Miracle-dz/UniFAR-FTUs huggingface dataset:
Prophage-Derived Regions in Curtobacterium Genomes: Good Things, Small Packages

Curtobacterium is a genus of Gram-positive bacteria within the order Actinomycetales. Some Curtobacterium species (C. flaccumfaciens, C. plantarum) are harmful pathogens of agricultural crops such as soybean, dry beans, peas, sugar beet and beetroot, which occur throughout the world. Bacteriophages (bacterial viruses) are considered to be potential curative agents to control the spread of harmful bacteria. Temperate bacteriophages integrate their genomes into bacterial chromosomes (prophages), sometimes substantially influencing bacterial lifestyle and pathogenicity. About 200 publicly available genomes of Curtobacterium species, including environmental metagenomic sequences, were inspected for the presence of sequences of possible prophage origin using bioinformatic methods. The comparison of the search results with several ubiquitous bacterial groups showed the relatively low level of the presence of prophage traces in Curtobacterium genomes. Genomic and phylogenetic analyses were undertaken for the evaluation of the evolutionary and taxonomic positioning of predicted prophages. The analyses indicated the relatedness of Curtobacterium prophage-derived sequences with temperate actinophages of siphoviral morphology. In most cases, the predicted prophages can represent novel phage taxa not described previously. One of the predicted temperate phages was induced from the Curtobacterium genome. Bioinformatic analysis of the modelled proteins encoded in prophage-derived regions led to the discovery of some 100 putative glycopolymer-degrading enzymes that contained enzymatic domains with predicted cell-wall- and cell-envelope-degrading activity; these included glycosidases and peptidases. These proteins can be considered for the experimental design of new antibacterials against Curtobacterium phytopathogens.
Diabatic states of a photoexcited retinal chromophore from ab initio many-body perturbation theory

We investigate the diabatic electronic states of a photoexcited molecule within a diabatization method originally proposed by Baer [Chem. Phys. Lett. 35, 112 (1975)]. A diabatization denotes a unitary transformation which allows for incorporating nonadiabatic effects into the quantum Hamiltonian, expressed in the adiabatic representation. A typical example is the treatment of avoided crossings in the potential-energy surface, for instance, in the case of the retinal chromophore. In this paper, we present analytical and numerical calculations for the diabatic states in the context of Green's-function-based ab initio many-body perturbation theory (density-functional theory plus GW method plus Bethe-Salpeter equation). We present the calculation of the adiabatic and diabatic lowest excited electronic states of the retinal chromophore molecule.
Marangoni convection and heat transfer in thin liquid films on heated walls with topography: Experiments and numerical study

Thermocapillary-induced motion in thin liquid films on a heated horizontal wall with parallel grooves on its upper surface is studied experimentally and numerically. The results of velocity and temperature measurements are reported. A numerical model for a liquid film on a structured wall is developed. The full incompressible Navier–Stokes equations and the energy equation are integrated by a finite difference algorithm, whereas the mobile gas-liquid interface is tracked by the volume-of-fluid method. The numerical model is verified by comparison with the experimental data showing a good agreement. The model is used to study flow patterns and film rupture caused by the thermocapillary forces. Heat transfer in the liquid is also investigated. In particular, it is found that the thermocapillary convection enhances heat transfer in liquid, though the effect depends on the shape of the wall surface.
Current Therapy and Liver Transplantation for Portopulmonary Hypertension in Japan

Portopulmonary hypertension (PoPH) and hepatopulmonary syndrome are severe pulmonary complications associated with liver cirrhosis (LC) and portal hypertension. Three key pathways, involving endothelin, nitric oxide, and prostacyclin, have been identified in the development and progression of pulmonary arterial hypertension (PAH). To obtain a good effect with PAH-specific drugs in PoPH patients, it is important to diagnose PoPH at an early stage and promptly initiate therapy. The majority of therapeutic drugs are contraindicated for Child-Pugh grade C LC, and their effects decrease in the severe PAH stage. Among many LC patients, the measurement of serum brain natriuretic peptide levels might be useful for detecting PoPH. Previously, liver transplantation (LT) for PoPH was contraindicated; however, the indications for LT are changing and now take into account how well the PoPH is controlled by therapeutic drugs. In Japan, new registration criteria for deceased-donor LT have been established for PoPH patients. PoPH patients with a mean pulmonary arterial pressure <35 mmHg and pulmonary vascular resistance <400 dyn/s/cm−5 are indicated for LT, regardless of whether they are using therapeutic drugs. Combined with PAH-specific drugs, LT may lead to excellent long-term outcomes in PoPH patients. We aimed to review current therapies for PoPH, including LT.
"Revoked just now!" Users' Behaviors Toward Fitness-Data Sharing with Third-Party Applications

The number of users of wearable activity trackers (WATs) has rapidly increased over the last decade. Although these devices enable their users to monitor their activities and health, they also raise new security and privacy concerns, given the sensitive data (e.g., steps, heart rate) they collect and the information that can be inferred from this data (e.g., diseases). In addition to sharing with the service providers (e.g., Fitbit), WAT users can share their fitness data with third-party applications (TPAs) and individuals. Understanding how and with whom users share their fitness data and what kind of approaches they take to preserve their privacy are key to assessing the underlying privacy risks and to further designing appropriate privacy-enhancing techniques. In this work, we perform, through a large-scale survey of N=628 WAT users, the first quantitative and qualitative analysis of users' awareness, understanding, attitudes, and behaviors toward fitness-data sharing with TPAs and individuals. By asking these users to draw their thoughts, we explore, in particular, users' practices and actual behaviors toward fitness-data sharing and their mental models. Our empirical results show that about half of WAT users underestimate the number of TPAs to which they have granted access to their data, and 63% share data with at least one TPA that they do not actively use (anymore). Furthermore, 29% of the users do not revoke TPA access to their data because they forget they gave access to it in the first place, and 8% were not even aware they could revoke access to their data. Finally, their mental models, as well as some of their answers, demonstrate substantial gaps in their understanding of the data-sharing process. Importantly, 67% of the respondents think that TPAs cannot access the fitness data that was collected before they granted access to it, whereas TPAs actually can do this.
The Cellular Abundance of Chemoreceptors, Chemosensory Signaling Proteins, Sensor Histidine Kinases, and Solute Binding Proteins of Pseudomonas aeruginosa Provides Insight into Sensory Preferences and Signaling Mechanisms

Chemosensory pathways and two-component systems are important bacterial signal transduction systems. In the human pathogen Pseudomonas aeruginosa, these systems control many virulence traits. Previous studies showed that inorganic phosphate (Pi) deficiency induces virulence. We report here the abundance of chemosensory and two-component signaling proteins of P. aeruginosa grown in Pi deficient and sufficient media. The cellular abundance of chemoreceptors differed greatly, since a 2400-fold difference between the most and least abundant receptors was observed. For many chemoreceptors, their amount varied with the growth condition. The amount of chemoreceptors did not correlate with the magnitude of chemotaxis to their cognate chemoeffectors. Of the four chemosensory pathways, proteins of the Che chemotaxis pathway were most abundant and showed little variation in different growth conditions. The abundance of chemoreceptors and solute binding proteins indicates a sensing preference for amino acids and polyamines. There was an excess of response regulators over sensor histidine kinases in two-component systems. In contrast, ratios of the response regulators CheY and CheB to the histidine kinase CheA of the Che pathway were all below 1, indicative of different signaling mechanisms. This study will serve as a reference for exploring sensing preferences and signaling mechanisms of other bacteria.
Natural Convection in an Anisotropic Porous Enclosure Due to Nonuniform Heating From the Bottom Wall

A comprehensive numerical investigation on the natural convection in a hydrodynamically anisotropic porous enclosure is presented. The flow is due to nonuniformly heated bottom wall and maintenance of constant temperature at cold vertical walls along with adiabatic top wall. Brinkman-extended non-Darcy model, including material derivative, is considered. The principal direction of the permeability tensor has been taken oblique to the gravity vector. The spectral element method has been adopted to solve numerically the governing conservative equations of mass, momentum, and energy by using a stream-function vorticity formulation. Special attention is given to understand the effect of anisotropic parameters on the heat transfer rate as well as flow configurations. The numerical experiments show that in the case of isotropic porous enclosure, the maximum rates of bottom as well as side heat transfers (Nu b and Nu s ) take place at the aspect ratio, A, of the enclosure equal to 1, which is, in general, not true in the case of anisotropic porous enclosures. The flow in the enclosure is governed by two different types of convective cells: rotating (i) clockwise and (ii) anticlockwise. Based on the value of media permeability as well as orientation angle, in the anisotropic case, one of the cells will dominate the other. In contrast to isotropic porous media, enhancement of flow convection in the anisotropic porous enclosure does not mean increasing the side heat transfer rate always. Furthermore, the results show that anisotropy causes significant changes in the bottom as well as side average Nusselt numbers. In particular, the present analysis shows that permeability orientation angle has a significant effect on the flow dynamics and temperature profile and consequently on the heat transfer rates.
Substance use and other correlates of HIV infection among transwomen and men who have sex with men in Perú: Implications for targeted HIV prevention strategies for transwomen

Characterization of HIV risk factors among transwomen and men who have sex with men (MSM) should be assessed separately and independently. However, due to several constraints, these populations continue to be conflated in clinical research and data. There are limited datasets globally powered to make such comparisons. The study aimed to use one of the largest surveys of transwomen and MSM in Latin America to determine differences in HIV risk and related correlates between the two populations. Secondary data analysis was completed using a cross-sectional biobehavioral survey of 4413 MSM and 714 transwomen living in Perú. Chi Square analysis of selected HIV correlates was conducted to examine differences between transwomen and MSM. Additionally, stratified binary logistic regression was used to split data for further comparative analyses of correlates associated with transwomen and MSM separately. HIV prevalence among transwomen was two-fold greater than among MSM (14.9% vs. 7.0%, p<0.001). Transwomen had a higher prevalence of most HIV risk factors assessed, including presence of alcohol dependence (16.4% vs. 19.0%; p < .001) and drug use in the past 3 months (17.0% vs. 14.9%). MSM were more likely to use marijuana (68.0% vs. 50.0%, p < .001), and transwomen were more likely to engage in inhaled cocaine use (70.0% vs. 51.1%, p < .001). The regression exposed differences in correlates driving sub-epidemics in transwomen vs. MSM, with a trend of substance use increasing HIV risk for transwomen only. Transwomen were more likely to be HIV-infected and had different risk factors from MSM. Targeted prevention strategies are needed for transwomen that are at highest risk. Additionally, further research is needed to determine if these observations in Perú regarding substance use patterns and the role of substance use in HIV risk relate to other trans populations globally.
The Levels of Anti-SARS-CoV-2 Spike Protein IgG Antibodies Before and After the Third Dose of Vaccination Against COVID-19

Purpose The COVID-19 pandemic has been going on for almost three years, and so far, many preventive and therapeutic strategies have been developed. The issue of subsequent booster vaccinations is currently being discussed. We aimed to analyze how the third dose of vaccination against COVID-19 correlates with the dynamics of IgG anti-SARS-CoV-2 spike protein antibody levels in a group of healthy people. Patients and Methods The prospective study included 93 participants before and after a second booster of COVID-19 vaccination, from whom 4 blood samples were collected at intervals. The levels of IgG anti-SARS-CoV-2 in serum were identified using the chemiluminescent immunoassay specific for the receptor-binding domain (RBD) of the S1 protein. The analysis of the results was performed using appropriate statistical methods, considering p <0.05 as a statistically significant value. Results The IgG levels were significantly higher and less diverse after the same follow-up time from the second booster vaccination compared to the first booster. The antibody levels were positively correlated with female, healthcare workers, the elderly and participants with a negative COVID-19 history. Furthermore, the increase in IgG antibodies after the second booster vaccination correlated inversely with the baseline level of antibodies before the vaccination. The latest results showed that antibody levels dropped 1.5-fold after approx. 10 months from the second booster vaccination but still remained at a protective level. Conclusion Booster vaccinations seem to better stimulate immune memory, and in the case of borderline IgG level induces the greatest increase in antibodies. It is worth considering the individual parameters of patients and measuring antibodies before vaccination.
A Recursive Procedure for Computing the Nonlinear Spectral Interactions of Progressive Finite‐Amplitude Waves in Nondispersive Fluids

A method for computing nonlinear interactions between the spectral lines of progressive finite‐amplitude waves in homogeneous media is developed via Burgers' equation. By means of Fourier analysis, this equation is reduced to a coupled set of ordinary nonlinear differential equations, which are then solved recursively using Airy's algorithm. The solution thus obtained has the form of a vector which initially contains the spectral amplitudes of the source waveform and is subsequently enriched by nonlinearly generated spectral components as the signal propagates through the medium. The utility of the method consists in the ease with which it can be implemented on a digital computer and its applicability to a wide variety of source waveforms.
Beyond the Myth of Legality? Framing Effects and Public Reactions to High Court Decisions in Europe

How do people respond to different decision-making processes in high courts? One long-standing view suggests that citizens expect courts to be neutral arbiters of legal controversies. Although the relevance of such “myth of legality” has been challenged, we know very little about the relationship between the portrayals of the motives of courts and justices and public attitudes in civil law countries. We explore this question in a pair of experiments in Norway and Portugal where we isolate the effects of different institutional frames from outcome favorability. We find that while partisan frames are detrimental to fairness perceptions and acceptance of decisions, depictions of judicial decision-making that emphasize policy goals do not adversely affect citizens’ responses in comparison with legalistic frames. The results suggest that, even in civil law systems, preserving the myth of legality may not be a necessary condition to elicit public support for judicial decisions.
Students' Challenges of Blended Learning Model in Higher Education

Blended learning is a general term for a method that combines the benefits of classroom learning with online learning. However, the combination of online and face-to-face educational components has caused problems over time. Some studies highlight the general limitations of the blended learning education model, but there is no clear insight into the challenges that exist in the blended learning online component. A systematic literature search was performed to identify obstacles to the online components of blended learning from a student's perspective. The biggest challenges students face are self-regulatory issues and the difficulty of learning technology. This study highlights the need for further research to address the problem of student blended learning.
Validation of an Uncertainty Propagation Method for Moving‐Boat Acoustic Doppler Current Profiler Discharge Measurements

The moving‐boat Acoustic Doppler Current Profiler (ADCP) gauging method is extensively used to measure the discharge of rivers and canals. Informed decisions related to water management require reliable estimates of the uncertainty of such measurements. The evaluation of the uncertainty is however a difficult task because of the complexity of the ADCP data workflow and the lack of reference discharges in rivers and canals. This study presents an evolution of the OURSIN method, which follows the framework of the Guide to the expression of Uncertainty in Measurement. The method has been implemented in the QRevInt software which provides an ADCP data quality review prior to the uncertainty analysis. As a computationally efficient alternative to the Monte Carlo approach, the uncertainty propagation combines elemental measurement uncertainty sources, transect‐to‐transect discharge variability, and estimation of the uncertainty of discharges in unmeasured areas by sensitivity analysis. The OURSIN uncertainty results are validated using empirical uncertainty estimates from two large‐scale repeated measures experiments with variable site and flow conditions. The mean and the 95% quantiles of the uncertainty differences are −0.4% [−4.4%; +2.5%]. The OURSIN method provides a comprehensive uncertainty budget that is helpful for understanding the relative impacts of error sources and defining strategies to minimize them. The method should be further evaluated with experiments in different conditions, and additional uncertainty components and options such as GPS reference for boat velocity could be implemented.
New method for reducing the general formula for lattice specific heat to the Einstein and Nernst- Lindemann approximations

To reduce the general formula for lattice specific heat to Einstein's formula of 1907, one traditionally models the spectrum of lattice modes-of-vibration as a set of independent oscillators all of one frequency, ν1. Not only is this a poor representation of a real solid, but no formula is provided for the frequency ν1, which has to be determined empirically. We offer a new and more compelling method for reducing the general formula to Einstein's formula. The reduction involves a simple mathematical approximation, proceeds without any reference to independent oscillators all of one frequency, and leads to a formula for the characteristic frequency, ν1, equal to the mean modal frequency. The mathematical approximation is valid at all but low temperatures, thereby providing insight into the failure of Einstein's formula at low temperatures. A simple extension of the new method leads to the NernstLindemann formula for specific heat, proposed in 1911 on the basis of trial and error and currently without a so.
Predicting Older Adults’ Mobile Payment Adoption: An Extended TAM Model

This study adopted an advanced model, combining the technology acceptance model, the theory of reasoned action, the diffusion of innovations, trust, and five aspects of perceived risk, to measure the factors that influence the behavioral intentions of older adults to use mobile payments. A total of 365 questionnaires were collected from older adults aged 55 years or older from 20 community care sites in central Taiwan. Partial least-squares structural equation modeling was used to test our research model. The results showed that attitude was the main determinant of M-payment in older adults. Moreover, increasing the usefulness, ease of use, and observability of M-payment helped older adults improve their attitudes toward M-payment, thereby increasing their intention to use it. Trust had a significant effect on the usefulness and ease of use of M-payment, while the main factors affecting trust were only performance and financial risks.
R-matrix calculation of low-energy electron collisions with phosphoric acid

Electron collision calculations are performed on two conformers of H3PO4, a weakly dipolar form with all OH groups pointing up and a strongly dipolar form where one OH group points down. Strong evidence is found for a broad shape resonance at about 7 eV for both conformers, although the precise parameters of this resonance are sensitive to the details of the target wavefunction used. Ten-state close-coupling calculations suggest the presence of very narrow Feshbach resonances in a similar energy region. Again both conformers behave similarly. Elastic and electronically inelastic cross sections are calculated for both conformers.
Accurate formula for dissipative interaction in frequency modulation atomic force microscopy

Much interest has recently focused on the viscosity of nano-confined liquids. Frequency modulation atomic force microscopy (FM-AFM) is a powerful technique that can detect variations in the conservative and dissipative forces between a nanometer-scale tip and a sample surface. We now present an accurate formula to convert the dissipation power of the cantilever measured during the experiment to damping of the tip-sample system. We demonstrated the conversion of the dissipation power versus tip-sample separation curve measured using a colloidal probe cantilever on a mica surface in water to the damping curve, which showed a good agreement with the theoretical curve. Moreover, we obtained the damping curve from the dissipation power curve measured on the hydration layers on the mica surface using a nanometer-scale tip, demonstrating that the formula allows us to quantitatively measure the viscosity of a nano-confined liquid using FM-AFM.