Miracle-dz/UniFAR-FTUs huggingface dataset:
MAXIMUM LIKELIHOOD TREES FROM DNA SEQUENCES: A PECULIAR STATISTICAL ESTIMATION PROBLEM

The parameter space of the phylogenetic tree estimation problem consists of three com? ponents, T, t, and 8. The tree topology T is a discrete entity that is not a proper statistical parameter but that can nevertheless be estimated using the maximum likelihood criterion. Its role is to specify the branch length parameters and the form of the likelihood function(s). Branch lengths t are conditional on T and are meaningful only for specific values of T. Parameters 8 in the model of nucleotide substitution are common to all the tree topologies and represent such values as the transition/trans version rate ratio. T and t thus represent the tree, and 8 represents the model. With typical DNA sequence data, differences in T have only a small effect on the likelihood, but changing 8 will influence the likelihood greatly. Estimates of 8 are also found to be insensitive to T, making it possible to obtain reliable estimates of 8 and to perform tests concerning the model (8) even if knowledge of the evolutionary relationship (T) is not available. In contrast, tests con? cerning t, such as testing the existence of a molecular clock, appear to be more difficult to perform when the true topology is unknown. In this paper, we explore the peculiarity of the parameter space of the tree estimation problem and suggest methods for overcoming some difficulties in? volved with tests concerning the model. We also address difficulties concerning hypothesis testing on T, i.e., evaluation of the reliability of the estimated tree topology. We note that estimation of and particularly tests concerning T depend critically on the assumed model. (Maximum likeli? hood; models; parameter space; consistency; sampling errors; hypothesis testing; nucleotide sub? stitution; phylogeny estimation; molecular systematics; molecular clock.)
Enhanced coupled-resonator-induced transparency and optical Fano resonance via intracavity backscattering

We look into the use of the intracavity backscattering in twin-coupled traveling wave microresonators (TWMRs) to generate enhanced coupled-resonator-induced transparency (CRIT) and optical Fano resonance (OFR). Intracavity backscattering makes it possible to either generate a single CRIT peak or a pair of CRIT peaks within one free spectral range in the transmission spectrum. The distance between the twin-CRIT peaks can be tuned by controlling the intracavity backscattering strength. Also, the use of intracavity backscattering allows the simultaneous production of both fast and slow light effects. In addition, it is found that the symmetric CRIT peaks can be reshaped into asymmetric OFR line shapes either by using TWMRs with different intracavity backscattering strengths when one input is launched into the circuit or by modulating the phase/amplitude difference between the dual contrapropagating inputs, which are launched into the circuit in the presence of intracavity backscattering. These allow switching between CRIT and OFR to be realized in the absence of gain or phase tuning elements in the cavities, unlike conventional twin-coupled TWMR systems.
A DESIGN FOR A SUSTAINED ASSESSMENT OF CLIMATE FORCING AND FEEDBACKS RELATED TO LAND USE AND LAND COVER CHANGE

Land use and land cover change (LULCC) significantly influences the climate system. Hence, to prepare the nation for future climate change and variability, a sustained assessment of LULCC and its climatic impacts needs to be undertaken. To address this objective, not only do we need to determine contemporary trends in land use and land cover that affect, or are affected by, weather and climate but also identify sectors and regions that are most affected by weather and climate variability. Moreover, it is critical that we recognize land cover and regions that are most vulnerable to climate change and how end-use practices are adapting to climate change. This paper identifies a series of steps that need to be undertaken to address these key items. In addition, national-scale institutional capabilities are identified and discussed. Included in the discussions are challenges and opportunities for collaboration among these institutions for a sustained assessment.
A Hamilton Path Embedding Algorithm on DCell

DCell has been proposed for enormous data centers as a server centric interconnection which can support millions of servers with high network capacity and provide good fault tolerance by only using commodity switches. In this paper, we study an attractive algorithm of finding Hamilton paths in dimensional. The time complexity of this algorithm is , where is the node number of DCellk .
Determination of piezoelectric material parameters using a combined measurement and simulation technique

In this paper we describe the extension of our parameter identification algorithm for extracting the full parameter set of piezoelectric materials. The scheme is based on the FE solution of the according partial differential equations and on impedance measurements on appropriate test transducers. The results obtained by applying the scheme to a multilayer stack actuator as well as an ultrasound array antenna material will demonstrate the applicability of the developed parameter identification scheme.
Statistical approach for angular position separability classes of EMG data

This paper focus on the application of a multivariate statistical analysis approach, based on Linear Discriminant Analysis (LDA), of EMG data that aims to identify the angular position of the elbow. Linear transformations applied to EMG signals of the Biceps brachii and Triceps brachii, acquired during flexion / extension movements, enabled good and reliable class separation for future classification.
An upwind numerical scheme for relativistic hydrodynamics with a general equation of state

This paper describes a simple, second-order, upwind scheme for the equations of special relativistic hydrodynamics in multidimensions. A linear solver is used for all Riemann problems except those that contain strong rarefactions and, unlike previous algorithms, it is not restricted to an equation of state with a constant ratio of specific heats. Test calculations show that the scheme is accurate for flows containing extremely strong shocks and with Lorentz factors of several hundred. It has been combined with an adaptive hierarchical grid, which makes it possible to use high resolution in any number of dimensions.
A multi-parametric segmentation tool dedicated to ultrasonic data

Ultrasound images segmentation can bring very useful information for diagnosis but is a difficult task. We propose in this paper a segmentation tool dedicated to ultrasonic data. Our software is based on a segmentation method that involves both multiresolution and multiparametric approaches. A multiparametric approach ensures the robustness of the method. Therefore, the segmentation tool is based on information connected to echo envelope characterization and acoustical characterization, the latter being calculated from the Radio-Frequency (RF) signal. The RF signal allows to calculate local information related to the acoustical properties of the investigated tissues. Several parametric images are build and involved in the segmentation process. The segmentation software is based on a previously presented method (Boukerroui et al. 2001). A Bayesian approach using a multiresolution Markov random field is implemented. The relevance of the several features calculated is shown by the mean of phantoms build with the FIELD II tool. We also present segmentation results on data provided by a technological platform that provides in-vivo multimodality imaging of small animals such as mice and rats. Results on the segmentation of liver mice ultrasonic data are presented.
Modeling and Control of Epitaxial Thin Film Growth

Thin film deposition is a manufacturing process in which tolerances may approach the size of individual atoms. The final film is highly sensitive to the processing conditions, which can be intentionally manipulated to control film properties. A lattice model of surface evolution during thin film growth captures many important features, including the nucleation and growth of clusters of atoms and the propagation of atomic-height steps. The dimension of this probabilistic master equation is too large to directly simulate for any physically realistic domain, and instead stochastic realizations of the lattice model are obtained with kinetic Monte Carlo simulations. In this thesis simpler representations of the master equation are developed for use in analysis and control. The static map between macroscopic process conditions and microscopic transition rates is first analyzed. In the limit of fast periodic process parameters, the surface responds only to the mean transition rates, and, since the map between process parameters and transition rates is nonlinear, new effective combinations of transition rates may be generated. These effective rates are the convex hull of the set of instantaneous rates. The map between transition rates and expected film properties is also studied. The dimension of a master equation can be reduced by eliminating or grouping configurations, yielding a reduced-order master equation that approximates the original one. A linear method for identifying the coefficients in a master equation is then developed, using only simulation data. These concepts are extended to generate low-order master equations that approximate the dynamic behavior seen in large Monte Carlo simulations. The models are then used to compute optimal time-varying process parameters. The thesis concludes with an experimental and modeling study of germanium film growth, using molecular beam epitaxy and reflection high-energy electron diffraction. Growth under continuous and pulsed flux is compared in experiment, and physical parameters for the lattice model are extracted. The pulsing accessible in the experiment does not trigger a change in growth mode, which is consistent with the Monte Carlo simulations. The simulations are then used to suggest other growth strategies to produce rougher or smoother surfaces.
Krull dimension of malcev-neumann rings

It is known that if R is a right noetherian ring, then the corresponding Malcev-Neumann ring R * ((G)) is right noetherian and r.K. dim(R) = r.K. dim(R * ((G))). We prove that the right noethe-rianness is a necessary condition for a Malcev-Neumann ring to have right Krull dimension. Also, we consider uniform dimension of Malcev-Neumann rings. The results obtained are applied to some other ring constructions
On the spectral (co)homology exact sequences of maps

Abstract. Using the inverse system approach of continuous maps, in this paper we study the (co)homological properties of continuous maps. Applications of the obtained results include the constructions of long exact sequences of continuous maps for homology pro-groups, cohomology inj-groups, Čech homology groups and Čech cohomology groups.
A FAST CONVERGENCE SCHEME FOR COUPLED ENERGY DOMAINS SIMULATION OF MEMS

Due to the massive demands from industry, the black-box based coupled energy domains simulation plays a more and more important role in the design of MEMS devices, and many numerical techniques have been developed so far for it. This paper presents a fast convergence scheme for coupled energy domains simulation of MEMS. This scheme is based on the relaxation approach but employs the Steffensen's acceleration technique to speed up the convergence procedure. In this paper, the details of this scheme are described as well as the relaxation and the multilevel Newton methods. The numerical examples show that the proposed scheme has equivalent convergence performance, sometimes even more efficient, as the multilevel Newton method, and much better than the relaxation method, especially for strong coupled or nonlinear situations, while keeping the advantage of easy programming.Copyright © 2006 by ASME
Retrieval of Cloud Cover Parameters from Multispectral Satellite Images

Abstract A technique is described for extracting cloud cover parameters from multispectral satellite radiometric measurements. Utilizing three channels (visible, 3.7 μm and 11 μm) from the AVHRR (Advanced Very High Resolution Radiometer) on NOAA polar orbiting satellites, it is shown that one can retrieve four parameters for each pixel: cloud fraction within the FOV, optical thickness cloud-top temperature and a microphysical model parameter. The last parameter is an index representing the properties of the cloud particle (e.g., size, shape, thermodynamic phase, etc.) and is determined primarily by the radiance at 3.7 μm. The other three parameters are extracted from the visible and 11 μm infrared radiances, utilizing the information contained in the two-dimensional scatter plot of the measured radiances. The solution is essentially one in which the distributions of optical thickness and cloud-top temperature are maximally clustered for each region, with cloud fraction for each pixel adjusted to achieve m.
Problems with the Asymptotic Theory of Maximum Likelihood Estimation in Integrated and Cointegrated Systems

Problems with the asymptotic theory of nonlinear maximum likelihood estimation in integrated and cointegrated systems are discussed in this paper. One problem is that standard proofs of consistency generally do not apply; another one is that, even if the consistency has been established, it can be difficult to deduce the limiting distribution of a maximum likelihood estimator from a conventional Taylor series expansion of the score vector. It is argued in this paper that the latter difficulty can generally be resolved if, in addition to consistency, an appropriate result of the order of consistency of the long-run parameter estimator of the model is available and the standardized sample information matrix satisfies a suitable extension of previous stochastic equicontinuity conditions. To make this idea applicable in particular cases, extensions of the author's recent stochastic equicontinuity results, relevant for many integrated and cointegrated systems with nonlinearities in parameters, are provided. As an illustration, a simple regression model with integrated and stationary regressors and nonlinearities in parameters is considered. In this model, the consistency and order of consistency of the long-run parameter estimator are obtained by employing extensions of well-known sufficient conditions for consistency. These conditions are applicable quite generally, and their verification in the special case of this paper suggests how to proceed in more complex models.
A stochastic Lagrangian model for acceleration in turbulent flows

A stochastic model is developed for the acceleration of a fluid particle in anisotropic and inhomogeneous turbulent flows. The model consists of an ordinary differential equation for velocity (which contains directly the acceleration due to the mean and rapid pressure gradients), and a stochastic model for the remainder of the acceleration, which is due to the slow pressure gradient and to viscosity. In addition to a rapid-pressure model, the stochastic model involves three tensor coefficients. For isotropic turbulence, the model reverts to that previously proposed by Sawford. At high Reynolds number the model is consistent with local isotropy and the Kolmogorov hypotheses, and tends to the generalized Langevin model for fluid-particle velocity. In this case two of the tensor coefficients are known in terms of the Kolmogorov constant C0, while the third is related to the coefficient in the generalized Langevin model. A complete analysis of the model is performed for homogeneous turbulent shear flow, for w.
Singularity formation in three-dimensional motion of a vortex sheet

The evolution of a small but finite three-dimensional disturbance on a flat uniform vortex sheet is analysed on the basis of a Lagrangian representation of the motion. The sheet at time t is expanded in a double periodic Fourier series: R(λ1, λ2, t) = (λ1, λ2, 0) + Σn,m An,m exp[i(nλ1 + δmλ2)], where λ1 and λ2 are Lagrangian parameters in the streamwise and spanwise directions, respectively, and δ is the aspect ratio of the periodic domain of the disturbance. By generalizing Moore's analysis for two-dimensional motion to three dimensions, we derive evolution equations for the Fourier coefficients An,m. The behaviour of An,m is investigated by both numerical integration of a set of truncated equations and a leading-order asymptotic analysis valid at large t. Both the numerical integration and the asymptotic analysis show that a singularity appears at a finite time tc = O(lnε−1) where ε is the amplitude of the initial disturbance. The singularity is such that An,0 = O(tc−1) behaves like n−5/2, while An,±1 = O(εtc) behaves like n−3/2 for large n. The evolution of A0,m(spanwise mode) is also studied by an asymptotic analysis valid at large t. The analysis shows that a singularity appears at a finite time t = O(ε−1) and the singularity is characterized by A0,2k ∝ k−5/2 for large k.
Laser pointing stability measured by an oblique-incidence optical transmittance difference technique

We describe an oblique-incidence optical transmittance technique for determining the pointing stability of a laser. In this technique, we follow the angular drift of a monochromatic laser beam by measuring the relative changes in transmittance through a parallel fused quartz window for s and p polarized components of the beam in response to the drift. This method is shown in the present experiment to have the sensitivity to detect angular changes in the range of 2 μ radians (1 μ radian=10−6 radian). To demonstrate this technique, we measured the angular drifts of two commercial intensity-stabilized He–Ne lasers.
Bayesian analysis of a multiple-recapture model

In the Bayesian analysis of a multiple-recapture census, different diffuse prior distributions can lead to markedly different inferences about the population size N. Through consideration of the Fisher information matrix it is shown that the number of captures in each sample typically provides little information about N. This suggests that if there is no prior information about capture probabilities, then knowledge of just the sample sizes and not the number of recaptures should leave the distribution of Nunchanged. A prior model that has this property is identified and the posterior distribution is examined. In particular, asymptotic estimates of the posterior mean and variance are derived. Differences between Bayesian and classical point and interval estimators are illustrated through examples.
Quadrupole-Strain Interaction in Rare Earth Hexaborides

Temperature dependence of the elastic constants in a series of rare earth hexaborides has been investigated by means of the ultrasonic method. The remarkable softening of the transverse C 44 mode in PrB 6 , NdB 6 , DyB 6 and HoB 6 has been discussed in connection with the cooperative Jahn-Teller effect due to the CEF ground state degenerated by the quadrupolar moment. The low temperature behavior of C 44 in Ce x La 1- x B 6 compounds is presented to show the Kondo effect on the quadrupolar moment of Γ 8 ground state. The anomaly of the bulk modulus C B in SmB 6 is related to the valence fluctuation state in the system.
Research of soil moisture retrieval in arid region on the moistureshed scale

Soil moisture is an indispensable parameter of water, heat and carbon cycle processes in the earth surface system, and plays a key role in the formation of run-off in arid areas. The retrieval of regional-scale soil moisture is significant in the monitoring of crop growth and drought in arid regions, and in the modeling of global climatic dynamic surface processes. The use of multi-source remote sensing data in the soil moisture retrieval can improve the accuracy of reversion and generally over perform the use of a single remote sensing data due to that the data acquired by different remote sensors can provide complementary information about the soil moisture. The co-reversion of multi-source remotely sensed data is a cutting-edge technique for soil moisture retrieval. This study tries to optimize and adjust the existing reversion models available for different land cover types. A co-reversion scheme model will be designed and used to retrieve soil moisture of different vegetation types of the arid area by using MODIS and AMSR-E remote sensing data. The downscaling strategy and field verification will be used to analyze the accuracy, uncertainty and sensitivity of the reversion models. The popularity and regionality of the model will be also examined to explore the possibility of the model used for large-scale and dynamic monitoring of soil moisture.
Three-dimensional beam propagation model for the optical path of light through a nematic liquid crystal

A three-dimensional beam propagation model is presented which, given a director profile, calculates the electric and magnetic fields for a light wave as it travels through a liquid crystal structure using a predictive-corrector Crank–Nicholson numerical method and adjusts for impedance effects in the direction of propagation. The results from the model are compared to both analytical solutions for simpler director profiles and other optical models for more complicated director profiles.
A new perturbation method for measuring microwave fields in free space

A perturbation method for measuring free-space microwave fields is described. A short thin metal rod forms the perturbing element. In order to avoid confusing the reflection from this rod with unwanted reflection the rod is arranged to spin about an axis perpendicular to its length. The perturbation of the field at the source is therefore modulated at a characteristic frequency, and by using an a.c. amplifier, steady reflections can be eliminated. The apparatus described operates at a wavelength of about 3.2 cm. Experimental results are given which verify the theory for linearly polarized waves. Extension of the method to elliptically polarized waves is possible in principle, but inherent ambiguities may be troublesome in practice.
Nonlinear extreme ground effect on thin wings of arbitrary aspect ratio

Air flows past a fixed thin body of a general planform, at a non-uniform small clearance from a plane ground surface. The flow beneath the body is described by a linear two-dimensional partial differential equation, in which the clearance appears as an input non-constant coefficient. Solutions are required subject to separate leading-edge and (nonlinear) trailing-edge boundary conditions, at the edge contour of the planform. The transition points between leading and trailing edge are not necessarily at the lateral extremities of this contour, and are to be determined as part of the solution. As an illustration, a solution is obtained for a circular planform with an exponentially varying clearance. The general problem is relevant to vehicle aerodynamics, especially for racing cars, and some qualitative discussion of the nature of the negative-lift ground-effect problem for such vehicles, and of the effect of ‘skirts’, is presented here.