Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution of tornado-like vortices in three-dimensional compressible rectangular cavity flows

Abstract The spatial structure and time evolution of tornado-like vortices in a three-dimensional cavity are studied by topological analysis and numerical simulation. The topology theory of the unsteady vortex in the rectangular coordinate system (Zhang, Zhang & Shu, J. Fluid Mech., vol. 639, 2009, pp. 343–372) is generalized to the curvilinear coordinate system. Two functions $\lambda (q_1,t)$ and $q(q_1,t)$ are obtained to determine the topology structure of the sectional streamline pattern in the cross-section perpendicular to the vortex axis and the meridional plane, respectively. The spiral direction of the sectional streamlines in the cross-section perpendicular to the vortex axis depends on the sign of $\lambda (q_1,t)$. The types of critical points in the meridional plane depend on the sign of $q(q_1,t)$. The relation between the critical points of the streamline pattern in the meridional plane and that in the cross-section perpendicular to the vortex axis is set up. The flow in a three-dimensional rectangular cavity is numerically simulated by solving the three-dimensional Navier–Stokes equations using high-order numerical methods. The spatial structures and the time evolutions of the tornado-like vortices in the cavity are analysed with our topology theory. Both the bubble type and spiral type of vortex breakdown are observed. They have a close relationship with the vortex structure in the cross-section perpendicular to the vortex axis. The bubble-type breakdown has a conical core and the core is non-axisymmetric in the sense of topology. A criterion for the bubble type and the spiral type based on the spatial structure characteristic of the two breakdown types is provided.
Psychological Stress and Perceived School Success During COVID-19 Among Parents of Children Who Are Deaf or Hard of Hearing

This study mainly explored psychological stress due to coronavirus disease 2019 (COVID-19) among parents of deaf and hard-of-hearing children and how it related to parents’ views of school success in mainland China. The Psychological Stress Questionnaire and Views of Social and Academic Success were administered to 213 parents of deaf and hard-of-hearing children. Results showed that parents’ and children’s characteristics were related to psychological stress due to COVID-19, which significantly negatively predicted parents’ views of school success. The contributions, limitations, and implications of the present research are discussed.
Moments of Mixture Periodic Autoregressive Models

This article deals with the study of some properties of a mixture periodically correlated autoregressive (MPAR S ) time series model, which extends the mixture time invariant parameter autoregressive (MAR) model, that has recently received a considerable interest from many economic time series analysts, to mixture periodic parameter autoregressive model. The aim behind this extension is to make the model able to capture, in addition to all features captured by the classical MAR model, the periodicity feature exhibited by the autocovariance structure of many encountered financial and environmental time series with eventual multimodal distributions. Our main contribution here is obtaining of the second moment periodically stationary condition for a MPAR S (K; 2,…, 2) model, furthermore the closed-form of the second moment is obtained.
Modeling Developable Mesh Surface by Lofting

In the metal building and garment industries, product model is required to be or closed to be developable surface (can be flattened onto planar patterns without any distortion, tear or stretch). Current work mainly focuses on interpolating only two curves with a narrow developable strip, and lose the generality of applications in industries, which often require N (N>2) curves to determine the final shape feature, and seek one interpolated developable surface. In this paper, a new developability degree criterion is introduced first and a novel lofting algorithm is proposed to model a quasi-developable mesh surface for the given characteristic curves. The curves are first adaptively sampled and then planar triangles are tiled to interpolate all sampling points. The optimal triangulation in terms of given criterion is mapped as one shortest-path finding graph problem, which can be solved by using well-known Dijkstra’s algorithm.
Radar Cross Section of Simple and Complex Targets in the C-band: A Comparison between Anechoic Chamber Measurements and Simulations

In order to validate RCS measurements performed in an anechoic chamber, experi- mental results are compared with simulations made using a commercial electromagnetic software package. The experimental part of this work was performed inside an anechoic chamber, with the radar operating in the C-band (6GHz). Two metallic targets, a cylindrical body with four square flns and a section of an air-to-air missile, were used for the RCS measurements. In order to improve the accuracy of the experimental data, an active noise suppressing system, based on the principle of phase cancellation, was used. The simulation software FEKO was used to calculate the RCS of models of these two targets. The comparison of simulations and experimental data shows good agreement between them, validating the experimental methods used in the collection of RCS data, as well as the results obtained with the simulation software.
The ER folding sensor UGGT1 acts on TAPBPR-chaperoned peptide-free MHC I

Adaptive immune responses are triggered by antigenic peptides presented on major histocompatibility complex class I (MHC I) at the surface of pathogen-infected or cancerous cells. Formation of stable peptide-MHC I complexes is facilitated by tapasin and TAPBPR, two related MHC I-specific chaperones that catalyze selective loading of suitable peptides onto MHC I in a process called peptide editing or proofreading. On their journey to the cell surface, MHC I complexes must pass a quality control step performed by UGGT1, which senses the folding status of the transiting N-linked glycoproteins in the endoplasmic reticulum (ER). UGGT1 reglucosylates non-native glycoproteins and thereby allows them to revisit the ER folding machinery. Here, we describe a reconstituted in-vitro system of purified human proteins that enabled us to delineate the function of TAPBPR during the UGGT1-catalyzed quality control and reglucosylation of MHC I. By combining glycoengineering with liquid chromatography-mass spectrometry, we show that TAPBPR promotes reglucosylation of peptide-free MHC I by UGGT1. Thus, UGGT1 cooperates with TAPBPR in fulfilling a crucial function in the quality control mechanisms of antigen processing and presentation.
Adaptive evolution of hearing genes highlights multiple evolutionary paths for dolphin echolocation in different environments

Echolocation was a key development in toothed whale evolution, favoring their ecological success and adaptive radiation across multiple habitats. Previous bioacoustic and morphological studies suggest that environmental pressures have influenced the evolution of echolocation in odontocetes. This hypothesis demands further investigation, especially regarding molecular mechanisms involved in odontocetes’ adaptive radiation across multiple habitats. Here we show that the coding sequences of four hearing genes involved in echolocation (CDH23, SLC26A5, TMC1 and CLDN14) have different signatures of molecular evolution among riverine, coastal and oceanic dolphins, suggesting that the evolutionary constraints of these habitats have shaped the genetic diversity underlying toothed whale sonars. Our comparative analysis across 37 odontocete species has revealed patterns of accelerated evolution within coastal and riverine lineages, supporting the hypothesis that these habitats generate specific selective pressures to sonar propagation, which are not found in the ocean (e.g., clutter and reverberation). Specific branches with sites under diversifying selection include: three coastal/estuarine species which have recently diverged from closely-related lineages inhabiting freshwater (Cephalorhynchus commersonii, Sotalia guianensis and Orcaella heinsohni - CDH23), and three species that operate specialized Narrow Band High Frequency Sonars (Phocoena sinus - SLC26A5, Neophocaena phocaenoides and Cephalorhynchus commersonii - CDH23). All positively selected lineages are coastal or estuarine from shallow waters (< 100), corroborating current knowledge on these species’ sonars. Among river dolphin branches, positive selection was found on specific sites of the genes CDH23 and SLC26A5, when compared to other cetaceans and Laurasiatherians. Finally, the detection of sites with different overall substitution rates (dN/dS) among river and marine dolphins, together with the finding of different amounts of positively selected sites in each environmental group, suggests distinct selective pressures acting in these groups in the molecular evolution of echolocation.
Missing data in amortized simulation-based neural posterior estimation

Amortized simulation-based neural posterior estimation provides a novel machine learning based approach for solving parameter estimation problems. It has been shown to be computationally efficient and able to handle complex models and data sets. Yet, the available approach cannot handle the in experimental studies ubiquitous case of missing data, and might provide incorrect posterior estimates. In this work, we discuss various ways of encoding missing data and integrate them into the training and inference process. We implement the approaches in the BayesFlow methodology, an amortized estimation framework based on invertible neural networks, and evaluate their performance on multiple test problems. We find that an approach in which the data vector is augmented with binary indicators of presence or absence of values performs the most robustly. Accordingly, we demonstrate that amortized simulation-based inference approaches are applicable even with missing data, and we provide a guideline for their handling, which is relevant for a broad spectrum of applications.
Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits

Changes in gene regulation have long been thought to underlie most phenotypic differences between species. Subterranean rodents, and in particular the naked mole-rat, have attracted substantial attention due to their proposed phenotypic adaptations, which include hypoxia tolerance, metabolic changes and cancer resistance. However, it is largely unknown what regulatory changes may associate with these phenotypic traits, and whether these are unique to the naked mole-rat, the mole-rat clade or also present in other mammals. Here, we investigate regulatory evolution in heart and liver from two African mole-rat species and two rodent outgroups using genome-wide epigenomic profiling. First, we adapted and applied a phylogenetic modeling approach to quantitatively compare epigenomic signals at orthologous regulatory elements, and identified thousands of promoter and enhancer regions with differential epigenomic activity in mole-rats. These elements associate with known mole-rat adaptation in metabolic and functional pathways, and suggest candidate genetic loci that may underlie mole-rat innovations. Second, we evaluated ancestral and species-specific regulatory changes in the study phylogeny, and report several candidate pathways experiencing stepwise remodeling during the evolution of mole-rats – such as the insulin and hypoxia response pathways. Third, we report non-orthologous regulatory elements overlap with lineage-specific repetitive elements and appear to modify metabolic pathways by rewiring of HNF4 and RAR/RXR transcription factor binding sites in mole-rats. These comparative analyses reveal how mole-rat regulatory evolution informs previously reported phenotypic adaptations. Moreover, the phylogenetic modeling framework we propose here improves upon the state-of-the-art by addressing known limitations of inter-species comparisons of epigenomic profiles, and has broad implications in the field of comparative functional genomics.
Systematic, Protein Activity-based Characterization of Single Cell State

While single-cell RNA sequencing provides a remarkable window on pathophysiologic tissue biology and heterogeneity, its high gene-dropout rate and low signal-to-noise ratio challenge quantitative analyses and mechanistic understanding. To address this issue, we developed PISCES, a platform for the network-based, single-cell analysis of mammalian tissue. PISCES accurately estimates the mechanistic contribution of regulatory and signaling proteins to cell state implementation and maintenance, based on the expression of their lineage-specific transcriptional targets, thus supporting discovery and visualization of Master Regulators of cell state and cell state transitions. Experimental validation assays, including by assessing concordance with antibody and CITE-Seq-based measurements, show significant improvement in the ability to identify rare subpopulations and to elucidate key lineage markers, compared to gene expression analysis. Systematic analysis of single cell profiles in the Human Protein Atlas (HPA) produced a comprehensive resource for human tissue studies, supporting fine-grain stratification of distinct cell states, molecular determinants, and surface markers.
Metagenomic Data Reveal Type I Polyketide Synthase Distributions Across Biomes

Microbial polyketide synthase (PKS) genes encode the biosynthesis of many biomedically important natural products, yet only a small fraction of nature’s polyketide biosynthetic potential has been realized. Much of this potential originates from type I PKSs (T1PKSs), which can be delineated into different classes and subclasses based on domain organization and structural features of the compounds encoded. Notably, phylogenetic relationships among PKS ketosynthase (KS) domains provide a method to classify the larger and more complex genes in which they occur. Increased access to large metagenomic datasets from diverse habitats provides opportunities to assess T1PKS biosynthetic diversity and distributions through the analysis of KS domain sequences. Here, we used the webtool NaPDoS2 to detect and classify over 35,000 type I KS domains from 137 metagenomic data sets reported from eight diverse biomes. We found biome-specific separation with soils enriched in modular cis-AT and hybrid cis-AT KSs relative to other biomes and marine sediments enriched in KSs associated with PUFA and enediyne biosynthesis. By extracting full-length KS domains, we linked the phylum Actinobacteria to soil-specific enediyne and cis-AT clades and identified enediyne and monomodular KSs in phyla from which the associated compound classes have not been reported. These sequences were phylogenetically distinct from those associated with experimentally characterized PKSs suggesting novel structures or enzyme functions remain to be discovered. Lastly, we employed our metagenome-extracted KS domains to evaluate commonly used type I KS PCR primers and identified modifications that could increase the KS sequence diversity recovered from amplicon libraries. Importance Polyketides are a crucial source of medicines, agrichemicals, and other commercial products. Advances in our understanding of polyketide biosynthesis coupled with the accumulation of metagenomic sequence data provide new opportunities to assess polyketide biosynthetic potential across biomes. Here, we used the webtool NaPDoS2 to assess type I PKS diversity and distributions by detecting and classifying KS domains across 137 metagenomes. We show that biomes are differentially enriched in KS domain classes, providing a roadmap for future biodiscovery strategies. Further, KS phylogenies reveal both biome-specific clades that do not include biochemically characterized PKSs, highlighting the biosynthetic potential of poorly explored environments. The large metagenome-derived KS dataset allowed us to identify regions of commonly used type I KS PCR primers that could be modified to capture a larger extent of KS diversity. These results facilitate both the search for novel polyketides and our understanding of the biogeographical distribution of PKSs across earth’s major biomes.
Natural stimuli drive concerted nonlinear responses in populations of retinal ganglion cells

The role of the vertebrate retina in early vision is generally described by the efficient coding theory, which predicts that the retina discards spatiotemporal correlations in natural scenes. It is unclear, however, whether the predicted decorrelation in the activity of ganglion cells, the retina’s output neurons, holds under gaze shifts, which dominate the natural visual input. We here show that species-specific gaze patterns in natural stimuli can drive strong and correlated spiking responses both within and across distinct types of ganglion cells in marmoset as well as mouse retina. These concerted responses violate efficient coding and signal fixation periods with locally high spatial contrast. Finally, novel model-based analyses of ganglion cell responses to natural stimuli reveal that the observed response correlations follow from nonlinear pooling of ganglion cell inputs. Our results reveal how concerted population activity can surpass efficient coding to detect gaze-related stimulus features.
Thermal plasticity of wing spot size in Drosophila guttifera: investigating the relevance to Wingless morphogen

Thermal plasticity of animal color patterns has been studied to investigate the molecular mechanisms of phenotypic plasticity. There are examples in which the formation of color patterns is controlled by a morphogen. The extracellular distribution of a morphogen can be plastic with temperature change. Whether alteration of morphogen distribution with temperature change produces thermal plasticity in color patterns has not been studied. To address this question, polka-dotted wing spots of Drosophila guttifera, whose inducer is wingless morphogen, can be a suitable model system. In this study, we reared D. guttifera at different temperatures to test whether wing spots show thermal plasticity. We found that wing size becomes larger and spot size adjusted with wing size becomes smaller at lower temperatures. We also changed the rearing temperature in the middle of the pupal period and found that the most sensitive developmental period for wing size and spot size is different. The results suggest that developmental mechanisms for the thermal plasticity of wing size and spot size are different. We also found that the most sensitive stage for spot size was part of the pupal period including stages at which wingless is expressed in the polka-dotted pattern. Therefore, it is suggested that temperature change might affect the process of specifying spot areas by Wingless in the extracellular region.
Worth the work? Monkeys discount rewards by a subjective adapting effort cost

All life must solve how to allocate limited energy resources to maximize benefits from scarce opportunities. Economic theory posits decision makers optimize choice by maximizing the subjective benefit (utility) of reward minus the subjective cost (disutility) of the required effort. While successful in many settings, this model does not fully account for how experience can alter reward-effort trade-offs. Here, we test how well the subtractive model of effort disutility explains the behavior of two male nonhuman primates (Macaca mulatta) in a binary choice task in which reward quantity and physical effort to obtain were varied. Applying random utility modeling to independently estimate reward utility and effort disutility, we show the subtractive effort model better explains out-of-sample choice behavior when compared with parabolic and exponential effort discounting. Furthermore, we demonstrate that effort disutility depends on previous experience of effort: in analogy to work from behavioral labor economics, we develop a model of reference-dependent effort disutility to explain the increased willingness to expend effort following previous experience of effortful options in a session. The result of this analysis suggests that monkeys discount reward by an effort cost that is measured relative to an expected effort learned from previous trials. When this subjective cost of effort, a function of context and experience, is accounted for, trial-by-trial choices can be explained by the subtractive cost model of effort. Therefore, in searching for net utility signals that may underpin effort-based decision-making in the brain, careful measurement of subjective effort costs is an essential first step. SIGNIFICANCE STATEMENT All decision-makers need to consider how much effort they need to expend when evaluating potential options. Economic theories suggest that the optimal way to choose is by cost-benefit analysis of reward against effort. To be able to do this efficiently over many decision contexts, this needs to be done flexibly, with appropriate adaptation to context and experience. Therefore, in aiming to understand how this might be achieved in the brain, it is important to first carefully measure the subjective cost of effort. Here, we show monkeys make reward-effort cost-benefit decisions, subtracting the subjective cost of effort from the subjective value of rewards. Moreover, the subjective cost of effort is dependent on the monkeys’ experience of effort in previous trials.
The Myb family genes in the rice pathogen Magnaporthe oryzae: Finding and deleting more family members involved in pathogenicity

Proteins with DNA binding Myb domains have been suggested in regulating development and stress responses. Magnaporthe oryzae is considered the most destructive pathogen of rice. We screened the genome for genes with Myb domains encoding since these can be needed for pathogenesis. We found Myb1-19. Only MoMyb1 was previously shown to be involved in pathogenesis. We succeeded in deleting 12 of the other 18 genes. MoMyb2 deletion affected mainly growth, while MoMyb13 or MoMyb15 deletions gave additional defects in conidiation and plant infection. However, RT-qPCR showed that none of the 19 Myb genes are negligibly expressed. Instead, they have different expression profiles hours post-infection when infecting rice plants. Considering this, the unchanged infection phenotype for 9 gene deletions surprised us, and we extended the analysis to expression co-regulation of all 19 Myb proteins and found 5 co-regulated groups of predicted Myb-domain proteins. MoMyb13 or MoMyb15 are discussed and motivated as candidates for further, more detailed studies with aims also outside of plant pathology. Referring to what is found in other eukaryotes, we finally discuss possible redundancy or compensatory regulations for many of the other Myb genes hiding or compensating for the effect of many complete deletions. IMPORTANCE Magnaporthe oryzae is considered the most important rice pathogen limiting rice production. Our study attempts to find all genes encoding a DNA-binding gene family called Myb, and we found 19, many of which have not been studied before. The Myb gene family is suspected to regulate stress responses the pathogen needs to overcome plant defenses. Inhibiting or disturbing these genes, if they are indeed regulatory, can open new ways of controlling the pathogen and learning more about its physiology and ecology.