| 1. |
- Uhlén, Mathias, et al.
(författare)
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The human secretome
- 2019
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Ingår i: Science Signaling. - : American Association for the Advancement of Science (AAAS). - 1945-0877 .- 1937-9145. ; 12:609
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Tidskriftsartikel (refereegranskat)abstract
- The proteins secreted by human cells (collectively referred to as the secretome) are important not only for the basic understanding of human biology but also for the identification of potential targets for future diagnostics and therapies. Here, we present a comprehensive analysis of proteins predicted to be secreted in human cells, which provides information about their final localization in the human body, including the proteins actively secreted to peripheral blood. The analysis suggests that a large number of the proteins of the secretome are not secreted out of the cell, but instead are retained intracellularly, whereas another large group of proteins were identified that are predicted to be retained locally at the tissue of expression and not secreted into the blood. Proteins detected in the human blood by mass spectrometry-based proteomics and antibody-based immuno-assays are also presented with estimates of their concentrations in the blood. The results are presented in an updated version 19 of the Human Protein Atlas in which each gene encoding a secretome protein is annotated to provide an open-access knowledge resource of the human secretome, including body-wide expression data, spatial localization data down to the single-cell and subcellular levels, and data about the presence of proteins that are detectable in the blood.
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| 2. |
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| 3. |
- Bergström, Lena, et al.
(författare)
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Report of the ICES/HELCOM Working Group on Integrated Assessments of the Baltic Sea (WGIAB)
- 2015
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The ICES/HELCOM Working Group on Integrated Assessments of the Baltic Sea(WGIAB) was established in 2007 as a forum for developing and combining ecosystembasedmanagement efforts for the Baltic Sea. The group intends to serve as a scientificcounterpart and support for the ICES Baltic Fisheries Assessment Working Group(WGBFAS) as well as for efforts and projects related to Integrated Ecosystem Assessments(IEA) within ICES and HELCOM. The group works in cooperation with similargroups within the ACOM/SCICOM Steering Group on Integrated Ecosystem Assessments(SSGIEA).The 2015 WGIAB meeting was held in Cádiz, Spain, from 9–13 March, back-to-backwith the meeting of its counterpart in the Working Group on Ecosystem Assessmentof Western European Shelf Seas (WGEAWESS). The meetings had joint sessions as wellas WG specific work, and some participants effectively participated in both meetings.The WGIAB meeting was attended by 27 participants from nine countries. The meetingwas chaired by Christian Möllmann, Germany, Laura Uusitalo, Finland and Lena Bergström,Sweden.This was the last year of the ongoing three-year Terms of Reference (ToR) for WGIAB.The main working activities in 2015 were to i) conduct studies on Baltic Sea ecosystemfunctioning with the goal to publish case studies from different parts of the Baltic Seain peer-reviewed journals, ii) work on the demonstration exercise to develop ecosystem-based assessment and advice for Baltic fish stocks focusing on cod (DEMO) withmultiple approaches, iii) plan further how to integrate the social and economic aspectsmore tightly in the WGIAB work, and iv) discuss the future focus and format of theWGIAB work.The Baltic ecosystem functioning activity focused on identifying and exploring keytrends and linkages in the Baltic Sea foodweb. This was pursued by presentation andfurther discussion of ongoing intersessional work on foodweb modelling and integratedanalyses, and by exercises to develop conceptual models Baltic Sea foodwebsand the links to ecosystem function. Long-term monitoring datasets on the abiotic andbiotic parts of the Baltic Sea Proper ecosystem were updated for use in the continuedwork to develop environmental indicators for fisheries and marine management.The focus of the DEMO 3 (DEMOnstration exercise for Integrated Ecosystem Assessmentand Advice of Baltic Sea cod) was on finding a way to use the results from theDEMO1 and DEMO2 workshops in short and midterm projections/scenarios of Balticcod dynamics based on different types of modelling, as well as designing methodologyand modelling data for practical implementation of Integrated Advice for Baltic cod.The WGIAB was positively inclined towards including social and economic aspectsinto the integrated assessment. Openings to this path were provided by presentationon ongoing project work, and discussing their linkages to ecological aspects. It wasseen as crucial that experts on social and economic analysis should be included andtake an active part in the future work of the group.The group concluded that its upcoming work should focus more closely on functionaldiversity, which was identified as a recurring issue in the Baltic Sea. This approach wasalso identified as a useful connection point between scientific and management aspectsin order for the group to continue serving as a forum for developing ecosystem-basedmanagement efforts in the Baltic Sea. A focus on functional diversity was also seen as2 | ICES WGIAB REPORT 2015a potentially feasible way of bringing together management aspects for different sectors,by linking to ecosystem services concepts.The group proposed Saskia Otto, Germany and Martin Lindegren, Denmark as newincoming Chairs, together with Lena Bergström, Sweden and Laura Uusitalo, Finland.Having four Chairs is justified due to the wide scope of the group's work, as well asthe increased work load due to the planned new foci.
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| 4. |
- Henningsson, Anna, et al.
(författare)
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Human tick-borne encephalitis and characterization of virus from biting tick
- 2016
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Ingår i: Emerging Infectious Diseases. - : Centers for Disease Control and Prevention (CDC). - 1080-6040 .- 1080-6059. ; 22:8, s. 1485-1487
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Tidskriftsartikel (refereegranskat)abstract
- We report a case of human tick-borne encephalitis (TBE) in which the TBE virus was isolated from the biting tick. Viral growth and sequence were characterized and compared with those of a reference strain. Virus isolation from ticks from patients with TBE may offer a new approach for studies of epidemiology and pathogenicity. © 2016, Centers for Disease Control and Prevention (CDC). All rights reserved.
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| 5. |
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| 6. |
- Nilsson, Erik, 1983-, et al.
(författare)
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Evaluating humidity and sea salt disturbances on CO2 flux measurements
- 2018
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Ingår i: Journal of Atmospheric and Oceanic Technology. - 0739-0572 .- 1520-0426. ; 35, s. 859-875
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Tidskriftsartikel (refereegranskat)abstract
- Global oceans are an important sink of atmospheric carbon dioxide (CO2). Therefore, understanding the air-sea flux of CO2 is a vital part in describing the global carbon balance. Eddy covariance (EC) measurements are often used to study CO2 fluxes from both land and ocean. CO2 are usually measured with infrared absorption sensors, which at the same time measure water vapor. Studies have shown that presence of water vapor fluctuations in the sampling air potentially result in erroneous CO2 flux measurements due to cross-sensitivity of the sensor. Here we compare measured CO2 fluxes from both enclosed path Li-Cor 7200 sensors and open-path Li-Cor 7500 instruments from an inland measurement site and a marine site. We also introduce new quality control criteria based upon a Relative Signal Strength Indicator (RSSI). The sampling gas in one of the Li-Cor 7200 instruments was dried by means of a multi-tube diffusion dryer so that the water vapor fluxes were close to zero. With this setup we investigated the effect that cross-sensitivity of the CO2 signal to water vapor can have on the CO2 fluxes. The dryer had no significant effect on the CO2 fluxes. We tested the hypothesis that the cross-sensitivity effect is caused by hygroscopic particles such as sea salt by spraying a saline solution on the windows of the Li-Cor 7200 instruments during the inland field test. Our results confirm earlier findings that sea salt contamination can affect CO2 fluxes significantly and confirm earlier findings, that drying the sampling air for the gas analyzer is an effective method to reduce this signal contamination.
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| 7. |
- Nybacka, Sanna, et al.
(författare)
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Carotenoids and alkylresorcinols as objective biomarkers of diet quality when assessing the validity of a web-based food record tool and a food frequency questionnaire in a middle-aged population
- 2016
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Ingår i: BMC Nutrition. - : Springer Science and Business Media LLC. - 2055-0928. ; 2:53
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundRecently, two web-based dietary assessment tools were developed; a 4-day food record tool (the Riksmaten method), and a food frequency questionnaire (MiniMeal-Q). The aim of this study was to use objective biomarkers to examine the ability of the two methods to capture habitual dietary intake.MethodsIn total, 200 individuals from the pilot study of the Swedish CArdioPulmonary bioImage Study (SCAPIS) participated. Plasma concentration of carotenoids were determined with high-performance liquid chromatography (HPLC) and used as biomarkers of fruit and vegetable intake. A gas chromatography mass spectrometry (GC-MS) method was used to quantify alkylresorcinol homologues, which were used as biomarkers of whole grain wheat and rye intake.ResultsThe correlations between energy-adjusted fruit and vegetable intakes and plasma carotenoid concentrations (except lycopene) were stronger amongst women than men (r = 0.46 and r = 0.20 for the Riksmaten method, and r = 0.50 and r = 0.31 for MiniMeal-Q, respectively). For whole grains, the correlations of energy-adjusted intakes and alkylresorcinols were higher using the Riksmaten method (r = 0.30 and r = 0.29 for women and men) than the MiniMeal-Q (r = 0.25 and r = 0.20, respectively). In regression analyses between plasma carotenoids (except lycopene) and reported intake of fruits and vegetables, the R2 were 21.6 % and 5.1 % for women and men by the Riksmaten method, and correspondingly, 18.0 % and 6.6 % by the MiniMeal-Q. In the final full models, adjusted for smoking and BMI, all regression models remained statistically significant. The regression analyses of plasma alkylresorcinols and reported intake of whole grains showed an R2 of 9.4 % and 9.7 % for women and men by the Riksmaten method, and correspondingly, 5.3 % and 8.4 % by the MiniMeal-Q. In the final full models, adjusted for smoking and age, all regression models remained statistically significant, except for women in MiniMeal-Q.ConclusionBoth dietary assessment methods were able to capture dietary intake based on food groups with a similar precision. Agreements with objective biomarkers ranged from low to moderate, depending on sex and diet quality indicator. While the ability to capture whole grain intake was weak for both methods and sexes, the assessment of vegetable and fruit intake performed in a satisfactory manner for women in both methods.
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| 8. |
- Nybacka, Sanna, et al.
(författare)
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Comparison of a web-based food record tool and a food-frequency questionnaire and objective validation using the doubly labelled water technique in a Swedish middle-aged population
- 2016
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Ingår i: Journal of Nutritional Science. - : Cambridge University Press (CUP). - 2048-6790. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Two web-based dietary assessment tools have been developed for use in large-scale studies: the Riksmaten method ( 4-d food record) and MiniMeal-Q ( food-frequency method). The aim of the present study was to examine the ability of these methods to capture energy intake against objectively measured total energy expenditure ( TEE) with the doubly labelled water technique ( TEEDLW), and to compare reported energy and macronutrient intake. This study was conducted within the pilot study of the Swedish CArdioPulmonary bioImage Study ( SCAPIS), which included 1111 randomly selected men and women aged 50-64 years from the Gothenburg general population. Of these, 200 were enrolled in the SCAPIS diet substudy. TEEDLW was measured in a subsample ( n 40). Compared with TEEDLW, both methods underestimated energy intake: -2.5 ( SD 2.9) MJ with the Riksmaten method; -2.3 ( SD 3.6) MJ with MiniMeal-Q. Mean reporting accuracy was 80 and 82 %, respectively. The correlation between reported energy intake and TEEDLW was r 0.4 for the Riksmaten method ( P < 0.05) and r 0.28 ( non-significant) for MiniMeal-Q. Women reported similar average intake of energy and macronutrients in both methods whereas men reported higher intakes with the Riksmaten method. Energy-adjusted correlations ranged from 0.14 ( polyunsaturated fat) to 0.77 ( alcohol). Bland-Altman plots showed acceptable agreement for energy and energy-adjusted protein and carbohydrate intake, whereas the agreement for fat intake was poorer. According to energy intake data, both methods displayed similar precision on energy intake reporting. However, MiniMeal-Q was less successful in ranking individuals than the Riksmaten method. The development of methods to achieve limited under-reporting is a major challenge for future research.
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| 9. |
- van der Valk, Ralf J P, et al.
(författare)
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A novel common variant in DCST2 is associated with length in early life and height in adulthood.
- 2015
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Ingår i: Human molecular genetics. - : Oxford University Press (OUP). - 1460-2083 .- 0964-6906. ; 24:4, s. 1155-68
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Tidskriftsartikel (refereegranskat)abstract
- Common genetic variants have been identified for adult height, but not much is known about the genetics of skeletal growth in early life. To identify common genetic variants that influence fetal skeletal growth, we meta-analyzed 22 genome-wide association studies (Stage 1; N = 28 459). We identified seven independent top single nucleotide polymorphisms (SNPs) (P < 1 × 10(-6)) for birth length, of which three were novel and four were in or near loci known to be associated with adult height (LCORL, PTCH1, GPR126 and HMGA2). The three novel SNPs were followed-up in nine replication studies (Stage 2; N = 11 995), with rs905938 in DC-STAMP domain containing 2 (DCST2) genome-wide significantly associated with birth length in a joint analysis (Stages 1 + 2; β = 0.046, SE = 0.008, P = 2.46 × 10(-8), explained variance = 0.05%). Rs905938 was also associated with infant length (N = 28 228; P = 5.54 × 10(-4)) and adult height (N = 127 513; P = 1.45 × 10(-5)). DCST2 is a DC-STAMP-like protein family member and DC-STAMP is an osteoclast cell-fusion regulator. Polygenic scores based on 180 SNPs previously associated with human adult stature explained 0.13% of variance in birth length. The same SNPs explained 2.95% of the variance of infant length. Of the 180 known adult height loci, 11 were genome-wide significantly associated with infant length (SF3B4, LCORL, SPAG17, C6orf173, PTCH1, GDF5, ZNFX1, HHIP, ACAN, HLA locus and HMGA2). This study highlights that common variation in DCST2 influences variation in early growth and adult height.
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| 10. |
- Wickman, Magnus, et al.
(författare)
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Detection of IgE Reactivity to a Handful of Allergen Molecules in Early Childhood Predicts Respiratory Allergy in Adolescence
- 2017
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Ingår i: EBioMedicine. - : Elsevier BV. - 2352-3964. ; 26, s. 91-99
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Tidskriftsartikel (refereegranskat)abstract
- Background: Sensitization in early childhood may precede respiratory allergy in adolescence.Methods: IgE reactivity against 132 allergen molecules was evaluated using the MeDALL microarray in sera obtained from a random sample of 786 children at the age of 4, 8 and 16 years in a population based birth cohort (BAMSE). Symptoms were analyzed by questionnaire at ages 4, 8 and 16 years. Clinically and independent relevant allergen molecules accounting for ≥ 90% of IgE reactivities in sensitized individuals and at all time-points were identified as risk molecules and used to predict respiratory allergy. The data was replicated in the Manchester Asthma and Allergy Study (MAAS) birth cohort by studying IgE reactivity with the use of a commercial IgE microarray. Sera were obtained from children at the ages of 3, 5, 8 and 11 years (N = 248) and the outcome was studied at 11 years.Findings: In the BAMSE cohort 4 risk molecules could be identified, i.e.: Ara h 1 (peanut), Bet v 1 (birch), Fel d 1 (cat), Phl p 1 (grass). For MAAS the corresponding number of molecules was 5: Der p 1 (dust mite), Der f 2 (dust mite), Phl p 1 (grass), Phl p 5 (grass), Fel d 1 (cat). In BAMSE, early IgE reactivity to ≥ 3 of 4 allergen molecules at four years predicted incident and persistent asthma and/or rhinitis at 16 years (87% and 95%, respectively). The corresponding proportions in the MAAS cohort at 16 years were 100% and 100%, respectively, for IgE reactivity to ≥ 3 of 5 risk molecules.Interpretations: IgE reactivity to a few allergen molecules early in life identifies children with a high risk of asthma and/or rhinitis at 16 years. These findings will be of importance for developing preventive strategies for asthma and rhinitis in children.
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