Miracle-dz/UniFAR-FTUs huggingface dataset:
Accurate docking is achieved by decoupling systematic sampling from scoring

OF THE DISSERTATION Accurate Docking is Achieved by Decoupling Systematic Sampling From Scoring by Jianwen A. Feng Doctor of Philosophy in Computational Biology Washington University in St. Louis, 2009 Research Advisor: Professor Garland R. Marshall This dissertation discusses two main projects from my thesis work. The first project focuses on the development of a small molecule docking program, SKATE, for drug discovery. The second project focuses on the critical analysis of the thermal stability of a mini-protein, FSD-1. SKATE is a novel approach to small molecule docking. It removes any inter-dependence between sampling and scoring to improve docking accuracy. SKATE systematically and exhaustively samples a ligand’s conformational, rotational and translational degrees of freedom, as constrained by a receptor pocket, to find sterically allowed poses. A total of 266 ligands were re-docked to their respective receptors to assess SKATE’s performance. The results show that SKATE was able to sample poses within 2 A RMSD of the native structure for 97% of the cases. The best performing scoring function was able to rank a pose that is within 2 A RMSD of the native structure as the top-scoring pose for 83% of the cases. Compared to published data, SKATE has a higher self-docking accuracy rate than or is at least comparable to GOLD, Glide,
Structure−Property Correlations in Bending and Brittle Organic Crystals

Bending of crystals of molecular solids occurs when the strength of intermolecular interactions in orthogonal directions is significantly different. We report here a survey of 60 molecular crystals and establish a causative correlation between bending and crystal packing. This group contains crystals with 4 and 8 A crystal axes and includes 1D, 2D, 3D, isostructural, polymorphic, stacked, interlocked, single, and multicomponent crystals and solvates. We found that 17 of these 60 crystals may be bent, whereas the rest are brittle and cannot be bent plastically. The bending crystals could be deformed into many shapes; sometimes, they could even be flattened upon themselves without breakage. A model for bending is proposed using the information obtained from X-ray diffraction, face indexing, and mechanical property measurements on both bending and non-bending (brittle) crystals. The bending and brittleness of these molecular crystals are discussed in comparison with the deformation behavior of metals. Molecu.
Variation of Nitrogen Use Efficiency and Its Relationships with Growth Characteristics in Rice Cultivars

This experiment was conducted to investigate the variation of nitrogen use efficiency, nitrogen uptake efficiency, physiological utilization efficiency and their relationships with growth characteristics in the 28 Korean rice cultivars. Nitrogen use efficiency of 28 rice cultivars was 47.74, nitrogen uptake efficiency was 0.71, and physiological utilization efficiency was 68.76 in average. Nitrogen use efficiency of rice cultivars had low variation ranged from 44.09 to 51.91, but nitrogen uptake efficiency were relatively high variation from 0.51 to 0.90, and physiological utilization efficiency was from 51.71 to 94.26. The high efficient group in nitrogen uptake efficiency whose value was calculated above 0.80 included Daeanbyeo, Seojinbyeo, Ansungbyeo, Dongjinbyeo, and Hwaanbyeo, while the low efficient group with below 0.60 was Kwanganbyeo, Sampyeongbyeo, Soorabyeo, and Hwasungbyeo. Hwasungbyeo, Sampyeongbyeo, Soorabyeo for physiological utilization efficiency were more efficient cultivars, while Daeanbyeo, Seojinbyeo, Ansungbyeo were less efficient cultivars. Nitrogen uptake efficiency had positive correlation coefficients between dry matter weight of plant (0.842), leaf area index (0.761), and leaf nitrogen content (0.599), respectively. Therefore, the dry matter weight of rice plant and leaf area index was important characters to evaluate nitrogen uptake efficiency in rice cultivars. Also, more efficient cultivar in nitrogen uptake had higher chlorophyll meter value, which was appeared dark green color.
Hydrogen Permeability and Delayed Failure of Polarized Martenstic Steels

Abstract Hydrogen permeability and delayed failure characteristics were directly correlated under cathodic and anodic polarization for 9-4-45 and 4340 high strength steels. At cathodic potentials they both exhibited the usual increased susceptibility to failure with increasing cathodic potential. With increasingly anodic applied potential, the 9-4-45 displayed decreased times to failure, increased hydrogen permeability and surface pitting. The time to failure in 4340 did not respond to anodic polarization, there was no hydrogen permeation, and no pitting. The concept of a generalized hydrogen embrittlement mechanism for stress corrosion cracking becomes increasingly attractive, since it is apparent that increased susceptibility to delayed failure under anodic potentials does not, per se, rule out the availability of hydrogen.
Asymmetry of rotational catalysis of single membrane-bound F0F1-ATP synthase

Synthesis of the cellular 'energy currency' ATP is catalyzed by membrane-bound F0F1-ATP synthases. The chemical reaction at three binding sites in the F1 part is coupled to proton translocation through the membrane-integrated F0 part by an internal rotation of subunits. We examined the rotary movements of the ε-subunit of the 'rotor' with respect to the b-subunits of the 'stator' by single-molecule fluorescence resonance energy transfer (FRET). Rotation of ε during ATP hydrolysis is divided into three major steps with constant FRET level corresponding to three binding sites. Different catalytic activities of the individual binding sites were observed depending on the relative orientation of the 'rotor'. Computer simulations of the FRET signals and non-equally distributed orientations of ε strongly corroborate asymmetry of catalysis in F0F1-ATP synthase.
Políticas de financiamento estudantil: análise de impacto do Fies no tempo de conclusão do ensino superior

Resumo Esse estudo avaliou o impacto do Fies no tempo total e no atraso da conclusão da educação superior dos alunos matriculados em cursos presenciais de instituições privadas, com base nas informações do Inep de 2007 a 2017. O tempo de conclusão é o total de anos que o aluno esteve matriculado, já o atraso refere-se ao número de anos que o estudante levou para concluir o curso além do prazo mínimo de integralização. O impacto estimado por score de propensão do Fies no tempo total foi em torno de 4 meses. Os resultados da variável atraso também indicaram um impacto positivo, porém com menor intensidade e significativo apenas na primeira fase do programa, de 2000 a 2009. Também foram realizadas estimativas pelo método de Lewbel (2012), na tentativa de lidar com o possível viés das características não observáveis que influenciam a decisão individual de participar do Fies. Os resultados indicaram uma possível superestimação dos resultados quando não são consideradas as características não observadas dos alunos.
Silica nanoparticle addition to control the calcium‐leaching in cement‐based materials

The calcium leaching of the cement hydrated matrix is of vital importance for constructions like water containers, dams, bridges, etc which have to be in contact with water during their lifetime. The aim of this work is the study of the reduction of such a negative phenomenon by the addition of silica nanoparticles. Several characterisation techniques such as 29Si MAS NMR, X‐ray diffraction, mercury intrusion porosimetry and EDX‐microanalysis have been used to evaluate the effect of the nanoparticles in the cement matrix nanostructure and in their impact on the evolution of the Ca leaching throughout time. Subsequent analysis of the results indicates that silica nanoparticles can reduce the Ca‐leaching both decreasing the amount of portlandite in the matrix and controlling the degradation rate of the C–S–H gel. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Variability in the Chemical Compositions of the Essential Oils of Five Ocimum Species from Tropical African Area

Abstract As part of our research on aromatic plants from Africa, we have analyzed, via GC and CG/MS, the essential oils from fresh leaves of five Ocimum species from tropical Africa: Ocimum basilicum L. , O. gratissimum L. , O. americanum L. (syn: O. canum Sims), O. lamiifolium Hochst. ex Benth. and O. minimum L. The chemical compositions of O. basilicum, O. gratissimum and O. minimum essential oils could be related to some chemotypes already defined for these three species: linalool- or methyl chavicol-types for the first species, thymol- or eugenol- or ocimenes/far- nesenes-types for the second one; finally, a high content of methyl chavicol (34.3%) and linalool (17.8%) was found in O. minimum oil, similar to that already described for a Brazilian species. On the other hand, an essential oil dominated by 1,8-cineole was described for the first time for a sample of O. americanum. Finally, the oil of O. lamiifolium, which was rich in sabinene, is chemically described for the first time.
The structural pressure dependence of potassium titanyl phosphate (KTP) to 8 GPa

The crystal structure of (KTP) has been determined as a function of pressure to 8 GPa at ambient temperature, using single-crystal x-ray diffraction techniques. The first-order isosymmetric phase transition, at 5.8 GPa, appears to have a strong effect on the compression mechanism of the structure: in the low-pressure phase the structure compresses by polyhedral tilting within the cross-linking chains while in the high-pressure phase relative translations and rotations of the chains themselves account for a significant proportion of the unit-cell volume reduction both at the transition and on further pressure increase. The distortion of the framework at the phase transition is accompanied by relatively large displacements of the potassium atoms to positions more closely related to the Pnan symmetry of the high-temperature phase. A comparison of the pressure-induced changes of the highly distorted octahedra with recent high-pressure optical measurements indicates that neither the lengths nor the orientations of the Ti - O bonds correlate, at least directly, with the observed variation of the second-harmonic-generating (SHG) power of the crystal. This strongly suggests that other regions of the structure may be important for the SHG properties.
Neutral electron trap generation in SiO2 by hot holes

Experimental evidence for neutral electron trap generation in SiO2 caused by injected holes is presented. The neutral electron traps are detected by Fowler–Nordheim (FN) tunneling electron injection after avalanche hole injection. The density of generated neutral traps increases with the number of injected holes, but does not saturate with that of the trapped holes. The centroid of generated neutral traps is found to be in the middle of the oxide. These results suggest that neutral traps are generated by the holes and not only by the recombination of electrons with trapped holes. The origin of neutral traps is considered to be associated with dipolar defects formed by SiO bond breaking under hole transport in the oxide.
Tellurium-125 solid-state NMR spectra and secondary bonding arrangements for some salts of the trimethyltelluronium and triphenyltelluronium cations

The preparation of several salts of the Me{sub 3}Te{sup +} and Ph{sub 3}Te{sup +} cations is reported along with {sup 125}Te static and CP/MAS solid-state NMR spectra of the Me{sub 3}Te{sup +} salts and {sup 125}Te CP/MAS spectra of the Ph{sub 3}Te{sup +} salts. In addition, crystal structures of the salts Me{sub 3}Te{sup +}Cl{sup {minus}} {times} H{sub 2}O (1), Me{sub 3}Te{sup +}I{sup {minus}} (2), Me{sub 3}Te{sup +}NO{sub 3}{sup {minus}} (3), Ph{sub 3}Te{sup +}NO{sub 3}{sup {minus}} (4), Ph{sub 3}Te{sup +}Cl{sup {minus}} {times}{1/2}CHCl{sub 3} (5), and (Ph{sub 3}Te){sub 2}SO{sub 4} {times} 5H{sub 2}O (6) have been determined to help in the interpretation of some of the above spectra. It is shown that secondary bonding interactions with the anions have significant and substantial influence on the geometries of the cations and their crystal packings and on the resulting NMR spectra in terms of the tellurium shielding tensors and isotropic chemical shifts and in the presence of log-range spin {1/2} to spin 3/2 couplings. These couplings are indicative of long-range covalent interactions between the anions and cations in this series of compounds. In particular, the {sup 125}Te CP/MAS spectrum of Me{sub 3}Te{sup +}Cl{sup {minus}} {times} H{sub 2}O consists of a septet due to couplingmore » to two equivalent chlorine atoms. In the case of 4 and 5 the presence of 4 and 2 crystallographically independent Te atoms is confirmed in the NMR spectra. 38 refs., 11 figs.« less
Bulk Synthesis of Monodisperse Ferrite Nanoparticles at Water−Organic Interfaces under Conventional and Microwave Hydrothermal Treatment and Their Surface Functionalization

Synthesis of monodisperse MFe2O4 (M =, Ni, Co, Mn) and γ-Fe2O3 nanoparticles at a water−toluene interface under conventional as well as microwave hydrothermal conditions using readily available nitrate or chloride salts and oleic acid as the dispersing agent is described. The ensuing particles were monodispersed with a size distribution ranging from 5 to 10 nm. The process is atom-efficient and can be scaled up to a level of several grams without downsizing the size and shape. The modulation of solubility profile of the particles was accomplished via functionalization using organic moieties. X-ray diffraction confirmed the formation of cubic spinel nanostructures. Particle sizes calculated from the Scherrer formula and TEM micrographs were comparable. ICP−AES studies confirmed that the ratios of Fe to Ni, Mn, and Co were approximately equal to 2. FT-IR confirmed the presence of oleic acid moieties on the surface of the synthesized particles. At room temperature, the particles were found to be superparamag.
Functionalized Room-Temperature Ionic Liquids for Lithium Secondary Battery Electrolyte Materials

Vinyl group-substituted room-temperature ionic liquids (RTILs) were used for aiming at fabrication of high-safety batteries. The imidazolium-based ionic liquids used in this study had a vinylmetylene group and another alkyl group on an imidazolium cation. The charge-discharge profiles of batteries composed of a LiCoO2 cathode were compared between the different RTILs to know the factors of RTIL influencing the battery performances. The charge/discharge efficiency of a graphite anode was also investigated for total evaluation of the battery performances.
Chemical Amendments and Process Controls To Reduce Ammonia Volatilization During In-House Composting

Composting inside high-rise, caged layer facilities can produce atmospheric ammonia (NH3) concentrations exceeding standards for human and poultry health. Control measures that reduce NH3 volatilization are necessary for in-house composting to be sustainable. Due to differences specific to in-house composting — low carbon to nitrogen ratios of composting material, continuous manure addition, and frequent turning — it is not known whether NH3 control measures used previously for poultry manure will work. The objectives of this study were to evaluate various amendment and process controls on NH3 produced during simulated in-house composting in the lab, and to evaluate select chemical control measures during composting inside a high-rise layer facility. Ten amendments (aluminum sulfate; chloride salts of aluminum, calcium, magnesium, and potassium; gypsum; sodium bisulfate; zeolite (clinoptilolite); straw; and cellulose) and four process controls (moisture; temperature; turning frequency; and particle size) were evaluated in lab incubations in 1 L vessels wherein samples of poultry manure compost were incubated to simulate composting. Vials of boric acid solution were used to capture NH3 evolved during incubations. With the exception of zeolite and cellulose, all amendments reduced NH3 capture. Low moisture and temperature also reduced NH3 capture, although managing temperature and moisture to achieve low NHg would adversely impact microbial activity and other desired benefits of composting. When evaluated inhouse, aluminum sulfate, calcium chloride and magnesium chloride did not reduce NH evolution from compost measured on three different dates with a gas sensor. Spatial variability along treated segments of windrow apparently masked amendment effects. At the end of a six-week composting cycle, total nitrogen content was higher in compost treated with aluminum sulfate than control or chloride salt treatments. Aluminum sulfate and process controls such as moisture content, carbon source and particle size have potential to reduce NH3 loss from poultry manure composted inside high-rise layer structures. In-house compost management to reduce NH3 volatilization must consider the cost of amendments, effectiveness, and impacts on the composting process.
Calcium sulfate-phosphate composites with enhanced water resistance

A novel method of processing gypsum, CaSO4·2H2O, is described, forming composites of calcium sulfate anhydrite crystallites bound by a water-resistant phosphate matrix. The materials have been characterised using various analytical techniques, including powder X-ray diffraction (PXRD), infrared spectroscopy, scanning electron microscopy and 31P solid-state nuclear magnetic resonance (NMR). While PXRD shows the major crystalline phase present in the composites is calcium sulfate anhydrite, the NMR shows the presence of a polyphosphate matrix, consistent with IR analysis. The NMR also allows the identification of an interfacial layer between the anhydrite crystallites and phosphate coating by comparison with the mixed sulfate-phosphate mineral ardealite, whose NMR spectra we also report. Comparison of conventional and proton-decoupled cross polarisation NMR spectra allows the presence and location of included protons to be probed. Physical measurements of mechanical strength show that addition of aluminium to the composite allows the formation of high density materials that have dry strength comparable to gypsum and no loss of strength on immersion in water.
Charge carrier generation in photosensitive amorphous molecular semiconductors

Thermalization process in photosensitive amorphous molecular semiconductors are theoretically considered from standpoint of their parameters, namely: thermalization time, thermalization length. The heat electron formed in consequence of absorption of the light quantum by semiconductor molecules loses his surplus energy in the time of inelastic interaction with neighbouring atoms. The results of theoretical predictions are confirmed by the experimental ones obtained for a number of molecular semiconductors (anthracene, pentacene, PVC, PEPC).
Chemical Recycling of Poly(ethylene terephthalate)

This paper reviews the state of the art in the field of chemical recycling of poly(ethylene terephthalate) (PET). Advantages of the chemical recycling of PET, the theoretical basis of the ester bond cleavage, and a wide spectrum of degrading agents and final products are presented. Chemical processes applied in polymer recycling are divided into six groups: methanolysis, glycolysis, hydrolysis, ammonolysis, aminolysis, and other methods. Numerous possibilities for the utilization of waste PET as a very useful raw chemical material are described on the basis of literature. A comparison of chemical recycling methods is carried out. The following aspects were taken into consideration: (i) flexibility in utilizing a variety of waste types, (ii) conditions necessary for degradation including safety requirements, (iii) economic aspects, and (iv) product versatility. A total of 108 references including 46 patents are cited in this paper.
Financing Multiple Heterogeneous Suppliers in Assembly Systems

Buyer finance has been practiced by manufacturers/assemblers for years; however, few papers have investigated the efficacy of buyer finance in an assembly system with multiple suppliers. This paper fills the literature gap by comparing buyer finance with bank finance in a supply chain with one assembler and multiple heterogeneous capital-constrained component suppliers. We characterize the equilibrium solutions for different financing schemes (i.e., buyer finance, bank finance, and no finance). We show that in buyer finance the assembler should charge the suppliers the lowest possible interest rate, which may be even below its own unit capital opportunity cost, leading to losses in financing suppliers. However, the assembler can benefit more from enhanced inventory backup and lower component purchasing prices resulted from the low buyer finance interest rate. We further compare the different financing schemes from the perspectives of assembler, (borrowing and non-borrowing) suppliers, and the whole supply chain. Our analysis reveals that the assembler may offer buyer finance even if its own unit capital opportunity cost is higher than banks’ risk-free interest rate. We also identify the conditions under which buyer finance is better than bank finance for each party as well as the whole supply chain, and demonstrate how the suppliers’ initial capitals, production costs, and their heterogeneities affect the assembler’s selection of the optimal financing scheme.
THE APPROACH TO SIMILAR TERTIARY CREEP RATES FOR ANTARCTIC CORE ICE AND LABORATORY PREPARED ICE

An account is given of ice deformation experiments in uniaxial compression. Samples studied include isotropic and anisotropic ice, laboratory prepared and from a core drilled at the summit of Law Dome, Antarctica. There are unexplained differences in the minimum strain rates attained by isotropic ices from the core and from the laboratory. Minimum strain rates for anisotropic ice are higher than for isotropic ice provided that the anisotropy is compatible with the stress configuration. In tertiary creep a constant strain rate is attained, associated with the development of a small circle girdle crystal orientation fabric, and an equilibrium crystal size. It is proposed that this tertiary creep is steady state.
Real-Time Measurements of Nonmetallic Fine Particulate Matter Adjacent to a Major Integrated Steelworks

A campaign took place in Wales (UK) in the spring of 2006 to characterize emissions from a major steelworks through atmospheric measurements. At no time during the measurements was the 24-h air quality standard for PM10 exceeded. However, real-time measurements of single particles by aerosol time-of-flight mass spectrometry (ATOFMS) allowed detection of particulate matter from the steelworks, which could be associated with specific emission areas within the works from measurements of wind direction. Three main wind sectors were identified with possible sources of emissions of fine nonmetallic particulate matter (PM < 1 μm). Characterization of the aerosol composition by a high resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) of the nonrefractory material associated with the specific plumes is also reported, along with results from other real-time techniques. The ATOFMS detected for the first time a unique elemental sulfur-rich particle type, likely to originate from the blast furnaces. AMS results, supported also by laboratory studies, confirm this finding by reporting elevated mass ratios m/z 64/48 and m/z 64/80. Two other novel ATOFMS particulate types were found to be associated with steelworks emissions. One was characterized by nitrogen-containing organic species, aromatic compounds, and high-molecular-weight (MW) polycyclic aromatic hydrocarbons (PAHs) and was associated with the sources in the area of the hot and cold mills. The second was found to be rich in organic carbon internally mixed with elemental carbon, nitrate, sulfate, and PAHs with lower MW. These particle types were likely related to the coke ovens and the basic oxygen steelmaking plant. Copyright 2012 American Association for Aerosol Research