Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure of an In Situ Phosphorus-Doped Silicon Ultrathin Film Analyzed Using Second Harmonic Generation and Simplified Bond-Hyperpolarizability Model

In fabricating advanced silicon (Si)-based metal–oxide semiconductors, the ability to inspect dopant distribution in Si ultrathin films (tens of nm) is crucial for monitoring the amount of dopant diffusion. Here, we perform an anisotropic reflective second harmonic generation (SHG) measurement to demonstrate the sensitivity of SHG to phosphorus (P) concentration within the range of 2.5×1017 to 1.6×1020 atoms/cm3. In addition, we propose an analysis method based on a simplified bond-hyperpolarizability model to interpret the results. The bond vector model that corresponds to the P vacancy clusters is built to calculate the SHG contribution from substitutionally incorporated P atoms. The effect of incorporating P into the Si lattice is reflected in the effective hyperpolarizability, lattice tilt, and deformation of this model. The fitting results of the intuitively defined coefficients exhibit a high correlation to the P concentration, indicating the potential of this model to resolve the properties in complex material compositions. Finally, a comparison with Fourier analysis is made to evaluate the advantages and disadvantages of this model. Combined anisotropic reflective SHG (Ani-RSHG) and the simplified bond-hyperpolarizability model (SBHM) can analyze the crystal structure of doped ultrathin films and provide a non-destructive nanophotonic way for in-line inspection.
Promising therapeutic potential of tumor suppressor microRNAs for malignant pleural mesothelioma

Malignant pleural mesothelioma (MPM) is an aggressive and recalcitrant surface neoplasm that defies current multimodality treatments. MicroRNAs (miRNAs) are small noncoding RNAs that epigenetically regulate multiple gene networks and cellular processes. In cancer, miRNA dysregulation is associated with tumorigenesis, with tumor suppressor miRNAs underexpressed or lost, while oncogenic miRNAs are overexpressed. Consequently, miRNAs have emerged as potential therapeutic candidates. Because loss of tumor suppressors predominates the pathophysiology of MPM, re-expressing tumor suppressor miRNAs could be an effective therapeutic strategy. This review highlights the most promising MPM-specific tumor suppressor miRNAs that could be developed into novel therapeutics, the supporting data, and what is known about their molecular mechanism(s).
The Emerging Roles of Extracellular Chaperones in Complement Regulation

The immune system is essential to protect organisms from internal and external threats. The rapidly acting, non-specific innate immune system includes complement, which initiates an inflammatory cascade and can form pores in the membranes of target cells to induce cell lysis. Regulation of protein homeostasis (proteostasis) is essential for normal cellular and organismal function, and has been implicated in processes controlling immunity and infection. Chaperones are key players in maintaining proteostasis in both the intra- and extracellular environments. Whilst intracellular proteostasis is well-characterised, the role of constitutively secreted extracellular chaperones (ECs) is less well understood. ECs may interact with invading pathogens, and elements of the subsequent immune response, including the complement pathway. Both ECs and complement can influence the progression of neurodegenerative diseases, including Alzheimer’s disease, Parkinson’s disease, Huntington’s disease and amyotrophic lateral sclerosis, as well as other diseases including kidney diseases and diabetes. This review will examine known and recently discovered ECs, and their roles in immunity, with a specific focus on the complement pathway.
Sampled-Data Output Feedback Leader-Following Scaled Consensus for Uncertain Nonlinear Multiagent Systems With Communication Delays and Noises

Communication delays and noises are common in practical problems. When they exist in the nonlinear multiagent system, this article addresses the leader-following scaled consensus problem. In the concerned system, nonlinearities can contain uncertainty and essential time-varying characteristic, and the output information is only available at sampling instants. In this article, we propose a class of time-varying gains to design the delay-dependent observer and control protocol, where a newly defined variable is used to cope with unknown noises. Under the output feedback control protocol, followers can asymptotically track the leader by assigned ratios. Different from existing works, the sampling period, communication delays, and noises are not restricted to a fixed upper bound. Two simulation examples are eventually presented to show the effectiveness of the proposed control protocol. Some future works can extend to general nonlinear systems with communication noises, and different time-varying delays.
A 3D posteriori error estimator for FEM solution of electromagnetic problems

We introduce a new method for computing a posteriori error estimator suitable for the finite‐element solution of 3D electromagnetic problems. We take into account both the error due to discontinuity on the elements' faces as well as the volumetric error. We demonstrate the efficiency of the error estimator. © 2003 Wiley Periodicals, Inc. Microwave Opt Technol Lett 36: 300–302, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10748
Integral sliding mode in systems operating under uncertainty conditions

The paper generalized a new sliding mode design concept, namely integral sliding mode (ISM). The order of the motion equation in ISM is equal to the order of the original system, rather than reduced by the number of dimension of the control input. As the result, robustness of the system can be guaranteed throughout an entire response of the system starting from the initial time instance. Uniform formulations of the ISM design principle are developed in the paper. It is shown through examples that our generalized ISM scheme enables a wide scope of application areas. In the case that the given control matrix can not be used directly for generating the sliding mode, the associated decoupling problem was also discussed based on the concept of sliding mode transformation. To alleviate chattering, we remove the discontinuous control action from the real control path and insert it to an internal dynamic process for generating the sliding mode.
Parametric Amplification of Magnetosonic Waves by an External, Transversal, Periodic Action

The influence of an external, transversal, periodic force on the local dynamics of magnetosonic waves is studied. We show that periodic, transversal plasma motions generated by this force lead to a periodical drift of the wavevector of the spatial Fourier harmonics in the local frame and, as a result, their amplitude is governed by Mathieu's equation. Thus, those harmonics with half the frequency of the external force have an exponential growth, and in consequence the energy of transversal oscillations can be transformed into the energy of magnetosonic waves. Some of the many applications of this mechanism to different astrophysical situations are discussed.
Inhibitory Effects of Pepper Mild Mottle Virus Infection by Supernatants of Five Bacterial Cultures in Capsicum annuum L.

Pepper mild mottle virus (PMMoV), one of the most prevalent viruses in chili pepper (Capsicum annuum L.) is a non-enveloped, rod-shaped, single-stranded positive-sense RNA virus classified in the genus Tobamovirus. The supernatants of five bacterial cultures (Pseudomonas putida [PP], Bacillus licheniformis [BLI], P. fluorescens [PF], Serratia marcescens [SER], and B. amyloliquifaciens [BA]) were analyzed to find novel antiviral agents to PMMoV in chili pepper. Foliar spraying with supernatants (1:1, v/v) obtained from Luria-Bertani broth cultures of PP, BLI, PF, SER, and BA inhibited PMMoV infection of chili pepper if applied before the PMMoV inoculation. Double-antibody sandwich enzyme-linked immunosorbent assay showed that treatments of five supernatants resulted in 51–66% reductions in PMMoV accumulation in the treated chili pepper. To identify key compounds in supernatants of PP, BLI, PF, SER, and BA, the supernatants were subjected to gas chromatography-mass spectrometry. The 24 different types of compounds were identified from the supernatants of PP, BLI, PF, SER, and BA. The compounds vary from supernatants of one bacterial culture to another which includes simple compounds—alkanes, ketones, alcohols, and an aromatic ring containing compounds. The compounds triggered the inhibitory effect on PMMoV propagation in chili pepper plants. In conclusion, the cultures could be used to further conduct tissue culture and field trial experiments as potential bio-control agents.
The Challenges of Modeling Defect Behavior and Plasticity across Spatial and Temporal Scales: A Case Study of Metal Bilayer Impact

Atomistic molecular dynamics (MD) and a microstructural dislocation density-based crystalline plasticity (DCP) framework were used together across time scales varying from picoseconds to nanoseconds and length scales spanning from angstroms to micrometers to model a buried copper–nickel interface subjected to high strain rates. The nucleation and evolution of defects, such as dislocations and stacking faults, as well as large inelastic strain accumulations and wave-induced stress reflections were physically represented in both approaches. Both methods showed similar qualitative behavior, such as defects originating along the impactor edges, a dominance of Shockley partial dislocations, and non-continuous dislocation distributions across the buried interface. The favorable comparison between methods justifies assumptions used in both, to model phenomena, such as the nucleation and interactions of single defects and partials with reflected tensile waves, based on MD predictions, which are consistent with the evolution of perfect and partial dislocation densities as predicted by DCP. This substantiates how the nanoscale as modeled by MD is representative of microstructural behavior as modeled by DCP.
Radiation background simulation and verification at the LHC: Examples from the ATLAS experiment and its upgrades

The high collision rates at the new energy and luminosity regime of the Large Hadron Collider (LHC) gives rise to unprecedented radiation environments, especially in the inner regions of the experiments. High fidelity particle transport codes such as FLUKA and GEANT4 are necessary for simulating the complex radiation environments in detail. The results are used for predicting detector system behaviour and performance over the lifetime of the project. In this paper the Monte Carlo tools used to simulate the radiation backgrounds are discussed and examples of the predictions in the ATLAS inner detector regions are shown. Also presented are the results of verification studies in which the fluence and dose predictions are compared with measurements using recent LHC data. It is shown that the level of agreement has exceeded expectations, with differences typically less than 30%, and always smaller than a factor of two. Finally, the radiation background situation for the ATLAS inner tracker at the future high luminosity upgrade of the LHC (HL-LHC) is discussed, as well as a simple parameterisation of silicon damage fluences to cover all collision energies.
Differences in color between early gastric cancer and cancer-suspected non-cancerous mucosa on linked color imaging

Abstract Background and study aims Linked color imaging (LCI) can enhance the original color of each area and may useful to detect tumorous lesions during esophagogastroduodenoscopy. However, LCI may also enhance cancer-suspected non-cancerous regional color change. We conducted a retrospective image analysis to investigate the color characteristics of early gastric cancer (EGC) and cancer-suspected non-cancerous mucosa (CSM) in LCI. Methods LCI images of both EGC and CSM were retrospectively collected from the database of the institution. Fifteen endoscopists individually judged each image as EGC or CSM. The color difference between the inside and outside of the lesions was measured by CIE-Lab analysis in both groups and compared. Results A total of 245 LCI images of EGC (169) and CSM (76) were extracted and randomly lined for image collection. The test by the endoscopists showed accuracy, sensitivity, and specificity of 64.0 %, 63.7 %, and 64.0 %, respectively. Although the color difference between EGC and CSM was almost the same (12.5 vs. 12.9, not significant), each parameter of ΔL (bright: –0.3 vs. –2.7, P < 0.001), Δa (Reddish: 7.2 vs. 9.6, P = 0.004), and Δb (Yellowish: 6.4 vs. 3.8, P < 0.001) was significantly different in the groups. The color feature of both positive ΔL and Δb to EGC showed accuracy, sensitivity, and specificity of 54.7 %, 39.6 %, 88.2%, respectively. Conclusions The total color difference was almost the same between EGC and CSM; however, their color tones were different on linked color imaging. Although the color characteristics of EGC had high specificity, they also had low sensitivity.
A three-dimensional solution of flows over wings with leading-edge vortex separation

The application of a new, general, potential flow computational technique to the solution of the subsonic, three-dimensional flow over wings with leading-edge vortex separation is presented. The present method is capable of predicting forces, moments, and detailed surface pressures on thin, sharp-edged wings of rather arbitrary planform. The wing geometry is arbitrary in the sense that leading and trailing edges may be curved or kinked and the wing may have arbitrary camber and twist. The method employs an inviscid flow model in which the wing, the rolled-up vortex sheets, and the wake are represented by piecewise continuous quadratic doublet sheet distributions. The Kutta condition is imposed along all wing edges. Strengths of the doublet distributions as well as shape and position of the free fortex sheet spirals are computed in iterative fashion starting with an assumed initial sheet geometry. The method is verified by numerous computed results.
Electron cyclotron emission temperature fluctuations associated with magnetic islands and real-time identification and control system

An important focus of the present research on thermonuclear fusion based on magnetic confinement is the control of rotating magnetic islands of low helical mode numbers m, n that are the nonlinear stage of resistive instabilities developing at magnetic surfaces where q = m/n. These perturbations are often driven by external resonant ‘error fields’ or mode coupling effects and maintained by local distortions of the current profile. The islands can be reduced in width or completely suppressed by a current driven by electron cyclotron waves accurately located within the island. A requisite for an effective control action is the ability to identify the relevant state variables (radial location, island amplitude, frequency and phase) in ‘real time’ and vary accordingly the control variables (wave beam power modulation and direction). Traditionally magnetohydrodynamic instabilities are monitored by external magnetic signals that however give no information about the radial location of the perturbation within the plasma. Here we describe the design of a real-time diagnostics/control device using an original algorithm for processing electron cyclotron emission signals to monitor temperature fluctuations and EC wave power deposition.
Quantitative Aspect of Bacillus subtilis σB Regulatory Network—A Computational Simulation

Simple Summary A kinetic, ordinary differential equation model of regulation of sigma factor σB of Bacillus subtilis is presented. The model was derived from chemical equations describing interactions among σB, its anti-sigma and anti-anti-sigma factors RsbW, RsbV and phosphatases RsbU, RsbP which transmit environmental signals. The model uses experimental time series of gene expression which allowed to model the response of the system to the changes of its parameters using real expression data. Abstract Bacillus subtilis is a model organism used to study molecular processes in prokaryotic cells. Sigma factor B, which associates with RNA polymerase, is one of the transcriptional regulators involved in the cell’s response to environmental stress. This study addresses the key question of how the levels of free SigB, which acts as the actual regulator of gene expression, are controlled. A set of chemical equations describing the network controlling the levels of free SigB was designed, leading to a set of differential equations quantifying the dynamics of the network. Utilizing a microarray-measured gene expression time series then allowed the simulation of the kinetic behavior of the network in real conditions and investigation of the role of phosphatases RsbU/RsbP transmitting the environmental signal and controlling the amounts of free SigB. Moreover, the role of kinetic constants controlling the formation of the molecular complexes, which consequently influence the amount of free SigB, was investigated. The simulation showed that although the total amount of sigma B is relatively high in the unstressed population, the amount of free SigB, which actually controls its regulon, is quite low. The simulation also allowed determination of the proportion of all the network members that were free or bound in complexes. While previously the qualitative features of B. subtilis SigB have been studied in detail, the kinetics of the network have mostly been ignored. In summary, the computational results based on experimental data provide a quantitative insight into the functioning of the SigB-dependent circuit and provide a roadmap for its further exploration in this industrially important bacterium.
What potential for improving sub‐seasonal predictions of the winter NAO?

The North Atlantic Oscillation (NAO) is the leading mode of variability across the Atlantic sector and is a key metric of extratropical forecast performance. Skilful predictions of the NAO are possible at medium‐range (1–2 weeks) and seasonal time scales. However, in a leading dynamical prediction system, we find that sub‐seasonal predictions (1 month NAO with a lead time of 20–30 days) are not statistically significant and represent a gap in forecast skill. In this study, we have investigated the potential for improving predictions using a large ensemble of dynamical hindcasts. First, we find that monthly predictions of the NAO are only weakly related to forecast errors at the medium‐range. This implies that improving medium‐range forecast performance is unlikely to drive significant improvements at longer lead times. Second, the Madden‐Julian Oscillation (MJO) is the leading mode of sub‐seasonal variability in the Tropics and projects onto the NAO with a lag of 10–15 days, but its teleconnection is only partially represented in current forecast systems. We, therefore, assess whether improved MJO‐NAO teleconnections are likely to lead to improved monthly NAO predictions. We find that even perfect MJO forecasts and teleconnections lead to only small improvements in NAO prediction skills. This work indicates that monthly timescales may represent a predictability gap for the NAO and hence the Euro‐Atlantic winter climate in which genuine skill improvements are difficult to achieve. Potential progress in this area could stem from currently unknown sources of skill and large initialised climate ensembles will be a vital tool for investigating these.
Study of a single-photon detector blinding attack with modulated bright light

In this paper, we present the research of the blinding attack on single photon avalanche diodes (SPAD) based on InGaAs structure which is used in quantum key distribution systems with modulated laser radiation. One of the variants of this attack is using continuous wave (CW) light but there is protection from it like monitoring of SPAD’s current. Thus, we use modulated CW radiations. Modulation allows us to establish parameters of blinding pulses. We studied the dependencies of the detector’s bias current on blinding pulse energy using different widths of light pulses in the range from 4ns to 20 ns than we applied various repetition rates which are 10 MHz, 5 MHz, 2.5 MHz, and 1MHz. Even we investigate this dependence using the not rectangular shape of pulses on repetition rates mentioned above.
Potential Novel N-Glycosylation Patterns Associated with the Emergence of New Genetic Variants of PRRSV-2 in the U.S

Glycosylation of proteins is a post-translational process where oligosaccharides are attached to proteins, potentially altering their folding, epitope availability, and immune recognition. In Porcine reproductive and respiratory syndrome virus-type 2 (PRRSV-2), positive selection pressure acts on amino acid sites potentially associated with immune escape through glycan shielding. Here, we describe the patterns of potential N-glycosylation sites over time and across different phylogenetic lineages of PRRSV-2 to better understand how these may contribute to patterns of coexistence and emergence of different lineages. We screened 19,179 PRRSV GP5 sequences (2004–2021) in silico for potential N-glycosylated sites. The emergence of novel combinations of N-glycosylated sites coincided with past PRRSV epidemics in the U.S. For lineage L1A, glycosylation at residues 32, 33, 44, 51, and 57 first appeared in 2012, but represented >62% of all L1A sequences by 2015, coinciding with the emergence of the L1A 1-7-4 strain that increased in prevalence from 8 to 86% of all L1A sequences from 2012 to 2015. The L1C 1-4-4 strain that emerged in 2020 also had a distinct N-glycosylation pattern (residues 32, 33, 44, and 51). From 2020 to 2021, this pattern was responsible for 44–47% of the L1C sequences, contrasting to <5% in years prior. Our findings support the hypothesis that antigenic evolution contributes to the sequential dominance of different PRRSV strains and that N-glycosylation patterns may partially account for antigenic differences amongst strains. Further studies on glycosylation and its effect on PRRSV GP5 folding are needed to further understand how glycosylation patterns shape PRRSV occurrence.
Tests for the exponential, Weibull and Gumbel distributions based on the stabilized probability plot

Goodness-of-fit procedures for composite testing of the exponential, Weibull and Gumbel distributions are investigated. These procedures are such that they can be used graphically with, and to aid interpretation of, probability plots. In the situations of interest here, the new procedure is generally more powerful than the KolmogorovSmirnov test, which appears to be the only other readily available goodness-of-fit procedure that can be used graphically with probability plots.
Beam manipulation and acceleration with Dielectric-Lined Waveguides

BEAM MANIPULATION AND ACCELERATION WITH DIELECTRIC-LINED WAVEGUIDES François Lemery, Ph.D. Department of Physics Northern Illinois University, 2015 Philippe Piot, Director The development of next-generation TeV+ electron accelerators will require either immense footprints based on conventional acceleraton techniques or the development of new higher–gradient acceleration methods. One possible alternative is beam-driven acceleration in a high-impedance medium such as a dielectric-lined-waveguide (DLW), where a highcharge bunch passes through a DLW and can excite gradients on the order of GV/m. An important characteristic of this acceleration class is the transformer ratio which characterizes the energy transfer of the scheme. This dissertation discusses alternative methods to improve the transformer ratio for beam-driven acceleration and also considers the use of DLWs for beam manipulation at low energy. NORTHERN ILLINOIS UNIVERSITY DE KALB, ILLINOIS