scholarly journals StrainHub: A phylogenetic tool to construct pathogen transmission networks

2019 ◽  
Author(s):  
Adriano de Bernardi Schneider ◽  
Colby T. Ford ◽  
Reilly Hostager ◽  
John Williams ◽  
Michael Cioce ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Control Strategies ◽  
Pathogen Transmission ◽  
Character State ◽  
Transmission Networks ◽  
Web Based ◽  
Centrality Metrics ◽  
Alternative Approach ◽  
Arbitrary Space ◽  
State Changes

SummaryIn exploring the epidemiology of infectious diseases, networks have been used to reconstruct contacts among individuals and/or populations. Summarizing networks using pathogen metadata (e.g., host species and place of isolation) and a phylogenetic tree is a nascent, alternative approach. In this paper, we introduce a tool for reconstructing transmission networks in arbitrary space from phylogenetic information and metadata. Our goals are to provide a means of deriving new insights and infection control strategies based on the dynamics of the pathogen lineages derived from networks and centrality metrics. We created a web-based application, called StrainHub, in which a user can input a phylogenetic tree based on genetic or other data along with characters derived from metadata using their preferred tree search method. StrainHub generates a transmission network based on character state changes in meta-data, such as place or source of isolation, mapped on the phylogenetic tree. The user has the option to calculate centrality metrics on the nodes including betweenness, closeness, degree, and a new metric, the source/hub ratio. The outputs include the network with values for metrics on its nodes and the tree with characters reconstructed. All of these results can be exported for further analysis.Availabilityhttps://github.com/abschneider/StrainHub and strainhub.io

scholarly journals StrainHub: a phylogenetic tool to construct pathogen transmission networks

2019 ◽  
Vol 36 (3) ◽  
pp. 945-947 ◽  
Author(s):  
Adriano de Bernardi Schneider ◽  
Colby T Ford ◽  
Reilly Hostager ◽  
John Williams ◽  
Michael Cioce ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Control Strategies ◽  
Pathogen Transmission ◽  
Character State ◽  
Transmission Networks ◽  
Web Based ◽  
Centrality Metrics ◽  
Alternative Approach ◽  
Arbitrary Space ◽  
State Changes

Abstract Summary In exploring the epidemiology of infectious diseases, networks have been used to reconstruct contacts among individuals and/or populations. Summarizing networks using pathogen metadata (e.g. host species and place of isolation) and a phylogenetic tree is a nascent, alternative approach. In this paper, we introduce a tool for reconstructing transmission networks in arbitrary space from phylogenetic information and metadata. Our goals are to provide a means of deriving new insights and infection control strategies based on the dynamics of the pathogen lineages derived from networks and centrality metrics. We created a web-based application, called StrainHub, in which a user can input a phylogenetic tree based on genetic or other data along with characters derived from metadata using their preferred tree search method. StrainHub generates a transmission network based on character state changes in metadata, such as place or source of isolation, mapped on the phylogenetic tree. The user has the option to calculate centrality metrics on the nodes including betweenness, closeness, degree and a new metric, the source/hub ratio. The outputs include the network with values for metrics on its nodes and the tree with characters reconstructed. All of these results can be exported for further analysis. Availability and implementation strainhub.io and https://github.com/abschneider/StrainHub.

scholarly journals A Darwinian Uncertainty Principle

2019 ◽  
Vol 69 (3) ◽  
pp. 521-529 ◽  
Author(s):  
Olivier Gascuel ◽  
Mike Steel
Keyword(s):  
Uncertainty Principle ◽  
Evolutionary Biology ◽  
Biochemical Properties ◽  
Simultaneous Estimation ◽  
Character State ◽  
Migration Routes ◽  
Region Of Origin ◽  
Large Classes ◽  
State Changes ◽  
Patterns And Processes

Abstract Reconstructing ancestral characters and traits along a phylogenetic tree is central to evolutionary biology. It is the key to understanding morphology changes among species, inferring ancestral biochemical properties of life, or recovering migration routes in phylogeography. The goal is 2-fold: to reconstruct the character state at the tree root (e.g., the region of origin of some species) and to understand the process of state changes along the tree (e.g., species flow between countries). We deal here with discrete characters, which are “unique,” as opposed to sequence characters (nucleotides or amino-acids), where we assume the same model for all the characters (or for large classes of characters with site-dependent models) and thus benefit from multiple information sources. In this framework, we use mathematics and simulations to demonstrate that although each goal can be achieved with high accuracy individually, it is generally impossible to accurately estimate both the root state and the rates of state changes along the tree branches, from the observed data at the tips of the tree. This is because the global rates of state changes along the branches that are optimal for the two estimation tasks have opposite trends, leading to a fundamental trade-off in accuracy. This inherent “Darwinian uncertainty principle” concerning the simultaneous estimation of “patterns” and “processes” governs ancestral reconstructions in biology. For certain tree shapes (typically speciation trees) the uncertainty of simultaneous estimation is reduced when more tips are present; however, for other tree shapes it does not (e.g., coalescent trees used in population genetics).

scholarly journals Ungulate use of locally infectious zones in a re-emerging anthrax risk area

2020 ◽  
Vol 7 (10) ◽  
pp. 200246 ◽  
Author(s):  
Morgan A. Walker ◽  
Maria Uribasterra ◽  
Valpa Asher ◽  
José Miguel Ponciano ◽  
Wayne M. Getz ◽  
...  
Keyword(s):  
Disease Transmission ◽  
Control Strategies ◽  
Pathogen Transmission ◽  
Camera Traps ◽  
Risk Area ◽  
Southwestern Montana ◽  
Increased Risk ◽  
Anthrax Spores ◽  
Causative Bacterium ◽  
And Control

Environmentally mediated indirect pathogen transmission is linked to host movement and foraging in areas where pathogens are maintained in the environment. In the case of anthrax, spores of the causative bacterium Bacillus anthracis are released into the environment following host death and create locally infectious zones (LIZs) around carcass sites; by grazing at LIZs, herbivores are potentially exposed to spores. Here, we used camera traps to assess how ungulate species use carcass sites in southwestern Montana and evaluated how these behaviours may promote indirect anthrax transmission, thus providing, to our knowledge, the first detailed documentation and study of the fine-scale mechanisms underlying foraging-based disease transmission in this ecosystem. We found that carcasses at LIZs significantly increased aboveground biomass of vegetation and concentrations of sodium and phosphorus, potentially making these sites more appealing to grazers. Host behavioural responses to LIZs varied depending on species, sex, season and carcass age; but, overall, our results demonstrated that carcasses or carcass sites serve as an attractant to herbivores in this system. Attraction to LIZs probably represents an increased risk of exposure to B. anthracis and, consequently, increased anthrax transmission rates. Accordingly, continued anthrax surveillance and control strategies are critical in this system.

Mental Phenomena as Changes of State in a Finite-State Machine

1986 ◽  
Vol 20 (2) ◽  
pp. 158-165 ◽  
Author(s):  
R. R. Kydd ◽  
J. J. Wright
Keyword(s):  
Finite State Machine ◽  
Conscious Experience ◽  
State Machine ◽  
Alternative Approach ◽  
Finite State ◽  
Biological Substrate ◽  
State Changes ◽  
Fundamental Unity ◽  
Mental Pathology ◽  
Changes Of State

This paper examines the classical functions of the psyche—cognition, affection and conation—from a phenomenological viewpoint and finds them to be defined each in terms of the other. It is held that this circularity of definition reflects the fundamental unity of conscious experience and, as a consequence, that the search for the biological substrate underlying individual functions too readily degenerates into a morphological and biochemical phrenology. An alternative approach, based on considerations from the field of artificial intelligence, is discussed. This approach provides a description of mental phenomena as changes of state in a finite-state machine, the next state being determined by both previous states and current inputs. This concept is shown to be compatible with the descriptions of conscious experience outlined in the phenomenology of Karl Jaspers. It is suggested that neurobiological investigations should be directed towards defining the processes by which state changes occur and further seeking to define mental pathology as aberrations of these dynamic processes.

Point Control of a One-Link Flexible Manipulator

1986 ◽  
Vol 53 (1) ◽  
pp. 23-27 ◽  
Author(s):  
S. B. Skaar ◽  
D. Tucker
Keyword(s):  
Transfer Functions ◽  
Control Strategies ◽  
Open Loop ◽  
Flexible Manipulator ◽  
Distributed Parameter ◽  
Loop Control ◽  
Control Approach ◽  
Alternative Approach ◽  
Single Link ◽  
Point Control

An alternative approach to the control of nonrigid, distributed parameter systems is presented. Transfer functions that relate the response of points on the system to a controlling force or torque are used in place of ordinary differential equations, which represent an approximation to the system dynamics. The implications of this “point control” approach are discussed with regard to plant modeling accuracy, uncontrolled regions, open-loop and closed-loop control strategies, system identification, and feedback estimation. Sample optimal control histories are illustrated for a single-link manipulator member with end load.

Prevention and control strategies for ticks and pathogen transmission

2015 ◽  
Vol 34 (1) ◽  
pp. 249-264 ◽  
Author(s):  
FUENTE J. DE LA FUENTE ◽  
K.M. KOCAN ◽  
M. CONTRERAS
Keyword(s):  
Prevention And Control ◽  
Control Strategies ◽  
Pathogen Transmission ◽  
And Control

scholarly journals Percolation-Based Risk Index for Pathogen Invasion: Application to Soilborne Disease in Propagation Systems

2013 ◽  
Vol 103 (10) ◽  
pp. 1012-1019 ◽  
Author(s):  
S. Poggi ◽  
F. M. Neri ◽  
V. Deytieux ◽  
A. Bates ◽  
W. Otten ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Control Strategies ◽  
Risk Index ◽  
Host Density ◽  
Transmission Probability ◽  
Pathogen Transmission ◽  
Soilborne Disease ◽  
Pathogen Invasion ◽  
Fungal Plant Pathogens ◽  
Set Up

Propagation systems for seedling growth play a major role in agriculture, and in notable cases (such as organic systems), are under constant threat from soil and seedborne fungal plant pathogens such as Rhizoctonia solani or Pythium spp. Yet, to date little is known that links the risk of disease invasion to the host density, which is an agronomic characteristic that can be readily controlled. We introduce here, for the first time in an agronomic system, a percolation framework to analyze the link. We set up an experiment to study the spread of the ubiquitous fungus R. solani in replicated propagation systems with different planting densities, and fit a percolation-based epidemiological model to the data using Bayesian inference methods. The estimated probability of pathogen transmission between infected and susceptible plants is used to calculate the risk of invasion. By comparing the transmission probability and the risk values obtained for different planting densities, we are able to give evidence of a nonlinear relationship between disease invasion and the inter-plant spacing, hence to demonstrate the existence of a spatial threshold for epidemic invasion. The implications and potential use of our methods for the evaluation of disease control strategies are discussed.

A Review of the Family Portulacaceae

1987 ◽  
Vol 35 (4) ◽  
pp. 383 ◽  
Author(s):  
R Carolin
Keyword(s):  
Character State ◽  
New Classification ◽  
The Family ◽  
State Changes ◽  
Biogeographical Analysis ◽  
Five Tribes

A number of attributes that has proved useful to delimit subfamilial taxa within the Portulacaceae are critically assessed and some little used ones are introduced. The attributes are polarised by an outgroup comparison and a Wagner tree constructed. Some reversals which occur on this tree are considered unacceptable and branches are moved to eliminate this factor, although a longer tree, in terms of character state changes, is produced. A phylogenetic sequence is proposed on this basis and a new classification of the family attempted. On the basis of these results it is suggested that: (1) the genus Calandrinia s.1. be divided into five genera; (2) the genera Talinaria and Anacampseros are closely related; (3) Talinum may not be a natural genus; (4) the family can be conveniently divided into five tribes. A biogeographical analysis indicates that closer floristic relationships exist between western America and Australia and between eastern America and Africa than between eastern and western America or between Australia and Africa.

Sign in / Sign up

Export Citation Format

Share Document