scholarly journals Integrative analysis of relative abundance data and presence-absence data of the microbiome using the LDM

2022 ◽  
Author(s):  
Zhengyi Zhu ◽  
Glen A Satten ◽  
Yi-Juan Hu
Keyword(s):  
Relative Abundance ◽  
R Package ◽  
Data Types ◽  
Omnibus Test ◽  
Testing Hypotheses ◽  
Abundance Data ◽  
Optimal Power ◽  
Wide Range ◽  
Individual Taxon ◽  
The Individual

We previously developed LDM for testing hypotheses about the microbiome that performs the test at both the community level and the individual taxon level. LDM can be applied to relative abundance data and presence-absence data separately, which work well when associated taxa are abundant and rare, respectively. Here we propose an omnibus test based on LDM that allows simultaneous consideration of data at different scales, thus offering optimal power across scenarios with different association mechanisms. The omnibus test is available for the wide range of data types and analyses that are supported by LDM. The omnibus test has been added to the R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM .

scholarly journals propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis

2017 ◽  
Author(s):  
Thomas Quinn ◽  
Mark F. Richardson ◽  
David Lovell ◽  
Tamsyn Crowley
Keyword(s):  
Data Analysis ◽  
Relative Abundance ◽  
Compositional Data ◽  
Life Sciences ◽  
Genomic Data ◽  
R Package ◽  
Compositional Data Analysis ◽  
Computationally Efficient ◽  
Abundance Data ◽  
Relative Abundances

AbstractIn the life sciences, many assays measure only the relative abundances of components for each sample. These data, called compositional data, require special handling in order to avoid misleading conclusions. For example, in the case of correlation, treating relative data like absolute data can lead to the discovery of falsely positive associations. Recently, researchers have proposed proportionality as a valid alternative to correlation for calculating pairwise association in relative data. Although the question of how to best measure proportionality remains open, we present here a computationally efficient R package that implements two proposed measures of proportionality. In an effort to advance the understanding and application of proportionality analysis, we review the mathematics behind proportionality, demonstrate its application to genomic data, and discuss some ongoing challenges in the analysis of relative abundance data.

scholarly journals JARA: ‘Just Another Red-List Assessment’

2019 ◽  
Author(s):  
Henning Winker ◽  
Nathan Pacoureau ◽  
Richard B. Sherley
Keyword(s):  
Relative Abundance ◽  
Extinction Risk ◽  
Decision Support Tool ◽  
R Package ◽  
Iucn Red List ◽  
Red List ◽  
Support Tool ◽  
Criterion A ◽  
Abundance Data ◽  
Abundance Indices

AbstractIdentifying species at risk of extinction is necessary to prioritise conservation efforts. The International Union for Conservation of Nature’s (IUCN) Red List of Threatened Species is the global standard for quantifying extinction risk, with many species categorised according to population reduction thresholds. We introduce the Bayesian state-space framework ‘JARA’ (Just Another Red-List Assessment). Designed as decision-support tool, JARA allows both process error and uncertainty to be incorporated into IUCN Red List assessments under criterion A. JARA is implemented via an R package that is designed to be easy to use, rapid and widely applicable, so conservation practitioners can apply it to their own count or relative abundance data. JARA outputs display easy to interpret graphics of the posterior probability of the population trend against the corresponding IUCN Red List categories, as well as additional graphics to describe the timeseries and model diagnostics. We illustrate JARA using three real-world examples: (1) relative abundance indices for two elasmobranchs, Yellowspotted SkateLeucoraja wallaceiand Whitespot SmoothhoundMustelus palumbes; (2) a comparison of standardized abundance indices for Atlantic Blue MarlinMakaira nigricansand (3) absolute abundance data for Cape GannetsMorus capensis. Finally, using a simulation experiment, we demonstrate how JARA provides greater accuracy than two approaches commonly used to assigning a Red List Status under criterion A. Tools like JARA can help further standardise Red List evaluations, increasing objectivity and lowering the risk of misclassification, with substantial benefits for global conservation efforts.

scholarly journals An omnibus test for the global null hypothesis

2018 ◽  
Vol 28 (8) ◽  
pp. 2292-2304 ◽  
Author(s):  
Andreas Futschik ◽  
Thomas Taus ◽  
Sonja Zehetmayer
Keyword(s):  
Null Hypothesis ◽  
A Priori ◽  
R Package ◽  
Test Statistics ◽  
Omnibus Test ◽  
Genetic Studies ◽  
Global Tests ◽  
Overall Performance ◽  
The Individual ◽  
Meta Analyses

Global hypothesis tests are a useful tool in the context of clinical trials, genetic studies, or meta-analyses, when researchers are not interested in testing individual hypotheses, but in testing whether none of the hypotheses is false. There are several possibilities how to test the global null hypothesis when the individual null hypotheses are independent. If it is assumed that many of the individual null hypotheses are false, combination tests have been recommended to maximize power. If, however, it is assumed that only one or a few null hypotheses are false, global tests based on individual test statistics are more powerful (e.g. Bonferroni or Simes test). However, usually there is no a priori knowledge on the number of false individual null hypotheses. We therefore propose an omnibus test based on cumulative sums of the transformed p-values. We show that this test yields an impressive overall performance. The proposed method is implemented in an R-package called omnibus.

The Orchard Plot: Cultivating a Forest Plot for Use in Ecology, Evolution and Beyond

2019 ◽  
Author(s):  
Shinichi Nakagawa ◽  
Malgorzata Lagisz ◽  
Rose E O'Dea ◽  
Joanna Rutkowska ◽  
Yefeng Yang ◽  
...  
Keyword(s):  
Meta Analysis ◽  
R Package ◽  
Effect Sizes ◽  
Forest Plot ◽  
Point Estimates ◽  
Aggregate Effect ◽  
The Individual ◽  
Meta Analyses ◽  
Heterogeneous Effect ◽  
Intuitive Interpretation

‘Classic’ forest plots show the effect sizes from individual studies and the aggregate effect from a meta-analysis. However, in ecology and evolution meta-analyses routinely contain over 100 effect sizes, making the classic forest plot of limited use. We surveyed 102 meta-analyses in ecology and evolution, finding that only 11% use the classic forest plot. Instead, most used a ‘forest-like plot’, showing point estimates (with 95% confidence intervals; CIs) from a series of subgroups or categories in a meta-regression. We propose a modification of the forest-like plot, which we name the ‘orchard plot’. Orchard plots, in addition to showing overall mean effects and CIs from meta-analyses/regressions, also includes 95% prediction intervals (PIs), and the individual effect sizes scaled by their precision. The PI allows the user and reader to see the range in which an effect size from a future study may be expected to fall. The PI, therefore, provides an intuitive interpretation of any heterogeneity in the data. Supplementing the PI, the inclusion of underlying effect sizes also allows the user to see any influential or outlying effect sizes. We showcase the orchard plot with example datasets from ecology and evolution, using the R package, orchard, including several functions for visualizing meta-analytic data using forest-plot derivatives. We consider the orchard plot as a variant on the classic forest plot, cultivated to the needs of meta-analysts in ecology and evolution. Hopefully, the orchard plot will prove fruitful for visualizing large collections of heterogeneous effect sizes regardless of the field of study.

Designing the Electricity Market with Energy Storage Devices

2020 ◽  
Vol 12 (12) ◽  
pp. 31-43
Author(s):  
Tatiana A. VASKOVSKAYA ◽  
◽  
Boris A. KLUS ◽  
Keyword(s):  
Energy Storage ◽  
Electricity Market ◽  
Power Flow ◽  
Optimal Power Flow ◽  
Storage Systems ◽  
Energy System ◽  
Energy Storage Systems ◽  
Storage Model ◽  
Optimal Power ◽  
Wide Range

The development of energy storage systems allows us to consider their usage for load profile leveling during operational planning on electricity markets. The paper proposes and analyses an application of an energy storage model to the electricity market in Russia with the focus on the day ahead market. We consider bidding, energy storage constraints for an optimal power flow problem, and locational marginal pricing. We show that the largest effect for the market and for the energy storage system would be gained by integration of the energy storage model into the market’s optimization models. The proposed theory has been tested on the optimal power flow model of the day ahead market in Russia of 10000-node Unified Energy System. It is shown that energy storage systems are in demand with a wide range of efficiencies and cycle costs.

THE VALUE OF LOVE IN THE SYSTEM OF FORMATION OF THE PROFESSIONAL MATURITY OF THE EDUCATOR

2020 ◽  
Vol 1 (10(79)) ◽  
pp. 12-18
Author(s):  
G. Bubyreva
Keyword(s):  
Russian Federation ◽  
The State ◽  
Educational Process ◽  
Wide Range ◽  
The Family ◽  
The Russian Federation ◽  
The Government ◽  
The Individual ◽  
The Right

The existing legislation determines the education as "an integral and focused process of teaching and upbringing, which represents a socially important value and shall be implemented so as to meet the interests of the individual, the family, the society and the state". However, even in this part, the meaning of the notion ‘socially significant benefit is not specified and allows for a wide range of interpretation [2]. Yet the more inconcrete is the answer to the question – "who and how should determine the interests of the individual, the family and even the state?" The national doctrine of education in the Russian Federation, which determined the goals of teaching and upbringing, the ways to attain them by means of the state policy regulating the field of education, the target achievements of the development of the educational system for the period up to 2025, approved by the Decree of the Government of the Russian Federation of October 4, 2000 #751, was abrogated by the Decree of the Government of the Russian Federation of March 29, 2014 #245 [7]. The new doctrine has not been developed so far. The RAE Academician A.B. Khutorsky believes that the absence of the national doctrine of education presents a threat to national security and a violation of the right of citizens to quality education. Accordingly, the teacher has to solve the problem of achieving the harmony of interests of the individual, the family, the society and the government on their own, which, however, judging by the officially published results, is the task that exceeds the abilities of the participants of the educational process.  The particular concern about the results of the patriotic upbringing served as a basis for the legislative initiative of the RF President V. V. Putin, who introduced the project of an amendment to the Law of RF "About Education of the Russian Federation" to the State Duma in 2020, regarding the quality of patriotic upbringing [3]. Patriotism, considered by the President of RF V. V. Putin as the only possible idea to unite the nation is "THE FEELING OF LOVE OF THE MOTHERLAND" and the readiness for every sacrifice and heroic deed for the sake of the interests of your Motherland. However, the practicing educators experience shortfalls in efficient methodologies of patriotic upbringing, which should let them bring up citizens, loving their Motherland more than themselves. The article is dedicated to solution to this problem based on the Value-sense paradigm of upbringing educational dynasty of the Kurbatovs [15].

Punk as Folk: Continuities and Tensions in the UK and Beyond

2020 ◽  
Author(s):  
Pete Dale
Keyword(s):  
Folk Music ◽  
Music Making ◽  
Collective Creativity ◽  
Living Tradition ◽  
Wide Range ◽  
The Us ◽  
The Common ◽  
The Individual ◽  
The Uk

Numerous claims have been made by a wide range of commentators that punk is somehow “a folk music” of some kind. Doubtless there are several continuities. Indeed, both tend to encourage amateur music-making, both often have affiliations with the Left, and both emerge at least partly from a collective/anti-competitive approach to music-making. However, there are also significant tensions between punk and folk as ideas/ideals and as applied in practice. Most obviously, punk makes claims to a “year zero” creativity (despite inevitably offering re-presentation of at least some existing elements in every instance), whereas folk music is supposed to carry forward a tradition (which, thankfully, is more recognized in recent decades as a subject-to-change “living tradition” than was the case in folk’s more purist periods). Politically, meanwhile, postwar folk has tended more toward a socialist and/or Marxist orientation, both in the US and UK, whereas punk has at least rhetorically claimed to be in favor of “anarchy” (in the UK, in particular). Collective creativity and competitive tendencies also differ between the two (perceived) genre areas. Although the folk scene’s “floor singer” tradition offers a dispersal of expressive opportunity comparable in some ways to the “anyone can do it” idea that gets associated with punk, the creative expectation of the individual within the group differs between the two. Punk has some similarities to folk, then, but there are tensions, too, and these are well worth examining if one is serious about testing out the common claim, in both folk and punk, that “anyone can do it.”

scholarly journals BloodGen3Module: Blood transcriptional module repertoire analysis and visualization using R

2021 ◽  
Author(s):  
Darawan Rinchai ◽  
Jessica Roelands ◽  
Mohammed Toufiq ◽  
Wouter Hendrickx ◽  
Matthew C Altman ◽  
...  
Keyword(s):  
Transcript Abundance ◽  
R Package ◽  
Supplementary Information ◽  
Illustrative Case ◽  
Bioinformatic Tools ◽  
Transcriptional Module ◽  
Wide Range ◽  
Downstream Analysis ◽  
Computing Module ◽  
Parallel Workflow

Abstract Motivation We previously described the construction and characterization of generic and reusable blood transcriptional module repertoires. More recently we released a third iteration (“BloodGen3” module repertoire) that comprises 382 functionally annotated gene sets (modules) and encompasses 14,168 transcripts. Custom bioinformatic tools are needed to support downstream analysis, visualization and interpretation relying on such fixed module repertoires. Results We have developed and describe here a R package, BloodGen3Module. The functions of our package permit group comparison analyses to be performed at the module-level, and to display the results as annotated fingerprint grid plots. A parallel workflow for computing module repertoire changes for individual samples rather than groups of samples is also available; these results are displayed as fingerprint heatmaps. An illustrative case is used to demonstrate the steps involved in generating blood transcriptome repertoire fingerprints of septic patients. Taken together, this resource could facilitate the analysis and interpretation of changes in blood transcript abundance observed across a wide range of pathological and physiological states. Availability The BloodGen3Module package and documentation are freely available from Github: https://github.com/Drinchai/BloodGen3Module Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals The OsERF115/AP2EREBP110 Transcription Factor Is Involved in the Multiple Stress Tolerance to Heat and Drought in Rice Plants

2021 ◽  
Vol 22 (13) ◽  
pp. 7181
Author(s):  
Seong-Im Park ◽  
Hyeok Jin Kwon ◽  
Mi Hyeon Cho ◽  
Ji Sun Song ◽  
Beom-Gi Kim ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Transcriptional Activation ◽  
Individual Plant ◽  
Hormone Signaling ◽  
Combined Stress ◽  
Drought Treatment ◽  
Wide Range ◽  
The Individual ◽  
Potential Use ◽  
Multiple Stress Tolerance

The AP2/EREBP family transcription factors play important roles in a wide range of stress tolerance and hormone signaling. In this study, a heat-inducible rice ERF gene was isolated and functionally characterized. The OsERF115/AP2EREBP110 was categorized to Group-IIIc of the rice AP2/EREBP family and strongly induced by heat and drought treatment. The OsERF115/AP2EREBP110 protein targeted to nuclei and suppressed the ABA-induced transcriptional activation of Rab16A promoter in rice protoplasts. Overexpression of OsERF115/AP2EREBP110 enhanced thermotolerance of seeds and vegetative growth stage plants. The OsERF115/AP2EREBP110 overexpressing (OE) plants exhibited higher proline level and increased expression of a proline biosynthesis P5CS1 gene. Phenotyping of water use dynamics of the individual plant indicates that the OsERF115/AP2EREBP110-OE plant exhibited better water saving traits under heat and drought combined stress. Our combined results suggest the potential use of OsERF115/AP2EREBP110 as a candidate gene for genetic engineering approaches to develop heat and drought stress-tolerant crops.

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