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Abstract The remarkable pace of genomic data generation is rapidly transforming our understanding of life at the micron scale. Yet this data stream also creates challenges for team science. A single microbe can have multiple versions of genome architecture, functional gene annotations, and gene identifiers; additionally, the lack of mechanisms for collating and preserving advances in this knowledge raises barriers to community coalescence around shared datasets. “Digital Microbes” are frameworks for interoperable and reproducible collaborative science through open source, community-curated data packages built on a (pan)genomic foundation. Housed within an integrative software environment, Digital Microbes ensure real-time alignment of research efforts for collaborative teams and facilitate novel scientific insights as new layers of data are added. Here we describe two Digital Microbes: 1) the heterotrophic marine bacteriumRuegeria pomeroyiDSS-3 with > 100 transcriptomic datasets from lab and field studies, and 2) the pangenome of the cosmopolitan marine heterotrophAlteromonascontaining 339 genomes. Examples demonstrate how an integrated framework collating public (pan)genome-informed data can generate novel and reproducible findings. 

An integrated analysis framework shows a strong association between within-population genetic variation and protein structure. 

Polysynthetic languages present a challenge for morphological analysis due to the complexity of their words and the lack of high-quality annotated datasets needed to build and/or evaluate computational models. The contribution of this work is twofold. First, using linguists’ help, we generate and contribute high-quality annotated data for two low-resource polysynthetic languages for two tasks: morphological segmentation and part-of-speech (POS) tagging. Second, we present the results of state-of-the-art unsupervised approaches for these two tasks on Adyghe and Inuktitut. Our findings show that for these polysynthetic languages, using linguistic priors helps the task of morphological segmentation and that using stems rather than words as the core unit of abstraction leads to superior performance on POS tagging. 

Polysynthetic languages present a challenge for morphological analysis due to the complexity of their words and the lack of high-quality annotated datasets needed to build and/or evaluate computational models. The contribution of this work is twofold. First, using linguists’ help, we generate and contribute high-quality annotated data for two low-resource polysynthetic languages for two tasks: morphological segmentation and part-of-speech (POS) tagging. Second, we present the results of state-of-the-art unsupervised approaches for these two tasks on Adyghe and Inuktitut. Our findings show that for these polysynthetic languages, using linguistic priors helps the task of morphological segmentation and that using stems rather than words as the core unit of abstraction leads to superior performance on POS tagging. 

Abstract How microbes adapt to a novel environment is a central question in evolutionary biology. Although adaptive evolution must be fueled by beneficial mutations, whether higher mutation rates facilitate the rate of adaptive evolution remains unclear. To address this question, we cultured Escherichia coli hypermutating populations, in which a defective methyl-directed mismatch repair pathway causes a 140-fold increase in single-nucleotide mutation rates. In parallel with wild-type E. coli, populations were cultured in tubes containing Luria-Bertani broth, a complex medium known to promote the evolution of subpopulation structure. After 900 days of evolution, in three transfer schemes with different population-size bottlenecks, hypermutators always exhibited similar levels of improved fitness as controls. Fluctuation tests revealed that the mutation rates of hypermutator lines converged evolutionarily on those of wild-type populations, which may have contributed to the absence of fitness differences. Further genome-sequence analysis revealed that, although hypermutator populations have higher rates of genomic evolution, this largely reflects strong genetic linkage. Despite these linkage effects, the evolved population exhibits parallelism in fixed mutations, including those potentially related to biofilm formation, transcription regulation, and mutation-rate evolution. Together, these results are generally inconsistent with a hypothesized positive relationship between the mutation rate and the adaptive speed of evolution, and provide insight into how clonal adaptation occurs in novel environments. 

Abstract Carrier concentration optimization has been an enduring challenge when developing newly discovered semiconductors for applications (e.g., thermoelectrics, transparent conductors, photovoltaics). This barrier has been particularly pernicious in the realm of high-throughput property prediction, where the carrier concentration is often assumed to be a free parameter and the limits are not predicted due to the high computational cost. In this work, we explore the application of machine learning for high-throughput carrier concentration range prediction. Bounding the model within diamond-like semiconductors, the learning set was developed from experimental carrier concentration data on 127 compounds ranging from unary to quaternary. The data were analyzed using various statistical and machine learning methods. Accurate predictions of carrier concentration ranges in diamond-like semiconductors are made within approximately one order of magnitude on average across bothp- andn-type dopability. The model fit to empirical data is analyzed to understand what drives trends in carrier concentration and compared with previous computational efforts. Finally, dopability predictions from this model are combined with high-throughput quality factor predictions to identify promising thermoelectric materials.