Computational models for inferring biochemical networks

Biochemical networks are of great practical importance. The interaction of biological compounds in cells has been enforced to a proper understanding by the numerous bioinformatics projects, which contributed to a vast amount of biological information. The construction of biochemical systems (systems of chemical reactions), which include both topology and kinetic constants of the chemical reactions, is NP-hard and is a well-studied system biology problem. In this paper, we propose a hybrid architecture, which combines genetic programming and simulated annealing in order to generate and optimize both the topology (the network) and the reaction rates of a biochemical system. Simulations and analysis of an artificial model and three real models (two models and the noisy version of one of them) show promising results for the proposed method.The Romanian National Authority for Scientific Research, CNDI–UEFISCDI, Project No. PN-II-PT-PCCA-2011-3.2-0917

Modeling mycorrhizal fungi dispersal by the mycophagous swamp wallaby (Wallabia bicolor)

Despite the importance of mammal-fungal interactions, tools to estimate the mammal-assisted dispersal distances of fungi are lacking. Many mammals actively consume fungal fruiting bodies, the spores of which remain viable after passage through their digestive tract. Many of these fungi form symbiotic relationships with trees and provide an array of other key ecosystem functions. We present a flexible, general model to predict the distance a mycophagous mammal would disperse fungal spores. We modelled the probability of spore dispersal by combining animal movement data from GPS-telemetry with data on spore gut-retention time. We test this model using an exemplar generalist mycophagist, the swamp wallaby (Wallabia bicolor). We show that swamp wallabies disperse fungal spores hundreds of metres—and occasionally up to 1265 m—from the point of consumption, distances that are ecologically significant for many mycorrhizal fungi. In addition to highlighting the ecological importance of swamp wallabies as dispersers of mycorrhizal fungi in eastern Australia, our simple modelling approach provides a novel and effective way of empirically describing spore dispersal by a mycophagous animal. This approach is applicable to the study of other animal-fungi interactions in other ecosystems.Funding provided by: Hermon Slade FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001109Award Number: HSF08-6Funding provided by: Australian Research CouncilCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100000923Award Number: DP0557022Methods are described in the published article

Climate change promotes parasitism in a coral symbiosis.

Coastal oceans are increasingly eutrophic, warm and acidic through the addition of anthropogenic nitrogen and carbon, respectively. Among the most sensitive taxa to these changes are scleractinian corals, which engineer the most biodiverse ecosystems on Earth. Corals' sensitivity is a consequence of their evolutionary investment in symbiosis with the dinoflagellate alga, Symbiodinium. Together, the coral holobiont has dominated oligotrophic tropical marine habitats. However, warming destabilizes this association and reduces coral fitness. It has been theorized that, when reefs become warm and eutrophic, mutualistic Symbiodinium sequester more resources for their own growth, thus parasitizing their hosts of nutrition. Here, we tested the hypothesis that sub-bleaching temperature and excess nitrogen promotes symbiont parasitism by measuring respiration (costs) and the assimilation and translocation of both carbon (energy) and nitrogen (growth; both benefits) within Orbicella faveolata hosting one of two Symbiodinium phylotypes using a dual stable isotope tracer incubation at ambient (26 °C) and sub-bleaching (31 °C) temperatures under elevated nitrate. Warming to 31 °C reduced holobiont net primary productivity (NPP) by 60% due to increased respiration which decreased host %carbon by 15% with no apparent cost to the symbiont. Concurrently, Symbiodinium carbon and nitrogen assimilation increased by 14 and 32%, respectively while increasing their mitotic index by 15%, whereas hosts did not gain a proportional increase in translocated photosynthates. We conclude that the disparity in benefits and costs to both partners is evidence of symbiont parasitism in the coral symbiosis and has major implications for the resilience of coral reefs under threat of global change

Dynamics of Flux Creep in Underdoped Single Crystals of Y_1-xPr_xBa_2Cu_3O_7-d

Transport as well as magnetic relaxation properties of the mixed state were studied on strongly underdoped Y_1-xPr_xBa_2Cu_3O_7-d crystals. We observed two correlated phenomena - a coupling transition and a transition to quantum creep. The distribution of transport current below the coupling transition is highly nonuniform, which facilitates quantum creep. We speculate that in the mixed state below the coupling transition, where dissipation is nonohmic, the current distribution may be unstable with respect to self-channeling resulting in the formation of very thin current-carrying layers.Comment: 11 pages, 9 figures, Submitted to Phys. Rev.

Investigating dietary life histories and mobility of children buried in St Gertrude Church Cemetery, Riga, Latvia (15th– 17th centuries AD)

Carbon and nitrogen isotope profiles were obtained from incremental dentine analysis of 19 non‐adults from a cemetery in Riga, Latvia. The research compared the life histories and diet between people buried in two mass graves and the general cemetery. The δ13C profiles of several children from the mass graves were similar but did not resemble the patterns seen in children from the general cemetery, suggesting that they probably represented a different population group. The rise in δ15N values towards the end of the life of four individuals from one mass grave suggests they were victims of an historically documented famine

Person Re-identification Using Clustering Ensemble Prototypes

Abstract. This paper presents an appearance-based model to deal with the person re-identification problem. Usually in a crowded scene, it is ob-served that, the appearances of most people are similar with regard to the combination of attire. In such situation it is a difficult task to distin-guish an individual from a group of alike looking individuals and yields an ambiguity in recognition for re-identification. The proper organiza-tion of the individuals based on the appearance characteristics leads to recognize the target individual by comparing with a particular group of similar looking individuals. To reconstruct a group of individual accord-ing to their appearance is a crucial task for person re-identification. In this work we focus on unsupervised based clustering ensemble approach for discovering prototypes where each prototype represents similar set of gallery image instances. The formation of each prototype depends upon the appearance characteristics of gallery instances. The estimation of k-NN classifier is employed to specify a prototype to a given probe image. The similarity measure computation is performed between the probe and a subset of gallery images, that shares the same prototype with the probe and thus reduces the number of comparisons. Re-identification perfor-mance on benchmark datasets are presented using cumulative matching characteristic (CMC) curves.

Absence of a Zero Temperature Vortex Solid Phase in Strongly Disordered Superconducting Bi Films

We present low temperature measurements of the resistance in magnetic field of superconducting ultrathin amorphous Bi films with normal state sheet resistances, $R_N$, near the resistance quantum, $R_Q={\hbar\over {e^2}}$. For $R_N<R_Q$, the tails of the resistive transitions show the thermally activated flux flow signature characteristic of defect motion in a vortex solid with a finite correlation length. When $R_N$ exceeds $R_Q$, the tails become non-activated. We conclude that in films where $R_N>R_Q$ there is no vortex solid and, hence, no zero resistance state in magnetic field. We describe how disorder induced quantum and/or mesoscopic fluctuations can eliminate the vortex solid and also discuss implications for the magnetic-field-tuned superconductor-insulator transition.Comment: REVTEX, 4 pages, 3 figure

Treatment response to indacaterol/glycopyrronium versus salmeterol/fluticasone in exacerbating COPD patients by gender: a post-hoc analysis in the FLAME study

Background: The burden of chronic obstructive lung disease (COPD) is increasing in women, with recent evidence suggesting gender differences in disease characteristics and potentially in treatment outcomes. Methods: FLAME was a 52-week randomized controlled trial in patients with severe-to-very-severe COPD and a history of exacerbations. In this post-hoc analysis, gender-based baseline differences and treatment outcomes between indacaterol/glycopyrronium 110/50 μg once daily (IND/GLY) and salmeterol/fluticasone 50/500 twice daily (SFC) were assessed in terms of rate of exacerbations, time-to-first exacerbation, lung function, health status, and rescue medication use. Results: This post-hoc analysis included 2557 men and 805 women. Baseline characteristics differed between genders, with women being younger, having better lung function and more often experiencing ≥2 exacerbations in the previous year. Compared with SFC, IND/GLY treatment was associated with reductions in the annualized rates of moderate/severe exacerbations (rate ratio [95% CI]: 0.81 [0.73–0.91], 0.89 [0.74–1.07] in men and women, respectively). Similarly, time-to-first moderate/severe exacerbation was also delayed (hazard ratio [95% CI]: 0.79 [0. 70–0.89] and 0.76 [0.63–0.91] in men and women, respectively). Results were similar for all (mild/moderate/severe) exacerbations. Improvements in lung function, health status and rescue medication use with IND/GLY vs SFC were comparable between men and women. The smaller sample size for women may account for some observed discrepancies in treatment responses. Conclusions: Although there were gender differences in baseline characteristics, IND/GLY demonstrated similar trends for exacerbation prevention and lung function improvement in men and women with moderate-to-verysevere COPD and a history of exacerbations compared with SFC. Small differences in the effects seen between genders may be attributed to the different sizes of the two groups and need to be further evaluated in randomized trials that are appropriately powered for gender analysis. Trial registration: Post hoc analysis of the FLAME study. ClinicalTrials.gov number: NCT01782326. Registered 1 February 2013