Miracle-dz/UniFAR-FTUs huggingface dataset:
In silico characterization, molecular docking, and dynamic simulation of a novel fungal cell-death suppressing effector, MoRlpA as potential cathepsin B-like cysteine protease inhibitor during rice blast infection

Abstract The blast fungus Magnaporthe oryzae is one of the most notorious pathogens affecting rice production worldwide. The cereal killer employs a special class of small secreted proteins called effectors to manipulate and perturb the host metabolism. In turn, the host plants trigger effector-triggered immunity (ETI) via localized cell death and hypersensitive response (HR). We have identified and characterized a novel secreted effector MoRlpA from M. oryzae by extensive in silico methods. The localization studies suggested that it is exclusively secreted in the host apoplasts. Interestingly, MoRlpA interacts with a protease, cathepsin B from rice with highest affinity. The 3D structural models of both the proteins were generated. Cathepsin B-like cysteine proteases are usually involved in programmed cell death (PCD) and autophagy in plants which lead to generation of HR upon infection. Our results suggest that MoRlpA interacts with rice cathepsin B-like cysteine protease and demolish the host counter-attack by suppressing cell death and HR during an active blast infection. This was further validated by molecular docking and molecular dynamic simulation analyses. The important residues involved in the rice-blast pathogen interactions were deciphered. Overall, this research highlights stable interactions between MoRlpA-OsCathB during rice blast pathogenesis and providing an insight into how this novel RlpA protease inhibitor-cum-effector modulates the host’s apoplast to invade the host tissues and establish a successful infection. Thus, this research will help to develop potential fungicide to block the binding region of MoRlpA target so that the cryptic pathogen would be recognized by the host. HIGHLIGHTS For the first time, a novel secreted effector protein, MoRlpA has been identified and characterised from M. oryzae in silico MoRlpA contains a rare lipoprotein A-like DPBB domain which is often an enzymatic domain in other systems MoRlpA as an apoplastic effector interacts with the rice protease OsCathB to suppress the cell death and hypersensitive response during rice blast infection The three-dimensional structures of both the MoRlpA and OsCathB proteins were predicted MoRlpA-OsCathB interactions were analysed by molecular docking and molecular dynamic simulation studies Communicated by Ramaswamy H. Sarma
Deep Manifold Harmonic Network With Dual Attention for Brain Disorder Classification

Numerous studies have shown that accurate analysis of neurological disorders contributes to the early diagnosis of brain disorders and provides a window to diagnose psychiatric disorders due to brain atrophy. The emergence of geometric deep learning approaches provides a new way to characterize geometric variations on brain networks. However, brain network data suffer from high heterogeneity and noise. Consequently, geometric deep learning methods struggle to identify discriminative and clinically meaningful representations from complex brain networks, resulting in poor diagnostic accuracy. Hence, the primary challenge in the diagnosis of brain diseases is to enhance the identification of discriminative features. To this end, this paper presents a dual-attention deep manifold harmonic discrimination (DA-DMHD) method for early diagnosis of neurodegenerative diseases. Here, a low-dimensional manifold projection is first learned to comprehensively exploit the geometric features of the brain network. Further, attention blocks with discrimination are proposed to learn a representation, which facilitates learning of group-dependent discriminant matrices to guide downstream analysis of group-specific references. Our proposed DA-DMHD model is evaluated on two independent datasets, ADNI and ADHD-200. Experimental results demonstrate that the model can tackle the hard-to-capture challenge of heterogeneous brain network topological differences and obtain excellent classifying performance in both accuracy and robustness compared with several existing state-of-the-art methods.
The GARD™skin assay: Investigation of the applicability domain for metals.

New approach methods (NAMs) for hazard identification of skin sensitizing chemicals have been adopted as test guidelines by the OECD during the last decade as alternatives to animal models. These models align to individual key events (KE) in the adverse outcome pathway (AOP) for skin sensitization for which the molecular initiating event (MIE) is covalent binding to proteins. As it currently stands, the AOP does not include mechanistic events of sensitization by metals, and limited information is available on whether NAMs accurately the predict sensitization potential of such molecules, which have been proposed to act via alternative mechanisms to organic chemicals. Methods for assessing the sensitization potential of metals would comprise valuable tools to support risk management within e.g., occupational settings during production of new metal salts or within the medical device industry to evaluate leachables from metal alloys. This paper describes a systematic evaluation of the applicability domain of the GARD™skin assay for assessment of metals. Hazard classifications were supplemented with an extended analysis of gene expression profiles induced by metal sensitizers to compare the induction of toxicity pathways between metals and organic sensitizers. Based on the results of this study, the accuracy, sensitivity, and specificity of GARD™skin for prediction of skin sensitizing hazard were 92% (12/13), 100% (7/7) and 83% (5/6), respectively. Thus, the performance of GARD™skin for assessment of metals was found to be similar to what is observed on conventional organic substances, providing support for inclusion of metals within the applicability domain of the test method.
Feasibility of endoscopic ultrasound-guided hepaticogastrostomy using a 22-gauge needle

This study aimed to evaluate the feasibility of performing endoscopic ultrasound-guided hepaticogastrostomy using a 22-gauge fine-needle aspiration needle. This was a single-center retrospective study. Fourteen patients who underwent endoscopic ultrasound-guided hepaticogastrostomy with a 22-gauge fine-needle aspiration needle were examined. Fourteen eligible patients were included in this study. The age of patients ranged from 55 to 93 years, with a median of 76 years. Of patients with existing underlying diseases, there were 8 cases of pancreatic cancer (57.1%), 2 cases of metastatic liver tumor (14.3%), 2 cases of bile duct stones (14.3%), 1 case of hilar cholangiocarcinoma (7.1%), and 1 case of gallbladder cancer (7.1%). Regarding gastrointestinal anatomy, there were 11 cases (78.6%) of normal and 3 cases (21.4%) of gastric resection with Roux-en-Y. Reasons for endoscopic ultrasound-guided hepaticogastrostomy were duodenal obstruction in 7 cases (50.0%), surgically altered anatomy in 3 cases (21.4%), and 4 cases (28.6%) of failed endoscopic retrograde cholangiopancreatography. Technical success was achieved in 11 cases (78.6%). Subsequently, 11 cases of technical success were analyzed. There were 5 cases of puncturing B2 (45.5%). The puncture bile duct diameter ranged from 3.1 to 5.7 mm, with a median of 4.4 mm. endoscopic ultrasound-guided antegrade procedures was combined with endoscopic ultrasound-guided hepaticogastrostomy in 2 cases (18.2%). Clinical success was achieved in all the cases. The procedure time ranged from 15 to 93 minutes, with a median duration of 35 minutes. Regarding the type of stent placed in hepaticogastrostomy, a plastic stent was placed in 10 cases (90.9%) and a metal stent was placed in 1 case (9.1%). Early adverse events occurred in 4 cases (36.4%), and all of these cases developed biliary peritonitis, late adverse events occurred in 1 case (9.1%), this was biloma. A change to a 0.025-inch guidewire during the procedure was required in 8 cases (72.7%). Esophageal puncture was not performed. endoscopic ultrasound-guided hepaticogastrostomy using a 22-gauge fine-needle aspiration needle is effective. However, in 72.7% of the cases started using the 0.018-inch guidewire, the guidewire was exchanged for a 0.025-inch guidewire during procedure.
Discrete CMC surfaces in R^3 and discrete minimal surfaces in S^3. A discrete Lawson correspondence

The main result of this paper is a discrete Lawson correspondence between discrete CMC surfaces in R^3 and discrete minimal surfaces in S^3. This is a correspondence between two discrete isothermic surfaces. We show that this correspondence is an isometry in the following sense: it preserves the metric coefficients introduced previously by Bobenko and Suris for isothermic nets. Exactly as in the smooth case, this is a correspondence between nets with the same Lax matrices, and the immersion formulas also coincide with the smooth case.
Effectiveness of home-based exercise delivered by digital health in older adults: a systematic review and meta-analysis

Abstract Background regular physical exercise is essential to maintain or improve functional capacity in older adults. Multimorbidity, functional limitation, social barriers and currently, coronavirus disease of 2019, among others, have increased the need for home-based exercise (HBE) programmes and digital health interventions (DHI). Our objective was to evaluate the effectiveness of HBE programs delivered by DHI on physical function, health-related quality of life (HRQoL) improvement and falls reduction in older adults. Design systematic review and meta-analysis. Participants community-dwelling older adults over 65 years. Intervention exercises at home through DHI. Outcomes measures physical function, HRQoL and falls. Results twenty-six studies have met the inclusion criteria, including 5,133 participants (range age 69.5 ± 4.0–83.0 ± 6.7). The HBE programmes delivered with DHI improve muscular strength (five times sit-to-stand test, −0.56 s, 95% confidence interval, CI −1.00 to −0.11; P = 0.01), functional capacity (Barthel index, 5.01 points, 95% CI 0.24–9.79; P = 0.04) and HRQoL (SMD 0.18; 95% CI 0.05–0.30; P = 0.004); and reduce events of falls (odds ratio, OR 0.77, 95% CI 0.64–0.93; P = 0.008). In addition, in the subgroup analysis, older adults with diseases improve mobility (SMD −0.23; 95% CI −0.45 to −0.01; P = 0.04), and balance (SMD 0.28; 95% CI 0.09–0.48; P = 0.004). Conclusion the HBE programmes carried out by DHI improve physical function in terms of lower extremity strength and functional capacity. It also significantly reduces the number of falls and improves the HRQoL. In addition, in analysis of only older adults with diseases, it also improves the balance and mobility.
Activity-adjusted crime rates show that public safety worsened in 2020

Significance The onset of the COVID-19 pandemic brought massive disruptions to economic and social life, including an unprecedented spike in homicides. Overall crime, however, was down. We resolve this apparent paradox by showing that after accounting for the fact that people were spending more time indoors in 2020, the risk of victimization in public actually increased. These recent changes in crime and activity provide a stark illustration of how conventional crime rates can fail to capture changes in public safety.
Deep wide-field imaging down to the oldest main sequence turn-offs in the Sculptor dwarf spheroidal galaxy

We present wide-field photometry of resolved stars in the nearby Sculptor dwarf spheroidal galaxy using CTIO/MOSAIC, going down to the oldest main sequence turn-off. The accurately flux calibrated wide field colour-magnitude diagrams can be used to constrain the ages of different stellar populations, and also their spatial distribution. The Sculptor dSph contains a predominantly ancient stellar population (>10 Gyr old) which can be easily resolved into individual stars. A galaxy dominated by an old population provides a clear view of ancient processes of galaxy formation unimpeded by overlying younger populations. By using spectroscopic metallicities of RGB stars in combination with our deep main sequence turn-off photometry we can constrain the ages of different stellar populations with particular accuracy. We find that the known metallicity gradient in Sculptor is well matched to an age gradient. This is the first time that this link with age has been directly quantified. This gradient has been previously observed as a variation in horizontal branch properties and is now confirmed to exist for main sequence turn-offs as well. It is likely the Sculptor dSph first formed an extended metal-poor population at the oldest times, and subsequent more metal-rich, younger stars were formed more towards the centre until the gas was depleted or lost roughly 7 Gyr ago. The fact that these clear radial gradients have been preserved up to the present day is consistent with the apparent lack of signs of recent tidal interactions.
APERTURE SYNTHESIS IMAGING OF V892 Tau AND PV Cep: DISK EVOLUTION

I present a study of two Herbig Ae stars that are in completely different evolutionary stages: V892 Tau and PV Cep. Using sub-arcsecond interferometric observations obtained with the Combined Array for Research in Millimeter-wave Astronomy at λ = 1.3 and 2.7 mm, I have for the first time resolved their disks. I deduce that the 5 Myr old V892 Tau has a low dust opacity index β = 1.1 and a disk mass of ∼0.03 M☉. These values correspond to the growth of its dust into large, up to centimeters size, structures. In contrast, the very young (a few ×105 yr) PV Cep has a quite high opacity index β = 1.75 and a more massive disk 0.8 M☉. PV Cep has the youngest resolved disk around any Herbig Ae star. Unlike the youngest T Tauri and Class 0 stars, which contain large and processed grains, the young Herbig Ae star, PV Cep, disk contains interstellar-medium-like unprocessed dust. This suggests that PV Cep's dust evolution is slower than T Tauri stars'. I also present high spatial resolution interferometric observations of the PV Cep outflow. The outflow inclination is consistent with the orientation of the known Herbig-Haro flow in that region, HH315.
Fe LINE DIAGNOSTICS OF CATACLYSMIC VARIABLES AND GALACTIC RIDGE X-RAY EMISSION

The properties of the Galactic Ridge X-ray Emission (GRXE) observed in the 2–10 keV band place fundamental constraints on various types of X-ray sources in the Milky Way. Although the primarily discrete origin of the emission is now well established, the responsible populations of these sources remain uncertain, especially at relatively low fluxes. To provide insights into this issue, we systematically characterize the Fe emission line properties of the candidate types of the sources in the solar neighborhood and compare them with those measured for the GRXE. Our source sample includes 6 symbiotic stars, 16 intermediate polars (IPs), 3 polars, 16 quiescent dwarf novae, and 4 active binaries (ABs); they are all observed with the Suzaku X-ray Observatory. The data of about one-fourth of these sources are analyzed for the first time. We find that the mean equivalent width (EW6.7) of the 6.7 keV line and the mean 7.0/6.7 keV line ratio are 107 ± 16.0 eV and 0.71 ± 0.04 for IPs and 221 ± 135 eV and 0.44 ± 0.14 for polars, respectively, which are all substantially different from those (490 ± 15 eV and 0.2 ± 0.08) for the GRXE. Instead, the GRXE values are better agreed by the EW6.7 (438 ± 84.6 eV) and the ratio (0.27 ± 0.06) observed for the DNe. We further find that the EW6.7 is strongly correlated with the 2–10 keV luminosity of the DNe, which can be characterized by the relation EW 6.7 = ( 438 ± 95 eV ) ( L / 10 31 erg s − 1 ) ( − 0.31 ± 0.15 ) ? > . Accounting for this correlation, the agreement can be improved further, especially when the contributions from other class sources to the GRXE are considered, which all have low EW6.7 values. We conclude that the GRXE mostly consists of typically faint but numerous DNe, plus ABs, while magnetic cataclysmic variables are probably mainly the high-flux representatives of the responsible populations and dominate the GRXE only in harder energy bands.
Myeloid cell subpopulations compensate each other for Ccr2‐deficiency in glioblastoma

Glioblastomas are high‐grade brain tumours that are characterised by the accumulation of brain‐resident microglia and peripheral macrophages. Recruitment of these myeloid cells can be facilitated by CCR2/CCL2 signalling. Besides the well‐known CCR2+ macrophages, we have identified microglia expressing CCR2 in glioma tissues. Thus, we investigated how Ccr2‐deficiency of one of the myeloid cell populations affects the other population and tumour biology.
Inverse problem for the Riemannian wave equation with Dirichlet data and Neumann data on disjoint sets

We consider the inverse problem to determine a smooth compact Riemannian manifold with boundary $(M, g)$ from a restriction $\Lambda_{\Src, \Rec}$ of the Dirichlet-to-Neumann operator for the wave equation on the manifold. Here $\Src$ and $\Rec$ are open sets in $\p M$ and the restriction $\Lambda_{\Src, \Rec}$ corresponds to the case where the Dirichlet data is supported on $\R_+\times \Src$ and the Neumann data is measured on $\R_+\times \Rec$. In the novel case where $\bar \Src \cap \bar \Rec = \emptyset$, we show that $\Lambda_{\Src, \Rec}$ determines the manifold $(M,g)$ uniquely, assuming that the wave equation is exactly controllable from the set of sources $\Src$. Moreover, we show that the exact controllability can be replaced by the Hassell-Tao condition for eigenvalues and eigenfunctions, that is, \lambda_j \le C \norm{\p_\nu \phi_j}_{L^2(\Src)}^2, \quad j =1, 2, . , where $\lambda_j$ are the Dirichlet eigenvalues and $(\phi_j)_{j=1}^\infty$ is an orthonormal basis of the corresponding eigenfunctions.
Laws of large numbers for the frog model on the complete graph

The frog model is a stochastic model for the spreading of an epidemic on a graph, in which a dormant particle starts to perform a simple random walk on the graph and to awake other particles, once it becomes active. We study two versions of the frog model on the complete graph with $N + 1$ vertices. In the first version we consider, active particles have geometrically distributed lifetimes. In the second version, the displacement of each awakened particle lasts until it hits a vertex already visited by the process. For each model, we prove that as $N \to \infty$, the trajectory of the process is well approximated by a three-dimensional discrete-time dynamical system. We also study the long-term behavior of the corresponding deterministic systems.
Symmetry breaking in a constrained Cheeger type isoperimetric inequality

We study the optimal constant in a Sobolev inequality for BV functions with zero mean value and vanishing outside a bounded open set. We are interested in finding the best possible embedding constant in terms of the measure of the domain alone. We set up an optimal shape problem and we completely characterize the behavior of optimal domains.
Two scenarios on a potential smoothness breakdown for the three-dimensional Navier–Stokes equations

In this paper we construct two families of initial data being arbitrarily large under any scaling-invariant norm for which their corresponding weak solution to the three-dimensional Navier-Stokes equations become smooth on either $[0,T_1]$ or $ [T_2,\infty)$, respectively, where $T_1$ and $T_2$ are two times prescribed previously. In particular, $T_1$ can be arbitrarily large and $T_2$ can be arbitrarily small. Therefore, possible formation of singularities would occur after a very long or short evolution time, respectively. We further prove that if a large part of the kinetic energy is consumed prior to the first (possible) blow-up time, then the global-in-time smoothness of the solutions follows for the two families of initial data.
Unsupervised Synthetic Acoustic Image Generation for Audio-Visual Scene Understanding

Acoustic images are an emergent data modality for multimodal scene understanding. Such images have the peculiarity of distinguishing the spectral signature of the sound coming from different directions in space, thus providing a richer information as compared to that derived from single or binaural microphones. However, acoustic images are typically generated by cumbersome and costly microphone arrays which are not as widespread as ordinary microphones. This paper shows that it is still possible to generate acoustic images from off-the-shelf cameras equipped with only a single microphone and how they can be exploited for audio-visual scene understanding. We propose three architectures inspired by Variational Autoencoder, U-Net and adversarial models, and we assess their advantages and drawbacks. Such models are trained to generate spatialized audio by conditioning them to the associated video sequence and its corresponding monaural audio track. Our models are trained using the data collected by a microphone array as ground truth. Thus they learn to mimic the output of an array of microphones in the very same conditions. We assess the quality of the generated acoustic images considering standard generation metrics and different downstream tasks (classification, cross-modal retrieval and sound localization). We also evaluate our proposed models by considering multimodal datasets containing acoustic images, as well as datasets containing just monaural audio signals and RGB video frames. In all of the addressed downstream tasks we obtain notable performances using the generated acoustic data, when compared to the state of the art and to the results obtained using real acoustic images as input.
An operator splitting scheme for the fractional kinetic Fokker-Planck equation

In this paper, we develop an operator splitting scheme for the fractional kinetic Fokker-Planck equation (FKFPE). The scheme consists of two phases: a fractional diffusion phase and a kinetic transport phase. The first phase is solved exactly using the convolution operator while the second one is solved approximately using a variational scheme that minimizes an energy functional with respect to a certain Kantorovich optimal transport cost functional. We prove the convergence of the scheme to a weak solution to FKFPE. As a by-product of our analysis, we also establish a variational formulation for a kinetic transport equation that is relevant in the second phase. Finally, we discuss some extensions of our analysis to more complex systems.
Efficient tensor tomography in fan-beam coordinates

We propose a thorough analysis of the tensor tomography problem on the Euclidean unit disk parameterized in fan-beam coordinates. This includes, for the inversion of the Radon transform over functions, using another range characterization first appearing in [Pestov-Uhlmann, IMRN 2004] to enforce in a fast way classical moment conditions at all orders. When considering direction-dependent integrands (e.g., tensors), a problem where injectivity no longer holds, we propose a suitable representative (other than the traditionally sought-after solenoidal candidate) to be reconstructed, as well as an efficient procedure to do so. Numerical examples illustrating the method are provided at the end.