| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)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. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Ahmad, Azeem, et al.
(författare)
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A Multi-factor Approach for Flaky Test Detection and Automated Root Cause Analysis
- 2021
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Ingår i: Proceedings - Asia-Pacific Software Engineering Conference, APSEC. - : IEEE COMPUTER SOC. - 1530-1362. ; , s. 338-348
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Konferensbidrag (refereegranskat)abstract
- Developers often spend time to determine whether test case failures are real failures or flaky. The flaky tests, also known as non-deterministic tests, switch their outcomes without any modification in the codebase, hence reducing the confidence of developers during maintenance as well as in the quality of a product. Re-running test cases to reveal flakiness is resource-consuming, unreliable and does not reveal the root causes of test flakiness. Our paper evaluates a multi-factor approach to identify flaky test executions implemented in a tool named MDF laker. The four factors are: trace-back coverage, flaky frequency, number of test smells, and test size. Based on the extracted factors, MDFlaker uses k-Nearest Neighbor (KNN) to determine whether failed test executions are flaky. We investigate MDFlaker in a case study with 2166 test executions from different open-source repositories. We evaluate the effectiveness of our flaky detection tool. We illustrate how the multi-factor approach can be used to reveal root causes for flakiness, and we conduct a qualitative comparison between MDF laker and other tools proposed in literature. Our results show that the combination of different factors can be used to identify flaky tests. Each factor has its own trade-off, e.g., trace-back leads to many true positives, while flaky frequency yields more true negatives. Therefore, specific combinations of factors enable classification for testers with limited information (e.g., not enough test history information).
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| 4. |
- Pan, Junxiu, et al.
(författare)
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pi-Extended Nonfullerene Acceptors for Efficient Organic Solar Cells with a High Open-Circuit Voltage of 0.94 V and a Low Energy Loss of 0.49 eV
- 2021
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Ingår i: ACS Applied Materials and Interfaces. - : AMER CHEMICAL SOC. - 1944-8244 .- 1944-8252. ; 13:19, s. 22531-22539
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Tidskriftsartikel (refereegranskat)abstract
- A combination of high open-circuit voltage (V-oc) and short-circuit current density (J(sc)) typically creates effective organic solar cells (OSCs). Y5, a member of the Y-series acceptors, can achieve high V-oc of 0.94 V with PM6 but low J(sc) of 12.8 mA cm(-2). To maintain the high V-oc while increasing the J(sc) of devices, we developed a new nonfullerene acceptor, namely, BTP-C2C4-N, by extending the conjugation of a Y5 molecule with a naphthalenebased end acceptor. In comparison with Y5-based devices, PM6:BTP-C2C4-N-based devices exhibited significantly higher J(sc) of 18.2 mA cm(-2) followed by a high V-oc. To further increase the photovoltaic properties of BTP-C2C4-N analogues, BTP-C4C6-N and BTP-C6C8-N molecules with better processability and film morphology are obtained by adjusting the alkyl branched chain length. The optimized OSCs based on BTP-C4C6-N with a moderate alkyl branched chain length exhibited the best PCE of 12.4% with a high V-oc of 0.94 V and J(sc) of 20.7 mA cm(-2). Notably, the devices achieved a low energy loss of 0.49 eV (0.51 eV for Y5 system) accompanied by a small nonradiative energy loss. The results indicate that nonfullerene acceptors with extended terminal motifs and optimized branched chain lengths can effectively enhance the performance of OSCs and reduce energy loss.
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| 5. |
- Shi, Yanan, et al.
(författare)
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Optimizing the Charge Carrier and Light Management of Nonfullerene Acceptors for Efficient Organic Solar Cells with Small Nonradiative Energy Losses
- 2021
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Ingår i: Solar RRL. - : WILEY-V C H VERLAG GMBH. - 2367-198X. ; 5:4
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Tidskriftsartikel (refereegranskat)abstract
- The photovoltaic properties and energy losses of organic solar cells (OSCs) based on nonfullerene acceptors (NFAs) are highly dependent on their molecular structures and aggregation morphologies. Charge carrier and light managements are important to optimize NFA molecules. Herein, four NFAs with different alkyl substituents and end groups, named BTP-C11-N2F, BTP-C9-N2F, BTP-C9-IC4F, and BTP-C9-N4F, are designed and synthesized by side-chain shortening, end-acceptor pi-extension, and fluorination. As a result, a favorable morphology is achieved in BTP-C9-N4F-based OSCs by using typical high bandgap polymer PM6 as a donor, and this system obtains the highest power conversion efficiency of 17.0% with a short circuit current (J(sc)) of 26.3 mA cm(-2), an open circuit current (V-oc) of 0.85 V, and a fill factor (FF) of 75.7%. In addition, its light (J(sc)) and charge carrier (V-oc x FF) managements relative to the Shockley-Queisser limit are also increased. Extending the conjugation of the end groups increased the energy levels of NFAs and enabled an E-loss of 0.50 eV with a nonradiative recombination loss of as low as 0.20 eV in BTP-C11-N2F-based OSCs. This work provides an efficient strategy to optimize the molecular structures of nonfullerene acceptors and further improve the properties of OSCs.
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