Miracle-dz/UniFAR-FTUs huggingface dataset:
Selection for cooperativity causes epistasis predominately between native contacts and enables epistasis-based structure reconstruction

Significance We investigated the relationship between cooperativity and epistasis and found low cooperativity results in high epistasis between nonnative contacts, whereas high cooperatively results in epistasis mainly between native contacts. This provides a mechanistic explanation for why epistasis measurements can be used to reconstruct protein structure. The structure of GB1 protein has been successfully reconstructed using epistasis measurements, and we calculated its epistasis distribution for a cooperative and a noncooperative model. The structure of the native state is clearly mapped out in the cooperative model but becomes obscured in the noncooperative model due to the presence of a folding intermediate. We thus conclude that using epistasis measurements to reconstruct the native state of proteins with stable intermediates may not be appropriate. Epistasis and cooperativity of folding both result from networks of energetic interactions in proteins. Epistasis results from energetic interactions among mutants, whereas cooperativity results from energetic interactions during folding that reduce the presence of intermediate states. The two concepts seem intuitively related, but it is unknown how they are related, particularly in terms of selection. To investigate their relationship, we simulated protein evolution under selection for cooperativity and separately under selection for epistasis. Strong selection for cooperativity created strong epistasis between contacts in the native structure but weakened epistasis between nonnative contacts. In contrast, selection for epistasis increased epistasis in both native and nonnative contacts and reduced cooperativity. Because epistasis can be used to predict protein structure only if it preferentially occurs in native contacts, this result indicates that selection for cooperativity may be key for predicting structure using epistasis. To evaluate this inference, we simulated the evolution of guanine nucleotide-binding protein (GB1) with and without cooperativity. With cooperativity, strong epistatic interactions clearly map out the native GB1 structure, while allowing the presence of intermediate states (low cooperativity) obscured the structure. This indicates that using epistasis measurements to reconstruct protein structure may be inappropriate for proteins with stable intermediates.
Removal of lead from aqueous solutions by spent tea leaves

Spent tea leaves from black and green tea were assessed for their potential to remove lead (II) from contaminated waters. Batch adsorption experiments made at temperatures between 5 and 40 °C and lead ion concentrations between 0.01 and 2 g/L showed that removal efficiencies higher than 95% can easily be achieved. The results were only marginally affected by the type of tea waste. At low lead loading the adsorption equilibrium was well described by the Langmuir equation, with a maximum adsorption capacity of 85–100 mg/g. A comparison with other adsorbents provided the following order for lead removal efficiency: black tea, coffee grounds > green tea > Fuller’s earth > activated carbon.
A matter of size? Health‐related quality of life after radical prostatectomy for patients with giant prostates

Evidence regarding the impact of giant prostate volume (PV) on outcome after radical prostatectomy (RP) is controversial with a lack of evidence on the impact of PV on health‐related quality of life (HRQOL). We aimed to assess the impact of giant PV on HRQOL and functional outcomes for men with prostate cancer (PC) undergoing RP.
Nonequilibrium Gas Dynamics and Molecular Simulation

This current and comprehensive book provides an updated treatment of molecular gas dynamics topics for aerospace engineers, or anyone researching high-temperature gas flows for hypersonic vehicles and propulsion systems. It demonstrates how the areas of quantum mechanics, kinetic theory, and statistical mechanics can combine in order to facilitate the study of nonequilibrium processes of internal energy relaxation and chemistry. All of these theoretical ideas are used to explain the direct simulation Monte Carlo (DSMC) method, a numerical technique based on molecular simulation. Because this text provides comprehensive coverage of the physical models available for use in the DSMC method, in addition to the equations and algorithms required to implement the DSMC numerical method, readers will learn to solve nonequilibrium flow problems and perform computer simulations, and obtain a more complete understanding of various physical modeling options for DSMC than is available in other texts.
Enhanced Electrochemical Properties of Non-stoichiometric Layered Perovskites, Sm1−xBaCo2O5+d, for IT-SOFC Cathodes

In this study, electrochemical properties of layered perovskites having non-stoichiometric compositions (Sm1−xBaCo2O5+d, x = 0, 0. 01, 0.02, 0.03, 0.04, 0.05, 0.10, and 0.15) were analyzed for the direct application of cathode materials for Intermediate Temperature-operating Solid Oxide Fuel Cells (IT-SOFC). From the Sm1−xBaCo2O5+d oxide systems calcined at 1,100°C for 8 h, single phase (SmBaCo2O5+d, SBCO_1) was maintained only in the case of the x = 0 composition. In the compositions of x = 0.05–0.10, BaCoO2.6 was mixed with the pattern of SBCO. In addition, in the composition of x = 0.15, it was confirmed that BaCoO2.6 and CoO phases coexisted with SBCO. In the compositions of Sm1−xBaCo2O5+d, the overall Area Specific Resistance (ASR) values decreased as the removal amount of Sm increased from x = 0–0.10; then, the values increased for compositions from x = 0.15. For example, the ASRs of SBCO_1, Sm0.95BaCo2O5+d (SBCO_0.95), Sm0.90BaCo2O5+d (SBCO_0.90), and Sm0.85BaCo2O5+d (SBCO_0.85) measured at 600°C were 0.301, 0.147, 0.119, and 0.179 Ω cm2, respectively. In particular, SBCO_0. 90 was found to have an excellent ASR property of about 0.035 Ω cm2 at 700°C. Typical properties of the metal–insulator transition (MIT) electrical conductivity were shown in all measured compositions. The temperature at which MIT occurred increased as the non-stoichiometric composition increased.
Predation and Resource Availability Interact to Drive Life-History Evolution in an Adaptive Radiation of Livebearing Fish

Predation risk and resource availability are two primary factors predicted by theory to drive the evolution of life histories. Yet, disentangling their roles in life-history evolution in the wild is challenging because (1) the two factors often co-vary across environments, and (2) environmental effects on phenotypes can mask patterns of genotypic evolution. Here, we use the model system of the post-Pleistocene radiation of Bahamas mosquitofish (Gambusia hubbsi) inhabiting blue holes to provide a strong test of the roles of predation and resources in life-history evolution, as the two factors do not co-vary in this system and we attempted to minimize environmental effects by raising eight populations under common laboratory conditions. We tested a priori predictions of predation- and resource-driven evolution in five life-history traits. We found that life-history evolution in Bahamas mosquitofish largely reflected complex interactions in the effects of predation and resource availability. High predation risk has driven the evolution of higher fecundity, smaller offspring size, more frequent reproduction, and slower growth rate—but this predation-driven divergence primarily occurred in environments with relatively high resource availability, and the effects of resources on life-history evolution was generally greater within environments having high predation risk. This implies that resource-driven selection on life histories overrides selection from predators when resources are particularly scarce. While several results matched a priori predictions, with the added nuance of interdependence among selective agents, some did not. For instance, only resource levels, not predation risk, explained evolutionary change in male age at maturity, with more rapid sexual maturation in higher-resource environments. We also found faster (not slower) juvenile growth rates within low-resource and low-predation environments, probably caused by selection in these high-competition scenarios favoring greater growth efficiency. Our approach, using common-garden experiments with a natural system of low- and high-predation populations that span a continuum of resource availability, provides a powerful way to deepen our understanding of life-history evolution. Overall, it appears that life-history evolution in this adaptive radiation has resulted from a complex interplay between predation and resources, underscoring the need for increased attention on more sophisticated interactions among selective agents in driving phenotypic diversification.
Hansenia weberbaueriana (Fedde ex H.Wolff) Pimenov & Kljuykov Extract Suppresses Proliferation of HepG2 Cells via the PTEN-PI3K-AKT Pathway Uncovered by Integrating Network Pharmacology and Iin Vitro Experiments

Previous studies have shown that Hansenia weberbaueriana (Fedde ex H.Wolff) Pimenov & Kljuykov extracts (HWEs) have antitumor activity, but their mechanism in vitro is still unclear. In this study, we first combined network pharmacology with experimental evaluation and applied a comprehensive strategy to explore and prove the therapeutic potential and potential mechanism of HWE. The mRNA expression profiles of PTEN, PIK3A, and AKT1 are from the Cancer Cell Line Encyclopedia (CCLE) of the Broad Institute. Our results showed that HWE has a good inhibition on HepG2 cells, and a slight inhibition on other cells. The results of the CCLE database showed that PTEN/PIK3A/AKT1 mRNA expression was up-regulated in HepG2 cells. Through further study, it was found that HWE increased the release of LDH, induced early and late apoptosis, and increased ROS levels in HepG2 cells. Western blot showed that HWE regulates the expression of mitochondrial apoptosis-related proteins. Meanwhile, the expression of PTEN was increased, and the expression of phosphorylated PI3K and Akt was down-regulated after HWE treatment. Our results show that HWE promotes HepG2 cell apoptosis via the PTEN-PI3K-Akt signaling pathway. This study is the first to report the potential role of HWE in the treatment of liver cancer.
Co-infection of H9N2 Influenza A Virus and Escherichia coli in a BALB/c Mouse Model Aggravates Lung Injury by Synergistic Effects

Pathogens that cause respiratory diseases in poultry are highly diversified, and co-infections with multiple pathogens are prevalent. The H9N2 strain of avian influenza virus (AIV) and Escherichia coli (E. coli) are common poultry pathogens that limit the development of the poultry industry. This study aimed to clarify the interaction between these two pathogens and their pathogenic mechanism using a mouse model. Co-infection with H9N2 AIV and E. coli significantly increased the mortality rate of mice compared to single viral or bacterial infections. It also led to the development of more severe lung lesions compared to single viral or bacterial infections. Co-infection further causes a storm of cytokines, which aggravates the host’s disease by dysregulating the JAK/STAT/SOCS and ERK1/2 pathways. Moreover, co-infection mutually benefited the virus and the bacteria by increasing their pathogen loads. Importantly, nitric oxide synthase 2 (NOS2) expression was also significantly enhanced by the co-infection. It played a key role in the rapid proliferation of E. coli in the presence of the co-infecting H9N2 virus. Therefore, our study underscores the role of NOS2 as a determinant for bacteria growth and illustrates its importance as an additional mechanism that enhances influenza virus-bacteria synergy. It further provides a scientific basis for investigating the synergistic infection mechanism between viruses and bacteria.
Real-World Methotrexate Dose on Clinical Effectiveness and Structural Damage of Certolizumab Pegol With Rheumatoid Arthritis

Objective: Rheumatoid arthritis (RA) treatments have markedly advanced with the introduction of biological agents, e. g. , tumor necrosis factor (TNF) inhibitors. TNF inhibitors are demonstrated to be quite effective in combination with methotrexate (MTX), and sufficient doses of both agents are important to control RA's disease activity. However, not all RA patients can be treated with high-dose MTX due to contraindications related to the antimetabolite action of MTX or to tolerability concerns. In daily practice, this has resulted in reduced effectiveness of TNF inhibitors. We sought to determine whether the concomitant use of dose of MTX affected the clinical effectiveness, retention rate, and side effects of certolizumab pegol (CZP) for treating RA in a real-world setting. CZP is a pegylated–conjugated Fab' fragment of a humanized anti-TNF antibody that has high affinity to TNF. Patients and Methods: We divided Japanese RA patients treated with CZP (n = 95, 25–83 years old) into groups based on those with (n = 65) and without (n = 30) concomitant MTX and those treated with a high dose (≥8 mg, n = 41) or low dose (1– <8 mg, n = 24) of MTX. We retrospectively analyzed the concomitant MTX doses' effects and side effects and the patient retention rate. Results: There were no significant differences among the CZP groups with and without MTX or the groups receiving the high vs. low MTX doses in the retention rate, the low disease activity rate, or the inhibitory effect in radiographic joint damage. Conclusion: CZP has the potential to be a useful biological agent to control RA's disease activity and the bone destruction in patients who cannot tolerate a sufficient MTX dose.
Comparative Analysis of Diagnostic Techniques for Melanoma Detection: A Systematic Review of Diagnostic Test Accuracy Studies and Meta-Analysis

Melanoma has the highest mortality rate among skin cancers, and early-diagnosis is essential to maximize survival rate. The current procedure for melanoma diagnosis is based on dermoscopy, i.e., a qualitative visual inspection of lesions with intrinsic limited diagnostic reliability and reproducibility. Other non-invasive diagnostic techniques may represent valuable solutions to retrieve additional objective information of a lesion. This review aims to compare the diagnostic performance of non-invasive techniques, alternative to dermoscopy, for melanoma detection in clinical settings. A systematic review of the available literature was performed using PubMed, Scopus and Google scholar databases (2010-September 2020). All human, in-vivo, non-invasive studies using techniques, alternative to dermoscopy, for melanoma diagnosis were included with no restriction on the recruited population. The reference standard was histology but dermoscopy was accepted only in case of benign lesions. Attributes of the analyzed studies were compared, and the quality was evaluated using CASP Checklist. For studies in which the investigated technique was implemented as a diagnostic tool (DTA studies), the QUADAS-2 tool was applied. For DTA studies that implemented a melanoma vs. other skin lesions classification task, a meta-analysis was performed reporting the SROC curves. Sixty-two references were included in the review, of which thirty-eight were analyzed using QUADAS-2. Study designs were: clinical trials (13), retrospective studies (10), prospective studies (8), pilot studies (10), multitiered study (1); the remain studies were proof of concept or had undefined study type. Studies were divided in categories based on the physical principle employed by each diagnostic technique. Twenty-nine out of thirty-eight DTA studies were included in the meta-analysis. Heterogeneity of studies' types, testing strategy, and diagnostic task limited the systematic comparison of the techniques. Based on the SROC curves, spectroscopy achieved the best performance in terms of sensitivity (93%, 95% CI 92.8–93.2%) and specificity (85.2%, 95%CI 84.9–85.5%), even though there was high concern regarding robustness of metrics. Reflectance-confocal-microscopy, instead, demonstrated higher robustness and a good diagnostic performance (sensitivity 88.2%, 80.3–93.1%; specificity 65.2%, 55–74.2%). Best practice recommendations were proposed to reduce bias in future DTA studies. Particular attention should be dedicated to widen the use of alternative techniques to conventional dermoscopy.
Exploring Sources of Satisfaction and Dissatisfaction in Airbnb Accommodation Using Unsupervised and Supervised Topic Modeling

This study aims to examine key attributes affecting Airbnb users' satisfaction and dissatisfaction through the analysis of online reviews. A corpus that comprises 59,766 Airbnb reviews form 27,980 listings located in 12 different cities is analyzed by using both Latent Dirichlet Allocation (LDA) and supervised LDA (sLDA) approach. Unlike previous LDA based Airbnb studies, this study examines positive and negative Airbnb reviews separately, and results reveal the heterogeneity of satisfaction and dissatisfaction attributes in Airbnb accommodation. In particular, the emergence of the topic “guest conflicts” in this study leads to a new direction in future sharing economy accommodation research, which is to study the interactions of different guests in a highly shared environment. The results of topic distribution analysis show that in different types of Airbnb properties, Airbnb users attach different importance to the same service attributes. The topic correlation analysis reveals that home like experience and help from the host are associated with Airbnb users' revisit intention. We determine attributes that have the strongest predictive power to Airbnb users' satisfaction and dissatisfaction through the sLDA analysis, which provides valuable managerial insights into priority setting when developing strategies to increase Airbnb users' satisfaction. Methodologically, this study contributes by illustrating how to employ novel approaches to transform social media data into useful knowledge about customer satisfaction, and the findings can provide valuable managerial implications for Airbnb practitioners.
Rapid and Sensitive Detection of Tomato Brown Rugose Fruit Virus in Tomato and Pepper Seeds by Reverse Transcription Loop-Mediated Isothermal Amplification Assays (Real Time and Visual) and Comparison With RT-PCR End-Point and RT-qPCR Methods

Tomato brown rugose fruit virus (ToBRFV) represents an emerging viral threat to the productivity of tomato and pepper protected cultivation worldwide. This virus has got the status of quarantine organism in the European Union (EU) countries. In particular, tomato and pepper seeds will need to be free of ToBRFV before entering the EU and before coming on the market. Thus, lab tests are needed. Here, we develop and validate a one-step reverse transcription LAMP platform for the detection of ToBRFV in tomato and pepper leaves, by real-time assay [reverse transcription loop-mediated isothermal amplification (RT-LAMP)] and visual screening (visual RT-LAMP). Moreover, these methods can also be applied successfully for ToBRFV detection in tomato and pepper seeds. The diagnostic specificity and sensitivity of both RT-LAMP and visual RT-LAMP are both 100%, with a detection limit of nearly 2.25 fg/μl, showing the same sensitivity as RT-qPCR Sybr Green, but 100 times more sensitive than end-point RT-PCR diagnostic methods. In artificially contaminated seeds, the proposed LAMP assays detected ToBRFV in 100% of contaminated seed lots, for up to 0.025–0.033% contamination rates in tomato and pepper, respectively. Our results demonstrate that the proposed LAMP assays are simple, inexpensive, and sensitive enough for the detection of ToBRFV, especially in seed health testing. Hence, these methods have great potential application in the routine detection of ToBRFV, both in seeds and plants, reducing the risk of epidemics.
Change in Evaluation Mode Can Cause a Cheerleader Effect

The cheerleader effect describes the phenomenon whereby faces are perceived as being more attractive when flanked by other faces than when they are perceived in isolation. At least four theories predict the cheerleader effect. Two visual memory processes could cause a cheerleader effect. First, visual information will sometimes be averaged in the visual memory: the averaging of faces could increase the perceived attractiveness of all the faces flanked by other faces. Second, information will often be combined into a higher-order concept. This hierarchical encoding suggests that information processing causes faces to appear more attractive when flanked by highly attractive faces. Two further explanations posit that comparison processes cause the cheerleader effect. While contrast effects predict that a difference between the target face and the flanking faces causes the cheerleader effect due to comparison processes, a change in the evaluation mode, which alters the standard of comparison between joint and separate evaluation of faces, could be sufficient for producing a cheerleader effect. This leads to the prediction that even when there is no contrast between the attractiveness of the target face and the flanking faces, a cheerleader effect could occur. The results of one experiment support this prediction. The findings of this study have practical implications, such as for individuals who post selfies on social media. An individual’s face will appear more attractive in a selfie taken with people of low attractiveness than in a selfie without other people, even when all the faces have equally low levels of attractiveness.
FSO Receiver With Adaptive Alignment Based on Pure Phased Holographic Imaging

This paper proposes a free space optical communication (FSO) receivier system with adaptive alignment based on pure phase holographic imaging. During the frame header transmission period, the optical phased array in this system performs specific holographic imaging on the receiving plane, which assist the system to undergo beam alignment. The system model has been built in this work, along with the receiving signal expression. Based on the physical model, we propose an algorithm for positioning calibration and the circuitous phased encoding for improvement of imaging quality and algorithm complexity.
The Contribution of Learning and Mental Health Variables in First-Year Students' Profiles

International studies focus on the successful transition into higher education, which is considered crucial for both the students and the educational institution in the context of students' learning and adjustment in higher education. The aim of the current study was to identify student profiles that include cognitive, metacognitive, and motivational aspects of learning, but also aspects of resilience, emotion dysregulation, and anxiety. The sample consists of 316 Greek undergraduate students (18.7% males and 81.3% females). The results showed four different (meta)-cognitive-emotional learner profiles: the emotionally stable and highly adaptive learner; the emotionally dysregulated and at risk learner; the emotionally dysregulated and highly adaptive learner; the emotionally stable and at risk learner. Emotionally dysregulated and at risk learner has a lower GPA than the emotional stable and highly adaptive learner, the emotionally dysregulated and highly adaptive learner and the emotionally stable and at risk learner.