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- 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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- Ojo, Kayode K, et al.
(författare)
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Transmission of malaria to mosquitoes blocked by bumped kinase inhibitors
- 2012
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Ingår i: Journal of Clinical Investigation. - : American Society for Clinical Investigation. - 0021-9738 .- 1558-8238. ; 122:6, s. 2301-2305
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Tidskriftsartikel (refereegranskat)abstract
- Effective control and eradication of malaria will require new tools to prevent transmission. Current antimalarial therapies targeting the asexual stage of Plasmodium do not prevent transmission of circulating gametocytes from infected humans to mosquitoes. Here, we describe a new class of transmission-blocking compounds, bumped kinase inhibitors (BKIs), which inhibit microgametocyte exflagellation. Oocyst formation and sporozoite production, necessary for transmission to mammals, were inhibited in mosquitoes fed on either BKI-1-treated human blood or mice treated with BKI-1. BKIs are hypothesized to act via inhibition of Plasmodium calcium-dependent protein kinase 4 and predicted to have little activity against mammalian kinases. Our data show that BKIs do not inhibit proliferation of mammalian cell lines and are well tolerated in mice. Used in combination with drugs active against asexual stages of Plasmodium, BKIs could prove an important tool for malaria control and eradication.
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- Bakke, PS, et al.
(författare)
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Recommendations for epidemiological studies on COPD
- 2011
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Ingår i: European Respiratory Journal. - : European Respiratory Society (ERS). - 1399-3003 .- 0903-1936. ; 38:6, s. 1261-1277
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Tidskriftsartikel (refereegranskat)abstract
- The prevalence of chronic obstructive pulmonary disease (COPD) has been extensively studied, especially in Western Europe and North America. Few of these data are directly comparable because of differences between the surveys regarding composition of study populations, diagnostic criteria of the disease and definitions of the risk factors. Few community studies have examined phenotypes of COPD and included other ways of characterising the disease beyond that of spirometry. The objective of the present Task Force report is to present recommendations for the performance of general population studies in COPD in order to facilitate comparable and valid estimates on COPD prevalence by various risk factors. Diagnostic criteria in epidemiological settings, and standardised methods to examine the disease and its potential risk factors are discussed. The paper also offers practical advice for planning and performing an epidemiological study on COPD. The main message of the paper is that thorough planning is worth half the study. It is crucial to stick to standardised methods and good quality control during sampling. We recommend collecting biological markers, depending on the specific objectives of the study. Finally, studies of COPD in the population at large should assess various phenotypes of the disease
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- Hiller, D., et al.
(författare)
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Absence of quantum confinement effects in the photoluminescence of Si3N4-embedded Si nanocrystals
- 2014
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Ingår i: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 115:20, s. 204301-
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Tidskriftsartikel (refereegranskat)abstract
- Superlattices of Si-rich silicon nitride and Si3N4 are prepared by plasma-enhanced chemical vapor deposition and, subsequently, annealed at 1150 degrees C to form size-controlled Si nanocrystals (Si NCs) embedded in amorphous Si3N4. Despite well defined structural properties, photoluminescence spectroscopy (PL) reveals inconsistencies with the typically applied model of quantum confined excitons in nitride-embedded Si NCs. Time-resolved PL measurements demonstrate 10(5) times faster time-constants than typical for the indirect band structure of Si NCs. Furthermore, a pure Si3N4 reference sample exhibits a similar PL peak as the Si NC samples. The origin of this luminescence is discussed in detail on the basis of radiative defects and Si3N4 band tail states in combination with optical absorption measurements. The apparent absence of PL from the Si NCs is explained conclusively using electron spin resonance data from the Si/Si3N4 interface defect literature. In addition, the role of Si3N4 valence band tail states as potential hole traps is discussed. Most strikingly, the PL peak blueshift with decreasing NC size, which is often observed in literature and typically attributed to quantum confinement (QC), is identified as optical artifact by transfer matrix method simulations of the PL spectra. Finally, criteria for a critical examination of a potential QC-related origin of the PL from Si3N4-embedded Si NCs are suggested.
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- Marto, João Pedro, et al.
(författare)
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Safety and Outcome of Revascularization Treatment in Patients With Acute Ischemic Stroke and COVID-19: The Global COVID-19 Stroke Registry.
- 2023
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Ingår i: Neurology. - 1526-632X. ; 100:7
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Tidskriftsartikel (refereegranskat)abstract
- COVID-19-related inflammation, endothelial dysfunction, and coagulopathy may increase the bleeding risk and lower the efficacy of revascularization treatments in patients with acute ischemic stroke (AIS). We aimed to evaluate the safety and outcomes of revascularization treatments in patients with AIS and COVID-19.This was a retrospective multicenter cohort study of consecutive patients with AIS receiving intravenous thrombolysis (IVT) and/or endovascular treatment (EVT) between March 2020 and June 2021 tested for severe acute respiratory syndrome coronavirus 2 infection. With a doubly robust model combining propensity score weighting and multivariate regression, we studied the association of COVID-19 with intracranial bleeding complications and clinical outcomes. Subgroup analyses were performed according to treatment groups (IVT-only and EVT).Of a total of 15,128 included patients from 105 centers, 853 (5.6%) were diagnosed with COVID-19; of those, 5,848 (38.7%) patients received IVT-only and 9,280 (61.3%) EVT (with or without IVT). Patients with COVID-19 had a higher rate of symptomatic intracerebral hemorrhage (SICH) (adjusted OR 1.53; 95% CI 1.16-2.01), symptomatic subarachnoid hemorrhage (SSAH) (OR 1.80; 95% CI 1.20-2.69), SICH and/or SSAH combined (OR 1.56; 95% CI 1.23-1.99), 24-hour mortality (OR 2.47; 95% CI 1.58-3.86), and 3-month mortality (OR 1.88; 95% CI 1.52-2.33). Patients with COVID-19 also had an unfavorable shift in the distribution of the modified Rankin score at 3 months (OR 1.42; 95% CI 1.26-1.60).Patients with AIS and COVID-19 showed higher rates of intracranial bleeding complications and worse clinical outcomes after revascularization treatments than contemporaneous non-COVID-19 patients receiving treatment. Current available data do not allow direct conclusions to be drawn on the effectiveness of revascularization treatments in patients with COVID-19 or to establish different treatment recommendations in this subgroup of patients with ischemic stroke. Our findings can be taken into consideration for treatment decisions, patient monitoring, and establishing prognosis.The study was registered under ClinicalTrials.gov identifier NCT04895462.
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- F., Durmo, et al.
(författare)
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Mutlimodality MR imaging for differentiation between brain tumor lesions
- 2016
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Ingår i: Neuroradiology. - : Springer Science and Business Media LLC. - 0028-3940 .- 1432-1920. ; 58:Suppl 1, s. 53-54
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Konferensbidrag (refereegranskat)abstract
- Purpose: Applying diffusion and perfusion metrics for evaluation of low-(LGG), high grade glioma (HGG) and metastases (MET) for differential diagnosis. Materials and Method: 43 patients (18HGG, 10 LGG, and 15MET) were included. MR data for tumour volume, perilesional edema, rCBF-, rCBV-, FLAIR-, FA-, ADC-maps were quantified by regions of interest (ROI). Measures of different parameters, and ratios, using contralateral white matter as denominator, were performed. A binary logistic regression model was constructed for multi-parametric analysis and ROCanalysis. Results: Significant difference was found for nADCt, rCBF, rCBV between LGG and HGG, nADCe between HGG and MET, and Ev, Ev-Tv ratio, nADCt, nADCe, rCBF, rCBV between LGG and MET. ROCanalysis for HGG compared to LGG showed 80 % sensitivity and 81.2 % specificity for nADCt, 100 % sensitivity and 100 % specificity for rCBF and 80 % sensitivity and 90 % specificity for rCBV. ROC-curves betweenMETand LGG showed sensitivity and specificity for Ev 73.3 % and 90 %, Ev-Tv ratio 80 % and 100 %, nADCt 90 % and 86.7 %, nADCe 80 % and 90 %, rCBF 93.3 % and 100 %, and rCBV 60 % and 100 %. Combining Ev, Ev-Tv ratio, nADCt, nADCe and rCBV between METand LGG gave 93.3%sensitivity and 100%specificity. Combining nADCt and rCBV between HGG and LGG 86.7 % sensitivity and 100 % specificity. Conclusion: Multi-parametric imaging protocols is an advantage for preoperative distinction of LGG, HGG and MET.
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- Vasefi, Fartash, et al.
(författare)
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Multimode optical dermoscopy (SkinSpect) analysis for skin with melanocytic nevus
- 2016
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Ingår i: Proceedings Volume 9711, Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues IX; 971110 (2016). - : SPIE - International Society for Optical Engineering.
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Konferensbidrag (refereegranskat)abstract
- We have developed a multimode dermoscope (SkinSpect™) capable of illuminating human skin samples in-vivo with spectrally-programmable linearly-polarized light at 33 wavelengths between 468nm and 857 nm. Diffusely reflected photons are separated into collinear and cross-polarized image paths and images captured for each illumination wavelength. In vivo human skin nevi (N = 20) were evaluated with the multimode dermoscope and melanin and hemoglobin concentrations were compared with Spatially Modulated Quantitative Spectroscopy (SMoQS) measurements. Both systems show low correlation between their melanin and hemoglobin concentrations, demonstrating the ability of the SkinSpect™ to separate these molecular signatures and thus act as a biologically plausible device capable of early onset melanoma detection.
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- Vasefi, Fartash, et al.
(författare)
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Separating melanin from hemodynamics in nevi using multimode hyperspectral dermoscopy and spatial frequency domain spectroscopy
- 2016
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Ingår i: Journal of Biomedical Optics. - : SPIE - International Society for Optical Engineering. - 1083-3668 .- 1560-2281. ; 21:11
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Tidskriftsartikel (refereegranskat)abstract
- Changes in the pattern and distribution of both melanocytes (pigment producing) and vasculature (hemoglobin containing) are important in distinguishing melanocytic proliferations. The ability to accurately measure melanin distribution at different depths and to distinguish it from hemoglobin is clearly important when assessing pigmented lesions (benign versus malignant). We have developed a multimode hyperspectral dermoscope (SkinSpect™) able to more accurately image both melanin and hemoglobin distribution in skin. SkinSpect uses both hyperspectral and polarization-sensitive measurements. SkinSpect’s higher accuracy has been obtained by correcting for the effect of melanin absorption on hemoglobin absorption in measurements of melanocytic nevi. In vivo human skin pigmented nevi (N=20) were evaluated with the SkinSpect, and measured melanin and hemoglobin concentrations were compared with spatial frequency domain spectroscopy (SFDS) measurements. We confirm that both systems show low correlation of hemoglobin concentrations with regions containing different melanin concentrations (R=0.13 for SFDS, R=0.07 for SkinSpect).
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