Using Annual Landsat Time Series for the Detection of Dry Forest Degradation Processes in South-Central Angola

Dry tropical forests undergo massive conversion and degradation processes. This also holds true for the extensive Miombo forests that cover large parts of Southern Africa. While the largest proportional area can be found in Angola, the country still struggles with food shortages, insufficient medical and educational supplies, as well as the ongoing reconstruction of infrastructure after 27 years of civil war. Especially in rural areas, the local population is therefore still heavily dependent on the consumption of natural resources, as well as subsistence agriculture. This leads, on one hand, to large areas of Miombo forests being converted for cultivation purposes, but on the other hand, to degradation processes due to the selective use of forest resources. While forest conversion in south-central rural Angola has already been quantitatively described, information about forest degradation is not yet available. This is due to the history of conflicts and the therewith connected research difficulties, as well as the remote location of this area. We apply an annual time series approach using Landsat data in south-central Angola not only to assess the current degradation status of the Miombo forests, but also to derive past developments reaching back to times of armed conflicts. We use the Disturbance Index based on tasseled cap transformation to exclude external influences like inter-annual variation of rainfall. Based on this time series, linear regression is calculated for forest areas unaffected by conversion, but also for the pre-conversion period of those areas that were used for cultivation purposes during the observation time. Metrics derived from linear regression are used to classify the study area according to their dominant modification processes. We compare our results to MODIS latent integral trends and to further products to derive information on underlying drivers. Around 13% of the Miombo forests are affected by degradation processes, especially along streets, in villages, and close to existing agriculture. However, areas in presumably remote and dense forest areas are also affected to a significant extent. A comparison with MODIS derived fire ignition data shows that they are most likely affected by recurring fires and less by selective timber extraction. We confirm that areas that are used for agriculture are more heavily disturbed by selective use beforehand than those that remain unaffected by conversion. The results can be substantiated by the MODIS latent integral trends and we also show that due to extent and location, the assessment of forest conversion is most likely not sufficient to provide good estimates for the loss of natural resources. View Full-Tex

Factor graph analysis of live cell-imaging data reveals mechanisms of cell fate decisions

Motivation: Cell fate decisions have a strong stochastic component. The identification of the underlying mechanisms therefore requires a rigorous statistical analysis of large ensembles of single cells that were tracked and phenotyped over time. Results: We introduce a probabilistic framework for testing elementary hypotheses on dynamic cell behavior using time-lapse cell-imaging data. Factor graphs, probabilistic graphical models, are used to properly account for cell lineage and cell phenotype information. Our model is applied to time-lapse movies of murine granulocyte-macrophage progenitor (GMP) cells. It decides between competing hypotheses on the mechanisms of their differentiation. Our results theoretically substantiate previous experimental observations that lineage instruction, not selection is the cause for the differentiation of GMP cells into mature monocytes or neutrophil granulocytes. Availability and implementation: The Matlab source code is available at http://treschgroup.de/Genealogies.html Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Differences across health care systems in outcome and cost-utility of surgical and conservative treatment of chronic low back pain: a study protocol

<p>Abstract</p> <p>Background</p> <p>There is little evidence on differences across health care systems in choice and outcome of the treatment of chronic low back pain (CLBP) with spinal surgery and conservative treatment as the main options. At least six randomised controlled trials comparing these two options have been performed; they show conflicting results without clear-cut evidence for superior effectiveness of any of the evaluated interventions and could not address whether treatment effect varied across patient subgroups. Cost-utility analyses display inconsistent results when comparing surgical and conservative treatment of CLBP. Due to its higher feasibility, we chose to conduct a prospective observational cohort study.</p> <p>Methods</p> <p>This study aims to examine if</p> <p>1. Differences across health care systems result in different treatment outcomes of surgical and conservative treatment of CLBP</p> <p>2. Patient characteristics (work-related, psychological factors, etc.) and co-interventions (physiotherapy, cognitive behavioural therapy, return-to-work programs, etc.) modify the outcome of treatment for CLBP</p> <p>3. Cost-utility in terms of quality-adjusted life years differs between surgical and conservative treatment of CLBP.</p> <p>This study will recruit 1000 patients from orthopaedic spine units, rehabilitation centres, and pain clinics in Switzerland and New Zealand. Effectiveness will be measured by the Oswestry Disability Index (ODI) at baseline and after six months. The change in ODI will be the primary endpoint of this study.</p> <p>Multiple linear regression models will be used, with the change in ODI from baseline to six months as the dependent variable and the type of health care system, type of treatment, patient characteristics, and co-interventions as independent variables. Interactions will be incorporated between type of treatment and different co-interventions and patient characteristics. Cost-utility will be measured with an index based on EQol-5D in combination with cost data.</p> <p>Conclusion</p> <p>This study will provide evidence if differences across health care systems in the outcome of treatment of CLBP exist. It will classify patients with CLBP into different clinical subgroups and help to identify specific target groups who might benefit from specific surgical or conservative interventions. Furthermore, cost-utility differences will be identified for different groups of patients with CLBP. Main results of this study should be replicated in future studies on CLBP.</p

Forest disturbance mapping using dense synthetic Landsat/MODIS time-series and permutation-based disturbance index detection

Spatio-temporal information on process-based forest loss is essential for a wide range of applications. Despite remote sensing being the only feasible means of monitoring forest change at regional or greater scales, there is no retrospectively available remote sensor that meets the demand of monitoring forests with the required spatial detail and guaranteed high temporal frequency. As an alternative, we employed the Spatial and Temporal Adaptive Reflectance Fusion Model (STARFM) to produce a dense synthetic time series by fusing Landsat and Moderate Resolution Imaging Spectroradiometer (MODIS) nadir Bidirectional Reflectance Distribution Function (BRDF) adjusted reflectance. Forest loss was detected by applying a multi-temporal disturbance detection approach implementing a Disturbance Index-based detection strategy. The detection thresholds were permutated with random numbers for the normal distribution in order to generate a multi-dimensional threshold confidence area. As a result, a more robust parameterization and a spatially more coherent detection could be achieved. (i) The original Landsat time series; (ii) synthetic time series; and a (iii) combined hybrid approach were used to identify the timing and extent of disturbances. The identified clearings in the Landsat detection were verified using an annual woodland clearing dataset from Queensland's Statewide Landcover and Trees Study. Disturbances caused by stand-replacing events were successfully identified. The increased temporal resolution of the synthetic time series indicated promising additional information on disturbance timing. The results of the hybrid detection unified the benefits of both approaches, i.e., the spatial quality and general accuracy of the Landsat detection and the increased temporal information of synthetic time series. Results indicated that a temporal improvement in the detection of the disturbance date could be achieved relative to the irregularly spaced Landsat data for sufficiently large patches

Land degradation and economic conditions of agricultural households in a marginal region of northern Greece

Land degradation is caused by and has impacts on both the social and natural components of coupled human-environment systems. However, few studies integrate both aspects simultaneously. The main objective of this study is to test a method to evaluate land degradation based on the integration of aggregate metrics of biophysical and socio-economic "degradation". We applied a framework that integrates the biophysical and socio-economic dimensions of land degradation to test the hypothesis that macro-economic policies, and in particular agricultural subsidies, are an important driving force of land degradation in marginal regions of the Mediterranean Europe. We analysed the influence of subsidies on the profitability of each crop and livestock type found in a sample of farms in a region of northern Greece. Spatial and socioeconomic data on agricultural households were collected to link remote sensing data and land degradation maps to socio-economic conditions of these households, as measured by the standard gross margin. The results demonstrate that subsidies provide a crucial socio-economic support to maintain the profitability of agricultural activities but may also promote land-use practices with damaging ecological impacts. Different levels of biophysical and socio-economic "degradation" were associated with different land use practices. The integration of the socio-economic and biophysical dimensions of land degradation reveals associations that would not be detectable if indicators along one dimension alone would be used. (C) 2008 Elsevier B.V. All rights reserved

Functional classification of genes exhibiting deviant expression levels in <i>hand</i>^<i>173</i> animals.

<p><i>Drosophila</i> Hand is apparently involved in regulating the expression of 545 genes with 385 genes being downregulated in <i>hand</i> mutants (<i>hand</i>^<i>173</i>) and 160 genes displaying an increased expression in the same line, compared to wild type. Functional classification of the corresponding protein products was done manually utilizing data from NCBI (<a href="http://www.ncbi.nlm.nih.gov/" target="_blank">http://www.ncbi.nlm.nih.gov/</a>) and Flybase (<a href="http://flybase.org/" target="_blank">http://flybase.org/</a>). Factors with yet unknown physiological functions are allocated to the category “assorted other”.</p

Relative expression of <i>Drosophila</i> homologs of selected vertebrate Hand target genes in <i>hand</i> mutant <i>Drosophila</i>, compared to wild type.

<p>Expression levels were assessed by Northern blot. Statistically relevant deviations are evident with respect to all genes tested. While <i>mef2</i> and <i>hedgehog</i> display an increased expression of 40.6% and 19.8% in <i>hand</i>^<i>173</i> animals, respectively, the expression of <i>cubitus interruptus</i> is decreased by 19.8% in the same line. Bars represent mean values ± SD of at least three independent experiments. Asterisks indicate statistical significance (Student´s <i>t</i>-test <i>P</i><0.05). Quantification of the relative band intensities in relation to the loading controls (ribosomal RNA, rRNA) was done by densitometric analysis.</p

The bHLH Transcription Factor Hand Regulates the Expression of Genes Critical to Heart and Muscle Function in <i>Drosophila melanogaster</i>

<div><p>Hand proteins belong to the highly conserved family of basic Helix-Loop-Helix transcription factors and are critical to distinct developmental processes, including cardiogenesis and neurogenesis in vertebrates. In <i>Drosophila melanogaster</i> a single orthologous <i>hand</i> gene is expressed with absence of the respective protein causing semilethality during early larval instars. Surviving adult animals suffer from shortened lifespan associated with a disorganized myofibrillar structure being apparent in the dorsal vessel, the wing hearts and in midgut tissue. Based on these data, the major biological significance of Hand seems to be related to muscle development, maintenance or function; however, up to now the physiological basis for Hand functionality remains elusive. Thus, the identification of genes whose expression is, directly or indirectly, regulated by Hand has considerable relevance with respect to understanding its biological functionality in flies and vertebrates. Beneficially, <i>hand</i> mutants are viable and exhibit affected tissues, which renders <i>Drosophila</i> an ideal model to investigate up- or downregulated target genes by a comparative microarray approach focusing on the respective tissues from mutant specimens. Our present work reveals for the first time that <i>Drosophila</i> Hand regulates the expression of numerous genes of diverse physiological relevancy, including distinct factors required for proper muscle development and function such as Zasp52 or Msp-300. These results relate Hand activity to muscle integrity and functionality and may thus be highly beneficial to the evaluation of corresponding <i>hand</i> phenotypes.</p></div

Relative expression of selected genes in hand mutant animals, compared to wild type.

<p>Expression levels were assessed by Northern blot. Statistically relevant deviations are evident with respect to all genes tested. While <i>akirin</i> displays an expression that is reduced by 40.5% in the <i>hand</i> mutant (<i>hand</i>^<i>173</i>), the expression of <i>kugelei</i> is lowered by 57.5%, that of <i>msp-300</i> by 65% and that of <i>multiplexin</i> by 28.5%, respectively. With regard to <i>zasp52</i>, two major transcripts are detected by the applied riboprobes with the larger one (arrow) being downregulated by 44.8% in the <i>hand</i> mutant and the smaller one (arrowhead) being upregulated by 34.9% in the same line. Bars represent mean values <u>+</u> SD of at least three independent experiments. Asterisks indicate statistical significance (Student´s <i>t</i>-test <i>P</i><0.05). Quantification of the relative band intensities in relation to the loading controls (ribosomal RNA, rRNA) was done by densitometric analysis.</p

Factor graph analysis of live cell-imaging data reveals mechanisms of cell fate decisions

Motivation: Cell fate decisions have a strong stochastic component. The identification of the underlying mechanisms therefore requires a rigorous statistical analysis of large ensembles of single cells that were tracked and phenotyped over time. Results: We introduce a probabilistic framework for testing elementary hypotheses on dynamic cell behavior using time-lapse cell-imaging data. Factor graphs, probabilistic graphical models, are used to properly account for cell lineage and cell phenotype information. Our model is applied to time-lapse movies of murine granulocyte-macrophage progenitor (GMP) cells. It decides between competing hypotheses on the mechanisms of their differentiation. Our results theoretically substantiate previous experimental observations that lineage instruction, not selection is the cause for the differentiation of GMP cells into mature monocytes or neutrophil granulocytes