The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity, biogeography, and molecular function. The National Institutes of Health Human Microbiome Project has provided one of the broadest such characterizations so far. Here we introduce a second wave of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to provide new characterizations of microbiome personalization. Strain identification revealed subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. This study furthers our knowledge of baseline human microbial diversity and enables an understanding of personalized microbiome function and dynamics.

 

Strains, functions and dynamics in the expanded Human Microbiome Project
Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, Jonathan Crabtree, Joshua Orvis, A. Brantley Hall, Arthur Brady, Heather H. Creasy, Carrie McCracken, Michelle G. Giglio, Daniel McDonald, Eric A. Franzosa, Rob Knight, Owen White & Curtis Huttenhower
Nature 550, 61–66 (05 October 2017)
doi:10.1038/nature23889

Source: www.nature.com

We demonstrate that exposure to the news media causes Americans to take public stands on specific issues, join national policy conversations, and express themselves publicly—all key components of democratic politics—more often than they would otherwise. After recruiting 48 mostly small media outlets, we chose groups of these outlets to write and publish articles on subjects we approved, on dates we randomly assigned. We estimated the causal effect on proximal measures, such as website pageviews and Twitter discussion of the articles’ specific subjects, and distal ones, such as national Twitter conversation in broad policy areas. Our intervention increased discussion in each broad policy area by ~62.7% (relative to a day’s volume), accounting for 13,166 additional posts over the treatment week, with similar effects across population subgroups.

 

How the news media activate public expression and influence national agendas
Gary King, Benjamin Schneer, Ariel White

Science  10 Nov 2017:
Vol. 358, Issue 6364, pp. 776-780
DOI: 10.1126/science.aao1100

Source: science.sciencemag.org

As debate rumbles on about how and how much poor statistics is to blame for poor reproducibility, Nature asked influential statisticians to recommend one change to improve science. The common theme? The problem is not our maths, but ourselves.

Source: www.nature.com

Imagine being able to shrink down to a small enough size to peer into the human body at the single-cell level. Now take a deep breath and plunge into that cell to see all of the ongoing biological processes, including the full complement of molecules and their locations within the cell. This has long been the realm of science fiction, but not for much longer. Recent technological advances now allow us to identify and visualize RNA transcripts, proteins, and other cellular components at the single-cell level. This has led to discoveries about the immune system, brain, and developmental processes and is poised to revolutionize our understanding of the entire human body.

 

A Fantastic Voyage in Genomics
Laura M. Zahn

Science  06 Oct 2017:
Vol. 358, Issue 6359, pp. 56-57
DOI: 10.1126/science.358.6359.56

Source: science.sciencemag.org

Governments and enterprises strongly rely on incentives to generate favorable outcomes from social and strategic interactions between individuals, for example climate or environmental friendly actions. The incentives are usually modeled by payoffs in strategical games, such as the prisoner’s dilemma or the harmony game. Adjusting the incentives by changing the payoff parameters e.g. through tax schemes can favor cooperation (harmony) over defection (prisoner’s dilemma). Here, we show that if individuals engage in strategic interactions in multiple domains, incentives can fail and the final outcome, cooperation or defection, is dominated by the initial state of the system. Our findings highlight the importance to take the multilayer structure of human interactions into account and emphasize the importance to rethink payoff-based incentives.

 

Failure of incentives in multiplex networks
Kaj-Kolja Kleineberg, Dirk Helbing

Source: arxiv.org