Bagging statistical network inference from large-scale gene expression data.

Modern biology and medicine aim at hunting molecular and cellular causes of biological functions and diseases. Gene regulatory networks (GRN) inferred from gene expression data are considered an important aid for this research by providing a map of molecular interactions. Hence, GRNs have the potential enabling and enhancing basic as well as applied research in the life sciences. In this paper, we introduce a new method called BC3NET for inferring causal gene regulatory networks from large-scale gene expression data. BC3NET is an ensemble method that is based on bagging the C3NET algorithm, which means it corresponds to a Bayesian approach with noninformative priors. In this study we demonstrate for a variety of simulated and biological gene expression data from S. cerevisiae that BC3NET is an important enhancement over other inference methods that is capable of capturing biochemical interactions from transcription regulation and protein-protein interaction sensibly. An implementation of BC3NET is freely available as an R package from the CRAN repository. © 2012 de Matos Simoes, Emmert-Streib.

Altered porphyrin excretion and histopathology of greylag geese (Anser anser) exposed to soil contaminated with lead and arsenic in the Guadalquivir Marshes, southwestern Spain

Greylag geese (Anser anser) in the Guadalquivir Marshes (southwestern Spain) can be exposed to sources of inorganic pollution such as heavy metals and arsenic from mining activities or Pb shot used for hunting. We have sampled 270 fecal excreta in different areas of the marshes in 2001 to 2002 to evaluate the exposure to Pb, Zn, Cu, Mn, and As and to determine its relationship with soil ingestion and with the excretion of porphyrins and biliverdin as biomarkers. These effects and the histopathology of liver, kidney, and pancreas were also studied in 50 geese shot in 2002 to 2004. None of the geese had ingested Pb shot in the gizzard. This contrasts with earlier samplings before the ban of Pb shot for waterfowl hunting in 2001 and the removal of Pb shot in points of the Doñana National Park (Spain) in 1999 to 2000. The highest exposure through direct soil ingestion to Pb and other studied elements was observed in samples from Entremuros, the area of the Doñana Natural Park affected by the Aznalcóllar mine spill in 1998. Birds from Entremuros also more frequently showed mononuclear infiltrates in liver and kidney than birds from the unaffected areas, although other more specific lesions of Pb or Zn poisoning were not observed. The excretion of coproporphyrins, especially of the isomer I, was positively related to the fecal As concentration, and the ratio of coproporphyrin III/I was positively related to fecal Pb concentration. Biliary protoporphyrin IX concentration was also slightly related to hepatic Pb concentration. This study reflects biological effects on terrestrial animals by the mining pollution in Doñana that can be monitored with the simple noninvasive sampling of feces.

Cold War Politics in Britain and the Contested Legacy of the Spanish Civil War

This article offers a sustained examination of how the vicissitudes of the Cold War shaped changing interpretations of the Spanish Civil War in Britain. Considering the perspectives of participants and historians, it focuses on the diverse strands of the Left that frequently drew on the civil war to attack each other and to make wider arguments about the global Cold War. First, with the aim of criticizing Communist take-overs in Eastern Europe in the late 1940s, the article analyzes retrospective assaults on Communist party tactics and Soviet foreign policy in Spain. Second, in order to argue that the Soviet Union took a counter-revolutionary line after 1956, it investigates the re-emergence of debates over the Spanish revolution. Third, to express disapproval of the United States, it examines the increasing use of the civil war as an analogy in Cold War international affairs from the 1960s. Fourth, in support of non-Soviet Left-of-Centre collaboration, most notably Eurocommunism in the 1970s and opposition to Margaret Thatcher’s Conservative government in the 1980s, it considers the renewed emphasis on the popular front. The trajectories of these debates reveal that, over time, the weight of the Left’s criticism moved from the Soviet Union towards the United States.

Water-hydrophobic compound interactions with the microbial cell

The structural interactions of biological macromolecules, their biochemical activities and, ultimately, the metabolic function of cellular systems are dependent upon weak inter- and intra-molecular forces such as hydrogen bonds, Van der Waals forces, and the hydrophobic effect. Water molecules, and those of hydrophobic substances such as hydrocarbons, can take part in and/or modify these interactions and thereby determine the operational and structural stability of the microbial cell and its macromolecular systems. We explain how the cytosol, plasma membrane and the extracellular solution form a material and energetic continuum; and discuss the behavior of hydrophobic substances of extracellular origin as they migrate into the plasma membrane and into the cell's interior. The adverse effects of substances with a log P octanol-water =2, that partition into the hydrophobic domains of biological macromolecules, are discussed in relation to microbial cell function; and we speculate whether the cellular stress that they induce is symmetrical or asymmetrical in nature. In the context of the microbial environment, we take a situational-functional approach to consider how hydrophobic stressors interact with the microbial cell, and what types of evasion tactics microbes can employ to minimize their inhibitory activities. Finally, we discuss the ecological implications of hydrocarbon-induced cellular stress for microbial systems.

Flexibility of Continental Navigation and Migration in European Mallards

The ontogeny of continent-wide navigation mechanisms of the individual organism, despite being crucial for the understanding of animal movement and migration, is still poorly understood. Several previous studies, mainly conducted on passerines, indicate that inexperienced, juvenile birds may not generally correct for displacement during fall migration. Waterbirds such as the mallard (Anas platyrhynchos, Linnaeus 1758) are more flexible in their migration behavior than most migratory songbirds, but previous experiments with waterbirds have not yet allowed clear conclusions about their navigation abilities. Here we tested whether immature mallard ducks correct for latitudinal displacement during fall migration within Europe. During two consecutive fall migration periods, we caught immature females on a stopover site in southeast Sweden, and translocated a group of them ca. 1,000 km to southern Germany. We followed the movements of the ducks via satellite GPS-tracking and observed their migration decisions during the fall and consecutive spring migration. The control animals released in Ottenby behaved as expected from banding recoveries: they continued migration during the winter and in spring returned to the population's breeding grounds in the Baltics and Northwest Russia. Contrary to the control animals, the translocated mallards did not continue migration and stayed at Lake Constance. In spring, three types of movement tactics could be observed: 61.5% of the ducks (16 of 26) stayed around Lake Constance, 27% (7 of 26) migrated in a northerly direction towards Sweden and 11.5% of the individuals (3 of 26) headed east for ca. 1,000 km and then north. We suggest that young female mallards flexibly adjust their migration tactics and develop a navigational map that allows them to return to their natal breeding area.

Attitudes and Ethics: Evaluating Knowledge and Regulatory Constructs in Planning Enforcement Practice

The departure point for the paper is the need to scrutinise previously unconsidered dimensions which are fundamental to understanding the dynamics of the planning enforcement system. Drawing upon emerging themes in regulation theory the paper fuses these with knowledge constructs. The rationale is that regulatory regimes must be informed by knowledge imparted from a range of sources and the resultant quality of decision making is inextricably linked to the robustness and completeness of the evidence base collated.
The theoretical analysis, coupled with proposed radical legislative changes, provides a lens for an empirical investigation which scrutinises tactics, strategies, operational mechanisms, attitudinal dimensions and ethics with a view to identifying key factors impacting upon enforcement efficacy. Prizes and pitfalls are identified in the course of the analysis and evaluation, with evidence-based remedies suggested where appropriate. The paper concludes by reflecting on the importance of theoretical synergy, epistemological advancement, taking cognisance of ethical and attitudinal challenges facing the planning profession; and, stresses the importance of identifying and bringing to book those who flagrantly breach the Code of Professional Conduct.

Étude des impacts écologiques du dynamisme spatio-temporel des habitats naturels sur la faune menacée du Complexe Zones Humides Mahavavy-Kinkony, Madagascar.

This study of the Mahavavy-Kinkony Wetland Complex (MKWC) assesses the impacts of habitat change on the resident globally threatened fauna. Located in Boeny Region, northwest Madagascar, the Complex encompasses a range of habitats including freshwater lakes, rivers, marshes, mangrove forests, and deciduous forest. Spatial modelling and analysis tools were used to (i) identify the important habitats for selected, threatened fauna, (ii) assess their change from 1950 to 2005, (iii) detect the causes of change, (iv) simulate changes to 2050 and (v) evaluate the impacts of change. The approach for prioritising potential habitats for threatened species used ecological science techniques assisted by the decision support software Marxan. Nineteen species were analysed: nine birds, three primates, three fish, three bats and one reptile. Based on knowledge of local land use, supervised classification of Landsat images from 2005 was used to classify the land use of the Complex. Simulations of land use change to 2050 were carried out based on the Land Change Modeler module in Idrisi Andes with the neural network algorithm. Changes in land use at site level have occurred over time but they are not significant. However, reductions in the extent of reed marshes at Lake Kinkony and forests at Tsiombikibo and Marofandroboka directly threaten the species that depend on these habitats. Long term change monitoring is recommended for the Mahavavy Delta, in order to evaluate the predictions through time. The future change of Andohaomby forest is of great concern and conservation actions are recommended as a high priority. Abnormal physicochemical properties were detected in lake Kinkony due to erosion of the four watersheds to the south, therefore an anti-erosion management plan is required for these watersheds. Among the species of global conservation concern, Sakalava rail (Amaurornis olivieri), Crowned sifaka (Propithecus coronatus) and dambabe (Paretroplus dambabe) are estimated the most affected, but at the site level Decken’s sifaka (Propithecus deckeni), kotsovato (Paretroplus kieneri) and Madagascan big-headed turtle (Erymnochelys madagascariensis) are also threatened. Local enforcement of national legislation on hunting means that MKWC is among the sites where the flying fox (Pteropus rufus) and Madagascan rousette (Rousettus madagascariensis) are well protected. Ecological restoration, ecological research and actions to reduce anthropogenic pressures are recommended.

Limits of Dissent, Perils of Activism: Spaces of Resistance and the New Security Logic

On 26 December 2003 an Israeli activist was shot by the Israeli Army while he was participating in a demonstration organized by Anarchists Against the Wall (AAtW) in the West Bank. This was the first time Israeli Soldiers have deliberately shot live bullets at a Jewish-Israeli activist. This paper is an attempt to understand the set of conditions, the enveloping frameworks, and the new discourses that have made this event, and similar shootings that soon followed, possible. Situating the actions of AAtW within a much wider context of securitization—of identities, movements, and bodies—we examine strategies of resistance which are deployed in highly securitized public spaces. We claim that an unexpected matrix of identity in which abnormality is configured as security threat render the bodies of activists especially precarious. The paper thus provides an account of the new rationales of security technologies and tactics which increasingly govern public spaces.

Holocene landscape intervention and plant food production strategies in island and mainland Southeast Asia

In the areas adjacent to the drowned Pleistocene continent of Sunda – present-day Mainland and Island SE Asia – the Austronesian Hypothesis of a diaspora of rice cultivators from Taiwan ∼4200 years ago has often been linked with the start of farming. Mounting evidence suggests that these developments should not be conflated and that alternative explanations should be considered, including indigenous inception of complex patterns of plant food production and early exchange of plants, animals, technology and genes. We review evidence for widespread forest disturbance in the Early Holocene which may accompany the beginnings of complex food-production. Although often insubstantial, evidence for incipient and developing management of rainforest vegetation and of developing complex relationships with plants is present, and early enough to suggest that during the Early to mid-Holocene this vast region was marked by different approaches to plant food production. The trajectory of the increasingly complex relationships between people and their food organisms was strongly locally contingent and in many cases did not result in the development of agricultural systems that were recognisable as such at the time of early European encounters. Diverse resource management economies in the Sunda and neighbouring regions appear to have accompanied rather than replaced a reliance on hunting and gathering. This, together with evidence for Early Holocene interaction between these neighbours, gives cause for us to question some authors continued adherence to a singular narrative of the Austronesian Hypothesis and the ‘Neolithisation’ of this part of the world. It also leads us to suggest that the forests of this vast region are, to an extent, a cultural artefact.

Zooarchaeology at the Niah Caves, Sarawak:Context and Research Issues INTRODUCTION

Extensive archaeological excavations in the Niah Caves (Sarawak, Malaysian Borneo) over the past 50 years have produced perhaps 750 000 fragments of vertebrate bone, one of the largest faunal assemblages in the region, This paper introduces a series of research studies examining different aspects of the Niah fauna, and discusses how they are contributing to, and shaping, regional research agendas relating to prehistoric environments and societies in Island Southeast Asia. Zooarchaeology has traditionally had a rather 'Cinderella' status here, but the ongoing programme of study of the Niah Caves fauna is demonstrating the remarkable potential of this material to address questions of Pleistocene and Holocene climate and environment, biodiversity, human activities within caves, people's engagement with the landscapes they inhabited as foragers and farmers, and the nature of the transition from foraging to farming. Copyright (C) 2009 John Wiley & Sons, Ltd.

The 'human revolution' in lowland tropical Southeast Asia:the antiquity and behavior of anatomically modern humans at Niah Cave (Sarawak, Borneo)

Recent research in Europe, Africa, and Southeast Asia suggests that we can no longer assume a direct and exclusive link between anatomically modern humans and behavioral modernity (the 'human revolution'), and assume that the presence of either one implies the presence of the other: discussions of the emergence of cultural complexity have to proceed with greater scrutiny of the evidence on a site-by-site basis to establish secure associations between the archaeology present there and the hominins who created it. This paper presents one such case study: Niah Cave in Sarawak on the island of Borneo, famous for the discovery in 1958 in the West Mouth of the Great Cave of a modern human skull, the 'Deep Skull,' controversially associated with radiocarbon dates of ca. 40,000 years before the present. A new chronostratigraphy has been developed through a re-investigation of the lithostratigraphy left by the earlier excavations, AMS-dating using three different comparative pre-treatments including ABOX of charcoal, and U-series using the Diffusion-Absorption model applied to fragments of bones from the Deep Skull itself. Stratigraphic reasons for earlier uncertainties about the antiquity of the skull are examined, and it is shown not to be an `intrusive' artifact. It was probably excavated from fluvial-pond-desiccation deposits that accumulated episodically in a shallow basin immediately behind the cave entrance lip, in a climate that ranged from times of comparative aridity with complete desiccation, to episodes of greater surface wetness, changes attributed to regional climatic fluctuations. Vegetation outside the cave varied significantly over time, including wet lowland forest, montane forest, savannah, and grassland. The new dates and the lithostratigraphy relate the Deep Skull to evidence of episodes of human activity that range in date from ca. 46,000 to ca. 34,000 years ago. Initial investigations of sediment scorching, pollen, palynomorphs, phytoliths, plant macrofossils, and starch grains recovered from existing exposures, and of vertebrates from the current and the earlier excavations, suggest that human foraging during these times was marked by habitat-tailored hunting technologies, the collection and processing of toxic plants for consumption, and, perhaps, the use of fire at some forest-edges. The Niah evidence demonstrates the sophisticated nature of the subsistence behavior developed by modern humans to exploit the tropical environments that they encountered in Southeast Asia, including rainforest. (c) 2006 Elsevier Ltd. All rights reserved.

Bone tool analysis

This article examines the osseous technologies that can be created from animal skeletons. 'Tool' status is accorded to a skeletal element or fragment that has been modified subsequent to its isolation from the carcass. Such anthropic adaptation may be deliberate (e.g., through manufacture) and/or appear as a result of utilization, and is granted in instances where these details cannot otherwise be ascribed to alternative nonanthropic causes. Implements can display a combination of traces from both human and natural sources and as such the study of them involves both zooarchaeological (i.e., via animal ecology, hunting, and butchery) and technological analysis.... As an exemplar of this, the following discussion will present some of the similarities and differences that exist between osseous and lithic raw materials and tool-blank production, and will situate both in an operational sequence of animal procurement and processing. It will then give an account of principal manufacturing techniques, methods for establishing tool function, and the phenomenon of 'pseudo tools'. © 2008 Copyright © 2008 Elsevier Inc.

The early exploitation of Southeast Asian mangroves:Bone technology from caves and open sites

This paper focuses on the contribution that the study of bone technology is making to the understanding of early tropical subsistence in Southeast Asia. Newly completed research suggests that during the period from the terminal Pleistocene to mid Holocene, bone tools may have featured prominently in coastal subsistence. There are indications that this technology may have had a particular association with hunting and gathering in the mangrove forests that proliferated along many coasts during this period. The study of these tools thus represents a rare chance to examine prehistoric extractive technologies, which are generally agreed to have been predominantly made on organic, nonpreserving media. The evidence presented also suggests that prehistoric foragers from this region possessed a good working understanding of the mechanical properties of bone and used bone implements where conditions and needs suited the parameters of this material. © 2005 by the University of Hawai'i Press.

Understanding Nonviolence

The use of nonviolent action is on the rise. From the Occupy Movement to the Arab Spring and mass protests on the streets of Brazil, activists across the world are increasingly using unarmed tactics to challenge oppressive, corrupt and unjust systems. But what exactly do we mean by nonviolence? How is it deployed and to what effect? Do nonviolent campaigns with political motivations differ from those driven by primarily economic concerns? What are the limits and opportunities for activists engaging in nonviolent action today? Is the growing number of nonviolence protests indicative of a new type of twenty-first century struggle or is it simply a passing trend?
Understanding Nonviolence: Contours and Contexts is the first book to offer a comprehensive introduction to nonviolence in theory and practice. Combining insightful analysis of key theoretical debates with fresh perspectives on contemporary and historical case studies, it explores the varied approaches, aims, and trajectories of nonviolent campaigns from Gandhi to the present day. With cutting-edge contributions from leading scholars and practitioners in the field, this accessible and lively book will be essential reading for activists, students and teachers of contentious politics, international security, and peace and conflict studies.