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1. Small rainfall changes drive substantial changes in plant coexistence

   https://doi.org/10.1038/s41586-022-05391-9  

   Van Dyke, Mary N.; Levine, Jonathan M.; Kraft, Nathan J. (November 2022, Nature)
2. Changes in Software Ecosystems

   https://doi.org/10.1184/R1/19799314.v1  

   Matute, Gabriel; Cheung, Alvin; Chasins, Sarah (June 2022, PLATEAU)
3. Changes in precipitation patterns can destabilize plant species coexistence via changes in plant–soil feedback

   https://doi.org/10.1038/s41559-022-01700-7  

   Dudenhöffer, Jan-Hendrik; Luecke, Noah C.; Crawford, Kerri M. (May 2022, Nature Ecology & Evolution)
4. Changes in gene body methylation do not correlate with changes in gene expression in Anthozoa or Hexapoda

   https://doi.org/10.1186/s12864-022-08474-z  

   Dixon, Groves; Matz, Mikhail (December 2022, BMC Genomics)

   Abstract Background As human activity alters the planet, there is a pressing need to understand how organisms adapt to environmental change. Of growing interest in this area is the role of epigenetic modifications, such as DNA methylation, in tailoring gene expression to fit novel conditions. Here, we reanalyzed nine invertebrate (Anthozoa and Hexapoda) datasets to validate a key prediction of this hypothesis: changes in DNA methylation in response to some condition correlate with changes in gene expression. Results In accord with previous observations, baseline levels of gene body methylation (GBM) positively correlated with transcription, and negatively correlated with transcriptional variation between conditions. Correlations between changes in GBM and transcription, however, were negligible. There was also no consistent negative correlation between methylation and transcription at the level of gene body methylation class (either highly- or lowly-methylated), anticipated under the previously described “seesaw hypothesis”. Conclusion Our results do not support the direct involvement of GBM in regulating dynamic transcriptional responses in invertebrates. If changes in DNA methylation regulate invertebrate transcription, the mechanism must involve additional factors or regulatory influences. 

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5. Identifying casualty changes in software patches

   https://doi.org/10.1145/3468264.3468624  

   Sejfia, Adriana; Zhao, Yixue; Medvidović, Nenad (August 2021, ESEC/FSE 2021: Proceedings of the 29th ACM Joint Meeting on European Software Engineering Conference and Symposium on the Foundations of Software Engineering)

   null (Ed.)

   Noise in software patches impacts their understanding, analysis, and use for tasks such as change prediction. Although several approaches have been developed to identify noise in patches, this issue has persisted. An analysis of a dataset of security patches for the Tomcat web server, which we further expanded with security patches from five additional systems, uncovered several kinds of previously unreported noise which we call nonessential casualty changes. These are changes that themselves do not alter the logic of the program but are necessitated by other changes made in the patch. In this paper, we provide a comprehensive taxonomy of casualty changes. We then develop CasCADe, an automated technique for automatically identifying casualty changes. We evaluate CasCADe with several publicly available datasets of patches and tools that focus on them. Our results show that CasCADe is highly accurate, that the kinds of noise it identifies occur relatively commonly in patches, and that removing this noise improves upon the evaluation results of a previously published change-based approach. 

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