An article published in BMCBioInformatics presents GraphSNP: an interactive visualisation tool which allows users to visualize single nucleotide polymorphism distances for investigating outbreak clusters and transmission routes.
To start using GraphSNP, users can simply drag and drop the SNP alignment and metadata file into the web page. The alignment file must contain a minimum of two fasta-formatted nucleotide sequences of equal length. Alternatively, a symmetric pairwise distance matrix can be uploaded if users precompute the distance using 3rd party tools.
Overall, the slowest process is visualising a complete graph of SNP distance , such as when the threshold is equal to the maximum distance. Generally, GraphSNP performs best on datasets containing less than 500 samples. With higher sample numbers the generated graphs become uninformative, limiting their usefulness to explore outbreaks and transmission events.GraphSNP performance on different sample size.
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Association between periodontitis and osteoporosis in United States adults from the National Health and Nutrition Examination Survey: a cross-sectional analysis - BMC Oral HealthObjective This cross-sectional study aimed to investigate the association between periodontitis and osteoporosis among US adults as well as the subgroup of menopausal women. Background Periodontitis and osteoporosis are both chronic inflammatory diseases characterized by local or systemic bone resorption. Since they share many risk factors, and the significant decrease in estrogen along with menopause is unfavorable for both diseases, it’s reasonable to assume that there exists some links between the two diseases, especially during the menopause. Methods We analyzed data from the National Health and Nutrition Examination Survey (NHANES) 2009–2010 and 2013–2014. Periodontitis (defined according to the CDC/AAP definition) and osteoporosis (assessed by the dual-energy radiation absorptiometry) data were available for 5736 participants, and 519 subjects were enrolled in the subgroup of menopausal women aged 45–60 years old. We used binary logistic regression analysis to examine the association between the two diseases both in crude and fully adjusted model. Results In the fully adjusted model, osteoporosis was significantly associated with an increased risk of periodontal disease (OR:1.66, 95% CI: 1.00–2.77) in the whole population. As to the subgroup of menopausal women, osteoporosis group had an adjusted OR of 9.66 (95% CI: 1.13–82.38) for developing severe periodontitis in the fully adjusted model. Conclusions Osteoporosis is significantly associated with periodontitis and the association is even more pronounced in menopausal women with severe periodontitis.
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Change in habitual intakes of flavonoid-rich foods and mortality in US males and females - BMC MedicineBackground Higher baseline intakes of flavonoid-rich foods and beverages are associated with a lower risk of chronic disease and mortality in observational studies. However, associations between changes in intakes and mortality remain unclear. We aimed to evaluate associations between 8-year changes in intakes of (1) individual flavonoid-rich foods and (2) a composite measure (termed the ‘flavodiet’) of foods and beverages that are known to be main contributors to flavonoid intake and subsequent total and cause-specific mortality. Methods We evaluated associations between 8-year changes in intakes of (1) individual flavonoid-rich foods and (2) a novel ‘flavodiet’ score and total and cause-specific mortality. We included 55,786 females from the Nurses’ Health Study (NHS) and 29,800 males from the Health Professionals Follow-up Study (HPFS), without chronic disease at baseline in our analyses. Using multivariable-adjusted Cox proportional hazard models, we examined associations of 8-year changes in intakes of (1) flavonoid-rich foods and (2) the flavodiet score with subsequent 2-year lagged 6-year risk of mortality adjusting for baseline intakes. Data were pooled using fixed-effects meta-analyses. Results We documented 15,293 deaths in the NHS and 8988 deaths in HPFS between 1986 and 2018. For blueberries, red wine and peppers, a 5%, 4% and 9% lower risk of mortality, respectively, was seen for each 3.5 servings/week increase in intakes while for tea, a 3% lower risk was seen for each 7 servings/week increase [Pooled HR (95% CI) for blueberries; 0.95 (0.91, 0.99); red wine: 0.96 (0.93, 0.99); peppers: 0.91 (0.88, 0.95); and tea: 0.97 (0.95, 0.98)]. Conversely, a 3.5 servings/week increase in intakes of onions and grapefruit plus grapefruit juice was associated with a 5% and 6% higher risk of total mortality, respectively. An increase of 3 servings per day in the flavodiet score was associated with an 8% lower risk of total mortality [Pooled HR: 0.92 (0.89, 0.96)], and
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Are dietary intake and nutritional status of specific polyunsaturated fatty acids correlated with sarcopenia outcomes in community-dwelling older adults with sarcopenia? – Exploratory results from ENHANce - BMC GeriatricsAims To explore the relationship between dietary polyunsaturated fatty acids (PUFAs) intake, nutritional PUFAs status and sarcopenia outcomes in sarcopenic older adults. Methods The Exercise and Nutrition for Healthy AgeiNg (ENHANce) is an ongoing 5-armed triple blinded randomized controlled trial, in sarcopenic older adults (| 65y) aiming to assess the effect of combined anabolic interventions (protein, omega-3 supplement and exercise) on physical performance in these adults, compared to single/placebo interventions. Baseline data were used for a secondary, exploratory, cross-sectional analysis. Dietary PUFAs intake was assessed with 4-day food records, status with RBC membrane fatty acids profiles. Spearman’s rho(ρ) correlation coefficients were calculated to explore associations of PUFAs intake and status with sarcopenia-defining parameters (muscle strength, mass and physical performance), physical activity (step count) and quality of life (SF-36, SarQoL). Results In total, 29 subjects (9♂/20♀, mean age 76.3 ± 5.4y) were included. Total omega-3 intake of participants (1.99 ± 0.99 g/d) was below the recommended intake (♂:2.8–5.6 g/d; ♀:2.2–4.4 g/d). Intake and status of PUFAs were not correlated. Regarding correlations with outcomes, α-linolenic acid status was inversely associated with appendicular lean mass (aLM) (ρ:-0.439; p = 0.017), whereas docosahexaenoic acid status was positively associated with aLM (ρ:0.388; p = 0.038). Some omega-3 PUFAs intake and status markers were positively associated with step count, SF-36 and SarQoL scores, whereas gamma-linolenic acid status was inversely associated with SF-36 physical component summary score (ρ = -0.426; p = 0.024). Conclusions Although intake of omega-3 and omega-6 was low, the present exploratory study generated new hypotheses for potential correlations of PUFAs intake and status with sarcopenia outcomes in older adults with sarcopenia.
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