Miracle-dz/UniFAR-FTUs huggingface dataset:
Congestion games with player-specific cost functions

We consider congestion games on graphs. In nonatomic games, we are given a set of infinitesimal players. Each player wants to go from one vertex to another by taking a route of minimal cost, the cost of a route depending on the number of players using it. In atomic splittable games, we are given a set of players with a non-negligible demand. Each player wants to ship his demand from one vertex to another by dividing it among different routes. In these games, we reach a Nash equilibrium when every player has chosen a minimal-cost strategy. The existence of a Nash equilibrium is ensured under mild conditions. The main issues are the uniqueness, the computation, the efficiency and the sensitivity of the Nash equilibrium. Many results are known in the specific case where all players are impacted in the same way by the congestion. The goal of this thesis is to generalize these results in the case where we allow player-specific cost functions. We obtain results on uniqueness of the equilibrium in nonatomic games. We give two algorithms able to compute a Nash equilibrium in nonatomic games when the cost functions are affine. We find a bound on the price of anarchy for some atomic splittable games, and prove that it is unbounded in general, even when the cost functions are affine. Finally we find results on the sensitivity of the equilibrium to the demand in atomic splittable games
SPECTRA OF STRONG MAGNETOHYDRODYNAMIC TURBULENCE FROM HIGH-RESOLUTION SIMULATIONS

Magnetohydrodynamic (MHD) turbulence is present in a variety of solar and astrophysical environments. Solar wind fluctuations with frequencies lower than 0.1 Hz are believed to be mostly governed by Alfvénic turbulence with particle transport depending on the power spectrum and the anisotropy of such turbulence. Recently, conflicting spectral slopes for the inertial range of MHD turbulence have been reported by different groups. Spectral shapes from earlier simulations showed that MHD turbulence is less scale-local compared with hydrodynamic turbulence. This is why higher-resolution simulations, and careful and rigorous numerical analysis is especially needed for the MHD case. In this Letter, we present two groups of simulations with resolution up to 40963, which are numerically well-resolved and have been analyzed with an exact and well-tested method of scaling study. Our results from both simulation groups indicate that the asymptotic power spectral slope for all energy-related quantities, such as total energy and residual energy, is around −1.7, close to Kolmogorov's −5/3. This suggests that residual energy is a constant fraction of the total energy and that in the asymptotic regime of Alfvénic turbulence magnetic and kinetic spectra have the same scaling. The −1.5 slope for energy and the −2 slope for residual energy, which have been suggested earlier, are incompatible with our numerics.
The Role of Faculty In Faculty–Student Engagement: Disaggregated Analyses by Ethnicity for Southeast Asian American College Students

Higher education institutions have struggled to support the degree completion of Southeast Asian American (SEAA) college students (Keo & Noguera, 2018), a population that has been historically understudied and underserved (Museus, 2014). Thus, increased attention to the success of this group of students is important. Research has indicated that faculty–student engagement is a contributing factor to degree completion (Price & Tovar, 2014). Given the importance of faculty–student engagement on degree completion, understanding its predictors can be important to begin addressing degree completion rates for SEAA college students. Some research on SEAA college students has suggested that faculty–student engagement is a function of the conditions created by faculty (Vang, 2018; Xiong & Wood, 2020). For example, students’ perceptions of the number of faculty who validate them were found to be a significant predictor of faculty–student engagement for SEAA students (Xiong & Wood, 2020). However, these studies have been limited in scope, focusing primarily on faculty validation and faculty belonging practices as predictors of faculty–student engagement. In addition to these practices, the current study included student perceptions of faculty relationship and welcoming engagement inside and outside of the classroom as predictor variables of faculty– student engagement. Research on faculty–student engagement that has included Asian American participants has infrequently disaggregated analyses by specific Asian ethnic groups (e.g., Chang, 2005; Cole, 2010). Analyses based on an aggregation of ethnic Asian populations may mask important ethnic differences. Therefore, disaggregated analyses for specific Asian ethnic groups are warranted since research has suggested the experiences of SEAA college students vary by ethnicity (Xiong, 2021). The current study analyzed faculty–student engagement data that could be disaggregated by Southeast Asian ethnic groups (e.g., Cambodian, Hmong, Laotian, Vietnamese) to examine ethnic differences. As such, the purpose of the current study was to examine how student perceptions of faculty practices predicted engagement with faculty and whether significant predictors of faculty–student engagement varied by ethnicity among SEAA college students. This study is the first to systematically examine these relationships for SEAA students. The current investigation is also the first empirical study to conduct disaggregated analyses on faculty–student
The Effects of Motivation, Career Decision-Making Self-Efficacy, and Self-Regulation on Learning Engagement of Junior College Students

Abstract:This study examined three influential factors of junior college students' learning engagement: (a) intrinsic and extrinsic motivation, (b) career decision-making self-efficacy (CDMSE), and (c) self-regulation. Participants included 206 students enrolled in the secretarial administration program in a junior college in South Korea. The primary research findings are as follows. First, intrinsic and extrinsic motivation positively influenced CDMSE. Intrinsic motivation influenced learning engagement through CDMSE and self-regulation; extrinsic motivation did not. Second, CDMSE influenced self-regulation and indirectly influenced learning engagement through self-regulation. Third, self-regulation had the largest effect on learning engagement. The findings highlight the need to examine and enhance students' self-regulation skills and help improve the learning engagement of junior college students. This study confirmed the significance of motivation, CDMSE, and self-regulation for junior college students' learning engagement.
Entrainment of bed sediment composed of very fine material

In an estuary bed composed of very fine sediment material, tidal currents cause active sediment transportation, bar morphology changes, and severe bank erosion. However, it is difficult to evaluate the erosion rate of a sediment bed composed of particles measuring five to several tens of micrometres using methodologies found in the available literature that estimate entrainment in the presence of fine sediment suspension. This paper proposes a new method to evaluate the erosion rate of a sediment bed composed of very fine material by introducing the concept of entrainment developed for density stratified flows. A series of flume experiments were conducted to investigate the erosion rates of bed material with water–sediment mixtures of different concentrations, sediment particle sizes, and overall Richardson numbers. The results of the flume experiments are compared with past theories and experimental results conducted for density stratified flows. The data show that the erosion rate of a water–sediment mixture is proportional to the inverse of the overall Richardson number, as proposed in previous studies on density stratified flows. In cases with a strong cohesion, the erosion rate can be evaluated using a modified Richardson number, introduced to evaluate the influence of viscosity on entrainment rates. The applicability of the proposed method is also tested by comparing the results of the present study with those of previous studies in terms of equilibrium suspended sediment concentration and size distributions of suspended sediment. The present results show that the proposed method can be used to evaluate not only the erosion rate of suspended sediment but also the characteristics of equilibrium transport processes.
Effect of time delay on dynamic of plant competition under allelopathy

In this paper, a mathematical model is applied to investigate the effect of density of allelochemicals on plant population involving delay. The model is constructed using a system of nonlinear delay differential equations. In the model, there are three state variables: plant populations (P1 & P2) and density of allelochemical (T). It is assumed that in the presence of density of allelochemicals, plant populations are affected. It further delays the conversion of resource into the density of allelochemicals and hence affects the plant population adversely. This effect is observed by using delay in the competition model. Equilibrium points are calculated. Using the Routh–Hurwitz theorem, certain explicit formulations defining the stability and path of the Hopf‐bifurcation periodic solutions at the positive equilibrium are obtained. Further, the direction of these bifurcating periodic solutions is also studied. Numerical simulation and graphical support are provided for analytical findings using MATLAB.
SARS-CoV-2 ORF3c impairs mitochondrial respiratory metabolism, oxidative stress and autophagic flow

Coronaviruses encode a variable number of accessory proteins that play a role in host-virus interactions, in the suppression of immune responses, or in immune evasion. Accessory proteins in SARS-CoV-2 consist of at least twelve viral proteins whose roles during infection have been extensively studied. Nevertheless, the role of the ORF3c accessory protein, an alternative open reading frame of ORF3a, has remained elusive. Herein, we characterized ORF3c in terms of cellular localization, host’s antiviral response modulation, and effects on mitochondrial metabolism. We show that ORF3c has a mitochondrial localization and alters mitochondrial metabolism, resulting in increased ROS production, block of the autophagic flux, and accumulation of autophagosomes/autolysosomes. Notably, we also found that ORF3c induces a shift from glucose to fatty acids oxidation and enhanced oxidative phosphorylation. This is similar to the condition observed in the chronic degenerative phase of COVID-19. Altogether these data suggest that ORF3c could be a key protein for SARS-CoV-2 pathogenesis and that it may play a role in disease progression.
Eye drift during fixation predicts visual acuity

Significance Healthy humans can visually resolve extremely fine patterns, in some cases with the relevant features spanning less than a single photoreceptor on the retina. This accomplishment is particularly remarkable considering that the eyes are never stationary. Ocular drift—a motion that eludes human awareness—shifts the stimulus across many photoreceptors during the acquisition of visual information. Here, we show that visual acuity depends on ocular drift. Natural variations in the amount of drift are associated with acuity both within and across subjects, so that individual acuity limits can be directly inferred from the amount of motion during fixation on a marker. Results closely follow the strength of the luminance modulations caused by ocular drift, providing support to long-standing dynamic theories of visual acuity.
Obsessive-Compulsive Disorder (OCD) is Associated with Increased Electroencephalographic (EEG) Delta and Theta Oscillatory Power but Reduced Delta Connectivity

Background Obsessive-Compulsive Disorder (OCD) is a mental health condition causing significant decline in the quality of life of sufferers and the limited knowledge on the pathophysiology hinders successful treatment. The aim of the current study was to examine electroencephalographic (EEG) findings of OCD to broaden our understanding of the disease. Methods Resting-state eyes-closed EEG data was recorded from 25 individuals with OCD and 27 healthy controls (HC). The 1/f arrhythmic activity was removed prior to computing oscillatory powers of all frequency bands (delta, theta, alpha, beta, gamma). Cluster-based permutation was used for between-group statistical analyses, and comparisons were performed for the 1/f slope and intercept parameters. Functional connectivity (FC) was measured using coherence and debiased weighted phase lag index (d-wPLI), and statistically analysed using the Network Based Statistic method. Results Compared to HC, the OCD group showed increased oscillatory power in the delta and theta bands in the fronto-temporal and parietal brain regions. However, there were no significant between-group findings in other bands or 1/f parameters. The coherence measure showed significantly reduced FC in the delta band in OCD compared to HC but the d-wPLI analysis showed no significant differences. Conclusions OCD is associated with raised oscillatory power in slow frequency bands in the fronto-temporal brain regions, which agrees with the previous literature and therefore is a potential biomarker. Although delta coherence was found to be lower in OCD, due to inconsistencies found between measures and the previous literature, further research is required to ascertain definitive conclusions.
A comprehensive view of cell-type-specific temporal dynamics in human and mouse brains

Progenitor cells play fundamental roles in preserving optimal organismal functions under normal, aging, and disease conditions. However, progenitor cells are incompletely characterized, especially in the brain, partly because conventional methods are restricted by inadequate throughput and resolution for deciphering cell-type-specific proliferation and differentiation dynamics in vivo. Here, we developed TrackerSci, a new technique that combines in vivo labeling of newborn cells with single-cell combinatorial indexing to profile the single-cell chromatin landscape and transcriptome of rare progenitor cells and track cellular differentiation trajectories in vivo. We applied TrackerSci to analyze the epigenetic and gene expression dynamics of newborn cells across entire mouse brains spanning three age stages and in a mouse model of Alzheimer’s disease. Leveraging the dataset, we identified diverse progenitor cell types less-characterized in conventional single cell analysis, and recovered their unique epigenetic signatures. We further quantified the cell-type-specific proliferation and differentiation potentials of progenitor cells, and identified the molecular programs underlying their aging-associated changes (e.g., reduced neurogenesis/oligodendrogenesis). Finally, we expanded our analysis to study progenitor cells in the aged human brain through profiling ∼800,000 single-cell transcriptomes across five anatomical regions from six aged human brains. We further explored the transcriptome signatures that are shared or divergent between human and mouse oligodendrogenesis, as well as the region-specific down-regulation of oligodendrogenesis in the human cerebellum. Together, the data provide an in-depth view of rare progenitor cells in mammalian brains. We anticipate TrackerSci will be broadly applicable to characterize cell-type-specific temporal dynamics in diverse systems.
MarR-Dependent Transcriptional Regulation of mmpSL5 Induces Ethionamide Resistance in Mycobacterium abscessus

Mycobacterium abscessus (Mabs) is an emerging nontuberculosis mycobacterial (NTM) pathogen responsible for a wide variety of respiratory and cutaneous infections that are difficult to treat with standard antibacterial therapy. Mabs has a high degree of both innate and acquired antibiotic resistance to most clinically relevant drugs, including standard anti-mycobacterial agents. Ethionamide (ETH), an inhibitor of mycolic acid biosynthesis, is currently utilized as a second-line agent for treating multidrug-resistant tuberculosis infections. ABSTRACT Mycobacterium abscessus (Mabs) is an emerging nontuberculosis mycobacterial (NTM) pathogen responsible for a wide variety of respiratory and cutaneous infections that are difficult to treat with standard antibacterial therapy. Mabs has a high degree of both innate and acquired antibiotic resistance to most clinically relevant drugs, including standard anti-mycobacterial agents. Ethionamide (ETH), an inhibitor of mycolic acid biosynthesis, is currently utilized as a second-line agent for treating multidrug-resistant tuberculosis infections. Here, we show that ETH displays activity against clinical strains of Mabs in vitro at concentrations that are >100× lower than other mycolic acid targeting drugs. Using transposon mutagenesis followed by transposon sequencing (Tn-Seq) and whole-genome sequencing of spontaneous ETH-resistant mutants, we identified MAB_2648c as a genetic determinant of ETH sensitivity in Mabs. MAB_2648c encodes a MarR family transcriptional regulator of the TetR class of regulators. We show that MAB_2648c represses expression of MAB_2649 (mmpS5) and MAB_2650 (mmpL5). Further, we show that derepression of these genes in MAB_2648c mutants confers resistance to ETH, but not other antibiotics. To identify determinants of resistance that may be shared across antibiotics with distinct mechanisms of action, we also performed Tn-Seq during treatment with amikacin and clarithromycin, drugs currently used clinically to treat Mabs. We found very little overlap in genes that modulate the sensitivity of Mabs to all three antibiotics, suggesting a high degree of specificity for resistance mechanisms in this emerging pathogen.
Raman microspectroscopy reveals unsaturation heterogeneity at the lipid droplet level and validates an in vitro model of bone marrow adipocyte subtypes

Bone marrow adipocytes (BMAds) constitute the most abundant stromal component of adult human bone marrow. Two subtypes of BMAds have been described, the more labile regulated adipocytes (rBMAds) and the more stable constitutive adipocytes (cBMAds), which develop earlier and are more resilient to environmental and metabolic disruptions. In vivo, rBMAds are enriched in saturated fatty acids, contain smaller lipid droplets (LDs) and more readily provide hematopoietic support than their cBMAd counterparts. Mouse models have been used for BMAds research, but isolation of primary BMAds presents many challenges, and thus in vitro models remain the current standard to study nuances of adipocyte differentiation. No in vitro model has yet been described for the study of rBMAds/cBMAds. Here, we present an in vitro model of BM adipogenesis with differential rBMAd and cBMAd-like characteristics. We used OP9 BM stromal cells derived from a (C57BL/6xC3H)F2-op/op mouse, which have been extensively characterized as feeder layer for hematopoiesis research. We observed similar canonical adipogenesis transcriptional signatures for spontaneously-differentiated (sOP9) and induced (iOP9) cultures, while fatty acid composition and desaturase expression of Scd1 and Fads2 differed at the population level. To resolve differences at the single adipocyte level we tested Raman microspectroscopy and show it constitutes a high-resolution method for studying adipogenesis in vitro in a label-free manner, with resolution to individual LDs. We found sOP9 adipocytes have lower unsaturation ratios, smaller LDs and higher hematopoietic support than iOP9 adipocytes, thus functionally resembling rBMAds, while iOP9 more closely resembled cBMAds. Validation in human primary samples confirmed a higher unsaturation ratio for lipids extracted from stable cBMAd-rich sites (femoral head upon hip-replacement surgery) versus labile rBMAds (iliac crest after chemotherapy). As a result, the 16:1/16:0 fatty acid unsaturation ratio, which was already shown to discriminate BMAd subtypes in rabbit and rat marrow, was validated to discriminate cBMAds from rBMAd in both the OP9 model in vitro system and in human samples. We expect our model will be useful for cBMAd and rBMAd studies, particularly where isolation of primary BMAds is a limiting step.
Type-specific EV-D68 real-time RT-PCR assay for the detection of all extant enterovirus D68 strains

Enterovirus D68 (EV-D68) has caused recurring respiratory disease outbreaks in the United States since 2014. The dominant circulating EV-D68 strain has evolved from clade B1 to the more recent B2 and B3 clades. As recurrent outbreaks and continued virus evolution are expected for EV-D68, a robust real-time PCR assay that detects known strains as well as potential emerging strains is critical for national surveillance and clinical diagnostics. We describe a type-specific EV-D68 real-time RT-PCR (rRT-PCR) assay termed CDC2022, which targets sequences encoding conserved amino acid regions of all extant EV-D68 strains. We targeted three motifs conserved among all strains in the last 60 years. The assay achieved 100% (270/270) sensitivity and 100% (344/344) specificity when tested with a collection of 613 respiratory specimens, compared to the gold-standard EV semi-nested VP1 PCR and sequencing assay (snPCR/Seq). CDC2022 gave negative results with 289/289 non-target viruses, including 104 EV A-D isolates, 165 rhinovirus (RV) isolates or clinical specimens, and 14 other common respiratory viruses. The assay can detect as few as 0.28 CCID50 per reaction. An in silico “phylo-primer-mismatch” analysis was performed to visualize primer/probe mismatches and to compare CDC2022 with other EV-D68 rRT-PCR assays, including the previous CDC assay (CDC2015) developed in 2014 for clade B1 strains. It showed that CDC2022 has the fewest primer/probe mismatches among all assays analyzed and is suitable for all clades. We additionally tested 11 EV-D68-positive clinical specimens from 2022 that were confirmed by snPCR/Seq, and all were detected. CDC2022 assay could provide a critical tool for molecular surveillance of EV-D68.