Constraints and entropy in a model of network evolution

Barab´asi-Albert’s ‘Scale Free’ model is the starting point for much of the accepted theory of the evolution of real world communication networks. Careful comparison of the theory with a wide range of real world networks, however, indicates that the model is in some cases, only a rough approximation to the dynamical evolution of real networks. In particular, the exponent γ of the power law distribution of degree is predicted by the model to be exactly 3, whereas in a number of real world networks it has values between 1.2 and 2.9. In addition, the degree distributions of real networks exhibit cut offs at high node degree, which indicates the existence of maximal node degrees for these networks. In this paper we propose a simple extension to the ‘Scale Free’ model, which offers better agreement with the experimental data. This improvement is satisfying, but the model still does not explain why the attachment probabilities should favor high degree nodes, or indeed how constraints arrive in non-physical networks. Using recent advances in the analysis of the entropy of graphs at the node level we propose a first principles derivation for the ‘Scale Free’ and ‘constraints’ model from thermodynamic principles, and demonstrate that both preferential attachment and constraints could arise as a natural consequence of the second law of thermodynamics

Gene × dietary pattern interactions in obesity: Analysis of up to 68 317 adults of European ancestry

Obesity is highly heritable. Genetic variants showing robust associations with obesity traits have been identified through genome-wide association studies. We investigated whether a composite score representing healthy diet modifies associations of these variants with obesity traits. Totally, 32 body mass index (BMI)- and 14 waist-hip ratio (WHR)-associated single nucleotide polymorphisms were genotyped, and genetic risk scores (GRS) were calculated in 18 cohorts of European ancestry (n = 68 317). Diet score was calculated based on self-reported intakes of whole grains, fish, fruits, vegetables, nuts/seeds (favorable) and red/processed meats, sweets, sugar-sweetened beverages and fried potatoes (unfavorable). Multivariable adjusted, linear regression within each cohort followed by inverse variance-weighted, fixed-effects meta-analysis was used to characterize: (a) associations of each GR

Meta-analysis of 49 549 individuals imputed with the 1000 Genomes Project reveals an exonic damaging variant in ANGPTL4 determining fasting TG levels

Background So far, more than 170 loci have been associated with circulating lipid levels through genomewide association studies (GWAS). These associations are largely driven by common variants, their function is often not known, and many are likely to be markers for the causal variants. In this study we aimed to identify more new rare and low-frequency functional variants associated with circulating lipid levels. Methods We used the 1000 Genomes Project as a reference panel for the imputations of GWAS data from ~60 000 individuals in the discovery stage and ~90 000 samples in the replication stage. Results Our study resu

1000 Genomes-based metaanalysis identifies 10 novel loci for kidney function

HapMap imputed genome-wide association studies (GWAS) have revealed >50 loci at which common variants with minor allele frequency >5% are associated with kidney function. GWAS using more complete reference sets for imputation, such as those from The 1000 Genomes project, promise to identify novel loci that have been missed by previous efforts. To investigate the value of such a more complete variant catalog, we conducted a GWAS meta-Analysis of kidney function based on the estimated glomerular filtration rate (EGFR) in 110,517 European ancestry participants using 1000 Genomes imputed data. We identified 10 novel loci with p-value < 5 × 10-8 previously missed by HapMap-based GWAS. Six of these loci (HOXD8, ARL15, PIK3R1, EYA4, ASTN2, and EPB41L3) are tagged by common SNPs unique to the 1000 Genomes reference panel. Using pathway analysis, we identified 39 significant (FDR < 0.05) genes and 127 significantly (FDR < 0.05) enriched gene sets, wh

Deepwater species. Handbook of fish age estimation protocols and validation methods

Assessment of individual age through the use of calcified structures (scales, otoliths, opercular bones, fin rays, etc.) has been proven to be very useful in assessing the status of any fish stock. According to Panfili et al. (2002), data on age and growth of fish are essential for understanding vital traits of species and populations (e.g. lifespan, age at recruitment, age at sexual maturity, reproduction periods, migrations, mortality) and the study of population demographic structure and its dynamics (e.g. age-based stock assessment). The age profile of a fish stock can be indicative of its general “health”, as one will expect to see evidence of a broad range of ages in a healthy population. A lack of young fish may indicate recruitment failure, which will have repercussions in future years, while a lack of older fish can signal overexploitation of the stock. Fisheries scientists are especially concerned with the dynamics of exploited populations, with the view to providing advice about the sustainable harvesting of the resource. In the ICES Area, this task is generally focused on providing a quantitative assessment and forecast on a stock, with age data at its core. Hilborn and Walters (1992) pointed out that the “aim of such studies is not only to assess the state of stocks and fisheries relative to historical states, biological reference points or management targets, but also to evaluate the consequences for both fish stocks and fishermen, of alternative management scenarios.” Therefore, it is clear that reliable age–length data are important for the management and sustainable exploitation of fish stocks. The need for reliable data is especially acute in times when stock levels are low and errors in predictions can have devastating effects on the resource

The H63D variant in the HFE gene predisposes to arthralgia, chondrocalcinosis and osteoarthritis

Objectives: To investigate the relation between the HFE C282Y and H63D variants with arthralgia and joint pathology in the population-based Rotterdam Study. Methods: From a cohort of 7983 people aged 55 years and over, 2095 randomly drawn subjects were genotyped for C282Y and H63D variants. We compared the frequency of arthralgia, and the presence of chondrocalcinosis, osteophytes, joint space narrowing and radiographic osteoarthritis in hand, hip and knee joints, and Heberden's nodes in carriers of HFE variants with that in non-carriers. Results: Overall, there was a significantly higher frequency of arthralgia (odds ratio 1.6; 95% CI 1.0 to 2.6), oligoarthralgia (2.3; 1.2 to 4.4) and Heberden's nodes (2.0; 1.1 to 3.8) in H63D homozygotes compared with non-carriers. In subjects aged 65 years or younger, H63D homozygotes had significantly more often polyarthralgia (3.1; 1.3 to 7.4), chondrocalcinosis in hip or knee joints (4.7; 1.2 to 18.5), and more hand joints with osteophytes (6.1±1.0 vs 4.4±0.3), space narrowing (2.8±0.5 vs 1.0±0.1), radiographic osteoarthritis (4.4±0.7 vs 2.0±0.2) and Heberden's nodes (3.1; 1.3 to 12.8) than non-carriers. We found no relation of arthralgia or joint pathology to C282Y, but compound heterozygotes had a significantly higher frequency of arthralgia (2.9; 1.0 to 9.3), chondrocalcinosis in hip joints (6.5; 1.8 to 22.3), and an increased number of osteophytes in knee (6.9±1.2, n = 5 vs 2.4±0.1) joints at a later age (>65 years). Conclusions: The HFE H63D variant may explain, at least in part, the prevalence of arthralgia in multiple joints sites, chondrocalcinosis, and hand osteoarthritis in the general population

Mutations in the hemochromatosis gene (HFE) and stroke

BACKGROUND AND PURPOSE: Increased serum iron is found to be a risk factor for stroke. Carriers of HFE C282Y and H63D mutations have elevated serum iron levels and may have an increased risk for stroke. We studied the association between HFE gene mutations, carotid atherosclerosis, and stroke. METHODS: We compared the frequency of the HFE C282Y and H63D gene mutations in 202 prevalent and incident cases of stro