Distribution Analysis Method Research Articles

Development of a distribution analysis method for metalloproteinase activity by combining wound blotting and zymography techniques：A pilot study in mice

Development of a distribution analysis method for metalloproteinase activity by combining wound blotting and zymography techniques：A pilot study in mice

Multi-fractal distribution analysis for pore structure characterization of tight sandstone—A case study of the Upper Paleozoic tight formations in the Longdong District, Ordos Basin

Abstract With proven gas potential, the gas charging and accumulation mechanisms for the Upper Paleozoic tight gas reservoir in the Longdong District of the Ordos Basin remain controversial. Pore structure is the most direct and critical factor that affects gas charging and accumulation in the reservoir. However, the pore structure characterization of tight sandstone is far more difficult than that for conventional reservoir rocks due to significant heterogeneity. The present work aims to introduce a new quantitative method for pore structure characterization that integrates multi-fractal distribution analysis, an effective and profitable method for quantitative heterogeneity analysis, and high-pressure mercury intrusion porosimetry (HPMIP). Twenty-one samples from targeted tight formations with different gas-bearing status were obtained for analysis. The results show that the best formations for gas charging and accumulation in the Upper Paleozoic tight sandstone formations in the Longdong District are the formations with more large pores, more homogeneous small pores, and well-developed micro-fractures. The existence of micro-fractures is the key factor that affects gas charging and accumulation. Tight sandstone samples were categorized into three types in accordance with the HPMIP curve configuration. Due to the high heterogeneity of pore structures, analyses based solely on HPMIP curve configuration has its shortcomings, which can be compensated by multi-fractal distribution analysis. The multi-fractal distribution of target tight formations could be interpreted as two linear segments, representing large pores and small pores. The separating points of the two segments vary from 0.1 μm to 0.5 μm in different samples due to different pore structures. Large pores are not ideal fractals in gas-bearing formations due to the existence of micro-fractures, whereas they are fractals in dry formations where micro-fractures are not developed. Small pores are all ideal fractals, with the highest heterogeneity in type γ samples and the lowest heterogeneity in type α samples. A conclusion was made in this work: if the slope of segment one in the multi-fractal distribution of mercury saturation (SHg) versus capillary pressure (PC) is larger than 1, this measure could be accepted as an empirical indicator for the existence of micro-fractures.

Illumination-related errors in limited-angle optical diffraction tomography.

In the paper, the design and tolerances of optical systems and scanning components used in limited-angle optical diffraction tomography are analyzed in order to improve the performance of the measurement systems and to encourage the application of tomography as a standard method for quantitative analysis of 3D refractive index distribution in biological microstructures. The first part of the presented analysis consists of component selection for the scanning device and optical system in the illumination part of the setup and the influence of the illumination wavefront on reconstruction quality. In the second part, the sensitivity of the tomographic reconstruction quality to three representative measurement-related errors based on synthetic data is demonstrated. Finally, a configuration of the system, selected to minimize reconstruction errors, is proposed and alignment tolerances simulated using the Monte Carlo method are provided.

A new method for analysis of dual pore size distributions in shale using nitrogen adsorption measurements

A new method is proposed to distinguish between cylindrical pores and slit pores of porous materials and obtain their individual pore size distributions (PSDs). The proposed method is based on nitrogen adsorption isotherms at 77.3K. First, we develop the conventional methods by utilizing both adsorption and desorption branches of the isotherms and deriving the volume distribution of the two types of pores. The method formulation and implementing procedure is given in detail. Then the isotherms of SBA-15 sample are used to verify the proposed method in the case of single-pore-type. Finally, the proposed method is applied to analyze the pore structure characterization of shale sample. The results depict that both the adsorbed quantity and pore volume are separated into two distinct parts contributed by cylindrical pores and slit pores respectively. That's to say, the proposed method can distinguish clearly between the two types of pores. This study can provide us a better understanding of the complicated pore structure of shale. Furthermore, it may have implications for shale gas production.

Inline method of droplet and particle size distribution analysis in dilute disperse systems

In the present article a measurement method of particle size distributions (PSD) in industrial installations which use a dispersed phase of low concentration (like spray dryers or spray scrubbers) is introduced. A new type of inline-measurement system has been developed and designed to work in spray drying conditions. A standard digital camera is used to record shadows of flowing particles inside the spray drying chamber. Collected images were analyzed by a newly developed software which recognizes particles only in the focus area and eliminates several types of artifacts. The constructed prototype of the PSD inline-analyzer was installed and used to monitor large laboratory scale spray dryer. All data collected by the designed system during the spray drying experiments were compared with data measured with an offline reference system to show accuracy of the new measurement technique.

Experimental investigation of energy distribution in continuous sinking EDM

Investigations into the fundamentals of the EDM process are often facing significant challenges due to the very small spatial and temporal scales in which it takes place. This also applies to the research on the distribution of the electrical energy of the discharges. This paper presents a novel method for the detailed experimental analysis of the energy distribution in continuous sinking EDM processes. For this purpose, sophisticated measurement methods for temperatures and electrical quantities were combined. Thus, the experimental setup was very close to realistic process conditions. The results of the obtained temperature profiles and the derived energy distribution are presented followed by variations of process parameters and a critical discussion to explain deviations.

A particle size distribution analysis method to quantitatively evaluate coagulation of fine particles in aqueous solutions

ABSTRACTA laser particle size analysis method was proposed to quantitatively evaluate the fine particles coagulation. Laser particle size analyzer was used to measure the particle size distribution of coal slime at different stirring rates and different concentrations of Ca2+ or Na+. The value of d10, d50, and d90 can be used to quantitatively evaluate the coagulation performance of fine particles, the greater value of d10, d50, and d90 they are, and the better coagulation performance it is. It was found that the addition of Ca2+ could promote easier coagulation for fine particles than the addition of Na+, and the best coagulation performance, in which d90 was greater than 700 µm, occurred at the conditions of 1000 rpm stirring speed and Ca2+ concentration above 5 mmol/L. It is because that the electronegativity of coal and clay particles would be weakened in the presence of Ca2+, and the electrostatic repulsive force of fine particles would be reduced, resulting in the fine particles becoming easy to coagulate. Moderate stirring speed could provide kinetic energy for particle to cross the energy barrier of two colloidal particles. On the contray, coagulated particles broke up when the stirring speed reached a high level.

Measurement of ion beam angular distribution at different helium gas pressures in a plasma focus device by large-area polycarbonate detectors

The paper presents an experimental study and analysis of full helium ion density angular distributions in a 4-kJ plasma focus device (PFD) at pressures of 10, 15, 25, and 30 mbar using large-area polycarbonate track detectors (PCTDs) (15-cm etchable diameter) processed by 50-Hz-HV electrochemical etching (ECE). Helium ion track distributions at different pressures, in particular, at the main axis of the PFD are presented. Maximum ion track density of ~4.4 × 104 tracks/cm2 was obtained in the PCTD placed 6 cm from the anode. The ion distributions for all pressures applied are ring-shaped, which is possibly due to the hollow cylindrical copper anode used. The large-area PCTD processed by ECE proves, at the present state-of-theart, a superior method for direct observation and analysis of ion distributions at a glance with minimum efforts and time. Some observations of the ion density distributions at different pressures are reported and discussed.

Sorption behavior of strontium ions in humic acid solutions

As shown by distribution, thermodynamic modeling, and dispersion analysis methods, the ability of freshly precipitated humic acid to take up Sr(II) ions is influenced by energy heterogeneity of its sorption sites, characteristic of both natural and synthetic samples. It is manifested in that the distribution coefficient Kd exceeds 1.9 × 104 mL g–1 at Sr(II) concentrations in solutions lower than 20 μg L–1 but is equal to 1.9 × 103 mL g–1 at Sr(II) concentrations higher than 1 mg L–1. In solutions with ultralow Sr(II) concentrations, humic acids exhibit high affinity for the humate complex Sr(HA) and do not interact with the complex Sr(HA)2.

Mass Spectrometry Imaging of Metabolites in Barley Grain Tissues.

Higher plants are composed of a multitude of tissues with particular functions, reflected by distinct profiles of transcripts, proteins, and metabolites. Although the rapid development of "omics" technologies has advanced plant science tremendously within recent years, analysis is frequently performed on whole organ or whole plant extracts, causing the loss of spatial information. Mass spectrometry-based imaging (MSI) approaches have become a powerful tool to decipher spatially resolved molecular information. Matrix-assisted laser desorption/ionization (MALDI) is the most widespread ionization method utilized for MSI and has recently been applied to plant science. A range of different plant organs and tissues has been successfully analyzed by MSI, and patterns of various classes of metabolites from primary and secondary metabolism have been obtained. This protocol describes a method for analysis of spatial metabolite distributions in cryosections of developing barley grains. Detailed procedures for sample preparation, mass spectrometry measurement, and data analysis are provided. © 2016 by John Wiley & Sons, Inc.

Temperature Field Probability Distribution Analysis Method for Refrigerated Compartment

In this paper, the distribution law of the temperature field in a city transportation reiterated truck is simulated by CFD simulation (Yi et.al,2015). The temperature distribution is analyzed, and the probability density is solved. It is found that the Gaussian distribution can be used to express and analyze the temperature field (Fel'dman, 1990). The Gaussian distribution model (Victor,2006) is established, and the probability distribution of the temperature field data measured by the Gaussian distribution model is analyzed. Finally, the accuracy of temperature field probability distribution statistics is verified through experiments.

Excited state proton transfer coupled with twisted intermolecular charge transfer for N,N-dimethylanilino-1,3-diketone in high polar acetonitrile solvent

In the present work, N,N-dimethylanilino-1,3-diketone (DMADK), a new chromophore of the unsymmetrically substituted 1,3-diketone [R. Ghosh and D. K. Palit, Photochem. Photobiol. Sci. 12 (2013) 987–995], has been investigated about the excited state proton transfer (ESPT) based on the time-dependent density functional theory (TDDFT) method. The experimental UV/Vis and emission spectra are well reproduced by the calculated vertical excitation energies in the S0 and S1 states. For the optimized Enol-B* structure, the twisted intermolecular charge transfer (TICT) process can be confirmed in the S1 state. Hydrogen bond strengthening has been testified in the S1 state based on comparing primary bond lengths and bond angles involved in the intramolecular hydrogen bond between the S0 state and the S1 state. Furthermore, infrared spectra (IR) at the OH stretching vibrational region and Molecular electrostatic potential surface (MEPS) based on our calculation also declare the phenomenon of hydrogen bond strengthening. The frontier molecular orbitals (MOs) analysis, MEPS, Mulliken's charge distribution analysis, Hirshfeld charge distribution analysis and Natural bond orbital (NBO) analysis methods manifest the intramolecular charge transfer, which reveals the tendency of excited state intramolecular proton transfer (ESIPT) process. The constructed PESs of both S0 and S1 states demonstrate that ground state intramolecular proton transfer (GSIPT) as well as reversed GSIPT processes exists in the S0 state, and the ESIPT coupled with the TICT process can occur in the S1 state rather than sequential ESIPT and TICT processes.

Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation

Molecular dynamics modeling of complex biological systems is limited by finite simulation time. The simulations are often trapped close to local energy minima separated by high energy barriers. Here, we introduce Hamiltonian replica exchange (H-REMD) with torsional flattening in the Binding Energy Distribution Analysis Method (BEDAM), to reduce energy barriers along torsional degrees of freedom and accelerate sampling of intramolecular degrees of freedom relevant to protein-ligand binding. The method is tested on a standard benchmark (T4 Lysozyme/L99A/p-xylene complex) and on a library of HIV-1 integrase complexes derived from the SAMPL4 blind challenge. We applied the torsional flattening strategy to 26 of the 53 known binders to the HIV Integrase LEDGF site found to have a binding energy landscape funneled toward the crystal structure. We show that our approach samples the conformational space more efficiently than the original method without flattening when starting from a poorly docked pose with incorrect ligand dihedral angle conformations. In these unfavorable cases convergence to a binding pose within 2-3 Å from the crystallographic pose is obtained within a few nanoseconds of the Hamiltonian replica exchange simulation. We found that torsional flattening is insufficient in cases where trapping is due to factors other than torsional energy, such as the formation of incorrect intramolecular hydrogen bonds and stacking. Work is in progress to generalize the approach to handle these cases and thereby make it more widely applicable.

Linguistic Aspects of Arabic-English Code Switching on Facebook and Radio in Australia

Code switching (CS) is a worldwide phenomenon wherein bilinguals utilize two languages within a single conversation and even within a single utterance in both formal and informal settings. The study investigates the linguistic aspects of CS among Arabic-English bilingual speakers in Australia. An integrated approach with both qualitative (conversation analysis) and quantitative (frequency distribution) analysis methods is employed for the purpose of this research. The data were collected from two sets of public resources that are recordings of free-flowing conversations in radio and chats on Facebook. The study concluded that CS is possible at various syntactic and discourse boundaries in these contexts despite the typological differences between the two languages. Nouns with noun phrases and interjections represented the largest number of switched elements in the corpus. In examining the theoretical aspects of Arabic-English CS, the data gave support to the congruence model while challenged the universality of the equivalence and the free morpheme models.

Synthesis of surface molecularly imprinting polymers for cordycepin and its application in separating cordycepin

Cordycepin is an antibiotic with excellent biological and pharmacological activities. In this work, surface imprinting technology was used for cordycepin purification. Gaussian 09 simulation software was used to screen out methacrylic acid and acrylamide as the functional monomers of molecularly imprinted polymers (MIPs). The synthesis was accomplished with modified silica gel as a matrix, cordycepin as a template, methacrylic acid and acrylamide as functional monomers, ethyleneglycol dimethacrylate as a crosslinking agent and azodiisobutyronitrile as an initiator. MIPs for cordycepin separation were characterized by scanning electron microscope, Fourier transform infrared spectroscopy, elemental analysis and the pore size distribution analysis method. Adsorption isotherms for cordycepin show that the adsorption capacity using an initial cordycepin concentration of 16mg/mL was 91.78mg/g. According to the adsorption kinetic curve, MIPs obtained the maximum adsorption amount at 95.37mg/g. In the adsorption kinetic experiments, adsorption reached equilibrium at 14h with a rapid increase up to 4–6h. The selectivity coefficients of MIPs were 3.14 (cordycepin versus inosine) and 3.74 (cordycepin versus adenosine). Experimental results indicated that the adsorption capacity and selectivity of MIPs were sufficient for the separation of cordycepin. MIPs were used to separate cordycepin from Cordyceps militaris. Cordycepin with 98% purity was obtained with the recovery of 25.67%. This result showed that MIPs prepared in this method have a good application prospect in the separation of cordycepin.

Theoretical investigation on ESIPT mechanism of a new fluorescent sensor in different solvents

In the present work, a new phenylbenzimidazole derivatized fluorescent sensor (L) (J. Lumin. 147 (2014) 179), has been investigated on the excited state proton transfer (ESPT) based on the time-dependent density functional theory (TDDFT) method. The calculated absorption and fluorescence spectra based on the TDDFT method are in agreement with the experimental results. Two kinds of structures of L chromophore are found in the first excited (S1) state, which may be due to the proton transfer reactive. Hydrogen bond strengthening has been testified in the S1 state based on comparing staple bond lengths and bond angles involved in hydrogen bonding between the S0 state and the S1 state. In addition, the calculated infrared spectra at the N–H stretching vibrational region and calculated hydrogen bond energy also declare the phenomenon of hydrogen bond strengthening. The frontier molecular orbitals (MOs) and Mulliken's charge distribution analysis method as well as natural bond orbital (NBO) demonstrate the charge distribution, which provides the tendency of ESIPT reaction. The potential energy surfaces of the S0 and S1 states are constructed to explain the mechanism of the proton transfer in the excited state in detail. In addition, the ESIPT process of sensor L is dependent on different solvents.

Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation.

The weighted histogram analysis method (WHAM) including its binless extension has been developed independently in several different contexts, and widely used in chemistry, physics, and statistics, for computing free energies and expectations from multiple ensembles. However, this method, while statistically efficient, is computationally costly or even infeasible when a large number, hundreds or more, of distributions are studied. We develop a locally WHAM (local WHAM) from the perspective of simulations of simulations (SOS), using generalized serial tempering (GST) to resample simulated data from multiple ensembles. The local WHAM equations based on one jump attempt per GST cycle can be solved by optimization algorithms orders of magnitude faster than standard implementations of global WHAM, but yield similarly accurate estimates of free energies to global WHAM estimates. Moreover, we propose an adaptive SOS procedure for solving local WHAM equations stochastically when multiple jump attempts are performed per GST cycle. Such a stochastic procedure can lead to more accurate estimates of equilibrium distributions than local WHAM with one jump attempt per cycle. The proposed methods are broadly applicable when the original data to be "WHAMMED" are obtained properly by any sampling algorithm including serial tempering and parallel tempering (replica exchange). To illustrate the methods, we estimated absolute binding free energies and binding energy distributions using the binding energy distribution analysis method from one and two dimensional replica exchange molecular dynamics simulations for the beta-cyclodextrin-heptanoate host-guest system. In addition to the computational advantage of handling large datasets, our two dimensional WHAM analysis also demonstrates that accurate results similar to those from well-converged data can be obtained from simulations for which sampling is limited and not fully equilibrated.

Electric field distribution and voltage breakdown modeling for any PN junction

Purpose – Scientists and engineers have been solving Poisson’s equation in PN junctions following two approaches: analytical solving or numerical methods. Although several efforts have been accomplished to offer accurate and fast analyses of the electric field distribution as a function of voltage bias and doping profiles, so far none achieved an analytic or semi-analytic solution to describe neither a double diffused PN junction nor a general case for any doping profile. The paper aims to discuss these issues. Design/methodology/approach – In this work, a double Gaussian doping distribution is first considered. However, such a doping profile leads to an implicit problem where Poisson’s equation cannot be solved analytically. A method is introduced and successfully applied, and compared to a finite element analysis. The approach is then generalized, where any doping profile can be considered. 2D and 3D extensions are also presented, when symmetries occur for the doping profile. Findings – These results and the approach here presented offer an efficient and accurate alternative to numerical methods for the modeling and simulation of mathematical equations arising in physics of semiconductor devices. Research limitations/implications – A general 3D extension in the case where no symmetry exists can be considered for further developments. Practical implications – The paper strongly simplify and ease the optimization and design of any PN junction. Originality/value – This paper provides a novel method for electric field distribution analysis.

ラマン散乱分光イメージング法による多色摺木版画の色材分子分布解析法の開発

錦絵をはじめとする多色摺木版画において，色材は木版画を特徴付ける重要な要素である．そのため，色材の分子構造および分子分布の詳細な解析が実現されれば，江戸時代の錦絵制作過程の重要な一部を推察することができる可能性がある．そこで本研究では，分子構造を強く反映した情報が得られるラマン散乱分光法に着目し，色材の分子構造と空間分布を同時に解析が可能な非侵襲的色材解析法の開発を行った．その結果，ラマン散乱分光法を用いることで色材の分子構造解析およびその空間分布を可視化することに成功した．特に，紙面内イメージングから紙の繊維上の色材分布を可視化することに成功した．また，紙面と垂直方向のイメージングから，色材の立体的空間分布を可視化することに成功した．さらに，膠含有/不含色材の空間分布の違いも明らかにし，色材分布に基づく摺刷技術解析の可能性を示した．以上の結果から，本手法は多色摺木版画制作技法の新たな解析手法となると考えられる．

Studying polyglutamine aggregation in Caenorhabditis elegans using an analytical ultracentrifuge equipped with fluorescence detection.

This work explores the heterogeneity of aggregation of polyglutamine fusion constructs in crude extracts of transgenic Caenorhabditis elegans animals. The work takes advantage of the recent technical advances in fluorescence detection for the analytical ultracentrifuge. Further, new sedimentation velocity methods, such as the multi-speed method for data capture and wide distribution analysis for data analysis, are applied to improve the resolution of the measures of heterogeneity over a wide range of sizes. The focus here is to test the ability to measure sedimentation of polyglutamine aggregates in complex mixtures as a prelude to future studies that will explore the effects of genetic manipulation and environment on aggregation and toxicity. Using sedimentation velocity methods, we can detect a wide range of aggregates, ranging from robust analysis of the monomer species through an intermediate and quite heterogeneous population of oligomeric species, and all the way up to detecting species that likely represent intact inclusion bodies based on comparison to an analysis of fluorescent puncta in living worms by confocal microscopy. Our results support the hypothesis that misfolding of expanded polyglutamine tracts into insoluble aggregates involves transitions through a number of stable intermediate structures, a model that accounts for how an aggregation pathway can lead to intermediates that can have varying toxic or protective attributes. An understanding of the details of intermediate and large-scale aggregation for polyglutamine sequences, as found in neurodegenerative diseases such as Huntington's Disease, will help to more precisely identify which aggregated species may be involved in toxicity and disease.