Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient calculation of two‐dimensional adiabatic and free energy maps: Application to the isomerization of the C13C14 and C15N16 bonds in the retinal of bacteriorhodopsin

Accurate calculation of potential energy and free‐energy profiles along reaction coordinates of biological processes such as enzymatic reactions or conformational changes is fundamental to the obtention of theoretical insight into protein function. We describe here the practical implementation of the Automatic Map Refinement Procedure (AMRP) and two‐dimensional Weighted Histogram Analysis Method (WHAM) for efficient computation of adiabatic potential energy and free‐energy maps, respectively. Methods for efficiently sampling configuration space with high‐energy barriers and for removing hysteresis in the case of periodic reaction coordinates are presented. The application of these techniques to the isomerization of the C13C14 and C15N16 bonds in the retinal of bacteriorhodopsin is described. In dark‐adapted bacteriorhodopsin (bR), the retinal moiety exists in two conformers, all‐trans and (13,15)cis, with the latter making ≃67% of the population. This experimental free energy difference is reproduced here to within kBT. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1644–1658, 1999
The Glucose-Lowering Effects of Coconut Oil: A Case Report and Review of the Literature

Background Coconut oil, a saturated fat comprised mostly of the medium-chain fatty acid, lauric acid, has become increasingly popular over the past few decades due to its touted anti-inflammatory, metabolic, and lipid-lowering properties. There have been many studies with mixed results evaluating the effects of coconut oil consumption on lipid metabolism and cardiometabolic risk. However, the effects on glucose metabolism are less clear. There are few trials on the effects of coconut oil on glucose homeostasis but no case reports prior to the current one. Case We present a case of a 66-year-old man with a history of type 2 diabetes managed with insulin who developed recurrent hypoglycemia and required reduction in insulin therapy quickly after consuming coconut oil supplementation. Conclusion This is the first known case report of coconut oil supplementation in a diabetic patient on insulin resulting in hypoglycemia. Review of the literature shows that coconut oil supplementation can have a favorable effect on glycemic control, possibly through phenolic compounds mediating anti-inflammatory effects. This effect is inconsistent throughout the studies reviewed, likely due to variations in types of coconut oil supplementation and scarcity of trials. Further research is required both in animal models and in humans before coconut oil intake is widely advised and popularized. This is especially true in patients with diabetes, who are at increased risk of cardiovascular disease, and in whom reduction in saturated fat intake is advised.
Two general methods for grand canonical ensemble simulation of molecules with internal flexibility

Two simulation methods are presented for generating a grand canonical ensemble of molecules with internal degrees of freedom. Molecular dynamics integration is used as a Monte Carlo perturbation move in these methods. The integration move helps to explore the intramolecular degrees of freedom with high acceptance ratios. The proofs of the acceptance criteria for both methods are presented. Tests are described to show that the simulation produces results matching an analytical solution for a simple test system. The method is further tested by predicting adsorption isotherms of n-butane in the zeolite silicalite. An example using these algorithms to generate adsorption isotherms of more complex chiral molecules in chiral zeolitelike materials is also presented.
Comparation of Anti-Inflammatory and Antioxidantactivities of Curcumin, Tetrahydrocurcuminand Octahydrocurcuminin LPS-Stimulated RAW264.7 Macrophages

Curcumin (CUR) possesses pronounced anti-inflammatory and antioxidant activities. Generally, the clinical application of CUR is restricted due to its apparent unstability and poor absorption, and the biological activities of CUR may be closely associated with its metabolites. Tetrahydrocurcumin (THC) and octahydrocurcumin (OHC) are two major hydrogenated metabolites of CUR with appreciable biological potentials. Here, we comparatively explored the anti-inflammatory and antioxidant activities of CUR, THC, and OHC in lipopolysaccharide- (LPS-) induced RAW264.7 macrophages. The results revealed that CUR, THC, and OHC dose-dependently inhibited the generation of NO and MCP-1 as well as the gene expression of MCP-1 and iNOS. Additionally, CUR, THC, and OHC significantly inhibited NF-κB activation and p38MAPK and ERK phosphorylation, while substantially upregulated the Nrf2 target gene expression (HO-1, NQO-1, GCLC, and GCLM). Nevertheless, zinc protoporphyrin (ZnPP), a typical HO-1 inhibitor, significantly reversed the alleviative effect of CUR, THC, and OHC on LPS-stimulated ROS generation. These results demonstrated that CUR, THC, and OHC exerted beneficial effect on LPS-stimulated inflammatory and oxidative responses, at least partially, through inhibiting the NF-κB and MAPKs pathways and activating Nrf2-regulated antioxidant gene expression. Particularly, THC and OHC might exert superior antioxidant and anti-inflammatory activities to CUR in LPS-stimulated RAW264.7 cells, which can be further explored to be a promising novel effective agent for inflammatory treatment.
A Modified Quasisteady Aerodynamic Model for a Sub-100 mg Insect-Inspired Flapping-Wing Robot

This study proposes a modified quasisteady aerodynamic model for the sub-100-milligram insect-inspired flapping-wing robot presented by the authors in a previous paper. The model, which is based on blade-element theory, considers the aerodynamic mechanisms of circulation, dissipation, and added-mass, as well as the inertial effect. The aerodynamic force and moment acting on the wing are calculated based on the two-degree-of-freedom (2-DOF) wing kinematics of flapping and rotating. In order to validate the model, we used a binocular high-speed photography system and a customized lift measurement system to perform simultaneous measurements of the wing kinematics and the lift of the robot under different input voltages. The results of these measurements were all in close agreement with the estimates generated by the proposed model. In addition, based on the model, this study analyzes the 2-DOF flapping-wing dynamics of the robot and provides an estimate of the passive rotation—the main factor in generating lift—from the measured flapping kinematics. The analysis also reveals that the calculated rotating kinematics of the wing under different input voltages accord well with the measured rotating kinematics. We expect that the model presented here will be useful in developing a control strategy for our sub-100 mg insect-inspired flapping-wing robot.
A comparative study of electrochemically formed and vacuum-deposited n-GaAs/Au Schottky barriers using ballistic electron emission microscopy (BEEM).

A comparative study between n-GaAs/Au contacts, formed by electrochemical deposition or by vacuum evaporation, is presented. The main parameter, the barrier height ? B, was determined using three methods, i.e.? classical current-voltage and capacitance-voltage measurements as well as STM-based ballistic electron emission microscopy (BEEM). The latter method allowed us to determine the distribution of ? B over the contact area on a nanometre scale and showed that the electrochemically made contacts are inhomogeneous. The main result, confirmed by the three methods, was that ? B was higher for the electrochemically deposited contacts than for the evaporated ones. This higher value is attributed to O- groups, present at the interface during the electrochemical metallization, and forming interfacial dipoles with the Au, leading to an increase of the barrier.
miRNA-451a and miRNA-125a Expression Levels in Ankylosing Spondylitis: Impact on Disease Diagnosis, Prognosis, and Outcomes

Background Early diagnosis of ankylosing spondylitis (AS) is yet not elucidated, with a potential diagnostic glance of microRNAs (miRNAs). Aim Study the expression profile of miRNA-451a and miRNA-125a in AS patients and their impact on disease activity and prognosis. Methods A cross-sectional study included 55 AS patients diagnosed according to modified New York criteria in 1984 with 55 matched healthy controls. History, clinical examination, and disease activity assessment with Bath ankylosing spondylitis disease activity index (BASDAI) were done. Full laboratory and radiological assessment along with expression profile of m iRNA-451a and miRNA-125a were tabulated and analyzed. Results Higher expression levels of miRNA-125a and lower of miRNA-451a in AS patients compared to controls. Furthermore, miRNA-125a expression was high in active AS patients compared to inactive patients and controls (7.0 ± 3.4 vs. 4.1 ± 2.1 vs. 2.6 ± 0.6, p < 0.001, respectively). miRNA-451a was significantly lower in active AS patients compared to inactive patients and controls (2.2 ± 1.1 vs. 4.1 ± 2.3 vs. 7.1 ± 4.5, respectively). Both miRNAs (miRNA-125a and miRNA-451a) had evident accuracy for AS diagnosis with areas under the curve (AUC) of 0.788 and 0.802, respectively. miRNA-125a had potential impact on AS activity with AUC of 0.777. Plasma levels of both miRNAs were able to distinguish AS patients with structural damage with AUCs 0.775 and 0.692, respectively. Conclusions Both miRNA-451a and miRNA-125a were found to be of great value as sensitive noninvasive diagnostic, prognostic, and disease burden biomarker of AS patients in Egypt with suggested further studies for future therapeutic implications.
A core competency model for clinical informationists

Objectives: Access to high-quality information improves the quality of patient care, but lack of time and sufficient skills in information seeking can prevent access to information by clinicians. To solve this problem, clinical informationists can provide high-quality, filtered information for clinical team members. This study identified the core competencies that clinical informationists need to effectively fulfill their roles on clinical teams. Methods: Participants were selected purposefully from clinicians and medical librarians. Data were collected through semi-structured interviews and analyzed using qualitative content analysis. Results: The authors identified six competencies—communication, research, education and training, domain knowledge, information services, and technology—which together were used to develop a “CREDIT” model of core competencies for clinical informationists. Conclusions: The CREDIT model can be used as criteria for evaluating the performance of clinical informationists as well as for developing and assessing clinical informationist educational programs and curriculums.
Beneficial Effects of Rosmarinic Acid on IPEC-J2 Cells Exposed to the Combination of Deoxynivalenol and T-2 Toxin

Mycotoxin contamination in feedstuffs is a worldwide problem that causes serious health issues both in humans and animals, and it contributes to serious economic losses. Deoxynivalenol (DON) and T-2 toxin (T-2) are major trichothecene mycotoxins and are known to challenge mainly intestinal barrier functions. Polyphenolic rosmarinic acid (RA) appeared to have antioxidant and anti-inflammatory properties in vitro. The aim of this study was to investigate protective effects of RA against DON and T-2 or combined mycotoxin-induced intestinal damage in nontumorigenic porcine cell line, IPEC-J2. It was ascertained that simultaneous treatment of DON and T-2 (DT2: 1 μmol/L DON + 5 nmol/L T − 2) for 48 h and 72 h reduced transepithelial electrical resistance of cell monolayer, which was restored by 50 μmol/L RA application. It was also found that DT2 for 48 h and 72 h could induce oxidative stress and elevate interleukin-6 (IL-6) and interleukin-8 (IL-8) levels significantly, which were alleviated by the administration of RA. DT2 administration contributed to the redistribution of claudin-1; however, occludin membranous localization was not altered by combined mycotoxin treatment. In conclusion, beneficial effect of RA was exerted on DT2-deteriorated cell monolayer integrity and on the perturbated redox status of IPEC-J2 cells.
Model of the selective laser sintering of bisphenol-A polycarbonate

Selective laser sintering (SLS) is a new additive process for rapidly preparing prototype parts by selectively fusing portions of layers of polymer powder with a rastered, modulated, CO 2 laser beam. Layer to layer fusion is important for achieving good mechanics properties. Generally, the fusion depth is found to be a function of laser beam overlap on adjacent scans, scan speed, and intensity. It is also a function of the kinetic rates of powder sintering and of heat transfer. A one-dimensional model of the SLS thermal process is presented that can accurately predict, to within 20%, the effect of these process and material parameters on experimentally observed fusion depths in bisphenol-A polycarbonate powders
A comprehensive experimental investigation of tubular entry flow of viscoelastic fluids: Part I. Vortex characteristics in stable flow

The characteristics of a vortex found at the entry of a 2:1 and 4:1 contraction for viscoelastic fluids is investigated. Two distinct flow regimes are identified in the contraction flow field: a vortex growth regime and a divergent flow regime. In the vortex flow regime, rheological forces are found to dominate the flow, with the vortex detachment length being a linear function of the Weissenberg number. In the divergent flow regime, the flow is found to diverge at the center line upstream of the vortex detachment plane, and the vortex size decreases with increasing flow rates. Inertial forces are important in the divergent flow regime. The entry flow characteristics for the 2:1 and 4:1 contraction are quantified in terms of the vortex detachment length as a function of Reynolds and Weissenberg number over the range of 0:2 < N′Re < 200 and 0.10 < NWS < 0.7.
Theoretical study of the effects of vibrational‐rotational interactions on the Raman spectrum of N2

A systematic study of the polarizability and polarizability derivatives of N2 is undertaken as a function of basis set and level of correlation treatment. The value obtained for the ratio of derivatives (re β′e/βe) of the polarizability anisotropy β=α∥−α⊥ is 3.15±0.2, which is larger than the two experimental estimates of 2.63±0.29 and 2.22±0.44.
Soil erosion prediction using MMF model on highly dissected hilly terrain of Ekiti environs in southwestern Nigeria

Assessment of soil erosion risk is important to formulate effective soil conservation plans for sustainable development. Information from remote sensing techniques can help decision makers prepare resource map accurately in less time and cost. GIS assists in linking those maps with other information related to geographic location and helps modeling, analyzing and solving complex problems. The objective of this study was to assess the potential of Morgan, Morgan and Finney (MMF) Model (Morgan et al., 1984) in predicting soil erosion in an agrarian Ekiti environment with highly dissected hilly and rolling terrain in southwestern Nigeria. Soil loss prediction by MMF approach involve factor maps from kinetic energy of rainfall, topsoil rooting depth, percentage rainfall contri-buting to permanent interception and stream flow, crop cover management factor, ratio of actual to potential evapotranspiration, soil moisture storage capacity. These were used to generate output maps like volume of overland flow, rate of soil detachment by raindrop impact and transport capacity of overland flow. Annual soil loss estimation was calculated by comparing two maps of soil detachment rate and transport capacity and taking the minimum value from them. Results showed that MMF model could predict erosion risks effectively in the highly dissected hilly and rolling landscape of Ekiti environ. Erosion was low in the area in spite of the landscape. The highest soil loss was 1.275 kgm-2 yr-1 from rock hill with slope greater than 15%. The lowest was 0.942 kgm-2 yr-1 at low lands covered with riparian forest. The average estimated annual soil loss of the study area was 1.112 kgm-2, which is less than tolerable standard of 1 kg 1233 m-2 yr-1. The MMF model shows that the current land-use/cover in Ekiti environs is sustainable because erosion risk is below the critical level. Key words: Soil erosion, MMF model, land use, hilly landscape, Nigeria.
Coupled channel bound states calculations for alkali dimers using the Fourier grid method

The Fourier grid Hamiltonian method is shown to be a powerful method to provide an accurate determination of the bound state spectra of coupled electronic states in alkali dimers. Using accurate ab initio potentials, the perturbations in the spectra of the coupled states A 1Σ+u and b 3Πu in Na2 are reproduced in excellent agreement with spectroscopic studies. A few predictions are also presented for the heavier species Cs2, for which a complete study, both experimental and theoretical, is still needed.
Opposite effects of successive hydration shells on the aqua ion structure of metal cations

The conformation adopted by water molecules around a metal ion in aqueous solution can be approached from a discrete representation of the solvent by studying the structure and stability of microsolvation clusters including a different number of water molecules. In this contribution, we present a quantum mechanics and ab initio molecular dynamics study on how the arrangement of water molecules around and shows preferentially a T h or S 6 symmetry depending on the number of hydration shells explicitly included in the calculation. The behaviour observed for both cases is the following: (1) for a cluster composed of the metal ion plus a first hydration shell, the preferred geometry shows a T h symmetry; (2) when a second hydration shell is added, a minimum can be found with an S 6 disposition of water molecules around the metal centre; (3) however, if a third hydration shell is considered a T h arrangement of water molecules around the central ion is strongly favoured. The structures of the different solvation complexes studied in this work are characterised. The preference for a T h or S 6 distribution of water ligands is rationalised in terms of total energies, interaction energies and the hydrogen bond network.
PZT Thin Film Preparation on Pt-Ti Electrode by RF Sputtering

Pt-Ti alloy films were studied for use as a lower electrode of the ferroelectric lead zirconate titanate (PZT) thin film capacitor. Pt-Ti alloy films with different Ti/Pt atomic ratios were first prepared by rf sputtering. Subsequently, PZT thin films were deposited also by rf magnetron sputtering on the Pt-Ti alloy metals. The Ti/Pt ratio in the alloy was found to strongly affect the crystal structure formation and the composition of the PZT thin films. The Ti/Pt ratio range from 0.02 to 0.17 was shown to bring about a preferable perovskite-type structure and a reproducible constant composition. The effect of Ti atoms in the Pt-Ti lower electrode was discussed in connection with the Pb atom evaporation rate.
Velocity dependence and rest time effect on nanoscale friction of ultrathin films at high sliding velocities

Micro∕nanoelectromechanical system devices and components often operate at high sliding velocities, and it requires the investigation of friction at high velocities. In this study, the velocity dependence of friction and the rest time effect on friction of hard diamondlike carbon films, soft perfluorodecyltrichlorosilane, and perfluoropolyether films were investigated up to 2×105μm∕s using an ultrahigh velocity stage and a high velocity stage. The velocity dependence of friction was found to vary with films and involve different mechanisms including adhesion due to solid-solid interaction, adhesion due to formation of meniscus bridges, atomic-scale stick slip, high velocity impact of the contacting asperities∕molecules, phase transformation∕tip jump, and viscoelastic shear. The increase in friction as a function of rest time was caused by continued growth and formation of water menisci bridges for the hydrophilic surfaces and continued deformation of soft films.
Nature of the Hydrogen Bond

Starting from a molecular orbital viewpoint, a general description is given of hydrogen bonds X—H···Y. The case of weak hydrogen bonds, as in associated liquids, is developed in detail, with the O–H···O bond as an example. The new feature in the treatment is the introduction of excited 2s and 2p orbitals of the hydrogen atom (Sec. II), the consequences of which, it is shown, provide a satisfactory account of the effects of hydrogen bonding both on the X—H stretching infrared band and on dipole moments (Sec. IV). The energy change accompanying hydrogen bond formation is considered as depending on the nature of the hybridization of the atomic orbitals involved (Sec. V). Again it is found that the experimental pattern is reproduced when the 2s and 2p orbitals of hydrogen are included. Moreover the behavior of the energy as a function of the hybridization parameters suggests a way in which the changes in the Xmdash;H bond and in the atom Y can account for the various properties observed in molecular associatio.
Ion chromatography as a tool for the investigation of unsymmetrical hydrazine degradation in soils

A new procedure for the determination of 1,1-dimethylhydrazine (UDMH) in soil samples was developed. This involves the distillation of UDMH from an alkaline suspension of soil and ion chromatographic analysis of the distillate. The separation was performed on a silica cation-exchanger column with ammonium acetate buffer solution as mobile phase and amperometric detection at +1.2 V. Hydrazine (Hy) and methylhydrazine (MH), which are decomposition products of UDMH, can be determined simultaneously. The limits of detection in aqueous solutions were 0.2, 0.5 and 1 µg L−1 for Hy, MH and UDMH, respectively. The developed technique was used for investigating the behaviour of UDMH in spills of rocket fuels on soils. It was found that the addition of 4 kg m−2 UDMH resulted in a 0.02% residue one year after the soil treatment. The vertical migration of UDMH in soil was less than 50 cm.
InP/InGaAs Composite Metal–Oxide–Semiconductor Field-Effect Transistors with Regrown Source and Al2O3 Gate Dielectric Exhibiting Maximum Drain Current Exceeding 1.3 mA/µm

We have realized InP/InGaAs composite-channel metal–oxide–semiconductor field-effect transistors with both selectively regrown n+-InGaAs source/drain regions and Al2O3 as a gate dielectric. A 100-nm-long channel was fabricated by laterally buried regrowth in a channel undercut by metalorganic vapor phase epitaxy. The carrier density of the regrown layer was 2.9×1019 cm-3. A drain current Id of 1.34 mA/µm was achieved at a drain voltage Vd of 1 V and a gate voltage Vg of 3 V. A transconductance gm of 817 µS/µm at Vd = 0.65 V was also observed at the same time. The improvement in the subthreshold slope can be explained by the decrease in dielectric/semiconductor interface trap density.