scholarly journals Formal Links between Feature Diversity and Phylogenetic Diversity

2020 ◽  
Author(s):  
Kristina Wicke ◽  
Arne Mooers ◽  
Mike Steel
Keyword(s):  
Phylogenetic Diversity ◽  
Cooperative Game Theory ◽  
Rapid Evolution ◽  
Short Paper ◽  
Simple Index ◽  
Branch Lengths ◽  
Shapley Values ◽  
Two Indices ◽  
Feature Evolution ◽  
The Relationship

AbstractThe extent to which phylogenetic diversity (PD) captures feature diversity (FD) is a topical and controversial question in biodiversity conservation. In this short paper, we formalise this question and establish a precise mathematical condition for FD (based on discrete characters) to coincide with PD. In this way, we make explicit the two main reasons why the two diversity measures might disagree for given data; namely, the presence of certain patterns of feature evolution and loss, and using temporal branch lengths for PD in settings that may not be appropriate (e.g. due to rapid evolution of certain features over short periods of time). Our paper also explores the relationship between the ‘Fair Proportion’ index of PD and a simple index of FD (both of which correspond to Shapley values in cooperative game theory). In a second mathematical result, we show that the two indices can take identical values for any phylogenetic tree, provided the branch lengths in the tree are chosen appropriately.

scholarly journals Formal Links between Feature Diversity and Phylogenetic Diversity

2020 ◽  
Author(s):  
Kristina Wicke ◽  
Arne Mooers ◽  
Mike Steel
Keyword(s):  
Phylogenetic Diversity ◽  
Cooperative Game Theory ◽  
Rapid Evolution ◽  
Short Paper ◽  
Simple Index ◽  
Evolutionary Distinctiveness ◽  
Branch Lengths ◽  
Shapley Values ◽  
Feature Evolution ◽  
The Relationship

Abstract The extent to which phylogenetic diversity (PD) captures feature diversity (FD) is a topical and controversial question in biodiversity conservation. In this short paper, we formalize this question and establish a precise mathematical condition for FD (based on discrete characters) to coincide with PD. In this way, we make explicit the two main reasons why the two diversity measures might disagree for given data; namely, the presence of certain patterns of feature evolution and loss, and using temporal branch lengths for PD in settings that may not be appropriate (e.g., due to rapid evolution of certain features over short periods of time). Our article also explores the relationship between the “Fair Proportion” index of PD and a simple index of FD (both of which correspond to Shapley values in cooperative game theory). In a second mathematical result, we show that the two indices can take identical values for any phylogenetic tree, provided the branch lengths in the tree are chosen appropriately. [Evolutionary distinctiveness; feature diversity; phylogenetic diversity; shapley value.]

scholarly journals Biological mechanisms linked to inflammation in cancer: Discovery of tumor microenvironment-related biomarkers and their clinical application in solid tumors

2020 ◽  
Vol 35 (1_suppl) ◽  
pp. 8-11 ◽  
Author(s):  
Paola Nisticò ◽  
Gennaro Ciliberto
Keyword(s):  
Tumor Microenvironment ◽  
Tumor Cells ◽  
Cancer Progression ◽  
Cancer Biology ◽  
Tumor Development ◽  
Short Paper ◽  
Great Relevance ◽  
Cellular Components ◽  
The Relationship

Our view of cancer biology radically shifted from a “cancer-cell-centric” vision to a view of cancer as an organ disease. The concept that genetic and/or epigenetic alterations, at the basis of cancerogenesis, are the main if not the exclusive drivers of cancer development and the principal targets of therapy, has now evolved to include the tumor microenvironment in which tumor cells can grow, proliferate, survive, and metastasize only within a favorable environment. The interplay between cancer cells and the non-cellular and cellular components of the tumor microenvironment plays a fundamental role in tumor development and evolution both at the primary site and at the level of metastasis. The shape of the tumor cells and tumor mass is the resultant of several contrasting forces either pro-tumoral or anti-tumoral which have at the level of the tumor microenvironment their battle field. This crucial role of tumor microenvironment composition in cancer progression also dictates whether immunotherapy with immune checkpoint inhibitor antibodies is going to be efficacious. Hence, tumor microenvironment deconvolution has become of great relevance in order to identify biomarkers predictive of efficacy of immunotherapy. In this short paper we will briefly review the relationship between inflammation and cancer, and will summarize in 10 short points the key concepts learned so far and the open challenges to be solved.

FUNDAMENTALS OF PLASMA ETCHING FOR SILICON TECHNOLOGY (PART 1)

1990 ◽  
Vol 01 (03n04) ◽  
pp. 303-345 ◽  
Author(s):  
ALEXANDER M. VOSHCHENKOV
Keyword(s):  
Plasma Etching ◽  
Technology Development ◽  
Rapid Evolution ◽  
Building Blocks ◽  
Semiconductor Technology ◽  
Silicon Technology ◽  
Wet Chemical ◽  
Basic Characteristics ◽  
Relationship Of ◽  
The Relationship

Over the past decade, as the rapid evolution of semiconductor technology has progressed towards submicron design rules, plasma (dry) etching has supplanted simple wet etching processes for the transfer of patterns. To understand the underlying need for development of plasma etching, a brief background of integrated semiconductor technology is presented. Along with a historical perspective of the evolution of plasma etching, the relationship of plasma etching to lithography needs, its basic characteristics and advantages over wet chemical processing are discussed. Following this, relevant concepts of plasma physics and chemistry, based on experience with plasma etching applications for silicon technology, which can be used as building blocks for technology development are described.

scholarly journals Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates

2017 ◽  
Author(s):  
Koichiro Tamura ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Relative Rate ◽  
Molecular Data ◽  
Evolutionary Rates ◽  
Divergence Times ◽  
Computationally Efficient ◽  
Molecular Sequence ◽  
Branch Lengths ◽  
Variable Evolutionary Rates ◽  
Relationship Of ◽  
The Relationship

AbstractRelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It showed excellent performance in estimating divergence times for both simulated and empirical molecular sequence datasets in which evolutionary rates varied extensively throughout the tree. RelTime is computationally efficient and scales well with increasing size of datasets. Until now, however, RelTime has not had a formal mathematical foundation. Here, we show that the basis of the RelTime approach is a relative rate framework (RRF) that combines comparisons of evolutionary rates in sister lineages with the principle of minimum rate change between an evolutionary lineage and its descendants. We present analytical solutions for estimating relative lineage rates and divergence times under RRF. We also discuss the relationship of RRF with other approaches, including the Bayesian framework. We conclude that RelTime will be also useful for phylogenies with branch lengths derived not only from molecular data, but also morphological and biochemical traits.

scholarly journals Rapid evolution and conserved function of the piRNA pathway

Open Biology ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 180181 ◽  
Author(s):  
Swapnil S. Parhad ◽  
William E. Theurkauf
Keyword(s):  
Phylogenetic Diversity ◽  
Gene Evolution ◽  
Rapid Evolution ◽  
Dna Breaks ◽  
Germline Development ◽  
Transposon Silencing ◽  
Core Function ◽  
Major Genome ◽  
Host Defence System ◽  
Pirna Pathway

Transposons are major genome constituents that can mobilize and trigger mutations, DNA breaks and chromosome rearrangements. Transposon silencing is particularly important in the germline, which is dedicated to transmission of the inherited genome. Piwi-interacting RNAs (piRNAs) guide a host defence system that transcriptionally and post-transcriptionally silences transposons during germline development. While germline control of transposons by the piRNA pathway is conserved, many piRNA pathway genes are evolving rapidly under positive selection, and the piRNA biogenesis machinery shows remarkable phylogenetic diversity. Conservation of core function combined with rapid gene evolution is characteristic of a host–pathogen arms race, suggesting that transposons and the piRNA pathway are engaged in an evolutionary tug of war that is driving divergence of the biogenesis machinery. Recent studies suggest that this process may produce biochemical incompatibilities that contribute to reproductive isolation and species divergence.

Corrigendum 1 (published 19 Sep 2018) and Corrigendum 2 (published 11 Dec 2018) to: Wildland fires behaviour: wind effect versus Byram’s convective number and consequences upon the regime of propagation

2018 ◽  
Vol 27 (12) ◽  
pp. 857
Author(s):  
D. Morvan ◽  
N. Frangieh
Keyword(s):  
Wind Velocity ◽  
Wildland Fire ◽  
Short Note ◽  
Short Paper ◽  
Speed Ratio ◽  
Wind Effect ◽  
Physical Parameters ◽  
Large Set ◽  
Wildland Fires ◽  
The Relationship

With fuel moisture content and slope, wind velocity (UW) is one of the major physical parameters that most affects the behaviour of wildland fires. The aim of this short paper was to revisit the relationship between the rate of spread (ROS) and the wind velocity, through the role played by the two forces governing the trajectory of the flame front and the plume, i.e. the buoyancy of the plume and the inertia due to wind. A large set of experimental data (at field and laboratory scale) from the literature was analysed, by introducing the ratio between these two forces, namely Byram's convective number NC and considering the relationship between the fire ROS/wind speed ratio and Byram's number. This short note was also an opportunity to make a point on particular issues, such as the existence of two regimes of propagation of surface fires (wind-driven fire vs plume-dominated fire), the relative importance of the two modes of heat transfer (by convection and radiation) on the propagation of a fire front, and others scientific debates animating the wildland fire community.

Effects of Response Uncertainty and Degree of Knowledge on Subjective Uncertainty

1968 ◽  
Vol 22 (3_suppl) ◽  
pp. 1081-1090 ◽  
Author(s):  
Robert D. Hoge ◽  
John T. Lanzetta
Keyword(s):  
Repeated Measures ◽  
Decision Time ◽  
Response Uncertainty ◽  
Subjective Uncertainty ◽  
Amount Of Information ◽  
Repeated Measures Design ◽  
Problem Presentation ◽  
Two Indices ◽  
The Relationship

The experiment was designed to examine the effects on subjective uncertainty of variations in response uncertainty and amount of information and to explore the relationship between two indices of subjective uncertainty, confidence in decision and decision time. 18 Ss were exposed to a 4-factor repeated measures design involving 6 levels of response uncertainty, 2 levels of ‘unknown information’, 2 levels of ‘known information’, and 2 orders of problem presentation. Confidence in decision was significantly affected by response uncertainty, ‘unknown information’, ‘known information’, and the interaction of the 2 information conditions. Decision time was significantly affected by response uncertainty and ‘known information.’

scholarly journals Wildland fires behaviour: wind effect versus Byram’s convective number and consequences upon the regime of propagation

2018 ◽  
Vol 27 (9) ◽  
pp. 636 ◽  
Author(s):  
D. Morvan ◽  
N. Frangieh
Keyword(s):  
Wind Velocity ◽  
Wildland Fire ◽  
Short Note ◽  
Short Paper ◽  
Speed Ratio ◽  
Wind Effect ◽  
Physical Parameters ◽  
Large Set ◽  
Wildland Fires ◽  
The Relationship

With fuel moisture content and slope, wind velocity (UW) is one of the major physical parameters that most affects the behaviour of wildland fires. The aim of this short paper was to revisit the relationship between the rate of spread (ROS) and the wind velocity, through the role played by the two forces governing the trajectory of the flame front and the plume, i.e. the buoyancy of the plume and the inertia due to wind. A large set of experimental data (at field and laboratory scale) from the literature was analysed, by introducing the ratio between these two forces, namely Byram’s convective number NC and considering the relationship between the fire ROS/wind speed ratio and Byram’s number. This short note was also an opportunity to make a point on particular issues, such as the existence of two regimes of propagation of surface fires (wind-driven fire vs plume-dominated fire), the relative importance of the two modes of heat transfer (by convection and radiation) on the propagation of a fire front, and others scientific debates animating the wildland fire community.

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