scholarly journals Robust and automatic definition of microbiome states

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6657 ◽  
Author(s):  
Beatriz García-Jiménez ◽  
Mark D. Wilkinson
Keyword(s):  
Microbial Populations ◽  
Ecological Niches ◽  
Rigorous Approach ◽  
State Identification ◽  
Individual Variations ◽  
Community Evolution ◽  
Final Output ◽  
Definition Of ◽  
Domain Independent ◽  
Monitoring Response

Analysis of microbiome dynamics would allow elucidation of patterns within microbial community evolution under a variety of biologically or economically important circumstances; however, this is currently hampered in part by the lack of rigorous, formal, yet generally-applicable approaches to discerning distinct configurations of complex microbial populations. Clustering approaches to define microbiome “community state-types” at a population-scale are widely used, though not yet standardized. Similarly, distinct variations within a state-type are well documented, but there is no rigorous approach to discriminating these more subtle variations in community structure. Finally, intra-individual variations with even fewer differences will likely be found in, for example, longitudinal data, and will correlate with important features such as sickness versus health. We propose an automated, generic, objective, domain-independent, and internally-validating procedure to define statistically distinct microbiome states within datasets containing any degree of phylotypic diversity. Robustness of state identification is objectively established by a combination of diverse techniques for stable cluster verification. To demonstrate the efficacy of our approach in detecting discreet states even in datasets containing highly similar bacterial communities, and to demonstrate the broad applicability of our method, we reuse eight distinct longitudinal microbiome datasets from a variety of ecological niches and species. We also demonstrate our algorithm’s flexibility by providing it distinct taxa subsets as clustering input, demonstrating that it operates on filtered or unfiltered data, and at a range of different taxonomic levels. The final output is a set of robustly defined states which can then be used as general biomarkers for a wide variety of downstream purposes such as association with disease, monitoring response to intervention, or identifying optimally performant populations.

scholarly journals Automatic definition of robust microbiome sub-states in longitudinal data

2018 ◽  
Author(s):  
Beatriz García-Jiménez ◽  
Mark D Wilkinson
Keyword(s):  
Microbial Community ◽  
Longitudinal Data ◽  
State Transition ◽  
Transition Dynamics ◽  
Stable Cluster ◽  
Broad Applicability ◽  
State Identification ◽  
Community Evolution ◽  
Definition Of ◽  
Domain Independent

The analysis of microbiome dynamics would allow us to elucidate patterns within microbial community evolution; however, microbiome state-transition dynamics have been scarcely studied. This is in part because a necessary first-step in such analyses has not been well-defined: how to deterministically describe a microbiome’s ”state”. Clustering in states have been widely studied, although no standard has been concluded yet. We propose a generic, domain-independent and automatic procedure to determine a reliable set of microbiome sub-states within a specific dataset, and with respect to the conditions of the study. The robustness of sub-state identification is established by the combination of diverse techniques for stable cluster verification. We reuse four distinct longitudinal microbiome datasets to demonstrate the broad applicability of our method, analysing results with different taxa subset allowing to adjust it depending on the application goal, and showing that the methodology provides a set of robust sub-states to examine in downstream studies about dynamics in microbiome.

scholarly journals Automatic definition of robust microbiome sub-states in longitudinal data

2018 ◽  
Author(s):  
Beatriz García-Jiménez ◽  
Mark D Wilkinson
Keyword(s):  
Microbial Community ◽  
Longitudinal Data ◽  
State Transition ◽  
Transition Dynamics ◽  
Stable Cluster ◽  
Broad Applicability ◽  
State Identification ◽  
Community Evolution ◽  
Definition Of ◽  
Domain Independent

The analysis of microbiome dynamics would allow us to elucidate patterns within microbial community evolution; however, microbiome state-transition dynamics have been scarcely studied. This is in part because a necessary first-step in such analyses has not been well-defined: how to deterministically describe a microbiome’s ”state”. Clustering in states have been widely studied, although no standard has been concluded yet. We propose a generic, domain-independent and automatic procedure to determine a reliable set of microbiome sub-states within a specific dataset, and with respect to the conditions of the study. The robustness of sub-state identification is established by the combination of diverse techniques for stable cluster verification. We reuse four distinct longitudinal microbiome datasets to demonstrate the broad applicability of our method, analysing results with different taxa subset allowing to adjust it depending on the application goal, and showing that the methodology provides a set of robust sub-states to examine in downstream studies about dynamics in microbiome.

scholarly journals Defining the niche for niche construction: evolutionary and ecological niches

2021 ◽  
Vol 36 (3) ◽  
Author(s):  
Rose Trappes
Keyword(s):  
Evolutionary Biology ◽  
Ecological Niche ◽  
Niche Construction ◽  
Habitat Degradation ◽  
Ecological Niches ◽  
Niche Concept ◽  
Definition Of ◽  
Compare And Contrast ◽  
Extreme Habitat

AbstractNiche construction theory (NCT) aims to transform and unite evolutionary biology and ecology. Much of the debate about NCT has focused on construction. Less attention has been accorded to the niche: what is it, exactly, that organisms are constructing? In this paper I compare and contrast the definition of the niche used in NCT with ecological niche definitions. NCT’s concept of the evolutionary niche is defined as the sum of selection pressures affecting a population. So defined, the evolutionary niche is narrower than the ecological niche. Moreover, when contrasted with a more restricted ecological niche concept, it has a slightly different extension. I point out three kinds of cases in which the evolutionary niche does not coincide with realized ecological niches: extreme habitat degradation, commensalism, and non-limiting or super-abundant resources. These conceptual differences affect the role of NCT in unifying ecology and evolutionary biology.

Interfacial behavior between particle and matrix in a composite rubber material

2011 ◽  
Vol 20 (1-3) ◽  
pp. 29-33
Author(s):  
Bartolomeo Trentadue
Keyword(s):  
Tensile Specimen ◽  
Interfacial Behavior ◽  
Rubber Material ◽  
Contour Integrals ◽  
Surrounding Matrix ◽  
Final Output ◽  
Definition Of ◽  
Electronic Holography ◽  
Creep Loading ◽  
Principal Strains

AbstractElectronic holography moiré is applied to the measurement of interfacial deformation field between an embedded particle and its surrounding matrix in a non-homogeneous rubber material. A tensile specimen is subjected to creep loading. The loads are applied in steps and measurements are carried out at equal intervals of time. The final output is provided by the Holo-Moiré Strain Analyzer and gives the principal strains and their directions in the region of observation. A definition of adhesion as an experimental measurable quantity through the evaluation of contour integrals is introduced.

scholarly journals Fitness, Extrinsic Complexity and Informing Science

10.28945/3668 ◽  
2017 ◽  
Vol 20 ◽  
pp. 037-061
Author(s):  
Grandon Gill ◽  
Matthew Mullarkey
Keyword(s):  
Best Practices ◽  
Evolutionary Biology ◽  
Resistance To Change ◽  
Academic Research ◽  
Future Research ◽  
Science Field ◽  
Rigorous Approach ◽  
Individual Effects ◽  
Research Stream ◽  
Definition Of

Aim/Purpose We establish a conceptually rigorous definition for the widely used but loosely defined term “fitness”. We then tie this definition to complexity, highlighting a number of important implications for the informing science transdiscipline. Background As informing science increasingly incorporates concepts of fitness and complexity in its research stream, rigorous discussion and definition of both terms is essential to effective communication. Methodology Our analysis consists principally of a synthesis of past work in the informing science field that incorporates concepts from evolutionary biology, economics and management. Contribution We provide a rigorous approach to defining fitness and introduce the construct “extrinsic complexity”, as a measure of the amount of information required to predict fitness, to more fully differentiate this form of complexity from other complexity constructs. We draw a number of conclusions regarding how behaviors under low and high extrinsic complexity will differ. Findings High extrinsic complexity environments are likely to produce behaviors that include resistance to change, imitation, turbulence and inequality. Recommendations for Practitioners As extrinsic complexity grows, effective search for problem solutions will increasingly dominate employing recommended solutions of “best practices”. Recommendation for Researchers As extrinsic complexity grows, research tools that rely on decomposing individual effects and hypothesis testing become increasingly unreliable. Impact on Society We raise concerns about society’s continuing investment in academic research that discounts the extrinsic complexity of the domains under study. Future Research We highlight a need for research to operationalize the concepts of fitness and complexity in practice.

A Rigorous Approach to the Definition of an International Vocational Master’s Degree in Information Security Management

2010 ◽  
Vol 1 (4) ◽  
pp. 1-17 ◽  
Author(s):  
Frédéric Girard ◽  
Bertrand Meunier ◽  
Duan Hua ◽  
Eric Dubois
Keyword(s):  
Information Security ◽  
Security Management ◽  
Holistic Approach ◽  
Learning Trajectory ◽  
Learning Program ◽  
Information Security Management ◽  
Security Officer ◽  
Rigorous Approach ◽  
Definition Of ◽  
New Education

In Luxembourg, like in many other countries, information security has become a central issue for private companies and public organizations. Today, information is the main asset of a company for its business and, at the same time, regulations are imposing more and more rules regarding its management. As a consequence, in Luxembourg, a clear need has emerged regarding the development of new learning trajectory fulfilling the requirements of the new job profile associated with a Chief Security Officer. This need was relayed by the national professional security association which asked for the development of a new education program targeting professional people engaged in a lifelong learning trajectory. The paper reports on the rigorous and scientific participatory approach for producing the adequate learning program meeting requirements elicited from the professional association members. The authors present the skills card that has been elaborated for capturing these requirements and the program, which has been built together with the University of Luxembourg for matching these requirements. This program proposes a holistic approach to information security management by including organization, human and technical security risks within the context of regulations and norms.

Problems in the Definition and Measurement of Poverty

1987 ◽  
Vol 16 (2) ◽  
pp. 147-164 ◽  
Author(s):  
David Piachaud
Keyword(s):  
Home Production ◽  
Social Consensus ◽  
Standard Methods ◽  
Individual Variations ◽  
Definition Of ◽  
Poverty Levels ◽  
Measurement Of Poverty

ABSTRACTThree approaches to defining poverty levels are discussed—social consensus approaches, budget standard methods, and behavioural approaches. Each addresses different questions and none, of itself, has provided—nor, it is argued, could ever provide—an objective definition of poverty. The paper then raises problems that have been largely neglected in defining poverty. First, the treatment of time and home production: the time and ability of individuals to prepare food or to wash and feed without assistance, for example, vary greatly depending on circumstances and in turn affect income needs. Choices and constraints affecting the household formations in which people live and their budgeting behaviour are also important in assessing poverty. Individual variations in behaviour need to be explicitly recognised if practical definitions of poverty levels are to be found. Finally, the paper condemns discussions of poverty that are part of the problem rather than part of the solution.

scholarly journals Fitness, Extrinsic Complexity and Informing Science

10.28945/3715 ◽  
2017 ◽  
Author(s):  
Grandon Gill ◽  
Matthew Mullarkey
Keyword(s):  
Best Practices ◽  
Evolutionary Biology ◽  
Resistance To Change ◽  
Academic Research ◽  
Future Research ◽  
Science Field ◽  
Rigorous Approach ◽  
Individual Effects ◽  
Research Stream ◽  
Definition Of

[This Proceedings paper was revised and published in Informing Science: the International Journal of an Emerging Transdiscipline (InfoSci)] Aim/Purpose: We establish a conceptually rigorous definition for the widely used but loosely defined term “fitness”. We then tie this definition to complexity, highlighting a number of important implications for the informing science transdiscipline. Background: As informing science increasingly incorporates concepts of fitness and complexity in its research stream, rigorous discussion and definition of both terms is essential to effective communication. Methodology: Our analysis consists principally of a synthesis of past work in the informing science field that incorporates concepts from evolutionary biology, economics and management. Contribution: We provide a rigorous approach to defining fitness and introduce the construct “extrinsic complexity”, as a measure of the amount of information required to predict fitness, to more fully differentiate this form of complexity from other complexity constructs. We draw a number of conclusions regarding how behaviors under low and high extrinsic complexity will differ. Findings: High extrinsic complexity environments are likely to produce behaviors that include resistance to change, imitation, turbulence and inequality. Recommendations for Practitioners: As extrinsic complexity grows, effective search for problem solutions will increasingly dominate employing recommended solutions of “best practices”. Recommendation for Researchers: As extrinsic complexity grows, research tools that rely on decomposing individual effects and hypothesis testing become increasingly unreliable. Impact on Society : We raise concerns about society’s continuing investment in academic research that discounts the extrinsic complexity of the domains under study. Future Research: We highlight a need for research to operationalize the concepts of fitness and complexity in practice.

scholarly journals THE FATE OF MYCOBACTERIUM TUBERCULOSIS IN MOUSE TISSUES AS DETERMINED BY THE MICROBIAL ENUMERATION TECHNIQUE

1956 ◽  
Vol 104 (5) ◽  
pp. 763-802 ◽  
Author(s):  
Robert M. McCune ◽  
Ralph Tompsett ◽  
Walsh McDermott
Keyword(s):  
Microbial Populations ◽  
Complete Disappearance ◽  
Antituberculous Drugs ◽  
Mouse Tissues ◽  
Two Factors ◽  
Posttreatment Period ◽  
Definition Of ◽  
Microbial Enumeration

Populations of tubercle bacilli of human origin exposed in vivo to pyrazinamide and a companion drug, vanished from the tissues of the mouse in so far as could be determined by microscopy, culture, or guinea pig subinoculation. The vanishing did not represent a complete elimination of the tubercle bacilli from all the animals. 90 days after the completion of treatment, tubercle bacilli could be cultured from approximately one-third of the animals examined at that time. This complete disappearance of the tubercle bacilli thus meets the definition of a truly latent infection in that the infection is present but is hidden beyond the limits of diagnostic reach. All but one of the strains of tubercle bacilli which survived in the animals and were detectable in the posttreatment period, were susceptible to pyrazinamide when tested under appropriate conditions in vitro. Only two factors could be identified which were essential for the uniform occurrence of the disappearance of tubercle bacilli: the administration of the pyrazinamide in a high daily dosage for at least eight of a total of 12 weeks of antimicrobial therapy; and the concurrent or prior exposure of the microbial populations to isoniazid or in some cases to other antituberculous drugs. The observations suggest that the ability of pyrazinamide-containing chemotherapies to bring about the disappearance of a tubercle bacillus is closely related to the occurrence of some alteration in the bacillus, essential for maximal pyrazinamide action, in response to environmental influences, including other antituberculous drugs present in the environment.

scholarly journals About Supergraphs. Part I

2018 ◽  
Vol 26 (2) ◽  
pp. 101-124
Author(s):  
Sebastian Koch
Keyword(s):  
Finite Sequence ◽  
Finite Graph ◽  
Mutual Understanding ◽  
Construction Operations ◽  
Rigorous Approach ◽  
Graph Properties ◽  
Definition Of ◽  
Disconnected Graphs ◽  
Theoretic Description ◽  
Innate Ability

Summary Drawing a finite graph is usually done by a finite sequence of the following three operations. 1. Draw a vertex of the graph. 2. Draw an edge between two vertices of the graph. 3. Draw an edge starting from a vertex of the graph and immediately draw a vertex at the other end of it. By this procedure any finite graph can be constructed. This property of graphs is so obvious that the author of this article has yet to find a reference where it is mentioned explicitly. In introductionary books (like [10], [5], [9]) as well as in advanced ones (like [4]), after the initial definition of graphs the examples are usually given by graphical representations rather than explicit set theoretic descriptions, assuming a mutual understanding how the representation is to be translated into a description fitting the definition. However, Mizar [2], [3] does not possess this innate ability of humans to translate pictures into graphs. Therefore, if one wants to create graphs in Mizar without directly providing a set theoretic description (i.e. using the createGraph functor), a rigorous approach to the constructing operations is required. In this paper supergraphs are defined as an inverse mode to subgraphs as given in [8]. The three graph construction operations are defined as modes extending Supergraph similar to how the various remove operations were introduced as submodes of Subgraph in [8]. Many theorems are proven that describe how graph properties are transferred to special supergraphs. In particular, to prove that disconnected graphs cannot become connected by adding an edge between two vertices that lie in the same component, the theory of replacing a part of a walk with another walk is introduced in the preliminaries.

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