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Using a starlike Be 6 Au 7 − cluster as a building block and following the bottom-up strategy, an intriguing two-dimensional (2D) binary s-block metal Be 2 Au monolayer with a P 6/ mmm space group was theoretically designed. Both the Be 6 Au 7 − cluster and the 2D monolayer are global minima featuring rule-breaking planar hexacoordinate motifs (anti-van't Hoff/Le Bel arrangement), and their high stabilities are attributed to good electron delocalization and electronic-stabilization-induced steric force. Strikingly, the Be 2 Au monolayer is a rare Dirac material with two perfect Dirac node-loops in the band structure and is a phonon-mediated superconductor with a critical temperature of 4.0 K. The critical temperature can be enhanced up to 11.0 K by applying compressive strain at only 1.6%. This study not only identifies a new binary s-block metal 2D material, namely Be 2 Au, which features planar hexacoordination, and a candidate superconducting material for further explorations, but also provides a new strategy to construct 2D materials with novel chemical bonding. 

Abstract Motivation Chromosomal patterning of gene expression in cancer can arise from aneuploidy, genome disorganization, or abnormal DNA methylation. To map such patterns, we introduce a weighted univariate clustering algorithm to guarantee linear runtime, optimality, and reproducibility. Results We present the chromosome clustering method, establish its optimality and runtime, and evaluate its performance. It uses dynamic programming enhanced with an algorithm to reduce search-space in-place to decrease runtime overhead. Using the method, we delineated outstanding genomic zones in 17 human cancer types. We identified strong continuity in dysregulation polarity—dominance by either up- or down-regulated genes in a zone—along chromosomes in all cancer types. Significantly polarized dysregulation zones specific to cancer types are found, offering potential diagnostic biomarkers. Unreported previously, a total of 109 loci with conserved dysregulation polarity across cancer types give insights into pan-cancer mechanisms. Efficient chromosomal clustering opens a window to characterize molecular patterns in cancer genome and beyond. Availability Weighted univariate clustering algorithms are implemented within the R package ‘Ckmeans.1d.dp’ (4.0.0 or above), freely available at https://cran.r-project.org/package=Ckmeans.1d.dp Supplementary information Supplementary data are available at Bioinformatics online. 

Functional dependency can lead to discoveries of new mechanisms not possible via symmetric association. Most asymmetric methods for causal direction inference are not driven by the function-versus-independence question. A recent exact functional test (EFT) was designed to detect functionally dependent patterns model-free with an exact null distribution. However, the EFT lacked a theoretical justification, had not been compared with other asymmetric methods, and was practically slow. Here, we prove the functional optimality of the EFT statistic, demonstrate its advantage in functional inference accuracy over five other methods, and develop a branch-and-bound algorithm with dynamic and quadratic programming to run at orders of magnitude faster than its previous implementation. Our results make it practical to answer the exact functional dependency question arising from discovery-driven artificial intelligence applications. Software that implements EFT is freely available in the R package 'FunChisq' (≥2.5.0) at https://cran.r-project.org/package=FunChisq 

Abstract The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii . The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology. 

Regression testing is an important but expensive activity in software development. Among various types of tests, web service tests are usually one of the most expensive (due to network communications) but widely adopted types of tests in commercial software development. Regression test selection (RTS) aims to reduce the number of tests which need to be retested by only running tests that are affected by code changes. Although a large number of RTS techniques have been proposed in the past few decades, these techniques have not been adopted on large-scale web service testing. This is because most existing RTS techniques either require direct code dependency between tests and code under test or cannot be applied on large scale systems with enough efficiency. In this paper, we present a novel RTS technique, TestSage, that performs RTS for web service tests on large scale commercial software. With a small overhead, TestSage is able to collect fine grained (function level) dependency between test and service under test that do not directly depend on each other. TestSage has also been successfully applied to large complex systems with over a million functions. We conducted experiments of TestSage on a large scale backend service at Google. Experimental results show that TestSage reduces 34% of testing time when running all AEC (Analysis, Execution and Collection) phases, 50% of testing time while running without collection phase. TestSage has been integrated with internal testing framework at Google and runs day-to-day at the company.