Infinite-Order Percolation and Giant Fluctuations in a Protein Interaction Network

We investigate a model protein interaction network whose links represent interactions between individual proteins. This network evolves by the functional duplication of proteins, supplemented by random link addition to account for mutations. When link addition is dominant, an infinite-order percolation transition arises as a function of the addition rate. In the opposite limit of high duplication rate, the network exhibits giant structural fluctuations in different realizations. For biologically-relevant growth rates, the node degree distribution has an algebraic tail with a peculiar rate dependence for the associated exponent.Comment: 4 pages, 2 figures, 2 column revtex format, to be submitted to PRL 1; reference added and minor rewording of the first paragraph; Title change and major reorganization (but no result changes) in response to referee comments; to be published in PR

Cost-effectiveness of lung transplantation in The Netherlands: a scenario analysis

STUDY OBJECTIVES: To calculate cost-effectiveness of scenarios concerning lung transplantation in The Netherlands. DESIGN: Microsimulation model predicting survival, quality of life, and costs with and without transplantation program, based on data of the Dutch lung transplantation program of 1990 to 1995. SETTING: Netherlands, University Hospital Groningen. PATIENTS: Included were 425 patients referred for lung transplantation, of whom 57 underwent transplantation. INTERVENTION: Lung transplantation. RESULTS: For the baseline scenario, the costs per life-year gained are G 194,000 (G=Netherlands guilders) and the costs per quality-adjusted life-year (QALY) gained are G 167,000. Restricting patient inflow ("policy scenario") lowers the costs per life-year gained: G 172,000 (costs per QALY gained: G 144,000). The supply of more donor lungs could reduce the costs per life-year gained to G 159,000 (G 135,000 per QALY gained; G1 =US $0.6, based on exchange rate at the time of the study). CONCLUSIONS: Lung transplantation is an expensive but effective intervention: survival and quality of life improve substantially after transplantation. The costs per life-year gained are relatively high, compared with other interventions and other types of transplantation. Restricting the patient inflow and/or raising donor supply improves cost-effectiveness to some degree. Limiting the extent of inpatient screening or lower future costs of immunosuppressives may slightly improve the cost-effectiveness of the program

Structure of a large social network

We study a social network consisting of over $10^4$ individuals, with a degree distribution exhibiting two power scaling regimes separated by a critical degree $k_{\rm crit}$, and a power law relation between degree and local clustering. We introduce a growing random model based on a local interaction mechanism that reproduces all of the observed scaling features and their exponents. Our results lend strong support to the idea that several very different networks are simultenously present in the human social network, and these need to be taken into account for successful modeling.Comment: 5 pages, 5 figure

CO oxidation activity of Pt/CeO2 catalysts below 0ºC: Platinum loading effects

Reducing the operating temperature of oxidation catalysts is important for designing energy efficient processes, extending catalyst lifetime, and abating pollutants, especially in cold climates. Herein, high CO oxidation activity at sub-ambient temperatures is reported for Pt/CeO2 catalysts with high content of Pt in the form of dispersed Pt2+ and Pt4+ centers. Whereas the reference 1 wt%Pt catalyst was active for CO oxidation only above 100ᵒC, the 8 and 20 wt%Pt catalysts converted 60 and 90 % of CO, respectively, below 0ᵒC. Ionic platinum was shown to facilitate oxygen release from ceria and lower the light-off temperature of the reaction occurring through the Mars-van-Krevelen mechanism. However, the remarkable activity observed at sub-ambient temperatures for the ≥8 wt%Pt catalysts is proposed to involve O2 and CO reactants weakly adsorbed on PtOx clusters. The synergies between ionic platinum and nanostructured ceria reported in this work advance the knowledge-driven design of catalysts for low-temperature oxidation reactions

Classification of protein interaction sentences via gaussian processes

The increase in the availability of protein interaction studies in textual format coupled with the demand for easier access to the key results has lead to a need for text mining solutions. In the text processing pipeline, classification is a key step for extraction of small sections of relevant text. Consequently, for the task of locating protein-protein interaction sentences, we examine the use of a classifier which has rarely been applied to text, the Gaussian processes (GPs). GPs are a non-parametric probabilistic analogue to the more popular support vector machines (SVMs). We find that GPs outperform the SVM and na\"ive Bayes classifiers on binary sentence data, whilst showing equivalent performance on abstract and multiclass sentence corpora. In addition, the lack of the margin parameter, which requires costly tuning, along with the principled multiclass extensions enabled by the probabilistic framework make GPs an appealing alternative worth of further adoption

Increased prevalence of advanced liver fibrosis in patients with psoriasis: A cross-sectional analysis from the rotterdam study

Prevalence of non-alcoholic fatty liver disease is increased in patients with psoriasis. However, it is not known how liver fibrosis correlates with psoriasis. This study investigated the association between psoriasis and liver fibrosis compared with participants without psoriasis within the population-based Rotterdam Study. All participants were screened for liver fibrosis using transient elastography. Liver stiffness > 9.5 kPa suggested advanced liver fibrosis. Psoriasis was identified using a validated algorithm. A total of 1,535 participants were included (mean age ± standard deviation 70.5 ± 7.9 years; 50.8% female; median body mass index 26.4 kg/ m2 (interquartile range 24.2–28.9)) of whom 74 (4.7%) had psoriasis. Prevalence of advanced liver fibrosis was 8.1% in psoriasis patients compared with 3.6% in the reference group (p = 0.05). The risk of advanced liver fibrosis in psoriasis patients remained comparable after adjustment for demographics, lifestyle characteristics and laboratory findings (odds ratio 2.57 (95% confidence interval 1.00–6.63). This study suggests that elderly people with psoriasis are twice as likely to have advanced liver fibrosis irrespective of common risk factors

CYP1A2 and coffee intake and the modifying effect of sex, age, and smoking

Background: The enzyme CYP1A2 (cytochrome 1A2) is involved in the metabolism of certain drugs and caffeine, and its activity can be influenced by factors such as sex, age, and smoking. The single nucleotide polymorphism (SNP) rs762551A>C, which has also been studied for its modifying effect on cardiovascular disease, has been reported to alter enzyme activity. Objective: The objective was to study the effect of CYP1A2, sex, age, and smoking on coffee intake. Design: Within the Rotterdam Study, a population-based cohort, all coffee drinkers for whom genome-wide association data were available were selected. Because SNP rs762551 was not on the Illumina 550 platform, SNP rs2472299 was used as a proxy, with the A allele of rs762551 linked to the G allele of rs2472299. Linear regression analyses were used to determine the effect and interaction of rs2472299, sex, age, and smoking on coffee intake. Adjusted geometric means of coffee intake were calculated per genotype for the different smoking and sex strata by using multivariable general linear models. A combined analysis, with the use of a "risk score,"was performed to determine the contribution of each separate factor. Results: rs2472299G>A, female sex, and nonsmoking were significantly inversely related to coffee intake. Coffee intake was lowest in nonsmoking women homozygous for rs2472299G>A (3.49 cups/d; ∼436 mL). All factors contributed almost linearly to the intake of coffee, with the highest coffee intake in smoking men without the A allele (5.32 cups/d; ∼665 mL). Conclusion: rs2472299G>A, linked to rs762551A>C, sex, age, and smoking significantly contribute to coffee intake

IgA N- and O-glycosylation profiling reveals no association with the pregnancy-related improvement in rheumatoid arthritis

Background: The Fc glycosylation of immunoglobulin G (IgG) is well known to associate with rheumatoid arthritis (RA) disease activity. The same may be true for other classes of Igs. In the present study, we sought to determine whether the glycosylation of IgA was different between healthy subjects and patients with RA, as well as whether it was associated with RA disease activity, in particular with the pregnancy-associated improvement thereof or the flare after delivery. Methods: A recently developed high-throughput method for glycoprofiling of IgA1 was applied to affinity-captured IgA from sera of patients with RA (n = 252) and healthy control subjects (n = 32) collected before, during and after pregnancy. Results: IgA1 O-glycans bore more sialic acids in patients with RA than in control subjects. In addition, levels of bisecting N-acetylglucosamine of the N-glycans at asparagine 144 were higher in the patients with RA. The levels of several N-glycosylation traits were shown to change with pregnancy, similar to what has been shown before for IgG. However, the changes in IgA glycosylation were not associated with improvement or a flare of disease activity. Conclusions: The glycosylation of IgA differs between patients with RA and healthy control subjects. However, our data suggest only a minor, if any, association of IgA glycosylation with RA disease activity

Why social networks are different from other types of networks

We argue that social networks differ from most other types of networks, including technological and biological networks, in two important ways. First, they have non-trivial clustering or network transitivity, and second, they show positive correlations, also called assortative mixing, between the degrees of adjacent vertices. Social networks are often divided into groups or communities, and it has recently been suggested that this division could account for the observed clustering. We demonstrate that group structure in networks can also account for degree correlations. We show using a simple model that we should expect assortative mixing in such networks whenever there is variation in the sizes of the groups and that the predicted level of assortative mixing compares well with that observed in real-world networks.Comment: 9 pages, 2 figure

Scalar meson dynamics in Chiral Perturbation Theory

A comparison of the linear sigma model (L$\sigma$M) and Chiral Perturbation Theory (ChPT) predictions for pion and kaon dynamics is presented. Lowest and next-to-leading order terms in the ChPT amplitudes are reproduced if one restricts to scalar resonance exchange. Some low energy constants of the order $p^4$ ChPT Lagrangian are fixed in terms of scalar meson masses. Present values of these low energy constants are compatible with the L$\sigma$M dynamics. We conclude that more accurate values would be most useful either to falsify the L$\sigma$M or to show its capability to shed some light on the controversial scalar physics.Comment: 9 pages, REVTeX 4.0. Final version accepted for publicatio