scholarly journals Leveraging Neural Networks in Preclinical Alcohol Research

2020 ◽  
Vol 10 (9) ◽  
pp. 578
Author(s):  
Lauren C. Smith ◽  
Adam Kimbrough

Alcohol use disorder is a pervasive healthcare issue with significant socioeconomic consequences. There is a plethora of neural imaging techniques available at the clinical and preclinical level, including magnetic resonance imaging and three-dimensional (3D) tissue imaging techniques. Network-based approaches can be applied to imaging data to create neural networks that model the functional and structural connectivity of the brain. These networks can be used to changes to brain-wide neural signaling caused by brain states associated with alcohol use. Neural networks can be further used to identify key brain regions or neural “hubs” involved in alcohol drinking. Here, we briefly review the current imaging and neurocircuit manipulation methods. Then, we discuss clinical and preclinical studies using network-based approaches related to substance use disorders and alcohol drinking. Finally, we discuss how preclinical 3D imaging in combination with network approaches can be applied alone and in combination with other approaches to better understand alcohol drinking.

Plant Methods ◽  
2019 ◽  
Vol 15 (1) ◽  
Author(s):  
Rachele Tofanelli ◽  
Athul Vijayan ◽  
Sebastian Scholz ◽  
Kay Schneitz

Abstract Background A salient topic in developmental biology relates to the molecular and genetic mechanisms that underlie tissue morphogenesis. Modern quantitative approaches to this central question frequently involve digital cellular models of the organ or tissue under study. The ovules of the model species Arabidopsis thaliana have long been established as a model system for the study of organogenesis in plants. While ovule development in Arabidopsis can be followed by a variety of different imaging techniques, no experimental strategy presently exists that enables an easy and straightforward investigation of the morphology of internal tissues of the ovule with cellular resolution. Results We developed a protocol for rapid and robust confocal microscopy of fixed Arabidopsis ovules of all stages. The method combines clearing of fixed ovules in ClearSee solution with marking the cell outline using the cell wall stain SCRI Renaissance 2200 and the nuclei with the stain TO-PRO-3 iodide. We further improved the microscopy by employing a homogenous immersion system aimed at minimizing refractive index differences. The method allows complete inspection of the cellular architecture even deep within the ovule. Using the new protocol we were able to generate digital three-dimensional models of ovules of various stages. Conclusions The protocol enables the quick and reproducible imaging of fixed Arabidopsis ovules of all developmental stages. From the imaging data three-dimensional digital ovule models with cellular resolution can be rapidly generated using image analysis software, for example MorphographX. Such digital models will provide the foundation for a future quantitative analysis of ovule morphogenesis in a model species.


2014 ◽  
Vol 2 (2) ◽  
pp. 91-103
Author(s):  
Krysta Ryzewski ◽  
Hassina Z. Bilheux ◽  
Susan N. Herringer ◽  
Jean-Christophe Bilheux ◽  
Lakeisha Walker ◽  
...  

AbstractNeutron imaging is a nondestructive application capable of producing two- and three-dimensional maps of archaeological objects’ external and internal structure, properties, and composition. This report presents the recent development of neutron imaging data collection and processing methods at Oak Ridge National Laboratory (ORNL), which have been advanced, in part, by information gathered from the experimental imaging of 25 archaeological objects over the past three years. The dual objectives of these imaging experiments included (1) establishing the first methodological procedures for the neutron imaging of archaeomaterials involving the CG-1D beamline and (2) further illustrating the potential of neutron imaging for archaeologists to use in the reverse engineering of ancient and historical objects. Examples of objects imaged in two and three dimensions are provided to highlight the application’s strengths and limitations for archaeological investigations, especially those that address ancient and historic technologies, materials science, and conservation issues.


Stroke ◽  
2021 ◽  
Author(s):  
Patrick Lyden ◽  
Alastair Buchan ◽  
Johannes Boltze ◽  
Marc Fisher ◽  

Despite years of basic research and pioneering clinical work, ischemic stroke remains a major public health concern. Prior STAIR (Stroke Treatment Academic Industry Roundtable) conferences identified both failures of clinical trial design and failures in preclinical assessment in developing putative ischemic stroke treatments. At STAIR XI, participants in workshop no. 1 Top Priorities for Neuroprotection sought to redefine the neuroprotection paradigm and given the paucity of evidence underlying preclinical assessment, offer consensus-based recommendations. STAIR proposes the term brain cytoprotection or cerebroprotection to replace the term neuroprotection when the intention of an investigation is to demonstrate that a new, candidate treatment benefits the entire brain. Although “time is still brain,” tissue imaging techniques have been developed to identify patients with both predicted core injury and penumbral, salvageable brain tissue, regardless of time after stroke symptom onset. STAIR XI workshop participants called this imaging approach a tissue window to select patients for recanalization. Elements of the neurovascular unit show differential vulnerability evolving over differing time scales in different brain regions. STAIR proposes the term target window to suggest therapies that target the different elements of the neurovascular unit at different times. Based on contemporary principles of rigor and transparency, the workshop updated, revised, and enhanced the STAIR preclinical recommendations for developing new treatments in 2 phases: an exploratory qualification phase and a definitive validation phase. For new, putative treatments, investigators should carefully characterize the mechanism of action, the pharmacokinetics/pharmacodynamics, demonstrate target engagement, and confirm penetration through the blood-brain barrier. Before clinical trials, testing of candidate molecules in stroke models could proceed in a comprehensive manner using animals of both sexes and to include significant variables such as age and comorbid conditions. Comprehensive preclinical assessment might include multicenter, collaborative testing, for example, network trials. In the absence of a proven cerebroprotective agent to use as a gold standard, however, it remains speculative whether such comprehensive preclinical assessment can effectively predict clinical outcome.


2018 ◽  
Author(s):  
Randall J. Ellis ◽  
Michael Michaelides

AbstractThe brain contains billions of neurons defined by diverse cytoarchitectural, anatomical, genetic, and functional properties. Sensory encoding and decoding are popular research areas in the fields of neuroscience, neuroprosthetics and artificial intelligence but the contribution of neuronal diversity to these processes is not well understood. Deciphering this contribution necessitates development of sophisticated neurotechnologies that can monitor brain physiology and behavior via simultaneous assessment of individual genetically-defined neurons during the presentation of discrete sensory cues and behavioral contexts. Neural networks are a powerful technique for formulating hierarchical representations of data using layers of nonlinear transformations. Here we leverage the availability of an unprecedented collection of neuronal activity data, derived from ∼25,000 individual genetically-defined neurons of the parcellated mouse visual cortex during the presentation of 118 unique and complex naturalistic scenes, to demonstrate that neural networks can be used to decode discrete visual scenes from neuronal calcium responses with high (∼96%) accuracy. Our findings highlight the novel use of neural networks for sensory decoding using neuronal calcium imaging data and reveal a neuroanatomical map of visual decoding strength traversing brain regions, cortical layers, neuron types, and time. Our findings also demonstrate the utility of feature selection in assigning contributions of neuronal diversity to visual decoding accuracy and the low requirement of network architecture complexity for high accuracy decoding in this experimental context.


2018 ◽  
Vol 38 (12) ◽  
pp. 2057-2072 ◽  
Author(s):  
Kazuto Masamoto ◽  
Alberto Vazquez

The cerebral microvasculature consists of pial vascular networks, parenchymal descending arterioles, ascending venules and parenchymal capillaries. This vascular compartmentalization is vital to precisely deliver blood to balance continuously varying neural demands in multiple brain regions. Optical imaging techniques have facilitated the investigation of dynamic spatial and temporal properties of microvascular functions in real time. Their combination with transgenic animal models encoding specific genetic targets have further strengthened the importance of optical methods for neurovascular research by allowing for the modulation and monitoring of neuro vascular function. Image analysis methods with three-dimensional reconstruction are also helping to understand the complexity of microscopic observations. Here, we review the compartmentalized cerebral microvascular responses to global perturbations as well as regional changes in response to neural activity to highlight the differences in vascular action sites. In addition, microvascular responses elicited by optical modulation of different cell-type targets are summarized with emphasis on variable spatiotemporal dynamics of microvascular responses. Finally, long-term changes in microvascular compartmentalization are discussed to help understand potential relationships between CBF disturbances and the development of neurodegenerative diseases and cognitive decline.


2021 ◽  
Vol 118 (13) ◽  
pp. e2100697118
Author(s):  
Shengze Cai ◽  
He Li ◽  
Fuyin Zheng ◽  
Fang Kong ◽  
Ming Dao ◽  
...  

Understanding the mechanics of blood flow is necessary for developing insights into mechanisms of physiology and vascular diseases in microcirculation. Given the limitations of technologies available for assessing in vivo flow fields, in vitro methods based on traditional microfluidic platforms have been developed to mimic physiological conditions. However, existing methods lack the capability to provide accurate assessment of these flow fields, particularly in vessels with complex geometries. Conventional approaches to quantify flow fields rely either on analyzing only visual images or on enforcing underlying physics without considering visualization data, which could compromise accuracy of predictions. Here, we present artificial-intelligence velocimetry (AIV) to quantify velocity and stress fields of blood flow by integrating the imaging data with underlying physics using physics-informed neural networks. We demonstrate the capability of AIV by quantifying hemodynamics in microchannels designed to mimic saccular-shaped microaneurysms (microaneurysm-on-a-chip, or MAOAC), which signify common manifestations of diabetic retinopathy, a leading cause of vision loss from blood-vessel damage in the retina in diabetic patients. We show that AIV can, without any a priori knowledge of the inlet and outlet boundary conditions, infer the two-dimensional (2D) flow fields from a sequence of 2D images of blood flow in MAOAC, but also can infer three-dimensional (3D) flow fields using only 2D images, thanks to the encoded physics laws. AIV provides a unique paradigm that seamlessly integrates images, experimental data, and underlying physics using neural networks to automatically analyze experimental data and infer key hemodynamic indicators that assess vascular injury.


2015 ◽  
Vol 8 (9) ◽  
pp. 959-964 ◽  
Author(s):  
Frédéric Clarençon ◽  
Franck Maizeroi-Eugène ◽  
Flavien Maingreaud ◽  
Damien Bresson ◽  
David Ayoub ◽  
...  

IntroductionConvex spherical anamorphosis is a barrel distortion that consists of the application of a plane surface on a convex hemisphere. Applied in vascular imaging of brain arteriovenous malformations (bAVMs), this deformation may help to ‘spread’ the nidus and surrounding vessels (arteries/veins) and thus to differentiate the different components of bAVMs more accurately.MethodsThe imaging data from 15 patients (8 male, 7 female; 14 supratentorial bAVMs, 1 infratentorial) were used to test the algorithm. The algorithm was applied to three-dimensional rotational angiography (3D-RA) volume rendering reconstructions in anteroposterior, lateral and oblique views and compared with regular 3D-RA and DSA. Arterial feeder and draining vein count and quality visualization of the main draining vein and intranidal aneurysms were compared between the three imaging techniques.ResultsAnamorphosis was able to depict more arterial feeders than 3D-RA alone (p=0.027). There was no statistically significant difference between 6 f/s DSA and anamorphosis for arterial feeder count. No difference was observed in draining vein count between the three imaging modalities. Visualization of the precise origin of the main draining vein was considered to be good in 67% of the cases with anamorphosis versus 47% and 33% for 6 f/s DSA and 3D-RA alone, respectively. Intranidal aneurysms were accurately depicted by anamorphosis (2 cases), whereas 6 f/s DSA and 3D-RA showed doubtful images in one and two additional cases, respectively, which were finally confirmed as focal venous ectasias on supraselective injection.ConclusionsAnamorphosis can help to visualize more precisely the main draining vein origin of the bAVM and depict more accurately intranidal aneurysms.


2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Eduardo Carabez ◽  
Miho Sugi ◽  
Isao Nambu ◽  
Yasuhiro Wada

From allowing basic communication to move through an environment, several attempts are being made in the field of brain-computer interfaces (BCI) to assist people that somehow find it difficult or impossible to perform certain activities. Focusing on these people as potential users of BCI, we obtained electroencephalogram (EEG) readings from nine healthy subjects who were presented with auditory stimuli via earphones from six different virtual directions. We presented the stimuli following the oddball paradigm to elicit P300 waves within the subject’s brain activity for later identification and classification using convolutional neural networks (CNN). The CNN models are given a novel single trial three-dimensional (3D) representation of the EEG data as an input, maintaining temporal and spatial information as close to the experimental setup as possible, a relevant characteristic as eliciting P300 has been shown to cause stronger activity in certain brain regions. Here, we present the results of CNN models using the proposed 3D input for three different stimuli presentation time intervals (500, 400, and 300 ms) and compare them to previous studies and other common classifiers. Our results show >80% accuracy for all the CNN models using the proposed 3D input in single trial P300 classification.


2021 ◽  
Vol 2021 ◽  
pp. 1-31
Author(s):  
Simon Wein ◽  
Gustavo Deco ◽  
Ana Maria Tomé ◽  
Markus Goldhacker ◽  
Wilhelm M. Malloni ◽  
...  

This short survey reviews the recent literature on the relationship between the brain structure and its functional dynamics. Imaging techniques such as diffusion tensor imaging (DTI) make it possible to reconstruct axonal fiber tracks and describe the structural connectivity (SC) between brain regions. By measuring fluctuations in neuronal activity, functional magnetic resonance imaging (fMRI) provides insights into the dynamics within this structural network. One key for a better understanding of brain mechanisms is to investigate how these fast dynamics emerge on a relatively stable structural backbone. So far, computational simulations and methods from graph theory have been mainly used for modeling this relationship. Machine learning techniques have already been established in neuroimaging for identifying functionally independent brain networks and classifying pathological brain states. This survey focuses on methods from machine learning, which contribute to our understanding of functional interactions between brain regions and their relation to the underlying anatomical substrate.


Gut ◽  
2019 ◽  
Vol 68 (9) ◽  
pp. 1701-1715 ◽  
Author(s):  
Emeran A Mayer ◽  
Jennifer Labus ◽  
Qasim Aziz ◽  
Irene Tracey ◽  
Lisa Kilpatrick ◽  
...  

Imaging of the living human brain is a powerful tool to probe the interactions between brain, gut and microbiome in health and in disorders of brain–gut interactions, in particular IBS. While altered signals from the viscera contribute to clinical symptoms, the brain integrates these interoceptive signals with emotional, cognitive and memory related inputs in a non-linear fashion to produce symptoms. Tremendous progress has occurred in the development of new imaging techniques that look at structural, functional and metabolic properties of brain regions and networks. Standardisation in image acquisition and advances in computational approaches has made it possible to study large data sets of imaging studies, identify network properties and integrate them with non-imaging data. These approaches are beginning to generate brain signatures in IBS that share some features with those obtained in other often overlapping chronic pain disorders such as urological pelvic pain syndromes and vulvodynia, suggesting shared mechanisms. Despite this progress, the identification of preclinical vulnerability factors and outcome predictors has been slow. To overcome current obstacles, the creation of consortia and the generation of standardised multisite repositories for brain imaging and metadata from multisite studies are required.


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