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| 3. |
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| 4. |
- 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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| 5. |
- Abbasi, Rasha, et al.
(författare)
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IceCube search for neutrinos from GRB 221009A
- 2023
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Ingår i: Proceedings of 38th International Cosmic Ray Conference - PoS(ICRC 2023). - : Sissa Medialab. ; , s. 1511-
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Konferensbidrag (refereegranskat)abstract
- GRB 221009A is the brightest Gamma Ray Burst (GRB) ever observed. The observed extremelyhigh flux of high and very-high-energy photons provide a unique opportunity to probe the predictedneutrino counterpart to the electromagnetic emission. We have used a variety of methods to searchfor neutrinos in coincidence with the GRB over several time windows during the precursor, promptand afterglow phases of the GRB. MeV scale neutrinos are studied using photo-multiplier ratescalers which are normally used to search for galactic core-collapse supernovae neutrinos. GeVneutrinos are searched starting with DeepCore triggers. These events don’t have directionallocalization, but instead can indicate an excess in the rate of events. 10 GeV - 1 TeV and >TeVneutrinos are searched using traditional neutrino point source methods which take into accountthe direction and time of events with DeepCore and the entire IceCube detector respectively. The>TeV results include both a fast-response analysis conducted by IceCube in real-time with timewindows of T0 − 1 to T0 + 2 hours and T0 ± 1 day around the time of GRB 221009A, as well asan offline analysis with 3 new time windows up to a time window of T0 − 1 to T0 + 14 days, thelongest time period we consider. The combination of observations by IceCube covers 9 ordersof magnitude in neutrino energy, from MeV to PeV, placing upper limits across the range forpredicted neutrino emission.
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| 7. |
- Aad, G, et al.
(författare)
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- 2015
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swepub:Mat__t
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| 8. |
- Ayoub, Ali, et al.
(författare)
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Effect of plasticizers and polymer blends for processing softwood kraft lignin as carbon fiber precursors
- 2021
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Ingår i: Cellulose. - : Springer Science and Business Media LLC. - 0969-0239 .- 1572-882X. ; 28:2, s. 1039-1053
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Tidskriftsartikel (refereegranskat)abstract
- Plasticizers depress the glass transition temperature (T-g) of polymers and produce a flowable material at lower temperatures. The use of plasticizers to depress T-g of lignin is important, since at high processing temperatures lignin crosslinks, making it intractable. The goal of this study was to assess plasticizers and polymer blends for the ability to retard a commercial softwood kraft lignin from crosslinking and also serve as thermal and rheological property modifiers during thermal processing in the attempt to produced moldable and spinnable lignin for lignin and carbon fiber products. The T-g of the lignin and the lignin mixed with various amounts of plasticizers and with different thermo-mechanical mixing were determined using differential scanning calorimetry. The T-g and the change in heat capacity at the glass transition (Delta C-p) decreased and increased, respectively, about linearly within this plasticizers range with increased plasticizer weight percentage. Gel permeation chromatography results for extruded lignin as well as extruded lignin-plasticizer blends with glycerol, N-allyurea, citric acid with and without sodium hypophosphite, and oleic acid indicate that the presence of these materials reduced the rate of molecular weight increase at temperatures between 100 and 200 degrees C. Continuous, homogenous films and fibers could be produced by thermal processing with plasticized lignin samples and plasticized lignin-polymer blends, but not with lignin alone. These fibers could be carbonized, yielding up to about 50% of carbon. The present findings have shown the advantages of plasticizers in thermally processing a commercial softwood kraft lignin.
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| 9. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 10. |
- Cheng, Jianlin, et al.
(författare)
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Estimation of model accuracy in CASP13
- 2019
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Ingår i: Proteins. - : Wiley. - 0887-3585 .- 1097-0134. ; 87:12, s. 1361-1377
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Tidskriftsartikel (refereegranskat)abstract
- Methods to reliably estimate the accuracy of 3D models of proteins are both a fundamental part of most protein folding pipelines and important for reliable identification of the best models when multiple pipelines are used. Here, we describe the progress made from CASP12 to CASP13 in the field of estimation of model accuracy (EMA) as seen from the progress of the most successful methods in CASP13. We show small but clear progress, that is, several methods perform better than the best methods from CASP12 when tested on CASP13 EMA targets. Some progress is driven by applying deep learning and residue‐residue contacts to model accuracy prediction. We show that the best EMA methods select better models than the best servers in CASP13, but that there exists a great potential to improve this further. Also, according to the evaluation criteria based on local similarities, such as lDDT and CAD, it is now clear that single model accuracy methods perform relatively better than consensus‐based methods.
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| 11. |
- Hou, Muzhou, et al.
(författare)
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Global Solar Radiation Prediction Using Hybrid Online Sequential Extreme Learning Machine Model
- 2018
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Ingår i: Energies. - : MDPI. - 1996-1073. ; 11:12
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Tidskriftsartikel (refereegranskat)abstract
- Accurate global solar radiation prediction is highly essential for related research on renewable energy sources. The cost implication and measurement expertise of global solar radiationemphasize that intelligence prediction models need to be applied. On the basis of long-term measured daily solar radiation data, this study uses a novel regularized online sequential extreme learning machine, integrated with variable forgetting factor (FOS-ELM), to predict global solar radiation at Bur Dedougou, in the Burkina Faso region. Bayesian Information Criterion (BIC) is applied to build the seven input combinations based on speed (Wspeed), maximum and minimum temperature (Tmax and Tmin), maximum and minimum humidity (Hmax and Hmin), evaporation (Eo) and vapor pressure deficiency (VPD). For the difference input parameters magnitudes, seven models were developed and evaluated for the optimal input combination. Various statistical indicators were computed for the prediction accuracy examination. The experimental results of the applied FOS-ELM model demonstrated a reliable prediction accuracy against the classical extreme learning machine (ELM) model for daily global solar radiation simulation. In fact, compared to classical ELM, the FOS-ELM model reported an enhancement in the root mean square error (RMSE) and mean absolute error(MAE) by (68.8–79.8%). In summary, the results clearly confirm the effectiveness of the FOS-ELM model, owing to the fixed internal tuning parameters.
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| 12. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 13. |
- Keasar, Chen, et al.
(författare)
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An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
- 2018
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Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research.
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| 14. |
- 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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| 15. |
- Rehfeld, Nadine, et al.
(författare)
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Round-Robin Study for Ice Adhesion Tests
- 2024
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Ingår i: Aerospace. - : Multidisciplinary Digital Publishing Institute (MDPI). - 2226-4310. ; 11:2
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Tidskriftsartikel (refereegranskat)abstract
- Ice adhesion tests are widely used to assess the performance of potential icephobic surfaces and coatings. A great variety of test designs have been developed and used over the past decades due to the lack of formal standards for these types of tests. In many cases, the aim of the research was not only to determine ice adhesion values, but also to understand the key surface properties correlated to low ice adhesion surfaces. Data from different measurement techniques had low correspondence between the results: Values varied by orders of magnitude and showed different relative relationships to one another. This study sought to provide a broad comparison of ice adhesion testing approaches by conducting different ice adhesion tests with identical test surfaces. A total of 15 test facilities participated in this round-robin study, and the results of 13 partners are summarized in this paper. For the test series, ice types (impact and static) as well as test parameters were harmonized to minimize the deviations between the test setups. Our findings are presented in this paper, and the ice- and test-specific results are discussed. This study can improve our understanding of test results and support the standardization process for ice adhesion strength measurements.
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| 17. |
- Steele, Julian A., et al.
(författare)
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How to GIWAXS: Grazing Incidence Wide Angle X-Ray Scattering Applied to Metal Halide Perovskite Thin Films
- 2023
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Ingår i: Advanced Energy Materials. - : WILEY-V C H VERLAG GMBH. - 1614-6832 .- 1614-6840. ; 13:27
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Tidskriftsartikel (refereegranskat)abstract
- The frequency of reports utilizing synchrotron-based grazing incident wide angle X-ray scattering (GIWAXS) to study metal halide perovskite thin films has exploded recently, as this technique has proven invaluable for understanding several structure-property relationships that fundamentally limit optoelectronic performance. The GIWAXS geometry and temporal resolution are also inherently compatible with in situ and operando setups (including ISOS protocols), and a relatively large halide perovskite research community has deployed GIWAXS to unravel important kinetic and dynamic features in these materials. Considering its rising popularity, the aim here is to accelerate the required learning curve for new experimentalists by clearly detailing the underlying analytical concepts which can be leveraged to maximize GIWAXS studies of polycrystalline thin films and devices. Motivated by the vast range of measurement conditions offered, together with the wide variety of compositions and structural motifs available (i.e., from single-crystal and polycrystalline systems, to quantum dots and layered superlatices), a comprehensive framework for conducting effective GIWAXS experiments is outlined for different purposes. It is anticipated that providing a clear perspective for this topic will help elevate the quality of future GIWAXS studies-which have become routine-and provide the impetus required to develop novel GIWAXS approaches to resolve unsettled scientific questions.
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| 18. |
- Wang, Fang, et al.
(författare)
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Emerging contaminants: A One Health perspective
- 2024
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Ingår i: Innovation. - 2666-6758. ; 5
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Forskningsöversikt (refereegranskat)abstract
- Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health. Despite global efforts to mitigate legacy pollutants, the continuous introduction of new substances remains a major threat to both people and the planet. In response, global initiatives are focusing on risk assessment and regulation of emerging contaminants, as demonstrated by the ongoing efforts to establish the UN's Intergovernmental Science-Policy Panel on Chemicals, Waste, and Pollution Prevention. This review identifies the sources and impacts of emerging contaminants on planetary health, emphasizing the importance of adopting a One Health approach. Strategies for monitoring and addressing these pollutants are discussed, underscoring the need for robust and socially equitable environmental policies at both regional and international levels. Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.
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| 19. |
- Aad, G., et al.
(författare)
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- 2011
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swepub:Mat__t (refereegranskat)
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