scholarly journals Identifying Brain Region Connectivity using Steiner Minimal Tree Approximation and a Genetic Algorithm

2019 ◽  
Author(s):  
Syed Islam ◽  
Dewan M. Sarwar
Keyword(s):  
Genetic Algorithm ◽  
Case Studies ◽  
Neurological Disease ◽  
Brain Regions ◽  
Regions Of Interest ◽  
Minimal Tree ◽  
Steiner Minimal Tree ◽  
Web Based ◽  
Connectivity Graph ◽  
The Brain

AbstractBackgroundComputation and visualization of connectivity among the brain regions is vital for tasks such as disease identification and drug discovery. An effective visualization can aid clinicians and biologists to perform these tasks addressing a genuine research and industrial need. In this paper, we present SMT-Neurophysiology, a web-based tool in a form of an approximation to the Steiner Minimal Tree (SMT) algorithm to search neurophysiology partonomy and connectivity graph in order to find biomedically-meaningful paths that could explain, to neurologists and neuroscientists, the mechanistic relationship, for example, among specific neurophysiological examinations. We also present SMT-Genetic, a web-based tool in a form of a Genetic Algorithm (GA) to find better paths than SMT-Neurophysiology.ResultsWe introduce an approximation to the SMT algorithm to identify the most parsimonious connectivity among the brain regions of interest. We have implemented our algorithm as a highly interactive web application called SMT-Neurophysiology that enables such computation and visualization. It operates on brain region connectivity dataset curated from the Neuroscience Information Framework (NIF) for four species – human, monkey, rat and bird. We present two case studies on finding the most biomedically-meaningful solutions that identifies connections among a set of brain regions over a specific route. The case studies demonstrate that SMT-Neurophysiology is able to find connection among brain regions of interest. Furthermore, SMT-Neurophysiology is modular and generic in nature allowing the underlying connectivity graph to model any data on which the tool can operate. In order to find better connections among a set of brain regions than SMT-Neurophysiology, we have implemented a web-based tool in a form of a GA called SMT-Genetic. We present further three case studies where SMT-Genetic finds better connections among a set of brain regions than SMT-Neurophysiology. SMT-Genetic gives better connections because SMT-Genetic finds global optimum whereas SMT-Neurophysiology finds local optimum although execution time of SMT-Genetic is higher than SMT-Neurophysiology.ConclusionOur analysis would provide key insights to clinical investigators about potential mechanisms underlying a particular neurological disease. The web-based tools and the underlying data are useful to clinicians and scientists to understand neurological disease mechanisms; discover pharmacological or surgical targets; and design diagnostic or therapeutic clinical trials. The source codes and links to the live tools are available at https://github.com/dewancse/connected-brain-regions and https://github.com/dewancse/SMT-Genetic.

scholarly journals Dissection of neuroinflammation in schizophrenia

BJPsych Open ◽  
2021 ◽  
Vol 7 (S1) ◽  
pp. S274-S275
Author(s):  
Fizah Muratib ◽  
Yuya Mizuno ◽  
Ines Carreira Figueiredo ◽  
Oliver Howes ◽  
Tiago Reis Marques
Keyword(s):  
Risk Factor ◽  
Grey Matter ◽  
Psychotic Disorders ◽  
Positive Association ◽  
Brain Regions ◽  
Regions Of Interest ◽  
Cannabis Use ◽  
Similar Response ◽  
Frequency Of Use ◽  
The Brain

AimsSchizophrenia is notoriously becoming one of the world's most debilitating mental disorders, affecting 1 in 100 people. There is increasing evidence that neuroinflammation plays a part in the pathogenesis of schizophrenia and other psychotic disorders; microglial activity acting as a marker for neuroinflammatory reactions in the brain. Furthermore, cannabis is an illicit substance that also evokes a similar response in the neuroimmune activity. This project explores how cannabis exposure influences an elevation in neuroinflammatory responses through TSPO levels, and whether this information can help us determine if cannabis use and increased TSPO levels can be associated with a risk factor for developing psychosis.Method55 participants (36 males and 19 females) were recruited from the community by the IRIS (Inflammatory Reaction in Schizophrenia) team at the IoPPN, King's College London, from which 34 patients with a diagnosis of schizophrenia and 21 healthy controls took part in the study. The eligible participants underwent clinical assessments and PET scanning, from which cannabis use history and PET data were collected. Participant neuroinflammatory levels are represented by [18F]DPA-714 volume and different regions of grey matter in the brain were analysed through multivariate analyses, the confounding variables being age and TSPO genotype.ResultA statistically significant association is shown between participants who have had exposure to cannabis and participants who have not had any exposure in their lifetime. The differences across the prioritised brain regions of interest were robust, the association appearing more apparent and statistically significant in the total (p = .00) and temporal grey matter (p = .00) regions of the brain. This may suggest that cannabis exposure influences the [18F]DPA-714 VT in the significant regions of interest. However, a negative association is seen with current use, the quantity of use, and the frequency of use.ConclusionThe initial findings for cannabis exposure show us a positive association with increased TSPO levels, however, limitations must be taken into account. Although we cannot readily establish that elevated TSPO levels in cannabis users can presently act as a risk factor marker for developing psychosis from this particular study, we can utilise this data to continue our research in disclosing a new system to predict the occurrence of psychosis.

scholarly journals Précis of Neuroconstructivism: How the Brain Constructs Cognition

2008 ◽  
Vol 31 (3) ◽  
pp. 321-331 ◽  
Author(s):  
Sylvain Sirois ◽  
Michael Spratling ◽  
Michael S. C. Thomas ◽  
Gert Westermann ◽  
Denis Mareschal ◽  
...  
Keyword(s):  
Cognitive Development ◽  
Case Studies ◽  
Brain Regions ◽  
Object Representations ◽  
Phonological Development ◽  
Contextual Influences ◽  
Guiding Principle ◽  
Levels Of Organization ◽  
Atypical Development ◽  
The Brain

AbstractNeuroconstructivism: How the Brain Constructs Cognition proposes a unifying framework for the study of cognitive development that brings together (1) constructivism (which views development as the progressive elaboration of increasingly complex structures), (2) cognitive neuroscience (which aims to understand the neural mechanisms underlying behavior), and (3) computational modeling (which proposes formal and explicit specifications of information processing). The guiding principle of our approach is context dependence, within and (in contrast to Marr [1982]) between levels of organization. We propose that three mechanisms guide the emergence of representations: competition, cooperation, and chronotopy; which themselves allow for two central processes: proactivity and progressive specialization. We suggest that the main outcome of development is partial representations, distributed across distinct functional circuits. This framework is derived by examining development at the level of single neurons, brain systems, and whole organisms. We use the terms encellment, embrainment, and embodiment to describe the higher-level contextual influences that act at each of these levels of organization. To illustrate these mechanisms in operation we provide case studies in early visual perception, infant habituation, phonological development, and object representations in infancy. Three further case studies are concerned with interactions between levels of explanation: social development, atypical development and within that, developmental dyslexia. We conclude that cognitive development arises from a dynamic, contextual change in embodied neural structures leading to partial representations across multiple brain regions and timescales, in response to proactively specified physical and social environment.

Gray matter blood flow change is unevenly distributed during moderate isocapnic hypoxia in humans

2008 ◽  
Vol 104 (1) ◽  
pp. 212-217 ◽  
Author(s):  
Andrew P. Binks ◽  
Vincent J. Cunningham ◽  
Lewis Adams ◽  
Robert B. Banzett
Keyword(s):  
Blood Flow ◽  
Nucleus Accumbens ◽  
Positron Emission Tomography Imaging ◽  
Occipital Lobe ◽  
Brain Regions ◽  
Functional Brain Imaging ◽  
Regions Of Interest ◽  
Breath Hold ◽  
Obstructive Sleep ◽  
The Brain

Hypoxia increases cerebral blood flow (CBF), but it is unknown whether this increase is uniform across all brain regions. We used H215O positron emission tomography imaging to measure absolute blood flow in 50 regions of interest across the human brain ( n = 5) during normoxia and moderate hypoxia. Pco2 was kept constant (∼44 Torr) throughout the study to avoid decreases in CBF associated with the hypocapnia that normally occurs with hypoxia. Breathing was controlled by mechanical ventilation. During hypoxia (inspired Po2 = 70 Torr), mean end-tidal Po2 fell to 45 ± 6.3 Torr (means ± SD). Mean global CBF increased from normoxic levels of 0.39 ± 0.13 to 0.45 ± 0.13 ml/g during hypoxia. Increases in regional CBF were not uniform and ranged from 9.9 ± 8.6% in the occipital lobe to 28.9 ± 10.3% in the nucleus accumbens. Regions of interest that were better perfused during normoxia generally showed a greater regional CBF response. Phylogenetically older regions of the brain tended to show larger vascular responses to hypoxia than evolutionary younger regions, e.g., the putamen, brain stem, thalamus, caudate nucleus, nucleus accumbens, and pallidum received greater than average increases in blood flow, while cortical regions generally received below average increases. The heterogeneous blood flow distribution during hypoxia may serve to protect regions of the brain with essential homeostatic roles. This may be relevant to conditions such as altitude, breath-hold diving, and obstructive sleep apnea, and may have implications for functional brain imaging studies that involve hypoxia.

scholarly journals Correlations Among mRNA Expression Levels of ATP7A, Serum Ceruloplasmin Levels, and Neuronal Metabolism in Unmedicated Major Depressive Disorder

2020 ◽  
Vol 23 (10) ◽  
pp. 642-652 ◽  
Author(s):  
Xuanjun Liu ◽  
Shuming Zhong ◽  
Lan Yan ◽  
Hui Zhao ◽  
Ying Wang ◽  
...  
Keyword(s):  
Major Depressive Disorder ◽  
Depressive Disorder ◽  
Mrna Expression ◽  
Brain Regions ◽  
Regions Of Interest ◽  
Major Depressive ◽  
Expression Levels ◽  
Neuronal Metabolism ◽  
The Brain ◽  
Mrna Expression Levels

Abstract Background Previous studies have found that elevated copper levels induce oxidation, which correlates with the occurrence of major depressive disorder (MDD). However, the mechanism of abnormal cerebral metabolism of MDD patients remains ambiguous. The main function of the enzyme ATPase copper-transporting alpha (ATP7A) is to transport copper across the membrane to retain copper homeostasis, which is closely associated with the onset of mental disorders and cognitive impairment. However, less is known regarding the association of ATP7A expression in MDD patients. Methods A total of 31 MDD patients and 21 healthy controls were recruited in the present study. Proton magnetic resonance spectroscopy was used to assess the concentration levels of N-acetylaspartate, choline (Cho), and creatine (Cr) in brain regions of interest, including prefrontal white matter (PWM), anterior cingulate cortex (ACC), thalamus, lentiform nucleus, and cerebellum. The mRNA expression levels of ATP7A were measured using polymerase chain reaction (SYBR Green method). The correlations between mRNA expression levels of ATP7A and/or ceruloplasmin levels and neuronal biochemical metabolite ratio in the brain regions of interest were evaluated. Results The decline in the mRNA expression levels of ATP7A and the increase in ceruloplasmin levels exhibited a significant correlation in MDD patients. In addition, negative correlations were noted between the decline in mRNA expression levels of ATP7A and the increased Cho/Cr ratios of the left PWM, right PWM, and right ACC in MDD patients. A positive correlation between elevated ceruloplasmin levels and increased Cho/Cr ratio of the left PWM was noted in MDD patients. Conclusions The findings suggested that the decline in the mRNA expression levels of ATP7A and the elevated ceruloplasmin levels induced oxidation that led to the disturbance of neuronal metabolism in the brain, which played important roles in the pathophysiology of MDD. The decline in the mRNA expression levels of ATP7A and the elevated ceruloplasmin levels affected neuronal membrane metabolic impairment in the left PWM, right PWM, and right ACC of MDD patients.

scholarly journals A tool for analyzing electrode tracks from slice histology

2018 ◽  
Author(s):  
Philip Shamash ◽  
Matteo Carandini ◽  
Kenneth D Harris ◽  
Nicholas A Steinmetz
Keyword(s):  
Data Analysis ◽  
Brain Slices ◽  
Brain Regions ◽  
Regions Of Interest ◽  
Brain Atlas ◽  
Essential Step ◽  
Pass Through ◽  
Manual Input ◽  
The Brain ◽  
Allen Mouse Brain Atlas

It is now possible to record from hundreds of neurons across multiple brain regions in a single electrophysiology experiment. An essential step in the ensuing data analysis is to assign recorded neurons to the correct brain regions. Brain regions are typically identified after the recordings by comparing images of brain slices to a reference atlas by eye. This introduces error, in particular when slices are not cut at a perfectly coronal angle or when electrode tracks span multiple slices. Here we introduce SHARP-Track, a tool to localize regions of interest and plot the brain regions they pass through. SHARP-Track offers a MATLAB user interface to explore the Allen Mouse Brain Atlas, register asymmetric slice images to the atlas using manual input, and interactively analyze electrode tracks. We find that it reduces error compared to localizing electrodes in a reference atlas by eye. See github.com/cortex-lab/allenCCF for the software and wiki.

scholarly journals Investigating Regional Specificity of Alzheimers Disease Pathology in the 5xFAD Mouse Model

2021 ◽  
Author(s):  
Araba Gyan ◽  
Emily D Glass ◽  
Tamara Stevenson ◽  
Geoffrey G Murphy ◽  
Shannon Moore
Keyword(s):  
Fluorescent Antibody ◽  
Brain Regions ◽  
Plaque Formation ◽  
Regions Of Interest ◽  
The Other ◽  
Alzheimers Disease ◽  
5Xfad Mouse ◽  
Regional Specificity ◽  
The Brain ◽  
Different Levels

Alzheimers disease (AD) is a neurodegenerative disease that affects cognition and memory. Mouse models such as 5xFAD, incorporate mutations found in familial or early-onset (EOAD) AD; these mutations increase the production of the toxic Aβ species that contributes to plaque formation in the brain. However, not all brain regions in the 5xAD animals accumulate plaques to the same degree. For example, the cerebellum appears to be resistant to AB plaque formation, while other regions such as the cortex and subiculum develop copious plaques. The mechanism(s) underlying this regional specificity remains unclear. Thus, we used a fluorescent antibody to APP/Aβ to quantify the amount of these proteins in several brain regions of interest, including subiculum, cortex, and cerebellum. We found that the cerebellum had less APP/Aβ than the other regions quantified, which demonstrates a correlation between the levels of APP/Aβ and plaque formation. Taken together, this suggests that the regional specificity of AD pathology may be a result of different levels of protein expression.

Vorläufige Ergebnisse von 99mTc-HMPAO-SPECT-Untersuchungen bei endogenen Psychosen

1989 ◽  
Vol 28 (03) ◽  
pp. 88-91
Author(s):  
J. Schröder ◽  
H. Henningsen ◽  
H. Sauer ◽  
P. Georgi ◽  
K.-R. Wilhelm
Keyword(s):  
Blood Flow ◽  
Cerebral Blood Flow ◽  
Regional Cerebral Blood Flow ◽  
Regions Of Interest ◽  
Post Mortem ◽  
Regional Cerebral Blood ◽  
Hmpao Spect ◽  
Endogenous Psychoses ◽  
The Brain ◽  
99Mtc Hmpao

18 psychopharmacologically treated patients (7 schizophrenics, 5 schizoaffectives, 6 depressives) were studied using 99mTc-HMPAO-SPECT of the brain. The regional cerebral blood flow was measured in three transversal sections (infra-/supraventricular, ventricular) within 6 regions of interest (ROI) respectively (one frontal, one parietal and one occipital in each hemisphere). Corresponding ROIs of the same section in each hemisphere were compared. In the schizophrenics there was a significantly reduced perfusion in the left frontal region of the infraventricular and ventricular section (p < 0.02) compared with the data of the depressives. The schizoaffectives took an intermediate place. Since the patients were treated with psychopharmaca, the result must be interpreted cautiously. However, our findings seem to be in accordance with post-mortem-, CT- and PET-studies presented in the literature. Our results suggest that 99mTc-HMPAO-SPECT may be helpful in finding cerebral abnormalities in endogenous psychoses.

TIMELESS BUILDINGS AND THE HUMAN BRAIN: The Effect of Spiritual Spaces on Human Brain Waves

2014 ◽  
Vol 8 (1) ◽  
pp. 133
Author(s):  
Sally M. Essawy ◽  
Basil Kamel ◽  
Mohamed S. Elsawy
Keyword(s):  
Human Brain ◽  
Case Studies ◽  
Spiritual Experience ◽  
Brain Wave ◽  
Human Comfort ◽  
Beliefs And Practices ◽  
Brain Waves ◽  
Space Design ◽  
State Of Mind ◽  
The Brain

Some buildings hold certain qualities of space design similar to those originated from nature in harmony with its surroundings. These buildings, mostly associated with religious beliefs and practices, allow for human comfort and a unique state of mind. This paper aims to verify such effect on the human brain. It concentrates on measuring brain waves when the user is located in several spots (coordinates) in some of these buildings. Several experiments are conducted on selected case studies to identify whether certain buildings affect the brain wave frequencies of their users or not. These are measured in terms of Brain Wave Frequency Charts through EEG Device. The changes identified on the brain were then translated into a brain diagram that reflects the spiritual experience all through the trip inside the selected buildings. This could then be used in architecture to enhance such unique quality.

Management of Glioblastoma Multiforme by Phytochemicals: Applications of Nanoparticle Based Targeted Drug Delivery System

2020 ◽  
Vol 21 ◽  
Author(s):  
Sayed Md Mumtaz ◽  
Gautam Bhardwaj ◽  
Shikha Goswami ◽  
Rajiv Kumar Tonk ◽  
Ramesh K. Goyal ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Glioblastoma Multiforme ◽  
Drug Delivery System ◽  
Delivery System ◽  
Genetic Disorder ◽  
Drug Regimen ◽  
Brain Regions ◽  
Radio Therapy ◽  
Novel Drug ◽  
The Brain

: The Glioblastoma Multiforme (GBM; grade IV astrocytoma) exhort tumor of star-shaped glial cell in the brain. It is a fast-growing tumor that spreads to nearby brain regions specifically to cerebral hemispheres in frontal and temporal lobes. The etiology of GBM is unknown, but major risk factors are genetic disorder like neurofibromatosis and schwanomatosis which develop the tumor in the nervous system. The management of GBM with chemo-radio therapy leads to resistance and current drug regimen like Temozolomide (TMZ) is less efficacious. The reasons behind failure of drugs are due to DNA alkylation in cell cycle by enzyme DNA guanidase and mitochondrial dysfunction. Naturally occurring bio-active compounds from plants known as phytochemicals, serve as vital sources for anti-cancer drugs. Some typical examples include taxol analogs, vinca alkaloids such as vincristine, vinblastine, podophyllotoxin analogs, camptothecin, curcumin, aloe emodin, quercetin, berberine e.t.c. These phytochemicals often act via regulating molecular pathways which are implicated in growth and progression of cancers. However the challenges posed by the presence of BBB/BBTB to restrict passage of these phytochemicals, culminates in their low bioavailability and relative toxicity. In this review we integrated nanotech as novel drug delivery system to deliver phytochemicals from traditional medicine to the specific site within the brain for the management of GBM.

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