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1. To Dereplicate or Not To Dereplicate?

   https://doi.org/10.1128/mSphere.00971-19  

   Evans, Jacob T.; Denef, Vincent J.; McMahon, Katherine (June 2020, mSphere)

   ABSTRACT Metagenome-assembled genomes (MAGs) expand our understanding of microbial diversity, evolution, and ecology. Concerns have been raised on how sequencing, assembly, binning, and quality assessment tools may result in MAGs that do not reflect single populations in nature. Here, we reflect on another issue, i.e., how to handle highly similar MAGs assembled from independent data sets. Obtaining multiple genomic representatives for a species is highly valuable, as it allows for population genomic analyses; however, when retaining genomes of closely related populations, it complicates MAG quality assessment and abundance inferences. We show that (i) published data sets contain a large fraction of MAGs sharing >99% average nucleotide identity, (ii) different software packages and parameters used to resolve this redundancy remove very different numbers of MAGs, and (iii) the removal of closely related genomes leads to losses of population-specific auxiliary genes. Finally, we highlight some approaches that can infer strain-specific dynamics across a sample series without dereplication. 

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2. To Stack or Not To Stack

   Afoakwa, Richard; Lu, Lejie; Wu, Hui; Huang, Michael (January 2019, International conference on parallel architectures and compilation techniques)
3. From division to ‘divergence’: to understand wood growth across timescales, we need to (learn to) manipulate it

   https://doi.org/10.1111/nph.20390  

   Buttò, Valentina; Peltier, Drew_M_P; Rademacher, Tim (January 2025, New Phytologist)

   Summary Wood formation is the Rosetta stone of tree physiology: a traceable, integrated record of physiological and morphological status. It also produces a large and persistent annual sink for terrestrial carbon, motivating predictive understanding. Xylogenesis studies have greatly expanded our knowledge of the intra‐annual controls on wood formation, while dendroecology has quantified the environmental drivers of multi‐annual variability. But these fields operate on different timescales, making it challenging to predict how short (e.g. turgor) and long timescale processes (e.g. disturbance) interactively influence wood formation. Toward this challenge, wood growth responses to natural climate events provide useful but incomplete explanations of tree growth variability. By contrast, direct manipulations of the tree vascular system have yielded unexpected insights, particularly outside of model species like boreal conifers, but they remain underutilized. To improve prediction of global wood formation, we argue for a new generation of experimental manipulations of wood growth across seasons, species, and ecosystems. Such manipulations should expand inference to diverse forests and capture inter‐ and intra‐specific differences in wood growth. We summarize the endogenous and exogenous factors influencing wood formation to guide future experimental design and hypotheses. We highlight key opportunities for manipulative studies integrating measurements from xylogenesis, dendroanatomy, dendroecology, and ecophysiology. 

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4. It Takes Two to Lie: One to Lie, and One to Listen

   Denis Peskov, Benny Cheng (January 2020, Proceedings of ACL)

   Trust is implicit in many online text conversations—striking up new friendships, or asking for tech support. But trust can be betrayed through deception. We study the language and dynamics of deception in the negotiation-based game Diplomacy, where seven players compete for world domination by forging and breaking alliances with each other. Our study with players from the Diplomacy community gathers 17,289 messages annotated by the sender for their intended truthfulness and by the receiver for their perceived truthfulness. Unlike existing datasets, this captures deception in long-lasting relationships, where the interlocutors strategically combine truth with lies to advance objectives. A model that uses power dynamics and conversational contexts can predict when a lie occurs nearly as well as human players. 

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5. To cut or to fill: a global optimization approach to topological simplification

   https://doi.org/10.1145/3414685.3417854  

   Dan Zeng, Erin Chambers (January 2020, ACM transactions on graphics)

   We present a novel algorithm for simplifying the topology of a 3D shape, which is characterized by the number of connected components, handles, and cavities. Existing methods either limit their modifications to be only cutting or only filling, or take a heuristic approach to decide where to cut or fill. We consider the problem of finding a globally optimal set of cuts and fills that achieve the simplest topology while minimizing geometric changes. We show that the problem can be formulated as graph labelling, and we solve it by a transformation to the Node-Weighted Steiner Tree problem. When tested on examples with varying levels of topological complexity, the algorithm shows notable improvement over existing simplification methods in both topological simplicity and geometric distortions. 

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