A primer for microbiome time-series analysis

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Coenen, A. R., Hu, S. K., Luo, E., Muratore, D., & Weitz, J. S. A primer for microbiome time-series analysis. Frontiers in Genetics, 11, (2020): 310, doi:10.3389/fgene.2020.00310.Time-series can provide critical insights into the structure and function of microbial communities. The analysis of temporal data warrants statistical considerations, distinct from comparative microbiome studies, to address ecological questions. This primer identifies unique challenges and approaches for analyzing microbiome time-series. In doing so, we focus on (1) identifying compositionally similar samples, (2) inferring putative interactions among populations, and (3) detecting periodic signals. We connect theory, code and data via a series of hands-on modules with a motivating biological question centered on marine microbial ecology. The topics of the modules include characterizing shifts in community structure and activity, identifying expression levels with a diel periodic signal, and identifying putative interactions within a complex community. Modules are presented as self-contained, open-access, interactive tutorials in R and Matlab. Throughout, we highlight statistical considerations for dealing with autocorrelated and compositional data, with an eye to improving the robustness of inferences from microbiome time-series. In doing so, we hope that this primer helps to broaden the use of time-series analytic methods within the microbial ecology research community.This work was supported by the Simons Foundation (SCOPE award ID 329108) and the National Science Foundation (NSF Bio Oc 1829636)

The ecological and biogeochemical state of the North Pacifi c Subtropical Gyre is linked to sea surface height

Sea surface height (SSH) is routinely measured from satellites and used to infer ocean currents, including eddies, that affect the distribution of organisms and substances in the ocean. SSH not only reflects the dynamics of the surface layer, but also is sensitive to the fluctuations of the main pycnocline; thus it is linked to events of nutrient upwelling. Beyond episodic upwelling events, it is not clear if and how SSH is linked to broader changes in the biogeochemical state of marine ecosystems. Our analysis of 23 years of satellite observations and biogeochemical measurements from the North Pacific Subtropical Gyre shows that SSH is associated with numerous biogeochemical changes in distinct layers of the water column. From the sea surface to the depth of the chlorophyll maximum, dissolved phosphorus and nitrogen enigmatically increase with SSH, enhancing the abundance of heterotrophic picoplankton. At the deep chlorophyll maximum, increases in SSH are associated with decreases in vertical gradients of inorganic nutrients, decreases in the abundance of eukaryotic phytoplankton, and increases in the abundance of prokaryotic phytoplankton. In waters below ∼100 m depth, increases in SSH are associated with increases in organic matter and decreases in inorganic nutrients, consistent with predicted consequences of the vertical displacement of isopycnal layers. Our analysis highlights how satellite measurements of SSH can be used to infer the ecological and biogeochemical state of open-ocean ecosystems

Multi-Party Argument from Experience

Abstract. A framework, PISA, for conducting dialogues to resolve disputes concerning the correct categorisation of particular cases, is described. Unlike previous systems to conduct such dialogues, which have typically involved only two agents, PISA allows any number of agents to take part, facilitating discussion of cases which permit many possible categorizations. A particular feature of the framework is that the agents argue directly from individual repositories of experiences rather than from a previously engineered knowledge base, as is the usual case, and so the knowledge engineering bottleneck is avoided. Argument from experience is enabled by real time data-mining conducted by individual agents to find reasons to support their viewpoints, and critique the arguments of other parties. Multiparty dialogues raise a number of significant issues, necessitating appropriate design choices. The paper describes how these issues were resolved in the protocol and implemented in PISA, and illustrates the operation of PISA using an example based of a dataset relating to nursery provision. Finally some experiments comparing PIS

Search for new physics in the lepton plus missing transverse momentum final state in proton-proton collisions at s\sqrt{s} = 13 TeV

A search for physics beyond the standard model (SM) in final states with an electron or muon and missing transverse momentum is presented. The analysis uses data from proton-proton collisions at a centre-of-mass energy of 13 TeV, collected with the CMS detector at the LHC in 2016-2018 and corresponding to an integrated luminosity of 138 fb$^{-1}$. No significant deviation from the SM prediction is observed. Model-independent limits are set on the production cross section of W' bosons decaying into lepton-plus-neutrino final states. Within the framework of the sequential standard model, with the combined results from the electron and muon decay channels a W' boson with mass less than 5.7 TeV is excluded at 95% confidence level. Results on a SM precision test, the determination of the oblique electroweak $W$ parameter, are presented using LHC data for the first time. These results together with those from the direct W' resonance search are used to extend existing constraints on composite Higgs scenarios. This is the first experimental exclusion on compositeness parameters using results from LHC data other than Higgs boson measurements

Search for new physics in the lepton plus missing transverse momentum final state in proton-proton collisions at s=\sqrt{s} = 13 TeV

International audienceA search for physics beyond the standard model (SM) in final states with an electron or muon and missing transverse momentum is presented. The analysis uses data from proton-proton collisions at a centre-of-mass energy of 13 TeV, collected with the CMS detector at the LHC in 2016-2018 and corresponding to an integrated luminosity of 138 fb$^{-1}$. No significant deviation from the SM prediction is observed. Model-independent limits are set on the production cross section of W' bosons decaying into lepton-plus-neutrino final states. Within the framework of the sequential standard model, with the combined results from the electron and muon decay channels a W' boson with mass less than 5.7 TeV is excluded at 95% confidence level. Results on a SM precision test, the determination of the oblique electroweak $W$ parameter, are presented using LHC data for the first time. These results together with those from the direct W' resonance search are used to extend existing constraints on composite Higgs scenarios. This is the first experimental exclusion on compositeness parameters using results from LHC data other than Higgs boson measurements

Search for new physics in the lepton plus missing transverse momentum final state in proton-proton collisions at s\sqrt{s} = 13 TeV

A search for physics beyond the standard model (SM) in final states with an electron or muon and missing transverse momentum is presented. The analysis uses data from proton-proton collisions at a centre-of-mass energy of 13 TeV, collected with the CMS detector at the LHC in 2016-2018 and corresponding to an integrated luminosity of 138 fb$^{-1}$. No significant deviation from the SM prediction is observed. Model-independent limits are set on the production cross section of W' bosons decaying into lepton-plus-neutrino final states. Within the framework of the sequential standard model, with the combined results from the electron and muon decay channels a W' boson with mass less than 5.7 TeV is excluded at 95% confidence level. Results on a SM precision test, the determination of the oblique electroweak $W$ parameter, are presented using LHC data for the first time. These results together with those from the direct W' resonance search are used to extend existing constraints on composite Higgs scenarios. This is the first experimental exclusion on compositeness parameters using results from LHC data other than Higgs boson measurements