Inference of evolutionary jumps in large phylogenies using Lévy processes

Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson’s hypothesis

Evidence of quasi-intramolecular redox reactions during thermal decomposition of ammonium hydroxodisulfitoferriate(III), (NH4)(2)[Fe(OH)(SO3)(2)]center dot H2O

Synthesis of ammonium hydroxodisulfitoferriate(III), (diammonium catena-{bis(mu (2)-sulfito-kappa O,kappa O)-mu (2)-hydroxo-kappa O-2}ferrate(III) monohydrate) (NH4)(2)[Fe(OH)(SO3)(2)]center dot H2O (compound 1) and its thermal behavior is reported. The compound is stable in air. Its thermal decomposition proceeds without the expected quasi-intramolecular oxidation of sulfite ion with ferric ions. The disproportionation reaction of the ammonium sulfite, formed from the evolved NH3, SO2 and H2O in the main decomposition stage of 1, results in the formation of ammonium sulfate and ammonium sulfide. The ammonium sulfide is unstable at the decomposition temperature of 1 (150 A degrees C) and transforms into NH3 and H2S which immediately forms elementary sulfur by reaction with SO2. The formation and decomposition of other intermediate compounds like (NH4)(2)SnOx (n = 2, x = 3 and n = 3, x = 6) results in the same decomposition products (S, SO2 and NH3). Two basic iron sulfates, formed in different ratios during synthesizing experiments performed under N-2 or in the presence of air, have been detected as solid intermediates which contain ammonium ions. The final decomposition product was proved to be alpha-Fe2O3 (mineral name hematite)

Hypoxia Modeling using Luo-Rudy II Cell Model

Abstract This study is aimed to present the development phases of hypoxia and anoxia using the dynamic Luo-Rudy II (LR) The calcium regulation mechanism is more sensitive to hypoxia than the potassium regulation, while the sodium regulation is the most robust among the investigated pump functionalities. Introduction In developed countries, the sudden cardiac death, mostly caused by ventricular fibrillation, represents the principal cause of mortality. Despite decades of intensive research, the mechanisms responsible for ventricular fibrillation are only partially discovered. Hypoxia represents an insufficient oxygen level in blood or tissue. In the presence of this pathological condition, despite adequate blood perfusion, the whole organism (generalized hypoxia) or a region of it (tissue hypoxia) suffers from reduced oxygen supply In a healthy organism hypoxia may develop during intensive physical exercises, or in the presence of oxygen deficiency in the atmosphere induced by high altitude. In these cases the arterial oxygen level may decrease substantially, however it rarely drops below physiological levels. Mild hypoxia increases heart and respiration rates. Hypoxia may also be caused by hypoventilation, pulmonary embolism, methemoglobinemia, carbon monoxide poisoning, histotoxic hypoxia and shunts in the pulmonary circulation A partial or total occlusion of a coronary artery yields to myocardial ischemia In order to understand the development phases of hypoxia, it is imperial to investigate the cellular functionality of the heart. A better understanding of the cardiac cell's biochemical properties enabled the development of various computational models. Several cardiac cell models have been published that describe the functionality of various cardiac cell types The large variances of events that may induce hypoxia inhibit the possibility to develop a generalized cell model, capable to treat all pathological cases. In order to handle such an inconvenient situation, we selected the Luo-Rudy II model • it can model ventricular cells; • it has a dynamic characteristic to model metabolic and electrophysiological changes; • includes all major ionic currents; • may have a good robustness; • demands relatively low computation power. Our goal in this paper is to study the development phases of hypoxia and anoxia using the dynamic LuoRudy II (LR) ventricular cell model. The rest of the paper is organized as follows: Section 2 gives a detailed description of the studied LR model for normal and pathological cases. We outline the effect on the generate

Self-Tuning Possibilistic c-Means Clustering Models

The relaxation of the probabilistic constraint of the fuzzy c-means clustering model was proposed to provide robust algorithms that are insensitive to strong noise and outlier data. These goals were achieved by the possibilistic c-means (PCM) algorithm, but these advantages came together with a sensitivity to cluster prototype initialization. According to the original recommendations, the probabilistic fuzzy c-means (FCM) algorithm should be applied to establish the cluster initialization and possibilistic penalty terms for PCM. However, when FCM fails to provide valid cluster prototypes due to the presence of noise, PCM has no chance to recover and produce a fine partition. This paper proposes a two-stage c-means clustering algorithm to tackle with most problems enumerated above. In the first stage called initialization, FCM with two modifications is performed: (1) extra cluster added for noisy data; (2) extra variable and constraint added to handle clusters of various diameters. In the second stage, a modified PCM algorithm is carried out, which also contains the cluster width tuning mechanism based on which it adaptively updates the possibilistic penalty terms. The proposed algorithm has less parameters than PCM when the number of clusters is c > 2. Numerical evaluation involving synthetic and standard test data sets proved the advantages of the proposed clustering model

Inference of Evolutionary Jumps in Large Phylogenies using Lévy Processes

Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson's hypothesis. [evolutionary jump; Lévy process; phenotypic evolution; punctuated equilibrium; quantitative traits