Search Results (98)

Background/Objectives: Magnetic resonance spectroscopy (MRS) is a valuable tool for studying metabolic processes in vivo. While numerous quantification methods exist, the advanced method for accurate, robust, and efficient spectral fitting (AMARES) is among the most used. This study introduces pyAMARES, an open-source Python implementation of AMARES, addressing the need for a flexible, user-friendly, and versatile MRS quantification tool within the Python ecosystem. Methods: PyAMARES was developed as a Python library, implementing the AMARES algorithm with additional features such as multiprocessing capabilities and customizable objective functions. The software was validated against established AMARES implementations (OXSA and jMRUI) using both simulated and in vivo MRS data. Monte Carlo simulations were conducted to assess robustness and accuracy across various signal-to-noise ratios and parameter perturbations. Results: PyAMARES utilizes spreadsheet-based prior knowledge and fitting parameter settings, enhancing flexibility and ease of use. It demonstrated comparable performance to existing software in terms of accuracy, precision, and computational efficiency. In addition to conventional AMARES fitting, pyAMARES supports fitting without prior knowledge, frequency-selective AMARES, and metabolite residual removal from mobile macromolecule (MM) spectra. Utilizing multiple CPU cores significantly enhances the performance of pyAMARES. Conclusions: PyAMARES offers a robust, flexible, and user-friendly solution for MRS quantification within the Python ecosystem. Its open-source nature, comprehensive documentation, and integration with popular data science tools enhance reproducibility and collaboration in MRS research. PyAMARES bridges the gap between traditional MRS fitting methods and modern machine learning frameworks, potentially accelerating advancements in metabolic studies and clinical applications. Full article

Background: Oral lichen planus (OLP) is a chronic inflammatory disease associated with the formation of symptomatic lesions in the mouth. P63 is essential for epidermal development and regeneration. Weak expression of this protein has been shown in OLP lesions. Photobiomodulation (PBM) therapy has been reported to reduce OLP symptoms, but its ability to correct the molecular perturbations of the disease has not been studied. This study aimed to evaluate the efficacy of PBM in OLP treatment by evaluating changes in p63 expression and their association with clinical response. Methods: Twenty OLP patients underwent PBM with a diode laser (810 nm), (0.50 W, 30 s, 1.2 J/cm²), 3 times weekly for a month. The treatment efficacy index (EI) was calculated based on pain-level values and clinical scores of lesions before and after therapy. Biopsies were taken before and after therapy, analyzed immunohistochemically for p63 expression, and compared with 10 healthy controls. Results: P63 levels in OLP lesions were significantly lower than those in normal oral mucosa. After treatment, the pain level and clinical scores of the lesions decreased significantly. The calculated EI showed PBM effectiveness in 90% of cases. Increased p63 positivity and staining intensity were observed after therapy. Conclusions: The established p63 deficiency in OLP lesions is likely an important molecular mechanism in the pathogenesis of the disease. Laser irradiation at 810 nm increased p63 expression to a level close to that found in the healthy epithelium and significantly improved the symptoms and clinical signs of OLP. All of this determines the effectiveness of PBM therapy in the management of OLP. Full article

Zinc oxide nanoparticles (NPs) are used in a wide range of consumer products and in biomedical applications, resulting in an increased production of these materials with potential for exposure, thus causing human health concerns. Although there are many reports on the size-related toxicity of ZnO NPs, the toxicity of different nanoforms of this chemical, toxicity mechanisms, and potency determinants need clarification to support health risk characterization. A set of well-characterized ZnO nanoforms (e.g., uncoated ca. 30, 45, and 53 nm; coated with silicon oil, stearic acid, and (3-aminopropyl) triethoxysilane) were screened for in vitro cytotoxicity in two cell types, human lung epithelial cells (A549), and mouse monocyte/macrophage (J774) cells. ZnO (bulk) and ZnCl₂ served as reference particles. Cytotoxicity was examined 24 h post-exposure by measuring CTB (viability), ATP (energy metabolism), and %LDH released (membrane integrity). Cellular oxidative stress (GSH-GSSG) and secreted proteins (targeted multiplex assay) were analyzed. Zinc oxide nanoform type-, dose-, and cell type-specific cytotoxic responses were seen, along with cellular oxidative stress. Cell-secreted protein profiles suggested ZnO NP exposure-related perturbations in signaling pathways relevant to inflammation/cell injury and corresponding biological processes, namely reactive oxygen species generation and apoptosis/necrosis, for some nanoforms, consistent with cellular oxidative stress and ATP status. The size, surface area, agglomeration state and metal contents of these ZnO nanoforms appeared to be physicochemical determinants of particle potencies. These findings warrant further research on high-content “OMICs” to validate and resolve toxicity pathways related to exposure to nanoforms to advance health risk-assessment efforts and to inform on safer materials. Full article

The increasing deployment of CubeSats in space missions necessitates the development of efficient and reliable orbital maneuvering techniques, particularly given the constraints on fuel capacity and computational resources. This paper presents a novel two-level control architecture designed to enhance the accuracy and robustness of CubeSat orbital maneuvers. The proposed method integrates a J₂-optimized sequence at the high level to leverage natural perturbative effects for fuel-efficient orbit corrections, with a gated recurrent unit (GRU)-based low-level controller that dynamically adjusts the maneuver sequence in real-time to account for unmodeled dynamics and external disturbances. A Kalman filter is employed to estimate the pointing accuracy, which represents the uncertainties in the thrust direction, enabling the GRU to compensate for these uncertainties and ensure precise maneuver execution. This integrated approach significantly enhances both the positional accuracy and fuel efficiency of CubeSat maneuvers. Unlike traditional methods, which either rely on extensive pre-mission planning or computationally expensive control algorithms, our architecture efficiently balances fuel consumption with real-time adaptability, making it well-suited for the resource constraints of CubeSat platforms. The effectiveness of the proposed approach is evaluated through a series of simulations, including an orbit correction scenario and a Monte Carlo analysis. The results demonstrate that the integrated J₂-GRU system significantly improves positional accuracy and reduces fuel consumption compared to traditional methods. Even under conditions of high uncertainty, the GRU-based control layer effectively compensates for errors in thrust direction, maintaining a low miss distance throughout the maneuvering period. Additionally, the GRU’s simpler architecture provides computational advantages over more complex models such as long short-term memory (LSTM) networks, making it more suitable for onboard CubeSat implementations. Full article

Multiple intermolecular H-bonding interactions play a pivotal role in determining the macroscopic state of ionic liquids (ILs). Hence, the relationship between the microscopic and the macroscopic properties is key for a rational design of new imidazolium ILs. In the present work, we investigated how the physicochemical property of hydroxyl-functionalized imidazolium chloride is connected to the molecular structure and intermolecular interactions. In the isolated ion pair, strong N-H···Cl H-bonding interactions are observed rather than H-bonding interactions at the acidic C₂-H site and alkyl-OH···Cl of the hydroxyl-functionalized imidazolium chloride. However, the N-H···Cl H-bonding interaction of the cation plays a significant role in ion-pair formations and polymeric clusters. For 3-(2-Hydroxy)-1H-imidazolium chloride (EtOHImCl), the oxygen atom (O) engages in two significant interactions within its homodimeric ion-pair cluster: N-H···O and alkyl OH···Cl. Vibrational spectroscopy and DFT calculations reveal that the chloride ion (Cl⁻) forms a hydrogen bond with the C2-H group via a C2-H···Cl interaction site. Natural Bond Orbital (NBO) analysis indicates that the O-H···Cl hydrogen-bonding interaction is crucial for the stability of the IL, with a second-order perturbation energy of approximately 133.8 kJ/mol. Additional computational studies using Atoms in Molecules (AIMs), non-covalent interaction (NCI) analysis, Electron Localization Function (ELF), and Localized Orbital Locator (LOL) provide significant insights into the properties and nature of non-covalent interactions in ILs. Ab initio molecular dynamics (AIMD) simulations of the IL demonstrate its stable states with relatively low energy values around −1680.6510 atomic units (a.u.) at both 100 fs and 400 fs due to O-H···Cl and C-H···Cl interactions. Full article

The benzene dimer (BD) is an archetypal model of π∙∙∙π and C–H∙∙∙π noncovalent interactions as they occur in its cofacial and perpendicular arrangements, respectively. The enthalpic stabilization of the related BD structures has been debated for a long time and is revisited here. The revisit is based on results of computations that apply the coupled-cluster theory with singles, doubles and perturbative triples [CCSD(T)] together with large basis sets and extrapolate results to the complete basis set (CBS) limit in order to accurately characterize the three most important stationary points of the intermolecular interaction energy (ΔE) surface of the BD, which correspond to the tilted T-shaped (TT), fully symmetric T-shaped (FT) and slipped-parallel (SP) structures. In the optimal geometries obtained by searching extensive sets of the CCSD(T)/CBS ΔE data of the TT, FT and SP arrangements, the resulting ΔE values were −11.84, −11.34 and −11.21 kJ/mol, respectively. The intrinsic strength of the intermolecular bonding in these configurations was evaluated by analyzing the distance dependence of the CCSD(T)/CBS ΔE data over wide ranges of intermonomer separations. In this way, regions of the relative distances that favor BD structures with either π∙∙∙π or C–H∙∙∙π interactions were found and discussed in a broader context. Full article

In a purely Keplerian picture, the anomalistic, draconitic and sidereal orbital periods of a test particle orbiting a massive body coincide with each other. Such degeneracy is removed when post-Keplerian perturbing acceleration enters the equations of motion, yielding generally different corrections to the Keplerian period for the three aforementioned characteristic orbital timescales. They are analytically worked out in the case of the accelerations induced by the general relativistic post-Newtonian gravitoelectromagnetic fields and, to the Newtonian level, by the oblateness of the central body. The resulting expressions hold for completely general orbital configurations and spatial orientations of the spin axis of the primary. Astronomical systems characterized by extremely accurate measurements of orbital periods like transiting exoplanets and binary pulsars may offer potentially viable scenarios for measuring such post-Keplerian features of motion, at least in principle. As an example, the sidereal period of the brown dwarf WD1032 + 011 b is currently known with an uncertainty as small as ≃${10}^{-5}\mathrm{s}$, while its predicted post-Newtonian gravitoelectric correction amounts to $0.07\mathrm{s}$; however, the accuracy with which the Keplerian period can be calculated is just 572 s. For double pulsar PSR J0737–3039, the largest relativistic correction to the anomalistic period amounts to a few tenths of a second, given a measurement error of such a characteristic orbital timescale as small as $\simeq {10}^{-6}\mathrm{s}$. On the other hand, the Keplerian term can be currently calculated just to a $\simeq 9$ s accuracy. In principle, measuring at least two of the three characteristic orbital periods for the same system independently would cancel out their common Keplerian component, provided that their difference is taken into account. Full article

Based on the Ψ-functions series method, a new numerical integration method for perturbed and damped second-order systems of differential equations is presented. This multistep method is defined for variable step and variable order (VSVO) and maintains the good properties of the Ψ-functions series method. In addition, it incorporates a recurring algebraic procedure to calculate the algorithm’s coefficients, which facilitates its implementation on the computer. The construction of Ψ-functions and the Ψ-functions series method are presented to address the construction of both explicit and implicit multistep methods and a predictor–corrector method. Three problems analogous to those solved by the Ψ-functions series method are analyzed, contrasting the results obtained with the exact solution of the problem or with its first integral. The first example is the integration of a quasi-periodic orbit. The second example is a Structural Dynamics problem associated with an earthquake, and the third example studies an equatorial satellite with perturbation J₂. This allows us to compare the good behavior of the new code with other prestige codes. Full article

The high diversity and biomass of organisms associated with coral communities depend directly on the maintenance or changes in the benthic composition. Over a decade, we evaluated the spatiotemporal variation in the benthic structure and composition of an insular coral community in the Northeastern Tropical Pacific. Our results show that local conditions drive spatiotemporal differences, and benthic organisms such as sponges, crustose coralline algae, octocorals, and hydrocorals all increased in abundance (cover) in response to negative thermal anomalies caused by the 2010–2011 La Niña event. In contrast, abnormally high temperatures, such as those recorded during the 2015–2016 El Niño Southern Oscillation (ENSO) event, explain the loss of scleractinian corals and crustose coralline algae coverage, which reduced the benthic groups’ richness (BGR), diversity (H’_BG), and evenness (J’_BG), with evidence of a consequent decrease in ecosystem function recorded the following year. Our analysis also showed that sites with high habitat heterogeneity harbored higher average BRG and H’_BG values and were less affected by environmental fluctuations than sites with high live scleractinian coral cover and lower BRG and H’_BG values. Therefore, the benthic structure was impacted differently by the same perturbation, and changes in the benthic community composition affected the groups associated with the community and ecological functions. More importantly, regional stressors such as the ENSO event caused only temporary changes in the benthic community structure, demonstrating the high resilience of the community to annual and interannual stressors. Full article

This study was conducted to elucidate the intestinal damage induced by the IPEC-J2 cell culture-passaged PDCoV. The results showed that PDCoV disrupted the intestinal structure and increased intestinal permeability, causing abnormalities in mucosal pathology. Additionally, PDCoV induced an imbalance in the intestinal flora and disturbed its stability. Microbial community profiling revealed bacterial enrichment (e.g., Proteobacteria) and reduction (e.g., Firmicutes and Bacteroidetes) in the PDCoV-inoculated piglet model. In addition, metabolomics analysis indicated that 82 named differential metabolites were successfully quantified, including 37 up-regulated and 45 down-regulated metabolites. Chenodeoxycholic acid, sphingosine, and oleanolic aldehyde levels were reduced in PDCoV-inoculated piglets, while phenylacetylglycine and geranylgeranyl-PP levels were elevated. Correlation analysis indicated a negative correlation between Escherichia-Shigella and choline, succinic acid, creatine, phenyllactate, and hippuric acid. Meanwhile, Escherichia-Shigella was positively correlated with acetylcholine, L-Glutamicacid, and N-Acetylmuramate. Roseburia, Lachnospiraceae_UCG-010, Blautia, and Limosilactobacillus were negatively and positively correlated with sphingosine, respectively. These data suggested PDCoV-inoculated piglets exhibited significant taxonomic perturbations in the gut microbiome, which may result in a significantly altered metabolomic profile. Full article

Roughly speaking, Ekeland’s Variational Principle (EkVP) (J. Math. Anal. Appl. 47 (1974), 324–353) asserts the existence of strict minima of some perturbed versions of lower semicontinuous functions defined on a complete metric space. Later, Pando Georgiev (J. Math. Anal. Appl. 131 (1988), no. 1, 1–21) and Tomonari Suzuki (J. Math. Anal. Appl. 320 (2006), no. 2, 787–794 and Nonlinear Anal. 72 (2010), no. 5, 2204–2209)) proved a Strong Ekeland Variational Principle, meaning the existence of strong minima for such perturbations. Please note that Suzuki also considered the case of functions defined on Banach spaces, emphasizing the key role played by reflexivity. In recent years, an increasing interest was manifested by many researchers to extend EkVP to the asymmetric case, i.e., to quasi-metric spaces (see references). Applications to optimization, behavioral sciences, and others were obtained. The aim of the present paper is to extend the strong Ekeland principle, both Georgiev’s and Suzuki’s versions, to the quasi-pseudometric case. At the end, we ask for the possibility of extending it to asymmetric normed spaces (i.e., the extension of Suzuki’s results). Full article

Accurate estimates of intermolecular interaction energy, ΔE, are crucial for modeling the properties of organic electronic materials and many other systems. For a diverse set of 50 dimers comprising up to 50 atoms (Set50-50, with 7 of its members being models of single-stacking junctions), benchmark ΔE data were compiled. They were obtained by the focal-point strategy, which involves computations using the canonical variant of the coupled cluster theory with singles, doubles, and perturbative triples [CCSD(T)] performed while applying a large basis set, along with extrapolations of the respective energy components to the complete basis set (CBS) limit. The resulting ΔE data were used to gauge the performance for the Set50-50 of several density-functional theory (DFT)-based approaches, and of one of the localized variants of the CCSD(T) method. This evaluation revealed that (1) the proposed “silver standard” approach, which employs the localized CCSD(T) method and CBS extrapolations, can be expected to provide accuracy better than two kJ/mol for absolute values of ΔE, and (2) from among the DFT techniques, computationally by far the cheapest approach (termed “ωB97X-3c/vDZP” by its authors) performed remarkably well. These findings are directly applicable in cost-effective yet reliable searches of the potential energy surfaces of noncovalent complexes. Full article

Irreversible perturbations in Langevin dynamics have been widely recognized for their role in accelerating convergence in simulations of multi-modal distributions $\pi \left(\theta \right)$. A commonly used and easily computed standard irreversible perturbation is $J\nabla log\pi \left(\theta \right)$, where J is a skew-symmetric matrix. However, Langevin dynamics employing a fixed-scale standard irreversible perturbation encounter a trade-off between local exploitation and global exploration, associated with small and large scales of standard irreversible perturbation, respectively. To address this trade-off, we introduce the adaptive irreversible perturbations Langevin dynamics, where the scale of the standard irreversible perturbation changes adaptively. Through numerical examples, we demonstrate that adaptive irreversible perturbations in Langevin dynamics can enhance performance compared to fixed-scale irreversible perturbations. Full article

Ground triplet 4,6-bis(trifluoromethyl)-1,3-phenylene bis(tert-butyl nitroxide) (TF2PBN) reacted with [Y(hfac)₃(H₂O)₂] (hfac = 1,1,1,5,5,5-hexafluoropentane-2,4-dionate), affording a doubly hydrogen-bonded adduct [Y(hfac)₃(H₂O)₂(TF2PBN)]. The biradical was recovered from the adduct through recrystallization. Crystallographic analysis indicates that the torsion angles (|θ| ≤ 90°) between the benzene ring and nitroxide groups were 74.9 and 84.8° in the adduct, which are larger than those of the starting material TF2PBN. Steric congestion due to o-trifluoromethyl groups gives rise to the reduction of π-conjugation. Two hydrogen bonds enhance this deformation. Susceptometry of the adduct indicates a ground singlet with 2J/k_B = −128(2) K, where 2J corresponds to the singlet–triplet gap. The observed magneto-structure relation is qualitatively consistent with Rajca’s pioneering work. A density functional theory calculation at the UB3LYP/6-311+G(2d,p) level using the atomic coordinates determined provided a result of 2J/k_B = −162.3 K for the adduct, whilst the corresponding calculation on intact TF2PBN provided +87.2 K. After a comparison among a few known compounds, the 2J vs. |θ| plot shows a negative slope with a critical torsion of 65(3)°. The ferro- and antiferromagnetic coupling contributions are balanced in TF2PBN, being responsible for ground-state interconversion by means of small structural perturbation like hydrogen bonds. Full article

This work systematically examines the interactions between a single argon atom and the edges and faces of cyclic H${}_2$O clusters containing three–five water molecules (Ar(H${}_2$O)${}_{n=3–5}$). Full geometry optimizations and subsequent harmonic vibrational frequency computations were performed using MP2 with a triple-$\zeta$ correlation consistent basis set augmented with diffuse functions on the heavy atoms (cc-pVTZ for H and aug-cc-pVTZ for O and Ar; denoted as haTZ). Optimized structures and harmonic vibrational frequencies were also obtained with the two-body–many-body (2b:Mb) and three-body–many-body (3b:Mb) techniques; here, high-level CCSD(T) computations capture up through the two-body or three-body contributions from the many-body expansion, respectively, while less demanding MP2 computations recover all higher-order contributions. Five unique stationary points have been identified in which Ar binds to the cyclic water trimer, along with four for (H${}_2$O)${}_4$ and three for (H${}_2$O)${}_5$. To the best of our knowledge, eleven of these twelve structures have been characterized here for the first time. Ar consistently binds more strongly to the faces than the edges of the cyclic (H${}_2$O)${}_n$ clusters, by as much as a factor of two. The 3b:Mb electronic energies computed with the haTZ basis set indicate that Ar binds to the faces of the water clusters by at least 3 kJ mol${}^{-1}$ and by nearly 6 kJ mol${}^{-1}$ for one Ar(H${}_2$O)${}_5$ complex. An analysis of the interaction energies for the different binding motifs based on symmetry-adapted perturbation theory (SAPT) indicates that dispersion interactions are primarily responsible for the observed trends. The binding of a single Ar atom to a face of these cyclic water clusters can induce perturbations to the harmonic vibrational frequencies on the order of 5 cm${}^{-1}$ for some hydrogen-bonded OH stretching frequencies. Full article