Miracle-dz/UniFAR-FTUs huggingface dataset:
Toward the semiquantitative estimation of binding constants guides for peptide peptide binding in aqueous solution

An expression is presented for the estimation of approximate binding constants for bimolecular associations in solution. The consequences of the approach have been examined for the bimolecular association of two peptide components in aqueous solution: specifically for the binding of two vancomycin group antibiotics, vancomycin itself and ristocetin A, to the peptide cell wall analogue ^V-Ac-D-AIa-D-AIa and related ligands. Uncertainties in the treatment are relatively large, but the physical insights gained into the binding process (in part with the aid of calorimetric data obtained by others) are enlightening. We conclude that for amide-amide hydrogen bond formation in aqueous solution at room temperature, the intrinsic binding energy is ca. 24 kJ mol"1 (an intrinsic binding constant of ca. 104); this process is almost completely driven by a favorable entropy change associated with the release of water molecules from the amide NH and CO groups involved in hydrogen bond formation. The bimolecular association of N-Ac-D-AIa-D-Ala with ristocetin A has a remarkably small entropy change at 298 K (TAS = 3 ± 1.5 kJ mol"1)- We conclude that the release of water from polar and hydrocarbon groups involved in the binding almost exactly compensates for (i) the unfavorable entropy change due to the freezing out of four rotors of /V-Ac-D-AIa-D-AIa upon binding and (ii) the unfavorable entropy change of a bimolecular association. A crude quantitation of these effects is presented. We also present an estimate of the increase in translational plus rotational free energy, as a function of the ligand mass, occurring when a ligand binds to a larger receptor. This quantity, fundamental to all binding processes, is relatively insensitive to the shape of the ligand. Extension of the approach will allow, in those cases where there is good complementarity between ligand and receptor, the prediction of approximate peptide-peptide binding constants in aqueous solution.
Binding pocket shape analysis for protein function prediction

Structural Genomics initiatives are generating an increasing number of protein structures with very limited biochemical characterisation. The analysis and functional assignment of protein structure is a key challenge and a major bottleneck towards the goal of well-annotated genomes. As shape plays a crucial rôle in biomolecular recognition and function, the development of shape analysis techniques is important for understanding protein structure-function relationships. Protein surfaces typically contain clefts of different shapes and sizes. It has been shown that for enzymes, the active site is commonly found in the largest cleft, Laskowski et al. (1996). This makes the detection of the active site relatively straightforward, and can be performed by a program such as SURFNET, Laskowski (1995). SURFNET does this by placing expandable spheres between protein atoms such that the radii of these spheres does not penetrate the two protein atoms or any nearby atoms. The union of all such spheres is used by SURFNET to describe the 3D cleft shape. Residue conservation can be used to improve the binding pocket prediction, Glaser et al. (2005). In this contribution, we present an efficient method for comparing protein binding pockets based on a spherical harmonics expansion. Binding pocket shapes are approximated as functions on the unit sphere by describing each surface point by its spherical coordinates and setting , Morris et al. (2005). The same methodology can be applied to enhance the description by including other properties such as the electrostatic potential, Ritchie and Kemp (1999, 2000).
Mg3MnH7, Containing the First Known Hexahydridomanganese(I) Complex.

Mg 3 MnH 7 was synthesised by reacting MgH 2 with manganese powder in a 3:1 molar ratio at 20 kbar and 1070 K for 120 min, and investigated by neutron powder diffraction on its deuteride. It crystallises with the hexagonal Mg 3 ReH 7 structure type (space group P6 3 /mmc, Z=2, a=4.7099(1), c=10.2861(3) A (hydride); a=4.6998(1), c=10.2590(2) A (deuteride). Manganese is nearly octahedrally co-ordinated by deuterium with bond distances of 1.629(3) A and bond angles of 89.17(14) and 90.83(2)°. An additional deuteride-anion is co-ordinated by five magnesium cations in a trigonal pyramidal way. Mg 3 MnH 7 decomposes between 530 K and 640 K under 1 bar hydrogen pressure into elemental manganese and magnesium. Its hydrogen storage efficiency is 5.2 wt % or 118.5 g H 2 l -1 .
Non‐destructive Crack detection using GMI sensor

In this study, the variation of the magnetic flux distribution in a magnetised ferromagnetic material which has inhomogeneity as a crack is studied using giant magnetoimpedance, GMI, sensor. The sensor was moved by a specially designed moving system. The amorphous (Co0.94Fe0.06)72.5Si12. 5B15 wire was used as a GMI sensor and 1 MHz with 5 mA ac current applied to the GMI sensor. A large decrease in the output voltage of the sensor circuit was observed when the sensor was moved on the top of the crack, after the further movement of the sensor the output voltage came back to the nearly previous value. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Adsorptive Stripping Voltammetric Determination of Imipramine and Amitriptiline at a Nanoclay Composite Carbon Ionic Liquid Electrode

A new carbon nanocomposite electrode has been designed by incorporation of montmorillonite nanoclay into a carbon ionic liquid electrode for the electrochemical determination of imipramine (IMP) and amitriptyline (AMT). They are expected to accumulate on the electrode surface through the cooperative interaction of ionic liquid and clay with the drugs. The proposed electrode also possesses attractive electrocatalytic effects towards the drugs especially AMT. Low detection limits of 19 nM for IMP and 24 nM for AMT were achieved. The proposed nanocomposite electrode exhibits good applicability for monitoring IMP and AMT in pharmaceutical formulations and blood serum samples.
STUDIES ON THE POTASSIUM-SUPPLYING CAPACITIES OF SOUTHERN ONTARIO SOILS. III. MEASUREMENT OF AVAILABLE K

This study was conducted to determine which of eight different extractants best described the K-supplying capacities of nine southern Ontario soils. The total amount of K extracted by eight crops of alfalfa grown in the greenhouse was related to soil K by regression techniques. The following procedures extracted increasingly higher average amounts of soil K: water; electro-ultrafiltration (EUF) at 20 °C (EUF-K-20) (37 μg K g−1); EUF at 80 °C (EUF-K-80) (83 μg K g−1); 2M NaCl (89 μg K g−1); 1M NH4OAc (131 μg K g−1); 0.1 M HNO3 (163 μg K g−1); seven sequential 7-min extractions with boiling 1 M HNO3 (Mactotal) (940 μg K g−1); and 0.2 M sodium tetra-phenyl boron (NaTPhB) (3248 μg K g−1). Of the eight extractants tested, the amount of K removed by EUF was the most closely associated to total K uptake; a multiple regression model with the logarithm of EUF-K-20 and the logarithm of EUF-K-80 as independent variables explained 97% of the total variation in K uptake. The K extracted by 2 M NaCl and by 0.1 M HNO3 a.
Evaluation of allometric equations of aboveground biomass in a semideciduous tropical forest of Yucatan.

The objectives of this study were to develop and compare allometric equations of aboveground biomass (AGB) for a semi-deciduous tropical forest of the ejido (system of communal or cooperative farming) San Agustin, Yucatan, Mexico, and to compare them to existing equations. Forty seven trees of 18 different species with diameters between 2.5 cm and 41.5 cm were selected. The diameter of each tree was measured before felling, and the height was estimated before and measured after felling. Fresh weight of each component (stem, branches, leaves) was measured in the field, and samples were taken to determine dry weight in the laboratory and to extrapolate to the whole individual. Six allometric equations with different functional forms were explored, and tested using the Akaike information criterion (AIC), adjusted R2 value and cross validation. The best equation yielded an AIC value of 48.36 and an adjusted R2 of 0.96. Crossvalidation showed an adjusted R2 value of 0.72 and a coefficient of agreement of 0.56. Unexpectedly, this equation is less precise than others used in the forests of the Yucatan Peninsula, including equations developed locally and in other continents, with very contrasting sample sizes. However, the best equation obtained in this study allows adequate estimates of AGB of the semideciduous tropical forests of Yucatan, especially for the largest trees, which are the most influential.
Evaluation of Different Sulphur Sources on Sunflower (Helianthus Annuus L.)

Sunflower is an important edible oilseed crop of the country and its oil is consider as premium because of its high poly unsaturated fatty acid content with high level of lenoleic acid and absence of linolenic acid . A field trial was conducted at the Agricultural Research Station, Junagadh Agricultural University, Amreli to study the "Evaluation of different sulphur sources on sunflower". The experimental was laidout inRandomized Block Design with four replications. There were 9 treatments comprising. The analysis of three year pooled data revealed that the treatment T8 40 kg sulphur/ ha through gypsum (266kg/ha) in soil addition with recommended dose of chemical fertilizer get higher oil content and higher yield of sunflower with higher BCR value.
Tissue Reflectivity Function Restoration from Fundamental and Harmonic Ultrasound Images

This paper addresses the problem of ultrasound (US) image restoration. In contrast to most of the existing approaches that only take into account fundamental radiofrequency (RF) data, the proposed method also considers harmonic US images. An algorithm based on the alternating direction of multipliers method (ADMM) is proposed to solve the joint deconvolution problem. Simulation results show the interest of the proposed approach when compared to classical US image restoration schemes based only on fundamental data.
Effect of varying solution calcium or magnesium concentrations in the presence or absence of aluminum on yield and plant calcium or magnesium concentrations in wheat

Abstract The effect of varying solution calcium (Ca) and magnesium (Mg) concentrations in the absence or presence of 10 μM aluminum (Al) was investigated in several experiments using a low ionic strength (2.7 × 10‐3 M) solution culture technique. Aluminium‐tolerant and Al‐sensitive lines of wheat (Triticum aestivum L.) were grown. In the absence of Al, top yields decreased when solution Ca concentrations were <50 μM or plant Ca concentrations were <2.0 mg/g. Top and root yields decreased when solution Mg concentrations were <50 μM or plant Mg concentrations were <1.5 mg/g. There were no differences between the lines in solution or plant concentrations at which yield declined. Increasing solution Ca concentrations decreased plant Mg concentrations in the tops (competitive ion effect) but increased plant Mg concentrations in the roots of wheat. This suggests that Ca is competing with Mg when Mg is transported from the roots. Increasing solution Mg concentrations decreased plant Ca concentrations in the tops.
Intrinsic secondary structure propensities of the amino acids, using statistical ϕ–ψ matrices: Comparison with experimental scales

Today there are several different experimental scales for the intrinsic α‐helix as well as β‐strand, propensities of the 20 amino acids obtained from the thermodynamic analysis of various model systems. These scales do not compare well with those extracted from statistical analysis of three‐dimensional structure databases. Possible explanations for this could be the limited size of the databases used, the definitions of intrinsic propensities, or the theoretical approach. Here we report a statistical determination of α‐helix and β‐strand propensities derived from the analysis of a database of 279 three‐dimensional structures. Contrary to what has been generally done, we have considered a particular residue as in α‐helix or β‐strand conformation by looking only at its dihedral angles (ϕ–ψ matrices). Neither the identity nor the conformation of the surrounding residues in the amino acid sequence has been taken into consideration. Pseudoenergy empirical scales have been calculated from the statistical propensities. These scales agree very well with the experimental ones in relative and absolute terms. Moreover, its correlation with the average of the experimental scales for α‐helix or β‐strand is as good as the correlations of the individual experimental scales with the average. These results show that by using a large enough database and a proper definition for the secondary structure propensities, it is possible to obtain a scale as good as any of experimental origin. Interestingly the ϕ–ψ analysis of the Ramachandran plot suggests that the amino acids could have different β‐strand propensities in different subregions of the β‐strand area. © 1994 Wiley‐Liss, Inc.
A Feasibility Study on a Continuous-flow-type Microwave Pretreatment System for Bioethanol Production from Woody Biomass

Efficient pretreatment prior to enzymatic saccharification process is essential for profitable bioethanol production from woody biomass. Microwave pretreatment is expected as an efficient and energy-cost-saving method to enhance enzymatic susceptibility. The objective of the present study is to develop an efficient, high-volume, and continuous microwave pretreatment system toward commercially-based bioethanol production. As a feasibility study, we developed prototypes of a continuous-flow-type microwave pretreatment system for bioethanol production from woody biomass. A unit of the microwave irradiation sections of a continuous-flow-type microwave pretreatment system was designed with a 3D electromagnetic simulator. Prototype experiments and quantitative estimation of energy balance were also conducted. Microwave pretreatment provided 45.9% of the total saccharide yield woody biomass weight by electric consumption of 552 kJ; whereas conventional heating pretreatment provides 43.6 % of the total saccharide yield by 498 kJ, when the mixture was composed of 70 g of woody biomass (Japanese cedar sapwood chips) and 770 g of solvents (ethylene glycol : phosphoric acid = 95 : 5). We estimated 14.8g of bioethanol and 439 kJ of bioethanol energy could be produced by the prototype microwave pretreatment. Although heat dissipation from the metal pipe to the air and the ratio of solvents to woody biomass are immediate problems, microwave is a future potential energy-saving pretreatment method without loss of the saccharide yield.
The effects of fire on biogenic soil emissions of nitric oxide and nitrous oxide

Measurements of biogenic soil emissions of nitric oxide (NO) and nitrous oxide (N2O) before and after a controlled burn conducted in a chaparral ecosystem on June 22, 1987, showed significantly enhanced emissions of both gases after the burn. Mean NO emissions from heavily burned and wetted (to simulate rainfall) sites exceeded 40 ng N m−2 s−1, an increase of 2 to 3 compared to preburn wetted site measurements. N2O emissions from burned and wetted sites ranged from 9 to 22 ng N m−2 s−1. Preburn N2O emissions from these wetted sites were all below the detection level of the instrumentation, indicating a flux below 2 ng N m−2 s−1. The flux of NO exceeded the N2O flux from burned wetted sites by factors ranging from 2.7 to 3.4. These measurements coupled with preburn and postburn measurements of ammonium and nitrate in the soil of this chaparral ecosystem and measurements of NO and N2O emissions obtained under controlled laboratory conditions suggest that the postfire enhancement of NO and N2O emissions is due to production of these gases by nitrifying bacteria.
Analysis of Microbial Community in Two-Phase Circulating Process for Hydrogen and Methane Fermentation

The structure of a microbial community during a two-phase circulating process for the hydrogen and methane fermentation of potato was investigated using a molecular biological approach. The process was performed using a mixing tank, a thermophilic acidogenic reactor (55°C) and a mesophilic methanogenic reactor (36°C) connected in series with the recirculation of methanogenic mixed liquor to the mixing tank. A continuous experiment was conducted by changing the process hydraulic retention time (HRT) stepwise from 56 days to 30 days, then 20 days and 15 days. A stable and high-rate hydrogen and methane fermentation was possible at a process HRT of 20 days with a hydrogen production rate of 3.6 l·l-1·d-1 and a methane production rate of 3.4 l·l-1·d-1. Denaturing gradient gel electrophoresis (DGGE) with 16S rRNA gene-targeted polymerase chain reaction (PCR) analysis was employed to identify the structure of a microbial community at various conditions for each reactor. Thermoanaerobacterium thermosaccharolyticum and Clostridium sporosphaeroides were considered to be the major hydrogen-producing bacteria in the thermophilic acidogenic reactor, whereas Methanosarcina siciliae and Methanoculleus bourgensis were considered, respectively, to be the acetate-utilizing and hydrogen-utilizing methanogenic archaea in the mesophilic methanogenic reactor.
Implementation of Self-expression Tool with Interactive Hangeul

Modern people communicate in a digital space without being limited by physical space and time. On the internet, people's desire for self-expression is getting bigger, and the most common self-expression tool is characters. Characters are visual materials to express human thoughts and desires. This study is a method to positively express the viewer's self in an interactive Hangeul system. The proposed system produces new formative shapes and meanings of Hangeul through the process of deconstructing and reconstructing the characters. Immediate character transformations that are synchronized with the motion of the viewer act as a tool of self-expression by inducing the viewer's active interaction repeatedly. Therefore, the proposed interactive Hangeul is more than enough to be used as a new graphic tool beyond the text to be read, and it is highly likely to develop into cultural contents using it.
Numerical Simulation of the Conditioning of Volatile Particles in Laminar Flow Tube Reactors

The conditioning of aerosol particles to a predefined composition and size can be considered as a standard problem in aerosol technology. Quite often aerosols generated by dispersing diluted solutions are conditioned in a subsequent flow reactor.To make the design of such reactors easier, a computer model was developed to simulate the behavior of particles with a volatile component during their passage through the reactor. The model is based on the assumption that part of the surface of the reactor is covered with a layer of the requested activity of the volatile component whose fraction has to be adjusted. The diffusion to or from this surface and the corresponding change of the particle size and composition is calculated for each streamline of the flow on the basis of a laminar flow profile. At the moment data for the system H 2 O/H 2 SO 4 are implemented in the model, but an extension to other systems can easily be done. Circular as well as annular flow cross sections can be taken into account.
Parametric study of the vacuum ultraviolet emission and electrical characteristics of a He–Xe microdischarge

Vacuum ultraviolet emission and electrical characteristics of a simple discharge configuration consisting of two planar cylindrical electrodes operated with a dc voltage have been measured over a wide range of He/Xe mixtures and discharge pressures. Breakdown characteristics are consistent with those found in the literature, however current–voltage characteristics and the inferred discharge resistivity suggest the presence of a complex process controlling electron emission at the cathode. Ultraviolet vacuum emission maps of atomic and molecular xenon at 147, 150, and 173 nm, respectively, have been measured as a function of pressure, from 60 to 500 Torr, and gas mixture, from pure Xe to 5% Xe in He. The calibrated ratios of each emission map help to visualize the zones of strongest ultraviolet emission over a wide range of operating conditions. One-dimensional simulations of the breakdown voltage and current discharge have been performed using the commercially available discharge-modeling package SIGLO. G.
Thermoelectric Harvesting and Seasonal Routing in Wireless Sensor Networks

We propose the use of embedded in-wall thermoelectric harvester to power the nodes of a wireless sensor network. We exploit significant temperature differences of indoor and outdoor environments in cold climates. We use real measurements to evaluate the use of the temperature difference as a proxy to heat flow through walls, and the feasibility of creating a network of in-wall thermoelectric harvesting sensors. We also discuss the seasonal availability of thermoelectric energy and get in depth to the issues and advantages this presents. We formulate the corresponding multi-commodity routing flow problem, where each commodity is data from every node, and using the indoor/outdoor temperature as a proxy we investigate the effect of fairness in routing. We also present a low overhead method of constructing a seasonally-aware routing scheme and study its performance. Finally we talk about techniques for predicting the incoming available energy in the future.
Investigating Antitermitic Compounds from Australian White Cypress Heartwood (Callitris glaucophylla Thompson et Johnson) Against Coptotermes formosanus Shiraki

Abstract Antitermitic activities of extracts obtained from the heartwood of Australian white cypress (Callitris glaucophylla Thompson et Johnson) were investigated in an attempt to detect and identify the presence of biologically active compounds against Coptotermes formosanus Shiraki. Extraction of compounds was achieved by successive extraction using dichloromethane and methanol. Three sesquiterpene alcohols, guaiol, α-eudesmol and β-eudesmol and two monoterpene acids, (−)-citronellic acid and geranic acid, were found in the C. glaucophylla heartwood extracts based on high performance liquid chromatography (HPLC) and gas chromatography/mass spectrometry (GC/MS) analysis. Antitermitic activity of each fraction obtained from methanol extracts was demonstrated by repellent and no-choice feeding tests. One of the strong termiticidal active compounds identified was columellarin and another sesquiterpene lactone fraction showed repellent activity.