open-source software that can archive and present the results of omic analyses with broad accommodation of study-specific analytical approaches and visualizations with useful exploration features.
    Results: We present OmicNavigator, an R package for the archival, visualization and interactive exploration of omic studies. OmicNavigator enables bioinformaticians to create web applications that interactively display their custom visualizations and analysis results linked with app-derived analytical tools, graphics, and tables. Studies created with OmicNavigator can be viewed within an interactive R session or hosted on a server for shared access.
    Conclusions: OmicNavigator can be found at https://github.com/abbvie-external/OmicNavigator.
    MeSH term(s) Software ; Computational Biology/methods ; User-Computer Interface ; Computer Graphics
    Language English
    Publishing date 2024-04-24
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-024-05743-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Nitrergic neurons of the forepaw representation in the rat somatosensory and motor cortices: A quantitative study.

    Guimaraes, Bárbara de Paula Pires Franco / Curado, Marco Rocha / Nogueira-Campos, Anaelli Aparecida / Houzel, Jean Christophe / Gattass, Ricardo

    The Journal of comparative neurology

    2021  Volume 529, Issue 13, Page(s) 3321–3335

    Abstract: Nitrergic neurons (NNs) are inhibitory neurons capable of releasing nitric oxide (NO) that are labeled with nicotinamide adenine dinucleotide phosphate diaphorase histochemistry. The rat primary somatosensory (S1) and motor (M1) cortices are a favorable ... ...

    Abstract Nitrergic neurons (NNs) are inhibitory neurons capable of releasing nitric oxide (NO) that are labeled with nicotinamide adenine dinucleotide phosphate diaphorase histochemistry. The rat primary somatosensory (S1) and motor (M1) cortices are a favorable model to investigate NN populations by comparing their morphology, since these areas share the border of forepaw representation. The distribution of the Type I NN of the forepaw representation in the S1 and M1 cortices of the rat in different laminar compartments and the morphological parameters related to the cell body and dendritic arborization were measured and compared. We observed that the neuronal density in the S1 (130 NN/mm
    MeSH term(s) Animals ; Forelimb/chemistry ; Forelimb/innervation ; Forelimb/metabolism ; Male ; Motor Cortex/chemistry ; Motor Cortex/cytology ; Motor Cortex/metabolism ; NADP/analysis ; NADP/metabolism ; Nitrergic Neurons/chemistry ; Nitrergic Neurons/metabolism ; Rats ; Rats, Wistar ; Somatosensory Cortex/chemistry ; Somatosensory Cortex/cytology ; Somatosensory Cortex/metabolism
    Chemical Substances NADP (53-59-8)
    Language English
    Publishing date 2021-05-31
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 3086-7
    ISSN 1096-9861 ; 0021-9967 ; 0092-7317
    ISSN (online) 1096-9861
    ISSN 0021-9967 ; 0092-7317
    DOI 10.1002/cne.25192
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: Anodal Transcranial Direct Current Stimulation Enhances Survival and Integration of Dopaminergic Cell Transplants in a Rat Parkinson Model.

    Winkler, Christian / Reis, Janine / Hoffmann, Nadin / Gellner, Anne-Kathrin / Münkel, Christian / Curado, Marco Rocha / Furlanetti, Luciano / Garcia, Joanna / Döbrössy, Máté D / Fritsch, Brita

    eNeuro

    2017  Volume 4, Issue 5

    Abstract: Restorative therapy concepts, such as cell based therapies aim to restitute impaired neurotransmission in neurodegenerative diseases. New strategies to enhance grafted cell survival and integration are still needed to improve functional recovery. Anodal ... ...

    Abstract Restorative therapy concepts, such as cell based therapies aim to restitute impaired neurotransmission in neurodegenerative diseases. New strategies to enhance grafted cell survival and integration are still needed to improve functional recovery. Anodal direct current stimulation (DCS) promotes neuronal activity and secretion of the trophic factor BDNF in the motor cortex. Transcranial DCS applied to the motor cortex transiently improves motor symptoms in Parkinson's disease (PD) patients. In this proof-of-concept study, we combine cell based therapy and noninvasive neuromodulation to assess whether neurotrophic support via transcranial DCS would enhance the restitution of striatal neurotransmission by fetal dopaminergic transplants in a rat Parkinson model. Transcranial DCS was applied daily for 20 min on 14 consecutive days following striatal transplantation of fetal ventral mesencephalic (fVM) cells derived from transgenic rat embryos ubiquitously expressing GFP. Anodal but not cathodal transcranial DCS significantly enhanced graft survival and dopaminergic reinnervation of the surrounding striatal tissue relative to sham stimulation. Behavioral recovery was more pronounced following anodal transcranial DCS, and behavioral effects correlated with the degree of striatal innervation. Our results suggest anodal transcranial DCS may help advance cell-based restorative therapies in neurodegenerative diseases. In particular, such an assistive approach may be beneficial for the already established cell transplantation therapy in PD.
    MeSH term(s) Adrenergic Agents/toxicity ; Animals ; Cell Survival ; Cell Transplantation/methods ; Disease Models, Animal ; Dopaminergic Neurons/physiology ; Dopaminergic Neurons/transplantation ; Female ; Green Fluorescent Proteins/genetics ; Green Fluorescent Proteins/metabolism ; Motor Activity ; Oxidopamine/toxicity ; Parkinson Disease/etiology ; Parkinson Disease/therapy ; Rats ; Rats, Sprague-Dawley ; Recovery of Function ; Transcranial Direct Current Stimulation/methods ; Tyrosine 3-Monooxygenase/metabolism
    Chemical Substances Adrenergic Agents ; Green Fluorescent Proteins (147336-22-9) ; Oxidopamine (8HW4YBZ748) ; Tyrosine 3-Monooxygenase (EC 1.14.16.2)
    Language English
    Publishing date 2017-09-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2800598-3
    ISSN 2373-2822 ; 2373-2822
    ISSN (online) 2373-2822
    ISSN 2373-2822
    DOI 10.1523/ENEURO.0063-17.2017
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Residual Upper Arm Motor Function Primes Innervation of Paretic Forearm Muscles in Chronic Stroke after Brain-Machine Interface (BMI) Training.

    Curado, Marco Rocha / Cossio, Eliana Garcia / Broetz, Doris / Agostini, Manuel / Cho, Woosang / Brasil, Fabricio Lima / Yilmaz, Oezge / Liberati, Giulia / Lepski, Guilherme / Birbaumer, Niels / Ramos-Murguialday, Ander

    PloS one

    2015  Volume 10, Issue 10, Page(s) e0140161

    Abstract: Background: Abnormal upper arm-forearm muscle synergies after stroke are poorly understood. We investigated whether upper arm function primes paralyzed forearm muscles in chronic stroke patients after Brain-Machine Interface (BMI)-based rehabilitation. ... ...

    Abstract Background: Abnormal upper arm-forearm muscle synergies after stroke are poorly understood. We investigated whether upper arm function primes paralyzed forearm muscles in chronic stroke patients after Brain-Machine Interface (BMI)-based rehabilitation. Shaping upper arm-forearm muscle synergies may support individualized motor rehabilitation strategies.
    Methods: Thirty-two chronic stroke patients with no active finger extensions were randomly assigned to experimental or sham groups and underwent daily BMI training followed by physiotherapy during four weeks. BMI sessions included desynchronization of ipsilesional brain activity and a robotic orthosis to move the paretic limb (experimental group, n = 16). In the sham group (n = 16) orthosis movements were random. Motor function was evaluated with electromyography (EMG) of forearm extensors, and upper arm and hand Fugl-Meyer assessment (FMA) scores. Patients performed distinct upper arm (e.g., shoulder flexion) and hand movements (finger extensions). Forearm EMG activity significantly higher during upper arm movements as compared to finger extensions was considered facilitation of forearm EMG activity. Intraclass correlation coefficient (ICC) was used to test inter-session reliability of facilitation of forearm EMG activity.
    Results: Facilitation of forearm EMG activity ICC ranges from 0.52 to 0.83, indicating fair to high reliability before intervention in both limbs. Facilitation of forearm muscles is higher in the paretic as compared to the healthy limb (p<0.001). Upper arm FMA scores predict facilitation of forearm muscles after intervention in both groups (significant correlations ranged from R = 0.752, p = 0.002 to R = 0.779, p = 0.001), but only in the experimental group upper arm FMA scores predict changes in facilitation of forearm muscles after intervention (R = 0.709, p = 0.002; R = 0.827, p<0.001).
    Conclusions: Residual upper arm motor function primes recruitment of paralyzed forearm muscles in chronic stroke patients and predicts changes in their recruitment after BMI training. This study suggests that changes in upper arm-forearm synergies contribute to stroke motor recovery, and provides candidacy guidelines for similar BMI-based clinical practice.
    MeSH term(s) Adult ; Aged ; Arm/physiopathology ; Brain-Computer Interfaces ; Chronic Disease ; Electromyography ; Female ; Forearm/innervation ; Forearm/physiopathology ; Hand/physiopathology ; Humans ; Male ; Middle Aged ; Movement ; Muscle, Skeletal/innervation ; Muscle, Skeletal/physiopathology ; Paresis/physiopathology ; Paresis/rehabilitation ; Physical Therapy Modalities ; Shoulder/physiopathology ; Stroke/physiopathology ; Stroke Rehabilitation ; Treatment Outcome
    Language English
    Publishing date 2015
    Publishing country United States
    Document type Journal Article ; Randomized Controlled Trial ; Research Support, Non-U.S. Gov't
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0140161
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  5. Article: Residual upper arm motor function primes innervation of paretic forearm muscles in chronic stroke after Brain-Machine Interface (BMI) training

    Curado, Marco Rocha / Cossio, Eliana Garcia / Broetz, Doris / Agostini, Manuel / Cho, Woosang / Brasil, Fabricio Lima / Yilmaz, Oezge / Liberati, Giulia / Lepski, Guilherme / Birbaumer, Niels / Ramos-Murguialday, Ander

    PLoS ONE

    2015  Volume 10, Issue 10, Page(s) No

    Abstract: Investigated whether upper arm function primes paralyzed forearm muscles in chronic stroke patients after brain-machine interface (BMI)-based rehabilitation. 32 chronic stroke patients with no active finger extensions were randomly assigned to ... ...

    Title translation Verbleibende motorische Funktion des Oberarms fördert Innervation paretischer Unterarmmuskeln bei chronischem Schlaganfall nach Training mit Hirn-Maschine-Schnittstelle
    Abstract Investigated whether upper arm function primes paralyzed forearm muscles in chronic stroke patients after brain-machine interface (BMI)-based rehabilitation. 32 chronic stroke patients with no active finger extensions were randomly assigned to experimental or sham groups and underwent daily BMI training followed by physiotherapy during four weeks. BMI sessions included desynchronization of ipsilesional brain activity and a robotic orthosis to move the paretic limb (experimental group with 16 subjects). In the sham group with 16 subjects orthosis movements were random. Patients performed distinct upper arm (for example, shoulder flexion) and hand movements (finger extensions). Forearm electromyography (EMG) activity significantly higher during upper arm movements as compared to finger extensions was considered facilitation of forearm EMG activity. Intraclass correlation coefficient (ICC) was used to test intersession reliability of facilitation of forearm EMG activity. Results show that facilitation of forearm EMG activity ICC ranges from 0.52 to 0.83, indicating fair to high reliability before intervention in both limbs. Facilitation of forearm muscles is higher in the paretic as compared to the healthy limb. Upper arm Fugl-Meyer assessment scores predict facilitation of forearm muscles after intervention in both groups, but only in the experimental group upper arm FMA scores predict changes in facilitation of forearm muscles after intervention. It is summarized that residual upper arm motor function primes recruitment of paralyzed forearm muscles in chronic stroke patients and predicts changes in their recruitment after BMI training. It is concluded that changes in upper arm-forearm synergies contribute to stroke motor recovery, and provides candidacy guidelines for similar BMI-based clinical practice.
    Keywords Arm (Anatomie) ; Arm (Anatomy) ; Cerebrovascular Accidents ; Electromyography ; Elektromyographie ; Genesung ; Hand ; Hand (Anatomy) ; Human Computer Interaction ; Mensch-Computer-Interaktion ; Neural Plasticity ; Neuronale Plastizität ; Paralyse ; Paralysis ; Recovery (Disorders) ; Rehabilitation ; Schlaganfall
    Language English
    Document type Article
    ZDB-ID 2267670-3
    ISSN 1932-6203
    ISSN 1932-6203
    Database PSYNDEX

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