Miracle-dz/UniFAR-FTUs huggingface dataset:
Type 17 Follicular Helper T (Tfh17) Cells are Superior for Memory Maintenance

A defining feature of successful vaccination is the ability to induce long-lived antigen- specific memory cells. Follicular helper T (Tfh) cells specialize in providing help to B cells in mounting protective humoral immunity in infection and after vaccination. Memory Tfh cells that retain the CXCR5 expression can confer protection through enhancing humoral response upon antigen re-exposure but how they are maintained is poorly understood. CXCR5+ memory Tfh cells in human blood are divided into Tfh1, Tfh2 and Tfh17 cells by the expression of chemokine receptors CXCR3 and CCR6 associated with Th1 and Th17 respectively. Here, we developed a new method to induce Tfh1, Tfh2 and Tfh17-like (iTfh1, iTfh2 and iTfh17) cells in vitro. Although all three iTfh subsets efficiently support antibody responses in recipient mice with immediate immunization, iTfh17 cells are superior to iTfh1 and iTfh2 cells in supporting antibody response to a later immunization after extended resting in vivo to mimic memory maintenance. Notably, the counterpart human Tfh17 cells are selectively enriched in CCR7+ central memory Tfh (TfhCM) with survival and proliferative advantages. Furthermore, the analysis of multiple human cohorts that received different vaccines for HBV, influenza virus, tetanus toxin or measles revealed that vaccine-specific Tfh17 cells outcompete Tfh1 or Tfh2 cells for the persistence in memory phase. Therefore, the complementary mouse and human results showing the advantage of Tfh17 cells in maintenance and memory function supports the notion that Tfh17-induced immunization might be preferable in vaccine development to confer long-term protection.
Sensitivity analysis of genome-scale metabolic flux prediction

TRIMER, Transcription Regulation Integrated with MEtabolic Regulation, is a genome-scale modeling pipeline targeting at metabolic engineering applications. Using TRIMER, regulated metabolic reactions can be effectively predicted by integrative modeling of metabolic reactions with Transcription Factor (TF)-gene regulatory network (TRN), where the TRN is modeled via Bayesian network (BN). In this paper, we focus on sensitivity analysis of metabolic flux prediction considering potential model uncertainty in TRIMER. We propose a computational strategy to construct the uncertainty class of TRN models based on the inferred regulatory order uncertainty when learning from given transcriptomic expression data and analyze the prediction sensitivity of the TRIMER pipeline for the metabolite yield of interest. The obtained sensitivity analyses can provide a useful guidance for Optimal Experimental Design (OED) to help acquire new data that can enhance TRN modeling and effectively achieve specific metabolic engineering objectives, including metabolite yield alterations. We have performed simulation experiments to demonstrate the effectiveness of our developed sensitivity analysis strategy and its potential to effectively guide OED. ACM Reference Format Puhua Niu, Maria J. Soto, Shuai Huang, Byung-Jun Yoon, Edward R. Dougherty,, Francis J. Alexander, Ian Blaby, Xiaoning Qian. 2018. Sensitivity analysis of genome-scale metabolic flux prediction. In Proceedings of Make sure to enter the correct conference title from your rights confirmation email (CNB-MAC 2022). ACM, New York, NY, USA, 9 pages. https://doi.org/XXXXXXX.XXXXXXX
The Molecular Structure of Anterograde Intraflagellar transport trains

Anterograde intraflagellar transport trains are essential for cilia assembly and maintenance. These trains are formed of 22 IFTA and IFTB proteins that link structural and signalling cargoes to microtubule motors for import into cilia. It remains unknown how the IFTA/B proteins are arranged into complexes and how these complexes polymerise into functional trains. Here, we use in situ cryo-electron tomography and Alphafold2 protein structure predictions to generate the first molecular model of the entire anterograde train. We show how the conformation of both IFTA and IFTB is dependent on lateral interactions with neighbouring repeats, suggesting that polymerization is required to cooperatively stabilize the complexes. The retrograde dynein motor binding site is a composite surface involving multiple IFTB repeats, ensuring that dynein can only form a strong interaction with IFTB upon train assembly. Finally, we reveal how IFTB extends two flexible tethers to maintain a connection with IFTA that can withstand the mechanical stresses present in actively beating cilia. Overall, our findings provide a framework for understanding the fundamental processes that are involved in cilia assembly.
A Tale of Two Trees: Modeling Apical and Basal Tree Contribution to L2/3 V1 Pyramidal Cell Orientation Selectivity

Pyramidal neurons, a mainstay of cortical regions, receive a plethora of inputs from various areas onto their morphologically distinct apical and basal trees. Both trees differentially contribute to the somatic response, defining distinct anatomical and possibly functional sub-units. To elucidate the contribution of each tree to the encoding of visual stimuli at the somatic level, we modeled the response pattern of a L2/3 V1 pyramidal neuron to orientation tuned synaptic input. Towards this goal, we used a morphologically detailed computational model of a single cell that replicates electrophysiological and two-photon imaging data. Our simulations predict a synergistic effect of apical and basal trees on somatic action potential generation: basal tree activity, in the form of either depolarization or dendritic spiking, is necessary for producing somatic activity, despite the fact that most somatic spikes are heavily driven by apical dendritic spikes. This model provides evidence for synergistic computations taking place in the basal and apical trees of the L2/3 V1 neuron along with mechanistic explanations for tree-specific contributions and emphasizes the potential role of predictive and attentional feedback input in these cells. Abstract Figure Graphical Representation of AP Generation in a L2/3 V1 Pyramidal Neuron Model Action potential generation requires the spatiotemporal coincidence of apical sodium spikes with either basal sodium spikes or significant basal depolarizations, allowing the neuron to respond to salient stimuli that may or may not be affected by attentional and/or predictive signals from higher-order areas.
Rapid Color Categorization in the Brain Revealed by Frequency-tagging-based EEG

The origin of color categories has been debated extensively. Linguistic relativists claim that color categories are shaped by the language we speak and that color terms subsequently affect our perception of color, while universalists postulate that color categories are independent of language and formed based on perceptual mechanisms. Our study adopted a sensitive frequency-tagging-based EEG paradigm where the color stimuli were presented sequentially at a fast speed of 10 Hz (SOA: 100 ms) to probe fast, feedforward processing of color categories. We showed that EEG responses to cross-category oddball colors at the frequency where the oddball stimuli were presented was significantly larger than the responses to within-category oddball colors. This finding suggested that the categories of color stimuli were likely to be encoded automatically and in a feedforward manner, as the color stimuli were only briefly flashed and irrelevant to the participants’ task. The findings support the view that the categorical processing of color emerges at the early perceptual stage.
Contribution of the eye and of opn4xa function to circadian photoentrainment in the diurnal zebrafish

The eye is instrumental for controlling circadian rhythms in mice and human. Here, we address the conservation of this function in the zebrafish, a diurnal vertebrate. Using lakritz (lak) mutant larvae, which lack retinal ganglion cells (RGCs), we show that while a functional eye contributes to masking, it is largely dispensable for the establishment of circadian rhythms of locomotor activity. Furthermore, the eye is dispensable for the induction of a phase delay following a pulse of white light at CT 16 but contributes to the induction of a phase advance upon a pulse of white light at CT21. Melanopsin photopigments are important mediators of photoentrainment, as shown in nocturnal mammals. One of the zebrafish melanopsin genes, opn4xa, is expressed in RGCs but also in photosensitive projection neurons in the pineal gland. Pineal opn4xa+ projection neurons function in a LIGHT ON manner in contrast to other projection neurons which function in a LIGHT OFF mode. We generated an opn4xa mutant in which the pineal LIGHT ON response is impaired. This mutation has no effect on masking and circadian rhythms of locomotor activity, or for the induction of phase shifts, but slightly modifies period length when larvae are subjected to constant light. Finally, analysis of opn4xa;lak double mutant larvae did not reveal redundancy between the function of the eye and opn4xa in the pineal for the control of phase shifts after light pulses. Our results support the idea that the eye is not the sole mediator of light influences on circadian rhythms of locomotor activity and highlight differences in the circadian system and photoentrainment of behaviour between different animal models. Author summary Experiments performed in mice have established a crucial role for the eye in general and melanopsin expressing cells in particular in the control of circadian rhythms most notably during photoentrainment, by which circadian rhythms adapt to a changing light environment. In marked contrast to this, we show that in zebrafish the eye and photosensitivity dependent on one of the melanopsin genes, opn4xa, which is expressed in both the eye and the pineal gland, are largely dispensable for correct circadian rhythms. These results provide insight that the light sensors orchestrating circadian rhythms of locomotor activity are different between animal models supporting that vertebrates might employ different molecular/cellular circuits for photoentrainment of behaviour depending on their phylogeny and/or temporal niche.
TOLD: Tamil Offensive Language Detection in Code-Mixed Social Media Comments using MBERT with Features based Selection

The immense growth in social media forums does increase the spread of offensive language. We detect and examine the challenges faced by automatic approaches for offensive language detection in the Tamil-English language. Among these difficulties are subtleties in code-mixed Tamil language, identifying what constitutes offensive, and handling the imbalanced data under the low resource language. This paper presents our work in the shared task of HASOC-Dravidian-CodeMix-FIRE 2021, where we explore different machine learning algorithms, deep learning techniques, and transfer learning models. We also explore various feature extraction techniques and utilize offensive features to perform this task. Our team SSN_NLP_MLRG has participated in task1 and classifies the code-mixed Tamil textual content into offensive or not-offensive. Our team best model is Multilingual BERT, and submission had a macro F1-score 0.84 of task1 of Tamil code-mixed language. Our team achieved the 3 𝑟𝑑 rank on the final test results in task1 for the Tamil code-mixed language.
The kinase occupancy of T cell coreceptors reconsidered

The sensitivity of the αβ T-cell receptor (TCR) is enhanced by the coreceptors CD4 and CD8αβ, which are expressed primarily by cells of the helper and cytotoxic T-cell lineages, respectively. The coreceptors bind to major histocompatibility complex (MHC) molecules and associate intracellularly with the Src-family kinase Lck, which catalyzes TCR phosphorylation during receptor triggering. Although coreceptor-kinase occupancy was initially believed to be high, a recent study suggested that most coreceptors exist in an Lck-free state, and that this low occupancy helps to effect TCR antigen discrimination. Here, using the same method, we found instead that the CD4-Lck interaction was stoichiometric (~100%) and that the CD8αβ-Lck interaction was also substantial (~60%). We confirmed our findings in live cells using fluorescence cross-correlation spectroscopy (FCCS) to measure coreceptor-Lck co-diffusion in situ. After introducing structurally guided mutations into the intracellular domain of CD4, we used FCCS to show that stoichiometric Lck coupling required an amphipathic α-helix present in CD4 but not CD8α. In double-positive cells expressing equal numbers of both coreceptors, but limiting amounts of kinase, CD4 out-competed CD8αβ for Lck. In T cells, TCR signaling induced CD4-Lck oligomerization but did not affect the high levels of CD4-Lck occupancy. These findings help settle the question of kinase occupancy and suggest that the binding advantages that CD4 has over CD8 could be important when Lck levels are limiting. Significance statement CD4 and CD8αβ are archetypal coreceptor proteins that potently enhance T-cell antigen sensitivity but how they function is still debated. A fundamental question that remains incompletely resolved is: what fractions of the coreceptors bind the signal-initiating kinase, Lck? Using in vitro assays and non-invasive fluorescence fluctuation spectroscopy in live cells, we show that most coreceptors are occupied by Lck at the surface of live cells. The structural basis for important differences in the kinase occupancy of CD4 and CD8αβ is also identified. These results provide important context for refining current models of both TCR antigen recognition and cell fate decisions made during thymopoiesis.
Mechanisms by Which Small Molecule Inhibitors Arrest Sec14 Phosphatidylinositol Transfer Protein Activity

Phosphatidylinositol transfer proteins (PITPs) promote phosphoinositide signaling by enhancing phosphatidylinositol (PtdIns) 4-OH kinase activities in producing signaling pools of PtdIns-4-phosphate. As such, PITPs are key regulators of lipid signaling in eukaryotic cells. While the PITP phospholipid exchange cycle is the engine that stimulates PtdIns 4-OH kinase activity, the protein and lipid dynamics associated with this critical process are not understood. Herein, we use an integrative structural approach that takes advantage of small molecule inhibitors (SMIs) directed against the major yeast PITP (Sec14) to gain new insights into the mechanics of the Sec14 phospholipid exchange cycle from the perspective of protein, phospholipid and SMI dynamics. Moreover, as Sec14 has emerged as an attractive target for next-generation antifungal drugs, the structures of Sec14 bound to SMIs of four different chemotypes reported in this study provide critical information required for structure-based design of next-generation lead compounds that target Sec14 PITPs of virulent fungi.
Drug–gene Interaction Screens Coupled to Tumor Data Analyses Identify the Most Clinically Relevant Cancer Vulnerabilities Driving Sensitivity to PARP Inhibition

Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) are currently indicated for the treatment of ovarian, breast, pancreatic and prostate cancers harbouring mutations in the tumour suppressor genes BRCA1 or BRCA2. In the case of ovarian and prostate cancers, their classification as homologous recombination repair (HRR) deficient (HRD) or mutated (HRRm) also makes PARPi an available treatment option beyond BRCA1 or BRCA2 mutational status. However, identification of the most relevant genetic alterations driving the HRD phenotype has proven difficult and recent data have shown that other genetic alterations not affecting HRR are also capable of driving PARPi responses. To gain insight into the genetics driving PARPi sensitivity, we performed CRISPR-Cas9 loss-of-function screens in 6 PARPi-insensitive cell lines and combined the output with published PARPi datasets from 8 additional cell lines. Ensuing exploration of the data identified 110 genes whose inactivation is strongly linked to sensitivity to PARPi. Parallel cell line generation of isogenic gene knockouts in ovarian and prostate cancer cell lines identified that inactivation of core HRR factors is required for driving in vitro PARPi responses comparable to the ones observed for BRCA1 or BRCA2 mutations. Moreover, pan-cancer genetic, transcriptomic and epigenetic data analyses of these 110 genes highlight the ones most frequently inactivated in tumours, making this study a valuable resource for prospective identification of potential PARPi-responsive patient populations. Importantly, our investigations uncover XRCC3 gene silencing as a potential new prognostic biomarker of PARPi sensitivity in prostate cancer. Statement of significance This study identifies tumour genetic backgrounds where to expand the use of PARP inhibitors beyond mutations in BRCA1 or BRCA2. This is achieved by combining the output of unbiased genome-wide loss-of-function CRISPR-Cas9 genetic screens with bioinformatics analysis of biallelic losses of the identified genes in public tumour datasets, unveiling loss of the DNA repair gene XRCC3 as a potential biomarker of PARP inhibitor sensitivity in prostate cancer.
Spectroscopic probes of isolated nonequilibrium quantum matter: Quantum quenches, Floquet states, and distribution functions

We investigate radio-frequency (rf) spectroscopy, metal-to-superconductor tunneling, and ARPES as probes of isolated out-of-equilibrium quantum systems, and examine the crucial role played by the nonequilibrium distribution function. As an example, we focus on the induced topological time-periodic (Floquet) phase in a 2D $p+ip$ superfluid, following an instantaneous quench of the coupling strength. The post-quench Cooper pairs occupy a linear combination of "ground" and "excited" Floquet states, with coefficients determined by the distribution function. While the Floquet bandstructure exhibits a single avoided crossing relative to the equilibrium case, the distribution function shows a population inversion of the Floquet bands at low energies. For a realization in ultracold atoms, these two features compensate, producing a bulk average rf signal that is well-captured by a quasi-equilibrium approximation. In particular, the rf spectrum shows a robust gap. The single crossing occurs because the quench-induced Floquet phase belongs to a particular class of soliton dynamics for the BCS equation. The population inversion is a consequence of this, and ensures the conservation of the pseudospin winding number. As a comparison, we compute the rf signal when only the lower Floquet band is occupied; in this case, the gap disappears for strong quenches. The tunneling signal in a solid state realization is ignorant of the distribution function, and can show wildly different behaviors. We also examine rf, tunneling, and ARPES for weak quenches, such that the resulting topological steady-state is characterized by a constant nonequilibrium order parameter. In a system with a boundary, tunneling reveals the Majorana edge states. However, the local rf signal due to the edge states is suppressed by a factor of the inverse system size, and is spatially deconfined throughout the bulk of the sample.
How talin allosterically activates vinculin

The talin-vinculin axis is a key mechanosensing component of cellular focal adhesions. How talin and vinculin respond to forces and regulate one another remains unclear. By combining single molecule magnetic tweezer experiments, Molecular Dynamics simulations, actin bundling assays, and adhesion assembly experiments in live cells, we here discover a two-ways allosteric network within vinculin as a regulator of the talin-vinculin interaction. We directly observe a maturation process of vinculin upon talin binding which reinforces the binding to talin at a rate of 0.03 s−1. This allosteric transition can compete with force-induced dissociation of vinculin from talin only at 7-10 pN. Mimicking the allosteric activation by mutation yields a vinculin molecule that bundles actin and localizes to focal adhesions in a force-independent manner. Hence, the allosteric switch confines talin-vinculin interactions and focal adhesion build-up to intermediate force levels. The ‘allosteric vinculin mutant’ is a valuable molecular tool to further dissect the mechanical and biochemical signalling circuits at focal adhesions and elsewhere.
Investigating the in vivo Spatial Distribution of Hippocampal Microstructure and Macrostructure

The hippocampus is classically divided into mesoscopic subfields which contain varying microstructure that contribute to their unique functional roles. It has been challenging to characterize this microstructure with current MR based neuroimaging techniques. In this work, we used a novel surface-based approach in the hippocampus to show distinct microstructural distributions of myelin, neurite density and dispersion, fractional anisotropy, and mean diffusivity using diffusion MRI. To get at this issue we used the Neurite Orientation Dispersion and Density Imaging (NODDI) model optimized for gray matter diffusivity and diffusion tensor imaging (DTI). We found that neurite dispersion was highest in the Cornu Ammonis (CA) 1 and subiculum subfields which likely captures the large heterogeneity of tangential and radial fibers, such as the Schaffer collaterals, perforant path, and pyramidal neurites. Neurite density and myelin content were highest in the subiculum and lowest in CA1, which may reflect known myeloarchitecture differences between these subfields. We show macrostructural measures of gyrification, thickness, and curvature which were in line with ex vivo descriptions of hippocampal anatomy. We employed a multivariate orthogonal projective non-negative matrix factorization (OPNNMF) approach to capture co-varying regions of macroand microstructure across the hippocampus. The clusters were highly variable along the medial-lateral (proximal-distal) direction, which is expected as there are known differences in morphology, cytoarchitectonic profiles, and connectivity. Long-axis (anterior-posterior) differences can also be seen in the OPNNMF components, where the body of the hippocampus has more parcellations than the head and tail. Finally, we show that by examining the main direction of diffusion relative to canonical hippocampal axes, we could identify microstructure that may map onto specific tangential fiber pathways, such as the Schaffer collaterals and perforant path. These results highlight the value of combining in vivo diffusion MRI with computational approaches for capturing hippocampal microstructure, which may provide useful features for understanding cognition and for diagnosis of disease states.
TraceTrack, an open-source software for batch processing, alignment and visualization of sanger sequencing chromatograms

Background Despite the advent of Next Generation Sequencing technology and its widespread applications, Sanger sequencing remains instrumental for molecular biology subcloning work in biological and medical research and indispensable for drug discovery campaigns. Although Sanger sequencing technology has been long established, existing software for processing and visualization of trace file chromatograms are limited in terms of functionality, scalability, and availability for commercial use. Results To fill this gap, we developed TraceTrack, an open-source web application tool for batch alignment, analysis and visualization of Sanger trace files. TraceTrack offers high throughput matching of trace files to reference sequences, rapid identification of mutations and an intuitive chromatogram analysis. Comparative analysis between TraceTrack and existing software tools highlights the advantages of TraceTrack with regards to batch processing, visualization and export functionalities. TraceTrack is available at https://github.com/Merck/TraceTrack and also at https://tracetrack.dichlab. org as a web application. Conclusion TraceTrack is a web application for batch processing and visualization of Sanger trace file chromatograms that meets the increasing demand of industrial sequence validation workflows in pharmaceutical settings.