| 1. |
- Abdellah, Tebani, et al.
(författare)
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Annotation of pituitary neuroendocrine tumors with genome-wide expression analysis
- 2021
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Ingår i: Acta neuropathologica communications. - : BioMed Central (BMC). - 2051-5960. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Pituitary neuroendocrine tumors (PitNETs) are common, generally benign tumors with complex clinical characteristics related to hormone hypersecretion and/or growing sellar tumor mass. PitNETs can be classified based on the expression pattern of anterior pituitary hormones and three main transcriptions factors (TF), SF1, PIT1 and TPIT that regulate differentiation of adenohypophysial cells. Here, we have extended this classification based on the global transcriptomics landscape using tumor tissue from a well-defined cohort comprising 51 PitNETs of different clinical and histological types. The molecular profiles were compared with current classification schemes based on immunohistochemistry. Our results identified three main clusters of PitNETs that were aligned with the main pituitary TFs expression patterns. Our analyses enabled further identification of specific genes and expression patterns, including both known and unknown genes, that could distinguish the three different classes of PitNETs. We conclude that the current classification of PitNETs based on the expression of SF1, PIT1 and TPIT reflects three distinct subtypes of PitNETs with different underlying biology and partly independent from the expression of corresponding hormones. The transcriptomic analysis reveals several potentially targetable tumor-driving genes with previously unknown role in pituitary tumorigenesis.
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| 2. |
- Albers, Eva, 1966, et al.
(författare)
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Cellular response in fresh water microalgae to polluting compounds of flue gas when used as carbon source
- 2012
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Ingår i: 15th Workshop of International Study Group for Systems Biology (ISGSB), September 25-28, Ameland, The Netherlands.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Attention has lately been given to the use of microalgae as provider of valuable biomass or as production organism. To be able to use algae in industrial production, especially of biofuels, the cultivation procedures need to be improved in terms of efficiency and minimization of production costs. To reach these goals understanding of both process conditions as well as biological response to such conditions is needed for optimization of algal cultivation. Carbon dioxide, the carbon source during phototrophic growth, should be provided at high levels to result in the high biomass concentrations needed for a feasible production. Suitable high-level sources of CO2 are flue gases from industrial activities, which when used for algal cultivation will be a way of carbon capture reducing CO2 emissions. However, flue gases contain additional components that may affect cellular activity negatively. The aim of this research is to understand the physiological behavior of microalgae in industrial conditions to be able to optimize cellular performance. This initial project was launched to provide basic information about response of several types of microalgae that could grow in fresh water conditions to the main gaseous pollutants in flue gas, NO and SO2. This knowledge would guide the selection for a deeper characterization of effect-response relations and control of metabolism in algae in response to industrial conditions. Ten strains of fresh water species and one marine were selected based on reported fast growth and interesting composition such as high levels of lipids. The algae were screened for growth and cellular composition in cultivations with fresh water mineral medium. Artificially produced flue gas, mimicking effluents of pulp mills, consisting of 15% CO2 with 100 ppm NO and 10 ppm SO2 included for the last period of the cultivations was bubbled into the cultures. All strains tested were able to grow and two Scenedesmus strains, an isolated strain from a nearby lake, Chorella protothecoides and Chlamydomonas reinhardtii exhibited the highest specific growth rates. The highest levels of cellular macromolecules were found in Chlorella emersonii (45% carbohydrates), Nannochloropsis salina and the local isolate (65% proteins), and Botrycoccus braunii (57% lipids). It can be concluded that all strains tested were able to grow in cultures with flue gas as carbon source, also the marine species Nannochloropsis salina, and that the gaseous components decrease pH which needs to be monitored carefully to avoid that large drops in pH inhibit algal growth.
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| 3. |
- Albers, Eva, 1966, et al.
(författare)
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Influence of flue gas mimicking effluents of paper mills on growth and cellular composition of fresh water species of microalgae
- 2012
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Ingår i: 9th European Workshop on Biotechnology of Microalgae, 4-5 June, Nuthetal, Germany.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- To be able to use algae in industrial production, especially of biofuels, the cultivation procedures need to be improved in terms of efficiency and minimization of production costs. One important factor is to reach as high biomass concentrations as possible e.g. by using high levels of carbon dioxide provided by flue gas. The aim of this project was to study the influence of flue gas simulated to mimic effluents of pulp mills on growth and cellular composition of microalgae. Ten strains of fresh water species and one marine were selected based on reported fast growth and interesting composition such as high levels of lipids. The algae were screened in cultivations with fresh water mineral medium and artificially produced flue gas bubbled into the cultures consisting of 15% CO2 with 100 ppm NO and 10 ppm SO2 included for the last period of the cultivations. All strains tested were able to grow and two Scenedesmus strains, an isolated strain from a nearby lake, Chorella protothecoides and Chlamydomonas reinhardtii exhibited the highest specific growth rates. The highest levels of cellular macromolecules were found in Chlorella emersonii (45% of carbohydrates), Nannochloropsis salina and the local isolate (65% of proteins), and Botrycoccus braunii (57% of lipids). It can be concluded that all strains tested were able to grow in cultures with flue gas as carbon source, also the marine species Nannochloropsis salina, and that the gaseous components decrease pH which needs to be monitored carefully to avoid that large drops in pH inhibit algal growth.
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| 4. |
- Andersson, Jonathan, et al.
(författare)
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Estimating the cold-induced brown adipose tissue glucose uptake rate measured by 18F-FDG PET using infrared thermography and water-fat separated MRI
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Brown adipose tissue (BAT) expends chemical energy to produce heat, which makes it a potential therapeutic target for combating metabolic dysfunction and overweight/obesity by increasing its metabolic activity. The most well-established method for measuring BAT metabolic activity is glucose uptake rate (GUR) measured using 18F-fluorodeoxyglucose (FDG) positron emission tomography (PET). However, this is expensive and exposes the subjects to potentially harmful radiation. Cheaper and safer methods are warranted for large-scale or longitudinal studies. Potential alternatives include infrared thermography (IRT) and magnetic resonance imaging (MRI). The aim of this study was to evaluate and further develop these techniques. Twelve healthy adult subjects were studied. The BAT GUR was measured using 18F-FDG PET during individualized cooling. The temperatures of the supraclavicular fossae and a control region were measured using IRT during a simple cooling protocol. The fat fraction and effective transverse relaxation rate of BAT were measured using MRI without any cooling intervention. Simple and multiple linear regressions were employed to evaluate how well the MRI and IRT measurements could estimate the GUR. Results showed that both IRT and MRI measurements correlated with the GUR. This suggest that these measurements may be suitable for estimating the cold-induced BAT GUR in future studies.
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| 5. |
- Brynolfsson, Patrik, et al.
(författare)
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Technical note : adapting a GE SIGNA PET/MR scanner for radiotherapy
- 2018
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Ingår i: Medical physics (Lancaster). - : Wiley-Blackwell Publishing Inc.. - 0094-2405. ; 45:8, s. 3546-3550
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Simultaneous collection of PET and MR data for radiotherapy purposes are useful for, for example, target definition and dose escalations. However, a prerequisite for using PET/MR in the radiotherapy workflow is the ability to image the patient in treatment position. The aim of this work was to adapt a GE SIGNA PET/MR scanner to image patients for radiotherapy treatment planning and evaluate the impact on signal-to-noise (SNR) of the MR images, and the accuracy of the PET attenuation correction. Method: A flat tabletop and a coil holder were developed to image patients in the treatment position, avoid patient contour deformation, and facilitate attenuation correction of flex coils. Attenuation corrections for the developed hardware and an anterior array flex coil were also measured and implemented to the PET/MR system to minimize PET quantitation errors. The reduction of SNR in the MR images due to the added distance between the coils and the patient was evaluated using a large homogenous saline-doped water phantom, and the activity quantitation errors in PET imaging were evaluated with and without the developed attenuation corrections. Result: We showed that the activity quantitation errors in PET imaging were within ±5% when correcting for attenuation of the flat tabletop, coil holder, and flex coil. The SNR of the MRI images were reduced to 74% using the tabletop, and 66% using the tabletop and coil holders. Conclusion: We present a tabletop and coil holder for an anterior array coil to be used with a GE SIGNA PET/MR scanner, for scanning patients in the radiotherapy work flow. Implementing attenuation correction of the added hardware from the radiotherapy setup leads to acceptable PET image quantitation. The drop in SNR in MR images may require adjustment of the imaging protocols.
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| 6. |
- Chami, Nathalie, et al.
(författare)
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Exome Genotyping Identifies Pleiotropic Variants Associated with Red Blood Cell Traits
- 2016
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 99:1, s. 8-21
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Tidskriftsartikel (refereegranskat)abstract
- Red blood cell (RBC) traits are important heritable clinical biomarkers and modifiers of disease severity. To identify coding genetic variants associated with these traits, we conducted meta-analyses of seven RBC phenotypes in 130,273 multi-ethnic individuals from studies genotyped on an exome array. After conditional analyses and replication in 27,480 independent individuals, we identified 16 new RBC variants. We found low-frequency missense variants in MAP1A (rs55707100, minor allele frequency [MAF] = 3.3%, p = 2 x 10(-10) for hemoglobin [HGB]) and HNF4A (rs1800961, MAF = 2.4%, p < 3 x 10(-8) for hematocrit [HCT] and HGB). In African Americans, we identified a nonsense variant in CD36 associated with higher RBC distribution width (rs3211938, MAF = 8.7%, p = 7 x 10(-11)) and showed that it is associated with lower CD36 expression and strong allelic imbalance in ex vivo differentiated human erythroblasts. We also identified a rare missense variant in ALAS2 (rs201062903, MAF = 0.2%) associated with lower mean corpuscular volume and mean corpuscular hemoglobin (p < 8 x 10(-9)). Mendelian mutations in ALAS2 are a cause of sideroblastic anemia and erythropoietic protoporphyria. Gene-based testing highlighted three rare missense variants in PKLR, a gene mutated in Mendelian non-spherocytic hemolytic anemia, associated with HGB and HCT (SKAT p < 8 x 10(-7)). These rare, low-frequency, and common RBC variants showed pleiotropy, being also associated with platelet, white blood cell, and lipid traits. Our association results and functional annotation suggest the involvement of new genes in human erythropoiesis. We also confirm that rare and low-frequency variants play a role in the architecture of complex human traits, although their phenotypic effect is generally smaller than originally anticipated.
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| 7. |
- Christiansen, Iben Maj, 1964-, et al.
(författare)
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The crosscurrents of Swedish mathematics teacher education
- 2021
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Ingår i: International perspectives on mathematics teacher education. - Waxhaw, NC, USA : Information Age Publishing. - 9781648026317 - 9781648026294 - 9781648026300 ; , s. 9-48
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Bokkapitel (refereegranskat)abstract
- As with any programs in teacher education, Swedish mathematics teacher education is influenced by changing political winds, developments in Information and Communication Technology (ICT), culture, history, PISA results, research-based program designs, and a fair amount of passion. Content and outcomes are nationally determined and include the requirement of a strong research foundation, but this is often not how practcing techers work, which exerts its own pull on teacher education. The specific implementations of programs take different forms at the universities that offer mathematics teacher education. In order to provide a comprehensive yet meaningful ntroduction to both the current system and current practices, we describe the overall organization of Swedish mathematics teacher education, and then offer short cases of implemented programs. To ensure inclusivity, the various parts are written by mathematics educators from the respective institutions. In this way, both variation across mathematicas teacher education for diffrent grade levels and variation across different institutions working with the same national directives can be distinguished. Issues such as the academization of teacher education are problematized, as are other forces that constitute the crosscurrents in Swedish mathematics teacher education.
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| 8. |
- Cossío, Fernando, et al.
(författare)
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VAI-B: a multicenter platform for the external validation of artificial intelligence algorithms in breast imaging
- 2023
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Ingår i: Journal of Medical Imaging. - : SPIE-SOC PHOTO-OPTICAL INSTRUMENTATION ENGINEERS. - 2329-4302 .- 2329-4310. ; 10:06
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Multiple vendors are currently offering artificial intelligence (AI) computer-aided systems for triage detection, diagnosis, and risk prediction of breast cancer based on screening mammography. There is an imminent need to establish validation platforms that enable fair and transparent testing of these systems against external data.Approach: We developed validation of artificial intelligence for breast imaging (VAI-B), a platform for independent validation of AI algorithms in breast imaging. The platform is a hybrid solution, with one part implemented in the cloud and another in an on-premises environment at Karolinska Institute. Cloud services provide the flexibility of scaling the computing power during inference time, while secure on-premises clinical data storage preserves their privacy. A MongoDB database and a python package were developed to store and manage the data on-premises. VAI-B requires four data components: radiological images, AI inferences, radiologist assessments, and cancer outcomes.Results: To pilot test VAI-B, we defined a case-control population based on 8080 patients diagnosed with breast cancer and 36,339 healthy women based on the Swedish national quality registry for breast cancer. Images and radiological assessments from more than 100,000 mammography examinations were extracted from hospitals in three regions of Sweden. The images were processed by AI systems from three vendors in a virtual private cloud to produce abnormality scores related to signs of cancer in the images. A total of 105,706 examinations have been processed and stored in the database.Conclusions: We have created a platform that will allow downstream evaluation of AI systems for breast cancer detection, which enables faster development cycles for participating vendors and safer AI adoption for participating hospitals. The platform was designed to be scalable and ready to be expanded should a new vendor want to evaluate their system or should a new hospital wish to obtain an evaluation of different AI systems on their images.
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| 9. |
- Cossío, Fernando, et al.
(författare)
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VAI-B: A multicenter platform for the external validation of artificial intelligence algorithms in breast imaging
- 2023
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Ingår i: Journal of Medical Imaging. - : SPIE-Intl Soc Optical Eng. - 2329-4302 .- 2329-4310. ; 10:6
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Multiple vendors are currently offering artificial intelligence (AI) computer-aided systems for triage detection, diagnosis, and risk prediction of breast cancer based on screening mammography. There is an imminent need to establish validation platforms that enable fair and transparent testing of these systems against external data. Approach: We developed validation of artificial intelligence for breast imaging (VAI-B), a platform for independent validation of AI algorithms in breast imaging. The platform is a hybrid solution, with one part implemented in the cloud and another in an on-premises environment at Karolinska Institute. Cloud services provide the flexibility of scaling the computing power during inference time, while secure on-premises clinical data storage preserves their privacy. A MongoDB database and a python package were developed to store and manage the data onpremises. VAI-B requires four data components: radiological images, AI inferences, radiologist assessments, and cancer outcomes. Results: To pilot test VAI-B, we defined a case-control population based on 8080 patients diagnosed with breast cancer and 36,339 healthy women based on the Swedish national quality registry for breast cancer. Images and radiological assessments from more than 100,000 mammography examinations were extracted from hospitals in three regions of Sweden. The images were processed by AI systems from three vendors in a virtual private cloud to produce abnormality scores related to signs of cancer in the images. A total of 105,706 examinations have been processed and stored in the database. Conclusions: We have created a platform that will allow downstream evaluation of AI systems for breast cancer detection, which enables faster development cycles for participating vendors and safer AI adoption for participating hospitals. The platform was designed to be scalable and ready to be expanded should a new vendor want to evaluate their system or should a new hospital wish to obtain an evaluation of different AI systems on their images.
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| 10. |
- Engström, Arvid, et al.
(författare)
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Temporal hybridity : footage with instant replay in real time
- 2010
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Ingår i: CHI '10 Proceedings of the SIGCHI Conference on Human Factors in Computing Systems. - New York, NY, USA : Association for Computing Machinery (ACM). - 9781605589299 ; , s. 1495-1504
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Konferensbidrag (refereegranskat)abstract
- In this paper we explore the production of streaming media that involves live and recorded content. To examine this, we report on how the production practices and process are conducted through an empirical study of the production of live television, involving the use of live and non-live media under highly time critical conditions. In explaining how this process is managed both as an individual and collective activity, we develop the concept of temporal hybridity to explain the properties of these kinds of production system and show how temporally separated media are used, understood and coordinated. Our analysis is examined in the light of recent developments in computing technology and we present some design implications to support amateur video production.
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