| 1. |
- Aad, G, et al.
(författare)
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- 2015
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swepub:Mat__t
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| 2. |
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| 3. |
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| 4. |
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| 5. |
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| 6. |
- Arndt, D. S., et al.
(författare)
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STATE OF THE CLIMATE IN 2017
- 2018
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Ingår i: Bulletin of The American Meteorological Society - (BAMS). - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 99:8, s. S1-S310
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Forskningsöversikt (refereegranskat)
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| 7. |
- Abbafati, Cristiana, et al.
(författare)
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- 2020
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Tidskriftsartikel (refereegranskat)
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| 8. |
- Liu, Y., et al.
(författare)
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The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data
- 2017
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Ingår i: Glycobiology. - : Oxford University Press (OUP). - 0959-6658 .- 1460-2423. ; 27:4, s. 280-284
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Tidskriftsartikel (refereegranskat)abstract
- MIRAGE (Minimum Information Required for A Glycomics Experiment) is an initiative that was created by experts in the fields of glycobiology, glycoanalytics and glycoinformatics to produce guidelines for reporting results from the diverse types of experiments and analyses used in structural and functional studies of glycans in the scientific literature. As a sequel to the guidelines for sample preparation (Struwe et al. 2016, Glycobiology, 26: 907-910) and mass spectrometry data (Kolarich et al. 2013, Mol. Cell Proteomics, 12: 991-995), here we present the first version of guidelines intended to improve the standards for reporting data from glycan microarray analyses. For each of eight areas in the workflow of a glycan microarray experiment, we provide guidelines for the minimal information that should be provided in reporting results. We hope that the MIRAGE glycan microarray guidelines proposed here will gain broad acceptance by the community, and will facilitate interpretation and reproducibility of the glycan microarray results with implications in comparison of data from different laboratories and eventual deposition of glycan microarray data in international databases.
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| 9. |
- York, W. S., et al.
(författare)
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MIRAGE: The minimum information required for a glycomics experiment
- 2014
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Ingår i: Glycobiology. - : Oxford University Press (OUP). - 0959-6658 .- 1460-2423. ; 24:5, s. 402-406
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Tidskriftsartikel (refereegranskat)abstract
- The MIRAGE (minimum information required for a glycomics experiment) initiative was founded in Seattle, WA, in November 2011 in order to develop guidelines for reporting the qualitative and quantitative results obtained by diverse types of glycomics analyses, including the conditions and techniques that were applied to prepare the glycans for analysis and generate the primary data along with the tools and parameters that were used to process and annotate this data. These guidelines must address a broad range of issues, as glycomics data are inherently complex and are generated using diverse methods, including mass spectrometry (MS), chromatography, glycan array-binding assays, nuclear magnetic resonance (NMR) and other rapidly developing technologies. The acceptance of these guidelines by scientists conducting research on biological systems in which glycans have a significant role will facilitate the evaluation and reproduction of glycomics experiments and data that is reported in scientific journals and uploaded to glycomics databases. As a first step, MIRAGE guidelines for glycan analysis by MS have been recently published (Kolarich D, Rapp E, Struwe WB, Haslam SM, Zaia J., et al. 2013. The minimum information required for a glycomics experiment (MIRAGE) project - Improving the standards for reporting mass spectrometry-based glycoanalytic data. Mol. Cell Proteomics. 12:991-995), allowing them to be implemented and evaluated in the context of real-world glycobiology research. In this paper, we set out the historical context, organization structure and overarching objectives of the MIRAGE initiative.
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| 10. |
- Brooks, BR, et al.
(författare)
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CHARMM: the biomolecular simulation program
- 2009
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Ingår i: Journal of computational chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 30:10, s. 1545-1614
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Tidskriftsartikel (refereegranskat)
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| 11. |
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| 12. |
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| 13. |
- Campbell, Matthew P, et al.
(författare)
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Toolboxes for a standardised and systematic study of glycans
- 2014
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Ingår i: BMC Bioinformatics. - 1471-2105. ; 15:Suppl. 1
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Tidskriftsartikel (refereegranskat)abstract
- Abstract Background Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation of structure analysis then calls for software development since adding meaning to large data collections in reasonable time requires corresponding bioinformatics methods and tools. Current glycobioinformatics resources do cover information on the structure and function of glycans, their interaction with proteins or their enzymatic synthesis. However, this information is partial, scattered and often difficult to find to for non-glycobiologists. Methods Following our diagnosis of the causes of the slow development of glycobioinformatics, we review the "objective" difficulties encountered in defining adequate formats for representing complex entities and developing efficient analysis software. Results Various solutions already implemented and strategies defined to bridge glycobiology with different fields and integrate the heterogeneous glyco-related information are presented. Conclusions Despite the initial stage of our integrative efforts, this paper highlights the rapid expansion of glycomics, the validity of existing resources and the bright future of glycobioinformatics.
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| 14. |
- Cespedes, PF, et al.
(författare)
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T-cell trans-synaptic vesicles are distinct and carry greater effector content than constitutive extracellular vesicles
- 2022
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1, s. 3460-
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Tidskriftsartikel (refereegranskat)abstract
- The immunological synapse is a molecular hub that facilitates the delivery of three activation signals, namely antigen, costimulation/corepression and cytokines, from antigen-presenting cells (APC) to T cells. T cells release a fourth class of signaling entities, trans-synaptic vesicles (tSV), to mediate bidirectional communication. Here we present bead-supported lipid bilayers (BSLB) as versatile synthetic APCs to capture, characterize and advance the understanding of tSV biogenesis. Specifically, the integration of juxtacrine signals, such as CD40 and antigen, results in the adaptive tailoring and release of tSV, which differ in size, yields and immune receptor cargo compared with steadily released extracellular vesicles (EVs). Focusing on CD40L+tSV as model effectors, we show that PD-L1 trans-presentation together with TSG101, ADAM10 and CD81 are key in determining CD40L vesicular release. Lastly, we find greater RNA-binding protein and microRNA content in tSV compared with EVs, supporting the specialized role of tSV as intercellular messengers.
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| 15. |
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| 16. |
- Kessler, Richard, et al.
(författare)
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First-Year Sloan Digital Sky Survey-II Supernova Results : Hubble Diagram and Cosmological Parameters
- 2009
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Ingår i: Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 185:1, s. 32-84
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Tidskriftsartikel (refereegranskat)abstract
- We present measurements of the Hubble diagram for 103 Type Ia supernovae (SNe) with redshifts 0.04 < z < 0.42, discovered during the first season (Fall 2005) of the Sloan Digital Sky Survey-II (SDSS-II) Supernova Survey. These data fill in the redshift "desert" between low- and high-redshift SN Ia surveys. Within the framework of the MLCS2K2 light-curve fitting method, we use the SDSS-II SN sample to infer the mean reddening parameter for host galaxies, RV = 2.18 ± 0.14stat ± 0.48syst, and find that the intrinsic distribution of host-galaxy extinction is well fitted by an exponential function, P(AV ) = exp(-AV /τV), with τV = 0.334 ± 0.088 mag. We combine the SDSS-II measurements with new distance estimates for published SN data from the ESSENCE survey, the Supernova Legacy Survey (SNLS), the Hubble Space Telescope (HST), and a compilation of Nearby SN Ia measurements. A new feature in our analysis is the use of detailed Monte Carlo simulations of all surveys to account for selection biases, including those from spectroscopic targeting. Combining the SN Hubble diagram with measurements of baryon acoustic oscillations from the SDSS Luminous Red Galaxy sample and with cosmic microwave background temperature anisotropy measurements from the Wilkinson Microwave Anisotropy Probe, we estimate the cosmological parameters w and ΩM, assuming a spatially flat cosmological model (FwCDM) with constant dark energy equation of state parameter, w. We also consider constraints upon ΩM and ΩΛ for a cosmological constant model (ΛCDM) with w = -1 and non-zero spatial curvature. For the FwCDM model and the combined sample of 288 SNe Ia, we find w = -0.76 ± 0.07(stat) ± 0.11(syst), ΩM = 0.307 ± 0.019(stat) ± 0.023(syst) using MLCS2K2 and w = -0.96 ± 0.06(stat) ± 0.12(syst), ΩM = 0.265 ± 0.016(stat) ± 0.025(syst) using the SALT-II fitter. We trace the discrepancy between these results to a difference in the rest-frame UV model combined with a different luminosity correction from color variations; these differences mostly affect the distance estimates for the SNLS and HST SNe. We present detailed discussions of systematic errors for both light-curve methods and find that they both show data-model discrepancies in rest-frame U band. For the SALT-II approach, we also see strong evidence for redshift-dependence of the color-luminosity parameter (β). Restricting the analysis to the 136 SNe Ia in the Nearby+SDSS-II samples, we find much better agreement between the two analysis methods but with larger uncertainties: w = -0.92 ± 0.13(stat)+0.10 -0.33(syst) for MLCS2K2 and w = -0.92 ± 0.11(stat)+0.07 -0.15 (syst) for SALT-II.
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| 17. |
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| 18. |
- Struwe, Weston B, et al.
(författare)
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The minimum information required for a glycomics experiment (MIRAGE) project: sample preparation guidelines for reliable reporting of glycomics datasets.
- 2016
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Ingår i: Glycobiology. - : Oxford University Press (OUP). - 1460-2423 .- 0959-6658. ; 26:9, s. 907-910
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Tidskriftsartikel (refereegranskat)abstract
- Theminimum information required for a glycomics experiment (MIRAGE) project was established in 2011 to provide guidelines to aid in data reporting from all types of experiments in glycomics research including mass spectrometry (MS), liquid chromatography, glycan arrays, data handling and sample preparation. MIRAGE is a concerted effort of the wider glycomics community that considers the adaptation of reporting guidelines as an important step towards critical evaluation and dissemination of datasets as well as broadening of experimental techniques worldwide. The MIRAGE Commission published reporting guidelines for MS data and here we outline guidelines for sample preparation. The sample preparation guidelines include all aspects of sample generation, purification and modification from biological and/or synthetic carbohydrate material. The application of MIRAGE sample preparation guidelines will lead to improved recording of experimental protocols and reporting of understandable and reproducible glycomics datasets.
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| 19. |
- van Bon, L., et al.
(författare)
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Distinct evolution of TLR-mediated dendritic cell cytokine secretion in patients with limited and diffuse cutaneous systemic sclerosis
- 2010
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Ingår i: Annals of the Rheumatic Diseases. - : BMJ. - 1468-2060 .- 0003-4967. ; 69:8, s. 1539-1547
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Tidskriftsartikel (refereegranskat)abstract
- Background Systemic sclerosis (SSc) is an autoimmune disease and accumulating evidence suggests a role for Toll-like receptor (TLR)-mediated activation of dendritic cells (DCs). Objective To map TLR-mediated cytokine responses of DCs from patients with SSc. Methods 45 patients with SSc were included. Patients were stratified as having diffuse cutaneous SSc (dSSc) or limited cutaneous SSc (lSSc) according to the extent of skin involvement, and further divided into those with late (> 3 years) or early disease (< 2 years). DCs were stimulated with ligands for TLR2, TLR3, TLR4, TLR7/8 or combinations. Plasma samples were collected from patients with SSc (n = 167) and measured for interleukin 6 (IL-6), tumour necrosis factor a (TNF alpha), IL-12, IL-10 and interferon gamma. Results Stimulation of DC subsets from patients with early lSSc and dSSc with ligands for TLR2, TLR3 or TLR4 resulted in higher secretion of IL-6 and TNF alpha compared with those having late disease or healthy controls. Remarkably, the production of IL-12 was lower upon stimulation with TLR ligands in most patients with SSc, whereas the secretion of IL-10 was very high in patients with the dSSc phenotype, particularly in those having early dSSc. The combination of various TLR ligands led to reduced cytokine secretion in all patients with SSc. Circulating levels of these cytokines further underscored the presence of differences between various SSc phenotypes. Discussion The altered TLR-mediated activation of DCs may be responsible for Th2 skewed T-cell activation in SSc that may be orchestrated by fibrogenic T-cell cytokines, such as IL-4 and IL-13. DC targeting could thus offer new avenues for therapeutic intervention.
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| 20. |
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| 21. |
- Winter-Vann, A. M., et al.
(författare)
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A small-molecule inhibitor of isoprenylcysteine carboxyl methyltransferase with antitumor activity in cancer cells
- 2005
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Ingår i: Proc Natl Acad Sci U S A. ; 102:12, s. 4336-4341
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Tidskriftsartikel (refereegranskat)abstract
- Many key regulatory proteins, including members of the Ras family of GTPases, are modified at their C terminus by a process termed prenylation. This processing is initiated by the addition of an isoprenoid lipid, and the proteins are further modified by a proteolytic event and methylation of the C-terminal prenylcysteine. Although the biological consequences of prenylation have been characterized extensively, the contributions of prenylcysteine methylation to the functions of the modified proteins are not well understood. This reaction is catalyzed by the enzyme isoprenylcysteine carboxyl methyltransferase (Icmt). Recent genetic disruption studies have provided strong evidence that blocking Icmt activity has profound consequences on oncogenic transformation. Here, we report the identification of a selective small-molecule inhibitor of Icmt, 2-[5-(3-methylphenyl)-1-octyl-1H-indol-3-yl]acetamide (cysmethynil). Cysmethynil treatment results in inhibition of cell growth in an Icmt-dependent fashion, demonstrating mechanism-based activity of the compound. Treatment of cancer cells with cysmethynil results in mislocalization of Ras and impaired epidermal growth factor signaling. In a human colon cancer cell line, cysmethynil treatment blocks anchorage-independent growth, and this effect is reversed by overexpression of Icmt. These findings provide a compelling rationale for development of Icmt inhibitors as another approach to anticancer drug development.
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| 22. |
- Barbieri, L, et al.
(författare)
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Two-dimensional TIRF-SIM-traction force microscopy (2D TIRF-SIM-TFM)
- 2021
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1, s. 2169-
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Tidskriftsartikel (refereegranskat)abstract
- Quantifying small, rapidly evolving forces generated by cells is a major challenge for the understanding of biomechanics and mechanobiology in health and disease. Traction force microscopy remains one of the most broadly applied force probing technologies but typically restricts itself to slow events over seconds and micron-scale displacements. Here, we improve >2-fold spatially and >10-fold temporally the resolution of planar cellular force probing compared to its related conventional modalities by combining fast two-dimensional total internal reflection fluorescence super-resolution structured illumination microscopy and traction force microscopy. This live-cell 2D TIRF-SIM-TFM methodology offers a combination of spatio-temporal resolution enhancement relevant to forces on the nano- and sub-second scales, opening up new aspects of mechanobiology to analysis.
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| 23. |
- Flynn, Alison B., et al.
(författare)
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Future Directions for Systems Thinking in Chemistry Education : Putting the Pieces Together
- 2019
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Ingår i: Journal of Chemical Education. - : AMER CHEMICAL SOC. - 0021-9584 .- 1938-1328. ; 96:12, s. 3000-3005
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Tidskriftsartikel (refereegranskat)abstract
- The International Union of Pure & Applied Chemistry (IUPAC) launched a global project in 2017 to infuse systems thinking into chemistry education, motivated in part by the desire to help equip chemists and citizens to better address the complex, global challenges our society currently faces. One important early outcome of the IUPAC Systems Thinking in Chemistry Education (STICE) project is this special issue of the Journal of Chemical Education, which provides a key reference point for the rapidly emerging literature on the incorporation of systems thinking into chemistry education, including its application to green and sustainable chemistry. The STICE project outcomes to date include reviewing systems thinking approaches in other STEM fields, articulating a framework for STICE, identifying aspects of learning theories relevant to learning systems thinking skills in chemistry, using systems thinking approaches to integrate green and sustainability chemistry concepts into university-level chemistry classrooms, and identifying considerations for assessing systems thinking in chemistry education. The authors of this article, who, with others, have provided leadership to the STICE project, conclude this Journal's special issue by briefly reviewing progress to date and identifying three main areas of future work for the application of systems thinking in chemistry education: (1) developing systems thinking resources for chemistry educators and students, (2) identifying chemistry education research needed to investigate and improve systems thinking approaches, and (3) investigating opportunities to apply chemistry-related systems thinking approaches in broader educational contexts. Our intention is to recommend potential opportunities, stimulate conversations, and motivate actions required to successfully equip learners with systems thinking skills in chemistry, such that these learners, citizens of our countries and our planet, are better positioned to interpret and address complex global challenges.
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| 24. |
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| 25. |
- Longo, Stefano, et al.
(författare)
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Sociology for sustainability science
- 2021
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Ingår i: Discover Sustainability. - : Springer Science and Business Media LLC. - 2662-9984. ; 2
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Tidskriftsartikel (refereegranskat)abstract
- Sociological insights are often underutilized in sustainability science. To further strengthen its commitment to interdisciplinary problem-driven, solutions-oriented research, sustainability science can better incorporate fundamental sociological conceptions into its core. We highlight four aspects of sociological thought that we consider crucial for advancing sustainability science research: (1) social construction and critical realism, (2) structure and agency, (3) historical specificity, and (4) collective action. We draw on examples from sociology to support a dynamic understanding of how social relations interact with the bio-geo-physical world. This necessary integration of sociological insights, we argue, is critical to generate comprehensive assessments of the causes and consequences of human-induced environmental change, and tend to be overlooked or oversimplified within the field of sustainability science. Beyond that, it can stimulate the development and implementation of viable solutions to sustainability challenges.
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| 26. |
- Longo, Stefano, 1969, et al.
(författare)
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Sociology for sustainability science
- 2021
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Ingår i: Discover Sustainability. - : Springer Science and Business Media LLC. - 2662-9984. ; 2
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Tidskriftsartikel (refereegranskat)abstract
- Sociological insights are often underutilized in sustainability science. To further strengthen its commitment to interdisciplinary problem-driven, solutions-oriented research, sustainability science can better incorporate fundamental sociological conceptions into its core. We highlight four aspects of sociological thought that we consider crucial for advancing sustainability science research: (1) social construction and critical realism, (2) structure and agency, (3) historical specificity, and (4) collective action. We draw on examples from sociology to support a dynamic understanding of how social relations interact with the bio-geo-physical world. This necessary integration of sociological insights, we argue, is critical to generate comprehensive assessments of the causes and consequences of human-induced environmental change, and tend to be overlooked or oversimplified within the field of sustainability science. Beyond that, it can stimulate the development and implementation of viable solutions to sustainability challenges.
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| 27. |
- McKee, Lauren, 1985-, et al.
(författare)
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Introducing endo-xylanase activity into an exo-acting arabinofuranosidase that targets side chains
- 2012
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : NATIONAL ACADEMY OF SCIENCES. - 0027-8424 .- 1091-6490. ; 109:17
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Tidskriftsartikel (refereegranskat)abstract
- The degradation of the plant cell wall by glycoside hydrolases is central to environmentally sustainable industries. The major polysaccharides of the plant cell wall are cellulose and xylan, a highly decorated beta-1,4-xylopyranose polymer. Glycoside hydrolases displaying multiple catalytic functions may simplify the enzymes required to degrade plant cell walls, increasing the industrial potential of these composite structures. Here we test the hypothesis that glycoside hydrolase family 43 (GH43) provides a suitable scaffold for introducing additional catalytic functions into enzymes that target complex structures in the plant cell wall. We report the crystal structure of Humicola insolens AXHd3 (HiAXHd3), a GH43 arabinofuranosidase that hydrolyses O3-linked arabinose of doubly substituted xylans, a feature of the polysaccharide that is recalcitrant to degradation. HiAXHd3 displays an N-terminal five-bladed beta-propeller domain and a C-terminal beta-sandwich domain. The interface between the domains comprises a xylan binding cleft that houses the active site pocket. Substrate specificity is conferred by a shallow arabinose binding pocket adjacent to the deep active site pocket, and through the orientation of the xylan backbone. Modification of the rim of the active site introduces endo-xylanase activity, whereas the resultant enzyme variant, Y166A, retains arabinofuranosidase activity. These data show that the active site of HiAXHd3 is tuned to hydrolyse arabinofuranosyl or xylosyl linkages, and it is the topology of the distal regions of the substrate binding surface that confers specificity. This report demonstrates that GH43 provides a platform for generating bespoke multifunctional enzymes that target industrially significant complex substrates, exemplified by the plant cell wall.
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| 28. |
- Truvé, Katarina, et al.
(författare)
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Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development-Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus
- 2016
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Ingår i: Plos Genetics. - : Public Library of Science (PLoS). - 1553-7404 .- 1553-7390. ; 12:5
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Tidskriftsartikel (refereegranskat)abstract
- Gliomas are the most common form of malignant primary brain tumors in humans and second most common in dogs, occurring with similar frequencies in both species. Dogs are valuable spontaneous models of human complex diseases including cancers and may provide insight into disease susceptibility and oncogenesis. Several brachycephalic breeds such as Boxer, Bulldog and Boston Terrier have an elevated risk of developing glioma, but others, including Pug and Pekingese, are not at higher risk. To identify glioma-associated genetic susceptibility factors, an across-breed genome-wide association study (GWAS) was performed on 39 dog glioma cases and 141 controls from 25 dog breeds, identifying a genome-wide significant locus on canine chromosome (CFA) 26 (p = 2.8 x 10(-8)). Targeted re-sequencing of the 3.4 Mb candidate region was performed, followed by genotyping of the 56 SNVs that best fit the association pattern between the re-sequenced cases and controls. We identified three candidate genes that were highly associated with glioma susceptibility: CAMKK2, P2RX7 and DENR. CAMKK2 showed reduced expression in both canine and human brain tumors, and a non-synonymous variant in P2RX7, previously demonstrated to have a 50% decrease in receptor function, was also associated with disease. Thus, one or more of these genes appear to affect glioma susceptibility.
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| 31. |
- York, A. M., et al.
(författare)
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Household bottled water consumption in Phoneix : a lifestyle choice
- 2011
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Ingår i: Water international. - : Informa UK Limited. - 0250-8060 .- 1941-1707. ; 36:6, s. 708-718
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Tidskriftsartikel (refereegranskat)abstract
- The demand for bottled water has grown tremendously in recent years, together with concern about its environmental impacts. The authors surveyed individuals in Phoenix, Arizona about their water consumption behaviour, socio-demographic characteristics, perception of water quality and trust in the government's willingness to respond to water quality issues. Using a logit model, the authors then tested the relationship between the respondents' characteristics and bottled water consumption for cooking and drinking in the home. Our results indicate that bottled water consumption reflects lifestyle choice not environmental concerns.
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