Prasun Kumar Roy

Bio: Prasun Kumar Roy is an academic researcher from National Brain Research Centre. The author has contributed to research in topics: Fractional anisotropy & Diffusion MRI. The author has an hindex of 8, co-authored 35 publications receiving 317 citations. Previous affiliations of Prasun Kumar Roy include Indian Institute of Technology (BHU) Varanasi & Indian Institute of Technology Delhi.

Magnetic resonance image enhancement using stochastic resonance in Fourier domain

Abstract: Objective In general, low-field MRI scanners such as the 0.5- and 1-T ones produce images that are poor in quality. The motivation of this study was to lessen the noise and enhance the signal such that the image quality is improved. Here, we propose a new approach using stochastic resonance (SR)-based transform in Fourier space for the enhancement of magnetic resonance images of brain lesions, by utilizing an optimized level of Gaussian fluctuation that maximizes signal-to-noise ratio (SNR). Materials and Methods We acquired the T1-weighted MR image of the brain in DICOM format. We processed the original MR image using the proposed SR procedure. We then tested our approach on about 60 patients of different age groups with different lesions, such as arteriovenous malformation, benign lesion and malignant tumor, and illustrated the image enhancement by using just-noticeable difference visually as well as by utilizing the relative enhancement factor quantitatively. Results Our method can restore the original image from noisy image and optimally enhance the edges or boundaries of the tissues, clarify indistinct structural brain lesions without producing ringing artifacts, as well as delineate the edematous area, active tumor zone, lesion heterogeneity or morphology, and vascular abnormality. The proposed technique improves the enhancement factor better than the conventional techniques like the Wiener- and wavelet-based procedures. Conclusions The proposed method can readily enhance the image fusing a unique constructive interaction of noise and signal, and enables improved diagnosis over conventional methods. The approach well illustrates the novel potential of using a small amount of Gaussian noise to improve the image quality.

Aging alterations in whole-brain networks during adulthood mapped with the minimum spanning tree indices : The interplay of density, connectivity cost and life-time trajectory

Abstract: The organizational network changes in the human brain across the lifespan have been mapped using functional and structural connectivity data. Brain network changes provide valuable insights into the processes underlying senescence. Nonetheless, the altered network density in the elderly severely compromises the usefulness of network analysis to study the aging brain. We successfully circumvented this problem by focusing on the critical structural network backbone, using a robust tree representation. Whole-brain networks' minimum spanning trees were determined in a dataset of diffusion-weighted images from 382 healthy subjects, ranging in age from 20.2 to 86.2 years. Tree-based metrics were compared with classical network metrics. In contrast to the tree-based metrics, classical metrics were highly influenced by age-related changes in network density. Tree-based metrics showed linear and non-linear correlation across adulthood and are in close accordance with results from previous histopathological characterizations of the changes in white matter integrity in the aging brain.

Age-Related Differences in White Matter Integrity in Healthy Human Brain: Evidence from Structural MRI and Diffusion Tensor Imaging.

Abstract: The aim is to investigate the relationship between microstructural white matter (WM) diffusivity indices and macrostructural WM volume (WMV) among healthy individuals (20–85 years). Whole-brain diffusion measures were calculated from diffusion tensor imaging using FMRIB software library while WMV was estimated through voxel-based morphometry, and voxel-based analysis was carried out using tract-based spatial statistics. Our results revealed that mean diffusivity, axial diffusivity, and radial diffusivity had shown good correlation with WMV but not for fractional anisotropy (FA). Voxel-wise tract-based spatial statistics analysis for FA showed a significant decrease in four regions for middle-aged group compared to young-aged group, in 22 regions for old-aged group compared to middle-aged group, and in 26 regions for old-aged group compared to young-aged group (P < 0.05). We found significantly lower WMV, FA, and mean diffusivity values in females than males and inverted-U trend for FA in males. We conclude differential age- and gender-related changes for structural WMV and WM diffusion indices.

Systems Biology of Immunomodulation for Post-Stroke Neuroplasticity: Multimodal Implications of Pharmacotherapy and Neurorehabilitation.

Abstract: AIMS: Recent studies indicate that anti-inflammatory drugs, act as a double-edged sword, not only exacerbating secondary brain injury but also contributing to neurological recovery after stroke. Our aim is to explore whether there is a beneficial role for neuroprotection and functional recovery using antiinflammatory drug along with neurorehabilitation therapy using transcranial direct current stimulation (tDCS) and repetitive transcranial magnetic stimulation (rTMS), so as to improve functional recovery after ischemic stroke. METHODS: We develop a computational systems biology approach from preclinical data using ordinary differential equations, to study the behavior of both phenotypes of microglia such as M1 type (pro-inflammatory) vis-a-vis M2 type (anti-inflammatory) under anti-inflammatory drug action (minocycline). We explore whether pharmacological treatment along with cerebral stimulation using tDCS and rTMS is beneficial or not. We utilize the systems pathway analysis of minocycline in NF-κB (nuclear factor kappa beta) signaling and neurorehabilitation therapy using tDCS and rTMS which act through brain-derived neurotrophic factor (BDNF) and tropomyosin-related kinase B (TrkB) signaling pathways. RESULTS: We demarcate the role of neuroinflammation and immunomodulation in post-stroke recovery, under minocycline activated microglia and neuroprotection together with improved neurogenesis, synaptogenesis and functional recovery under the action of rTMS or tDCS. We elucidate the feasibility of utilizing rTMS/tDCS to increase neuroprotection across the reperfusion stage during minocycline administration. We delineate that the signaling pathways of minocycline by modulation of inflammatory genes in NF-κB and proteins activated by tDCS and rTMS through BDNF, Trk-B and Calmodulin kinase (CaMK) signaling. Utilizing systems biology approach, we show the activation pathways for pharmacotherapy (minocycline) and neurorehabilitation (rTMS applied to ipsilesional cortex and tDCS) results into increased neuronal and synaptic activity that commonly occur through activation of N-methyl-D-aspartate (NMDA) receptors. We construe that considerable additive neuroprotection effect would be obtained and delayed reperfusion injury can be remedied, if one uses multimodal intervention of minocycline together with tDCS and rTMS. CONCLUSION: Additive beneficial effect is thus noticed for pharmacotherapy along with neurorehabilitation therapy, by maneuvering the dynamics of immunomodulation using anti-inflammatory drug and cerebral stimulation for augmenting the functional recovery after stroke, which may engender clinical applicability for enhancing plasticity, rehabilitation and neurorestoration.

A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility.

Abstract: There is great need for coordination around standards and best practices in neuroscience to support efforts to make neuroscience a data-centric discipline. Major brain initiatives launched around the world are poised to generate huge stores of neuroscience data. At the same time, neuroscience, like many domains in biomedicine, is confronting the issues of transparency, rigor, and reproducibility. Widely used, validated standards and best practices are key to addressing the challenges in both big and small data science, as they are essential for integrating diverse data and for developing a robust, effective, and sustainable infrastructure to support open and reproducible neuroscience. However, developing community standards and gaining their adoption is difficult. The current landscape is characterized both by a lack of robust, validated standards and a plethora of overlapping, underdeveloped, untested and underutilized standards and best practices. The International Neuroinformatics Coordinating Facility (INCF), an independent organization dedicated to promoting data sharing through the coordination of infrastructure and standards, has recently implemented a formal procedure for evaluating and endorsing community standards and best practices in support of the FAIR principles. By formally serving as a standards organization dedicated to open and FAIR neuroscience, INCF helps evaluate, promulgate, and coordinate standards and best practices across neuroscience. Here, we provide an overview of the process and discuss how neuroscience can benefit from having a dedicated standards body.

Effects of aging on functional and structural brain connectivity.

Abstract: Over the past decade there has been an enormous rise in the application of functional and structural connectivity approaches to explore the brain's intrinsic organization in healthy and clinical populations. The notion underlying the application of these approaches to study aging is that subtle age-related disruption of the brain's regional integrity and information flow across the brain, are expressed by age-related differences in functional and structural connectivity. In this review I will discus recent advances in our understanding of how age affects our brain's intrinsic organization, and I will share my perspective on potential challenges and future directions of the field.

Application of Graph Theory for Identifying Connectivity Patterns in Human Brain Networks: A Systematic Review.

Abstract: Background: Analysis of the human connectome using functional magnetic resonance imaging (fMRI) started in the mid-1990s and attracted increasing attention in attempts to discover the neural underpinnings of human cognition and neurological disorders. In general, brain connectivity patterns from fMRI data are classified as statistical dependencies (functional connectivity) or causal interactions (effective connectivity) among various neural units. Computational methods, especially graph theory-based methods, have recently played a significant role in understanding brain connectivity architecture. Objectives: Thanks to the emergence of graph theoretical analysis, the main purpose of the current paper is to systematically review how brain properties can emerge through the interactions of distinct neuronal units in various cognitive and neurological applications using fMRI. Moreover, this article provides an overview of the existing functional and effective connectivity methods used to construct the brain network, along with their advantages and pitfalls. Methods: In this systematic review, the databases Science Direct, Scopus, arXiv, Google Scholar, IEEE Xplore, PsycINFO, PubMed, and SpringerLink are employed for exploring the evolution of computational methods in human brain connectivity from 1990 to the present, focusing on graph theory. The Cochrane Collaboration's tool was used to assess the risk of bias in individual studies. Results: Our results show that graph theory and its implications in cognitive neuroscience have attracted the attention of researchers since 2009 (as the Human Connectome Project launched), because of their prominent capability in characterizing the behavior of complex brain systems. Although graph theoretical approach can be generally applied to either functional or effective connectivity patterns during rest or task performance, to date, most articles have focused on the resting-state functional connectivity. Conclusions: This review provides an insight into how to utilize graph theoretical measures to make neurobiological inferences regarding the mechanisms underlying human cognition and behavior as well as different brain disorders.

Optimal imaging parameters for fibre-orientation estimation in diffusion MRI

Abstract: This study uses Monte Carlo simulations to investigate the optimal value of the diffusion weighting factor b for estimating white-matter fiber orientations using diffusion MRI with a standard spherical sampling scheme. We devise an algorithm for determining the optimal echo time, pulse width, and pulse separation in the pulsed-gradient spin-echo sequence for a specific value of b. The Monte Carlo simulations provide an estimate of the optimal value of b for recovering one and two fiber orientations. We show that the optimum is largely independent of the noise level in the measurements and the number of gradient directions and that the optimum depends only weakly on the diffusion anisotropy, the maximum gradient strength, and the spin-spin relaxation time. The optimum depends strongly on the mean diffusivity. In brain tissue, the optima we estimate are in the ranges [0.7, 1.0] x 10(9) s m(-2) and [2.2, 2.8] x 10(9) s m(-2) for the one- and two-fiber cases, respectively. The best b for estimating the fractional anisotropy is slightly higher than for estimating fiber directions in the one-fiber case and slightly lower in the two-fiber case. To estimate Tr(D) in the one-fiber case, the optimal setting is higher still. Simulations suggest that a ratio of high to low b measurements of 5 to 1 is a good compromise for measuring fiber directions and size and shape indices.

Development of brain structural connectivity between ages 12 and 30: A 4-Tesla diffusion imaging study in 439 adolescents and adults

Abstract: Understanding how the brain matures in healthy individuals is critical for evaluating deviations from normal development in psychiatric and neurodevelopmental disorders. The brain's anatomical networks are profoundly re-modeled between childhood and adulthood, and diffusion tractography offers unprecedented power to reconstruct these networks and neural pathways in vivo. Here we tracked changes in structural connectivity and network efficiency in 439 right-handed individuals aged 12 to 30 (211 female/126 male adults, mean age=23.6, SD=2.19; 31 female/24 male 12 year olds, mean age=12.3, SD=0.18; and 25 female/22 male 16 year olds, mean age=16.2, SD=0.37). All participants were scanned with high angular resolution diffusion imaging (HARDI) at 4 T. After we performed whole brain tractography, 70 cortical gyral-based regions of interest were extracted from each participant's co-registered anatomical scans. The proportion of fiber connections between all pairs of cortical regions, or nodes, was found to create symmetric fiber density matrices, reflecting the structural brain network. From those 70 × 70 matrices we computed graph theory metrics characterizing structural connectivity. Several key global and nodal metrics changed across development, showing increased network integration, with some connections pruned and others strengthened. The increases and decreases in fiber density, however, were not distributed proportionally across the brain. The frontal cortex had a disproportionate number of decreases in fiber density while the temporal cortex had a disproportionate number of increases in fiber density. This large-scale analysis of the developing structural connectome offers a foundation to develop statistical criteria for aberrant brain connectivity as the human brain matures.