Miracle-dz/UniFAR-FTUs huggingface dataset:
A complex tissue-specific interplay between the Arabidopsis transcription factors AtMYB68, AtHB23, and AtPHL1 modulates primary and lateral root development and adaptation to salinity

Adaptation to soil is a well-regulated process vital for plant life. AtHB23 is a homeodomain-leucine zipper I transcription factor (TF), previously revealed as crucial for plant survival in front of salinity conditions. We wondered whether this TF has partners to achieve this essential function. A TF cDNA library screening, Y2H, BiFC, and CoIP assays were complemented with expression analyses and phenotypic characterizations of silenced, mutant, overexpressor, and crossed plants in normal and salinity conditions. We revealed that AtHB23, AtPHL1, and AtMYB68 interact with each other, modulating root development and salinity response. The encoding genes coexpress in specific root tissues and developmental stages. In normal conditions, amiR68 silenced plants have less initiated roots, the opposite phenotype to that showed by amiR23 ones. AtMYB68 and AtPHL1 play contrary roles in lateral root elongation. Under salinity, where AtHB23 plays a crucial positive function, AtMYB68 cooperates with it, whereas AtPHL1 obstructs its action impacting survival ability and supporting the complex interaction between AtHB23, AtPHL1, and AtMYB68 in the primary and lateral roots. The root adaptation capability was associated with the amyloplast state. We identified new molecular players that through a complex relationship determine Arabidopsis root architecture and survival ability in salinity conditions.
Single-Molecule Super-Resolution Microscopy Reveals Formation of NS2B3 Protein Clusters on Mitochondrial Network Leading to its Fragmentation during the Onset of Dengue (Denv-2) Viral Infection

NS2B3 is a key protein complex essential for proteolytic activity and processing of viral polyprotein during dengue type 2 (Denv-2) infection. The underlying mechanism involved in the early onset (first 48 hrs) of dengue pathogenesis was studied using single molecule-based super-resolution microscopy to understand the Denv-2 infection. The study was conducted on NIH3T3 cells transfected by two distinct photoactivable fusion plasmid DNAs (mEos3.2 − NS2B3 and PAGFP − NS2B3). Studies demonstrated that the formation of NS2B3 clusters on the mitochondrial network induces its fragmentation. The NS2B3 complex acts as a protease that clips specific sites of mitofusin (MFN1/2) proteins, responsible for fusion which holds the network together, disrupting the mitochondrial network. Statistical analysis of super-resolution data (images) estimates an average NS2B3 cluster area of ≈ 0.050 μm2 with a density of ≈ 3500mol. /μm2, and an average of ≈ 120 molecules per cluster. Based on the present study, we hypothesize that the formation of clusters and the associated cluster-related parameters are critical in promoting mitochondrial fragmentation. Overall, the single molecule-based super-resolution study helped reveal the basic mechanism of single-molecule (NS2B3) clustering during the onset of dengue viral infection. Understanding the underlying biophysical mechanism of NS2B3 clustering at the single molecule level may help decipher potential drug targets and the mechanisms of action to disrupt the NS2B3 clusters, which may ultimately usher the way to contain/treat dengue viral infection. Statement of Significance The arrival of single molecule based super-resolution microscopy techniques have advanced the field of cell biology, and our understanding of sub-cellular processes with single molecule precision. Here, we report the first ever application of super-resolution microscopy to visualize NS2B3 clusters that lead to the fragmentation of mitochondrial network. To facilitate this study, two new photoactivable probes (mEos3.2 − NS2B3 and PAGFP − NS2B3) with key protein complex, NS2B3 of dengue virus were developed. The study involves cell transfection studies and single molecule imaging. The proposed study is expected to decipher potential drug candidates and the mechanisms of action to disrupt the NS2B3 clusters, which may ultimately usher the way to contain/treat dengue viral infection.
Interleukin-17 signaling influences CD8+ T cell immunity and tumor progression according to the IL-17 receptor subunit expression pattern in cancer cells

The role of IL-17 mediated immune responses in cancer is conflicting as pre-clinical and clinical results show tumor-promoting as wel as tumor-repressing functions. Herein, we used syngeneic tumor models from different tissue origins as a tool to evaluate the role of IL-17 signaling in cancer progression, dissecting the effects in cancer cell growth and tumor immunity. We show that absence of IL-17RA or IL-17A/F expression in the host has contrasting effects in the in vivo growth of different tumor types. We observed that lack of IL-17A/F-IL-17RA signaling in host cells changed the expression pattern of several mediators within the tumor microenvironment in a cancer-type specific manner. Deficiencies in host IL-17RA or IL-17A/F expression resulted in reduced antitumor CD8+ T cell immunity in all cancer models and in tumor-specific changes in several lymphoid cell populations. These findings were associated to particular patterns of expression of cytokines (IL-17A and IL-17F) and receptor subunits (IL-17RA, IL-17RC and IL-17RD) of the IL-17 family in the injected tumor cell lines that, in turn, dictated tumor cell responsiveness to IL-17. We identified IL-17RC as an important determinant of the IL-17-mediated transcriptional response in tumor cells and; consequently, as a predictive biomarker of the overall effect of IL-17 signaling in tumor progression. Our findings contribute to unraveling the molecular mechanisms underlying the divergent activities of IL-17 in cancer and provide rational targets for immunotherapies based on personalized approaches.
Study of Tip Vortex Cavitation Inception Using Navier-Stokes Computation and Bubble Dynamics Model

The Rayleigh-Plesset bubble dynamics equation coupled with the bubble motion equation developed by Johnson and Hsieh was applied to study the real flow effects on the prediction of cavitation inception in tip vortex flows. A three-dimensional steady-state tip vortex flow obtained from a Reynolds-Averaged Navier-Stokes computation was used as a prescribed flow field through which the bubble was passively convected. A “window of opportunity” through which a candidate bubble must pass in order to be drawn into the tip-vortex core and cavitate was determined for different initial bubble sizes. It was found that bubbles with larger initial size can be entrained into the tip-vortex core from a larger window size and also had a higher cavitation inception number.
GIM3D: A 3D Dataset for Garment Segmentation

The 3D cloth segmentation task is particularly challenging due to the extreme variation of shapes, even among the same category of clothes. Several data-driven methods try to cope with this problem but they have to face the lack of available data capable to generalize to the variety of real-world data. For this reason, we present GIM3D (Garments In Motion 3D), a synthetic dataset of clothed 3D human characters in different poses. The over 4000 3D models in this dataset are produced by a physical simulation of clothes with different fabrics, sizes, and tightness, using animated human avatars having a large variety of shapes. Our dataset is composed of single meshes created to simulate 3D scans, with labels for the separate clothes and the visible body parts. We also provide an evaluation of the use of GIM3D as a training set on garment segmentation tasks using state-of-the-art data-driven methods for both meshes and point clouds.
Not Quite Lost in Translation: Mistranslation Alters Adaptive Landscape Topography and the Dynamics of Evolution

Mistranslation – the erroneous incorporation of amino acids into nascent proteins – is a source of protein variation that is orders of magnitude more frequent than DNA mutation. Like other sources of nongenetic variation, it can affect adaptive evolution. We study the evolutionary consequences of mistranslation with experimental data on mistranslation rates applied to three empirical adaptive landscapes. We find that mistranslation generally flattens adaptive landscapes by reducing the fitness of high fitness genotypes and increasing that of low fitness genotypes, but it does not affect all genotypes equally. Most importantly, it increases genetic variation available to selection by rendering many neutral DNA mutations non-neutral. Mistranslation also renders some beneficial mutations deleterious and vice versa. It increases the probability of fixation of 3 to 8 percent of beneficial mutations. Even though mistranslation increases the incidence of epistasis, it also allows populations evolving on a rugged landscape to evolve modestly higher fitness. Our observations show that mistranslation is an important source of non-genetic variation that can affect adaptive evolution on fitness landscapes in multiple ways.
Wolbachia endosymbionts manipulate GSC self-renewal and differentiation to reinforce host fertility

The alphaproteobacterium Wolbachia pipientis infects arthropod and nematode species worldwide, making it a key target for host biological control. Wolbachia-driven host reproductive manipulations, such as cytoplasmic incompatibility (CI), are credited for catapulting these intracellular bacteria to high frequencies in host populations. Positive, perhaps mutualistic, reproductive manipulations also increase infection frequencies, but are not well understood. Here, we identify molecular and cellular mechanisms by which Wolbachia influences the molecularly distinct processes of GSC self renewal and differentiation. We demonstrate that wMel infection rescues the fertility of flies lacking the translational regulator mei-P26, and is sufficient to sustain infertile homozygous mei-P26-knockdown stocks indefinitely. Cytology revealed that wMel mitigates the impact of mei-P26 loss through restoring proper pMad, Bam, Sxl, and Orb expression. In OreR files with wild-type fertility, wMel infection elevates lifetime egg hatch rates. Exploring these phenotypes through dual-RNAseq experiments revealed that wMel infection rescues and offsets many gene expression changes induced by mei-P26 loss at the mRNA level. Overall, we show that wMel infection beneficially reinforces host fertility at mRNA, protein, and phenotypic levels, and these mechanisms may promote the emergence of mutualism and the breakdown of host reproductive manipulations. Graphical Abstract Highlights ● The wMel strain of Wolbachia restores fertility in females and males deficient for the essential translational regulator meiotic-P26 ● Mei-P26’s germline maintenance and oocyte cyst differentiation functions are genetically rescued by wMel infection ● Perturbed pMad, Sxl, Bam, and Orb protein expression are mitigated by wMel infection ● wMel infection elevates lifetime egg lay and hatch rates in OreR flies ● Ovary transcriptomes reveal wMel infection restores or offsets changes in gene expression induced by the loss of functional mei-P26 Significance Statement Wolbachia bacterial symbionts are being harnessed as biological control agents through the use of their costly manipulations to host fertility. Here, we reveal that the wMel strain can have a beneficial impact on fruit fly development in both mutant and wild-type flies. This phenotype is essential to the long-term use of these bacteria for host population control.
Direct neural perturbations reveal a dynamical mechanism for robust computation

The rich repertoire of skilled mammalian behavior is the product of neural circuits that generate robust and flexible patterns of activity distributed across populations of neurons. Decades of associative studies have linked many behaviors to specific patterns of population activity, but association alone cannot reveal the dynamical mechanisms that shape those patterns. Are local neural circuits high-dimensional dynamical reservoirs able to generate arbitrary superpositions of patterns with appropriate excitation? Or might circuit dynamics be shaped in response to behavioral context so as to generate only the low-dimensional patterns needed for the task at hand? Here, we address these questions within primate motor cortex by delivering optogenetic and electrical microstimulation perturbations during reaching behavior. We develop a novel analytic approach that relates measured activity to theoretically tractable, dynamical models of excitatory and inhibitory neurons. This computational model captures the dynamical effects of these perturbations and demonstrates that motor cortical activity during reaching is shaped by a self-contained, low-dimensional dynamical system. The subspace containing task-relevant dynamics proves to be oriented so as to be robust to strong non-normal amplification within cortical circuits. This task dynamics space exhibits a privileged causal relationship with behavior, in that stimulation in motor cortex perturb reach kinematics only to the extent that it alters neural states within this subspace. Our results resolve long-standing questions about the dynamical structure of cortical activity associated with movement, and illuminate the dynamical perturbation experiments needed to understand how neural circuits throughout the brain generate complex behavior.
Surface energies in microstructure of martensite

A continuum model for laminate geometry in microstructure of martensite, employing energy minimization, is presented. Ansatzes for twin interface energies as well as grain boundary energy are proposed. The model is applied to predict scale properties and geometrical characteristics of refinement and accommodation of microstructure. (© 2011 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Minimax character of the two‐sample χ2‐test

We consider the problem of testing equality of the mean vectors of two multivariate normal populations when covariates are present and the covariance matrix is known. As an application of the Hunt-Stein theorem it is shown that the χ2--test of level a maximizes, among all level a tests, the minimum power on each of the contours where the χ2--test has constant power. A corollary is that the χ2--test is most stringent level a.
Long-Run Performance of Bayesian Model Averaging

Abstract : Hjort and Claeskens (HC) argue that statistical inference conditional on a single selected model underestimates uncertainty, and that model averaging is the way to remedy this; we strongly agree. They point out that Bayesian model averaging (BMA) has been the dominant approach to this, but argue that its performance has been inadequately studied, and propose an alternative, Frequentist Model Averaging (FMA). We point out, however, that there is a substantial literature on the performance of BMA, consisting of three main threads: general theoretical results, simulation studies, and evaluation of out-of-sample performance. The theoretical results are scattered, and we summarize them. The results have been quite consistent: BMA has tended to outperform competing methods for model selection and taking account of model uncertainty. The theoretical results depend on the assumption that the "practical distribution" over which the performance of methods is assessed is the same as the prior distribution used, and we investigate sensitivity of results to this assumption in a simple normal example; they turn out not to be unduly sensitive.
Cloud Conditions Favoring Secondary Ice Particle Production in Tropical Maritime Convection

AbstractProgress in understanding the formation of ice in lower-tropospheric clouds is slowed by the difficulties in characterizing the many complex interactions that lead to ice initiation and to the dynamic, non-steady-state nature of the clouds. The present study characterizes the conditions where secondary ice particles, specifically identified as needle or thin columnar types, are observed in tropical maritime convection with modest liquid water contents during the Ice in Clouds Experiment-Tropical (ICE-T), based out of St. Croix, U.S. Virgin Islands, and the NASA African Monsoon Multidisciplinary Analyses (NAMMA) in 2006 sampling from Cape Verde, Africa. The properties of the cloud droplet populations relevant to the secondary ice production process and the ice particle populations are characterized as a function of temperature and vertical velocity. These secondary ice particles are observed primarily in regions of low liquid water content and weak vertical velocities. Two situations are examined i.
Extensions of incomplete oblique projections method for solving rank-deficient least-squares problems

The aim of this paper is to extend the applicability of an algorithm for solving inconsistent linear systems to the rank-deficient case, by employing incomplete projections onto the set of solutions of the augmented system $ Ax-r=b$. The extended algorithm converges to the unique minimal norm solution of the least squares solutions. For that purpose, incomplete oblique projections are used, defined by means of matrices that penalize the norm of the residuals. The theoretical properties of the new algorithm are analyzed, and numerical experiences are presented comparing its performance with some well-known projection methods.
The Casimir Effect and Its Applications

The Casimir effect is analyzed. This effect consists of a polarization of the vacuum of quantized fields which arises as a result of a change in the spectrum of vacuum oscillations when the quantization volume is bounded or the topology of the space is non-Euclidean. Calculations of the effect for manifolds of various configurations and for fields with various spins are reported. Various definitions of the Casimir vacuum energy in the presence of walls are discussed. The quantum field theory of Casimir forces is generalized to incorporate the dispersion properties of the medium. Applications of the Casimir effect in various branches of physics are reviewed: from the theory of molecular forces to cosmology and elementary particle physics, including the bag model and supersymmetry.
Ion/ion and electron/ion cross‐field instabilities near the lower hybrid frequency

Instabilities near the lower hybrid frequency are investigated by numerically solving the linear Vlasov electromagnetic dispersion equation. The configuration is that of two unmagnetized ion components, a less dense beam and a more dense core, streaming across a uniform magnetic field with magnetized electrons in the zero momentum frame. All three components are considered to have similar temperatures. This paper studies the parametric dependences of maximum growth rate for three distinct modes: the electron/ion beam modified two-stream instability, the electron/ion core modified two-stream instability, and the ion/ion lower hybrid instability. In the electrostatic limit the electron/beam instability has a lower threshold and larger growth rate than its electron/core counterpart. Except near equal beam and core densities, our results also suggest that the electron/beam instability has a maximum growth rate that is equal to or greater than that of the ion/ion instability for all plasma beta values. Thus the electron/beam modified two-stream instability is a likely candidate to account for the presence of lower hybrid fluctuations in the foot of the earth's bow shock at low beta.
Scalable uncertainty estimation for nonlinear inverse problems using parameter reduction, constraint mapping, and geometric sampling: Marine controlled-source electromagnetic examples

We have developed a new uncertainty estimation method that accounts for nonlinearity inherent in most geophysical problems, allows for the explicit search of model posterior space, is scalable, and maintains computational efficiencies on the order of deterministic inverse solutions. We accomplish this by combining an efficient parameter reduction technique, a parameter constraint mapping routine, a sparse geometric sampling scheme, and an efficient forward solver. In order to reduce our model domain and determine an independent basis, we implement both a typical principal component analysis, which factorizes the model covariance matrix, and an alternative compression method, based on singular-value decomposition, which acts on training models, directly, and is storage efficient. Once we have a reduced base, we map parameter constraints, from our original model domain, to this reduced domain to define a bounded geometric region of feasible model space. We utilize an optimal scheme to sample this reduced mo.
Spatio-temporal breakdown in surface DBDs: evidence of collective effect

This paper presents an experimental investigation of the plasma ignition in a dielectric barrier surface discharge in air at atmospheric pressure. CCD pictures of the discharge are compared with electrical measurements. A detailed study of the current peaks during the positive half period of the applied voltage has been performed. CCD pictures of single discharges events have been taken. They show synchronous breakdowns of plasma filaments, corresponding to current intensities of several amperes. It is shown that each plasma filament transfers a current of about 40 mA. The influence of adsorbed electrons on the synchronization of the plasma filaments is discussed. The length of the filaments increases during the half period and can be plotted as a linear function of the difference between applied and ignition voltages. The differences between the discharges of positive and negative half periods are presented. The discharges of the negative half period consist of diffuse spots of shorter lengths and are characterized by low currents (several milliamperes), and individual breakdowns.
Detection of a Rotor Crack Using a Harmonic Excitation and Nonlinear Vibration Analysis

Detection of a rotor crack based on the nonlinear vibration diagnosis using harmonic excitation force is investigated. The open-close mechanism of crack is firstly modeled by a piecewise linear function. In addition, another approximation crack model using a power series function that is convenient for the theoretical analysis is used. When the power series function crack model is used, the equations of motion of a cracked rotor have linear and nonlinear parametric terms. In this paper, a harmonic excitation force is applied to the cracked rotor and its excitation frequency is swept, and the nonlinear resonances due to crack are investigated. The occurrence of various types of nonlinear resonances due to crack are clarified, and types of these resonances, their resonance points, and dominant frequency component of these resonances are clarified numerically and experimentally. Furthermore, nonlinear theoretical analyses are performed for these nonlinear resonances, and it is clarified that the amplitudes of these nonlinear resonances depend on the nonlinear parametric characteristics of rotor crack. These results enable us to detect a rotor crack without stopping the system during on-line operation.
Mobility of Holes and Electrons in High Electric Fields

The 6eld dependence of mobility has been determined for electrons and holes in both germanium and silicon. The observed critical Geld at 298 K beyond which p varies as E & is 900 volts/cm for n-type germanium, 1400 volts/cm for P-type germanium, 2500 volts/cm for tr-type silicon, and 7500 volts/cm for P-type silicon. These values of critical field are between two to four times those calculated on the basis of spherical constant energy surfaces in the Brillouin zone. A saturation drift velocity of 6(10)s cm/sec is observed in germanium which is in good agreement with predictions based on scattering by the optical modes. Data on n-type germanium at 20'K show a range over which impurity scattering decreases and the mobility increases with field until lattice scattering dominates as at the higher temperatures.