| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Jangali, Mostafa, et al.
(author)
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Automated Generation and Evaluation of JMH Microbenchmark Suites From Unit Tests
- 2023
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In: IEEE Transactions on Software Engineering. - 0098-5589 .- 1939-3520. ; 49:4, s. 1704-1725
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Journal article (peer-reviewed)abstract
- Performance is a crucial non-functional requirement of many software systems. Despite the widespread use of performance testing, developers still struggle to construct and evaluate the quality of performance tests. To address these two major challenges, we implement a framework, dubbed ju2jmh, to automatically generate performance microbenchmarks from JUnit tests and use mutation testing to study the quality of generated microbenchmarks. Specifically, we compare our ju2jmh generated benchmarks to manually written JMH benchmarks and to automatically generated JMH benchmarks using the AutoJMH framework, as well as directly measuring system performance with JUnit tests. For this purpose, we have conducted a study on three subjects (Rxjava, Eclipse-collections, and Zipkin) with $\sim$454 K source lines of code (SLOC), 2,417 JMH benchmarks (including manually written and generated AutoJMH benchmarks) and 35,084 JUnit tests. Our results show that the ju2jmh generated JMH benchmarks consistently outperform using the execution time and throughput of JUnit tests as a proxy of performance and JMH benchmarks automatically generated using the AutoJMH framework while being comparable to JMH benchmarks manually written by developers in terms of tests’ stability and ability to detect performance bugs. Nevertheless, ju2jmh benchmarks are able to cover more of the software applications than manually written JMH benchmarks during the microbenchmark execution. Furthermore, ju2jmh benchmarks are generated automatically, while manually written JMH benchmarks requires many hours of hard work and attention; therefore our study can reduce developers’ effort to construct microbenchmarks. In addition, we identify three factors (too low test workload, unstable tests and limited mutant coverage) that affect a benchmark’s ability to detect performance bugs. To the best of our knowledge, this is the first study aimed at assisting developers in fully automated microbenchmark creation and assessing microbenchmark quality for performance testing.
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| 3. |
- Pang, Kanglei, 1993-, et al.
(author)
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Redirecting configuration of atomically dispersed selenium catalytic sites for efficient hydrazine oxidation
- 2024
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In: Matter. - 2590-2393 .- 2590-2385. ; 7:2, s. 655-667
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Journal article (peer-reviewed)abstract
- Understanding the reconstruction of surface sites is crucial for gaining insights into the true active sites and catalytic mechanisms. While extensive research has been conducted on reconstruction behaviors of atomically dispersed metallic catalytic sites, limited attention has been paid to non-metallic ones despite their potential catalytic activity comparable or even superior to their noble-metal counterpart. Herein, we report a carbonaceous, atomically dispersed non-metallic selenium catalyst that displayed exceptional catalytic activity in the hydrazine oxidation reaction (HzOR) in alkaline media, outperforming the noble-metal Pt catalysts. In situ X-ray absorption spectroscopy (XAS) and Fourier transform infrared spectroscopy revealed that the pristine SeC4 site pre-adsorbs an ∗OH ligand, followed by HzOR occurring on the other side of the OH–SeC4. Theoretical calculations proposed that the pre-adsorbed ∗OH group pulls electrons from the Se site, resulting in a more positively charged Se and a higher polarity of Se–C bonds, thereby enhancing surface reactivity toward HzO/R.
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| 4. |
- Tang, Qingquan, et al.
(author)
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Templated synthesis of cyclic poly(ionic liquid)s
- 2019
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In: Reactive & functional polymers. - : Elsevier BV. - 1381-5148 .- 1873-166X. ; 138, s. 1-8
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Journal article (peer-reviewed)abstract
- Charged cyclic polymers, e.g. cyclic DNAs and polypeptides, play enabling roles in organisms, but their synthesis was challenging due to the well-known polyelectrolyte effect. To tackle the challenge, we developed a templated method to synthesize a library of imidazolium and pyridinium based cyclic poly(ionic liquid)s. Cyclic templates, cyclic polyimidazole and poly(2-pyridine), were synthesized first through ring-closure method by light-induced Diels - Alder click reaction. Through quaternization of cyclic templates followed by anion metathesis, the cyclic poly(ionic liquid)s were synthesized, which paired with varied counter anions.
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| 5. |
- Tang, Qingquan, et al.
(author)
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Topological Effects on Cyclic Co-Poly(ionic liquid)s Self-Assembly
- 2023
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In: Macromolecular Chemistry and Physics. - : Wiley. - 1022-1352 .- 1521-3935. ; 224:3
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Journal article (peer-reviewed)abstract
- Topological geometry of poly(ionic liquid)s (PILs), such as brush-like, knot-like, hyperbranched and randomly coiled, often exerts a strong influence on their self-assembly behaviors. As a primary topological form, the cyclic topology-derived effects have not been investigated on PILs, which concerns synergy of charges and zero chain end. Herein, linear and cyclic poly(ionic liquid) copolymers (co-PILs) with randomly distributed counter anions of B(Ph)4− and Br− by a template method in combination with a follow-up partial anion exchange is prepared. The self-assembly phenomena of linear and cyclic co-PILs are studied in selective solvents, where the hydrophobic counter anions B(Ph)4− and hydrophilic counter anions Br− aggregated to form cores and corona in the assembled nanospheres, showing the average size of cyclic co-PILs nanospheres is 46.2% smaller (≈120 nm) than linear co-PILs nano-assemblies (≈176 nm). Based on the CGMD simulations, the authors speculate that the spherical aggregates are formed by transitioning from micelles with gradient block-like structures, which formed by enriched hydrophobic counter anions in the core and enriched hydrophilic counter anions in the corona. These results indicate a novel synergy of topology effects and dynamic anion movements, as revealed by cyclic co-PIL self-assembly in this work.
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| 6. |
- Tang, Weiyi, et al.
(author)
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Database of nitrification and nitrifiers in the global ocean
- 2023
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In: EARTH SYSTEM SCIENCE DATA. - 1866-3508 .- 1866-3516. ; 15:11, s. 5039-5077
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Journal article (peer-reviewed)abstract
- As a key biogeochemical pathway in the marine nitrogen cycle, nitrification (ammonia oxidation and nitrite oxidation) converts the most reduced form of nitrogen - ammonium-ammonia (NH-NH3) - into the oxidized species nitrite (NO) and nitrate (NO). In the ocean, these processes are mainly performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB). By transforming nitrogen speciation and providing substrates for nitrogen removal, nitrification affects microbial community structure; marine productivity (including chemoautotrophic carbon fixation); and the production of a powerful greenhouse gas, nitrous oxide (N2O). Nitrification is hypothesized to be regulated by temperature, oxygen, light, substrate concentration, substrate flux, pH and other environmental factors. Although the number of field observations from various oceanic regions has increased considerably over the last few decades, a global synthesis is lacking, and understanding how environmental factors control nitrification remains elusive. Therefore, we have compiled a database of nitrification rates and nitrifier abundance in the global ocean from published literature and unpublished datasets. This database includes 2393 and 1006 measurements of ammonia oxidation and nitrite oxidation rates and 2242 and 631 quantifications of ammonia oxidizers and nitrite oxidizers, respectively. This community effort confirms and enhances our understanding of the spatial distribution of nitrification and nitrifiers and their corresponding drivers such as the important role of substrate concentration in controlling nitrification rates and nitrifier abundance. Some conundrums are also revealed, including the inconsistent observations of light limitation and high rates of nitrite oxidation reported from anoxic waters. This database can be used to constrain the distribution of marine nitrification, to evaluate and improve biogeochemical models of nitrification, and to quantify the impact of nitrification on ecosystem functions like marine productivity and N2O production. This database additionally sets a baseline for comparison with future observations and guides future exploration (e.g., measurements in the poorly sampled regions such as the Indian Ocean and method comparison and/or standardization). The database is publicly available at the Zenodo repository: https://doi.org/10.5281/zenodo.8355912 (Tang et al., 2023).
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