Miracle-dz/UniFAR-FTUs huggingface dataset:
Artificial acoustic stiffness reduction in fully compressible, direct numerical simulation of combustion

A pseudo-compressibility method is proposed to modify the acoustic time step restriction found in fully compressible, explicit flow solvers. The method manipulates terms in the governing equations of orderMa2, whereMais a characteristic flow Mach number. A decrease in the speed of acoustic waves is obtained by adding an extra term in the balance equation for total energy. This term is proportional to flow dilatation and uses a decomposition of the dilatational field into an acoustic component and a component due to heat transfer. The present method is a variation of the pressure gradient scaling (PGS) method proposed in Ramshawet al(1985 Pressure gradient scaling method for fluid flowwith nearly uniform pressureJ. Comput. Phys.58 361–76). It achieves gains in computational efficiencies similar to PGS: at the cost of a slightly more involved right-hand-side computation, the numerical time step increases by a full order of magnitude. It also features the added benefit of preserving the hydrodynamic pressure field. The original and modified PGS methods are implemented into a parallel direct numerical simulation solver developed for applications to turbulent reacting flows with detailed chemical kinetics. The performance of the pseudo-compressibility methods is illustrated in a series of test problems ranging from isothermal sound propagation to laminar premixed flame problems.
THREE-FLUID, THREE-DIMENSIONAL MAGNETOHYDRODYNAMIC SOLAR WIND MODEL WITH EDDY VISCOSITY AND TURBULENT RESISTIVITY

We have developed a three-fluid, three-dimensional magnetohydrodynamic solar wind model that incorporates turbulence transport, eddy viscosity, turbulent resistivity, and turbulent heating. The solar wind plasma is described as a system of co-moving solar wind protons, electrons, and interstellar pickup protons, with separate energy equations for each species. Numerical steady-state solutions of Reynolds-averaged solar wind equations coupled with turbulence transport equations for turbulence energy, cross helicity, and correlation length are obtained by the time relaxation method in the corotating with the Sun frame of reference in the region from 0.3 to 100 AU (but still inside the termination shock). The model equations include the effects of electron heat conduction, Coulomb collisions, photoionization of interstellar hydrogen atoms and their charge exchange with the solar wind protons, turbulence energy generation by pickup protons, and turbulent heating of solar wind protons and electrons. The turbulence transport model is based on the Reynolds decomposition and turbulence phenomenologies that describe the conversion of fluctuation energy into heat due to a turbulent cascade. In addition to using separate energy equations for the solar wind protons and electrons, a significant improvement over our previous work is that the turbulence model now uses an eddy viscosity approximation for the Reynolds stress tensor and the mean turbulent electric field. The approximation allows the turbulence model to account for driving of turbulence by large-scale velocity gradients. Using either a dipole approximation for the solar magnetic field or synoptic solar magnetograms from the Wilcox Solar Observatory for assigning boundary conditions at the coronal base, we apply the model to study the global structure of the solar wind and its three-dimensional properties, including embedded turbulence, heating, and acceleration throughout the heliosphere. The model results are compared with plasma and magnetic field observations on WIND, Ulysses, and Voyager 2 spacecraft.
Long time approximations for solutions of wave equations associated with the Steklov spectral homogenization problems

The interest in the use of quasimodes, or almost frequencies and almost eigenfunctions, to describe asymptotics for low‐frequency and high‐frequency vibrations in certain singularly perturbed spectral problems, which depend on a small parameter ε, has been recently highlighted in many papers. In this paper we deal with the low frequencies for a Steklov‐type eigenvalue homogenization problem: we consider harmonic functions in a bounded domain of ℝ2, and strongly alternating boundary conditions of the Dirichlet and Steklov type on a part of the boundary. The spectral parameter appears in the boundary condition on small segments Tε of size O(ε) periodically distributed along the boundary; ε also measures the periodicity of the structure. We consider associated second‐order evolution problems on spaces of traces that depend on ε, and we provide estimates for the time t in which standing waves, constructed from quasimodes, approach their solutions uε(t) as ε→0. Copyright © 2009 John Wiley & Sons, Ltd.
Phylogenetic relationships and further unknown diversity of diplostomids (Diplostomida: Diplostomidae) parasitic in kingfishers

Abstract Kingfishers (Alcedinidae Rafinesque) are common inhabitants of wetlands and are known to be definitive hosts to a wide range of digeneans that parasitize fish as second intermediate hosts. Among these digeneans, members of the Diplostomidae Poirier, 1886 (diplostomids) are particularly common. Recent studies of diplostomids collected from kingfishers have revealed that they are probably more diverse than currently known. This particularly concerns the genera Crassiphiala Van Haitsma, 1925 and Uvulifer Yamaguti, 1934. In the present work, we studied seven diplostomid taxa from kingfishers in Brazil, the USA and the Philippines. Partial DNA sequences of the nuclear large ribosomal subunit (28S) and mitochondrial cytochrome c oxidase I (cox1) genes were obtained, and 28S sequences were used to study the phylogenetic interrelationships of these diplostomids. We provide the first DNA sequences from Uvulifer semicircumcisus Dubois et Rausch, 1950 and a member of Subuvulifer Dubois, 1952. Pseudocrassiphiala n. gen. is erected for a previously recognized species-level lineage of Crassiphiala and a new generic diagnosis of Crassiphiala is provided. Crassiphiala jeffreybelli n. sp. , Crassiphiala wecksteini n. sp. and Pseudocrassiphiala tulipifera n. sp. are described, and a description of newly collected, high-quality specimens of Crassiphiala bulboglossa Van Haitsma, 1925 (the type-species of the genus) is provided.
Instability of a thin film of chemotactic active suspension

Abstract In this paper, we analyse the instability of a thin-film suspension of micro-swimmers subjected to an attractant gradient. The imposed attractant gradient introduces a preferential swimming direction for the swimmers, resulting in an anisotropic orientation field. By modelling the swimmers as force dipoles, the study by Kasyap & Koch (Phys. Rev. Lett., vol. 108, issue 3, 2012, 038101, J. Fluid Mech., vol. 741, 2014, pp. 619–657) found an instability arising from the coupling between the active stress associated with an anisotropic orientation field and perturbations to the swimmer density field. In this work we begin by presenting a stability analysis that calculates the modification of this instability in the presence of an interface. We then detail the presence of a new mode of instability that arises solely from the deformation of the interface mediated by the active stress in the suspension. The resulting hydrodynamic instabilities in the system are observed to be sensitive to the direction of the attractant gradient relative to the interface. Furthermore, we show that the coupling between the two modes involving a jump in interfacial viscous stresses and normal stress differences within the suspension allows for an instability to manifest in a suspension of chemotactic pullers, previously thought to be unconditionally stable. We then use a long-wave theory to write down a set of nonlinear equations governing the film evolution. The numerical solution of the system using the long-wave theory aids in explaining the mechanism associated with the instability in addition to validating the predictions from the linear stability theory.
Calibration of consonant perception to room reverberation

Purpose We examined how consonant perception is affected by a preceding speech carrier simulated in the same or a different room, for a broad range of consonants. Carrier room, carrier length, and carrier length/target room uncertainty were manipulated. A phonetic feature analysis tested which phonetic categories are most influenced by the acoustic context of the carrier. Method Two experiments were performed, each with 9 participants. Targets consisted of vowel-consonant (VC) syllables presented in one of 2 strongly reverberant rooms, preceded by a VC carrier presented either in the same room, a different reverberant room, or an anechoic room. In Experiment 1 the carrier length and the target room randomly varied from trial to trial while in Experiment 2 they were fixed within blocks of trials. Results Compared to the no-carrier condition, a consistent carrier provided only a small advantage for consonant perception, whereas inconsistent carriers disrupted performance significantly. For a different-room carrier, carrier length had an effect; performance dropped significantly in the 2-VC compared to the 4-VC carrier length. The only effect of carrier uncertainty was an overall drop in performance. Phonetic analysis showed that an inconsistent carrier significantly degraded identification of the manner of articulation, especially for stop consonants, and, in one of the rooms, also of voicing. Conclusions Calibration of consonant perception to strong reverberation is exhibited through disruptions in perception when the room is switched. The strength of calibration varies across different consonants and phonetic features, as well as across rooms and durations of exposure to a given room.
Cortical Synaptic Mechanism for Chronic Pain and Anxiety in Parkinson’s Disease

Zhaoxiang Zhou1,2,3, Qiyu Chen4, Qin Liu1, Pingyi Xu1, Jingshan Lu2,4, Min Zhuo1,2,3,4 1Department of Neurology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510130, Guangdong Province, China; 2Center for Neuron and Disease, Frontier Institutes of Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shaanxi Province, China; 3Department of Physiology, Faculty of Medicine, University of Toronto, Medical Science Building, 1 King’s College Circle, Toronto M5S 1A8, Ontario, Canada; 4Institute of Brain Research, Qingdao International Academician Park, Qingdao 266102, Shandong Province, China
Scalable fabrication of self-assembled GeSn vertical nanowires for nanophotonic applications

Abstract In this work, scalable fabrication of self-assembled GeSn vertical nanowires (NWs) based on rapid thermal annealing (RTA) and inductively coupled-plasma (ICP) dry etching was proposed. After thermal treatment of molecular-beam-epitaxy-grown GeSn, self-assembled Sn nanodots (NDs) were formed on surface and the spontaneous emission from GeSn direct band was enhanced by ∼5-fold. Employing the self-assembled Sn NDs as template, vertical GeSn NWs with a diameter of 25 ± 6 nm and a density of 2.8 × 109 cm−2 were obtained by Cl-based ICP dry etching technique. A prototype GeSn NW photodetector (PD) with rapid switching ability was demonstrated and the optoelectronic performance of Ge NW PD was systematically studied. The GeSn NW PD exhibited an ultralow dark current density of ∼33 nA/cm2 with a responsivity of 0.245 A/W and a high specific detectivity of 2.40 × 1012 cm Hz1/2 W−1 at 1550 nm under −1 V at 77 K. The results prove that this method is prospective for low-cost and scalable fabrication of GeSn NWs, which are promising for near infrared or short wavelength infrared nanophotonic devices.
Stability of asynchronous dynamical systems with rate constraints and applications

A class of asynchronous dynamical systems with rate constraints that is a modification of the class defined by Hassibi et al. (1999) is introduced. A numerical procedure for a quadratic stability analysis, based on a combination of LMI and a genetic algorithm is proposed. Applications to networked control systems with packet dropout and to convergence of asynchronous fixed point iterations are described. The results obtained are put in perspective as well as compared with those obtained earlier in the literature.
Dynamical modelling of proliferative-invasive plasticity and IFNγ signaling in melanoma reveals mechanisms of PD-L1 expression heterogeneity

Phenotypic heterogeneity of melanoma cells contributes to drug tolerance, increased metastasis, and immune evasion in patients with progressive disease. Diverse mechanisms have been individually reported to shape extensive intra- and inter-tumoral phenotypic heterogeneity, such as IFNγ signaling and proliferative to invasive transition, but how their crosstalk impacts tumor progression remains largely elusive. Here, we integrate dynamical systems modeling with transcriptomic data analysis at bulk and single-cell levels to investigate underlying mechanisms behind phenotypic heterogeneity in melanoma and its impact on adaptation to targeted therapy and immune checkpoint inhibitors. We construct a minimal core regulatory network involving transcription factors implicated in this process and identify the multiple “attractors” in the phenotypic landscape enabled by this network. Our model predictions about synergistic control of PD-L1 by IFNγ signaling and proliferative to invasive transition were validated experimentally in three melanoma cell lines – MALME3, SK-MEL-5 and A375. We demonstrate that the emergent dynamics of our regulatory network comprising MITF, SOX10, SOX9, JUN and ZEB1 can recapitulate experimental observations about the co-existence of diverse phenotypes (proliferative, neural crest-like, invasive) and reversible cell-state transitions among them, including in response to targeted therapy and immune checkpoint inhibitors. These phenotypes have varied levels of PD-L1, driving heterogeneity in immune-suppression. This heterogeneity in PD-L1 can be aggravated by combinatorial dynamics of these regulators with IFNγ signaling. Our model predictions about changes in proliferative to invasive transition and PD-L1 levels as melanoma cells evade targeted therapy and immune checkpoint inhibitors were validated in multiple data sets from in vitro and in vivo experiments. Our calibrated dynamical model offers a platform to test combinatorial therapies and provide rational avenues for the treatment of metastatic melanoma. This improved understanding of crosstalk among PD-L1 expression, proliferative to invasive transition and IFNγ signaling can be leveraged to improve the clinical management of therapy-resistant and metastatic melanoma.
Carbohydrate distribution via SWEET17 is critical for Arabidopsis inflorescence branching under drought

Sugars Will Eventually be Exported Transporters (SWEETs) are the most recently discovered family of plant sugar transporters. Functioning as uniporters and thus facilitating the diffusion of sugars across cell membranes, SWEETs play an important role in various physiological processes such as abiotic stress adaptation. AtSWEET17, a vacuolar fructose facilitator, was shown to be involved in the modulation of the root system during drought. Moreover, overexpression of a homolog from apple results in increased drought tolerance of tomato plants. Therefore, SWEET17 appears to be essential for the plant’s drought response. Nevertheless, the role and function of SWEET17 in aboveground tissues under drought stress to date remains enigmatic. By combining gene expression analysis with analysis of the sugar profile of various aboveground tissues, we uncovered a putative role of SWEET17 in the carbohydrate supply, and thus cauline branch emergence and growth, particularly during periods of carbon limitation as occurs under drought stress. SWEET17 thereby being of critical importance for maintaining efficient reproduction under drought stress. Highlight The fructose transporter SWEET17 supports shoot branching by increasing mobilization of carbohydrates from vacuoles to supply the newly forming inflorescence branch, thereby maintaining efficient reproduction under drought stress.
Single Molecule Mechanics and Kinetics of Cardiac Myosin Interacting with Regulated Thin Filaments

The cardiac cycle is a tightly regulated process wherein the heart generates force to pump blood to the body during systole and then relaxes during diastole. Disruption of this finely tuned cycle can lead to a range of diseases including cardiomyopathies and heart failure. Cardiac contraction is driven by the molecular motor myosin, which pulls regulated thin filaments in a calcium-dependent manner. In some muscle and non-muscle myosins, regulatory proteins on actin tune the kinetics, mechanics, and load dependence of the myosin working stroke; however, it is not well understood whether or how thin filament regulatory proteins tune the mechanics of the cardiac myosin motor. To address this critical gap in knowledge, we used single-molecule techniques to measure the kinetics and mechanics of the substeps of the cardiac myosin working stroke in the presence and absence of thin filament regulatory proteins. We found that regulatory proteins gate the calcium-dependent interactions between myosin and the thin filament. At physiologically relevant ATP concentrations, cardiac myosin’s mechanics and unloaded kinetics are not affected by thin filament regulatory proteins. We also measured the load-dependent kinetics of cardiac myosin at physiologically relevant ATP concentrations using an isometric optical clamp, and we found that thin filament regulatory proteins do not affect either the identity or magnitude of myosin’s primary load-dependent transition. Interestingly, at low ATP concentrations, thin filament regulatory proteins have a small effect on actomyosin dissociation kinetics, suggesting a mechanism beyond simple steric blocking. These results have important implications for both disease modeling and computational models of muscle contraction. Significance Statement Human heart contraction is powered by the molecular motor β-cardiac myosin, which pulls on thin filaments consisting of actin and the regulatory proteins troponin and tropomyosin. In some muscle and non-muscle systems, these regulatory proteins tune the kinetics, mechanics, and load dependence of the myosin working stroke. Despite having a central role in health and disease, it is not well understood whether the mechanics or kinetics of β-cardiac myosin are affected by regulatory proteins. We show that regulatory proteins do not affect the mechanics or load-dependent kinetics of the working stroke at physiologically relevant ATP concentrations; however, they can affect the kinetics at low ATP concentrations, suggesting a mechanism beyond simple steric blocking. This has important implications for modeling of cardiac physiology and diseases.
Steady-state polypeptide transfer from the translocon to the membrane

In concert with irreversible non-equilibrium peptide translation by the ribosome, the nascent polypeptide chain may integrate into the membrane or translocate to the other side of the membrane, facilitated by the conserved protein translocation channel SecYEG in bacteria and Sec61 in eukaryotes. Assuming equilibrium for the decision processes yielded the biological hydrophobicity scale, reflecting free-energy differences ΔG between the pore interior and membrane. Yet kinetic effects and molecular dynamic simulations suggested that a nascent polypeptide could not sample the two separate environments a sufficient number of times for partitioning in equilibrium. Here we tested the hypothesis employing purified and reconstituted SecYEG harboring a stalled ribosome nascent chain (RNC). The SecYEG-RNC complex was open in a de-energized membrane, allowing ion flow. Application of a membrane potential closed the channel if nascent chain hydrophobicity permitted membrane integration. Taking the ratio of steady-state to initial ion conductances as a measure of nascent chain hydrophobicity, we found ΔG for KvAP’s voltage sensor (4th helix harboring four arginines) and FtsQ’s transmembrane helix to be equal to 0.3 and –2.1 kcal/mol, respectively. Thus, ΔG observed in our minimalistic system agrees very well with the position-dependent amino acid contribution of the biological hydrophobicity scale. Characteristic sampling times of ~2 s appear sufficient to reach a steady state for a ~20 amino acid-long segment invalidating the hypothesis of insufficient sampling.
Aclarubicin stimulates RNA polymerase II elongation at closely spaced divergent promoters

Anthracyclines are a class of widely prescribed anti-cancer drugs that disrupt chromatin by intercalating into DNA and enhancing nucleosome turnover. To understand the molecular consequences of anthracycline-mediated chromatin disruption, we utilized CUT&Tag to profile RNA polymerase II during anthracycline treatment in Drosophila cells. We observed that treatment with the anthracycline aclarubicin leads to elevated levels of elongating RNA polymerase II and changes in chromatin accessibility. We found that promoter proximity and orientation impacts chromatin changes during aclarubicin treatment, as closely spaced divergent promoter pairs show greater chromatin changes when compared to codirectionally-oriented tandem promoters. We also found that aclarubicin treatment changes the distribution of non-canonical DNA G-quadruplex structures both at promoters and at G-rich pericentromeric repeats. Our work suggests that the anti-cancer activity of aclarubicin is driven by the effects of nucleosome disruption on RNA polymerase II, chromatin accessibility and DNA structures.
Evolutionary history of the Brachyury gene in Hydrozoa: duplications, divergence and neofunctionalization

Brachyury, a member of T-box gene family, is widely known for its major role in mesoderm specification in bilaterians. It is also present in non-bilaterian metazoans, such as cnidarians, where it acts as a component of an axial patterning system. In this study, we present a phylogenetic analysis of Brachyury genes within phylum Cnidaria, investigate differential expression and address a functional framework of Brachyury paralogs in hydrozoan Dynamena pumila. Our analysis indicates two duplication events of Brachyury in the cnidarian lineage: in the common ancestor of the Medusozoa clade and at the base of the class Hydrozoa. We designate result of the first step as Brachyury2 and of the second as Brachyury3. Brachyury1 and 2 display a conservative expression pattern marking the oral pole of the body axis in D. pumila. On the contrary, Brachyury3 expression was detected in scattered presumably nerve cells of the D. pumila larva. Pharmacological modulations indicated that Brachyury3 is not under regulation of cWnt signalling in contrast to the other two Brachyury genes. Divergence in expression patterns and regulation suggest neofunctionalization of Brachyury3 in hydrozoans.