Biology subjects

Kumar, R.

Publications and source records attributed to Kumar, R..

At least 235 records · Page 13Linked to original sources

bioRxiv2021

hnRNPA1 regulates early translation to replication switch in SARS-CoV-2 life cycle

Our study suggests that methylation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA is essential for its optimal replication in the target cells. Heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1, an RNA-binding protein) was shown to mediate deposition of N6-methyladenosine (m6A) in internal SARS-CoV-2 RNA. The levels of hNRNPA1 expression and extent of methylation varied, depending on the course of SARS-CoV-2 life cycle. The recruitment of eIF4E (translational initiation factor) facilitated viral RNA translation at 1 hour post infection (1 hpi). However, at 2 hpi, methylation of internal SARS-CoV-2 RNA recruited hNRNPA1 which facilitated viral RNA transcription but resulted in translational repression, a phenomenon contributing in understanding the early translation to replication switch in the viral life cycle. Besides, the abrogation of methylation also produced a defective 5 cap of viral RNA which failed to interact with eIF4E, thereby resulting in a decreased synthesis of viral proteins. To conclude, methylation of the internal and 5 cap of SARS-CoV-2 RNA was shown to regulate transcription and translation of SARS-CoV-2 in a time dependent manner. IMPORTANCERNA modifications are found in all life forms and have been linked to development, health and diseases. Our study reveals that internal SARS-CoV-2 RNA methylation (m6A) is essential for interaction with hNRNPA1 to effectively synthesize viral genome. Besides, m6A-marked RNA and hRNPA1 interaction was also shown to regulate early translation to replication switch in SARS-CoV-2 life cycle. Blocking SARS-CoV-2 RNA methylation resulted in reduced virus yield, suggesting epitranscriptomic machinery (methylation) facilitates SARS-CoV-2 replication and might represent potential target for new antiviral drugs against COVID-19.

microbiology↗

bioRxiv2021

A bacterial derived plant- mimicking cytokinin hormone regulates social behaviour in a rice pathogen

Many plant-associated bacteria produce plant- mimicking hormones which are involved in modulating host physiology. However, their function in modulating bacterial physiology has not been reported. Here we show that the XopQ protein, a type-III effector of the rice pathogen, Xanthomonas oryzae pv. oryzae (Xoo), is involved in cytokinin biosynthesis. Xoo produces and secretes an active form of cytokinin which enables the bacterium to maintain a planktonic lifestyle and promotes virulence. RNA-seq analysis indicates that the cytokinin produced by Xoo is required for the regulation of several genes which are involved in biofilm formation. We have also identified the Xoo isopentenyl transferase gene, which is involved in the cytokinin biosynthesis pathway and is required for maintaining planktonic behaviour and virulence. Furthermore, mutations in the predicted cytokinin receptor kinase (PcrK) and the downstream response regulator (PcrR) of Xoo phenocopy the cytokinin biosynthetic mutants, but are not complemented by supplementation with exogenous cytokinin. Cytokinin biosynthetic functions are encoded in a number of diverse bacterial genomes suggesting that cytokinin may be a widespread signalling molecule in the bacterial kingdom.

microbiology↗

bioRxiv2021

Single cell multi-omics analysis of chromothriptic medulloblastoma highlights genomic and transcriptomic consequences of genome instability

Chromothripsis is a form of genome instability, whereby a presumably single catastrophic event generates extensive genomic rearrangements of one or few chromosome(s). However, little is known about the heterogeneity of chromothripsis across different clones from the same tumor, as well as changes in response to treatment. We analyzed single-cell genomic and transcriptomic alterations linked with chromothripsis in human p53-deficient medulloblastoma (n=7). We reconstructed the order of somatic events, identified early alterations likely linked to chromothripsis and depicted the contribution of chromothripsis to malignancy. We characterized subclonal variation of chromothripsis and its effects on double-minute chromosomes, cancer drivers and putatively druggable targets. Furthermore, we highlighted the causative role and the fitness consequences of specific rearrangements in neural progenitors. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/449944v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@9d30e4org.highwire.dtl.DTLVardef@1f4d34eorg.highwire.dtl.DTLVardef@5cd50corg.highwire.dtl.DTLVardef@a71a81_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2021

In silico model for predicting IL-2 inducing peptides in human

Interleukin-2 (IL-2) based immunotherapy has been approved for treating certain types of cancer, as IL-2 plays a crucial role in regulating the immune system. In this study, we developed a method for predicting IL-2-inducing peptides. Our method was trained, tested, and validated on a main dataset containing 6,574 experimentally validated Major histocompatibility complex (MHC) binders, including 3,429 IL-2-inducing and 3,145 non-inducing peptides. A primary analysis of IL-2 inducing and non-inducing peptides revealed that certain residues, such as alanine and leucine, are more abundant in IL-2-inducing peptides. Initially, we developed alignment-based methods, which demonstrated high precision but limited coverage. Subsequently, we developed artificial intelligence-based models, including machine learning (ML), deep learning (DL), and large language models (LLM), to predict IL-2-inducing peptides. Our Extra Tree-based model, developed using dipeptide composition and peptide length, achieved a maximum AUC of 0.82. Finally, we constructed ensemble models that combined artificial intelligence and alignment-based methods. Our best ensemble model, which integrates the Extra Tree-based model with MERCI, achieved the highest AUC of 0.84 and an MCC of 0.51 on the main dataset. One limitation of the main dataset is that both IL-2-inducing and non-inducing peptides are MHC binders. To address this limitation, we created two additional datasets: Alternate Dataset 1, consisting of 3,429 IL-2-inducing peptides and 3,429 non-inducing peptides (MHC non-binders), and Alternate Dataset 2, consisting of 3,429 IL-2-inducing peptides and 3,439 non-inducing peptides (MHC binders + MHC non-binders). Our best ensemble model achieved AUCs of 0.9 and 0.8 with MCCs of 0.61 and 0.44 on Alternate Datasets 1 and 2, respectively. To assist the scientific community, we have integrated the best models from this study into a standalone software and web server, IL2pred, which enables users to predict, scan, and design IL-2-inducing peptides (https://webs.iiitd.edu.in/raghava/il2pred/). HighlightsO_LIDevelopment of alignment-based techniques for predicting IL-2-inducing peptides. C_LIO_LIIdentification of amino acid patterns associated with IL-2 induction. C_LIO_LIImplementation of machine learning, deep learning, and LLM-based models for peptide prediction. C_LIO_LIEnsemble approaches combining alignment-based and AI-driven methods and integration into the webserver. C_LI

bioinformatics↗

bioRxiv2021

Mapping QTLs for phenotypic and morpho-physiological traits related to grain yield under late sown conditions in wheat (Triticum aestivum L.)

The elevating temperature makes heat stress one of the major issues for wheat production globally. To elucidate genetic basis and map heat tolerance traits, a set of 166 doubled haploid lines (DHLs) derived from the cross between PBW3438/IC252874 was used. The population was evaluated under Normal sown (NS) and late sown (LS) conditions, by exposing to heat stress during rabi season. The canopy temperature (CT) showed positive correlations with grain yield, whereas Soil plant analysis development (SPAD) was not significantly correlated and associated with GY in both the normal and late sown conditions. Composite interval mapping (CIM) identified total 12 Quantitative trait loci (QTLs) viz., 2 (Normal sown), 10 (late sown) mapped on linkage groups 1A, 1D, 2B, 2D, 3B, 4D, 5B and 6D, during both the crop seasons 2017-18 and 2018-19. Combining the results of these QTLs revealed a major stable QTL for grain yield (GY) on chromosome 3B with 11.84% to 21.24% explaining phenotypic variance under both sowing conditions. QTL for CT and SPAD was detected on chromosome 1A while QTL for GY on chromosome 3B and 5B. The identified QTLs in the genomic regions could be targeted for genetic improvement and marker assisted selection for heat tolerance in wheat. The tools like SPAD and CT could be exploited to screen the large number of breeding lines.

plant biology↗

bioRxiv2021

Prediction of pancreatic adenocarcinoma patient risk status using alternative splicing events

In literature, several mRNA, miRNA, lncRNA based biomarkers are identified by genomic analysis to stratify the patients into high and low risk groups of pancreatic adenocarcinoma (PAAD). The identified biomarkers are of limited use in terms of sensitivity and prediction ability. Thus, we aimed to identify the prognostic alternative splicing events and their related mutations in the PAAD. PAAD splicing data of 174 samples (17874 AS events in 6209 genes) and corresponding clinical information was obtained from the SpliceSeq and The Cancer Genome Atlas (TCGA), respectively. Prognostic-index based modeling was used to obtain the best predictive models for the seven AS types. However, model based on multiple spliced events genes (APP; LATS1; MRPL4; LAS1L; STARD10; PHF21A; NMRAL1) outperformed the single event models with a remarkable HR of 9.13 (p-value = 6.42e-10) as well as other existing models. Results from g:Profiler suggest that transcription factors ZF5, ER81, E2F-1/2/3, ER81, Erg, and PEA3 are most related to the prognostic spliced genes. We also identified 565 mutations across 160 spliced genes that have a strong association with the prognostic AS events. The analysis revealed that around 560 of these mutations were not reported before in context to splice event/region. Overall, we conclude that altered AS events may serve as strong indicators for overall survival in pancreatic cancer patients, and novel linkage of the known mutations to the survival-related AS events may provide a new dimension to the advancement of diagnostic and therapeutic interventions in these patients.

bioinformatics↗

bioRxiv2021

Aggregation state of Mycobacterium tuberculosis impacts host immunity and augments pulmonary disease pathology

Phagocytosis of Mycobacterium tuberculosis (Mtb) aggregates, rather than similar numbers of single bacilli, induces host macrophage death and favors bacterial growth. Here, we examined whether aggregation contributes to enhanced Mtb pathogenicity in vivo in rabbit lungs. Rabbits were exposed to infectious aerosols containing mainly Mtb-aggregates (Mtb-AG) or Mtb-single cells (Mtb-SC). The lung bacterial load, histology, and immune cell composition were investigated over time. Genome-wide transcriptome analysis, cellular and tissue-level assays, and immunofluorescent imaging were performed on lung tissue to define and compare differential immune activation and pathogenesis between Mtb-AG and Mtb-SC infection. Lung bacillary loads, disease scores, lesion size, and structure were significantly higher in Mtb-AG than in Mtb-SC infected animals. A differential immune cell distribution and activation were noted in the lungs and spleen of the two groups of infected animals. Mtb-AG infected animals also showed early induction of inflammatory network genes associated with necrosis and reduced host cell viability. Consistently, larger lung granulomas with clumped Mtb, extensive necrotic foci, and elevated matrix metalloproteases expression were observed in Mtb-AG infected rabbits. Our findings suggest that bacillary aggregation increases Mtb fitness for improved growth and accelerated lung inflammation and cell death, thereby exacerbating disease pathology in the lungs.

microbiology↗

bioRxiv2021

Occurrence, functionality, and abundance of the TERT promoter mutations

Telomere shortening at chromosomal ends due to the constraints of the DNA replication process acts as a tumor suppressor by restricting the replicative potential in primary cells. Cancers evade that limitation primarily through the reactivation of telomerase via different mechanisms. Mutations within the promoter of the telomerase reverse transcriptase (TERT) gene represent a definite mechanism for the ribonucleic enzyme regeneration predominantly in cancers that arise from tissues with low rates of self-renewal. The promoter mutations cause a moderate increase in TERT transcription and consequent telomerase upregulation to the levels sufficient to delay replicative senescence but not prevent bulk telomere shortening and genomic instability. Since the discovery, a staggering number of studies and publications have resolved the discrete aspects, effects, and clinical relevance of the TERT promoter mutations. The promoter mutations link transcription of TERT with oncogenic pathways, associate with markers of poor outcome, and define patients with reduced survivals in several cancers. In this review, we discuss the occurrence and impact of the promoter mutations and highlight the mechanism of TERT activation. We further deliberate on the foundational question of the abundance of the TERT promoter mutations and a general dearth of functional mutations within noncoding sequences, as evident from pan-cancer analysis of the whole-genomes. We posit that the favorable genomic constellation within the TERT promoter may be less than a common occurrence in other noncoding functional elements. The evolutionary constraints limit the functional fraction within the human genome, hence the lack of abundant mutations outside the coding sequences.

cancer biology↗

bioRxiv2021

High-density spinal cord stimulation selectively activates lower urinary tract afferents

Epidural spinal cord stimulation (SCS) has recently been reported as a potential intervention to improve limb and autonomic functions, with lumbar stimulation improving locomotion and thoracic stimulation regulating blood pressure. We asked whether sacral SCS could be used to target the lower urinary tract. Here we show that high-density epidural SCS over the sacral spinal cord and cauda equina of anesthetized cats evokes responses in nerves innervating the bladder and urethra and that these nerves can be activated selectively. Sacral epidural SCS always recruited the pelvic and pudendal nerves and selectively recruited these nerves in all but one animal. Individual branches of the pudendal nerve were always recruited as well. Electrodes that selectively recruited specific peripheral nerves were spatially clustered on the arrays, suggesting anatomically organized sensory pathways. This selective recruitment demonstrates a mechanism to directly modulate bladder and urethral function through known reflex pathways, which could be used to restore bladder and urethral function after injury or disease.

bioengineering↗

bioRxiv2021

Computational investigation reveals that the mutant strains of SARS-CoV2 are highly infectious than wildtype

Remarkable infectivity of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV2) is due to the rapid emergence of various strains, thus enable the virus to rule the world. Over the course of SARS-CoV2 pandemic, the scientific communities worldwide are responding to newly emerging genetic variants. However, the mechanism behind the persistent infection of these variants is still not known due to the paucity of study of these variants at molecular level. In this scenario, computational methods have immense utility in understanding the molecular and functional properties of different variants. Therefore, in this study various mutants (MTs) of SpikeS1 receptor binding domain (RBD) of highly infectious SARS-CoV2 strains were carried and elucidated the protein structure and dynamics using molecular dynamics (MD) approach. MD simulation study showed that all MTs exhibited stable structures with altered functional properties. Furthermore, the binding strength of different MTs along with WT (wildtype) was revealed through protein-protein docking and observed that MTs showed high binding affinities than WT. Hence, this study shed light on the molecular basis of infection caused by different variants of SARS-CoV2, which might play an important role in to cease the transmission and pathogenesis of virus and also implicate in rational designing of a specific drug.

bioinformatics↗

bioRxiv2021

A synergistic interaction between HDAC- and PARP inhibitors in childhood tumors with chromothripsis

Chromothripsis is a form of genomic instability characterized by the occurrence of tens to hundreds of clustered DNA double-strand breaks in a one-off catastrophic event. Rearrangements associated with chromothripsis are detectable in numerous tumor entities and linked with poor prognosis in some of these, such as Sonic Hedgehog medulloblastoma, neuroblastoma and osteosarcoma. Hence, there is a need for therapeutic strategies eliminating tumor cells with chromothripsis. Defects in DNA double-strand break repair, and in particular homologous recombination repair, have been linked with chromothripsis. Targeting DNA repair deficiencies by synthetic lethality approaches, we performed a synergy screen using drug libraries (n = 375 compounds, 15 models) combined with either a PARP inhibitor or cisplatin. This revealed a synergistic interaction between the HDAC inhibitor romidepsin and PARP inhibition. Functional assays, transcriptome analyses, and in vivo validation in patient-derived xenograft mouse models confirmed the efficacy of the combinatorial treatment.

cancer biology↗

bioRxiv2021

Brevibacillin 2V, a novel antimicrobial lipopeptide with an exceptional low hemolytic activity

Bacterial non-ribosomally produced peptides (NRPs) form a rich source of antibiotics, including more than twenty of these antibiotics that are used in the clinic, such as penicillin G, colistin, vancomycin, and chloramphenicol. Here we report the identification, purification, and characterization of a novel NRP, i.e., brevibacillin 2V, from Brevibacillus laterosporus DSM 25. Brevibacillin 2V has strong antimicrobial activity against Gram-positive bacterial pathogens, including difficult-to-treat antibiotic-resistant Enterococcus faecium, Enterococcus faecalis, and Staphylococcus aureus. Notably, brevibacillin 2V has a much lower hemolytic activity to eukaryotic cells than previously reported NRPs of the lipo-tridecapeptide family, including other brevibacillins, which makes it a promising candidate for antibiotic development. In addition, our results demonstrate that brevibacillins display synergistic action with established antibiotics against Gram-negative bacterial pathogens. Thus, we identified and characterized a novel and promising antibiotic candidate (brevibacillin 2V) with a low hemolytic activity, which can be used either on its own or as a template for further total synthesis and modification.

microbiology↗

bioRxiv2021

Quantifying control circuit regulation in the human brain.

As a field, control systems engineering has developed quantitative methods to characterize the regulation of systems or processes, whose functioning is ubiquitous within synthetic systems. In this context, a control circuit is objectively "well regulated" when discrepancy between desired and achieved output trajectories is minimized, and "robust" to the degree that it is able to regulate well in response to a wide range of stimuli. Most psychiatric disorders are assumed to reflect dysregulation of brain circuits. Yet, probing circuit regulation requires fundamentally different analytic strategies than the correlations relied upon for analyses of connectivity and their resultant networks. Here, we demonstrate how well-established methods for system identification in control systems engineering may be applied to functional magnetic resonance imaging (fMRI) data to extract generative computational models of human brain circuits. These provide two quantitative measures of direct relevance for psychiatric disorders: a circuits sensitivity to external perturbation and its dysregulation.

neuroscience↗

bioRxiv2021

α1-COP delivers sphingolipid modifiers and controls plasmodesmal callose deposition in Arabidopsis

Callose is a plant cell wall polymer in the form of {beta}-1,3-glucan, which regulates symplasmic channel size at plasmodesmata (PD). It plays a crucial role in a variety of processes in plants through the regulation of intercelluar symplasmic continuity. However, how to maintain callose homeostasis at PD in the molecular levels is poorly understood. To further elucidate the mechanism of PD callose homeostasis, we screened and identified an Arabidopsis mutant plant that exhibited excessive callose deposition at PD. Based on the Next-generation sequencing (NGS)-based mapping, other mutant allele analysis, and complementation assay, the mutated gene was shown to be 1-COP, which encodes a member of the COPI coatomer complex comprised of , {beta}, {beta}', {gamma}, {delta}, {varepsilon}, and {zeta} subunits. Since there is no report on the link between COPI and callose/PD, it was extremely curious to know the roles of 1-COP or COPI in PD regulation through callose deposition. Here, we report that loss-of-function of 1-COP directly elevates the callose accumulation at PD by affecting subcellular protein localization of callose degradation enzyme PdBG2. This process is linked to ERH1, an inositol phosphoryl ceramide synthase (IPCS), and glucosylceramide synthase (GCS) functions through physical interactions with the 1-COP protein. In addition, the loss-of-function of 1-COP also alters the subcellular localization of ERH1 and GCS proteins, results in a reduction of GlcCers and GlcHCers molecules, which are the key SL species for lipid raft formation. According to our findings, we propose that 1-COP protein, together with the SL modifiers controlling lipid raft compositions, regulates the function of GPI-anchored PD proteins and hence the callose turnover at PD and symplastic movement of biomolecules. Our findings provide the first key clue to link the COPI-mediated intracellular trafficking pathway to the callose-mediated intercellular signaling pathway through PD. One-sentence summaryPlant-specific coatomer protein functions as a negative regulator of callose accumulation by regulating the translocation of sphingolipid enzymes.

cell biology↗

bioRxiv2021

Effect of Pre-harvest Calcium Chloride and Salicylic Acid Spray on Morphological and Biochemical Traits of Guava (Psidium guajava)

Guava is a small, tropical fruit tree grown in various tropical and subtropical regions. Salicylic acid (SA) is a phenolic compound that enhances disease resistance and delays the fruit ripening process. Calcium is an essential cell component that delays ripening, particularly softening of the fruit. The effect of foliar spray of CaCl2, and SA, on the physical and biochemical traits of guava was investigated in the present investigation. The application of CaCl2 2% + SA 2mM was more effective as compared with both when applied alone. The data were recorded on fruit set (%), fruit weight (g), fruit length (cm), fruit diameter (cm), fruit yield (kg), ripening period (days), TSS, acidity, total sugar, ascorbic acid, nitrogen, phosphorus, potassium. CaCl2 2% + SA 2mM was showed better performance in all cases, followed by SA 2mM and CaCl2 2%. Overall, this work determines the influence on guava's essential traits by pre-harvest calcium chloride and salicylic acid.

biochemistry↗

bioRxiv2021

Fiber-associated Lachnospiraceae reduce colon tumorigenesis by modulation of the tumor-immune microenvironment

Patients with colorectal cancer (CRC) harbor gut microbiomes that differ in structure and function from those of healthy individuals, suggesting this altered microbiome could contribute to tumorigenesis. Despite increasing evidence implicating the gut microbiome in CRC, the collective role of different microbial consortia in CRC carcinogenesis is unclear. We have previously described these consortia as co-abundance groups that co-exist at different abundance levels in the same patient. Here, we report that tumor biopsy tissue from patients with a "high-risk" Pathogen-type microbiome had a different immune transcriptome and immune cell infiltrate from those with a "low-risk" Lachnospiraceae-type microbiome. Transplantation from patients of the two fecal microbiome types into mice with an orthotopic tumor differentially affected tumor growth and the systemic anti-tumor immune response. The differences in tumor volume and immunophenotype between mice receiving the high-risk and the low-risk microbiome correlated with differences in the engrafted human microbial species and predicted microbiome-encoded metabolites in the two groups. Of twelve taxa whose abundance in recipient mice led to increased tumor onset, seven corresponded with differentially abundant taxa in a global dataset of 325 CRC patients versus 310 healthy controls. These data suggest that the enrichment for a Lachnospiraceae-type configuration of the gut microbiome may influence colon cancer progression and disease outcome by modulating the local and systemic anti-tumor immune response. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/432654v2_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1de9ff5org.highwire.dtl.DTLVardef@d790d5org.highwire.dtl.DTLVardef@65be8aorg.highwire.dtl.DTLVardef@1c096da_HPS_FORMAT_FIGEXP M_FIG C_FIG Proposed model of how the high-risk Pathogen and low-risk Lachnospiraceae CAGs differentially modulate the tumor immune response.

microbiology↗

bioRxiv2021

Synthesis, Physiochemical and Biological evaluation of Inclusion Complex of Benzyl Isothiocyanate encapsulated in cyclodextrins for triple negative breast cancer

Benzyl isothiocyanate (BITC), an organic dietary compound, is allied with a major role in the potential chemopreventive effects. BITC has acknowledged rising attention as a therapeutic compound to be used in medicine because of its high potency and characteristic biopharmaceutical properties, like high permeability with marginal aqueous solubility. The highly volatile and hydrophobic nature brought a need to provide a suitable delivery-matrix to BITC to exploit its pharmacological potential to the fullest. It has been successfully incorporated in {beta}-CD and HP-{beta}-CD using acoustic forces and thoroughly characterized using UV-vis spectroscopy, FTIR, DSC, TEM, and SAXS. The complexation helped in masking the acute odour, achieving a controlled release of BITC, and made its use viable by prolonging the retention time and thereby sustaining the biological effects. Different models like Higuchi, first-order kinetic decay, Korsmeyer-Peppas model were applied, suggesting a diffusion-controlled mechanism of release. Also, the bioaccessibility and stability of BITC in an in vitro digestion model was evaluated. The main objective of the present work was to systemically study the credibility of BITC-CD complexes in well-established tumor mimicking 2D cell culture models and produce a conclusive report on its chemotherapeutic activity. The in vitro anti-cancer activity of BITC and the formed sonochemical complexes was confirmed by MTT assay and further evaluated using apoptosis assay and production of ROS like moieties. Cell cycle analysis was done to evaluate the growth inhibitory mechanism of BITC. Strikingly, BITC and its complexes showcased ROS generation and lysosome-mediated cell death. Effect on cell migration was assessed using wound healing assay. The results promptly suggest the functional efficacy of the CDs in releasing BITC and attest the ability of the complexes to provide alternate to otherwise remedially sparse triple-negative breast cancer.

cancer biology↗

bioRxiv2021

Parameter estimation for correlated Ornstein-Uhlenbeck time-series

In this article, we develop a Maximum likelihood (ML) approach to estimate parameters from correlated time traces that originate from coupled Ornstein-Uhlenbeck processes. The most common technique to characterize the correlation between time-series is to calculate the Pearson correlation coefficient. Here we show that for time series with memory (or a characteristic relaxation time), our method gives more reliable results, but also results in coupling coefficients and their uncertainties given the data. We investigate how these uncertainties depend on the number of samples, the relaxation times and sampling time. To validate our analytic results, we performed simulations over a wide range of correlation coefficients both using our maximum likelihood solutions and Markov-Chain Monte-Carlo (MCMC) simulations. We found that both ML and MCMC result in the same parameter estimations. We also found that when analyzing the same data, the ML and MCMC uncertainties are strongly correlated, while ML underestimates the uncertainties by a factor of 1.5 to 3 over a large range of parameters. For large datasets, we can therfore use the less computationally expensive maximum likelihood method to run over the whole dataset, and then we can use MCMC on a few samples to determine the factor by which the ML method underestimates the uncertainties. To illustrate the application of our method, we apply it to time series of brain activation using fMRI measurements of the human default mode network. We show that our method significantly improves the interpretation of multi-subject measurements of correlations between brain regions by providing parameter confidence intervals for individual measurements, which allows for distinguishing between the variance from differences between subjects from variance due to measurement error.

neuroscience↗