Miracle-dz/UniFAR-FTUs huggingface dataset:
The Kelch/Nrf2 Antioxidant System as a Target for Some Marine Fungal Metabolites

Marine fungal metabolites often exhibit antioxidant activity, but their effects on the Keap1/Nrf2 cellular system are rarely studied, possibly due to insufficient isolated amounts. In this work, we used a bioinformatics approach to evaluate the ability of some promising cytoprotective compounds to bind Kelch domain of Keap1 protein, and thus inhibit its interaction with Nrf2. The molecular docking data suggested that gliorosein, niveoglaucin A, 6-hydroxy-N-acetyl-β-oxotryptamine, 4-hydroxyscytalone and 4-hydroxy-6-dehydroxyscytalone can form the hydrogen building with Arg415 or Arg483 amino acid residues of P1-P2 sub-pockets in the Nrf2 binding site of Keap1′s Kelch domain. These positions of the small molecules in the Kelch domain of Keap1 can inhibit the interaction of Keap1 with Nrf2 and enhance the nuclear translocation of Nrf2 from cytosol that can result in overexpression of relative genes. This assumption, based on virtual screening of a number of low molecular weight metabolites of marine fungi, makes them promising for further studies.
Shallow water waves generated by subaerial solid landslides

SUMMARY Subaerial landslides are common events, which may generate very large water waves. The numerical modelling and simulation of these events are thus of primary interest for forecasting and mitigation of tsunami disasters. In this paper, we aim at describing these extreme events using a simplified shallow water model to derive relevant scaling laws. To cope with the problem,twodifferentnumericalcodesareemployed:one,SPHysics,isbasedonaLagrangian meshless approach to accurately describe the impact stage whereas the other, Gerris, based on a two-phase finite-volume method is used to study the propagation of the wave. To validate Gerris for this very particular problem, two numerical cases of the literature are reproduced: a vertical sinking box and a 2-D wedge sliding down a slope. Then, to get insights into the problem of subaerial landslide-generated tsunamis and to further validate the codes for this case of landslides, a series of experiments is conducted in a water wave tank and successfully compared with the results of both codes. Based on a simplified approach, we derive different scaling laws in excellent agreement with the experiments and numerical simulations.
Modeling the effect of suspended sediment stratification on bottom exchange processes

A vertical gradient of suspended sediment concentration often exists in estuaries, particularly within the bottom boundary layer where sediment erosion and deposition take place. This results in a vertical density gradient and hence modification of the flow. However, this important effect has often been ignored in past sediment studies. Because of this and because of other empirical assumptions, exisiting erosion models cannot be used as predictive tools. This paper employs a simplified second-order closure model to simulate the effect of sediment-induced stratification on bottom boundary layer dynamics, and particularly the erosion process. Numerical models, which employ the concept of Richardson number dependent eddy viscosity, have been developed in the past for stratified flows. These models require a large number of data for tuning parameters of the eddy viscosity formula. The simplified second-order closure model used here consists of the dynamic equations of motion for mean variables (velocity, temperature, salinity, density, and suspended sediment concentration) and turbulent quantities of turbulent kinetic energy and turbulence macroscale. Model constants are thus invariant owing to the added physics. Model simulations of laboratory sediment-laden boundary layers indicate that, as sediments are eroded or resuspended from the bottom, a vertical gradient of suspended sediment concentration can lead to a significant reduction of the turbulent shear stresses and a slowdown of the erosion-resuspension process. Hence significant error may be contained in some empirical sediment erosion rate formulae, which were derived by ignoring flow-sediment interactions. Simulations of a wave boundary layer and a thermally stratified boundary layer, obtained with the same numerical model, are also presented. There is good agreement between measured and simulated mean and turbulent quantities in both cases.
Gravity wave characteristics over the equator observed during CPEA campaign using simultaneous multiple stations data

The vertical and temporal variations of inertia-gravity waves are studied by means of an intensive radiosonde campaign con-ducted from 10 April to 09 May 2004 at ﬁve sites, including the Equatorial Atmosphere radar (EAR) site at Koto Tabang (0.2oS, 100.32oE) in west Sumatra, Indonesia. The four other balloon sounding sites are located about 75-400 km away from EAR. Dominant gravity waves with periods 2-3 days and vertical wavelengths of about 3-5 km showing clear downward phase propagation were detected, particularly in the upper troposphere and lower stratosphere (UTLS) region. The gravity wave energy is found to become the largest at around 20 km altitude, although the enhancement was not continuous, but intermittent. The wave activity was similar at all the ﬁve sites with a slight phase shift, which suggests that the horizontal scale of the wave is larger than the distance between the sites. We have applied a correlative analysis to delineate the horizontal propagation characteristics of gravity waves, and estimated the horizontal wavelength to be about 1700 km propagating towards 30o south from the east during 26-30 April 2004 which is further veriﬁed by hodograph analysis for individual proﬁles. During 10-14 April 2004 and 5-9 May 2004, horizontal wavelength and direction of the propagation is found to be 2700 km and 3250 km and, 26oand 3o north from the east, respectively. The spatial and temporal variations of the convection, which is thought to be a major source for the generation of gravity waves, is also studied using satellite data of outgoing long-wave radiation (OLR). We noticed clear eastward advection of large super cloud clusters (SCCs) from the Indian Ocean to the maritime continent, sometimes moving towards the observational sites. The source of the gravity waves is strongly related to this slowly eastward-advecting tropospheric convection implying that the wave activity we are looking in the UTLS region is already generated by far distant sources located west of EAR. We also present a case study where large wave activity did not correspond to the particular cloud convection.
Thunderstorm electrification: A case study

The paper presents interpretation of triple Doppler radar observations of a thunderstorm that occurred at the Kennedy Space Center, Florida. Precipitation particle motions inside the storm, as evaluated from the three radial velocity radar data sets, are presented in a selected vertical plane throughout the storm development. These data are interpreted and compared with observations of VHF radio emission sources and lightning charge centers derived from an earlier analysis (Krehbiel, 1981). The main feature of the particle motion field is the persistence, at nearly the same altitude throughout the entire period of analysis, of a “balance level” characterized by a zero value of the precipitation particle mean vertical velocity. Further analysis based on considerations of radar reflectivity and air velocity suggests the presence, at this altitude, of relatively large precipitation particles suspended in an updraft. The lightning negative charge centers appear to be less than 1 km above the particle balance level.
Precipitation Reproducibility over Tropical Oceans and Its Relationship to the Double ITCZ Problem in CMIP3 and MIROC5 Climate Models

AbstractPrecipitation reproducibility over the tropical oceans in climate models is examined. Models participating in phase 3 of the Coupled Model Intercomparison Project (CMIP3) and the current (fifth) version Model for Interdisciplinary Research on Climate (MIROC5) developed by the Atmosphere and Ocean Research Institute, National Institute for Environmental Studies, and Research Institute for Global Change (AORI/NIES/RIGC) are analyzed. Scores of a pattern similarity between precipitation in the models and that in observations are evaluated. The low score models (LSMs) overestimate (underestimate) precipitation over large-scale subsidence (ascending) regions compared to the high score models (HSMs). The sensitivity of deep convection to sea surface temperature (SST) and large-scale subsidence is examined; analysis suggests that dynamical suppression of deep convection by the entrainment of environmental dry air over the subsidence region is very weak, and deep convection follows SST closely in LSMs. Fo.
Krauklis wave in a trilayer

ABSTRACTThe Krauklis wave is a slow dispersive wave mode that propagates in a fluid layer bounded by elastic media. The guided properties of this wave and its ability to generate very short wavelengths at seismic frequency range predict possibility of resonances in fluid-filled rock fractures. Study of Krauklis wave properties at laboratory scales requires evaluation of its propagation velocities in models with finite and thin elastic walls. Analysis of an exact solution for a fluid-filled trilayer with equal thickness plates reveals existence of the Krauklis waves in such a model, as well as another mode which propagates mostly in the solid part. Both propagation modes exist at all frequencies. We derived and verified various asymptotic solutions by comparing their dependencies on layer thicknesses and frequency with the exact numerical solution. Analytical and computational results demonstrate that in a 60-cm-long model, the first resonant frequency can be below 10 Hz. This result suggests that the Krau.
Calcium storage in multivesicular endo-lysosome

It is now established that endo-lysosomes, also referred to as late endosomes, serve as intracellular calcium store, in addition to the endoplasmic reticulum. While abundant calcium-binding proteins provide the latter compartment with its calcium storage capacity, essentially nothing is known about the mechanism responsible for calcium storage in endo-lysosomes. In this paper, we propose that the structural organization of endo-lysosomal membranes drives the calcium storage capacity of the compartment. Indeed, endo-lysosomes exhibit a characteristic multivesicular ultrastructure, with intralumenal membranes providing a large amount of additional bilayer surface. We used a theoretical approach to investigate the calcium storage capacity of endosomes, using known calcium binding affinities for bilayers and morphological data on endo-lysosome membrane organization. Finally, we tested our predictions experimentally after Sorting Nexin 3 depletion to decrease the intralumenal membrane content. We conclude that the major negatively-charge lipids and proteins of endo-lysosomes serve as calcium-binding molecules in the acidic calcium stores of mammalian cells, while the large surface area of intralumenal membranes provide the necessary storage capacity.
A homogeneity test applied to precipitation data

In climate research it is important to have access to reliable data which are free from artificial trends or changes. One way of checking the reliability of a climate series is to compare it with surrounding stations. This is the idea behind all tests of the relative homogeneity. Here we will present a simple homogeneity test and apply it to a precipitation data set from south-western Sweden. More precisely we will apply it to ratios between station values and some reference values. The reference value is a form of a mean value from surrounding stations. It is found valuable to include short and incomplete series in the reference value. The test can be used as an instrument for quality control as far as the mean level of, for instance, precipitation is concerned. In practice it should be used along with the available station history. Several non-homogeneities are present in these series and probably reflect a serious source of uncertainty in studies of climatic trends and climatic change all over the world. The significant breaks varied from 5 to 25 per cent for this data set. An example illustrates the importance of using relevant climatic normals that refer to the present measurement conditions in constructing maps of anomalies.
Climate change scenarios from a regional climate model: Estimating change in runoff in southern Africa

This paper describes an analysis of different ways of constructing climate change scenarios using output from three climate models. It focuses on using the HadRM3H regional climate model applied across southern Africa and a macroscale runoff model operating at a scale of 0.5 × 0.5° to simulate river runoff. HadRM3H has a spatial resolution of 0.44 × 0.44° and is driven by boundary conditions from HadAM3H, a global atmosphere general circulation model with a spatial resolution of 1.875 × 1.25°. This, in turn, used sea-surface boundary conditions from HadCM3, a coupled global ocean-atmosphere general circulation model that operates at a spatial resolution of 3.75 × 2.5°. Sixteen climate scenarios were constructed from the three models, representing different combinations of model scale, whether the climate model simulations were used directly or changes were applied to an observed baseline, and whether observed or simulated variations from year-to-year were used. The different ways of deriving climate scenarios from a single initial climate model experiment result in a range in change in average annual runoff at a location of at least 10%, and often more than 20%. There is a clear difference in the large-scale spatial pattern of change in runoff from HadCM3 to HadRM3H. Many of the climate features in HadRM3H are already present in HadAM3H simulations, as would be expected from the experimental design. This suggests that for studies over a large geographic domain, an intermediate-resolution global climate model can produce useful scenarios for impact assessments. HadRM3H overestimates rainfall across much of southern Africa and so results in too much runoff: This leads to smaller estimates of future change in runoff than arise when changes in climate are applied to an observed climate baseline. It is concluded that under these circumstances it is preferable to apply modeled changes in climate to observed data to construct climate scenarios rather than derive these directly from the regional climate model simulations. Incorporating increases in interannual variability as simulated by HadRM3H leads to little change in simulated annual mean runoff. However, it has a larger impact on the frequency distributions of runoff, with extreme flows predicted to increase more than mean flows and even to increase in areas where the mean flow decreases. This demonstrates the importance of considering not only changes in mean climate but also climate variability.
MORPHOLOGY, PHYSIOCHEMICAL CHARACTERISTICS, AND FERTILITY OF SOILS FROM QUATERNARY LIMESTONE IN LEYTE, PHILIPPINES

Very few studies have been conducted on the nature and characteristics of soils from Quaternary limestones in geologically young islands in the humid tropics. This study examined a hillslope in Leyte, Philippines, with soils from Quaternary (Late Pleistocene) limestone and evaluated their morphology, physiochemical characteristics, and fertility constraints. We evaluated six pedons representing different slope positions, such as summit, shoulder, upper backslope, middle backslope, lower backslope, and footslope. Our data indicate that the soils in the upper slopes (summit, shoulder, and upper backslope) have thin solum, black surface horizon, clayey texture, granular structure, high organic matter and N, high Ca and CaCO3 contents, low contents of nutrients like P, K, Fe, Mn, and B, and are neutral to alkaline pH values. According to Soil Taxonomy, the soils are classified as Typic Calciudolls (summit) and Rendollic Eutrudepts (shoulder and upper backslope), but all three pedons are classified as Calcaric Phaeozems in the World Reference Base system. Conversely, the soils on the lower slopes (footslope and middle and lower backslopes) have thicker solum and higher clay content. They have subangular blocky structures, which turn hard when dry and become plastic and sticky when wet. Like the soils on the upper slopes, they also have neutral to strongly alkaline pH values, have high organic matter, N, Ca, and CaCO3 contents, but are generally low in nutrient contents. They are classified as Typic Eutrudepts (source, Soil Taxonomy) or Calcaric Cambisols (source, World Reference Base). Most soils have high rock fragment contents in their profile. Results also show substantial variations of solum depth at short distances along the slope (i.e., from summit to footslope) and across the slope. The solum depth variability helps explain the commonly observed variations of crop growth in limestone areas. The high clay content of these relatively young soils suggests contribution from limestone parent material and possibly volcanic ash from past eruptions of nearby volcanoes. Our results show that soils developed from limestone have both physical and chemical fertility constraints to upland crop production, which differ between soils even in the same landscape. The overall results indicate that the characteristics and fertility constraints of soils from Quaternary limestones in our study site are largely the influence of the slope position, chemical characteristic of the limestone parent material, and human activities.
pNeurFill: Enhanced Neural Network Model-Based Dummy Filling Synthesis With Perimeter Adjustment

Dummy filling is widely applied to significantly improve the planarity of topographic patterns for the chemical mechanical polishing (CMP) process in VLSI manufacturing. In the dummy filling flow, dummy synthesis works as the key step to adjust the post- CMP profile height. However, existing dummy synthesis optimization approaches usually fail to balance the filling quality and efficiency. This article proposes a novel model-based dummy filling synthesis framework NeurFill, integrated with multiple starting points-sequential quadratic programming (MSP-SQP) optimization solver. Inside this framework, a full-chip CMP simulator is first migrated to the neural network, achieving $8134\times $ speedup on gradient calculation by backward propagation. Entrenched in the CMP neural network models, we further implement an improved version of NeurFill (pNeurFill) to alleviate the post- CMP height variation caused by dummy perimeter. After each iteration of dummy density optimization, an additional perimeter adjustment based on a given candidate dummy pattern set is applied to search for the optimal perimeter fill amount. The experimental results show that the proposed NeurFill outperforms existing rule- and model-based methods. The extra perimeter adjustment strategy in pNeurFill can achieve an average 66. 97Å decreasing in height variation and 8.92% quality improvement compared to NeurFill. This will provide guidance for DFM so as to increase IC chip yield.
Paediatric COVID-19 Outcomes: Haematology Parameters, Mortality Rates, and Hospitalization Duration

The global COVID-19 pandemic has strained healthcare systems around the globe, necessitating extensive research into the variables that affect patient outcomes. This study examines the relationships between key haematology parameters, duration of hospital stay (LOS), and mortality rates in COVID-19 cases in paediatric patients. Researchers analyse relationships between independent variables (COVID-19 status, age, sex) and dependent variables (mortality, LOS, coagulation parameters, WBC count, RBC parameters) using multivariate regression models. Although the R-square values (0.6–3.7%) indicate limited explanatory power, coefficients with statistical significance establish the impact of independent variables on outcomes. Age emerges as a crucial predictor of mortality; the mortality rate decreases by 1.768% per age group. Both COVID-19 status and age have an inverse relationship with length of stay, emphasising the milder hospitalisation of children. Platelet counts decline with age and male gender, potentially revealing the influence of COVID-19 on haematological markers. There are significant correlations between COVID-19 status, age, gender and coagulation measures. Lower prothrombin time and D-dimer concentrations in elder COVID-19 patients are indicative of distinct coagulation profiles. WBC and RBC parameters exhibit correlations with variables: COVID-19-positive patients have lower WBC counts, whereas male COVID-19-positive patients have higher RBC counts. In addition, correlations exist between independent variables and the red cell distribution width, mean corpuscular volume, and mean corpuscular haemoglobin. However, there is no correlation between mean corpuscular haemoglobin concentration and outcomes, indicating complex interactions between haematological markers and outcomes. In essence, this study underlines the importance of age in COVID-19 mortality, provides novel insights into platelet counts, and emphasises the complexity of the relationships between haematological parameters and disease outcomes.
Behavior of a Drosophila melanogaster transposable element in Saccharomyces cerevisiae

The Drosophila melanogaster transposable element 412 is transiently unstable in Saccharomyces cerevisiae when present on a freely replicating plasmid. The 412 element undergoes recombination to form two circular molecules, a 412 deletion plasmid and, presumably, a 412 circle. The 412 deletion plasmid contains a single long terminal repeat which most likely is the result of homologous recombination within the long terminal repeats. This recombination occurs at or shortly after transformation and is independent of both the RAD52 gene product and the Flp gene of 2 micron DNA.
Enhanced Land Vehicle Positioning in Challenging GNSS Urban Environments Utilizing Automotive Radars

Positioning services for land vehicle navigation have long relied on global navigation satellite systems (GNSS); however, GNSS cannot maintain an accurate position while travelling under bridges, around tall buildings and under tree canopies due to signal blockage or multipath. Integration with the onboard motion sensors can bridge the positioning solution for a short duration but cannot sustain adequate positioning performance during extended GNSS outages. The proposed research overcomes the limitations of current positioning technologies for land vehicles by integrating a GNSS receiver, onboard motion sensors, and an electronic scanning radar (ESR) used in present land vehicles for adaptive cruise control. A new ESR-based static object detection method is developed using newly designed criteria to estimate the forward velocity. We also propose a radar odometry method to obtain the vehicle position based on the radar scans. Integration with onboard motion sensors based on Extended Kalman filtering (EKF) is designed and realized to achieve accurate positioning in degraded vision and challenging GNSS environments. The proposed multi-sensor positioning solution is examined using several road test trajectories in challenging urban environments in Toronto. It shows RMS error as low as 3 m over more than 90% of the traveled distance.