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| 2. |
- Agirre, Jon, et al.
(författare)
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The CCP4 suite: integrative software for macromolecular crystallography
- 2023
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Ingår i: Acta Crystallographica Section D. - : INT UNION CRYSTALLOGRAPHY. - 2059-7983. ; 79, s. 449-461
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Tidskriftsartikel (refereegranskat)abstract
- The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.
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| 3. |
- 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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| 4. |
- Ferrando, Carlos, et al.
(författare)
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Effects of oxygen on post-surgical infections during an individualised perioperative open-lung ventilatory strategy : a randomised controlled trial
- 2020
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Ingår i: British Journal of Anaesthesia. - : ELSEVIER SCI LTD. - 0007-0912 .- 1471-6771. ; 124:1, s. 110-120
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Tidskriftsartikel (refereegranskat)abstract
- Background: We aimed to examine whether using a high fraction of inspired oxygen (FIO2) in the context of an individualised intra- and postoperative open-lung ventilation approach could decrease surgical site infection (SSI) in patients scheduled for abdominal surgery. Methods: We performed a multicentre, randomised controlled clinical trial in a network of 21 university hospitals from June 6, 2017 to July 19, 2018. Patients undergoing abdominal surgery were randomly assigned to receive a high (0.80) or conventional (0.3) FIO2 during the intraoperative period and during the first 3 postoperative hours. All patients were mechanically ventilated with an open-lung strategy, which included recruitment manoeuvres and individualised positive end-expiratory pressure for the best respiratory-system compliance, and individualised continuous postoperative airway pressure for adequate peripheral oxyhaemoglobin saturation. The primary outcome was the prevalence of SSI within the first 7 postoperative days. The secondary outcomes were composites of systemic complications, length of intensive care and hospital stay, and 6-month mortality. Results: We enrolled 740 subjects: 371 in the high FIO2 group and 369 in the low FIO2 group. Data from 717 subjects were available for final analysis. The rate of SSI during the first postoperative week did not differ between high (8.9%) and low (9.4%) FIO2 groups (relative risk [RR]: 0.94; 95% confidence interval [CI]: 0.59-1.50; P=0.90]). Secondary outcomes, such as atelectasis (7.7% vs 9.8%; RR: 0.77; 95% CI: 0.48-1.25; P=0.38) and myocardial ischaemia (0.6% [n=2] vs 0% [n=0]; P=0.47) did not differ between groups. Conclusions: An oxygenation strategy using high FIO2 compared with conventional FIO2 did not reduce postoperative SSIs in abdominal surgery. No differences in secondary outcomes or adverse events were found.
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| 5. |
- Megido, Loerto, et al.
(författare)
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Understanding and utilizing the biomolecule/nanosystems interface: Soft materials and coatings for controlled drug release
- 2017
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Ingår i: Nanotechnologies in Preventive and Regenerative Medicine: An Emerging Big Picture. - 9780323480642 ; , s. 244-260
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Combining biomolecules with materials used in medicine allows for local control of the biological response and can be used for modulating the host immune response, a major challenge in the efficacy of many medical devices. In Subchapter 3.1, we will review different methods used to attach biomolecules to materials, focusing on protein conjugation methods. We will begin by describing noncovalent immobilization strategies, including encapsulation within biomaterials and adsorption to material surfaces. We will then discuss strategies to covalently attach biomolecules to materials via the use of specific functional groups, thus enhancing the stability of the interaction. Finally, we will describe emerging methods to site specifically immobilize biomolecules to materials such that proteins are presented in an oriented manner, improving their overall functionality. Throughout the subchapter, we will emphasize the advantages and disadvantages of each technique, successes achieved, as well as the challenges remaining in this growing field.During last years, increasing development of nanoparticles as targeted drug delivery agents, has led to a wide amount of studies involving their characterization to the application as novel therapeutic agents. Hence, the nanoparticles interact with biological environments when they enter in the human body, and then proteins bind to the nanomaterial surface forming the protein corona. Protein corona has a great relevance in the interaction and function of the nanoparticle-drug conjugates. In fact, its characterization is one of the main challenges for nanoscience development. Herein, it is reviewed the main proteomic methods described for quantify and qualify the protein corona formed around nanoparticles to better understand the process of interaction with the biological media, and to decipher key parameters to control the effects of the protein corona.In Subchapter 3.3, the structure and working principles of coatings for controlled drug release in oral drug administration are presented. The release mechanisms, including diffusion, dissolution, osmotic pumping, and swelling are described. The soft materials used in the majority of controlled drug release formulations are natural and synthetic polymers. They are presented here and examples of specific polymers applied in controlled release formulations are provided. There is also a section containing characterization of soft materials using in situ electron microscopy for studying water transport through coatings at high-spatial resolution. The reason for this is that the detailed properties and release mechanisms of the controlled release depend on the material nanostructure. The in situ characterization gives access not only the information about the nanostructure but also the direct correlation between structure and properties on different length scales. Finally, an overview of the present major challenges and future possibilities concerning controlled drug release formulations is presented.Targeting cancer cells with functional nanoprobes possessing a targeting drug unit and an imaging moiety carries great potential for early detection, accurate diagnosis, and targeted therapy of various diseases. Given their nanoscopic dimensions, ultrasmall particles ( < 100nm) are in general well suited for interactions with the cells; however, the current challenge of the nanomedicine is to transform inorganic nanoparticles of metals (e.g., gold) or metal oxide (e.g., magnetite) into signal-generating vectors. Engineered nanostructures can act as vehicles for a large number of signaling centers and/or targeting units thereby offering unique opportunity to enhance the sensitivity by locally enhancing the density of signal groups. For this purpose, creation of surface groups enabling chemical attachment of antibodies or other targeting biomolecules are essential that will allow the delivery of therapeutic payloads to the diseased sites. Multimodal nanoprobes functionalized with different diagnostic and therapeutic options within a single nanoparticle followed by their functionalization with organic ligands and biomolecules can provide specific uptake and high sensitivity toward anatomical information. However, the vision of making clinical theranostics a routine clinical procedure is encumbered by limited stability of complex nanoparticles in biological milieu and lack of standardization of therapy response. Despite the widely acclaimed advantages of integrating diagnostic imaging, drug delivery, and therapeutic monitoring in a single nanotheranostic probe, the clinical utilization of engineered nanoprobes demands concerted efforts in the domains of nanoparticle and surface chemistry/charge, new chelator ligands, pharmaceutical technology, radioactive labeling of nanovectors, biokinetics, and pharmacodynamics of nanoprobes, and biological tests (cell tests and animal models).
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| 6. |
- Vialas, Vital, et al.
(författare)
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A multicentric study to evaluate the use of relative retention times in targeted proteomics
- 2017
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Ingår i: Journal of Proteomics. - : Elsevier BV. - 1874-3919. ; 152, s. 138-149
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Tidskriftsartikel (refereegranskat)abstract
- Despite the maturity reached by targeted proteomic strategies, reliable and standardized protocols are urgently needed to enhance reproducibility among different laboratories and analytical platforms, facilitating a more widespread use in biomedical research. To achieve this goal, the use of dimensionless relative retention times (iRT), defined on the basis of peptide standard retention times (RT), has lately emerged as a powerful tool. The robustness, reproducibility and utility of this strategy were examined for the first time in a multicentric setting, involving 28 laboratories that included 24 of the Spanish network of proteomics laboratories (ProteoRed-ISCIII). According to the results obtained in this study, dimensionless retention time values (iRTs) demonstrated to be a useful tool for transferring and sharing peptide retention times across different chromatographic set-ups both intra- and inter-laboratories. iRT values also showed very low variability over long time periods. Furthermore, parallel quantitative analyses showed a high reproducibility despite the variety of experimental strategies used, either MRM (multiple reaction monitoring) or pseudoMRM, and the diversity of analytical platforms employed. Biological significance From the very beginning of proteomics as an analytical science there has been a growing interest in developing standardized methods and experimental procedures in order to ensure the highest quality and reproducibility of the results. In this regard, the recent (2012) introduction of the dimensionless retention time concept has been a significant advance. In our multicentric (28 laboratories) study we explore the usefulness of this concept in the context of a targeted proteomics experiment, demonstrating that dimensionless retention time values is a useful tool for transferring and sharing peptide retention times across different chromatographic set-ups.
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