Miracle-dz/UniFAR-FTUs huggingface dataset:
Free energy of helical transmembrane peptide dimerization in OPLS-AA/Berger force field simulations: inaccuracy and implications for partner-specific Lennard-Jones parameters between peptides and lipids

Abstract Interactions between transmembrane (TM) peptides are important in biophysical chemistry, but there are few studies assessing atomistic simulation parameters concerning the energetics of interactions of TM helical peptides. Our potential of mean force analysis using OPLS-AA protein/Berger lipid force fields (FFs) shows that the dimerisation energy of (AALALAA)3 helical peptides in the dioleoylphosphatidylcholine bilayer is −4.4 kJ/mol, which was much smaller than the reported experimental value (−12.7 kJ/mol), thus calling for improvement of parameters of the combined FFs. As each of the FFs has been independently developed, we then tested the effects of downscaling the Lennard-Jones (LJ) energy terms between the OPLS-AA atoms and Berger lipid atoms, preserving the parameters within each FF. A 0.9-fold rescaling of the LJ energies was found to render the dimerisation energy close to the experimental value. Solvation of backbone atoms as well as side chain atoms in lipids is crucial for the TM helix interaction. In similar analyses, GROMOS 53A6 FF exhibited as weak dimerisation propensity (~−5.2 kJ/mol) as OPLS-AA/Berger, but CHARMM36 showed relatively accurate propensity (~−9.9 kJ/mol). Challenges and strategies in rendering the TM interaction energy realistic within the framework of current FFs are discussed.
The Effects of COVID-19 and Continuous Auditing on Employees' Compliance with the Internal Control System: The Moderating Role of Conscientiousness

The trend towards continuous auditing of business operations is growing. In economically demanding times, organizations aim to improve compliance with internal controls. Our study investigates whether continuous auditing and a (COVID19) crisis situation interact with the personality trait conscientiousness among auditees to influence compliance with internal controls. We conducted a between-subjects experiment manipulating audit frequency (continuous vs. traditional audit) and the current business situation (business as usual vs. crisis) and received 125 complete responses from sales professionals. We found that the effect of a crisis situation on the likelihood to engage in non-compliance with internal controls is conditional on conscientiousness, while continuous auditing does not seem to interact with the trait of conscientiousness. Specifically, we observe that less conscientious individuals who are operating under a crisis condition and continuously audited are likelier to engage in non-compliance with internal controls. In contrast, individuals with a high level of conscientiousness were more likely to comply with internal controls when continuously audited in the context of a crisis.
Stuck in the Wisdom of Crowds: Information, Knowledge, and Heuristics

Collective knowledge is significantly affected by information about others’ viewpoints. However, under what conditions does the “wisdom of crowds” help versus harm knowledge of factual information? In this experiment, we present subjects with the task of answering 50 factual true or false trivia questions, with the potential opportunity to revise their answers after receiving different levels of information about other subjects’ answers and self-assessed confidence levels from an independent session. We find that information about others’ answers improves performance on easy questions, but tends to harm performance on difficult questions. In addition, information about answers provided by other subjects mainly improves performance for those with lower initial knowledge levels. Subjects in our Moderate-Information condition outperform those in either the Low or High-Information conditions, implying an optimal level of social information provision, in which the Majority Rule and Maximum Confidence rule complement one another. Although the Maximum Confidence rule can improve performance, yielding the lowest overall error rate out of the heuristics considered, subjects generally underutilize the information on other subjects’ confidence levels in favor of the Majority Rule heuristic. These findings shed light on possible directions for policies that can cultivate factual knowledge on online opinion platforms.
Production of Hydrogen and Nanocarbon from Catalytic Decomposition of Methane over a Ni–Fe/Al2O3 Catalyst

A Ni–Fe–Al catalyst derived from a hydrotalcite-like structured precursor prepared with a co-precipitation technique is employed in the methane catalytic decomposition reaction producing carbon nanofibers (CNFs) and COx-free hydrogen. The effect of doping with iron on the activity and stability is investigated. The performance of the catalyst is evaluated with a temperature-programmed reaction and a constant temperature reaction. The catalyst with a Ni/Fe/Al mole ratio of 2:1:1 shows an extremely stable activity and is still active after 210 h of reaction. The carbon yield on this catalyst reaches 562 g of C/g of catalyst. The post-reaction characterization results indicate that the Ni–Fe alloy is formed in the Ni–Fe–Al catalyst and is proposed to be the active phase for the CNF growth. The addition of an appropriate amount of Fe may enhance the carbon diffusion rate and decrease the carbon formation rate. Thus, the balance among the carbon atom formation, diffusion, and precipitation rates is maintained,.
Graph-based Pattern Detection in Spatio-Temporal Phenomena

RÉSUMÉ. Les modèles spatio-temporels (ST) sont souvent utilisés pour analyser les phénomènes ST. Une de ces techniques d’analyse consiste à détecter des motifs dans le phénomène pour comprendre son évolution et modéliser le comportement de ses en-tités dans l’espace et le temps. Dans cet article, nous nous concentrons sur l’utilisation d’une représentation fondée sur les graphes dynamiques pour la modélisation des phé-nomènes ST, au sein duquel des motifs structurels, également modélisés sous forme de graphes dynamiques, peuvent être détectés. Nous illustrons le concept de motif par deux exemples applicatifs - le traﬁc routier et les sports collectifs. Pour chacun d’eux, nous présentons une modélisation du graphe ainsi que des motifs associés. Ensuite, nous formalisons le problème de la détection de motifs comme celui de l’isomorphisme de sous-graphe pour les graphes dynamiques. Enﬁn, nous présentons les résultats de notre algorithme pour résoudre ce problème. Les premiers résultats décrits dans cet article, qui sont obtenus en utilisant les graphes aléatoires, présentent une base de référence pour les futurs tests de l’algorithme. ABSTRACT. Spatio-temporal (ST) models are often used for analyzing ST phenomena. One such analysis technique is to detect patterns in the phenomenon to understand its evolution and model the behaviour of its entities over space-time. In this paper, we focus on using a dynamic graph-based representation for modeling ST phenomena, within which structural patterns, also modeled using dynamic graphs, can be detected. We illustrate the concept of pattern using two applications - road traﬃc and invasive team sports. For both these applications, we present the graph model as well as the corresponding patterns. Then we formalize the problem of pattern detection as that of subgraph isomorphism for dynamic graphs. Finally, we present the results of our algorithm to solve this problem. The initial results described in this paper, obtained using random graphs, present a baseline for the future tests of the algorithm.
Pain as memory: neuroplasticity of central sensitization as a therapeutic target

One of the crucial cellular processes for major symptoms of pain, like hyperalgesia and allodynia, is considered as a phenomenon of sensitization. Key processes for pain memory stabilizing are peripheral and central sensitizations. Mechanical hypersensitivity and allodynia to light touch after central sensitization are pathologic in that they are evoked by Aβ low threshold mechanoreceptors, which normally do not produce painful sensations. Peripheral sensitization allows low-intensity stimuli to produce pain by activating Aδ and C nociceptors whereas central sensitization allows normal low-threshold Aβ mechanoreceptors to produce pain as a result of changes in sensory processing in the spinal cord. During peripheral and central sensitization, the receptive fields of dorsal horn neurons expand beyond the site of injury into surrounding uninjured tissue. The clinical result of all above changes is hyperalgesia, allodynia, spontaneous pain, referred pain and sympathetically maintained pain. These persistent sensory responses to noxious stimuli are a form of memory, the memory for pain. Long-lasting synaptic plasticity as long-term potentiation at spinal and supraspinal levels could be providing the neuronal basis for persistent pain and pain memory. Thus, it will be particularly important to know how to regulate long-lasting plastic changes in the spinal cord, thalamus and cortex. Molecular mechanisms of these plastic processes could be main targets for new therapeutic drugs in pain relief. This review presents findings from recent studies that examined the possibility of relations between pain and memory.
Characterization of As-Doped p-Type ZnO by X-ray Absorption Near-Edge Structure Spectroscopy: Theory

Vaithianathan et al. [Appl. Phys. Lett. 88, 112103 (2006)] measured x-ray absorption near-edge structure (XANES) of As-doped ZnO and analyzed it as evidence for AsO acceptors. However, upon carrying out first principles calculations, we found that the simulated XANES spectrum for AsO is very different from that observed. Instead, the simulated spectrum for AsZn–2VZn defect complex, which is predicted to be an acceptor [S. Limpijumnong et al., Phys. Rev. Lett. 92, 155504 (2004)], is far more consistent with the XANES data. The combination of our study, with the XANES of Vaithianathan et al. might be, until now, the strongest support for the AsZn–2VZn model.
The Intrinsic Viscosity of Polyamidoamine Dendrimer

The intrinsic viscosities of a group of polyamidoamine PAMAM dendrimer, having ethylenediamine as the core, have been investigated. The intrinsic viscosity of G =0.5~4.5 PAMAM shows a maximum at G =2~3, while the ammonium quanternaries show a minimum there. The hydrodynamic radii of PAMAM calculated from intrinsic viscosity, increase approximately linearly with dendrimer generation.
Multi-scale analysis of acoustic emission signals in dense-phase pneumatic conveying of pulverized coal at high pressure

Acoustic emission technique in conjunction with multiscale processing method has been utilized to investigate the flow behavior of the dense-phase pneumatic conveying system at high pressure. A clearly defined classification of microscale, mesoscale, and macroscale signals has been put forward with the aid of wavelet transform and V statistics analysis. The detailed signals d1–d4, d5–d7, d8–d10 were recomposed into the microscale, mesoscale, and macroscale signals, respectively, which represent microscale particle-wall interactions, mesoscale interaction between gas phase and solid phase (such as bubbles, plugs, dunes), and macroscale flow-induced pipe vibration. Further analysis shows that as the mass flow rate of pulverized coal increases, the energy fraction (energy of detailed signal divided by the energy of original signal) of microscale signals decreases while that of mesoscale signals increases, which indicates that particles are more likely to move as particle aggregates than individual particles when mass flow rate increases. © 2016 American Institute of Chemical Engineers AIChE J, 62: 2635–2648, 2016
Methanol production via bioelectrocatalytic reduction of carbon dioxide: Role of carbonic anhydrase in improving electrode performance

Electrocatalytic production of methanol from CO2 has recently been studied. This paper focuses on understanding the role of carbonic anhydrase to efficiently facilitate uptake of CO2, which can be the rate determining step. The three oxidoreductase enzymes responsible for CO2 reduction to methanol are formate, aldehyde, and alcohol dehydrogenase. This enzyme cascade was coupled to a poly(neutral red) modified electrode to regenerate NADH. We have found that the dehydrogenases alone can achieve reduction of CO2, but the process is accelerated by the addition of carbonic anhydrase. As researchers focus on electrofuels, carbonic anhydrase will likely improve performance. VC 2011 The Electrochemical Society. [DOI: 10.1149/1.3537463] All rights reserved.
Factors Ruling Protein Adsorption

Abstract In this short review an introduction to the phenomenon of protein adsorption will be given. Protein adsorption often plays the central role in a wide variety of processes occurring in medicine, biochemistry, biotechnology and daily life. The main types of interactions ruling protein adsorption are summarized in this review and the principles of a few powerful experimental techniques to characterize protein adsorbates are outlined. Taking the silica/water interface as an example, the driving forces for protein adsorption are discussed on the basis of recent experimental results. Finally, the interactions of proteins with polyelectrolyte brushes are described. These brushes combine favourable properties of other interfaces and permit a controlled immobilization of protein molecules.
Détection des croisements de fibre en IRM de diffusion par décomposition de tenseur : Approche analytique

L'IRM de diffusion (IRMd) est l'unique modalite qui permet d'explorer les structures neuronales de la substance blanche in-vivo et de maniere non-invasive. La diffusion a d'abord ete modelisee par le modele du tenseur de diffusion du second ordre (DTI). Toutefois, ce modele trouve rapidement ses limites dans les zones, nombreuses, ou les fibres de la matiere blanche se croisent. Pour surmonter cette limite et reconstruire les croisements de fibres, differentes approches ont ete proposees telles que: l'imagerie a resonance magnetique (IRM) a haute resolution angulaire (HARDI) et les tenseurs d'ordre superieur (HOT) ; ces methodes permettent de reconstruire des fonctions telle que la fonction de distribution d'orientation de fibre (FOD) dont les maxima s'alignent sur les orientations des fibres multiples. Dans ce travail, on se propose d'extraire les directions des fibres caracterisees par les maxima de la fonction FOD. Pour cela, une approche analytique de decomposition de tenseur symetrique a ete implementee et efficacement adaptee pour extraire les directions des fibres avec precision. Differents resultats obtenus sur des donnees synthetiques et reelles illustrent l'efficacite de la methode.
Spatial distribution of the chemical properties of the soil and of soybean yield in the field

The aim of this study was to evaluate the spatial dependence between chemical properties of the soil and yield components in the soybean using precision farming techniques. Samples of the soil and plants were taken from georeferenced points to determine the chemical properties of the soil and the yield components. The results were submitted to Pearson correlation analysis, descriptive statistics and geostatistics. The coefficient of variation showed a wide range of distribution for the chemical attributes of the soil, with the highest indices being found for the levels of available phosphorus (102%) and potassium (72.65%). Soil pH and organic matter showed a coefficient of variation of 5.96 and 15.93% respectively. Semivariogram analysis of the yield components (productivity, 1,000-seed weight and number of seeds) and the chemical properties of the soil (organic matter, pH, phosphorus, potassium, calcium, magnesium, boron, manganese and zinc) fitted the spherical model with moderate spatial dependence, with values ranging from 200 to 700 m. Spatial distribution by means of map interpolation was efficient in evaluating spatial variability, allowing the identification and quantification of regions of low and high productivity in the production area, together with the distribution of soil attributes and their respective levels of availability to the soybean plants.
Anomalous electronic structure of the positive muon in antimony : evidence for an isolated kondo impurity

The anomalous electronic structure of a positive muon in the semimetal antimony was investigated by the SR (Muon Spin Rotation/Relaxation) technique. Precise mea surements of the giant muon Knight shift (K=+1.4%) were made as a function of temperature (2-20 K) and magnetic field (18-21 kG) with the applied magnetic field parallel to the ê-axis of the antimony single crystal. No de Haas-van Alphen oscillations were observed at a temperature of 3 K, which indicates the electron spin density on the muon does not scale simply with the magnetic susceptibility of the conduction electrons. An upper limit of 0.2% of K, can be placed on the amplitude of the K, de Haas-van Alphen oscillations. The measured K, varies weakly with temperature below 10 K. The data were fit in three different ways. The best fit is to the form K = 1/(a + bT 2 + cT 4) with parameters a=7.167(3) x i0, b=6.4(7) x 1O K2, and c=1.8(2) x 10 K4. A fit to an Arrhenius Law of the form 1— Ae/T yields a pre-exponential of 0.47(4) and an activation temperature Ea/kB of 40(2) K. If one fits to an expression for the Kondo susceptibility of the form K = a(1/2IrTK — 0.433T 2/) at low temperatures (2-10 K) one obtains a parameter a=14.0(0.3) K and a Kondo temperature TK=160(3) K. Together with existing measurements of K at higher temperatures (90-180 K) we ob serve a crossover from a weakly temperature dependent Pauli paramagnetic behaviour below 10 K to a Curie-like behaviour above 90 K. This crossover is characteristic of a Kondo impurity indicating the anomalous electronic structure of a positive muon in antimony may be due to muonium formation, in which a local moment is centered on or near the muon. Within context of this model estimates of the hyperfine parameters (A 11 =259,7(4) MHz and A±=129.9(2) MHz) for muonium in antimony are similar to
Cerebellar preference of luminal A and B type and basal ganglial preference of HER2-positive type breast cancer-derived brain metastases

The purpose of the current study was to investigate the hypothesis that the spatial distribution of brain metastases could be affected by the biological subtypes of breast cancer. CT (n=1) or MRI (n=66) images of 67 patients with a total of 437 treatment-naive brain metastases from breast cancer were retrospectively reviewed. Patients were grouped according to the biological subtype of the tumor [luminal A, 28; luminal B, 9; human epidermal growth factor receptor 2 (HER2) positive, 14; triple-negative breast cancer (TNBC), 16]. All images were standardized to the human brain MRI atlas provided by the Montreal Neurological Institute 152 database. The distribution pattern of brain metastases after image standardization was analyzed. The cerebellum and the frontal lobe were more commonly affected by breast cancer brain metastases. Brain metastases from luminal A and B types of breast cancer arose more often in the cerebellum. Brain metastases from HER2-positive type breast cancer occurred more often in the putamen and the thalamus and less frequently in the cerebellum than other types (P=0.0057). The subtypes of breast cancer are related to differences in the spatial distributions of their brain metastases. These differences may be utilized to plan different cranial irradiation strategies according to the breast cancer subtypes.
Health‐related quality‐of‐life questionnaires for deep vein thrombosis and pulmonary embolism: A systematic review on questionnaire development and methodology

To improve the quality and accuracy of the patient‐reported outcome measures that assess health‐related quality of life (HRQoL), guidelines have been developed to standardize the development and validation process. Considering the increasing importance of HRQoL questionnaires in research, we set out to review the literature and evaluate whether existing questionnaires developed for deep vein thrombosis (DVT) and pulmonary embolism (PE) fulfill state‐of‐the‐art requirements. The literature search was conducted in March 2019 and updated in September 2020. Seven databases were searched. No time limit was set for the search to include all available questionnaires. The inclusion criteria were original publications describing the development of disease‐specific HRQoL questionnaires specific to DVT or PE in adults and available in English. The questionnaires were assessed to determine whether they fulfill the requirements in the latest guidelines. A total of 3826 references were identified. After the exclusion process, 15 papers were reviewed in full, of which 7 were included. Four questionnaires were developed for chronic venous disease, two were specific to DVT, and one was specific to PE. Most questionnaires we found in this review, fulfilled some but none fulfilled all recommendations in existing guidelines. Because the development of current available HRQoL questionnaires specific to DVT or PE do not fulfil all recommendations of existing guidelines, there is room for improvements within this field. Such improvements could likely enhance the quality associated with the use of these end points in clinical trials and practice.
TiO2 – do we have to worry about it? One of the important aetiological factors in inflammatory bowel disease

TiO2 in the food industry, designated as E171, is widely used in the production of chewing gums, sweets, and icing. It is absorbed through food ingestion and the respiratory tract. There are also reports that TiO2 nanoparticles can reach the dermis through damaged epidermis. It demonstrates the ability to accumulate in some internal organs, like spleen, liver, and kidneys, depending on its size and structure. It may have pro-inflammatory, cytotoxic, and genotoxic effects. A change in the composition of the host’s intestinal microflora is also observed after exposure to high doses of TiO2. There are some differences in TiO2 intake with food around the world, but most data indicate higher consumption of this additive by children. Due to the small amount of research and the fact that most of the analyses were carried out using animal models, it is necessary to plan future observations of long-term exposure of the TiO2 molecule.
Biochanin A Regulates Cholesterol Metabolism Further Delays the Progression of Nonalcoholic Fatty Liver Disease

Purpose To discover the possible target of biochanin A (BCA) in the lipid metabolism pathway and further explore its mechanism to nonalcoholic fatty liver disease (NAFLD). Methods We adopted a high-fat and high-glucose diet for 12 weeks to build the NAFLD rat model, which was then treated with different proportions of BCA for 4 weeks. General condition, body weight, Lee index, and liver index were then evaluated. Furthermore, blood lipid level and insulin resistance (IR) were detected. Moreover, hematoxylin and eosin and oil red O staining were used to observe the pathological changes in the liver. Finally, Western blotting was used to detect the protein expression levels of CYP7A1, HMGCR, LDLR, PPAR-α, PPAR-γ, and SREBP-1c in the liver. Results The vital signs of rats in each group were stable. The treatment with BCA effectively reduced Lee index and liver index (F = 104.781, P < 0.05); however, the weight was not effected in each group. Additionally, BCA effectively reduced the related lipid metabolism indexes of NAFLD, such as total cholesterol (TC), triglyceride (TG), low-density lipoprotein (LDL), blood glucose, insulin, IR (F =12.463 (TC), 6.909 [TG], and 15.3 effected 75 [LDL], P < 0.05), and increased HDL (F = 11.580, P < 0.05). We observed that BCA could significantly improve steatosis and inflammatory cell infiltration in liver slices. Furthermore, BCA significantly increased the CYP7A1, LDLR, and PPAR-α protein expression in the liver and downregulated the HMGCR, SREBP-1c, and PPAR-γ protein expression. Conclusion BCA could delay the liver damage of NAFLD induced by a high-fat diet, regulate the blood lipid level, and improve the expression of lipid metabolism-related genes in rats.