Miracle-dz/UniFAR-FTUs huggingface dataset:
The subsystem quantum chemistry program Serenity

SERENITY [J Comput Chem. 2018;39:788–798] is an open‐source quantum chemistry software that provides an extensive development platform focused on quantum‐mechanical multilevel and embedding approaches. In this study, we give an overview over the developments done in Serenity since its original publication in 2018. This includes efficient electronic‐structure methods for ground states such as multilevel domain‐based local pair natural orbital coupled cluster and Møller–Plesset perturbation theory as well as the multistate frozen‐density embedding quasi‐diabatization method. For the description of excited states, SERENITY features various subsystem‐based methods such as embedding variants of coupled time‐dependent density‐functional theory, approximate second‐order coupled cluster theory and the second‐order algebraic diagrammatic construction technique as well as GW/Bethe–Salpeter equation approaches. SERENITY's modular structure allows combining these methods with density‐functional theory (DFT)‐based embedding through various practical realizations and variants of subsystem DFT including frozen‐density embedding, potential‐reconstruction techniques and projection‐based embedding.
Design of a Strong Robust Wireless Power Transfer System With Wide-Range Output Regulation Based on Dual-Band Architecture

With the continuous development of wireless power transfer (WPT) equipment in the direction of miniaturization, how to adapt the traditional sensitive Class E system to high-voltage, high-power and wide-range adjustable output occasions has become a crucial research issue. Here, compared with the other two, the difficulty of improving the system robustness under the large power fluctuation and achieving the system's wide-range output voltage regulation is much greatly. Aiming at the above difficulties, a novel dual-band system architecture based on power synthesis is proposed, the power variation of the megahertz WPT subsystem is actively compressed by the kilohertz WPT subsystem with strong robustness and the high-frequency subsystem only needs to bear relatively low power fluctuations, thereby reducing the difficulty of system design and ensuring the efficient operation. Meanwhile, compared with the traditional system, the buck circuit only needs to perform partial power regulation to achieve the wide range of voltage output. To verify the feasibility of the proposed architecture, a 200 W experimental prototype was built, with a maximum efficiency of 89%.
Compact Tri-Band Claw-Shaped Monopole Antenna for Wlan/wimax Applications

A compact microstrip-fed tri-band printed monopole antenna is presented for wireless applications in wireless local area network (WLAN) and worldwide interoperability for microwave access (WiMAX) applications simultaneously. The antenna is composed of a novel claw-shaped monopole and a modified rectangular ground plane. The three arms of the antenna generate three desired resonate frequencies and exhibit a relatively independence while being tuned separately. The antenna is simple in configuration outlining an overall size of 38 × 30 × 1.6 mm3. The measured 10 dB bandwidth for return loss is from 2.35 to 2.72, 3.34 to 3.7, and 4.81 to 6.74 GHz for WiMAX and WLAN applications. Good radiation characteristics and antenna gains for the operating bands have been obtained. Effects of varying the monopole dimensions on the antenna performance have also been studied.
WO3 Nanopores Array Modified by Au Trisoctahedral NPs: Formation, Characterization and SERS Application

The WO3 nanopores array was obtained by an anodization method in aqueous solution with addition of F- ions. Several factors affecting the final morphology of the samples were tested such as potential, time, and F- concentrations. The morphology of the formed nanopores arrays was examined by SEM microscopy. It was found that the optimal time of anodization process is in the range of 0.5–1 h. The nanopores size increased with the increasing potential. The XPS measurements do not show any contamination by F- on the surface, which is common for WOx samples formed by an anodization method. Such a layer was successfully modified by anisotropic gold trisoctahedral NPs of various sizes. The Au NPs were obtained by seed-mediated growth method. The shape and size of Au NPs was analysed by TEM microscopy and optical properties by UV-VIS spectroscopy. It was found that the WO3-Au platform has excellent SERS activity. The R6G molecules could be detected even in the range of 10−9 M.
Long-Term Spatiotemporal Variability of Whitings in Lake Geneva from Multispectral Remote Sensing and Machine Learning

Whiting events are massive calcite precipitation events turning hardwater lake waters to a milky turquoise color. Herein, we use a multispectral remote sensing approach to describe the spatial and temporal occurrences of whitings in Lake Geneva from 2013 to 2021. Landsat-8, Sentinel-2, and Sentinel-3 sensors are combined to derive the AreaBGR index and identify whitings using appropriate filters. 95% of the detected whitings are located in the northeastern part of the lake and occur in a highly reproducible environmental setting. An extended time series of whitings in the last 60 years is reconstructed from a random forest algorithm and analyzed through a Bayesian decomposition for annual and seasonal trends. The annual number of whiting days between 1958 and 2021 does not follow any particular monotonic trend. The inter-annual changes of whiting occurrences significantly correlate to the Western Mediterranean Oscillation Index. Spring whitings have increased since 2000 and significantly follow the Atlantic Multidecadal Oscillation index. Future climate change in the Mediterranean Sea and the Atlantic Ocean could induce more variable and earlier whiting events in Lake Geneva.
Data-Driven Version of Neyman's Smooth Test of Fit

Abstract Neyman's smooth test for testing uniformity is a recognized goodness-of-fit procedure. As stated by LaRiccia, the test can be viewed as a compromise between omnibus test procedures, with generally low power in all directions, and procedures whose power is focused in the direction of a specific alternative. The basic idea behind this test is to embed the null density into, say, a k-dimensional exponential family and then to construct an asymptotically optimal test for the parametric testing problem. The resulting procedure is Neyman's test with k components. The most difficult problem related with using this test is the choice of k. Recommendations in statistical literature are sometimes confusing. Some authors advocate a small number of components, whereas others show that in some situations a larger number of components is profitable. All existing suggestions concerning how to select k exploit in fact some preliminary knowledge about a possible alternative. In this article, a new data-driven met.
A self-organizing cluster process

The state of the self-organizing cluster process is a (cid:12)nite subset of points in a bounded region. This subset represents an evolving discrete approximation to a continuous probability distribution in the region. The dynamics of the process is determined by an independent sequence of random points in the region chosen according to the distribution. At each time step the random point attracts the nearest point in the (cid:12)nite set. In this way the subset learns to approximate its environment. It is shown that initial states approach each other exponentially fast for all time with probability one. Thus all memory of the initial state is lost; the environment alone determines future history.
Preterm infants at low risk for early-onset sepsis differ in early fecal microbiome assembly

ABSTRACT Antibiotics are administered near-universally to very low birth weight (VLBW) infants after birth for suspected early-onset sepsis (EOS). We previously identified a phenotypic group of VLBW infants, referred to as low-risk for EOS (LRE), whose risk of EOS is low enough to avoid routine antibiotic initiation. In this cohort study, we compared 18 such infants with 30 infants categorized as non-LRE to determine if the lower risk of pathogen transmission at birth is accompanied by differences in microbiome acquisition and development. We did shotgun metagenomic sequencing of 361 fecal samples obtained serially. LRE infants had a higher human-to-bacterial DNA ratio than non-LRE infants in fecal samples on days 1–3 after birth, confirming lower bacterial acquisition among LRE infants. The microbial diversity and composition in samples from days 4–7 differed between the groups with a predominance of Staphylococcus epidermidis in LRE infants and Enterobacteriaceae sp. in non-LRE infants. Compositional differences were congruent with the distribution of virulence factors and antibiotic resistant genes. After the first week, the overall composition was similar, but changes in relative abundance for several taxa with increasing age differed between groups. Of the nine late-onset bacteremia episodes, eight occurred in non-LRE infants. Species isolated from the blood culture was detected in the pre-antibiotic fecal samples of the infant for all episodes, though these species were also found in infants without bacteremia. In conclusion, LRE infants present a distinct pattern of microbiome development that is aligned with their low risk for EOS. Further investigation to determine the impact of these differences on later outcomes such as late-onset bacteremia is warranted.
Significance of Basal Membrane Permeability of Epithelial Cells in Predicting Intestinal Drug Absorption

Drug absorption from the gastrointestinal tract is often restricted by efflux transport by P-glycoprotein (P-gp) and metabolism by CYP3A4. Both localize in the epithelial cells, and thus, their activities are directly affected by the intracellular drug concentration, which should be regulated by the ratio of permeability between apical (A) and basal (B) membranes. In this study, using Caco-2 cells with forced expression of CYP3A4, we assessed the transcellular permeation of A-to-B and B-to-A directions and the efflux from the preloaded cells to both sides of 12 representative P-gp or CYP3A4 substrate drugs and obtained the parameters for permeabilities, transport, metabolism, and unbound fraction in the enterocytes (fent) using simultaneous and dynamic model analysis. The membrane permeability ratios for B to A (RBA) and fent varied by 8.8-fold and by more than 3000-fold, respectively, among the drugs. The RBA values for digoxin, repaglinide, fexofenadine, and atorvastatin were greater than 1.0 (3.44, 2.39, 2.27, and 1.90, respectively) in the presence of a P-gp inhibitor, thus suggesting the potential involvement of transporters in the B membrane. The Michaelis constant for quinidine for P-gp transport was 0.077 µM for the intracellular unbound concentration. These parameters were used to predict overall intestinal availability (FAFG) by applying an intestinal pharmacokinetic model, advanced translocation model (ATOM), in which permeability of A and B membranes accounted separately. The model predicted changes in the absorption location for P-gp substrates according to its inhibition, and FAFG values of 10 of 12 drugs, including quinidine at varying doses, were explained appropriately. SIGNIFICANCE STATEMENT Pharmacokinetics has improved predictability by identifying the molecular entities of metabolism and transport and by using mathematical models to appropriately describe drug concentrations at the locations where they act. However, analyses of intestinal absorption so far have not been able to accurately consider the concentrations in the epithelial cells where P-glycoprotein and CYP3A4 exert effects. In this study, the limitation was removed by measuring the apical and basal membrane permeability separately and then analyzing these values using new appropriate models.
On the rationality homotopy type of configuration spaces

In this article we prove that the rational homotopy type of the configuration space of n distinct points on a smooth projective variety X over C is determined by the rational cohomology ring of X together with its canonical orientation class. This strengthens a previous result of Fulton and MacPherson [FM] (see previous issue in this volume). A few words are due on the history of differential graded algebras. By a DGA we shall mean a graded-commutative differential graded algebra. Fulton and MacPherson [FM] gave a model F(n) for the space F(X, n) by resolving the singularities of the inclusion F(X, n) C Xn and using a result of Morgan [M] on the rational homotopy type of smooth quasiprojective varieties over C. Surprisingly the DGA F(n) depended not only on H*X and its orientation class, but also on the Chern classes of X. Fulton suggested that one should be able to find another explicit model of F(X, n) independent of Chern classes. The DGA used here, E(n), was found independently by the author and by Totaro [T]. Totaro's idea was to study the Leray spectral sequence of the inclusion F(X, n) C Xn. By a weight-filtration argument he showed that the only nontrivial differential in this spectral sequence is d2m. The E2 term with the differential d2m is isomorphic to E(n). Thus, by a result of Deligne [D2], H*E(n) ' H*F(X, n) as rings. Finally the relations (1)-(3) of Theorem 1.2 are much older than any of the results mentioned above. They were discovered by F. Cohen [C] (see also [CLMa]) in the study of configuration spaces of IR'. What happens could be described by saying that H*F(X, n) for a smooth projective variety X is related to H*F(lR2m, n) in the "simplest possible way. "
Metric-Based Mathematical Derivation of Efficient Airfoil Design Variables

Within an aerodynamic shape optimization framework, an efficient shape parameterization and deformation scheme is critical to allow flexible deformation of the surface with the maximum possible design space coverage. Numerous approaches have been developed for the geometric representation of airfoils. A fundamental approach is considered here from the geometric perspective; and a method is presented to allow the derivation of efficient, generic, and orthogonal airfoil geometric design variables. This is achieved by the mathematical decomposition of a training library. The resulting geometric modes are independent of a parameterization scheme, surface and volume mesh, and flow solver; thus, they are generally applicable. However, these modes are dependent on the training library, and so a benchmark performance measure, called the airfoil technology factor, has also been incorporated into the scheme to allow intelligent metric-based filtering, or design space reduction, of the training library to ensure eff.
Repeated evolution of blanched coloration in a lizard across independent white‐sand habitats

Abstract The White Sands lizards of New Mexico are a rare and classic example of convergent evolution where three species have evolved blanched coloration on the white gypsum dunes. Until now, no geological replicate of the pattern had been described. However, one of the White Sands species, the lesser earless lizard (Holbrookia maculata), has been discovered to also inhabit the Salt Basin Dunes of Texas, where it has also evolved a blanched morph. We here present a first phenotypic and genetic description of the Salt Basin Dunes population of H. maculata. Phylogenetic inference based on a housekeeping gene (ND4) and a classic candidate gene in the melanin‐synthesis pathway (Melanocortin 1 Receptor; Mc1r) shows the newly discovered population as an independent lineage, with no evidence of genetic parallelism in the coding region of Mc1r. Initial morphological data suggest that while this population displays convergent evolution in blanched coloration, there are divergent patterns in limb length and habitat use behavior between the gypsum environments. Our findings present the White Sands/Salt Basin Dunes as an exceptionally promising comparative model for studies of adaptation and convergent evolution.
Kinetic modulation of bacterial hydrolases by microbial community structure in coastal waters

Abstract In this study, we hypothesized that shifts in the kinetic parameters of extracellular hydrolytic enzymes may occur as a consequence of seasonal environmental disturbances and would reflect the level of adaptation of the bacterial community to the organic matter of the ecosystem. We measured the activities of enzymes that play a key role in the bacterial growth (leucine aminopeptidase, β‐ and α‐glucosidases) in surface coastal waters of the Eastern Cantabrian Sea and determined their kinetic parameters by computing kinetic models of distinct complexity. Our results revealed the existence of two clearly distinct enzymatic systems operating at different substrate concentrations: a high‐affinity system prevailing at low substrate concentrations and a low‐affinity system characteristic of high substrate concentrations. These findings could be the result of distinct functional bacterial assemblages growing concurrently under sharp gradients of high‐molecular‐weight compounds. We constructed an ecological network based on contemporaneous and time‐delayed correlations to explore the associations between the kinetic parameters and the environmental variables. The analysis revealed that the recurring phytoplankton blooms registered throughout the seasonal cycle trigger the wax and wane of those members of the bacterial community able to synthesize and secrete specific enzymes.
Biocidal Activity of Tannic Acid-Prepared Silver Nanoparticles towards Pathogens Isolated from Patients with Exacerbations of Chronic Rhinosinusitis

The microbiome’s significance in chronic rhinosinusitis (CRS) is unclear. Antimicrobials are recommended in acute exacerbations of the disease (AECRS). Increasing rates of antibiotic resistance have stimulated research on alternative therapeutic options, including silver nanoparticles (AgNPs). However, there are concerns regarding the safety of silver administration. The aim of this study was to assess the biological activity of tannic acid-prepared AgNPs (TA-AgNPs) towards sinonasal pathogens and nasal epithelial cells (HNEpC). The minimal inhibitory concentration (MIC) for pathogens isolated from patients with AECRS was approximated using the well diffusion method. The cytotoxicity of TA-AgNPswas evaluated using an MTT assay and trypan blue exclusion. A total of 48 clinical isolates and 4 reference strains were included in the study (Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Klebsiellaoxytoca, Acinetobacter baumannii, Serratia marcescens, Enterobacter cloacae). The results of the studies revealed that the MIC values differed between isolates, even within the same species. All the isolates were sensitive to TA-AgNPs in concentrations non-toxic to human cells during 24 h exposition. However, 48 h exposure to TA-AgNPs increased toxicity to HNEpC, narrowing their therapeutic window and enabling 19% of pathogens to resist the TA-AgNPs’ biocidal action. It was concluded that TA-AgNPs are non-toxic for the investigated eukaryotic cells after short-term exposure and effective against most pathogens isolated from patients with AECRS, but sensitivity testing may be necessary before application.
Analysis of Repeated Categorical Measurements with Conditional Likelihood Methods

Abstract This article presents a method for analyzing repeated measures with categorical responses based on maximizing a conditional likelihood. Many existing methods for analyzing repeated categorical responses, such as those proposed by Duncan (1980, 1985), Bishop, Fienberg, and Holland (1975), and Cochran (1950) are special cases of the method based on the conditional likelihood approach. This article explores the relationships among the various methods and extends several of the existing methods. The conditional likelihood approach is used to analyze data from a four-wave panel study with trichotomous responses. The data, taken from Fienberg, Bromet, Follmann, Lambert, and May (1985), are from an investigation of the psychological effects of the accident at the Three Mile Island nuclear power plant in the spring of 1979. In this example, methods are presented for checking the assumption of local independence in the model used for the conditional likelihood analysis. With an extension of the results of.
A Comparative Study of Generalized Coordinates for Solving the Inverse- Kinematics Problem of a 6R Robot Manipulator

This paper studies two different approaches to the inverse- kinematics problem for a six-degree-of-freedom robot manip ulator having three revolute joint axes intersecting at the wrist. One method uses three rotational generalized coordi nates to describe the orientation of the body. The other method uses equivalent Euler parameters with one constraint equation. These two approaches have been incorporated into two different computer algorithms, and the results from each are compared on the basis of computational complexity, time simulation, singularity, etc. It was found that Euler parame ters were less efficient than three rotational angles for solving the inverse-kinematics problem of the robot considered, and that the physical singularities caused by the robot mecha nism could not be eliminated by using either of the two ap proaches.
MXene-Based Ink Design for Printed Applications

MXenes are a class of two-dimensional nanomaterials with a rich chemistry, hydrophilic surface and mechano-ceramic nature, and have been employed in a wide variety of applications ranging from medical and sensing devises to electronics, supercapacitors, electromagnetic shielding, and environmental applications, to name a few. To date, the main focus has mostly been paid to studying the chemical and physical properties of MXenes and MXene-based hybrids, while relatively less attention has been paid to the optimal application forms of these materials. It has been frequently observed that MXenes show great potential as inks when dispersed in solution. The present paper aims to comprehensively review the recent knowledge about the properties, applications and future horizon of inks based on 2D MXene sheets. In terms of the layout of the current paper, 2D MXenes have briefly been presented and followed by introducing the formulation of MXene inks, the process of turning MAX to MXene, and ink compositions and preparations. The chemical, tribological and rheological properties have been deeply discussed with an eye to the recent developments of the MXene inks in energy, health and sensing applications. The review ends with a summary of research pitfalls, challenges, and future directions in this area.
An Adequate Dispersive Wave Scheme for Tsunami Simulation

In tsunami research, dispersive wave theory is used to numerically simulate transoceanic and near-field propagation by soliton fission. Many numerical schemes have been proposed to solve the dispersive wave effect, but there has been no reliable criterion for selecting an adequate scheme. To address this, we derive exact numerical stability solutions to the linear finite difference equations of dispersive wave theory by using several numerical methods. Characteristics of the truncation error and the numerical stability of the methods are discussed, and the leap-frog implicit scheme appears to be applicable to practical problems due to its superior stability. A new numerical model that uses an implicit scheme is proposed based on the above results. The dispersive term in the equation of motion is solved by a Poisson-type differential equation and the model can be extended to the nonlinear physics. This model is validated by being compared to the conventional models, and it is applied to a Tonankai-Nankai tsunami as an example of a practical problem. The model shows excellent agreement with both the linear analytical solution and the laboratory experiments. Furthermore, the solutions to this model require less computing time than those of the conventional models.