Miracle-dz/UniFAR-FTUs huggingface dataset:
Predictable outcomes of warbler hybridization: Synthesis and an exceptional Yellow × Black-throated Blue Warbler (Setophaga petechia × S. caerulescens) pairing

ABSTRACT Hybridization can have profound effects on biological diversity. However, predictable inheritance of plumage traits remains poorly understood, especially for rare hybrids. We reviewed the literature and compiled a comprehensive list of hybrids from the New World warbler family Parulidae, a diverse radiation of songbirds with divergent plumage traits. We used our compilation to analyze modes of inheritance in wing bar patterns and carotenoid coloration. Finally, we describe an unusual hybrid from the University of New Mexico in Albuquerque, New Mexico, southwestern USA. We identified evidence of hybridization in 44 of 47 (93%) North American parulid species, with the highest number of hybrids found in the genus Setophaga. Plumage patterns between hybrid offspring and parental forms in our 2 focal traits were predictable, supporting the identification of our hybrid as a Yellow × Black-throated Blue Warbler (S. petechia × S. caerulescens). We based our identification on the extent and pattern of white in the tail, a prominent white wing flag, and our ability to confidently rule out all other alternative parentals. Our results suggest that phenotypes of rare hybrid warblers likely have some degree of predictability.
Social Media Context Collapse: The Consequential Differences Between Context Collusion Versus Context Collision

Context collapse blurs the boundaries between public, private, and professional selves and has emerged as an important research focus in relation to vocational identity. However, the conditions under which context collapse occur have been empirically neglected in the literature. Utilizing Davis and Jurgenson’s theoretical framework of context collapse (i.e., context collusion and context collision) and Erving Goffman’s theory of face-work, this study seeks to determine the consequential outcomes associated with the different context collapse conditions in two phases (Quasi-experimental in Phase 1 and open-ended questions in Phase 2). Specifically, a quasi-experimental study with scenarios was used to examine whether intentionality within context collusion and context collision influenced participants’ perception of loss of face and affect. First-year tertiary students (N = 151) who were also working were randomly selected from a capital state university student population and asked to respond to hypothetical online context collapse scenarios. Multivariate analysis of variance was conducted and the results indicated that context collapse has significant impact on participants’ loss of face and affect (emotion). In addition, a follow-up analysis of variance reveals partial support for the significant impact of context collapse on loss of face and affect.
Students in Danger: Binge Drinking Behaviour and Associated Factors in Hungary

Abstract Introduction Among young adults, high rates of binge drinking were observed in certain European countries. Binge drinking is associated with several health problems (unplanned pregnancy, HIV infections, problems with memory, and injuries). The aim of this questionnaire-based study was to measure the frequency of binge drinking and its association with sociodemographic, familial, lifestyle factors and school performance among secondary and university students (n=2449) in Csongrád County, Hungary. Methods In this cross-sectional study the students’ sociodemographic data, parents’ educational and economic level, and students’ academic performance and self-reported use of tobacco, drugs, and alcohol were collected by a questionnaire. Descriptive statistics and multivariable binary logistic regression analyses were applied using SPSS 24.0 software. Results Altogether 2449 Hungarian secondary school students and university students participated in the study. Nearly one-third of the students were classified as binge drinkers, significantly more male university students. Tobacco or illicit drug use resulted in higher odds of being a binge drinker in both subgroups. Poor school performance and binge drinking were significantly correlated especially among secondary school students. Conclusions Targeting alcohol, tobacco, and illicit drug use together, including education, parent interventions, and public health policies, are crucial in the prevention of possible serious consequences.
Uplifting Us: A BIPOC Game Design Case Study

In this short paper, we share our experiences designing a game for and about students of color at predominantly white institutions as a case study for a BIPOC-centric game design process. Through our design process, we encountered tensions in game design. For example, the frequency and relative inconsequence of physically violent death harmfully emphasizing real-world trauma in a game where all the main characters are people of color. We also encountered exciting opportunities in how we might create game experiences truly centering people of color. For example, the surprisingly novel delight of designing and creating slice-of-life narrative scenes in which people of color interact and thrive. We share how we work through these tensions and opportunities in order to open a conversation around game design processes by and for people of color as ways to uplift ourselves and our communities.
Questgram [Qg]: Toward a Mixed-Initiative Quest Generation Tool

Quests are a core element in many games, especially role-playing and adventure games, where quests drive the gameplay and story, engage the player in the game’s narrative, and in most cases, act as a bridge between different game elements. The automatic generation of quests and objectives is an interesting challenge since this can extend the lifetime of games such as in Skyrim, or can help create unique experiences such as in AI Dungeon. This work presents Questgram [Qg], a mixed-initiative prototype tool for creating quests using grammars combined in a mixed-initiative level design tool. We evaluated our tool quantitatively by assessing the generated quests and qualitatively through a small user study. Human designers evaluated the system by creating quests manually, automatically, and through mixed-initiative. Our results show the Questgram’s potential, which creates diverse, valid, and interesting quests using quest patterns. Likewise, it helps engage designers in the quest design process, fosters their creativity by inspiring them, and enhance the level generation facet of the Evolutionary Dungeon Designer with steps towards intertwining both level and quest design.
Mean flow structure and velocity–bed shear stress maxima phase difference in smooth wall, transitionally turbulent oscillatory boundary layers: direct numerical simulations

Abstract Direct numerical simulations of oscillatory boundary-layer flows in the transitional regime were performed to explain discrepancies in the literature regarding the phase difference ${\rm \Delta} \phi$ between the bed-shear stress and free-stream velocity maxima. Recent experimental observations in smooth bed oscillatory boundary-layer (OBL) flows, showed a significant change in the widely used ${\rm \Delta} \phi$ diagram (Mier et al., J. Fluid Mech., vol. 922, 2021, A29). However, the limitations of the point-wise measurement technique did not allow us to associate this finding with the turbulent kinetic energy budget and to detect the approach to a ‘near-equilibrium’ condition, defined in a narrow sense herein. Direct numerical simulation results suggest that a phase lag occurs as the result of a delayed and incomplete transition of OBL flows to a stage that mimics the fully turbulent regime. Data from the literature were also used to support the presence of the phase lag and propose a new ${\rm \Delta} \phi$ diagram. Simulations performed for ${\textit {Re}}_{\delta }=671$ confirmed the sensitivity in the development of self-sustained turbulence on the background disturbances ($\textit{Re}_{\delta}=U_{o}\delta/\nu$, where $\delta=[2\nu/\omega]^{1/2}$ is the Stokes' length, $U_{o}$ is the maximum free stream velocity of the oscillation, $\nu$ is the kinematic viscosity and $\omega=2{\rm \pi}/T$ is the angular velocity based on the period of the oscillation T). Variations of the mean velocity slope and intersect values for oscillatory flows are also explained in terms of the proximity to near-equilibrium conditions. Relaminarization and transition effects can significantly delay the development of OBL flows, resulting in an incomplete transition. The shape and defect factors are examined as diagnostic parameters for conditions that allow the formation of a logarithmic profile with the universal von Kármán constant and intersect. These findings are of relevance for environmental fluid mechanics and coastal morphodynamics/engineering applications.
nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models

Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for biological reality. Another significant downside to time-reversible models is that they do not allow inference of rooted trees without outgroups. In this paper, we introduce a maximum likelihood approach nQMaker, an extension of the recently published QMaker method, that allows the estimation of time non-reversible amino acid substitution models and rooted phylogenetic trees from a set of protein sequence alignments. We show that the non-reversible models estimated with nQMaker are a much better fit to empirical alignments than pre-existing reversible models, across a wide range of datasets including mammals, birds, plants, fungi, and other taxa, and that the improvements in model fit scale with the size of the dataset. Notably, for the recently published plant and bird trees, these non-reversible models correctly recovered the commonly known root placements with very high statistical support without the need to use an outgroup. We provide nQMaker as an easy-to-use feature in the IQ-TREE software (http://www.iqtree.org), allowing users to estimate non-reversible models and rooted phylogenies from their own protein datasets.
Sonic Hedgehog Pathway Modulation Normalizes Expression of Olig2 in Rostrally Patterned NPCs With Trisomy 21

The intellectual disability found in people with Down syndrome (DS) is associated with a decrease in white matter in the central nervous system. To study the mechanism of this myelination deficit, we differentiated two isogenic lines of induced pluripotent stem cells (iPSCs) derived from people with DS into brain-like and spinal cord-like neural progenitor cells (NPCs) and promoted a transition towards oligodendroglial fate by activating the Sonic hedgehog (SHH) pathway. In the spinal cord-like trisomic cells, we found no difference in expression of OLIG2 or NKX2.2, two transcription factors essential for commitment to the oligodendrocyte (OL) lineage. However, in the brain-like trisomic NPCs, OLIG2 is significantly upregulated and is associated with reduced expression of NKX2.2. We found that this gene dysregulation and block in NPC transition can be normalized by increasing the concentration of a SHH pathway agonist (SAG) during differentiation. These results underscore the importance of regional and cell type differences in gene expression in DS and demonstrate that modulation of SHH signaling in trisomic cells can rescue an early perturbed step in neural lineage specification in DS.
Antennapedia and optix regulate metallic silver wing scale development and cell shape in Bicyclus anynana butterflies

Butterfly wing scale cells can develop very intricate cuticular nanostructures that interact with light to produce structural colors including silvery hues, but the genetic basis of such nanostructures is mostly unexplored. Here, we first identified that optix is necessary for metallic scale development in the butterfly Bicyclus anynana. We then characterized different subtypes of wildtype metallic silver scales and addressed the function of five genes – apterous A, Ultrabithorax, doublesex, Antennapedia, and optix – in the differentiation of silver scales, at a single-cell resolution, by leveraging crispants that exhibited either ectopic gains or losses of silver scales. Wildtype silver scales were generally rounded and had low amounts of pigmentation, exhibiting a common ultrastructural modification for metallic broadband reflectance, i.e., an undulatory air layer enclosed by an upper and lower lamina. Our results indicated that the varying air layer thickness was the important parameter of the bilaminate scale for producing a broadband reflectance across visible wavelengths. While a single lamina of the appropriate thickness could also produce broadband colors, the bilaminate structure is advantageous as it increases the overall reflectivity. Crispant brown scales differed from wildtype silver scales via the loss of the continuous upper lamina, increased lower lamina thickness, and increased pigmentation. The reverse was seen when brown scales became silver. We identified Antennapedia and optix as high-level regulators in the network differentiating different silver scale subtypes and determining overall cell shape in both sexes. In addition, Antp exhibits a novel, post-embryonic role in the determination of ridge and crossrib orientation.
A Single-Cell Approach Reveals Variation in Cellular Phage-Producing Capacities

Virus burst size, a component of viral fitness, is the average number of viral particles released from a single infected cell. In this study, we estimated bacteriophage lambda (λ) burst size mean and distribution at different lysis times. To estimate phage λ burst sizes at single-cell level, we employed a lysis-deficient E. coli lysogen, which allowed chemical lysis at desired times after the induction of lytic cycle. Induced cultures of E. coli lysogen were diluted and aliquoted into the wells of 96-well plates. A high dilution rate results in mostly empty wells and minimizes the probability of having multiple cells in wells that do receive cells. Burst size was estimated by titering single-cell lysates obtained after chemical lysis at desired times. Our data shows that the viral burst size initially increases exponentially with the lysis time, and then saturates at longer lysis times. We also demonstrate that cell-to-cell variation or “noise” in lysis timing does not significantly contribute to the burst size noise. The burst size noise remains constant with increasing mean burst size. The most likely explanation for the experimentally observed constant burst size noise is that cell-to-cell differences in burst size originate from differences in cellular capacity to produce phages. The mean burst size measured at different lysis times is positively correlated to cell volume, which may determine the cellular phage production capacity. However, experiments controlling for cell size indicates that there are other factors in addition to cell size that determine this cellular capacity. ARTICLE IMPORTANCE Phages produce offspring by hijacking a cell’s replicative machinery. Previously, it was noted that the variation in the number of phages produced by single infected cells far exceeded cell size variation. It has been hypothesized that this variation is a consequence of variation in the timing of host cell lysis. Here we show that cell-to-cell variation in lysis timing does not significantly contribute to the burst size variation. We suggest that the constant burst size variation across different host lysis times results from cell-to-cell differences in capacity to produce phages. We find that the mean burst size measured at different lysis times is positively correlated to cell volume, which may determine the cellular phage production capacity. However, experiments controlling for cell size indicates that there are other factors in addition to cell size that determine this cellular capacity.
Ochratoxin A induces behavioral and neurochemical changes in adult zebrafish

Ochratoxin A (OTA) is a mycotoxin produced by species of filamentous fungi widely found as a contaminant in food and with high toxic potential. Studies have shown that this toxin cause kidney and liver damage, however, data on the effects of exposure to OTA on the central nervous system are still scarce. Zebrafish (Danio rerio) is a teleost often used in translational research due to its physiological, genetic, and behavioral homology with mammals, in addition to being useful as an environmental bioindicator. Thus, this study aimed to investigate the effects of exposure to OTA on behavioral and neurochemical parameters in adult zebrafish. The animals were treated with different doses of OTA (1.38, 2.77, and 5.53 mg/kg) and submitted to behavioral evaluations in the open tank and social interaction tests. Subsequently, they were euthanized, and the brains were used to assess markers associated with oxidative status. In the open tank test OTA induced changes in distance, absolute turn angle, mean speed, and time-freezing. However, no significant effects were observed in the social interaction test. Moreover, OTA also induced alterations in neurochemical parameters with changes in non-protein thiols (NPSH), glutathione peroxidase (GPx), glutathione-S-transferase (GST), and glutathione reductase (GR). This study showed that OTA can affect neurobiological aspects in zebrafish even at low doses.
Concentration fluctuations due to size-dependent gene expression and cell-size control mechanisms

Intracellular reaction rates depend on concentrations and hence their levels are often regulated. However classical models of stochastic gene expression lack a cell size description and cannot be used to predict noise in concentrations. Here, we construct a model of gene product dynamics that includes a description of cell growth, cell division, size-dependent gene expression, gene dosage compensation, and size control mechanisms that can vary with the cell cycle phase. We obtain expressions for the approximate distributions and power spectra of concentration fluctuations which lead to insight into the emergence of concentration homeostasis. Furthermore, we find that (i) the conditions necessary to suppress cell division-induced concentration oscillations are difficult to achieve; (ii) mRNA concentration and number distributions can have different number of modes; (iii) certain size control strategies are ideal because they maintain constant mean concentrations whilst minimising concentration noise. Predictions are confirmed using lineage data for E. coli, fission yeast and budding yeast.
Unravelling the microphysics of polar mesospheric cloud formation

Abstract. Polar mesospheric clouds are the highest water ice clouds occurring in the terrestrial atmosphere. They form in the polar summer mesopause, the coldest region in the atmosphere. It has long been assumed that these clouds form by heterogeneous nucleation on meteoric smoke particles which are the remnants of material ablated from meteoroids in the upper atmosphere. However, until now little was known about the properties of these nanometre-sized particles and application of the classical theory for heterogeneous ice nucleation was impacted by large uncertainties. In this work, we performed laboratory measurements on the heterogeneous ice formation process at mesopause conditions on small (r=1 to 3 nm) iron silicate nanoparticles serving as meteoric smoke analogues. We observe that ice growth on these particles sets in for saturation ratios with respect to hexagonal ice below Sh=50, a value that is commonly exceeded during the polar mesospheric cloud season, affirming meteoric smoke particles as likely nuclei for heterogeneous ice formation in mesospheric clouds. We present a simple ice-activation model based on the Kelvin–Thomson equation that takes into account the water coverage of iron silicates of various compositions. The activation model reproduces the experimental data very well using bulk properties of compact amorphous solid water. This is in line with the finding from our previous study that ice formation on iron silicate nanoparticles occurs by condensation of amorphous solid water rather than by nucleation of crystalline ice at mesopause conditions. Using the activation model, we also show that for iron silicate particles with dry radius larger than r=0.6 nm the nanoparticle charge has no significant effect on the ice-activation threshold.
Random walks on weighted networks: a survey of local and non-local dynamics

In this article, we present a survey of different types of random walk models with local and non-local transitions on undirected weighted networks. We present a general approach by defining the dynamics as a discrete-time Markovian process with transition probabilities expressed in terms of a symmetric matrix of weights. In the first part, we describe the matrices of weights that define local random walk dynamics like the normal random walk, biased random walks and preferential navigation, random walks in the context of digital image processing and maximum entropy random walks. In addition, we explore non-local random walks, like Lévy flights on networks, fractional transport through the new formalism of fractional graph Laplacians, and applications in the context of human mobility. Explicit relations for the stationary probability distribution, the mean first passage time and global times to characterize random walks are obtained in terms of the elements of the matrix of weights and its respective eigenvalues and eigenvectors. Finally, we apply the results to the analysis of particular local and non-local random walk dynamics, and we discuss their capacity to explore several types of networks. Our results allow us to study and compare the global dynamics of different types of random walk models.
Traumatic Brain Injury: Mechanisms of Glial Response

Traumatic brain injury (TBI) is a heterogeneous disorder that involves brain damage due to external forces. TBI is the main factor of death and morbidity in young males with a high incidence worldwide. TBI causes central nervous system (CNS) damage under a variety of mechanisms, including synaptic dysfunction, protein aggregation, mitochondrial dysfunction, oxidative stress, and neuroinflammation. Glial cells comprise most cells in CNS, which are mediators in the brain’s response to TBI. In the CNS are present astrocytes, microglia, oligodendrocytes, and polydendrocytes (NG2 cells). Astrocytes play critical roles in brain’s ion and water homeostasis, energy metabolism, blood-brain barrier, and immune response. In response to TBI, astrocytes change their morphology and protein expression. Microglia are the primary immune cells in the CNS with phagocytic activity. After TBI, microglia also change their morphology and release both pro and anti-inflammatory mediators. Oligodendrocytes are the myelin producers of the CNS, promoting axonal support. TBI causes oligodendrocyte apoptosis, demyelination, and axonal transport disruption. There are also various interactions between these glial cells and neurons in response to TBI that contribute to the pathophysiology of TBI. In this review, we summarize several glial hallmarks relevant for understanding the brain injury and neuronal damage under TBI conditions.