Self organising maps for visualising and modelling

The paper describes the motivation of SOMs (Self Organising Maps) and how they are generally more accessible due to the wider available modern, more powerful, cost-effective computers. Their advantages compared to Principal Components Analysis and Partial Least Squares are discussed. These allow application to non-linear data, are not so dependent on least squares solutions, normality of errors and less influenced by outliers. In addition there are a wide variety of intuitive methods for visualisation that allow full use of the map space. Modern problems in analytical chemistry include applications to cultural heritage studies, environmental, metabolomic and biological problems result in complex datasets. Methods for visualising maps are described including best matching units, hit histograms, unified distance matrices and component planes. Supervised SOMs for classification including multifactor data and variable selection are discussed as is their use in Quality Control. The paper is illustrated using four case studies, namely the Near Infrared of food, the thermal analysis of polymers, metabolomic analysis of saliva using NMR, and on-line HPLC for pharmaceutical process monitoring

Energy Sprawl or Energy Efficiency: Climate Policy Impacts on Natural Habitat for the United States of America

Concern over climate change has led the U.S. to consider a cap-and-trade system to regulate emissions. Here we illustrate the land-use impact to U.S. habitat types of new energy development resulting from different U.S. energy policies. We estimated the total new land area needed by 2030 to produce energy, under current law and under various cap-and-trade policies, and then partitioned the area impacted among habitat types with geospatial data on the feasibility of production. The land-use intensity of different energy production techniques varies over three orders of magnitude, from 1.9–2.8 km2/TW hr/yr for nuclear power to 788–1000 km2/TW hr/yr for biodiesel from soy. In all scenarios, temperate deciduous forests and temperate grasslands will be most impacted by future energy development, although the magnitude of impact by wind, biomass, and coal to different habitat types is policy-specific. Regardless of the existence or structure of a cap-and-trade bill, at least 206,000 km2 will be impacted without substantial increases in energy efficiency, which saves at least 7.6 km2 per TW hr of electricity conserved annually and 27.5 km2 per TW hr of liquid fuels conserved annually. Climate policy that reduces carbon dioxide emissions may increase the areal impact of energy, although the magnitude of this potential side effect may be substantially mitigated by increases in energy efficiency. The possibility of widespread energy sprawl increases the need for energy conservation, appropriate siting, sustainable production practices, and compensatory mitigation offsets

Assessing the ecological risks from the persistence and spread of feral populations of insect-resistant transgenic maize

One source of potential harm from the cultivation of transgenic crops is their dispersal, persistence and spread in non-agricultural land. Ecological damage may result from such spread if the abundance of valued species is reduced. The ability of a plant to spread in non-agricultural habitats is called its invasiveness potential. The risks posed by the invasiveness potential of transgenic crops are assessed by comparing in agronomic field trials the phenotypes of the crops with the phenotypes of genetically similar non-transgenic crops known to have low invasiveness potential. If the transgenic and non-transgenic crops are similar in traits believed to control invasiveness potential, it may be concluded that the transgenic crop has low invasiveness potential and poses negligible ecological risk via persistence and spread in non-agricultural habitats. If the phenotype of the transgenic crop is outside the range of the non-transgenic comparators for the traits controlling invasiveness potential, or if the comparative approach is regarded as inadequate for reasons of risk perception or risk communication, experiments that simulate the dispersal of the crop into non-agricultural habitats may be necessary. We describe such an experiment for several commercial insect-resistant transgenic maize events in conditions similar to those found in maize-growing regions of Mexico. As expected from comparative risk assessments, the transgenic maize was found to behave similarly to non-transgenic maize and to be non-invasive. The value of this experiment in assessing and communicating the negligible ecological risk posed by the low invasiveness potential of insect-resistant transgenic maize in Mexico is discussed

Paving (through) Amazonia: Neoliberal Urbanism and the Reperipheralization of Roraima

This paper examines the neoliberal reshaping of infrastructure provision in Brazil's extreme north since the mid-1990s, when roadway investments resulted in unprecedented regional connectivity. The BR-174 upgrade, the era's most important project, marked a transition from resource-based developmentalism to free-market transnationalism. Primarily concerned with urban competitiveness, the federal government funded the trunk roadway's paving to facilitate manufacturing exports from Manaus. While an effort was made to minimize deforestation, planners sidelined development implications in adjacent Roraima. The state's urban system has thus experienced reperipheralization and intensified primacy. Market-led growth now compounds the inheritance of hierarchical centralism and ongoing governmental neglect. Our study shows a vast territory dependent on primate cities for basic goods and services. Travelling with Roraimans from bypassed towns, we detected long-distance passenger transportation and surface logistics with selective routes. Heterogeneous Roraiman (im)mobilities comprise middle-class tourism and heightened consumerism as well as informal mobility tactics and transnational circulations of precarious labor. The paper exhorts neoliberal urbanism research to look beyond both Euro America's metropoles and their Global South counterparts. Urbanization dynamics in Brazil's extreme north demonstrate that market-disciplined investments to globalize cities produce far-reaching spatial effects. These are felt even by functionally-articulated-yet-marginalized peripheries in ostensibly remote locations

Isomorphic diffuse glioma is a morphologically and molecularly distinct tumour entity with recurrent gene fusions of MYBL1 or MYB and a benign disease course

The “isomorphic subtype of diffuse astrocytoma” was identified histologically in 2004 as a supratentorial, highly differentiated glioma with low cellularity, low proliferation and focal diffuse brain infiltration. Patients typically had seizures since childhood and all were operated on as adults. To define the position of these lesions among brain tumours, we histologically, molecularly and clinically analysed 26 histologically prototypical isomorphic diffuse gliomas. Immunohistochemically, they were GFAP-positive, MAP2-, OLIG2- and CD34-negative, nuclear ATRX-expression was retained and proliferation was low. All 24 cases sequenced were IDH-wildtype. In cluster analyses of DNA methylation data, isomorphic diffuse gliomas formed a group clearly distinct from other glial/glio-neuronal brain tumours and normal hemispheric tissue, most closely related to paediatric MYB/MYBL1-altered diffuse astrocytomas and angiocentric gliomas. Half of the isomorphic diffuse gliomas had copy number alterations of MYBL1 or MYB (13/25, 52%). Gene fusions of MYBL1 or MYB with various gene partners were identified in 11/22 (50%) and were associated with an increased RNA-expression of the respective MYB-family gene. Integrating copy number alterations and available RNA sequencing data, 20/26 (77%) of isomorphic diffuse gliomas demonstrated MYBL1 (54%) or MYB (23%) alterations. Clinically, 89% of patients were seizure-free after surgery and all had a good outcome. In summary, we here define a distinct benign tumour class belonging to the family of MYB/MYBL1-altered gliomas. Isomorphic diffuse glioma occurs both in children and adults, has a concise morphology, frequent MYBL1 and MYB alterations and a specific DNA methylation profile. As an exclusively histological diagnosis may be very challenging and as paediatric MYB/MYBL1-altered diffuse astrocytomas may have the same gene fusions, we consider DNA methylation profiling very helpful for their identification

Potential impact of invasive alien species on ecosystem services provided by a tropical forested ecosystem: a case study from Montserrat

Local stakeholders at the important but vulnerable Centre Hills on Montserrat consider that the continued presence of feral livestock (particularly goats and pigs) may lead to widespread replacement of the reserve’s native vegetation by invasive alien trees (Java plum and guava), and consequent negative impacts on native animal species. Since 2009, a hunting programme to control the feral livestock has been in operation. However long-term funding is not assured. Here, we estimate the effect of feral livestock control on ecosystem services provided by the forest to evaluate whether the biodiversity conservation rationale for continuation of the control programme is supported by an economic case. A new practical tool (Toolkit for Ecosystem Service Site-based Assessment) was employed to measure and compare ecosystem service provision between two states of the reserve (i.e. presence and absence of feral livestock control) to estimate the net consequences of the hunting programme on ecosystem services provided by the forest. Based on this we estimate that cessation of feral livestock management would substantially reduce the net benefits provided by the site, including a 46 % reduction in nature-based tourism (from $419,000 to$228,000) and 36 % reduction in harvested wild meat (from $205,000 to$132,000). The overall net benefit generated from annual ecosystem service flows associated with livestock control in thereserve, minus the management cost, was $214,000 per year. We conclude that continued feral livestock control is important for maintaining the current level of ecosystem services provided by the reserve

A multi-scale modelling framework to guide management of plant invasions in a transboundary context

Background Attention has recently been drawn to the issue of transboundary invasions, where species introduced and naturalized in one country cross international borders and become problematic in neighbouring countries. Robust modelling frameworks, able to identify the environmental drivers of invasion and forecast the current and future potential distribution of invasive species, are needed to study and manage invasions. Limitations due to the lack of species distribution and environmental data, or assumptions of modelling tools, often constrain the reliability of model predictions. Methods We present a multiscale spatial modelling framework for transboundary invasions, incorporating robust modelling frameworks (Multimodel Inference and Ensemble Modelling) to overcome some of the limitations. The framework is illustrated using Hakea sericea Schrad. (Proteaceae), a shrub or small tree native to Australia and invasive in several regions of the world, including the Iberian Peninsula. Two study scales were considered: regional scale (western Iberia, including mainland Portugal and Galicia) and local scale (northwest Portugal). At the regional scale, the relative importance of environmental predictors sets was evaluated and ranked to determine the main general drivers for the species distribution, while the importance of each environmental predictor was assessed at the local scale. The potential distribution of H. sericea was spatially projected for both scale areas. Results Model projections for western Iberia suggest that a large area is environmentally suitable in both Portugal and Spain. Climate and landscape composition sets were the most important determinants of this regional distribution of the species. Conversely, a geological predictor (schist lithology) was more important in explaining its local-scale distribution. Conclusions After being introduced to Portugal, H. sericea has become a transboundary invader by expanding in parts of Galicia (Spain). The fact that a larger area is predicted as environmentally suitable in Spain raises concerns regarding its potential continued expansion. This highlights the importance of transboundary cooperation in the early management of invasions. By reliably identifying drivers and providing spatial projections of invasion at multiple scales, this framework provides insights for the study and management of biological invasions, including the assessment of transboundary invasion risk.This work was funded by FEDER funds through the Operational Programme for Competitiveness Factors - COMPETE and by National Funds through FCT - Foundation for Science and Technology under the project PTDC/AAGMAA/4539/2012 / FCOMP-01-0124-FEDER-027863 (IND_CHANGE). J. Vicente is supported by POPH/FSE funds and by National Funds through FCT - Foundation for Science and Technology through Post-doctoral grant SFRH/BPD/84044/2012. D.M. Richardson acknowledges support from the DST-NRF Centre of Excellence for Invasion Biology and the National Research Foundation (grant 85417).info:eu-repo/semantics/publishedVersio