| 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. |
- Thompson, Luke R., et al.
(författare)
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A communal catalogue reveals Earth's multiscale microbial diversity
- 2017
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 551:7681, s. 457-463
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Tidskriftsartikel (refereegranskat)abstract
- © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
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| 3. |
- Gutierrez-Gutierrez, Belen, et al.
(författare)
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Propensity Score and Desirability of Outcome Ranking Analysis of Ertapenem for Treatment of Nonsevere Bacteremic Urinary Tract Infections Due to Extended-Spectrum-Beta-Lactamase-Producing Enterobacterales in Kidney Transplant Recipients
- 2021
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Ingår i: Antimicrobial Agents and Chemotherapy. - : American Society for Microbiology. - 0066-4804 .- 1098-6596. ; 65:11
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Tidskriftsartikel (refereegranskat)abstract
- There are scarce data on the efficacy of ertapenem in the treatment of bacteremia due to extended-spectrum-beta-lactamase (ESBL)-producing Enterobacterales (ESBL-E) in kidney transplant (KT) recipients. We evaluated the association between treatment with ertapenem or meropenem and clinical cure in KT recipients with nonsevere bacteremic urinary tract infections (B-UTI) caused by ESBL-E. We performed a registered, retrospective, international (29 centers in 14 countries) cohort study (INCREMENT-SOT, NCT02852902). The association between targeted therapy with ertapenem versus meropenem and clinical cure at day 14 (the principal outcome) was studied by logistic regression. Propensity score matching and desirability of outcome ranking (DOOR) analyses were also performed. A total of 201 patients were included; only 1 patient (treated with meropenem) in the cohort died. Clinical cure at day 14 was reached in 45/100 (45%) and 51/101 (50.5%) of patients treated with ertapenem and meropenem, respectively (adjusted OR 1.29; 95% CI 0.51 to 3.22; P = 0.76); the propensity score-matched cohort included 55 pairs (adjusted OR for clinical cure at day 14, 1.18; 95% CI 0.43 to 3.29; P = 0.74). In this cohort, the proportion of cases treated with ertapenem with better DOOR than with meropenem was 49.7% (95% CI, 40.4 to 59.1%) when hospital stay was considered. It ranged from 59 to 67% in different scenarios of a modified (weights-based) DOOR sensitivity analysis when potential ecological advantage or cost was considered in addition to outcome. In conclusion, targeted therapy with ertapenem appears as effective as meropenem to treat nonsevere B-UTI due to ESBL-E in KT recipients and may have some advantages.
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| 4. |
- Perez-Nadales, Elena, et al.
(författare)
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Predictors of mortality in solid organ transplant recipients with bloodstream infections due to carbapenemase-producing Enterobacterales : The impact of cytomegalovirus disease and lymphopenia
- 2020
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Ingår i: American Journal of Transplantation. - : WILEY. - 1600-6135 .- 1600-6143. ; 20:6, s. 1629-1641
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Tidskriftsartikel (refereegranskat)abstract
- Treatment of carbapenemase-producing Enterobacterales bloodstream infections in solid organ transplant recipients is challenging. The objective of this study was to develop a specific score to predict mortality in solid organ transplant recipients with carbapenemase-producing Enterobacterales bloodstream infections. A multinational, retrospective (2004-2016) cohort study (INCREMENT-SOT, ClinicalTrials.gov NCT02852902) was performed. The main outcome variable was 30-day all-cause mortality. The INCREMENT-SOT-CPE score was developed using logistic regression. The global cohort included 216 patients. The final logistic regression model included the following variables: INCREMENT-CPE mortality score >= 8 (8 points), no source control (3 points), inappropriate empirical therapy (2 points), cytomegalovirus disease (7 points), lymphopenia (4 points), and the interaction between INCREMENT-CPE score >= 8 and CMV disease (minus 7 points). This score showed an area under the receiver operating characteristic curve of 0.82 (95% confidence interval [CI] 0.76-0.88) and classified patients into 3 strata: 0-7 (low mortality), 8-11 (high mortality), and 12-17 (very-high mortality). We performed a stratified analysis of the effect of monotherapy vs combination therapy among 165 patients who received appropriate therapy. Monotherapy was associated with higher mortality only in the very-high (adjusted hazard ratio [HR] 2.82, 95% CI 1.13-7.06, P = .03) and high (HR 9.93, 95% CI 2.08-47.40, P = .004) mortality risk strata. A score-based algorithm is provided for therapy guidance.
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| 5. |
- Colomé, Núria, et al.
(författare)
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Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis
- 2022
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Ingår i: Journal of Proteomics. - : Elsevier. - 1874-3919 .- 1876-7737. ; 251
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Tidskriftsartikel (refereegranskat)abstract
- Global analysis of protein phosphorylation by mass spectrometry proteomic techniques has emerged in the last decades as a powerful tool in biological and biomedical research. However, there are several factors that make the global study of the phosphoproteome more challenging than measuring non-modified proteins. The low stoichiometry of the phosphorylated species and the need to retrieve residue specific information require particular attention on sample preparation, data acquisition and processing to ensure reproducibility, qualitative and quantitative robustness and ample phosphoproteome coverage in phosphoproteomic workflows. Aiming to investigate the effect of different variables in the performance of proteome wide phosphoprotein analysis protocols, ProteoRed-ISCIII and EuPA launched the Proteomics Multicentric Experiment 11 (PME11). A reference sample consisting of a yeast protein extract spiked in with different amounts of a phosphomix standard (Sigma/Merck) was distributed to 31 laboratories around the globe. Thirty-six datasets from 23 laboratories were analyzed. Our results indicate the suitability of the PME11 reference sample to benchmark and optimize phosphoproteomics strategies, weighing the influence of different factors, as well as to rank intra and inter laboratory performance.
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| 6. |
- Crespo, Alejandro J., et al.
(författare)
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On the state-of-the-art of CFD simulations for wave energy converters within the open-source numerical framework of DualSPHysics
- 2023
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Ingår i: Proceedings of the 15th European Wave and Tidal Energy Conference, Bilbao, 3-7 September 2023. - : European Wave and Tidal Energy Conference.
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Konferensbidrag (refereegranskat)abstract
- There are currently several types of devices capable of harnessing wave energy, exploiting a broad variety of physical transformation processes. These devices – known as Wave Energy Converters (WECs) – are developed to maximize their power output. However, there are still uncertainties about their response and survivability to loads induced by adverse environmental conditions, with a consequent increase of the Levelized Cost of Energy (LCOE), which prevents in fact their commercial diffusion. As evidenced by a large body of research, marine renewable energy devices need to have more robust design practices. To address this issue, we propose the CFD-based DualSPHysics toolbox as a support in the design stages. DualSPHysics is high-fidelity software inherently suited to numerically address most challenges posed by multiphysics simulations, which are required to reliably predict WEC response in situations well beyond operational conditions. It should be noted that WECs, generally, may be connected to the seabed and comprise mechanical systems named Power Take-Offs (PTO) used to convert the energy from waves into electricity or other usable energies. To reproduce these features, DualSPHysics benefits from coupling with the multiphysics library Project Chrono and the dynamic mooring model Moordyn+. In this work, the augmented DualSPHysics framework is utilised to simulate a range of very different types of WECs with a variety of elements, such as catenary connections, taut mooring lines, or linear and nonlinear PTO actuators. Version 5.2 of the open-source licensed code was recently released, making the numerical framework publicly available as one unit. This work aims to provide a numerical review of past applications, and to demonstrate how the same open-source code is able to simulate very different technologies.Specifically, this paper proposes routine modeling and validation procedures using the SPH-based solver DualSPHysics applied to five different WEC types: i) a moored point absorber (PA); ii) an oscillating wave surge converter (OWSC); iii) a floating OWSC (so called FOSWEC); iv) a wave energy hyperbaric converter (WEHC); and v) a multi-body attenuator (so called Multi-float M4). For each device listed above, we provide validation proof against physical model data for various components of the floater(s) and PTO related quantities, performed under specific sea conditions that aim to challenge their survivability. Within the scope of this research, we present the WEC response with respect to the degrees of freedom that really matter for each of the floatings due to hydrodynamic interactions (i.e., heave, surge, and pitch), along with quantities more intimately connected to the anchoring systems (e.g., line tension) or the mechanical apparatus (e.g., end-stopper force). The quality of the results, the discussion built upon them and the demonstrated solver exploitability to a wide range of WECs show that one software model can run all cases using the exact same methodology, which is of great value for the marine energy R&D community. Finally, we discuss future research objectives, which include the implementation of automation to apply open control systems and possible applications to subsets of WEC farm arrays and other floating energy harnessing devices.
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| 7. |
- de Amorim Lima, Nayane Maria, et al.
(författare)
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Light-Emitting Porphyrin Derivative Obtained from a Subproduct of the Cashew Nut Shell Liquid : A Promising Material for OLED Applications
- 2019
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Ingår i: Materials. - : MDPI. - 1996-1944. ; 12:7
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Tidskriftsartikel (refereegranskat)abstract
- In this work, the meso-tetra[4-(2-(3-n-pentadecylphenoxy)ethoxy]phenylporphyrin (H2P), obtained from the cashew nut shell liquid (CNSL), and its zinc (ZnP) and copper (CuP) metallic complexes, were applied as emitting layers in organic light emitting diodes (OLEDs). These compounds were characterized via optical and electrochemical analysis and the electroluminescent properties of the device have been studied. We performed a cyclic voltammetry analysis to determine the Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) energy levels for the porphyrins, in order to select the proper materials to assemble the device. H2P and ZnP presented fluorescence emission band in the red region, from 601 nm to 718 nm. Moreover, we verified that the introduction of bulky substituents hinders the - stacking, favoring the emission in the film. In addition, the strongest emitter, ZnP, presented a threshold voltage of 4 V and the maximum irradiance of 10 W cm(-2) with a current density (J) of 15 mA cm(-2) at 10 V. The CuP complex showed to be a favorable material for the design of OLEDs in the infrared. These results suggest that the porphyrins derived from a renewable source, such as CNSL, is a promising material to be used in organic optoelectronic devices such as OLEDs.
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