Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating the Reliability of MM-PB/GB-SA Method for the Protein-Ligand Binding Free Energies Using Penicillopepsin-Inhibitor ligands

: An accurate prediction of the ligand-receptor binding free energies (ΔG) is a critical step in the early stages of rational drug design. The Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) method is a popular approach to estimate ΔG. However, correlations between the predicted and the experimental ΔG are variable. The goal of this study is to investigate various approaches to optimize accuracy of the MM-GBSA method. A molecular dynamic (MD) simulations protocol was applied using penicillopepsin receptor against its inhibitor ligands, repeated 50 times for each complex system. After that, ΔG of the five inhibitors were predicted using MM-GBSA method. Moreover, a diverse ΔG values were calculated from the replicate MD simulations of each system. The results were showed correlations not only between the predicted and the experimental binding affinities of the systems but also between the predicted values and root-mean-square deviation. In addition, statistical analysis was evaluated the sample size.
Private Control Benefits

We construct a new index for measuring managers’ private control benefits (PCB) and examine how these benefits affect corporate performance and policies. Our index mitigates various potential biases associated with measurement of PCB in the literature. Consistent with theoretical predictions, firms whose CEOs enjoy more PCB experience poorer operating and stock return performance and reduced value. They use less debt financing and make fewer risky investments, resulting in higher cash holdings and lower firm risk. They also adopt more non-delay antitakeover provisions and pay more to employees. The evidence highlights the importance of PCB for firm valuation and decision-making. JEL classification: G11; G30; G31; G32; J31
Variational Monte Carlo method for fermionic models combined with tensor networks and applications to the hole-doped two-dimensional Hubbard model

The conventional tensor-network states employ real-space product states as reference wave functions. Here, we propose a many-variable variational Monte Carlo (mVMC) method combined with tensor networks by taking advantages of both to study fermionic models. The variational wave function is composed of a pair product wave function operated by real space correlation factors and tensor networks. Moreover, we can apply quantum number projections, such as spin, momentum and lattice symmetry projections, to recover the symmetry of the wave function to further improve the accuracy. We benchmark our method for one- and two-dimensional Hubbard models, which show significant improvement over the results obtained individually either by mVMC or by tensor network. We have applied the present method to hole doped Hubbard model on the square lattice, which indicates the stripe charge/spin order coexisting with a weak $d$-wave superconducting order in the ground state for the doping concentration less than 0.3, where the stripe oscillation period gets longer with increasing hole concentration. The charge homogeneous and highly superconducting state also exists as a metastable excited state for the doping concentration less than 0.25.
Updating and structure in non-monotonic theories

The challenge we address is how to support non-monotonic reasoning tasks over large-scale knowledge bases of rich expressive form. We identify a central problem of updating: which parts of the previous retractable conclusions are safe, i.e., unaffected, when various new axioms are added? This problem is important not only for the task of belief maintenance and revision, but also for specification and for inference. The difficulty arises because non-monotonicity implies potential globality of conflicting interaction. We attack the problem at a logical level, choosing the circumscription formalism as our vehicle of analysis for its mathematical convenience and expressive power. This dissertation provides a primary groundwork for implementing circumscriptive (and other) non-monotonic reasoning systems that go beyond previous ones in several respects: to perform forward inference and to maintain a body of valid conclusions, as well as to answer queries, for more expressively complex and larger-scale theories. Our major results build sequentially. (1) We extend the circumscription formalism by generalizing the idea of prioritization (relative precedence) so as to enable, for example, the more adequate representation of source reliability and of default inheritance networks. (2) We show that non-monotonic theories are hierarchically decomposable in a manner analogous to programming languages with side effects. (3) We demonstrate several broad cases of safeties of updating, including updating with new default rules. Enabling conditions include syntactic independence and positivity, as well as relative prioritization. (4) We define a generalized "assumption-based" truth maintenance scheme to support inference and belief revision.
Unique shape changes during freezing of a nanofluid droplet

Understanding the dynamics during freezing of nanofluid droplets is of importance from a fundamental and practical viewpoint. While the freezing of a water droplet has been extensively studied, little information is available about the characteristics of freezing a nanofluid droplet. Here, we report unique shape changes observed during the freezing process of a nanofluid droplet. Instead of forming a pointy tip on the frozen deionized water droplet, we found that the top of a frozen nanofluid droplet exhibits a flat plateau shape and such plateau becomes larger with increasing nanoparticle concentration. We ascribe this characteristic shape change to an outward Marangoni flow which moves liquid from the droplet interior to its vertexes, thus engendering the volume redistribution and shape changes. Moreover, we also observed a particle ring pattern formed during freezing of a nanofluid droplet, which is similar to the well-known coffee stain phenomenon occurring during evaporation of a water droplet with dispersed particles. We believe our reported phenomena are not only of fundamental interest but have potential applications in the freezing of nanofluids for energy storage and developing nanofluid based new microfabrication methods.
Holographic Quantum Matter

We present a review of theories of states of quantum matter without quasiparticle excitations. Solvable examples of such states are provided through a holographic duality with gravitational theories in an emergent spatial dimension. We review the duality between gravitational backgrounds and the various states of quantum matter which live on the boundary. We then describe quantum matter at a fixed commensurate density (often described by conformal field theories), and also compressible quantum matter with variable density, providing an extensive discussion of transport in both cases. We present a unified discussion of the holographic theory of transport with memory matrix and hydrodynamic methods, allowing a direct connection to experimentally realized quantum matter. We also explore other important challenges in non-quasiparticle physics, including symmetry broken phases such as superconductors and non-equilibrium dynamics.
Numerically calibrated model for propagation of a relativistic unmagnetized jet in dense media

Relativistic jets reside in high-energy astrophysical systems of all scales. Their interaction with the surrounding media is critical as it determines the jet evolution, observable signature, and feedback on the environment. During its motion the interaction of the jet with the ambient media inflates a highly pressurized cocoon, which under certain conditions collimates the jet and strongly affects its propagation. Recently, Bromberg et al. (2011) derived a general simplified (semi)analytic solution for the evolution of the jet and the cocoon in case of an unmagnetized jet that propagates in a medium with a range of density profiles. In this work we use a large suite of 2D and 3D relativistic hydrodynamic simulations in order to test the validity and accuracy of this model. We discuss the similarities and differences between the analytic model and numerical simulations and also, to some extent, between 2D and 3D simulations. Our main finding is that although the analytic model is highly simplified, it properly predicts the evolution of the main ingredients of the jet-cocoon system, including its temporal evolution and the transition between various regimes (e.g., collimated to uncollimated). The analytic solution predicts a jet head velocity that is faster by a factor of about 3 compared to the simulations, as long as the head velocity is Newtonian. We use the results of the simulations to calibrate the analytic model which significantly increases its accuracy. We provide an applet that calculates semi-analytically the propagation of a jet in an arbitrary density profile defined by the user at this http URL
Mean-field dynamical density functional theory

We examine the out-of-equilibrium dynamical evolution of density profiles of ultrasoft particles under time-varying external confining potentials in three spatial dimensions. The theoretical formalism employed is the dynamical density functional theory (DDFT) of Marini, Bettolo, Marconi and Tarazona (1999 J. Chem. Phys. 110 8032), supplied by an equilibrium excess free energy functional that is essentially exact. We complement our theoretical analysis by carrying out extensive Brownian dynamics simulations. We find excellent agreement between theory and simulations for the whole time evolution of density profiles, demonstrating thereby the validity of the DDFT when an accurate equilibrium free energy functional is employed.
New cosmological constraints on primordial black holes

We update the constraints on the fraction of the Universe going into primordial black holes in the mass range 10{sup 9}-10{sup 17} g associated with the effects of their evaporations on big bang nucleosynthesis and the extragalactic photon background. We include for the first time all the effects of quark and gluon emission by black holes on these constraints and account for the latest observational developments. We then discuss the other constraints in this mass range and show that these are weaker than the nucleosynthesis and photon background limits, apart from a small range 10{sup 13}-10{sup 14} g, where the damping of cosmic microwave background anisotropies dominates. Finally we review the gravitational and astrophysical effects of nonevaporating primordial black holes, updating constraints over the broader mass range 1-10{sup 50} g.
A Possible experimental test of quantized gravity

While it is widely believed that gravity should ultimately be treated as a quantum theory, there remains a possibility that general relativity should not be quantized. If this is the case, the coupling of classical gravity to the expectation value of the quantum stress-energy tensor will naturally lead to nonlinearities in the Schrodinger equation. By numerically investigating time evolution in the nonrelativistic "Schrodinger-Newton" approximation, we show that such nonlinearities may be observable in the next generation of molecular interferometry experiments.
Off-shell effects on the interaction of Nambu-Goldstone bosons and $D$ mesons

The Bethe-Salpeter equation in unitarized chiral perturbation theory is usually solved with the so-called on-shell approximation. The underlying argument is that the off-shell effects can be absorbed by the corresponding coupling constants and physical masses, which has been corroborated by the success of unitarized chiral perturbation theory in describing a variety of physical phenomena. Such an approximation needs to be scrutinized when applied to study the light-quark mass evolution of physical observables, as routinely performed nowadays. In the present work, we propose to solve the Bethe-Salpeter equation with the full off-shell terms of the chiral potentials and apply this formalism to the description of the latest $n_f=2+1$ lattice QCD (LQCD) data on the scattering lengths of Nambu-Goldstone bosons off $D$ mesons. It is shown that the LQCD data can be better described in this formalism than in the widely used on-shell approximation. On the other hand, no qualitative difference between the on-shell and off-shell approaches is observed for the light-quark mass evolution of the scattering lengths, given the limited LQCD data and their relatively large uncertainties. We also show that the light-quark mass dependence of the $D^*_{s0}(2317)$ remains essentially the same in both approaches.
Changes in built-up areas and population in a typical mountainous region—a case study of Liping County, Southwest China

: Mountainous regions surrounded by various natural environments are sensitive to anthropogenic disturbances. This study aims to investigate recent changes in built-up areas and population in Liping County, a typical mountainous region in Southwest China since 2000 by Landsat time series and township-level census data. We found that built-up areas have continuously expanded whereas the population has decreased, which may imply excessive human impacts on this region.
Lecture notes on Mather's theory for Lagrangian systems

These are introductory lecture notes on Mather's theory for Tonelli Lagrangian and Hamiltonian systems. They are based on a series of lectures given by the author at Universit\`a degli Studi di Napoli "Federico II" (April 2009), at University of Cambridge (academic year 2009-2010) and at Universitat Polit\`ecnica de Catalunya (June 2010).
Modeling the adoption of medical wearable devices among the senior adults: Using hybrid SEM-neural network approach

The world is witnessing an increasing number of senior adult residents who experience health issues. Healthcare innovation facilitates monitoring the health conditions of senior adults and reducing the burden on healthcare institutions. The study explored the effect of health improvement expectancy, effort expectancy, price value, perceived vulnerability, health consciousness, and perceived reliability on the intention and adoption of medical wearable devices (MWD) among senior adults in China. Furthermore, a cross-sectional design was adopted, while quantitative data was collected from 304 senior adults through an online survey. A hybrid approach of partial least square structural equational modeling and artificial neural network-based analysis technique was adopted. The findings demonstrated that health improvement expectancy, perceived vulnerability, price value, and perceived reliability significantly affected the intention to adopt MWDs. Moreover, the intention to adopt MWDs significantly positively affected the actual adoption of MWDs among senior adults. Although the moderating effect of the pre-existing conditions and income between the intention to use MWDs and actual adoption of MWDs was positive, it was not statistically significant. The artificial neural network analysis has proven that perceived reliability, price value, and vulnerability are the most critical factors contributing to the intention to use MWDs. The current study offered valuable insights into the factors affecting the intention and adoption of MWDs among senior adults. Following that, theoretical and practical contributions were documented to improve the ease of use and price value for the prospective users of MWDs. The correct healthcare policies could curtail the influx of senior adults into the hospital and empower these adults to track and manage their health issues at home.
Avian models for brain mechanisms underlying altered social behavior in autism

The current review is an update on experimental approaches in which birds serve as model species for the investigation of typical failure symptoms associated with autism spectrum disorder (ASD). The discussion is focused on deficiencies of social behavior, from social interactions of domestic chicks, based on visual and auditory cues, to vocal communication in songbirds. Two groups of pathogenetic/risk factors are discussed: 1) non-genetic (environmental/epigenetic) factors, exemplified by embryonic exposure to valproic acid (VPA), and 2) genetic factors, represented by a list of candidate genes and signaling pathways of diagnostic or predictive value in ASD patients. Given the similarities of birds as experimental models to humans (visual orientation, vocal learning, social cohesions), avian models usefully contribute toward the elucidation of the neural systems and developmental factors underlying ASD, improving the applicability of preclinical results obtained on laboratory rodents. Furthermore, they may predict potential susceptibility factors worthy of investigation (both by animal studies and by monitoring human babies at risk), with potential therapeutic consequence.
Mono- and biallelic germline variants of DNA glycosylase genes in colon adenomatous polyposis families from two continents

Recently, biallelic germline variants of the DNA glycosylase genes MUTYH and NTHL1 were linked to polyposis susceptibility. Significant fractions remain without a molecular explanation, warranting searches for underlying causes. We used exome sequencing to investigate clinically well-defined adenomatous polyposis cases and families from Finland (N=34), Chile (N=21), and Argentina (N=12), all with known susceptibility genes excluded. Nine index cases (13%) revealed germline variants with proven or possible pathogenicity in the DNA glycosylase genes, involving NEIL1 (mono- or biallelic) in 3 cases, MUTYH (monoallelic) in 3 cases, NTHL1 (biallelic) in 1 case, and OGG1 (monoallelic) in 2 cases. NTHL1 was affected with the well-established, pathogenic c.268C>T, p.(Gln90Ter) variant. A recurrent heterozygous NEIL1 c.506G>A, p.(Gly169Asp) variant was observed in two families. In a Finnish family, the variant occurred in trans with a truncating NEIL1 variant (c.821delT). In an Argentine family, the variant co-occurred with a genomic deletion of exons 2 – 11 of PMS2. Mutational signatures in tumor tissues complied with biological functions reported for NEIL1. Our results suggest that germline variants in DNA glycosylase genes may occur in a non-negligible proportion of unexplained colon polyposis cases and may predispose to tumor development.
What does current science tell us about the accuracy, reliability, and completeness of intoxicated witnesses? A case example of the murder of a prime minister

Generally, the testimony of intoxicated witnesses has been considered relatively unreliable, but recent research has nuanced the knowledge base regarding these vulnerable witnesses. Purpose To demonstrate the application of recent research findings regarding intoxicated witnesses to the statements made by a key witness to the murder of Olof Palme, Sweden's prime minister, in 1986. An additional purpose was to illustrate the use of a nuanced calculation of blood alcohol concentration (BAC) for researchers. Methods The Palme murder has been debated since the crime was committed and no one has yet been sentenced. One of the witnesses was intoxicated and to estimate a range for his BAC at the time, a comprehensive BAC calculation was conducted in this study to illustrate important factors to consider in these types of cases. Results Through the demonstration of the use of a nuanced BAC formula and by applying recent research results from studies on intoxicated witnesses, it was estimated that the possible BAC of the witness in the Palme-case at the time of the witnessed crime ranged between BAC = 0 to BAC = 0.13, depending on the type of alcoholic beverage consumed and whether the witness was a social or heavy drinker. This puts the witness either well within the span of maintained completeness as well as maintained accuracy rate (if considering: lowest dose and heavy drinker), or slightly exceeding this span into the BAC-range of reduced completeness but maintained accuracy rate (if considering: highest dose and social drinker). He was questioned immediately, and thereafter repeatedly, and he reported similar information throughout the interviews, which is in line with previous results on information maintenance over repeated interviews among intoxicated witnesses. Conclusion The current case example shows how recent research on intoxicated witnesses can be applied in praxis, illustrating important factors for legal practitioners to consider when interpreting information from intoxicated witnesses. It also provides legal practitioners and researchers with an example of a structured approach to more nuanced BAC-calculations.
Psychological assessment in infertility: A systematic review and meta-analysis

Infertility is a prevalent worldwide health issue and is defined by the World Health Organization (WHO) as a global health problem. Considering the importance of the psychological dimensions of infertility, various measurement tools have been used to measure the variables involved in infertility, of which the most widely used are the following: the Symptom Checklist 90 (SCL90), the Brief Symptom Inventory (BSI), the State-Trait Anxiety Inventory Form (STAI), and the Depression Anxiety Stress Scale (DASS). Therefore, given the problems of infertile people in terms of psychological dimensions, the aim of this meta-analysis was to assess the psychological assessment score in infertility. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol, we applied an online database with no time restriction. Data were gathered using a random-effect model to estimate the standard mean difference (SMD) for the evaluation of the strength of association analyses. Our data demonstrated a significant higher SCL90 score (CISCL90: 0.96, 0.34–1.57, heterogeneity: 94%, pheterogeneity < 0.001), and a non-significant higher DASS score (CIAnxiety: 0.82, -0.14 to 1.79; CIDepression: 0.8, -0.28 to 1.87; and CIStress: 0.82, -0.24 to 1.88). It is essential to seek for strategies to help infertile patients overcome their infertility-related psychological problems.
Prevalence of psychopathy in a community sample of Spanish adults: Definitions and measurements matter

The main objective of this work is to examine the prevalence of psychopathy in the general adult population from the main currently existing theoretical perspectives of psychopathy, using for this purpose the five-factor or Big Five model as a common language that allows the comparison and integration of the personality traits considered as defining psychopathy by these different perspectives. The NEO Personality Inventory-Revised (NEO PI-R) was applied to a sample of 682 adults of the general Spanish population. The prevalence of clinical and subclinical psychopathy was calculated according to six different definitions of these two constructs based on Hare’s, Lilienfeld’s, triarchic, and DSM-5-hybrid models, and the simultaneous presence of a minimum number of personality traits that differed from the sample mean by one standard deviation. Prevalence rates for the different definitions were consistently low, indicating that the prevalence of clinical psychopathy in the general Spanish population is around 0.55%, and that of subclinical psychopathy is around 1.65%. There were no significant sex differences in the prevalence of psychopathy. These results question the alarmist claims that warn about the existence in society of a very high number of people with psychopathy who can cause many social, economic, physical, and psychological damage to others.
Improving Efficiency by Shrinkage: The James--Stein and Ridge Regression Estimators

Introduction to shrinkage estimators: the Stein paradox the ridge estimators of Hoerl and Kennard. Estimation for a single linear model: the James-Stein estimator for a single model ridge estimators from different general points of view improving the James-Stein estimator - the positive parts. Other linear model setups: the simultaneous estimation problem precision of individual estimators the multivariate model other linear model setups.