Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation of foam filled tube model and optimization result using Weibull distribution

*Corresponding Author https://doi.org/10.1590/1679-78256174 Abstract Passenger safety and low fuel consumption rate are the most important factors that need to be considered when designing modern transportations. This study validates the crash behavior and optimum values of foam-filled structures under the dynamic oblique impact using the Weibull distribution. The optimization method aimed to absorb maximum energy with minimum peak crushing force. Furthermore, the metamodel and optimization techniques such as RBF and NSGA-II were used to ensure accurate validation of the Weibull distribution method. The result showed that the finite element model is comparable to the experimental data in the reference, while the metamodel method, which is directly verified, affects optimization results. The Weibull distribution method shows that the optimum value and the simulation have good accuracy or R Weibull 3 RESULT AND DISCUSSION 3.1 Deformation modes Figure 4 shows the numerical reaction or deformation modes for empty double, foam-filled double and single tubes under oblique loading with an impact angle of 0°, 10°, 20°, 30°, and 40°. All numerical models of the tubular structure in the progressive fall mode are stacked by rigid walls with loading angles of 0° and 10°, while 30° and 40° are categorized in the global bending modes. The loading angle of 20° is a transitional area between the progressive fall and the global bending collapse modes. The examined deformation modes show that the tube configuration has similar geometry and material as those under oblique static quasi-loading. The deformation mode for the 0° loading angle is a progressive axial collapse mode. Assuming it is 10°, the tubes form folds progressively, and at the final stage, they bend slightly towards the center, as shown in Figures 4a and b. At 30° and 40°, the bend is more significant at the tube portion where global mode
Seed fate and seedling recruitment in monkey latrines in rustic cocoa plantations and rain forest in southern Mexico

Abstract Primates are important seed dispersers in natural ecosystems and agro-ecosystems, but the latter scenario remains under-studied. The degree to which primates favour plant regeneration greatly depends on post-dispersal processes. The main objective of this study was to compare patterns of seed/seedling fate and seedling recruitment in two habitats of the black howler monkey (Alouatta pigra Lawrence 1933), rustic cocoa and rain forest, and two types of seed-deposition locations, monkey latrines and control locations. Field experiments were carried out within the non-overlapping home ranges of six monkey groups, three in cocoa and three in forest. Seed and seedling fates were assessed for one focal tree species, Brosimum lactescens. The probabilities of seed survival (0.52), germination (0.72), seedling establishment (0.73) and early seedling survival (0.38) were not affected by habitat or seed-deposition location. Late seedling survival was similar in the two habitats but was higher in control locations (0.22) than in latrines (0.09). In cocoa, 4641 seedlings of 59 species were recorded, in forest 3280 seedlings of 68 species. Seedling recruitment was similar in both habitats, but latrines had higher densities than control locations. The importance of agro-ecosystems with low management intensity for the maintenance of ecological processes in anthropogenic landscapes is discussed.
Molecular typing of methicillin and vancomycin-resistant
Staphylococcus aureus isolated from clinical specimens by doublelocus
sequence typing (DLST) method

Methicillin-resistant Staphylococcus aureus (MRSA) strains are the essential cause of infections in communities and hospitals. The present study was conducted to determine the molecular typing of MRSA, isolated from hospitalized patients, using the double-locus sequence typing (DLST). In total, 280 S. aureus isolated from clinical specimens by phenotypic (catalase, coagulase, DNase, oxacillin, vancomycin screening agar and antibiotic disk diffusion), and molecular methods (PCR for determining the mecA, vanA and nuc genes). The DLST and sequencing was performed for MRSA containing mecA. Out of 280 specimens, confirmed as Staphylococcus aureus (S. aureus), 123 (43.9%) strains were MRSA. The highest resistance toward the erythromycin (15 μg), followed by ciprofloxacin (5 μg), clindamycin (2 μg), tetracycline (30 μg), gentamicin (10 μg) and rifampicin (5 μg), was 98.3%, 97.5%, 94.3%, 90.2%, 83.7% and 41.4%, respectively. Also, the least resistance (0%) was observed in each of teicoplanin (30 μg), linzolide (30 μg), and vancomycin (30 μg). All (100%) of MRSA strains had the mecA, and none of them have had the vanA. The results of DLST showed that the most common sequence types were BPH 2003 and 0217. The DLST type 18-32 was a significant cluster of MRSA. By sequencing MRSA and comparing the dominant types via the DLST, it is possible to establish the etiology of the disease in a much shorter time, and prevent the complications of the disease. Therefore, the combination of partial sequences of clfB and spa can serve as useful genetic markers for MRSA typing. It concluded that the MRSA in our region was relatively high, but no vancomycin resistance was found. The majority of the MRSA DLST type was 18–32.
Gaps and limitations in the use of restoration scenarios: a review

The use of scenarios to evaluate restoration effects on biodiversity and ecosystem services (ES) is fundamental to improve restoration practices. Here we developed a systematic review to verify the existence of gaps and limitations in the use of scenarios for environmental restoration, and assess the state of the science of “restoration scenarios” and implications for future research. From 419 studies reviewed, most were held in developed countries, using exploratory scenarios at the regional scale, actively restoring ES and habitat at “habitat, ecosystems or communities” at landscape level, targeting forests and fragmented landscapes. The main gaps we identified were: few studies in tropical, marine, and urban environments, despite their importance for biodiversity and ES; few reports on global scales using target‐seeking approach, despite the existence of global targets; small number of studies considered invertebrates and invasive species, neglecting many ecosystem services and disservices; lack of participatory and cost‐effectiveness studies, revealing a disconnection between restoration research and socioeconomic context. The gaps identified might prevent the widespread use of scenarios for restoration planning, particularly the limited scales of analysis, the lack of participatory approaches, and weak cost consideration. We encourage the use of target‐seeking scenarios, with clear objectives, stimulating collaboration among stakeholders seeking cost‐effective restoration alternatives.
Mechanosensitive fluorescent probes

Green fluorescent protein (GFP) mutants have become the most widely used fluorescence markers in the life sciences, and although they are becoming increasingly popular as mechanical force or strain probes, there is little direct information on how their fluorescence changes when mechanically stretched. Here we derive high-resolution structural models of the mechanical intermediate states of stretched GFP using steered molecular dynamics (SMD) simulations. These structures were used to produce mutants of EGFP and EYFP that mimic GFP’s different mechanical intermediates. A spectroscopic analysis revealed that a population of EGFP molecules with a missing N-terminal α-helix was significantly dimmed, while the fluorescence lifetime characteristic of the anionic chromophore state remained unaffected. This suggests that N-terminal deletions switch the protonation state of the chromophore, and how the fluorescence of GFP molecules in response to mechanical disturbance might be turned off. INTRODUCTION Since the discovery that GFP can be used to monitor gene expression and protein localization in living organisms[1], GFP and its mutants have become the most widely used fluorescence markers to identify how protein expression levels and their spatial organization within cells and tissues are altered. When mapping spatial distributions of GFP-tagged protein within cells, the lack of GFP fluorescence is typically interpreted as an absence of the tagged protein in that region. Since a large fraction of proteins outside and within cells are not free to move but are physically connected to other proteins, mechanical forces generated by cells or acting on cells can stretch and unfold proteins[2,3,4,5,6,7]. Furthermore,
Molecular dynamics of NaCl (B1 and B2) and MgO (B1) melting: Two-phase simulation

Abstract Melting of NaCl and MgO has been simulated with a two-phase molecular dynamics method at constant pressure using newly developed interaction potentials. Equations of state for NaCl and MgO simulated by molecular dynamics are in good agreement with available experimental data. Equations of state for MgO and NaCl were obtained by fitting simulated volumetric properties at pressures and temperatures up to 300 kbar and 3000 K (for NaCl) and 2000 kbar and 7000 K (for MgO). The pressure dependence of the melting temperature was predicted up to 1000 and 1400 kbar for NaCl and MgO, respectively. Crystallization and melting were observed without hysteresis. The simulated melting curve of NaCl is fully consistent with experimental measurements. The pressure dependence of the melting temperature of MgO is consistent with experimental data at 1 bar and previous theoretical estimations by Jackson (1977) and Ohtani (1983). The melting temperature of MgO is substantially higher than that determined by Zerr and Boehler (1994) (by 1000 K at 300 kbar) and substantially lower than that predicted by Cohen and Gong (1994) (by 1500 Kat 300 kbar). The melting temperature of MgO at the pressure of the core-mantle boundary is calculated to be 6900 ± 200 K. The procedures for simulation of melting of NaCl and MgO, starting from a calculation of the interatomic potential and ending with analysis of results, are identical.
Modeling of ultrasound tomographic imaging for non-destructive inspection of underwater structures

In non-destructive inspection regular ultrasound techniques provide detection and estimate size of specific defects or undesired objects in different structures. The method of tomographic imaging modeled in this paper can provide the correct position and shape of the object inside underwater structures to be inspected. The proposed method is based on 2-D full waveform inversion of reflected ultrasound field registered by the array of sensors at a short distance from the target object. The computationally intensive algorithm for tomographic image reconstruction is described and tested with focus on underwater pipeline ultrasound inspection. The results of numerical modeling using parallel calculations and physical modeling are presented and discussed.
The planalto hermit, Phaethornis pretrei – a key species in a Neotropical savanna community in Central Brazil

ABSTRACT Among vertebrate pollinators, hummingbirds are the most important group in the Neotropics as they use a wide spectrum of plant species. The hummingbird Phaethornis pretrei (Phaethornithinae) was studied in a Neotropical savanna of Central Brazil. The objectives were to: (1) record the flowering period of species used by P. pretrei as food resources and establish whether this hummingbird is their exclusive visitor; (2) determine the return time of P. pretrei to a given plant species and the number of P. pretrei that use the same individual plant; (3) assess the pollen loads transported by P. pretrei; and (4) verify whether this hummingbird is resident in the area. The flowering period of plants used by P. pretrei was recorded for 22 months between 2007 and 2008. Focal observations were made concomitantly with capture and marking of hummingbirds and collection of pollen loads using adhesive tape. Phaethornis pretrei was recorded visiting 21 plant species, being the exclusive visitor of two species and performing more than 90% of visits to another four. Nineteen of those plant species were also visited by seven other hummingbird species. The return time of P. pretrei to typically ornithophilous flowers was around 1 hour and visits to the same plants were made by two or sometimes three individuals. Phaethornis pretrei may transport pollen of up to 10 species on its bill. This hummingbird is resident in the study area and promotes the flow of pollen, favouring the reproduction of several plant species. Therefore, it is a pollinator of great importance for this plant community, being a key species in the area in question.
New Simplified and Generalized Three-Dimensional Space Vector Modulation Algorithm for Multilevel Four-Leg Diode Clamped Converter

This article aims to propose a new simplified and generalized three-dimensional space vector modulation (3DSVM) for four-leg multilevel diode clamped converter (FL-DCC). The idea is to use the three-dimensional space vector diagram of the multilevel FL-DCC in αβγ space, while all calculation stages of the 3DSVM algorithm will be carried out in a new frame called ρστ. The proposed 3DSVM algorithm provides, for any inverter level, 1) simple way to calculate the duration time; 2) automatic generation of the adjacent switching states; 3) balancing the dc capacitor voltages, and 4) switching sequence definition without prism and tetrahedron identification stage. All 3DSVM steps are implemented in only one sector, thanks to the proposed new reference voltage vector. Such feature makes possible to build a generalized 3DSVM that can be implemented with minimum computational burden in simple embedded digital platforms. Simulation and experimental results are provided to demonstrate the proposed concept.
Magnetic Field Enhancement Characteristic of an Axially Parallel Hybrid Excitation DC Generator

The magnetic field enhancement characteristic of an axially parallel hybrid excitation generator (APHEG) is revealed and analyzed in this article. The APHEG consists of a permanent magnet machine part (PMMP), a flux modulation machine part (FMMP), and a diode rectifier. The magnetic fields of the two parts are interactional despite the independent flux paths, which provides the possibility to enhance the FMMP field at the expense of weakening the PMMP field. By taking advantage of that, the combination of the PMMP and FMMP can effectively boost the output power in the defined voltage-boost region as the weakening of the PMMP field is negligible. In addition, the magnetic field of the FMMP can be further enhanced by regulating the rotor shift angle. Based on the analysis of the phasor diagrams, it is found that the flux amplitudes and phase displacement angles of the two parts are mutually restrictive and decide the optimized rotor shift angle range of the APHEG. Finally, a prototype APHEG has been developed, and the experiments verify the phasor diagrams and simulation analysis.
Fine Mapping of the brachytic Locus on the Tomato Genome

Mechanization of farm work is increasingly demanded for the current system of fresh-market tomato (Solanum lycopersicum) production. One essential element for the adoption of mechanical harvest of fresh-market tomatoes is modification of plant architecture so that the crop can be grown without staking. To address this in the current production system, the stem length should be reduced. The tomato brachytic (br) locus has been shown to be a primary source of reducing stem length. To improve the effectiveness of marker-assisted selection (MAS) for the br-mediated trait and to provide resources for cloning this gene, we fine-mapped br to the tomato genome. Fine mapping of br to chromosome 1 was initiated by a survey of genome-wide single-nucleotide polymorphisms (SNPs) shown to be polymorphic between the br phenotype and normal using the tomato array, identifying the interval that harbors br. Genetic markers that flank the locus further permitted saturation of the interval. Twenty-six fixed homozygous recombinant lines were identified together in two different populations and tested with those markers. These efforts resulted in the first report that the br is fine-mapped to a 763-kb physical interval of tomato reference genome. The identified markers close to the br in the present study will be significant resources for MAS and gene cloning research.
Side-Information Aided Compressed Multi-User Detection for Up-Link Grant-Free NOMA

Grant-free non-orthogonal multiple access (NOMA) is considered as one of the most important methodologies for the machine-type communications (MTC). In the field of MTC, compressed sensing based multi-user detection (CS-MUD) has been recognized as an excellent candidate for joint user activity and data detection, since many users sporadically transmit short-size data packets at low rates. This article focuses on the CS-MUD problem in the up-link grant-free NOMA scenario, where users are (in)-active randomly in each time slot yet with high temporal correlation. First, we investigate the CS framework to fully extract the underlying side information in the temporal correlation and propose a novel CS-MUD algorithm. Then, to mitigate the performance degradation due to the imperfect channel estimation in practice, the proposed algorithm is further extended by utilizing the perturbed CS, where the impact of channel estimation errors is modeled as certain perturbation in the measurement matrix. Different from most of the state-of-the-art CS-MUD algorithms, both proposed algorithms can apply even in the absence of prior knowledge on the number of active users. Simulation results indicate that the proposed algorithms achieve better performance than the existing CS-MUD methods. Their convergence and complexity issues are also discussed theoretically and numerically.
Performance of preferential flow models in predicting infiltration through a remolded soil with artificial macropores

Preferential flow in soils contributes to water and contaminant leaching to groundwater and subsurface drains. At practical scales, preferential flow is often neglected due to the lack of consensus or guidance on how to simulate this process. Dual‐permeability (DP) approaches are a standard, but their applicability in practice is limited by the large number of parameters involved. The source‐responsive (SR) model simulates preferential flow as flow films along the walls of macropores that interact with the soil matrix. The objective of this study was to evaluate the ability of the SR model and a DP model with calibration limited to macropore parameters to simulate hydrologic variables of interest for practical applications. Infiltration experiments were conducted in a 150‐cm‐long by 50‐cm‐wide by 40‐cm‐deep soil column with vertical artificial macropores, with preferential flow being the most prevalent flow process. Two macropore configurations and various rainfall rates were tested. The DP model provided relatively accurate predictions of the bottom drainage rates, but inaccurate soil parameter estimates resulted in poor predictions of matrix flow. Critical limitations in the SR model formulation were highlighted, and the model was revised. The refined SR model provided accurate predictions of bottom drainage rates and water contents under steady‐state rainfall. The DP model with a reduced calibration appeared valid to estimate subsurface fluxes with negligible matrix flow. The SR model applicability is limited to steady‐state scenarios with negligible matrix flow. Critical developments are needed for the SR model to be applicable in practice.
IRREVERSIBILITY AND MONITORING IN DYNAMIC GAMES: EXPERIMENTAL EVIDENCE

This paper provides experimental evidence on the impacts of irreversibility and imperfect monitoring on the efficiency and the equity of repeated public goods game. We find that irreversibility and imperfect monitoring both lead to inefficient and unequal outcomes through different channels. Irreversibility lowers public goods contribution in earlier periods and makes the initial-period contribution gap between two players long-lasting. Imperfect monitoring hampers conditional cooperation and reduces group contribution persistently. A finite mixture estimation with conditional cooperator provides a coherent account of the treatment effects.
Agonist binding affinity determines palmitoylation of the glucagon-like peptide-1 receptor and its functional interaction with plasma membrane nanodomains in pancreatic beta cells

The glucagon-like peptide-1 receptor (GLP-1R), a key pharmacological target in type 2 diabetes and obesity, is known to undergo palmitoylation by covalent ligation of an acyl chain to cysteine 438 in its carboxyl-terminal tail. Work with other GPCRs indicates that palmitoylation can be dynamically regulated to allow receptors to partition into plasma membrane nanodomains that act as signaling hotspots. Here, we demonstrate that the palmitoylated state of the GLP-1R is increased by agonist binding, leading to its segregation and clustering into plasma membrane signaling nanodomains before undergoing internalization in a clathrin-dependent manner. Both GLP-1R signaling and trafficking are modulated by strategies targeting nanodomain segregation and cluster formation, including depletion of cholesterol or expression of a palmitoylation-defective GLP-1R mutant. Differences in receptor binding affinity exhibited by biased GLP-1R agonists, and modulation of binding kinetics with the positive allosteric modulator BETP, influence GLP-1R palmitoylation, clustering, nanodomain signaling, and internalization. Downstream effects on insulin secretion from pancreatic beta cells indicate that these processes are relevant to GLP-1R physiological actions and might be therapeutically targetable.
Effect of Direct-Fed Microbials and Monensin on In vitro Fermentation of a High-Forage Diet

An in vitro experiment was conducted to determine effects of directfed microbials (DFM) on rumen fermentation of a forage-based diet in the presence and absence of monensin (MON). Treatments included DFM (0 and 50,000 cfu; primarily Lactobacillus acidophilus and Enterococcus faecium) and monensin (0 and 5 ppm) and were applied directly to the appropriate flask. Substrates (80:20 forage: concentrate) were incubated for 30 h. Measurements included serial gas pressure, and terminal CH4 production, pH, and volatile fatty acid (VFA) and NH3 concentrations. Interactions between DFM and MON were absent (P>0.10) for gas production and fermentation end products, except for a tendency for DFM to increase total VFA concentration without, but not with MON (interaction between DFM and MON; P=0.07). Addition of DFM did not affect (P>0.10) gas production or fermentative end products except for a tendency (P=0.08) for a slight increase in proportion of isovalerate. >Contrariwise, MON decreased (P<0.001) total gas and CH4 production. Similarly, MON decreased (P<0.001) total VFA and NH3 concentrations, and molar proportions of acetate and butyrate and increased (P<0.001) proportions of propionate, valerate, isobutyrate, and isovalerate. Independently, DFM and MON increased (P<0.001) end point pH, resulting in an additive effect when the two treatments were combined. Addition of MON altered fermentation in a predictable fashion and was not influenced by the addition of DFM. In contrast, fermentation characteristics were largely unaffected by DFM with two exceptions: a slight increase in total VFA in the absence of MON and a small increase in pH that appeared to occur through a different mechanism than that for MON.