Biology subjects

Bhattacharya, J.

Publications and source records attributed to Bhattacharya, J..

24 records · Page 2Linked to original sources

bioRxiv2020

Geospatial HIV-1 subtype C gp120 sequence diversity and its predicated impact on broadly neutralizing antibody sensitivity

Evolving diversity in globally circulating HIV-1 subtypes presents formidable challenge in defining and developing neutralizing antibodies for prevention and treatment. HIV-1 subtype C is responsible for majority of global HIV-1 infections. Broadly neutralizing antibodies (bnAbs) capable of neutralizing distinct HIV-1 subtypes by targeting conserved vulnerable epitopes on viral envelope protein (Env) are being considered as promising antiviral agents for prevention and treatment. In the present study, we examined the diversity in genetic signatures and attributes that differentiate region-specific global HIV-1 subtype C gp120 sequences associated with virus neutralization outcomes to key bnAbs having distinct epitope specificities. A total of 1814 full length HIV-1 subtype C gp120 sequence from 37 countries were retrieved from Los Alamos National Laboratory HIV database (www.hiv.lanl.gov). The amino acid sequences were assessed for their phylogenetic association, variable loop lengths and prevalence of potential N-linked glycosylation sites (pNLGS). Responses of these sequences to bnAbs were predicted with a machine learning algorithm bNAb-ReP and compared with those reported in the CATNAP database. Phylogenetically, sequences from Asian countries including India clustered together however differed significantly when compared with pan African subtype C sequences. Variable loop lengths within Indian and African clusters were distinct from each other, specifically V1, V2 and V4 loops. Furthermore, V1V2 and V2 alone sequences were also found to vary significantly in their charges. Pairwise analyses at each of the 25 pNLG sites indicated distinct country specific profiles. Highly significant differences (p<0.001***) were observed in prevalence of four pNLGS (N130, N295, N392 and N448) between South Africa and India, having most disease burden associated with subtype C. Our findings highlight that the distinctly evolving clusters within global intra-subtype C gp120 sequences are likely to influence the disparate region-specific sensitivity of circulating HIV-1 subtype C to bnAbs.

bioinformatics↗

bioRxiv2020

Dynamics of the COVID -19 Related Publications

BackgroundThis study aims to analyze the dynamics of the published articles and preprints of Covid-19 related literature from different scientific databases and sharing platforms. MethodsThe PubMed, Elsevier, and Research Gate (RG) databases were under consideration in this study over a specific time. Analyses were carried out on the number of publications as (a) function of time (day), (b) journals and (c) authors. Doubling time of the number of publications was analyzed for PubMed "all articles" and Elsevier published articles. Analyzed databases were (1A) PubMed "all articles" (01/12/2019-12/06/2020) (1B) PubMed Review articles (01/12/2019-2/5/2020) and (1C) PubMed Clinical Trials (01/01/2020-30/06/2020) (2) Elsevier all publications (01/12/2019-25/05/2020) (3) RG (Article, Pre Print, Technical Report) (15/04/2020-30/4/2020). FindingsTotal publications in the observation period for PubMed, Elsevier, and RG were 23000, 5898 and 5393 respectively. The average number of publications/day for PubMed, Elsevier and RG were 70.0 {+/-}128.6, 77.6{+/-}125.3 and 255.6{+/-}205.8 respectively. PubMed shows an avalanche in the number of publication around May 10, number of publications jumped from 6.0{+/-}8.4/day to 282.5{+/-}110.3/day. The average doubling time for PubMed, Elsevier, and RG was 10.3{+/-}4 days, 20.6 days, and 2.3{+/-}2.0 days respectively. In PubMed average articles/journal was 5.2{+/-}10.3 and top 20 authors representing 935 articles are of Chinese descent. The average number of publications per author for PubMed, Elsevier, and RG was 1.2{+/-}1.4, 1.3{+/-}0.9, and 1.1{+/-}0.4 respectively. Subgroup analysis, PubMed review articles mean and median review time for each article were <0|17{+/-}17|77> and 13.9 days respectively; and reducing at a rate of-0.21 days (count)/day. InterpretationAlthough the disease has been known for around 6 months, the number of publications related to the Covid-19 until now is huge and growing very fast with time. It is essential to rationalize the publications scientifically by the researchers, authors, reviewers, and publishing houses. FundingNone

scientific communication and education↗

bioRxiv2020

Causally Linking Neural Dominance to Perceptual Dominance in a Multisensory Conflict

When different senses are in conflict, one sense may dominate the perception of other sense, but it is not known whether the sensory cortex associated with the dominant modality exerts directional influence, at the functional brain level, over the sensory cortex associated with the dominated modality; in short, the link between sensory dominance and neuronal dominance is not established. In a task involving audio-visual conflict, using magnetoencephalography recordings in humans, we first demonstrated that the neuronal dominance - visual cortex being functionally influenced by the auditory cortex - was associated with the sensory dominance - participants visual perception being qualitatively altered by sound. Further, we found that prestimulus auditory-to-visual connectivity could predict the perceptual outcome on a trial-by-trial basis. Subsequently, we performed an effective connectivity-guided neurofeedback electroencephalography experiment and showed that participants who were briefly trained to increase the neuronal dominance from auditory to visual cortex also showed higher sensory, i.e. auditory, dominance during the conflict task immediately after the training. The results shed new light into the interactive neuronal nature of multisensory integration and open up exciting opportunities by enhancing or suppressing targeted mental functions subserved by effective connectivity.

neuroscience↗

bioRxiv2020

Linking flexibility of brain networks to cognitive development in preschool children

Recent studies of functional connectivity networks (FCNs) suggest that the reconfiguration of brain network across time, both at rest and during task, is linked with cognition in human adults. In this study, we tested this prediction, i.e. cognitive ability is associated with a flexible brain network in preschool children of 3-4 years - a critical age, representing a blossoming period for brain development. We recorded magnetoen-cephalogram (MEG) data from 88 preschoolers, and assessed their cognitive ability by a battery of cognitive tests. We estimated FCNs obtained from the source reconstructed MEG recordings, and characterized the temporal variability at each node using a novel path-based measure of temporal variability; the latter captures reconfiguration of the nodes interactions to the rest of the network across time. Using connectome predictive modeling, we demonstrated that the temporal variability of fronto-temporal nodes in the dynamic FCN can reliably predict out-of-scanner performance of short-term memory and attention distractability in novel participants. Further, we observed that the network-level temporal variability increased with age, while individual nodes exhibited an inverse relationship between temporal variability and node centrality. These results demonstrate that functional brain networks, and especially their reconfiguration ability, are important to cognition at an early but a critical stage of human brain development.

neuroscience↗

bioRxiv2018

Cardiac afferent activity modulates early neural signature of error detection during skilled performance

Behavioral adaptations during performance rely on predicting and evaluating the consequences of our actions through action monitoring. Previous studies revealed that proprioceptive and exteroceptive signals contribute to error-monitoring processes, which are implemented in the posterior medial frontal cortex. Interestingly, errors trigger changes in autonomic nervous system activity such as pupil dilation or heartbeat deceleration. Yet, the contribution of implicit interoceptive signals of bodily states to error-monitoring during ongoing performance has been overlooked. This is more surprising given the evidence on the relevance of interoceptive signals for the modulation of perceptual, affective and cognitive processes.\n\nWe investigated whether cardiovascular interoceptive signals influence the neural correlates of error processing during performance, with an emphasis on the early stages of error processing. We recorded participants electroencephalography and electrocardiogram during the performance of highly-trained music pieces in musicians. Previous event-related potential (ERP) studies revealed that pitch errors during skilled musical performance are preceded by an error detection signal, the pre-error-negativity (preERN), and followed by a later error positivity (PE). In this study, by combining ERP, source localization and multivariate pattern classification analysis, we found that the error-correct ERP waveform had a larger amplitude within 40-100 ms following errors in the systolic period of the cardiac cycle. This component could be decoded from single-trials, was dissociated from the preERN and PE, and stemmed from the inferior parietal cortex, which is a region implicated in cardiac autonomic regulation. In addition, the cardiac phase influenced behavioral alterations resulting from errors, with a smaller post-error slowing and less perturbed velocity in keystrokes following pitch errors in the systole phase of the cardiac cycle. This study provides the first evidence of preconscious visceral information modulating neural and behavioral responses related to early error monitoring during skilled performance.

neuroscience↗

bioRxiv2017

Systematic Identification of Correlates of HIV-1 Infection: An X-Wide Association Study in Zambia

BackgroundHIV-1 remains the leading cause of death among adults in Sub-Saharan Africa, and over 1 million people are infected annually. Better identification of at-risk groups could benefit prevention and treatment programmes. We systematically identified factors related to HIV-1 infection in two nationally representative cohorts of women that participated in Zambias Demographic and Health Surveys (DHS).\n\nMethodsWe conducted a comprehensive analysis to identify and replicate the association of 1,415 social, economic, environmental, and behavioral indicators with HIV-1 status. We used the 2007 and 2013-2014 DHS surveys conducted among 5,715 and 15,433 Zambian women, respectively (727 indicators in 2007; 688 in 2013-2014; 688 in both). We used false discovery rate criteria to identify indicators that are strongly associated with HIV-1 in univariate and multivariate models in the entire population, as well as in subgroups stratified by wealth, residence, age, and history of HIV-1 testing.\n\nFindingsIn the univariate analysis we identified 102 and 182 variables that are associated with HIV-1 in the 2007 and 2013-2014 surveys, respectively, among which 79 were associated in both. Variables that were associated with HIV-1 status in all full-sample models (unadjusted and adjusted) as well as in at least 17 out of 18 subgroups include being formerly in a union (adjusted OR 2007 2.8, p<10-16; 2013-2014 2.8, p<10-29), widowhood (adjusted OR 2007 3.7, p<10-12; 2013-2014 4.2, p<10-30), history of genital ulcers in the last 12 months (adjusted 2007 OR 2.4, p<10-5; 2013-2014 2.2, p<10-6), and having a woman for the head of the household (2007 OR 1.7, p<10-7; 2013-2014 OR 2.1, p<10-26), while owning a bicycle (adjusted 2007 OR 0.6, p<10-6; 2013-2014 0.6, p<10-8) and currently breastfeeding (adjusted 2007 OR 0.5, p<10-9; 2013-2014 0.4, p<10-26) were associated with decreased risk. Using the identified variables, area under the curve for HIV-1 positivity ranged from 0.76 to 0.82.\n\nInterpretationOur X-wide association study in Zambian women identifies multiple under-recognized factors correlated with HIV-1 infection in 2007 and 2013-2014, including widowhood, breastfeeding, and being the head of the household. These variables could be used to improve HIV-1 testing and identification programs.

epidemiology↗