Root Digger: a root placement program for phylogenetic trees

Background In phylogenetic analysis, it is common to infer unrooted trees. However, knowing the root location is desirable for downstream analyses and interpretation. There exist several methods to recover a root, such as molecular clock analysis (including midpoint rooting) or rooting the tree using an outgroup. Non-reversible Markov models can also be used to compute the likelihood of a potential root position. Results We present a software called which uses a non-reversible Markov model to compute the most likely root location on a given tree and to infer a confidence value for each possible root placement. We find that is successful at finding roots when compared to similar tools such as IQ-TREE and MAD, and will occasionally outperform them. Additionally, we find that the exhaustive mode of is useful in quantifying and explaining uncertainty in rooting positions. Conclusions can be used on an existing phylogeny to find a root, or to asses the uncertainty of the root placement. is available under the MIT licence at https://www.github.com/computations/root_digger.

Crown Lengthening Procedure: Report of Two Cases

Crown lengthening is a surgical procedure designed to increase the extent of the supragingival tooth structure, so that the clinician can restore the tooth. Crown lengthening procedure is done to maintain normal biologic width and increase crown length for retention of prosthesis. Various techniques have been proposed to perform CLP, such as gingivectomy, undisplaced flap with or without osseous reduction, apically repositioned flap with or without bone reduction, and orthodontic forced eruption with or without fibrotomy. Selection of one of this CLP technique depends upon esthetics, clinical ratio of crown to root, structure of root, location of furcation, position of tooth and the capacity of the tooth to be restored. This case report illustrate two different methods of doing crown lengthening procedure the selection of case depends upon various soft tissue and hard tissue parameters. Owing to the various advantages, disadvantages and associated limitation with different methods, we opted for surgical CLP with scalpel method. Uneventful healing was observed in both our cases. No post-operative complications was observed in both cases. Thus to conclude success rate of CLP is high but appropriate selection of case is required. In our case report both the methods of CLP shows significant result in increasing the crown length and maintaining the biological width.

A root location-based framework for degradation modeling of dynamic systems with predictive maintenance perspective

This paper considers dynamic systems widely used in industry for which the behavior can be approximated to a second order differential equation. The components of such a system suffer from random faults and failures due to wear, age or usage. These events impact the dynamic behavior which is interpreted as a modification of the initial differential equation with random coefficients. At given times, the system is solicited and its output – the only source of information – is measured to infer the position of equation roots in the complex plane. The Euclidian distance between the current and initial positions of a root is proposed as a new indicator reflecting the gradual deterioration of system performance. Such an indicator presents stochastic trajectories in time according to the random evolution of the root location in complex plane. More especially, these trajectories can be modeled by an univariate non-linear diffusion process if underlying degradation sources are assumed to be homogeneous Gamma processes. Based on this model, the system remaining useful lifetime is assessed. Two predictive maintenance policies are also designed showing the feasibility to easily maintain dynamic systems solely on the system output.

RootDigger: a root placement program for phylogenetic trees

SummaryIn phylogenetic analysis, it is common to infer unrooted trees. Thus, it is unknown which node is the most recent common ancestor of all the taxa in the phylogeny. However, knowing the root location is desirable for downstream analyses and interpretation. There exist several methods to recover a root, such as midpoint rooting or rooting the tree at an outgroup. Non-reversible Markov models can also be used to compute the likelihood of a potential root position. We present a software called RootDigger which uses a non-reversible Markov model to compute the most likely root location on a given tree and to infer a confidence value for each possible root placement.Availability and implementationRootDigger is available under the MIT licence at https://github.com/computations/root_digger

Effect of Particle Damping Technique on 1 kW Wind Turbine Blade using 3 mm Balls

Particle damping technique is first time use for study of vibration suppression in 1 kW wind turbine blade for using change of percentage fill of particles parameter. External container is attached on blade and fills the container using three different percentage changes as 10, 50 and 90 using 3mm spherical ball size. Blade is mounted at root location on electromagnetic shaker and accelerometer is located randomly on blade at 600 mm position from tip of blade. With damping results are compared with without damping and finding out the cases where vibration suppression takes place.

Fixed Point Polynomials of Permutation Groups

In this paper we study, given a group $G$ of permutations of a finite set, the so-called fixed point polynomial $\sum_{i=0}^{n}f_{i}x^{i}$, where $f_{i}$ is the number of permutations in $G$ which have exactly $i$ fixed points. In particular, we investigate how root location relates to properties of the permutation group. We show that for a large family of such groups most roots are close to the unit circle and roughly uniformly distributed round it. We prove that many families of such polynomials have few real roots. We show that many of these polynomials are irreducible when the group acts transitively. We close by indicating some future directions of this research. A corrigendum was appended to this paper on 10th October 2014.