iTriplet, a rule-based nucleic acid sequence motif finder

<p>Abstract</p> <p>Background</p> <p>With the advent of high throughput sequencing techniques, large amounts of sequencing data are readily available for analysis. Natural biological signals are intrinsically highly variable making their complete identification a computationally challenging problem. Many attempts in using statistical or combinatorial approaches have been made with great success in the past. However, identifying highly degenerate and long (>20 nucleotides) motifs still remains an unmet challenge as high degeneracy will diminish statistical significance of biological signals and increasing motif size will cause combinatorial explosion. In this report, we present a novel rule-based method that is focused on finding degenerate and long motifs. Our proposed method, named iTriplet, avoids costly enumeration present in existing combinatorial methods and is amenable to parallel processing.</p> <p>Results</p> <p>We have conducted a comprehensive assessment on the performance and sensitivity-specificity of iTriplet in analyzing artificial and real biological sequences in various genomic regions. The results show that iTriplet is able to solve challenging cases. Furthermore we have confirmed the utility of iTriplet by showing it accurately predicts polyA-site-related motifs using a dual Luciferase reporter assay.</p> <p>Conclusion</p> <p>iTriplet is a novel rule-based combinatorial or enumerative motif finding method that is able to process highly degenerate and long motifs that have resisted analysis by other methods. In addition, iTriplet is distinguished from other methods of the same family by its parallelizability, which allows it to leverage the power of today's readily available high-performance computing systems.</p

Secondary literacy across the curriculum: Challenges and possibilities

This paper discusses the challenges and possibilities attendant upon successfully implementing literacy across the curriculum initiatives – or ‘school language policies’ as they have come to be known - particularly at the secondary or high school level. It provides a theoretical background to these issues, exploring previous academic discussions of school language policies, and highlights key areas of concern as well as opportunity with respect to school implementation of such policies. As such, it provides a necessary conceptual background to the subsequent papers in this special issue, which focus upon the Secondary Schools’ Literacy Initiative (SSLI) – a New Zealand funded programme that aims to establish cross-curricular language and literacy policies in secondary schools

Boson stars in massive dilatonic gravity

We study equilibrium configurations of boson stars in the framework of a class scalar-tensor theories of gravity with massive gravitational scalar (dilaton). In particular we investigate the influence of the mass of the dilaton on the boson star structure. We find that the masses of the boson stars in presence of dilaton are close to those in general relativity and they are sensitive to the ratio of the boson mass to the dilaton mass within a typical few percent. It turns out also that the boson star structure is mainly sensitive to the mass term of the dilaton potential rather to the exact form of the potential.Comment: 9 pages, latex, 9 figures, one figure dropped, new comments added, new references added, typos correcte

Recurrence risk of occult micrometastases and isolated tumor cells in early stage endometrial cancer: A case control study

Objectives: To determine whether previously undetected occult micrometastasis (MM) or isolated tumor cells (ITC) is associated with increased recurrence odds in stage I-II endometrioid adenocarcinoma. Methods: Women with recurrent stage I/II EC who had complete pelvic and para-aortic were identified as the outcome of interest. A case-control study was designed with the exposure defined as occult MM/ITC not seen on original nodal pathology. Controls were found by frequency-matching in a 1:2 case control ratio. Original nodal slides were re-reviewed, stained and tested with immunohistochemical to detect occult MM/ITC and the odds of associated recurrence was calculated. Results: Of 153 included, 50 with and 103 without recurrence, there was no difference in age (p = 0.46), race (p = 0.24), stage (p = 0.75), FIGO grade (p = 0.64), lymphovascular space invasion (LVSI); p = 1.00, or GOG 99 high-intermediate risk (HIR) criteria (p = 0.35). A total of 18 ITC (11.8%) and 3 MM (2.0%) not previously identified were found in 19 patients. Finding occult MM/ITC was not associated with more lymph nodes (LN) removed (p = 0.67) or tumor grade (p = 0.48) but was significantly associated with stage (p \u3c 0.01). LVSI (p = 0.09) and meeting high-intermediate risk criteria (p = 0.09), were closely associated but not statistically significant. Isolated ITC were not associated with increased odds for recurrence (OR 0.71, CL: 0.20 - 2.22, p = 0.57), recurrence free survival (RFS) (p = 0.85) or overall survival (OS) (p = 0.92). Conclusions: In early-stage EC, identification of occult MM or ITC is uncommon and associated with stage. The presence of ITC was not associated with increased odds of recurrence. Adjusting stage or treatment may avoided based on ITC alone. Isolated MM were rare in our population, and further investigation is warranted

Options for National Parks and Reserves for Adapting to Climate Change

Past and present climate has shaped the valued ecosystems currently protected in parks and reserves, but future climate change will redefine these conditions. Continued conservation as climate changes will require thinking differently about resource management than we have in the past; we present some logical steps and tools for doing so. Three critical tenets underpin future management plans and activities: (1) climate patterns of the past will not be the climate patterns of the future; (2) climate defines the environment and influences future trajectories of the distributions of species and their habitats; (3) specific management actions may help increase the resilience of some natural resources, but fundamental changes in species and their environment may be inevitable. Science-based management will be necessary because past experience may not serve as a guide for novel future conditions. Identifying resources and processes at risk, defining thresholds and reference conditions, and establishing monitoring and assessment programs are among the types of scientific practices needed to support a broadened portfolio of management activities. In addition to the control and hedging management strategies commonly in use today, we recommend adaptive management wherever possible. Adaptive management increases our ability to address the multiple scales at which species and processes function, and increases the speed of knowledge transfer among scientists and managers. Scenario planning provides a broad forward-thinking framework from which the most appropriate management tools can be chosen. The scope of climate change effects will require a shared vision among regional partners. Preparing for and adapting to climate change is as much a cultural and intellectual challenge as an ecological challenge

Charged Scalar-Tensor Boson Stars: Equilibrium, Stability and Evolution

We study charged boson stars in scalar-tensor (ST) gravitational theories. We analyse the weak field limit of the solutions and analytically show that there is a maximum charge to mass ratio for the bosons above which the weak field solutions are not stable. This charge limit can be greater than the GR limit for a wide class of ST theories. We numerically investigate strong field solutions in both the Brans Dicke and power law ST theories. We find that the charge limit decreases with increasing central boson density. We discuss the gravitational evolution of charged and uncharged boson stars in a cosmological setting and show how, at any point in its evolution, the physical properties of the star may be calculated by a rescaling of a solution whose asymptotic value of the scalar field is equal to its initial asymptotic value. We focus on evolution in which the particle number of the star is conserved and we find that the energy and central density of the star decreases as the cosmological time increases. We also analyse the appearance of the scalarization phenomenon recently discovered for neutron stars configurations and, finally, we give a short discussion on how making the correct choice of mass influences the argument over which conformal frame, the Einstein frame or the Jordan frame, is physical.Comment: RevTeX, 27 pages, 9 postscript figures. Minor revisions and updated references. Accepted for publication in Phys. Rev.

Boson Stars in General Scalar-Tensor Gravitation: Equilibrium Configurations

We study equilibrium configurations of boson stars in the framework of general scalar-tensor theories of gravitation. We analyse several possible couplings, with acceptable weak field limit and, when known, nucleosynthesis bounds, in order to work in the cosmologically more realistic cases of this kind of theories. We found that for general scalar-tensor gravitation, the range of masses boson stars might have is comparable with the general relativistic case. We also analyse the possible formation of boson stars along different eras of cosmic evolution, allowing for the effective gravitational constant far out form the star to deviate from its current value. In these cases, we found that the boson stars masses are sensitive to this kind of variations, within a typical few percent. We also study cases in which the coupling is implicitly defined, through the dependence on the radial coordinate, allowing it to have significant variations in the radius of the structure.Comment: 19 pages in latex, 3 figures -postscript- may be sent via e-mail upon reques

Green technologies for sustainable water management: Introduction and overview

© 2016 American Society of Civil Engineers. This chapter presents the background, current development and future opportunities of green technologies and issues to facilitate strategic planning of sustainable water management systems. It describes the fundamental concepts and current and future applications of green technologies for sustainable improvement in water management. The chapter discusses the appropriate approaches and policies in achieving sustainable objectives and promoting green design and supplies for water utilization. Sustainable water management has received great attention over recent years because of its substantial benefits to the environment, society, and economy. Improvements in water management are likely to come from green technologies fueled by individual curiosity, dedicated effort, and opportunities within a strategic program supported by national and international agencies, universities, and industries. These innovations can significantly contribute to less nonrenewable resource requirement, reduced carbon footprint, greenhouse gas emissions and costs, minimized water losses, and enhanced removal of contaminants