Miracle-dz/UniFAR-FTUs huggingface dataset:
Simulation Study about Event-by-Event Mass Separation of Cosmic Rays using Several Mass Sensitive Air-Shower Observables

Specific observables of extensive air showers, such as the depth of shower maximum and relative size of the air-shower muonic component, are sensitive to the mass of the primary cosmic-ray particle and therefore provide an avenue for cosmic-ray mass composition analyses. The separation power between proton, helium, oxygen, and iron cosmic rays, on an event-by-event basis, was studied using exact knowledge of mass sensitive air-shower observables determined from CORSIKA simulations at the sites of the IceCube Neutrino Observatory at the South Pole and the Pierre Auger Observatory in Argentina. The simulations cover shower energies from 10 PeV to a few EeV and a wide range of zenith angles, relevant to the next generation upgrades to the IceCube and Auger observatories. Combined knowledge of all studied mass sensitive observables yields promising mass separation power, even when accounting for typical reconstruction uncertainties of the observables. The combination of shower maximum and muon observables is of particular importance for event-by-event mass discrimination, while high-energy muons ( > 500 GeV), measurable by IceCube, serve as an important mass sensitive observable on their own. This motivates equipping the next generation of air-shower arrays with multiple detection techniques for the simultaneous measurement of these shower observables.
A higher-order interpolation method for simulated radio signals of air showers

high-precision cosmic-ray measurements using the radio emission of air showers such as done with LOFAR and envisioned for the Square Kilometre Array (SKA), simulating ensembles of air showers takes considerable CPU time. In particular, simulating every antenna position would become intractable for the 60,000 antennas at SKA. We present a higher-order algorithm for interpolating radio signals of air showers simulated on a radial (polar) grid. It allows to interpolate the full pulse signal in each antenna/polarization along any position in the footprint. It provides significant improvement over existing, linear methods. From a set of simulated showers analyzed from 30 to 500 MHz, we show that simulating about 200 antennas is sufficient to represent signals at any relevant position to high accuracy. Thus, by reducing simulation time for SKA by a factor ∼ 300, it offers a relevant extension to radio simulation codes
Molecular Modeling Insights into Metal-Organic Frameworks (MOFs) as a Potential Matrix for Immobilization of Lipase: An In Silico Study

Simple Summary In recent years, a significant amount of attention has been directed toward MOFs as a potential matrix for the immobilization of enzymes. As per the literature, structures based on metal-organic frameworks (MOFs) offer hydrophobic interaction between lipases and the organic component of the MOF. To ascertain the optimal approach for enhancing the robustness and stability of biocatalysts, it is imperative to gain insights into the molecular interactions between enzymes and ligands. In this regard, the computational methodology proves to be an invaluable asset. A review of the literature reveals numerous reports discussing the interaction between lipase and various ligands. However, there is a lack of available research examining the interaction between lipase and MOF. Hence, it is imperative to comprehend the interplay between Candida rugosa lipase (CRL) and the Zeolitic imidazolate framework (ZIF-8) in order to investigate its industrial practicality. This article presents a comprehensive investigation of the utilization of molecular modeling methodologies, specifically molecular docking and molecular dynamics (MD) simulation, for the purpose of studying the interaction between CRL and ZIF-8. Abstract CRL is a highly versatile enzyme that finds extensive utility in numerous industries, which is attributed to its selectivity and catalytic efficiency, which have been impeded by the impracticality of its implementation, leading to a loss of native catalytic activity and non-reusability. Enzyme immobilization is a necessary step for enabling its reuse, and it provides methods for regulating the biocatalyst’s functional efficacy in a synthetic setting. MOFs represent a novel category of porous materials possessing distinct superlative features that make MOFs an optimal host matrix for developing enzyme-MOF composites. In this study, we employed molecular modeling approaches, for instance, molecular docking and MD simulation, to explore the interactions between CRL and a specific MOF, ZIF-8. The present study involved conducting secondary structural analysis and homology modeling of CRL, followed by docking ZIF-8 with CRL. The results of the molecular docking analysis indicate that ZIF-8 was situated within the active site pocket of CRL, where it formed hydrogen bonds with Val-81, Phe-87, Ser-91, Asp-231, Thr-132, Lue-297, Phe-296, Phe-344, Thr-347, and Ser-450. The MD simulation analysis revealed that the CRL and ZIF-8 docked complex exhibited stability over the entire simulation period, and all interactions presented in the initial docked complex were maintained throughout the simulation. The findings derived from this investigation could promote comprehension of the molecular mechanisms underlying the interaction between CRL and ZIF-8 as well as the development of immobilized CRL for diverse industrial purposes.
UTILIZATION OF CRAB CAVITIES IN THE DESIGNED QBA LATTICE OF TAIWAN PHOTON SOURCE

A pair of superconducting transverse deflecting RF cavities has been studied in the QBA low emittance lattice of 3 GeV TPS for generating ultra short X-ray pulses. During numerous turns of the electron tracking, the nonlinear effects between the cavities, the energy spread, the momentum compaction factor, and the synchrotron radiation effects are taken into account. The configuration with positioning the RF deflectors between the QBA cells in each super-period as an optimum arrangement gives rise to better quality electron bunches and radiated photon pulses. The FWHM of the radiated photon pulses of about 540 fs with an acceptable intensity (70% transmission) is attained by optimizing the compression optical elements of the TPS photon beamline.
A Bayesian Significance Test for Multinomial Distributions

SUMMARY A Bayesian significance test for multinomial distributions is discussed, together with the results of 18 numerical experiments in which the test is compared with non-Bayesian methods. Several different non-Bayesian criteria are considered because the circumstances under which their tail-area probabilities can be conveniently approximated differ from one to the other. A provisional empirical formula, connecting the Bayes factors with the tailarea probabilities, is found to be correct within a factor of 6 in the 18 experiments. As a by-product, a new non-Bayesian statistic is suggested by the theory, and its asymptotic distribution obtained. It seems to be useful sometimes when chi-squared is not, although chi-squared also has a Bayesian justification for large samples. The work originated in, and is relevant to, the problem of the estimation of multinomial probabilities, but significance tests are a better proving ground for assumptions concerning the initial (prior) distribution of the physical probabilities.
Potential of Bacterial Cellulose in Reconstructive Surgery of Body Integumentary System: Preliminary Studies in Animals

The aim of the study is to present the preliminary results of the in vivo application of Komagataeibacter xylinum E25 bacterial cellulose (BC) as a replacement material for produced defects during operations. Three pigs (sus scrofa domestica) had the same defects in the ear cartilage (4 × 4 cm) and in the rectus abdominis muscle (6 × 10 cm) with BC membranes implanted into them. The time of observation of the condition of the animals was 3 months. Implantation sites did not show clinical signs of complications in the form of inflammation or necrosis. Histologically, a normal scar was produced as a result of the material healing into the host’s body. In one case, no residual implant material was found at the site of implantation, and the remodeled scar confirmed healing. No systemic inflammatory reaction was observed in any of the animals. The host organism’s reaction to the bacterial cellulose allows us to believe that it meets the expectations as a material that can be widely used in reconstructive surgery. Nevertheless, this requires further research on a larger group and also using other foreign bodies. The next step would be an experiment on a group consisting of people.
Identification of the gut microbiota affecting Salmonella pullorum and their relationship with reproductive performance in hens

Introduction Pullorum disease is one of the common bacterial infectious diseases caused by Salmonella pullorum (S. pullorum), which can result in a decrease in the reproductive performance of laying hens, thus causing considerable economic losses. However, studies about the characteristics of intestinal microbiota with pullorum and their potential association with reproductive performance in hens are still limited. This study was to identify the gut microbiota associated with S. pullorum in poultry. Methods A total of 30 hens with S. pullorum-negative (PN) and 30 hens with S. pullorum-positive (PP) were analyzed for hatching eggs laid in 2 weeks (HEL), fertilization eggs (FE), chick number (CN), and microbial structure. Results There were significant differences in HEL (p < 0.01), FE (p < 0.01), and CN (p < 0.01) between PP and PN. Histomorphological observations showed abnormal morphology of the ovaries and fallopian tubes and low integrity of epithelial tissue in the ileum and cecum in PP. 16S rRNA gene sequencing revealed that beneficial cecal microbes, such as Bacteroides, Desulfovibrio, and Megamonas, were positively correlated with reproductive performance and had lower abundance in PP (p = 0.001). Furthermore, diminished phosphotransferase system (PTS) and pentose phosphate pathway, butanoate metabolism and oxidative phosphorylation were also found in PP. Discussion Taken together, this study clarified the morphological characteristics of the reproductive tract and intestines of chickens infected with S. pullorum and preliminarily explored the potential association between cecal microbiota and reproductive performance in hens. Our data may provide a reference for revealing the intestinal microbial characteristics of hens in resisting pullorum and exploring novel approaches to infection control in future studies.
Moment Problem and Its Applications to Risk Assessment

ABSTRACT This article discusses how to assess risk by computing the best upper and lower bounds on the expected value E[φ(X)], subject to the constraints E[Xi] = μi for i = 0, 1, 2, …, n. φ(x) can take the form of the indicator function in which the bounds on are calculated and the form φ(x) = (ϕ(x) − K)+ in which the bounds on financial payments are found. We solve the moment bounds on through three methods: the semidefinite programming method, the moment-matching method, and the linear approximation method. We show that for practical purposes, these methods provide numerically equivalent results. We explore the accuracy of bounds in terms of the number of moments considered. We investigate the usefulness of the moment method by comparing the moment bounds with the “point” estimate provided by the Johnson system of distributions. In addition, we propose a simpler formulation for the unimodal bounds on compared to the existing formulations in the literature. For those problems that could be solved both analytically and numerically given the first few moments, our comparisons between the numerical and analytical results call attention to the potential differences between these two methodologies. Our analysis indicates the numerical bounds could deviate from their corresponding analytical counterparts. The accuracy of numerical bounds is sensitive to the volatility of X. The more volatile the random variable X is, the looser the numerical bounds are, compared to their closed-form solutions.
Triangular Silver Nanoplates as a Bioanalytical Tool: Potential COVID-19 Detection

Nanotechnology offers new possibilities in molecular diagnostics, with nanoparticles gaining attention as biosensor upgrades. This study evaluates gold-coated silver nanoplates coated with PEG for enhanced protection, aiming to detect Spike protein with higher sensitivity, and emphasizes the importance of considering complex environments and appropriate controls for specific binding and accurate analysis. The sensitivity of antibody-coated PEGAuTSNPs as tools for immunoassays is demonstrated through fibronectin (Fn)– anti-fibronectin binding within an isolated extracellular matrix as a complex and native environment of Fn. Moreover, the optimal functionalization volume of Spike protein was determined (4 µg/mL of PEGAuTSNP). Anti-Spike was added to confirm binding, while the TJP1 protein was used as a negative control. The same experiment was used in the presence of horse serum to simulate a complex environment. According to Localized Surface Plasmon Resonance analysis and Dynamic Light Scattering size measurements, anti-Spike exhibited a stronger affinity for the nanoplates, causing TJP1 to be replaced by the antibody on the nanoplates’ surface. Future research will involve exploring alternative complex environments, filtering larger molecules, and the optimization of immunoassay performance.
Transcriptome sequencing and functional verification revealed the roles of exogenous magnesium in tobacco anti-PVY infection

Potato virus Y (PVY) infection causes necrosis and curling of leaves, which seriously affect the yield and quality of Solanaceous crops. The roles of nutrient elements in the regulation of plant resistance to virus infection has been widely reported, while the mechanisms are poorly studied. Previous studies in our laboratory have demonstrated that foliar spraying of MgSO4 could induce Nicotiana tabacum resistance to PVY by increasing the activity of defense-related enzymes. Consistent with the results, we found that exogenous magnesium (Mg) had a certain effect on N. tabacum anti-PVY infection. Meanwhile, Illumina RNA sequencing revealed that Mg induced resistance to PVY infection was mainly by regulating carbohydrate metabolism and transportation, nitrogen metabolism, Ca2+ signal transduction and oxidative phosphorylation. Moreover, we used virus-induced gene silencing assays to verify the function of homologs of five N. tabacum genes involved in above pathways in N. benthamiana. The results showed that NbTPS and NbGBE were conducive to PVY infection, while NbPPases and NbNR were related to resistance to PVY infection. These results suggested a novel strategy for resistance to PVY infection and provided a theoretical basis for virus-resistance breeding.
Dysregulated miRNA and mRNA Expression Affect Overlapping Pathways in a Huntington’s Disease Model

Huntington’s disease (HD) is a fatal neurodegenerative disorder caused by the expansion of a CAG trinucleotide repeat in the Huntingtin gene. Transcriptional dysregulation is one of the main cellular processes affected by mutant Huntingtin (mHtt). In this study, we investigate the alterations in miRNA and mRNA expression levels in a Drosophila model of HD by RNA sequencing and assess the functional effects of misregulated miRNAs in vivo. We found that in head samples of HD flies, the level of 32 miRNAs changed significantly; half of these were upregulated, while the other half were downregulated. After comparing miRNA and mRNA expression data, we discovered similarities in the impacted molecular pathways. Additionally, we observed that the putative targets of almost all dysregulated miRNAs were overrepresented among the upregulated mRNAs. We tested the effects of overexpression of five misregulated miRNAs in the HD model and found that while mir-10 and mir-219 enhanced, mir-137, mir-305, and mir-1010 ameliorated mHtt-induced phenotypes. Based on our results, we propose that while altered expression of mir-10, mir-137, and mir-1010 might be part of HD pathology, the upregulation of mir-305 might serve as a compensatory mechanism as a response to mHtt-induced transcriptional dysregulation.
A free boundary problem involving a cusp. Part II: Local analysis

We consider a stationary free boundary problem describing the stationary flow of fresh and salt water in a porous medium. The salt water is supposed to be stagnant, while the fresh water on top of it is drawn into wells. In a previous work it has been shown, that for pumping rates Q < Q cr a solution with smooth interface exists. In this part we study the case Q = Q cr in two dimensions. We show that the interface has isolated singularities. At each singularity the free boundary develops a cusp or becomes vertical. By means of local analysis techniques we obtain the asymptotic behaviour of the free boundary at these singularities.
Microfluidic metamaterial sensor: Selective trapping and remote sensing of microparticles

We experimentally demonstrate the integration of a microfluidic trap array on top of metamaterial resonators for size selective trapping and remote sensing of microparticles. A split-ring resonator (SRR) design supports strongly confined electric field in the capacitive split gap at the fundamental inductive-capacitive resonance mode. The tightly confined electric field in the SRR gap forms a hot-spot that has become an enabling platform for sensing applications. Here, we extend the concept of metamaterial sensing to “trapping and sensing” by fabricating trapezoidal shaped structures near the split gap that enables trapping of microparticles in the split-gap region of each SRR. The proposed microfluidic metamaterial sensor enables sensing of different refractive index microparticles in terms of change in the transmitted amplitude and resonance frequency of the fundamental resonance mode operating in the terahertz spectral region. The proposed approach exploits the advantages offered by microfluidics, meta.
Influence of teaching activities, environmental conditions and class schedules on teacher stress measured with a smartwatch: a pilot study

To recognize and assess the job stressors that teachers face in daily practice is essential. One of the most used objective measures of stress is the heart rate (HR). This pilot study explored the use of a wearable device (smartwatch) to monitor the HR of two teachers over two weeks in the classroom. Educational context variables (subject, class size, timetable, activity learning performed) and environment variables (temperature, humidity, sun irradiance) were related with HR. The results showed significant differences on HR among the teachers according to the educational activity, time of the day, or day of the week. The environmental variables were related differently in each of the participants. The study showed the practical implications of using a smartwatch, or smart bracelet, in the field of education. It provides systematic data that be analyzed and linked to other variables, opening the possibility of measuring real-time stress in the classroom, as an alternative or complement to stress self-reports.
ZOMETAG: Zone-Based Memory Tagging for Fast, Deterministic Detection of Spatial Memory Violations on ARM

Against spatial memory violations threatening a vast amount of legacy software, various safety solutions have been suggested for decades. However, their practical uses have been impeded by diverse reasons, such as significant overheads and mandatory modifications of existing architectures. Accordingly, there has been a clear need for a practical safety solution that is fast enough and yet runs on commodity systems for its wide applicability in the field. As an effort to meet this need, a major processor vendor, ARM, recently announced a hardware extension, called Memory Tagging Extension (MTE), that helps engineers to implement efficient safety solutions. However, due to lack of hardware tags to isolate all data objects, MTE either resorts to a probabilistic memory safety guarantee, which is susceptible to a security loophole, or suffers from severe performance degradation to guarantee deterministic security. The aim of our work is to develop a MTE-based deterministic spatial safety solution, called ZOMETAG, with high efficiency by capitalizing on salient architectural features. Our key idea for fast, deterministic safety is to somehow assign permanently all objects unique tags throughout program execution. For this, ZOMETAG first divides the data memory into a number of small regions, called zones, and distributes data objects over the zones subject to certain constraints (to be discussed later). Then, we extend the notion of a tag in a way that each object stored with MTE tag <inline-formula> <tex-math notation="LaTeX">$t$ </tex-math></inline-formula> in zone <inline-formula> <tex-math notation="LaTeX">$z$ </tex-math></inline-formula> is uniquely assigned the zone-tag pair <<inline-formula> <tex-math notation="LaTeX">$z$ </tex-math></inline-formula>,<inline-formula> <tex-math notation="LaTeX">$t$ </tex-math></inline-formula>> as a new tag. To work with this new tag assignment, we devise a novel mechanism, called two-layer isolation, that is basically a combination of MTE-based tagging (for one-layer of isolation) with zone-based tagging (for the other) both of which collaborate together to ensure spatial safety for all objects by preventing a pointer currently assigned one zone-tag pair from erroneously referring to objects assigned different pairs. Our experimental results are quite encouraging. ZOMETAG enforces deterministic spatial safety with overheads of 35% in SPEC CPU2006 and merely of 6% in real world applications like nginx.
Altered interhemispheric functional connectivity in patients with comitant exotropia before and after surgery: a resting-state fMRI study

Purpose To assess the interhemispheric homotopic connectivity alterations in patients with comitant exotropia (CE) before and after surgery, using resting-state functional magnetic resonance imaging (rs-fMRI) with voxel-mirrored homotopic connectivity (VMHC). Methods Thirty-four patients with CE and twenty-four well-matched healthy controls (HCs) were enrolled to undergo a preoperative rs-fMRI scan. The rs-fMRI scan was performed again in twenty-four patients 1 month after surgery. The VMHC method was applied to evaluate the group differences of interhemispheric functional connectivity. The correlations between VMHC values and clinical variables were analyzed in the patient group. Results Compared with HCs, 34 patients with CE showed significantly increased VMHC values in occipital lobe (cuneus/superior occipital gyrus/middle occipital gyrus/calcarine), cerebellar area 8/cerebellar Crus1 area, and cerebellar Crus1 area. In CE group, VMHC in the cuneus was positively correlated with stereoacuity (r = 0.417, P = 0.014), meanwhile VMHC in the cerebellar Crus1 area was positively correlated with stereoacuity (r = 0.395, P = 0.021). One month after surgery, the 24 CE patients with follow-up showed decreased VMHC values in the cuneus and superior occipital gyrus compared with preoperative collection, meanwhile, non-significant difference compared with HCs. Conclusion Our study revealed the interhemispheric homotopic connectivity changes of patients with CE in the occipital lobe and cerebellum before and after surgery. The findings may provide a new perspective for the neurological alterations of CE.