Miracle-dz/UniFAR-FTUs huggingface dataset:
Composition of nasopharyngeal microbiota in individuals with SARS-CoV-2 infection across three COVID-19 waves in India

Multiple variants of the SARS-CoV-2 virus have been plaguing the world through successive waves of infection over the past three years. Studies by independent research groups across geographies have shown that the microbiome composition in COVID-19 patients (CP) differ from that of healthy individuals (CN). However, such observations were based on limited-sized sample-sets collected primarily from the early days of the pandemic. Here, we study the nasopharyngeal microbiota in COVID-19 patients, wherein the samples have been collected across the three COVID-19 waves witnessed in India, which were driven by different variants of concern. We also present the variations in microbiota of symptomatic vs asymptomatic COVID-19 patients. The nasopharyngeal swabs were collected from 589 subjects providing samples for diagnostics purposes at Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India. CP showed a marked shift in the microbial diversity and composition compared to CN, in a wave-dependent manner. Rickettsiaceae was the only family that was noted to be consistently depleted in CP samples across the waves. The genera Staphylococcus, Anhydrobacter, Thermus, and Aerococcus were observed to be highly abundant in the symptomatic CP patients when compared to the asymptomatic group. In general, we observed a decrease in the burden of opportunistic pathogens in the host microbiota during the later waves of infection. To our knowledge, this is the first longitudinal study which was designed to understand the relation between the evolving nature of the virus and the changes in the human nasopharyngeal microbiota. Such studies not only pave way for better understanding of the disease pathophysiology but also help gather preliminary evidence on whether interventions to the host microbiota can help in better protection or faster recovery.
Neural correlates of face perception modeled with a convolutional recurrent neural network

Objective. Event-related potential (ERP) sensitivity to faces is predominantly characterized by an N170 peak that has greater amplitude and shorter latency when elicited by human faces than images of other objects. We aimed to develop a computational model of visual ERP generation to study this phenomenon which consisted of a three-dimensional convolutional neural network (CNN) connected to a recurrent neural network (RNN). Approach. The CNN provided image representation learning, complimenting sequence learning of the RNN for modeling visually-evoked potentials. We used open-access data from ERP Compendium of Open Resources and Experiments (40 subjects) to develop the model, generated synthetic images for simulating experiments with a generative adversarial network, then collected additional data (16 subjects) to validate predictions of these simulations. For modeling, visual stimuli presented during ERP experiments were represented as sequences of images (time x pixels). These were provided as inputs to the model. By filtering and pooling over spatial dimensions, the CNN transformed these inputs into sequences of vectors that were passed to the RNN. The ERP waveforms evoked by visual stimuli were provided to the RNN as labels for supervised learning. The whole model was trained end-to-end using data from the open-access dataset to reproduce ERP waveforms evoked by visual events. Main results. Cross-validation model outputs strongly correlated with open-access (r = 0.98) and validation study data (r = 0.78). Open-access and validation study data correlated similarly (r = 0.81). Some aspects of model behavior were consistent with neural recordings while others were not, suggesting promising albeit limited capacity for modeling the neurophysiology of face-sensitive ERP generation. Significance. The approach developed in this work is potentially of significant value for visual neuroscience research, where it may be adapted for multiple contexts to study computational relationships between visual stimuli and evoked neural activity.
Structural mechanism of LIN28B nucleosome targeting by OCT4 for pluripotency

Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of how pioneer factors recognize the in vivo nucleosomal DNA targets is unknown. Here, we determine the high-resolution structures of the nucleosome containing human LIN28B DNA and its complexes with the OCT4 DNA binding region. Three OCT4s bind the pre-positioned nucleosome by recognizing non-canonical DNA motifs. Two use their POUS domains by forming extensive hydrogen bonds. The other uses the POUS-loop-POUHD region; POUHD serves as a wedge to unwrap ∼25 base pair DNA. Biochemical studies suggest that multiple OCT4s cooperatively open the H1-condensed nucleosome array containing the LIN28B nucleosome. Our study suggests a mechanism whereby OCT4s target the LIN28B nucleosome by forming multivalent interactions with nucleosomal motifs, unwrapping nucleosomal DNA, evicting H1, and cooperatively open closed chromatin to initiate cell reprogramming.
Label-free single-cell live imaging reveals fast metabolic switch in T lymphocytes

T cell activation induces a metabolic switch generating energy required for proliferation, survival, and fueling their functions. Thus, it is essential to monitor metabolism associated to subcellular functional and structural changes. We used non-invasive label-free two-photon fluorescence lifetime microscopy (2P-FLIM) to map the spatial and temporal dynamics of the metabolic NADH co-enzyme during T lymphocyte activation. 2P-FLIM measurements of the protein-bound and free NADH ratios provides a readout of the redox state (NAD+/ NADH) of the cells, and thus of their OXPHOS and glycolysis rates. Using this method, we followed the dynamics of fraction of bound NADH (fb NADH) in live single cells. Comparing fb NADH between resting and activated T cells, we show that T cell activation induces a rapid switch toward glycolysis. The switch takes only 10 minutes and remains stable for at least one hour. Three-dimensional (3D) analysis revealed that the intracellular distribution of fb NADH is symmetrically distributed in resting cells, whereas increases at the contact zone in activated cells. Finally, we show that fb NADH negatively correlates with spreading of activated T cells, suggesting a link between actin remodeling and metabolic changes. This study shows that 2P-FLIM measurement of fb NADH is well suited to follow a fast metabolic switch in 3D, in single T lymphocytes with subcellular resolution.
gp120 envelope glycoproteins of HIV-1 Group M Subtype A and Subtype B differentially affect gene expression in human vascular endothelial cells

Cardiovascular complications are seen among human immunodeficiency virus (HIV)-positive individuals who can now survive longer due to successful antiretroviral therapies. Among them, pulmonary arterial hypertension (PAH) is a fatal disease characterized by increased blood pressure in the lung circulation due to vasoconstriction and vascular wall remodeling, resulting in the overworking of the heart. The prevalence of PAH in the HIVpositive population is dramatically higher than that in the general population. While HIV-1 Group M Subtype B is the most prevalent subtype in western countries, the majority of HIV-1 infections in eastern Africa and former Soviet Union countries are caused by Subtype A. Research on the mechanism of vascular complications in the HIV-positive population, especially in the context of subtype differences, however, has not been rigorous. Much of the research on HIV has focused on Subtype B and information on the molecular mechanisms of Subtype A is non-existent. The lack of such knowledge results in health disparities in the development of therapeutic strategies to prevent/treat HIV complications. The present study examined the effects of HIV-1 viral fusion protein gp120 of Subtypes A and B on cultured human pulmonary artery endothelial cells by performing protein arrays. We found that the gene expression changes caused by the gp120s of Subtypes A and B are different. Specifically, Subtype A is a more potent downregulator of perostasin, matrix metalloproteinase-2 (MMP-2), and ErbB/Her3 than Subtype B, while Subtype B is more effective in downregulating monocyte chemotactic protein-2 (MCP-2/CCL8), MCP-3 (CCL7), and thymus- and activation-regulated chemokine (TARC/CCL17) proteins. This is the first report of gp120 proteins affecting host cells in an HIV subtype-specific manner, opening up the possibility that vascular complications may occur differently in HIV patients throughout the world.
Single-cell transcriptional analysis of lamina propria lymphocytes in the jejunum reveals ILC-like cells in pigs

Pigs are the most suitable model to study various therapeutic strategies and drugs for human beings, while knowledge about tissue- and cell-type-specific transcriptomes and heterogeneity is poorly available. Here, we focused on the intestinal immunity of pigs. Through single-cell sequencing (scRNA-seq) and flow cytometry analysis of the types of immune cells in the jejunum of pigs, we found that innate lymphoid cells (ILCs) existed in the lamina propria lymphocytes (LPLs) of the jejunum. Then, through flow sorting of Live/Dead (L/D)-Lineage(LIN)-CD45+ cells and scRNA-seq, we found that ILCs in the porcine jejunum were mainly ILC3s, with a small number of ILC1s, ILC2s, and NK cells. Through a gene expression map, we found that ILCs coexpressed IL-7Rα, ID2, and other genes and differentially expressed RORC, GATA3, and other genes but did not express the CD3 gene. According to their gene expression profiles, ILC3s can be divided into four subgroups, and genes such as CXCL8, CXCL2, IL-22, IL-17, and NCR2 are differentially expressed. To further detect and identify ILC3s, we prepared RORC monoclonal antibodies and verified the classification of ILCs in the porcine jejunum subgroup and the expression of related hallmark genes at the protein level by flow cytometry. For systematically characterizing of ILCs in the porcine intestines, we combined our pig ILCs dataset with publicly available human and mice ILCs data and identified that the humans and pigs ILCs shared more common features than those mice ILCs in gene signatures and cell states. For the first time, our results showed in detail the gene expression of porcine jejunal ILCs, the subtype classification of ILCs, and the markers of various ILCs, which provides a basis for an in-depth exploration of porcine intestinal mucosal immunity. Graphical abstract
Directed differentiation of human hindbrain neuroepithelial stem cells recapitulates cerebellar granule neurogenesis

Cerebellar granule neurons (CGNs) are the most abundant neurons in the human brain and modulate cerebellar output to the motor cortex. Dysregulation of CGN development underlies movement disorders and medulloblastomas. It is suspected that these disorders arise in progenitor states of the CGN lineage, for which human models are lacking. Here, we have differentiated human hindbrain neuroepithelial stem (hbNES) cells to CGNs in vitro using soluble growth factors, recapitulating key progenitor states in the lineage. We show that hbNES cells are not lineage committed and retain rhombomere 1 (r1) regional identity. Upon differentiation, hbNES cells first transit through a rhombic lip (RL) progenitor state at day 7, demonstrating human specific sub-ventricular cell identities. This RL state is followed by an ATOH1+ CGN progenitor state at day 14. By the end of a 56-day differentiation procedure, we obtain mature neurons expressing CGN markers GABAAa6 and vGLUT2. These neurons generate spontaneous and evoked action potentials. A small fraction of endpoint neurons were unipolar brush cells (UBC). We noted maintenance of a RL population throughout differentiation, as is consistent with human development. We show that sonic hedgehog (SHH) promotes γ-aminobutyric acid (GABA)-ergic lineage specification and is a positive regulator of CGN progenitor proliferation. Interestingly, we observed that functional neuronal maturation is impaired by either elevated or absent SHH signaling. Impaired maturation under high SHH levels represents the potential of our system to model cerebellar tumorigenesis. Further, our data suggest a potential pro-differentiation role of SHH within a certain concentration range. Our work is, to our knowledge, the first detailed temporal characterization of the complete human CGN lineage in vitro. Our system recapitulates developmentally relevant progenitor states and is a new tool to model this specific cerebellar lineage, and how it may be disrupted to cause human disease.
Water entry of two-dimensional bodies

A numerical method for studying water entry of a two-dimensional body of arbitrary cross-section is presented. It is a nonlinear boundary element method with a jet flow approximation. The method has been verified by comparisons with new similarity solution results for wedges with deadrise angles varying from 4° to 81°. A simple asymptotic solution for small deadrise angles α based on Wagner (1932) agrees with the similarity solution for small α.
EFNB1 level affects drug response in DLBCL cell lines

Targeted therapy was a promising therapy for aggressive B-cell lymphoma. However, drug resistance was still an unavoidable problem. Here, we explored the effect of EFNB1 on drug response. Analysis of IC50 data showed that high level of EFNB1 was associated with resistance to most targeted drugs targeting BCR in human DLBCL cell lines. Drug response assay showed that Efnb1 could enhance SRC phosphorylation and increased the sensitivity of cells to SRC inhibitors. Meanwhile, Efnb1 could sensitize cells to most cytotoxic drugs, especially DOX and VCR. Efnb1 could confer cells sensitivity to VCR by enhancing the phosphorylation of Stmn1 at serine 28. Survival analysis revealed that the expression level of genes phosphorylated in Efnb1 cells were associated with poor prognosis of human DLBC. Together, this study revealed that EFNB1 level, as a non-genetic mechanism, greatly affected drug response of targeted drugs and cytotoxic drugs through the phosphorylation network. Our findings would provide important insights into EFNB1-SRC activated B-cell lymphoma and efficacy evaluation.
Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen B. burgdorferi

Transcription termination is an essential and dynamic process that can tune gene expression in response to diverse molecular signals. Yet, the genomic positions, molecular mechanisms, and regulatory consequences of termination have only been studied thoroughly in model bacteria. We employed complementary RNA-seq approaches to map RNA ends for the transcriptome of the spirochete Borrelia burgdorferi – the etiological agent of Lyme disease. By systematically mapping B. burgdorferi RNA ends at single nucleotide resolution, we delineated complex gene arrangements and operons and mapped untranslated regions (UTRs) and small RNAs (sRNAs). We experimentally tested modes of B. burgdorferi transcription termination and compared our findings to observations in E. coli, P. aeruginosa, and B. subtilis. We discovered 63% of B. burgdorferi RNA 3′ ends map upstream or internal to open reading frames (ORFs), suggesting novel mechanisms of regulation. Northern analysis confirmed the presence of stable 5′ derived RNAs from mRNAs encoding gene products involved in the unique infectious cycle of B. burgdorferi. We suggest these RNAs resulted from premature termination and regulatory events, including forms of cis-acting regulation. For example, we documented that the polyamine spermidine globally influences the generation of truncated mRNAs. In one case, we showed that high spermidine concentrations increased levels of RNA fragments derived from an mRNA encoding a spermidine import system, with a concomitant decrease in levels of the full- length mRNA. Collectively, our findings revealed new insight into transcription termination and uncovered an abundance of potential RNA regulators.
Apolipoprotein E O-glycosylation is associated with amyloid plaques and APOE genotype

Although the APOE ε4 allele is the strongest genetic risk factor for sporadic Alzheimer’s disease (AD), the relationship between apolipoprotein (apoE) and AD pathophysiology is not yet fully understood. Relatively little is known about the apoE protein species, including post-translational modifications, that exist in the human periphery and CNS. To better understand these apoE species, we developed a LC-MS/MS assay that simultaneously quantifies both unmodified and O-glycosylated apoE peptides. The study cohort included 47 older individuals (age 75.6 ± 5.7 years [mean ± standard deviation]), including 23 individuals (49%) with cognitive impairment. Paired plasma and cerebrospinal fluid samples underwent analysis. We quantified O-glycosylation of two apoE protein residues – one in the hinge region and one in the C-terminal region – and found that glycosylation occupancy of the hinge region in the plasma was significantly correlated with plasma total apoE levels, APOE genotype and amyloid status as determined by CSF Aβ42/Aβ40. A model with plasma glycosylation occupancy, plasma total apoE concentration, and APOE genotype distinguished amyloid status with an AUROC of 0.89. These results suggest that plasma apoE glycosylation levels could be a marker of brain amyloidosis, and that apoE glycosylation may play a role in the pathophysiology of AD. Highlights Simultaneous quantification of unmodified and O-glycosylated apoE via LC-MS/MS. Total plasma apoE varies by APOE genotype in an isoform, dose-dependent fashion. CNS-derived apoE is more extensively O-glycosylated than peripherally derived apoE. Hinge region glycosylation occupancy of plasma apoE is associated with amyloidosis.
Versatile electrical stimulator for cardiac tissue engineering—Investigation of charge-balanced monophasic and biphasic electrical stimulations

The application of biomimetic physical stimuli replicating the in vivo dynamic microenvironment is crucial for the in vitro development of functional cardiac tissues. In particular, pulsed electrical stimulation (ES) has been shown to improve the functional properties of in vitro cultured cardiomyocytes. However, commercially available electrical stimulators are expensive and cumbersome devices while customized solutions often allow limited parameter tunability, constraining the investigation of different ES protocols. The goal of this study was to develop a versatile compact electrical stimulator (ELETTRA) for biomimetic cardiac tissue engineering approaches, designed for delivering controlled parallelizable ES at a competitive cost. ELETTRA is based on an open-source micro-controller running custom software and is combinable with different cell/tissue culture set-ups, allowing simultaneously testing different ES patterns on multiple samples. In particular, customized culture chambers were appositely designed and manufactured for investigating the influence of monophasic and biphasic pulsed ES on cardiac cell monolayers. Finite element analysis was performed for characterizing the spatial distributions of the electrical field and the current density within the culture chamber. Performance tests confirmed the accuracy, compliance, and reliability of the ES parameters delivered by ELETTRA. Biological tests were performed on neonatal rat cardiac cells, electrically stimulated for 4 days, by comparing, for the first time, the monophasic waveform (electric field = 5 V/cm) to biphasic waveforms by matching either the absolute value of the electric field variation (biphasic ES at ±2.5 V/cm) or the total delivered charge (biphasic ES at ±5 V/cm). Findings suggested that monophasic ES at 5 V/cm and, particularly, charge-balanced biphasic ES at ±5 V/cm were effective in enhancing electrical functionality of stimulated cardiac cells and in promoting synchronous contraction.
Imputing Missing Answers in the World Values Survey

Questionnaire surveys are useful for many areas of science, in particular social sciences. Such surveys are often the prime means of gathering data directly from participants, however, they are prone to missing data, which could be caused by many reasons: (i) an error by survey administrators, (ii) participants not responding to certain questions, (iii) acts of nature and, (iv) etc. In order to keep the full survey sample, researchers must often use imputation to deal with the missing data problem. Methods for imputation can sometimes offer reasonable estimates for the missing data, however, in the case of the survey: (i) imputation can add high noise to the data, (ii) imputation becomes unreliable when more than 40% of the data is missing. This work attempts to address these issues by evaluating if the usage of matrix completion methods stemming from collaborative filtering (CF) in recommender systems can yield more accurate imputations of survey data. The rationale for the usage of these methods is (i) the similarity between the problem framing, methods and data representation used in CF and survey imputation; (ii) the effectiveness of CF-based methods in recommender systems. We use data from the World Values Survey, a valuable dataset in social science of high volume and veracity, to compare (i) one simple approach to imputation, (ii) two established imputation approaches (iii) two CF matrix completion techniques. The results show that our chosen CF matrix completion techniques perform overall comparable, but not better than existing imputation techniques for the case of survey imputation. The matrix completion techniques, however, might prove useful in niche situations, such as in the imputation of non-ordinal question answers. The right technique for imputation often depends on the problem, these results beckon the consideration of CF-based techniques in future research on survey imputation.
Effects of chemical reaction in thermal and mass diffusion of micropolar fluid saturated in porous regime with radiation and ohmic heating

The present paper analyzes the chemically reacting free convection MHD micropolar flow, heat and mass transfer in porous medium past an infinite vertical plate with radiation and viscous dissipation. The non-linear coupled partial differential equations are solved numerically using an implicit finite difference scheme known as Keller-box method. The results for concentration, transverse velocity, angular velocity and temperature are obtained and effects of various parameters on these functions are presented graphically. The numerical discussion with physical interpretations for the influence of various parameters also presented.
Towards Interaction-based User Embeddings in Sequential Recommender Models

All transductive recommender systems are unable to make predictions for users who were not included in the training sample due to the process of learning user-specific embeddings. In this paper, we propose a new method for replacing identity-based user embeddings in existing sequential models with interaction-based user vectors trained purely on interaction sequences. Such vectors are composed of user interactions using GRU layers with adjusted dropout and maximum item sequence length. This approach is substantially more efficient and does not require retraining when new users appear. Extensive experiments on three open-source datasets demonstrate noticeable improvement in quality metrics for the most of selected state-of-the-art sequential recommender models