scholarly journals COREMIC: a web-tool to search for a root-zone associated CORE MICrobiome

2017 ◽  
Author(s):  
Richard R. Rodrigues ◽  
Nyle C. Rodgers ◽  
Xiaowei Wu ◽  
Mark A. Williams
Keyword(s):  
Root Zone ◽  
Growth Promotion ◽  
Niche Partitioning ◽  
Web Tool ◽  
Core Microbiome ◽  
Exact Test ◽  
The Core ◽  
Using Data ◽  
User Friendly

AbstractMicrobial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the burgeoning growth of information from databases, our tool “COREMIC” meets a great need in the search for understanding niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly statistically robust web-tool (http://coremic2.appspot.com), developed using Google App Engine, to help in the process of database mining to identify the “core microbiome” associated with a given habitat. A case study is presented using data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs) to identify a core switchgrass microbiome. Even across a diverse set of soils (5 environments), and conservative statistical criteria (presence in more than 90% samples and FDR q-val < 0.05% for Fisher’s exact test) a core set of bacteria associated with switchgrass was observed. These included, among others, closely related taxa from Lysobacter spp., Mesorhizobium spp, and Chitinophagaceae. These bacteria have been shown to have functions related to the production of bacterial and fungal antibiotics and plant growth promotion. COREMIC can be used as a hypothesis generating or confirmatory tool that shows great potential for identifying taxa that may be important to the functioning of a habitat (e.g. host plant). The case study, in conclusion, shows that COREMIC can identify key habitat-specific microbes across diverse samples, using currently available databases and a unique freely available software.

scholarly journals COREMIC: a web-tool to search for a niche associated CORE MICrobiome

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4395 ◽  
Author(s):  
Richard R. Rodrigues ◽  
Nyle C. Rodgers ◽  
Xiaowei Wu ◽  
Mark A. Williams
Keyword(s):  
Growth Promotion ◽  
Niche Partitioning ◽  
Web Tool ◽  
Core Microbiome ◽  
Exact Test ◽  
The Core ◽  
Link Type ◽  
Using Data ◽  
User Friendly

Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the burgeoning growth of information from databases, our tool “COREMIC” meets a great need in the search for understanding niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly statistically robust web-tool (http://coremic2.appspot.com or http://core-mic.com), developed using Google App Engine, to help in the process of database mining to identify the “core microbiome” associated with a given habitat. A case study is presented using data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs) to identify a core switchgrass microbiome. Even across a diverse set of soils (five environments), and conservative statistical criteria (presence in more than 90% samples and FDR q-val <0.05% for Fisher’s exact test) a core set of bacteria associated with switchgrass was observed. These included, among others, closely related taxa from Lysobacter spp., Mesorhizobium spp, and Chitinophagaceae. These bacteria have been shown to have functions related to the production of bacterial and fungal antibiotics and plant growth promotion. COREMIC can be used as a hypothesis generating or confirmatory tool that shows great potential for identifying taxa that may be important to the functioning of a habitat (e.g. host plant). The case study, in conclusion, shows that COREMIC can identify key habitat-specific microbes across diverse samples, using currently available databases and a unique freely available software.

Classification as Evaluation

2011 ◽  
pp. 41-62 ◽  
Author(s):  
Sari Hakkarainen ◽  
Darijus Strasunskas ◽  
Lillian Hella ◽  
Stine Tuxen
Keyword(s):  
Web Applications ◽  
Evaluation Criteria ◽  
Web Based ◽  
Classification Approach ◽  
The Core ◽  
Ontology Language ◽  
Ontology Building ◽  
Using Data

Ontology is the core component in Semantic Web applications. The employment of an ontology building method affects the quality of ontology and the applicability of ontology language. A weighted classification approach for ontology building guidelines is presented in this chapter. The evaluation criteria are based on an existing classification scheme of a semiotic framework for evaluating the quality of conceptual models. A sample of Web-based ontology building method guidelines is evaluated in general and experimented with using data from a case study in particular. Directions for further refinement of ontology building methods are discussed.

scholarly journals Examining the Core Dilemmas Hindering Big Data-related Transformations in Public-Sector Organisations

2019 ◽  
Vol 12 (2) ◽  
pp. 131-156 ◽  
Author(s):  
Päivikki Kuoppakangas ◽  
Tony Kinder ◽  
Jari Stenvall ◽  
Ilpo Laitinen ◽  
Olli-Pekka Ruuskanen ◽  
...  
Keyword(s):  
Big Data ◽  
Risk Taking ◽  
Service Provision ◽  
Data Driven ◽  
The Core ◽  
Management Approaches ◽  
Using Data ◽  
Public Organisations ◽  
Managerial System

AbstractThis study examines public organisations planning big data-driven transformations in their service provision. Without radical structural change or managerial system changes, leaders face dilemmas: simply bolting on big data makes little difference. This study is based on a qualitative empirical case study using data collected from the cities of Helsinki and Tampere in Finland. The three core dilemma pairs detected and connected to the big data-related organisational changes are: (1) repetitive continuity vs. visionary change, (2) risk-taking vs. security-seeking and (3) technology-based development vs. human-based development. This study suggests that organisational readiness involves not only capabilities; instead, readiness involves absorbing knowledge, making decisions, handling ambiguities, managing dilemmas. Thus, big data-related transformations in public organisations require embracing the world of dilemmas, since selected and cancelled experiments may each have valuable outcomes. The capability to act on intentions is a prerequisite for readiness; however, a preparedness to detect and address dilemmas is central to big data-related transformations. Thus, the ability to make dilemma decisions is a more complicated characteristic of readiness. In conclusion, our data analysis suggests that traditional public organisational and chance management approaches produce unsolved dilemmas in big data-related organisational changes.

Concepts and Consequences of a Core Gut Microbiota for Animal Growth and Development

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Daphne Perlman ◽  
Marina Martínez-Álvaro ◽  
Sarah Moraïs ◽  
Ianina Altshuler ◽  
Live H. Hagen ◽  
...  
Keyword(s):  
Growth And Development ◽  
Annual Review ◽  
Publication Date ◽  
Core Microbiome ◽  
Host Environment ◽  
The Core ◽  
Genomic Architecture ◽  
Animal Growth ◽  
Potential Factors

Animal microbiomes are occasionally considered as an extension of host anatomy, physiology, and even their genomic architecture. Their compositions encompass variable and constant portions when examined across multiple hosts. The latter, termed the core microbiome, is viewed as more accommodated to its host environment and suggested to benefit host fitness. Nevertheless, discrepancies in its definitions, characteristics, and importance to its hosts exist across studies. We survey studies that characterize the core microbiome, detail its current definitions and available methods to identify it, and emphasize the crucial need to upgrade and standardize the methodologies among studies. We highlight ruminants as a case study and discuss the link between the core microbiome and host physiology and genetics, as well as potential factors that shape it. We conclude with main directives of action to better understand the host–core microbiome axis and acquire the necessary insights into its controlled modulation. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

A case study of global ULF pulsations using data from space-borne and ground-based magnetometers and a SuperDARN radar

2011 ◽  
Vol 17 (6) ◽  
pp. 54-67
Author(s):  
A.S. Potapov ◽  
◽  
E. Amata ◽  
T.N. Polyushkina ◽  
I. Coco ◽  
...  
Keyword(s):  
Using Data

Possessing the Iconic Book

2012 ◽  
Vol 6 (1-3) ◽  
pp. 309-329
Author(s):  
Claudia V. Camp
Keyword(s):  
Second Century ◽  
Religious Literature ◽  
Ben Sira ◽  
The Core ◽  
The Bible ◽  
Iconic Status ◽  
The Voice ◽  
Woman Wisdom ◽  
Martin Marty

I propose that the notion of possession adds an important ideological nuance to the analyses of iconic books set forth by Martin Marty (1980) and, more recently, by James Watts (2006). Using the early second century BCE book of Sirach as a case study, I tease out some of the symbolic dynamics through which the Bible achieved iconic status in the first place, that is, the conditions in which significance was attached to its material, finite shape. For Ben Sira, this symbolism was deeply tied to his honor-shame ethos in which women posed a threat to the honor of his eternal name, a threat resolved through his possession of Torah figured as the Woman Wisdom. What my analysis suggests is that the conflicted perceptions of gender in Ben Sira’s text is fundamental to his appropriation of, and attempt to produce, authoritative religious literature, and thus essential for understanding his relationship to this emerging canon. Torah, conceived as female, was the core of this canon, but Ben Sira adds his own literary production to this female “body” (or feminized corpus, if you will), becoming the voice of both through the experience of perfect possession.

Optimales Layout einer Walderschliessung

2016 ◽  
Vol 167 (5) ◽  
pp. 294-301
Author(s):  
Leo Bont
Keyword(s):  
Road Network ◽  
Spatial Arrangement ◽  
Problem Situation ◽  
Optimal Layout ◽  
Forest Road ◽  
The Road ◽  
Network Cost ◽  
User Friendly ◽  
Short Time

Optimal layout of a forest road network The road network is the backbone of forest management. When creating or redesigning a forest road network, one important question is how to shape the layout, this means to fix the spatial arrangement and the dimensioning standard of the roads. We consider two kinds of layout problems. First, new forest road network in an area without any such development yet, and second, redesign of existing road network for actual requirements. For each problem situation, we will present a method that allows to detect automatically the optimal road and harvesting layout. The method aims to identify a road network that concurrently minimizes the harvesting cost, the road network cost (construction and maintenance) and the hauling cost over the entire life cycle. Ecological issues can be considered as well. The method will be presented and discussed with the help of two case studies. The main benefit of the application of optimization tools consists in an objective-based planning, which allows to check and compare different scenarios and objectives within a short time. The responses coming from the case study regions were highly positive: practitioners suggest to make those methods a standard practice and to further develop the prototype to a user-friendly expert software.

Sign in / Sign up

Export Citation Format

Share Document