| 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. |
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- 2019
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Journal article (peer-reviewed)
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| 4. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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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| 5. |
- Greenhalgh, David G., et al.
(author)
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Surviving Sepsis After Burn Campaign
- 2023
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In: Burns. - : Elsevier. - 0305-4179 .- 1879-1409. ; 49:7, s. 1487-1524
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Journal article (peer-reviewed)abstract
- Introduction: The Surviving Sepsis Campaign was developed to improve outcomes for all patients with sepsis. Despite sepsis being the primary cause of death after thermal injury, burns have always been excluded from the Surviving Sepsis efforts. To improve sepsis outcomes in burn patients, an international group of burn experts developed the Surviving Sepsis After Burn Campaign (SSABC) as a testable guideline to improve burn sepsis outcomes. Methods: The International Society for Burn Injuries (ISBI) reached out to regional or na-tional burn organizations to recommend members to participate in the program. Two members of the ISBI developed specific "patient/population, intervention, comparison and out-come" (PICO) questions that paralleled the 2021 Surviving Sepsis Campaign [1]. SSABC parti-cipants were asked to search the current literature and rate its quality for each topic. At the Congress of the ISBI, in Guadalajara, Mexico, August 28, 2022, a majority of the participants met to create "statements" based on the literature. The "summary statements" were then sent to all members for comment with the hope of developing an 80% consensus. After four reviews, a consensus statement for each topic was created or "no consensus" was reported. Results: The committee developed sixty statements within fourteen topics that provide guidance for the early treatment of sepsis in burn patients. These statements should be used to improve the care of sepsis in burn patients. The statements should not be considered as "static" comments but should rather be used as guidelines for future testing of the best treatments for in burn should be on a basis. Conclusion: Members of the burn community from the around the world have developed the Surviving Sepsis After Burn Campaign guidelines with the goal of improving the outcome of sepsis in burn patients. (c) 2023 Elsevier Ltd and ISBI. All rights reserved.
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| 6. |
- Lobanov, Victor P., et al.
(author)
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Sturgeon and paddlefish: Review of research on broodstock and early life stage management
- 2023
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In: Aquaculture and Fisheries. - 2096-1758 .- 2468-550X.
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Research review (peer-reviewed)abstract
- Sturgeon aquaculture has taken a parallel yet unique path relative to other teleost rearing. One of the driving factors has been the fact that virtually all extant species are facing extinction; thus, laws concerning the transport and processing of sturgeon are stringent. As a result, most sturgeon companies vertically integrate the farming process from hatchery to harvest, in contrast to the production of other commercial fish species (e.g., trout, sea bass, salmon), where farmers tend to purchase fry from producers specialized only in the production of that life stage and sell product to unaffiliated fish processors. Sturgeon aquaculture is furthermore unique in the extremely high value of the main product (caviar). The secondary product (meat) also surpasses other finfish aquaculture products' average price per weight. These expensive outputs reveal the greatest challenge in production — an exceptionally long time to market from larvae to harvestable adults. For all their rigor and robustness as juveniles and adults, sturgeon species are highly fragile during larval stages. Due to the unique legal framework around sturgeon cultivation, aquaculturists often specialize in regional species, although some hybrids have achieved global popularity. This lends to a heterogenous swath of literature on best cultivation and management practices, especially at early growth stages. Nonetheless, the role of aquaculture as both a food source and restocking program to thwart further extinction of sturgeon species has hardly been fully tapped. In light of the many challenges, this review examines recent advances in sturgeon farming with an emphasis on broodstock and early life-stage management to summarize studies that can help researchers and farmers assess the industry's current state.
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| 7. |
- Metsch, Thijs, et al.
(author)
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Apex lake : a framework for enabling smart orchestration
- 2015
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In: Proceedings of the Industry Track of the 16th ACM/IFIP/USENIX Middleware Conference. - New York, USA : Association for Computing Machinery (ACM). - 9781450337274 ; , s. 1-7
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Conference paper (peer-reviewed)abstract
- The introduction of a Software-defined infrastructures brings additional challenges to the management of cloud infrastructure. With the impending convergence of telecommunications and cloud infrastructures, datacenters become an essential part of an overall integrated environment. The potential scale of such environments has significant implications as traditional orchestration approaches cannot scale appropriately. However, the combination of infrastructure topology, fine-grained operational data and advanced analytics, has the potential to deliver a scalable approach to facilitate orchestration and resource management. In this paper we introduce Apex Lake, a framework designed to address the question of "how to efficiently define and maintain a physical and logical resource and service landscape enriched by operational data, to support orchestration for optimized service delivery?" We also demonstrate with a use-case illustrating how functionalities provided by Apex Lake can be used dealing with performance anomalies.
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| 8. |
- Pacheco, Victor
(author)
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Processing–Structure–Properties Relationship in Metal Additive Manufacturing
- 2021
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Doctoral thesis (other academic/artistic)abstract
- The last three decades have seen the transition of additive manufacturing, from applications exclusively in rapid-prototyping to an emerging production method in the manufacturing industry that is rapidly gaining more relevance. Within additive manufacturing methods, selective laser melting (SLM) is one of the most widely used and mature technologies and is the focus of this thesis. In particular, this work aims at characterizing novel microstructures and/or alloys produced with SLM and to understand how the process parameters influence the microstructure and properties.Hitherto, the most prevalent material selection approach for SLM has been the use and optimization of well-known alloys, such as steels, Ni- and Ti-based alloys, among others. Favorable microstructures are usually achieved with a combination of appropriate parameters and post-processing techniques. Another approach, especially interesting from a research perspective, is the exploration of materials and microstructures suited for the inherent characteristics of SLM. In alignment with the latter strategy, three types of materials are successfully produced and analyzed in this work: the amorphous Zr-based AMZ4 alloy, 316L stainless steel with strong preferential orientation (i.e., similar orientation of the crystalline structure of the grains) and the intermetallic MnAl(C) with strong preferential orientation. The latter contains a ferromagnetic phase with potential applications as a permanent magnet.SLM was found to be an effective method to produce the amorphous phase in the Zr59.3Cu28.8Al10.4Nb1.5 system (AMZ4). The laser power and oxygen impurities were found to have a central role in the formation of crystalline particles in the amorphous matrix. These crystalline particles and the oxygen impurities reduced the thermal stability of the alloy in comparison to specimens fabricated by suction casting. For the more conventional 316L stainless steel, it was demonstrated that the scan strategy can be used to influence the type of texture, with a notable effect on the mechanical properties. In the case of MnAl(C), it was established that the high temperature polymorph – ε-phase, can be retained during the printing process. This phase can be subsequently transformed to the ferromagnetic τ-phase with annealing procedures. It was observed that a strong preferred orientation of the ε-phase can be achieved, although it did not translate into a strong texture in the τ-phase (after the heat treatments). The research methodology used in this thesis and the findings regarding the processing–structure–properties relationship in SLM provide an important reference for future studies of novel materials and microstructures produced by additive manufacturing.
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| 9. |
- Zamora, Juan Carlos, et al.
(author)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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In: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Journal article (peer-reviewed)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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