| 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. |
- Jones, Daniel O.B., et al.
(författare)
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Environment, ecology, and potential effectiveness of an area protected from deep-sea mining (Clarion Clipperton Zone, abyssal Pacific)
- 2021
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Ingår i: Progress in Oceanography. - : Elsevier BV. - 0079-6611. ; 197:September-October 2021
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Tidskriftsartikel (refereegranskat)abstract
- To protect the range of habitats, species, and ecosystem functions in the Clarion Clipperton Zone (CCZ), a region of interest for deep-sea polymetallic nodule mining in the Pacific, nine Areas of Particular Environmental Interest (APEIs) have been designated by the International Seabed Authority (ISA). The APEIs are remote, rarely visited and poorly understood. Here we present and synthesise all available observations made at APEI-6, the most north eastern APEI in the network, and assess its representativity of mining contract areas in the eastern CCZ. The two studied regions of APEI-6 have a variable morphology, typical of the CCZ, with hills, plains and occasional seamounts. The seafloor is predominantly covered by fine-grained sediments, and includes small but abundant polymetallic nodules, as well as exposed bedrock. The oceanographic parameters investigated appear broadly similar across the region although some differences in deep-water mass separation were evident between APEI-6 and some contract areas. Sediment biogeochemistry is broadly similar across the area in the parameters investigated, except for oxygen penetration depth, which reached >2 m at the study sites within APEI-6, deeper than that found at UK1 and GSR contract areas. The ecology of study sites in APEI-6 differs from that reported from UK1 and TOML-D contract areas, with differences in community composition of microbes, macrofauna, xenophyophores and metazoan megafauna. Some species were shared between areas although connectivity appears limited. We show that, from the available information, APEI-6 is partially representative of the exploration areas to the south yet is distinctly different in several key characteristics. As a result, additional APEIs may be warranted and caution may need to be taken in relying on the APEI network alone for conservation, with other management activities required to help mitigate the impacts of mining in the CCZ.
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| 3. |
- Banerjee, Ambar, 1985-, et al.
(författare)
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Accessing metal-specific orbital interactions in C–H activation with resonant inelastic X-ray scattering
- 2024
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Ingår i: Chemical Science. - : Royal Society of Chemistry. - 2041-6520 .- 2041-6539. ; 15:7, s. 2398-2409
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Tidskriftsartikel (refereegranskat)abstract
- Photochemically prepared transition-metal complexes are known to be effective at cleaving the strong C–H bonds of organic molecules in room temperature solutions. There is also ample theoretical evidence that the two-way, metal to ligand (MLCT) and ligand to metal (LMCT), charge-transfer between an incoming alkane C–H group and the transition metal is the decisive interaction in the C–H activation reaction. What is missing, however, are experimental methods to directly probe these interactions in order to reveal what determines reactivity of intermediates and the rate of the reaction. Here, using quantum chemical simulations we predict and propose future time-resolved valence-to-core resonant inelastic X-ray scattering (VtC-RIXS) experiments at the transition metal L-edge as a method to provide a full account of the evolution of metal–alkane interactions during transition-metal mediated C–H activation reactions. For the model system cyclopentadienyl rhodium dicarbonyl (CpRh(CO)2), we demonstrate, by simulating the VtC-RIXS signatures of key intermediates in the C–H activation pathway, how the Rh-centered valence-excited states accessible through VtC-RIXS directly reflect changes in donation and back-donation between the alkane C–H group and the transition metal as the reaction proceeds via those intermediates. We benchmark and validate our quantum chemical simulations against experimental steady-state measurements of CpRh(CO)2 and Rh(acac)(CO)2 (where acac is acetylacetonate). Our study constitutes the first step towards establishing VtC-RIXS as a new experimental observable for probing reactivity of C–H activation reactions. More generally, the study further motivates the use of time-resolved VtC-RIXS to follow the valence electronic structure evolution along photochemical, photoinitiated and photocatalytic reactions with transition metal complexes.
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| 4. |
- Bribiesca-Contreras, Guadalupe, et al.
(författare)
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Biogeography and Connectivity Across Habitat Types and Geographical Scales in Pacific Abyssal Scavenging Amphipods
- 2021
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Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Recently, there has been a resurgent interest in the exploration of deep-sea mineral deposits, particularly polymetallic nodules in the Clarion-Clipperton Zone (CCZ), central Pacific. Accurate environmental impact assessment is critical to the effective management of a new industry and depends on a sound understanding of species taxonomy, biogeography, and connectivity across a range of scales. Connectivity is a particularly important parameter in determining ecosystem resilience, as it helps to define the ability of a system to recover post-impact. Scavenging amphipods in the superfamilies Alicelloidea Lowry and De Broyer, 2008 and Lysianassoidea Dana, 1849 contribute to a unique and abundant scavenging community in abyssal ecosystems. They are relatively easy to sample and in recent years have become the target of several molecular and taxonomic studies, but are poorly studied in the CCZ. Here, a molecular approach is used to identify and delimit species, and to investigate evolutionary relationships of scavenging amphipods from both abyssal plain and deep (>3000 m) seamount habitats in three APEIs (Areas of Particular Environmental Interest, i.e., designated conservation areas) in the western CCZ. A total of 17 different morphospecies of scavenging amphipods were identified, which include at least 30 genetic species delimited by a fragment of the cytochrome c oxidase subunit I (COI) barcode gene. The scavenging communities sampled in the western CCZ included the most common species (Abyssorchomene gerulicorbis (Shulenberger and Barnard, 1976), A. chevreuxi (Stebbing, 1906), Paralicella caperesca Shulenberger and Barnard, 1976, and P. tenuipes Chevreux, 1908) reported for other ocean basins. Only four morphospecies, representing five genetic species, were shared between APEIs 1, 4, and 7. The two abyssal plain sites at APEIs 4 and 7 were dominated by two and three of the most common scavenging species, respectively, while the APEI 1 seamount site was dominated by two species potentially new to science that appeared to be endemic to the site. The presence of common species in all sites and high genetic diversity, yet little geographic structuring, indicate connectivity over evolutionary time scales between the areas, which span about 1500 km. Similar to recent studies, the differences in amphipod assemblages found between the seamount and abyssal sites suggest that ecological conditions on seamounts generate distinct community compositions.
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| 5. |
- Fritze, Stefan, et al.
(författare)
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Elemental distribution and fracture properties of magnetron sputtered carbon supersaturated tungsten films
- 2024
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Ingår i: Surface & Coatings Technology. - : Elsevier BV. - 0257-8972 .- 1879-3347. ; 477
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Tidskriftsartikel (refereegranskat)abstract
- The combination of strength and toughness is a major driving force for alloy design of protective coatings, and nanocrystalline tungsten (W)-alloys have shown to be promising candidates for combining strength and toughness. Here we investigate the elemental distribution and the fracture toughness of carbon (C) alloyed W thin films prepared by non-reactive magnetron sputtering. W:C films with up to ~4 at.% C crystallize in a body-centered-cubic structure with a strong 〈hh0〉texture, and no additional carbide phases are observed in the diffraction pattern. Atom probe tomography and X-ray photoelectron spectroscopy confirmed the formation of such a supersaturated solid solution. The pure W film has a hardness ~13 GPa and the W:C films exhibit a peak hardness of ~24 GPa. In-situ micromechanical cantilever bending tests show that the fracture toughness decreases from ~4.5 MPa·m1/2 for the W film to ~3.1 MPa·m1/2 for W:C films. The results show that C can significantly enhance the hardness of W thin films while retaining a high fracture toughness.
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| 6. |
- Jay, Raphael, et al.
(författare)
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Tracking C–H activation with orbital resolution
- 2023
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6648, s. 955-960
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Tidskriftsartikel (refereegranskat)abstract
- Transition metal reactivity toward carbon-hydrogen (C-H) bonds hinges on the interplay of electron donation and withdrawal at the metal center. Manipulating this reactivity in a controlled way is difficult because the hypothesized metal-alkane charge-transfer interactions are challenging to access experimentally. Using time-resolved x-ray spectroscopy, we track the charge-transfer interactions during C-H activation of octane by a cyclopentadienyl rhodium carbonyl complex. Changes in oxidation state as well as valence-orbital energies and character emerge in the data on a femtosecond to nanosecond timescale. The x-ray spectroscopic signatures reflect how alkane-to-metal donation determines metal-alkane complex stability and how metal-to-alkane back-donation facilitates C-H bond cleavage by oxidative addition. The ability to dissect charge-transfer interactions on an orbital level provides opportunities for manipulating C-H reactivity at transition metals.
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| 7. |
- Michael Ayas, Hamdy, 1994, et al.
(författare)
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An empirical investigation on the competences and roles of practitioners in Microservices-based Architectures
- 2024
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Ingår i: Journal of Systems and Software. - 0164-1212. ; 213
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Tidskriftsartikel (refereegranskat)abstract
- Microservices-based Architectures (MSAs) are gaining popularity since, among others, they enable rapid and independent delivery of software at scale, facilitating the delivery of business value. Additionally, there are attempts towards understanding practitioners’ roles and technical knowledge. MSAs call for affinity in several technologies as well as business domains. This diversity makes it challenging to scope and describe the roles of practitioners. In addition, practitioners often do not receive training and contents of MSA training remain largely undefined, even though there are challenges in finding or developing relevant technical expertise. In this research, we determine the different technical roles that are required in MSAs, along with their detailed competences. We use public online forums (e.g., StackOverflow), where developers share technical knowledge. We analyze 13,517 public profiles of software engineers, deriving their technical competences. Our taxonomy of technical competences in MSAs, contains 11 competences clusters, organized in 3 collections of competences — Web Technologies, DevOps, and Data Technologies. In addition, we derive the roles of microservice practitioners and the characteristics of their roles. Our findings organize the technical competences of MSAs practitioners and determine the training topics and combination of topics that can prepare engineers for MSAs.
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| 8. |
- Michael Ayas, Hamdy, 1994, et al.
(författare)
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An empirical study of the systemic and technical migration towards microservices
- 2023
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Ingår i: Empirical Software Engineering. - 1382-3256 .- 1573-7616. ; 28:4
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Tidskriftsartikel (refereegranskat)abstract
- ContextAs many organizations modernize their software architecture and transition to the cloud, migrations towards microservices become more popular. Even though such migrations help to achieve organizational agility and effectiveness in software development, they are also highly complex, long-running, and multi-faceted.ObjectiveIn this study we aim to comprehensively map the journey towards microservices and describe in detail what such a migration entails. In particular, we aim to discuss not only the technical migration, but also the long-term journey of change, on a systemic level.MethodOur research method is an inductive, qualitative study on two data sources. Two main methodological steps take place - interviews and analysis of discussions from StackOverflow. The analysis of both, the 19 interviews and 215 StackOverflow discussions, is based on techniques found in grounded theory.ResultsOur results depict the migration journey, as it materializes within the migrating organization, from structural changes to specific technical changes that take place in the work of engineers. We provide an overview of how microservices migrations take place as well as a deconstruction of high level modes of change to specific solution outcomes. Our theory contains 2 modes of change taking place in migration iterations, 14 activities and 53 solution outcomes of engineers. One of our findings is on the architectural change that is iterative and needs both a long and short term perspective, including both business and technical understanding. In addition, we found that a big proportion of the technical migration has to do with setting up supporting artifacts and changing the paradigm that software is developed.
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| 9. |
- Michael Ayas, Hamdy, 1994, et al.
(författare)
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The Perceived Impact and Sequence of Activities When Transitioning to Microservices
- 2023
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Ingår i: Proceedings - 17th IEEE International Conference on Service-Oriented System Engineering, SOSE 2023. ; , s. 156-160
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Konferensbidrag (refereegranskat)abstract
- Microservices migrations are often present in organizations that want to modernize and integrate their software systems. There is little empirical evidence showing how migration projects take place. Investigating migration activities and the perceived impact of migrations from practitioners is important to understand how migration projects materialize. In this study, we ask 54 practitioners about their views on specific aspects of microservices migrations. Specifically, we derive the sequence of migration activities as well as the perceived impact of microservices on the development process. Database refactoring, back-end refactoring, and setting up DevOps tend to take place before front-end refactoring, setting up communication patterns, and splitting teams. In addition, aligning teams with profitable value propositions, improving the testing process, and having fewer dependencies between teams are among the prominent impact areas of microservices. Our results call for further empirical research in understanding transitions toward MSAs.
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