Discrete time piecewise affine models of genetic regulatory networks

We introduce simple models of genetic regulatory networks and we proceed to the mathematical analysis of their dynamics. The models are discrete time dynamical systems generated by piecewise affine contracting mappings whose variables represent gene expression levels. When compared to other models of regulatory networks, these models have an additional parameter which is identified as quantifying interaction delays. In spite of their simplicity, their dynamics presents a rich variety of behaviours. This phenomenology is not limited to piecewise affine model but extends to smooth nonlinear discrete time models of regulatory networks. In a first step, our analysis concerns general properties of networks on arbitrary graphs (characterisation of the attractor, symbolic dynamics, Lyapunov stability, structural stability, symmetries, etc). In a second step, focus is made on simple circuits for which the attractor and its changes with parameters are described. In the negative circuit of 2 genes, a thorough study is presented which concern stable (quasi-)periodic oscillations governed by rotations on the unit circle -- with a rotation number depending continuously and monotonically on threshold parameters. These regular oscillations exist in negative circuits with arbitrary number of genes where they are most likely to be observed in genetic systems with non-negligible delay effects.Comment: 34 page

Heuristic-based firefly algorithm for bound constrained nonlinear binary optimization

Firefly algorithm (FA) is a metaheuristic for global optimization. In this paper,we address the practical testing of aheuristic-based FA (HBFA) for computing optimaof discrete nonlinear optimization problems,where the discrete variables are of binary type. An important issue in FA is the formulation of attractiveness of each firefly which in turn affects its movement in the search space. Dynamic updating schemes are proposed for two parameters, one from the attractiveness term and the other from the randomization term. Three simple heuristics capable of transforming real continuous variables into binary ones are analyzed. A new sigmoid ‘erf’ function is proposed. In the context of FA, three different implementations to incorporate the heuristics for binary variables into the algorithm are proposed. Based on a set of benchmark problems, a comparison is carried out with other binary dealing metaheuristics. The results demonstrate that the proposed HBFA is efficient and outperforms binary versions of differential evolution (DE) and particle swarm optimization (PSO). The HBFA also compares very favorably with angle modulated version of DE and PSO. It is shown that the variant of HBFA based on the sigmoid ‘erf’ function with ‘movements in continuous space’ is the best, both in terms of computational requirements and accuracy.Fundação para a Ciência e a Tecnologia (FCT

Coating ZnO:Zn Nanoparticles with Alumina for Polymer Protection

Using a modified preparation large nanoparticles of ZnO and ZnO:Zn were coated (without destroying the luminescent properties of the latter), but the coating is a layer of AZO not Al2O3. Large nanoparticles of ZnO:Zn were coated with a layer of ZnO by using only (NH4)HCO3 in the absence of Al2SO4

Young people's opinions of cancer care in England: the BRIGHTLIGHT cohort

OBJECTIVES: The BRIGHTLIGHT cohort study was the national evaluation of cancer services for teenager and young adults (TYA). This was analysis of free-text survey data to better understand their experiences of cancer care. DESIGN: Cohort study SETTING: National Health Service hospitals delivering cancer care in England PARTICIPANTS: 830 young people newly diagnosed with cancer. INTERVENTIONS: Exposure to specialist care in the first 6 months after diagnosis defined as care in a TYA Principal Treatment Centre (PTC). This was categorised as follows: all care in a TYA-PTC (ALL-TYA-PTC), no care in a TYA-PTC (NO-TYA-PTC) so care delivered in a children/adult unit only and some care in a TYA-PTC with additional care in a children's/adult unit (SOME-TYA-PTC). PRIMARY OUTCOME: Data were collected through the BRIGHTLIGHT survey included free-text questions which asked patients 'what was the best aspects of their experiences of care' and 'what aspects could be improved'. These comments were analysed using content analysis. Themes were compared between categories of care, then ranked in order of frequency, ranging from the most endorsed to the least. RESULTS: Overall, young people were most positive about their healthcare team, while the area highlighted for improvement was diagnostic experience. Differences between the three groups suggested those who had some or all treatment in a TYA-PTC valued the place of care. Regardless of where TYA were treated their healthcare teams were favourably viewed. Age appropriate place of care was highlighted to be of value for those in PTCs. CONCLUSIONS: These data show the value young people placed on the care they received in TYA specific wards. Young people who accessed some or all of their care in a TYA-PTC highly endorsed their place of care as one of the best elements of their care, and it is further emphasised by those who had shared care who experienced difficulty with lack of age-appropriate care when treated outside the TYA-PTC

Sex, Body Image, and Relationships: A BRIGHTLIGHT Workshop on Information and Support Needs of Adolescents and Young Adults

PURPOSE: Discovering sexuality and romantic relationships are important development milestones in adolescence and young adulthood. A cancer diagnosis imposes obstacles for young people such as changes in their sexual function due to the disease and/or side effects of treatment, body image concerns, and interpersonal relationship difficulties. This can cause psychological distress and can impact on quality of life. We aimed to explore sexual health information and support needs of adolescents and young adults with cancer. METHODS: Five young people aged 16-24 years, with a previous cancer diagnosis when aged 13-22 years, attended an in-depth 4-hour workshop. The framework approach was used to analyze workshop transcripts. RESULTS: Three overarching themes emerged: (i) information sharing; (ii) contexts and relationships (influencing factors); and (iii) information sharing preferences. Information shared by healthcare professionals was focused on a medicalized view of sex with symptoms, infection control, and protected sex at its core. Young people had unanswered questions related to sexual function, the impact of cancer and how to manage it, and about pleasure, body image, and relationships. Parents' presence at clinical consultations inhibited discussions about sex. Young people wanted professionals who were comfortable to talk about sex with them. CONCLUSION: Young people exhibited significant unmet needs around information provision on sex, body image, and relationships. They wanted information to be given by professionals and access to online resources. Development of training for professionals and resources to support young people requires further work

Ecological Factors Influencing Wild Pig Damage to Planted Pine and Hardwood Seedlings

Expanding wild pig (Sus scrofa) populations across the southern United States has the potential to impact longleaf pine (Pinus palustris) restoration efforts. The depredation of planted pine seedlings is the most widespread and economically costly damage caused by wild pigs in forest plantations. A better understanding of the ecological factors affecting depredation rates will allow managers to implement best management practices to reduce seedling mortality from wild pigs at their most vulnerable stage of growth. From March 2016 to March 2017, we evaluated wild pig preferences for planted pine and hardwood species at a 34.4-ha cutover site and 4.7-ha pecan (Carya illinoinensis) orchard in Bullock County, Alabama, USA. Wild pig damage differed for the 5 seedling species tested, with longleaf and cherrybark oak (Quercus pagodaefolia) being the most preferred. Ninety one percent of seedlings destroyed by wild pigs were from the cutover site. Wild pigs at the cutover site experienced substantially more hunting pressure compared to those at the other site. We believe the debris scattering practices of the logging crew following a clearcut created a desirable foraging environment that led to the initial discovery of the seedlings. The short-term protection and minimization of seedling depredation in young forest plantations may be the most realistic solution to reducing the impact of wild pigs on forestry and timber resources

An expert botanical feature extraction technique based on phenetic features for identifying plant species

In this paper, we present a new method to recognise the leaf type and identify plant species using phenetic parts of the leaf; lobes, apex and base detection. Most of the research in this area focuses on the popular features such as the shape, colour, vein, and texture, which consumes large amounts of computational processing and are not efficient, especially in the Acer database with a high complexity structure of the leaves. This paper is focused on phenetic parts of the leaf which increases accuracy. Detecting the local maxima and local minima are done based on Centroid Contour Distance for Every Boundary Point, using north and south region to recognise the apex and base. Digital morphology is used to measure the leaf shape and the leaf margin. Centroid Contour Gradient is presented to extract the curvature of leaf apex and base. We analyse 32 leaf images of tropical plants and evaluated with two different datasets, Flavia, and Acer. The best accuracy obtained is 94.76% and 82.6% respectively. Experimental results show the effectiveness of the proposed technique without considering the commonly used features with high computational cost

The role of nuclear receptors in the differentiation of oligodendrocyteprecursor cells derived from fetal and adult neural stem cells.

Oligodendrocyte precursor cells (OPCs) differentiation from multipotent neural stem cells (NSCs) into mature oligodendrocytes is driven by thyroid hormone and mediated by thyroid hormone receptors (TRs). We show that several nuclear receptors display strong changes in expression levels between fetal and adult NSCs, with an overexpression of TR\u3b2 and a lower expression of RXR\u3b3 in adult. Such changes may determine the reduced capacity of adult OPCs to differentiate as supported by reduced yield of maturation and compromised mRNA expression of key genes. RXR\u3b3 may be the determinant of these differences, on the evidence of reduced number of mature oligodendrocytes and increased number of proliferating OPCs in RXR\u3b3-/- cultures. Such data also points to RXR\u3b3 as an important regulator of the cell cycle exit, as proved by the dysregulation of T3-induced cell cycle exit-related genes. Our data highlight the biological differences between fetal and adult OPCs and demonstrate the essential role of RXR\u3b3 in the T3-mediated OPCs maturation process