Biology subjects

Sengupta, R.

Publications and source records attributed to Sengupta, R..

18 recordsLinked to original sources

bioRxiv2026

Amaranthus viridis-derived phytopriming reprograms redox homeostasis and limits arsenic accumulation in rice

Arsenic (As) poses a major threat to rice productivity and food safety due to its high bioaccumulation potential and subsequent entry into the human food chain. In rice, As impairs seed germination, disrupts morpho-anatomical development, and induces oxidative stress. This study evaluates seed priming with an aqueous extract of the agricultural weed Amaranthus viridis (AvE) as a sustainable strategy to alleviate As-induced phytotoxicity. AvE priming significantly improved germination (71-75%) and morpho-physiological performance under As stress. It reduced oxidative stress markers, including H2O2 (21-38%), malondialdehyde (13-26%), and proline (18.9-44.7%), while increasing antioxidant metabolites, polyphenols and glutathione by up to 2.34-fold and 41%, respectively. Microscopy confirmed restoration of cellular integrity and anatomical organisation in primed seedlings. ICP-OES analysis showed that AvE priming reduced root As uptake by up to 39%, root-to-shoot translocation by up to 58%, and grain As accumulation by up to 95% compared with unprimed plants. qRT-PCR revealed modulation of genes involved in As homeostasis, indicating coordinated physiological and transcriptional responses. Importantly, improved agronomic performance further demonstrated the translational potential of this approach. This study provides the first evidence that A. viridis extract is a cost-effective, sustainable biostimulant for producing low-As rice in contaminated regions.

plant biology↗

bioRxiv2026

Reverse DTNB assay: a novel in vitrobiochemical approach to detect oxidized thiol modifications

The participation of sulfhydryl or thiol functions in a multitude of protein posttranslational modifications, although reflects on the redox versatility of cysteine residues, but their assessment in a dynamic cellular milieu involving the facile inter-conversion of SH to SSG, S-S, SNO, and S-R has been overwhelmingly difficult despite theirimplications in protein folding, enzyme structure and function, signalling and detoxification pathways, and pathophysiological ramifications.The current methodology, in contrast to a wide variety of cumbersome and prolonged techniques,repurposes the conventional DTNB assay for a hassle-free qualitative and quantitative analysisof redox-modified single or multiple susceptible thiol residues of cysteines in pure proteins as well as in a complex mixture of proteins.In this study, we document the thiol content, bearing the susceptibility to undergo reversible, oxidative thiol modifications, utilizing reverse DTNB assay in cell-free lysates and purified proteins that might provide a possible framework for dissecting the physiological phenomena behind the concealment of the susceptible cysteines through their redox-modified forms.

biochemistry↗

bioRxiv2026

Assessing the physiological S nitrosoproteome reveals nitric oxide mediated regulatory networks in rice

Nitric oxide metabolism-based protein post-translational modifications, such as reversible S- nitrosylation, have been at the pinnacle of plant redox research owing to their significant correlation with seed dormancy, interaction with other signaling molecules, plant development and metabolism, biotic and abiotic plant stress responses, immune defense responses against plant pathogens, and senescence. The rapid interconversion of reactive nitrogen species, the abrogation of nitric oxide homeostasis by exogenous supplementation of NO donors and scavengers, the lack of spatio-temporal specificity of NO signaling, and the limited bioavailability or assay sensitivity for detection often limit the effectiveness of identifying and characterizing S-nitrosothiols in plants. Hitherto unknown, we report the first experimental evidence of the total in vivo S-nitrosoproteome in Oryza sativa L. subsp. indica, comprising 134 PSNOs, enriched with 169 putative sites susceptible to S-nitrosylation, without any exogenous supplementation of NO donors. In the present study, mercuric salt- driven facile decomposition of S-nitrosoproteins in the presence of nitrone spin trap 5,5- dimethyl-1-pyrroline N-oxide, resulting in the synthesis of DMPO-nitrone adducts with PSNO-derived protein thiyl radicals in O. sativa, has been demonstrated as an efficient and novel strategy for characterizing the PSNOs using mass spectrometry analysis. The evidence of physiological levels of PSNOs was further re-examined in a bi-directional qualitative and quantitative approach involving the 2,3-diaminonaphthalene assay in tandem with fluorescence-based visualization and fluorometric quantification. In silico analyses, involving both functional enrichment and pathway prediction analyses, have furthermore revealed unique protein-protein interaction networks and signaling pathways among the S- nitrosoproteome candidates and their predictable physiological roles in O. sativa indica, awaiting further in vitro validation for their functional correlation in response to S- nitrosylation. In conclusion, the present study provides novel evidence of nitric oxide signaling in rice cultivars under physiological conditions, bringing new insights into the potential in vivo transnitrosylation of regulatory or active-site cysteine thiols.

biochemistry↗

bioRxiv2024

Predicting purification process fit of monoclonal antibodies using machine learning

0In early stage development of therapeutic monoclonal antibodies, assessment of ease of purification process development typically requires extensive experimentation. However, upstream protein expression and downstream purification experiments are often in conflict with timeline pressures and material constraints, limiting the number of molecules and process conditions that can reasonably be assessed. Recently, high-throughput batch-binding screen data along with improved molecular descriptors have enabled development of robust quantitative structure-property relationship (QSPR) models which predict monoclonal antibody chromatographic binding behavior from the amino acid sequence. This work describes a QSPR strategy for in silico monoclonal antibody purification process fit assessment. Principal Component Analysis is applied to extract a one-dimensional basis for comparison of molecular chromatographic binding behavior from multi-dimensional high-throughput batch-binding screen data. Kernel Ridge Regression is employed to predict the first principal component for new molecular sequences. This workflow is demonstrated with a set of 97 monoclonal antibodies for five chromatography resins in two salt types across a range of pH and salt concentrations. Model development benchmarks four descriptor sets from biophysical structural models and protein language models. The investigation illustrates the value QSPR models can provide to purification process fit assessment, and selection of resins and operating conditions from sequence alone.

bioinformatics↗

bioRxiv2022

Contribution of the Golgi apparatus in morphogenesis of a virus induced cytopathic vacuolar system

The Golgi apparatus (GA) in mammalian cells is pericentrosomally anchored and exhibits a stacked architecture. During infections by members of the alphavirus genus, the host cell GA is thought to give rise to distinct mobile pleomorphic vacuoles known as CPV-II (cytopathic vesicle-II) via unknown morphological steps. To dissect this, we adopted a phased electron tomography approach to image multiple overlapping volumes of a cell infected with Venezuelan equine encephalitis virus (VEEV) and complemented it with localization of peroxidase tagged Golgi marker. Analysis of the tomograms revealed a pattern of progressive cisternal bending into double-lamellar vesicles as a central process underpinning the biogenesis and the morphological complexity of this vacuolar system. Here we propose a model for the conversion of GA to CPV-II that reveals a unique pathway of intracellular virus envelopment. Our result has implications for alphavirus virus induced displacement of Golgi cisternae to the plasma membrane to aid viral egress operating late in the infection cycle.

microbiology↗

bioRxiv2021

Development of Microbiome Biomarkers for IgA: a Joint Modeling Approach

Our aim in this study is to develop predictive microbiome biomarkers for intestinal IgA levels. In this article, a operational taxonomic units(OTU)-specific (family-specific) and time-specific joint model is presented as a tool to model the association between OTU (or family) and biological response (measured by IgA level) taking into account the treatment group (Control or PAT) of the subjects. The model allows detecting OTUs (families) that are associated with the IgA; for some OTUs (families), the association is driven by the treatment while for others the association reflects the correlation between the OTUs (families) and IgA.The results of the analysis reveal that: (1) the observed diversity of S24-7 family can be used as a biomarker to classify samples according to treatment group for days 6 and 12; (2) the treatment effect induces the corrlelation between the S24-7 diversity and the IgA level at day 20; (3) The OTUs that are identified to be significantly differentially abundant (FDR level of 0.05) between the two treatment groups for days 12 and 20 are all part of the S24-7 family, although most of the differentially abundant ones at day 1 are from the Lactobacillaceae family; (4) only the Lachnospiraceae family diversity at day 6, and 20 can be used as predictive biomarker for the IgA level at day 20; (5) New.ReferenceOTU513, correlated with the IgA level at day 20, since day 12, belongs to the Lachnospiraceae family and all other OTUs among the top 10 significantly associated OTUs at day 20 are from the S24-7 family; (6) the observed alpha diversity at day 6 is significantly differentially abundant and can be used as predictive biomarker for IgA level at day 20.

microbiology↗

bioRxiv2020

Age-Associated Insolubility of Parkin in Human Midbrain is Linked to Redox Balance and Sequestration of Reactive Dopamine Metabolites

The mechanisms by which parkin protects the adult human brain from Parkinson disease remain incompletely understood. We hypothesized that parkin cysteines participate in redox reactions, which are reflected in its posttranslational modifications. We found that in human control brain, including the S. nigra, parkin is largely insoluble after age 40 years, which is linked to its oxidation, e.g., at Cys95 and Cys253. In mice, oxidative stress increases posttranslational modifications at parkin cysteines and reduces its solubility. Oxidation of recombinant parkin also promotes insolubility and aggregate formation, but in parallel, lowers hydrogen peroxide (H2O2). This thiol-based redox activity is diminished by parkin point mutants, e.g., p.C431F and p.G328E. Intriguingly, in parkin-deficient human brain H2O2 concentrations are elevated. In prkn-null mice, H2O2 levels are dysregulated under oxidative stress conditions, such as acutely by MPTP-toxin exposure or chronically due to a second genetic hit. In dopamine toxicity studies, wild-type parkin, but not disease-linked mutants, protects human dopaminergic M17 cells, in part through lowering H2O2. Parkin also neutralizes reactive, electrophilic dopamine metabolites via adduct formation, which occurs foremost at primate-specific Cys95. Further, wild-type but not p.C95A-mutant parkin augments melanin formation. In sections of normal, adult human midbrain, parkin specifically co-localizes with neuromelanin pigment, frequently within LAMP-3/CD63+ lysosomes. We conclude that oxidative modifications of parkin cysteines are associated with protective outcomes, which include the reduction of H2O2, conjugation of reactive dopamine metabolites, sequestration of radicals within insoluble aggregates, and increased melanin formation. The loss of these redox effects may augment oxidative stress in dopamine producing neurons of mutant PRKN allele carriers, thereby contributing to neurodegeneration.

neuroscience↗

bioRxiv2020

SARS-CoV-2 viral budding and entry can be modeled using virus-like particles

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first discovered in December 2019 in Wuhan, China and expeditiously spread across the globe causing a global pandemic. While a select agent designation has not been made for SARS-CoV-2, closely related SARS-CoV-1 and MERS coronaviruses are classified as Risk Group 3 select agents, which restricts use of the live viruses to BSL-3 facilities. Such BSL-3 classification make SARS-CoV-2 research inaccessible to the majority of functioning research laboratories in the US; this becomes problematic when the collective scientific effort needs to be focused on such in the face of a pandemic. In this work, we assessed the four structural proteins from SARS-CoV-2 for their ability to form viruslike particles (VLPs) from human cells to form a competent system for BSL-2 studies of SARS-CoV-2. Herein, we provide methods and resources of producing, purifying, fluorescently and APEX2-labeling of SARS-CoV-2 VLPs for the evaluation of mechanisms of viral budding and entry as well as assessment of drug inhibitors under BSL-2 conditions.

microbiology↗

bioRxiv2020

Strategy guides feature recall of a single object in working memory task

Over past couple of decades our understanding of visual working memory (VWM), and working memory in general, has been predominantly in line with the capacity debate. We recently opened a new line of inquiry regarding the recall of a single object to go beyond the capacity debate, and showed that a series of feature probe questions about a single object yields poorer recall later in the sequence (Sengupta et al, 2020). In the current work we focused on another aspect of sequential feature recall - mainly regarding whether recall can be improved by asking the same question twice. To that end, we chose to focus on two features - color and location, and we contrasted repeat and non-repeat (from the standpoint of feature questions) trials in a series of two experiments. In repeat trials either color or location would be probed twice consecutively. In non-repeat trials color and location probes were presented one after the other in random order. In all trials the stimulus was a small colored oriented line presented for 1 sec in a location within 4o of visual angle. The recall of color and location were mapped onto continuous variable like Sengupta et al, 2020 - for instance, color recall was mapped onto a color wheel. In the first experiment, we used an unaltered color wheel when the color question was repeated. For the second experiment, we used a rotated color wheels for two consecutive color recall trials. We observed an increase in recall error for both repeat and non-repeat condition for location when the probe was at the second question in both experiments. However, color recall error did not increase for second repeat question condition in Experiment 1 as opposed to the non-repeat condition. On the other hand, in Experiment 2 we observed the expected increase in recall error for both repeat and non repeat condition for color probe at the second question. This maybe due to the fact that participants used an anchoring strategy in Experiment 1 by remembering where they clicked on the color wheel in the first question. The rotation of color wheel in second experiment destroys the anchor leading to the aforementioned result. The results show that trying to recall the same feature again leads to degradation of recall accuracy for both color and location, and human beings may use different strategies for recall in working memory tasks.

animal behavior and cognition↗

bioRxiv2020

Parkinson Disease-Linked Parkin Mediates Redox Reactions That Lower Oxidative Stress In Mammalian Brain

We recently hypothesized that parkin plays a role in redox homeostasis and provided evidence that it directly reduces hydrogen peroxide (H2O2) in vitro. Here, we examined this anti-oxidant activity in vivo. Informed by findings in human brain, we demonstrate that elevated oxidative stress promotes parkin insolubility in mice. In normal mouse brain parkin was partially oxidized, e.g., at cysteines 195 and 252, which was augmented by oxidative stress. Although under basal conditions H2O2 levels were unchanged in adult prkn-/- brain, a parkin-dependent reduction of cytosolic H2O2 was observed when mitochondria were impaired, either due to neurotoxicant exposure (MPTP) or Sod2 haploinsufficiency. In accordance, markers of oxidative stress, e.g., protein carbonylation and nitrotyrosination, were elevated in the cytosol but not in mitochondria from prkn-/- mice. Nevertheless, this rise in oxidative stress led to changes in mitochondrial enzyme activities and the metabolism of glutathione in cells and mammalian brain. In parkins absence reduced glutathione concentrations were increased including in human cortex. This compensation was not due to new glutathione synthesis but attributed to elevated oxidized glutathione (GSSG)-reductase activity. Moreover, we discovered that parkin also recycled GSSG to its reduced form. With this reaction, parkin became S-glutathionylated, e.g., at cysteines 59 and human-specific 95. This oxidative modification was reversed by glutaredoxin. Our results demonstrate that cytosolic parkin mediates anti-oxidant reactions including H2O2 reduction and glutathione regeneration. These reducing activities lead to a range of oxidative modifications in parkin itself. In parkin-deficient brain oxidative stress rises despite changes to maintain redox balance.

neuroscience↗

bioRxiv2020

Temporal dynamics of ensemble statistics calculation using a neural network model

Computing summary or ensemble statistics of a visual scene is often automatic and a hard necessity for stable perceptual life of a cognitive agent. Although computationally the process should be as simple as applying a filter as it were to a perceived scene, the issue of mechanism of summary statistics is complicated by the fact that we can seamlessly switch from summarizing to individuation while computing the ensemble averages across multiple reference frames. In the current work we have investigated the possibility of a neural network that can also switch between individuation and summarization. We have chosen a computational model previously used for enumeration/individuation (Sengupta et al, 2014) in order to show possibility of extracting summary statistics using two different measures from the network. The results also shed a light on possible temporal dynamics of ensemble perception.

animal behavior and cognition↗

bioRxiv2020

Oxidative Modifications of Parkin Underlie its Selective Neuroprotection in Adult Human Brain

The mechanisms by which Parkinson disease-linked parkin confers neuroprotection of human dopamine cells remain elusive. We hypothesized that its cysteines mediate multiple anti-oxidant effects in the midbrain. By studying >60 control specimens, we found that in adult human brain - but not in skeletal muscle- parkin is mostly aggregated and insoluble due to oxidative modifications, such as at C253. In vitro, parkins oxidation directly reduces hydrogen peroxide (H2O2) to water. In parkin-deficient human brain, H2O2 concentrations are elevated. In dopamine toxicity studies, wild-type parkin -but not disease-associated mutants-prevents neural death by lowering H2O2 and sequestering radicals within insoluble aggregates. Parkin conjugates dopamine metabolites at the human-specific residue C95 and augments melanin formation in vitro. Using epitope-mapped antibodies, we found that in adult Substantia nigra neurons parkin localizes to neuromelanin within LAMP-3/CD63-positive lysosomes. We conclude that parkins own oxidation, previously considered a loss-of-function event, underlies three neuroprotective effects in adult midbrain: its cysteines participate in H2O2 reduction, dopamine radical conjugation and the formation of neuromelanin.

neuroscience↗

bioRxiv2020

Recalling a single object: going beyond the capacity debate

Working memory is now established as a limited capacity system. The debate regarding working memory has been largely between slots and resource based models. The resource model suggests that as the number of items increases, precision of recall decreases because neural resources are dynamically allocate to all the objects needed for task. Slot model on the other hand implies that an item is stored either with the highest precision or not at all. If both these models stand true then quality of memory performance would be near perfect for a single object. However, that may not be the case. In the current work, we investigated recall accuracy for feature(s) of a single object in three successive experiments. In all three experiments, the memory array consisted of a single colored oriented short line presented a short distance away from the center of the display for 1 sec. We probed recall of features from the set of color, location, orientation, and size. In experiment 1 number of recall question varied between 1 - 4 with the order randomized in each trial. In experiment 2 we chose to probe only two feature recall questions, whereas only one recall question was probed for the third experiment. In experiment 3 we varied the delay before the recall probe between 1 and 2 s. The recall response for each feature was mapped on to a continuous variable. Subjects used a color wheel to respond to color, on-screen mouse click to indicate center of the line location, click away from the center to indicate size, and a mouse click to the periphery of centered circle to indicate orientation with the slant of the resulting radial line. We calculated z-scores of errors for each feature for every subject separately. In experiment 1 that for color, location, and size the errors increase significantly with the position of the questions asked. In experiment 2, the errors increased significantly between questions for color and location (but not for orientation and size). In experiment 3, we did not see any significant increase in error with recall probe delay. Overall run-time for each trial was within 10 secs, well within the limits of operation of working memory. This drop in performance poses questions for memory mechanisms proposed by slot and resource models as both would predict near-perfect recall within the time-period for the trials.

animal behavior and cognition↗

bioRxiv2019

N-terminal autoprocessing and acetylation of MARTX Makes-Caterpillars Floppy-like effector is stimulated by ADP-Ribosylation Factor 1 in advance of Golgi fragmentation

Studies have successfully elucidated the mechanism of action of several effector domains that comprise the MARTX toxins of Vibrio vulnificus. However, the biochemical linkage between the cysteine proteolytic activity of Makes Caterpillars Floppy-like (MCF) effector and its cellular effects remains unknown. In this study, we identify the host cell factors that activate in vivo and in vitro MCF autoprocessing as ADP-Ribosylation Factor 1 (ARF1) and ADP-ribosylation Factor 3 (ARF3). Autoprocessing activity is enhanced when ARF1 is in its active (GTP-bound) form compared to the inactive (GDP-bound) form. Subsequent to auto-cleavage, MCF is acetylated on its exposed N-terminal glycine residue. Acetylation apparently does not dictate subcellular localization, as MCF is found localized throughout the cell. However, the cleaved form of MCF gains the ability to bind to the specialized lipid phosphatidylinositol 5-phosphate enriched in Golgi and other membranes necessary for endocytic trafficking, suggesting a fraction of MCF may be subcellular localized. Traditional thin-section electron microscopy, high-resolution cryoAPEX localization, and fluorescent microscopy show that MCF causes Golgi dispersal resulting in extensive vesiculation. In addition, host mitochondria are disrupted and fragmented. Surprisingly, ARF1 is not itself processed or post-translationally modified by MCF. Further, only catalytically inactive MCF stably associates with ARF1, thus serving as a substrate trap. Our data indicate that ARF1 is a cross-kingdom activator of MCF, but reveal that MCF mediates cytotoxicity likely by directly targeting another yet to be identified protein. This study begins to elucidate the biochemical activity of this important domain and gives insight into how it may promote disease progression.

microbiology↗

bioRxiv2019

Alpha-Synuclein is a Target of Fic-mediated Adenylylation/AMPylation: Implications for Parkinson’s Disease

During disease, cells experience various stresses that manifest as an accumulation of misfolded proteins and eventually lead to cell death. To combat this stress, cells activate a pathway called UPR (Unfolded Protein Response) that functions to maintain ER (endoplasmic reticulum) homeostasis and determines cell fate. We recently reported a hitherto unknown mechanism of regulating ER stress via a novel post-translational modification (PTM) called Fic-mediated Adenylylation/AMPylation. Specifically, we showed that the human Fic (filamentation induced by cAMP) protein, HYPE/FicD, catalyzes the addition of an AMP (adenosine monophosphate) to the ER chaperone, BiP, to alter the cells UPR-mediated response to misfolded proteins. Here, we report that we have now identified a second target for HYPE - alpha-Synuclein (Syn), a presynaptic protein involved in Parkinsons disease (PD). Aggregated Syn has been shown to induce ER stress and elicit neurotoxicity in PD models. We show that HYPE adenylylates Syn and reduces phenotypes associated with Syn aggregation in vitro, suggesting a possible mechanism by which cells cope with Syn toxicity.\n\nHIGHLIGHTSO_LIAggregated forms of the presynaptic protein Syn cause neurotoxicity and induce ER stress in cellular and animal models of Parkinsons disease.\nC_LIO_LIWe have identified Syn as a novel target for the human Fic protein, HYPE, a key regulator of ER homeostasis.\nC_LIO_LIHYPE adenylylates Syn and reduces the aggregation of recombinant Syn\nC_LIO_LIFic-mediated adenylylation/AMPylation is a possible mechanism by which cells cope with Syn toxicity.\nC_LI\n\nGraphic Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

biochemistry↗

bioRxiv2019

CryoAPEX - an electron tomography tool for subcellular localization of membrane proteins

We describe a method, termed cryoAPEX, that couples chemical fixation and high pressure freezing of cells with peroxidase-tagging (APEX) to allow precise localization of membrane proteins in the context of a well-preserved subcellular membrane architecture. Further, cryoAPEX is compatible with electron tomography. As an example, we apply cryoAPEX to obtain a high-resolution three-dimensional contextual map of the human Fic (filamentation induced by cAMP) protein, HYPE/FicD. HYPE is a single pass membrane protein that localizes to the endoplasmic reticulum (ER) lumen and regulates the unfolded protein response. Alternate cellular locations for HYPE have been suggested. CryoAPEX analysis shows that, under normal/resting conditions, HYPE localizes robustly within the subdomains of the ER and is not detected in the secretory pathway or other organelles. CryoAPEX is broadly applicable for assessing both lumenal and cytosol-facing membrane proteins.\n\nSummary statementCryoAPEX couples localization of peroxidase-tagged membrane proteins at high-resolution with 3D structural analysis, within an optimally preserved cellular context.

cell biology↗

bioRxiv2018

Exogenous attention facilitates performance through dissociable sensitivity and bias mechanisms

Selective attention enables prioritizing the most important information for differential sensory processing and decision-making. Here, we address an active debate regarding whether attention reflects a unitary phenomenon or involves the operation of dissociable sensory enhancement (perceptual sensitivity) and decisional gating (choice bias) processes. We developed a multialternative task in which participants detected and localized orientation changes in gratings at one of four spatial locations. Exogenous attention cues (high contrast flashes) preceded or followed the change events in close temporal proximity. Analysis of participants behavior with a multidimensional signal detection model revealed markedly distinct effects of exogenous cueing on perceptual sensitivity and choice bias. Whereas sensitivity enhancement was localized to the stimulus proximal to the exogenous cue, bias enhancement occurred even for distal stimuli in the cued hemifield. Modulations of sensitivity and bias were uncorrelated at both cued and uncued locations. Finally, exogenous cueing produced reaction time benefits only at the cued location and costs only at locations contralateral to the cue. These disparate effects of exogenous cueing on sensitivity, bias and reaction times could be parsimoniously explained within the framework of a diffusion-decision model, in which the drift rate was determined by a linear combination of sensitivity and bias at each location. Exogenous cueing effects on sensitivity and bias differed systematically from previously reported effects of endogenous cueing. We propose that the search for shared neural substrates of exogenous and endogenous attention would benefit from investigating neural correlates of their component sensory and decisional mechanisms.\n\nSignificance statementWhen we voluntarily direct attention \"endogenously\", we are able to better perceive stimuli at the attended location (sensitivity), and to prioritize information from that location for guiding behavioral decisions (bias). But when a salient stimulus, such as a flash of lightning, captures our attention \"exogenously\", does it also produce these same effects? To answer this question, we designed a multiple alternative task in which task events occurred in close conjunction with salient exogenous cues (high contrast flashes). We discovered that exogenous attention enhanced both sensitivity and bias for cued stimuli, but each of these changes followed distinct spatial patterns across locations. Our results provide novel insights into component processes of exogenous attention and motivate the search for their neural correlates.

neuroscience↗

bioRxiv2017

From Neural Network To Psychophysics Of Time: Exploring Emergent Properties Of RNNs Using Novel Hamiltonian Formalism

The stability analysis of dynamical neural network systems generally follows the route of finding a suitable Liapunov function after the fashion Hopfields famous paper on content addressable memory network or by finding conditions that make divergent solutions impossible. For the current work we focused on biological recurrent neural networks (bRNNs) that require transient external inputs (Cohen-Grossberg networks). In the current work we have proposed a general method to construct Liapunov functions for recurrent neural network with the help of a physically meaningful Hamiltonian function. This construct allows us to explore the emergent properties of the recurrent network (e.g., parameter configuration needed for winner-take-all competition in a leaky accumulator design) beyond that available in standard stability analysis, while also comparing well with standard stability analysis (ordinary differential equation approach) as a special case of the general stability constraint derived from the Hamiltonian formulation. We also show that the Cohen-Grossberg Liapunov function can be derived naturally from the Hamiltonian formalism. A strength of the construct comes from its usability as a predictor for behavior in psychophysical experiments involving numerosity and temporal duration judgements.

neuroscience↗