Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular simulations of DEAH-box helicases reveal control of domain flexibility by ligands: RNA, ATP, ADP, and G-patch proteins

Abstract DEAH-box helicases use the energy from ATP hydrolysis to translocate along RNA strands. They are composed of tandem RecA-like domains and a C-terminal domain connected by flexible linkers, and the activity of several DEAH-box helicases is regulated by cofactors called G-patch proteins. We used all-atom molecular dynamics simulations of the helicases Prp43, Prp22, and DHX15 in various liganded states to investigate how RNA, ADP, ATP, or G-patch proteins influence their conformational dynamics. The simulations suggest that apo helicases are highly flexible, whereas binding of RNA renders the helicases more rigid. ATP and ADP control the stability of the RecA1–RecA2 interface, but they have only a smaller effect on domain flexibility in absence of a RecA1–RecA2 interface. Binding of a G-patch protein to DHX15 imposes a more structured conformational ensemble, characterized by more defined relative domain arrangements and by an increased conformational stability of the RNA tunnel. However, the effect of the G-patch protein on domain dynamics is far more subtle as compared to the effects of RNA or ATP/ADP. The simulations characterize DEAH-box helicase as dynamic machines whose conformational ensembles are strongly defined by the presence of RNA, ATP, or ADP and only fine-tuned by the presence of G-patch proteins.
Pipe Flow Development and Transition in CoSmaPipe Facility

The current research focuses on understanding the transition of pipe flow by using a triggering device. In particular, a transition rod was installed within the CoSma‐Pipe at the Brandenburg University of Technology Cottbus‐Senftenberg. The effect of the transition rod, which has a variable height perpendicular to the axis at the pipe inlet, was examined in a range of 2,500 ≤ Re ≤ 31,000 where Re is the Reynolds number based on the mean velocity, the diameter, and the air's viscosity. This study used constant temperature hot‐wire anemometry to measure the flow. The observed effect of the transition rod was compared to previously published work in which a ring obstacle was used. The main objective of this research is to improve our understanding of the transition of pipe flow by using a triggering device such as the transition rod. By studying the effect of the transition rod on the flow, researchers can gain valuable insights into the dynamics of the transition from laminar to turbulent flow and its implications for various practical applications. This could ultimately lead to the development of more effective ways of controlling and mitigating turbulence in piping systems, engines, turbines, and other applications.
SOME METEOROLOGICAL RELATIONSHIPS IN THE PREDICTION OF TORNADOES

Abstract Synoptic surface and upper air features are analyzed in relation to tornado occurrences. The findings are incorporated into a forecasting system by means of which a preliminary alert forecast of tornado areas can be issued in the early morning hours for the period 1100–2300 CST. Basically, the forecast is derived through the prognostic locations of favorable surface parameters relative to the cold axis a t 200 mb. In a test of the system on independent data, most of the multiple outbreaks of tornadoes are correctly predicted.
Edge-Based HTSO Model via Markov Decision Process Using Q-Learning

Task scheduling using edge is a multidomain process that involves analysis of task patterns, edge Virtual Machine (VM) specific capabilities, task dependencies, scheduling constraints, and other context-specific requirements. These requirements are aggregated by various Machine Learning Models (MLMs) to generate task-toedge schedules for effective load-balancing operations. But most existing models do not perform the multiparametric analysis while deciding these schedules. Due to this characteristic, efficient models, w.r. t. one parameter, show inefficiencies for other parameters. Some models incorporate multiparametric analysis, but their computational complexity is higher, which limits their applicability when used for edge computing-based high-speed task scheduling scenarios. To overcome these limitations, a novel Q-Learning Model for Edge-Based Heterogeneous Task Specific Offloading (HTSO) via Markov Decision Process (MDP) is discussed in this text. The proposed model initially categorizes tasks as per their application-specific use cases, which decides their priority clusters. These priority-based clusters are used to decide sleep schedules for high-capacity edge nodes, and edge computing devices. All these decisions are taken by central cloud processors, which assists in maintaining synchronization between connected edge computing devices. Based on task priority levels and the computational efficiency of edge devices, the Q-Learning Model is able to identify mapping schedules between tasks & edge devices. The MDP Model
Sediment-laden fresh water above salt water: linear stability analysis

Abstract When a layer of particle-laden fresh water is placed above clear, saline water, both Rayleigh–Taylor and double diffusive fingering instabilities may arise. For quasi-steady base profiles, we obtain linear stability results for such situations by means of a rational spectral approximation method with adaptively chosen grid points, which is able to resolve multiple steep gradients in the base state density profile. In the absence of salinity and for a step-like concentration profile, the dominant parameter is the ratio of the particle settling velocity to the viscous velocity scale. As long as this ratio is small, particle settling has a negligible influence on the instability growth. However, when the particles settle more rapidly than the instability grows, the growth rate decreases inversely proportional to the settling velocity. This damping effect is a result of the smearing of the vorticity field, which in turn is caused by the deposition of vorticity onto the fluid elements passing through the interface between clear and particle-laden fluid. In the presence of a stably stratified salinity field, this picture changes dramatically. An important new parameter is the ratio of the particle settling velocity to the diffusive spreading velocity of the salinity, or alternatively the ratio of the unstable layer thickness to the diffusive interface thickness of the salinity profile. As long as this quantity does not exceed unity, the instability of the system and the most amplified wavenumber are primarily determined by double diffusive effects. In contrast to situations without salinity, particle settling can have a destabilizing effect and significantly increase the growth rate. Scaling laws obtained from the linear stability results are seen to be largely consistent with earlier experimental observations and theoretical arguments put forward by other authors. For unstable layer thicknesses much larger than the salinity interface thickness, the particle and salinity interfaces become increasingly decoupled, and the dominant instability mode becomes Rayleigh–Taylor-like, centred at the lower boundary of the particle-laden flow region.
Plant Disease Detection Over Multiple Datasets Using AlexNet

Plants diseases are responsible for huge loss of crop yield. Manual inspection of plant disease is a time taken and inefficient process. Image processing and machine learning-based approaches have been offered as a solution for creating such automated plant disease detection systems. Plant diseases leads to change in color and texture of leave, this property is used for developing plant disease detection systems. Deep learning models such as Visual Geometry Group (VGG) and ResNET are extensively used in this field. However, most of these models are not scalable as they are either focused on disease classification on a particular crop or dataset. The focus of this study is to showcase a new method for identifying leaf diseases. AlexNet is used in the system's development, and it is trained and verified using data from many sources. Results indicate improved performance as compared to previously published works.
Does World Heritage inscription promote regional tourism? Evidence from China

Using the panel data from 2002 to 2018 of 287 prefecture-level cities in China and the propensity score matching–difference-in-differences method, our study sought to reexamine the effect of World Heritage inscription on regional tourism. The results show that World Heritage sites improve regional tourism significantly, further confirmed by a series of robustness tests. However, the arrival and revenue effects of World Heritage inscription on inbound tourism are not significant. Moreover, World Heritage sites generate significant tourism economic benefits for the eastern and western regions in China but not for the central region. Last, a mechanism analysis shows that tourism public services increase the arrival and revenue effects significantly. The conclusions provide important insights for governments and tourism operators regarding the sustainable development of World Heritage sites and regional tourism.
The effects of attrition and ball milling on the properties of magnesium diboride

Commercially produced magnesium diboride powder was modified by attrition milling and ball milling in propan-2-ol for various durations. These powders were characterized by means of particle size distribution measurements using laser diffraction, impurity analysis using x-ray diffraction, energy dispersive spectroscopy and x-ray photoelectron spectroscopy, and scanning electron microscopy, and were then used to produce magnesium diboride samples through pressureless heat treatment at peak temperatures up to 1100 °C. X-ray diffraction, scanning electron microscopy, Vickers hardness measurements, and density measurements using the Archimedes method were used to characterize the properties of the samples, and a determination of their superconducting properties using the magnetization method was carried out. Magnesium diboride produced from powder milled under certain conditions had a higher Jc, mag than samples produced from as-purchased powder, but the relationship between the milling duration or energy and the superconducting performance is a complex one, affected by both the particle size and the impurity content of the starting powder.
Inverse shape design for heat conduction problems via the ball spine algorithm

ABSTRACT In this article, a novel iterative physical-based method is introduced for solving inverse heat conduction problems. The method extends the ball spine algorithm concept, originally developed for inverse fluid flow problems, to inverse heat conduction problems by employing a subtle physical-sense rule. The inverse problem is described as a heat source embedded within a solid medium with known temperature distribution. The object is to find a body configuration satisfying a prescribed heat flux originated from a heat source along the outer surface. Performance of the proposed method is evaluated by solving many 2-D inverse heat conduction problems in which known heat flux distribution along the unknown surface is directly related to the Biot number and surface temperature distribution arbitrarily determined by the user. Results show that the proposed method has a truly low computational cost accompanied with a high convergence rate.
Genetic and environmental manipulation of Arabidopsis hybridization barriers uncovers antagonistic functions in endosperm cellularization

Speciation by reproductive isolation can occur by hybridization barriers acting in the endosperm of the developing seed. The nuclear endosperm is a nutrient sink, accumulating sugars from surrounding tissues, and undergoes coordinated cellularization, switching to serve as a nutrient source for the developing embryo. Tight regulation of cellularization is therefore vital for seed and embryonic development. Here we show that hybrid seeds from crosses between Arabidopsis thaliana as maternal contributor and A. arenosa or A. lyrata as pollen donors result in an endosperm based post-zygotic hybridization barrier that gives rise to a reduced seed germination rate. Hybrid seeds display opposite endosperm cellularization phenotypes, with late cellularization in crosses with A. arenosa and early cellularization in crosses with A. lyrata. Stage specific endosperm reporters display temporally ectopic expression in developing hybrid endosperm, in accordance with the early and late cellularization phenotypes, confirming a disturbance of the source-sink endosperm phase change. We demonstrate that the hybrid barrier is under the influence of abiotic factors, and show that a temperature gradient leads to diametrically opposed cellularization phenotype responses in hybrid endosperm with A. arenosa or A. lyrata as pollen donors. Furthermore, different A. thaliana accession genotypes also enhance or diminish seed viability in the two hybrid cross-types, emphasizing that both genetic and environmental cues control the hybridization barrier. We have identified an A. thaliana MADS-BOX type I family single locus that is required for diametrically opposed cellularization phenotype responses in hybrid endosperm. Loss of AGAMOUS-LIKE 35 significantly affects the germination rate of hybrid seeds in opposite directions when transmitted through the A. thaliana endosperm, and is suggested to be a locus that promotes cellularization as part of an endosperm based mechanism involved in post-zygotic hybrid barriers. The role of temperature in hybrid speciation and the identification of distinct loci in control of hybrid failure have great potential to aid the introduction of advantageous traits in breeding research and to support models to predict hybrid admixture in a changing global climate.
Are probiotics beneficial for obese patients with major depressive disorder? Opinion for future implications and strategies

COPYRIGHT © 2023 Kaunang, Setiawan, Mayulu, Leonita, Wijaya, Yusuf, Mahira, Yudisthira, Gunawan, Taslim, Purnomo, Sabrina, Amalia, Permatasari and Nurkolis. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Are probiotics beneficial for obese patients with major depressive disorder? Opinion for future implications and strategies
Axial spondyloarthritis in patients with recurrent fever attacks: data from the AIDA network registry for undifferentiated autoInflammatory diseases (USAIDs)

Beckground Despite the recent advances in the field of autoinflammatory diseases, most patients with recurrent fever episodes do not have any defined diagnosis. The present study aims at describing a cohort of patients suffering from apparently unexplained recurrent fever, in whom non-radiographic axial spondylarthritis (SpA) represented the unique diagnosis identified after a complete clinical and radiologic assessment. Materials and methods Patients’ data were obtained from the international registry on Undifferentiated Systemic AutoInflammatory Diseases (USAIDs) developed by the AutoInflammatory Disease Alliance (AIDA) network. Results A total of 54 patients with recurrent fever episodes were also affected by non-radiographic axial SpA according to the international classification criteria. SpA was diagnosed after the start of fever episodes in all cases; the mean age at the diagnosis of axial SpA was 39.9 ± 14.8 years with a diagnostic delay of 9.3 years. The highest body temperature reached during flares was 42°C, with a mean temperature of 38.8 ± 1.1°C. The most frequent manifestations associated to fever were: arthralgia in 33 (61.1%) cases, myalgia in 24 (44.4%) cases, arthritis in 22 (40.7%) cases, headache in 15 (27.8%) cases, diarrhea in 14 (25.9%) cases, abdominal pain in 13 (24.1%) cases, and skin rash in 12 (22.1%) cases. Twenty-four (44.4%) patients have taken daily or on-demand non-steroidal anti-inflammatory drugs (NSAIDs) and 31 (57.4%) patients have been treated with daily or on demand oral glucocorticoids. Colchicine was used in 28 (51.8%) patients, while other conventional disease modifying anti-rheumatic drugs (cDMARDs) were employed in 28 (51.8%) patients. Forty (74.1%) patients underwent anti-tumor necrosis factor (TNF) agents and 11 (20.4%) were treated with interleukin (IL)-1 inhibitors. The response to TNF inhibitors on recurrent fever episodes appeared more effective than that observed with anti-IL-1 agents; colchicine and other cDMARDs were more useful when combined with biotechnological agents. Conclusion Signs and symptoms referring to axial SpA should be inquired in patients with apparently unexplained recurrent fever episodes. The specific treatment for axial SpA may lead to a remarkable improvement in the severity and/or frequency of fever episodes in patients with unexplained fevers and concomitant axial SpA.
Molecular mechanism and research progress on pharmacology of ferulic acid in liver diseases

Ferulic acid (FA) is a natural polyphenol, a derivative of cinnamic acid, widely found in Angelica, Chuanxiong and other fruits, vegetables and traditional Chinese medicine. FA contains methoxy, 4-hydroxy and carboxylic acid functional groups that bind covalently to neighbouring adjacent unsaturated Cationic C and play a key role in many diseases related to oxidative stress. Numerous studies have shown that ferulic acid protects liver cells and inhibits liver injury, liver fibrosis, hepatotoxicity and hepatocyte apoptosis caused by various factors. FA has protective effects on liver injury induced by acetaminophen, methotrexate, antituberculosis drugs, diosbulbin B and tripterygium wilfordii, mainly through the signal pathways related to TLR4/NF-κB and Keap1/Nrf2. FA also has protective effects on carbon tetrachloride, concanavalin A and septic liver injury. FA pretreatment can protect hepatocytes from radiation damage, protects the liver from damage caused by fluoride, cadmium and aflatoxin b1. At the same time, FA can inhibit liver fibrosis, inhibit liver steatosis and reduce lipid toxicity, improve insulin resistance in the liver and exert the effect of anti-liver cancer. In addition, signalling pathways such as Akt/FoxO1, AMPK, PPAR γ, Smad2/3 and Caspase-3 have been shown to be vital molecular targets for FA involvement in improving various liver diseases. Recent advances in the pharmacological effects of ferulic acid and its derivatives on liver diseases were reviewed. The results will provide guidance for the clinical application of ferulic acid and its derivatives in the treatment of liver diseases.
Kinetic Characterization of Heat Bath and the Energetics of Thermal Ratchet Models

Langevin equations have been employed to describe thermally fluctuating systems, such as thermal ratchet models . Their role of the heat bath in these contexts has not been clearly understood. We introduce an approach to this issue and, by using it, propose a method to study the energetics of those models. As a example, we calculate the efficiency of energy conversion of “Feynman's ratchet”.
m6A reader proteins: the executive factors in modulating viral replication and host immune response

N6-Methyladenosine (m6A) modification is the most abundant covalent modification of RNA. It is a reversible and dynamic process induced by various cellular stresses including viral infection. Many m6A methylations have been discovered, including on the genome of RNA viruses and on RNA transcripts of DNA viruses, and these methylations play a positive or negative role on the viral life cycle depending on the viral species. The m6A machinery, including the writer, eraser, and reader proteins, achieves its gene regulatory role by functioning in an orchestrated manner. Notably, data suggest that the biological effects of m6A on target mRNAs predominantly depend on the recognition and binding of different m6A readers. These readers include, but are not limited to, the YT521-B homology (YTH) domain family, heterogeneous nuclear ribonucleoproteins (HNRNPs), insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs), and many others discovered recently. Indeed, m6A readers have been recognized not only as regulators of RNA metabolism but also as participants in a variety of biological processes, although some of these reported roles are still controversial. Here, we will summarize the recent advances in the discovery, classification, and functional characterization of m6A reader proteins, particularly focusing on their roles and mechanisms of action in RNA metabolism, gene expression, and viral replication. In addition, we also briefly discuss the m6A-associated host immune responses in viral infection.
Post-viral idiopathic purpura fulminans is associated with inherited thrombophilia and anti-cardiolipin antibodies

Introduction Idiopathic purpura fulminans (IPF) is a rare and severe coagulation disorder, associated with transient anti-protein S (anti-PS) antibodies in the context of post-viral infection such as varicella. Anti-protein S antibodies are frequently found in the context of varicella, in contrast with the rarity of IPF. Other factors such as anti-phospholipid antibodies (APL) and inherited thrombophilia may be associated with severe vascular complication. Method This is an ancillary study of a French multicenter retrospective series and systematic review of literature. We analyzed patients who were tested for inherited thrombophilia, namely antithrombin, protein C, protein S deficiency; prothrombin gene G20210A polymorphism (FII:G20210A),Factor V R506Q polymorphism (FV:R506Q); and/or for APL (lupus anticoagulant (LA), anti-cardiolipin antibodies (ACL), or anti-beta 2-GPI antibodies (Aβ2GP1). Results Among the 25 patients tested for inherited thrombophilia, 7 (28%) had positive results. Three had FV R506Q, two FII:G20210A, one compound heterozygote FV:R506Q associated to FII:G20210A, and one protein C deficiency. APL testing was performed in 32 patients. It was positive in 19 patients (59%): 17 ACL (53%), 5 LA (16%), 4 Aβ2GP1 (13%). The risk of severe complications was not associated with presence of inherited thrombophilia or APL presence, with RR: 0.8 [95% CI: 0.37–1.71], p = 1 and RR: 0.7 [95% CI: 0.33–1.51], p = 0.39, respectively. We found a high prevalence of inherited thrombophilia or APL in a population of patients with IPF. However, we do not find an association with the occurrence of severe vascular complications or venous thromboembolism.