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1. CNSBench: A cloud native storage benchmark native storage

   Alex Merenstein, Vasily Tarasov (February 2021, Proceedings of the 19th USENIX Conference on File and Storage Technologies (FAST '20))

   null (Ed.)

   Modern hybrid cloud infrastructures require software to be easily portable between heterogeneous clusters. Application containerization is a proven technology to provide this portability for the functionalities of an application. However, to ensure performance portability, dependable verification of a cluster's performance under realistic workloads is required. Such verification is usually achieved through benchmarking the target environment and its storage in particular, as I/O is often the slowest component in an application. Alas, existing storage benchmarks are not suitable to generate cloud native workloads as they do not generate any storage control operations (e.g., volume or snapshot creation), cannot easily orchestrate a high number of simultaneously running distinct workloads, and are limited in their ability to dynamically change workload characteristics during a run. In this paper, we present the design and prototype for the first-ever Cloud Native Storage Benchmark—CNSBench. CNSBench treats control operations as first-class citizens and allows to easily combine traditional storage benchmark workloads with user-defined control operation workloads. As CNSBench is a cloud native application itself, it natively supports orchestration of different control and I/O workload combinations at scale. We built a prototype of CNSBench for Kubernetes, leveraging several existing containerized storage benchmarks for data and metadata I/O generation. We demonstrate CNSBench's usefulness with case studies of Ceph and OpenEBS, two popular storage providers for Kubernetes, uncovering and analyzing previously unknown performance characteristics. 

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2. Native Microbes Amplify Native Seedling Establishment and Diversity While Inhibiting a Non-Native Grass

   https://doi.org/10.3390/plants12051184  

   Koziol, Liz; McKenna, Thomas P.; Bever, James D. (March 2023, Plants)

   Although several studies have shown increased native plant establishment with native microbe soil amendments, few studies have investigated how microbes can alter seedling recruitment and establishment in the presence of a non-native competitor. In this study, the effect of microbial communities on seedling biomass and diversity was assessed by seeding pots with both native prairie seeds and a non-native grass that commonly invades US grassland restorations, Setaria faberi. Soil in the pots was inoculated with whole soil collections from ex-arable land, late successional arbuscular mycorrhizal (AM) fungi isolated from a nearby tallgrass prairie, with both prairie AM fungi and ex-arable whole soil, or with a sterile soil (control). We hypothesized (1) late successional plants would benefit from native AM fungi, (2) that non-native plants would outcompete native plants in ex-arable soils, and (3) early successional plants would be unresponsive to microbes. Overall, native plant abundance, late successional plant abundance, and total diversity were greatest in the native AM fungi+ ex-arable soil treatment. These increases led to decreased abundance of the non-native grass S. faberi. These results highlight the importance of late successional native microbes on native seed establishment and demonstrate that microbes can be harnessed to improve both plant community diversity and resistance to invasion during the nascent stages of restoration. 

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3. Non-uniform consumption of a novel, non-native seaweed by native consumers

   https://doi.org/10.1007/s10530-024-03484-2  

   Haram, Linsey E; Kinney, Kaitlin; Montgomery, Timothy; Sotka, Erik E; Byers, James E (January 2025, Biological Invasions)
4. MASH Native: a unified solution for native top-down proteomics data processing

   https://doi.org/10.1093/bioinformatics/btad359  

   Larson, Eli J; Pergande, Melissa R; Moss, Michelle E; Rossler, Kalina J; Wenger, R Kent; Krichel, Boris; Josyer, Harini; Melby, Jake A; Roberts, David S; Pike, Kyndalanne; et al (June 2023, Bioinformatics)

   Kelso, Janet (Ed.)

   Abstract MotivationNative top-down proteomics (nTDP) integrates native mass spectrometry (nMS) with top-down proteomics (TDP) to provide comprehensive analysis of protein complexes together with proteoform identification and characterization. Despite significant advances in nMS and TDP software developments, a unified and user-friendly software package for analysis of nTDP data remains lacking. ResultsWe have developed MASH Native to provide a unified solution for nTDP to process complex datasets with database searching capabilities in a user-friendly interface. MASH Native supports various data formats and incorporates multiple options for deconvolution, database searching, and spectral summing to provide a “one-stop shop” for characterizing both native protein complexes and proteoforms. Availability and implementationThe MASH Native app, video tutorials, written tutorials, and additional documentation are freely available for download at https://labs.wisc.edu/gelab/MASH_Explorer/MASHSoftware.php. All data files shown in user tutorials are included with the MASH Native software in the download .zip file. 

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5. A global analysis of elevational distribution of non-native versus native plants

   https://doi.org/10.1111/jbi.13145  

   Guo, Qinfeng; Fei, Songlin; Shen, Zehao; Iannone, III, Basil V.; Knott, Jonathan; Chown, Steven L. (April 2018, Journal of Biogeography)