| 11. |
- De Marchi, Tommaso, et al.
(författare)
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Proteogenomic Workflow Reveals Molecular Phenotypes Related to Breast Cancer Mammographic Appearance
- 2021
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 20:5, s. 2983-3001
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Tidskriftsartikel (refereegranskat)abstract
- Proteogenomic approaches have enabled the generat̲ion of novel information levels when compared to single omics studies although burdened by extensive experimental efforts. Here, we improved a data-independent acquisition mass spectrometry proteogenomic workflow to reveal distinct molecular features related to mammographic appearances in breast cancer. Our results reveal splicing processes detectable at the protein level and highlight quantitation and pathway complementarity between RNA and protein data. Furthermore, we confirm previously detected enrichments of molecular pathways associated with estrogen receptor-dependent activity and provide novel evidence of epithelial-to-mesenchymal activity in mammography-detected spiculated tumors. Several transcript-protein pairs displayed radically different abundances depending on the overall clinical properties of the tumor. These results demonstrate that there are differentially regulated protein networks in clinically relevant tumor subgroups, which in turn alter both cancer biology and the abundance of biomarker candidates and drug targets.
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| 12. |
- De Marchi, Tommaso, et al.
(författare)
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Proteogenomics decodes the evolution of human ipsilateral breast cancer
- 2023
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Ipsilateral breast tumor recurrence (IBTR) is a clinically important event, where an isolated in-breast recurrence is a potentially curable event but associated with an increased risk of distant metastasis and breast cancer death. It remains unclear if IBTRs are associated with molecular changes that can be explored as a resource for precision medicine strategies. Here, we employed proteogenomics to analyze a cohort of 27 primary breast cancers and their matched IBTRs to define proteogenomic determinants of molecular tumor evolution. Our analyses revealed a relationship between hormonal receptors status and proliferation levels resulting in the gain of somatic mutations and copy number. This in turn re-programmed the transcriptome and proteome towards a highly replicating and genomically unstable IBTRs, possibly enhanced by APOBEC3B. In order to investigate the origins of IBTRs, a second analysis that included primaries with no recurrence pinpointed proliferation and immune infiltration as predictive of IBTR. In conclusion, our study shows that breast tumors evolve into different IBTRs depending on hormonal status and proliferation and that immune cell infiltration and Ki-67 are significantly elevated in primary tumors that develop IBTR. These results can serve as a starting point to explore markers to predict IBTR formation and stratify patients for adjuvant therapy.
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| 13. |
- Dima, Elijs, et al.
(författare)
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LIFE: A Flexible Testbed For Light Field Evaluation
- 2018
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Konferensbidrag (refereegranskat)abstract
- Recording and imaging the 3D world has led to the use of light fields. Capturing, distributing and presenting light field data is challenging, and requires an evaluation platform. We define a framework for real-time processing, and present the design and implementation of a light field evaluation system. In order to serve as a testbed, the system is designed to be flexible, scalable, and able to model various end-to-end light field systems. This flexibility is achieved by encapsulating processes and devices in discrete framework systems. The modular capture system supports multiple camera types, general-purpose data processing, and streaming to network interfaces. The cloud system allows for parallel transcoding and distribution of streams. The presentation system encapsulates rendering and display specifics. The real-time ability was tested in a latency measurement; the capture and presentation systems process and stream frames within a 40 ms limit.
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| 14. |
- Durcik, Martina, et al.
(författare)
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New Dual Inhibitors of Bacterial Topoisomerases with Broad-Spectrum Antibacterial Activity and In Vivo Efficacy against Vancomycin-Intermediate Staphylococcus aureus
- 2023
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Ingår i: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 66:6, s. 3968-3994
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Tidskriftsartikel (refereegranskat)abstract
- A new series of dual low nanomolar benzothiazole inhibitors of bacterial DNA gyrase and topoisomerase IV were developed. The resulting compounds show excellent broad-spectrum antibacterial activities against Gram-positive Enterococcus faecalis, Enterococcus faecium and multidrug resistant (MDR) Staphylococcus aureus strains [best compound minimal inhibitory concentrations (MICs): range, <0.03125–0.25 μg/mL] and against the Gram-negatives Acinetobacter baumannii and Klebsiella pneumoniae (best compound MICs: range, 1–4 μg/mL). Lead compound 7a was identified with favorable solubility and plasma protein binding, good metabolic stability, selectivity for bacterial topoisomerases, and no toxicity issues. The crystal structure of 7a in complex with Pseudomonas aeruginosa GyrB24 revealed its binding mode at the ATP-binding site. Expanded profiling of 7a and 7h showed potent antibacterial activity against over 100 MDR and non-MDR strains of A. baumannii and several other Gram-positive and Gram-negative strains. Ultimately, in vivo efficacy of 7a in a mouse model of vancomycin-intermediate S. aureus thigh infection was also demonstrated.
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| 15. |
- Eklundh, Lars, et al.
(författare)
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Analysing vegetation changes in the Sahel using sensor data from Landsat and NOAA
- 2005
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Konferensbidrag (refereegranskat)abstract
- The semi-arid Sahel zone of Africa has suffered several periods of severe drought since about 1950. We have analyzed AVHRR Normalized Difference Vegetation Index (NDVI) over the Sahel for the period 1982-2002, and found extensive areas of increasing NDVI. To verify these changes we have analyzed Landsat TM and ETM+ scenes from 1984-1986 and 1999-2001 for areas in the Sudan, Central African Republic, Niger, Mali and Mauritania. Changes in the Landsat data were analysed by visual interpretation and change vector analysis. In areas of positive AVHRR NDVI change the analysis of Landsat data generally showed a transition from barren or sparse vegetation to a denser vegetation cover. Rainfall had increased over the course of time in several of these areas. In some areas visual interpretation indicated an expansion of agricultural land.
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| 16. |
- Eklundh, Lars, et al.
(författare)
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High resolution mapping of vegetation dynamics from Sentinel-2
- 2012
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Ingår i: Proceedings of 1st Sentinel-2 Preparatory Symposium. - 0379-6566. - 9789290922711 ; 707 SP
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Konferensbidrag (refereegranskat)abstract
- The aim of this work is to develop and test a method for generation of information on vegetation dynamics from high-spatial resolution data, such as Sentinel-2. In order to accomplish this, Sentinel-2 data were simulated from existing SPOT HRG and HRVIR scenes over Sweden. We used TIMESAT, a well-tested computer package for generating smooth seasonal profiles and generation of seasonality parameters, like start and end, length, amplitude, integrated values, seasonal maximum, derivatives, etc. The processing works on a pixel-by-pixel basis and is resistant to clouds and noise. Data gaps are handled, and quality information can be included to increase the fidelity of the fits. The pilot study demonstrated that TIMESAT was successful in fitting smooth model functions to the data, and generating seasonality parameters for the test area at 10 × 10 m resolution. We conclude that TIMESAT will be useful for generating vegetation dynamics data from high-spatial resolution data such as Sentinel-2. The smooth seasonal profiles will be extremely useful for driving high-resolution biophysical vegetation models, and the seasonality parameters will be excellent for change detection, and for studying trends in vegetation productivity and seasonality.
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| 17. |
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| 18. |
- Eriksson, Mikael, et al.
(författare)
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The MAX IV Facility
- 2013
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Ingår i: 11th International Conference on Synchrotron Radiation Instrumentation (SRI 2012). - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 425
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Konferensbidrag (refereegranskat)abstract
- The MAX IV synchrotron radiation facility is currently being constructed in Lund, Sweden. The accelerator park consists of a 3 GeV linac injector and 2 storage rings operated at 1.5 and 3 GeV respectively. The linac injector will also be used for the generation of short Xray pulses. Close to 30 straight sections will be available for IDs at the rings. The three machines mentioned above are described below with some emphasis on the effort to create a very small emittance in the 3 GeV ring. Some unconventional technical solutions imposed by the emittance minimisation are discussed.
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| 19. |
- Eriksson, Mikael, et al.
(författare)
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The MAX IV Synchrotron Light Source
- 2011
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Ingår i: [Host publication title missing]. - 9789290833666 ; , s. 3026-3028
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Konferensbidrag (refereegranskat)abstract
- The MAX IV synchrotron radiation facility is currently being constructed in Lund, Sweden. It consists of a 3 GeV linac injector and 2 storage rings operated at 1.5 and 3 GeV respectively. The linac injector will also be used for the generation of short X-ray pulses. The three machines mentioned above are described with some emphasis on the effort to create a very small emittance in the 3 GeV ring. Some unconventional technical solutions will also be presented.
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| 20. |
- Gräsbeck, Anne, et al.
(författare)
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Dementia in First-Degree Relatives of Patients with Frontotemporal Dementia. A Family History Study.
- 2005
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Ingår i: Dementia and Geriatric Cognitive Disorders. - : S. Karger AG. - 1420-8008 .- 1421-9824. ; 19:2-3, s. 145-153
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Tidskriftsartikel (refereegranskat)abstract
- Several studies have found a clustering of dementia in relatives of patients with frontotemporal dementia (FTD). This study analysed the familial aggregation of FTD specifically as well as the occurrence of dementia in general in first-degree relatives of patients with FTD. A family history study was carried out on 478 first-degree relatives of 74 index patients suffering from FTD. Cases of organic dementia and of FTD were diagnosed according to internationally accepted diagnostic criteria. Age- and sex-specific incidences of organic dementia and of FTD were calculated as was the proportion of FTD in relation to organic dementia in general; comparisons with clinical and population studies were made. There was a tenfold increase in the incidence of FTD in the first-degree relatives of FTD patients compared with the incidence of FTD in a population study. The proportion of FTD in relation to all types of organic dementia was much higher in relatives of FTD patients compared to the corresponding proportions in clinical and population-based studies. There was a small, non-significant difference between the present family history study and the population studies as regards the incidence of organic dementia. The findings suggest that hereditary and/or shared environmental factors are strongly involved in the aetiology of FTD. There were no indications of familial clustering of organic dementia in general in relatives of FTD patients.
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