Combining ASTER multispectral imagery analysis and support vector machines for rapid and cost-effective post-fire assessment: a case study from the Greek wildland fires of 2007

Remote sensing is increasingly being used as a cost-effective and practical solution for the rapid evaluation of impacts from wildland fires. The present study investigates the use of the support vector machine (SVM) classification method with multispectral data from the Advanced Spectral Emission and Reflection Radiometer (ASTER) for obtaining a rapid and cost effective post-fire assessment in a Mediterranean setting. A further objective is to perform a detailed intercomparison of available burnt area datasets for one of the most catastrophic forest fire events that occurred near the Greek capital during the summer of 2007. For this purpose, two ASTER scenes were acquired, one before and one closely after the fire episode. Cartography of the burnt area was obtained by classifying each multi-band ASTER image into a number of discrete classes using the SVM classifier supported by land use/cover information from the CORINE 2000 land nomenclature. Overall verification of the derived thematic maps based on the classification statistics yielded results with a mean overall accuracy of 94.6% and a mean Kappa coefficient of 0.93. In addition, the burnt area estimate derived from the post-fire ASTER image was found to have an average difference of 9.63% from those reported by other operationally-offered burnt area datasets available for the test region

A multi-model approach to stakeholder engagement in complex environmental problems

We describe the different types of models we used as part of an effort to inform policy-making aiming at the management of the Ningaloo coast in the Gascoyne region, Western Australia. This provides an overview of how these models interact, the different roles they cover, how they fit into a full decision making process and what we learnt about the stakeholders involved in our project via their use. When modelling is explicitly used to address socio-ecological issues, the key determinant of success is whether the models, their results and recommendations are taken up by stakeholders; such uptake in turn depends on addressing stakeholders’ concerns, on engaging them in the project, on ensuring they feel ownership of the decision process at large, and that they understand and trust the modelling effort. This observation has guided our approach and has resulted in treating ‘building a model’ as the catalyst, rather than the final aim, of the process. In other words, extensive interactions in order to introduce, showcase, discuss and tune the model used for final decision making have represented both a requirement and an opportunity to ensure (i) model relevance, (ii) its acceptance, (iii) that all information available in the stakeholder team was accounted for and (iv) that stakeholders holding different levels of understanding of modelling, what it does and what it can provide to decision-making could develop an informed opinion on its use. To fulfil these roles we developed five broad classes of models: conceptual models, toy-models, singlesystem models, shuttle-models and a full-system model. In conceptual models the main drivers of a system are highlighted for subsequent representation as components of the full-system model. This usually results in a diagram summarising our understanding of how the system works. In toy-models a problem is simplified in such a way that only a handful of components are included. The purpose of these models is mostly educational: we want to understand how each component affects the problem and in order to achieve this, we temporarily renounce a satisfactory understanding of the overall problem. In single-system models we include a fairly detailed representation of a single component of the system (in our case recreational fishing and tourism); these models can be used to introduce stakeholders to modelling, provide temporary results from the study of a single activity, which will feed into the development of the final full-system model, or address sector-specific issues. In shuttle-models, we include the minimum number of processes we believe are crucial for a basic understanding of the overall problem. We know these models are still too simple for full system description, but they provide a sufficient understanding to enable us to contemplate, build and use the more complex models needed for full problem description. The term ‘shuttle’ refers to taking us from a minimum to a full description of the problem, a journey which is necessary both to developers in model definition and parameterisation and to stakeholders in the interpretation of the final full-system model results. Finally, the full-system model includes all information collected through the project and addresses all scenarios of stakeholders concern, and whose definition has been greatly eased by use of the ‘simpler’ models. As an example, a conceptual model may identify fishing and tourism as the main drivers of a region; a toymodel may describe how catches affect fish stocks; a single-system model may include the effect of gear, regulations and other processes affecting recreational fishing; a shuttle-model may include a simplified representation of the interaction between fishing, tourism, and infrastructure development on the overall health of the local ecosystem; this will gradually ‘take’ us to comprehend the ‘full’ model which may include tourism pressure, fish market values, climate effect, larger food-webs, etc

Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species.

Bdelloid rotifers are a class of microscopic invertebrates that have existed for millions of years apparently without sex or meiosis. They inhabit a variety of temporary and permanent freshwater habitats globally, and many species are remarkably tolerant of desiccation. Bdelloids offer an opportunity to better understand the evolution of sex and recombination, but previous work has emphasised desiccation as the cause of several unusual genomic features in this group. Here, we present high-quality whole-genome sequences of 3 bdelloid species: Rotaria macrura and R. magnacalcarata, which are both desiccation intolerant, and Adineta ricciae, which is desiccation tolerant. In combination with the published assembly of A. vaga, which is also desiccation tolerant, we apply a comparative genomics approach to evaluate the potential effects of desiccation tolerance and asexuality on genome evolution in bdelloids. We find that ancestral tetraploidy is conserved among all 4 bdelloid species, but homologous divergence in obligately aquatic Rotaria genomes is unexpectedly low. This finding is contrary to current models regarding the role of desiccation in shaping bdelloid genomes. In addition, we find that homologous regions in A. ricciae are largely collinear and do not form palindromic repeats as observed in the published A. vaga assembly. Consequently, several features interpreted as genomic evidence for long-term ameiotic evolution are not general to all bdelloid species, even within the same genus. Finally, we substantiate previous findings of high levels of horizontally transferred nonmetazoan genes in both desiccating and nondesiccating bdelloid species and show that this unusual feature is not shared by other animal phyla, even those with desiccation-tolerant representatives. These comparisons call into question the proposed role of desiccation in mediating horizontal genetic transfer

A prospective evaluation of the predictive value of faecal calprotectin in quiescent Crohn’s disease

Background: The faecal calprotectin (FC) test is a non-invasive marker for gastrointestinal inflammation. Aim: To determine whether higher FC levels in individuals with quiescent Crohn’s disease are associated with clinical relapse over the ensuing 12 months.<p></p> Methods: A single centre prospective study was undertaken in Crohn's disease patients in clinical remission attending for routine review. The receiver operating characteristic (ROC) curve for the primary endpoint of clinical relapse by 12 months, based on FC at baseline, was calculated. Kaplan-Meier curves of time to relapse were based on the resulting optimal FC cutoff for predicting relapse.<p></p> Results: Of 97 patients recruited, 92 were either followed up for 12 months without relapsing, or reached the primary endpoint within that period. Of these, 10 (11%) had relapsed by 12 months. The median FC was lower for non-relapsers, 96µg/g (IQR 39-237), than for relapsers, 414µg/g (IQR 259-590), (p=0.005). The area under the ROC curve to predict relapse using FC was 77.4%. An optimal cutoff FC value of 240µg/g to predict relapse of quiescent Crohn’s had sensitivity of 80.0% and specificity of 74.4%. Negative predictive value was 96.8% and positive predictive value was 27.6%. FC≥240μg/g was associated with likelihood of relapse 5.7 (95% CI 1.9-17.3) times higher within 2.3 years than lower values (p=0.002).<p></p> Conclusions: In this prospective dataset, FC appears to be a useful, non-invasive tool to help identify quiescent Crohn’s disease patients at a low risk of relapse over the ensuing 12 months. FC of 240µg/g was the optimal cutoff in this cohort.<p></p&gt

Molecular subtypes, metastatic pattern and patient age in breast cancer: An analysis of italian network of cancer registries (airtum) data

Breast cancer stage at diagnosis, patient age and molecular tumor subtype influence disease progression. The aim of this study was to analyze the relationships between these factors and survival in breast cancer patients among the Italian population using data from the AIRTUM national database. We enrolled women with primary breast cancer from 17 population‐based cancer registries. Patients were subdivided into older (>69 years), middle (50–69 years) and younger age groups (<50 years) and their primary tumors categorized into four molecular subtypes based on hormone receptor (HR) and human epidermal growth factor receptor 2 (HER2) status. There were 8831 patients diagnosed between 2010 and 2012 included. The most represented age group was 50– 69 years (41.7%). In 5735 cases the molecular subtype was identified: HER2–/HR+ was the most frequent (66.2%) and HER2+/HR− the least (6.2%). Of the 390 women with metastases at diagnosis, 38% had simultaneous involvement of multiple sites, independent of age and molecular profile. In women with a single metastatic site, bone (20% of cases), liver (11%), lung (7%) and brain (3%) were the most frequent. In the studied age groups with different receptor expression profiles, the tumor metastasized to target organs with differing frequencies, affecting survival. Five‐year survival was lowest in women with triple‐negative (HER2−/HR–) tumors and women with brain metastases at diagnosis

Biomass burning fuel consumption rates: a field measurement database

Landscape fires show large variability in the amount of biomass or fuel consumed per unit area burned. Fuel consumption (FC) depends on the biomass available to burn and the fraction of the biomass that is actually combusted, and can be combined with estimates of area burned to assess emissions. While burned area can be detected from space and estimates are becoming more reliable due to improved algorithms and sensors, FC is usually modeled or taken selectively from the literature. We compiled the peerreviewed literature on FC for various biomes and fuel categories to understand FC and its variability better, and to provide a database that can be used to constrain biogeochemical models with fire modules. We compiled in total 77 studies covering 11 biomes including savanna (15 studies, average FC of 4.6 t DM (dry matter) ha 1 with a standard deviation of 2.2),tropical forest (n = 19, FC = 126 +/- 77),temperate forest (n = 12, FC = 58 +/- 72),boreal forest (n = 16, FC = 35 +/- 24),pasture (n = 4, FC = 28 +/- 9.3),shifting cultivation (n = 2, FC = 23, with a range of 4.0-43),crop residue (n = 4, FC = 6.5 +/- 9.0),chaparral (n = 3, FC = 27 +/- 19),tropical peatland (n = 4, FC = 314 +/- 196),boreal peatland (n = 2, FC = 42 [42-43]),and tundra (n = 1, FC = 40). Within biomes the regional variability in the number of measurements was sometimes large, with e. g. only three measurement locations in boreal Russia and 35 sites in North America. Substantial regional differences in FC were found within the defined biomes: for example, FC of temperate pine forests in the USA was 37% lower than Australian forests dominated by eucalypt trees. Besides showing the differences between biomes, FC estimates were also grouped into different fuel classes. Our results highlight the large variability in FC, not only between biomes but also within biomes and fuel classes. This implies that substantial uncertainties are associated with using biome-averaged values to represent FC for whole biomes. Comparing the compiled FC values with co-located Global Fire Emissions Database version 3 (GFED3) FC indicates that modeling studies that aim to represent variability in FC also within biomes, still require improvements as they have difficulty in representing the dynamics governing FC

Paroxysmal Nocturnal Hemoglobinuria (Pnh) : Brain Mri Ischemic Lesions in Neurologically Asymtomatic Patients

This study investigated for the first time brain ischemic involvement in 19 consecutive neurologically asymptomatic PNH patients by non-enhanced cerebral MRI, and by intracranial arterial and venous angio-MRI. Eleven cases (58%, 7 aged 5 mm, and 5 cases a score >4 by the age-related white matter changes (ARWMC) scale. Compared with age and sex-matched controls (1:2 ratio), patients showed an increased frequency of periventricular WM vascular degeneration (32% versus 5.2%, p = 0.04) and of severe lesions (ARWMC scale score >4) (26% versus 2.6%, p = 0.05), and a higher overall ARWMC scale score (3.5 \uc2\ub1 1.07 versus 2.0 \uc2\ub1 0.8, mean \uc2\ub1 SD, p < 0.0001). Notably, vascular abnormalities suspected for prior partial venous thrombosis, were observed in PNH cases only. MRI lesions were not related to blood counts, hemolytic markers, clone size, disease duration, and therapy with eculizumab. Neurological examination was unremarkable in all patients but one (Parkinson disease). Psychiatric assessment revealed a case of generalized anxiety disorder, 1 bipolar disorder type 2, and 1 adjustment disorder. In conclusion, brain MRI may be useful at diagnosis and during the course of the disease to explore subclinical neurological involvement

Shotgun Proteomics Identifies Serum Fibronectin as a Candidate Diagnostic Biomarker for Inclusion in Future Multiplex Tests for Ectopic Pregnancy

Ectopic pregnancy (EP) is difficult to diagnose early and accurately. Women often present at emergency departments in early pregnancy with a 'pregnancy of unknown location' (PUL), and diagnosis and exclusion of EP is challenging due to a lack of reliable biomarkers. The objective of this study was to identify novel diagnostic biomarkers for EP. Shotgun proteomics, incorporating combinatorial-ligand library pre-fractionation, was used to interrogate pooled sera (n = 40) from women undergoing surgery for EP, termination of viable intrauterine pregnancy and management of non-viable intrauterine pregnancy. Western blot was used to validate results in individual sera. ELISAs were developed to interrogate sera from women with PUL (n = 120). Sera were collected at time of first symptomatic presentation and categorized according to pregnancy outcome. The main outcome measures were differences between groups and area under the receiver operating curve (ROC). Proteomics identified six biomarker candidates. Western blot detected significant differences in levels of two of these candidates. ELISA of sera from second cohort revealed that these differences were only significant for one of these candidates, fibronectin. ROC analysis of ability of fibronectin to discriminate EP from other pregnancy outcomes suggested that fibronectin has diagnostic potential (ROC 0.6439; 95% CI 0.5090 to 0.7788; P>0.05), becoming significant when 'ambiguous' medically managed PUL excluded from analysis (ROC 0.6538; 95% CI 0.5158 to 0.7918; P<0.05). Fibronectin may make a useful adjunct to future multiplex EP diagnostic tests

Quantitative iTRAQ-Based Proteomic Identification of Candidate Biomarkers for Diabetic Nephropathy in Plasma of Type 1 Diabetic Patients

# The Author(s) 2010. This article is published with open access at Springerlink.com Introduction As part of a clinical proteomics programme focused on diabetes and its complications, it was our goal to investigate the proteome of plasma in order to find improved candidate biomarkers to predict diabetic nephropathy. Methods Proteins derived from plasma from a crosssectiona