Evaluating functional network inference using simulations of complex biological systems.

MOTIVATION: Although many network inference algorithms have been presented in the bioinformatics literature, no suitable approach has been formulated for evaluating their effectiveness at recovering models of complex biological systems from limited data. To overcome this limitation, we propose an approach to evaluate network inference algorithms according to their ability to recover a complex functional network from biologically reasonable simulated data. RESULTS: We designed a simulator to generate data representing a complex biological system at multiple levels of organization: behaviour, neural anatomy, brain electrophysiology, and gene expression of songbirds. About 90% of the simulated variables are unregulated by other variables in the system and are included simply as distracters. We sampled the simulated data at intervals as one would sample from a biological system in practice, and then used the sampled data to evaluate the effectiveness of an algorithm we developed for functional network inference. We found that our algorithm is highly effective at recovering the functional network structure of the simulated system-including the irrelevance of unregulated variables-from sampled data alone. To assess the reproducibility of these results, we tested our inference algorithm on 50 separately simulated sets of data and it consistently recovered almost perfectly the complex functional network structure underlying the simulated data. To our knowledge, this is the first approach for evaluating the effectiveness of functional network inference algorithms at recovering models from limited data. Our simulation approach also enables researchers a priori to design experiments and data-collection protocols that are amenable to functional network inference.

Biological parameters and glomalin levels as quality indicators in a soil implanted with exotic forest species in Argentine Patagonia

p.83-88

Biological and demographic response of aphids Nasonovia ribisnigri (Mosley) and Aulacorthum solani (Kaltenbach) (Hemiptera : Aphididae) on lettuce commercial cultivars under laboratory conditions

p.17-24

Biological and demographic response of aphids Nasonovia ribisnigri (Mosley) and Aulacorthum solani (Kaltenbach) (Hemiptera : Aphididae) on lettuce commercial cultivars under laboratory conditions

p.17-24

Structural and biological investigation of ferrocene-substituted 3-methylidene-1,3-dihydro-2H-indol-2-ones

The Knoevenagel condensation of 1,3-dihydro-2H-indol-2-one with ferrocene carboxaldehyde afforded an approximate 2:1 mixture of the geometrical isomers (E)- and (Z)-3-ferrocenylmethylidene-1,3-dihydro-2H-indol-2-one respectively in an overall 67% yield; the air and solution-stable isomers were readily separated by preparative thin layer chromatography and their structures were unequivocally elucidated in solution, by (1)H NMR spectroscopy, and in the solid phase, by X-ray crystallography; both isomers of displayed in vitro toxicity against B16 melanoma and Vero cell lines in the micromolar range and inhibited the kinase VEGFR-2 with IC(50) values of ca. 200 nM.

Tourism is it the ‘new’ driver for regeneration?

Article explores how tourism might be the key driver to urban regeneration in towns and cities as economic crisis deepens.

Review paper: role of aluminum in glass-ionomer dental cements and its biological effects

The role of aluminum in glass-ionomers and resin-modified glass-ionomers for dentistry is reviewed. Aluminum is included in the glass component of these materials in the form of Al(2)O(3) to confer basicity on the glass and enable the glass to take part in the acid-base setting reactions. Results of studies of these reactions by FTIR and magic-angle spinning (MAS)-NMR spectroscopy are reported and the role of aluminum is discussed in detail. Aluminum has been shown to be present in the glasses in predominantly 4-coordination, as well as 5- and 6-coordination, and during setting a proportion of this is converted to 6-coordinate species within the matrix of the cement. Despite this, mature cements may contain detectable amounts of both 4- and 5-coordinate aluminum. Aluminum has been found to be leached from glass-ionomer cements, with greater amounts being released under acidic conditions. It may be associated with fluoride, with which it is known to complex strongly. Aluminum that enters the body via the gastro-intestinal tract is mainly excreted, and only about 1% ingested aluminum crosses the gut wall. Calculation shows that, if a glass-ionomer filling dissolved completely over 5 years, it would add only an extra 0.5% of the recommended maximum intake of aluminum to an adult patient. This leads to the conclusion that the release of aluminum from either type of glass-ionomer cement in the mouth poses a negligible health hazard.

Epilobium parviflorum Schreb. - in vitro study of biological action

Epilobium parviflorum Schreb. (Onagraceae) is used for the treatment of benign prostatic hyperplasia (BPH), which is regarded as an endocrine disorder caused by age-related hormone imbalance and increased oxidative damage [1,2,3]. Epilobium can moderate the obstructive and the irritative symptoms of BPH [1] but its biological action is not entirely identified. E. parviflorum is rich in phytosterols, flavonoids (myricetin, quercetin, kaempferol and their glycosides), phenolic acids, catechins, ellagi- and gallotannins [4]. The potential biological effects of Epilobium parviflorum Schreb. have been investigated, in respect to its antioxidant, anti-inflammatory, enzyme-inhibitory and anti-androgenic effect. The whole-plant water extract showed higher antioxidant effect (IC50=1.65±0.05µg/mL) in DPPH assay than Trolox or ascorbic acid and inhibited the lipid peroxidation examined in TBA assay (IC50=2.31±0.18mg/mL). In concentrations 0.20-15.00µg/mL the extract possessed a protective effect comparable to catalase enzyme (2500 IU/mL), against oxidative damage generated on fibroblast cells. The examination of the COX-inhibitory effect showed that E. parviflorum had an anti-inflammatory effect (IC50=1.38±0.08µg/mL). Investigation of steroid receptor binding ability and the aromatase enzyme-inhibition showed negative results in the concentration range examined.