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nlme : Linear and nonlinear mixed effects models

S. Debroy
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The article was published on 2006-01-01 and is currently open access. It has received 9437 citations till now.

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Functional guild classification predicts the enzymatic role of fungi in litter and soil biogeochemistry

TL;DR: The hypothesis that key biological features of fungi - evolutionary history, functional guild, and abundance of functional genes – can predict the biogeochemical activity of fungal species during decay is tested and quantifying the specific functional guilds of fungi in soil is suggested.
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Rapid thermal adaptation in photosymbionts of reef-building corals.

TL;DR: Using a reciprocal transplant design, it is shown that the upper temperature tolerance and temperature tolerance range of Symbiodinium C1 increased after ~80 asexual generations (2.5 years) of laboratory thermal selection, and the cause behind its limited transference to the coral holobiont in this genotypes is important next steps for developing methods that aim to increase coral bleaching tolerance.
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Predicting cyanobacterial dynamics in the face of global change: the importance of scale and environmental context

TL;DR: In this paper, the authors applied linear and nonlinear mixed-effect modeling techniques to seasonal time-series data from multiple lakes and found that the results showed that due to predictable interactions among nutrients and temperature, polymictic and dimictic lakes are expected to respond differently to future climate warming and eutrophication.
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Metagenome-Wide Association of Microbial Determinants of Host Phenotype in Drosophila melanogaster

TL;DR: The utility of MGWA is demonstrated for identifying bacterial determinants of host traits and mechanistic insight is provided into how gut microbiota modulate the nutritional status of a model host.