Miracle-dz/UniFAR-FTUs huggingface dataset:
A time-frequency calculus for time-varying systems and non-stationary processes with applications

This thesis introduces an approximate time-frequency calculus for underspread linear time-varying systems (i.e., time-varying systems that effect only small time-frequency shifts of the input signal) and underspread nonstationary random processes (i.e., nonstationary processes that feature only small time-frequency correlations). After briefly describing the major difficulties encountered with time-varying systems and nonstationary processes, we introduce an extended definition of underspread systems. Our extended underspread concept is based on weighted integrals and moments of the system’s generalized spreading function. Subsequently, numerous approximations are presented which show that in the case of underspread systems the generalized Weyl symbol constitutes an approximate time-frequency transfer function. As a mathematical underpinning of our transfer function approximations, we provide bounds on the associated approximation errors that involve the previously defined weighted integrals and moments of the generalized spreading function. We then consider nonstationary random processes and provide an extended definition of underspread processes. This extended underspread concept is based on weighted integrals and moments of the generalized expected ambiguity function of the process. Subsequently, two fundamental classes of time-varying power spectra are introduced and analyzed: “type I” spectra that extend the generalized Wigner-Ville spectrum and “type II” spectra that extend the generalized evolutionary spectrum. We show that in the case of underspread processes, the various members of these two classes of spectra are approximately equivalent to each other and (at least) approximately satisfy several desirable properties. Our approximations are again supported by bounds on the associated approximation errors. These bounds are formulated in terms of the previously defined weighted integrals and moments of the generalized expected ambiguity function. The definition and analysis of time-frequency coherence functions concludes our discussion of time-varying power spectra. Finally, we illustrate the practical relevance of our theoretical findings by considering several applications in the areas of statistical signal processing and wireless communications. These applications include nonstationary signal estimation and detection, the sounding of mobile radio channels, multicarrier communications over time-varying channels, and the analysis of car engine signals.
Nuclear export inhibition jumbles epithelial–mesenchymal states and gives rise to migratory disorder in healthy epithelia

Epithelial-mesenchymal (E-M) phenotypes govern collective cellular behaviors to facilitate diverse tissue functions, including embryogenesis, wound healing, and cancer invasion. Cellular E-M state is regulated by dynamic nucleocytoplasmic transport of corresponding E-M factors; yet, it remains unknown how concurrently trapping these factors affects epithelia at the macroscale. To explore this question, we performed nuclear export inhibition (NEI) via Leptomycin B treatment, which biases nuclear localization of CRM1- associated E-M factors. We examined changes in collective cell migration across a range of substrate stiffnesses. Our results show that NEI fosters an atypical E-M state wherein cells concurrently strengthen intercellular adhesions and develop mechanoactive characteristics. Following NEI, soft substrates elevate collective migration for up to 24 h, while stiffer substrates reduce migration at all timepoints. We demonstrate that excluding Yes-associated protein 1 from NEI shifts affected cells toward an epithelial phenotype. Meanwhile, removing α-catenin maintains NEI’s intercellular adhesion strengthening and mechanoactivation capabilities, but prevents mechanoactive characteristics from reaching collective behavior. Overall, our results show that NEI disrupts epithelial migration through competition between intercellular adhesions, mechanoactivation, and cell-cell coordination. Ultimately, these findings of mechanoactive NEI outcomes for healthy cells could warrant additional investigation in the context of NEI-centered cancer therapies.
Characterization of environmental effects on flowering and plant architecture in an everbearing strawberry F1-hybrid by meristem dissection and gene expression analysis

Floral transition in the cultivated everbearing strawberry is a hot topic because these genotypes flower perpetually and are difficult to maintain in a non-flowering state. However, it has rarely been studied using morphogenetic and molecular analyses simultaneously. We therefore examined morphogenetic effects and the activation of genes involved in floral induction and initiation in seedlings of an everbearing F1-hybrid. Seedlings were grown at 12, 19, and 26°C under 10-h SD and 20-h LD conditions. We observed a strong environmental influence on meristem development and a FLOWERING LOCUS T1 (FaFT1)–SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (FaSOC1) pathway similar to that in the everbearing woodland strawberry. The everbearing cultivar showed typical features of a quantitative LD plant, flowering earlier under LD than SD conditions at all temperatures. We also found that floral induction is facilitated by FaFT1 upregulation under LD conditions, while FaSOC1 upregulation in the apex leads to photoperiod-independent floral initiation. Moreover, we confirmed the strawberry meristem identity gene FRUITFULL (FaFUL) can also be used as an early indicator of floral initiation in EB cultivars. This study also highlights the advantages of using seed-propagated F1-hybrids for genetic studies because are genetically identical, and not biased by a previous flowering history.
Juvenile Shank3 KO Mice Adopt Distinct Hunting Strategies during Prey Capture Learning

Abstract Mice are opportunistic omnivores that readily learn to hunt and eat insects such as crickets. The details of how mice learn these behaviors and how these behaviors may differ in strains with altered neuroplasticity are unclear. We quantified the behavior of juvenile wild-type (WT) and Shank3 knock-out (KO) mice as they learned to hunt crickets during the critical period for ocular dominance plasticity. This stage involves heightened cortical plasticity including homeostatic synaptic scaling, which requires Shank3, a glutamatergic synaptic protein that, when mutated, produces Phelan-McDermid syndrome and is often comorbid with autism spectrum disorder (ASD). Both strains showed interest in examining live and dead crickets and learned to hunt. Shank3 knock-out mice took longer to become proficient, and, after 5 d, did not achieve the efficiency of wild-type mice in either time-to-capture or distance-to-capture. Shank3 knock-out mice also exhibited different characteristics when pursuing crickets that could not be explained by a simple motor deficit. Although both genotypes moved at the same average speed when approaching a cricket, Shank3 KO mice paused more often, did not begin final accelerations toward crickets as early, and did not close the distance gap to the cricket as quickly as wild-type mice. These differences in Shank3 KO mice are reminiscent of some behavioral characteristics of individuals with ASD as they perform complex tasks, such as slower action initiation and completion. This paradigm will be useful for exploring the neural circuit mechanisms that underlie these learning and performance differences in monogenic ASD rodent models.
A prefrontal network model operating near steady and oscillatory states links spike desynchronization and synaptic deficits in schizophrenia

Schizophrenia results in part from a failure of prefrontal networks but we lack full understanding of how disruptions at a synaptic level cause failures at the network level. This is a crucial gap in our understanding because it prevents us from discovering how genetic mutations and environmental risks that alter synaptic function cause prefrontal network to fail in schizophrenia. To address that question, we developed a recurrent spiking network model of prefrontal local circuits that can explain the link between NMDAR synaptic and spike timing deficits we recently observed in a pharmacological monkey model of prefrontal network failure in schizophrenia. We analyze how the balance between AMPA and NMDA components of recurrent excitation and GABA inhibition in the network influence spike timing to inform the biological data. We show that reducing recurrent NMDAR synaptic currents prevents the network from shifting from a steady to oscillatory state in response to extrinsic inputs such as might occur during behavior. This explains how NMDAR synaptic deficits, implicated by genetic evidence as causal in schizophrenia, could prevent the emergence of 0-lag synchronous spiking in prefrontal local circuits during behavior, potentially disconnecting those circuits via spike-timing dependent mechanisms in the human disease.
Distinct airway progenitor cells drive epithelial heterogeneity in the developing human lung

Recent advances using single cell genomic approaches have identified new epithelial cell types and uncovered cellular heterogeneity in the murine and human lung (1). Here, using scRNA-seq and microscopy we identify and describe a secretory-like cell that is enriched in the small airways of the developing human lung and identified by the unique co-expression of SCGB3A2/SFTPB/CFTR. To place these cells in the hierarchy of airway development, we apply a single cell barcode-based lineage tracing method track the fate of SCGB3A2/SFTPB/CFTR cells during airway organoid differentiation in vitro (2). Lineage tracing revealed that these cells have distinct developmental potential from basal cells, giving rise predominantly to pulmonary neuroendocrine cells (PNECs) and a subset of multiciliated cells distinguished by high C6 and low MUC16 expression. We conclude that SCGB3A2/SFTPB/CFTR cells act as a progenitor cell contributing to the cellular diversity and heterogeneity in the developing human airway. SIGNIFICANCE STATEMENT The current study identifies a novel secretory cell type that is present predominantly in the small airway of the developing human lung. These secretory cells are defined by co-expression of SCGB3A2/SFTPB/CFTR, and functional studies show that this cell gives rise to pulmonary neuroendocrine cells and a sub-population of multiciliated cells, thereby leading to cellular heterogeneity.
Dissection of insular cortex layer 5 reveals two sublayers with opposing modulatory roles in appetitive behavior

The insular cortex (insula) is known to play a modulatory role in motivated behaviors including feeding and drinking. Previous studies have revealed that the anterior and posterior subregions of the insula have differential subcortical efferents and roles, yet the anatomical and functional heterogeneity among the cortical layers remains poorly understood. Here, we show that layer 5 of the mouse dysgranular insula has two distinct neuronal subpopulations along the entire anterior-posterior axis: the upper layer (L5a) population, expressing NECAB1, projects bilaterally to the lateral and capsular divisions of the central amygdala, and the deeper layer (L5b) population, expressing CTIP2, projects ipsilaterally to the parasubthalamic nucleus and the medial division of the central amygdala. Optogenetically activating L5a and L5b neuronal populations in thirsty mice led to suppressed and facilitated water spout licking, respectively, in a single-spout test. However, the opto-activation induced no avoidance against or preference for the spout paired with the opto-stimulation in a two-spout choice test, indicating no induction of emotional valences by the opto-activation per se. Our results suggest sublayer-specific bidirectional modulatory roles of insula layer 5 in the motivational aspect of appetitive behavior.
Instability Analysis of a Low-Density Gas Jet Injected into a High-Density Gas

The objective of this study was to determine the effects of buoyancy on the absolute instability of low-density gas jets injected into high-density gas mediums. Most of the existing analyses of low-density gas jets injected into a high-density ambient have been carried out neglecting effects of gravity. In order to investigate the influence of gravity on the near-injector development of the flow, a linear temporal stability analysis and a spatio-temporal stability analysis of a low-density round jet injected into a high-density ambient gas were performed. The flow was assumed to be isothermal and locally parallel; viscous and diffusive effects were ignored. The variables were represented as the sum of the mean value and a normal-mode small disturbance. An ordinary differential equation governing the amplitude of the pressure disturbance was derived. The velocity and density profiles in the shear layer, and the Froude number (signifying the effects of gravity) were the three important parameters in this equation. Together with the boundary conditions, an eigenvalue problem was formulated. Assuming that the velocity and density profiles in the shear layer to be represented by hyperbolic tangent functions, the eigenvalue problem was solved for various values of Froude number. The temporal growth rates and the phase velocity of the disturbances were obtained. It was found that the presence of variable density within the shear layer resulted in an increase in the temporal amplification rate of the disturbances and an increase in the range of unstable frequencies, accompanied by a reduction in the phase velocities of the disturbances. Also, the temporal growth rates of the disturbances were increased as the Froude number was reduced (i.e. gravitational effects increased), indicating the destabilizing role played by gravity. The spatio-temporal stability analysis was performed to determine the nature of the absolute instability of the jet. The roles of the density ratio, Froude number, Schmidt number, and the lateral shift between the density and velocity profiles on the jet's absolute instability were determined. Comparisons of the results with previous experimental studies show good agreement when the effects of these variables are combined together. Thus, the combination of these variables determines how absolutely unstable the jet will be. Experiments were carried out to observe the qualitative differences between a round low-density gas jet injected into a high-density gas (helium jet injected into air) and a round constant density jet (air jet injected into air). Flow visualizations and velocity measurements in the near-injector region of the helium jet show more mixing and spreading of the helium jet than the air jet. The vortex structures develop and contribute to the jet spreading causing the helium jet to oscillate.
Immediate Early Proteins of Herpes Simplex Virus Transiently Repress Viral Transcription before Subsequent Activation

HSV-1 transcription during productive replication is believed to comprise a series of activation steps leading to a specific sequence of gene expression. Here, we show that virion components and IE gene products ICP0, ICP4, and ICP22 first repress viral gene transcription to various degrees before subsequently activating specific gene subsets. ABSTRACT Herpes simplex virus 1 (HSV-1) utilizes cellular RNA polymerase II (Pol) to transcribe its genes in one of two phases. In the latent phase, viral transcription is highly restricted, but during the productive lytic phase, more than 80 genes are expressed in a temporally coordinated cascade. In this study, we used Precision nuclear Run On followed by deep Sequencing (PRO-Seq) to characterize early viral transcriptional events using HSV-1 immediate early (IE) gene mutants, corresponding genetically repaired viruses, and wild-type virus. Unexpectedly, in the absence of the IE genes ICP4, ICP22, and ICP0 at 1.5 hours postinfection (hpi), we observed high levels of aberrant transcriptional activity across the mutant viral genomes but substantially less on either wild-type or the congenic repaired virus genomes. This feature was particularly prominent in the absence of ICP4 expression. Cycloheximide treatment during infection with both the ICP4 and ICP22 mutants and their respective genetic repairs did not alter the relative distribution of Pol activity, but it increased overall activity across both viral genomes, indicating that both virion components and at least some de novo protein synthesis were required for full repression. Overall, these data reveal that prior to their role in transcriptional activation, IE gene products and virion components first repress transcription and that the HSV-1 lytic transcriptional cascade is mediated through subsequent derepression steps. IMPORTANCE HSV-1 transcription during productive replication is believed to comprise a series of activation steps leading to a specific sequence of gene expression. Here, we show that virion components and IE gene products ICP0, ICP4, and ICP22 first repress viral gene transcription to various degrees before subsequently activating specific gene subsets. It follows that the entire HSV transcriptional program involves a series of steps to sequentially reverse this repression. This previously uncharacterized repressive activity of IE genes very early in infection may represent an important checkpoint allowing HSV-1 to orchestrate either the robust lytic transcriptional cascade or the more restricted transcriptional program during latency.
Structural features stabilized by divalent cation coordination within hepatitis E virus ORF1 are critical for viral replication

Hepatitis E virus (HEV) is an RNA virus responsible for over 20 million infections annually. HEV’s open reading frame (ORF)1 polyprotein is essential for genome replication, though it is unknown how the different subdomains function within a structural context. Our data show that ORF1 operates as a multifunctional protein, which is not subject to proteolytic processing. Supporting this model, scanning mutagenesis performed on the putative papain-like cysteine protease (pPCP) domain revealed six cysteines essential for viral replication. Our data are consistent with their role in divalent metal ion coordination, which governs local and interdomain interactions that are critical for the overall structure of ORF1; further, the “pPCP” domain can only rescue viral genome replication in trans when expressed in the context of the full-length ORF1 protein but not as an individual subdomain. Taken together our work provides a comprehensive model of the structure and function of HEV ORF1. Significance Statement The development of non-teratogenic and potent antiviral therapies against HEV have been hindered by an incomplete understanding of the viral replication cycle. Our work provides a mechanistic insight into the complex replicative cycle of this understudied human pathogen and identifies a novel domain-domain interaction that is vital for replicative fitness.
Solving the Puzzle: A New Measure of Trade Distance in the Gravity Equation

The gravity equation model is a workhorse tool that has been used many times in international trade. However, one philosophical and empirical question that arises when this theory is applied in this ? eld is what is the relevant measure of distance. This question is easily solved in physics, which is the ? eld where this theory was originally developed, but there is not clear answer in international trade. Therefore, we propose an index of distance based on principal component analysis that summarizes in one factor information related to geographical, cultural, political and economic variables that might a? ect international trade between countries. We use this index as proxy of distance, and Gross Domestic Product as proxy of mass, and we run some panel data exercises between 1995 and 2000 for 10 Latin American economies. Estimations indicate that the sign of the load factors in the principal component analysis are intuitively plausible, and that panel data exercises give sensible robust outcomes.
Off-manifold coding in visual cortex revealed by sleep

Low-dimensional neural manifolds are controversial in part because it is unclear how to reconcile them with high-dimensional representations observed in areas such as primary visual cortex (V1). We addressed this by recording neuronal activity in V1 during slow-wave sleep, enabling us to identify internally-generated low-dimensional manifold structure and evaluate its role during visual processing. We found that movements and visual stimuli were both encoded in the “on-manifold” subspace preserved during sleep. However, only stimuli were encoded in the “off-manifold” subspace, which contains activity patterns that are less likely than chance to occur spontaneously during sleep. This off-manifold activity comprises sparse firing in neurons with the strongest low-dimensional modulation by movement, which paradoxically prevents movement-evoked activity from interfering with stimulus representations. These results reveal an unexpected link between low-dimensional dynamics and sparse coding, which together create a protected off-manifold coding space keeping high-dimensional representations separable from movement-evoked activity.
Bootstrap bandwidth selection in kernel hazard rate estimation

The purpose of this study is to thoroughly discuss kernel hazard function estimation, both in the complete sample case as well as in the presence of random right censoring. Most of the focus is on the very important task of automatic bandwidth selection. Two existing selectors, least-squares cross validation as described by Patil (1993a) and Patil (1993b), as well as the bootstrap bandwidth selector of Gonzalez-Manteiga, Cao and Marron (1996) will be discussed. The bandwidth selector of Hall and Robinson (2009), which uses bootstrap aggregation (or “bagging”), will be extended to and evaluated in the setting of kernel hazard rate estimation. We will also make a simple proposal for a bootstrap bandwidth selector. The performance of these bandwidth selectors will be compared empirically in a simulation study. The findings and conclusions of this study are reported.
efficient heterogeneous catalyst for the degradation of methyl blue in water in the presence of peroxymonosulfate ion

ZnCo-ZIFs was successfully synthesized by a solvothermal method in methanol solvent at room conditions and determined physical–chemical properties by a series of characterization techniques. The catalytic activity of ZnCo-ZIFs on Methyl Blue (MB) degradation in the presence of peroxymonosulfate (PMS) was examined by variation of the effective factors including ZnCo-ZIFs dosage, mass ratio of ZnCoZIFs:PMS, temperature, reaction time and initial MB concentration. The result showed that MB was mostly degraded at initial MB concentration of 50 mg L−1 with catalyst dosage of 50 mg L−1 and ZnCo-ZIFs:PMS ratio of 1:3 at room temperature within 20 min of reaction. The main mechanism for dye degradation was the Fenton-like reaction via major active species SO4· ̅ (sulfate free radical) generated from PMS by Co2+ metal centers in the catalyst frameworks. The ZnCo-ZIFs showed highly efficient catalytic activity and stability compared to both homogeneous (cobalt salt, zinc salt and 2-methylimidazole) and heterogeneous (ZIF-67, ZIF-8, zeolite ZMS-5 and activated carbon) catalysts. The recyclability of the catalyst also showed an impressive result with 93.6% at the 5th recycle. To the best of our knowledge, ZnCo-ZIFs associated with PMS was first reported as a novel Fenton-like heterogeneous catalyst for MB degradation in water. * Huynh Vu Thanh Luong lhvthanh@ctu.edu. vn 1 Applied Chemical Engineering Lab, College of Engineering, Can Tho University, Can Tho 900000, Vietnam 2 Department of Chemical Engineering, College of Engineering, Can Tho University, Can Tho 900000, Vietnam 3 Department of Chemistry, College of Natural Sciences, Can Tho University, Can Tho 900000, Vietnam Reaction Kinetics, Mechanisms and Catalysis 1 3 Graphical abstract