Evolutionary robustness of differentiation in genetic regulatory networks

We investigate the ability of artificial Genetic Regulatory Networks (GRNs) to evolve differentiation. The proposed GRN model supports non-linear interaction between regulating factors, thereby facilitating the realization of complex regulatory logics. As a proof of concept we evolve GRNs of this kind to follow different pathways, producing two kinds of periodic dynamics in response to minimal differences in external input. Furthermore we find that successive increases in environmental pressure for differentiation, allowing a lineage to adapt gradually, compared to an immediate requirement for a switch between behaviors, yields better results on average. Apart from better success there is also less variability in performance, the latter indicating an increase in evolutionary robustness

Civil society and public health research in the European Union new member states

Introduction Civil society organisations (CSOs) are not-for-profit organisations working for the public interest with concerns complementary to public health. We investigated the contribution of CSOs in public health research. Methods Within a European project STEPS (Strengthening Engagement with Public Health Research), CSOs with interests in health were identified in the new member states of the European Union (Estonia, Latvia, Lithuania, Poland, Hungary, Slovakia, Czech Republic, Slovenia, Romania, Bulgaria, Malta and Cyprus) and workshops organised, held in their own languages. The reports of the workshops were translated into English, and drawn together through a framework analysis. Results CSOs can contribute in all stages of the research cycle, through championship, priority-setting, capacity building and generation of resources, sharing and application of the research results, and dissemination across their network of contacts. There have been successful CSO-researcher collaborations in public health fields. Funding is important, and ministries of health and public institutions should interact more with CSOs. Barriers include attitudes, technical understanding across public health fields. Discussion There is little European empirical literature linking health CSOs and research: our results indicate benefits and further opportunities. In contrast to biomedicine’s link with industry, public health research can align with civil society in not-for-profit research. CSOs are important for European integration, and their contribution should be better recognised at international level

Predictors of Early Numeracy: Applied Measures in Two Childcare Contexts

The purpose of the current research was: (1) To assess differences in early numeracy, phonological awareness, receptive language, executive functioning, and working memory for children in two childcare settings (family and center); (2) To determine whether applied measures of phonological awareness and executive functioning could serve as predictors of numeracy performance. Children (N = 89) ranging in age from 39 to 75 months were recruited from state-licensed childcare centers and family childcare homes. Teacher ratings of executive functioning were significantly related to early number skills, phonological awareness, and receptive language, but none of the parent ratings were significantly related to the child scores. The overall model did not differ between center and family childcare children. Phonological awareness was a significant predictor of number skills for both younger and older children. Receptive language skills were the best predictor of early numeracy performance for younger children and the best predictor for older children was phonological working memory measured by a non-words repetition task. These results suggest a connection between children’s numeracy skills and a developmental change from receptive language skills to phonological working memory skills

Solitonic excitations in the Haldane phase of a S=1 chain

We study low-lying excitations in the 1D $S=1$ antiferromagnetic valence-bond-solid (VBS) model. In a numerical calculation on finite systems the lowest excitations are found to form a discrete triplet branch, separated from the higher-lying continuum. The dispersion of these triplet excitations can be satisfactorily reproduced by assuming approximate wave functions. These wave functions are shown to correspond to moving hidden domain walls, i.e. to one-soliton excitations.Comment: RevTex 3.0, 24 pages, 2 figures on request by fax or mai

Analysis of Clock-Regulated Genes in Neurospora Reveals Widespread Posttranscriptional Control of Metabolic Potential

Neurospora crassa has been for decades a principal model for filamentous fungal genetics and physiology as well as for understanding the mechanism of circadian clocks. Eukaryotic fungal and animal clocks comprise transcription-translation-based feedback loops that control rhythmic transcription of a substantial fraction of these transcriptomes, yielding the changes in protein abundance that mediate circadian regulation of physiology and metabolism: Understanding circadian control of gene expression is key to understanding eukaryotic, including fungal, physiology. Indeed, the isolation of clock-controlled genes (ccgs) was pioneered in Neurospora where circadian output begins with binding of the core circadian transcription factor WCC to a subset of ccg promoters, including those of many transcription factors. High temporal resolution (2-h) sampling over 48 h using RNA sequencing (RNA-Seq) identified circadianly expressed genes in Neurospora, revealing that from ∼10% to as much 40% of the transcriptome can be expressed under circadian control. Functional classifications of these genes revealed strong enrichment in pathways involving metabolism, protein synthesis, and stress responses; in broad terms, daytime metabolic potential favors catabolism, energy production, and precursor assembly, whereas night activities favor biosynthesis of cellular components and growth. Discriminative regular expression motif elicitation (DREME) identified key promoter motifs highly correlated with the temporal regulation of ccgs. Correlations between ccg abundance from RNA-Seq, the degree of ccg-promoter activation as reported by ccg-promoter-luciferase fusions, and binding of WCC as measured by ChIP-Seq, are not strong. Therefore, although circadian activation is critical to ccg rhythmicity, posttranscriptional regulation plays a major role in determining rhythmicity at the mRNA level

Scarring on invariant manifolds for perturbed quantized hyperbolic toral automorphisms

We exhibit scarring for certain nonlinear ergodic toral automorphisms. There are perturbed quantized hyperbolic toral automorphisms preserving certain co-isotropic submanifolds. The classical dynamics is ergodic, hence in the semiclassical limit almost all eigenstates converge to the volume measure of the torus. Nevertheless, we show that for each of the invariant submanifolds, there are also eigenstates which localize and converge to the volume measure of the corresponding submanifold.Comment: 17 page

Effect of rapidly resorbable bone substitute materials on the temporal expression of the osteoblastic phenotype \u3cem\u3ein vitro\u3c/em\u3e

Ideally, bioactive ceramics for use in alveolar ridge augmentation should possess the ability to activate bone formation and, thus, cause the differentiation of osteoprogenitor cells into osteoblasts at their surfaces. Therefore, in order to evaluate the osteogenic potential of novel bone substitute materials, it is important to examine their effect on osteoblastic differentiation. This study examines the effect of rapidly resorbable calcium–alkali– orthophosphates on osteoblastic phenotype expression and compares this behavior to that of ß-tricalcium phosphate (TCP) and bioactive glass 45S5. Test materials were three materials (denominated GB14, GB9, GB9/25) with a crystalline phase Ca2KNa(PO4)2 and with a small amorphous portion containing either magnesium potassium phosphate (GB14) or silica phosphate (GB9 and GB9/25, which also contains Ca2P2O7); and a material with a novel crystalline phase Ca10[K/Na](PO4)7 (material denominated 352i). SaOS-2 human bone cells were grown on the substrata for 3, 7, 14, and 21 days, counted, and probed for an array of osteogenic markers. GB9 had the greatest stimulatory effect on osteoblastic proliferation and differentiation, suggesting that this material possesses the highest potency to enhance osteogenesis. GB14 and 352i supported osteoblast differentiation to the same or a higher degree than TCP, whereas, similar to bioactive glass 45S5, GB9/25 displayed a greater stimulatory effect on osteoblastic phenotype expression, indicating that GB9/25 is also an excellent material for promoting osteogenesis

Preschool Mathematics Performance and Executive Function: Rural-Urban Comparisons across Time

This longitudinal study examined the relationship between executive function (EF) and mathematics with rural and urban preschool children. A panel of direct and indirect EF measures were used to compare how well individual measures, as well as analytic approaches, predicted both numeracy and geometry skill. One hundred eighteen children, ages 39 to 68 months, were given EF and mathematics assessments twice, approximately six months apart, concurrent to their teachers completing an indirect assessment of EF for each child. Results suggest: (1) the child’s age determines if a panel of direct EF measures is a better predictor of numeracy and geometry skills than a single EF measure, (2) geometry and numeracy skill are influenced differently by contextual factors, and (3) the EF-geometry link may develop about six months later than the EF-numeracy connection. As the relationship between preschool age EF and mathematics is better understood, efforts can be made to improve the aspects of EF connected to mathematics skill, which may aid in performance

Using the Hadamard and related transforms for simplifying the spectrum of the quantum baker's map

We rationalize the somewhat surprising efficacy of the Hadamard transform in simplifying the eigenstates of the quantum baker's map, a paradigmatic model of quantum chaos. This allows us to construct closely related, but new, transforms that do significantly better, thus nearly solving for many states of the quantum baker's map. These new transforms, which combine the standard Fourier and Hadamard transforms in an interesting manner, are constructed from eigenvectors of the shift permutation operator that are also simultaneous eigenvectors of bit-flip (parity) and possess bit-reversal (time-reversal) symmetry.Comment: Version to appear in J. Phys. A. Added discussions; modified title; corrected minor error