Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical characteristics of turbulent mixing in spherical and cylindrical converging Richtmyer–Meshkov instabilities

Abstract In this paper, the Richtmyer–Meshkov instabilities in spherical and cylindrical converging geometries with a Mach number of approximately 1.5 are investigated by using the high resolution implicit large eddy simulation method, and the influence of the geometric effect on the turbulent mixing is investigated. The heavy fluid is sulphur hexafluoride (SF6), and the light fluid is nitrogen (N2). The shock wave converges from the heavy fluid into the light fluid. The Atwood number is 0.678. The total structured and uniform Cartesian grid node number in the main computational domain is 20483. In addition, to avoid the influence of boundary reflection, a sufficiently long sponge layer with 50 non-uniform coarse grids is added for each non-periodic boundary. Present numerical simulations have high and nonlinear initial perturbation levels, which rapidly lead to turbulent mixing in the mixing layers. Firstly, some physical-variable mean profiles, including mass fraction, Taylor Reynolds number, turbulent kinetic energy, enstrophy and helicity, are provided. Second, the mixing characteristics in the spherical and cylindrical turbulent mixing layers are investigated, such as molecular mixing fraction, efficiency Atwood number, turbulent mass-flux velocity and density self-correlation. Then, Reynolds stress and anisotropy are also investigated. Finally, the radial velocity, velocity divergence and enstrophy in the spherical and cylindrical turbulent mixing layers are studied using the method of conditional statistical analysis. Present numerical results show that the geometric effect has a great influence on the converging Richtmyer–Meshkov instability mixing layers.
How Preservice Teachers Begin to Develop Equitable Visions for Teaching Multilingual Learners

ABSTRACT Given the growing numbers of multilingual learners in public school classrooms and persistent nationwide shortages of ESL-endorsed teachers, it is essential that preservice teachers (PSTs) are prepared to teach multilingual learners in equitable, effective ways. Visioning can help with this, but before developing visions that include being teachers of multilingual learners, PSTs must first develop metacognitive awareness of their beliefs about multilingualism and multilingual learners in the classroom. Using historically situated social practice and translanguaging pedagogy as framing, this study surveyed final-year PSTs pursuing elementary education or special education certification on four dimensions of beliefs about multilingualism: embracing the interconnected nature of language with culture and identity, valuing multilingualism, understanding language demand in content classrooms, and feeling responsible for language teaching. Results revealed contradictory beliefs about multilingual learners that were influenced by PSTs’ backgrounds and experiences, including whether they were pursuing an ESL endorsement and their second language proficiency. We call on teacher preparation programs to re-examine their curriculum in order to better prepare all PSTs to work with multilingual learners. Teacher educators can begin this work by helping PSTs become metacognitive about their beliefs as an essential first step to developing equitable visions for teaching multilingual learners.
Rethinking ‘supply and demand’ of technical and vocational education and training: insights from a company survey in three manufacturing sectors in South Africa

ABSTRACT This paper presents the results of a company survey focused on the role of technical and vocational education and training (TVET) in industrial transformation and growth in three manufacturing sectors in South Africa. We find two main patterns from our data: Those companies that take training seriously do this in a comprehensive way and reflect on this training as a combination of formal, informal, and on-the-job training. Second, the industries in which the majority of companies report use of TVET qualifications for hiring and in-house training are those in which training is integral to industrial strategy pertaining to new technologies, work-organisation, and products rather than as an adjunct to these core industry imperatives. These patterns have implications for policy, which tends in South Africa, like many countries, to be strongly focused on formal TVET provision, with little consideration of the broader picture of training, and with little sectoral specificity and little integration into economic development strategies. This also has implications for research into TVET, which, especially in the African context, has tended to look at formal provision on its own rather than as one component of a broader set of vocational skills development interventions.
Conformations, inter-molecular structure and hydrogen bond dynamics of neutral and cationic poly(vinyl amine) in aqueous solution

ABSTRACT Intermolecular structure, hydration and conformations of Poly(vinylamine) (PVAm) in neutral as well as protonated (cationic) condition as polyelectrolyte in dilute aqueous solution, were studied via single-chain atomistic molecular dynamics simulations in explicit solvent. A parametric study of atomic partial charges was carried out at different values of degree-of-ionisation (f) of the amine group. A modification of generic GROMOS force-field is developed. The unusual non-monotonic behaviour of radius-of-gyration with an increase in f is captured, in agreement with experimental results of intrinsic viscosity. Cooperative solvation of PVAm chain occurs with an increase in f as assisted by counter-ion condensation. Three different regimes of the variation of radius-of-gyration of PVAm with change in f are identified. Changes in polymer-water hydrogen bonding is not the dominant effect for the behaviour of chain-size variation. The non-monotonous expansion of PVAm is attributed to the complex interplay between hydrogen bonding and intermolecular structure of polymer chain, water and counter-ions, all of which provide a cooperative solvation of the chain. With an increase in f at the higher range, the formation of ion pairs produces salt-bridges and bends in the chain, as well as ion-pair–ion-pair repulsion extending the chain at complete ionisation.
Graduate employability in Europe: the role of human capital, institutional reputation and network ties in European graduate labour markets

ABSTRACT The link between higher education and employment is central to the understanding of social stratification and social mobility. We use three theories to analyse the importance of education and credentials in recruitment decisions in European graduate labour markets: human capital (HC), network capital (NC) and reputational capital (RC) theory. Latent class modelling was applied to data from over 5,000 European private-sector companies to allow segmentation. The results identify four groups of companies using different HC, NC and RC mixes in the recruitment process. A ‘complementary effect’ was found between these forms of capital at the time of recruitment. Company classes, however, vary in their emphasis on different types of capital according to their characteristics. The article further contributes to the literature by exploring how national political economies relate to segmentation patterns, and questioning some of the central tenets of the Varieties of Capitalism literature.
Airborne transmission of SARS-CoV-2 in indoor environments: A comprehensive review

The COVID-19 pandemic has caused millions of deaths and great economic loss globally. There has been substantial evidence supporting the airborne transmission of SARS-CoV-2. Airborne route has been considered as a major transmission pathway, which can spread the disease over a longer distance and time. The viral loads in the respiratory tract of a virus carrier are typically below 109 RNA copies/mL and are related to the emission rate of pathogens. Most particles expelled during respiratory activities are smaller than 1–2 µm in diameter. Viral aerosols can remain infectious for hours under typical indoor conditions. Sunlight contributes greatly to the viability inactivation of SARS-CoV-2. The outbreaks in different scenarios are reviewed based on existing data. Most outbreaks were related to long-term care facilities, K-12 schools, restaurants, retail facilities, and offices. The Wells-Riley model for estimating the risk of airborne transmission is introduced, along with model parameters such as the quanta generation rate, virus-containing particle size distribution, and inactivation rate. The effectiveness of various IAQ control strategies for mitigating the airborne transmission risk is analyzed, including PPE, ventilation strategies, partitions, air cleaning, and disinfection technologies, and occupancy control strategies. Both benefits and costs should be considered in designing the control strategies.
Social framing effects in decision making

Human decisions are known to be strongly influenced by the manner in which options are presented, the “framing effect”. Here, we ask whether decision-makers are also influenced by how advice from other knowledgeable agents are framed, a “social framing effect”. For example, do students learn better from a teacher who often frames advice by emphasizing appetitive outcomes, or do they learn better from another teacher who usually emphasizes avoiding options that can be harmful to their progress? We study the computational and neural mechanisms by which framing of advice affect decision-making, social learning, and trust. We found that human participants are more likely to trust and follow an adviser who often uses an appetitive frame for advice compared with another one who often uses an aversive frame. This social framing effect is implemented through a modulation of the integrative abilities of the ventromedial prefrontal cortex. At the time of choice, this region combines information learned via personal experiences of reward with social information, but the combination differs depending on the social framing of advice. Personally-acquired information is weighted more strongly when dealing with an adviser who uses an aversive frame. The findings suggest that social advice is systematically incorporated into our decisions, while being affected by biases similar to those influencing individual value-based learning.
Evaluation of calcium-sensitive adenylyl cyclase AC1 and AC8 mRNA expression in the anterior cingulate cortex of mice with neuropathic pain

The anterior cingulate cortex (ACC) is a critical region of the brain for the emotional and affective components of pain in rodents and humans. Hyperactivity in this region has been observed in neuropathic pain states in both patients and animal models and ablation of this region from cingulotomy, or inhibition with genetics or pharmacology can diminish pain and anxiety. Two adenylyl cyclases (AC), AC1 and AC8 play an important role in regulating nociception and anxiety-like behaviors through an action in the ACC, as genetic and pharmacological targeting of these enzymes reduces mechanical hypersensitivity and anxietylike behavior, respectively. However, the distribution of these ACs in the ACC has not been studied in the context of neuropathic pain. To address this gap in knowledge, we conducted RNAscope in situ hybridization to assess AC1 and AC8 mRNA distribution in mice with spared nerve injury (SNI). Given the key role of AC1 in nociception in neuropathic, inflammatory and visceral pain animal models, we hypothesized that AC1 would be upregulated in the ACC of mice following nerve injury. This hypothesis was also founded on data showing increased AC1 expression in the ACC of mice with zymosan-induced visceral inflammation. We found that AC1 and AC8 are widely expressed in many regions of the mouse brain including the hippocampus, ACC, medial prefrontal cortex and midbrain regions, but AC1 is more highly expressed. Contrary to our hypothesis, SNI causes an increase in AC8 mRNA expression in NMDAR-2B (Nr2b) positive neurons in the contralateral ACC but does not affect AC1 mRNA expression. Our findings show that changes in Adcy1 mRNA expression in the ACC are insufficient to explain the important role of this AC in mechanical hypersensitivity in mice following nerve injury and suggest a potential unappreciated role of AC8 in regulation of ACC synaptic changes after nerve injury.
Structures of core eukaryotic protein complexes

Protein-protein interactions play critical roles in biology, but despite decades of effort, the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions that have not yet been identified. Here, we take advantage of recent advances in proteome-wide amino acid coevolution analysis and deep-learning-based structure modeling to systematically identify and build accurate models of core eukaryotic protein complexes, as represented within the Saccharomyces cerevisiae proteome. We use a combination of RoseTTAFold and AlphaFold to screen through paired multiple sequence alignments for 8.3 million pairs of S. cerevisiae proteins and build models for strongly predicted protein assemblies with two to five components. Comparison to existing interaction and structural data suggests that these predictions are likely to be quite accurate. We provide structure models spanning almost all key processes in Eukaryotic cells for 104 protein assemblies which have not been previously identified, and 608 which have not been structurally characterized. One-sentence summary We take advantage of recent advances in proteome-wide amino acid coevolution analysis and deep-learning-based structure modeling to systematically identify and build accurate models of core eukaryotic protein complexes.
Morphological control of receptor-mediated endocytosis

Receptor-mediated endocytosis is the primary process for nanoparticle uptake in cells and one of the main entry mechanisms for viral infection. The cell membrane adheres to the particle (nanoparticle or virus) and then wraps it to form a vesicle delivered to the cytosol. Previous findings identified a minimum radius for a spherical particle below which endocytosis cannot occur. This is due to the insufficient driving force, from receptor-ligand affinity, to overcome the energy barrier created by membrane bending. In this paper, we extend this result to the case of clathrin-mediated endocytosis, which is the most common pathway for virus entry. Moreover, we investigate the effect of ligand inhibitors on the particle surface, motivated by viral antibodies, peptides or phage capsids nanoparticles. We determine the necessary conditions for endocytosis by considering the additional energy barrier due to the membrane bending to wrap such inhibiting protrusions. We find that the density and size of inhibitors determine the size range of internalized particles, and endocytosis is completely blocked above critical thresholds. The assembly of a clathrin coat with a spontaneous curvature increases the energy barrier and sets a maximum particle size (in agreement with experimental observations on smooth particles). Our investigation suggests that morphological considerations can inform the optimal design of neutralizing viral antibodies and new strategies for targeted nanomedicine.
A novel approach to develop wheat chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in doubled haploid introgression lines

Many wild relative species are being used in pre-breeding programmes to increase the genetic diversity of wheat. Genotyping tools such as single nucleotide polymorphism (SNP)-based arrays and molecular markers have been widely used to characterise wheat-wild relative introgression lines. However, due to the polyploid nature of the recipient wheat genome, it is difficult to develop SNP-based KASP markers that are codominant to track the introgressions from the wild species. Previous attempts to develop KASP markers have involved both exome- and PCR-amplicon-based sequencing of the wild species. But chromosome-specific KASPs assays have been hindered by homoeologous SNPs within the wheat genome. This study involved whole genome sequencing of the diploid wheat wild relative Amblyopyrum muticum and development of a SNP discovery pipeline that generated ∼38,000 SNPs in single-copy wheat genome sequences. New assays were designed to increase the density of Am. muticum polymorphic KASP markers. With a goal of one marker per 60 Mbp, 335 new KASP assays were validated as functional. Together with assays validated in previous studies, 498 well distributed chromosome-specific markers were used to recharacterize previously genotyped wheat-Am. muticum doubled haploid (DH) introgression lines. The chromosome specific nature of the KASP markers allowed clarification of which wheat chromosomes were involved with recombination events or substituted with Am. muticum chromosomes and the higher density of markers allowed detection of new small introgressions in these DH lines. Key Message A novel methodology to generate chromosome-specific SNPs between wheat and its wild relative Amblyopyrum muticum and their use in the development of KASP markers to genotype wheat-Am. muticum introgression lines.
Regulation of Blos1 by IRE1 prevents the accumulation of Huntingtin protein aggregates

Huntington’s disease is characterized by accumulation of the aggregation-prone mutant Huntingtin (mHTT) protein. Here, we show that expression of mHTT in mouse cultured cells activates IRE1, the transmembrane sensor of stress in the endoplasmic reticulum, leading to degradation of the Blos1 mRNA and repositioning of lysosomes and late endosomes toward the microtubule organizing center. Overriding Blos1 degradation results in excessive accumulation of mHTT aggregates in both cultured cells and primary neurons. Although mHTT is degraded by macroautophagy when highly expressed, we show that prior to the formation of large aggregates, mHTT is degraded via an ESCRT-dependent, macroautophagy-independent pathway consistent with endosomal microautophagy. This pathway is enhanced by Blos1 degradation and appears to protect cells from a toxic, less aggregated form of mHTT. Condensed title Blos1 regulation protects from Huntingtin aggregation Short summary Here the authors demonstrate that the regulation of Blos1 by the unfolded protein response prevents the excessive accumulation of Huntingtin, the protein that underlies Huntington’s disease. This pathway involves the macroautophagy-independent degradation of Huntingtin prior to its forming large aggregates.
Ensemble–function relationships to evaluate catalysis in the ketosteroid isomerase oxyanion hole

Following decades of insights from structure–function studies, there is now a need to progress from a static to dynamic view of enzymes. Comparison of prior cryo X-ray structures suggested that deleterious effects from ketosteroid isomerase (KSI) mutants arise from misalignment of the oxyanion hole catalytic residue, Y16. However, multi-conformer models from room temperature X-ray diffraction revealed an ensemble of Y16 conformers indistinguishable from WT for Y32F/Y57F KSI and a distinct, non-native ensemble for Y16 in Y57F KSI. Functional analyses suggested rate effects arise from weakened hydrogen bonding, due to disruption of the Y16/Y57/Y32 hydrogen bond network, and repositioning of the general base. In general, catalytic changes can be deconvoluted into effects on the probability of occupying a state (P-effects) and the reactivity of each state (k-effects). Our results underscore the need for ensemble–function analysis to decipher enzyme function and ultimately manipulate their extraordinary capabilities.
TES-1/Tes protects junctional actin networks under tension from self-injury during epidermal morphogenesis in the C. elegans embryo

During embryonic morphogenesis, the integrity of epithelial tissues depends on the ability of cells in tissue sheets to undergo rapid changes in cell shape while preventing self-injury to junctional actin networks. LIM domain-containing repeat (LCR) proteins are recruited to sites of strained actin filaments in cultured cells [1–3], and are therefore promising candidates for mediating self-healing of actin networks, but whether they play similar roles in living organisms has not been determined. Here, we establish roles for Caenorhabditis elegans TES-1/Tes, an actin-binding LCR protein present at apical junctions, during epithelial morphogenesis. TES-1::GFP is recruited to apical junctions during embryonic elongation, when junctions are under tension; in embryos in which stochastic failure of cell elongation occurs, TES-1 is only strongly recruited to junctions in cells that successfully elongate, and recruitment is severely compromised in genetic backgrounds in which cell shape changes do not successfully occur. tes-1 mutant embryos display junctional F-actin defects, and loss of TES-1 strongly enhances tension-dependent injury of junctional actin networks in hypomorphic mutant backgrounds for CCC components, suggesting that TES-1 helps to prevent self-injury of junctional actin networks during rapid cell shape change. Consistent with such role, a fragment of TES-1 containing its LIM domains localizes to stress fiber strain sites (SFSS) in cultured vertebrate cells. Together, these data establish TES-1 as a tension-sensitive stabilizer of the junctional actin cytoskeleton during embryonic morphogenesis.
Loss of the cleaved-protamine 2 domain leads to incomplete histone-to-protamine exchange and infertility in mice

Protamines are unique sperm-specific proteins that package and protect paternal chromatin until fertilization. A subset of mammalian species expresses two protamines (PRM1 and PRM2), while in others PRM1 is sufficient for sperm chromatin packaging. Alterations of the species-specific ratio between PRM1 and PRM2 are associated with infertility. Unlike PRM1, PRM2 is generated as a precursor protein consisting of a highly conserved N-terminal domain, termed cleaved PRM2 (cP2), which is consecutively trimmed off during chromatin condensation. The carboxyterminal part, called mature PRM2 (mP2), interacts with DNA and together with PRM1, mediates chromatin-hypercondensation. The removal of the cP2 domain is believed to be imperative for proper chromatin condensation, yet, the role of cP2 is not yet understood. We generated mice lacking the cP2 domain while the mP2 is still expressed. We show that the cP2 domain is indispensable for complete sperm chromatin protamination and male mouse fertility. cP2 deficient sperm show incomplete PRM2 incorporation, resulting in a severely altered protamine ratio, retention of transition proteins and aberrant retention of the testis specific histone variant H2A.L. 2. During epididymal transit, cP2 deficient sperm seem to undergo ROS mediated degradation leading to complete DNA fragmentation. The cP2 domain therefore seems to be a key aspect in the complex crosstalk between histones, transition proteins and protamines during sperm chromatin condensation. Overall, we present the first step towards understanding the role of the cP2 domain in paternal chromatin packaging and open up avenues for further research.