Measurement of the electric conductivity of tungsten in a continuous liquid-to-gas transition

A method is developed that makes it possible to investigate the transition of a metal from a condensed to a gaseous phase while maintaining almost uniform temperature and pressure distributions in the sample. The method consists in the pulsed Joule heating of a sample in the form of a thin foil strip placed between two relatively thick glass plates. This method is used to measure the conductivity of tungsten in a process during which the pressure in the sample is maintained at a level of 40–60 kbar and the density of the sample decreases from the normal solid density to a density 20 to 30 times lower. It is found that, along the 40-kbar isobar, the density dependence of the conductivity of tungsten changes radically at a certain density value, at which it has a pronounced kink. At the kink, the density of tungsten is approximately ten times lower than its characteristic solid density, and the internal energy is about two times the sublimation energy. The method makes it possible to carry out experiments with the almost isobaric heating of tungsten in the parameter range in which the effect in question takes place. No such effect is detected in nonisobaric processes.     

Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta

We describe a method based on Rosetta structure refinement for generating high-resolution, all-atom protein models from electron cryomicroscopy density maps. A local measure of the fit of a model to the density is used to directly guide structure refinement and to identify regions incompatible with the density that are then targeted for extensive rebuilding. Over a range of test cases using both simulated and experimentally generated data, the method consistently increases the accuracy of starting models generated either by comparative modeling or by hand-tracing the density. The method can achieve near-atomic resolution starting from density maps at 4-6 Å resolution.     

Optimization of DNA immobilization on gold electrodes for label-free detection by electrochemical impedance spectroscopy

The ability to immobilize DNA probes onto gold substrates at an optimum surface density is key in the development of a wide range of DNA biosensors. We present a method to accurately control probe DNA surface density by the simultaneous co-immobilization of thiol modified probes and mercaptohexanol. Probe surface density is controlled by the thiol molar ratio in solution, with a linear relationship between thiol molar ratio and probe density spanning (1-9) x10(12)/cm2. The probe surface density per microscopic surface area was determined using chronocoulometry, and a detailed analysis of the method presented. Using this sample preparation method, the effect of probe density and hybridization on the charge transfer resistance with the negatively charged ferri/ferrocyanide redox couple was determined. Above a threshold probe surface density of 2.5 x 10(12)/cm2, electrostatic repulsion from the negatively charged DNA modulates the charge transfer resistance, allowing hybridization to be detected. Below the threshold density no change in charge transfer resistance with probe density or with hybridization occurs. The probe surface density was optimized to obtain the maximum percentage change in charge transfer resistance with hybridization.     

Pooling local expert opinions for estimating mammal densities in tropical rainforests

Methods currently used for assessing wildlife density in rainforests are time and money consuming. The precision of the most commonly used methods is disputed, but accepted because more exact methods are not available. In this study a new method of wildlife density estimation is explained. The new method is less time and money consuming, but yields comparable results with classical methods. The method was tested in the field in Cameroon and compared with transect surveys in the area and with relevant literature. The Pooled Local Expert Opinion (PLEO) method is based on the knowledge of local experts. A number of hunters were asked to estimate wildlife abundance in a specified area, after which the density/km² was calculated for 33 wildlife species. These estimates were pooled and extrapolated for the whole study area. Elephant (Loxodonta africana) density outside the National Park was estimated to be 0.06 animals/km², and 0.3 inside. Buffalo (Syncerus caffer) density for the study area was estimated at 0.2 animals/km² and gorilla (Gorilla gorilla) density at 1.05 per km². Transect surveys carried out at the same time for considerably more money, taking far more time, produced too few data to calculate densities. The evaluation of the PLEO method was favourable and the method offers a substitute for conventional methods of estimating wildlife density in rainforests. The methodology is simple and it can be incorporated in many tropical biodiversity and conservation projects. It can also be used for long-term monitoring of wildlife status in a given area. In contrast with classical methods, the PLEO method is low in cost and assures local ownership of the results.     

Simple method to measure power density entering a plane biological sample at millimeter wavelengths

A simple method for measuring microwave power density is described. It is applicable to situations where exposure of samples in the near field of a horn is necessary. A transmitted power method is used to calibrate the power density entering the surface of the sample. Once the calibration is available, the power density is known in terms of the incident and reflected powers within the waveguide. The calibration has been carried out for liquid samples in a quartz cell. Formulas for calculating specific absorption rate (SAR) are derived in terms of the power density and the complex dielectric constant of the sample. An error analysis is also given.     

基于核密度估算的路网格局与景观破碎化分析

道路网络的发展是导致区域景观破碎化程度加剧的重要因素,如何定量表征道路网络特征及其破碎化效应是道路生态学的一个关键科学问题。本研究以珠江三角洲核心区为案例,采用核密度估算(KDE)结合道路密度指数方法,探讨了区域路网格局及其对景观破碎化的影响。结果表明:KDE法能有效识别和提取高密度路网热点区域;道路密度指数分析显示,道路密度与景观破碎化之间存在较强的相关性;道路密度与KDE法结合能突破传统基于行政边界计算道路密度的局限,为研究路网特征及其景观破碎化程度提供了一个很好的量化工具。     

Assisted assignment of ligands corresponding to unknown electron density

A semi-automated computational procedure to assist in the identification of bound ligands from unknown electron density has been developed. The atomic surface surrounding the density blob is compared to a library of three-dimensional ligand binding surfaces extracted from the Protein Data Bank (PDB). Ligands corresponding to surfaces which share physicochemical texture and geometric shape similarities are considered for assignment. The method is benchmarked against a set of well represented ligands from the PDB, in which we show that we can identify the correct ligand based on the corresponding binding surface. Finally, we apply the method during model building and refinement stages from structural genomics targets in which unknown density blobs were discovered. A semi-automated computational method is described which aims to assist crystallographers with assigning the identity of a ligand corresponding to unknown electron density. Using shape and physicochemical similarity assessments between the protein surface surrounding the density and a database of known ligand binding surfaces, a plausible list of candidate ligands are identified for consideration. The method is validated against highly observed ligands from the Protein Data Bank and results are shown from its use in a high-throughput structural genomics pipeline.     

Adenosine triphosphate content of Mycobacterium leprae by percoll buoyant density centrifugation.

Thirty nine untreated patients of bacilliferous leprosy with a mean bacteriological index of 4.8 and morphological index of 1.3% formed the study group. Adenosine triphosphate assay was carried out by (i) enzyme treatment method in 18 patients and (ii) percoll buoyant density gradient method in 21 patients. ATP content obtained by percoll buoyant density gradient method was significantly higher than that obtained by enzyme treatment method. Percoll buoyant density centrifugation for purification and isolation of bacilli from human leproma is simplier, quicker and can serve as an alternate method of enzyme treatment.     

Estimating trophic link density from quantitative but incomplete diet data

The trophic link density and the stability of food webs are thought to be related, but the nature of this relation is controversial. This article introduces a method for estimating the link density from diet tables which do not cover the complete food web and do not resolve all diet items to species level. A simple formula for the error of this estimate is derived. Link density is determined as a function of a threshold diet fraction below which diet items are ignored ("diet partitioning function"). Furthermore, analytic relationships between this threshold-dependent link density and the generality distribution of food webs are established. A preliminary application of the method to field data suggests that empirical results relating link density to diversity might need to be revisited.     

Critical Point Analysis of Calculated Electron Density Maps at Medium Resolution: Application to Shape Analysis of Zeolite-Like Systems

A method, derived from the procedure implemented in the program ORCRIT which was originally developed by C.K. Johnson, is presented for the topological analysis of zeolite electron density maps. This method is an approach to shape analysis of zeolitic frameworks through the location, identification, and linkage of critical points (points where the gradient of the density vanishes) in medium resolution electron density maps. It is observed that, at 3 Å resolution, tetrahedral sites and oxygen atoms generate peaks (density maxima) and passes (saddle points), respectively. The definition of ellipsoids, built at each peak location from their three local density curvatures, is used to generate a void volume wherein atomic or molecular probes can interact. The energetic behaviour of probes of several sizes interacting with ferrierite and mordenite is qualitatively studied through a pseudo- Lennard-Jones potential approximation.Electronic Supplementary Material available.     

Use of track counts and camera traps to estimate the abundance of roe deer in North-Eastern Italy: are they effective methods?

Population density of European roe deer Capreolus capreolus was estimated in six forest areas of North-Eastern Italy through the use of different methods. The most effective method to estimate a population density is always case-dependent and, thus, varies across study areas. Particularly, drive count and vantage point count estimates (i.e. counts by hunters) have been reported to be the most effective to assess deer densities in woodlands, but they require a high volunteer human presence, which limit their feasibility. Results of count by hunters were thus compared with estimates obtained through camera trapping and track counts. Surveys were all carried out between 2014 and 2015. The three-used method provided us with comparable density results, suggesting that they all may be applied in the study area. Track-count survey was shown to be—with equal effectiveness—the cheapest method to infer roe deer density in forest areas (i.e. near 28% cheaper than camera trapping). As to our study sites, we therefore suggest that the proposal of track-count method might provide wildlife managers with a cost-effective alternative to other count methods to estimate roe deer population density. However, it is noteworthy that track-count method may also lead to lower density estimates than the drive counts; an apparent difference in the accuracy between methods needs to be considered when choosing for a certain count method.     

Wet and dry bacterial spore densities determined by buoyant sedimentation

The wet densities of various types of dormant bacterial spores and reference particles were determined by centrifugal buoyant sedimentation in density gradient solutions of three commercial media of high chemical density. With Metrizamide or Renografin, the wet density values for the spores and permeable Sephadex beads were higher than those obtained by a reference direct mass method, and some spore populations were separated into several density bands. With Percoll, all of the wet density values were about the same as those obtained by the direct mass method, and only single density bands resulted. The differences were due to the partial permeation of Metrizamide and Renografin, but not Percoll, into the spores and the permeable Sephadex beads. Consequently, the wet density of the entire spore was accurately represented only by the values obtained with the Percoll gradient and the direct mass method. The dry densities of the spores and particles were determined by gravity buoyant sedimentation in a gradient of two organic solvents, one of high and the other of low chemical density. All of the dry density values obtained by this method were about the same as those obtained by the direct mass method.     

Wet and dry bacterial spore densities determined by buoyant sedimentation.

The wet densities of various types of dormant bacterial spores and reference particles were determined by centrifugal buoyant sedimentation in density gradient solutions of three commercial media of high chemical density. With Metrizamide or Renografin, the wet density values for the spores and permeable Sephadex beads were higher than those obtained by a reference direct mass method, and some spore populations were separated into several density bands. With Percoll, all of the wet density values were about the same as those obtained by the direct mass method, and only single density bands resulted. The differences were due to the partial permeation of Metrizamide and Renografin, but not Percoll, into the spores and the permeable Sephadex beads. Consequently, the wet density of the entire spore was accurately represented only by the values obtained with the Percoll gradient and the direct mass method. The dry densities of the spores and particles were determined by gravity buoyant sedimentation in a gradient of two organic solvents, one of high and the other of low chemical density. All of the dry density values obtained by this method were about the same as those obtained by the direct mass method.     

Computational analysis of density gradient distribution profiles

A method is presented for the construction of distribution profiles following subcellular fractionation by density gradient centrifugation. The method allows reconstruction of the frequency-density distributions over user-defined density limits, enabling averaging of results from multiple experiments. An alternative format for data presentation, that of relative concentration versus density, is also introduced. This overcomes some practical problems associated with frequency-density distribution profiles. The technique utilizes a direct noniterative approach to curve fitting and can easily be implemented on microcomputers.     

Diagnostics of plasma oscillations by the field of surface waves guided by a dielectric waveguide

The potentialities of the diagnostic method for determining the plasma parameters by recording the surface waves guided by a dielectric waveguide and scattered by plasma oscillations are discussed. The use of surface (slowed) waves makes it possible to improve both the sensitivity and spatial resolution of measurements. The scattering is the most intense near the waveguide cutoff, at which the dependence of the wave propagation constant on the plasma density is the steepest. It is shown experimentally that the method proposed makes it possible to determine the discharge plasma density and electron energy and to estimate the amplitude of the RF field of the plasma waves forming the discharge and the amplitude of plasma density oscillations in these waves. The data obtained from the measurements of the amplitudes of both high-and low-frequency plasma density oscillations by the proposed method agree satisfactorily with theoretical predictions. The experimental data on the plasma density are confirmed by other diagnostic measurements. The ways of reducing measurement errors are proposed.     

A likelihood approach to estimating animal density from binary acoustic transects

We propose an approximate maximum likelihood method for estimating animal density and abundance from binary passive acoustic transects, when both the probability of detection and the range of detection are unknown. The transect survey is purposely designed so that successive data points are dependent, and this dependence is exploited to simultaneously estimate density, range of detection, and probability of detection. The data are assumed to follow a homogeneous Poisson process in space, and a second-order Markov approximation to the likelihood is used. Simulations show that this method has small bias under the assumptions used to derive the likelihood, although it performs better when the probability of detection is close to 1. The effects of violations of these assumptions are also investigated, and the approach is found to be sensitive to spatial trends in density and clustering. The method is illustrated using real acoustic data from a survey of sperm and humpback whales.     

Obtaining source current density related to irregularly structured electromagnetic target field inside human body using hybrid inverse/FDTD method

Inverse method is inherently suitable for calculating the distribution of source current density related with an irregularly structured electromagnetic target field. However, the present form of inverse method cannot calculate complex field–tissue interactions. A novel hybrid inverse/finite-difference time domain (FDTD) method that can calculate the complex field–tissue interactions for the inverse design of source current density related with an irregularly structured electromagnetic target field is proposed. A Huygens’ equivalent surface is established as a bridge to combine the inverse and FDTD method. Distribution of the radiofrequency (RF) magnetic field on the Huygens’ equivalent surface is obtained using the FDTD method by considering the complex field–tissue interactions within the human body model. The obtained magnetic field distributed on the Huygens’ equivalent surface is regarded as the next target. The current density on the designated source surface is derived using the inverse method. The homogeneity of target magnetic field and specific energy absorption rate are calculated to verify the proposed method.     

Estimating population density from indirect sign: track counts and the Formozov–Malyshev–Pereleshin formula

For many purposes it is often desirable to estimate animal population densities over large areas. Where total counts are not possible and sightings are relatively rare, a range of methods exists to estimate densities from indirect sign. Such methods are frequently unreliable and usually require independent calibration or confirmation. We present an analytical method for estimating population density from track counts. The method, widely known in the Russian Federation but not in the English language scientific literature, requires counts of tracks of known age, together with estimates of animal daily travel distances. We use simulations to verify the theoretical basis of the approach and to indicate potential precision that may be achieved. We illustrate application of the approach using a large data set on ungulate track counts in the Russian Far East. We suggest that under most circumstances, nonparametric bootstrapping will be the most appropriate method for deriving estimates of confidence intervals about density estimates. As with other approaches to estimating density from indirect sign, the method that we discuss is vulnerable to violations of an array of underlying assumptions. However, it is easily applied and could represent an important method by which the relationship between indices of abundance and absolute density can be understood.     

A maximum entropy method for inverting Laplace transforms of probability density functions

This papers presents a maximum entropy method for invertingLaplace transforms of density functions of positive random variables.The maximum entropy density is very flexible and can assumea variety of different shapes. Accurate approximations to thetrue density can be obtained even when only a few transformvalues are available. Numerical evidence is provided for gamma,lognormal, inverse Gaussian and Pareto distributions.