| 1. |
- Cossarizza, A., et al.
(författare)
-
Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)
- 2019
-
Ingår i: European Journal of Immunology. - : Wiley. - 0014-2980 .- 1521-4141. ; 49:10, s. 1457-1973
-
Tidskriftsartikel (refereegranskat)abstract
- These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer-reviewed by leading experts in the field, making this an essential research companion.
|
|
| 2. |
|
|
| 3. |
|
|
| 4. |
- Polymeris, A. A., et al.
(författare)
-
Intravenous thrombolysis for suspected ischemic stroke with seizure at onset
- 2019
-
Ingår i: Annals of Neurology. - : Wiley. - 0364-5134 .- 1531-8249. ; 86:5, s. 770-779
-
Tidskriftsartikel (refereegranskat)abstract
- Objective Seizure at onset (SaO) has been considered a relative contraindication for intravenous thrombolysis (IVT) in patients with acute ischemic stroke, although this appraisal is not evidence based. Here, we investigated the prognostic significance of SaO in patients treated with IVT for suspected ischemic stroke. Methods In this multicenter, IVT-registry-based study we assessed the association between SaO and symptomatic intracranial hemorrhage (sICH, European Cooperative Acute Stroke Study II definition), 3-month mortality, and 3-month functional outcome on the modified Rankin Scale (mRS) using unadjusted and adjusted logistic regression, coarsened exact matching, and inverse probability weighted analyses. Results Among 10,074 IVT-treated patients, 146 (1.5%) had SaO. SaO patients had significantly higher National Institutes of Health Stroke Scale score and glucose on admission, and more often female sex, prior stroke, and prior functional dependence than non-SaO patients. In unadjusted analysis, they had generally less favorable outcomes. After controlling for confounders in adjusted, matched, and weighted analyses, all associations between SaO and any of the outcomes disappeared, including sICH (odds ratio [OR](unadjusted) = 1.53 [95% confidence interval (CI) = 0.74-3.14], ORadjusted = 0.52 [95% CI = 0.13-2.16], ORmatched = 0.68 [95% CI = 0.15-3.03], ORweighted = 0.95 [95% CI = 0.39-2.32]), mortality (ORunadjusted = 1.49 [95% CI = 1.00-2.24], ORadjusted = 0.98 [95% CI = 0.5-1.92], ORmatched = 1.13 [95% CI = 0.55-2.33], ORweighted = 1.17 [95% CI = 0.73-1.88]), and functional outcome (mRS >= 3/ordinal mRS: ORunadjusted = 1.33 [95% CI = 0.96-1.84]/1.35 [95% CI = 1.01-1.81], ORadjusted = 0.78 [95% CI = 0.45-1.32]/0.78 [95% CI = 0.52-1.16], ORmatched = 0.75 [95% CI = 0.43-1.32]/0.45 [95% CI = 0.10-2.06], ORweighted = 0.87 [95% CI = 0.57-1.34]/1.00 [95% CI = 0.66-1.52]). These results were consistent regardless of whether patients had an eventual diagnosis of ischemic stroke (89/146) or stroke mimic (57/146 SaO patients). Interpretation SaO was not an independent predictor of poor prognosis. Withholding IVT from patients with assumed ischemic stroke presenting with SaO seems unjustified. ANN NEUROL 2019
|
|
| 5. |
- Falk, H., et al.
(författare)
-
TACLeBench : A benchmark collection to support worst-case execution time research
- 2016
-
Ingår i: OpenAccess Series in Informatics. - 9783959770255 ; , s. 2.1-2.10
-
Konferensbidrag (refereegranskat)abstract
- Engineering related research, such as research on worst-case execution time, uses experimentation to evaluate ideas. For these experiments we need example programs. Furthermore, to make the research experimentation repeatable those programs shall be made publicly available. We collected open-source programs, adapted them to a common coding style, and provide the collection in open-source. The benchmark collection is called TACLeBench and is available from GitHub in version 1.9 at the publication date of this paper. One of the main features of TACLeBench is that all programs are self-contained without any dependencies on standard libraries or an operating system.
|
|
| 6. |
- Tulstrup, M., et al.
(författare)
-
NT5C2 germline variants alter thiopurine metabolism and are associated with acquired NT5C2 relapse mutations in childhood acute lymphoblastic leukaemia
- 2018
-
Ingår i: Leukemia. - : Springer Science and Business Media LLC. - 0887-6924 .- 1476-5551. ; 32:12, s. 2527-2535
-
Tidskriftsartikel (refereegranskat)abstract
- The antileukaemic drug 6-mercaptopurine is converted into thioguanine nucleotides (TGN) and incorporated into DNA (DNA-TG), the active end metabolite. In a series of genome-wide association studies, we analysed time-weighted means ((wm)) of erythrocyte concentrations of TGN (Ery-TGN) and DNA-TG in 1009 patients undergoing maintenance therapy for acute lymphoblastic leukaemia (ALL). In discovery analyses (454 patients), the propensity for DNA-TG incorporation ((wm)DNA-TG/(wm)Ery-TGN ratio) was significantly associated with three intronic SNPs in NT5C2 (top hit: rs72846714; P - 2.09 x 10(-10), minor allele frequency 15%). In validation analyses (555 patients), this association remained significant during both early and late maintenance therapy (P - 8.4 x 10(-6) and 1.3 x 10(-3), respectively). The association was mostly driven by differences in (wm)Ery-TGN, but in regression analyses adjusted for wmEry-TGN (P < 0.0001), rs72846714-A genotype was also associated with a higher (wm)DNA-TG (P - 0.029). Targeted sequencing of NT5C2 did not identify any missense variants associated with rs72846714 or (wm)Ery-TGN/(wm)DNA-TG. rs72846714 was not associated with relapse risk, but in a separate cohort of 180 children with relapsed ALL, rs72846714-A genotype was associated with increased occurrence of relapse-specific NT5C2 gain-of-function mutations that reduce cytosol TGN levels (P = 0.03). These observations highlight the impact of both germline and acquired mutations in drug metabolism and disease trajectory.
|
|
| 7. |
- Kaminski, M., et al.
(författare)
-
Investigation of the beta-pinene photooxidation by OH in the atmosphere simulation chamber SAPHIR
- 2017
-
Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 17:11, s. 6631-6650
-
Tidskriftsartikel (refereegranskat)abstract
- Besides isoprene, monoterpenes are the nonmethane volatile organic compounds (VOCs) with the highest global emission rates. Due to their high reactivity towards OH, monoterpenes can dominate the radical chemistry of the atmosphere in forested areas. In the present study the photochemical degradation mechanism of beta-pinene was investigated in the Julich atmosphere simulation chamber SAPHIR (Simulation of Atmospheric PHotochemistry In a large Reaction Chamber). One focus of this study is on the OH budget in the degradation process. Therefore, the SAPHIR chamber was equipped with instrumentation to measure radicals (OH, HO2, RO2), the total OH reactivity, important OH precursors (O-3, HONO, HCHO), the parent VOC beta-pinene, its main oxidation products, acetone and nopinone and photolysis frequencies. All experiments were carried out under low-NO conditions (<= 300 ppt) and at atmospheric beta-pinene concentrations (<= 5 ppb) with and without addition of ozone. For the investigation of the OH budget, the OH production and destruction rates were calculated from measured quantities. Within the limits of accuracy of the instruments, the OH budget was balanced in all beta-pinene oxidation experiments. However, even though the OH budget was closed, simulation results from the Master Chemical Mechanism (MCM) 3.2 showed that the OH production and destruction rates were underestimated by the model. The measured OH and HO2 concentrations were underestimated by up to a factor of 2, whereas the total OH reactivity was slightly overestimated because the model predicted a nopinone mixing ratio which was 3 times higher than measured. A new, theory-derived, first-generation product distribution by Vereecken and Peeters (2012) was able to reproduce the measured nopinone time series and the total OH reactivity. Nevertheless, the measured OH and HO2 concentrations remained underestimated by the numerical simulations. These observations together with the fact that the measured OH budget was closed suggest the existence of unaccounted sources of HO2. Although the mechanism of additional HO2 formation could not be resolved, our model studies suggest that an activated alkoxy radical intermediate proposed in the model of Vereecken and Peeters (2012) generates HO2 in a new pathway, whose importance has been underestimated so far. The proposed reaction path involves unimolecular rearrangement and decomposition reactions and photolysis of dicarbonyl products, yielding additional HO2 and CO. Further experiments and quantum chemical calculations have to be made to completely unravel the pathway of HO2 formation.
|
|
| 8. |
- Novelli, A., et al.
(författare)
-
Evaluation of OH and HO2 concentrations and their budgets during photooxidation of 2-methyl-3-butene-2-ol (MBO) in the atmospheric simulation chamber SAPHIR
- 2018
-
Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 18:15, s. 11409-11422
-
Tidskriftsartikel (refereegranskat)abstract
- Several previous field studies have reported unexpectedly large concentrations of hydroxyl and hydroperoxyl radicals (OH and HO2, respectively) in forested environments that could not be explained by the traditional oxidation mechanisms that largely underestimated the observations. These environments were characterized by large concentrations of biogenic volatile organic compounds (BVOC) and low nitrogen oxide concentration. In isoprene-dominated environments, models developed to simulate atmospheric photochemistry generally underestimated the observed OH radical concentrations. In contrast, HO2 radical concentration showed large discrepancies with model simulations mainly in non-isoprene-dominated forested environments. An abundant BVOC emitted by lodgepole and ponderosa pines is 2-methyl- 3-butene-2-ol (MBO), observed in large concentrations for studies where the HO2 concentration was poorly described by model simulations. In this work, the photooxidation of MBO by OH was investigated for NO concentrations lower than 200 pptv in the atmospheric simulation chamber SAPHIR at Forschungszentrum Julich. Measurements of OH and HO2 radicals, OH reactivity (kO(H)), MBO, OH precursors, and organic products (acetone and formaldehyde) were used to test our current understanding of the OH-oxidation mechanisms for MBO by comparing measurements with model calculations. All the measured trace gases agreed well with the model results (within 15 %) indicating a well understood mechanism for the MBO oxidation by OH. Therefore, the oxidation of MBO cannot contribute to reconciling the unexplained high OH and HO2 radical concentrations found in previous field studies.
|
|
| 9. |
- Rolletter, M., et al.
(författare)
-
Investigation of the alpha-pinene photooxidation by OH in the atmospheric simulation chamber SAPHIR
- 2019
-
Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 19:18, s. 11635-11649
-
Tidskriftsartikel (refereegranskat)abstract
- The photooxidation of the most abundant monoterpene, alpha-pinene, by the hydroxyl radical (OH) was investigated at atmospheric concentrations in the atmospheric simulation chamber SAPHIR. Concentrations of nitric oxide (NO) were below 120 pptv. Yields of organic oxidation products are determined from measured time series giving values of 0.11 +/- 0.05, 0.19 +/- 0.06, and 0.05 +/- 0.03 for formaldehyde, acetone, and pinonaldehyde, respectively. The pinonaldehyde yield is at the low side of yields measured in previous laboratory studies, ranging from 0.06 to 0.87. These studies were mostly performed at reactant concentrations much higher than observed in the atmosphere. Time series of measured radical and trace-gas concentrations are compared to results from model calculations applying the Master Chemical Mechanism (MCM) 3.3.1. The model predicts pinonaldehyde mixing ratios that are at least a factor of 4 higher than measured values. At the same time, modeled hydroxyl and hydroperoxy (HO2) radical concentrations are approximately 25 % lower than measured values. Vereecken et al. (2007) suggested a shift of the initial organic peroxy radical (RO2) distribution towards RO2 species that do not yield pinonaldehyde but produce other organic products. Implementing these modifications reduces the model-measurement gap of pinonaldehyde by 20 % and also improves the agreement in modeled and measured radical concentrations by 10 %. However, the chemical oxidation mechanism needs further adjustment to explain observed radical and pinonaldehyde concentrations. This could be achieved by adjusting the initial RO2 distribution, but could also be done by implementing alternative reaction channels of RO2 species that currently lead to the formation of pinonaldehyde in the model.
|
|
