Miracle-dz/UniFAR-FTUs huggingface dataset:
Examination of certain terms appearing in Reynolds' equations under unsteady conditions and their implications for micrometeorology

Reynolds' equations are generally valid only when the bar operator represents an ensemble average. Such averages are rarely calculated in practice, the usual approach (especially in micrometeorology) being to calculate a time average instead. When conditions are at all unsteady, this practice necessitates consideration of additional terms in the expression for the Reynolds flux. It is shown, with the aid of a series of rapid-response measurements of wind and temperature, that these terms are not necessarily negligible and that under unsteady conditions the complete Reynolds flux expression may differ considerably from the quantity generally computed; also, the vertical gradients of the two quantities will differ. A quantitative criterion of steadiness is proposed and is shown to be highly correlated with the difference between the complete Reynolds flux and the quantity usually calculated.
Grey matter reshaping of language-related regions depends on tumor lateralization

A brain tumor in the left hemisphere can decrease language laterality as assessed with fMRI. However, it remains unclear whether or not this decreased language laterality is associated with a structural reshaping of the grey matter, particularly within the language network. Here, we examine if the disruption of language hubs exclusively affects macrostructural properties of contralateral homologues (as suggested by previous research), or whether it affects both hemispheres. This study uses voxel-based morphometry applied to high-resolution MR T1-weighted MPRAGE images from 31 adult patients left-dominant for language. Eighteen patients had brain tumors in the left hemisphere, and 13 had tumors in the right hemisphere. A cohort of 71 healthy individuals matched on age and sex was used as a baseline. We defined 10 ROIs per hemisphere known to subserve language function. Two separate repeated-measures ANOVAs were conducted with the volume per region as the dependent variables. For the patients, tumor lateralization (right versus left) served as a between-subject factor. The current study demonstrated that the presence of a brain tumor generates a global volumetric change affecting left language regions and their contralateral homologues. These changes are mediated by the lateralization of the lesion. Our findings suggest that compensatory functional mechanisms are supported by the rearrangement of the grey matter, although future longitudinal research should determine the temporal course of such changes.
In vivo tracing of the ascending vagal projections to the brain with manganese enhanced magnetic resonance imaging

The vagus nerve, the primary neural pathway mediating brain-body interactions, plays an essential role in transmitting bodily signals to the brain. Despite its significance, our understanding of the detailed organization and functionality of vagal afferent projections remains incomplete. In this study, we utilized manganese-enhanced magnetic resonance imaging (MEMRI) as a non-invasive method for tracing vagal nerve projections to the brainstem in vivo and assessing their functional dependence on cervical vagus nerve stimulation (VNS). Manganese chloride solution was injected into the nodose ganglion of rats, and T1-weighted MRI scans were performed 12 and 24 hours post-injection. Our findings reveal that vagal afferent neurons can uptake and transport manganese ions, serving as a surrogate for calcium ions, to the nucleus tractus solitarius (NTS) in the brainstem. In the absence of VNS, we observed significant contrast enhancements of around 19 to 24% in the NTS ipsilateral to the injection side. Application of VNS for four hours further promoted nerve activity, leading to greater contrast enhancements of 40 to 43% in the NTS. These results underline the potential of MEMRI for high-resolution, activity-dependent tracing of vagal afferents, providing a valuable tool for the structural and functional assessment of the vagus nerve and its influence on brain activity.
Aurora kinase A/AURKA interacts with the mitochondrial ATP synthase to regulate energy metabolism and cell death

Cancer cells often hijack metabolic pathways to obtain the energy required to sustain their proliferation. Understanding the molecular mechanisms underlying cancer cell metabolism is key to fine-tune the metabolic preference of specific tumors, and potentially offer new therapeutic strategies. Here, we show that the pharmacological inhibition of mitochondrial Complex V delays the cell cycle by arresting breast cancer cell models in the G0/G1 phase. Under these conditions, the abundance of the multifunctional protein Aurora kinase A/AURKA is specifically lowered. We then demonstrate that AURKA directly interacts with the mitochondrial Complex V core subunits ATP5F1A and ATP5F1B. Altering the AURKA/ATPF1A/ATPF1B nexus is sufficient to trigger G0/G1 arrest, and this is accompanied by decreased glycolysis and mitochondrial respiration rates. Last, we discover that the roles of the AURKA/ATPF1A/ATPF1B nexus depend on the specific metabolic propensity of triple-negative breast cancer cell lines, where they correlate with cell fate. On one hand, the nexus induces G0/G1 arrest in cells relying on oxidative phosphorylation as the main source of energy. On the other hand, it allows to bypass cell cycle arrest and it triggers cell death in cells with a glycolytic metabolism. Altogether, we provide evidence that AURKA and mitochondrial Complex V subunits cooperate to maintain cell metabolism in breast cancer cells. Our work paves the way to novel anti-cancer therapies targeting the AURKA/ATPF1A/ATPF1B nexus to lower cancer cell metabolism and proliferation.
Lianas in tropical dry forests have higher embolism resistance but similar hydraulic efficiency than lianas in rainforests

Lianas are increasing in relative abundance and biomass, mainly in seasonally dry forests, but it is unclear if this is associated with their hydraulic strategy. Here, we ask whether liana of seasonally dry forests are safer and more efficient in water transport than those of rainforest, which could explain liana distribution patterns and their recent increases. We measured hydraulic traits on five pairs of congeneric liana species (tribe Bignonieae) on one seasonal dry Atlantic forest and one Amazon rainforest. The predawn and minimum water potential, and the water potential at which 50% of the maximum gas amount was discharged were, on average, more negative in the liana species of the seasonal forest. However, these patterns were not constant at the genus level. The positive hydraulic safety margins and hydraulic efficiency were similar among species congeners across sites. The Bignonieae lianas studied likely experience equally low levels of embolism during drought, and maintain a high conductive capacity with efficient use of xylem space, which may favor survival and growth across tropical forests. The likely evolutionary convergence of high hydraulic safety associated with the opportunistic strategy of rapid growth, especially in disturbed areas can favor the abundant liana species in seasonal forests. Highlight Tropical forest liana species have high hydraulic efficiency and high interspecific variability in hydraulic safety. Despite this variability, some seasonal forest liana species have greater hydraulic safety than rainforest lianas, indicating an evolutionary convergence across lineages.
Congruent visual cues speed dynamic motor adaptation

Motor adaptation to novel dynamics occurs rapidly using sensed errors to update the current motor memory. This adaption is strongly driven by proprioceptive and visual signals, that indicate errors in the motor memory. Here we extend this previous work by investigating whether the presence of additional visual cues could increase the rate of motor adaptation, specifically when the visual motion cue is congruent with the dynamics. Six groups of participants performed reaching movements while grasping the handle of a robotic manipulandum while an additional cue (red object) was connected to the cursor. After a baseline, either a unidirectional (3 groups) or bidirectional (3 groups) velocity dependent force field was applied during the reach. For each group, the movement of the red object relative to the cursor was either congruent with the force field dynamics, incongruent with the force field dynamics or constant (fixed distance). Participants adapted more to the unidirectional force fields than to the bidirectional force field groups. However, across both force fields, groups in which the visual cues matched the type of force field (congruent visual cue) exhibited higher final adaptation level at the end of learning compared to either the control or incongruent conditions. In all groups, we observed an additional congruent cue assisted the formation of the motor memory of the external dynamics. We then demonstrate that a state estimation based model that integrates proprioceptive and visual information can successfully replicate the experimental data. New & Noteworthy We demonstrate that adaptation to novel dynamics is stronger when additional online visual cues that are congruent with the dynamics are presented during adaptation, compared to either a constant or incongruent visual cue. This effect was found regardless of whether a bidirectional or unidirectional velocity dependent force field was presented to the participants. We propose that this effect might arise through the inclusion of this additional visual cue information within the state estimation process.
A Role for the V0 Sector of the V-ATPase in Neuroexocytosis: Exogenous V0d Blocks Complexin and SNARE Interactions with V0c

V-ATPase is an important factor in synaptic vesicle acidification and is implicated in synaptic transmission. Rotation of the extra-membranous V1 sector drives proton transfer through the membrane-embedded multi-subunit V0 sector of the V-ATPase. Intra-vesicular protons are then used to drive neurotransmitter uptake by synaptic vesicles. V0a and V0c, two membrane subunits of the V0 sector have been shown to interact with SNARE proteins and their photo-inactivation rapidly impairs synaptic transmission. V0d, a soluble subunit of the V0 sector strongly interacts with its membrane embedded subunits and is crucial for the canonic proton transfer activity of the V-ATPase. Our investigations show that the loop 1.2 of V0c interacts with complexin, a major partner of the SNARE machinery and that V0d1 binding to V0c inhibits this interaction, as well as V0c association with SNARE complex. Injection of recombinant V0d1 in rat superior cervical ganglion neurons rapidly reduced neurotransmission. In chromaffin cells, V0d1 overexpression and V0c silencing modified in a comparable manner several parameters of unitary exocytotic events. Our data suggest that V0c subunit promotes exocytosis via interactions with complexin and SNAREs and that this activity can be antagonized by exogenous V0d.
MPK12 in stomatal CO2 signaling: function beyond its kinase activity

Protein phosphorylation by kinases is a major molecular switch mechanism involved in the regulation of stomatal opening and closure. Previous research defined interaction between MAP kinase 12 and Raf-like kinase HT1 as a required step for stomatal movements by changes in CO2 concentration. However, whether MPK12 kinase activity is required for regulation of CO2-induced stomatal responses warrants in depth investigation. We apply genetic, biochemical, and structural modeling approaches to examining the non-catalytic role of MPK12 in guard cell CO2 signaling that relies on allosteric inhibition of HT1. We show that CO2/HCO3−-enhanced MPK12 interaction with HT1 is independent of its phosphor-transfer activity. By analyzing gas exchange of plant lines expressing various kinase-dead and constitutively active versions of MPK12 in a plant line where MPK12 is deleted, we confirmed that CO2-dependent stomatal responses rely on MPK12’s ability to bind to HT1 but not its kinase activity. We also demonstrate that purified MPK12 and HT1 proteins form a heterodimer in the presence of CO2/HCO3− and present structural modeling that explains the MPK12:HT1 interaction interface. These data add to the model that MPK12 kinase-activity-independent interaction with HT1 functions as a molecular switch by which stomatal guard cells sense changes in atmospheric CO2 concentration.
The core effector RipE1 of Ralstonia solanacearum interacts with and cleaves Exo70B1 and is recognized by the Ptr1 immune receptor

Ralstonia solanacearum depends on numerous virulence factors, also known as effectors, to promote disease in a wide range of economically important host plants. Although some of these effectors have been characterized, none have yet been shown to target the host’s secretion machinery. Here, we used an extended library of NLR plant immune receptor integrated domains (IDs), to identify new effector targets. The screen uncovered that the core effector RipE1, of the R. solanacearum species complex, among other targets, associates with Arabidopsis exocyst component Exo70B1. RipE1, in accordance with its predicted cysteine protease activity, cleaves Exo70B1 in vitro and also promotes Exo70B1 degradation in planta. RipE1 enzymatic activity additionally results in the activation of TN2-dependent ectopic cell death. TN2 is an atypical NLR that has been proposed to guard Exo70B1. Despite the fact that RipE1 has been previously reported to activate defense responses in model plant species, we present here a Nicotiana species, in which RipE1 expression does not activate cell death. In addition, we discovered that RipE1 is recognized by Ptr1, a Nicotiana benthamiana CC-NLR, via its cysteine protease activity. Overall, this study uncovers a new RipE1 host target and a new RipE1-activated NLR while providing evidence and novel tools to advance in-depth studies of RipE1 and homologous effectors. Author Summary Bacterial wilt disease caused by Ralstonia solanacearum, poses a serious global threat for a wide range of agriculturally important plant species. This Gram-negative bacterium utilizes a collection of Type III Secretion System (T3SS) effectors to manipulate host cell defense and physiology. In this study, we searched for new subcellular plant targets of the core R. solanacearum effector RipE1, a cysteine protease. We discovered that RipE1 has multiple potential eukaryotic targets and further elucidated its association with the host exocyst complex. Using Artificial Intelligence (AI)-based predictions and performing both in vitro and in planta assays, we found that RipE1 promotes the degradation of plant exocyst component Exo70B1 through its enzymatic activity. Apart from being the first report of a R. solanacearum effector targeting a component of the host secretion machinery, our findings also identify an NLR from a model plant species that is able to recognize RipE1 protease activity and provide evidence that can lead to the discovery of additional RipE1 targets inside the host cell.
Functional trajectories during innate spinal cord repair

Adult zebrafish are capable of anatomical and functional recovery following severe spinal cord injury. Axon growth, glial bridging and adult neurogenesis are hallmarks of cellular regeneration during spinal cord repair. However, the correlation between these cellular regenerative processes and functional recovery remains to be elucidated. Whereas the majority of established functional regeneration metrics measure swim capacity, we hypothesize that gait quality is more directly related to neurological health. Here, we performed a longitudinal swim tracking study for 60 individual zebrafish spanning 8 weeks of spinal cord regeneration. Multiple swim parameters as well as axonal and glial bridging were integrated. We established rostral compensation as a new gait quality metric that highly correlates with functional recovery. Tensor component analysis of longitudinal data supports a correspondence between functional recovery trajectories and neurological outcomes. Moreover, our studies predicted and validated that a subset of functional regeneration parameters measured 1 to 2 weeks post-injury is sufficient to predict the regenerative outcomes of individual animals at 8 weeks post-injury. Our findings established new functional regeneration parameters and generated a comprehensive correlative database between various functional and cellular regeneration outputs.
Stokes's Theorem Applied to Microlensing of Finite Sources

The computation of the magnification of a finite source by an arbitrary gravitational lens can be reduced from a two-dimensional to a one-dimensional integral using a generalization of Stokes's thereom. For a large source lensed by a planetary system whose planet lies at the position where one of the two images would be in the absence of a planet, the integral can be done analytically. If the planet lies at the position of the major (unperturbed) images, the excess flux is the same as it would be for an isolated planet. If the planet lies at the minor image, there is no excess flux.
Anisotropic etching of polymers in SO2/O2 plasmas: Hypotheses on surface mechanisms

A study of the anisotropy of the etching of resists in SO2‐based plasmas is performed in a distributed electron‐cyclotron‐resonance plasma excited at 2.45 GHz with independent radio frequency biasing at 13.56 MHz. Emphasis is put on the comparison of the profiles and etch rates obtained in pure oxygen and SO2‐containing plasmas as a function of substrate temperature and ion bombardment energy. For a constant ion bombardment intensity, a significant decrease in the etch rate obtained using pure SO2 plasmas is observed as compared to pure O2 plasmas. The evolution of the etch rate with ion energy also shows quite different behavior. In contrast to pure oxygen plasmas, perfect anisotropic profiles can be obtained on cooled substrates with SO2‐containing gas mixtures. A likely explanation for these results is to assume that sulfur acts as a passivating layer at temperatures close to or below room temperature. The surface mechanisms involved in this sulfur passivation and the conditions required to obtain an e.
Multiple-Criterion Method for Determining Structural Damage

A new multiple-criterion updating method that minimizes the Euclidean norm of the error vector obtained by adding the normalized eigenproblem equation and equation of motion with equal weighting functions is proposed. The method is applied to detecting damage in structures and is tested on an unsymmetrical H-shaped structure. It is found that the multiple-criterion updating method predicts the presence, the position, and the extent of damage. The multiple-criterion method is compared to the frequency-response function method and the modal property-based method by using the coordinate modal assurance criterion and the modal assurance criterion. The multiple-criterion method was found to give better results than the other two methods. This is because it was better able to detect damage on the structure than the modal property method (which failed to detect multiple-damage cases) and gave results that were less noisy, i.e., less updating to undamaged elements, than the frequency-response method.
Inertial cavitation dose produced ex vivo in rabbit ear arteries with optison

Ultrasound‐induced inertial cavitation (IC) effects were studied ex vivo in rabbit ear arteries with the addition of ultrasound contrast agents (UCAs). Ears were removed from New Zealand white rabbits immediately after being euthanized under a protocol approved by the University of Washington IACUC. The auricular arteries were perfused with varying concentration of UCA (Optison) in saline and exposed to 1.155‐MHz pulsed high‐intensity focused ultrasound (HIFU) with constant PRF (10 Hz), pulse length (20 cycles), and total treatment time (20 s). Experiments were performed for variable peak negative acoustic pressure (P−) (from 0.19 to 3.31 Mpa) and Optison volume concentration (0% [saline only], 0.1%, 0.2%, 0.5%, and 1%). Cavitation activity was quantified by IC Dose (cumulated root‐mean‐squared [rms] broadband noise amplitude in a particular band in the frequency domain). The results showed that (1) IC activity was induced much more easily with the addition of Optison, even at low volume concentration, su.
Linear functional state observer for time-delay systems

A new linear functional state observer for time-delay systems is introduced in this paper. It is shown that the observer converges, with any prescribed stability margin, to any number of linear functionals when some conditions are met. The design procedure is simple and can be easily implemented. Numerical examples are given to illustrate the properties of the new observer and its advantages over existing observer design techniques in the literature.
A new upper bound for the harmonious chromatic number

A harmonious coloring of a simple graph G is a proper vertex coloring such that each pair of colors appears together on at most one edge. The harmonious chromatic number h(G) is the least number of colors in such a coloring. We obtain a new upper bound for the harmonious chromatic number of general graphs. © 1998 John Wiley & Sons, Inc. J Graph Theory 29: 257–261, 1998
The optical and X-ray content of the 1992 May 1 gamma-ray burst error box

A gamma-ray burst which occurred on 1992 May 1 was observed by three spacecraft in the third interplanetary network, and rapidly localized to a small error box. The coordinates were promptly circulated to a wide astronomical community, and radio, optical, and X-ray counterpart searches were carried out. A weak X-ray source was found in the error box, and two radio sources are discovered outside the error box, but in alignment with the X-ray source. The X-ray source position contains approximately 25 optical objects down to 23d magnitude. We discuss the prospects for identifying the burster counterpart.
Analysis of a wire antenna in the presence of a body of revolution

The problem of an arbitrarily oriented thin-wire antenna located near a body of revolution is analyzed. The usual integrodifferential equation for a thin wire in unbounded space is generalized to account for scattering from the nearby body. The presence of the body is accounted for by a numerical dyadic Green's function. The modified wire equation is solved by standard numerical techniques to obtain the current distribution on the wire. The effects of various bodies on input admittance are compared with results for an isolated antenna. Measured and theoretical input admittance data for a monopole near several different bodies of revolution are found to be in good agreement.
Diacetone acrylamide-based non-toxic holographic photopolymer

A new low-toxicity diacetone acrylamide-based photopolymer is developed and characterized. The environmentallycompatible photopolymer has been modified with the inclusion of glycerol. The incorporation of glycerol results in a uniform maximum refractive index modulation for recording intensities in the range of 1-20 mW/cm2. This may be attributed to glycerol's nature as a plasticizer, which allows for faster diffusion of un-reacted monomer within the grating during holographic recording. An optimum recording intensity of 0.5 mW/cm2 is observed for exposure energies of 20- 60 mW/cm2. The modified photopolymer achieves a refractive index modulation of 2.2×10-3, with diffraction efficiencies up to 90 % in 100 μm layers. The photopolymer layers containing glycerol have improved stability and optical quality.
Information capacity of Bragg holograms in planar optics

The analysis of structural information of planar holograms (i.e., “surface” holograms in integrated optics) is presented by using Ewald’s construction and a grating vector uncertainty theorem. The influences of the geometry and the material constants of the holographic system, the modulation transfer function, and dimensions of the hologram are given. A new approach to the transfer of information, connected with multimode operation, is presented.