Miracle-dz/UniFAR-FTUs huggingface dataset:
Density functional theory with London dispersion corrections

Dispersion corrections to standard Kohn–Sham density functional theory (DFT) are reviewed. The focus is on computationally efficient methods for large systems that do not depend on virtual orbitals or rely on separated fragments. The recommended approaches (van der Waals density functional and DFT‐D) are asymptotically correct and can be used in combination with standard or slightly modified (short‐range) exchange–correlation functionals. The importance of the dispersion energy in intramolecular cases (conformational problems and thermochemistry) is highlighted. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 211‐228 DOI: 10.1002/wcms.30
Heat-shock transformation of Escherichia coli in nanolitre droplets formed in a capillary-composited microfluidic device

This work describes an improved method for monodispersed water-in-oil droplet formation and collection using a composite microfluidic device composed of a poly(dimethylsiloxane) (PDMS) microfluidic device and a commercially available quartz capillary. The application of the method to chemical heat-shock (CaCl2-dependent) transformation of Escherichia coli (E. coli) is also presented. With this approach, tunable and uniform different-sized droplets were generated and conveniently collected into a capillary for subsequent experiments. Characterization of droplet size and formation frequency exhibits that droplet behavior is strongly dependent on the ratio (R) of aqueous phase flow rate (Qaq) to oil phase flow rate (Qo). An increase in R induces droplet size and droplet formation frequency increase, which agrees well with a theoretical calculation. To illustrate the application of this droplet-based device in biological fields, as a case study, we also apply this device to the study of heat-shock E. coli transformation. Results demonstrate that plasmid DNA can be effectively transformed into E. coli, and a similar transformation efficiency with the traditional tube-based method can be obtained. This technique provides a new way for droplet generation and easy collection, as well as functional genomics studies by taking advantage of the high throughput of droplet microfluidics.
The relationship between HMW glutenin subunit composition and the bread‐making quality of British‐grown wheat varieties

Based on previous work, which related individual HMW glutenin subunits to bread-making quality by genetical analysis, quality scores were assigned to each of the commonly occurring subunits. The grain proteins of 84 home-grown wheat varieties were fractionated by SDS—PAGE to determine their HMW glutenin subunit composition. The quality scores of each of the subunits were summed to create a Glu-1 quality score for each variety. The results indicated that 47-60% of the variation in the independently established bread-making qualities of this set of varieties could be accounted for by variation in HMW subunits of glutenin. The presence or absence in the varieties of a translocated chromosome, which consisted of the long arm of 1B and the short arm of 1R from rye, was also established because of its known association with poor bread-making quality. A correction factor was applied to the Glu-1 quality score of those varieties that contained the 1 BLURS chromosome. The variations in the rye-adjusted Glu-1 quality scores were compared with those of the bread-making qualities of the varieties, and the proportion of variation in quality accounted for was raised to 55-67%. The Glu-1 quality score and the biscuit-making qualities of the same set of varieties were negatively related. The results are discussed in relation to future strategies recommended to wheat breeders for developing new varieties with improved bread-making quality.
Length preferences and periodicity in β‐strands. Antiparallel edge β‐sheets are more likely to finish in non‐hydrogen bonded rings

We analysed the length distributions of different types of beta-strand in a high resolution, non-homologous set of 500 protein structures, finding differences in their mean lengths. Antiparallel edge strands in strand-turn-strand motifs show a preference for an even number of residues. This propensity is enhanced if the length is corrected for beta-bulges, which insert an extra residue into the strand. Residues in antiparallel edge beta-strands alternate between being in hydrogen bonded and non-hydrogen bonded rings. Antiparallel edges with an even number of residues are more likely to have their final beta residue in a non-hydrogen bonded ring. This suggests that non-hydrogen bonded rings are intrinsically more stable than hydrogen bonded rings, perhaps because its side chain packing is closer. Therefore, we suggest that a simple way to increase beta-hairpin stability, or the stability of an antiparallel edge strand, is to have a non-hydrogen bonded ring at the end of the strand.
The phase behaviour of 1-alkyl-3-methylimidazolium tetrafluoroborates; ionic liquids and ionic liquid crystals

Air- and water-stable 1-alkyl-3-methylimidazolium tetrafluoroborate salts with the general formula [Cn-mim][BF4] (n = 0–18) have been prepared by metathesis from the corresponding chloride or bromide salts. The salts have been characterised by 1H NMR and IR spectroscopy, microanalysis, polarising optical microscopy and differential scanning calorimetry. Those with short alkyl chains (n = 2–10) are isotropic ionic liquids at room temperature and exhibit a wide liquid range, whereas the longer chain analogues are low melting mesomorphic crystalline solids which display an enantiotropic smectic A mesophase. The thermal range of the mesophase increases with increasing chain length and in the case of the longest chain salt prepared, [C18-mim][BF4], the mesophase range is ca. 150 °C.
Identifying annual peaks in dielectric profiles with a selection curve

Abstract A novel ‘selection curve’ method is developed to interpret annual layers in the West Antarctic ice sheet (WAIS) Divide ice core based on dielectric properties (DEP). Because dielectric measurements are non-contact and represent the integrated response of the ice volume, they are particularly useful for the brittle zone of the core. Seasonal differences in ice chemistry create an annual signal in DEP, though multiple peaks of varying strength within a year may complicate the interpretation of annual layers. The selection curve algorithm uses a spline curve whose shape selects successive annual peaks in plots of DEP. This spline curve was scaled to the average annual-layer thickness at a given depth, where the layer thickness was best estimated using the fast Fourier transform (FFT) power spectrum within a sliding 10 m window. To explore the accuracy and stability of the method, several spline curves were generated from varying lengths of calibration data taken from multiple depths in the WAIS core. Using 50 m of manually interpreted calibration data, the selection curve method matched a manual interpretation throughout the entire 1200 m dataset to within 2% root-mean-square error (RMSE). This method is equally applicable to glaciochemical and other time/depth series measurements.
Determination of the elastic constants of cereal grains in a uniaxial compression test

Stress-strain relationships of bulk of seeds were examined under conditions of uniaxial compression with addi- tional measurement of lateral stress. Tests were performed on wheat, rye, barley, oats and rapeseed for five levels of moisture content in a range from 6 to 20%. A constitutive stress-strain relationship formulated for sand was found to describe adequately the 'en masse' mechanical behavior of grain. The elastic constants of the material (Young's modulus E and Poisson's ratio ) were determined using the linear phase of the unloading of the sample. Values of the modulus of elasticity E of cereal grains were found in a range from 10.4 to 23.6 MPa and decreasing with an increase in moisture content. Values of E for rapeseed ranged from 9 to 6.6 MPa for moisture contents of 6 and 15%, respectively. Values of Poisson's ratio of cereal grains were found in a range from 0.22 (wheat - 10.8% of m.c.) to 0.15 (barley - 15.3% of m.c.), while in the case of rapeseed, values of ranged from 0.24 for 6% to 0.10 for 15% of m.c.
Modeling of the Furfural Refining Process for Lubricating Oils

Abstract The effect of operation temperature and furfural/oil ratio on a single-stage furfural refining process for two distillates was studied. The acid number, basic nitrogen, refractive index and aniline point of each of the distillates and the refined oils were measured. They were assumed as four oil components, and the liquid-liquid equilibrium data and corresponding partition coefficients of the pseudo-components could be determined through mass conservation equations and simulated based on the artificial neural networks method. A multistage mathematical model for the refining process was established and solved numerically to give the refined oil quality and recovery under various furfural/oil ratios, temperatures, and stages, which showed a good agreement with those obtained from a pilot plant and the separatory funnel experiments under similar operation conditions. This paper may provide a useful way to assist in determining the optimum conditions and designing plant for the furfural refining process.
Point defects in uranium dioxide

Formation energies of oxygen and uranium vacancies, interstitials and Frenkel pairs as well as Schottky trio defect energies in uranium dioxide are calculated by means of the linear muffin-tin orbital supercell method in the atomic sphere approximation. These ab initio results are in qualitative agreement with experiment and they confirm previous calculations based on semiempirical interaction models. Nevertheless, the gap between some experimental and theoretical values is still not resolved.
Tobacco Smoking and Associated Factors among In-school Adolescents in Vietnam in 2013 and 2019

Tobacco smoking is one of the most dangerous risk behaviors, leading to many adverse human health consequences. The aims of this study is to estimate the prevalence of tobacco smoking and related factor among adolescents aged 13-17 years in Vietnam. The data were from two rounds of the Vietnam Global School-based Student Health Survey (GSHS) that is the nationally representative survey conducted in 2013 and 2019. The logistic regressions were carried out to identify factors associated with tobacco smoking among study participants. We found the prevalence of current smoking (water pipe and cigarettes) reduced significantly from 5.4% (95% CI: 4.0-7.2) in 2013 to 2.8% (95% CI: 2.2-3.6) in 2019. In 2019, 2.6% of students used electronic cigarette products in the last 30 days. Factors associated with higher odds of current smoking status included study year, gender, parental monitoring, loneliness, suicide attempt, sexual intercourse, truancy, alcohol drinking. Similar patterns were found in e-cigarette use. Smoking among adolescents in Vietnam reduced between 2013 and 2019. Further follow-up studies are needed to confirm the causal factors of the reduction and e-cigarettes use.
The effect of Origanum onites L., Rosmarinus officinalis L. and Schinus molle L. on in vitro digestibility in lamb

The objective of this study was to evaluate the effects of different levels of aromatic plants (AP);“Origanum onites L. (ORE), Rosmarinus officinalis L. (ROS) and Schinus molle L. (SHN)” on in vitro gas production (GP), organic matter digestibility (OMD) and net energy lactation (NEL) using an in vitro gas-production method. Two rumen-fistulated sheep were used in the experiment. The sheep were fed with 60% of alfalfa hay and 40% of concentrate feed twice daily. Five different levels of ORE, ROS, and SHN were added to the concentrate (CON) to produce 200 mg KM (C - without , AP; 1 - 0.02 mg AP + 198 mg CON; 2 - 0.04 mg AP + 196 mg CON; 3 - 0.06 mg AP + 194 mg CON; 4 - 0.08 mg AP + 192 mg CON; 5 0.10 mg AP + 190 mg CON). The volume of gas produced was recorded at 2, 4, 8, 12, and 24 h after incubation. The results showed that, GP, OMD and NEL contents decreased significantly as the level of ORE, ROS, and SHN added to CON increased. It was concluded that, ORE, ROS, and SHN are potential supplements that alter rumen fermentation. To obtain exact results, the findings obtained under in vitro conditions should be supported by in vivo studies.
A PEACH STONE ACTIVATED CARBON CHEMICALLY MODIFIED TO ADSORB AQUEOUS AMMONIA

The oxidation of an activated carbon prepared from peach stones as well as the adsorption of aqueous ammonia using untreated and modified carbons is described here in. Boehm method in conjunction with temperature-programmed desorption (TPD) were mainly used to assess the chemical changes. These methods were complemented by chemical analysis, pH measurements and FT-IR spectra. Textural characterization was obtained from CO2 and N2 adsorption. Chemical modifications performed under the same experimental conditions with aqueous solutions of HNO3 and H2O2 indicated evidences that carboxylic acids like group formation is enhanced by short periods of time of HNO3 treatment at temperatures about 353 K followed by a mild oven-dry process in atmospheric air. The activated carbon modified under such conditions resulted to be the best ammonia adsorbent
A phase one trial of carfilzomib, bendamustine, and dexamethasone in relapsed and/or refractory multiple myeloma

AP-HP, GHU Paris-Saclay, Hôpital Bicêtre, Service de Médecine Interne et Immunologie Clinique, Le Kremlin Bicêtre, France INSERM, Institut National de la Santé et de la Recherche Médicale Université Paris Saclay (COMUE), Le Kremlin-Bicêtre, France CEA, DSV/iMETI, IDMIT, Fontenay-aux-Roses, France Neurology Department, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Paris Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France INSERM U1195 & Paris Saclay University, Le Kremlin Bicêtre, France Faculté de Médecine, Université Paris Saclay, Le Kremlin Bicêtre, France
Simulations of Polymer Cyclization by Brownian Dynamics

The dynamic characteristics of polymers in dilute solution, such as the end-to-end distance relaxation time, τ m , and the time of diffusion-controlled cyclization, τ a , were studied using Brownian dynamics simulations. The major goal was to estimate the effect of the impenetrability of the chain backbone on the dynamic properties. We compared several models of polymer chains: phantom ones with and without excluded volume and a nonphantom model with excluded volume. The hydrodynamic interaction between chain segments was not taken into account. The impenetrability of a chain is found to have a small effect on the magnitude of τ m . For sufficiently long chains, τ m exceeded the value for phantom chains by factor of 1.5. The ratio τ a /τ m remained the same for the phantom and nonphantom models. On the other hand, the excluded volume effect changed the dependence of τ m on the chain contour length, in accordance with the known theoretical conclusions. In addition, the presence of excluded volume caused a 2-fold increase of the scaling factor between τ a and τ m for sufficiently long chains. This scaling factor and, consequently, τ a appeared to be reciprocally proportional to the reaction radius R. When the reaction radius is close to the statistical segment length λ, τ a was estimated as τ a = ζ(l/R)τ m , where the coefficient ζ is equal to 1.3 ± 0.2 and 2.6 ± 0.3 for chains without and with excluded volume, respectively.
Sodium deficiency in Na0.5Bi0.5TiO3

The mechanism of solid-state synthesis for Na0.5Bi0. 5TiO3 was investigated using X-ray powder diffraction, scanning electron microscopy and wavelength-dispersive X-ray spectroscopy. The results showed that a Na0.5−xBi0.5TiO3−x/2 homogeneity region, with Na0.5Bi0. 5TiO3 and Na0.47Bi0. 5TiO3−δ as the end-members (0 ≤ x ≤ 0.03), exists in the Na2O–Bi2O3–TiO2 system. The formation of any member from the homogeneity region starts with the formation of the deficient end-member, i.e., Na0.47Bi0. 5TiO3−δ. However, the reaction continues toward a nominal composition when a sufficiently high temperature and/or a long firing time are used. The conversion of the latter reaction may be followed by the observation of the crystal symmetry, which changes from the cubic-like toward the rhombohedral as the reaction proceeds from Na0.47Bi0. 5TiO3−δ to Na0.5Bi0. 5TiO3. Differences in the dielectric, ferroelectric and piezoelectric properties were observed for the samples from the homogeneity region, and these can be related to the stoichiometry variation along the homogeneity region and thus to the variation in the vacancy concentration. The most striking difference is the change in the piezoelectric constant d33, which increases from 82 pC N−1 to 97 pC N−1 as the composition of the ceramics changes from Na0.5Bi0. 5TiO3 to Na0.47Bi0. 5TiO3−δ.
Controls on the Sorption, Desorption and Mineralization of Low‐Molecular‐Weight Organic Acids in Variable‐Charge Soils

Understanding the controls on interactions between soluble organic compounds and the solid soil matrix is important in understanding soil organic matter dynamics in general, including specific impacts on pedogenic processes, nutrient bioavailability, and C sequestration. This study investigated the pH-dependent relationship between low-molecular-weight organic acids (LMWOAs) and variable-charge soils as a control on the retention of an otherwise highly mobile and bioavailable class of organic compounds. Sorption isotherms of three LMWOAs (one amino acid [glycine], one monocarboxylic acid [propionic acid], and one dicarboxylic acid [malonic acid]) were generated for three forest soils using batch equilibration techniques. Before equilibration, soils were saturated with KCl to control for competing ions, and both soils and solutions were adjusted to one of three pH levels (4.0, 6.0, or 8.0 ± 0.1). Bioavailability was assessed by generating desorption isotherms for each LMWOA-pH combination as well as through laboratory incubations for mineralization rates. Results indicate that sorption of the three LMWOAs followed the general trend: malonic acid » glycine > propionic acid. Sorption tended to increase with acidity and short-range-ordered aluminosilicate content, and was correlated (r = 0.69, P < 0.001) with the magnitude of the difference between the positive charge on the mineral surface and the negative charge of the LMWOA. This trend remained true for the amino acid, which demonstrated sorptive maximums that were more strongly correlated with anion exchange (r = 0.62, P = 0.1) than cation exchange (r = 0.05, P = 0.9). These observations, coupled with decreased desorption and lower mineralization rates at lower pH levels, suggest the potential for an electrostatic mechanism to contribute to the abiotic retention of organic matter in variable-charge soils under acidic conditions.
Reflectivity and absorption coefficient of a borosilicate glass during 60Co-γ irradiation calculated from data measured by an integrating sphere

Before and after 11 kGy 60Co-γ irradiation as well as after 150°C bleaching, reflectivity and absorption coefficient of a borosilicate glass were calculated from the intensity of transmitted light and the intensity of reflected light measured using an integrating sphere. The irradiation induced absorption in the studied wavelength range, while it only made the reflectivity change obviously in the range 4.5–5.6 eV (275–221 nm). The absorption coefficient spectrum and the reflectivity spectrum of the irradiated glass both recovered to a degree after 150°C bleaching. The relative error of irradiation-induced absorption coefficient calculated neglecting reflectivity change was studied, and the relative errors in the studied wavelength range theoretically increase when the thickness of glass sheet decreases, so if irradiation-induced absorption coefficients are studied using a thin glass sheet, reflectivity changes should be considered. The band gap of the glass was studied using Mott and Davis's theory, and it was found to reduce after irradiation, then after 150°C bleaching, it increased but still smaller than the one before irradiation.
Design and development of novel reactive amine nanocontainers for a self-healing epoxy adhesive: self-repairing investigation using the lap shear test

A self-healing epoxy adhesive is reported based on a commercial structural adhesive which has the ability to heal under room temperature conditions. Various reactive amine nanocontainers were achieved via a simple and novel double emulsion technique and characterized by spectroscopic study. The effect of the shell wall structure of the nanocontainers on the adhesion properties of the epoxy adhesive in steel–steel, aluminum–aluminum and copper–copper metal junctions was studied in detail. Virgin fracture toughness and recovery of fracture toughness of the adhesives were evaluated through lap shear strength test. The overall results open the door for the application of the lap shear strength test in self-healing adhesives. For further investigation, the self-healing ability of the fabricated adhesives was characterized by FT-IR, fluorescence and SEM microscopy.
Total Viable Count and Concentration of Enteric Bacteria in Bottom Sediments from the Czarna Hańcza River , Northeast Poland

Studies were carried out to determine counts of TVC 20°C, TVC 37°C, TC, FC, FS and Clostridium perfringens in bottom sediments of the Czarna Haricza River, from about 1 cm layer, at 10 stations located in Suwatki region (stations 1 and 2), in the villages Sobolewo (stations 3 and 4), the old river bed of the Czarna Hancza and its inflow to Lake Wigry (stations 5 and 6), and in the villages Czerwony Folwark, Mackowa Ruda, Buda Ruska and Wysoki Most (stations 7-10) east of Lake Wigry. Bottom sediments from stations 1 -4 and 7-10 were mostly sandy, while at stations 5 and 6 they dominated by silty clay. Studies were carried out in 1995 and 1996, at monthly intervals with the exception of winter. Water was examined at the same time. All groups of indicatory bacteria were 100-1000 times more numerous in the bottom sediments than in water. They were usually least numerous in sandy bottom sediments, especially in the villages Buda Ruska and Wysoki Most (stations 9 and 10), and the highest in silty clay sediments in the region of the old Czarna Hancza bed and its inflow to Lake Wigry (stations 5 and 6). Minimal and maximal counts of indicatory bacteria were noted in different months upon particular sampling stations. Only sometimes curves of their numbers corresponded to the respective courves of bacteria counts in water. It is suggested that sanitary and bacteriological studies of water should be supplemented by respective studies of the surface layer of bottom sediments.
A Robust Homotopy Continuation Method for Seeking All Real Roots of Unconstrained Systems of Nonlinear Algebraic and Transcendental Equations

A new homotopy developed for finding all real roots to a single nonlinear equation is extended to a system of nonlinear algebraic and transcendental equations written as f{x} = 0 to find all real roots, including those on isolas. To reach roots that may lie on isolas, the functions are squared. This causes all roots to be bifurcation points that are connected to each other through stemming branches. As a result, a new system of homotopy functions, including numerous bifurcation points, is formed as H{x,t} = (x − x0)(1 + f2 − t), where x0 is the starting point. Because the functions are squared, many systems of equations must be solved to find a starting point on a reduced system of homotopy functions written as H{x,t} = 1 + f2 − t. Therefore, robustness is achieved at the expense of increased computation time. To improve the efficiency of the algorithm, the Levenberg−Marquardt method is used to find the starting point for the reduced homotopy system by solving a system of nonlinear equations with the degr.