| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Strategies to improve usability and preserve accuracy in biological sequence databases
- 2016
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Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 16:18, s. 2454-2460
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Tidskriftsartikel (refereegranskat)abstract
- Biology is increasingly dependent on large-scale analysis, such as proteomics, creating a requirement for efficient bioinformatics. Bioinformatic predictions of biological functions rely upon correctly annotated database sequences, and the presence of inaccurately annotated or otherwise poorly described sequences introduces noise and bias to biological analyses. Accurate annotations are, for example, pivotal for correct identifications of polypeptide fragments. However, standards for how sequence databases are organized and presented are currently insufficient. Here, we propose five strategies to address fundamental issues in the annotation of sequence databases: (i) to clearly separate experimentally verified and unverified sequence entries; (ii) to enable a system for tracing the origins of annotations; (iii) to separate entries with high-quality, informative annotation from less useful ones; (iv) to integrate automated quality-control software whenever such tools exist; and (v) to facilitate post-submission editing of annotations and metadata associated with sequences. We believe that implementation of these strategies, for example as requirements for publication of database papers, would enable biology to better take advantage of large-scale data.
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| 3. |
- Aberšek, Nina, et al.
(författare)
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Calprotectin levels in amniotic fluid in relation to intra-amniotic inflammation and infection in women with preterm labor with intact membranes: A retrospective cohort study
- 2022
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Ingår i: European Journal of Obstetrics & Gynecology and Reproductive Biology. - : Elsevier BV. - 1872-7654 .- 0301-2115. ; 272, s. 24-29
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To evaluate the concentrations of calprotectin in amniotic fluid with respect to intra-amniotic inflammation and infection and to assess the presence or absence of bacteria in the amnio-chorionic niche with respect to presence or absence of intra-amniotic inflammation. Study design: Seventy-nine women with singleton pregnancies and preterm labor with intact membranes (PTL) were included in the study. Amniotic fluid was collected at the time of admission by amniocentesis and calprotectin levels were analyzed from frozen/thawed samples using ELISA. Interleukin (IL)-6 concentration was measured by point-of-care test. Samples from amniotic fluid and the amnio-chorionic niche (space between amniotic and chorionic membranes) were microbiologically analyzed. Microbial invasion of the amniotic cavity (MIAC) was diagnosed based on a positive PCR result for Ureaplasma species, Mycoplasma hominis, 16S rRNA or positive culture. Intra-amniotic inflammation (IAI) was defined as amniotic fluid point-of-care IL-6 concentration ≥ 745 pg/mL. The cohort of included women was divided into 4 subgroups based on the presence or absence of IAI/MIAC; i) intra-amniotic infection, ii) sterile IAI, iii) intra-amniotic colonization and iv) neither MIAC nor IAI. Results: Women with intra-amniotic infection had a significantly higher intra-amniotic calprotectin concentration (median; 101.6 µg/mL) compared with women with sterile IAI (median; 9.2 µg/mL), women with intra-amniotic colonization (median; 2.6 µg/mL) and women with neither MIAC nor IAI (median 4.6 µg/mL) (p = 0.001). Moreover, significantly higher amniotic fluid calprotectin concentration was seen in women who delivered within 7 days (p = 0.003). A significant negative correlation was found between amniotic fluid calprotectin and gestational age at delivery (rho = 0.32, p = 0.003). Relatively more bacteria in the amnio-chorionic niche were found in the sterile IAI group compared with the other groups. Conclusions: Calprotectin concentrations in amniotic fluid were significantly higher in the intra-amniotic infection group compared with the other groups. Moreover, the bacterial presence in the amnio-chorionic niche was higher in IAI group.
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| 4. |
- Bakidou, Anna, 1996, et al.
(författare)
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On Scene Injury Severity Prediction (OSISP) model for trauma developed using the Swedish Trauma Registry
- 2023
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Ingår i: BMC Medical Informatics and Decision Making. - 1472-6947. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Providing optimal care for trauma, the leading cause of death for young adults, remains a challenge e.g., due to field triage limitations in assessing a patient’s condition and deciding on transport destination. Data-driven On Scene Injury Severity Prediction (OSISP) models for motor vehicle crashes have shown potential for providing real-time decision support. The objective of this study is therefore to evaluate if an Artificial Intelligence (AI) based clinical decision support system can identify severely injured trauma patients in the prehospital setting. Methods: The Swedish Trauma Registry was used to train and validate five models – Logistic Regression, Random Forest, XGBoost, Support Vector Machine and Artificial Neural Network – in a stratified 10-fold cross validation setting and hold-out analysis. The models performed binary classification of the New Injury Severity Score and were evaluated using accuracy metrics, area under the receiver operating characteristic curve (AUC) and Precision-Recall curve (AUCPR), and under- and overtriage rates. Results: There were 75,602 registrations between 2013–2020 and 47,357 (62.6%) remained after eligibility criteria were applied. Models were based on 21 predictors, including injury location. From the clinical outcome, about 40% of patientswere undertriaged and 46% were overtriaged. Models demonstrated potential for improved triaging and yielded AUC between 0.80–0.89 and AUCPR between 0.43–0.62. Conclusions: AI based OSISP models have potential to provide support during assessment of injury severity. The findings may be used for developing tools to complement field triage protocols, with potential to improve prehospital trauma care and thereby reduce morbidity and mortality for a large patient population.
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| 5. |
- Barman, Malin, 1983, et al.
(författare)
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No association between allergy and current 25-hydroxy vitamin D in serum or vitamin D intake
- 2015
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Ingår i: Acta Paediatrica. - : Wiley. - 0803-5253 .- 1651-2227. ; 104:4, s. 405-413
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Tidskriftsartikel (refereegranskat)abstract
- Aim Vitamin D may be involved in allergy development, but there is conflicting evidence. We investigated if dietary intake of vitamin D and levels of 25OHD in serum differed between allergic and nonallergic adolescents and if serum 25OHD correlated with dietary intake of vitamin D or season of blood sampling. Methods Serum 25-hydroxy vitamin D (25OHD) levels were analysed in 13-year-old subjects with atopic eczema (n = 55), respiratory allergy (n = 55) or no allergy (n = 55). Intake of fat-containing foods was assessed by food-frequency questionnaires, and total daily vitamin D intake was calculated. Logistic regression was used to adjust for gender, parental allergy and time of blood sampling. Results Subjects with atopic eczema or respiratory allergy did not differ from nonallergic controls regarding serum 25OHD levels or calculated vitamin D intake. Subjects sampled in the autumn had significantly higher levels of serum 25OHD than subjects sampled in the winter or spring. Serum 25OHD levels correlated to consumption of vitamin D-fortified lean milk (p = 0.001). Conclusion The findings suggest no association between allergy and 25OHD levels in serum or vitamin D intake in adolescents. Serum 25OHD levels correlated to intake of vitamin D-fortified lean milk.
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| 6. |
- Barman, Malin, 1983, et al.
(författare)
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Nutritional impact on Immunological maturation during Childhood in relation to the Environment (NICE): a prospective birth cohort in northern Sweden
- 2018
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Ingår i: BMJ Open. - : BMJ. - 2044-6055 .- 2044-6055. ; 8:10
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Tidskriftsartikel (refereegranskat)abstract
- © Author(s) (or their employer(s)) 2018. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ. INTRODUCTION: Prenatal and neonatal environmental factors, such as nutrition, microbes and toxicants, may affect health throughout life. Many diseases, such as allergy and impaired child development, may be programmed already in utero or during early infancy. Birth cohorts are important tools to study associations between early life exposure and disease risk. Here, we describe the study protocol of the prospective birth cohort, 'Nutritional impact on Immunological maturation during Childhood in relation to the Environment' (NICE). The primary aim of the NICE cohort is to clarify the effect of key environmental exposures-diet, microbes and environmental toxicants-during pregnancy and early childhood, on the maturation of the infant's immune system, including initiation of sensitisation and allergy as well as some secondary outcomes: infant growth, obesity, neurological development and oral health.METHODS AND ANALYSIS: The NICE cohort will recruit about 650 families during mid-pregnancy. The principal inclusion criterion will be planned birth at the Sunderby Hospital in the north of Sweden, during 2015-2018. Questionnaires data and biological samples will be collected at 10 time-points, from pregnancy until the children reach 4 years of age. Samples will be collected primarily from mothers and children, and from fathers. Biological samples include blood, urine, placenta, breast milk, meconium, faeces, saliva and hair. Information regarding allergic heredity, diet, socioeconomic status, lifestyle including smoking, siblings, pet ownership, etc will be collected using questionnaires. Sensitisation to common allergens will be assessed by skin prick testing and allergic disease will be diagnosed by a paediatrician at 1 and 4 years of age. At 4 years of age, the children will also be examined regarding growth, neurobehavioural and neurophysiological status and oral health.ETHICS AND DISSEMINATION: The NICE cohort has been approved by the Regional Ethical Review Board in Umeå, Sweden (2013/18-31M). Results will be disseminated through peer-reviewed journals and communicated on scientific conferences.
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| 7. |
- Barman, Malin, 1983, et al.
(författare)
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Serum fatty acid profile does not reflect seafood intake in adolescents with atopic eczema.
- 2014
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Ingår i: Acta Paediatrica, International Journal of Paediatrics. - : Wiley. - 0803-5253 .- 1651-2227. ; 103:9, s. 968-976
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Tidskriftsartikel (refereegranskat)abstract
- AIM:Long-chain polyunsaturated fatty acids (LCPUFAs) are immunomodulatory, but their role in allergy development is controversial. We investigated whether proportions of LCPUFAs in serum phospholipids were related to allergic diagnosis, seafood intake and LCPUFA proportions in cord blood.METHODS:Serum was obtained from 148 birth cohort children at 13 years of age. Forty had atopic eczema, 53 had respiratory allergy, and 55 were nonallergic. Proportions of LCPUFAs were determined in serum phospholipids; cord blood from 128 of the individuals was previously analysed. Seafood intake was estimated using questionnaires.RESULTS:Allergic and nonallergic individuals did not differ significantly regarding individual LCPUFAs. However, arachidonic acid over docosahexaenoic acid (DHA) ratio was higher in allergic, compared with nonallergic, adolescents. In nonallergic individuals, LCPUFA proportions in cord serum and adolescent serum correlated weakly. In individuals with atopic eczema and respiratory allergy, these correlations were weak or absent. A moderate correlation between seafood intake and serum DHA was seen in nonallergic individuals and those with respiratory allergy, but not in those with atopic eczema.CONCLUSION:Serum LCPUFA pattern was similar in allergic and nonallergic adolescents. Fatty acid metabolism may be altered in atopic eczema subjects, suggested by poor correlations between fatty acid intake and serum levels.
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| 8. |
- Bauer, Brigitte, 1978, et al.
(författare)
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Modification and expulsion of keratins by human epidermal keratinocytes upon hapten exposure in vitro.
- 2011
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Ingår i: Chemical research in toxicology. - : American Chemical Society (ACS). - 1520-5010 .- 0893-228X. ; 24:5, s. 737-43
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Tidskriftsartikel (refereegranskat)abstract
- Allergic contact dermatitis is the most prevalent form of human immunotoxicity. It is caused by reactive low molecular weight chemicals, that is, haptens, coming in contact with the skin where hapten-peptide complexes are formed, activating the immune system. By using sensitizing fluorescent thiol-reactive haptens, that is, bromobimanes, we show how keratinocytes respond to hapten exposure in vitro and reveal, for the first time in a living system, an exact site of haptenation. Rapid internalization and reaction of haptens with keratin filaments were visualized. Subsequently, keratinocytes respond in vitro to hapten exposure by release of membrane blebs, which contain haptenated keratins 5 and 14. Particularly, cysteine 54 of K5 was found to be a specific target. A mechanism is proposed where neoepitopes, otherwise hidden from the immune system, are released after hapten exposure via keratinocyte blebbing. The observed expulsion of modified keratins by keratinocytes in vitro might play a role during hapten sensitization in vivo and should be subject to further investigations.
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| 9. |
- Björklund, Henrik, 1973, et al.
(författare)
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Formal and informal communication in a project organisation: The case of a large construction project
- 2006
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Ingår i: Proceedings of IRNOP VII Project Research Conference, October 11-13, Xian, China. - 712103252X
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Konferensbidrag (refereegranskat)abstract
- In larger projects, where large numbers of project participants are involved, it is important to have a well functioning project organisation. The more complex a project is the more planning and control is needed. The study presented in this paper investigates an installation company’s formal and informal communication when constructing a new power plant for district heating, in Göteborg, Sweden. This is done in order to understand the informal communication and its effect on the project organisation. Literature reviews and interviews with managers involved in the project have been done. The results of the study indicate that the actual organisational structure differs from the planned structure in terms of communication paths. Actors involved, tend to contact each other beside the formal chain of order. A well functioning project team with established informal communication paths might be a possibility to achieve success in projects.
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| 10. |
- Calvén, Anna, et al.
(författare)
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Adolescents' attitudes, preferences and perceived behaviours regarding healthy eating and whole grains from a gender and health interest perspective
- 2023
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Ingår i: Food & Nutrition Research. - 1654-6628 .- 1654-661X. ; 67:8988, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- Background: A healthy diet is important not only for the growth and development of the human body but also for the prevention of chronic diseases. However, most Swedish adolescents do not follow dietary recommendations, especially the intake of whole grain is very low. To create targeted conditions for healthy food choices amongst adolescents, comprehensive knowledge of factors related to adolescents' unhealthy and healthy eating is needed. Objective: To investigate adolescents' attitudes, preferences and perceived behaviours regarding healthy eating, with a specific focus on whole grains and to evaluate differences between genders and between adolescents with higher versus lower health interest. Design: A total of 1,178 Swedish adolescents responded to a questionnaire about their attitudes, preferences and perceived behabviours towards healthy eating and whole grains, and their general interest in nutrition and health.Results of girls and boys were compared, as well as adolescents with a higher versus lower health interest. Results: Displays information about healthy eating among adolescents and a comprehensive set of factors that may affect their ability to eat healthier. Overall, adolescents had a positive attitude towards food and health, but less than half felt that they managed to eat healthy. The consumption of different whole grain products was low, although the willingness to eat healthier and more whole grain was high. The most reported barrier to healthy eating, as well as increasing whole grain intake, was the unavailability of tasty healthy products, taste being even more important for adolescents with a low health interest than those with a high interest. Whole grain consumption and factors increasing the willingness of whole grain consumption were most prominent not only in adolescents with high health interest but also in girls compared with boys. Conclusion: The results show good potential to improve dietary habits amongst adolescents. Taste and availability of healthy products were rated the most important, whilst knowledge about the products' healthiness was rated the least important, especially amongst those with low health interest. By focusing on the attitudes and preferences of adolescents, the effectiveness may increase of initiatives to improve their dietary habits.
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