scholarly journals TreeBASEdmp: A Toolkit for Phyloinformatic Research

2018 ◽  
Author(s):  
William H. Piel ◽  
Rutger A. Vos
Keyword(s):  
Matrix Representation ◽  
New Approach ◽  
Substantial Body ◽  
Phylogenetic Data ◽  
Nested Sets

AbstractOver the last 20 years, TreeBASE has acquired a substantial body of phylogenetic data, including more than 20,000 published phylogenies. Given latency issues and limited options when it comes to querying the database remotely, a simplified and consolidated version of the database, here called TreeBASEdmp, is made available for download, allowing biologists to design custom analyses of the data on their local computers. The database is indexed to support searching for phylogenetic topologies using nested sets and closure tables. Here we propose a new approach to find broadly-defined phylogenetic patterns, a method we call Generic Topological Querying, which allows the user to find hypotheses of relationship without being constrained to use particular sets of specific taxa. Additionally, we normalize as many leaf nodes as possible to an equivalent species rank identifier to assist in supertree synthesis. Our example script rapidly assembles sets of trees and generates a matrix representation of them for subsequent supertree generation.

scholarly journals Dynamic Phasors Estimation Based on Taylor-Fourier Expansion and Gram Matrix Representation

2018 ◽  
Vol 2018 ◽  
pp. 1-17 ◽  
Author(s):  
Predrag Petrović ◽  
Nada Damljanović
Keyword(s):  
Matrix Representation ◽  
Series Representation ◽  
Gram Matrix ◽  
New Approach ◽  
Dynamic Phasors ◽  
New Strategy ◽  
Analytical Expressions ◽  
Numerical Complexity ◽  
Algebra Of Matrices

The paper presents a new approach to estimation of the dynamic power phasors parameters. The observed system is modelled in algebra of matrices related to its Taylor-Fourier-trigonometric series representation. The proposed algorithm for determination of the unknown phasors parameters is based on the analytical expressions for elements of the Gram’s matrix associated with this system. The numerical complexity and algorithm time are determined and it is shown that new strategy for calculation of Gram’s matrix increases the accuracy of estimation, as well as the speed of the algorithm with respect to the classical way of introducing the Gram’s matrix. Several simulation examples of power system signals with a time-varying amplitude and phase parameters are given by which the robustness and accuracy of the new algorithm are confirmed.

State Matrix Representation of Assembly and Robot Planning

Robotica ◽  
1995 ◽  
Vol 13 (3) ◽  
pp. 259-272 ◽  
Author(s):  
S. M. Noorhosseini ◽  
A. S. Malowany
Keyword(s):  
Matrix Representation ◽  
Assembly Planning ◽  
Assembly Process ◽  
State Matrix ◽  
Goal Structures ◽  
Planning Time ◽  
New Approach ◽  
Planning Methods ◽  
Simple Matrix ◽  
Matrix Manipulation

SummaryA new approach to represent assembly called state matrix representation and an algorithm for automatic robot assembly planning based on this representation is proposed. The state matrix representation of assembly is configured by considering the inter-relationships of parts and objects involved in the initial and the goal structures. Thanks to this new representation, the planning lgorithm is straightforward and can be easily and efficiently implemented with simple matrix manipulation. Unlike other planning methods, the actions involved in the assembly process are not defined in advance but are generated at planning time. The syntax of actions are designed so that while directly reflecting the semantics of actions, they can be easily manipulated by the planner. Two examples of how to plan an assembly based on this representation are given in the paper.

scholarly journals Random Construction of Interpolating Sets for High-Dimensional Integration

2014 ◽  
Vol 51 (01) ◽  
pp. 92-105 ◽  
Author(s):  
Mark Huber ◽  
Sarah Schott
Keyword(s):  
Bayesian Methods ◽  
Extensive Study ◽  
High Dimensional ◽  
Posterior Distributions ◽  
New Approach ◽  
Random Samples ◽  
Normalizing Constants ◽  
Nested Sets ◽  
Random Construction ◽  
Dimensional Integral

Computing the value of a high-dimensional integral can often be reduced to the problem of finding the ratio between the measures of two sets. Monte Carlo methods are often used to approximate this ratio, but often one set will be exponentially larger than the other, which leads to an exponentially large variance. A standard method of dealing with this problem is to interpolate between the sets with a sequence of nested sets where neighboring sets have relative measures bounded above by a constant. Choosing such a well-balanced sequence can rarely be done without extensive study of a problem. Here a new approach that automatically obtains such sets is presented. These well-balanced sets allow for faster approximation algorithms for integrals and sums using fewer samples, and better tempering and annealing Markov chains for generating random samples. Applications, such as finding the partition function of the Ising model and normalizing constants for posterior distributions in Bayesian methods, are discussed.

scholarly journals Random Construction of Interpolating Sets for High-Dimensional Integration

2014 ◽  
Vol 51 (1) ◽  
pp. 92-105 ◽  
Author(s):  
Mark Huber ◽  
Sarah Schott
Keyword(s):  
Bayesian Methods ◽  
Extensive Study ◽  
High Dimensional ◽  
Posterior Distributions ◽  
New Approach ◽  
Random Samples ◽  
Normalizing Constants ◽  
Nested Sets ◽  
Random Construction ◽  
Dimensional Integral

Computing the value of a high-dimensional integral can often be reduced to the problem of finding the ratio between the measures of two sets. Monte Carlo methods are often used to approximate this ratio, but often one set will be exponentially larger than the other, which leads to an exponentially large variance. A standard method of dealing with this problem is to interpolate between the sets with a sequence of nested sets where neighboring sets have relative measures bounded above by a constant. Choosing such a well-balanced sequence can rarely be done without extensive study of a problem. Here a new approach that automatically obtains such sets is presented. These well-balanced sets allow for faster approximation algorithms for integrals and sums using fewer samples, and better tempering and annealing Markov chains for generating random samples. Applications, such as finding the partition function of the Ising model and normalizing constants for posterior distributions in Bayesian methods, are discussed.

scholarly journals A new approach to identifying the local structure of multidimensional chaotic time series

2021 ◽  
Vol 2142 (1) ◽  
pp. 012011
Author(s):  
A V Makshanov ◽  
A E Zhuravlev ◽  
L N Tyndykar
Keyword(s):  
Decision Making ◽  
Time Series ◽  
Fine Structure ◽  
Local Structure ◽  
Matrix Representation ◽  
Data Matrix ◽  
New Approach ◽  
Time Dynamics ◽  
Multidimensional Time Series ◽  
Different Origins

Abstract The paper is devoted to the solution of the problems of mathematical supply of decision making during multichannel monitoring of large-scaled systems. The work also deals with space-time dynamics of multidimensional time series of different origins. Highly dynamical chaotic processes whose fine structure cannot be revealed by standard spectral methods are regarded. Technologies for dimension reduction based on data matrix representation on the first singular basis and multiple regression in projections’ space are developed.

Stellar Evolution

1962 ◽  
Vol 11 (02) ◽  
pp. 137-143
Author(s):  
M. Schwarzschild
Keyword(s):  
Solar System ◽  
Stellar Evolution ◽  
Space Craft ◽  
New Techniques ◽  
Substantial Body ◽  
Individual Stars ◽  
The Past ◽  
Evolution Of Galaxies ◽  
History Of ◽  
Fast Flow

It is perhaps one of the most important characteristics of the past decade in astronomy that the evolution of some major classes of astronomical objects has become accessible to detailed research. The theory of the evolution of individual stars has developed into a substantial body of quantitative investigations. The evolution of galaxies, particularly of our own, has clearly become a subject for serious research. Even the history of the solar system, this close-by intriguing puzzle, may soon make the transition from being a subject of speculation to being a subject of detailed study in view of the fast flow of new data obtained with new techniques, including space-craft.

The O–C diagrams of minor planets − a new approach to modelling the rotation

1999 ◽  
Vol 173 ◽  
pp. 185-188
Author(s):  
Gy. Szabó ◽  
K. Sárneczky ◽  
L.L. Kiss
Keyword(s):  
Error Analysis ◽  
Time Dependence ◽  
Theoretical Work ◽  
Minor Planet ◽  
Minor Planets ◽  
New Approach ◽  
Preliminary Results ◽  
Ccd Observations

AbstractA widely used tool in studying quasi-monoperiodic processes is the O–C diagram. This paper deals with the application of this diagram in minor planet studies. The main difference between our approach and the classical O–C diagram is that we transform the epoch (=time) dependence into the geocentric longitude domain. We outline a rotation modelling using this modified O–C and illustrate the abilities with detailed error analysis. The primary assumption, that the monotonity and the shape of this diagram is (almost) independent of the geometry of the asteroids is discussed and tested. The monotonity enables an unambiguous distinction between the prograde and retrograde rotation, thus the four-fold (or in some cases the two-fold) ambiguities can be avoided. This turned out to be the main advantage of the O–C examination. As an extension to the theoretical work, we present some preliminary results on 1727 Mette based on new CCD observations.

A New Approach to the Demonstration of Oxidase-Localization Using Tannic Acid Or Catechin

1973 ◽  
Vol 31 ◽  
pp. 698-699
Author(s):  
V. Mizuhira ◽  
Y. Futaesaku
Keyword(s):  
Cross Section ◽  
Tannic Acid ◽  
Elastic Fiber ◽  
The Other ◽  
New Approach ◽  
Tissue Block ◽  
Active Reaction ◽  
The Cross

Previously we reported that tannic acid is a very effective fixative for proteins including polypeptides. Especially, in the cross section of microtubules, thirteen submits in A-tubule and eleven in B-tubule could be observed very clearly. An elastic fiber could be demonstrated very clearly, as an electron opaque, homogeneous fiber. However, tannic acid did not penetrate into the deep portion of the tissue-block. So we tried Catechin. This shows almost the same chemical natures as that of proteins, as tannic acid. Moreover, we thought that catechin should have two active-reaction sites, one is phenol,and the other is catechole. Catechole site should react with osmium, to make Os- black. Phenol-site should react with peroxidase existing perhydroxide.

Processing Immunoperoxidase Labeled Cell Monolayers and Cryostat Sesctions For Electron Microscopy

1985 ◽  
Vol 43 ◽  
pp. 714-715
Author(s):  
K. Chien ◽  
R. Van de Velde ◽  
I.P. Shintaku ◽  
A.F. Sassoon
Keyword(s):  
Cell Monolayer ◽  
Cell Types ◽  
Surface Antigens ◽  
Immunoperoxidase Method ◽  
Reaction Step ◽  
Hot Plate ◽  
Air Drying ◽  
New Approach ◽  
Cell Monolayers ◽  
Glass Slides

Immunoelectron microscopy of neoplastic lymphoma cells is valuable for precise localization of surface antigens and identification of cell types. We have developed a new approach in which the immunohistochemical staining can be evaluated prior to embedding for EM and desired area subsequently selected for ultrathin sectioning.A freshly prepared lymphoma cell suspension is spun onto polylysine hydrobromide- coated glass slides by cytocentrifugation and immediately fixed without air drying in polylysine paraformaldehyde (PLP) fixative. After rinsing in PBS, slides are stained by a 3-step immunoperoxidase method. Cell monolayer is then fixed in buffered 3% glutaraldehyde prior to DAB reaction. After the DAB reaction step, wet monolayers can be examined under LM for presence of brown reaction product and selected monolayers then processed by routine methods for EM and embedded with the Chien Re-embedding Mold. After the polymerization, the epoxy blocks are easily separated from the glass slides by heatingon a 100°C hot plate for 20 seconds.

TEM study of a biofilm on copper corrosion

1996 ◽  
Vol 54 ◽  
pp. 220-221
Author(s):  
W. A. Chiou ◽  
N. Kohyama ◽  
B. Little ◽  
P. Wagner ◽  
M. Meshii
Keyword(s):  
Marine Bacterium ◽  
Culture Medium ◽  
Copper Alloys ◽  
Pure Copper ◽  
Localized Corrosion ◽  
Natural Seawater ◽  
Copper Corrosion ◽  
New Approach ◽  
The Past ◽  
Copper Tolerant

The corrosion of copper and copper alloys in a marine environment is of great concern because of their widespread use in heat exchangers and steam condensers in which natural seawater is the coolant. It has become increasingly evident that microorganisms play an important role in the corrosion of a number of metals and alloys under a variety of environments. For the past 15 years the use of SEM has proven to be useful in studying biofilms and spatial relationships between bacteria and localized corrosion of metals. Little information, however, has been obtained using TEM capitalizing on its higher spacial resolution and the transmission observation of interfaces. The research presented herein is the first step of this new approach in studying the corrosion with biological influence in pure copper.Commercially produced copper (Cu, 99%) foils of approximately 120 μm thick exposed to a copper-tolerant marine bacterium, Oceanospirillum, and an abiotic culture medium were subsampled (1 cm × 1 cm) for this study along with unexposed control samples.

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