Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop algorithms to solve the relevant problems. In particular, we introduce a new algorithm that solves a "subcoloring" problem for expressing the difference between the taxonomy and phylogeny at a given rank. This algorithm improves upon the current best algorithm in terms of asymptotic complexity for the parameter regime of interest; we also describe a branch-and-bound algorithm that saves orders of magnitude in computation on real data sets. We also develop a formalism and an algorithm for rooting phylogenetic trees according to a taxonomy. All of these algorithms are implemented in freely-available software.Comment: Version submitted to Algorithms for Molecular Biology. A number of fixes from previous versio

A comparison of sacral neuromodulation vs. transvaginal electrical stimulation for the treatment of refractory overactive bladder: The impact on quality of life, body image, sexual function, and emotional well-being

Overactive bladder syndrome (OAB) is defined by the presence of urinary urgency, with or without urge incontinence, usually accompanied by an increase in urinary frequency and nocturia in the absence of urinary tract infections (UTI) or other diseases. The overall prevalence of OAB symptoms in the female population is reported to be 16.6% and increases with advancing age and menopause. The aetiology of OAB is not fully understood and is likely to affect a heterogeneous population of patients due to changes to their central and peripheral nervous systems. Although OAB is frequently associated with female sexual dysfunction (FSD), its real impact on sexual function in women has been evaluated only in a few studies. The first line of treatment for OAB includes behavioural modification and physical therapy, either as monotherapies or in combination. Many patients who have not had success in managing their symptoms with more conservative therapies may decide to resort to third-line treatments for refractory OAB. These treatments include neuromodulation therapies, particularly transvaginal electrical stimulation (TES) and sacral neuromodulation (SN). The aim of this short commentary is to provide an overview of the effectiveness of these treatments and of their impact on quality of life, body image, sexual function, and emotional well-being

VIP: An Experiment to Search for a Violation of the Pauli Exclusion Principle

The Pauli Exclusion Principle is a basic principle of Quantum Mechanics, and its validity has never been seriously challenged. However, given its fundamental standing, it is very important to check it as thoroughly as possible. Here we describe the VIP (VIolation of the Pauli exclusion principle) experiment, an improved version of the Ramberg and Snow experiment (E. Ramberg and G. Snow, {\it Phys. Lett. B} {\bf 238}, 438 (1990)); VIP has just completed the installation at the Gran Sasso underground laboratory, and aims to test the Pauli Exclusion Principle for electrons with unprecedented accuracy, down to $\beta^2/2 \approx 10^{-30} - 10^{-31}$. We report preliminary experimental results and briefly discuss some of the implications of a possible violation.Comment: Plenary talk presented by E. Milotti at Meson 2006, Cracow, 9-13 June 200

New experimental limit on the Pauli Exclusion Principle violation by electrons

The Pauli Exclusion Principle (PEP) is one of the basic principles of modern physics and, even if there are no compelling reasons to doubt its validity, it is still debated today because an intuitive, elementary explanation is still missing, and because of its unique stand among the basic symmetries of physics. The present paper reports a new limit on the probability that PEP is violated by electrons, in a search for a shifted K$_\alpha$ line in copper: the presence of this line in the soft X-ray copper fluorescence would signal a transition to a ground state already occupied by 2 electrons. The obtained value, ${1/2} \beta^{2} \leq 4.5\times 10^{-28}$, improves the existing limit by almost two orders of magnitude.Comment: submitted to Phys. Lett.

The Size Variance Relationship of Business Firm Growth Rates

The relationship between the size and the variance of firm growth rates is known to follow an approximate power-law behavior $\sigma(S) \sim S^{-\beta(S)}$ where $S$ is the firm size and $\beta(S)\approx 0.2$ is an exponent weakly dependent on $S$. Here we show how a model of proportional growth which treats firms as classes composed of various number of units of variable size, can explain this size-variance dependence. In general, the model predicts that $\beta(S)$ must exhibit a crossover from $\beta(0)=0$ to $\beta(\infty)=1/2$. For a realistic set of parameters, $\beta(S)$ is approximately constant and can vary in the range from 0.14 to 0.2 depending on the average number of units in the firm. We test the model with a unique industry specific database in which firm sales are given in terms of the sum of the sales of all their products. We find that the model is consistent with the empirically observed size-variance relationship

New experimental limit on Pauli Exclusion Principle violation by electrons (the VIP experiment)

The Pauli Exclusion Principle is one of the basic principles of modern physics and is at the very basis of our understanding of matter: thus it is fundamental importance to test the limits of its validity. Here we present the VIP (Violation of the Pauli Exclusion Principle) experiment, where we search for anomalous X-rays emitted by copper atoms in a conductor: any detection of these anomalous X-rays would mark a Pauli-forbidden transition. ] VIP is currently taking data at the Gran Sasso underground laboratories, and its scientific goal is to improve by at least four orders of magnitude the previous limit on the probability of Pauli violating transitions, bringing it into the 10**-29 - 10**-30 region. First experimental results, together with future plans, are presented.Comment: To appear in proceedings of the XLVI International Winter Meeting on Nuclear Physics, Bormio, Italy, January 20-26, 200

The VIP Experiment

The Pauli Exclusion Principle (PEP) is a basic principle of Quantum Mechanics, and its validity has never been seriously challenged. However, given its importance, it is very important to check it as thoroughly as possible. Here we describe the VIP (Violation of PEP) experiment, an improved version of the Ramberg and Snow experiment (Ramberg and Snow, Phys. Lett. B238 (1990) 438); VIP shall be performed at the Gran Sasso underground laboratories, and aims to test the Pauli Exclusion Principle for electrons with unprecedented accuracy, down to $\frac{\beta^2}{2} \sim 10^{-30}$Comment: 7 pages, 5 figures, PDF only, presented by Edoardo Milotti to the conference "Quantum Theory: reconsideration of foundations-3", Vaxjo (Sweden), June, 6-11 200

Testing the Pauli Exclusion Principle for Electrons

One of the fundamental rules of nature and a pillar in the foundation of quantum theory and thus of modern physics is represented by the Pauli Exclusion Principle. We know that this principle is extremely well fulfilled due to many observations. Numerous experiments were performed to search for tiny violation of this rule in various systems. The experiment VIP at the Gran Sasso underground laboratory is searching for possible small violations of the Pauli Exclusion Principle for electrons leading to forbidden X-ray transitions in copper atoms. VIP is aiming at a test of the Pauli Exclusion Principle for electrons with high accuracy, down to the level of 10$^{-29}$ - 10$^{-30}$, thus improving the previous limit by 3-4 orders of magnitude. The experimental method, results obtained so far and new developments within VIP2 (follow-up experiment at Gran Sasso, in preparation) to further increase the precision by 2 orders of magnitude will be presented.Comment: Proceedings DISCRETE 2012-Third Symposium on Prospects in the Physics of Discrete Symmetries, Lisbon, December 3-7, 201