Branching Diagram Research Articles

DIAGRAM FILOGENIK HASIL SEKUENS BASA DNA MENGGUNAKAN PROGRAM MEGA-7 (MOLECULAR EVOLUTIONARY GENETICS ANALYSIS)

Sequencing techniques Deoxyribonucleic Acid (DNA) at this time is a method to identify the genetic basis of living beings, including to determine the accurate genetic relationship of several DNA sequence data. Kinship clearly and easily can be expressed in the form of a phylogenetic tree diagram (Phylogenetic Tree). This diagram represents kinship obtained from the elektroferogram process of electrophoresis sequencing of DNA bases. From some sequences experimental results using sequence analysis application program gradually, starting from installing, editing, and alignment so as to obtain the analysis and phylogenetic branching diagram view. This study uses a sequence analysis program Mega-7 (Molecular Evolutionary Genetics Analysis) to obtain a phylogenetic diagram for high accuracy and relatively easy to operate. This program can translate image data into nucleotide bases that shows the kinship of the distance the nearest branch with a standard sequence. The major advantage of this program is that it can do some analysis in a single program.

Time-Based Joining Method for Generating Phylogenetic Trees of Architectural Plans

AbstractA method has been developed for automatically generating a phylogenetic tree of architectural plans based on graph theory, according to the properties of the plans and the timing of their appearance. A phylogenetic tree of architectural plans is a branching diagram that shows transitions of the architectural plans by period. In previous studies, researchers analyzed structural similarities and differences between architectural plans by comparing one floor plan to another. Such manual classification processes sometimes result in inconsistent classifications and are inefficient, especially when a large number of plans are compared and analyzed. In this paper, a new algorithmic approach is proposed, termed the time-based joining (TBJ) method, for quantitatively evaluating structural similarities between architectural plans and creating a phylogenetic tree of the analyzed architectural plans. The validity and consistency of the TBJ method’s results were tested by generating a phylogenetic tree of 422 ...

Cellular Bases for Algebras with a Jones Basic Construction

We construct analogues for the Brauer, BMW, partition, and Jones–Temperley–Lieb algebras of the Murphy basis of the Hecke algebra of the symmetric group. The bases are cellular bases indexed by paths on branching diagrams, and compatible with restriction of cell modules. The Jucys–Murphy elements for each class of algebras act by triangular matrices on the Murphy basis.

Correlated Pair States Formed by Singlet Fission and Exciton-Exciton Annihilation.

Singlet fission to form a pair of triplet excitations on two neighboring molecules and the reverse process, triplet-triplet annihilation to upconvert excitation, have been extensively studied. Comparatively little work has sought to examine the properties of the intermediate state in both of these processes-the bimolecular pair state. Here, the eigenstates constituting the manifold of 16 bimolecular pair excitations and their relative energies in the weak-coupling regime are reported. The lowest-energy states obtained from the branching diagram method are the triplet pairs with overall singlet spin |X1⟩ ≈ (1)[TT] and quintet spin |Q⟩ ≈ (5)[TT]. It is shown that triplet pair states can be separated by a triplet-triplet energy-transfer mechanism to give a separated, yet entangled triplet pair (1)[T···T]. Independent triplets are produced by decoherence of the separated triplet pair. Recombination of independent triplets by exciton-exciton annihilation to form the correlated triplet pair (i.e., nongeminate recombination) happens with 1/3 of the rate of either triplet migration or recombination of the separated correlated triplet pair (geminate recombination).

Estimation of Phyletic Trees from Cladograms and Birth Orders

Abstract The purpose of computational phylogenetics is to assemble a branching diagram or tree that represents a hypothesis regarding the evolutionary relationships of an entity set. Phyletic trees and cladograms are well-known methods for expressing phyletic relationships. Although many estimating methods for cladograms have been proposed, few studies have examined automatic estimation of phyletic trees because, in our opinion, most biological entities do not have birth year information. On the other hand, targets in cultural phylogenetics may have birth year information. Therefore, we propose a method to estimate phyletic trees for cultural phylogenetics using estimated cladograms and birth order information. First, we define necessary conditions for estimating phyletic trees from cladograms and birth order. We then propose an algorithm for estimating phyletic trees that satisfy these conditions. We demonstrate that the phyletic trees estimated by the proposed algorithm satisfy the defined conditions. Our experimental results show that the proposed estimation method obtained approximately 70% estimation accuracy for some targets.

Modeling and Solving of Non-Linear Vibration Model of the Multi-Clearance and Bend and Torsion Coupled Gear-Driven System

Comprehensively taking the effects of variable rigidities, tooth flank clearances, bearing clearances, contact rigidities, and other multiple non-linear factors into account, it built a bend and torsion coupled gear-driven system’s dynamics analysis model in use of lumped mass method. After dimensionless dealing, it solved this dynamic model by the method of fifth order adaptive variable step (Runge-Kutta) method, and then it obtained system vibratory responses’ time domain diagrams, frequency domain diagrams, phase map, Poincare diagram, fast Fourier transformation (FFT) diagrams, and system branch diagrams under different parameters. All of them analyzed the effects of parameter variations on gearing system’s dynamic characteristics, and it provided a foundation for gearing system dynamic optimum designs.

A discontinuity associated with the capillary deformation of microstructures

Capillary forces are known to deform microstructures. In this work, we consider the deformation of a microstructure idealized as a double cantilever beam (DCB) caused by a liquid droplet at the free end. When the volume of the liquid is small, a discontinuity may appear in the deflection of the DCB. As the volume of the small droplet is gradually decreased in a quasi-static fashion, a discontinuous decrease in the beam deflection is observed, accompanied by an abrupt movement of one of the menisci. For small droplets, a discontinuity from low to high deflection may be observed when the ratio of the capillary force to the elastic restoring force increases. The discontinuity, attributed to the nonlinear nature of the equations governing the beam deformation, is important for determining whether the DCB will collapse as the capillary loading increases. An analysis using energy and branching diagrams is performed to help understand the occurrence of the discontinuity.

JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison

BackgroundCross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or co-regulated sets of genes, suggest annotations of previously un-annotated genes, and help to identify horizontal gene transfer events across microbial species. Existing tools to investigate genomic contexts, however, lack features for dynamically comparing and exploring genomic regions from multiple species. As DNA sequencing technologies improve and the number of whole sequenced microbial genomes increases, a user-friendly genome context comparison platform designed for use by a broad range of users promises to satisfy a growing need in the biological community.ResultsHere we present JContextExplorer: a tool that organizes genomic contexts into branching diagrams. We implement several alternative context-comparison and tree rendering algorithms, and allow for easy transitioning between different clustering algorithms. To facilitate genomic context analysis, our tool implements GUI features, such as text search filtering, point-and-click interrogation of individual contexts, and genomic visualization via a multi-genome browser. We demonstrate a use case of our tool by attempting to resolve annotation ambiguities between two highly homologous yet functionally distinct genes in a set of 22 alpha and gamma proteobacteria.ConclusionsJContextExplorer should enable a broad range of users to analyze and explore genomic contexts. The program has been tested on Windows, Mac, and Linux operating systems, and is implemented both as an executable JAR file and java WebStart. Program executables, source code, and documentation is available at http://www.bme.ucdavis.edu/facciotti/resources_data/software/.

A History in 230 Trees Trees of Life A Visual History of Evolution by Theodore W. Pietsch Johns Hopkins University Press, Baltimore, MD, 2012. 372 pp. $69.95, £36.50. ISBN 9781421404790.

Presenting examples from the past 450 years, Pietsch surveys the use of branching diagrams to convey relationships among organisms.

On spin wavefunctions and young orthogonal matrices

Electron spin wavefunctions are expressed in the Young orthogonal representation. The normalization factor is calculated. An explicit expression for the first column elements of the Young orthogonal matrices is obtained by a comparison to the branching diagram wavefunctions. These matrix elements are used in a multideterminant representation of the total wavefunction. © 2012 Wiley Periodicals, Inc.

Trees of life: a visual history of evolution

For the past 450 years, tree-like branching diagrams have been created to show the complex and surprising interrelationships of organisms, both living and fossil, viruses and bacteria to birds and mammals. This stunning book celebrates the manifest beauty, intrinsic interest, and human ingenuity of these exquisite trees of life. Theodore W. Pietsch has chosen 230 trees of life - among thousands of possible contenders - dating the sixteenth century to the present day. His arrangement gives readers a visual sense of the historical development of these diagrams and shows how, in Darwin's words, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved. Pietsch's brief, accessible prose accompanies the diverse trees to fully reveal the engrossing history of human theories of evolution. Over the centuries, trees of life appeared in a wide variety of forms; some were revered as iconic while others incited intense controversy. The earliest examples were meant to portray the imagined temporal order in which God created life on Earth. More recent scientific trees represent hypothetical histories of life. Never before has the full spectrum of trees of life been brought together in a single volume. Pietsch has spent decades collecting and researching the origin and meaning of these evolutionary trees and presents a visually breathtaking and intellectually brilliant history of the form.

On the representation matrices for the symmetric group adapted to electron‐pair and electron‐group wave functions using graphical methods of spin algebras

AbstractUsing graphical methods of spin algebras, we present a direct method for the determination of the representation matrices of the symmetric group in a basis adapted to electron‐pair and electron‐group wave functions. In particular, we consider nonstandard representations adapted to $S_{n_1 } \times S_{n_2 } \times \ldots \times S_{n_\ell }$ where n1 + n2 + … + nℓ = n. The Serber coupling scheme based on S2 × S2 × …× S2 is a special case suited for electron‐pair wave functions. Our approach exploiting graphical methods of spin algebras is contrasted with the use of Young diagrams and tableaux, Yamanouchi symbols and branching diagrams. © 2012 Wiley Periodicals, Inc.

An SAO-based text mining approach to building a technology tree for technology planning

A technology tree (TechTree) is a branching diagram that expresses relationships among product components, technologies, or functions of a technology in a specific technology area. A TechTree identifies strategic core technologies and is a useful tool to support decision making in a given market environment for organizations with specified capabilities. However, existing TechTrees generally overemphasize qualitative and expert-dependent knowledge rather than incorporating quantitative and objective information. In addition, the traditional process of developing a TechTree requires vast amounts of information, which costs considerably in terms of time, and cannot provide integrated information from a variety of technological perspectives simultaneously. To remedy these problems, this research presents a text mining approach based on Subject–Action–Object (SAO) structures; this approach develops a TechTree by extracting and analyzing SAO structures from patent documents. The extracted SAO structures are categorized by similarities, and are identified by the type of technological implications. To demonstrate the feasibility of the proposed approach, we developed a TechTree regarding Proton Exchange Fuel Cell technology.

Fast Routing System Research and Application Based on Pro-E

A fast automatic routing method based on skeleton model in virtual environment is introduced in this paper. By defining the properties of the stent, electronic connector and electronic equipment of the routing solid model, the routing factors are obtained and skeleton is built. Then, the cables can generated automatically based on the connection relationship and cable attributes. This method can bring out the connection between electronic connector node tables and 3D model, managing the network path, flexible modification of 3D routing features, 3D routing automatically, and generating cable branch diagrams. The routing efficiency can be improved and the length of the cables inosculates with the actual one perfectly, which is of great value in engineering.

Cellularity and the Jones basic construction

We establish a framework for cellularity of algebras related to the Jones basic construction. Our framework allows a uniform proof of cellularity of Brauer algebras, ordinary and cyclotomic BMW algebras, walled Brauer algebras, partition algebras, and others. Our cellular bases are labeled by paths on certain branching diagrams rather than by tangles. Moreover, for the class of algebras that we study, we show that the cellular structures are compatible with restriction and induction of modules.

The series, the network, and the tree: changing metaphors of order in nature

The history of biological systematics documents a continuing tension between classifications in terms of nested hierarchies congruent with branching diagrams (the ‘Tree of Life’) versus reticulated relations. The recognition of conflicting character distribution led to the dissolution of the scala naturae into reticulated systems, which were then transformed into phylogenetic trees by the addition of a vertical axis. The cladistic revolution in systematics resulted in a representation of phylogeny as a strictly bifurcating pattern (cladogram). Due to the ubiquity of character conflict—at the genetic or morphological level, or at any level in between—some characters will necessarily have to be discarded (qua noise) in favor of others in support of a strictly bifurcating phylogenetic tree. Pattern analysts will seek maximal congruence in the distribution of characters (ultimately of any kind) relative to a branching tree-topology; process explainers will call such tree-topologies into question by reference to incompatible evolutionary processes. Pattern analysts will argue that process explanations must not be brought to bear on pattern reconstruction; process explainers will insist that the reconstructed pattern requires a process explanation to become scientifically relevant, i.e., relevant to evolutionary theory. The core question driving the current debate about the adequacy of the ‘Tree of Life’ metaphor seems to be whether the systematic dichotomization of the living world is an adequate representation of the complex evolutionary history of global biodiversity. In ‘Questioning the Tree of Life’, it seems beneficial to draw at least four conceptual distinctions: pattern reconstruction versus process explanation as different epistemological approaches to the study of phylogeny; open versus closed systems as expressions of different kinds of population (species) structures; phylogenetic trees versus cladograms as representations of evolutionary processes versus patterns of relationships; and genes versus species as expressions of different levels of causal integration and evolutionary transformation.

Who Should Be Targeted for CKD Screening? Impact of Diabetes, Hypertension, and Cardiovascular Disease

To address the highly complex interrelated nature of chronic kidney disease (CKD) and diabetes, hypertension, and cardiovascular disease, we examined CKD prevalence by the predictive effect of demographic factors, comorbid conditions, and CKD risk factors by using National Health and Nutrition Examination Survey (NHANES) 1999-2004 data. NHANES is a nationally representative cross-sectional series of surveys with a complex stratified multistage sampling design. NHANES 1999-2004 participants (n = 15,332; age > or = 20 years) were interviewed in their homes and asked to participate in standardized medical examinations in mobile centers and provide samples for laboratory tests. Weighted logistic regression modeling was used to assess the importance of individual CKD risk factors. Multiple logistic regressions were performed on patient cohorts, with increasing levels of CKD severity defined by means of estimated glomerular filtration rate. A branching diagram was constructed to address the distribution of CKD grouped by diabetes, hypertension, and cardiovascular disease status. CKD prevalence increases with age (39.2% for age > or = 60 years). For ages 20 to 59 years, CKD prevalence was greater for participants with diabetes (33.8%) than for those without diabetes (8.2%) and for participants with both diabetes and hypertension (43%) than for diabetic participants without hypertension (25.5%) or nondiabetic participants with hypertension (15.2%). The prevalence was 6.8% for nondiabetic participants without hypertension. Effects of cardiovascular disease are less dramatic when hypertension and diabetes are considered. A CKD screening approach targeting individuals 60 years and older or those with diabetes or hypertension likely would be useful from a public health standpoint.

MODAL MODELLING OF THE NONLINEAR RESONANT FLUID SLOSHING IN A RECTANGULAR TANK II: SECONDARY RESONANCE

In Part I of this work [Math. Mod. Meth. Appl. Sci.15 (2005) 1431–1458], we studied periodic (steady-state) solutions of an asymptotic nonlinear modal system which describes two-dimensional resonant sloshing in a rectangular tank. The system was derived by Faltinsen et al. (2000) under the assumption that the primary excited (lowest) natural mode gives the largest contribution to the wave patterns. We found that this assumption is not true in a certain frequency domain due to internal (secondary) resonance leading to an amplification of the second mode. This frequency domain can also be identified for the critical depth-to-breath ratio h = 0.3368 … which was discussed in Part I. In Part II, this secondary resonance is modelled by a double-dominant modal system by Faltinsen and Timokha (2001). A comparative analysis with the results from Part I is presented. The emphasis is placed on the case of the mentioned critical ratio when a double turning point arises in the branching diagram. The appearance of the double turning point explains why classical laboratory experiments by Fultz (1962) underestimate the value of the critical depth.

Ancestor-descendant relationships and the reconstruction of the Tree of Life

The reconstruction of the Tree of Life has been a primary goal in biology since Darwin coined the expression, the “great Tree of Life” in On the Origin of Species : “The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species….As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications” (Darwin 1859: pp. 129–130). Ernst Haeckel was the first biologist who attempted to reconstruct the Darwinian Tree of Life. However, he could not reach his goal because his method of tree reconstruction was deeply anchored in the pre-Darwinian scala naturae (Dayrat 2003). A segment of the Darwinian Tree of Life is illustrated in the unique figure published in On the Origin of Species . This figure, which Darwin referred to as a “branching diagram,” represents ancestor-descendant relationships (ADR). Pointing out that Darwin's Tree of Life represents ADR is not controversial. It simply is a fact. However, it might be more controversial to point out a paradoxical situation: why does an overwhelming majority of the trees currently published represent sister-group relationships (SGR)? Given that reconstructing the Darwinian Tree of Life is one of today's foremost goals in systematic biology, one would expect that the reconstruction of ADR would arouse greater interest among biologists. Certainly, only SGR can be …

Numerical Analysis of Axisymmetric Buckling of a Conical Shell under Radial Compression

The nonlinear boundary-value problem of the axisymmetric buckling of a simply supported conical shell (dome) under a radial compressive load applied to the supported edge is formulated for a system of six first-order ordinary differential equations for independent fields of finite displacements and rotations. Multivalued solutions are obtained using the shooting method with specified accuracy. For various values of the loading parameter, bifurcation of the solutions of the problem is studied and a parametric branching diagram is constructed. The buckling modes are obtained for three branches of the solution. Curves of the buckling modes corresponding to three isolated branches of the solution are given.