| 1. |
- Brunius, Carl, 1974, et al.
(författare)
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Prediction and modeling of pre-analytical sampling errors as a strategy to improve plasma NMR metabolomics data
- 2017
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1460-2059 .- 1367-4811. ; 33:22, s. 3567-3574
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Tidskriftsartikel (refereegranskat)abstract
- Biobanks are important infrastructures for life science research. Optimal sample handling regarding e.g. collection and processing of biological samples is highly complex, with many variables that could alter sample integrity and even more complex when considering multiple study centers or using legacy samples with limited documentation on sample management. Novel means to understand and take into account such variability would enable high-quality research on archived samples. This study investigated whether pre-analytical sample variability could be predicted and reduced by modeling alterations in the plasma metabolome, measured by NMR, as a function of pre-centrifugation conditions (1-36 h pre-centrifugation delay time at 4 A degrees C and 22 A degrees C) in 16 individuals. Pre-centrifugation temperature and delay times were predicted using random forest modeling and performance was validated on independent samples. Alterations in the metabolome were modeled at each temperature using a cluster-based approach, revealing reproducible effects of delay time on energy metabolism intermediates at both temperatures, but more pronounced at 22 A degrees C. Moreover, pre-centrifugation delay at 4 A degrees C resulted in large, specific variability at 3 h, predominantly of lipids. Pre-analytical sample handling error correction resulted in significant improvement of data quality, particularly at 22 A degrees C. This approach offers the possibility to predict pre-centrifugation delay temperature and time in biobanked samples before use in costly downstream applications. Moreover, the results suggest potential to decrease the impact of undesired, delay-induced variability. However, these findings need to be validated in multiple, large sample sets and with analytical techniques covering a wider range of the metabolome, such as LC-MS.
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| 2. |
- Enlund, Karolina Brunius, et al.
(författare)
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Dental home care in dogs-a questionnaire study among Swedish dog owners, veterinarians and veterinary nurses
- 2020
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Ingår i: BMC Veterinary Research. - : Springer Science and Business Media LLC. - 1746-6148. ; 16:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Periodontal disease remains one of the dog's most common health issues, even though it is largely preventable by tooth brushing. Implementation of daily tooth brushing would not only improve animal welfare, but also reduce veterinary costs for the owner. There is a paucity of studies investigating attitudes, opinions and practices of dog owners, veterinarians, and veterinary nurses regarding preventative dental home care in dogs. The objective of this study was to investigate these parameters in Sweden, thereby providing a basis for improved prophylactic strategies. Methods Validated questionnaire surveys were distributed to all Swedish dog owners (n = 209,263), veterinarians (n = 3657) and veterinary nurses (n = 1650) with e-mail addresses in the national registry. The response rates were 32% for dog owners and veterinarians, and 38% for veterinary nurses. The survey questions concerned attitudes, opinions and practices regarding dental home care, including whether dog owners received information concerning dental home care or not, and if this information resulted in implementation. Results Attitudes, opinions and practices regarding dental home care are presented for Swedish dog owners, veterinarians, and veterinary nurses. A fundamental finding was that the absolute majority of Swedish dog owners do not perform adequate prophylactic dental home care. Considerable discrepancies were identified in the opinions of veterinary health practitioners and dog owners regarding attitudes towards dental home care and conveying of information. Several areas for improvement in the communication between dog owners and veterinary health practitioners concerning dental home care were identified. Conclusion Our results illustrates the need for validated methods to increase dog owner compliance with dental home care recommendations. We also see a need of further education, regarding canine dental home care, among veterinarians, veterinary nurses, and dog owners. The results from this unique study constitute an important foundation for future development of prophylactic strategies, with the ultimate goal to improve dental health, and thereby animal welfare, in dogs.
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| 3. |
- Enlund, Karolina Brunius, et al.
(författare)
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Development and validation of two questionnaires: Dental home care and dental health in Swedish dogs
- 2019
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203 .- 1932-6203. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Background: Dental disease is one of the most common health problems in dogs. However, no studies have investigated the attitudes, opinions and practices of dog owners, veterinarians and veterinary nurses regarding dental health and preventative dental home care in dogs. The objective of this study was therefore to develop and validate questionnaires for this purpose, in accordance with survey methodology guidelines. Methods: Questionnaire items were determined based on the authors' academic knowledge and clinical experience, and modified throughout the validation process. Several measures were taken to reduce sampling, coverage, measurement and non-response errors. Content validity was assessed by Subject-Matter Experts (SME) and cognitive interviews were conducted in accordance with the “think-aloud protocol”. Non-response analysis was performed using several methods. Results: Constructs were identified using exploratory factor analysis and two predefined constructs from the dog owner questionnaire were confirmed “Dog owners' attitudes towards brushing their dog's teeth” (Cronbach's α = 0.86) and “Dog owners' assessment of their dog's dental health” (α = 0.76). Additionally, exploratory factor analysis identified three potential constructs. In the veterinary health practitioner questionnaire, two constructs were identified: “Veterinary health practitioners' attitudes towards dental chews and dental feed” (α = 0.78) and “Veterinary health practitioners' attitudes and opinions on dental problems and dental cleaning” (α = 0.73). Non-response analysis showed a higher proportion of women in the sample of dog owners and veterinarians compared to the target populations. Veterinarians in the sample were also younger. In contrast, gender and age distributions in veterinary nurses did not differ between sample and target. Conclusion: The validation presented in this work showed that the developed questionnaires could be used as accurate and reliable tools for measuring attitudes and practices regarding dental home care in dogs among Swedish dog owners, veterinarians and veterinary nurses.
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| 4. |
- Enlund, Karolina Brunius, et al.
(författare)
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Dog Owners' Perspectives on Canine Dental Health : A Questionnaire Study in Sweden
- 2020
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Ingår i: Frontiers in Veterinary Science. - : Frontiers Media SA. - 2297-1769. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Periodontal disease is one of the most common diseases affecting dogs, with a reported prevalence of at least 80% in dogs over 3 years of age. However, there is a lack of studies regarding dog owners' assessment of their dog's dental health, and whether they perceive clinical signs often associated with periodontal disease, i.e., dental calculus, halitosis or mobile or lost teeth. A validated questionnaire survey was distributed to all Swedish dog owners with email addresses in the national registry (n = 209,263). The response rate was 32%. The survey questions concerned opinions and practices regarding canine dental health, including assessment of dental health parameters and dog owners' ability to examine their dog's mouth. A construct (α = 0.76) was used to investigate dog owners' assessed symptoms of their dog's dental health in relation to background factors. Half of the respondents rated their dog's dental health as very good. However, one in four dog owners experienced difficulties when inspecting the dog's teeth. The most common reason for this difficulty was stated to be an uncooperative dog. Almost half of the dog owners reported halitosis to some degree in their dog, and almost four in ten owners reported dental calculus. One in eight dogs had been previously anesthetized for dental cleaning, and one in 12 dogs had experienced problems with gum disease, according to the owners. Owners' assessment varied significantly with the dog's age, weight, breed, breed group, sex, and concurrent disease. Owner-related factors that influenced the assessment of the dog's dental health were age, gender, education, county (urban/rural), and whether they were breeders or not. Dog owners with smaller dogs, older dogs and certain breeds predisposed to periodontal disease assessed their dog's dental health as worse than their counterparts, which is in agreement with previously reported higher prevalence of dental disease in these groups. This indicates that dog owners are able to perform relative assessment of their dog's dental health status. Our results also highlight the need for routine professional assessment of periodontal health, as well as education of dog owners and training of dogs to accept dental care procedures.
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| 5. |
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| 6. |
- Enlund, Karolina Brunius, et al.
(författare)
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Professional dental cleaning in dogs: clinical routines among Swedish veterinarians and veterinary nurses
- 2020
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Ingår i: Acta Veterinaria Scandinavica. - : Springer Science and Business Media LLC. - 1751-0147 .- 0044-605X. ; 62:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Dental disease is very common in dogs and veterinary professional dental cleaning and examination, together with daily dental home care, is the foundation for good dental health. To our knowledge, no previous study has investigated professional dental cleaning routines in small animal veterinary practice. A validated questionnaire survey was distributed to all veterinarians and veterinary nurses with registered e-mail addresses in the Swedish national registry (veterinarians; n = 3657, veterinary nurses; n = 1650). Response rates were 32% for veterinarians (V) and 38% for veterinary nurses (VN). Results: In total, 73% (V)/96% (VN) of respondents reported that professional dental cleaning was performed at their work place under general anesthesia, and 27% (V)/18% (VN) that dental cleaning was performed under sedation. Of the respondents, 43% (V)/96% (VN) considered regular dental cleaning under general anesthesia fairly or very important, and 49% (V)/47% (VN) stated that it was sometimes important for good dental health in dogs. A majority of respondents, 84% (V)/97% (VN), reported that dental extractions were performed at their clinic, and 72% (V)/90% (VN) had access to dental radiography equipment. Conclusion: A majority of Swedish veterinarians and veterinary nurses perform professional dental cleaning under general anesthesia with access to dental radiography equipment, in accordance with national and international recommendations. However, a considerable proportion of professional dental cleanings were performed under sedation only, and extractions performed without access to dental radiography equipment were common, suggesting several areas of improvement in the routines in Swedish veterinary clinics and hospitals. Our results clearly indicate the need for improved educational efforts to increase the awareness among veterinary health professionals regarding guidelines and official recommendations in canine dental care.
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| 7. |
- Rådjursöga, Millie, 1977, et al.
(författare)
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The H-1 NMR serum metabolomics response to a two meal challenge: a cross-over dietary intervention study in healthy human volunteers
- 2019
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Ingår i: Nutrition Journal. - : Springer Science and Business Media LLC. - 1475-2891. ; 18:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Metabolomics represents a powerful tool for exploring modulation of the human metabolome in response to food intake. However, the choice of multivariate statistical approach is not always evident, especially for complex experimental designs with repeated measurements per individual. Here we have investigated the serum metabolic responses to two breakfast meals: an egg and ham based breakfast and a cereal based breakfast using three different multivariate approaches based on the Projections to Latent Structures framework. Methods: In a cross over design, 24 healthy volunteers ate the egg and ham breakfast and cereal breakfast on four occasions each. Postprandial serum samples were subjected to metabolite profiling using H-1 nuclear magnetic resonance spectroscopy and metabolites were identified using 2D nuclear magnetic resonance spectroscopy. Metabolic profiles were analyzed using Orthogonal Projections to Latent Structures with Discriminant Analysis and Effect Projections and ANOVA-decomposed Projections to Latent Structures. Results: The Orthogonal Projections to Latent Structures with Discriminant Analysis model correctly classified 92 and 90% of the samples from the cereal breakfast and egg and ham breakfast, respectively, but confounded dietary effects with inter-personal variability. Orthogonal Projections to Latent Structures with Effect Projections removed inter-personal variability and performed perfect classification between breakfasts, however at the expense of comparing means of respective breakfasts instead of all samples. ANOVA-decomposed Projections to Latent Structures managed to remove inter-personal variability and predicted 99% of all individual samples correctly. Proline, tyrosine, and N-acetylated amino acids were found in higher concentration after consumption of the cereal breakfast while creatine, methanol, and isoleucine were found in higher concentration after the egg and ham breakfast. Conclusions: Our results demonstrate that the choice of statistical method will influence the results and adequate methods need to be employed to manage sample dependency and repeated measurements in cross-over studies. In addition, H-1 nuclear magnetic resonance serum metabolomics could reproducibly characterize postprandial metabolic profiles and identify discriminatory metabolites largely reflecting dietary composition.
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| 8. |
- Almanza-Aguilera, Enrique, et al.
(författare)
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Impact in Plasma Metabolome as Effect of Lifestyle Intervention for Weight-Loss Reveals Metabolic Benefits in Metabolically Healthy Obese Women
- 2018
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3907 .- 1535-3893. ; 17:8, s. 2600-2610
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Tidskriftsartikel (refereegranskat)abstract
- Little is known regarding metabolic benefits of weight loss (WL) on the metabolically healthy obese (MHO) patients. We aimed to examine the impact of a lifestyle weight loss (LWL) treatment on the plasma metabolomic profile in MHO individuals. Plasma samples from 57 MHO women allocated to an intensive LWL treatment group (TG, hypocaloric Mediterranean diet and regular physical activity, n = 30) or to a control group (CG, general recommendations of a healthy diet and physical activity, n = 27) were analyzed using an untargeted1H NMR metabolomics approach at baseline, after 3 months (intervention), and 12 months (follow-up). The impact of the LWL intervention on plasma metabolome was statistically significant at 3 months but not at follow-up and included higher levels of formate and phosphocreatine and lower levels of LDL/VLDL (signals) and trimethylamine in the TG. These metabolites were also correlated with WL. Higher myo-inositol, methylguanidine, and 3-hydroxybutyrate, and lower proline, were also found in the TG; higher levels of hippurate and asparagine, and lower levels of 2-hydroxybutyrate and creatine, were associated with WL. The current findings suggest that an intensive LWL treatment, and the consequent WL, leads to an improved plasma metabolic profile in MHO women through its impact on energy, amino acid, lipoprotein, and microbial metabolism.
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| 9. |
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| 10. |
- Bodén, Stina, et al.
(författare)
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Dietary patterns, untargeted metabolite profiles and their association with colorectal cancer risk
- 2024
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322 .- 2045-2322. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- We investigated data-driven and hypothesis-driven dietary patterns and their association to plasma metabolite profiles and subsequent colorectal cancer (CRC) risk in 680 CRC cases and individually matched controls. Dietary patterns were identified from combined exploratory/confirmatory factor analysis. We assessed association to LC–MS metabolic profiles by random forest regression and to CRC risk by multivariable conditional logistic regression. Principal component analysis was used on metabolite features selected to reflect dietary exposures. Component scores were associated to CRC risk and dietary exposures using partial Spearman correlation. We identified 12 data-driven dietary patterns, of which a breakfast food pattern showed an inverse association with CRC risk (OR per standard deviation increase 0.89, 95% CI 0.80–1.00, p = 0.04). This pattern was also inversely associated with risk of distal colon cancer (0.75, 0.61–0.96, p = 0.01) and was more pronounced in women (0.69, 0.49–0.96, p = 0.03). Associations between meat, fast-food, fruit soup/rice patterns and CRC risk were modified by tumor location in women. Alcohol as well as fruit and vegetables associated with metabolite profiles (Q2 0.22 and 0.26, respectively). One metabolite reflecting alcohol intake associated with increased CRC risk, whereas three metabolites reflecting fiber, wholegrain, and fruit and vegetables associated with decreased CRC risk.
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| 11. |
- Brunius, Carl, 1974, et al.
(författare)
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Targeted and untargeted metabolomics for specific food intake assessment whole grains as an example
- 2017
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Ingår i: Advances in the Assessment of Dietary Intake. - Boca Raton : CRC Press, 2017. : CRC Press. - 9781498749329 ; , s. 315-336
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- This chapter provides an overview of the current available knowledge about alternative approaches to address food intakes by using dietary biomarkers. Biomarkers of whole grain intake identified by targeted and untargeted metabolomics approaches will be used as illustrative examples. The chapter addresses discovery, validation, and implementation of biomarkers of specific foods using targeted, and with particular emphasis, untargeted metabolomics approaches with whole grain foods as an example of a food category important to human health. The choice of experimental design for biomarker discovery will have a large impact on the choice of statistical techniques, what can be found in the data, and also on workload of study participants and researchers. The gold standard for statistical modeling validation is to use external validation, i.e. that separate datasets are used for model construction and validation. The chapter outlines a suggested approach to discover urinary biomarkers of specific food consumption using whole grain rye consumption in a healthy, free-living population as an example.
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| 12. |
- Cheng, Ken, 1987, et al.
(författare)
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An LC-QToF MS based method for untargeted metabolomics of human fecal samples
- 2020
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Ingår i: Metabolomics. - : Springer Science and Business Media LLC. - 1573-3882 .- 1573-3890. ; 16:4
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Consensus in sample preparation for untargeted human fecal metabolomics is lacking. Objectives: To obtain sample preparation with broad metabolite coverage for high-throughput LC–MS. Methods: Extraction solvent, solvent ratio and fresh frozen-vs-lyophilized samples were evaluated by metabolite feature quality. Results: Methanol at 5 mL per g wet feces provided a wide metabolite coverage with optimal balance between signal intensity and saturation for both fresh frozen and lyophilized samples. Lyophilization did not affect SCFA and is recommended because of convenience in normalizing to dry matter. Conclusion: The suggested sample preparation is simple, efficient and suitable for large-scale human fecal metabolomics.
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| 13. |
- Eriksen, Anne Kirstine, et al.
(författare)
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Effects of whole-grain wheat, rye, and lignan supplementation on cardiometabolic risk factors in men with metabolic syndrome: A randomized crossover trial
- 2020
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Ingår i: American Journal of Clinical Nutrition. - : Elsevier BV. - 0002-9165 .- 1938-3207. ; 111:4, s. 864-876
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Tidskriftsartikel (refereegranskat)abstract
- A whole-grain (WG)-rich diet has shown to have potential for both prevention and treatment of the metabolic syndrome (MetS), which is a cluster of risk factors that increase the risk of type 2 diabetes and cardiovascular disease. Different WGs may have different health effects. WG rye, in particular, may improve glucose homeostasis and blood lipids, possibly mediated through fermentable dietary fiber and lignans. Recent studies have also suggested a crucial role of the gut microbiota in response to WG. Objectives: The aim was to investigate WG rye, alone and with lignan supplements [secoisolariciresinol diglucoside (SDG)], and WG wheat diets on glucose tolerance [oral-glucose-tolerance test (OGTT)], other cardiometabolic outcomes, enterolignans, and microbiota composition. Moreover, we exploratively evaluated the role of gut microbiota enterotypes in response to intervention diets. Methods: Forty men with MetS risk profile were randomly assigned to WG diets in an 8-wk crossover study. The rye diet was supplemented with 280 mg SDG at weeks 4-8. Effects of treatment were evaluated by mixed-effects modeling, and effects on microbiota composition and the role of gut microbiota as a predictor of response to treatment were analyzed by random forest plots. Results: The WG rye diet (± SDG supplements) did not affect the OGTT compared with WG wheat. Total and LDL cholesterol were lowered (-0.06 and -0.09 mmol/L, respectively; P < 0.05) after WG rye compared with WG wheat after 4 wk but not after 8 wk. WG rye resulted in higher abundance of Bifidobacterium [fold-change (FC) = 2.58, P < 0.001] compared with baseline and lower abundance of Clostridium genus compared with WG wheat (FC = 0.54, P = 0.02). The explorative analyses suggest that baseline enterotype is associated with total and LDL-cholesterol response to diet. Conclusions: WG rye, alone or with SDG supplementation, compared with WG wheat did not affect glucose metabolism but caused transient LDL-cholesterol reduction. The effect of WG diets appeared to differ according to enterotype. This trial was registered at www.clinicaltrials.gov as NCT02987595.
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| 14. |
- Esberg, Anders, et al.
(författare)
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Carbonic Anhydrase 6 Gene Variation influences Oral Microbiota Composition and Caries Risk in Swedish adolescents
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Carbonic anhydrase VI (CA6) catalyses the reversible hydration of carbon dioxide in saliva with possible pH regulation, taste perception, and tooth formation effects. This study assessed effects of variation in the CA6 gene on oral microbiota and specifically the acidophilic and caries-associated Streptococcus mutans in 17-year old Swedish adolescents (n = 154). Associations with caries status and secreted CA6 protein were also evaluated. Single Nucleotide Polymorphisms (27 SNPs in 5 haploblocks) and saliva and tooth biofilm microbiota from Illumina MiSeq 16S rDNA (V3-V4) sequencing and culturing were analysed. Haploblock 4 (rs10864376, rs3737665, rs12138897) CCC associated with low prevalence of S. mutans (OR (95% CI): 0.5 (0.3, 0.8)), and caries (OR 0.6 (0.3, 0.9)), whereas haploblock 4 TTG associated with high prevalence of S. mutans (OR: 2.7 (1.2, 5.9)) and caries (OR: 2.3 (1.2, 4.4)). The TTG-haploblock 4 (represented by rs12138897(G)) was characterized by S. mutans, Scardovia wiggsiae, Treponema sp. HOT268, Tannerella sp. HOT286, Veillonella gp.1 compared with the CCC-haploblock 4 (represented by rs12138897(C)). Secreted CA6 in saliva was weakly linked to CA6 gene variation. In conclusion, the results indicate that CA6 gene polymorphisms influence S. mutans colonization, tooth biofilm microbiota composition and risk of dental caries in Swedish adolescents.
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| 15. |
- Fernández-Ochoa, Álvaro, et al.
(författare)
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A case report of switching from specific vendor-based to R-based pipelines for untargeted LC-MS metabolomics
- 2020
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Ingår i: Metabolites. - : MDPI AG. - 2218-1989 .- 2218-1989. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Data pre-processing of the LC-MS data is a critical step in untargeted metabolomics studies in order to achieve correct biological interpretations. Several tools have been developed for pre-processing, and these can be classified into either commercial or open source software. This case report aims to compare two specific methodologies, Agilent Profinder vs. R pipeline, for a metabolomic study with a large number of samples. Specifically, 369 plasma samples were analyzed by HPLC-ESI-QTOF-MS. The collected data were pre-processed by both methodologies and later evaluated by several parameters (number of peaks, degree of missingness, quality of the peaks, degree of misalignments, and robustness in multivariate models). The vendor software was characterized by ease of use, friendly interface and good quality of the graphs. The open source methodology could more effectively correct the drifts due to between and within batch effects. In addition, the evaluated statistical methods achieved better classification results with higher parsimony for the open source methodology, indicating higher data quality. Although both methodologies have strengths and weaknesses, the open source methodology seems to be more appropriate for studies with a large number of samples mainly due to its higher capacity and versatility that allows combining different packages, functions, and methods in a single environment.
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| 16. |
- Fernandez-Ochoa, Alvaro, et al.
(författare)
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Metabolic Disturbances in Urinary and Plasma Samples from Seven Different Systemic Autoimmune Diseases Detected by HPLC-ESI-QTOF-MS
- 2020
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3907 .- 1535-3893. ; 19:8, s. 3220-3229
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Tidskriftsartikel (refereegranskat)abstract
- Systemic autoimmune diseases (SADs) are characterized by dysfunctioning of the immune system, which causes damage in several tissues and organs. Among these pathologies are systemic lupus erythematosus (SLE), systemic sclerosis or scleroderma, Sjogren's syndrome, rheumatoid arthritis, primary antiphospholipid syndrome (PAPS), mixed connective tissue disease (MCTD), and undifferentiated connective tissue disease (UCTD). Early diagnosis is difficult due to similarity in symptoms, signs, and clinical test results. Hence, our aim was to search for differentiating metabolites of these diseases in plasma and urine samples. We performed metabolomic profiling by liquid chromatography-mass spectrometry (LC-MS) of samples from 228 SADs patients and 55 healthy volunteers. Multivariate PLS models were applied to investigate classification accuracies and identify metabolites differentiating SADs and healthy controls. Furthermore, we specifically investigated UCTD against the other SADs. PLS models were able to classify most SADs vs healthy controls (area under the roc curve (AUC) > 0.7), with the exception of MCTD and PAPS. Differentiating metabolites consisted predominantly of unsaturated fatty acids, acylglycines, acylcarnitines, and amino acids. In accordance with the difficulties in defining UCTD, the UCTD metabolome did not differentiate well from the other SADs. However, most UCTD cases were dassified as SLE, suggesting that metabolomics may provide a tool to reassess UCTD diagnosis into other conditions for more well-informed therapeutic strategies.
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| 17. |
- González-Domínguez, Álvaro, et al.
(författare)
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QComics: Recommendations and Guidelines for Robust, Easily Implementable and Reportable Quality Control of Metabolomics Data
- 2024
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Ingår i: Analytical Chemistry. - 0003-2700 .- 1520-6882. ; 96:3, s. 1064-1072
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Tidskriftsartikel (refereegranskat)abstract
- The implementation of quality control strategies is crucial to ensure the reproducibility, accuracy, and meaningfulness of metabolomics data. However, this pivotal step is often overlooked within the metabolomics workflow and frequently relies on the use of nonstandardized and poorly reported protocols. To address current limitations in this respect, we have developed QComics, a robust, easily implementable and reportable method for monitoring and controlling data quality. The protocol operates in various sequential steps aimed to (i) correct for background noise and carryover, (ii) detect signal drifts and “out-of-control” observations, (iii) deal with missing data, (iv) remove outliers, (v) monitor quality markers to identify samples affected by improper collection, preprocessing, or storage, and (vi) assess overall data quality in terms of precision and accuracy. Notably, this tool considers important issues often neglected along quality control, such as the need of separately handling missing values and truly absent data to avoid losing relevant biological information, as well as the large impact that preanalytical factors may elicit on metabolomics results. Altogether, the guidelines compiled in QComics might contribute to establishing gold standard recommendations and best practices for quality control within the metabolomics community.
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| 18. |
- Hallingström, Maria, et al.
(författare)
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Metabolomic profiles of mid-trimester amniotic fluid are not associated with subsequent spontaneous preterm delivery or gestational duration at delivery
- 2022
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Ingår i: Journal of Maternal-Fetal and Neonatal Medicine. - : Informa UK Limited. - 1476-7058 .- 1476-4954. ; 35:11, s. 2054-2062
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Tidskriftsartikel (refereegranskat)abstract
- Introduction:Spontaneous preterm delivery (<37 gestational weeks) has a multifactorial etiology with still incompletely identified pathways. Amniotic fluid is a biofluid with great potential for insights into the feto-maternal milieu. It is rich in metabolites, and metabolic consequences of inflammation is yet researched only to a limited extent. Metabolomic profiling provides opportunities to identify potential biomarkers of inflammatory conditioned pregnancy complications such as spontaneous preterm delivery. Objective:The aim of this study was to perform metabolomic profiling of amniotic fluid from uncomplicated singleton pregnancies in the mid-trimester to identify potential biomarkers associated with spontaneous preterm delivery and gestational duration at delivery. A secondary aim was to replicate previously reported mid-trimester amniotic fluid metabolic biomarkers of spontaneous preterm delivery in asymptomatic women. Method:A nested case-control study was performed within a larger cohort study of asymptomatic pregnant women undergoing mid-trimester genetic amniocentesis at 14-19 gestational weeks in Gothenburg, Sweden. Medical records were used to obtain clinical data and delivery outcome variables. Amniotic fluid samples from women with a subsequent spontaneous preterm delivery (n = 37) were matched with amniotic fluid samples from women with a subsequent spontaneous delivery at term (n = 37). Amniotic fluid samples underwent untargeted metabolomic analyses using liquid chromatography-mass spectrometry. Multivariate random forest analyses were used for data processing. A secondary targeted analysis was performed, aiming to replicate previously reported mid-trimester amniotic fluid metabolic biomarkers in women with a subsequent spontaneous preterm delivery. Results:Multivariate analysis did not distinguish the samples from women with a subsequent spontaneous preterm delivery from those with a subsequent term delivery. Neither was the metabolic profile associated with gestational duration at delivery. Potential metabolic biomarker candidates were identified from four publications by two different research groups relating mid-trimester amniotic fluid metabolomes to spontaneous PTD, of which fifteen markers were included in the secondary analysis. None of these were replicated. Conclusions:Metabolomic profiles of early mid-trimester amniotic fluid were not associated with spontaneous preterm delivery or gestational duration at delivery in this cohort.
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| 19. |
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| 20. |
- Harlid, Sophia, 1978-, et al.
(författare)
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A two-tiered targeted proteomics approach to identify pre-diagnostic biomarkers of colorectal cancer risk
- 2021
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Colorectal cancer prognosis is dependent on stage, and measures to improve early detection are urgently needed. Using prospectively collected plasma samples from the population-based Northern Sweden Health and Disease Study, we evaluated protein biomarkers in relation to colorectal cancer risk. Applying a two-tiered approach, we analyzed 160 proteins in matched sequential samples from 58 incident colorectal cancer case–control pairs. Twenty-one proteins selected from both this discovery phase and the literature were then analyzed in a validation set of 450 case–control pairs. Odds ratios were estimated by conditional logistic regression. LASSO regression and ROC analysis were used for multi-marker analyses. In the main validation analysis, no proteins retained statistical significance. However, exploratory subgroup analyses showed associations between FGF-21 and colon cancer risk (multivariable OR per 1 SD: 1.23 95% CI 1.03–1.47) as well as between PPY and rectal cancer risk (multivariable OR per 1 SD: 1.47 95% CI 1.12–1.92). Adding protein markers to basic risk predictive models increased performance modestly. Our results highlight the challenge of developing biomarkers that are effective in the asymptomatic, prediagnostic window of opportunity for early detection of colorectal cancer. Distinguishing between cancer subtypes may improve prediction accuracy. However, single biomarkers or small panels may not be sufficient for effective precision screening.
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| 21. |
- Hartvigsson, Olle, 1991, et al.
(författare)
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Associations of maternal and infant metabolomes with immune maturation and allergy development at 12 months in the Swedish NICE-cohort
- 2021
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Allergic diseases are the most common chronic diseases in childrenin the Western world, but little is know about what factors influence immune maturation and allergy development. We therefore aimed to associate infant and maternal metabolomes to T- and B-cell subpopulations and allergy diagnosis. We performed liquid chromatography-mass spectrometry based untargeted metabolomics on blood plasma from mothers (third trimester, n = 605; delivery, n = 558) and from the umbilical cord (n = 366). The measured metabolomes were associated to T- and B-cell subpopulations up to 4 months after delivery and to doctor´s diagnosed eczema, food allergy and asthma at one year of age using random forest analysis. Maternal and cord plasma at delivery could predict the number of CD24+CD38low memory B-cells (p = 0.033, n = 26 and p = 0.009, n = 22), but future allergy status could not be distinguished from any of the three measured metabolomes. Replication of previous literature findings showed hypoxanthine to be upregulated in the umbilical cord of children with subsequent asthma. This exploratory study suggests foetal immune programming occuring during pregnancy as the metabolomic profiles of mothers and infants at delivery related to infants’ B-cell maturation.
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| 22. |
- Hartvigsson, Olle, 1991, et al.
(författare)
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Associations of the placental metabolome with immune maturation up to one year of age in the Swedish NICE-cohort
- 2024
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Ingår i: Metabolomics. - : Springer Nature. - 1573-3882 .- 1573-3890. ; 20:2
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Allergies and other immune-mediated diseases are thought to result from incomplete maturation of the immune system early in life. We previously showed that infants’ metabolites at birth were associated with immune cell subtypes during infancy. The placenta supplies the fetus with nutrients, but may also provide immune maturation signals. Objectives: To examine the relationship between metabolites in placental villous tissue and immune maturation during the first year of life and infant and maternal characteristics (gestational length, birth weight, sex, parity, maternal age, and BMI). Methods: Untargeted metabolomics was measured using Liquid Chromatography-Mass Spectrometry. Subpopulations of T and B cells were measured using flow cytometry at birth, 48 h, one, four, and 12 months. Random forest analysis was used to link the metabolomics data with the T and B cell sub populations as well as infant and maternal characteristics. Results: Modest associations (Q2 = 0.2–0.3) were found between the placental metabolome and kappa-deleting recombination excision circles (KREC) at birth and naïve B cells and memory T cells at 12 months. Weak associations were observed between the placental metabolome and sex and parity. Still, most metabolite features of interest were of low intensity compared to associations previously found in cord blood, suggesting that underlying metabolites were not of placental origin. Conclusion: Our results indicate that metabolomic measurements of the placenta may not effectively recognize metabolites important for immune maturation.
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| 23. |
- Hartvigsson, Olle, 1991, et al.
(författare)
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Differences between Arterial and Venous Umbilical Cord Plasma Metabolome and Association with Parity
- 2022
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Ingår i: Metabolites. - : MDPI AG. - 2218-1989 .- 2218-1989. ; 12:2
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Tidskriftsartikel (refereegranskat)abstract
- Umbilical cord blood is frequently used in health monitoring of the neonate. Results may be affected by the proportion of arterial and venous cord blood, the venous blood coming from the mother to supply oxygen and nutrients to the infant, and the arterial carrying waste products from the fetus. Here, we sampled arterial and venous umbilical cords separately from 48 newly delivered infants and examined plasma metabolomes using GC-MS/MS metabolomics. We investigated differences in metabolomes between arterial and venous blood and their associations with gestational length, birth weight, sex, and whether the baby was the first born or not, as well as maternal age and BMI. Using multilevel random forest analysis, a classification rate of 79% was achieved for arteriovenous differences (p = 0.004). Several monosaccharides had higher concentrations in the arterial cord plasma while amino acids were higher in venous plasma, suggesting that the main differences in the measured arterial and venous plasma metabolomes are related to amino acid and energy metabolism. Venous cord plasma metabolites related to energy metabolism were positively associated with parity (77% classification rate, p = 0.004) while arterial cord plasma metabolites were not. This underlines the importance of defining cord blood type for metabolomic studies.
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| 24. |
- Hålldin, Elin, et al.
(författare)
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Factors Explaining Interpersonal Variation in Plasma Enterolactone Concentrations in Humans
- 2019
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Ingår i: Molecular Nutrition and Food Research. - : Wiley. - 1613-4125 .- 1613-4133. ; 63:16
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Forskningsöversikt (refereegranskat)abstract
- Lignans are diphenolic plant compounds with potential health modulating properties that are absorbed to the circulation and metabolized to the enterolignans enterodiol (END) and enterolactone (ENL) by gut microbiota. Epidemiological studies have inconsistently shown that a high lignan intake and circulating ENL are associated with reduced risk of breast-, prostate-, and colorectal cancer as well as cardiovascular disease and total and cause-specific mortality. Inconsistencies can be due to interpersonal variation of ENL formation or responses. The aim of this review is to identify and evaluate the impact of factors influencing variability in plasma concentrations of the main enterolignan, ENL. The main determinants of plasma ENL concentrations are intake of lignan and lignan-rich foods, composition and activity of intestinal microflora, antimicrobial use, nutrient intake, BMI, smoking, sex, and age. Composition and activity of the intestinal microbiota appear to be the most critical factor governing interpersonal variability in plasma ENL concentration followed by the use of antibiotics. Future studies with combined data from gut microbiota and metabolomics with food intake and life style data can be used to estimate the relative contribution of the different factors to ENL concentration in quantitative terms.
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| 25. |
- Iversen, Kia Noehr, 1987, et al.
(författare)
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Appetite and Subsequent Food Intake Were Unaffected by the Amount of Sourdough and Rye in Soft Bread-A Randomized Cross-Over Breakfast Study
- 2018
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Ingår i: Nutrients. - : MDPI AG. - 2072-6643 .- 2072-6643. ; 10:11
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Tidskriftsartikel (refereegranskat)abstract
- Sourdough fermented bread has been suggested to have beneficial health effects, in part mediated by increased satiety in the postprandial phase, but only limited research has been conducted to verify this. The current study aimed to investigate the effect of the amounts of sourdough and rye in soft bread on postprandial appetite. On 6 occasions, 23 healthy volunteers consumed 5 different test breads, with varying amount of rye and sourdough, and a yeast-fermented refined wheat control bread as part of a breakfast meal. The sourdough ranged between 9⁻51% of dough weight and rye content between 35⁻48% of flour weight. Appetite was recorded using visual analogue scales from immediately before breakfast and every 30 min the following 4 h. An ad libitum lunch was served 4 h after the breakfast meal, from which voluntary energy intake was measured. While some of the test breads resulted in lower hunger ratings and increased sense of fullness compared to the refined wheat bread, there were no differences between the test breads. The content of rye in the test breads differed within a narrow range, which might explain the lack of a consistent effect of rye on appetite. Microstructural examination of the test breads showed an increased aggregation of proteins in the breads with high content of sourdough, indicating additional changes to the breads, beyond change in pH, which may counteract the potential effect of decreased pH in the bread on appetite. In conclusion, our study does not support an effect of sourdough on appetite and ad libitum food intake.
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