Biology subjects

Holla, B.

Publications and source records attributed to Holla, B..

5 recordsLinked to original sources

bioRxiv2022

Federated analysis in COINSTAC reveals functional network connectivity and spectral links to smoking and alcohol consumption in nearly 2,000 adolescent brains

With the growth of decentralized/federated analysis approaches in neuroimaging, the opportunities to study brain disorders using data from multiple sites has grown multi-fold. One such initiative is the Neuromark, a fully automated spatially constrained independent component analysis (ICA) that is used to link brain network abnormalities among different datasets, studies, and disorders while leveraging subject-specific networks. In this study, we implement the neuromark pipeline in COINSTAC, an open-source neuroimaging framework for collaborative/decentralized analysis. Decentralized analysis of nearly 2000 resting-state functional magnetic resonance imaging datasets collected at different sites across two cohorts and co-located in different countries was performed to study the resting brain functional network connectivity changes in adolescents who smoke and consume alcohol. Results showed hypoconnectivity across the majority of networks including sensory, default mode, and subcortical domains, more for alcohol than smoking, and decreased low frequency power. These findings suggest that global reduced synchronization is associated with both tobacco and alcohol use. This work demonstrates the utility and incentives associated with large-scale decentralized collaborations spanning multiple sites.

bioinformatics↗

bioRxiv2020

Protocol for Magnetic Resonance Imaging Acquisition, Quality Assurance, and Quality Check for the Accelerator Program for Discovery in Brain Disorders using Stem Cells

ObjectiveThe Accelerator Program for Discovery in Brain Disorders using Stem Cells (ADBS) is a longitudinal study focused on collecting and analysing clinical, neuropsychological, neurophysiological, and multimodal neuroimaging data from five cohorts of patients with major psychiatric disorders from genetically high-risk families, their unaffected first-degree relatives, and healthy subjects. Here, we present a complete description of the acquisition of multimodal MRI data along with the quality assurance (QA) and quality check (QC) procedures that we are following in this study. MethodsThe QA procedure consists of monitoring of different quantitative measurements using an agar gel and a geometrical phantom. For the already acquired data from human subjects, we describe QC steps for each imaging modality. To quantify reliability of outcome measurements, we perform test-retest reliability on human volunteers. ResultsWe have presented results from analysis of phantom data and test-retest reliability on a human volunteer. Results show consistency in data acquisition and reliable quantification of different outcome measurements. ConclusionThe acquisition protocol and QA-QC procedures described here can yield consistent and reliable outcome measures. We hope to acquire and eventually release high quality longitudinal neuroimaging dataset that will serve the scientific community and pave the way for interesting discoveries.

neuroscience↗

bioRxiv2020

A series of five population-specific Indian brain templates and atlases spanning ages 6 to 60 years

Anatomical brain templates are commonly used as references in neurological MRI studies, for bringing data into a common space for group-level statistics and coordinate reporting. Given the inherent variability in brain morphology across age and geography, it is important to have templates that are as representative as possible for both age and population. A representative-template increases the accuracy of alignment, decreases distortions as well as potential biases in final coordinate reports. In this study, we developed and validated a new set of T1w Indian brain templates (IBT) from a large number of brain scans (total n=466) acquired across different locations and multiple 3T MRI scanners in India. A new tool in AFNI, make_template_dask.py, was created to efficiently make five age-specific IBTs (ages 6-60 years) as well as maximum probability map (MPM) atlases for each template; for each age-groups template-atlas pair, there is both a "population-average" and a "typical" version. Validation experiments on an independent Indian structural and functional-MRI dataset show the appropriateness of IBTs for spatial normalization of Indian brains. The results indicate significant structural differences when comparing the IBTs and MNI template, with these differences being maximal along the Anterior-Posterior and Inferior-Superior axes, but minimal Left-Right. For each age-group, the MPM brain atlases provide reasonably good representation of the native-space volumes in the IBT space, except in a few regions with high inter-subject variability. These findings provide evidence to support the use of age and population-specific templates in human brain mapping studies. This dataset is made publicly available (https://hollabharath.github.io/IndiaBrainTemplates). HighlightsO_LIA new set of age-specific T1w Indian brain templates for ages 6-60 yr are developed and validated. C_LIO_LIA new AFNI tool, make_template_dask.py, for the creation of group-based templates. C_LIO_LIMaximum probability map atlases are also provided for each template. C_LIO_LIResults indicate the appropriateness of Indian templates for spatial normalization of Indian brains C_LI

neuroscience↗

bioRxiv2019

Decentralized multi-site VBM analysis during adolescence shows structural changes linked to age, body mass index, and smoking: A COINSTAC analysis

In the recent past, there has been an upward trend in developing frameworks that enable neuroimaging researchers to address challenging questions by leveraging data across multiple sites all over the world. One such framework, Collaborative Informatics and Neuroimaging Suite Toolkit for Anonymous Computation (COINSTAC), provides a platform to analyze neuroimaging data stored locally across multiple organizations without the need for pooling the data at any point during the analysis. In this paper, we perform a decentralized voxel-based morphometry analysis of structural magnetic resonance imaging data across two different sites to understand the structural changes in the brain as linked to age, body mass index and smoking. Results produced by the decentralized analysis are contrasted with similar findings in literature. This work showcases the potential benefits of performing multi-voxel and multivariate analyses of large-scale neuroimaging data located at multiple sites.

neuroscience↗

bioRxiv2019

Adverse childhood experiences in families with multiple members diagnosed to have psychiatric illnesses

ObjectiveAdverse Childhood Experiences (ACEs) are linked to the development of a number of psychiatric illnesses in adulthood. Our study examined the pattern of ACEs and their relation to the age of onset (AAO) of major psychiatric conditions in individuals from families that had [≥] 2 first degree relatives with major psychiatric conditions (multiplex families) identified as part of an ongoing longitudinal study.\n\nMethodsOur sample consisted of 509 individuals from 215 families. Of these, 268 were affected i.e diagnosed with bipolar disorder (BPAD) (n=61), obsessive-compulsive disorder (OCD) (n=58), schizophrenia (n=52), substance dependence (SUD) (n=59), or co-occurring diagnoses (n=38); while 241 were at-risk first degree relatives (FDRs) who were either unaffected (n=210) or had other depressive or anxiety disorders (n=31). All individuals were evaluated using the Adverse Childhood Experiences - International Questionnaire (ACE-IQ) and ACE binary and frequency scores were calculated.\n\nResultsIt was seen that affected males, as a group, had the greatest ACE scores in our sample. A cox mixed-effects model fit by gender revealed that higher ACE binary and frequency scores were associated with significantly increased risk for an earlier AAO of psychiatric diagnoses in males. A similar model that evaluated the effect of diagnosis revealed an earlier AAO in OCD and SUD, but not in schizophrenia and BPAD.\n\nConclusionsOur study indicates that ACEs brought forward the onset of major psychiatric conditions in men and in individuals diagnosed with OCD and SUD. Ongoing longitudinal assessments in FDRs from these families are expected to identify mechanisms underlying this relationship.

neuroscience↗