Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome Analysis and Functional Characterization Reveal That Peclg Gene Contributes to the Virulence of Penicillium expansum on Apple Fruits

Penicillium expansum is the causal agent of blue mold decay on apple fruits and is also known to be the major producer of patulin, a mycotoxin that represents serious hazard to human health. Several mechanisms have been suggested to explain the pathogenesis of P. expansum in host plants. Secreted effector proteins are vital for the pathogenicity of many fungal pathogens through manipulating their hosts for efficient colonization. In this study, we performed a RNA-Seq analysis followed by computational prediction of effector proteins from P. expansum during infection of the host apple fruits, and a total of 212 and 268 candidate effector protein genes were identified at 6 and 9 h after inoculation (hai), respectively. One of the candidate effector protein genes was identified as a concanavalin A-like lectin/glucanase (Peclg), which was dramatically induced during the pathogen–host interaction. Targeted knockout of Peclg resulted in significant reduction in conidial production and germination relative to the wild type. Further studies showed that in addition to salt stress, the mutant was much more sensitive to SDS and Congo red, suggesting a defect in cell wall integrity. Pathogenicity assays revealed that the ΔPeclg mutant showed significant decrease in virulence and infectious growth on apple fruits. All these results suggest that Peclg is required for fungal growth, stress response, and the virulence of P. expansum.
A Hybrid Piezoelectric and Electromagnetic Broadband Harvester with Double Cantilever Beams

Vibration-energy harvesting is an effective strategy for replacing batteries and provides a long-term power supply to microelectronic devices. Harvesting vibration energy from human motions has attracted research attention in recent years. Here, a novel low-frequency hybrid piezoelectric and electromagnetic broadband harvester is proposed. Two parallel piezoelectric cantilever beams support the harvester and capture environmental vibration energy based on the piezoelectric effect. A permanent magnet is connected by springs to the two beams, and a fixed coil surrounds the moving permanent magnet, enabling energy conversion via the electromagnetic effect and the proof mass. The parameters influencing the output power of the harvester are optimized numerically to boost the harvester’s performance. The output power of the proposed hybrid harvester is compared with that of a piezoelectric harvester and an electromagnetic harvester. The simulation results show that the output power is significantly higher for the hybrid harvester than for the piezoelectric and electromagnetic harvesters, and the bandwidth is broader owing to the double cantilevers. An experiment is conducted using a prototype of the hybrid harvester to evaluate its output power. The results show multiple resonant peaks, an extended bandwidth, and a maximum power of 6.28 mW. In contrast, the maximum harvested power of the piezoelectric harvester is only 5.15 mW at 9.6 Hz.
Nonaffine response of skeletal muscles on the ‘descending limb’

Tetanized muscle myofibrils are often modeled as one-dimensional chains where springs represent half-sarcomeres (HS). The force–length relation for individual HSs (isometric tetanus) is known to have a ‘descending limb’, a segment with an apparently negative stiffness. Despite the potential mechanical instability on the descending limb, the isometric tetanus is usually interpreted as describing an affine deformation. At the same time, active stretching during tetanus around the descending limb is known to produce non-affine sarcomere patterns. In view of this paradox, the question whether the mechanical behavior of a myofibril can be interpreted as a response of a single contractile unit has been a subject of considerable controversy over the last 50 years. In this paper we question the claim that the isometric tetanus describes homogeneous configurations of the HS chain. To distinguish between the multitudes of non-affine equilibrium states available to this mechanical system, we propose to use the concept of a stored mechanical energy. While the notion of energy is natural from a mechanical point of view, physiologists have resisted it so far on the grounds that the contractile elements are active. We discuss how this objection can be overcome and show that the appropriately defined stored energy of a tetanized myofibril with N contractile units has exponentially many local minima. We then argue that the ruggedness of the ensuing energy landscape is responsible for the experimentally observed history dependence and hysteresis in the mechanical response of a tetanized muscle near the descending limb. A nonlocal extension of the chain model, accounting for surrounding tissues, shows that both the ground states and the marginally stable states are fine mixtures of short and long HSs. These mixtures are homogeneous at the macro-scale and inhomogeneous at the micro-scale and we show that the negative overall slope of the step-wise tetanus can coexist with a positive instantaneous stiffness. A salient feature of the nonlocal model is that the variation of the degree of non-uniformity with elongation follows a complete devil’s staircase.
Improvement of Spatial Memory and Cognitive Function in Mice via the Intervention of Milk Fat Globule Membrane

With the improvement of living standards, dietary interventions have become an appropriate approach to enhance memory and cognitive performance. The present study investigated the potential mechanisms of spatial memory and cognitive function improvement with the milk fat globule membrane (MFGM) intervention in mice. The Morris water maze experiment revealed that the trajectories of mice in group M were more disordered. Also, the immunohistochemical results demonstrated a significantly higher number of neurons in group M compared with group C, especially in the hippocampal dentate gyrus (DG) area. It is suggested that MFGM enhanced mice’s spatial memory and cognition from macroscopic behavior and microscopic cytology, respectively. Meanwhile, 47 differentially expressed proteins (DEPs) were identified, including 20 upregulated and 27 downregulated proteins. Upregulated (Sorbs 2, Rab 39, and Cacna 1e) and downregulated (Hp and Lrg 1) DEPs may improve spatial memory and cognition in mice by promoting synapse formation and increasing neurotransmitter receptors. KEGG enrichment analysis of the DEPs identified seven signaling pathways that were significantly enriched (p < 0.05). One of these pathways was neuroactive ligand-receptor interactions, which are strongly associated with improved spatial memory and cognitive performance. These findings give some new insights and references to the potential mechanisms of spatial memory and cognitive enhancement by MFGM.
IGF-1 Controls Metabolic Homeostasis and Survival in HEI-OC1 Auditory Cells through AKT and mTOR Signaling

Insulin-like growth factor 1 (IGF-1) is a trophic factor for the nervous system where it exerts pleiotropic effects, including the regulation of metabolic homeostasis. IGF-1 deficiency induces morphological alterations in the cochlea, apoptosis and hearing loss. While multiple studies have addressed the role of IGF-1 in hearing protection, its potential function in the modulation of otic metabolism remains unclear. Here, we report that “House Ear Institute-organ of Corti 1” (HEI-OC1) auditory cells express IGF-system genes that are regulated during their differentiation. Upon binding to its high-affinity receptor IGF1R, IGF-1 activates AKT and mTOR signaling to stimulate anabolism and, concomitantly, to reduce autophagic catabolism in HEI-OC1 progenitor cells. Notably, IGF-1 stimulation during HEI-OC1 differentiation to mature otic cells sustained both constructive metabolism and autophagic flux, possibly to favor cell remodeling. IGF1R engagement and downstream AKT signaling promoted HEI-OC1 cell survival by maintaining redox balance, even when cells were challenged with the ototoxic agent cisplatin. Our findings establish that IGF-1 not only serves an important function in otic metabolic homeostasis but also activates antioxidant defense mechanisms to promote hair cell survival during the stress response to insults.
Forces in Molecules

Formulas have been developed to calculate the forces in a molecular system directly, rather than indirectly through the agency of energy. This permits an independent calculation of the slope of the curves of energy vs. position of the nuclei, and may thus increase the accuracy, or decrease the labor involved in the calculation of these curves. The force on a nucleus in an atomic system is shown to be just the classical electrostatic force that would be exerted on this nucleus by other nuclei and by the electrons' charge distribution. Qualitative implications of this are discussed.
Optical Spectroscopy of the X-Ray Transient GS 2023+338 (=V404 Cygni)

Spectroscopic observations of V404 Cygni obtained during the decline from a major outburst are presented. The spectral evolution is followed over the period from 1989 July to 1990 May and a spectrum characteristic of emission from an accretion disk in a close binary system is found. V404 Cyg displays a smooth continuum, lacking in stellar absorption features, with broad, double-peaked Balmer, He, and Fe emission lines whose velocity widths increased with time. The increasing line widths is interpreted as evidence for a decrease in the outer radius of the disk's emission-line region
Organogermanium THGP Induces Differentiation into M1 Macrophages and Suppresses the Proliferation of Melanoma Cells via Phagocytosis

M1 macrophages are an important cell type related to tumor immunology and are known to phagocytose cancer cells. In previous studies, the organogermanium compound poly-trans-[(2-carboxyethyl)germasesquioxane] (Ge-132) and its hydrolysate, 3-(trihydroxygermyl) propanoic acid (THGP), have been reported to exert antitumor effects by activating NK cells and macrophages through the induction of IFN-γ activity in vivo. However, the detailed molecular mechanism has not been clarified. In this study, we found that macrophages differentiate into the M1 phenotype via NF-κB activation under long-term culture in the presence of THGP in vitro and in vivo. Furthermore, long-term culture with THGP increases the ability of RAW 264.7 cells to suppress B16 4A5 melanoma cell proliferation. These mechanisms indicate that THGP promotes the M1 polarization of macrophages and suppresses the expression of signal-regulatory protein alpha (SIRP-α) in macrophages and CD47 in cancers. Based on these results, THGP may be considered a new regulatory reagent that suppresses tumor immunity.
Altered Fatty Acid Oxidation in Lymphocyte Populations of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a disabling multisystem illness in which individuals are plagued with fatigue, inflammatory symptoms, cognitive dysfunction, and the hallmark symptom, post-exertional malaise. While the cause of this disease remains unknown, there is evidence of a potential infectious component that, along with patient symptoms and common onsets of the disease, implicates immune system dysfunction. To further our understanding of the state of ME/CFS lymphocytes, we characterized the role of fatty acids in isolated Natural Killer cells, CD4+ T cells, and CD8+ T cells in circulation and after overnight stimulation, through implicit perturbations to fatty acid oxidation. We examined samples obtained from at least 8 and as many as 20 subjects for immune cell fatty acid characterization in a variety of experiments and found that all three isolated cell types increased their utilization of lipids and levels of pertinent proteins involved in this metabolic pathway in ME/CFS samples, particularly during higher energy demands and activation. In T cells, we characterized the cell populations contributing to these metabolic shifts, which included CD4+ memory cells, CD4+ effector cells, CD8+ naïve cells, and CD8+ memory cells. We also discovered that patients with ME/CFS and healthy control samples had significant correlations between measurements of CD4+ T cell fatty acid metabolism and demographic data. These findings provide support for metabolic dysfunction in ME/CFS immune cells. We further hypothesize about the consequences that these altered fuel dependencies may have on T and NK cell effector function, which may shed light on the illness’s mechanism of action.
Robust Three-impulse Sequence Input Shaper Design

This article presents an unsophisticated method for tuning the amplitudes and time locations of a three-impulse sequence input shaper. The method helps to solve the insufficient constraint equations directly. A wide range of shapers can be obtained using the proposed method, including Zero Vibration (ZV), Zero Vibration Derivative (ZVD) and Extra Insensitive (EI) or Specified Insensitive (SI) shapers. The impulse amplitudes can be produced without additional derivative constraints or an initial penalty of residual vibration. It is also shown that a more robust input shaper can be obtained using the new algorithm. Experimental results from a step motor are used to support the numerical solutions.
Comparison of pre‐ and post‐processors for ensemble streamflow prediction

This study conducted a broad review of the pre‐ and post‐processor methods for ensemble streamflow prediction using a Korean case study. Categorical forecasts offered by the Korea Meteorogical Administration and deterministic forecasts of a regional climate model called Seoul National University Regional Climate Model(SNURCM) were selected as climate forecast information for the pre‐processors and incorporated into Ensemble Streamflow Prediction(ESP) runs with the TANK hydrologic model. The post‐processors were then used to minimize a possible error propagated through the streamflow generation. The application results show that use of the post‐processor more effectively reduced the uncertainty of the no‐processor ESP than use of the pre‐processor, especially in dry season. Copyright © 2010 Royal Meteorological Society
Meaningful local signalling in sinoatrial node identified by random matrix theory and PCA

The sinoatrial node (SAN) is the pacemaker of the heart. Recently calcium signals, believed to be crucially important in rhythm generation, have been imaged in intact SAN and shown to be heterogeneous in various regions of the SAN with a lot of analysis relying on visual inspection rather than mathematical tools. Here we apply methods of random matrix theory (RMT) developed for financial data and various biological data sets including β-cell collectives and electroencephalograms (EEG) to analyse correlations in SAN calcium signals using eigenvalues and eigenvectors of the correlation matrix. We use principal component analysis to locate signalling modules corresponding to localization properties the eigenvectors corresponding to high eigenvalues. We find that the top eigenvector captures the global behaviour of the SAN i.e. action potential (AP) induced calcium transient. In some cases, the eigenvector corresponding to the second highest eigenvalue yields a pacemaker region whose calcium signals predict the AP. Furthermore, using new analytic methods, we study the relationship between covariance coefficients and distance, and find that even inside the central zone, there are non-trivial long range correlations, indicating intercellular interactions in most cases. Lastly, we perform an analysis of nearest-neighbour eigenvalue distances and find that it coincides with universal Wigner surmise under all available experimental conditions, while the number variance, which captures eigenvalue correlations, is sensitive to experimental conditions. Thus RMT application to SAN allows to remove noise and the global effects of the AP-induced calcium transient and thereby isolate the local and meaningful correlations in calcium signalling.
Disk Dissipation, Giant Planet Formation, and Star Formation Rate Fluctuations in the 3 Myr History of Gould’s Belt

Although episodic star formation (SF) has been suggested for nearby SF regions, a panoramic view of the recent episodic SF history in the solar neighborhood is still missing. By uniformly constraining the slope α of infrared spectral energy distributions (SEDs) of young stellar objects (YSOs) in the 13 largest Gould’s Belt (GB) protoclusters surveyed by the Spitzer Space Telescope, we have constructed a cluster-averaged histogram of α representing the YSO evolution lifetime as a function of the α value. Complementary to the traditional SED classification scheme (0, i, f, ii, and iii) that is based on different α values, a staging scheme (A, B, C, D, and E) of SED evolution is proposed on the basis of the α statistical features that can be better matched to the physical stages of disk dissipation and giant planet formation. This has also allowed us to unravel the fluctuations of SF rate (SFR) in the 3 Myr history of these GB protoclusters. Diverse evolutionary patterns such as single peaks, double peaks, and ongoing acceleration of SFR are revealed. The SFR fluctuations are between 20% and 60% (∼40% on average) and no dependence on the average SFR or the number of SFR episodes is found. However, spatially close protoclusters tend to have similar SFR fluctuation trends, indicating that the driving force of the fluctuations should be at size scales beyond the typical cluster sizes of several parsecs.
Direct numerical simulation of the pulsatile flow through an aortic bileaflet mechanical heart valve

This work focuses on the direct numerical simulation of the pulsatile flow through a bileaflet mechanical heart valve under physiological conditions and in a realistic aortic root geometry. The motion of the valve leaflets has been computed from the forces exerted by the fluid on the structure both being considered as a single dynamical system. To this purpose the immersed boundary method, combined with a fluid–structure interaction algorithm, has shown to be an inexpensive and accurate technique for such complex flows. Several complete flow cycles have been simulated in order to collect enough phase-averaged statistics, and the results are in good agreement with experimental data obtained for a similar configuration. The flow analysis, strongly relying on the data accessibility provided by the numerical simulation, shows how some features of the leaflets motion depend on the flow dynamics and that the criteria for the red cell damages caused by the valve need to be formulated using very detailed analysis. In particular, it is shown that the standard Eulerian computation of the Reynolds stresses, usually employed to assess the risk of haemolysis, might not be adequate on several counts: (i) Reynolds stresses are only one part of the solicitation, the other part being the viscous stresses, (ii) the characteristic scales of the two solicitations are very different and the Reynolds stresses act on lengths much larger than the red cells diameter and (iii) the Eulerian zonal assessment of the stresses completely misses the information of time exposure to the solicitation which is a fundamental ingredient for the phenomenon of haemolysis. Accordingly, the trajectories of several fluid particles have been tracked in a Lagrangian way and the pointwise instantaneous viscous stress tensor has been computed along the paths. The tensor has been then reduced to an equivalent scalar using the von Mises criterion, and the blood damage index has been evaluated following Grigioni et al. (Biomech. Model Mechanobiol., vol. 4, 2005, p. 249).
Anomalous diffusion of charged particles in a strong magnetic field

A self-consistent mode-coupling theory is used to calculate the coefficient of self-diffusion in a three-dimensional classical one-component plasma subjected to an external magnetic field. For asymptotically large fields a Bohm-like behavior is found for diffusion in the plane perpendicular to the magnetic field. The experimental consequences of these results are discussed.
SOME REMARKS CONCERNING REFLECTIONLESS STURM–LIOUVILLE POTENTIALS

We consider the class of reflectionless Sturm–Liouville potentials and the subclass consisting of "Sato–Segal–Wilson" potentials. We construct illustrative examples lying in these classes, in particular we adapt the constructions of Craig and Levitan to the Sturm–Liouville case. We also discuss an inverse problem of Kotani type in the context of Sato–Segal–Wilson potentials.
Growth of zinc blende MgS/ZnSe single quantum wells by molecular-beam epitaxy using ZnS as a sulphur source

Zinc blende MgS has been grown on GaAs by molecular beam epitaxy using a novel method where the sources were Mg and ZnS. A reaction at the surface results in the formation of MgS layers with a Zn content estimated by secondary ion mass spectrometry and Auger spectroscopy to be between 0.5% and 2%. Double crystal x-ray rocking curve measurements of ZnSe/MgS/ZnSe layers show layers with good crystallinity. Using this growth technique layers up to 67 nm thick have been grown. Photoluminescence measurements of MgS/ZnSe/MgS single-quantum-well structures show that the confinement of the heavy hole excitons can be as large as 430 meV for a 1.7 nm well.
Origin of transonic buffet on aerofoils

Buffeting flow on transonic aerofoils serves as a model problem for the more complex three-dimensional flows responsible for aeroplane buffet. The origins of transonic aerofoil buffet are linked to a global instability, which leads to shock oscillations and dramatic lift fluctuations. The problem is analysed using the Reynolds-averaged Navier–Stokes equations, which for the foreseeable future are a necessary approximation to cover the high Reynolds numbers at which transonic buffet occurs. These equations have been shown to reproduce the key physics of transonic aerofoil flows. Results from global-stability analysis are shown to be in good agreement with experiments and numerical simulations. The stability boundary, as a function of the Mach number and angle of attack, consists of an upper and a lower branch – the lower branch shows features consistent with a supercritical bifurcation. The unstable modes provide insight into the basic character of buffeting flow at near-critical conditions and are consistent with fully nonlinear simulations. The results provide further evidence linking the transonic buffet onset to a global instability.
Envelopes and reduced-rank regression

We incorporate the nascent idea of envelopes (Cook et al., Statist. Sinica 20, 927–1010) into reduced-rank regression by proposing a reduced-rank envelope model, which is a hybrid of reduced-rank and envelope regressions. The proposed model has total number of parameters no more than either of reduced-rank regression or envelope regression. The resulting estimator is at least as efficient as both existing estimators. The methodology of this paper can be adapted to other envelope models, such as partial envelopes (Su & Cook, Biometrika 98, 133–46) and envelopes in predictor space (Cook et al., J. R. Statist. Soc. B 75, 851–77).
True worst-case circuit tolerance analysis using genetic algorithms and affine arithmetic

In this paper, a new approach to the calculation of the true worst case in circuit tolerance analysis (TWC-CTA) with parameters characterized by large uncertainties is presented. It is based on the joint use of genetic algorithms (GAs) and affine arithmetic (AA). The GAs are used to minimize the underestimation error which affects stochastic methods while the AA is applied to minimize the overestimation error which affects interval arithmetic methods in TWC-CTA problems. The joint GA-AA approach presented in this paper ensures a reliable TWC evaluation.