Essential proteins identification method based on four-order distances and subcellular localization information

Essential proteins are inseparable in cell growth and survival. The study of essential proteins is important for understanding cellular functions and biological mechanisms. Therefore, various computable methods have been proposed to identify essential proteins. Unfortunately, most methods based on network topology only consider the interactions between a protein and its neighboring proteins, and not the interactions with its higher-order distance proteins. In this paper, we propose the DSEP algorithm in which we integrated network topology properties and subcellular localization information in protein–protein interaction(PPI) networks based on four-order distances, and then used random walks to identify the essential proteins. We also propose a method to calculate the finite-order distance of the network, which can greatly reduce the time complexity of our algorithm. We conducted a comprehensive comparison of the DSEP algorithm with 11 existing classical algorithms to identify essential proteins with multiple evaluation methods. The results show that DSEP is superior to these 11 methods.

Extended Lorenz majorization and frequencies of distances in an undirected network

Purpose:To contribute to the study of networks and graphs.Design/methodology/approach:We apply standard mathematical thinking.Findings:We show that the distance distribution in an undirected network Lorenz majorizes the one of a chain.As a consequence,the average and median distances in any such network are smaller than or equal to those of a chain.Research limitations:We restricted our investigations to undirected,unweighted networks.Practical implications:We are convinced that these results are useful in the study of small worlds and the so-called six degrees of separation property.Originality/value:To the best of our knowledge our research contains new network results,especially those related to frequencies of distances.

Robust free-space optical frequency transfer in time-varying link distances conditions

Future inter-satellite clock comparison on high orbit will require optical time and frequency transmission technology between moving objects.Here,we demonstrate robust optical frequency transmission under the condition of variable link distance.This variable link is accomplished by the relative motion of a single telescope fixed on the experimental platform to a corner-cube reflector(CCR)installed on a sliding guide.Two acousto–optic modulators with different frequencies are used to separate forward signal from backward signal.With active phase noise suppression,when the CCR moves back and forth at a constant velocity of 20 cm/s and an acceleration of 20 cm/s^(2),we achieve the best frequency stability of 1.9×10^(-16) at 1 s and 7.9×10^(-19) at 1000 s indoors.This work paves the way for future studying optical frequency transfer between ultra-high-orbit satellites.

Multi-Attribute Couplings-Based Euclidean and Nominal Distances for Unlabeled Nominal Data

Learning unlabeled data is a significant challenge that needs to han-dle complicated relationships between nominal values and attributes.Increas-ingly,recent research on learning value relations within and between attributes has shown significant improvement in clustering and outlier detection,etc.However,typical existing work relies on learning pairwise value relations but weakens or overlooks the direct couplings between multiple attributes.This paper thus proposes two novel and flexible multi-attribute couplings-based distance(MCD)metrics,which learn the multi-attribute couplings and their strengths in nominal data based on information theories:self-information,entropy,and mutual information,for measuring both numerical and nominal distances.MCD enables the application of numerical and nominal clustering methods on nominal data and quantifies the influence of involving and filtering multi-attribute couplings on distance learning and clustering perfor-mance.Substantial experiments evidence the above conclusions on 15 data sets against seven state-of-the-art distance measures with various feature selection methods for both numerical and nominal clustering.

Influences of Different Distances between Ridges or Plants on Yield of Sweet Potatoes

Based on the combination test of various distances between ridges or plants, the influences of corresponding cultivation techniques on the per unit area yield of a variety of sweet potatoes Xushu 22 in Xianning City were analyzed. The results show that different distances between ridges or plants had significant effects on the per unit area yield of Xushu 22; when the distances between ridges and plants for Xushu 22 planted in the city were 80 and 21 cm respectively, the per u- nit area yield of Xushu 22 was the highest, up to 48 340.7 kg/hm2.

Investigation of True Ni^(2+)-Halide Distances in Alkali Halide Lattices

Using the μKα model of Ni2+-6X- cluster, the true distances between impurity Ni2+ cation and halide anion in alkali halide lattices are estimated from the optical spectra data. The results suggest that the true impurity cation- ligand anion distances are close to the sum of ionic radii of the impurity cation and ligand anion but not the cation - anion distance of the perfect lattices in the case of that the ionic radius of host cation is more larger than that of impurity cation

Effect of Distances from Different Trees Species on the Properties of Mollic Horizon

The study area is located in Duhok province-Kurdistan region-Northern Iraq and including two locations the first location is situated in Galbook village and the vegetation cover is trees of （Quercus aegilops L.）, the second location is situated in Koradeer village that covered with threes of Prunus dulcis （Mill.） Webb.. Disturbed surface soil samples at depth 0-30 cm were collected at four different distances （1, 5, 10 and 15 m） from the tree with randomized selection three trees in each study location. Soil organic matter decreases with increasing distances from tree in both locations under two different trees species, which is attributed to the effect of tree crown. Ordinarily, organic matter content in both locations correspond to the requirements of Mollisols. Statistical analysis of data showed significant differences in organic matter content between locations. Cation exchange capacity is high under tree crown and decreasing with distances from tree in both locations, as a result of decreasing organic matter and increasing calcium carbonate with distances. Commonly soil pH is slightly increased with increasing distances from tree because of increasing calcium carbonate with distances and decreasing organic matter content. Calcium was not uniform with distances and Mg decreasing with distances in both locations. The values of fine clay/coarse clay and fine clay/total clay of soil samples confirm development of the soils under study. Porosity percentage under tree crown is high and decreasing with distances. Soil bulk density was increased with distances in both locations, as a result of decreasing organic matter content with distances. This study aims to explain the effect of tree distances and species on the mollic horizon properties.

Cosmological Distances in Closed Model of the Universe

Four Cosmological distances were determined in the light of the closed cosmic model which was presented in a previous study. Each of these distances was obtained in terms of the redshift of an extragalactic object. It is found that the luminosity distance of the extragalactic object in the closed cosmic model, the observed model and model are approximately the same up to z = 0.1535. However, the luminosity distance in the close cosmic model approximately agrees with its value in the observed model up to z = 0.6442. Estimations of the horizon distance of the universe, the total mass and the mass of matter within the horizon distance, the equivalent numbers of the Milky Way-like galaxies and the Coma-like clusters of galaxies to the mass of matter were computed in the closed cosmic model at the present time.

Cosmological Distances in Five General Cosmic Models

Four cosmological distances were investigated in the light of the five general cosmic models which were developed in a previous study. These are the proper distance, luminosity distance, angular diameter distance and distance modulus. Each of these distances was studied in terms of the redshift of the extragalactic objects. Estimations of the horizon distance of the universe, the total mass and the mass of matter within the horizon distance, the equivalent numbers of the Milky Way-like galaxies and the Coma-like clusters of galaxies to the mass of matter were determined in the general models at the present time.

Distances Scale Determination for a Planetary Nebula in Galactic Bulge

Planetary Nebulae (PN) distances represent the fundamental parameter for the determination the physical properties of the central star of PN. In this paper the distances scale to Planetary Nebulae in the Galactic bulge were calculated related to previous distances scales. The proposed distance scale was done by recalibrated the previous distance scale technique CKS/D82. This scale limited for nearby PN (D ≤ 3.5 kpc), so the surface fluxes less than other distance scales. With these criteria the results showed that the proposed distance scale is more accurate than other scales related to the observations for adopted sample of PN distances, also the limit of ionized radius (Rio) for all both optically thick and optically thin in the rang of sizes (0.45 > Rio (pc) > 0.03).

Information-Based Numerical Distances between Equilibrium and Non-Equilibrium States

We consider a typical master equation describing thermal time-evolution. In parallel, we also consider a quasi static canonical description of the same problem. We are able to devise a way of numerically comparing these two treatments and concoct a distance-measure between them. In this way, one is in a position to know how far or close equilibrium and off-equilibrium can get. The first, rather surprising observation, is that our systems lose structural details as N grows. Also, the time-evolution of the distance between the two pertinent probability distributions is quite sensitive to the heating-cooling process.

Assessment of different genetic distances in constructing cotton core subset by genotypic values

One hundred and sixty-eight genotypes of cotton from the same growing region were used as a germplasm group to study the validity of different genetic distances in constructing cotton core subset. Mixed linear model approach was employed to unbiasedly predict genotypic values of 20 traits for eliminating the environmental effect. Six commonly used genetic distances(Euclidean,standardized Euclidean,Mahalanobis,city block,cosine and correlation distances) combining four commonly used hierarchical cluster methods(single distance,complete distance,unweighted pair-group average and Ward's methods) were used in the least distance stepwise sampling(LDSS) method for constructing different core subsets. The analyses of variance(ANOVA) of different evaluating parameters showed that the validities of cosine and correlation distances were inferior to those of Euclidean,standardized Euclidean,Mahalanobis and city block distances. Standardized Euclidean distance was slightly more effective than Euclidean,Mahalanobis and city block distances. The principal analysis validated standardized Euclidean distance in the course of constructing practical core subsets. The covariance matrix of accessions might be ill-conditioned when Mahalanobis distance was used to calculate genetic distance at low sampling percentages,which led to bias in small-sized core subset construction. The standardized Euclidean distance is recommended in core subset construction with LDSS method.

An Improved DV-Hop Localization Algorithm Based on Hop Distances Correction

DV-Hop localization algorithm has greater localization error which estimates distance from an unknown node to the different anchor nodes by using estimated average size of a hop to achieve the location of the unknown node.So an improved DV-Hop localization algorithm based on correctional average size of a hop,HDCDV-Hop algorithm,is proposed.The improved algorithm corrects the estimated distance between the unknown node and different anchor nodes based on fractional hop count information and relatively accurate coordinates of the anchor nodes information,and it uses the improved Differential Evolution algorithm to get the estimate location of unknown nodes so as to further reduce the localization error.Simulation results show that our proposed algorithm have lower localization error and higher localization accuracy compared with the original DV-Hop algorithm and other classical improved algorithms.

Changes in Runout Distances of Debris Flows over Time in the Wenchuan Earthquake Zone

A large number of debris flows occurred in the Wenchuan earthquake zone after the 12 May 2008 earthquake.The risks posed by these debris flows were rather high.An appropriate model is required to predict the possible runout distance and impacted area.This paper describes a study on the runout characteristics of the debris flows that occurred in the Wenchuan earthquake zone over the past four years.A total of 120 debris flows are analyzed.Separate multivariate regression models are established for the runout distances of hill-slope debris flows and channelized debris flows.The control variables include type of debris flow,debris flow volume,and elevation difference.Comparison of the debris flows occurring before and after the earthquake shows that the runout distance increased after the earthquake due to sufficient material supply and increased mobility of the source materials.In addition,the runout distances of annual debris flow events in 2008,2010 and 2011 are analyzed and compared.There is a tendency that the runout distance decreases over time due to the decreasing source material volume and possible changes of debris flow type.Comparison between the debris flows in the earthquake zone and the debris flows in Swiss Alps,Canada,Austria,and Japan shows that the former have a smaller mobility.

Fuzzy distances based FMAGDM compromise ratio method and application

An extended compromise ratio method（CRM） based on fuzzy distances is developed to solve fuzzy multi-attribute group decision making problems in which weights of attributes and ratings of alternatives on attributes are expressed with values of linguistic variables parameterized using triangular fuzzy numbers.A compromise solution is determined by introducing the ranking index based on the concept that the chosen alternative should be as close as possible to the positive ideal solution and as far away from the negative ideal solution as possible simultaneously.This proposed method is compared with other existing methods to show its feasibility and effectiveness and illustrated with an example of the military route selection problem as one of the possible applications.

Fixed Point Results by Altering Distances in Fuzzy Metric Spaces

We establish fixed point theorems in complete fuzzy metric space by using notion of altering distance, initiated by Khan et al. [Bull. Austral. Math. Soc. 30 (1984), 1-9]. Also, we find an affirmative answer in fuzzy metric space to the problem of Sastry [TamkangJ. Math., 31(3) (2000), 243-250].

Minimum Time Overtaking Problem of Vehicle Handling Inverse Dynamics Based on Two Kinds of Safe Distances

Overtaking accidents caused by improper operations performed by a driver occur frequently. However, most stud?ies on overtaking safety have neglected research into driver control input. A novel method is proposed to obtain the driver control input during the overtaking process. Meanwhile, to improve the safety of overtaking, two types of safe distances, and the time of the overtaking are considered. Path constraints are established when considering the two types of safe distances. An optimal control model is established to solve the minimum time maneuver under multiple constraints. Using the Gauss pseudospectral method, the optimal control problem is converted into a nonlinear pro?gramming problem, which is then solved through sequential quadratic programming(SQP). In addition, the e ective?ness of the proposed method is verified based on the results of a Carsim simulation. The simulation results show that by adopting an inverse dynamics method to solve the manipulation problem of the vehicle’s minimum overtaking time, the manipulation capability of a vehicle in completing an overtaking safely within the minimum time can be obtained. This method can provide a reference for research into the active safety of manned and unmanned vehicles.

Entanglement dynamics of a three-qubit system with different interatomic distances

We investigate the tripartite entanglement dynamics of three two-level atoms in a multi-mode vacuum field. By considering the influences of the interatomic distance and the initial condition on the lower bound of concurrence and the tripartite negativity, we show that an optimal interatomic distance can be found to minimize the collective damping. Interestingly, at the same optimal distance, the tripartite entanglement would be maximized in the open dynamics process. In the case of shorter interatomic distance, the tripartite entanglement can display the oscillatory behavior in the initial short-time limit and be trapped in a stationary value in the long-time limit. In addition, the tripartite entanglement for the general situation with different interatomic distances is also discussed.

Minimum Clearance Offsets for Providing Desired Stopping Sight Distances at Simple Curves with Variable Operating Speeds

Lateral clearance on the inside of horizontal curves is required by all geometric design guidelines in order to provide at least stopping sight distance. There already exist graphical models, analytical models, and design charts for determining minimum clearance offsets to meet the requirement. Some of these models determine the offsets based on constant design sight distance values on the assumption that drivers negotiate horizontal curves at constant speed. Therefore, those models are suitable for sites where there is no difference in speeds between tangent and curved sections. Past studies have reported that there are sites where drivers decelerate on entering horizontal curves and accelerate on departing from the curves. At those sites stopping sight distance for a given driver varies with driver location due to variable speed. This paper presents an analytical model and a chart for determining minimum offsets needed to provide desired sight distances at horizontal curves with variable operating speeds. At those sites the offsets yield roadside clearance boundaries that have transition arcs with performances that are similar to those of elliptical arcs. Therefore, practitioners may choose to use elliptical equations or equations and the chart developed herein. Results of this study will be of value to practitioners in the area of roadside design.

Computations of wall distances by solving a transport equation

Computations of wall distances still play a key role in modern turbulence modeling. Motivated by the expense involved in the computation, an approach solving partial differential equations is considered. An Euler-like transport equation is proposed based on the Eikonal equation. Thus, the efficient algorithms and code components developed for solving transport equations such as Euler and Navier-Stokes equations can be reused. This article provides a detailed implementation of the transport equation in the Cartesian coordinates based on the code of computational fluid dynamics for missiles （MI- CFD） of Beihang University. The transport equation is robust and rapidly convergent by the implicit lower-upper symmetric Gauss-Seidel （LUSGS） time advancement and upwind spatial discretization. Geometric derivatives must also be upwind determined to ensure accuracy. Special treatments on initial and boundary conditions are discussed. This distance solving approach is successfully applied on several complex geometries with 1-1 blocking or overset grids.