Global and threshold-free transcriptional regulatory networks reconstruction through integrating ChIP-Chip and expression data

Inferring transcriptional regulatory networks from high-throughput biological data is a major challenge to bioinformatics today. To address this challenge, we developed TReNGO (Transcriptional Regulatory Networks reconstruction based on Global Optimization), a global and threshold-free algorithm with simulated annealing for inferring regulatory networks by the integration of ChIP-chip and expression data. Superior to existing methods, TReNGO was expected to find the optimal structure of transcriptional regulatory networks without any arbitrary thresholds or predetermined number of transcriptional modules (TMs). TReNGO was applied to both synthetic data and real yeast data in the rapamycin response. In these applications, we demonstrated an improved functional coherence of TMs and TF (transcription factor)- target predictions by TReNGO when compared to GRAM, COGRIM or to analyzing ChIP-chip data alone. We also demonstrated the ability of TReNGO to discover unexpected biological processes that TFs may be involved in and to also identify interesting novel combinations of TFs.

The intriguing and forgotten international exchanges in the master plan for the reconstruction of Skopje

At 5:17AM on Friday 26 July 1963, Skopje was struck by an earthquake, which in 17 seconds destroyed approximately 75% of the urban fabric, and changed the course of its history from an unknown town to a city of international focus. Immediate actions and a formidable level of local organization; an unprecedented pouring in of aid from the other Yugoslav republics and from individual nations and organisations; and a monumental role for the United Nations in the co-ordination of international , architectural and urban planning expertise for the city's large-scale and long-term reconstruction, laid the foundation for what has been called 'a precise Marxist revolutionary situation' .1 The detail of the paper concerns Stage 4, Replanning 1963 to 1966 of the planning strategy that was organised into five stages, and has a major interest in the invited United Nations (UN) international competition ~o redesign approximately two square kilometres of the city centre.2 Action is associated with activity as productivity, but in Skopje added to this were symbolic human acts and heroic action such that its inhabitants regained their city and importantly a new position as city in the world.

Image reconstruction using Loop subdivision

It is an ultimate objective to reconstruct an image with high quality using a compact representation, which is the basic step in image-manipulation fields. We propose an effective vectorization based approach to reconstruct an image using a triangular mesh associated with Loop subdivision scheme in the present paper. With an initial control mesh obtained by simplifying a dense mesh from a quality-preserved triangulation, we produce the final optimal control mesh by optimizing a mesh over topologies and colors to approximate the given image. The main advantages of the approach include: (1) the reconstruction of an image is not restricted to be aligned with image coordinate axes; (2) a high order continuous function is defined over a triangle instead of a bilinear interpolation; (3) it is a compact and vector-based representation easy to edit and transmit. Experimental results are presented to confirm the effectiveness of the method. Comparisons with the bi-cubic spline and the mesh simplification methods demonstrate the merits of our method in reconstruction quality and representation size.

Reconstruction over ruins : rebuilding Dresden's Frauenkirche

The debate over the reconstruction of Dresden’s Frauenkirche, the city’s landmark Protestant cathedral destroyed by aerial bombing in 1945, exemplifies the conflicts inherent in the treatment of war-related cultural heritage. Although initially preserved only by virtue of some local citizens’ determination to rebuild the church, in time the Frauenkirche ruins emerged in their own right as an arresting antiwar symbol and one of the foremost sites of war memory and commemoration in the divided Germany. This development created a certain conundrum, for if the church ever were to be rebuilt such a project could only materialise by disturbing the ruins, which supporters claimed were deserving of preservation in their unaltered state. With the advent of reunification, the kind of heritage to be preserved at the site—and the way in which it was to be conserved—came under renewed and reintensified scrutiny and debate. By tracing the shifting dynamics during a half-century of debate over how the Frauenkirche site should be conserved, this chapter examines the impact that struggles over war memory and commemoration can have on cultural heritage. It surveys the arguments for and against rebuilding the Frauenkirche before, during, and after reunification, and considers what aspirations conflicting sides had for expressing personal, national, and international memories of war, loss, and the German national past. Finally, it explores how anastylosis rebuilding principles were used to find a compromise by incorporating, somewhat controversially, parts of the existing ruins into the new church after a local citizens’ initiative successfully appealed for worldwide support to reconstruct the Frauenkirche in the wake of Germany’s reunification.

Kenzo Tange's forgotten master plan for the reconstruction of Skopje

After the 1963 earthquake, which is said to have destroyed seventy-five per cent of the urban fabric, Skopje, capital city of the Republic of Macedonia (then in Yugoslavia) became a centre of architectural activity. The United Nations held a limited competition for the reconstruction of Skopje, inviting four foreign firms and four Yugoslavian firms to participate. Tange's submission received sixty per cent of the first prize, co-operating with Yugoslav architects to develop the design idea. What can this project tell us about modernism re-inscribed in Japan, and the kinds of internationalism that the United Nations constructed? Japanese Metabolism, of which Tange was a pioneer, heralded Japan as a new centre for innovation in architecture; a new nationalism re-oriented the suffering after Hiroshima and Nagasaki. Tange developed and realised in Skopje the striking planning ideas he began in his Tokyo Bay proposal. This article examines Tange's master plan for Skopje. It argues that his key elements, the City Wall and the City Gate, exemplify Tange's drive for a new vision in the context of destruction, and that these remain definitive elements today even in the context of a messy transition from a communist to a capitalist society.

Climate change and sea turtles : a 150-year reconstruction of incubation temperatures at a major marine turtle rookery

Sea turtles show temperature dependent sex determination. Using an empirical relationship between sand and air temperature, we reconstructed the nest temperatures since 1855 at Ascension Island, a major green turtle (Chelonia mydas) rookery. Our results show that inter-beach thermal variations, previously ascribed to the albedo of the sand, which varies hugely from one beach to another, have persisted for the last century. Reconstructed nest temperatures varied by only 0.5 °C on individual beaches over the course of the nesting season, while the temperature difference between two key nesting beaches was always around 3 °C. Hence inter-beach thermal variations are the main factor causing a large range of incubation temperatures at this rookery. There was a general warming trend for nests, with a mean increase in reconstructed nest temperatures for different months of between 0.36 and 0.49 °C for the last 100 years.

Resistance and reconstruction: Older women talk about childhood sexual abuse

Research which explores the experiences of women, who have experienced childhood sexual abuse is, in the main, focused on young and middle aged women. The perspectives of older women is often absent or hidden in the literature. This study explores the experiences of 16 Australian women aged 57 years and older who have experienced childhood sexual abuse. It aims to privilege their views and highlight their particular contexts in order to redress professional assumptions regarding the notions of recovery. Additionally, in discussing their experiences, the women contribute to insights regarding the patterns of inequality which are produced as a result of dominant discourses that promote ageist and sexist prescriptions in the construction of the self. These insights demonstrate how the women have resisted a range of oppressive patterns in their everyday lives. The study follows a feminist research framework and aims to contribute to the fields of social work practice and critical feminist gerontology.

Recognition, resistance and reconstruction : an introduction to subjectivities and social justice

The aim of this book is to examine new forms of resistance to social injustices in contemporary Western societies. Resistance requires agency, and agency is grounded in notions of the subject and subjectivity. It is a premise of this book that new and/or reconstructed forms of subjectivity are required to challenge social relations of subordination and domination.
Subjectivity is primarily based on lived experience. While subjectivity is sometimes used to explore individualistic strategies for personal meaning, we argue that subjectivity is central to political struggles against regimes of power. Thus, understanding how subjects are constituted is important in fostering the capacity of critical reflection and social transformation.
Our aim  is to understand the relationship between subjectivity and the wider social order. The relationship between the psyche and society is one of the most challenging issues facing social theory. While there is a variety of theoretical approaches to subjectivity, those that explore the links between the subject and society are the most promising in developing strategies for resistance. In this introductory chapter, we review and interrogate what we believe are the most important theoretical approaches to subjectivity, drawing upon Marxism, critical theory, feminism, postcolonialism and post-structuralism. Our aim in this book is not to develop a new theory of subjectivities. Rather, we are more concerned with investigating how diverse subjectivities are constructed and reconstructed.

Effects of Mitochondrial DNA Rate Variation on Reconstruction of Pleistocene Demographic History in a Social Avian Species, Pomatostomus superciliosus

Mitochondrial sequence data is often used to reconstruct the demographic history of Pleistocene populations in an effort to understand how species have responded to past climate change events. However, departures from neutral equilibrium conditions can confound evolutionary inference in species with structured populations or those that have experienced periods of population expansion or decline. Selection can affect patterns of mitochondrial DNA variation and variable mutation rates among mitochondrial genes can compromise inferences drawn from single markers. We investigated the contribution of these factors to patterns of mitochondrial variation and estimates of time to most recent common ancestor (TMRCA) for two clades in a co-operatively breeding avian species, the white-browed babbler Pomatostomus superciliosus. Both the protein-coding ND3 gene and hypervariable domain I control region sequences showed departures from neutral expectations within the superciliosus clade, and a two-fold difference in TMRCA estimates. Bayesian phylogenetic analysis provided evidence of departure from a strict clock model of molecular evolution in domain I, leading to an over-estimation of TMRCA for the superciliosus clade at this marker. Our results suggest mitochondrial studies that attempt to reconstruct Pleistocene demographic histories should rigorously evaluate data for departures from neutral equilibrium expectations, including variation in evolutionary rates across multiple markers. Failure to do so can lead to serious errors in the estimation of evolutionary parameters and subsequent demographic inferences concerning the role of climate as a driver of evolutionary change. These effects may be especially pronounced in species with complex social structures occupying heterogeneous environments. We propose that environmentally driven differences in social structure may explain observed differences in evolutionary rate of domain I sequences, resulting from longer than expected retention times for matriarchal lineages in the superciliosus clade.