Miracle-dz/UniFAR-FTUs huggingface dataset:
Variation at Extra-epitopic Amino Acid Residues Influences Suppression of Influenza Virus Replication by M158-66 Epitope-Specific CD8+ T Lymphocytes

ABSTRACT Influenza virus-specific CD8+ T lymphocytes (CTLs) contribute to clearance of influenza virus infections and reduce disease severity. Variation at amino acid residues located in or outside CTL epitopes has been shown to affect viral recognition by virus-specific CTLs. In the present study, we investigated the effect of naturally occurring variation at residues outside the conserved immunodominant and HLA*0201-restricted M158-66 epitope, located in the influenza virus M1 protein, on the extent of virus replication in the presence of CTLs specific for the epitope. To this end, we used isogenic viruses with an M1 gene segment derived from either an avian or a human influenza virus, HLA-transgenic human epithelial cells, human T cell clones specific for the M158-66 epitope or a control epitope, and a novel, purposely developed in vitro system to coculture influenza virus-infected cells with T cells. We found that the M gene segment of a human influenza A/H3N2 virus afforded the virus the capacity to replicate better in the presence of M158-66-specific CTLs than the M gene segment of avian viruses. These findings are in concordance with previously observed differential CTL activation, caused by variation at extra-epitopic residues, and may reflect an immune adaptation strategy of human influenza viruses that allows them to cope with potent CTL immunity to the M158-66 epitope in HLA-A*0201-positive individuals, resulting in increased virus replication and shedding and possibly increasing disease severity. IMPORTANCE Influenza viruses are among the leading causes of acute respiratory tract infections. CD8+ T lymphocytes display a high degree of cross-reactivity with influenza A viruses of various subtypes and are considered an important correlate of protection. Unraveling viral immune evasion strategies and identifying signs of immune adaptation are important for defining the role of CD8+ T lymphocytes in affording protection more accurately. Improving our insight into the interaction between influenza viruses and virus-specific CD8+ T lymphocyte immunity may help to advance our understanding of influenza virus epidemiology, aid in risk assessment of potentially pandemic influenza virus strains, and benefit the design of vaccines that induce more broadly protective immunity.
Modifying Thermal Switchability of Liquid Crystalline Nanoparticles by Alkyl Ligands Variation

By coating plasmonic nanoparticles (NPs) with thermally responsive liquid crystals (LCs) it is possible to prepare reversibly reconfigurable plasmonic nanomaterials with prospective applications in optoelectronic devices. However, simple and versatile methods to precisely tailor properties of liquid-crystalline nanoparticles (LC NPs) are still required. Here, we report a new method for tuning structural properties of assemblies of nanoparticles grafted with a mixture of promesogenic and alkyl thiols, by varying design of the latter. As a model system, we used Ag and Au nanoparticles that were coated with three-ring promesogenic molecules and dodecanethiol ligand. These LC NPs self-assemble into switchable lamellar (Ag NPs) or tetragonal (Au NPs) aggregates, as determined with small angle X-ray diffraction and transmission electron microscopy. Reconfigurable assemblies of Au NPs with different unit cell symmetry (orthorombic) are formed if hexadecanethiol and 1H,1H,2H,2H-perfluorodecanethiol were used in the place of dodecanethiol; in the case of Ag NPs the use of 11-hydroxyundecanethiol promotes formation of a lamellar structure as in the reference system, although with substantially broader range of thermal stability (140 vs. 90 °C). Our results underline the importance of alkyl ligand functionalities in determining structural properties of liquid-crystalline nanoparticles, and, more generally, broaden the scope of synthetic tools available for tailoring properties of reversibly reconfigurable plasmonic nanomaterials.
RESEARCH OF 4D C/C COMPOSITE MATERIAL THROAT INSERT BY MIX WEAVED WITH CARBON FIBRE AND AXIAL CARBON ROD

The throat insert material made by 4D preform,by mix weaved with carbon fibre and axial carbon rod,the preform is densified with the process of high-pressure pitch impregnation and carbonization.The production cost of the material is low,and the density of its reached to 1.93～1.94g/cm~3,the ablation properties increased by 20%～50% Compared With 4D C/C throat insert material by mix weaved with carbon fibre and radial carbon rod.The material can be applied for high-pressure and high-flow rate nozzle of solid rocket motor in a tow cost.
Particle swarm optimization with particles having quantum behavior

In this paper, inspired by the analysis of convergence of PSO, we study the individual particle of a PSO system moving in a quantum multidimensional space and establish a quantum delta potential well model for PSO. After that, a trial method of parameter control and QDPSO is proposed. The experiment result shows much advantage of QDPSO to the traditional PSO.
The satiety effect of disguised liquid preloads administered acutely and differing only in their nutrient content tended to be weaker for lipids but did not differ between proteins and carbohydrates in human subjects.

Whether protein is the macronutrient with the strongest satiety effect remains a matter of debate because of the diversity of study designs employed. The aim of the present study was to compare the effect of different liquid preloads made up of proteins, fats or carbohydrates only, under stringently controlled conditions, on satiety. Fifty-six subjects participated in the present study which consisted of four randomised test days, i.e. 1 d per macronutrient and one control day. During each test day, the subjects were required to consume the preload in full, and then their subsequent food intake was measured. The volunteers were divided into two groups: the first (T0) group, which consumed the preload immediately before lunch, and the second (T1) group, which consumed it 1 h beforehand. The main results showed that the participants consumed significantly less at lunch following the consumption of all three preloads than on the no-preload day, and consumed less after the consumption of the carbohydrate preload than after the consumption of the lipid preload. When energy from the preload was included, overall energy intake was significantly greater in all the three preload conditions than in the situation involving no preload, with only partial compensation for preload energy in all conditions. Total daily energy intake was highest after the lipid preload ingestion, but this could be a chance finding since it was not significantly higher than that observed after protein or carbohydrate preload ingestion. No significant effects of the interval between the preload and test meal ingestion were found. These results do not confirm the greater satiety effect of proteins than of carbohydrates, but partially confirm the weaker effect of fats.
Diode Laser and Periodontal Regeneration-Assisted Management of Implant Complications in Anterior Maxilla

Dental implant is being considered successful if the patient is pleased with both of its functional and esthetic outcome. As implant complications (such as peri-implantitis, inappropriate implant position, wrong angulation, and implant location too close to anatomical structures) have been frequently encountered in dental practice, therefore, thorough knowledge to manage such complications is the key prerequisite to prevent the failure of implant. The present case report discussed the etiology, diagnosis of early peri-implantitis, and periodontal abscess with their successful management through periodontal regeneration and diode laser-assisted therapy.
Plasmonic Absorption Enhancement in Elliptical Graphene Arrays

In this paper, we come up with a wavelength tunable absorber which is made up of periodically elliptical graphene arrays in the far-infrared and terahertz regions. Through simulation, we find that we can increase the length of long axis of the ellipse, raise the incidence angles of TM- and TE-polarization (TM- and TE-polarization indicate the direction of the incident electric field along the direction of the x and the y axis, respectively.) within certain limits, and increase the chemical potential of graphene, so as to enhance the absorption of light in the elliptical graphene arrays. We also compare the absorption spectra of the original structure and the complementary structure, and find that the absorption of the original structure is higher than that of the complementary structure. In the end, we study the changes in the absorption rate of the double layer structure of the elliptical array with the increase in the thickness of SiO2. The elliptical array structure can be applied to tunable spectral detectors, filters and sensors at far-infrared and terahertz wavelengths.
Ionic basis of ryanodine's negative chronotropic effect on pacemaker cells isolated from the sinoatrial node.

Spontaneous electrical activity and indo 1 fluorescence ratios were recorded simultaneously in cultured pacemaker cells isolated from the rabbit sinoatrial node. Ryanodine (10 μM) reduced the amplitude of action potential-induced intracellular Ca2+([Formula: see text]) transients by 19 ± 3%, increased the time constant for their decay by 51 ± 5%, and slowed spontaneous firing by 32 ± 3%. 1,2-Bis(2-aminophenoxy)ethane- N, N, N', N'-tetraacetic acid (BAPTA)-acetoxymethyl ester (AM; 25 μM) inhibited the [Formula: see text] transients and slowed spontaneous firing by 28 ± 4%. Ryanodine did not alter hyperpolarization-activated or time-independent inward current, but it reduced the sum of L- and T-type Ca2+ currents ( I Ca,L and I Ca,T) in both the presence and absence of BAPTA-AM. In contrast, I Ca,L was unchanged by ryanodine. Slow inward current tails, presumed to be Na/Ca exchange current ( I Na/Ca), were abolished by BAPTA or ryanodine. The results suggest that a decrement of I Ca,T, due to reduction of the intracellular Ca2+ concentration or a direct effect of ryanodine on T-type Ca2+channels, contributes to the negative chronotropic effect. Another possibility, based primarily on theory and results in other preparations, is that a reduction of I Na/Ca, as a consequence of the smaller action potential-induced[Formula: see text] transients, contributes to the effect of ryanodine.
Comparison of airway deposition distributions of particles in healthy and diseased workers in an Egyptian industrial site

Abstract The objective of this study is the prediction and comparison of airway deposition patterns of an industrial aerosol in healthy workers and workers suffering from silicosis. Mass concentrations and related size distributions of particulate matter were measured in the industrial area of Samalut in Minia, Egypt. A novel stochastic lung deposition model, simulating the symptoms of silicosis by chronic bronchial (Br) obstruction and emphysema in the acinar (Ac) region, was applied to compute mass deposition fractions, deposition density, deposition rate and deposition density rate distributions in healthy and diseased workers. In the case of healthy workers, both mass deposition fractions and deposition rates are highest in the first half of the Ac region of the lung, while the corresponding deposition density and deposition density rate distributions exhibit a maximum in the large Br airways. In the case of diseased lungs, bullous emphysema causes a large deposition peak in the region of the bronchioli respiratorii. Regional mass deposition fractions adopt maximum values in the extrathoracic region, except during mouth breathing for bullous emphysema, where Ac deposition can be the most prominent. In general, lung deposition is significantly higher in diseased than in healthy lungs. Indeed, workers suffering from silicosis receive significantly higher Ac doses than healthy workers exposed to the same aerosol. Thus, this illness may progress faster if a diseased worker remains in a strongly polluted area.
Mackinac: a bridge between ModelSEED and COBRApy to generate and analyze genome-scale metabolic models

Summary: Reconstructing and analyzing a large number of genome‐scale metabolic models is a fundamental part of the integrated study of microbial communities; however, two of the most widely used frameworks for building and analyzing models use different metabolic network representations. Here we describe Mackinac, a Python package that combines ModelSEED's ability to automatically reconstruct metabolic models with COBRApy's advanced analysis capabilities to bridge the differences between the two frameworks and facilitate the study of the metabolic potential of microorganisms. Availability and Implementation: This package works with Python 2.7, 3.4, and 3.5 on MacOS, Linux and Windows. The source code is available from https://github.com/mmundy42/mackinac. Contact: mundy.michael@mayo.edu or soares.maria@mayo.edu
ATP releases HSP-72 from protein aggregates after renal ischemia.

The pattern of 72-kDa heat-shock protein (HSP-72) induction after renal ischemia suggests a role in restoring cell structure. HSP-72 activity in the repair and release from denatured and aggregated proteins requires ATP. Protein aggregates were purified from normal and ischemic rat renal cortex. The addition of ATP to cortical homogenates reduced HSP-72, Na+-K+-ATPase, and actin in aggregates subsequently isolated, suggesting that their interaction is ATP dependent. Altering ATP hydrolysis in the purified aggregates, however, had different effects. ATP released HSP-72 during reflow and preserved Na+-K+-ATPase association with aggregates at 2 h but had no effect in controls or at 6 h reflow and caused no change in actin. These results indicate that HSP-72 complexes with aggregated cellular proteins in an ATP-dependent manner and suggests that enhancing HSP-72 function after ischemic renal injury assists refolding and stabilization of Na+-K+-ATPase or aggregated elements of the cytoskeleton, allowing reassembly into a more organized state.
Quantifying Information and Uncertainty

We examine ways to measure the amount of information generated by a piece of news and the amount of uncertainty implicit in a given belief. Say a measure of information is valid if it corresponds to the value of news in some decision problem. Say a measure of uncertainty is valid if it corresponds to expected utility loss from not knowing the state in some decision problem. We axiomatically characterize all valid measures of information and uncertainty. We show that if measures of information and uncertainty arise from the same decision problem, then they are coupled in that the expected reduction in uncertainty always equals the expected amount of information generated. We provide explicit formulas for the measure of information that is coupled with any given measure of uncertainty and vice versa. Finally, we show that valid measures of information are the only payment schemes that never provide incentives to delay information revelation. (JEL D81, D83)
Glucose and glutamine provide similar proportions of energy to mucosal cells of rat small intestine.

The objectives of this study were to establish a reliable method for quantifying glycolytic flux in intestinal epithelial cells, to determine the proportion of energy provided to small intestine epithelial cells by glucose vs. glutamine, and to determine whether there was an energetic advantage to having both substrates present simultaneously. There was substantial retention of 3H in alanine and lactate when [2-3H]glucose was used as tracer for quantifying glycolysis, and the magnitude of the3H retention was influenced by the presence of other substrates and metabolites. Detritiation was at least 99% complete, however, when [3-3H]glucose was used as tracer in this system and the tritium was recovered as3H2O. Glycolytic flux was six- to sevenfold higher in cells of the proximal than distal small intestine but was not significantly different for young adult (4 mo) vs. aged adult (24 mo) rats. Net ATP production from exogenous substrates was higher when both glucose and glutamine were present simultaneously than when either substrate was present alone, and glucose was calculated to provide 50-60% of the net ATP produced from these two substrates. Most of the energy produced from glucose was produced via the anaerobic metabolic pathways (78% for glucose alone, 95% with glucose and glutamine). Net energy production was calculated to be 10% lower in cells from aged animals than in those from young animals, since CO2 production from these major substrates was lower in cells from aged animals.
Chronic nitric oxide inhibition with l-NAME: effects on autonomic control of the cardiovascular system.

To determine whether increased sympathetic activity contributes to the hypertension induced by chronic exposure to moderate nitric oxide synthase (NOS) inhibition, various indexes of autonomic function were measured in rats given the NOS inhibitor N G-nitro-l-arginine methyl ester (l-NAME, 10 mg/100 ml, ≅16 mg ⋅ kg-1 ⋅ day-1) in the drinking water. One week of treatment raised blood pressure (139 ± 3 vs. 106 ± 1 mmHg; P < 0.01) and lowered heart rate (319 ± 4 vs. 379 ± 6 beats/min, P < 0.01). l-NAME had no effect on cardiac sympathetic tone, but elevated cardiac parasympathetic tone (-73 ± 4 vs. -56 ± 7 beats/min; P< 0.05). Depressor responses to ganglionic blockade were greater inl-NAME-treated rats (-50 ± 5 vs. -34 ± 5 mmHg; P < 0.05), whereas resting plasma, renal, and adrenal catecholamine values did not differ between groups. Treated rats also showed evidence of reduced baroreflex sympathetic stimulation of heart rate during hypotension and reduced parasympathetic activation during hypertension. Together, these data provide only very limited, indirect evidence that sympathetic stimulation contributes to the hypertension associated with moderate NOS inhibition.
The 5′ and 3′ Untranslated Regions of the Flaviviral Genome

Flaviviruses are enveloped arthropod-borne viruses with a single-stranded, positive-sense RNA genome that can cause serious illness in humans and animals. The 11 kb 5′ capped RNA genome consists of a single open reading frame (ORF), and is flanked by 5′ and 3′ untranslated regions (UTR). The ORF is a polyprotein that is processed into three structural and seven non-structural proteins. The UTRs have been shown to be important for viral replication and immune modulation. Both of these regions consist of elements that are essential for genome cyclization, resulting in initiation of RNA synthesis. Genome mutation studies have been employed to investigate each component of the essential elements to show the necessity of each component and its role in viral RNA replication and growth. Furthermore, the highly structured 3′UTR is responsible for the generation of subgenomic flavivirus RNA (sfRNA) that helps the virus evade host immune response, thereby affecting viral pathogenesis. In addition, changes within the 3′UTR have been shown to affect transmissibility between vector and host, which can influence the development of vaccines.
Structure and phase behavior of fluids in porous media.

XVII CHAPTER 1 INTRODUCTION . 1 1.1 SIMULATION METHODS . 5 1.1.1 Isobaric‐Isothermal Ensemble Monte Carlo . 6 1.1.2 Grand Canonical Ensemble Monte Carlo . 8 1.1. 3 Gibbs Ensemble Monte Carlo . 10 1.1. 4 Gibbs‐Duhem Integration . 12 1.1. 5 Quenched Molecular Dynamics . 14 1.2 FREEZING AND MELTING OF CONFINED FLUIDS . 14 CHAPTER 2 GENERAL METHODOLOGY . 21 2.1 DIMENSIONLESS UNITS . 21 2.2 PERIODIC BOUNDARY CONDITIONS . 23
Clinical value of patient-specific three-dimensional printing of congenital heart disease: Quantitative and qualitative assessments

Objective Current diagnostic assessment tools remain suboptimal in demonstrating complex morphology of congenital heart disease (CHD). This limitation has posed several challenges in preoperative planning, communication in medical practice, and medical education. This study aims to investigate the dimensional accuracy and the clinical value of 3D printed model of CHD in the above three areas. Methods Using cardiac computed tomography angiography (CCTA) data, a patient-specific 3D model of a 20-month-old boy with double outlet right ventricle was printed in Tango Plus material. Pearson correlation coefficient was used to evaluate correlation of the quantitative measurements taken at analogous anatomical locations between the CCTA images pre- and post-3D printing. Qualitative analysis was conducted by distributing surveys to six health professionals (two radiologists, two cardiologists and two cardiac surgeons) and three medical academics to assess the clinical value of the 3D printed model in these three areas. Results Excellent correlation (r = 0.99) was noted in the measurements between CCTA and 3D printed model, with a mean difference of 0.23 mm. Four out of six health professionals found the model to be useful in facilitating preoperative planning, while all of them thought that the model would be invaluable in enhancing patient-doctor communication. All three medical academics found the model to be helpful in teaching, and thought that the students will be able to learn the pathology quicker with better understanding. Conclusion The complex cardiac anatomy can be accurately replicated in flexible material using 3D printing technology. 3D printed heart models could serve as an excellent tool in facilitating preoperative planning, communication in medical practice, and medical education, although further studies with inclusion of more clinical cases are needed.
EVIDENCE FORBACTERIAL CAUSATION OFADVERSEPULPAL RESPONSES INRESIN-BASED DENTALRESTORATIONS

Thewidespread useofresin andresin-monomers forbonding ofdental restorations todentin hasoccurred because ofafundamental shift intheviewthat injury tothepulpisinduced byrestorative procedures. While, formanyyears, thetoxic effects ofrestorative materials werethought tobeofcrucial importance inthedevelopment ofadverse pulpal respon- ses, thekeyrole ofbacterial leakage attherestoration-tooth interface isnowwell-recognized. Consequently, ifoptimal condi- tions forthepreservation ofpulpal health aretobeensured, dental restorations should provide animpervious seal against the surrounding tooth structure. However, polymerization shrinkage andcontraction stresses induced during setting, aswell asa variety oftechnical difficulties encountered during theclinical operation, often produce less thanperfect results. Therefore, modernrestorative procedures involving resin andresin-bonded restoratives muststill rely ontheability ofthepulptocope with theinjurious elements towhich itmaybeexposed during andafter theprocedure. This review examines factors that may govern thepulp's response torestorative procedures that involve adhesive technologies. Anassessment ismadeoftherisks involved asfar asthecontinued vital function ofthepulpisconcerned. Itisconcluded that anintact, although thin, wall ofpri- mary dentin often enables thepulptoovercome bothtoxic material effects andtheinfluences ofbacterial leakage. Incontrast, thepulpmaynotdoequally well following capping ofopenexposures withresin composites. Adearth ofcontrolled clinical studies inthis areaofdentistry calls forconfirmation that pulpal health prevails over thelongtermfollowing theuseoftotal- etchandresin-bonding techniques.