| 1. |
- Huttenhain, Ruth, et al.
(författare)
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A targeted mass spectrometry strategy for developing proteomic biomarkers : a case study of epithelial ovarian cancer
- 2019
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Ingår i: Molecular and Cellular Proteomics. - 1535-9484. ; 18:9, s. 1836-1850
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Tidskriftsartikel (refereegranskat)abstract
- Protein biomarkers for epithelial ovarian cancer are critical for the early detection of the cancer to improve patient prognosis and for the clinical management of the disease to monitor treatment response and to detect recurrences. Unfortunately, the discovery of protein biomarkers is hampered by the limited availability of reliable and sensitive assays needed for the reproducible quantification of proteins in complex biological matrices such as blood plasma. In recent years, targeted mass spectrometry, exemplified by Selected Reaction Monitoring (SRM) has emerged as a method, capable of overcoming this limitation. Here, we present a comprehensive SRM-based strategy for developing plasma-based protein biomarkers for epithelial ovarian cancer and illustrate how the SRM platform, when combined with rigorous experimental design and statistical analysis, can result in detection of predictive analytes.Our biomarker development strategy first involved a discovery-driven proteomic effort to derive potential N-glycoprotein biomarker candidates for plasma-based detection of human ovarian cancer from a genetically engineered mouse model of endometrioid ovarian cancer, which accurately recapitulates the human disease. Next, 65 candidate markers selected from proteins of different abundance in the discovery dataset were reproducibly quantified with SRM assays across a large cohort of over 200 plasma samples from ovarian cancer patients and healthy controls. Finally, these measurements were used to derive a 5-protein signature for distinguishing individuals with epithelial ovarian cancer from healthy controls. The sensitivity of the candidate biomarker signature in combination with CA125 ELISA-based measurements currently used in clinic, exceeded that of CA125 ELISA-based measurements alone. The SRM-based strategy in this study is broadly applicable. It can be used in any study that requires accurate and reproducible quantification of selected proteins in a high-throughput and multiplexed fashion.
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| 2. |
- Abelev, Betty, et al.
(författare)
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Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV
- 2012
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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :11
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Tidskriftsartikel (refereegranskat)abstract
- The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
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| 3. |
- Abelev, Betty, et al.
(författare)
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Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC
- 2012
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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :7
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Tidskriftsartikel (refereegranskat)abstract
- We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
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| 4. |
- Becker, Kathrin, et al.
(författare)
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Dental care during COVID-19 pandemic : survey of experts' opinion.
- 2020
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Ingår i: Clinical Oral Implants Research. - : John Wiley & Sons. - 0905-7161 .- 1600-0501. ; 31:12, s. 1253-1260
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: The current COVID-19 outbreak in conjunction with the need to provide safe dental treatments, and the limited knowledge on the efficacy of protective measures has posed dentists into a challenging situation. Therefore, the present article aimed at collecting experiences and recommendations of front-line clinical experts on critical aspects of dental treatment provision during pandemic.MATERIAL & METHODS: , 2020.RESULTS: A total of 27 experts from different European countries completed the survey. The transmission risk of SARS-CoV-2 in dental settings for aerosol generating procedures was considered high by all experts except two. For aerosol-free and aerosol generating procedures, more than 80% of the experts recommended face protection and caps for every single treatment. For aerosol-generating procedures, additional measures (FFP2/FFP3 masks and gowns) were suggested by the vast majority of the experts. To reduce transmission risk, all experts recommended limiting aerosol-generating procedures and reducing the number of patients in waiting areas as well as hand hygiene for the patients.CONCLUSION: The limitation of aerosol-generating procedures along with the usage of adequate personal protection equipment was considered to be crucial to protect dental health care providers and patients, thus reducing the transmission risk of COVID-19.
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| 5. |
- Brunello, Giulia, et al.
(författare)
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Dental care during COVID-19 pandemic : follow-up survey of experts' opinion
- 2021
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Ingår i: Clinical Oral Implants Research. - : John Wiley & Sons. - 0905-7161 .- 1600-0501. ; 32:S21, s. 342-352
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: The purpose of the present survey is to give an update of European experts' opinion on infection control and prevention in dentistry during second wave of pandemic. The secondary aim was to analyse how experts' opinion changed in the light of the new scientific evidence since the first wave.MATERIAL & METHODS: An anonymous online 14-item questionnaire was sent to a total of 27 leading academic experts in Oral (and Maxillofacial) Surgery from different European countries, who had completed a previous survey in April-May 2020. The questionnaire covered the topics of dental setting safety, personal protective equipment (PPE), and patient-related measures to minimise transmission risk. Data collection took place in November-February 2020/21.RESULTS: 26 experts participated in the follow-up survey. The overall transmission risk in dental settings was scored significantly lower compared to the initial survey (P<0.05), though the risk associated with aerosol generating procedures (AGP) was still considered to be high. Maximum PPE was less frequently recommended for non-AGP (P<0.05), whereas the majority of experts still recommended FFP2/FFP3 masks (80.8%), face shields or goggles (88.5%), gowns (61.5%), and caps (57.7%) for AGP. Most of the experts also found mouth rinse relevant (73.1%) and reported to be using it prior to treatment (76.9%). No uniform opinion was found regarding the relevance of COVID-19 testing of staff and patients.CONCLUSION: With the continuation of dental care provision, transmission risk has been scored lower compared to the first wave of pandemic. However, high risk is still assumed for AGP, and maximum PPE remained advised for the respective treatments.
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| 6. |
- Godoy, Patricio, et al.
(författare)
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Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME
- 2013
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Ingår i: Archives of Toxicology. - : Springer Science and Business Media LLC. - 0340-5761 .- 1432-0738. ; 87:8, s. 1315-1530
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Forskningsöversikt (refereegranskat)abstract
- This review encompasses the most important advances in liver functions and hepatotoxicity and analyzes which mechanisms can be studied in vitro. In a complex architecture of nested, zonated lobules, the liver consists of approximately 80 % hepatocytes and 20 % non-parenchymal cells, the latter being involved in a secondary phase that may dramatically aggravate the initial damage. Hepatotoxicity, as well as hepatic metabolism, is controlled by a set of nuclear receptors (including PXR, CAR, HNF-4 alpha, FXR, LXR, SHP, VDR and PPAR) and signaling pathways. When isolating liver cells, some pathways are activated, e.g., the RAS/MEK/ERK pathway, whereas others are silenced (e.g. HNF-4 alpha), resulting in up- and downregulation of hundreds of genes. An understanding of these changes is crucial for a correct interpretation of in vitro data. The possibilities and limitations of the most useful liver in vitro systems are summarized, including three-dimensional culture techniques, co-cultures with non-parenchymal cells, hepatospheres, precision cut liver slices and the isolated perfused liver. Also discussed is how closely hepatoma, stem cell and iPS cell-derived hepatocyte-like-cells resemble real hepatocytes. Finally, a summary is given of the state of the art of liver in vitro and mathematical modeling systems that are currently used in the pharmaceutical industry with an emphasis on drug metabolism, prediction of clearance, drug interaction, transporter studies and hepatotoxicity. One key message is that despite our enthusiasm for in vitro systems, we must never lose sight of the in vivo situation. Although hepatocytes have been isolated for decades, the hunt for relevant alternative systems has only just begun.
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| 7. |
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| 8. |
- Ludewig, Kristin, et al.
(författare)
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Phenology and morphology of the invasive legume Lupinus polyphyllus along a latitudinal gradient in Europe
- 2022
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Ingår i: NeoBiota. - : Pensoft Publishers. - 1619-0033 .- 1314-2488. ; 78
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Tidskriftsartikel (refereegranskat)abstract
- Plant phenology, i. e. the timing of life cycle events, is related to individual fitness and species distributionranges. Temperature is one of the most important drivers of plant phenology together with day length.The adaptation of their phenology may be important for the success of invasive plant species. The presentstudy aims at understanding how the performance and the phenology of the invasive legume Lupinuspolyphyllus vary with latitude. We sampled data across a >2000 km latitudinal gradient from Centralto Northern Europe. We quantified variation in phenology of flowering and fruiting of L. polyphyllususing >1600 digital photos of inflorescences from 220 individual plants observed weekly at 22 sites. Theday of the year at which different phenological phases were reached, increased 1.3–1.8 days per degreelatitude, whereas the growing degree days (gdd) required for these phenological phases decreased 5–16 gddper degree latitude. However, this difference disappeared, when the day length of each day included inthe calculation of gdd was considered. The day of the year of the earliest and the latest climatic zone toreach any of the three studied phenological phases differed by 23–30 days and temperature requirementsto reach these stages differed between 62 and 236 gdd. Probably, the invasion of this species will furtherincrease in the northern part of Europe over the next decades due to climate warming. For invasive speciescontrol, our results suggest that in countries with a large latitudinal extent, the mowing date should shiftby ca. one week per 500 km at sites with similar elevations.
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| 9. |
- Ludewig, Kristin, et al.
(författare)
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Phenology of Lupinus polyphyllus from Central to Northern Europe
- 2022
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Annan publikationabstract
- Plant phenology, i. e. the timing of life cycle events, is related to individual fitness and species distribution ranges. Among the environmental factors, phenology is mostly driven by temperature and day length. Rapid adaptation of their phenology may also be important for the success of invasive plant species. Our main aim was to understand how the performance, timing, and temperature dependence of the phenology of the invasive legume Lupinus polyphyllus varies with latitude. L. polyphyllus is one of the most frequent invasive species in Europe, and the gained information may help to make management more effective by adjustments to latitude and phenology.Methods:We quantified variation in phenology across a >2000 km latitudinal gradient from Central to Northern Europe. We sampled data of flowering and fruiting of L. polyphyllus using >1600 digital photos of inflorescences from 220 individual plants observed weekly at 22 locations. We calculated the accumulated growing degree days for each observation date at each site from the temperature data of the meteorological stations, which are listed in the metadata of the dataset.
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| 10. |
- Reid, Cameron J, et al.
(författare)
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A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58
- 2022
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Escherichia coli ST58 has recently emerged as a globally disseminated uropathogen that often progresses to sepsis. Unlike most pandemic extra-intestinal pathogenic E. coli (ExPEC), which belong to pathogenic phylogroup B2, ST58 belongs to the environmental/commensal phylogroup B1. Here, we present a pan-genomic analysis of a global collection of 752 ST58 isolates from diverse sources. We identify a large ST58 sub-lineage characterized by near ubiquitous carriage of ColV plasmids, which carry genes encoding virulence factors, and by a distinct accessory genome including genes typical of the Yersiniabactin High Pathogenicity Island. This sub-lineage includes three-quarters of all ExPEC sequences in our study and has a broad host range, although poultry and porcine sources predominate. By contrast, strains isolated from cattle often lack ColV plasmids. Our data indicate that ColV plasmid acquisition contributed to the divergence of the major ST58 sub-lineage, and different sub-lineages inhabit poultry, swine and cattle.
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| 11. |
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| 12. |
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| 13. |
- Schwarz, Frank, et al.
(författare)
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Efficacy of air polishing for the non-surgical treatment of peri-implant diseases : a systematic review
- 2015
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Ingår i: Journal of Clinical Periodontology. - : John Wiley & Sons. - 0303-6979 .- 1600-051X. ; 42:10, s. 951-959
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Forskningsöversikt (refereegranskat)abstract
- Focused Question: In patients suffering from peri-implant diseases, what is the efficacy of air polishing on changing signs of inflammation compared with control treatments (i.e. alternative measures for plaque removal with or without adjunctive antiseptic and/or antibiotic therapy)? Material & Methods: After electronic database and hand search, 10 full-text articles were independently screened by two reviewers. Finally, a total of five studies (six publications) fulfilled the inclusion criteria. The weighted mean difference (WMD) [p; 95% CI] in bleeding on probing-(BOP) (primary outcome) and probing pocket depth-(PD) reductions was estimated using a random effect model. Results: All studies reported on residual BOP scores after therapy. A narrative data synthesis did not reveal any major improvement of bleeding index/BOP or disease resolution following air polishing over mechanical debridement at mucositis sites. At peri-implantitis sites, WMD in BOP reduction between test and control (mechanical debridement with or without local antiseptic therapy, Er:YAG laser) groups was -23.83% [p = 0.048; 95% CI (-47.47, -0.20)] favouring air polishing over control measures. Conclusions: While glycine powder air polishing is as effective as the control treatments at mucositis sites, it may improve the efficacy of non-surgical treatment of peri-implantitis over the control measures investigated. A complete disease resolution was commonly not obtained.
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| 14. |
- Schwarz, Frank, et al.
(författare)
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Recommendations on the clinical application of air polishing for the management of peri-implant mucositis and peri-implantitis
- 2016
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Ingår i: Quintessence International. - : Quintessence Publishing Company. - 0033-6572 .- 1936-7163. ; 47:4, s. 293-296
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Tidskriftsartikel (refereegranskat)abstract
- Air polishing was introduced as an alternative approach for the supra- and submucosal biofilm management at dental implants. An international expert meeting involving competent clinicians and researchers took place during the EUROPERIO 8 conference in London, UK, on 4 June 2015. Prior to this meeting a comprehensive systematic review dealing with the efficacy of air polishing in the treatment of peri-implant mucositis and peri-implantitis was prepared and served as a basis for the group discussions. This paper summarizes the consensus statements and practical recommendations on the clinical application of air polishing for the management of peri-implant mucositis and peri-implantitis.
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