WorldWideScience

Sample records for transcriptional landscape estimation

  1. Transcriptional landscape estimation from tiling array data using a model of signal shift and drift

    DEFF Research Database (Denmark)

    Rasmussen, Simon; Jarmer, Hanne Østergaard; Nicolas, P

    2009-01-01

    MOTIVATION: High-density oligonucleotide tiling array technology holds the promise of a better description of the complexity and the dynamics of transcriptional landscapes. In organisms such as bacteria and yeasts, transcription can be measured on a genome-wide scale with a resolution >25 bp...

  2. The transcriptional landscape

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2011-01-01

    The application of new and less biased methods to study the transcriptional output from genomes, such as tiling arrays and deep sequencing, has revealed that most of the genome is transcribed and that there is substantial overlap of transcripts derived from the two strands of DNA. In protein coding...... regions, the map of transcripts is very complex due to small transcripts from the flanking ends of the transcription unit, the use of multiple start and stop sites for the main transcript, production of multiple functional RNA molecules from the same primary transcript, and RNA molecules made...... by independent transcription from within the unit. In genomic regions separating those that encode proteins or highly abundant RNA molecules with known function, transcripts are generally of low abundance and short-lived. In most of these cases, it is unclear to what extent a function is related to transcription...

  3. Transcriptional landscape of glomerular parietal epithelial cells.

    Directory of Open Access Journals (Sweden)

    Sina A Gharib

    Full Text Available Very little is known about the function of glomerular parietal epithelial cells (PECs. In this study, we performed genome-wide expression analysis on PEC-enriched capsulated vs. PEC-deprived decapsulated rat glomeruli to determine the transcriptional state of PECs under normal conditions. We identified hundreds of differentially expressed genes that mapped to distinct biologic modules including development, tight junction, ion transport, and metabolic processes. Since developmental programs were highly enriched in PECs, we characterized several of their candidate members at the protein level. Collectively, our findings confirm that PECs are multifaceted cells and help define their diverse functional repertoire.

  4. Transcriptional landscapes of Axolotl (Ambystoma mexicanum).

    Science.gov (United States)

    Caballero-Pérez, Juan; Espinal-Centeno, Annie; Falcon, Francisco; García-Ortega, Luis F; Curiel-Quesada, Everardo; Cruz-Hernández, Andrés; Bako, Laszlo; Chen, Xuemei; Martínez, Octavio; Alberto Arteaga-Vázquez, Mario; Herrera-Estrella, Luis; Cruz-Ramírez, Alfredo

    2018-01-15

    The axolotl (Ambystoma mexicanum) is the vertebrate model system with the highest regeneration capacity. Experimental tools established over the past 100 years have been fundamental to start unraveling the cellular and molecular basis of tissue and limb regeneration. In the absence of a reference genome for the Axolotl, transcriptomic analysis become fundamental to understand the genetic basis of regeneration. Here we present one of the most diverse transcriptomic data sets for Axolotl by profiling coding and non-coding RNAs from diverse tissues. We reconstructed a population of 115,906 putative protein coding mRNAs as full ORFs (including isoforms). We also identified 352 conserved miRNAs and 297 novel putative mature miRNAs. Systematic enrichment analysis of gene expression allowed us to identify tissue-specific protein-coding transcripts. We also found putative novel and conserved microRNAs which potentially target mRNAs which are reported as important disease candidates in heart and liver. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Dataset of transcriptional landscape of B cell early activation

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    Alexander S. Garruss

    2015-09-01

    Full Text Available Signaling via B cell receptors (BCR and Toll-like receptors (TLRs result in activation of B cells with distinct physiological outcomes, but transcriptional regulatory mechanisms that drive activation and distinguish these pathways remain unknown. At early time points after BCR and TLR ligand exposure, 0.5 and 2 h, RNA-seq was performed allowing observations on rapid transcriptional changes. At 2 h, ChIP-seq was performed to allow observations on important regulatory mechanisms potentially driving transcriptional change. The dataset includes RNA-seq, ChIP-seq of control (Input, RNA Pol II, H3K4me3, H3K27me3, and a separate RNA-seq for miRNA expression, which can be found at Gene Expression Omnibus Dataset GSE61608. Here, we provide details on the experimental and analysis methods used to obtain and analyze this dataset and to examine the transcriptional landscape of B cell early activation.

  6. Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages

    KAUST Repository

    Roy, Sugata

    2018-04-24

    Mycobacterium tuberculosis (Mtb) infection reveals complex and dynamic host-pathogen interactions, leading to host protection or pathogenesis. Using a unique transcriptome technology (CAGE), we investigated the promoter-based transcriptional landscape of IFNγ (M1) or IL-4/IL-13 (M2) stimulated macrophages during Mtb infection in a time-kinetic manner. Mtb infection widely and drastically altered macrophage-specific gene expression, which is far larger than that of M1 or M2 activations. Gene Ontology enrichment analysis for Mtb-induced differentially expressed genes revealed various terms, related to host-protection and inflammation, enriched in up-regulated genes. On the other hand, terms related to dis-regulation of cellular functions were enriched in down-regulated genes. Differential expression analysis revealed known as well as novel transcription factor genes in Mtb infection, many of them significantly down-regulated. IFNγ or IL-4/IL-13 pre-stimulation induce additional differentially expressed genes in Mtb-infected macrophages. Cluster analysis uncovered significant numbers, prolonging their expressional changes. Furthermore, Mtb infection augmented cytokine-mediated M1 and M2 pre-activations. In addition, we identified unique transcriptional features of Mtb-mediated differentially expressed lncRNAs. In summary we provide a comprehensive in depth gene expression/regulation profile in Mtb-infected macrophages, an important step forward for a better understanding of host-pathogen interaction dynamics in Mtb infection.

  7. A General Model for Estimating Macroevolutionary Landscapes.

    Science.gov (United States)

    Boucher, Florian C; Démery, Vincent; Conti, Elena; Harmon, Luke J; Uyeda, Josef

    2018-03-01

    The evolution of quantitative characters over long timescales is often studied using stochastic diffusion models. The current toolbox available to students of macroevolution is however limited to two main models: Brownian motion and the Ornstein-Uhlenbeck process, plus some of their extensions. Here, we present a very general model for inferring the dynamics of quantitative characters evolving under both random diffusion and deterministic forces of any possible shape and strength, which can accommodate interesting evolutionary scenarios like directional trends, disruptive selection, or macroevolutionary landscapes with multiple peaks. This model is based on a general partial differential equation widely used in statistical mechanics: the Fokker-Planck equation, also known in population genetics as the Kolmogorov forward equation. We thus call the model FPK, for Fokker-Planck-Kolmogorov. We first explain how this model can be used to describe macroevolutionary landscapes over which quantitative traits evolve and, more importantly, we detail how it can be fitted to empirical data. Using simulations, we show that the model has good behavior both in terms of discrimination from alternative models and in terms of parameter inference. We provide R code to fit the model to empirical data using either maximum-likelihood or Bayesian estimation, and illustrate the use of this code with two empirical examples of body mass evolution in mammals. FPK should greatly expand the set of macroevolutionary scenarios that can be studied since it opens the way to estimating macroevolutionary landscapes of any conceivable shape. [Adaptation; bounds; diffusion; FPK model; macroevolution; maximum-likelihood estimation; MCMC methods; phylogenetic comparative data; selection.].

  8. Sequence2Vec: A novel embedding approach for modeling transcription factor binding affinity landscape

    KAUST Repository

    Dai, Hanjun; Umarov, Ramzan; Kuwahara, Hiroyuki; Li, Yu; Song, Le; Gao, Xin

    2017-01-01

    Motivation: An accurate characterization of transcription factor (TF)-DNA affinity landscape is crucial to a quantitative understanding of the molecular mechanisms underpinning endogenous gene regulation. While recent advances in biotechnology have

  9. Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages

    KAUST Repository

    Roy, Sugata; Schmeier, Sebastian; Kaczkowski, Bogumil; Arner, Erik; Alam, Tanvir; Ozturk, Mumin; Tamgue, Ousman; Parihar, Suraj P.; Kawaji, Hideya; Itoh, Masayoshi; Lassmann, Timo; Carninci, Piero; Hayashizaki, Yoshihide; Forrest, Alistair R. R.; Guler, Reto; Bajic, Vladimir B.; Brombacher, Frank; Suzuki, Harukazu

    2018-01-01

    landscape of IFNγ (M1) or IL-4/IL-13 (M2) stimulated macrophages during Mtb infection in a time-kinetic manner. Mtb infection widely and drastically altered macrophage-specific gene expression, which is far larger than that of M1 or M2 activations. Gene

  10. Landscape of transcriptional deregulations in the preeclamptic placenta.

    Directory of Open Access Journals (Sweden)

    Daniel Vaiman

    Full Text Available Preeclampsia is a pregnancy disease affecting 5 to 8% of pregnant women and a leading cause of both maternal and fetal mortality and morbidity. Because of a default in the process of implantation, the placenta of preeclamptic women undergoes insufficient vascularization. This results in placental ischemia, inflammation and subsequent release of placental debris and vasoactive factors in the maternal circulation causing a systemic endothelial activation. Several microarray studies have analyzed the transcriptome of the preeclamptic placentas to identify genes which could be involved in placental dysfunction. In this study, we compared the data from publicly available microarray analyses to obtain a consensus list of modified genes. This allowed to identify consistently modified genes in the preeclamptic placenta. Of these, 67 were up-regulated and 31 down-regulated. Assuming that changes in the transcription level of co-expressed genes may result from the coordinated action of a limited number of transcription factors, we looked for over-represented putative transcription factor binding sites in the promoters of these genes. Indeed, we found that the promoters of up-regulated genes are enriched in putative binding sites for NFkB, CREB, ANRT, REEB1, SP1, and AP-2. In the promoters of down-regulated genes, the most prevalent putative binding sites are those of MZF-1, NFYA, E2F1 and MEF2A. These transcriptions factors are known to regulate specific biological pathways such as cell responses to inflammation, hypoxia, DNA damage and proliferation. We discuss here the molecular mechanisms of action of these transcription factors and how they can be related to the placental dysfunction in the context of preeclampsia.

  11. The transcriptional landscape of hematopoietic stem cell ontogeny

    Science.gov (United States)

    McKinney-Freeman, Shannon; Cahan, Patrick; Li, Hu; Lacadie, Scott A.; Huang, Hsuan-Ting; Curran, Matthew; Loewer, Sabine; Naveiras, Olaia; Kathrein, Katie L.; Konantz, Martina; Langdon, Erin M.; Lengerke, Claudia; Zon, Leonard I.; Collins, James J.; Daley, George Q.

    2012-01-01

    Transcriptome analysis of adult hematopoietic stem cells (HSC) and their progeny has revealed mechanisms of blood differentiation and leukemogenesis, but a similar analysis of HSC development is lacking. Here, we acquired the transcriptomes of developing HSC purified from >2500 murine embryos and adult mice. We found that embryonic hematopoietic elements clustered into three distinct transcriptional states characteristic of the definitive yolk sac, HSCs undergoing specification, and definitive HSCs. We applied a network biology-based analysis to reconstruct the gene regulatory networks of sequential stages of HSC development and functionally validated candidate transcriptional regulators of HSC ontogeny by morpholino-mediated knock-down in zebrafish embryos. Moreover, we found that HSCs from in vitro differentiated embryonic stem cells closely resemble definitive HSC, yet lack a Notch-signaling signature, likely accounting for their defective lymphopoiesis. Our analysis and web resource (http://hsc.hms.harvard.edu) will enhance efforts to identify regulators of HSC ontogeny and facilitate the engineering of hematopoietic specification. PMID:23122293

  12. The Transcriptional Landscape of the Production Organism Pseudomonas putida

    DEFF Research Database (Denmark)

    D'Arrigo, Isotta

    Bacterial cell factories represent a valid alternative to fossil fuel-based production. A promising bacterium that can be optimized as cell factory is Pseudomonas putida. However, its development in bioproduction applications poses some challenges including a clear understanding of the bacterial...... system biology. This thesis has the aim of facilitating the development of P. putida KT2440 as a bacterial cell factory by investigating the transcriptome of the bacterium under different conditions (e.g. growth and stress). The main goals are the identification of differentially expressed genes, which...... provide information on bacterial adaptation to different environments, and the identification of non-coding RNAs, which regulate gene expression. This work focuses on several aspects of P. putida highlighting genomic features such as transcription start sites (TSSs), RNA regulatory elements...

  13. Inferring the transcriptional landscape of bovine skeletal muscle by integrating co-expression networks.

    Directory of Open Access Journals (Sweden)

    Nicholas J Hudson

    Full Text Available BACKGROUND: Despite modern technologies and novel computational approaches, decoding causal transcriptional regulation remains challenging. This is particularly true for less well studied organisms and when only gene expression data is available. In muscle a small number of well characterised transcription factors are proposed to regulate development. Therefore, muscle appears to be a tractable system for proposing new computational approaches. METHODOLOGY/PRINCIPAL FINDINGS: Here we report a simple algorithm that asks "which transcriptional regulator has the highest average absolute co-expression correlation to the genes in a co-expression module?" It correctly infers a number of known causal regulators of fundamental biological processes, including cell cycle activity (E2F1, glycolysis (HLF, mitochondrial transcription (TFB2M, adipogenesis (PIAS1, neuronal development (TLX3, immune function (IRF1 and vasculogenesis (SOX17, within a skeletal muscle context. However, none of the canonical pro-myogenic transcription factors (MYOD1, MYOG, MYF5, MYF6 and MEF2C were linked to muscle structural gene expression modules. Co-expression values were computed using developing bovine muscle from 60 days post conception (early foetal to 30 months post natal (adulthood for two breeds of cattle, in addition to a nutritional comparison with a third breed. A number of transcriptional landscapes were constructed and integrated into an always correlated landscape. One notable feature was a 'metabolic axis' formed from glycolysis genes at one end, nuclear-encoded mitochondrial protein genes at the other, and centrally tethered by mitochondrially-encoded mitochondrial protein genes. CONCLUSIONS/SIGNIFICANCE: The new module-to-regulator algorithm complements our recently described Regulatory Impact Factor analysis. Together with a simple examination of a co-expression module's contents, these three gene expression approaches are starting to illuminate the in vivo

  14. Estimating restorable wetland water storage at landscape scales

    Science.gov (United States)

    Jones, Charles Nathan; Evenson, Grey R.; McLaughlin, Daniel L.; Vanderhoof, Melanie; Lang, Megan W.; McCarty, Greg W.; Golden, Heather E.; Lane, Charles R.; Alexander, Laurie C.

    2018-01-01

    Globally, hydrologic modifications such as ditching and subsurface drainage have significantly reduced wetland water storage capacity (i.e., volume of surface water a wetland can retain) and consequent wetland functions. While wetland area has been well documented across many landscapes and used to guide restoration efforts, few studies have directly quantified the associated wetland storage capacity. Here, we present a novel raster-based approach to quantify both contemporary and potential (i.e., restorable) storage capacities of individual depressional basins across landscapes. We demonstrate the utility of this method by applying it to the Delmarva Peninsula, a region punctuated by both depressional wetlands and drainage ditches. Across the entire peninsula, we estimated that restoration (i.e., plugging ditches) could increase storage capacity by 80%. Focusing on an individual watershed, we found that over 59% of restorable storage capacity occurs within 20 m of the drainage network, and that 93% occurs within 1 m elevation of the drainage network. Our demonstration highlights widespread ditching in this landscape, spatial patterns of both contemporary and potential storage capacities, and clear opportunities for hydrologic restoration. In Delmarva and more broadly, our novel approach can inform targeted landscape-scale conservation and restoration efforts to optimize hydrologically mediated wetland functions.

  15. Sequence2Vec: A novel embedding approach for modeling transcription factor binding affinity landscape

    KAUST Repository

    Dai, Hanjun

    2017-07-26

    Motivation: An accurate characterization of transcription factor (TF)-DNA affinity landscape is crucial to a quantitative understanding of the molecular mechanisms underpinning endogenous gene regulation. While recent advances in biotechnology have brought the opportunity for building binding affinity prediction methods, the accurate characterization of TF-DNA binding affinity landscape still remains a challenging problem. Results: Here we propose a novel sequence embedding approach for modeling the transcription factor binding affinity landscape. Our method represents DNA binding sequences as a hidden Markov model (HMM) which captures both position specific information and long-range dependency in the sequence. A cornerstone of our method is a novel message passing-like embedding algorithm, called Sequence2Vec, which maps these HMMs into a common nonlinear feature space and uses these embedded features to build a predictive model. Our method is a novel combination of the strength of probabilistic graphical models, feature space embedding and deep learning. We conducted comprehensive experiments on over 90 large-scale TF-DNA data sets which were measured by different high-throughput experimental technologies. Sequence2Vec outperforms alternative machine learning methods as well as the state-of-the-art binding affinity prediction methods.

  16. A transcription factor collective defines the HSN serotonergic neuron regulatory landscape.

    Science.gov (United States)

    Lloret-Fernández, Carla; Maicas, Miren; Mora-Martínez, Carlos; Artacho, Alejandro; Jimeno-Martín, Ángela; Chirivella, Laura; Weinberg, Peter; Flames, Nuria

    2018-03-22

    Cell differentiation is controlled by individual transcription factors (TFs) that together activate a selection of enhancers in specific cell types. How these combinations of TFs identify and activate their target sequences remains poorly understood. Here, we identify the cis -regulatory transcriptional code that controls the differentiation of serotonergic HSN neurons in Caenorhabditis elegans . Activation of the HSN transcriptome is directly orchestrated by a collective of six TFs. Binding site clusters for this TF collective form a regulatory signature that is sufficient for de novo identification of HSN neuron functional enhancers. Among C. elegans neurons, the HSN transcriptome most closely resembles that of mouse serotonergic neurons. Mouse orthologs of the HSN TF collective also regulate serotonergic differentiation and can functionally substitute for their worm counterparts which suggests deep homology. Our results identify rules governing the regulatory landscape of a critically important neuronal type in two species separated by over 700 million years. © 2018, Lloret-Fernández et al.

  17. Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape.

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    Scarlet S Shell

    2015-11-01

    Full Text Available RNA-seq technologies have provided significant insight into the transcription networks of mycobacteria. However, such studies provide no definitive information on the translational landscape. Here, we use a combination of high-throughput transcriptome and proteome-profiling approaches to more rigorously understand protein expression in two mycobacterial species. RNA-seq and ribosome profiling in Mycobacterium smegmatis, and transcription start site (TSS mapping and N-terminal peptide mass spectrometry in Mycobacterium tuberculosis, provide complementary, empirical datasets to examine the congruence of transcription and translation in the Mycobacterium genus. We find that nearly one-quarter of mycobacterial transcripts are leaderless, lacking a 5' untranslated region (UTR and Shine-Dalgarno ribosome-binding site. Our data indicate that leaderless translation is a major feature of mycobacterial genomes and is comparably robust to leadered initiation. Using translational reporters to systematically probe the cis-sequence requirements of leaderless translation initiation in mycobacteria, we find that an ATG or GTG at the mRNA 5' end is both necessary and sufficient. This criterion, together with our ribosome occupancy data, suggests that mycobacteria encode hundreds of small, unannotated proteins at the 5' ends of transcripts. The conservation of small proteins in both mycobacterial species tested suggests that some play important roles in mycobacterial physiology. Our translational-reporter system further indicates that mycobacterial leadered translation initiation requires a Shine Dalgarno site in the 5' UTR and that ATG, GTG, TTG, and ATT codons can robustly initiate translation. Our combined approaches provide the first comprehensive view of mycobacterial gene structures and their non-canonical mechanisms of protein expression.

  18. Reliability and precision of pellet-group counts for estimating landscape-level deer density

    Science.gov (United States)

    David S. deCalesta

    2013-01-01

    This study provides hitherto unavailable methodology for reliably and precisely estimating deer density within forested landscapes, enabling quantitative rather than qualitative deer management. Reliability and precision of the deer pellet-group technique were evaluated in 1 small and 2 large forested landscapes. Density estimates, adjusted to reflect deer harvest and...

  19. Genomic and transcriptional landscape of P2RY8-CRLF2-positive childhood acute lymphoblastic leukemia

    Science.gov (United States)

    Vesely, C; Frech, C; Eckert, C; Cario, G; Mecklenbräuker, A; zur Stadt, U; Nebral, K; Kraler, F; Fischer, S; Attarbaschi, A; Schuster, M; Bock, C; Cavé, H; von Stackelberg, A; Schrappe, M; Horstmann, M A; Mann, G; Haas, O A; Panzer-Grümayer, R

    2017-01-01

    Children with P2RY8-CRLF2-positive acute lymphoblastic leukemia have an increased relapse risk. Their mutational and transcriptional landscape, as well as the respective patterns at relapse remain largely elusive. We, therefore, performed an integrated analysis of whole-exome and RNA sequencing in 41 major clone fusion-positive cases including 19 matched diagnosis/relapse pairs. We detected a variety of frequently subclonal and highly instable JAK/STAT but also RTK/Ras pathway-activating mutations in 76% of cases at diagnosis and virtually all relapses. Unlike P2RY8-CRLF2 that was lost in 32% of relapses, all other genomic alterations affecting lymphoid development (58%) and cell cycle (39%) remained stable. Only IKZF1 alterations predominated in relapsing cases (P=0.001) and increased from initially 36 to 58% in matched cases. IKZF1’s critical role is further corroborated by its specific transcriptional signature comprising stem cell features with signs of impaired lymphoid differentiation, enhanced focal adhesion, activated hypoxia pathway, deregulated cell cycle and increased drug resistance. Our findings support the notion that P2RY8-CRLF2 is dispensable for relapse development and instead highlight the prominent rank of IKZF1 for relapse development by mediating self-renewal and homing to the bone marrow niche. Consequently, reverting aberrant IKAROS signaling or its disparate programs emerges as an attractive potential treatment option in these leukemias. PMID:27899802

  20. Hydrologic Landscape Classification to Estimate Bristol Bay Watershed Hydrology

    Science.gov (United States)

    The use of hydrologic landscapes has proven to be a useful tool for broad scale assessment and classification of landscapes across the United States. These classification systems help organize larger geographical areas into areas of similar hydrologic characteristics based on cl...

  1. Global parameter estimation for thermodynamic models of transcriptional regulation.

    Science.gov (United States)

    Suleimenov, Yerzhan; Ay, Ahmet; Samee, Md Abul Hassan; Dresch, Jacqueline M; Sinha, Saurabh; Arnosti, David N

    2013-07-15

    Deciphering the mechanisms involved in gene regulation holds the key to understanding the control of central biological processes, including human disease, population variation, and the evolution of morphological innovations. New experimental techniques including whole genome sequencing and transcriptome analysis have enabled comprehensive modeling approaches to study gene regulation. In many cases, it is useful to be able to assign biological significance to the inferred model parameters, but such interpretation should take into account features that affect these parameters, including model construction and sensitivity, the type of fitness calculation, and the effectiveness of parameter estimation. This last point is often neglected, as estimation methods are often selected for historical reasons or for computational ease. Here, we compare the performance of two parameter estimation techniques broadly representative of local and global approaches, namely, a quasi-Newton/Nelder-Mead simplex (QN/NMS) method and a covariance matrix adaptation-evolutionary strategy (CMA-ES) method. The estimation methods were applied to a set of thermodynamic models of gene transcription applied to regulatory elements active in the Drosophila embryo. Measuring overall fit, the global CMA-ES method performed significantly better than the local QN/NMS method on high quality data sets, but this difference was negligible on lower quality data sets with increased noise or on data sets simplified by stringent thresholding. Our results suggest that the choice of parameter estimation technique for evaluation of gene expression models depends both on quality of data, the nature of the models [again, remains to be established] and the aims of the modeling effort. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation.

    Science.gov (United States)

    Yu, Bingfei; Zhang, Kai; Milner, J Justin; Toma, Clara; Chen, Runqiang; Scott-Browne, James P; Pereira, Renata M; Crotty, Shane; Chang, John T; Pipkin, Matthew E; Wang, Wei; Goldrath, Ananda W

    2017-05-01

    Dynamic changes in the expression of transcription factors (TFs) can influence the specification of distinct CD8 + T cell fates, but the observation of equivalent expression of TFs among differentially fated precursor cells suggests additional underlying mechanisms. Here we profiled the genome-wide histone modifications, open chromatin and gene expression of naive, terminal-effector, memory-precursor and memory CD8 + T cell populations induced during the in vivo response to bacterial infection. Integration of these data suggested that the expression and binding of TFs contributed to the establishment of subset-specific enhancers during differentiation. We developed a new bioinformatics method using the PageRank algorithm to reveal key TFs that influence the generation of effector and memory populations. The TFs YY1 and Nr3c1, both constitutively expressed during CD8 + T cell differentiation, regulated the formation of terminal-effector cell fates and memory-precursor cell fates, respectively. Our data define the epigenetic landscape of differentiation intermediates and facilitate the identification of TFs with previously unappreciated roles in CD8 + T cell differentiation.

  3. Epigenetic landscapes reveal transcription factors regulating CD8+ T cell differentiation

    Science.gov (United States)

    Yu, Bingfei; Zhang, Kai; Milner, J. Justin; Toma, Clara; Chen, Runqiang; Scott-Browne, James P.; Pereira, Renata M.; Crotty, Shane; Chang, John T.; Pipkin, Matthew E.; Wang, Wei; Goldrath, Ananda W.

    2017-01-01

    Dynamic changes in the expression of transcription factors (TFs) can influence specification of distinct CD8+ T cell fates, but the observation of equivalent expression of TF among differentially-fated precursor cells suggests additional underlying mechanisms. Here, we profiled genome-wide histone modifications, open chromatin and gene expression of naive, terminal-effector, memory-precursor and memory CD8+ T cell populations induced during the in vivo response to bacterial infection. Integration of these data suggested that TF expression and binding contributed to establishment of subset-specific enhancers during differentiation. We developed a new bioinformatics method using the PageRank algorithm to reveal novel TFs influencing the generation of effector and memory populations. The TFs YY1 and Nr3c1, both constitutively expressed during CD8+ T cell differentiation, regulated the formation of terminal-effector and memory-precursor cell-fates, respectively. Our data define the epigenetic landscape of differentiation intermediates, facilitating identification of TFs with previously unappreciated roles in CD8+ T cell differentiation. PMID:28288100

  4. Patent landscape of countermeasures against smallpox and estimation of grant attraction capability through patent landscape data.

    Science.gov (United States)

    Mayburd, Anatoly L; Kedia, Govind; Evans, Haydn W; Kaslival, Pritesh C

    2010-11-01

    The study was concerned with countermeasures against a possible smallpox outbreak. In the process of assessment 18 landscaping sectors were defined and described, the advantages and drawbacks of the corresponding countermeasures being reviewed. The data of the previously published influenza landscape were revisited. The current economic climate of deficit cutting (austerity) also puts emphasis on the optimization of capital investment. We used the materials of the landscape to define and analyze metrics of capital placement optimization. Value score was obtained by fitting patent landscape internals to the sale price of individual patents. Success score was obtained as a product of a-priori parameters that measure likelihood of emergence of a marketable product in a technological sector. Both scores were combined in a qualitative metric. Our methodology defined weight as a product of the sector size by the success score. We hypothesized - based on the material of two landscapes- that a life cycle of a technology begins in IP space with a high patent quality low volume "bud" of low weight, reaches maximum weight and then weight falls again when the technology becomes outdated. The weight and the annual dynamic of weight can serve a measure of investment risk and return. In this report we modeled investment by issue of government grants or purchase of patents by government. In the smallpox landscape the number of patents purchased by government agencies was the highest in the sectors with the highest weight and the trend was confirmed by the count of NIH grants issued in support of the technological sectors. In the influenza landscape only grant issue count was statistically meaningful and the trend was also confirmed. To better fit the grant support levels, the weight expression was optimized by using training coefficients. We propose to use value scores for evaluation of individual patent publications/company portfolios and to use weights for assessment of

  5. Noncoding RNA in the Transcriptional Landscape of Human Neural Progenitor Cell Differentiation

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    Patrick eHecht

    2015-10-01

    Full Text Available Increasing evidence suggests that noncoding RNAs play key roles in cellular processes, particularly in the brain. The present study used RNA sequencing to identify the transcriptional landscape of two human neural progenitor cell lines, SK-N-SH and ReNcell CX, as they differentiate into human cortical projection neurons. Protein coding genes were found to account for 54.8% and 57.0% of expressed genes, respectively, and alignment of RNA sequencing reads revealed that only 25.5-28.1% mapped to exonic regions of the genome. Differential expression analysis in the two cell lines identified altered gene expression in both protein coding and noncoding RNAs as they undergo neural differentiation with 222 differentially expressed genes observed in SK-N-SH cells and 19 differentially expressed genes in ReNcell CX. Interestingly, genes showing differential expression in SK-N-SH cells are enriched in genes implicated in autism spectrum disorder, but not in gene sets related to cancer or Alzheimer’s disease. Weighted gene co-expression network analysis (WGCNA was used to detect modules of co-expressed protein coding and noncoding RNAs in SK-N-SH cells and found four modules to be associated with neural differentiation. These modules contain varying levels of noncoding RNAs ranging from 10.7% to 49.7% with gene ontology suggesting roles in numerous cellular processes important for differentiation. These results indicate that noncoding RNAs are highly expressed in human neural progenitor cells and likely hold key regulatory roles in gene networks underlying neural differentiation and neurodevelopmental disorders.

  6. Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis

    LENUS (Irish Health Repository)

    Guida, Alessandro

    2011-12-22

    Abstract Background Candida parapsilosis is one of the most common causes of Candida infection worldwide. However, the genome sequence annotation was made without experimental validation and little is known about the transcriptional landscape. The transcriptional response of C. parapsilosis to hypoxic (low oxygen) conditions, such as those encountered in the host, is also relatively unexplored. Results We used next generation sequencing (RNA-seq) to determine the transcriptional profile of C. parapsilosis growing in several conditions including different media, temperatures and oxygen concentrations. We identified 395 novel protein-coding sequences that had not previously been annotated. We removed > 300 unsupported gene models, and corrected approximately 900. We mapped the 5\\' and 3\\' UTR for thousands of genes. We also identified 422 introns, including two introns in the 3\\' UTR of one gene. This is the first report of 3\\' UTR introns in the Saccharomycotina. Comparing the introns in coding sequences with other species shows that small numbers have been gained and lost throughout evolution. Our analysis also identified a number of novel transcriptional active regions (nTARs). We used both RNA-seq and microarray analysis to determine the transcriptional profile of cells grown in normoxic and hypoxic conditions in rich media, and we showed that there was a high correlation between the approaches. We also generated a knockout of the UPC2 transcriptional regulator, and we found that similar to C. albicans, Upc2 is required for conferring resistance to azole drugs, and for regulation of expression of the ergosterol pathway in hypoxia. Conclusion We provide the first detailed annotation of the C. parapsilosis genome, based on gene predictions and transcriptional analysis. We identified a number of novel ORFs and other transcribed regions, and detected transcripts from approximately 90% of the annotated protein coding genes. We found that the transcription factor

  7. Global effects of the CSR-1 RNA interference pathway on the transcriptional landscape.

    Science.gov (United States)

    Cecere, Germano; Hoersch, Sebastian; O'Keeffe, Sean; Sachidanandam, Ravi; Grishok, Alla

    2014-04-01

    Argonaute proteins and their small RNA cofactors short interfering RNAs are known to inhibit gene expression at the transcriptional and post-transcriptional levels. In Caenorhabditis elegans, the Argonaute CSR-1 binds thousands of endogenous siRNAs (endo-siRNAs) that are antisense to germline transcripts. However, its role in gene expression regulation remains controversial. Here we used genome-wide profiling of nascent RNA transcripts and found that the CSR-1 RNA interference pathway promoted sense-oriented RNA polymerase II transcription. Moreover, a loss of CSR-1 function resulted in global increase in antisense transcription and ectopic transcription of silent chromatin domains, which led to reduced chromatin incorporation of centromere-specific histone H3. On the basis of these findings, we propose that the CSR-1 pathway helps maintain the directionality of active transcription, thereby propagating the distinction between transcriptionally active and silent genomic regions.

  8. Global effects of the CSR-1 RNA interference pathway on transcriptional landscape

    Science.gov (United States)

    Cecere, Germano; Hoersch, Sebastian; O’Keeffe, Sean; Sachidanandam, Ravi; Grishok, Alla

    2014-01-01

    Argonaute proteins and their small RNA co-factors short interfering RNAs (siRNAs) are known to inhibit gene expression at the transcriptional and post-transcriptional levels. In Caenorhabditis elegans, the Argonaute CSR-1 binds thousands of endogenous siRNAs (endo-siRNAs) antisense to germline transcripts and associates with chromatin in a siRNA-dependent manner. However, its role in gene expression regulation remains controversial. Here, we used a genome-wide profiling of nascent RNA transcripts to demonstrate that the CSR-1 RNAi pathway promotes sense-oriented Pol II transcription. Moreover, a loss of CSR-1 function resulted in global increase in antisense transcription and ectopic transcription of silent chromatin domains, which led to reduced chromatin incorporation of centromere-specific histone H3. Based on these findings, we propose that the CSR-1 pathway has a role in maintaining the directionality of active transcription thereby propagating the distinction between transcriptionally active and silent genomic regions. PMID:24681887

  9. Using genetic data to estimate diffusion rates in heterogeneous landscapes.

    Science.gov (United States)

    Roques, L; Walker, E; Franck, P; Soubeyrand, S; Klein, E K

    2016-08-01

    Having a precise knowledge of the dispersal ability of a population in a heterogeneous environment is of critical importance in agroecology and conservation biology as it can provide management tools to limit the effects of pests or to increase the survival of endangered species. In this paper, we propose a mechanistic-statistical method to estimate space-dependent diffusion parameters of spatially-explicit models based on stochastic differential equations, using genetic data. Dividing the total population into subpopulations corresponding to different habitat patches with known allele frequencies, the expected proportions of individuals from each subpopulation at each position is computed by solving a system of reaction-diffusion equations. Modelling the capture and genotyping of the individuals with a statistical approach, we derive a numerically tractable formula for the likelihood function associated with the diffusion parameters. In a simulated environment made of three types of regions, each associated with a different diffusion coefficient, we successfully estimate the diffusion parameters with a maximum-likelihood approach. Although higher genetic differentiation among subpopulations leads to more accurate estimations, once a certain level of differentiation has been reached, the finite size of the genotyped population becomes the limiting factor for accurate estimation.

  10. Timber volume and aboveground live tree biomass estimations for landscape analyses in the Pacific Northwest

    Science.gov (United States)

    Xiaoping Zhou; Miles A. Hemstrom

    2010-01-01

    Timber availability, aboveground tree biomass, and changes in aboveground carbon pools are important consequences of landscape management. There are several models available for calculating tree volume and aboveground tree biomass pools. This paper documents species-specific regional equations for tree volume and aboveground live tree biomass estimation that might be...

  11. Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

    NARCIS (Netherlands)

    C. Nepal (Chirag); Y. Hadzhiev (Yavor); C. Previti (Christopher); V. Haberle (Vanja); N. Li (Nan); H. Takahashi (Hiroyuki); A.M. Suzuki (Ana Maria); Y. Sheng (Ying); R.F. Abdelhamid (Rehab); S. Anand (Santosh); P.A. Gehrig (Paola A.); A. Akalin (Altuna); C. Kockx (Christel); A. Van Der Sloot (Antoine); W.F.J. van IJcken (Wilfred); O. Armant (Olivier); S. Rastegar (Sepand); C. Watson (Craig); U. Strähle (Uwe); E. Stupka (Elia); P. Carninci (Piero); B. Lenhard (Boris); F. Müller (Ferenc)

    2013-01-01

    textabstractSpatiotemporal control of gene expression is central to animal development. Core promoters represent a previously unanticipated regulatory level by interacting with cis-regulatory elements and transcription initiation in different physiological and developmental contexts. Here, we

  12. Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003.

    Science.gov (United States)

    Bottacini, Francesca; Zomer, Aldert; Milani, Christian; Ferrario, Chiara; Lugli, Gabriele Andrea; Egan, Muireann; Ventura, Marco; van Sinderen, Douwe

    2017-12-28

    Bifidobacterium breve represents a common member of the infant gut microbiota and its presence in the gut has been associated with host well being. For this reason it is relevant to investigate and understand the molecular mechanisms underlying the establishment, persistence and activities of this gut commensal in the host environment. The assessment of vegetative promoters in the bifidobacterial prototype Bifidobacterium breve UCC2003 was performed employing a combination of RNA tiling array analysis and cDNA sequencing. Canonical -10 (TATAAT) and -35 (TTGACA) sequences were identified upstream of transcribed genes or operons, where deviations from this consensus correspond to transcription level variations. A Random Forest analysis assigned the -10 region of B. breve promoters as the element most impacting on the level of transcription, followed by the spacer length and the 5'-UTR length of transcripts. Furthermore, our transcriptome study also identified rho-independent termination as the most common and effective termination signal of highly and moderately transcribed operons in B. breve. The present study allowed us to identify genes and operons that are actively transcribed in this organism during logarithmic growth, and link promoter elements with levels of transcription of essential genes in this organism. As homologs of many of our identified genes are present across the whole genus Bifidobacterium, our dataset constitutes a transcriptomic reference to be used for future investigations of gene expression in members of this genus.

  13. From the Beauty of Genomic Landscapes to the Strength of Transcriptional Mechanisms.

    Science.gov (United States)

    Natoli, Gioacchino

    2016-03-24

    Genomic analyses are commonly used to infer trends and broad rules underlying transcriptional control. The innovative approach by Tong et al. to interrogate genomic datasets allows extracting mechanistic information on the specific regulation of individual genes. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Estimating Net Primary Production of Swedish Forest Landscapes by Combining Mechanistic Modeling and Remote Sensing

    DEFF Research Database (Denmark)

    Tagesson, Håkan Torbern; Smith, Benjamin; Løfgren, Anders

    2009-01-01

    and the Beer-Lambert law. LAI estimates were compared with satellite-extrapolated field estimates of LAI, and the results were generally acceptable. NPP estimates directly from the dynamic vegetation model and estimates obtained by combining the model estimates with remote sensing information were, on average......The aim of this study was to investigate a combination of satellite images of leaf area index (LAI) with processbased vegetation modeling for the accurate assessment of the carbon balances of Swedish forest ecosystems at the scale of a landscape. Monthly climatologic data were used as inputs...... in a dynamic vegetation model, the Lund Potsdam Jena-General Ecosystem Simulator. Model estimates of net primary production (NPP) and the fraction of absorbed photosynthetic active radiation were constrained by combining them with satellite-based LAI images using a general light use efficiency (LUE) model...

  15. Use of non-contacting electromagnetic inductive method for estimating soil moisture across a landscape

    International Nuclear Information System (INIS)

    Khakural, B.R.; Robert, P.C.; Hugins, D.R.

    1998-01-01

    There is a growing interest in real-time estimation of soil moisture for site-specific crop management. Non-contacting electromagnetic inductive (EMI) methods have potentials to provide real-time estimate of soil profile water contents. Soil profile water contents were monitored with a neutron probe at selected sites. A Geonics LTD EM-38 terrain meter was used to record bulk soil electrical conductivity (EC(A)) readings across a soil-landscape in West central Minnesota with variable moisture regimes. The relationships among EC(A), selected soil and landscape properties were examined. Bulk soil electrical conductivity (0-1.0 and 0-0.5 m) was negatively correlated with relative elevation. It was positively correlated with soil profile (1.0 m) clay content and negatively correlated with soil profile coarse fragments (2 mm) and sand content. There was significant linear relationship between ECA (0-1.0 and 0-0.5) and soil profile water storage. Soil water storage estimated from ECA reflected changes in landscape and soil characteristics

  16. Three-dimensional habitat structure and landscape genetics: a step forward in estimating functional connectivity.

    Science.gov (United States)

    Milanesi, P; Holderegger, R; Bollmann, K; Gugerli, F; Zellweger, F

    2017-02-01

    Estimating connectivity among fragmented habitat patches is crucial for evaluating the functionality of ecological networks. However, current estimates of landscape resistance to animal movement and dispersal lack landscape-level data on local habitat structure. Here, we used a landscape genetics approach to show that high-fidelity habitat structure maps derived from Light Detection and Ranging (LiDAR) data critically improve functional connectivity estimates compared to conventional land cover data. We related pairwise genetic distances of 128 Capercaillie (Tetrao urogallus) genotypes to least-cost path distances at multiple scales derived from land cover data. Resulting β values of linear mixed effects models ranged from 0.372 to 0.495, while those derived from LiDAR ranged from 0.558 to 0.758. The identification and conservation of functional ecological networks suffering from habitat fragmentation and homogenization will thus benefit from the growing availability of detailed and contiguous data on three-dimensional habitat structure and associated habitat quality. © 2016 by the Ecological Society of America.

  17. Estimating wildfire risk on a Mojave Desert landscape using remote sensing and field sampling

    Science.gov (United States)

    Van Linn, Peter F.; Nussear, Kenneth E.; Esque, Todd C.; DeFalco, Lesley A.; Inman, Richard D.; Abella, Scott R.

    2013-01-01

    Predicting wildfires that affect broad landscapes is important for allocating suppression resources and guiding land management. Wildfire prediction in the south-western United States is of specific concern because of the increasing prevalence and severe effects of fire on desert shrublands and the current lack of accurate fire prediction tools. We developed a fire risk model to predict fire occurrence in a north-eastern Mojave Desert landscape. First we developed a spatial model using remote sensing data to predict fuel loads based on field estimates of fuels. We then modelled fire risk (interactions of fuel characteristics and environmental conditions conducive to wildfire) using satellite imagery, our model of fuel loads, and spatial data on ignition potential (lightning strikes and distance to roads), topography (elevation and aspect) and climate (maximum and minimum temperatures). The risk model was developed during a fire year at our study landscape and validated at a nearby landscape; model performance was accurate and similar at both sites. This study demonstrates that remote sensing techniques used in combination with field surveys can accurately predict wildfire risk in the Mojave Desert and may be applicable to other arid and semiarid lands where wildfires are prevalent.

  18. Combining laser microdissection and RNA-seq to chart the transcriptional landscape of fungal development

    Science.gov (United States)

    2012-01-01

    Background During sexual development, filamentous ascomycetes form complex, three-dimensional fruiting bodies for the protection and dispersal of sexual spores. Fruiting bodies contain a number of cell types not found in vegetative mycelium, and these morphological differences are thought to be mediated by changes in gene expression. However, little is known about the spatial distribution of gene expression in fungal development. Here, we used laser microdissection (LM) and RNA-seq to determine gene expression patterns in young fruiting bodies (protoperithecia) and non-reproductive mycelia of the ascomycete Sordaria macrospora. Results Quantitative analysis showed major differences in the gene expression patterns between protoperithecia and total mycelium. Among the genes strongly up-regulated in protoperithecia were the pheromone precursor genes ppg1 and ppg2. The up-regulation was confirmed by fluorescence microscopy of egfp expression under the control of ppg1 regulatory sequences. RNA-seq analysis of protoperithecia from the sterile mutant pro1 showed that many genes that are differentially regulated in these structures are under the genetic control of transcription factor PRO1. Conclusions We have generated transcriptional profiles of young fungal sexual structures using a combination of LM and RNA-seq. This allowed a high spatial resolution and sensitivity, and yielded a detailed picture of gene expression during development. Our data revealed significant differences in gene expression between protoperithecia and non-reproductive mycelia, and showed that the transcription factor PRO1 is involved in the regulation of many genes expressed specifically in sexual structures. The LM/RNA-seq approach will also be relevant to other eukaryotic systems in which multicellular development is investigated. PMID:23016559

  19. Combining laser microdissection and RNA-seq to chart the transcriptional landscape of fungal development

    Directory of Open Access Journals (Sweden)

    Teichert Ines

    2012-09-01

    Full Text Available Abstract Background During sexual development, filamentous ascomycetes form complex, three-dimensional fruiting bodies for the protection and dispersal of sexual spores. Fruiting bodies contain a number of cell types not found in vegetative mycelium, and these morphological differences are thought to be mediated by changes in gene expression. However, little is known about the spatial distribution of gene expression in fungal development. Here, we used laser microdissection (LM and RNA-seq to determine gene expression patterns in young fruiting bodies (protoperithecia and non-reproductive mycelia of the ascomycete Sordaria macrospora. Results Quantitative analysis showed major differences in the gene expression patterns between protoperithecia and total mycelium. Among the genes strongly up-regulated in protoperithecia were the pheromone precursor genes ppg1 and ppg2. The up-regulation was confirmed by fluorescence microscopy of egfp expression under the control of ppg1 regulatory sequences. RNA-seq analysis of protoperithecia from the sterile mutant pro1 showed that many genes that are differentially regulated in these structures are under the genetic control of transcription factor PRO1. Conclusions We have generated transcriptional profiles of young fungal sexual structures using a combination of LM and RNA-seq. This allowed a high spatial resolution and sensitivity, and yielded a detailed picture of gene expression during development. Our data revealed significant differences in gene expression between protoperithecia and non-reproductive mycelia, and showed that the transcription factor PRO1 is involved in the regulation of many genes expressed specifically in sexual structures. The LM/RNA-seq approach will also be relevant to other eukaryotic systems in which multicellular development is investigated.

  20. LocExpress: a web server for efficiently estimating expression of novel transcripts.

    Science.gov (United States)

    Hou, Mei; Tian, Feng; Jiang, Shuai; Kong, Lei; Yang, Dechang; Gao, Ge

    2016-12-22

    The temporal and spatial-specific expression pattern of a transcript in multiple tissues and cell types can indicate key clues about its function. While several gene atlas available online as pre-computed databases for known gene models, it's still challenging to get expression profile for previously uncharacterized (i.e. novel) transcripts efficiently. Here we developed LocExpress, a web server for efficiently estimating expression of novel transcripts across multiple tissues and cell types in human (20 normal tissues/cells types and 14 cell lines) as well as in mouse (24 normal tissues/cell types and nine cell lines). As a wrapper to RNA-Seq quantification algorithm, LocExpress efficiently reduces the time cost by making abundance estimation calls increasingly within the minimum spanning bundle region of input transcripts. For a given novel gene model, such local context-oriented strategy allows LocExpress to estimate its FPKMs in hundreds of samples within minutes on a standard Linux box, making an online web server possible. To the best of our knowledge, LocExpress is the only web server to provide nearly real-time expression estimation for novel transcripts in common tissues and cell types. The server is publicly available at http://loc-express.cbi.pku.edu.cn .

  1. Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation

    Directory of Open Access Journals (Sweden)

    Hisham Mohammed

    2017-08-01

    Full Text Available The mouse inner cell mass (ICM segregates into the epiblast and primitive endoderm (PrE lineages coincident with implantation of the embryo. The epiblast subsequently undergoes considerable expansion of cell numbers prior to gastrulation. To investigate underlying regulatory principles, we performed systematic single-cell RNA sequencing (seq of conceptuses from E3.5 to E6.5. The epiblast shows reactivation and subsequent inactivation of the X chromosome, with Zfp57 expression associated with reactivation and inactivation together with other candidate regulators. At E6.5, the transition from epiblast to primitive streak is linked with decreased expression of polycomb subunits, suggesting a key regulatory role. Notably, our analyses suggest elevated transcriptional noise at E3.5 and within the non-committed epiblast at E6.5, coinciding with exit from pluripotency. By contrast, E6.5 primitive streak cells became highly synchronized and exhibit a shortened G1 cell-cycle phase, consistent with accelerated proliferation. Our study systematically charts transcriptional noise and uncovers molecular processes associated with early lineage decisions.

  2. Transcriptional landscape of ncRNA and Repeat elements in somatic cells

    KAUST Repository

    Ghosheh, Yanal

    2016-12-01

    The advancement of Nucleic acids (DNA and RNA) sequencing technology has enabled many projects targeted towards the identification of genome structure and transcriptome complexity of organisms. The first conclusions of the human and mouse projects have underscored two important, yet unexpected, findings. First, while almost the entire genome is transcribed, only 5% of it encodes for proteins. Thereby, most transcripts are noncoding RNA. This includes both short RNA (<200 nucleotides (nt)) comprising piRNAs; microRNAs (miRNAs); endogenous Short Interfering RNAs (siRNAs) among others, and includes lncRNA (>200nt). Second, a significant portion of the mammalian genome (45%) is composed of Repeat Elements (REs). RE are mostly relics of ancestral viruses that during evolution have invaded the host genome by producing thousands of copies. Their roles within their host genomes have yet to be fully explored considering that they sometimes produce lncRNA, and have been shown to influence expression at the transcriptional and post-transcriptional levels. Moreover, because some REs can still mobilize within host genomes, host genomes have evolved mechanisms, mainly epigenetic, to maintain REs under tight control. Recent reports indicate that REs activity is regulated in somatic cells, particularily in the brain, suggesting a physiological role of RE mobilization during normal development. In this thesis, I focus on the analysis of ncRNAs, specifically REs; piRNAs; lncRNAs in human and mouse post-mitotic somatic cells. The main aspects of this analysis are: Using sRNA-Seq, I show that piRNAs, a class of ncRNAs responsible for the silencing of Transposable elements (TEs) in testes, are present also in adult mouse brain. Furthermore, their regulation shows only a subset of testes piRNAs are expressed in the brain and may be controlled by known neurogenesis factors. To investigate the dynamics of the transcriptome during cellular differentiation, I examined deep RNA-Seq and Cap

  3. Urban Landscape Spatial Pattern Estimation of Cities in Shandong Province Using Nighttime Luminosity Data

    Science.gov (United States)

    Fan, J.; He, H.; Hu, T.; Li, G.; Gao, H.; Zhao, X.

    2017-09-01

    China's cities have been undergoing rapid and intense urbanization processes in the past few decades. Shandong is a coastal province which is located in East China with big economy and population scales, and which also plays an important role in the rapid process of China's modernization. The DMSP/OLS dataset has been widely used for the urban development assessments in long time-series and large spatial scales situations. In this paper, we used a time series of nighttime light data to estimate the landscape spatial pattern changes of cities in Shandong province from 1994 to 2012. Nine landscape metrics were calculated and analyzed to figure out the spatial patterns of urban area developments of the cities in Shandong province. The landscape metrics include the number of patches (NP), the landscape total area (TA), the aggregation index (AI), the largest patch index (LPI), the mean patch area (AREA_MN), the landscape shape index (LSI), the total edge length (TE), the edge density (ED), and the mean radius of gyration (GYRATE_MN). The experimental results reveal that, in 1994-2012, the total urban area of cities in Shandong province expanded for 1.17 times, the average urban area increased by about 93.00%, the average annual growth rate of the TE metric is 2.67 %, while the ED metric decreased about 1.44 % annually. Bigger cities in this area show relative slower urbanization development processes, such as Jinan and Qingdao. Coastal cities represented much more rapid expansion velocities than inland cities. In the middle area of Shandong province, the connectivity between developed urban areas was constantly increased.

  4. URBAN LANDSCAPE SPATIAL PATTERN ESTIMATION OF CITIES IN SHANDONG PROVINCE USING NIGHTTIME LUMINOSITY DATA

    Directory of Open Access Journals (Sweden)

    J. Fan

    2017-09-01

    Full Text Available China’s cities have been undergoing rapid and intense urbanization processes in the past few decades. Shandong is a coastal province which is located in East China with big economy and population scales, and which also plays an important role in the rapid process of China’s modernization. The DMSP/OLS dataset has been widely used for the urban development assessments in long time-series and large spatial scales situations. In this paper, we used a time series of nighttime light data to estimate the landscape spatial pattern changes of cities in Shandong province from 1994 to 2012. Nine landscape metrics were calculated and analyzed to figure out the spatial patterns of urban area developments of the cities in Shandong province. The landscape metrics include the number of patches (NP, the landscape total area (TA, the aggregation index (AI, the largest patch index (LPI, the mean patch area (AREA_MN, the landscape shape index (LSI, the total edge length (TE, the edge density (ED, and the mean radius of gyration (GYRATE_MN. The experimental results reveal that, in 1994–2012, the total urban area of cities in Shandong province expanded for 1.17 times, the average urban area increased by about 93.00%, the average annual growth rate of the TE metric is 2.67 %, while the ED metric decreased about 1.44 % annually. Bigger cities in this area show relative slower urbanization development processes, such as Jinan and Qingdao. Coastal cities represented much more rapid expansion velocities than inland cities. In the middle area of Shandong province, the connectivity between developed urban areas was constantly increased.

  5. Estimation of Remote Microclimates from Weather Station Data with Applications to Landscape Architecture.

    Science.gov (United States)

    Brown, Robert Douglas

    Several components of a system for quantitative application of climatic statistics to landscape planning and design (CLIMACS) have been developed. One component model (MICROSIM) estimated the microclimate at the top of a remote crop using physically-based models and inputs of weather station data. Temperatures at the top of unstressed, uniform crops on flat terrain within 1600 m of a recording weather station were estimated within 1.0 C 96% of the time for a corn crop and 92% of the time for a soybean crop. Crop top winds were estimated within 0.4 m/s 92% of the time for corn and 100% of the time for soybean. This is of sufficient accuracy for application in landscape planning and design models. A physically-based model (COMFA) was developed for the determination of outdoor human thermal comfort from microclimate inputs. Estimated versus measured comfort levels in a wide range of environments agreed with a correlation coefficient of r = 0.91. Using these components, the CLIMACS concept has been applied to a typical planning example. Microclimate data were generated from weather station information using MICROSIM, then input to COMFA and to a house energy consumption model called HOTCAN to derive quantitative climatic justification for design decisions.

  6. The transcriptional landscape of seasonal coat colour moult in the snowshoe hare.

    Science.gov (United States)

    Ferreira, Mafalda S; Alves, Paulo C; Callahan, Colin M; Marques, João P; Mills, L Scott; Good, Jeffrey M; Melo-Ferreira, José

    2017-08-01

    Seasonal coat colour change is an important adaptation to seasonally changing environments but the evolution of this and other circannual traits remains poorly understood. In this study, we use gene expression to understand seasonal coat colour moulting in wild snowshoe hares (Lepus americanus). We used hair colour to follow the progression of the moult, simultaneously sampling skin from three moulting stages in hares collected during the peak of the spring moult from white winter to brown summer pelage. Using RNA sequencing, we tested whether patterns of expression were consistent with predictions based on the established phases of the hair growth cycle. We found functionally consistent clustering across skin types, with 766 genes differentially expressed between moult stages. "White" pelage showed more differentially expressed genes that were upregulated relative to other skin types, involved in the transition between late telogen (quiescent stage) and the onset of anagen (proliferative stage). Skin samples from transitional "intermediate" and "brown" pelage were transcriptionally similar and resembled the regressive transition to catagen (regressive stage). We also detected differential expression of several key circadian clock and pigmentation genes, providing important means to dissect the bases of alternate seasonal colour morphs. Our results reveal that pelage colour is a useful biomarker for seasonal change but that there is a consistent lag between the main gene expression waves and change in visible coat colour. These experiments establish that developmental sampling from natural populations of nonmodel organisms can provide a crucial resource to dissect the genetic basis and evolution of complex seasonally changing traits. © 2017 John Wiley & Sons Ltd.

  7. An individual-based modelling approach to estimate landscape connectivity for bighorn sheep (Ovis canadensis

    Directory of Open Access Journals (Sweden)

    Corrie H. Allen

    2016-05-01

    Full Text Available Background. Preserving connectivity, or the ability of a landscape to support species movement, is among the most commonly recommended strategies to reduce the negative effects of climate change and human land use development on species. Connectivity analyses have traditionally used a corridor-based approach and rely heavily on least cost path modeling and circuit theory to delineate corridors. Individual-based models are gaining popularity as a potentially more ecologically realistic method of estimating landscape connectivity. However, this remains a relatively unexplored approach. We sought to explore the utility of a simple, individual-based model as a land-use management support tool in identifying and implementing landscape connectivity. Methods. We created an individual-based model of bighorn sheep (Ovis canadensis that simulates a bighorn sheep traversing a landscape by following simple movement rules. The model was calibrated for bighorn sheep in the Okanagan Valley, British Columbia, Canada, a region containing isolated herds that are vital to conservation of the species in its northern range. Simulations were run to determine baseline connectivity between subpopulations in the study area. We then applied the model to explore two land management scenarios on simulated connectivity: restoring natural fire regimes and identifying appropriate sites for interventions that would increase road permeability for bighorn sheep. Results. This model suggests there are no continuous areas of good habitat between current subpopulations of sheep in the study area; however, a series of stepping-stones or circuitous routes could facilitate movement between subpopulations and into currently unoccupied, yet suitable, bighorn habitat. Restoring natural fire regimes or mimicking fire with prescribed burns and tree removal could considerably increase bighorn connectivity in this area. Moreover, several key road crossing sites that could benefit from

  8. Impact of sampling strategy on stream load estimates in till landscape of the Midwest

    Science.gov (United States)

    Vidon, P.; Hubbard, L.E.; Soyeux, E.

    2009-01-01

    Accurately estimating various solute loads in streams during storms is critical to accurately determine maximum daily loads for regulatory purposes. This study investigates the impact of sampling strategy on solute load estimates in streams in the US Midwest. Three different solute types (nitrate, magnesium, and dissolved organic carbon (DOC)) and three sampling strategies are assessed. Regardless of the method, the average error on nitrate loads is higher than for magnesium or DOC loads, and all three methods generally underestimate DOC loads and overestimate magnesium loads. Increasing sampling frequency only slightly improves the accuracy of solute load estimates but generally improves the precision of load calculations. This type of investigation is critical for water management and environmental assessment so error on solute load calculations can be taken into account by landscape managers, and sampling strategies optimized as a function of monitoring objectives. ?? 2008 Springer Science+Business Media B.V.

  9. Estimating landscape-scale impacts of agricultural management on soil carbon using measurements and models

    Science.gov (United States)

    Schipanski, M.; Rosenzweig, S. T.; Robertson, A. D.; Sherrod, L. A.; Ghimire, R.; McMaster, G. S.

    2017-12-01

    Agriculture covers 40% of Earth's ice-free land area and has broad impacts on global biogeochemical cycles. While some agricultural management changes are small in scale or impact, others have the potential to shift biogeochemical cycles at landscape and larger scales if widely adopted. Understanding which management practices have the potential to contribute to climate change adaptation and mitigation while maintaining productivity requires scaling up estimates spatially and temporally. We used on-farm, long-term, and landscape scale datasets to estimate how crop rotations impact soil organic carbon (SOC) accumulation rates under current and future climate scenarios across the semi-arid Central and Southern Great Plains. We used a stratified, landscape-scale soil sampling approach across 96 farm fields to evaluate crop rotation intensity effects on SOC pools and pesticide inputs. Replacing traditional wheat-fallow rotations with more diverse, continuously cropped rotations increased SOC by 17% and 12% in 0-10 cm and 0-20 cm depths, respectively, and reduced herbicide use by 50%. Using USDA Cropland Data Layer, we estimated soil C accumulation and pesticide reduction potentials of shifting to more intensive rotations. We also used a 30-year cropping systems experiment to calibrate and validate the Daycent model to evaluate rotation intensify effects under future climate change scenarios. The model estimated greater SOC accumulation rates under continuously cropped rotations, but SOC stocks peaked and then declined for all cropping systems beyond 2050 under future climate scenarios. Perennial grasslands were the only system estimated to maintain SOC levels in the future. In the Southern High Plains, soil C declined despite increasing input intensity under current weather while modest gains were simulated under future climate for sorghum-based cropping systems. Our findings highlight the potential vulnerability of semi-arid regions to climate change, which will be

  10. Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis.

    Science.gov (United States)

    Cochain, Clément; Vafadarnejad, Ehsan; Arampatzi, Panagiota; Jaroslav, Pelisek; Winkels, Holger; Ley, Klaus; Wolf, Dennis; Saliba, Antoine-Emmanuel; Zernecke, Alma

    2018-03-15

    Rationale: It is assumed that atherosclerotic arteries contain several macrophage subsets endowed with specific functions. The precise identity of these subsets is poorly characterized as they ha ve been defined by the expression of a restricted number of markers. Objective: We have applied single-cell RNA-seq as an unbiased profiling strategy to interrogate and classify aortic macrophage heterogeneity at the single-cell level in atherosclerosis. Methods and Results: We performed single-cell RNA sequencing of total aortic CD45 + cells extracted from the non-diseased (chow fed) and atherosclerotic (11 weeks of high fat diet) aorta of Ldlr -/- mice. Unsupervised clustering singled out 13 distinct aortic cell clusters. Among the myeloid cell populations, Resident-like macrophages with a gene expression profile similar to aortic resident macrophages were found in healthy and diseased aortae, whereas monocytes, monocyte-derived dendritic cells (MoDC), and two populations of macrophages were almost exclusively detectable in atherosclerotic aortae, comprising Inflammatory macrophages showing enrichment in I l1b , and previously undescribed TREM2 hi macrophages. Differential gene expression and gene ontology enrichment analyses revealed specific gene expression patterns distinguishing these three macrophage subsets and MoDC, and uncovered putative functions of each cell type. Notably, TREM2 hi macrophages appeared to be endowed with specialized functions in lipid metabolism and catabolism, and presented a gene expression signature reminiscent of osteoclasts, suggesting a role in lesion calcification. TREM2 expression was moreover detected in human lesional macrophages. Importantly, these macrophage populations were present also in advanced atherosclerosis and in Apoe -/- aortae, indicating relevance of our findings in different stages of atherosclerosis and mouse models. Conclusions: These data unprecedentedly uncovered the transcriptional landscape and phenotypic

  11. Evaluation of alternative approaches for landscape-scale biomass estimation in a mixed-species northern forest

    Science.gov (United States)

    Coeli M. Hoover; Mark J. Ducey; R. Andy Colter; Mariko Yamasaki

    2018-01-01

    There is growing interest in estimating and mapping biomass and carbon content of forests across large landscapes. LiDAR-based inventory methods are increasingly common and have been successfully implemented in multiple forest types. Asner et al. (2011) developed a simple universal forest carbon estimation method for tropical forests that reduces the amount of required...

  12. Sensitivity of landscape resistance estimates based on point selection functions to scale and behavioral state: Pumas as a case study

    Science.gov (United States)

    Katherine A. Zeller; Kevin McGarigal; Paul Beier; Samuel A. Cushman; T. Winston Vickers; Walter M. Boyce

    2014-01-01

    Estimating landscape resistance to animal movement is the foundation for connectivity modeling, and resource selection functions based on point data are commonly used to empirically estimate resistance. In this study, we used GPS data points acquired at 5-min intervals from radiocollared pumas in southern California to model context-dependent point selection...

  13. How can streamflow and climate-landscape data be used to estimate baseflow mean response time?

    Science.gov (United States)

    Zhang, Runrun; Chen, Xi; Zhang, Zhicai; Soulsby, Chris; Gao, Man

    2018-02-01

    Mean response time (MRT) is a metric describing the propagation of catchment hydraulic behavior that reflects both hydro-climatic conditions and catchment characteristics. To provide a comprehensive understanding of catchment response over a longer-time scale for hydraulic processes, the MRT function for baseflow generation was derived using an instantaneous unit hydrograph (IUH) model that describes the subsurface response to effective rainfall inputs. IUH parameters were estimated based on the "match test" between the autocorrelation function (ACFs) derived from the filtered base flow time series and from the IUH parameters, under the GLUE framework. Regionalization of MRT was conducted using estimates and hydroclimate-landscape indices in 22 sub-basins of the Jinghe River Basin (JRB) in the Loess Plateau of northwest China. Results indicate there is strong equifinality in determination of the best parameter sets but the median values of the MRT estimates are relatively stable in the acceptable range of the parameters. MRTs vary markedly over the studied sub-basins, ranging from tens of days to more than a year. Climate, topography and geomorphology were identified as three first-order controls on recharge-baseflow response processes. Human activities involving the cultivation of permanent crops may elongate the baseflow MRT and hence increase the dynamic storage. Cross validation suggests the model can be used to estimate MRTs in ungauged catchments in similar regions of throughout the Loess Plateau. The proposed method provides a systematic approach for MRT estimation and regionalization in terms of hydroclimate and catchment characteristics, which is helpful in the sustainable water resources utilization and ecological protection in the Loess Plateau.

  14. Estimation of real evapotranspiration and its variation in Mediterranean landscapes of central-southern Chile

    Science.gov (United States)

    Olivera-Guerra, L.; Mattar, C.; Galleguillos, M.

    2014-05-01

    Evapotranspiration (ETd) is a key controller in the ecohydrological processes of semi-arid landscapes. This is the case of the dry land in Chile's central-southern zone, where forestry, farming and livestock activities must adapt to precipitation with considerable year-on-year variations. In this study, the spatial distribution of ETd was estimated in relation to the land use map and physical parameters of the soil. The ETd was estimated through the Simplified Surface Energy Balance Index (S-SEBI) using data from weather stations and remote data provided by the ASTER and MODIS sensors for November 2004 and 2006, respectively. The spatial variability of ETd was compared among different plant types, soil textural classes and depths using non-parametric statistical tests. In this comparison, the highest rates of ETd were obtained in the forest covers with values of 7.3 ± 0.8 and 8.4 ± 0.8 mm d-1 for 2004 and 2006, respectively. The lowest values were estimated for pastures and shrublands with values of 3.5 ± 1.2 mm d-1 and for crops with rates of 4.4 ± 1.6 mm d-1. Comparison of the ETd of the native forest covers and plantations of exotic species showed statistically significant differences; however, no great variation was noted, at least in the study months. Additionally, the highest rates of ETd were found in the clay loam textures (6.0 ± 1.8 and 6.4 ± 2.0 mm d-1) and the lowest rates in the sandy loam soils (3.7 ± 1.6 and 3.9 ± 1.6 mm d-1) for 2004 and 2006, respectively. The results enable analysis of the spatial patterns of the landscape in terms of the relation between water consumption, ET and the biophysical characteristics of a Mediterranean ecosystem. These results form part of the creation of tools useful in the optimization of decision-making for the management and planning of water resources and soil use in territories with few measuring instruments.

  15. A deterministic method for estimating free energy genetic network landscapes with applications to cell commitment and reprogramming paths.

    Science.gov (United States)

    Olariu, Victor; Manesso, Erica; Peterson, Carsten

    2017-06-01

    Depicting developmental processes as movements in free energy genetic landscapes is an illustrative tool. However, exploring such landscapes to obtain quantitative or even qualitative predictions is hampered by the lack of free energy functions corresponding to the biochemical Michaelis-Menten or Hill rate equations for the dynamics. Being armed with energy landscapes defined by a network and its interactions would open up the possibility of swiftly identifying cell states and computing optimal paths, including those of cell reprogramming, thereby avoiding exhaustive trial-and-error simulations with rate equations for different parameter sets. It turns out that sigmoidal rate equations do have approximate free energy associations. With this replacement of rate equations, we develop a deterministic method for estimating the free energy surfaces of systems of interacting genes at different noise levels or temperatures. Once such free energy landscape estimates have been established, we adapt a shortest path algorithm to determine optimal routes in the landscapes. We explore the method on three circuits for haematopoiesis and embryonic stem cell development for commitment and reprogramming scenarios and illustrate how the method can be used to determine sequential steps for onsets of external factors, essential for efficient reprogramming.

  16. Integrating animal movement with habitat suitability for estimating dynamic landscape connectivity

    Science.gov (United States)

    van Toor, Mariëlle L.; Kranstauber, Bart; Newman, Scott H.; Prosser, Diann J.; Takekawa, John Y.; Technitis, Georgios; Weibel, Robert; Wikelski, Martin; Safi, Kamran

    2018-01-01

    Context High-resolution animal movement data are becoming increasingly available, yet having a multitude of empirical trajectories alone does not allow us to easily predict animal movement. To answer ecological and evolutionary questions at a population level, quantitative estimates of a species’ potential to link patches or populations are of importance. Objectives We introduce an approach that combines movement-informed simulated trajectories with an environment-informed estimate of the trajectories’ plausibility to derive connectivity. Using the example of bar-headed geese we estimated migratory connectivity at a landscape level throughout the annual cycle in their native range. Methods We used tracking data of bar-headed geese to develop a multi-state movement model and to estimate temporally explicit habitat suitability within the species’ range. We simulated migratory movements between range fragments, and calculated a measure we called route viability. The results are compared to expectations derived from published literature. Results Simulated migrations matched empirical trajectories in key characteristics such as stopover duration. The viability of the simulated trajectories was similar to that of the empirical trajectories. We found that, overall, the migratory connectivity was higher within the breeding than in wintering areas, corroborating previous findings for this species. Conclusions We show how empirical tracking data and environmental information can be fused for meaningful predictions of animal movements throughout the year and even outside the spatial range of the available data. Beyond predicting migratory connectivity, our framework will prove useful for modelling ecological processes facilitated by animal movement, such as seed dispersal or disease ecology.

  17. Shaping the landscape of the Escherichia coli chromosome: replication-transcription encounters in cells with an ectopic replication origin

    DEFF Research Database (Denmark)

    Ivanova, Darja; Taylor, Toni; Smith, Sarah L

    2015-01-01

    Each cell division requires the unwinding of millions of DNA base pairs to allow chromosome duplication and gene transcription. As DNA replication and transcription share the same template, conflicts between both processes are unavoidable and head-on collisions are thought to be particularly...

  18. What's the FOX Got to Do with the KITten? Regulating the Lineage-Specific Transcriptional Landscape in GIST.

    Science.gov (United States)

    Lee, Donna M; Duensing, Anette

    2018-02-01

    Transcriptional regulation of the KIT receptor tyrosine kinase, a master regulator in gastrointestinal stromal tumors (GIST) and their precursors, the interstitial cells of Cajal (ICC), is part of a positive feedback loop involving the transcription factor ETV1. A new study now shows that the forkhead box (FOX) family transcription factor FOXF1 not only is an upstream regulator of ETV1 and hence ICC/GIST lineage-specific gene transcription, but also functions as lineage-specific pioneer factor with an active role in chromatin rearrangement to facilitate ETV1 binding and transcriptional activity. Cancer Discov; 8(2); 146-9. ©2018 AACR See related article by Ran et al., p. 234 . ©2018 American Association for Cancer Research.

  19. Repeated holdout Cross-Validation of Model to Estimate Risk of Lyme Disease by Landscape Attributes

    Science.gov (United States)

    We previously modeled Lyme disease (LD) risk at the landscape scale; here we evaluate the model's overall goodness-of-fit using holdout validation. Landscapes were characterized within road-bounded analysis units (AU). Observed LD cases (obsLD) were ascertained per AU. Data were ...

  20. Methane emissions from termites - landscape level estimates and methods of measurement

    Science.gov (United States)

    Jamali, Hizbullah; Livesley, Stephen J.; Hutley, Lindsay B.; Arndt, Stefan K.

    2013-04-01

    Termites contribute between mound-building termite species diurnally and seasonally in tropical savannas in the Northern Territory, Australia. Our results showed that there were significant diel and seasonal variations of methane emissions from termite mounds and we observed large species-specific differences. On a diurnal basis, methane fluxes were least at the coolest time of the day and greatest at the warmest for all species for both wet and dry seasons. We observed a strong and significant positive correlation between methane flux and mound temperature for all species. Fluxes in the wet season were 5-26-fold greater than those in the dry season and this was related to population dynamics of the termites. We observed significant relationships between mound methane flux and mound carbon dioxide flux, enabling the prediction of methane flux from measured carbon dioxide flux. However, these relationships were clearly termite species specific. We also determined significant relationships between mound flux and gas concentration inside mound, for both gases, and for all termite species, thereby enabling the prediction of flux from measured mound internal gas concentration. However, these relationships were also termite species specific. Consequently, there was no generic relationship that would enable an easier prediction of methane flux from termite mounds. On a landscape scale we estimated that termites were a methane source of +0.24 kg methane-C ha-1 year-1 whilst savanna soils were a methane sink of 1.14 kg methane-C ha-1 year-1. Termites therefore only offset 21% of methane consumed by savanna soil resulting in net sink strength of -0.90 kg methane-C ha-1 year-1 for these savannas. Assuming a similar contribution of termites in the savannas and tropical rain forests worldwide, termites would globally produce around 27 Tg CO2-e year-1, which is 0.2% of the global methane source budget or an order of magnitude smaller than many of the previous estimates.

  1. A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana

    DEFF Research Database (Denmark)

    Lindemose, Søren; Jensen, Michael Krogh; de Velde, Jan Van

    2014-01-01

    regulatory networks of 12 NAC transcription factors. Our data offer specific single-base resolution fingerprints for most TFs studied and indicate that NAC DNA-binding specificities might be predicted from their DNA-binding domain's sequence. The developed methodology, including the application......Target gene identification for transcription factors is a prerequisite for the systems wide understanding of organismal behaviour. NAM-ATAF1/2-CUC2 (NAC) transcription factors are amongst the largest transcription factor families in plants, yet limited data exist from unbiased approaches to resolve...... the DNA-binding preferences of individual members. Here, we present a TF-target gene identification workflow based on the integration of novel protein binding microarray data with gene expression and multi-species promoter sequence conservation to identify the DNA-binding specificities and the gene...

  2. EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering.

    Science.gov (United States)

    Lee, Soohyun; Seo, Chae Hwa; Alver, Burak Han; Lee, Sanghyuk; Park, Peter J

    2015-09-03

    RNA-seq has been widely used for genome-wide expression profiling. RNA-seq data typically consists of tens of millions of short sequenced reads from different transcripts. However, due to sequence similarity among genes and among isoforms, the source of a given read is often ambiguous. Existing approaches for estimating expression levels from RNA-seq reads tend to compromise between accuracy and computational cost. We introduce a new approach for quantifying transcript abundance from RNA-seq data. EMSAR (Estimation by Mappability-based Segmentation And Reclustering) groups reads according to the set of transcripts to which they are mapped and finds maximum likelihood estimates using a joint Poisson model for each optimal set of segments of transcripts. The method uses nearly all mapped reads, including those mapped to multiple genes. With an efficient transcriptome indexing based on modified suffix arrays, EMSAR minimizes the use of CPU time and memory while achieving accuracy comparable to the best existing methods. EMSAR is a method for quantifying transcripts from RNA-seq data with high accuracy and low computational cost. EMSAR is available at https://github.com/parklab/emsar.

  3. Estimating effective landscape distances and movement corridors: Comparison of habitat and genetic data

    Science.gov (United States)

    Maria C. Mateo-Sanchez; Niko Balkenhol; Samuel Cushman; Trinidad Perez; Ana Dominguez; Santiago Saura

    2015-01-01

    Resistance models provide a key foundation for landscape connectivity analyses and are widely used to delineate wildlife corridors. Currently, there is no general consensus regarding the most effective empirical methods to parameterize resistance models, but habitat data (species’ presence data and related habitat suitability models) and genetic data are the...

  4. Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates.

    Directory of Open Access Journals (Sweden)

    Andreas Tuerk

    2017-05-01

    Full Text Available Accuracy of transcript quantification with RNA-Seq is negatively affected by positional fragment bias. This article introduces Mix2 (rd. "mixquare", a transcript quantification method which uses a mixture of probability distributions to model and thereby neutralize the effects of positional fragment bias. The parameters of Mix2 are trained by Expectation Maximization resulting in simultaneous transcript abundance and bias estimates. We compare Mix2 to Cufflinks, RSEM, eXpress and PennSeq; state-of-the-art quantification methods implementing some form of bias correction. On four synthetic biases we show that the accuracy of Mix2 overall exceeds the accuracy of the other methods and that its bias estimates converge to the correct solution. We further evaluate Mix2 on real RNA-Seq data from the Microarray and Sequencing Quality Control (MAQC, SEQC Consortia. On MAQC data, Mix2 achieves improved correlation to qPCR measurements with a relative increase in R2 between 4% and 50%. Mix2 also yields repeatable concentration estimates across technical replicates with a relative increase in R2 between 8% and 47% and reduced standard deviation across the full concentration range. We further observe more accurate detection of differential expression with a relative increase in true positives between 74% and 378% for 5% false positives. In addition, Mix2 reveals 5 dominant biases in MAQC data deviating from the common assumption of a uniform fragment distribution. On SEQC data, Mix2 yields higher consistency between measured and predicted concentration ratios. A relative error of 20% or less is obtained for 51% of transcripts by Mix2, 40% of transcripts by Cufflinks and RSEM and 30% by eXpress. Titration order consistency is correct for 47% of transcripts for Mix2, 41% for Cufflinks and RSEM and 34% for eXpress. We, further, observe improved repeatability across laboratory sites with a relative increase in R2 between 8% and 44% and reduced standard deviation.

  5. Modelling and estimating pollen movement in oilseed rape (Brassica napus) at the landscape scale using genetic markers.

    Science.gov (United States)

    Devaux, C; Lavigne, C; Austerlitz, F; Klein, E K

    2007-02-01

    Understanding patterns of pollen movement at the landscape scale is important for establishing management rules following the release of genetically modified (GM) crops. We use here a mating model adapted to cultivated species to estimate dispersal kernels from the genotypes of the progenies of male-sterile plants positioned at different sampling sites within a 10 x 10-km oilseed rape production area. Half of the pollen clouds sampled by the male-sterile plants originated from uncharacterized pollen sources that could consist of both large volunteer and feral populations, and fields within and outside the study area. The geometric dispersal kernel was the most appropriate to predict pollen movement in the study area. It predicted a much larger proportion of long-distance pollination than previously fitted dispersal kernels. This best-fitting mating model underestimated the level of differentiation among pollen clouds but could predict its spatial structure. The estimation method was validated on simulated genotypic data, and proved to provide good estimates of both the shape of the dispersal kernel and the rate and composition of pollen issued from uncharacterized pollen sources. The best dispersal kernel fitted here, the geometric kernel, should now be integrated into models that aim at predicting gene flow at the landscape level, in particular between GM and non-GM crops.

  6. Estimating Carbon Stocks and Atmospheric Exchange of Depressional Marshes on the Central Florida Landscape

    Science.gov (United States)

    Benscoter, B.; McClellan, M. D.; Benavides, V.; Harshbarger, D.; Comas, X.

    2014-12-01

    Depressional marshes are ubiquitous throughout central and south Florida. Often distributed within a matrix of sandy pine flatwoods and hammocks, these wetlands have a seasonally variable water table, alternating between inundation and complete drydown. Though these landforms are typically small individually, they comprise a substantial component of the landscape and provide vital habitat for an array of flora and fauna. Given their fluctuating hydrology, conditions for soil and plant carbon (C) exchange mechanisms can vary greatly both spatially and temporally. In this study, we are developing a C budget for depressional marsh landforms by assessing ecosystem carbon exchange along an ecotone gradient and quantifying belowground C stocks using non-invasive geophysical methods (ground penetrating radar, GPR) at the Disney Wilderness Preserve (DWP) in Kissimmee, FL, USA. Using a series of closed chambers transecting the marsh from the center outward into the surrounding flatwoods, we are quantifying the effects of seasonal water table change on the magnitude of C exchange. Three dimensional GPR surveys were used to quantify peat layer thickness, and were constrained with direct core sampling to verify subsurface lithology and to assess peat C content. Using the relationship between landform surface area and belowground C volume, we assessed the cumulative C storage in depressional marshes across the DWP landscape. In conjunction with a nearby eddy covariance tower and seasonal hydrologic data, these response functions will help to evaluate the contribution of these small but widespread landscape features on regional C cycling.

  7. Impact of Land Use Change to the Soil Erosion Estimation for Cultural Landscapes: Case Study of Paphos Disrict in Cyprus

    Science.gov (United States)

    Cuca, B.; Agapiou, A.

    2017-05-01

    In 2006 UNESCO report has identified soil loss as one of the main threats of climate change with possible impact to natural and cultural heritage. The study illustrated in this paper shows the results from geomatic perspective, applying an interdisciplinary approach undertaken in order to identify major natural hazards affecting cultural landscapes and archaeological heritage in rural areas in Cyprus. In particular, Earth Observation (EO) and ground-based methods were identified and applied for mapping, monitoring and estimation of the possible soil loss caused by soil erosion. Special attention was given to the land use/land cover factor (C) and its impact on the overall estimation of the soil-loss. Cover factor represents the effect of soil-disturbing activities, plants, crop sequence and productivity level, soil cover and subsurface bio-mass on soil erosion. Urban areas have a definite role in retarding the recharge process, leading to increased runoff and soil loss in the broader area. On the other hand, natural vegetation plays a predominant role in reducing water erosion. The land use change was estimated based on the difference of the NDVI value between Landsat 5 TM and Sentinel-2 data for the period between 1980s' until today. Cover factor was then estimated for both periods and significant land use changes were further examined in areas of significant cultural and natural landscape value. The results were then compared in order to study the impact of land use change on the soil erosion and hence on the soil loss rate in the selected areas.

  8. Estimating the Cumulative Ecological Effect of Local Scale Landscape Changes in South Florida

    Science.gov (United States)

    Hogan, Dianna M.; Labiosa, William; Pearlstine, Leonard; Hallac, David; Strong, David; Hearn, Paul; Bernknopf, Richard

    2012-01-01

    Ecosystem restoration in south Florida is a state and national priority centered on the Everglades wetlands. However, urban development pressures affect the restoration potential and remaining habitat functions of the natural undeveloped areas. Land use (LU) planning often focuses at the local level, but a better understanding of the cumulative effects of small projects at the landscape level is needed to support ecosystem restoration and preservation. The South Florida Ecosystem Portfolio Model (SFL EPM) is a regional LU planning tool developed to help stakeholders visualize LU scenario evaluation and improve communication about regional effects of LU decisions. One component of the SFL EPM is ecological value (EV), which is evaluated through modeled ecological criteria related to ecosystem services using metrics for (1) biodiversity potential, (2) threatened and endangered species, (3) rare and unique habitats, (4) landscape pattern and fragmentation, (5) water quality buffer potential, and (6) ecological restoration potential. In this article, we demonstrate the calculation of EV using two case studies: (1) assessing altered EV in the Biscayne Gateway area by comparing 2004 LU to potential LU in 2025 and 2050, and (2) the cumulative impact of adding limestone mines south of Miami. Our analyses spatially convey changing regional EV resulting from conversion of local natural and agricultural areas to urban, industrial, or extractive use. Different simulated local LU scenarios may result in different alterations in calculated regional EV. These case studies demonstrate methods that may facilitate evaluation of potential future LU patterns and incorporate EV into decision making.

  9. Landscape-scale estimation of denitrification rates and nitrous oxide to dinitrogen ratio at Georgia and Pennsylvania LTAR sites

    Science.gov (United States)

    Dell, C. J.; Groffman, P. M.; Strickland, T.; Kleinman, P. J. A.; Bosch, D. D.; Bryant, R.

    2015-12-01

    Denitrification results in a significant loss of plant-available nitrogen from agricultural systems and contributes to climate change, due to the emissions of both the potent greenhouse gas nitrous oxide (N2O) and environmentally benign dinitrogen (N2). However total quantities of the gases emitted and the ratio of N2:N2O are often not clearly understood, because N2 emissions cannot be directly measured in the field because of the high background level of N2 in the atmosphere. While variability in soil conditions across landscapes, especially water content and aeration, is believed to greatly impact both total denitrification rates and N2:N2O, the measurement limitations have prevented a clear understanding of landscape-scale emissions of denitrification products. The Cary Institute has developed an approach where soil core are maintained in a sealed system with an N2-free airstream, allowing emitted N2 and N2O emissions to be measured without interference from atmospheric N2. Emissions of the gases are measured under a range of oxygen concentrations and soil water contents. Laboratory responses can then be correlated with measured field conditions at the sampling points and resulting emission estimates extrapolated to the field-scale. Measurements are currently being conducted on peanut/cotton rotations, dairy forage rotations (silage corn/alfalfa), and bioenergy crops (switchgrass and miscanthus) at Long Term Agricultural Research (LTAR) sites at Tifton, GA and University Park, PA.

  10. Towards regional, error-bounded landscape carbon storage estimates for data-deficient areas of the world.

    Directory of Open Access Journals (Sweden)

    Simon Willcock

    Full Text Available Monitoring landscape carbon storage is critical for supporting and validating climate change mitigation policies. These may be aimed at reducing deforestation and degradation, or increasing terrestrial carbon storage at local, regional and global levels. However, due to data-deficiencies, default global carbon storage values for given land cover types such as 'lowland tropical forest' are often used, termed 'Tier 1 type' analyses by the Intergovernmental Panel on Climate Change (IPCC. Such estimates may be erroneous when used at regional scales. Furthermore uncertainty assessments are rarely provided leading to estimates of land cover change carbon fluxes of unknown precision which may undermine efforts to properly evaluate land cover policies aimed at altering land cover dynamics. Here, we present a repeatable method to estimate carbon storage values and associated 95% confidence intervals (CI for all five IPCC carbon pools (aboveground live carbon, litter, coarse woody debris, belowground live carbon and soil carbon for data-deficient regions, using a combination of existing inventory data and systematic literature searches, weighted to ensure the final values are regionally specific. The method meets the IPCC 'Tier 2' reporting standard. We use this method to estimate carbon storage over an area of33.9 million hectares of eastern Tanzania, reporting values for 30 land cover types. We estimate that this area stored 6.33 (5.92-6.74 Pg C in the year 2000. Carbon storage estimates for the same study area extracted from five published Africa-wide or global studies show a mean carbon storage value of ∼50% of that reported using our regional values, with four of the five studies reporting lower carbon storage values. This suggests that carbon storage may have been underestimated for this region of Africa. Our study demonstrates the importance of obtaining regionally appropriate carbon storage estimates, and shows how such values can be produced

  11. Mixed-species allometric equations and estimation of aboveground biomass and carbon stocks in restoring degraded landscape in northern Ethiopia

    Science.gov (United States)

    Mokria, Mulugeta; Mekuria, Wolde; Gebrekirstos, Aster; Aynekulu, Ermias; Belay, Beyene; Gashaw, Tadesse; Bräuning, Achim

    2018-02-01

    Accurate biomass estimation is critical to quantify the changes in biomass and carbon stocks following the restoration of degraded landscapes. However, there is lack of site-specific allometric equations for the estimation of aboveground biomass (AGB), which consequently limits our understanding of the contributions of restoration efforts in mitigating climate change. This study was conducted in northwestern Ethiopia to develop a multi-species allometric equation and investigate the spatial and temporal variation of C-stocks following the restoration of degraded landscapes. We harvested and weighed 84 trees from eleven dominant species from six grazing exclosures and adjacent communal grazing land. We observed that AGB correlates significantly with diameter at stump height D 30 (R 2 = 0.78 P < 0.01), and tree height H (R 2 = 0.41, P < 0.05). Our best model, which includes D 30 and H as predictors explained 82% of the variations in AGB. This model produced the lowest bias with narrow ranges of errors across different diameter classes. Estimated C-stock showed a significant positive correlation with stem density (R 2 = 0.80, P < 0.01) and basal area (R 2 = 0.84, P < 0.01). At the watershed level, the mean C-stock was 3.8 (±0.5) Mg C ha-1. Plot-level C-stocks varied between 0.1 and 13.7 Mg C ha-1. Estimated C-stocks in three- and seven-year-old exclosures exceeded estimated C-stock in the communal grazing land by 50%. The species that contribute most to C-stocks were Leucaena sp. (28%), Calpurnia aurea (21%), Euclea racemosa (20.9%), and Dodonaea angustifolia (15.8%). The equations developed in this study allow monitoring changes in C-stocks and C-sequestration following the implementation of restoration practices in northern Ethiopia over space and time. The estimated C-stocks can be used as a reference against which future changes in C-stocks can be compared.

  12. Impact of flow routing on catchment area calculations, slope estimates, and numerical simulations of landscape development

    Science.gov (United States)

    Shelef, Eitan; Hilley, George E.

    2013-12-01

    Flow routing across real or modeled topography determines the modeled discharge and wetness index and thus plays a central role in predicting surface lowering rate, runoff generation, likelihood of slope failure, and transition from hillslope to channel forming processes. In this contribution, we compare commonly used flow-routing rules as well as a new routing rule, to commonly used benchmarks. We also compare results for different routing rules using Airborne Laser Swath Mapping (ALSM) topography to explore the impact of different flow-routing schemes on inferring the generation of saturation overland flow and the transition between hillslope to channel forming processes, as well as on location of saturation overland flow. Finally, we examined the impact of flow-routing and slope-calculation rules on modeled topography produced by Geomorphic Transport Law (GTL)-based simulations. We found that different rules produce substantive differences in the structure of the modeled topography and flow patterns over ALSM data. Our results highlight the impact of flow-routing and slope-calculation rules on modeled topography, as well as on calculated geomorphic metrics across real landscapes. As such, studies that use a variety of routing rules to analyze and simulate topography are necessary to determine those aspects that most strongly depend on a chosen routing rule.

  13. A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data

    Directory of Open Access Journals (Sweden)

    Chandra Nagasuma R

    2009-02-01

    Full Text Available Abstract Background A genetic network can be represented as a directed graph in which a node corresponds to a gene and a directed edge specifies the direction of influence of one gene on another. The reconstruction of such networks from transcript profiling data remains an important yet challenging endeavor. A transcript profile specifies the abundances of many genes in a biological sample of interest. Prevailing strategies for learning the structure of a genetic network from high-dimensional transcript profiling data assume sparsity and linearity. Many methods consider relatively small directed graphs, inferring graphs with up to a few hundred nodes. This work examines large undirected graphs representations of genetic networks, graphs with many thousands of nodes where an undirected edge between two nodes does not indicate the direction of influence, and the problem of estimating the structure of such a sparse linear genetic network (SLGN from transcript profiling data. Results The structure learning task is cast as a sparse linear regression problem which is then posed as a LASSO (l1-constrained fitting problem and solved finally by formulating a Linear Program (LP. A bound on the Generalization Error of this approach is given in terms of the Leave-One-Out Error. The accuracy and utility of LP-SLGNs is assessed quantitatively and qualitatively using simulated and real data. The Dialogue for Reverse Engineering Assessments and Methods (DREAM initiative provides gold standard data sets and evaluation metrics that enable and facilitate the comparison of algorithms for deducing the structure of networks. The structures of LP-SLGNs estimated from the INSILICO1, INSILICO2 and INSILICO3 simulated DREAM2 data sets are comparable to those proposed by the first and/or second ranked teams in the DREAM2 competition. The structures of LP-SLGNs estimated from two published Saccharomyces cerevisae cell cycle transcript profiling data sets capture known

  14. Estimating the similarity of alternative Affymetrix probe sets using transcriptional networks

    Science.gov (United States)

    2013-01-01

    Background The usefulness of the data from Affymetrix microarray analysis depends largely on the reliability of the files describing the correspondence between probe sets, genes and transcripts. Particularly, when a gene is targeted by several probe sets, these files should give information about the similarity of each alternative probe set pair. Transcriptional networks integrate the multiple correlations that exist between all probe sets and supply much more information than a simple correlation coefficient calculated for two series of signals. In this study, we used the PSAWN (Probe Set Assignment With Networks) programme we developed to investigate whether similarity of alternative probe sets resulted in some specific properties. Findings PSAWNpy delivered a full textual description of each probe set and information on the number and properties of secondary targets. PSAWNml calculated the similarity of each alternative probe set pair and allowed finding relationships between similarity and localisation of probes in common transcripts or exons. Similar alternative probe sets had very low negative correlation, high positive correlation and similar neighbourhood overlap. Using these properties, we devised a test that allowed grouping similar probe sets in a given network. By considering several networks, additional information concerning the similarity reproducibility was obtained, which allowed defining the actual similarity of alternative probe set pairs. In particular, we calculated the common localisation of probes in exons and in known transcripts and we showed that similarity was correctly correlated with them. The information collected on all pairs of alternative probe sets in the most popular 3’ IVT Affymetrix chips is available in tabular form at http://bns.crbm.cnrs.fr/download.html. Conclusions These processed data can be used to obtain a finer interpretation when comparing microarray data between biological conditions. They are particularly well

  15. Estimating the similarity of alternative Affymetrix probe sets using transcriptional networks.

    Science.gov (United States)

    Bellis, Michel

    2013-03-21

    The usefulness of the data from Affymetrix microarray analysis depends largely on the reliability of the files describing the correspondence between probe sets, genes and transcripts. Particularly, when a gene is targeted by several probe sets, these files should give information about the similarity of each alternative probe set pair. Transcriptional networks integrate the multiple correlations that exist between all probe sets and supply much more information than a simple correlation coefficient calculated for two series of signals. In this study, we used the PSAWN (Probe Set Assignment With Networks) programme we developed to investigate whether similarity of alternative probe sets resulted in some specific properties. PSAWNpy delivered a full textual description of each probe set and information on the number and properties of secondary targets. PSAWNml calculated the similarity of each alternative probe set pair and allowed finding relationships between similarity and localisation of probes in common transcripts or exons. Similar alternative probe sets had very low negative correlation, high positive correlation and similar neighbourhood overlap. Using these properties, we devised a test that allowed grouping similar probe sets in a given network. By considering several networks, additional information concerning the similarity reproducibility was obtained, which allowed defining the actual similarity of alternative probe set pairs. In particular, we calculated the common localisation of probes in exons and in known transcripts and we showed that similarity was correctly correlated with them. The information collected on all pairs of alternative probe sets in the most popular 3' IVT Affymetrix chips is available in tabular form at http://bns.crbm.cnrs.fr/download.html. These processed data can be used to obtain a finer interpretation when comparing microarray data between biological conditions. They are particularly well adapted for searching 3' alternative

  16. Soil carbon storage estimation in a forested watershed using quantitative soil-landscape modeling

    Science.gov (United States)

    James A. Thompson; Randall K. Kolka

    2005-01-01

    Carbon storage in soils is important to forest ecosystems. Moreover, forest soils may serve as important C sinks for ameliorating excess atmospheric CO2. Spatial estimates of soil organic C (SOC) storage have traditionally relied upon soil survey maps and laboratory characterization data. This approach does not account for inherent variability...

  17. Urban Growth in a Fragmented Landscape: Estimating the Relationship between Landscape Pattern and Urban Land Use Change in Germany, 2000-2006

    Science.gov (United States)

    Keller, R.

    2013-12-01

    One of the highest priorities in the conservation and management of biodiversity, natural resources and other vital ecosystem services is the assessment of the mechanisms that drive urban land use change. Using key landscape indicators, this study addresses why urban land increased 6 percent overall in Germany from 2000-2006. Building on regional science and economic geography research, I develop a model of landscape change that integrates remotely sensed and other geospatial data, and socioeconomic data in a spatial autoregressive model to explain the variance in urban land use change observed in German kreise (counties) over the past decade. The results reveal three key landscape mechanisms that drive urban land use change across Germany, aligning with those observed in US studies: (1) the level of fragmentation, (2) the share of designated protected areas, and (3) the share of prime soil. First, as fragmentation of once continuous habitats in the landscape increases, extensive urban growth follows. Second, designated protected areas have the perverse effect of hastening urbanization in surrounding areas. Third, greater shares of prime, productive soil experienced less urban land take over the 6 year period, an effect that is stronger in the former East Germany, where the agricultural sector remains large. The results suggest that policy makers concentrate their conservation efforts on preexisting fragmented land with high shares of protected areas in Germany to effectively stem urban land take. Given that comparative studies of land use change are vital for the scientific community to grasp the wider global process of urbanization and coincident ecological impacts, the methodology employed here is easily exportable to land cover and land use research programs in other fields and geographic areas. Key words: Urban land use change, Ecosystem services, Landscape fragmentation, Remote sensing, Spatial regression models, GermanyOLS and Spatial Autoregressive Model

  18. Scaling wood volume estimates from inventory plots to landscapes with airborne LiDAR in temperate deciduous forest

    Directory of Open Access Journals (Sweden)

    Shaun R. Levick

    2016-05-01

    Full Text Available Abstract Background Monitoring and managing carbon stocks in forested ecosystems requires accurate and repeatable quantification of the spatial distribution of wood volume at landscape to regional scales. Grid-based forest inventory networks have provided valuable records of forest structure and dynamics at individual plot scales, but in isolation they may not represent the carbon dynamics of heterogeneous landscapes encompassing diverse land-management strategies and site conditions. Airborne LiDAR has greatly enhanced forest structural characterisation and, in conjunction with field-based inventories, it provides avenues for monitoring carbon over broader spatial scales. Here we aim to enhance the integration of airborne LiDAR surveying with field-based inventories by exploring the effect of inventory plot size and number on the relationship between field-estimated and LiDAR-predicted wood volume in deciduous broad-leafed forest in central Germany. Results Estimation of wood volume from airborne LiDAR was most robust (R2 = 0.92, RMSE = 50.57 m3 ha−1 ~14.13 Mg C ha−1 when trained and tested with 1 ha experimental plot data (n = 50. Predictions based on a more extensive (n = 1100 plot network with considerably smaller (0.05 ha plots were inferior (R2 = 0.68, RMSE = 101.01 ~28.09 Mg C ha−1. Differences between the 1 and 0.05 ha volume models from LiDAR were negligible however at the scale of individual land-management units. Sample size permutation tests showed that increasing the number of inventory plots above 350 for the 0.05 ha plots returned no improvement in R2 and RMSE variability of the LiDAR-predicted wood volume model. Conclusions Our results from this study confirm the utility of LiDAR for estimating wood volume in deciduous broad-leafed forest, but highlight the challenges associated with field plot size and number in establishing robust relationships between airborne LiDAR and field derived wood volume. We

  19. Scaling wood volume estimates from inventory plots to landscapes with airborne LiDAR in temperate deciduous forest.

    Science.gov (United States)

    Levick, Shaun R; Hessenmöller, Dominik; Schulze, E-Detlef

    2016-12-01

    Monitoring and managing carbon stocks in forested ecosystems requires accurate and repeatable quantification of the spatial distribution of wood volume at landscape to regional scales. Grid-based forest inventory networks have provided valuable records of forest structure and dynamics at individual plot scales, but in isolation they may not represent the carbon dynamics of heterogeneous landscapes encompassing diverse land-management strategies and site conditions. Airborne LiDAR has greatly enhanced forest structural characterisation and, in conjunction with field-based inventories, it provides avenues for monitoring carbon over broader spatial scales. Here we aim to enhance the integration of airborne LiDAR surveying with field-based inventories by exploring the effect of inventory plot size and number on the relationship between field-estimated and LiDAR-predicted wood volume in deciduous broad-leafed forest in central Germany. Estimation of wood volume from airborne LiDAR was most robust (R 2  = 0.92, RMSE = 50.57 m 3 ha -1  ~14.13 Mg C ha -1 ) when trained and tested with 1 ha experimental plot data (n = 50). Predictions based on a more extensive (n = 1100) plot network with considerably smaller (0.05 ha) plots were inferior (R 2  = 0.68, RMSE = 101.01 ~28.09 Mg C ha -1 ). Differences between the 1 and 0.05 ha volume models from LiDAR were negligible however at the scale of individual land-management units. Sample size permutation tests showed that increasing the number of inventory plots above 350 for the 0.05 ha plots returned no improvement in R 2 and RMSE variability of the LiDAR-predicted wood volume model. Our results from this study confirm the utility of LiDAR for estimating wood volume in deciduous broad-leafed forest, but highlight the challenges associated with field plot size and number in establishing robust relationships between airborne LiDAR and field derived wood volume. We are moving into a forest management era where

  20. Relative pollen productivity estimates in the modern agricultural landscape of Central Bohemia (Czech Republic)

    Czech Academy of Sciences Publication Activity Database

    Abraham, V.; Kozáková, Radka

    2012-01-01

    Roč. 179, JUL 1 (2012), s. 1-12 ISSN 0034-6667 R&D Projects: GA AV ČR IAAX00020701; GA AV ČR IAAX00050801 Institutional research plan: CEZ:AV0Z80020508 Keywords : relative pollen productivity estimates * Central Bohemia * moss polsters * pollen-vegetation relationship * relevant source area of pollen Subject RIV: EH - Ecology, Behaviour Impact factor: 1.933, year: 2012

  1. Estimating suitable environments for invasive plant species across large landscapes: a remote sensing strategy using Landsat 7 ETM+

    Science.gov (United States)

    Young, Kendal E.; Abbott, Laurie B.; Caldwell, Colleen A.; Schrader, T. Scott

    2013-01-01

    The key to reducing ecological and economic damage caused by invasive plant species is to locate and eradicate new invasions before they threaten native biodiversity and ecological processes. We used Landsat Enhanced Thematic Mapper Plus imagery to estimate suitable environments for four invasive plants in Big Bend National Park, southwest Texas, using a presence-only modeling approach. Giant reed (Arundo donax), Lehmann lovegrass (Eragrostis lehmanniana), horehound (Marrubium vulgare) and buffelgrass (Pennisteum ciliare) were selected for remote sensing spatial analyses. Multiple dates/seasons of imagery were used to account for habitat conditions within the study area and to capture phenological differences among targeted species and the surrounding landscape. Individual species models had high (0.91 to 0.99) discriminative ability to differentiate invasive plant suitable environments from random background locations. Average test area under the receiver operating characteristic curve (AUC) ranged from 0.91 to 0.99, indicating that plant predictive models exhibited high discriminative ability to differentiate suitable environments for invasive plant species from random locations. Omission rates ranged from <1.0 to 18%. We demonstrated that useful models estimating suitable environments for invasive plants may be created with <50 occurrence locations and that reliable modeling using presence-only datasets can be powerful tools for land managers.

  2. Daily Landsat-scale evapotranspiration estimation over a forested landscape in North Carolina, USA, using multi-satellite data fusion

    Science.gov (United States)

    Yun Yang; Martha C. Anderson; Feng Gao; Christopher R. Hain; Kathryn A. Semmens; William P. Kustas; Asko Noormets; Randolph H. Wynne; Valerie A. Thomas; Ge Sun

    2017-01-01

    As a primary flux in the global water cycle, evapotranspiration (ET) connects hydrologic and biological processes and is directly affected by water and land management, land use change and climate variability. Satellite remote sensing provides an effective means for diagnosing ET patterns over heterogeneous landscapes; however, limitations on the spatial and temporal...

  3. Landscape Studio

    DEFF Research Database (Denmark)

    Hansen, Peter Lundsgaard

    2017-01-01

    Landscape studio documents is the biography of the method 'design conversation' and contributes to the way we work with landscapes. The blog communicates renewed landscape didactics and leads to the innovation of design practices.......Landscape studio documents is the biography of the method 'design conversation' and contributes to the way we work with landscapes. The blog communicates renewed landscape didactics and leads to the innovation of design practices....

  4. Landscape Ecology

    DEFF Research Database (Denmark)

    Christensen, Andreas Aagaard; Brandt, Jesper; Svenningsen, Stig Roar

    2017-01-01

    Landscape ecology is an interdisciplinary field of research and practice that deals with the mutual association between the spatial configuration and ecological functioning of landscapes, exploring and describing processes involved in the differentiation of spaces within landscapes......, and the ecological significance of the patterns which are generated by such processes. In landscape ecology, perspectives drawn from existing academic disciplines are integrated based on a common, spatially explicit mode of analysis developed from classical holistic geography, emphasizing spatial and landscape...... pattern analysis and ecological interaction of land units. The landscape is seen as a holon: an assemblage of interrelated phenomena, both cultural and biophysical, that together form a complex whole. Enduring challenges to landscape ecology include the need to develop a systematic approach able...

  5. A mixed-modes approach for estimating hiking on trails through diverse forest landscapes: the case of the Appalachian Trail

    Science.gov (United States)

    Stanley J. Zarnoch; J.M. Bowker; H. Ken. Cordell

    2011-01-01

    Many hiking trails traverse the forests and public lands across North America. It has therefore become important for federal management to gain an understanding of total use on these trails. However, there has never been a formal attempt to estimate hiking on these long, backcountry trails. This paper presents an approach that utilizes two survey instruments (exit-site...

  6. Towards Regional, Error-Bounded Landscape Carbon Storage Estimates for Data-Deficient Areas of the World

    DEFF Research Database (Denmark)

    Willcock, Simon; Phillips, Oliver L.; Platts, Philip J.

    2012-01-01

    estimates for the same study area extracted from five published Africa-wide or global studies show a mean carbon storage value of ∼50% of that reported using our regional values, with four of the five studies reporting lower carbon storage values. This suggests that carbon storage may have been...

  7. Estimating suitable environments for invasive plant species across large landscapes: A remote sensing strategy using Landsat 7 ETM+

    Science.gov (United States)

    The key to reducing ecological and economic damage caused by invasive plant species is to locate and eradicate new invasions before they threaten native biodiversity and ecological processes. We used Landsat Enhanced Thematic Mapper Plus imagery to estimate suitable environments for four invasive pl...

  8. Estimating sample size for landscape-scale mark-recapture studies of North American migratory tree bats

    Science.gov (United States)

    Ellison, Laura E.; Lukacs, Paul M.

    2014-01-01

    Concern for migratory tree-roosting bats in North America has grown because of possible population declines from wind energy development. This concern has driven interest in estimating population-level changes. Mark-recapture methodology is one possible analytical framework for assessing bat population changes, but sample size requirements to produce reliable estimates have not been estimated. To illustrate the sample sizes necessary for a mark-recapture-based monitoring program we conducted power analyses using a statistical model that allows reencounters of live and dead marked individuals. We ran 1,000 simulations for each of five broad sample size categories in a Burnham joint model, and then compared the proportion of simulations in which 95% confidence intervals overlapped between and among years for a 4-year study. Additionally, we conducted sensitivity analyses of sample size to various capture probabilities and recovery probabilities. More than 50,000 individuals per year would need to be captured and released to accurately determine 10% and 15% declines in annual survival. To detect more dramatic declines of 33% or 50% survival over four years, then sample sizes of 25,000 or 10,000 per year, respectively, would be sufficient. Sensitivity analyses reveal that increasing recovery of dead marked individuals may be more valuable than increasing capture probability of marked individuals. Because of the extraordinary effort that would be required, we advise caution should such a mark-recapture effort be initiated because of the difficulty in attaining reliable estimates. We make recommendations for what techniques show the most promise for mark-recapture studies of bats because some techniques violate the assumptions of mark-recapture methodology when used to mark bats.

  9. Estimation of daily maximum and minimum air temperatures in urban landscapes using MODIS time series satellite data

    Science.gov (United States)

    Yoo, Cheolhee; Im, Jungho; Park, Seonyoung; Quackenbush, Lindi J.

    2018-03-01

    Urban air temperature is considered a significant variable for a variety of urban issues, and analyzing the spatial patterns of air temperature is important for urban planning and management. However, insufficient weather stations limit accurate spatial representation of temperature within a heterogeneous city. This study used a random forest machine learning approach to estimate daily maximum and minimum air temperatures (Tmax and Tmin) for two megacities with different climate characteristics: Los Angeles, USA, and Seoul, South Korea. This study used eight time-series land surface temperature (LST) data from Moderate Resolution Imaging Spectroradiometer (MODIS), with seven auxiliary variables: elevation, solar radiation, normalized difference vegetation index, latitude, longitude, aspect, and the percentage of impervious area. We found different relationships between the eight time-series LSTs with Tmax/Tmin for the two cities, and designed eight schemes with different input LST variables. The schemes were evaluated using the coefficient of determination (R2) and Root Mean Square Error (RMSE) from 10-fold cross-validation. The best schemes produced R2 of 0.850 and 0.777 and RMSE of 1.7 °C and 1.2 °C for Tmax and Tmin in Los Angeles, and R2 of 0.728 and 0.767 and RMSE of 1.1 °C and 1.2 °C for Tmax and Tmin in Seoul, respectively. LSTs obtained the day before were crucial for estimating daily urban air temperature. Estimated air temperature patterns showed that Tmax was highly dependent on the geographic factors (e.g., sea breeze, mountains) of the two cities, while Tmin showed marginally distinct temperature differences between built-up and vegetated areas in the two cities.

  10. Mapping and estimating land change between 2001 and 2013 in a heterogeneous landscape in West Africa: Loss of forestlands and capacity building opportunities

    Science.gov (United States)

    Badjana, Hèou Maléki; Olofsson, Pontus; Woodcock, Curtis E.; Helmschrot, Joerg; Wala, Kpérkouma; Akpagana, Koffi

    2017-12-01

    In West Africa, accurate classification of land cover and land change remains a big challenge due to the patchy and heterogeneous nature of the landscape. Limited data availability, human resources and technical capacities, further exacerbate the challenge. The result is a region that is among the more understudied areas in the world, which in turn has resulted in a lack of appropriate information required for sustainable natural resources management. The objective of this paper is to explore open source software and easy-to-implement approaches to mapping and estimation of land change that are transferrable to local institutions to increase capacity in the region, and to provide updated information on the regional land surface dynamics. To achieve these objectives, stable land cover and land change between 2001 and 2013 in the Kara River Basin in Togo and Benin were mapped by direct multitemporal classification of Landsat data by parameterization and evaluation of two machine-learning algorithms. Areas of land cover and change were estimated by application of an unbiased estimator to sample data following international guidelines. A prerequisite for all tools and methods was implementation in an open source environment, and adherence to international guidelines for reporting land surface activities. Findings include a recommendation of the Random Forests algorithm as implemented in Orfeo Toolbox, and a stratified estimation protocol - all executed in the QGIS graphical use interface. It was found that despite an estimated reforestation of 10,0727 ± 3480 ha (95% confidence interval), the combined rate of forest and savannah loss amounted to 56,271 ± 9405 ha (representing a 16% loss of the forestlands present in 2001), resulting in a rather sharp net loss of forestlands in the study area. These dynamics had not been estimated prior to this study, and the results will provide useful information for decision making pertaining to natural resources management, land

  11. Enhancing the Simplified Surface Energy Balance (SSEB) Approach for Estimating Landscape ET: Validation with the METRIC model

    Science.gov (United States)

    Senay, Gabriel B.; Budde, Michael E.; Verdin, James P.

    2011-01-01

    Evapotranspiration (ET) can be derived from satellite data using surface energy balance principles. METRIC (Mapping EvapoTranspiration at high Resolution with Internalized Calibration) is one of the most widely used models available in the literature to estimate ET from satellite imagery. The Simplified Surface Energy Balance (SSEB) model is much easier and less expensive to implement. The main purpose of this research was to present an enhanced version of the Simplified Surface Energy Balance (SSEB) model and to evaluate its performance using the established METRIC model. In this study, SSEB and METRIC ET fractions were compared using 7 Landsat images acquired for south central Idaho during the 2003 growing season. The enhanced SSEB model compared well with the METRIC model output exhibiting an r2 improvement from 0.83 to 0.90 in less complex topography (elevation less than 2000 m) and with an improvement of r2 from 0.27 to 0.38 in more complex (mountain) areas with elevation greater than 2000 m. Independent evaluation showed that both models exhibited higher variation in complex topographic regions, although more with SSEB than with METRIC. The higher ET fraction variation in the complex mountainous regions highlighted the difficulty of capturing the radiation and heat transfer physics on steep slopes having variable aspect with the simple index model, and the need to conduct more research. However, the temporal consistency of the results suggests that the SSEB model can be used on a wide range of elevation (more successfully up 2000 m) to detect anomalies in space and time for water resources management and monitoring such as for drought early warning systems in data scarce regions. SSEB has a potential for operational agro-hydrologic applications to estimate ET with inputs of surface temperature, NDVI, DEM and reference ET.

  12. Landscape Ecology

    DEFF Research Database (Denmark)

    Christensen, Andreas Aagaard; Brandt, Jesper; Svenningsen, Stig Roar

    2017-01-01

    , and the ecological significance of the patterns which are generated by such processes. In landscape ecology, perspectives drawn from existing academic disciplines are integrated based on a common, spatially explicit mode of analysis developed from classical holistic geography, emphasizing spatial and landscape...... to translate positivist readings of the environment and hermeneutical perspectives on socioecological interaction into a common framework or terminology....

  13. Alanine-scanning mutagenesis of human signal transducer and activator of transcription 1 to estimate loss- or gain-of-function variants.

    Science.gov (United States)

    Kagawa, Reiko; Fujiki, Ryoji; Tsumura, Miyuki; Sakata, Sonoko; Nishimura, Shiho; Itan, Yuval; Kong, Xiao-Fei; Kato, Zenichiro; Ohnishi, Hidenori; Hirata, Osamu; Saito, Satoshi; Ikeda, Maiko; El Baghdadi, Jamila; Bousfiha, Aziz; Fujiwara, Kaori; Oleastro, Matias; Yancoski, Judith; Perez, Laura; Danielian, Silvia; Ailal, Fatima; Takada, Hidetoshi; Hara, Toshiro; Puel, Anne; Boisson-Dupuis, Stéphanie; Bustamante, Jacinta; Casanova, Jean-Laurent; Ohara, Osamu; Okada, Satoshi; Kobayashi, Masao

    2017-07-01

    Germline heterozygous mutations in human signal transducer and activator of transcription 1 (STAT1) can cause loss of function (LOF), as in patients with Mendelian susceptibility to mycobacterial diseases, or gain of function (GOF), as in patients with chronic mucocutaneous candidiasis. LOF and GOF mutations are equally rare and can affect the same domains of STAT1, especially the coiled-coil domain (CCD) and DNA-binding domain (DBD). Moreover, 6% of patients with chronic mucocutaneous candidiasis with a GOF STAT1 mutation have mycobacterial disease, obscuring the functional significance of the identified STAT1 mutations. Current computational approaches, such as combined annotation-dependent depletion, do not distinguish LOF and GOF variants. We estimated variations in the CCD/DBD of STAT1. We mutagenized 342 individual wild-type amino acids in the CCD/DBD (45.6% of full-length STAT1) to alanine and tested the mutants for STAT1 transcriptional activity. Of these 342 mutants, 201 were neutral, 30 were LOF, and 111 were GOF mutations in a luciferase assay. This assay system correctly estimated all previously reported LOF mutations (100%) and slightly fewer GOF mutations (78.1%) in the CCD/DBD of STAT1. We found that GOF alanine mutants occurred at the interface of the antiparallel STAT1 dimer, suggesting that they destabilize this dimer. This assay also precisely predicted the effect of 2 hypomorphic and dominant negative mutations, E157K and G250E, in the CCD of STAT1 that we found in 2 unrelated patients with Mendelian susceptibility to mycobacterial diseases. The systematic alanine-scanning assay is a useful tool to estimate the GOF or LOF status and the effect of heterozygous missense mutations in STAT1 identified in patients with severe infectious diseases, including mycobacterial and fungal diseases. Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  14. Estimation of Tissue Distribution of mRNA Transcripts for Desaturase and Elongase Enzymes in Channa striata (Bloch, 1793 Fingerlings using PCR Technique

    Directory of Open Access Journals (Sweden)

    M. Aliyu-Paiko

    2013-06-01

    Full Text Available Fish species are varied in their capacity to biosynthesize n-3 highlyunsaturated fatty acids (HUFA such as eicosapentaenoic and docosahexaenoic acids (EPA & DHA that are crucial to the health and well-being of all higher vertebrates. Experts report that HUFA metabolism involves enzyme-mediated fatty acyl desaturation (FAD and elongation (FAE processes. In previous studies, different workers cloned, characterized, identified and reported several genes for FAD and FAE enzymes in different fish species such as Atlantic salmon, gilthead seabream, rainbow trout and zebrafish, and also demonstrated the up- and down-regulation in the activity of these enzymes in response to fluctuations in dietary HUFA. In this paper, we report on the expression of genes (mRNA transcripts for FAD and FAE enzymes in different tissues of Channa striata (Bloch, 1793 fingerling, to evaluate the tissues of the fish in which activity of both enzymes are high. To achieve this objective, we used conventional polymerase chain reaction (PCR technique to isolate and quantify the absolute copy number for each gene transcripts from 8 different tissues of the fish (reared with a commercial feed. Our estimate show that the distribution of the 2 enzyme transcripts were significantly (P < 0.05 higher in the liver and brain of C. striata than detected in the 6 other tissues evaluated (muscle, ovary, testis, intestine, kidney and skin. Subsequently, we discuss here extensively, the implication of this observation with respect to the use of vegetable oils (VO as substitute to fish oil (FO in diets for freshwater fish species.

  15. The legacy of logging--estimating arboreal lichen occurrence in a boreal multiple-use landscape on a two century scale.

    Science.gov (United States)

    Horstkotte, Tim; Moen, Jon; Lämås, Tomas; Helle, Timo

    2011-01-01

    In northern Sweden, the availability of arboreal lichens (Bryoria fuscescens, Alectoria sarmentosa) as winter grazing resources is an important element in reindeer husbandry. With the industrialization of forestry, forests rich in arboreal lichens have diminished considerably. Here, we analyze how forestry has impacted lichen availability from the 1920's to the present day and model its future development assuming different forest management scenarios.We recorded the current occurrence of B. fuscescens in 144 sampling plots, stratified by forest age class and dominant tree species in a 26,600 ha boreal forest landscape that is used for both reindeer herding and forestry. Lichen abundance was visually estimated in four classes: none, sparse, moderate and abundant. A binary logistic model using forest age as the independent variable was developed to predict the probability of lichens being present. Using this model, we found that lichens were present in stands that are at least 63 years old. Because of the relative paucity of stands rich in arboreal lichens, it was not possible to reliably determine how age affects the variation in abundance of older forest stands. The historical development of forests where arboreal lichens could potentially occur was studied using historic forestry records dating back 80 years. Between 1926 and the present day, forestry has reduced the cover of forests older than 60 years from 84% to 34%. The likely future spatial coverage of these stands over the next 120 years was estimated for two different management scenarios and an unmanaged reference scenario, using the Heureka strategic planning program. Under both the "business as usual" scenario and that involving more intensive forestry, continued decreases in lichen availability are projected. Our results emphasize the importance of alternative forestry practices, such as prolonged rotation periods, to increase the availability of arboreal lichens as a grazing resource for reindeer.

  16. The legacy of logging--estimating arboreal lichen occurrence in a boreal multiple-use landscape on a two century scale.

    Directory of Open Access Journals (Sweden)

    Tim Horstkotte

    Full Text Available In northern Sweden, the availability of arboreal lichens (Bryoria fuscescens, Alectoria sarmentosa as winter grazing resources is an important element in reindeer husbandry. With the industrialization of forestry, forests rich in arboreal lichens have diminished considerably. Here, we analyze how forestry has impacted lichen availability from the 1920's to the present day and model its future development assuming different forest management scenarios.We recorded the current occurrence of B. fuscescens in 144 sampling plots, stratified by forest age class and dominant tree species in a 26,600 ha boreal forest landscape that is used for both reindeer herding and forestry. Lichen abundance was visually estimated in four classes: none, sparse, moderate and abundant. A binary logistic model using forest age as the independent variable was developed to predict the probability of lichens being present. Using this model, we found that lichens were present in stands that are at least 63 years old. Because of the relative paucity of stands rich in arboreal lichens, it was not possible to reliably determine how age affects the variation in abundance of older forest stands. The historical development of forests where arboreal lichens could potentially occur was studied using historic forestry records dating back 80 years. Between 1926 and the present day, forestry has reduced the cover of forests older than 60 years from 84% to 34%. The likely future spatial coverage of these stands over the next 120 years was estimated for two different management scenarios and an unmanaged reference scenario, using the Heureka strategic planning program. Under both the "business as usual" scenario and that involving more intensive forestry, continued decreases in lichen availability are projected. Our results emphasize the importance of alternative forestry practices, such as prolonged rotation periods, to increase the availability of arboreal lichens as a grazing

  17. The Legacy of Logging—Estimating Arboreal Lichen Occurrence in a Boreal Multiple-Use Landscape on a Two Century Scale

    Science.gov (United States)

    Horstkotte, Tim; Moen, Jon; Lämås, Tomas; Helle, Timo

    2011-01-01

    In northern Sweden, the availability of arboreal lichens (Bryoria fuscescens, Alectoria sarmentosa) as winter grazing resources is an important element in reindeer husbandry. With the industrialization of forestry, forests rich in arboreal lichens have diminished considerably. Here, we analyze how forestry has impacted lichen availability from the 1920's to the present day and model its future development assuming different forest management scenarios. We recorded the current occurrence of B. fuscescens in 144 sampling plots, stratified by forest age class and dominant tree species in a 26,600 ha boreal forest landscape that is used for both reindeer herding and forestry. Lichen abundance was visually estimated in four classes: none, sparse, moderate and abundant. A binary logistic model using forest age as the independent variable was developed to predict the probability of lichens being present. Using this model, we found that lichens were present in stands that are at least 63 years old. Because of the relative paucity of stands rich in arboreal lichens, it was not possible to reliably determine how age affects the variation in abundance of older forest stands. The historical development of forests where arboreal lichens could potentially occur was studied using historic forestry records dating back 80 years. Between 1926 and the present day, forestry has reduced the cover of forests older than 60 years from 84% to 34%. The likely future spatial coverage of these stands over the next 120 years was estimated for two different management scenarios and an unmanaged reference scenario, using the Heureka strategic planning program. Under both the “business as usual” scenario and that involving more intensive forestry, continued decreases in lichen availability are projected. Our results emphasize the importance of alternative forestry practices, such as prolonged rotation periods, to increase the availability of arboreal lichens as a grazing resource for reindeer

  18. Systematic clustering of transcription start site landscapes

    DEFF Research Database (Denmark)

    Zhao, Xiaobei; Valen, Eivind; Parker, Brian J

    2011-01-01

    and earlier studies have shown that the TSSDs have biological implications in both regulation and function. However, no systematic study has been made to explore how many types of TSSDs and by extension core promoters exist and to understand which biological features distinguish them. In this study, we...... two-class separations of promoter based on TSS distributions are motivated, but the ultra-sharp TSS distributions will confound downstream analyses if not removed....

  19. Proposed Method for Estimating Health-Promoting Glucosinolates and Hydrolysis Products in Broccoli (Brassica oleracea var. italica) Using Relative Transcript Abundance.

    Science.gov (United States)

    Becker, Talon M; Jeffery, Elizabeth H; Juvik, John A

    2017-01-18

    Due to the importance of glucosinolates and their hydrolysis products in human nutrition and plant defense, optimizing the content of these compounds is a frequent breeding objective for Brassica crops. Toward this goal, we investigated the feasibility of using models built from relative transcript abundance data for the prediction of glucosinolate and hydrolysis product concentrations in broccoli. We report that predictive models explaining at least 50% of the variation for a number of glucosinolates and their hydrolysis products can be built for prediction within the same season, but prediction accuracy decreased when using models built from one season's data for prediction of an opposing season. This method of phytochemical profile prediction could potentially allow for lower phytochemical phenotyping costs and larger breeding populations. This, in turn, could improve selection efficiency for phase II induction potential, a type of chemopreventive bioactivity, by allowing for the quick and relatively cheap content estimation of phytochemicals known to influence the trait.

  20. Industrious Landscaping

    DEFF Research Database (Denmark)

    Brichet, Nathalia Sofie; Hastrup, Frida

    2018-01-01

    This article has a twofold ambition. It offers a history of landscaping at Søby brown coal beds—a former mining site in western Denmark—and a methodological discussion of how to write such a study. Exploring this specific industrial landscape through a series of projects that have made different...... natural resources appear, we show that even what is recognized as resources shifts over time according to radically different and unpredictable agendas. This indicates that the Søby landscape is fundamentally volatile, as its resourcefulness has been seen interchangeably to shift between the brown coal...... business, inexpensive estates for practically savvy people, pasture for grazing, and recreational forest, among other things. We discuss these rifts in landscape history, motivated by what we refer to as industriousness, to show that, at sites such as Søby, both natural resources and historical...

  1. Electromagnetic Landscape

    DEFF Research Database (Denmark)

    Cermak, Daniel; Okutsu, Ayaka; Jørgensen, Stina Marie Hasse

    2015-01-01

    Daniel Cermak-Sassenrath, Ayaka Okutsu, Stina Hasse. Electromagnetic Landscape - In-between Signal, Noise and Environment. Installation and artist talk. 21th International Symposium on Electronic Art (ISEA) 2015, Vancouver, CAN, Aug 14-18, 2015.......Daniel Cermak-Sassenrath, Ayaka Okutsu, Stina Hasse. Electromagnetic Landscape - In-between Signal, Noise and Environment. Installation and artist talk. 21th International Symposium on Electronic Art (ISEA) 2015, Vancouver, CAN, Aug 14-18, 2015....

  2. Nordic Landscape

    DEFF Research Database (Denmark)

    Hjortshøj, Rasmus

    2017-01-01

    This Box Set NORDIC LANDSCAPE presents Nordic Territories, a project by Rasmus Hjortshøj, exploring the man-made landscapes of the coastal territories and the entanglement of society and nature in times where it is no longer merely mankind subjected to nature, but where nature is equally being...... territories is not only their transient nature, but also the warm currents of the Gulf Stream making these northern shorelines habitable for human settlements....

  3. Estimating Landscape Fire Particulate Matter (PM) Emissions over Southern Africa using MSG-SEVIRI Fire Radiative Power (FRP) and MODIS Aerosol Optical Thickness Observations

    Science.gov (United States)

    Mota, Bernardo; Wooster, Martin J.

    2016-04-01

    The approach to estimating landscape fire fuel consumption based on the remotely sensed fire radiative power (FRP) thermal energy release rate, as opposed to burned area, is now relatively widely used in studies of fire emissions, including operationally within the Copernicus Atmosphere Monitoring Service (CAMS). Nevertheless, there are still limitations to the approach, including uncertainties associated with using only the few daily overpasses typically provided by polar orbiting satellite systems, the conversion between FRP and smoke emissions, and the increased likelihood that the more frequent data from geostationary systems fails to detect the (probably highly numerous) smaller (i.e. low FRP) component of a regions fire regime. In this study, we address these limitations to directly estimate fire emissions of Particular Matter (PM; or smoke aerosols) by presenting an approach combining the "bottom-up" FRP observations available every 15 minutes across Africa from the Meteosat Spinning Enhanced Visible and Infrared Imager (SEVIRI) Fire Radiative Product (FRP) processed at the EUMETSAT LSA SAF, and the "top-down" aerosol optical thickness (AOT) measures of the fire plumes themselves as measured by the Moderate-resolution Imaging Spectro-radiometer (MODIS) sensors aboard the Terra (MOD04_L2) and Aqua (MYD04_L2) satellites. We determine PM emission coefficients that relate directly to FRP measures by combining these two datasets, and the use of the almost continuous geostationary FRP observations allows us to do this without recourse to (uncertain) data on wind speed at the (unknown) height of the matching plume. We also develop compensation factors to address the detection limitations of small/low intensity (low FRP) fires, and remove the need to estimate fuel consumption by going directly from FRP to PM emissions. We derive the smoke PM emissions coefficients per land cover class by comparing the total fire radiative energy (FRE) released from individual fires

  4. Changing Landscapes, Changing Landscape's Story

    Czech Academy of Sciences Publication Activity Database

    Lapka, Miloslav; Cudlínová, Eva

    2003-01-01

    Roč. 28, č. 3 (2003), s. 323-328 ISSN 0142-6397. [Symposium on Sustainable Landscapes in an Enlarged Europe. Nové Hrady, 12.09.2001-14.09.2001] R&D Projects: GA MŠk ME 530 Grant - others:GA-(XE) QLK5-CT-2000-01211-SPRITE Institutional research plan: CEZ:AV0Z5039906 Keywords : Landscape stability * narrative approach * socio-economic typology Subject RIV: DO - Wilderness Conservation

  5. Estimating volume of deposits associated with landslides on volcanic landscapes in the SW flank of the volcano Pico de Orizaba, Puebla-Veracruz

    Directory of Open Access Journals (Sweden)

    Gabriel Legorreta Paulín

    2017-03-01

    Full Text Available Landslides that occur along river systems are very common and have the potential to cause harm to human, to its infrastructure or affect their socio-economic activity. This dynamic is magnified in territories where morphological contrasts are very marked; as in the border between the mountains and subhorizontal land. This is especially true for volcanic terrains where volcanic activity can trigger voluminous landslides along stream systems by sector and flank collapse and where high seasonal rainfall on terrains covered by poorly consolidated materials produces small but hazardous landslides and debris flows that occur continually along stream systems during the volcanic repose periods. Those type of landslides can deliver volumes of hundreds and millions cubic meters that create a potentially hazardous situation for people and property down the valleys. The study of landslides in volcanic terrains through a Geographic Information System (GIS and under a geomorphological criterion, have allowed to develop a comprehensive methodology linked to the development of multi-temporal inventory, with susceptibility and volume estimation of displaced material. The aim of this research is to develop a method (protocol for landslide susceptibility and landslide volume assessment of potentially unstable volcanic landscapes in order to be helpful in mitigating landslide damages to human settlements. Pico de Orizaba volcano is the highest volcano in Mexico. The volcano has been affected by large flank collapse landslides throughout its geological history. These events have partially destroyed the cone as it happened in Bezymianny volcano and St. Elena volcano. In this volcano, the risk associated with landslide and debris flows, is increased by the growing of human settlements along the hillslopes and by the subsistence agriculture, and deforestation. This situation is favored by a volcanic calm that has lasted 147 years, approximate. These conditions create a

  6. Adaptive evolution of transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Berg Johannes

    2004-10-01

    Full Text Available Abstract Background The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks in the evolution of complex regulatory networks. We study a theoretical model for the sequence evolution of binding sites by point mutations. The approach is based on biophysical models for the binding of transcription factors to DNA. Hence we derive empirically grounded fitness landscapes, which enter a population genetics model including mutations, genetic drift, and selection. Results We show that the selection for factor binding generically leads to specific correlations between nucleotide frequencies at different positions of a binding site. We demonstrate the possibility of rapid adaptive evolution generating a new binding site for a given transcription factor by point mutations. The evolutionary time required is estimated in terms of the neutral (background mutation rate, the selection coefficient, and the effective population size. Conclusions The efficiency of binding site formation is seen to depend on two joint conditions: the binding site motif must be short enough and the promoter region must be long enough. These constraints on promoter architecture are indeed seen in eukaryotic systems. Furthermore, we analyse the adaptive evolution of genetic switches and of signal integration through binding cooperativity between different sites. Experimental tests of this picture involving the statistics of polymorphisms and phylogenies of sites are discussed.

  7. Contemporary danish landscape research

    DEFF Research Database (Denmark)

    Vejre, H.; Brandt, J.

    2004-01-01

    Danish landscape research blossomed during the 1990’ies thanks to several transdisciplinary research programmes involving several institutions. The main themes of the programmes encompassed Landscape change, landscape and biological diversity, nature and landscape management, use and monitoring...

  8. Electromagnetic Landscape

    DEFF Research Database (Denmark)

    Cermak, Daniel; Okutsu, Ayaka; Hasse, Stina

    2015-01-01

    Electromagnetic Landscape demonstrates in direct, tangible and immediate ways effects of the disruption of the familiar. An ubiquitous technological medium, FM radio, is turned into an alien and unfamiliar one. Audience participation, the environment, radio signals and noise create a site...

  9. Changing Landscape

    DEFF Research Database (Denmark)

    Tunby Gulbrandsen, Ib; Kamstrup, Andreas; Koed Madsen, Anders

    with an analysis of the changing organizational landscape created by new ICT’s like Google, Facebook, Wikipedia, iPods, smart phones and Wi-Fi. Based on five netno- and ethno-graphic investigations of the intertwinement of ICT’s and organizational work, we point to three features that have changed the scene: new...

  10. Disposable Landscapes

    Science.gov (United States)

    Kevin T. Smith

    2008-01-01

    Whether we are a traditionalist or on the cutting edge of landscape care, we need to take a deep breath and think about what we are trying to achieve, before we select a specific treatment or practice for tree care. We should measure that treatment or practice against what we know about the tree system. I say "system" because the recent years of Modern...

  11. Transcriptional networks and chromatin remodeling controlling adipogenesis

    DEFF Research Database (Denmark)

    Siersbæk, Rasmus; Nielsen, Ronni; Mandrup, Susanne

    2012-01-01

    Adipocyte differentiation is tightly controlled by a transcriptional cascade, which directs the extensive reprogramming of gene expression required to convert fibroblast-like precursor cells into mature lipid-laden adipocytes. Recent global analyses of transcription factor binding and chromatin...... remodeling have revealed 'snapshots' of this cascade and the chromatin landscape at specific time-points of differentiation. These studies demonstrate that multiple adipogenic transcription factors co-occupy hotspots characterized by an open chromatin structure and specific epigenetic modifications....... Such transcription factor hotspots are likely to represent key signaling nodes which integrate multiple adipogenic signals at specific chromatin sites, thereby facilitating coordinated action on gene expression....

  12. Cuban Landscapes

    DEFF Research Database (Denmark)

    Scarpaci, Joseph L.; Portela, Armando

    This accessible book offers a vivid geographic portrait of Cuba, exploring the island’s streetscapes, sugar cane fields, beaches, and rural settlements; its billboards, government buildings, and national landmarks. The authors illuminate how natural and built landscapes have shaped Cuban identity...... (cubanidad), and vice versa. They provide a unique perspective on Cuba’s distinct historical periods and political economies, from the colonial period through republicanism and today’s socialist era. Compelling topics include the legacies of slavery and the sugar industry, the past and future of urban...

  13. PESP Landscaping Initiative

    Science.gov (United States)

    Landscaping practices can positively or negatively affect local environments and human health. The Landscaping Initiative seeks to enhance benefits of landscaping while reducing need for pesticides, fertilizers, etc., by working with partners.

  14. Estimation of Cs-137 hillslope patterns of Polesje landscapes using geo-information modeling techniques (on example of the Bryansk region)

    Science.gov (United States)

    Linnik, Vitaly; Nenko, Kristina; Sokolov, Alexander; Saveliev, Anatoly

    2015-04-01

    In the result of Chernobyl disaster on 26 April 1986 many regions of Ukraine, Belarus and Russia were contaminated by radionuclides. Vast areas of farmlands and woodlands were contaminated in Russia. The deposited radionuclides continue to cause concern about the possible contamination of food (in particular, mushrooms and berries). But the radioactive materials are also an ideal marker for understanding of hillslope processes in natural and seminatural landscapes. Model area chosen for the research (Opolje landscapes located in the central part of the Bryansk region) is characterized by relatively low levels of Cs-137 contamination. It just 4-33 times higher than global fallout which was equal 1,75 kBq/m2 in 1986 . According the results of air gamma survey (grid size: 100 m x100 m), which was done in 1993, it was explicitly to identify that the processes of Cs-137 lateral migration took place due to nearly fourfold increase of Cs-137 in the lower slope in comparison with the surface of the watershed during a seven-year period after Chernobyl accident. Erosion processes which define Cs-137 pattern in the lowest part of hillslope depend upon such parameters as slope, hillslope forms, vegetation, land use and the roads, which intersect a streamline. GIS-modeling of Cs-137 was carried out in SAGA software. The spatial modeling resolution was equal 100x100 m according the air-gamma data. SRTM data was resampled to a grid 100x100 m. Erosion rates were the highest on the slope of southern exposure. There the processes of lateral migration are more intensive and observed within the entire slope. The main contribution in receipt of Cs-137 to floodplain on the northern slopes comes only from the lower part of the slope and gullies and ravines network. We have used geo-information modeling techniques and some kind of interpolation and statistical models to predict or understand forming of Cs-137 spatial patterns and trends in soil erosion. To study the role of some

  15. Visualizing phylogenetic tree landscapes.

    Science.gov (United States)

    Wilgenbusch, James C; Huang, Wen; Gallivan, Kyle A

    2017-02-02

    Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. We introduce several dimensionality reduction methods to visualize in 2- and 3-dimensions the relationship among competing phylogenies obtained from gene partitions found in three mid- to large-size mitochondrial genome alignments. We test the performance of these dimensionality reduction methods by applying several goodness-of-fit measures. The intrinsic dimensionality of each data set is also estimated to determine whether projections in 2- and 3-dimensions can be expected to reveal meaningful relationships among trees from different data partitions. Several new approaches to aid in the comparison of different phylogenetic landscapes are presented. Curvilinear Components Analysis (CCA) and a stochastic gradient decent (SGD) optimization method give the best representation of the original tree-to-tree distance matrix for each of the three- mitochondrial genome alignments and greatly outperformed the method currently used to visualize tree landscapes. The CCA + SGD method converged at least as fast as previously applied methods for visualizing tree landscapes. We demonstrate for all three mtDNA alignments that 3D

  16. UAV-Based Estimation of Carbon Exports from Heterogeneous Soil Landscapes--A Case Study from the CarboZALF Experimental Area.

    Science.gov (United States)

    Wehrhan, Marc; Rauneker, Philipp; Sommer, Michael

    2016-02-19

    The advantages of remote sensing using Unmanned Aerial Vehicles (UAVs) are a high spatial resolution of images, temporal flexibility and narrow-band spectral data from different wavelengths domains. This enables the detection of spatio-temporal dynamics of environmental variables, like plant-related carbon dynamics in agricultural landscapes. In this paper, we quantify spatial patterns of fresh phytomass and related carbon (C) export using imagery captured by a 12-band multispectral camera mounted on the fixed wing UAV Carolo P360. The study was performed in 2014 at the experimental area CarboZALF-D in NE Germany. From radiometrically corrected and calibrated images of lucerne (Medicago sativa), the performance of four commonly used vegetation indices (VIs) was tested using band combinations of six near-infrared bands. The highest correlation between ground-based measurements of fresh phytomass of lucerne and VIs was obtained for the Enhanced Vegetation Index (EVI) using near-infrared band b899. The resulting map was transformed into dry phytomass and finally upscaled to total C export by harvest. The observed spatial variability at field- and plot-scale could be attributed to small-scale soil heterogeneity in part.

  17. Calculation of Configurational Entropy in Complex Landscapes

    Directory of Open Access Journals (Sweden)

    Samuel A Cushman

    2018-04-01

    Full Text Available Entropy and the second law of thermodynamics are fundamental concepts that underlie all natural processes and patterns. Recent research has shown how the entropy of a landscape mosaic can be calculated using the Boltzmann equation, with the entropy of a lattice mosaic equal to the logarithm of the number of ways a lattice with a given dimensionality and number of classes can be arranged to produce the same total amount of edge between cells of different classes. However, that work seemed to also suggest that the feasibility of applying this method to real landscapes was limited due to intractably large numbers of possible arrangements of raster cells in large landscapes. Here I extend that work by showing that: (1 the proportion of arrangements rather than the number with a given amount of edge length provides a means to calculate unbiased relative configurational entropy, obviating the need to compute all possible configurations of a landscape lattice; (2 the edge lengths of randomized landscape mosaics are normally distributed, following the central limit theorem; and (3 given this normal distribution it is possible to fit parametric probability density functions to estimate the expected proportion of randomized configurations that have any given edge length, enabling the calculation of configurational entropy on any landscape regardless of size or number of classes. I evaluate the boundary limits (4 for this normal approximation for small landscapes with a small proportion of a minority class and show it holds under all realistic landscape conditions. I further (5 demonstrate that this relationship holds for a sample of real landscapes that vary in size, patch richness, and evenness of area in each cover type, and (6 I show that the mean and standard deviation of the normally distributed edge lengths can be predicted nearly perfectly as a function of the size, patch richness and diversity of a landscape. Finally, (7 I show that the

  18. MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples.

    Science.gov (United States)

    Behr, Jonas; Kahles, André; Zhong, Yi; Sreedharan, Vipin T; Drewe, Philipp; Rätsch, Gunnar

    2013-10-15

    High-throughput sequencing of mRNA (RNA-Seq) has led to tremendous improvements in the detection of expressed genes and reconstruction of RNA transcripts. However, the extensive dynamic range of gene expression, technical limitations and biases, as well as the observed complexity of the transcriptional landscape, pose profound computational challenges for transcriptome reconstruction. We present the novel framework MITIE (Mixed Integer Transcript IdEntification) for simultaneous transcript reconstruction and quantification. We define a likelihood function based on the negative binomial distribution, use a regularization approach to select a few transcripts collectively explaining the observed read data and show how to find the optimal solution using Mixed Integer Programming. MITIE can (i) take advantage of known transcripts, (ii) reconstruct and quantify transcripts simultaneously in multiple samples, and (iii) resolve the location of multi-mapping reads. It is designed for genome- and assembly-based transcriptome reconstruction. We present an extensive study based on realistic simulated RNA-Seq data. When compared with state-of-the-art approaches, MITIE proves to be significantly more sensitive and overall more accurate. Moreover, MITIE yields substantial performance gains when used with multiple samples. We applied our system to 38 Drosophila melanogaster modENCODE RNA-Seq libraries and estimated the sensitivity of reconstructing omitted transcript annotations and the specificity with respect to annotated transcripts. Our results corroborate that a well-motivated objective paired with appropriate optimization techniques lead to significant improvements over the state-of-the-art in transcriptome reconstruction. MITIE is implemented in C++ and is available from http://bioweb.me/mitie under the GPL license.

  19. Characterizing European cultural landscapes

    DEFF Research Database (Denmark)

    Tieskens, Koen F.; Schulp, Catharina J E; Levers, Christian

    2017-01-01

    intensification and land abandonment. To prevent the loss of cultural landscapes, knowledge on the location of different types of cultural landscapes is needed. In this paper, we present a characterization of European cultural landscapes based on the prevalence of three key dimensions of cultural landscapes......Almost all rural areas in Europe have been shaped or altered by humans and can be considered cultural landscapes, many of which now are considered to entail valuable cultural heritage. Current dynamics in land management have put cultural landscapes under a huge pressure of agricultural...... the three dimensions into a continuous “cultural landscape index” that allows for a characterization of Europe's rural landscapes. The characterization identifies hotspots of cultural landscapes, where all three dimensions are present, such as in the Mediterranean. On the other hand, Eastern and Northern...

  20. Spatiotemporal Changes in Atmospheric Deposition Rates Across The Czech Republic Estimated in The Selected Biomonitoring Campaigns. Examples of Results Available For Landscape Ecology and Land Use Planning

    Directory of Open Access Journals (Sweden)

    Suchara Ivan

    2015-11-01

    Full Text Available Several large-scale and fine-scale biomonitoring surveys were carried out in the Czech Republic to estimate current and long-term accumulated atmospheric deposition rates using moss, spruce bark and forest floor humus as bioindicators since the end of 1980s. The results of the bioindicator analyses significantly correlated with available figures of deposition rates detected at the EMEP or Czech national measurement stations.

  1. Research using energy landscape

    International Nuclear Information System (INIS)

    Kim, Hack Jin

    2007-01-01

    Energy landscape is a theoretical tool used for the study of systems where cooperative processes occur such as liquid, glass, clusters, and protein. Theoretical and experimental researches related to energy landscape are introduced in this review

  2. Lines of landscape organisation

    DEFF Research Database (Denmark)

    Løvschal, Mette

    2015-01-01

    This paper offers a landscape analysis of the earliest linear landscape boundaries on Skovbjerg Moraine, Denmark, during the first millennium BC. Using Delaunay triangulation as well as classic distribution analyses, it demonstrates that landscape boundaries articulated already established use-pa...

  3. Tensor modes on the string theory landscape

    International Nuclear Information System (INIS)

    Westphal, Alexander

    2012-06-01

    We attempt an estimate for the distribution of the tensor mode fraction r over the landscape of vacua in string theory. The dynamics of eternal inflation and quantum tunneling lead to a kind of democracy on the landscape, providing no bias towards large-field or small-field inflation regardless of the class of measure. The tensor mode fraction then follows the number frequency distributions of inflationary mechanisms of string theory over the landscape. We show that an estimate of the relative number frequencies for small-field vs large-field inflation, while unattainable on the whole landscape, may be within reach as a regional answer for warped Calabi-Yau flux compactifications of type IIB string theory.

  4. Tensor modes on the string theory landscape

    Energy Technology Data Exchange (ETDEWEB)

    Westphal, Alexander

    2012-06-15

    We attempt an estimate for the distribution of the tensor mode fraction r over the landscape of vacua in string theory. The dynamics of eternal inflation and quantum tunneling lead to a kind of democracy on the landscape, providing no bias towards large-field or small-field inflation regardless of the class of measure. The tensor mode fraction then follows the number frequency distributions of inflationary mechanisms of string theory over the landscape. We show that an estimate of the relative number frequencies for small-field vs large-field inflation, while unattainable on the whole landscape, may be within reach as a regional answer for warped Calabi-Yau flux compactifications of type IIB string theory.

  5. Flowscapes : Infrastructure as landscape, landscape as infrastructure. Graduation Lab Landscape Architecture 2012/2013

    NARCIS (Netherlands)

    Nijhuis, S.; Jauslin, D.; De Vries, C.

    2012-01-01

    Flowscapes explores infrastructure as a type of landscape and landscape as a type of infrastructure, and is focused on landscape architectonic design of transportation-, green- and water infrastructures. These landscape infrastructures are considered armatures for urban and rural development. With

  6. Estimating the Consequences of Fire Exclusion for Food Crop Production, Soil Fertility, and Fallow Recovery in Shifting Cultivation Landscapes in the Humid Tropics

    Science.gov (United States)

    Norgrove, Lindsey; Hauser, Stefan

    2015-03-01

    In the Congo Basin, smallholder farmers practice slash-and-burn shifting cultivation. Yet, deliberate burning might no longer be sustainable under reduced fallow scenarios. We synthesized data from the Forest Margins Benchmark Area (FMBA), comprising 1.54 million hectares (ha), in southern Cameroon and assessed the impact of fire exclusion on yield, labor inputs, soil fertility, ecosystem carbon stocks, and fallow recovery indicators in two common field types (plantain and maize) under both current and reduced fallow scenarios. While we could not distinguish between impacts of standard farmer burning practice and fire exclusion treatments for the current fallow scenario, we concluded that fire exclusion would lead to higher yields, higher ecosystem carbon stocks as well as potentially faster fallow recovery under the reduced fallow scenario. While its implementation would increase labor requirements, we estimated increased revenues of 421 and 388 US ha-1 for plantain and maize, respectively. Applied to the FMBA, and assuming a 6-year reduced fallow scenario, fire exclusion in plantain fields would potentially retain 240,464 Mg more ecosystem carbon, comprising topsoil carbon plus tree biomass carbon, than standard farmer practice. Results demonstrate a potential "win-win scenario" where yield benefits, albeit modest, and conservation benefits can be obtained simultaneously. This could be considered as a transitional phase towards higher input use and thus higher yielding systems.

  7. Circumpolar distribution and carbon storage of thermokarst landscapes

    Science.gov (United States)

    Olefeldt, David; Goswami, S.; Grosse, G.; Hayes, D.; Hugelius, G.; Kuhry, P.; McGuire, A. David; Romanovsky, V.E.; Sannel, A.B.K.; Schuur, E.A.G.; Turetsky, M.R.

    2016-01-01

    Thermokarst is the process whereby the thawing of ice-rich permafrost ground causes land subsidence, resulting in development of distinctive landforms. Accelerated thermokarst due to climate change will damage infrastructure, but also impact hydrology, ecology and biogeochemistry. Here, we present a circumpolar assessment of the distribution of thermokarst landscapes, defined as landscapes comprised of current thermokarst landforms and areas susceptible to future thermokarst development. At 3.6 × 106 km2, thermokarst landscapes are estimated to cover ∼20% of the northern permafrost region, with approximately equal contributions from three landscape types where characteristic wetland, lake and hillslope thermokarst landforms occur. We estimate that approximately half of the below-ground organic carbon within the study region is stored in thermokarst landscapes. Our results highlight the importance of explicitly considering thermokarst when assessing impacts of climate change, including future landscape greenhouse gas emissions, and provide a means for assessing such impacts at the circumpolar scale.

  8. Why Landscape Beauty Matters

    Directory of Open Access Journals (Sweden)

    Angelika Krebs

    2014-11-01

    Full Text Available This philosophical paper explores the aesthetic argument for landscape conservation. The main claim is that the experience of beautiful landscapes is an essential part of the good human life. Beautiful landscapes make us feel at home in the world. Their great and irreplaceable value lies therein. To establish this claim, the concepts of landscape and “Stimmung” are clarified. It is shown how “Stimmung” (in the sense of mood is infused into landscape (as atmosphere and how we respond to it aesthetically. We respond by resonating or feeling at home. The paper ends by indicating how art can help us to better appreciate landscape beauty. This is done by way of an example from contemporary nature poetry, Michael Donhauser’s Variationen in Prosa, which begins with “Und was da war, es nahm uns an” (“And what was there accepted us”.

  9. Condensed landscape experience

    DEFF Research Database (Denmark)

    Earon, Ofri

    2011-01-01

    ‘Re-thinking interaction between landscape and urban buildings’ participates in an interdisciplinary discourse about the theoretical and practical advantages of openly juxtaposing landscape and architecture without having one more advanced in importance. Recently, the greenification of buildings...... demands, quality of space, mixture of functions, urban complexity, public life and cultural heritage. In order to launch such an approach, an understanding of the spatial, social and environmental significance of a radical re-thinking of relationships between architecture and landscape is necessary...

  10. Inland drift sand landscapes

    NARCIS (Netherlands)

    Fanta, J.; Siepel, H.

    2010-01-01

    Man has had a complex relationship with inland drift sands through the ages. For some centuries these landscapes were seen as a threat to society, especially agriculture and housing. At present we conserve these landscapes as important Natura 2000 priority habitats. In this book you may find these

  11. Principles of landscape architecture

    NARCIS (Netherlands)

    Nijhuis, S.

    2013-01-01

    The Department of Urbanism at the Faculty of Architecture and Built Environment, TU Delft considers urbanism as a planning and design oriented activity towards urban and rural landscapes. It aims to enhance, restore or create landscapes from a perspective of sustainable development, so as to guide,

  12. Nature and landscape protection

    International Nuclear Information System (INIS)

    Klinda, J.; Lieskovska, Z.

    1998-01-01

    In accordance with National Council of the Slovak Republic Act N. 287/1994 Coll. on Nature and Landscape Protection, the system of complex nature landscape protection has been designed based on five levels of protection. Categories of protected areas as well as cultural monuments in the Slovak Republic are reviewed.Slovak contribution to the world heritage is included

  13. Globalization and Landscape Architecture

    OpenAIRE

    Robert R. Hewitt

    2014-01-01

    The literature review examines globalization and landscape architecture as discourse, samples its various meanings, and proposes methods to identify and contextualize its specific literature. Methodologically, the review surveys published articles and books by leading authors and within the WorldCat.org Database associated with landscape architecture and globalization, analyzing survey results for comprehensive concept...

  14. Glossary on agricultural landscapes.

    NARCIS (Netherlands)

    Kruse, A.; Centeri, C.; Renes, J.; Roth, M.; Printsman, A.; Palang, H.; Benito Jorda, M.-D.; Verlarde, M.D.; Kruckenberg, H.

    2010-01-01

    T he following glossary of terms related to the European agricultural landscape shall serve as a common basis for all parties, working in or on agricultural landscapes. Some of the terms are quite common and sometimes used in our every day language, but they often have different meanings in

  15. Empirical methods for modeling landscape change, ecosystem services, and biodiversity

    Science.gov (United States)

    David Lewis; Ralph. Alig

    2009-01-01

    The purpose of this paper is to synthesize recent economics research aimed at integrating discrete-choice econometric models of land-use change with spatially-explicit landscape simulations and quantitative ecology. This research explicitly models changes in the spatial pattern of landscapes in two steps: 1) econometric estimation of parcel-scale transition...

  16. Integrating social, economic, and ecological values across large landscapes

    Science.gov (United States)

    Jessica E. Halofsky; Megan K. Creutzburg; Miles A. Hemstrom

    2014-01-01

    The Integrated Landscape Assessment Project (ILAP) was a multiyear effort to produce information, maps, and models to help land managers, policymakers, and others conduct mid- to broad-scale (e.g., watersheds to states and larger areas) prioritization of land management actions, perform landscape assessments, and estimate cumulative effects of management actions for...

  17. Statistical topography of fitness landscapes

    OpenAIRE

    Franke, Jasper

    2011-01-01

    Fitness landscapes are generalized energy landscapes that play an important conceptual role in evolutionary biology. These landscapes provide a relation between the genetic configuration of an organism and that organism’s adaptive properties. In this work, global topographical features of these fitness landscapes are investigated using theoretical models. The resulting predictions are compared to empirical landscapes. It is shown that these landscapes allow, at least with respe...

  18. Urban Landscape Perspectives

    Directory of Open Access Journals (Sweden)

    Frederick Steiner

    2014-03-01

    Full Text Available Cities present significant opportunities for new landscape perspectives that can help inform conservation and development decisions. Early in the twenty-first century, the majority of the planet’s population became urban as more people lived in city-regions for the first time in our history. As the global population increases, so does this urbanization. The environmental challenges of population and urban growth are profound. Landscapes represent a synthesis of natural and cultural processes. Cities are certainly cultural phenomena. Historically, cities provided refuge from nature. The expanding field of urban ecology, coupled with landscape ecology, can enhance how the dual natural and cultural dimensions of landscapes in cities are understood. Furthermore, concepts such as ecosystem services and green infrastructure are proving useful for urban landscape planning and design. Examples from Dayton, Ohio; Brooklyn, New York; and Austin, Texas are presented.

  19. Vacuum selection on axionic landscapes

    International Nuclear Information System (INIS)

    Wang, Gaoyuan; Battefeld, Thorsten

    2016-01-01

    We compute the distribution of minima that are reached dynamically on multi-field axionic landscapes, both numerically and analytically. Such landscapes are well suited for inflationary model building due to the presence of shift symmetries and possible alignment effects (the KNP mechanism). The resulting distribution of dynamically reached minima differs considerably from the naive expectation based on counting all vacua. These differences are more pronounced in the presence of many fields due to dynamical selection effects: while low lying minima are preferred as fields roll down the potential, trajectories are also more likely to get trapped by one of the many nearby minima. We show that common analytic arguments based on random matrix theory in the large D-limit to estimate the distribution of minima are insufficient for quantitative arguments pertaining to the dynamically reached ones. This discrepancy is not restricted to axionic potentials. We provide an empirical expression for the expectation value of such dynamically reached minimas' height and argue that the cosmological constant problem is not alleviated in the absence of anthropic arguments. We further comment on the likelihood of inflation on axionic landscapes in the large D-limit

  20. Genomic regulatory landscapes and chromosomal rearrangements

    DEFF Research Database (Denmark)

    Ladegaard, Elisabete L Engenheiro

    2008-01-01

    The main objectives of the PhD study are to identify and characterise chromosomal rearrangements within evolutionarily conserved regulatory landscapes around genes involved in the regulation of transcription and/or development (trans-dev genes). A frequent feature of trans-dev genes is that they ......The main objectives of the PhD study are to identify and characterise chromosomal rearrangements within evolutionarily conserved regulatory landscapes around genes involved in the regulation of transcription and/or development (trans-dev genes). A frequent feature of trans-dev genes...... the complex spatio-temporal expression of the associated trans-dev gene. Rare chromosomal breakpoints that disrupt the integrity of these regulatory landscapes may be used as a tool, not only to make genotype-phenotype associations, but also to link the associated phenotype with the position and tissue...... specificity of the individual CNEs. In this PhD study I have studied several chromosomal rearrangements with breakpoints in the vicinity of trans-dev genes. This included chromosomal rearrangements compatible with known phenotype-genotype associations (Rieger syndrome-PITX2, Mowat-Wilson syndrome-ZEB2...

  1. A multispecies framework for landscape conservation planning.

    Science.gov (United States)

    Schwenk, W Scott; Donovan, Therese M

    2011-10-01

    Rapidly changing landscapes have spurred the need for quantitative methods for conservation assessment and planning that encompass large spatial extents. We devised and tested a multispecies framework for conservation planning to complement single-species assessments and ecosystem-level approaches. Our framework consisted of 4 elements: sampling to effectively estimate population parameters, measuring how human activity affects landscapes at multiple scales, analyzing the relation between landscape characteristics and individual species occurrences, and evaluating and comparing the responses of multiple species to landscape modification. We applied the approach to a community of terrestrial birds across 25,000 km(2) with a range of intensities of human development. Human modification of land cover, road density, and other elements of the landscape, measured at multiple spatial extents, had large effects on occupancy of the 67 species studied. Forest composition within 1 km of points had a strong effect on occupancy of many species and a range of negative, intermediate, and positive associations. Road density within 1 km of points, percent evergreen forest within 300 m, and distance from patch edge were also strongly associated with occupancy for many species. We used the occupancy results to group species into 11 guilds that shared patterns of association with landscape characteristics. Our multispecies approach to conservation planning allowed us to quantify the trade-offs of different scenarios of land-cover change in terms of species occupancy. Conservation Biology © 2011 Society for Conservation Biology. No claim to original US government works.

  2. Planetary Landscape Geography

    Science.gov (United States)

    Hargitai, H.

    INTRODUCTION Landscape is one of the most often used category in physical ge- ography. The term "landshap" was introduced by Dutch painters in the 15-16th cen- tury. [1] The elements that build up a landscape (or environment) on Earth consists of natural (biogenic and abiogenic - lithologic, atmospheric, hydrologic) and artificial (antropogenic) factors. Landscape is a complex system of these different elements. The same lithology makes different landscapes under different climatic conditions. If the same conditions are present, the same landscape type will appear. Landscapes build up a hierarchic system and cover the whole surface. On Earth, landscapes can be classified and qualified according to their characteristics: relief forms (morphology), and its potential economic value. Aesthetic and subjective parameters can also be considered. Using the data from landers and data from orbiters we can now classify planetary landscapes (these can be used as geologic mapping units as well). By looking at a unknown landscape, we can determine the processes that created it and its development history. This was the case in the Pathfinder/Sojourner panoramas. [2]. DISCUSSION Planetary landscape evolution. We can draw a raw landscape develop- ment history by adding the different landscape building elements to each other. This has a strong connection with the planet's thermal evolution (age of the planet or the present surface materials) and with orbital parameters (distance from the central star, orbit excentricity etc). This way we can build a complex system in which we use differ- ent evolutional stages of lithologic, atmospheric, hydrologic and biogenic conditions which determine the given - Solar System or exoplanetary - landscape. Landscape elements. "Simple" landscapes can be found on asteroids: no linear horizon is present (not differentiated body, only impact structures), no atmosphere (therefore no atmospheric scattering - black sky as part of the landscape) and no

  3. The transcriptional landscape of age in human peripheral blood

    NARCIS (Netherlands)

    M.J. Peters (Marjolein); R. Joehanes (Roby); L.C. Pilling (Luke); C. Schurmann (Claudia); K.N. Conneely (Karen N.); J.E. Powell (Joseph); E. Reinmaa (Eva); G.L. Sutphin (George L.); A. Zhernakova (Alexandra); K. Schramm (Katharina); Y.A. Wilson (Yana A.); S. Kobes (Sayuko); T. Tukiainen (Taru); Y.F.M. Ramos (Yolande); H.H.H. Göring (Harald H.); M. Fornage (Myriam); Y. Liu (YongMei); S.A. Gharib (Sina); B.E. Stranger (Barbara); P.L. de Jager (Philip); A. Aviv (Abraham); D. Levy (Daniel); J. Murabito (Joanne); P.J. Munson (Peter J.); T. Huan (Tianxiao); A. Hofman (Albert); A.G. Uitterlinden (André); F. Rivadeneira Ramirez (Fernando); J. van Rooij (Jeroen); L. Stolk (Lisette); L. Broer (Linda); M.M.P.J. Verbiest (Michael); M. Jhamai (Mila); P.P. Arp (Pascal); A. Metspalu (Andres); L. Tserel (Liina); L. Milani (Lili); N.J. Samani (Nilesh); P. Peterson (Pärt); S. Kasela (Silva); V. Codd (Veryan); A. Peters (Annette); C.K. Ward-Caviness (Cavin K.); C. Herder (Christian); M. Waldenberger (Melanie); M. Roden (Michael); P. Singmann (Paula); S. Zeilinger (Sonja); T. Illig (Thomas); G. Homuth (Georg); H.J. Grabe (Hans Jörgen); H. Völzke (Henry); L. Steil (Leif); T. Kocher (Thomas); A. Murray (Anna); D. Melzer (David); H. Yaghootkar (Hanieh); S. Bandinelli; E.K. Moses (Eric); J.W. Kent (Jack); J.E. Curran (Joanne); M.P. Johnson (Matthew); S. Williams-Blangero (Sarah); H.J. Westra (Harm-Jan); A.F. McRae (Allan F.); J.A. Smith (Jennifer A); S.L.R. Kardia (Sharon); I. Hovatta (Iiris); M. Perola (Markus); S. Ripatti (Samuli); V. Salomaa (Veikko); A.K. Henders (Anjali); N.G. Martin (Nicholas); A.K. Smith (Alicia K.); D. Mehta (Divya); E.B. Binder (Elisabeth B.); K.M. Nylocks (K. Maria); E.M. Kennedy (Elizabeth M.); T. Klengel (Torsten); J. Ding (Jingzhong); A. Suchy-Dicey (Astrid); D. Enquobahrie; J. Brody (Jennifer); J.I. Rotter (Jerome I.); Y.-D.I. Chen (Yii-Der I.); J.J. Houwing-Duistermaat (Jeanine); M. Kloppenburg (Margreet); P.E. Slagboom (Eline); Q. Helmer (Quinta); W. den Hollander (Wouter); S. Bean (Shannon); T. Raj (Towfique); N. Bakhshi (Noman); Q.P. Wang (Qiao Ping); L.J. Oyston (Lisa J.); B.M. Psaty (Bruce); R.P. Tracy (Russell); G.W. Montgomery (Grant); S.T. Turner (Stephen); J. Blangero (John); I. Meulenbelt (Ingrid); K.J. Ressler (Kerry); J. Yang (Jian); L. Franke (Lude); J. Kettunen (Johannes); P.M. Visscher (Peter); G.G. Neely (G. Gregory); R. Korstanje (Ron); R.L. Hanson (Robert L.); H. Prokisch (Holger); L. Ferrucci (Luigi); T. Esko (Tõnu); A. Teumer (Alexander); J.B.J. van Meurs (Joyce); A.D. Johnson (Andrew D.); M.A. Nalls (Michael); D.G. Hernandez (Dena); M.R. Cookson (Mark); R.J. Gibbs (Raphael J.); J. Hardy (John); A. Ramasamy (Adaikalavan); A.B. Zonderman (Alan B.); A. Dillman (Allissa); B. Traynor (Bryan); C. Smith (Colin); D.L. Longo (Dan L.); D. Trabzuni (Danyah); J.C. Troncoso (Juan); M.P. van der Brug (Marcel); M.E. Weale (Michael); R. O'Brien (Richard); R. Johnson (Robert); R. Walker (Robert); R.H. Zielke (Ronald H.); S. Arepalli (Sampath); M. Ryten (Mina); A. Singleton

    2015-01-01

    textabstractDisease incidences increase with age, but the molecular characteristics of ageing that lead to increased disease susceptibility remain inadequately understood. Here we perform a whole-blood gene expression meta-analysis in 14,983 individuals of European ancestry (including replication)

  4. The transcriptional landscape of age in human peripheral blood

    NARCIS (Netherlands)

    Peters, Marjolein J.; Joehanes, Roby; Pilling, Luke C.; Schurmann, Claudia; Conneely, Karen N.; Powell, Joseph; Reinmaa, Eva; Sutphin, George L.; Zhernakova, Alexandra; Schramm, Katharina; Wilson, Yana A.; Kobes, Sayuko; Tukiainen, Taru; Ramos, Yolande F.; Goering, Harald H. H.; Fornage, Myriam; Liu, Yongmei; Gharib, Sina A.; Stranger, Barbara E.; De Jager, Philip L.; Aviv, Abraham; Levy, Daniel; Murabito, Joanne M.; Munson, Peter J.; Huan, Tianxiao; Hofman, Albert; Uitterlinden, Andre G.; Rivadeneira, Fernando; van Rooij, Jeroen; Stolk, Lisette; Broer, Linda; Verbiest, Michael M. P. J.; Jhamai, Mila; Arp, Pascal; Metspalu, Andres; Tserel, Liina; Milani, Lili; Samani, Nilesh J.; Peterson, Paert; Kasela, Silva; Codd, Veryan; Peters, Annette; Ward-Caviness, Cavin K.; Herder, Christian; Waldenberger, Melanie; Roden, Michael; Singmann, Paula; Zeilinger, Sonja; Westra, Harm-Jan; Franke, Lude

    2015-01-01

    Disease incidences increase with age, but the molecular characteristics of ageing that lead to increased disease susceptibility remain inadequately understood. Here we perform a whole-blood gene expression meta-analysis in 14,983 individuals of European ancestry (including replication) and identify

  5. The Transcriptional Landscape of p53 Signalling Pathway

    Directory of Open Access Journals (Sweden)

    Chizu Tanikawa

    2017-06-01

    Full Text Available Although recent cancer genomics studies have identified a large number of genes that were mutated in human cancers, p53 remains as the most frequently mutated gene. To further elucidate the p53-signalling network, we performed transcriptome analysis on 24 tissues in p53+/+ or p53−/− mice after whole-body X-ray irradiation. Here we found transactivation of a total of 3551 genes in one or more of the 24 tissues only in p53+/+ mice, while 2576 genes were downregulated. p53 mRNA expression level in each tissue was significantly associated with the number of genes upregulated by irradiation. Annotation using TCGA (The Cancer Genome Atlas database revealed that p53 negatively regulated mRNA expression of several cancer therapeutic targets or pathways such as BTK, SYK, and CTLA4 in breast cancer tissues. In addition, stomach exhibited the induction of Krt6, Krt16, and Krt17 as well as loricrin, an epidermal differentiation marker, after the X-ray irradiation only in p53+/+ mice, implying a mechanism to protect damaged tissues by rapid induction of differentiation. Our comprehensive transcriptome analysis elucidated tissue specific roles of p53 and its signalling networks in DNA-damage response that will enhance our understanding of cancer biology.

  6. The single-cell transcriptional landscape of hematopoiesis

    NARCIS (Netherlands)

    Baron, Chloé Sophie

    2018-01-01

    Hematopoietic stem cells (HSCs) are responsible for the production of all mature hematopoietic cells during the entire life of an organism. It is now known that HSCs are generated from a specific subset of endothelial cells in the main arteries of the developing mouse and zebrafish embryos. In the

  7. Biomass yield from an urban landscape

    Science.gov (United States)

    Utilizing biomass from urban landscapes could significantly contribute to the nation’s renewable energy needs. In 2007, an experiment was begun to evaluate the biomass production from a bermudagrass, Cynodon dactylon var. dactylon (L.) Pers., lawn in Woodward, Oklahoma and to estimate the potential...

  8. Landscape equivalent of the shoving model

    DEFF Research Database (Denmark)

    Dyre, Jeppe; Olsen, Niels Boye

    2004-01-01

    It is shown that the shoving model expression for the average relaxation time of viscous liquids, according to which the activation energy is proportional to the instantaneous shear modulus, follows largely from a classical "landscape" estimation of barrier heights from curvature at energy minima...

  9. Welfare Landscape and Communities

    DEFF Research Database (Denmark)

    Braae, Ellen Marie

    2017-01-01

    Danish housing developments of the post-war era were a cornerstone in the implementation of the welfare vision and the overall urban and landscape planning in the post-war period. The new city was a horizontal city and – as it will be my primary ambition to show – a green and landscape-like city....... The landscape came, in Denmark, to play a prominent role and became synonymous with ‘The Good Life’, but it also presented a number of moral imperatives. The article concerns how communities and community feelings found their expression in the Danish ‘welfare landscapes’....

  10. Weathering and landscape evolution

    Science.gov (United States)

    Turkington, Alice V.; Phillips, Jonathan D.; Campbell, Sean W.

    2005-04-01

    In recognition of the fundamental control exerted by weathering on landscape evolution and topographic development, the 35th Binghamton Geomorphology Symposium was convened under the theme of Weathering and Landscape Evolution. The papers and posters presented at the conference imparted the state-of-the-art in weathering geomorphology, tackled the issue of scale linkage in geomorphic studies and offered a vehicle for interdisciplinary communication on research into weathering and landscape evolution. The papers included in this special issue are encapsulated here under the general themes of weathering mantles, weathering and relative dating, weathering and denudation, weathering processes and controls and the 'big picture'.

  11. Landscape metrics application in ecological and visual landscape assessment

    Directory of Open Access Journals (Sweden)

    Gavrilović Suzana

    2017-01-01

    Full Text Available The development of landscape-ecological approach application in spatial planning provides exact theoretical and empirical evidence for monitoring ecological consequences of natural and/or anthropogenic factors, particularly changes in spatial structures caused by them. Landscape pattern which feature diverse landscape values is the holder of the unique landscape character at different spatial levels and represents a perceptual domain for its users. Using the landscape metrics, the parameters of landscape composition and configuration are mathematical algorithms that quantify the specific spatial characteristics used for interpretation of landscape features and processes (physical and ecological aspect, as well as forms (visual aspect and the meaning (cognitive aspect of the landscape. Landscape metrics has been applied mostly in the ecological and biodiversity assessments as well as in the determination of the level of structural change of landscape, but more and more applied in the assessment of the visual character of the landscape. Based on a review of relevant literature, the aim of this work is to show the main trends of landscape metrics within the aspect of ecological and visual assessments. The research methodology is based on the analysis, classification and systematization of the research studies published from 2000 to 2016, where the landscape metrics is applied: (1 the analysis of landscape pattern and its changes, (2 the analysis of biodiversity and habitat function and (3 a visual landscape assessment. By selecting representative metric parameters for the landscape composition and configuration, for each category is formed the basis for further landscape metrics research and application for the integrated ecological and visual assessment of the landscape values. Contemporary conceptualization of the landscape is seen holistically, and the future research should be directed towards the development of integrated landscape assessment

  12. Landscape genetics and limiting factors

    Science.gov (United States)

    Samuel A. Cushman; Andrew J. Shirk; Erin L. Landguth

    2013-01-01

    Population connectivity is mediated by the movement of organisms or propagules through landscapes. However, little is known about how variation in the pattern of landscape mosaics affects the detectability of landscape genetic relationships. The goal of this paper is to explore the impacts of limiting factors on landscape genetic processes using simulation...

  13. Condensed landscape experience

    DEFF Research Database (Denmark)

    Earon, Ofri

    2011-01-01

    demands, quality of space, mixture of functions, urban complexity, public life and cultural heritage. In order to launch such an approach, an understanding of the spatial, social and environmental significance of a radical re-thinking of relationships between architecture and landscape is necessary...... is becoming a standard in contemporary architecture. Merging architecture and landscape has turned into a principle for an ecological / sustainable architecture. Yet, my aspiration is to achieve a wider interaction involving an application of a wider range of perspectives, such as: urban identity, social......‘Re-thinking interaction between landscape and urban buildings’ participates in an interdisciplinary discourse about the theoretical and practical advantages of openly juxtaposing landscape and architecture without having one more advanced in importance. Recently, the greenification of buildings...

  14. PNW Hydrologic Landscape Class

    Data.gov (United States)

    U.S. Environmental Protection Agency — Work has been done to expand the hydrologic landscapes (HLs) concept and to develop an approach for using it to address streamflow vulnerability from climate change....

  15. Appropriate complexity landscape modeling

    NARCIS (Netherlands)

    Larsen, Laurel G.; Eppinga, Maarten B.; Passalacqua, Paola; Getz, Wayne M.; Rose, Kenneth A.; Liang, Man

    Advances in computing technology, new and ongoing restoration initiatives, concerns about climate change's effects, and the increasing interdisciplinarity of research have encouraged the development of landscape-scale mechanistic models of coupled ecological-geophysical systems. However,

  16. Exploring Energy Landscapes

    Science.gov (United States)

    Wales, David J.

    2018-04-01

    Recent advances in the potential energy landscapes approach are highlighted, including both theoretical and computational contributions. Treating the high dimensionality of molecular and condensed matter systems of contemporary interest is important for understanding how emergent properties are encoded in the landscape and for calculating these properties while faithfully representing barriers between different morphologies. The pathways characterized in full dimensionality, which are used to construct kinetic transition networks, may prove useful in guiding such calculations. The energy landscape perspective has also produced new procedures for structure prediction and analysis of thermodynamic properties. Basin-hopping global optimization, with alternative acceptance criteria and generalizations to multiple metric spaces, has been used to treat systems ranging from biomolecules to nanoalloy clusters and condensed matter. This review also illustrates how all this methodology, developed in the context of chemical physics, can be transferred to landscapes defined by cost functions associated with machine learning.

  17. Conserving tigers in working landscapes.

    Science.gov (United States)

    Chanchani, Pranav; Noon, Barry R; Bailey, Larissa L; Warrier, Rekha A

    2016-06-01

    Tiger (Panthera tigris) conservation efforts in Asia are focused on protected areas embedded in human-dominated landscapes. A system of protected areas is an effective conservation strategy for many endangered species if the network is large enough to support stable metapopulations. The long-term conservation of tigers requires that the species be able to meet some of its life-history needs beyond the boundaries of small protected areas and within the working landscape, including multiple-use forests with logging and high human use. However, understanding of factors that promote or limit the occurrence of tigers in working landscapes is incomplete. We assessed the relative influence of protection status, prey occurrence, extent of grasslands, intensity of human use, and patch connectivity on tiger occurrence in the 5400 km(2) Central Terai Landscape of India, adjacent to Nepal. Two observer teams independently surveyed 1009 km of forest trails and water courses distributed across 60 166-km(2) cells. In each cell, the teams recorded detection of tiger signs along evenly spaced trail segments. We used occupancy models that permitted multiscale analysis of spatially correlated data to estimate cell-scale occupancy and segment-scale habitat use by tigers as a function of management and environmental covariates. Prey availability and habitat quality, rather than protected-area designation, influenced tiger occupancy. Tiger occupancy was low in some protected areas in India that were connected to extensive areas of tiger habitat in Nepal, which brings into question the efficacy of current protection and management strategies in both India and Nepal. At a finer spatial scale, tiger habitat use was high in trail segments associated with abundant prey and large grasslands, but it declined as human and livestock use increased. We speculate that riparian grasslands may provide tigers with critical refugia from human activity in the daytime and thereby promote tiger occurrence

  18. Digital landscapes of imagination

    OpenAIRE

    Starlight Vattano

    2014-01-01

    Urban landscapes that exist in the expression of an imaginative sequence define their shape through the digital representation. These hyperreal dimensions, combine imagination and representation as constituents a new reality, which follows the utopian, suprematist and constructivist theories, where the two-dimensional dynamics is transformed into an infinite space in which the imagination creates new forms. Although interpretations of the urban landscape film, put in place a correspondence be...

  19. New infrastructures, new landscapes

    Directory of Open Access Journals (Sweden)

    Chiara Nifosì

    2014-06-01

    Full Text Available New infrastructures, new landscapes AbstractThe paper will discuss one recent Italian project that share a common background: the relevance of the existing maritime landscape as a non negotiable value. The studies will be discussed in details a feasibility study for the new port in Monfalcone. National infrastructural policies emphasize competitiveness and connection as a central issue incultural, economic and political development of communities . Based on networks and system development along passageways that make up the European infrastructural armor; the two are considered at the meantime as cause and effect of "territorialisation”. These two views are obviously mutually dependent. It's hard to think about a strong attractiveness out of the network, and to be part of the latter encourages competitiveness. Nonetheless this has proved to be conflictual when landscape values and the related attractiveness are considered.The presented case study project, is pursuing the ambition to promote a new approach in realizing large infrastructures; its double role is to improve connectivity and to generate lasting and positive impact on the local regions. It deal with issues of inter-modality and the construction of nodes and lines which connects Europe, and its markets.Reverting the usual approach which consider landscape project as as a way to mitigate or to compensate for the infrastructure, the goal is to succeed in realizing large infrastructural works by conceiving them as an occasion to reinterpret a region or, as extraordinary opportunities, to build new landscapes.The strategy proposed consists in achieving structural images based on the reinforcement of the environmental and historical-landscape systems. Starting from the reinterpretation of local maritime context and resources it is possible not just to preserve the attractiveness of a specific landscape but also to conceive infrastructure in a more efficient way. 

  20. Semiotics in landscape design

    Directory of Open Access Journals (Sweden)

    Karsten Jorgensen

    1997-03-01

    Full Text Available This paper claims that concepts of language can help us create better and more relevant landscape design. It is based on research undertaken by Karsten Jørgensen (1989, and subsequent studies carried out at the department of Land Use and Landscape Planning at the Agricultural University in Norway. The 'signs' that constitute the design language are categorised using the analytical vocabulary of landscape design; for example, elements, materials, effects and shapes. Studies of these signs are based on elements of semiotics and cognitive science, especially the Umwelt-theories developed by Jakob von Uexküll (Hoffmeyer 1994. We are constantly exposed to numerous signs of different kinds. Everywhere in society we see signs around us; for example, traffic signs, advertising signs and logos. It is therefore relevant to introduce the term 'semiosphere' in order to focus on the significance of semiosis at all levels of activity in the world, from cellular activities, to complex systems of development such as those found in a population. This study focuses on the semantic aspects of landscape architecture. In explaining the meaning of a statement, it is useful to have a set of rules or 'codes' to correlate a specific expression with a specific interpretation. These codes may be based on conventions, or on similarity between or stylisation of objects, such as natural or cultural landscapes. In any case, they are based on the interpreter's language and 'mind-structure'. At a general level, it is only possible to study sign content. To analyse meaning in landscape design you have to look at the context; for example, the overall composition of a garden or park and the situation, which includes the interpreter's cultural background, their experiences and so on. In other words, you have to analyse a specific case to be able to speak reasonably about meaning in landscape (designs.

  1. European landscape architecture and territorial strategies for water landscapes

    DEFF Research Database (Denmark)

    Diedrich, Lisa Babette

    2010-01-01

    This article sums up the author’s lecture at the 2009 Sydney Resilient Water Landscapes Symposium and presents a series of realized or planned European landscape architectural and urbanistic projects on water landscapes taken from the recently published book On Site/ Landscape Architecture Europe...... and accompanying reflections. The hypothesis is that further scientific research can help defining weaknesses and strengths of the existing water landscape designs in terms of resilience, extract principles and tools, improve the weak ones and communicate the strong ones and develop general quality criteria...... and tools for future resilient water landscapes....

  2. Geomorpho-Landscapes

    Science.gov (United States)

    Farabollini, Piero; Lugeri, Francesca; Amadio, Vittorio

    2014-05-01

    Landscape is the object of human perceptions, being the image of spatial organization of elements and structures: mankind lives the first approach with the environment, viewing and feeling the landscape. Many definitions of landscape have been given over time: in this case we refer to the Landscape defined as the result of interaction among physical, biotic and anthropic phenomena acting in a different spatial-temporal scale (Foreman & Godron) Following an Aristotelic approach in studying nature, we can assert that " Shape is synthesis": so it is possible to read the land features as the expression of the endogenous and exogenous processes that mould earth surfaces; moreover, Landscape is the result of the interaction of natural and cultural components, and conditions the spatial-temporal development of a region. The study of the Landscape offers results useful in order to promote sustainable development, ecotourism, enhancement of natural and cultural heritage, popularization of the scientific knowledge. In Italy, a very important GIS-based tool to represent the territory is the "Carta della Natura" ("Map of Nature", presently coordinated by the ISPRA) that aims at assessing the state of the whole Italian territory, analyzing Landscape. The methodology follows a holistic approach, taking into consideration all the components of a landscape and then integrating the information. Each individual landscape, studied at different scales, shows distinctive elements: structural, which depend on physical form and specific spatial organization; functional, which depend on relationships created between biotic and abiotic elements, and dynamic, which depend on the successive evolution of the structure. The identification of the landscape units, recognized at different scales of analysis, allows an evaluation of the state of the land, referring to the dual risk/resource which characterizes the Italian country. An interesting opportunity is to discover those areas of unusual

  3. Globalization and Landscape Architecture

    Directory of Open Access Journals (Sweden)

    Robert R. Hewitt

    2014-02-01

    Full Text Available The literature review examines globalization and landscape architecture as discourse, samples its various meanings, and proposes methods to identify and contextualize its specific literature. Methodologically, the review surveys published articles and books by leading authors and within the WorldCat.org Database associated with landscape architecture and globalization, analyzing survey results for comprehensive conceptual and co-relational frameworks. Three “higher order” dimensions frame the review’s conceptual organization, facilitating the organization of subordinate/subtopical areas of interest useful for comparative analysis. Comparative analysis of the literature suggests an uneven clustering of discipline-related subject matter across the literature’s “higher order” dimensions, with a much smaller body of literature related to landscape architecture confined primarily to topics associated with the dispersion of global phenomena. A subcomponent of this smaller body of literature is associated with other fields of study, but inferentially related to landscape architecture. The review offers separate references and bibliographies for globalization literature in general and globalization and landscape architecture literature, specifically.

  4. Qualifying Urban Landscapes

    DEFF Research Database (Denmark)

    Clemmensen, Thomas Juel; Nielsen, Tom; Daugaard, Morten

    2010-01-01

    The article presents an attempt to develop alternatives to the dominant planning and design principles used in building and rebuilding the contemporary urban landscape. The basic idea is that the ‘forces of modernisation’ driving current development might result in a broader and more interesting...... for contemporary urban landscape design practice....... to the task of constructing and improving things. With this goal, a set of objectives based in important insights from recent urban theory are formulated constituting the normative spine of the analysis of a number of found situations as basis for formulating eight generic concepts of qualification...

  5. Digital landscapes of imagination

    Directory of Open Access Journals (Sweden)

    Starlight Vattano

    2014-05-01

    Full Text Available Urban landscapes that exist in the expression of an imaginative sequence define their shape through the digital representation. These hyperreal dimensions, combine imagination and representation as constituents a new reality, which follows the utopian, suprematist and constructivist theories, where the two-dimensional dynamics is transformed into an infinite space in which the imagination creates new forms. Although interpretations of the urban landscape film, put in place a correspondence between reality and virtuality, into the modeling of spatial movements, from which do not arise contraries, but only interdependencies. It is a particular type of representation that takes shape via the digital in motion and provides new tools for urban representation.

  6. Imagine A Collective Landscape

    Directory of Open Access Journals (Sweden)

    Manuela Silvia Campanini

    2010-03-01

    Full Text Available Iceland plays a key role in the circumpolar context. The research investigates the fields of both the icelandic cultural landscape perception and the icelandic cultural identity. It considers the book Ultima thule; or, a summer in Iceland and Ólafur Elíasson art works as two sides of a same medal: the Iceland on the brain concept (F. Burton. The transition from a cultural identity to a collective landscape identity is investigated analysing Imagine J. Lennon's song which inspired Yõko Ono's work art titled Imagine Peace Tower.

  7. Selecting Landscape Plants: Shade Trees

    OpenAIRE

    Relf, Diane; Appleton, Bonnie Lee, 1948-2012; Close, David

    2015-01-01

    Because of the permanency of trees and their importance in the landscape, care must be taken to select the best species for each situation. This publication goes over how to choose landscape trees that are shade tolerant.

  8. Transcriptional regulation by competing transcription factor modules.

    Directory of Open Access Journals (Sweden)

    Rutger Hermsen

    2006-12-01

    Full Text Available Gene regulatory networks lie at the heart of cellular computation. In these networks, intracellular and extracellular signals are integrated by transcription factors, which control the expression of transcription units by binding to cis-regulatory regions on the DNA. The designs of both eukaryotic and prokaryotic cis-regulatory regions are usually highly complex. They frequently consist of both repetitive and overlapping transcription factor binding sites. To unravel the design principles of these promoter architectures, we have designed in silico prokaryotic transcriptional logic gates with predefined input-output relations using an evolutionary algorithm. The resulting cis-regulatory designs are often composed of modules that consist of tandem arrays of binding sites to which the transcription factors bind cooperatively. Moreover, these modules often overlap with each other, leading to competition between them. Our analysis thus identifies a new signal integration motif that is based upon the interplay between intramodular cooperativity and intermodular competition. We show that this signal integration mechanism drastically enhances the capacity of cis-regulatory domains to integrate signals. Our results provide a possible explanation for the complexity of promoter architectures and could be used for the rational design of synthetic gene circuits.

  9. Biogenic VOC Emissions from Tropical Landscapes

    Science.gov (United States)

    Guenther, A.; Greenberg, J.; Harley, P.; Otter, L.; Vanni Gatti, L.; Baker, B.

    2003-04-01

    Biogenic VOC have an important role in determining the chemical composition of atmosphere. As a result, these compounds are important for visibility, biogeochemical cycling, climate and radiative forcing, and the health of the biosphere. Tropical landscapes are estimated to release about 80% of total global biogenic VOC emissions but have been investigated to lesser extent than temperate regions. Tropical VOC emissions are particularly important due to the strong vertical transport and the rapid landuse change that is occurring there. This presentation will provide an overview of field measurements of biogenic VOC emissions from tropical landscapes in Amazonia (Large-scale Biosphere-atmosphere experiment in Amazonia, LBA) Central (EXPRESSO) and Southern (SAFARI 2000) Africa, Asia and Central America. Flux measurement methods include leaf-scale (enclosure measurements), canopy-scale (above canopy tower measurements), landscape-scale (tethered balloon), and regional-scale (aircraft measurements) observations. Typical midday isoprene emission rates for different landscapes vary by more than a factor of 20 with the lowest emissions observed from degraded forests. Emissions of alpha-pinene vary by a similar amount with the highest emissions associated with landscapes dominated by light dependent monoterpene emitting plants. Isoprene emissions tend to be higher for neotropical forests (Amazon and Costa Rica) in comparison to Africa and Asian tropical forests but considerable differences are observed within regions. Strong seasonal variations were observed in both the Congo and the Amazon rainforests with peak emissions during the dry seasons. Substantial emissions of light dependent monoterpenes, methanol and acetone are characteristic of at least some tropical landscapes.

  10. Landscape metrics for three-dimension urban pattern recognition

    Science.gov (United States)

    Liu, M.; Hu, Y.; Zhang, W.; Li, C.

    2017-12-01

    Understanding how landscape pattern determines population or ecosystem dynamics is crucial for managing our landscapes. Urban areas are becoming increasingly dominant social-ecological systems, so it is important to understand patterns of urbanization. Most studies of urban landscape pattern examine land-use maps in two dimensions because the acquisition of 3-dimensional information is difficult. We used Brista software based on Quickbird images and aerial photos to interpret the height of buildings, thus incorporating a 3-dimensional approach. We estimated the feasibility and accuracy of this approach. A total of 164,345 buildings in the Liaoning central urban agglomeration of China, which included seven cities, were measured. Twelve landscape metrics were proposed or chosen to describe the urban landscape patterns in 2- and 3-dimensional scales. The ecological and social meaning of landscape metrics were analyzed with multiple correlation analysis. The results showed that classification accuracy compared with field surveys was 87.6%, which means this method for interpreting building height was acceptable. The metrics effectively reflected the urban architecture in relation to number of buildings, area, height, 3-D shape and diversity aspects. We were able to describe the urban characteristics of each city with these metrics. The metrics also captured ecological and social meanings. The proposed landscape metrics provided a new method for urban landscape analysis in three dimensions.

  11. Qualifying Urban Landscapes

    DEFF Research Database (Denmark)

    Juel Clemmensen, Thomas; Daugaard, Morten; Nielsen, Tom

    This paper is based on a research project aimed at contributing to the qualification of the aesthetical value of the contemporary urban landscape. We see our work as part of a tradition within the architectural profession of making explorative projects, which combines analysis of the contemporary...

  12. A landscape analysis plan

    Science.gov (United States)

    Nancy E. Fleenor

    2002-01-01

    A Landscape Analysis Plan (LAP) sets out broad guidelines for project development within boundaries of the Kings River Sustainable Forest Ecosystems Project. The plan must be a dynamic, living document, subject to change as new information arises over the course of this very long-term project (several decades). Two watersheds, each of 32,000 acres, were dedicated to...

  13. Ecology, recreation and landscape

    Energy Technology Data Exchange (ETDEWEB)

    Satchell, J E

    1983-01-01

    The article is dedicated to the problems of combining mass tourism in certain countries of Western Europe and environmental protection (OOS) requirements. The ecological damage from recreation is examined and the throughput of the medium is evaluated. The author proposes development of regulable, managable and controllable recreation use of natural resources and landscapes using selective advertising of the recreation sites.

  14. Landscape Planning of Schoolyards

    Science.gov (United States)

    Kopeva, A.; Khrapko, O.; Ivanova, O.

    2017-11-01

    The optimal landscape architecture planning of schoolyards allows for creation of favorable conditions for children personal development and physical fitness. The key principles of schoolyard landscape planning, same as for other areas intended for children, are as follows: establishment of a favorable microclimate, safety, aesthetic and educational environment. Green spaces play an essential role in this respect as they are essential to sanitary, hygienic, structural, and spatial planning performing decorative, artistic, cognitive, and educational functions in these areas. Various types of landscape plantings are used in school areas: borders, lawns, beds, vines, ornamental arrangements, and various potted plants. Children’s safety is the key principle when selecting a landscape design type and the plants’ range. Any allergenic, poisonous, thorny, strong-smelling or life-threatening plants are excluded. Plants on school grounds can serve as visual aids for studies. Drought-resistant, attractive, colorful, abundantly blooming plants with variable leaf texture are preferred. Ornamental trees and shrubs as well as perennials and annuals provide a broad plant range for school grounds.

  15. Landscape Assessment (LA)

    Science.gov (United States)

    Carl H. Key; Nathan C. Benson

    2006-01-01

    Landscape Assessment primarily addresses the need to identify and quantify fire effects over large areas, at times involving many burns. In contrast to individual case studies, the ability to compare results is emphasized along with the capacity to aggregate information across broad regions and over time. Results show the spatial heterogeneity of burns and how fire...

  16. Landscapes in transition

    NARCIS (Netherlands)

    Padfield, Rory; Drew, Simon; Syayuti, Khadijah; Page, Susan; Evers, Stephanie; Campos-Arceiz, Ahimsa; Kangayatkarasu, Nagulendran; Sayok, Alex; Hansen, Sune; Schouten, Greetje; Maulidia, Martha; Papargyropoulou, Effie; Tham, Mun Hou

    2016-01-01

    The recent Southeast Asian haze crisis has generated intense public scrutiny over the rate, methods and types of landscape change in the tropics. Debate has centred on the environmental impacts of large-scale agricultural expansion, particularly the associated loss of high carbon stock forest and

  17. WRKY transcription factors

    Science.gov (United States)

    Bakshi, Madhunita; Oelmüller, Ralf

    2014-01-01

    WRKY transcription factors are one of the largest families of transcriptional regulators found exclusively in plants. They have diverse biological functions in plant disease resistance, abiotic stress responses, nutrient deprivation, senescence, seed and trichome development, embryogenesis, as well as additional developmental and hormone-controlled processes. WRKYs can act as transcriptional activators or repressors, in various homo- and heterodimer combinations. Here we review recent progress on the function of WRKY transcription factors in Arabidopsis and other plant species such as rice, potato, and parsley, with a special focus on abiotic, developmental, and hormone-regulated processes. PMID:24492469

  18. Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer's disease.

    Science.gov (United States)

    Alkallas, Rached; Fish, Lisa; Goodarzi, Hani; Najafabadi, Hamed S

    2017-10-13

    The abundance of mRNA is mainly determined by the rates of RNA transcription and decay. Here, we present a method for unbiased estimation of differential mRNA decay rate from RNA-sequencing data by modeling the kinetics of mRNA metabolism. We show that in all primary human tissues tested, and particularly in the central nervous system, many pathways are regulated at the mRNA stability level. We present a parsimonious regulatory model consisting of two RNA-binding proteins and four microRNAs that modulate the mRNA stability landscape of the brain, which suggests a new link between RBFOX proteins and Alzheimer's disease. We show that downregulation of RBFOX1 leads to destabilization of mRNAs encoding for synaptic transmission proteins, which may contribute to the loss of synaptic function in Alzheimer's disease. RBFOX1 downregulation is more likely to occur in older and female individuals, consistent with the association of Alzheimer's disease with age and gender."mRNA abundance is determined by the rates of transcription and decay. Here, the authors propose a method for estimating the rate of differential mRNA decay from RNA-seq data and model mRNA stability in the brain, suggesting a link between mRNA stability and Alzheimer's disease."

  19. Chapter 4: Overview of the vegetation management treatment economic analysis module in the integrated landscape assessment project

    Science.gov (United States)

    Xiaoping Zhou; Miles A. Hemstrom

    2014-01-01

    Forest land provides various ecosystem services, including timber, biomass, and carbon sequestration. Estimating trends in these ecosystem services is essential for assessing potential outcomes of landscape management scenarios. However, the state-and transition models used in the Integrated Landscape Assessment Project for simulating landscape changes over time do not...

  20. Landscape Evolution Modelling-LAPSUS

    Energy Technology Data Exchange (ETDEWEB)

    Baartman, J. E. M.; Temme, A. J. A. M.; Schoorl, J. M.; Claessens, L.; Viveen, W.; Gorp, W. van; Veldkamp, A.

    2009-07-01

    Landscape evolution modelling can make the consequences of landscape evolution hypotheses explicit and theoretically allows for their falsification and improvement. ideally, landscape evolution models (LEMs) combine the results of all relevant landscape forming processes into an ever-adapting digital landscape (e.g. DEM). These processes may act on different spatial and temporal scales. LAPSUS is such a LEM. Processes that have in different studies been included in LAPSUS are water erosion and deposition, landslide activity, creep, solidification, weathering, tectonics and tillage. Process descriptions are as simple and generic as possible, ensuring wide applicability. (Author) 25 refs.

  1. Landscape Evolution Modelling-LAPSUS

    International Nuclear Information System (INIS)

    Baartman, J. E. M.; Temme, A. J. A. M.; Schoorl, J. M.; Claessens, L.; Viveen, W.; Gorp, W. van; Veldkamp, A.

    2009-01-01

    Landscape evolution modelling can make the consequences of landscape evolution hypotheses explicit and theoretically allows for their falsification and improvement. ideally, landscape evolution models (LEMs) combine the results of all relevant landscape forming processes into an ever-adapting digital landscape (e.g. DEM). These processes may act on different spatial and temporal scales. LAPSUS is such a LEM. Processes that have in different studies been included in LAPSUS are water erosion and deposition, landslide activity, creep, solidification, weathering, tectonics and tillage. Process descriptions are as simple and generic as possible, ensuring wide applicability. (Author) 25 refs.

  2. Driving the Landscape

    Science.gov (United States)

    Haff, P. K.

    2012-12-01

    Technological modification of the earth's surface (e.g., agriculture, urbanization) is an old story in human history, but what about the future? The future of landscape in an accelerating technological world, beyond a relatively short time horizon, lies hidden behind an impenetrable veil of complexity. Sufficiently complex dynamics generates not only the trajectory of a variable of interest (e.g., vegetation cover) but also the environment in which that variable evolves (e.g., background climate). There is no way to anticipate what variables will define that environment—the dynamics creates its own variables. We are always open to surprise by a change of conditions we thought or assumed were fixed or by the appearance of new phenomena of whose possible existence we had been unaware or thought unlikely. This is especially true under the influence of technology, where novelty is the rule. Lack of direct long-term predictability of landscape change does not, however, mean we cannot say anything about its future. The presence of persistence (finite time scales) in a system means that prediction by a calibrated numerical model should be good for a limited period of time barring bad luck or faulty implementation. Short-term prediction, despite its limitations, provides an option for dealing with the longer-term future. If a computer-controlled car tries to drive itself from New York to Los Angeles, no conceivable (or possible) stand-alone software can be constructed to predict a priori the space-time trajectory of the vehicle. Yet the drive is normally completed easily by most drivers. The trip is successfully completed because each in a series of very short (linear) steps can be "corrected" on the fly by the driver, who takes her cues from the environment to keep the car on the road and headed toward its destination. This metaphor differs in a fundamental way from the usual notion of predicting geomorphic change, because it involves a goal—to reach a desired

  3. Ecological Functions of Landscapes

    Science.gov (United States)

    Kiryushin, V. I.

    2018-01-01

    Ecological functions of landscapes are considered a system of processes ensuring the development, preservation, and evolution of ecosystems and the biosphere as a whole. The concept of biogeocenosis can be considered a model that integrates biotic and environmental functions. The most general biogeocenotic functions specify the biodiversity, biotic links, self-organization, and evolution of ecosystems. Close interaction between biocenosis and the biotope (ecotope) is ensured by the continuous exchange of matter, energy, and information. Ecotope determines the biocenosis. The group of ecotopic functions includes atmospheric (gas exchange, heat exchange, hydroatmospheric, climate-forming), lithospheric (geodynamic, geophysical, and geochemical), hydrologic and hydrogeologic functions of landscape and ecotopic functions of soils. Bioecological functions emerge as a result of the biotope and ecotope interaction; these are the bioproductive, destructive, organoaccumulative, biochemical (gas, concentration, redox, biochemical, biopedological), pedogenetic, and energy functions

  4. Conceiving Landscape through Film

    DEFF Research Database (Denmark)

    Farsø, Mads; Munck Petersen, Rikke

    2015-01-01

    This article shows how the media of film can be integrated, explored and can add value to architectural design studios and practice. It elucidates how film may offer an alternative position in architecture, where landscapes and cities are thought, planned and developed in closer relation...... to their spatial and sensory effects on humans. It underscores that the film camera can work as a kind of amplifier of how we, with our bodies, perceive space and project space. In the “Landscape Film” Studio at University of Copenhagen the film medium was tested as a combined registration and design tool...... for a new Nature Park south of Copenhagen. The final studio films and designs show how resonate recordings of sound, time and a bodily presence may simulate an Einfühling that inspires an alternative architecture of relations: the ambient, the changeable and the volatile. They also emphasize that an ability...

  5. Landscape & Imagination: riflettere insieme

    Directory of Open Access Journals (Sweden)

    Mariella Zoppi

    2015-10-01

    Full Text Available In Paris, at La Villette University, was four-days of debate on 2-4 Mai 2013, in which faculty members of all the world discussed on methods and experiences in teaching landscape. The conference was organized in multiple sessions: history, theories, representation, process, science and governance. All the fields discussed were related to the main problem of the identity of territories in the landscape project -from the theories to the practices- and applied in a very large range of different situations: from the rural world between conservation and transformations to the coastal areas under the pressure of tourism, from the ecology in the city life renovation to the land use control and project by community and the emergency management in natural catastrophes.

  6. Identification Of Minangkabau Landscape Characters

    Science.gov (United States)

    Asrina, M.; Gunawan, A.; Aris, Munandar

    2017-10-01

    Minangkabau is one of cultures in indonesia which occupies landscape intact. Landscape of Minangkabau have a very close relationship with the culture of the people. Uniqueness of Minangkabau culture and landscape forming an inseparable characterunity. The landscape is necessarily identified to know the inherent landscape characters. The objective of this study was to identify the character of the Minangkabau landscape characterizes its uniqueness. The study was conducted by using descriptive method comprised literature review and field observasion. Observed the landscape characters comprised two main features, they were major and minor features. Indetification of the features was conducted in two original areas (darek) of the Minangkabau traditional society. The research results showed that major features or natural features of the landscape were predominantly landform, landcover, and hidrology. All luhak (districts) of Minangkabau showed similar main features such as hill, canyon, lake, valley, and forest. The existence of natural features such as hills, canyon and valleys characterizes the nature of minangkabau landscape. Minor features formed by Minangkabau cultural society were agricultural land and settlement. Rumah gadang (big house) is one of famous minor features characterizes the Minangkabau culture. In addition, several historical artefacts of building and others structure may strengthen uniqueness of the Minangkabau landscape character, such as The royal palace, inscription, and tunnels.

  7. Comparison of Transcription Factor Binding Site Models

    KAUST Repository

    Bhuyan, Sharifulislam

    2012-05-01

    Modeling of transcription factor binding sites (TFBSs) and TFBS prediction on genomic sequences are important steps to elucidate transcription regulatory mechanism. Dependency of transcription regulation on a great number of factors such as chemical specificity, molecular structure, genomic and epigenetic characteristics, long distance interaction, makes this a challenging problem. Different experimental procedures generate evidence that DNA-binding domains of transcription factors show considerable DNA sequence specificity. Probabilistic modeling of TFBSs has been moderately successful in identifying patterns from a family of sequences. In this study, we compare performances of different probabilistic models and try to estimate their efficacy over experimental TFBSs data. We build a pipeline to calculate sensitivity and specificity from aligned TFBS sequences for several probabilistic models, such as Markov chains, hidden Markov models, Bayesian networks. Our work, containing relevant statistics and evaluation for the models, can help researchers to choose the most appropriate model for the problem at hand.

  8. Dysfunctional transcripts are formed by alternative polyadenylation in OPMD

    OpenAIRE

    Raz, Vered; Dickson, George; ’t Hoen, Peter A.C.

    2017-01-01

    Post-transcription mRNA processing in the 3’-untranslated region (UTR) of transcripts alters mRNA landscape. Alternative polyadenylation (APA) utilization in the 3’-UTR often leads to shorter 3’-UTR affecting mRNA stability, a process that is regulated by PABPN1. In skeletal muscles PABPN1 levels reduce with age and a greater decrease in found in Oculopharyngeal muscular dystrophy (OPMD). OPMD is a late onset autosomal dominant myopathy caused by expansion mutation in PABPN1. In OPMD models a...

  9. Incorporating Bioenergy in Sustainable Landscape Designs Workshop Two: Agricultural Landscapes

    Energy Technology Data Exchange (ETDEWEB)

    None

    2015-08-01

    The Bioenergy Technologies Office hosted two workshops on Incorporating Bioenergy in Sustainable Landscape Designs with Oak Ridge and Argonne National Laboratories in 2014. The second workshop focused on agricultural landscapes and took place in Argonne, IL from June 24—26, 2014. The workshop brought together experts to discuss how landscape design can contribute to the deployment and assessment of sustainable bioenergy. This report summarizes the discussions that occurred at this particular workshop.

  10. Integrated landscape initiatives in Europe

    DEFF Research Database (Denmark)

    García-Martín, María; Bieling, Claudia; Hart, Abigail

    2016-01-01

    Landscapes are linked to human well-being in a multitude of ways, some of which are challenged by global market forces and traditional management approaches. In response to this situation there has been a rise in local initiatives to sustain the values of landscape. The aim of this paper is to pr......Landscapes are linked to human well-being in a multitude of ways, some of which are challenged by global market forces and traditional management approaches. In response to this situation there has been a rise in local initiatives to sustain the values of landscape. The aim of this paper...... searches and canvassing of European umbrella organisations; followed by an online survey of representatives from the identified initiatives (n??=??71). Our results show that the most relevant characteristics of integrated landscape initiatives in Europe are: a holistic approach to landscape management...

  11. Transcriptional and Chromatin Dynamics of Muscle Regeneration After Severe Trauma

    Science.gov (United States)

    2016-10-12

    02127. 2Broad Institute of MIT and Harvard, Cambridge , MA 02142, Harvard Stem Cell Institute, Cambridge , MA 02138, Dept. of Stem Cell and...Regenerative Biology, Harvard University, Cambridge , MA 02138. 3United States Army Institute of Environmental Medicine - Military Performance Division, Natick...throughout the regenerative process in a mouse model of traumatic muscle injury. We first illustrate how the transcriptional landscape of coding and

  12. Flowscapes: Designing infrastructure as landscape

    OpenAIRE

    Nijhuis, S.; Jauslin, D.T.; Van der Hoeven, F.D.

    2015-01-01

    Social, cultural and technological developments of our society are demanding a fundamental review of the planning and design of its landscapes and infrastructures, in particular in relation to environmental issues and sustainability. Transportation, green and water infrastructures are important agents that facilitate processes that shape the built environment and its contemporary landscapes. With movement and flows at the core, these landscape infrastructures facilitate aesthetic, functional,...

  13. Modelling Geomorphic Systems: Landscape Evolution

    OpenAIRE

    Valters, Declan

    2016-01-01

    Landscape evolution models (LEMs) present the geomorphologist with a means of investigating how landscapes evolve in response to external forcings, such as climate and tectonics, as well as internal process laws. LEMs typically incorporate a range of different geomorphic transport laws integrated in a way that simulates the evolution of a 3D terrain surface forward through time. The strengths of LEMs as research tools lie in their ability to rapidly test many different hypotheses of landscape...

  14. Energy landscape Allgaeu; Energielandschaft Allgaeu

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2013-04-01

    In tandems with questions on the energy policy turnaround, the topics cultural landscape history, morphology, actual land use, tourism, settlement development or infrastructure are summarized in regional concepts and designs to a consistent landscape. Thus, a true integration of renewable energies in the landscape enhances existing or creates completely new landscape qualities. Energy supply shall be understood as a component of the every day life world. The energy supply shall not be hidden any more, but it rather should be communicated as the brand 'Allgaeu'.

  15. The Value of Landscape Essence

    Directory of Open Access Journals (Sweden)

    Maria da Conceição Marques Freire

    2014-08-01

    Full Text Available A new approach to interpreting the landscape is examined by accepting its complexity through inductive reasoning. While attempting to identify the essence of the landscape in the city and municipality of Óbidos, Portugal, several architectural recommendations of Venturi (2004 have been adapted as a framework for understanding this landscape. These will then guide the process of landscape transformation through:•••using the concepts of closed and contained spaces and the concept of fluid space;•recognising the existence of interstitial open spaces;•using those elements which are common to the distinct typologies of space;•defining the components that should be respected and those that can be respected;•observing landscape as a whole , while emphasising the relationship between the parts and the whole; and•rejecting simplification in the landscape transformation process.valuing the ambiguity incorporating the complexity Underlying this approach is the belief that the process of transformation must be based on the essence of each landscape. This implies the use of elements and structures of the landscape which are related to ecological, morphological and cultural systems. These elements and structures represent points of reference which should be considered in the process of landscape transformation.

  16. Impressionist Landscape Cartography

    Science.gov (United States)

    Todd, Stella W.

    2018-05-01

    Cartography helps to show us the world in which we reside by providing us a framework to explore space. We can select myriad themes to represent what is relevant to our lives: physical characteristics, human behaviors, hazards, opportunities. Themes are represented on a continuum between real-world images and pure abstractions. How we define cartography and what we expect from it changes with society and technology. We are now inundated with data but we still struggle with expressing our personal geographic experiences through cartography. In this age of information we have become more cognizant of our individual experience of place and our need to determine our own paths and therefore create our own maps. In order to reflect our journey we can add individual details to cartographic products or generalize information to concentrate on what is meaningful to us. Since time and space are interrelated we experience geography by viewing the landscape as changing scenes over time. This experience is both spatial and temporal since we experience geography by moving through space. Experiencing each scene is a separate event. This paper expands the personalization of maps to include our impressions of the travel experience. Rather than add art to cartography it provides geographic reference to art. It explores the use of a series of quick sketches drawn while traveling along roads using a single drawing pad to produce a time series of interpreted landscapes. With the use of geographic time stamps from global positioning systems these sketches are converted from a drawing to a map documenting the path of movement. Although the map scale varies between sketch entries each scene impression can be linked to one or more maps of consistent scale. The result is an artistic piece that expresses a dynamic geographic experience that can be viewed in conjunction with more traditional maps. Unlike mental maps which are constructed from memory, these maps reflect our direct impressions

  17. Experimental Rugged Fitness Landscape in Protein Sequence Space

    Science.gov (United States)

    Hayashi, Yuuki; Aita, Takuyo; Toyota, Hitoshi; Husimi, Yuzuru; Urabe, Itaru; Yomo, Tetsuya

    2006-01-01

    The fitness landscape in sequence space determines the process of biomolecular evolution. To plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein D2 domain, which is essential for phage infection. After 20 cycles of random substitution at sites 12–130 of the initial random polypeptide and selection for infectivity, the selected phage showed a 1.7×104-fold increase in infectivity, defined as the number of infected cells per ml of phage suspension. Fitness was defined as the logarithm of infectivity, and we analyzed (1) the dependence of stationary fitness on library size, which increased gradually, and (2) the time course of changes in fitness in transitional phases, based on an original theory regarding the evolutionary dynamics in Kauffman's n-k fitness landscape model. In the landscape model, single mutations at single sites among n sites affect the contribution of k other sites to fitness. Based on the results of these analyses, k was estimated to be 18–24. According to the estimated parameters, the landscape was plotted as a smooth surface up to a relative fitness of 0.4 of the global peak, whereas the landscape had a highly rugged surface with many local peaks above this relative fitness value. Based on the landscapes of these two different surfaces, it appears possible for adaptive walks with only random substitutions to climb with relative ease up to the middle region of the fitness landscape from any primordial or random sequence, whereas an enormous range of sequence diversity is required to climb further up the rugged surface above the middle region. PMID:17183728

  18. Experimental rugged fitness landscape in protein sequence space.

    Science.gov (United States)

    Hayashi, Yuuki; Aita, Takuyo; Toyota, Hitoshi; Husimi, Yuzuru; Urabe, Itaru; Yomo, Tetsuya

    2006-12-20

    The fitness landscape in sequence space determines the process of biomolecular evolution. To plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein D2 domain, which is essential for phage infection. After 20 cycles of random substitution at sites 12-130 of the initial random polypeptide and selection for infectivity, the selected phage showed a 1.7x10(4)-fold increase in infectivity, defined as the number of infected cells per ml of phage suspension. Fitness was defined as the logarithm of infectivity, and we analyzed (1) the dependence of stationary fitness on library size, which increased gradually, and (2) the time course of changes in fitness in transitional phases, based on an original theory regarding the evolutionary dynamics in Kauffman's n-k fitness landscape model. In the landscape model, single mutations at single sites among n sites affect the contribution of k other sites to fitness. Based on the results of these analyses, k was estimated to be 18-24. According to the estimated parameters, the landscape was plotted as a smooth surface up to a relative fitness of 0.4 of the global peak, whereas the landscape had a highly rugged surface with many local peaks above this relative fitness value. Based on the landscapes of these two different surfaces, it appears possible for adaptive walks with only random substitutions to climb with relative ease up to the middle region of the fitness landscape from any primordial or random sequence, whereas an enormous range of sequence diversity is required to climb further up the rugged surface above the middle region.

  19. Experimental rugged fitness landscape in protein sequence space.

    Directory of Open Access Journals (Sweden)

    Yuuki Hayashi

    Full Text Available The fitness landscape in sequence space determines the process of biomolecular evolution. To plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein D2 domain, which is essential for phage infection. After 20 cycles of random substitution at sites 12-130 of the initial random polypeptide and selection for infectivity, the selected phage showed a 1.7x10(4-fold increase in infectivity, defined as the number of infected cells per ml of phage suspension. Fitness was defined as the logarithm of infectivity, and we analyzed (1 the dependence of stationary fitness on library size, which increased gradually, and (2 the time course of changes in fitness in transitional phases, based on an original theory regarding the evolutionary dynamics in Kauffman's n-k fitness landscape model. In the landscape model, single mutations at single sites among n sites affect the contribution of k other sites to fitness. Based on the results of these analyses, k was estimated to be 18-24. According to the estimated parameters, the landscape was plotted as a smooth surface up to a relative fitness of 0.4 of the global peak, whereas the landscape had a highly rugged surface with many local peaks above this relative fitness value. Based on the landscapes of these two different surfaces, it appears possible for adaptive walks with only random substitutions to climb with relative ease up to the middle region of the fitness landscape from any primordial or random sequence, whereas an enormous range of sequence diversity is required to climb further up the rugged surface above the middle region.

  20. Landscape encodings enhance optimization.

    Directory of Open Access Journals (Sweden)

    Konstantin Klemm

    Full Text Available Hard combinatorial optimization problems deal with the search for the minimum cost solutions (ground states of discrete systems under strong constraints. A transformation of state variables may enhance computational tractability. It has been argued that these state encodings are to be chosen invertible to retain the original size of the state space. Here we show how redundant non-invertible encodings enhance optimization by enriching the density of low-energy states. In addition, smooth landscapes may be established on encoded state spaces to guide local search dynamics towards the ground state.

  1. The Anti-Landscape

    DEFF Research Database (Denmark)

    There have always been some uninhabitable places, but in the last century human beings have produced many more of them. These anti-landscapes have proliferated to include the sandy wastes of what was once the Aral Sea, severely polluted irrigated lands, open pit mines, blighted nuclear zones...... that no longer sustain life. This history includes T. S. Eliot’s Wasteland and Cormac McCarthy’s The Road as well as air pollution, recycled railway lines, photography and landfills. It links theories of aesthetics, politics, tourism, history, geography, and literature into the new synthesis of the environmental...

  2. Landscapes of the Anthropocene

    DEFF Research Database (Denmark)

    Pawson, Eric; Christensen, Andreas Aagaard

    2014-01-01

    since the 1840s, when indigenous forests were transformed into improved landscapes of sown grass. The chapter is shaped by a broad question. What can be learned from this place about the ways in which people have exercised and are coming to terms with what Gibson-Graham and Roelvink describe as our...... of the shifting balance of ecological agency in favour of humans during the Anthropocene. Banks Peninsula on the east coast of New Zealand’s South Island was first settled by Polynesian peoples within the last few hundred years. The nature of their footprint contrasts with the dramatic change wrought by Europeans...

  3. Stonehenge and its Landscape

    Science.gov (United States)

    Ruggles, Clive L. N.

    In the 1960s and 1970s, Stonehenge polarized academic opinion between those (mainly astronomers) who claimed it demonstrated great astronomical sophistication and those (mainly archaeologists) who denied it had anything to do with astronomy apart from the solstitial alignment of its main axis. Now, several decades later, links to the annual passage of the sun are generally recognized as an essential part of the function and meaning not only of Stonehenge but also of several other nearby monuments, giving us important insights into beliefs and actions relating to the seasonal cycle by the prehistoric communities who populated this chalkland landscape in the third millennium BC Links to the moon remain more debatable.

  4. Reprogramming the chromatin landscape

    DEFF Research Database (Denmark)

    Miranda, Tina B; Voss, Ty C; Sung, Myong-Hee

    2013-01-01

    , mechanistic details defining the cellular interactions between ER and GR are poorly understood. We investigated genome-wide binding profiles for ER and GR upon coactivation and characterized the status of the chromatin landscape. We describe a novel mechanism dictating the molecular interplay between ER...... and GR. Upon induction, GR modulates access of ER to specific sites in the genome by reorganization of the chromatin configuration for these elements. Binding to these newly accessible sites occurs either by direct recognition of ER response elements or indirectly through interactions with other factors...

  5. Landscape Encodings Enhance Optimization

    Science.gov (United States)

    Klemm, Konstantin; Mehta, Anita; Stadler, Peter F.

    2012-01-01

    Hard combinatorial optimization problems deal with the search for the minimum cost solutions (ground states) of discrete systems under strong constraints. A transformation of state variables may enhance computational tractability. It has been argued that these state encodings are to be chosen invertible to retain the original size of the state space. Here we show how redundant non-invertible encodings enhance optimization by enriching the density of low-energy states. In addition, smooth landscapes may be established on encoded state spaces to guide local search dynamics towards the ground state. PMID:22496860

  6. Editorial: Mapping the Intellectual Landscape of Landscape and Urban Planning

    Science.gov (United States)

    Paul H. Gobster; Wei-Ning. Xiang

    2012-01-01

    Maps are central to our understanding of landscapes. When this Editorship began to revise the journal's Aims and Scope for presentation in a forthcoming editorial, we sought ways in which we could identify the core knowledge base and boundaries, however permeable, of what the journal community considers to be Landscape and Urban Planning (LAND). Strategically, we...

  7. Landscape Painting in Evaluation of Changes in Landscape

    Czech Academy of Sciences Publication Activity Database

    Lacina, Jan; Halas, Petr

    2015-01-01

    Roč. 8, č. 2 (2015), s. 60-68 ISSN 1803-2427 Institutional support: RVO:68145535 Keywords : landscape painting * landscape ecology * land-use changes * biodiversity Subject RIV: DE - Earth Magnetism, Geodesy, Geography http://www.degruyter.com/view/j/jlecol.2015.8.issue-2/jlecol-2015-0009/jlecol-2015-0009. xml

  8. Changing landscape in the Three Gorges Reservoir Area of Yangtze River from 1977 to 2005: Land use/land cover, vegetation cover changes estimated using multi-source satellite data

    Science.gov (United States)

    Zhang, Jixian; Zhengjun, Liu; Xiaoxia, Sun

    2009-12-01

    The eco-environment in the Three Gorges Reservoir Area (TGRA) in China has received much attention due to the construction of the Three Gorges Hydropower Station. Land use/land cover changes (LUCC) are a major cause of ecological environmental changes. In this paper, the spatial landscape dynamics from 1978 to 2005 in this area are monitored and recent changes are analyzed, using the Landsat TM (MSS) images of 1978, 1988, 1995, 2000 and 2005. Vegetation cover fractions for a vegetation cover analysis are retrieved from MODIS/Terra imagery from 2000 to 2006, being the period before and after the rising water level of the reservoir. Several analytical indices have been used to analyze spatial and temporal changes. Results indicate that cropland, woodland, and grassland areas reduced continuously over the past 30 years, while river and built-up area increased by 2.79% and 4.45% from 2000 to 2005, respectively. The built-up area increased at the cost of decreased cropland, woodland and grassland. The vegetation cover fraction increased slightly. We conclude that significant changes in land use/land cover have occurred in the Three Gorges Reservoir Area. The main cause is a continuous economic and urban/rural development, followed by environmental management policies after construction of the Three Gorges Dam.

  9. Cultural Landscape and Migration

    Directory of Open Access Journals (Sweden)

    Gunnar Haaland

    2011-04-01

    Full Text Available This paper focus on the way Nepalese migrants in Myanmar use features of the natural environment in their homeland in metaphoric constructions of a cultural landscape expressing ethnic identity. It is through such "symbolic work" that perceptions of "ethnoscapes" are shaped and indoctrinated. Although the appeal is to symbols that can serve to foster the importance of Nepaliness as a basis for belonging to an imagined community, this does not mean that the caste/ethnicity interaction boundaries are broken down. It does mean however that sectors of activities where such boundaries are made relevant have been changed and so has the cultural content organized through such interaction boundaries. Ethnoscapes do not exist by themselves from a 'primordial' past; they require ongoing expression and confirmation. Features of a natural environment most migrants have never seen is used as sources for spinning compelling webs of significance extolling the values of belonging to a group that shares a common past in that environment. I shall here present material of an ethnoscape very different from what is experienced in Nepal, namely Nepalese multi-caste/ethnic communities among Kachins, Shans, Burmese, Indian and Chinese traders in the Kachin state of Northern Myanmar. Keywords: Nepali migrants; Myanmar; ethnic identity; cultural landscape DOI: 10.3126/dsaj.v4i0.4515 Dhaulagiri Journal of Sociology and Anthropology Vol.4 2010 pp.99-110

  10. The Data Science Landscape

    Science.gov (United States)

    Mentzel, C.

    2017-12-01

    Modern scientific data continue to increase in volume, variety, and velocity, and though the hype of big data has subsided, its usefulness for scientific discovery has only just begun. Harnessing these data for new insights, more efficient decision making, and other mission critical uses requires a combination of skills and expertise, often labeled data science. Data science can be thought of as a combination of statistics, computation and the domain from which the data relate, and so is a true interdisciplinary pursuit. Though it has reaped large benefits in companies able to afford the high cost of the severely limited talent pool, it suffers from lack of support in mission driven organizations. Not purely in any one historical field, data science is proving difficult to find a home in traditional university academic departments and other research organizations. The landscape of data science efforts, from academia, industry and government, can be characterized as nascent, enthusiastic, uneven, and highly competitive. Part of the challenge in documenting these trends is the lack of agreement about what data science is, and who is a data scientist. Defining these terms too closely and too early runs the risk of cutting off a tremendous amount of productive creativity, but waiting too long leaves many people without a sustainable career, and many organizations without the necessary skills to gain value from their data. This talk will explore the landscape of data science efforts in the US, including how organizations are building and sustaining data science teams.

  11. Landscape Evolution of Titan

    Science.gov (United States)

    Moore, Jeffrey

    2012-01-01

    Titan may have acquired its massive atmosphere relatively recently in solar system history. The warming sun may have been key to generating Titan's atmosphere over time, starting from a thin atmosphere with condensed surface volatiles like Triton, with increased luminosity releasing methane, and then large amounts of nitrogen (perhaps suddenly), into the atmosphere. This thick atmosphere, initially with much more methane than at present, resulted in global fluvial erosion that has over time retreated towards the poles with the removal of methane from the atmosphere. Basement rock, as manifested by bright, rough, ridges, scarps, crenulated blocks, or aligned massifs, mostly appears within 30 degrees of the equator. This landscape was intensely eroded by fluvial processes as evidenced by numerous valley systems, fan-like depositional features and regularly-spaced ridges (crenulated terrain). Much of this bedrock landscape, however, is mantled by dunes, suggesting that fluvial erosion no longer dominates in equatorial regions. High midlatitude regions on Titan exhibit dissected sedimentary plains at a number of localities, suggesting deposition (perhaps by sediment eroded from equatorial regions) followed by erosion. The polar regions are mainly dominated by deposits of fluvial and lacustrine sediment. Fluvial processes are active in polar areas as evidenced by alkane lakes and occasional cloud cover.

  12. Branches of the landscape

    International Nuclear Information System (INIS)

    Dine, Michael; O'Neil, Deva; Sun Zheng

    2005-01-01

    With respect to the question of supersymmetry breaking, there are three branches of the flux landscape. On one of these, if one requires small cosmological constant, supersymmetry breaking is predominantly at the fundamental scale; on another, the distribution is roughly flat on a logarithmic scale; on the third, the preponderance of vacua are at very low scale. A priori, as we will explain, one can say little about the first branch. The vast majority of these states are not accessible even to crude, approximate analysis. On the other two branches one can hope to do better. But as a result of the lack of access to branch one, and our poor understanding of cosmology, we can at best conjecture about whether string theory predicts low energy supersymmetry or not. If we hypothesize that are on branch two or three, distinctive predictions may be possible. We comment of the status of naturalness within the landscape, deriving, for example, the statistics of the first branch from simple effective field theory reasoning

  13. Urban landscape as palimpsest

    Directory of Open Access Journals (Sweden)

    Daniel-Gabriel Vâlceanu

    2014-12-01

    Full Text Available The current urban morphology and the identity building of the city construction can be designed as a palimpsest; the spatial development stages of urban systems represent the result of their evolution over time. The characteristics of urban palimpsest depend mainly on the emergent factors that influenced the territorial dynamics and the configuration of urban bodies. Urban life and its quality are directly influenced by spatial and temporal factors of the city evolution. For this reason the study aims to achieve a research to explain the concept of urban palimpsest and the current morphology of urban tissue because they are products of landscape transformations along the history. The current knowledge on urban palimpsest characteristics is very important and useful to plan the current and future evolution of urban systems. The case study presents a vast view on the history of spatial development and urban system as well as a dynamics of the landscape interconditioned by the elements of such development in the context of reference historical eras

  14. Norwegian millstone quarry landscapes

    Science.gov (United States)

    Heldal, Tom; Meyer, Gurli; Grenne, Tor

    2013-04-01

    Rotary querns and millstones were used in Norway since just after the Roman Period until the last millstone was made in the 1930s. Throughout all this time millstone mining was fundamental for daily life: millstones were needed to grind grain, our most important food source. We can find millstone quarries in many places in the country from coast to mountain. Some of them cover many square kilometers and count hundreds of quarries as physical testimonies of a long and great production history. Other quarries are small and hardly visible. Some of this history is known through written and oral tradition, but most of it is hidden and must be reconstructed from the traces we can find in the landscape today. The Millstone project has put these quarry landscapes on the map, and conducted a range of case studies, including characterization of archaeological features connected to the quarrying, interpretation of quarrying techniques and evolution of such and establishing distribution and trade patterns by the aid of geological provenance. The project also turned out to be a successful cooperation between different disciplines, in particular geology and archaeology.

  15. Sustainability, Smart Growth, and Landscape Architecture

    Science.gov (United States)

    Sustainability, Smart Growth, and Landscape Architecture is an overview course for landscape architecture students interested in sustainability in landscape architecture and how it might apply to smart growth principles in urban, suburban, and rural areas

  16. Changing wind-power landscapes

    DEFF Research Database (Denmark)

    Möller, Bernd

    2006-01-01

    of determining the likely visual-impact on landscapes and population, taking into account that there is no clear threshold for perceived adverse visual-impact. A geographical information system (GIS) has been used to build a regional landscape model for Northern Jutland County, which is used to assess visibility...

  17. Marc Treib: Representing Landscape Architecture

    DEFF Research Database (Denmark)

    Braae, Ellen Marie

    2008-01-01

    The editor of Representing Landscape Architecture, Marc Treib, argues that there is good reason to evaluate the standard practices of representation that landscape architects have been using for so long. In the rush to the promised land of computer design these practices are now in danger of being...

  18. Caribbean landscapes and their biodiversity

    Science.gov (United States)

    A. E. Lugo; E. H. Helmer; E. Santiago Valentín

    2012-01-01

    Both the biodiversity and the landscapes of the Caribbean have been greatly modified as a consequence of human activity. In this essay we provide an overview of the natural landscapes and biodiversity of the Caribbean and discuss how human activity has affected both. Our Caribbean geographic focus is on the insular Caribbean and the biodiversity focus is on the flora,...

  19. Future landscapes: opportunities and challenges

    Science.gov (United States)

    John Stanturf

    2015-01-01

    The global magnitude of degraded and deforested areas is best approached by restoring landscapes. Heightened international perception of the importance of forests and trees outside forests (e.g., woodlands, on farms) demands new approaches to future landscapes. The current need for forest restoration is two billion ha; most opportunities are mosaic restoration in the...

  20. Landscape in a Lacquer Box

    Science.gov (United States)

    Savage, Martha

    2010-01-01

    A symbolic dry landscape garden of Eastern origin holds a special fascination for the author's middle-school students, which is why the author chose to create a project exploring this view of nature. A dry landscape garden, or "karesansui," is an arrangement of rocks, worn by nature and surrounded by a "sea" of sand, raked into patterns…

  1. Contingent Diversity on Anthropic Landscapes

    Directory of Open Access Journals (Sweden)

    William Balée

    2010-02-01

    Full Text Available Behaviorally modern human beings have lived in Amazonia for thousands of years. Significant dynamics in species turnovers due to human-mediated disturbance were associated with the ultimate emergence and expansion of agrarian technologies in prehistory. Such disturbances initiated primary and secondary landscape transformations in various locales of the Amazon region. Diversity in these locales can be understood by accepting the initial premise of contingency, expressed as unprecedented human agency and human history. These effects can be accessed through the archaeological record and in the study of living languages. In addition, landscape transformation can be demonstrated in the study of traditional knowledge (TK. One way of elucidating TK distinctions between anthropic and nonanthropic landscapes concerns elicitation of differential labeling of these landscapes and more significantly, elicitation of the specific contents, such as trees, occurring in these landscapes. Freelisting is a method which can be used to distinguish the differential species compositions of landscapes resulting from human-mediated disturbance vs. those which do not evince records of human agency and history. The TK of the Ka’apor Indians of Amazonian Brazil as revealed in freelisting exercises shows differentiation of anthropogenic from high forests as well as a recognition of diversity in the anthropogenic forests. This suggests that the agents of human-mediated disturbance and landscape transformation in traditional Amazonia encode diversity and contingency into their TK, which encoding reflects past cultural influence on landscape and society over time.

  2. Erosion and sedimentation effects on soil : organic carbon redistribution in a complex landscape of western Ecuador

    NARCIS (Netherlands)

    Corre, M.D.; Schoorl, J.M.; Koning, de F.; López-Ulloa, M.; Veldkamp, E.

    2015-01-01

    This study was conducted to evaluate how land-use changes affect the distribution of SOC within a complex tropical landscape through the processes of erosion and sedimentation. The objectives were: (i) to estimate the present SOC storage at a landscape scale using predictors such as slope,

  3. Fitness Landscapes of Functional RNAs

    Directory of Open Access Journals (Sweden)

    Ádám Kun

    2015-08-01

    Full Text Available The notion of fitness landscapes, a map between genotype and fitness, was proposed more than 80 years ago. For most of this time data was only available for a few alleles, and thus we had only a restricted view of the whole fitness landscape. Recently, advances in genetics and molecular biology allow a more detailed view of them. Here we review experimental and theoretical studies of fitness landscapes of functional RNAs, especially aptamers and ribozymes. We find that RNA structures can be divided into critical structures, connecting structures, neutral structures and forbidden structures. Such characterisation, coupled with theoretical sequence-to-structure predictions, allows us to construct the whole fitness landscape. Fitness landscapes then can be used to study evolution, and in our case the development of the RNA world.

  4. Modeling Aquatic Macroinvertebrate Richness Using Landscape Attributes

    Directory of Open Access Journals (Sweden)

    Marcia S. Meixler

    2015-01-01

    Full Text Available We used a rapid, repeatable, and inexpensive geographic information system (GIS approach to predict aquatic macroinvertebrate family richness using the landscape attributes stream gradient, riparian forest cover, and water quality. Stream segments in the Allegheny River basin were classified into eight habitat classes using these three landscape attributes. Biological databases linking macroinvertebrate families with habitat classes were developed using life habits, feeding guilds, and water quality preferences and tolerances for each family. The biological databases provided a link between fauna and habitat enabling estimation of family composition in each habitat class and hence richness predictions for each stream segment. No difference was detected between field collected and modeled predictions of macroinvertebrate families in a paired t-test. Further, predicted stream gradient, riparian forest cover, and total phosphorus, total nitrogen, and suspended sediment classifications matched observed classifications much more often than by chance alone. High gradient streams with forested riparian zones and good water quality were predicted to have the greatest macroinvertebrate family richness and changes in water quality were predicted to have the greatest impact on richness. Our findings indicate that our model can provide meaningful landscape scale macroinvertebrate family richness predictions from widely available data for use in focusing conservation planning efforts.

  5. A Classification of Landscape Services to Support Local Landscape Planning

    Directory of Open Access Journals (Sweden)

    María Vallés-Planells

    2014-03-01

    Full Text Available The ecosystem services approach has been proven successful to measure the contributions of nature and greenery to human well-being. Ecosystems have an effect on quality of life, but landscapes also, as a broader concept, may contribute to people's well-being. The concept of landscape services, compared to ecosystem services, involves the social dimension of landscape and the spatial pattern resulting from both natural and human processes in the provision of benefits for human-well being. Our aim is to develop a classification for landscape services. The proposed typology of services is built on the Common International Classification of Ecosystem Services (CICES and on a critical review of existing literature on human well-being dimensions, existing ecosystem service classifications, and landscape perception. Three themes of landscape services are defined, each divided into several groups: provisioning, regulation and maintenance, cultural and social life fulfillment, with the latter focusing on health, enjoyment, and personal and social fulfillment. A special emphasis is made on cultural services, which are especially important when applied to landscape and which have received less attention.

  6. The Transcription Factor Encyclopedia

    DEFF Research Database (Denmark)

    Yusuf, Dimas; Butland, Stefanie L; Swanson, Magdalena I

    2012-01-01

    mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written......ABSTRACT: Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130...

  7. The European nanometrology landscape.

    Science.gov (United States)

    Leach, Richard K; Boyd, Robert; Burke, Theresa; Danzebrink, Hans-Ulrich; Dirscherl, Kai; Dziomba, Thorsten; Gee, Mark; Koenders, Ludger; Morazzani, Valérie; Pidduck, Allan; Roy, Debdulal; Unger, Wolfgang E S; Yacoot, Andrew

    2011-02-11

    This review paper summarizes the European nanometrology landscape from a technical perspective. Dimensional and chemical nanometrology are discussed first as they underpin many of the developments in other areas of nanometrology. Applications for the measurement of thin film parameters are followed by two of the most widely relevant families of functional properties: measurement of mechanical and electrical properties at the nanoscale. Nanostructured materials and surfaces, which are seen as key materials areas having specific metrology challenges, are covered next. The final section describes biological nanometrology, which is perhaps the most interdisciplinary applications area, and presents unique challenges. Within each area, a review is provided of current status, the capabilities and limitations of current techniques and instruments, and future directions being driven by emerging industrial measurement requirements. Issues of traceability, standardization, national and international programmes, regulation and skills development will be discussed in a future paper.

  8. The European nanometrology landscape

    Science.gov (United States)

    Leach, Richard K.; Boyd, Robert; Burke, Theresa; Danzebrink, Hans-Ulrich; Dirscherl, Kai; Dziomba, Thorsten; Gee, Mark; Koenders, Ludger; Morazzani, Valérie; Pidduck, Allan; Roy, Debdulal; Unger, Wolfgang E. S.; Yacoot, Andrew

    2011-02-01

    This review paper summarizes the European nanometrology landscape from a technical perspective. Dimensional and chemical nanometrology are discussed first as they underpin many of the developments in other areas of nanometrology. Applications for the measurement of thin film parameters are followed by two of the most widely relevant families of functional properties: measurement of mechanical and electrical properties at the nanoscale. Nanostructured materials and surfaces, which are seen as key materials areas having specific metrology challenges, are covered next. The final section describes biological nanometrology, which is perhaps the most interdisciplinary applications area, and presents unique challenges. Within each area, a review is provided of current status, the capabilities and limitations of current techniques and instruments, and future directions being driven by emerging industrial measurement requirements. Issues of traceability, standardization, national and international programmes, regulation and skills development will be discussed in a future paper.

  9. The European nanometrology landscape

    International Nuclear Information System (INIS)

    Leach, Richard K; Boyd, Robert; Gee, Mark; Roy, Debdulal; Yacoot, Andrew; Burke, Theresa; Danzebrink, Hans-Ulrich; Dziomba, Thorsten; Koenders, Ludger; Dirscherl, Kai; Morazzani, Valerie; Pidduck, Allan; Unger, Wolfgang E S

    2011-01-01

    This review paper summarizes the European nanometrology landscape from a technical perspective. Dimensional and chemical nanometrology are discussed first as they underpin many of the developments in other areas of nanometrology. Applications for the measurement of thin film parameters are followed by two of the most widely relevant families of functional properties: measurement of mechanical and electrical properties at the nanoscale. Nanostructured materials and surfaces, which are seen as key materials areas having specific metrology challenges, are covered next. The final section describes biological nanometrology, which is perhaps the most interdisciplinary applications area, and presents unique challenges. Within each area, a review is provided of current status, the capabilities and limitations of current techniques and instruments, and future directions being driven by emerging industrial measurement requirements. Issues of traceability, standardization, national and international programmes, regulation and skills development will be discussed in a future paper. (topical review)

  10. The European nanometrology landscape

    Energy Technology Data Exchange (ETDEWEB)

    Leach, Richard K; Boyd, Robert; Gee, Mark; Roy, Debdulal; Yacoot, Andrew [National Physical Laboratory (United Kingdom); Burke, Theresa [European Society for Precision Engineering and Nanotechnology (United Kingdom); Danzebrink, Hans-Ulrich; Dziomba, Thorsten; Koenders, Ludger [Physikalisch-Technische Bundesanstalt (Germany); Dirscherl, Kai [Danish Fundamental Metrology (Denmark); Morazzani, Valerie [Laboratoire National de Metrologie et d' Essais (France); Pidduck, Allan [QinetiQ (United Kingdom); Unger, Wolfgang E S, E-mail: richard.leach@npl.co.uk [Federal Institute for Materials Research and Testing (Germany)

    2011-02-11

    This review paper summarizes the European nanometrology landscape from a technical perspective. Dimensional and chemical nanometrology are discussed first as they underpin many of the developments in other areas of nanometrology. Applications for the measurement of thin film parameters are followed by two of the most widely relevant families of functional properties: measurement of mechanical and electrical properties at the nanoscale. Nanostructured materials and surfaces, which are seen as key materials areas having specific metrology challenges, are covered next. The final section describes biological nanometrology, which is perhaps the most interdisciplinary applications area, and presents unique challenges. Within each area, a review is provided of current status, the capabilities and limitations of current techniques and instruments, and future directions being driven by emerging industrial measurement requirements. Issues of traceability, standardization, national and international programmes, regulation and skills development will be discussed in a future paper. (topical review)

  11. Data anonymization patent landscape

    Directory of Open Access Journals (Sweden)

    Mirjana Pejić Bach

    2017-01-01

    Full Text Available The omnipresent, unstoppable increase in digital data has led to a greater understanding of the importance of data privacy. Different approaches are used to implement data privacy. The goal of this paper is to develop a data anonymization patent landscape, by determining the following: (i the trend in data anonymization patenting, (ii the type of technical content protected in data anonymization, (iii the organizations and countries most active in patenting data anonymization know-how; and (iv the topics emerging most often in patent titles. Patents from the PatSeer database relating to data anonymization from 2001 to 2015 were analyzed. We used the longitudinal approach in combination with text mining techniques to develop a data anonymization patent landscape. The results indicated the following. The number of single patent families is growing with a high increase after 2010, thus indicating a positive trend in the area of patenting data anonymization solutions. The majority of patenting activities relate to the G Physics section. Organizations from the USA and Japan assigned the majority of patents related to data anonymization. The results of text mining indicate that the most often used word in titles of data anonymization patents are “anonym*, “method”, “data” and “system”. Several additional words that indicated the most frequent topics related to data anonymization were: “equipment”, “software”, “protection”, “identification”, or “encryption”, and specific topics such as “community”, “medical”, or “service”.

  12. Buildings Interoperability Landscape

    Energy Technology Data Exchange (ETDEWEB)

    Hardin, Dave [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Stephan, Eric G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Wang, Weimin [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Corbin, Charles D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Widergren, Steven E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-12-31

    Through its Building Technologies Office (BTO), the United States Department of Energy’s Office of Energy Efficiency and Renewable Energy (DOE-EERE) is sponsoring an effort to advance interoperability for the integration of intelligent buildings equipment and automation systems, understanding the importance of integration frameworks and product ecosystems to this cause. This is important to BTO’s mission to enhance energy efficiency and save energy for economic and environmental purposes. For connected buildings ecosystems of products and services from various manufacturers to flourish, the ICT aspects of the equipment need to integrate and operate simply and reliably. Within the concepts of interoperability lie the specification, development, and certification of equipment with standards-based interfaces that connect and work. Beyond this, a healthy community of stakeholders that contribute to and use interoperability work products must be developed. On May 1, 2014, the DOE convened a technical meeting to take stock of the current state of interoperability of connected equipment and systems in buildings. Several insights from that meeting helped facilitate a draft description of the landscape of interoperability for connected buildings, which focuses mainly on small and medium commercial buildings. This document revises the February 2015 landscape document to address reviewer comments, incorporate important insights from the Buildings Interoperability Vision technical meeting, and capture thoughts from that meeting about the topics to be addressed in a buildings interoperability vision. In particular, greater attention is paid to the state of information modeling in buildings and the great potential for near-term benefits in this area from progress and community alignment.

  13. Landscape-scale forest disturbance regimes in southern Peruvian Amazonia.

    Science.gov (United States)

    Boyd, Doreen S; Hill, Ross A; Hopkinson, Chris; Baker, Timothy R

    2013-10-01

    Landscape-scale gap-size frequency distributions in tropical forests are a poorly studied but key ecological variable. Currently, a scale gap currently exists between local-scale field-based studies and those employing regional-scale medium-resolution satellite data. Data at landscape scales but of fine resolution would, however, facilitate investigation into a range of ecological questions relating to gap dynamics. These include whether canopy disturbances captured in permanent sample plots (PSPs) are representative of those in their surrounding landscape, and whether disturbance regimes vary with forest type. Here, therefore, we employ airborne LiDAR data captured over 142.5 km2 of mature, swamp, and regenerating forests in southeast Peru to assess the landscape-scale disturbance at a sampling resolution of up to 2 m. We find that this landscape is characterized by large numbers of small gaps; large disturbance events are insignificant and infrequent. Of the total number of gaps that are 2 m2 or larger in area, just 0.45% were larger than 100 m2, with a power-law exponent (alpha) value of the gap-size frequency distribution of 2.22. However, differences in disturbance regimes are seen among different forest types, with a significant difference in the alpha value of the gap-size frequency distribution observed for the swamp/regenerating forests compared with the mature forests at higher elevations. Although a relatively small area of the total forest of this region was investigated here, this study presents an unprecedented assessment of this landscape with respect to its gap dynamics. This is particularly pertinent given the range of forest types present in the landscape and the differences observed. The coupling of detailed insights into forest properties and growth provided by PSPs with the broader statistics of disturbance events using remote sensing is recommended as a strong basis for scaling-up estimates of landscape and regional-scale carbon balance.

  14. An anatomic transcriptional atlas of human glioblastoma.

    Science.gov (United States)

    Puchalski, Ralph B; Shah, Nameeta; Miller, Jeremy; Dalley, Rachel; Nomura, Steve R; Yoon, Jae-Guen; Smith, Kimberly A; Lankerovich, Michael; Bertagnolli, Darren; Bickley, Kris; Boe, Andrew F; Brouner, Krissy; Butler, Stephanie; Caldejon, Shiella; Chapin, Mike; Datta, Suvro; Dee, Nick; Desta, Tsega; Dolbeare, Tim; Dotson, Nadezhda; Ebbert, Amanda; Feng, David; Feng, Xu; Fisher, Michael; Gee, Garrett; Goldy, Jeff; Gourley, Lindsey; Gregor, Benjamin W; Gu, Guangyu; Hejazinia, Nika; Hohmann, John; Hothi, Parvinder; Howard, Robert; Joines, Kevin; Kriedberg, Ali; Kuan, Leonard; Lau, Chris; Lee, Felix; Lee, Hwahyung; Lemon, Tracy; Long, Fuhui; Mastan, Naveed; Mott, Erika; Murthy, Chantal; Ngo, Kiet; Olson, Eric; Reding, Melissa; Riley, Zack; Rosen, David; Sandman, David; Shapovalova, Nadiya; Slaughterbeck, Clifford R; Sodt, Andrew; Stockdale, Graham; Szafer, Aaron; Wakeman, Wayne; Wohnoutka, Paul E; White, Steven J; Marsh, Don; Rostomily, Robert C; Ng, Lydia; Dang, Chinh; Jones, Allan; Keogh, Bart; Gittleman, Haley R; Barnholtz-Sloan, Jill S; Cimino, Patrick J; Uppin, Megha S; Keene, C Dirk; Farrokhi, Farrokh R; Lathia, Justin D; Berens, Michael E; Iavarone, Antonio; Bernard, Amy; Lein, Ed; Phillips, John W; Rostad, Steven W; Cobbs, Charles; Hawrylycz, Michael J; Foltz, Greg D

    2018-05-11

    Glioblastoma is an aggressive brain tumor that carries a poor prognosis. The tumor's molecular and cellular landscapes are complex, and their relationships to histologic features routinely used for diagnosis are unclear. We present the Ivy Glioblastoma Atlas, an anatomically based transcriptional atlas of human glioblastoma that aligns individual histologic features with genomic alterations and gene expression patterns, thus assigning molecular information to the most important morphologic hallmarks of the tumor. The atlas and its clinical and genomic database are freely accessible online data resources that will serve as a valuable platform for future investigations of glioblastoma pathogenesis, diagnosis, and treatment. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  15. [Landscape classification: research progress and development trend].

    Science.gov (United States)

    Liang, Fa-Chao; Liu, Li-Ming

    2011-06-01

    Landscape classification is the basis of the researches on landscape structure, process, and function, and also, the prerequisite for landscape evaluation, planning, protection, and management, directly affecting the precision and practicability of landscape research. This paper reviewed the research progress on the landscape classification system, theory, and methodology, and summarized the key problems and deficiencies of current researches. Some major landscape classification systems, e. g. , LANMAP and MUFIC, were introduced and discussed. It was suggested that a qualitative and quantitative comprehensive classification based on the ideology of functional structure shape and on the integral consideration of landscape classification utility, landscape function, landscape structure, physiogeographical factors, and human disturbance intensity should be the major research directions in the future. The integration of mapping, 3S technology, quantitative mathematics modeling, computer artificial intelligence, and professional knowledge to enhance the precision of landscape classification would be the key issues and the development trend in the researches of landscape classification.

  16. Evolution of a Lowland Karst Landscape; A Mass-Balance Approach

    Science.gov (United States)

    Chamberlin, C.; Heffernan, J. B.; Cohen, M. J.; Quintero, C.; Pain, A.

    2016-12-01

    Karst landscapes are highly soluble, and are vulnerable to biological acid production as a major driving factor in their evolution. Big Cypress National Park (BICY) is a low-lying karst landscape in southern Florida displaying a distinctive morphology of isolated depressions likely influenced by biology. The goal of this study is to constrain timescales of landform development in BICY. This question was addressed through the construction of landscape-scale elemental budgets for both calcium and phosphorus. Precipitation and export fluxes were calculated using available chemistry and hydrology data, and stocks were calculated from a combination of existing data, field measurements, and laboratory chemical analysis. Estimates of expected mass export given no biological acid production and given an equivalent production of 100% of GPP were compared with observed rates. Current standing stocks of phosphorus are dominated by a large soil pool, and contain 500 Gg P. Inputs are largely dominated by precipitation, and 8000 years are necessary to accumulate standing stocks of phosphorus given modern fluxes. Calcium flux is vastly dominated by dissolution of the limestone bedrock, and though some calcium is retained in the soil, most is exported. Using LiDAR generated estimates of volume loss across the landscape and current export rates, an estimated 15,000 years would be necessary to create the modern landscape. Both of these estimates indicate that the BICY landscape is geologically very young. The different behaviors of these elements (calcium is largely exported, while phosphorus is largely retained) lend additional confidence to estimates of denudation rates of the landscape. These estimates can be even closer reconciled if calcium redistribution over the landscape is allowed for. This estimate is compared to the two bounding conditions for biological weathering to indicate a likely level of biological importance to landscape development in this system.

  17. Basal transcription machinery

    Indian Academy of Sciences (India)

    2007-03-29

    Mar 29, 2007 ... The holoenzyme of prokaryotic RNA polymerase consists of the core enzyme, made of two , , ' and subunits, which lacks promoter selectivity and a sigma () subunit which enables the core enzyme to initiate transcription in a promoter dependent fashion. A stress sigma factor s, in prokaryotes ...

  18. Machine Dictation and Transcription.

    Science.gov (United States)

    Harvey, Evelyn; And Others

    This instructional package contains both an instructor's manual and a student's manual for a course in machine dictation and transcription. The instructor's manual contains an overview with tips on teaching the course, letters for dictation, and a key to the letters. The student's manual contains an overview of the course and of the skills needed…

  19. Transcriptional Regulation in Haematopoiesis:

    DEFF Research Database (Denmark)

    Lauridsen, Felicia K B

    with the capacity to both self-renew and differentiate. This thesis is built upon two studies, which investigate two different aspects of the haematopoietic system; heterogeneity within the HSC compartment (presented in manuscript I), and the interplay between transcription factors controlling granulocyte/ monocyte...

  20. Efficient species-level monitoring at the landscape scale

    Science.gov (United States)

    Barry R. Noon; Larissa L. Bailey; Thomas D. Sisk; Kevin S. McKelvey

    2012-01-01

    Monitoring the population trends of multiple animal species at a landscape scale is prohibitively expensive. However, advances in survey design, statistical methods, and the ability to estimate species presence on the basis of detection­nondetection data have greatly increased the feasibility of species-level monitoring. For example, recent advances in monitoring make...

  1. Densification and state transition across the Missouri Ozarks landscape

    Science.gov (United States)

    Brice B. Hanberry; John M. Kabrick; Hong S. He

    2014-01-01

    World-wide, some biomes are densifying, or increasing in dense woody vegetation, and shifting to alternative stable states. We quantified densification and state transition between forests ecosystems in historical (ca. 1815-1850) and current (2004-2008) surveys of the Missouri Ozark Highlands, a 5-million ha landscape in southern Missouri, USA. To estimate density of...

  2. Landscape mapping MAV using single image perspective cues

    CSIR Research Space (South Africa)

    Tekane, YC

    2015-01-01

    Full Text Available in order to do mapping, our method does require a 3D model. Instead, our method first classifies the type of site the MAV is in, and the uses vision algorithms based on perspective cues to estimate the landscape location and the do mapping. We tested our...

  3. Log sampling methods and software for stand and landscape analyses.

    Science.gov (United States)

    Lisa J. Bate; Torolf R. Torgersen; Michael J. Wisdom; Edward O. Garton; Shawn C. Clabough

    2008-01-01

    We describe methods for efficient, accurate sampling of logs at landscape and stand scales to estimate density, total length, cover, volume, and weight. Our methods focus on optimizing the sampling effort by choosing an appropriate sampling method and transect length for specific forest conditions and objectives. Sampling methods include the line-intersect method and...

  4. Landscape characterization and biodiversity research

    Energy Technology Data Exchange (ETDEWEB)

    Dale, V.H. [Oak Ridge National Lab., TN (United States); Offerman, H. [Univ. of Maryland, College Park, MD (United States). Geography Dept.; Frohn, R. [Univ. of California, Santa Barbara, CA (United States); Gardner, R.H. [Appalachian Environmental Lab., Frostburg, MD (United States)

    1995-03-01

    Rapid deforestation often produces landscape-level changes in forest characteristics and structure, including area, distribution, and forest habitat types. Changes in landscape pattern through fragmentation or aggregation of natural habitats can alter patterns of abundance for single species and entire communities. Examples of single-species effects include increased predation along the forest edge, the decline in the number of species with poor dispersal mechanisms, and the spread of exotic species that have deleterious effects (e.g., gypsy moth). A decrease in the size and number of natural habitat patches increases the probability of local extirpation and loss of diversity of native species, whereas a decline in connectivity between habitat patches can negatively affect species persistence. Thus, there is empirical justification for managing entire landscapes, not just individual habitat types, in order to insure that native plant and animal diversity is maintained. A landscape is defined as an area composed of a mosaic of interacting ecosystems, or patches, with the heterogeneity among the patches significantly affecting biotic and abiotic processes in the landscape. Patches comprising a landscape are usually composed of discrete areas of relatively homogeneous environmental conditions and must be defined in terms of the organisms of interest. A large body of theoretical work in landscape ecology has provided a wealth of methods for quantifying spatial characteristics of landscapes. Recent advances in remote sensing and geographic information systems allow these methods to be applied over large areas. The objectives of this paper are to present a brief overview of common measures of landscape characteristics, to explore the new technology available for their calculation, to provide examples of their application, and to call attention to the need for collection of spatially-explicit field data.

  5. Detecting novel low-abundant transcripts in Drosophila

    DEFF Research Database (Denmark)

    Lee, Sanggyu; Bao, Jingyue; Zhou, Guolin

    2005-01-01

    Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244......,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue. From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55% of the 40,823 unique SAGE tags are novel without matches in currently known Drosophila transcripts...... in the Drosophila genome. Our study reveals the presence of a significant number of novel low-abundant transcripts in Drosophila, and highlights the need to isolate these novel low-abundant transcripts for further biological studies. Udgivelsesdato: 2005-Jun...

  6. Landscape services as boundary concept in landscape governance: Building social capital in collaboration and adapting the landscape

    NARCIS (Netherlands)

    Westerink, Judith; Opdam, Paul; Rooij, Van Sabine; Steingröver, Eveliene

    2017-01-01

    The landscape services concept provides a lens to study relations within the social-ecological networks that landscapes are, and to identify stakeholders as either providers or beneficiaries. However, landscape services can also be used as a boundary concept in collaborative landscape governance. We

  7. Multifunctional landscape practice and accessibility in manorial landscapes

    DEFF Research Database (Denmark)

    Brandt, Jesper; Svenningsen, Stig Roar; Christensen, Andreas Aagaard

    . However classical manorial estates seems to represent an opposite trend. Allthough working at the same market conditions as other large specialized holdings developed through the process of structural rationalization, they have often maintained and elaborated a land use strategy based on a multifunctional...... use of the potential ecosystem services present within their domain. The targeted combination of agriculture, forestry, hunting rents, rental housing, and a variety of recreational activities influences makes a certain public accessibility to an integrated part of this strategy, diverging from...... the multifunctional landscape strategy supporting a certain public access. A study of this thesis is presented based on an analysis of multifunctionality, landscape development and accessibility in Danish Manorial landscapes and eventual linkages between their multifunctional landscape strategy, their history...

  8. Beyond Landscape MacArchitecture: new languages, new landscapes

    Directory of Open Access Journals (Sweden)

    Simon Rackham

    1996-03-01

    Full Text Available The sine qua non of landscape architecture is respect for the genius loci, but even in the landscape, as in architecture and society more generally, a process of cultural homogenisation has been taking place. Against this process, a resurgence of interest in minority languages in Europe can be seen as an assertion of pride, and a desire to preserve difference. In Scotland, landscape architects are attempting to reinterpret Scottish and northern European urban design influences and materials: in effect to develop a new regional dialect for the new landscapes. Rooted in sound design principles and materials which respond to and reflect the climate, way of life and traditions of the place, design languages can communicate effectively about cultural values and differences.

  9. Decision making on fitness landscapes

    Science.gov (United States)

    Arthur, R.; Sibani, P.

    2017-04-01

    We discuss fitness landscapes and how they can be modified to account for co-evolution. We are interested in using the landscape as a way to model rational decision making in a toy economic system. We develop a model very similar to the Tangled Nature Model of Christensen et al. that we call the Tangled Decision Model. This is a natural setting for our discussion of co-evolutionary fitness landscapes. We use a Monte Carlo step to simulate decision making and investigate two different decision making procedures.

  10. Studying landscape architecture in Denmark

    DEFF Research Database (Denmark)

    Braae, Ellen Marie; Hare, Richard Andrew

    2010-01-01

    s demanded large numbers of landscape architects. Today landscape architecture education addresses current challenges of climate change and the need for sustainable development where an understanding of natural systems is seen as essential for future urbanisation processes in evermore innovative......Landscape architecture is a well-established profession in Denmark. From the early 20th Century the profession developed steadily. However, it was 1960 before a separate education was established. This proved timely as the immense physical development of the Danish welfare state of the 1970s and 80...

  11. Decision Making on Fitness Landscapes

    DEFF Research Database (Denmark)

    Arthur, Rudy; Sibani, Paolo

    2017-01-01

    We discuss fitness landscapes and how they can be modified to account for co-evolution. We are interested in using the landscape as a way to model rational decision making in a toy economic system. We develop a model very similar to the Tangled Nature Model of Christensen et. al. that we call...... the Tangled Decision Model. This is a natural setting for our discussion of co-evolutionary fitness landscapes. We use a Monte Carlo step to simulate decision making and investigate two different decision making procedures....

  12. Connecting Brabant's cover sand landscapes through landscape history

    Science.gov (United States)

    Heskes, Erik; van den Ancker, Hanneke; Jungerius, Pieter Dirk; Harthoorn, Jaap; Maes, Bert; Leenders, Karel; de Jongh, Piet; Kluiving, Sjoerd; van den Oetelaar, Ger

    2015-04-01

    Noord-Brabant has the largest variety of cover sand landscapes in The Netherlands, and probably in Western Europe. During the Last Ice Age the area was not covered by land ice and a polar desert developed in which sand dunes buried the existing river landscapes. Some of these polar dune landscapes experienced a geomorphological and soil development that remained virtually untouched up to the present day, such as the low parabolic dunes of the Strabrechtse Heide or the later and higher dunes of the Oisterwijkse Vennen. As Noord-Brabant lies on the fringe of a tectonic basin, the thickness of cover sand deposits in the Centrale Slenk, part of a rift through Europe, amounts up to 20 metres. Cover sand deposits along the fault lines cause the special phenomenon of 'wijst' to develop, in which the higher grounds are wetter than the boarding lower grounds. Since 4000 BC humans settled in these cover sand landscapes and made use of its small-scale variety. An example are the prehistoric finds on the flanks and the historic towns on top of the 'donken' in northwest Noord-Brabant, where the cover sand landscapes are buried by river and marine deposits and only the peaks of the dunes protrude as donken. Or the church of Handel that is built beside a 'wijst' source and a site of pilgrimage since living memory. Or the 'essen' and plaggen agriculture that developed along the stream valleys of Noord-Brabant from 1300 AD onwards, giving rise to geomorphological features as 'randwallen' and plaggen soils of more than a metre thickness. Each region of Brabant each has its own approach in attracting tourists and has not yet used this common landscape history to connect, manage and promote their territories. We propose a landscape-historical approach to develop a national or European Geopark Brabants' cover sand landscapes, in which each region focuses on a specific part of the landscape history of Brabant, that stretches from the Late Weichselian polar desert when the dune

  13. The influence of landscape characteristics and home-range size on the quantification of landscape-genetics relationships

    Science.gov (United States)

    Tabitha A. Graves; Tzeidle N. Wasserman; Milton Cezar Ribeiro; Erin L. Landguth; Stephen F. Spear; Niko Balkenhol; Colleen B. Higgins; Marie-Josee Fortin; Samuel A. Cushman; Lisette P. Waits

    2012-01-01

    A common approach used to estimate landscape resistance involves comparing correlations of ecological and genetic distances calculated among individuals of a species. However, the location of sampled individuals may contain some degree of spatial uncertainty due to the natural variation of animals moving through their home range ormeasurement error in plant or animal...

  14. Dynamic analysis of stochastic transcription cycles.

    Directory of Open Access Journals (Sweden)

    Claire V Harper

    2011-04-01

    Full Text Available In individual mammalian cells the expression of some genes such as prolactin is highly variable over time and has been suggested to occur in stochastic pulses. To investigate the origins of this behavior and to understand its functional relevance, we quantitatively analyzed this variability using new mathematical tools that allowed us to reconstruct dynamic transcription rates of different reporter genes controlled by identical promoters in the same living cell. Quantitative microscopic analysis of two reporter genes, firefly luciferase and destabilized EGFP, was used to analyze the dynamics of prolactin promoter-directed gene expression in living individual clonal and primary pituitary cells over periods of up to 25 h. We quantified the time-dependence and cyclicity of the transcription pulses and estimated the length and variation of active and inactive transcription phases. We showed an average cycle period of approximately 11 h and demonstrated that while the measured time distribution of active phases agreed with commonly accepted models of transcription, the inactive phases were differently distributed and showed strong memory, with a refractory period of transcriptional inactivation close to 3 h. Cycles in transcription occurred at two distinct prolactin-promoter controlled reporter genes in the same individual clonal or primary cells. However, the timing of the cycles was independent and out-of-phase. For the first time, we have analyzed transcription dynamics from two equivalent loci in real-time in single cells. In unstimulated conditions, cells showed independent transcription dynamics at each locus. A key result from these analyses was the evidence for a minimum refractory period in the inactive-phase of transcription. The response to acute signals and the result of manipulation of histone acetylation was consistent with the hypothesis that this refractory period corresponded to a phase of chromatin remodeling which significantly

  15. LANDSCAPE PLANNING IN UKRAINE: THE FIRST LANDSCAPE-PLANNING PROGRAM

    Directory of Open Access Journals (Sweden)

    Leonid Rudenko

    2013-01-01

    Full Text Available The paper presents the results of the first, in Ukraine; project on landscape planning widely accepted in European countries. Under the project implemented in 2010–2013, a landscape-planning program has been developed for the Cherkassy oblast. This is the first document of this kind in Ukraine. The program is mainly based on the experience of the German and Russian schools of landscape planning and on research and assessment conducted by the authors, which allowed identifying approaches to landscape planning, principles of the national policy, and characteristics and potential of environmentally friendly planning in Ukraine. The paper discusses the main phases of the work on the development of the landscape program for the oblast. It also identifies the main stages and key concepts and principles of landscape planning. The paper presents the results of integrated research on the identification and classification of conflicts in land use and the integral concept of the developmental goals for the oblast. The results can be the foundation for adopting management decisions and development of action plans for the lower hierarchal branches.

  16. Energy landscapes in a crowded world

    NARCIS (Netherlands)

    Pasqualetti, Martin; Stremke, Sven

    2018-01-01

    One of the main drivers of landscape transformation has been our demand for energy. We refer to the results of such transformations as "energy landscapes". This paper examines the definition of energy landscapes within a conceptual framework, proposes a classification of energy landscapes, and

  17. Perspectives on landscape identity, a conceptual challenge

    NARCIS (Netherlands)

    Stobbelaar, D.J.; Pedroli, B.

    2011-01-01

    The concept of landscape identity is often referred to in landscape policy and planning. A clear definition of the concept is lacking however. This is problematic because the term ‘landscape identity’ can have many different meanings and thus easily lead to confusion. We define landscape identity as

  18. Bipolarity and Ambivalence in Landscape Architecture

    NARCIS (Netherlands)

    Koh, J.

    2010-01-01

    Our discipline of landscape architecture contains bipolarity, not only in terms of landscape and architecture but also because the idea of landscape is both aesthetic and scientific. Furthermore, within landscape architecture there is a gap between design (as implied by architecture) and planning

  19. Flowscapes : Designing infrastructure as landscape

    NARCIS (Netherlands)

    Nijhuis, S.; Jauslin, D.T.; Van der Hoeven, F.D.

    2015-01-01

    Social, cultural and technological developments of our society are demanding a fundamental review of the planning and design of its landscapes and infrastructures, in particular in relation to environmental issues and sustainability. Transportation, green and water infrastructures are important

  20. Qualified Health Plan (QHP) Landscape

    Data.gov (United States)

    U.S. Department of Health & Human Services — QHP Landscape Files present basic information about certified Qualified Health Plans and Stand-alone Dental Plans for individuals-families and small businesses...

  1. The evolving landscape of banking

    NARCIS (Netherlands)

    Boot, A.W.A.; Marinč, M.

    2008-01-01

    The structure of the financial services industry is in flux. Liberalization, deregulation, and advances in information technology have changed the financial landscape dramatically. Interbank competition has heated up and banks face increasing competition from nonbanking financial institutions and

  2. Greenhouse warming and landscape care

    Science.gov (United States)

    Kevin T. Smith

    2009-01-01

    Climate change is one of the few truly planetary processes that influence the assessments and actions of governments and of everyday citizens. Principles and practices of ecological landscaping fit well with concern about hte effects of climate change.

  3. Distributed denitrification in a northeastern agricultural landscape

    Science.gov (United States)

    Anderson, T. R.; Groffman, P. M.; Walter, M. T.

    2011-12-01

    Denitrification may be an important sink of anthropogenic nitrogen (N) in eastern US watersheds. Denitrification occurs primarily under anaerobic conditions by heterotrophic microbes, and is therefore expected to be vigorous in wet soils containing large amounts of organic carbon. Actual rates of denitrification, however, have been difficult to quantify, and remain one of the critical unresolved N processes at the landscape scale. We measured denitrification rates in situ along hydrologic flow paths and across gradients of hydroperiodicities, i.e., frequencies and durations of saturated conditions, at Cornell University's Teaching & Research Center in Harford, NY (an active dairy farm). Denitrification rates were measured monthly using the 15N push-pull method from 14 mini-piezometers arrayed along a gradient of hydroperiodicity as indicated by a soil topographic index (STI). Measured rates of denitrification were spatially variable across sites and ranged from undetectable to over 4500 μg N/kg soil/day with a mean of 572 ± 167 μg N/kg soil/day. Mean rates of denitrification increased with STI, which ranged from 8.7 to 23.0 across our mini-piezometer sites. This relationship was used to estimate denitrification rates across the landscape and resolve a missing piece of the N budget for the farm. Only 14% of the farm fell into areas of STI greater than 8.7; however, denitrification in these areas account for more than 60% of the missing N balance for the entire landscape. Improved understanding of the distribution and magnitudes of denitrification in agricultural landscapes has good potential to facilitate new, novel, and better management practices for controlling N loading to streams and rivers. Indeed, the very areas that appear to have a propensity to harbor denitrification, i.e., areas prone to be wet, are often artificially drained as part of standard agricultural practices which reduces the frequency that these areas are likely to be anaerobic and

  4. Aeolian Landscape Change in West Greenland

    Science.gov (United States)

    Heindel, Ruth Chaves

    In the Arctic, aeolian processes can be important drivers of landscape change. Soil deflation, the removal of fine-grained sediment by wind, is one aeolian process that has had a profound impact in the Arctic. While soil deflation has been well studied in Iceland, our understanding of aeolian processes across the rest of the Arctic remains limited. Kangerlussuaq, West Greenland, provides an opportunity to study the mechanisms and impacts of soil deflation without direct anthropogenic influence. In Kangerlussuaq, strong katabatic winds have resulted in distinct erosional landforms, here referred to as deflation patches, that are largely devoid of vascular plants and are dominated by biological soil crusts. This dissertation considers the geomorphic and ecological impacts of soil deflation through an interdisciplinary framework. I show that deflation patches are a critical component of the Kangerlussuaq ecosystem, accounting for 22% of the terrestrial landscape and impacting vegetation dynamics by providing habitat for graminoid, herbaceous, and lichen species. Deflation patches formed roughly 230-800 years ago, during a period of cold, dry, and windy climate conditions. Deflation patches expand across the landscape when the active margin, or scarp, becomes undercut and collapses. I estimate that rates of patch expansion are roughly 2.5 cm yr-1, and that geomorphic change can be detected even over the short time period of two years. I suggest that an erosional threshold exists because climate conditions required for initial deflation-patch formation are harsher than those required for continued patch expansion. The future trajectory of deflation patches depends on the role of the biological soil crust as either a successional facilitator or a long-term landscape cover, as well as future climate conditions. While the biological soil crusts slightly enrich soil fertility over time, they decrease soil moisture and create an impenetrable soil surface, which may inhibit

  5. Titan Polar Landscape Evolution

    Science.gov (United States)

    Moore, Jeffrey M.

    2016-01-01

    With the ongoing Cassini-era observations and studies of Titan it is clear that the intensity and distribution of surface processes (particularly fluvial erosion by methane and Aeolian transport) has changed through time. Currently however, alternate hypotheses substantially differ among specific scenarios with respect to the effects of atmospheric evolution, seasonal changes, and endogenic processes. We have studied the evolution of Titan's polar region through a combination of analysis of imaging, elevation data, and geomorphic mapping, spatially explicit simulations of landform evolution, and quantitative comparison of the simulated landscapes with corresponding Titan morphology. We have quantitatively evaluated alternate scenarios for the landform evolution of Titan's polar terrain. The investigations have been guided by recent geomorphic mapping and topographic characterization of the polar regions that are used to frame hypotheses of process interactions, which have been evaluated using simulation modeling. Topographic information about Titan's polar region is be based on SAR-Topography and altimetry archived on PDS, SAR-based stereo radar-grammetry, radar-sounding lake depth measurements, and superposition relationships between geomorphologic map units, which we will use to create a generalized topographic map.

  6. PSEUDO-CODEWORD LANDSCAPE

    Energy Technology Data Exchange (ETDEWEB)

    CHERTKOV, MICHAEL [Los Alamos National Laboratory; STEPANOV, MIKHAIL [Los Alamos National Laboratory

    2007-01-10

    The authors discuss performance of Low-Density-Parity-Check (LDPC) codes decoded by Linear Programming (LP) decoding at moderate and large Signal-to-Noise-Ratios (SNR). Frame-Error-Rate (FER) dependence on SNR and the noise space landscape of the coding/decoding scheme are analyzed by a combination of the previously introduced instanton/pseudo-codeword-search method and a new 'dendro' trick. To reduce complexity of the LP decoding for a code with high-degree checks, {ge} 5, they introduce its dendro-LDPC counterpart, that is the code performing identifically to the original one under Maximum-A-Posteriori (MAP) decoding but having reduced (down to three) check connectivity degree. Analyzing number of popular LDPC codes and their dendro versions performing over the Additive-White-Gaussian-Noise (AWGN) channel, they observed two qualitatively different regimes: (i) error-floor sets early, at relatively low SNR, and (ii) FER decays with SNR increase faster at moderate SNR than at the largest SNR. They explain these regimes in terms of the pseudo-codeword spectra of the codes.

  7. Saddleworth, Responding to a Landscape

    OpenAIRE

    Murray, Matthew

    2017-01-01

    Matthew Murray's Landscape publication Saddleworth, Responding To A Landscape. Forward by Martin Barnes Senior Curator of Photographs at The Victoria and Albert Museum, London, Artist Richard Billingham and Maartje van den Heuvel Curator Photography and Media Culture -Leiden Institute. \\ud \\ud ‘Every trip I have taken to Saddleworth Moor over four years has encapsulated each season, weather and cloud pattern, rain, sunshine, snow, early morning clear skies and the sense of the bitter cold of ...

  8. The Industrial Engineering publishing landscape

    OpenAIRE

    Claasen, Schalk

    2012-01-01

    Looking at the Industrial Engineering publishing landscape through the window of Google Search, an interesting panorama unfolds. The view that I took is actually just a peek and therefore my description of what I saw is not meant to be comprehensive. The African landscape is empty except for the South African Journal of Industrial Engineering (SAJIE). This is an extraordinary situation if compared to the South American continent where there are Industrial Engineering journals in at least ...

  9. The landscapes of tourism space

    OpenAIRE

    Włodarczyk, Bogdan

    2009-01-01

    The author attempts to define the term ‘tourism landscape’. It is treated as an important attribute of tourism space therefore, apart from its definition, the author presents its characteristic features and various types of such spaces with differing tourism landscapes. The landscapes of tourism space are treated not only as tourism assets or attractions, but also as the consequences of tourism activity on the natural and cultural environment.

  10. DNA Topoisomerases in Transcription

    DEFF Research Database (Denmark)

    Rødgaard, Morten Terpager

    2015-01-01

    This Ph.D. thesis summarizes the main results of my studies on the interplay between DNA topoisomerases and transcription. The work was performed from 2011 to 2015 at Aarhus University in the Laboratory of Genome Research, and was supervised by associate professor Anni H. Andersen. Most of the ex......This Ph.D. thesis summarizes the main results of my studies on the interplay between DNA topoisomerases and transcription. The work was performed from 2011 to 2015 at Aarhus University in the Laboratory of Genome Research, and was supervised by associate professor Anni H. Andersen. Most...... topoisomerase-DNA cleavage complex. The second study is an investigation of how topoisomerases influence gene regulation by keeping the genome in an optimal topological state....

  11. Deciphering Transcriptional Regulation

    DEFF Research Database (Denmark)

    Valen, Eivind

    The myriad of cells in the human body are all made from the same blueprint: the human genome. At the heart of this diversity lies the concept of gene regulation, the process in which it is decided which genes are used where and when. Genes do not function as on/off buttons, but more like a volume...... mostly near the start of the gene known as the promoter. This region contains patterns scattered in the DNA that the TFs can recognize and bind to. Such binding can prompt the assembly of the pre-initiation complex which ultimately leads to transcription of the gene. In order to achieve the regulation...... on what characterizes a hippocampus promoter. Pairing CAGE with TF binding site prediction we identi¿ed a likely key regulator of hippocampus. Finally, we developed a method for CAGE exploration. While the DeepCAGE library characterized a full 1.4 million transcription initiation events it did not capture...

  12. A human transcription factor in search mode.

    Science.gov (United States)

    Hauser, Kevin; Essuman, Bernard; He, Yiqing; Coutsias, Evangelos; Garcia-Diaz, Miguel; Simmerling, Carlos

    2016-01-08

    Transcription factors (TF) can change shape to bind and recognize DNA, shifting the energy landscape from a weak binding, rapid search mode to a higher affinity recognition mode. However, the mechanism(s) driving this conformational change remains unresolved and in most cases high-resolution structures of the non-specific complexes are unavailable. Here, we investigate the conformational switch of the human mitochondrial transcription termination factor MTERF1, which has a modular, superhelical topology complementary to DNA. Our goal was to characterize the details of the non-specific search mode to complement the crystal structure of the specific binding complex, providing a basis for understanding the recognition mechanism. In the specific complex, MTERF1 binds a significantly distorted and unwound DNA structure, exhibiting a protein conformation incompatible with binding to B-form DNA. In contrast, our simulations of apo MTERF1 revealed significant flexibility, sampling structures with superhelical pitch and radius complementary to the major groove of B-DNA. Docking these structures to B-DNA followed by unrestrained MD simulations led to a stable complex in which MTERF1 was observed to undergo spontaneous diffusion on the DNA. Overall, the data support an MTERF1-DNA binding and recognition mechanism driven by intrinsic dynamics of the MTERF1 superhelical topology. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Editorial: Entropy in Landscape Ecology

    Directory of Open Access Journals (Sweden)

    Samuel A. Cushman

    2018-04-01

    Full Text Available Entropy and the second law of thermodynamics are the central organizing principles of nature, but the ideas and implications of the second law are poorly developed in landscape ecology. The purpose of this Special Issue “Entropy in Landscape Ecology” in Entropy is to bring together current research on applications of thermodynamics in landscape ecology, to consolidate current knowledge and identify key areas for future research. The special issue contains six articles, which cover a broad range of topics including relationships between entropy and evolution, connections between fractal geometry and entropy, new approaches to calculate configurational entropy of landscapes, example analyses of computing entropy of landscapes, and using entropy in the context of optimal landscape planning. Collectively these papers provide a broad range of contributions to the nascent field of ecological thermodynamics. Formalizing the connections between entropy and ecology are in a very early stage, and that this special issue contains papers that address several centrally important ideas, and provides seminal work that will be a foundation for the future development of ecological and evolutionary thermodynamics.

  14. Landscape Visualisation on the Internet

    Science.gov (United States)

    Imhof, M. P.; Cox, M. T.; Harvey, D. W.; Heemskerk, G. E.; Pettit, C. J.

    2012-07-01

    The Victorian Resources Online (VRO) website (http://www.dpi.vic.gov.au/vro) is the principal means for accessing landscapebased information in Victoria. In this paper we introduce a range of online landscape visualisations that have been developed to enhance existing static web content around the nature and distribution of Victoria's landforms and soils as well as associated processes. Flash is used to develop online visualisations that include interactive landscape panoramas, animations of soil and landscape processes and videos of experts explaining features in the field as well as landscape "flyovers". The use of interactive visualisations adds rich information multimedia content to otherwise static pages and offers the potential to improve user's appreciation and understanding of soil and landscapes. Visualisation is becoming a key component of knowledge management activities associated with VRO - proving useful for both "knowledge capture" (from subject matter specialists) and "knowledge transfer" to a diverse user base. A range of useful visualisation products have been made available online, with varying degrees of interactivity and suited to a variety of users. The use of video files, animation and interactive visualisations is adding rich information content to otherwise static web pages. These information products offer new possibilities to enhance learning of landscapes and the effectiveness of these will be tested as the next phase of development.

  15. Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function.

    Directory of Open Access Journals (Sweden)

    Giulio Quarta

    Full Text Available Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way in which sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we compute energy landscapes, which describe the accessible secondary structures for a range of sequence lengths, to analyze the transcriptional process as a given sequence elongates to full length. In line with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: low-barrier landscape with an ensemble of different conformations in equilibrium before encountering a substrate; barrier-free landscape in which a direct, dominant "downhill" pathway to the minimum free energy structure is apparent; and a barrier-dominated landscape with two isolated conformational states, each associated with a different biological function. Sharing concepts with the "new view" of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved in various riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design.

  16. Transcriptional networks controlling adipocyte differentiation

    DEFF Research Database (Denmark)

    Siersbæk, R; Mandrup, Susanne

    2011-01-01

    " of the transcription factor networks operating at specific time points during adipogenesis. Using such global "snapshots," we have demonstrated that dramatic remodeling of the chromatin template occurs within the first few hours following adipogenic stimulation and that many of the early transcription factors bind...... in a cooperative fashion to transcription factor hotspots. Such hotspots are likely to represent key chromatin nodes, where many adipogenic signaling pathways converge to drive the adipogenic transcriptional reprogramming....

  17. The Evolution of Bony Vertebrate Enhancers at Odds with Their Coding Sequence Landscape.

    Science.gov (United States)

    Yousaf, Aisha; Sohail Raza, Muhammad; Ali Abbasi, Amir

    2015-08-06

    Enhancers lie at the heart of transcriptional and developmental gene regulation. Therefore, changes in enhancer sequences usually disrupt the target gene expression and result in disease phenotypes. Despite the well-established role of enhancers in development and disease, evolutionary sequence studies are lacking. The current study attempts to unravel the puzzle of bony vertebrates' conserved noncoding elements (CNE) enhancer evolution. Bayesian phylogenetics of enhancer sequences spotlights promising interordinal relationships among placental mammals, proposing a closer relationship between humans and laurasiatherians while placing rodents at the basal position. Clock-based estimates of enhancer evolution provided a dynamic picture of interspecific rate changes across the bony vertebrate lineage. Moreover, coelacanth in the study augmented our appreciation of the vertebrate cis-regulatory evolution during water-land transition. Intriguingly, we observed a pronounced upsurge in enhancer evolution in land-dwelling vertebrates. These novel findings triggered us to further investigate the evolutionary trend of coding as well as CNE nonenhancer repertoires, to highlight the relative evolutionary dynamics of diverse genomic landscapes. Surprisingly, the evolutionary rates of enhancer sequences were clearly at odds with those of the coding and the CNE nonenhancer sequences during vertebrate adaptation to land, with land vertebrates exhibiting significantly reduced rates of coding sequence evolution in comparison to their fast evolving regulatory landscape. The observed variation in tetrapod cis-regulatory elements caused the fine-tuning of associated gene regulatory networks. Therefore, the increased evolutionary rate of tetrapods' enhancer sequences might be responsible for the variation in developmental regulatory circuits during the process of vertebrate adaptation to land. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for

  18. A meta-analysis of crop pest and natural enemy response to landscape complexity.

    Science.gov (United States)

    Chaplin-Kramer, Rebecca; O'Rourke, Megan E; Blitzer, Eleanor J; Kremen, Claire

    2011-09-01

    Many studies in recent years have investigated the relationship between landscape complexity and pests, natural enemies and/or pest control. However, no quantitative synthesis of this literature beyond simple vote-count methods yet exists. We conducted a meta-analysis of 46 landscape-level studies, and found that natural enemies have a strong positive response to landscape complexity. Generalist enemies show consistent positive responses to landscape complexity across all scales measured, while specialist enemies respond more strongly to landscape complexity at smaller scales. Generalist enemy response to natural habitat also tends to occur at larger spatial scales than for specialist enemies, suggesting that land management strategies to enhance natural pest control should differ depending on whether the dominant enemies are generalists or specialists. The positive response of natural enemies does not necessarily translate into pest control, since pest abundances show no significant response to landscape complexity. Very few landscape-scale studies have estimated enemy impact on pest populations, however, limiting our understanding of the effects of landscape on pest control. We suggest focusing future research efforts on measuring population dynamics rather than static counts to better characterise the relationship between landscape complexity and pest control services from natural enemies. © 2011 Blackwell Publishing Ltd/CNRS.

  19. The shifting beverage landscape.

    Science.gov (United States)

    Storey, Maureen

    2010-04-26

    STOREY, M.L. The shifting beverage landscape. PHYSIOL BEHAV, 2010. - Simultaneous lifestyle changes have occurred in the last few decades, creating an imbalance in energy intake and energy expenditure that has led to overweight and obesity. Trends in the food supply show that total daily calories available per capita increased 28% since 1970. Total energy intake among men and women has also increased dramatically since that time. Some have suggested that intake of beverages has had a disproportional impact on obesity. Data collected by the Beverage Marketing Corporation between 1988-2008 demonstrate that, in reality, fewer calories per ounce are being produced by the beverage industry. Moreover, data from the National Cancer Institute show that soft drink intake represents 5.5% of daily calories. Data from NHANES 1999-2003 vs. 2003-06 may demonstrate a shift in beverage consumption for age/gender groups, ages 6 to>60years. The beverages provided in schools have significantly changed since 2006 when the beverage industry implemented School Beverage Guidelines. This voluntary action has removed full-calorie soft drinks from participating schools across the country. This shift to lower-calorie and smaller-portion beverages in school has led to a significant decrease in total beverage calories in schools. These data support the concept that to prevent and treat obesity, public health efforts should focus on energy balance and that a narrow focus on sweetened beverages is unlikely to have any meaningful impact on this complex problem. Copyright 2010 Elsevier Inc. All rights reserved.

  20. Monotonicity of fitness landscapes and mutation rate control.

    Science.gov (United States)

    Belavkin, Roman V; Channon, Alastair; Aston, Elizabeth; Aston, John; Krašovec, Rok; Knight, Christopher G

    2016-12-01

    A common view in evolutionary biology is that mutation rates are minimised. However, studies in combinatorial optimisation and search have shown a clear advantage of using variable mutation rates as a control parameter to optimise the performance of evolutionary algorithms. Much biological theory in this area is based on Ronald Fisher's work, who used Euclidean geometry to study the relation between mutation size and expected fitness of the offspring in infinite phenotypic spaces. Here we reconsider this theory based on the alternative geometry of discrete and finite spaces of DNA sequences. First, we consider the geometric case of fitness being isomorphic to distance from an optimum, and show how problems of optimal mutation rate control can be solved exactly or approximately depending on additional constraints of the problem. Then we consider the general case of fitness communicating only partial information about the distance. We define weak monotonicity of fitness landscapes and prove that this property holds in all landscapes that are continuous and open at the optimum. This theoretical result motivates our hypothesis that optimal mutation rate functions in such landscapes will increase when fitness decreases in some neighbourhood of an optimum, resembling the control functions derived in the geometric case. We test this hypothesis experimentally by analysing approximately optimal mutation rate control functions in 115 complete landscapes of binding scores between DNA sequences and transcription factors. Our findings support the hypothesis and find that the increase of mutation rate is more rapid in landscapes that are less monotonic (more rugged). We discuss the relevance of these findings to living organisms.

  1. Preliminary estimating the contemporary sedimentation trend in dry valley bottoms of first-order catchments of different landscape zones of the Russian Plain using the 137Cs as a chronomarker

    Science.gov (United States)

    Sharifullin, A.; Gusarov, A.; Gafurov, A.; Essuman-Quainoo, B.

    2018-01-01

    A general trend of erosion processes over the last 50-60 years can be estimated by dating sediments washed off from arable lands and accumulated in the first-order dry valleys bottoms. Three small (first-order) catchments were chosen as objects of the study. They are located, respectively, in the southern part of the taiga zone, the zone of temperate broad-leaf forests and the forest-steppe zone of the Russian Plain. To date the sediments accumulated in the bottoms the radioactive caesium-137 (137Cs) of global (since 1954) and Chernobyl origin (1986) had been used as a chronomarker. The average (for all the catchments) sedimentation rates during the global 137Cs fallout period (1963(1954)-1986) are at least 0.88-2.71 cm per year.For the period that has passed since the Chernobyl accident (1986-2015(2016)) the average rates were 0.15-1.07 cm per year. The greatest reduction in the sedimentation rates is observed in the subzone of the southern taiga, the lowest one is in the forest-steppe zone of the Russian Plain. The main reason for such significant reduction in the rates of sedimentation of the soil erosion products in the dry valley bottoms was a reduction of surface runoff within the catchments during a snowmelt period, as well as crop-rotation changes there.

  2. Can porosity affect the hyperspectral signature of sandy landscapes?

    Science.gov (United States)

    Baranoski, Gladimir V. G.; Kimmel, Bradley W.

    2017-10-01

    Porosity is a fundamental property of sand deposits found in a wide range of landscapes, from beaches to dune fields. As a primary determinant of the density and permeability of sediments, it represents a central element in geophysical studies involving basin modeling and coastal erosion as well as geoaccoustics and geochemical investigations aiming at the understanding of sediment transport and water diffusion properties of sandy landscapes. These applications highlight the importance of obtaining reliable porosity estimations, which remains an elusive task, notably through remote sensing. In this work, we aim to contribute to the strengthening of the knowledge basis required for the development of new technologies for the remote monitoring of environmentally-triggered changes in sandy landscapes. Accordingly, we employ an in silico investigation approach to assess the effects of porosity variations on the reflectance of sandy landscapes in the visible and near-infrared spectral domains. More specifically, we perform predictive computer simulations using SPLITS, a hyperspectral light transport model for particulate materials that takes into account actual sand characterization data. To the best of our knowledge, this work represents the first comprehensive investigation relating porosity to the reflectance responses of sandy landscapes. Our findings indicate that the putative dependence of these responses on porosity may be considerably less pronounced than its dependence on other properties such as grain size and shape. Hence, future initiatives for the remote quantification of porosity will likely require reflectance sensors with a high degree of sensitivity.

  3. Epigenetic Inheritance Across the Landscape

    Directory of Open Access Journals (Sweden)

    Amy Vaughn Whipple

    2016-10-01

    Full Text Available The study of epigenomic variation at the landscape-level in plants may add important insight to studies of adaptive variation. A major goal of landscape genomic studies is to identify genomic regions contributing to adaptive variation across the landscape. Heritable variation in epigenetic marks, resulting in transgenerational plasticity, can influence fitness-related traits. Epigenetic marks are influenced by the genome, the environment, and their interaction, and can be inherited independently of the genome. Thus, epigenomic variation likely influences the heritability of many adaptive traits, but the extent of this influence remains largely unknown. Here we summarize the relevance of epigenetic inheritance to ecological and evolutionary processes, and review the literature on landscape-level patterns of epigenetic variation. Landscape-level patterns of epigenomic variation in plants generally show greater levels of isolation by distance and isolation by environment then is found for the genome, but the causes of these patterns are not yet clear. Linkage between the environment and epigenomic variation has been clearly shown within a single generation, but demonstrating transgenerational inheritance requires more complex breeding and/or experimental designs. Transgenerational epigenetic variation may alter the interpretation of landscape genomic studies that rely upon phenotypic analyses, but should have less influence on landscape genomic approaches that rely upon outlier analyses or genome-environment associations. We suggest that multi-generation common garden experiments conducted across multiple environments will allow researchers to understand which parts of the epigenome are inherited, as well as to parse out the relative contribution of heritable epigenetic variation to the phenotype.

  4. Epigenetic Inheritance across the Landscape.

    Science.gov (United States)

    Whipple, Amy V; Holeski, Liza M

    2016-01-01

    The study of epigenomic variation at the landscape-level in plants may add important insight to studies of adaptive variation. A major goal of landscape genomic studies is to identify genomic regions contributing to adaptive variation across the landscape. Heritable variation in epigenetic marks, resulting in transgenerational plasticity, can influence fitness-related traits. Epigenetic marks are influenced by the genome, the environment, and their interaction, and can be inherited independently of the genome. Thus, epigenomic variation likely influences the heritability of many adaptive traits, but the extent of this influence remains largely unknown. Here, we summarize the relevance of epigenetic inheritance to ecological and evolutionary processes, and review the literature on landscape-level patterns of epigenetic variation. Landscape-level patterns of epigenomic variation in plants generally show greater levels of isolation by distance and isolation by environment then is found for the genome, but the causes of these patterns are not yet clear. Linkage between the environment and epigenomic variation has been clearly shown within a single generation, but demonstrating transgenerational inheritance requires more complex breeding and/or experimental designs. Transgenerational epigenetic variation may alter the interpretation of landscape genomic studies that rely upon phenotypic analyses, but should have less influence on landscape genomic approaches that rely upon outlier analyses or genome-environment associations. We suggest that multi-generation common garden experiments conducted across multiple environments will allow researchers to understand which parts of the epigenome are inherited, as well as to parse out the relative contribution of heritable epigenetic variation to the phenotype.

  5. A Genome-Scale Resource for the Functional Characterization of Arabidopsis Transcription Factors

    Directory of Open Access Journals (Sweden)

    Jose L. Pruneda-Paz

    2014-07-01

    Full Text Available Extensive transcriptional networks play major roles in cellular and organismal functions. Transcript levels are in part determined by the combinatorial and overlapping functions of multiple transcription factors (TFs bound to gene promoters. Thus, TF-promoter interactions provide the basic molecular wiring of transcriptional regulatory networks. In plants, discovery of the functional roles of TFs is limited by an increased complexity of network circuitry due to a significant expansion of TF families. Here, we present the construction of a comprehensive collection of Arabidopsis TFs clones created to provide a versatile resource for uncovering TF biological functions. We leveraged this collection by implementing a high-throughput DNA binding assay and identified direct regulators of a key clock gene (CCA1 that provide molecular links between different signaling modules and the circadian clock. The resources introduced in this work will significantly contribute to a better understanding of the transcriptional regulatory landscape of plant genomes.

  6. Landscape Ecology and problems of European cultural landscapes

    DEFF Research Database (Denmark)

    Brandt, Jesper

    2011-01-01

    by practical problems of European cultural – especial agricultural – landscapes since the rise of the environmental movement. Central themes have been the consequences of technological and structural changes within European agriculture for the landscape and the development of habitats and dispersal...... Problemstellungen basieren auf multifunktionalen Nutzungskonzepten ruraler Landschaften, besonders im Hinblick auf Suburbanisierungsprozesse. Eine Anzahl untereinander vergleichbarer Projekte, mit parallelen bis ähnlichen Ausprägungen innerhalb Dänemarks und weiteerer europäischer Länder, werden exemplarisch...

  7. Navigating the Interface Between Landscape Genetics and Landscape Genomics

    Directory of Open Access Journals (Sweden)

    Andrew Storfer

    2018-03-01

    Full Text Available As next-generation sequencing data become increasingly available for non-model organisms, a shift has occurred in the focus of studies of the geographic distribution of genetic variation. Whereas landscape genetics studies primarily focus on testing the effects of landscape variables on gene flow and genetic population structure, landscape genomics studies focus on detecting candidate genes under selection that indicate possible local adaptation. Navigating the transition between landscape genomics and landscape genetics can be challenging. The number of molecular markers analyzed has shifted from what used to be a few dozen loci to thousands of loci and even full genomes. Although genome scale data can be separated into sets of neutral loci for analyses of gene flow and population structure and putative loci under selection for inference of local adaptation, there are inherent differences in the questions that are addressed in the two study frameworks. We discuss these differences and their implications for study design, marker choice and downstream analysis methods. Similar to the rapid proliferation of analysis methods in the early development of landscape genetics, new analytical methods for detection of selection in landscape genomics studies are burgeoning. We focus on genome scan methods for detection of selection, and in particular, outlier differentiation methods and genetic-environment association tests because they are the most widely used. Use of genome scan methods requires an understanding of the potential mismatches between the biology of a species and assumptions inherent in analytical methods used, which can lead to high false positive rates of detected loci under selection. Key to choosing appropriate genome scan methods is an understanding of the underlying demographic structure of study populations, and such data can be obtained using neutral loci from the generated genome-wide data or prior knowledge of a species

  8. Landscape Environmental Assessment Framework

    Energy Technology Data Exchange (ETDEWEB)

    2017-07-20

    LEAF Version 2.0 is a framework comprising of three models RUSLE2, WEPS, and AGNPS. The framework can predict row crop, crop residue, and energy crop yields at a sub-field resolutions for various combinations of soil, climate and crop management and residue harvesting practices. It estimates the loss of soil, carbon, and nutrients to the atmosphere, to the groundwater, and to runoff. It also models the overland flow of water and washed-off sediments, nutrients and other chemicals to provide estimates of sediment, nutrient, and chemical loadings to water bodies within a watershed. AGNPS model and wash-off calculations are the new additions to this version of LEAF. Development of LEAF software is supported by DOE's BETO program.

  9. Anurans in a Subarctic Tundra Landscape Near Cape Churchill, Manitoba

    Science.gov (United States)

    Reiter, M.E.; Boal, C.W.; Andersen, D.E.

    2008-01-01

    Distribution, abundance, and habitat relationships of anurans inhabiting subarctic regions are poorly understood, and anuran monitoring protocols developed for temperate regions may not be applicable across large roadless areas of northern landscapes. In addition, arctic and subarctic regions of North America are predicted to experience changes in climate and, in some areas, are experiencing habitat alteration due to high rates of herbivory by breeding and migrating waterfowl. To better understand subarctic anuran abundance, distribution, and habitat associations, we conducted anuran calling surveys in the Cape Churchill region of Wapusk National Park, Manitoba, Canada, in 2004 and 2005. We conducted surveys along ~l-km transects distributed across three landscape types (coastal tundra, interior sedge meadow-tundra, and boreal forest-tundra interface) to estimate densities and probabilities of detection of Boreal Chorus Frogs (Pseudacris maculata) and Wood Frogs (Lithobates sylvaticus). We detected a Wood Frog or Boreal Chorus Frog on 22 (87%) of 26 transects surveyed, but probability of detection varied between years and species and among landscape types. Estimated densities of both species increased from the coastal zone inland toward the boreal forest edge. Our results suggest anurans occur across all three landscape types in our study area, but that species-specific spatial patterns exist in their abundances. Considerations for both spatial and temporal variation in abundance and detection probability need to be incorporated into surveys and monitoring programs for subarctic anurans.

  10. Learning free energy landscapes using artificial neural networks.

    Science.gov (United States)

    Sidky, Hythem; Whitmer, Jonathan K

    2018-03-14

    Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to varied free energy landscapes. Further, user-specified parameters are in general non-intuitive yet significantly affect the convergence rate and accuracy of the free energy estimate. Here we propose a novel method, wherein artificial neural networks (ANNs) are used to develop an adaptive biasing potential which learns free energy landscapes. We demonstrate that this method is capable of rapidly adapting to complex free energy landscapes and is not prone to boundary or oscillation problems. The method is made robust to hyperparameters and overfitting through Bayesian regularization which penalizes network weights and auto-regulates the number of effective parameters in the network. ANN sampling represents a promising innovative approach which can resolve complex free energy landscapes in less time than conventional approaches while requiring minimal user input.

  11. Learning free energy landscapes using artificial neural networks

    Science.gov (United States)

    Sidky, Hythem; Whitmer, Jonathan K.

    2018-03-01

    Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to varied free energy landscapes. Further, user-specified parameters are in general non-intuitive yet significantly affect the convergence rate and accuracy of the free energy estimate. Here we propose a novel method, wherein artificial neural networks (ANNs) are used to develop an adaptive biasing potential which learns free energy landscapes. We demonstrate that this method is capable of rapidly adapting to complex free energy landscapes and is not prone to boundary or oscillation problems. The method is made robust to hyperparameters and overfitting through Bayesian regularization which penalizes network weights and auto-regulates the number of effective parameters in the network. ANN sampling represents a promising innovative approach which can resolve complex free energy landscapes in less time than conventional approaches while requiring minimal user input.

  12. Fitness landscapes among many options under social influence.

    Science.gov (United States)

    Caiado, Camila C S; Brock, William A; Bentley, R Alexander; O'Brien, Michael J

    2016-09-21

    Cultural learning represents a novel problem in that an optimal decision depends not only on intrinsic utility of the decision/behavior but also on transparency of costs and benefits, the degree of social versus individual learning, and the relative popularity of each possible choice in a population. In terms of a fitness-landscape function, this recursive relationship means that multiple equilibria can exist. Here we use discrete-choice theory to construct a fitness-landscape function for a bi-axial decision-making map that plots the magnitude of social influence in the learning process against the costs and payoffs of decisions. Specifically, we use econometric and statistical methods to estimate not only the fitness function but also movements along the map axes. To search for these equilibria, we employ a hill-climbing algorithm that leads to the expected values of optimal decisions, which we define as peaks on the fitness landscape. We illustrate how estimation of a measure of transparency, a measure of social influence, and the associated fitness landscape can be accomplished using panel data sets. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Urban Landscapes and Sustainable Cities

    Directory of Open Access Journals (Sweden)

    Erik Andersson

    2006-06-01

    Full Text Available Ecological research targeting sustainable urban landscapes needs to include findings and methods from many lines of ecological research, such as the link between biodiversity and ecosystem function, the role of humans in ecosystems, landscape connectivity, and resilience. This paper reviews and highlights the importance of these issues for sustainable use of ecosystem services, which is argued to be one aspect of sustainable cities. The paper stresses the need to include social and economic factors when analyzing urban landscapes. Spatially explicit data can be used to assess the roles different green areas have in providing people with ecosystem services, and whether people actually have access to the services. Such data can also be used to assess connectivity and heterogeneity, both argued to be central for continuous, long-term provision of these services, and to determine the role urban form has for sustainability.

  14. Transcript structure and domain display: a customizable transcript visualization tool.

    Science.gov (United States)

    Watanabe, Kenneth A; Ma, Kaiwang; Homayouni, Arielle; Rushton, Paul J; Shen, Qingxi J

    2016-07-01

    Transcript Structure and Domain Display (TSDD) is a publicly available, web-based program that provides publication quality images of transcript structures and domains. TSDD is capable of producing transcript structures from GFF/GFF3 and BED files. Alternatively, the GFF files of several model organisms have been pre-loaded so that users only needs to enter the locus IDs of the transcripts to be displayed. Visualization of transcripts provides many benefits to researchers, ranging from evolutionary analysis of DNA-binding domains to predictive function modeling. TSDD is freely available for non-commercial users at http://shenlab.sols.unlv.edu/shenlab/software/TSD/transcript_display.html : jeffery.shen@unlv.nevada.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  15. Legible landscapes: the use of narratives in landscape design for leisure and tourism in Dutch cultural landscapes.

    NARCIS (Netherlands)

    Brinkhuijsen, M.

    2007-01-01

    Nowadays, leisure and tourism have become significant factors in rural development, which is manifest in the ‘commodification’ of landscapes. However, leisure and tourist markets are very competitive and consumers increasingly demand high quality, unique and memorable experiences. Landscape

  16. Reading fitness landscape diagrams through HSAB concepts

    Energy Technology Data Exchange (ETDEWEB)

    Vigneresse, Jean-Louis, E-mail: jean-louis.vigneresse@univ-lorraine.fr

    2014-10-31

    Highlights: • Qualitative information from HSAB descriptors. • 2D–3D diagrams using chemical descriptors (χ, η, ω, α) and principles (MHP, mEP, mPP). • Estimate of the energy exchange during reaction paths. • Examples from complex systems (geochemistry). - Abstract: Fitness landscapes are conceived as range of mountains, with local peaks and valleys. In terms of potential, such topographic variations indicate places of local instability or stability. The chemical potential, or electronegativity, its value changed of sign, carries similar information. In addition to chemical descriptors defined through hard-soft acid-base (HSAB) concepts and computed through density functional theory (DFT), the principles that rule chemical reactions allow the design of such landscape diagrams. The simplest diagram uses electrophilicity and hardness as coordinates. It allows examining the influence of maximum hardness or minimum electrophilicity principles. A third dimension is introduced within such a diagram by mapping the topography of electronegativity, polarizability or charge exchange. Introducing charge exchange during chemical reactions, or mapping a third parameter (f.i. polarizability) reinforces the information carried by a simple binary diagram. Examples of such diagrams are provided, using data from Earth Sciences, simple oxides or ligands.

  17. Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels

    KAUST Repository

    Wang, Xiaolei

    2014-12-12

    Background: A quantitative understanding of interactions between transcription factors (TFs) and their DNA binding sites is key to the rational design of gene regulatory networks. Recent advances in high-throughput technologies have enabled high-resolution measurements of protein-DNA binding affinity. Importantly, such experiments revealed the complex nature of TF-DNA interactions, whereby the effects of nucleotide changes on the binding affinity were observed to be context dependent. A systematic method to give high-quality estimates of such complex affinity landscapes is, thus, essential to the control of gene expression and the advance of synthetic biology. Results: Here, we propose a two-round prediction method that is based on support vector regression (SVR) with weighted degree (WD) kernels. In the first round, a WD kernel with shifts and mismatches is used with SVR to detect the importance of subsequences with different lengths at different positions. The subsequences identified as important in the first round are then fed into a second WD kernel to fit the experimentally measured affinities. To our knowledge, this is the first attempt to increase the accuracy of the affinity prediction by applying two rounds of string kernels and by identifying a small number of crucial k-mers. The proposed method was tested by predicting the binding affinity landscape of Gcn4p in Saccharomyces cerevisiae using datasets from HiTS-FLIP. Our method explicitly identified important subsequences and showed significant performance improvements when compared with other state-of-the-art methods. Based on the identified important subsequences, we discovered two surprisingly stable 10-mers and one sensitive 10-mer which were not reported before. Further test on four other TFs in S. cerevisiae demonstrated the generality of our method. Conclusion: We proposed in this paper a two-round method to quantitatively model the DNA binding affinity landscape. Since the ability to modify

  18. Energy Landscape of Social Balance

    Science.gov (United States)

    Marvel, Seth A.; Strogatz, Steven H.; Kleinberg, Jon M.

    2009-11-01

    We model a close-knit community of friends and enemies as a fully connected network with positive and negative signs on its edges. Theories from social psychology suggest that certain sign patterns are more stable than others. This notion of social “balance” allows us to define an energy landscape for such networks. Its structure is complex: numerical experiments reveal a landscape dimpled with local minima of widely varying energy levels. We derive rigorous bounds on the energies of these local minima and prove that they have a modular structure that can be used to classify them.

  19. Energy landscape of social balance.

    Science.gov (United States)

    Marvel, Seth A; Strogatz, Steven H; Kleinberg, Jon M

    2009-11-06

    We model a close-knit community of friends and enemies as a fully connected network with positive and negative signs on its edges. Theories from social psychology suggest that certain sign patterns are more stable than others. This notion of social "balance" allows us to define an energy landscape for such networks. Its structure is complex: numerical experiments reveal a landscape dimpled with local minima of widely varying energy levels. We derive rigorous bounds on the energies of these local minima and prove that they have a modular structure that can be used to classify them.

  20. Chapter 9. The landscape sector

    International Nuclear Information System (INIS)

    Larivaille, Pierrette

    1980-01-01

    The object of this work is to examine the interactions between the activities of the electric industry (generating, transmission and distribution) and the environment, whilst showing to what extent the facilities are likely to affect it adversely and describing the measures taken to lessen the detrimental effects. The chapter devoted to the 'landscape' includes a section covering the electricity generating facilities, and among these, the nuclear power stations. The studies carried out on the main units of insertion into the site are presented, particularly the landscaping involved in setting up a power station [fr

  1. Cooling towers in the landscape

    International Nuclear Information System (INIS)

    Boernke, F.

    1977-01-01

    The cooling tower as a large technical construction is one of the most original industrial buildings. It sticks out as an outlandish element in our building landscape, a giant which cannot be compared with the traditional forms of technical buildings. If it is constructed as a reinforced-concrete hyperboloid, its shape goes beyond all limits of building construction. Judgment of these highly individual constructions is only possible by applying a novel standard breaking completely with tradition. This new scale of height and dimension in industrial construction, and in particular the modern cooling tower, requires painstaking care and design and adaptation to the landscape around it. (orig.) [de

  2. Landscape history and archaeology of open field landscapes in Europe

    NARCIS (Netherlands)

    Renes, J.|info:eu-repo/dai/nl/071365303

    2016-01-01

    The landscapes of open fields were the grain baskets of medieval Europe. The term ‘open fields’ refers to the large arable fields that have an open character because the individual parcels of the owners were not surrounded by hedges, woodbanks, drystone walls or other visible boundaries. In this

  3. Regulation of circadian clock transcriptional output by CLOCK:BMAL1

    Science.gov (United States)

    Trott, Alexandra J.

    2018-01-01

    The mammalian circadian clock relies on the transcription factor CLOCK:BMAL1 to coordinate the rhythmic expression of 15% of the transcriptome and control the daily regulation of biological functions. The recent characterization of CLOCK:BMAL1 cistrome revealed that although CLOCK:BMAL1 binds synchronously to all of its target genes, its transcriptional output is highly heterogeneous. By performing a meta-analysis of several independent genome-wide datasets, we found that the binding of other transcription factors at CLOCK:BMAL1 enhancers likely contribute to the heterogeneity of CLOCK:BMAL1 transcriptional output. While CLOCK:BMAL1 rhythmic DNA binding promotes rhythmic nucleosome removal, it is not sufficient to generate transcriptionally active enhancers as assessed by H3K27ac signal, RNA Polymerase II recruitment, and eRNA expression. Instead, the transcriptional activity of CLOCK:BMAL1 enhancers appears to rely on the activity of ubiquitously expressed transcription factors, and not tissue-specific transcription factors, recruited at nearby binding sites. The contribution of other transcription factors is exemplified by how fasting, which effects several transcription factors but not CLOCK:BMAL1, either decreases or increases the amplitude of many rhythmically expressed CLOCK:BMAL1 target genes. Together, our analysis suggests that CLOCK:BMAL1 promotes a transcriptionally permissive chromatin landscape that primes its target genes for transcription activation rather than directly activating transcription, and provides a new framework to explain how environmental or pathological conditions can reprogram the rhythmic expression of clock-controlled genes. PMID:29300726

  4. Thermal Infrared Remote Sensing for Analysis of Landscape Ecological Processes: Methods and Applications

    Science.gov (United States)

    Quattrochi, Dale A.; Luvall, Jeffrey C.

    1998-01-01

    Thermal Infrared (TIR) remote sensing data can provide important measurements of surface energy fluxes and temperatures, which are integral to understanding landscape processes and responses. One example of this is the successful application of TIR remote sensing data to estimate evapotranspiration and soil moisture, where results from a number of studies suggest that satellite-based measurements from TIR remote sensing data can lead to more accurate regional-scale estimates of daily evapotranspiration. With further refinement in analytical techniques and models, the use of TIR data from airborne and satellite sensors could be very useful for parameterizing surface moisture conditions and developing better simulations of landscape energy exchange over a variety of conditions and space and time scales. Thus, TIR remote sensing data can significantly contribute to the observation, measurement, and analysis of energy balance characteristics (i.e., the fluxes and redistribution of thermal energy within and across the land surface) as an implicit and important aspect of landscape dynamics and landscape functioning. The application of TIR remote sensing data in landscape ecological studies has been limited, however, for several fundamental reasons that relate primarily to the perceived difficulty in use and availability of these data by the landscape ecology community, and from the fragmentation of references on TIR remote sensing throughout the scientific literature. It is our purpose here to provide evidence from work that has employed TIR remote sensing for analysis of landscape characteristics to illustrate how these data can provide important data for the improved measurement of landscape energy response and energy flux relationships. We examine the direct or indirect use of TIR remote sensing data to analyze landscape biophysical characteristics, thereby offering some insight on how these data can be used more robustly to further the understanding and modeling of

  5. NitroScape: A model to integrate nitrogen transfers and transformations in rural landscapes

    Energy Technology Data Exchange (ETDEWEB)

    Duretz, S. [INRA-AgroParisTech, UMR 1091 Environnement et Grandes Cultures (EGC), 78850 Thiverval-Grignon (France); Drouet, J.L., E-mail: Jean-Louis.Drouet@grignon.inra.fr [INRA-AgroParisTech, UMR 1091 Environnement et Grandes Cultures (EGC), 78850 Thiverval-Grignon (France); Durand, P. [INRA-AgroCampus, UMR 1069 Sol Agro et hydrosysteme Spatialisation (SAS), 35042 Rennes cedex (France); Hutchings, N.J. [Department of Agroecology, Faculty of Agricultural Sciences, University of Aarhus (AU), Blichers Alle, 8830 Tjele (Denmark); Theobald, M.R. [Department of Chemistry and Agricultural Analysis, Technical University of Madrid (UPM), 28040 Madrid (Spain); Centre for Ecology and Hydrology (CEH), Bush Estate, Penicuik, Midlothian EH26 0QB (United Kingdom); Salmon-Monviola, J. [INRA-AgroCampus, UMR 1069 Sol Agro et hydrosysteme Spatialisation (SAS), 35042 Rennes cedex (France); Dragosits, U. [Centre for Ecology and Hydrology (CEH), Bush Estate, Penicuik, Midlothian EH26 0QB (United Kingdom); Maury, O. [INRA-AgroParisTech, UMR 1091 Environnement et Grandes Cultures (EGC), 78850 Thiverval-Grignon (France); Sutton, M.A. [Centre for Ecology and Hydrology (CEH), Bush Estate, Penicuik, Midlothian EH26 0QB (United Kingdom); Cellier, P. [INRA-AgroParisTech, UMR 1091 Environnement et Grandes Cultures (EGC), 78850 Thiverval-Grignon (France)

    2011-11-15

    Modelling nitrogen transfer and transformation at the landscape scale is relevant to estimate the mobility of the reactive forms of nitrogen (N{sub r}) and the associated threats to the environment. Here we describe the development of a spatially and temporally explicit model to integrate N{sub r} transfer and transformation at the landscape scale. The model couples four existing models, to simulate atmospheric, farm, agro-ecosystem and hydrological N{sub r} fluxes and transformations within a landscape. Simulations were carried out on a theoretical landscape consisting of pig-crop farms interspersed with unmanaged ecosystems. Simulation results illustrated the effect of spatial interactions between landscape elements on N{sub r} fluxes and losses to the environment. More than 10% of the total N{sub 2}O emissions were due to indirect emissions. The nitrogen budgets and transformations of the unmanaged ecosystems varied considerably, depending on their location within the landscape. The model represents a new tool for assessing the effect of changes in landscape structure on N{sub r} fluxes. - Highlights: > The landscape scale is relevant to study how spatial interactions affect N{sub r} fate. > The NitroScape model integrates N{sub r} transfer and transformation at landscape scale. > NitroScape couples existing atmospheric, farm, agro-ecosystem and hydrological models. > Data exchanges within NitroScape are dynamic and spatially distributed. > More than 10% of the simulated N{sub 2}O emissions are due to indirect emissions. - A model integrating terrestrial, hydrological and atmospheric processes of N{sub r} transfer and transformation at the landscape scale has been developed to simulate the effect of spatial interactions between landscape elements on N{sub r} fate.

  6. Scale-Free Relationships between Social and Landscape Factors in Urban Systems

    Directory of Open Access Journals (Sweden)

    Chunzhu Wei

    2017-01-01

    Full Text Available Urban planners and ecologists have long debated the relationship between the structure of urban landscapes and social activities. There have, however, been very few discussions as to whether any such relationships might depend on the scales of observation. This work applies a hierarchical zoning technique to data from the city of Quito, Ecuador, to examine how relationships between typical spatial landscape metrics and social indicators depend on zoning scales. Our results showed that the estimates of both landscape heterogeneity features and social indicators significantly depend on the zoning scale. The mean values of the typical landscape metrics and the social indicators all exhibited predictable responses to a changing zoning scale, suggesting a consistent and significant scaling relationship within the multiple zoning scales. Yet relationships between these pairs of variables remain notably invariant to scale. This quantitative demonstration of the scale-free nature of the relationship between landscape characteristics and social indicators furthers our understanding of the relationships between landscape structures and social aspects of urban spaces, including deprivation and public service accessibility. The relationships between social indicators and one typical landscape aggregation metric (represented as the percentage of like adjacencies were nevertheless significantly dependent on scale, suggesting the importance of zoning scale decisions for analyzing the relationships between the social indicators and the landscape characteristics related with landscape adjacency. Aside from this typical landscape aggregation metric, the general invariance to the zoning scale of relationships between landscape structures and socioeconomic indicators in Quito suggests the importance of applying these scale-free relationships in understanding complex socio-ecological systems in other cities, which are shaped by the conflated influences of both

  7. NitroScape: A model to integrate nitrogen transfers and transformations in rural landscapes

    International Nuclear Information System (INIS)

    Duretz, S.; Drouet, J.L.; Durand, P.; Hutchings, N.J.; Theobald, M.R.; Salmon-Monviola, J.; Dragosits, U.; Maury, O.; Sutton, M.A.; Cellier, P.

    2011-01-01

    Modelling nitrogen transfer and transformation at the landscape scale is relevant to estimate the mobility of the reactive forms of nitrogen (N r ) and the associated threats to the environment. Here we describe the development of a spatially and temporally explicit model to integrate N r transfer and transformation at the landscape scale. The model couples four existing models, to simulate atmospheric, farm, agro-ecosystem and hydrological N r fluxes and transformations within a landscape. Simulations were carried out on a theoretical landscape consisting of pig-crop farms interspersed with unmanaged ecosystems. Simulation results illustrated the effect of spatial interactions between landscape elements on N r fluxes and losses to the environment. More than 10% of the total N 2 O emissions were due to indirect emissions. The nitrogen budgets and transformations of the unmanaged ecosystems varied considerably, depending on their location within the landscape. The model represents a new tool for assessing the effect of changes in landscape structure on N r fluxes. - Highlights: → The landscape scale is relevant to study how spatial interactions affect N r fate. → The NitroScape model integrates N r transfer and transformation at landscape scale. → NitroScape couples existing atmospheric, farm, agro-ecosystem and hydrological models. → Data exchanges within NitroScape are dynamic and spatially distributed. → More than 10% of the simulated N 2 O emissions are due to indirect emissions. - A model integrating terrestrial, hydrological and atmospheric processes of N r transfer and transformation at the landscape scale has been developed to simulate the effect of spatial interactions between landscape elements on N r fate.

  8. landscape incorporation in the environmental impact studies

    International Nuclear Information System (INIS)

    Gutierrez G, Luz Angela

    2000-01-01

    A general overview on landscape analysis showing the two principal approaches to their study, the article emphasize on the need of taking landscape in consideration on the making of the environmental impact study of any project of development

  9. Nucleocytoplasmic shuttling of transcription factors

    DEFF Research Database (Denmark)

    Cartwright, P; Helin, K

    2000-01-01

    To elicit the transcriptional response following intra- or extracellular stimuli, the signals need to be transmitted to their site of action within the nucleus. The nucleocytoplasmic shuttling of transcription factors is a mechanism mediating this process. The activation and inactivation...... of the transcriptional response is essential for cells to progress through the cell cycle in a normal manner. The involvement of cytoplasmic and nuclear accessory molecules, and the general nuclear membrane transport components, are essential for this process. Although nuclear import and export for different...... transcription factor families are regulated by similar mechanisms, there are several differences that allow for the specific activation of each transcription factor. This review discusses the general import and export pathways found to be common amongst many different transcription factors, and highlights...

  10. Transcriptional Silencing of Retroviral Vectors

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Duch, M.; Pedersen, F.S.

    1996-01-01

    . Extinction of long-term vector expression has been observed after implantation of transduced hematopoietic cells as well as fibroblasts, myoblasts and hepatocytes. Here we review the influence of vector structure, integration site and cell type on transcriptional silencing. While down-regulation of proviral...... transcription is known from a number of cellular and animal models, major insight has been gained from studies in the germ line and embryonal cells of the mouse. Key elements for the transfer and expression of retroviral vectors, such as the viral transcriptional enhancer and the binding site for the t......RNA primer for reverse transcription may have a major influence on transcriptional silencing. Alterations of these elements of the vector backbone as well as the use of internal promoter elements from housekeeping genes may contribute to reduce transcriptional silencing. The use of cell culture and animal...

  11. DNA topology and transcription

    Science.gov (United States)

    Kouzine, Fedor; Levens, David; Baranello, Laura

    2014-01-01

    Chromatin is a complex assembly that compacts DNA inside the nucleus while providing the necessary level of accessibility to regulatory factors conscripted by cellular signaling systems. In this superstructure, DNA is the subject of mechanical forces applied by variety of molecular motors. Rather than being a rigid stick, DNA possesses dynamic structural variability that could be harnessed during critical steps of genome functioning. The strong relationship between DNA structure and key genomic processes necessitates the study of physical constrains acting on the double helix. Here we provide insight into the source, dynamics, and biology of DNA topological domains in the eukaryotic cells and summarize their possible involvement in gene transcription. We emphasize recent studies that might inspire and impact future experiments on the involvement of DNA topology in cellular functions. PMID:24755522

  12. Eukaryotic transcription factors

    DEFF Research Database (Denmark)

    Staby, Lasse; O'Shea, Charlotte; Willemoës, Martin

    2017-01-01

    Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains...... regions with function-related, short sequence motifs and molecular recognition features with structural propensities. This review focuses on molecular aspects of TFs, which represent paradigms of ID-related features. Through specific examples, we review how the ID-associated flexibility of TFs enables....... It is furthermore emphasized how classic biochemical concepts like allostery, conformational selection, induced fit, and feedback regulation are undergoing a revival with the appreciation of ID. The review also describes the most recent advances based on computational simulations of ID-based interaction mechanisms...

  13. Coulomb Mechanics And Landscape Geometry Explain Landslide Size Distribution

    Science.gov (United States)

    Jeandet, L.; Steer, P.; Lague, D.; Davy, P.

    2017-12-01

    It is generally observed that the dimensions of large bedrock landslides follow power-law scaling relationships. In particular, the non-cumulative frequency distribution (PDF) of bedrock landslide area is well characterized by a negative power-law above a critical size, with an exponent 2.4. However, the respective role of bedrock mechanical properties, landscape shape and triggering mechanisms on the scaling properties of landslide dimensions are still poorly understood. Yet, unravelling the factors that control this distribution is required to better estimate the total volume of landslides triggered by large earthquakes or storms. To tackle this issue, we develop a simple probabilistic 1D approach to compute the PDF of rupture depths in a given landscape. The model is applied to randomly sampled points along hillslopes of studied digital elevation models. At each point location, the model determines the range of depth and angle leading to unstable rupture planes, by applying a simple Mohr-Coulomb rupture criterion only to the rupture planes that intersect downhill surface topography. This model therefore accounts for both rock mechanical properties, friction and cohesion, and landscape shape. We show that this model leads to realistic landslide depth distribution, with a power-law arising when the number of samples is high enough. The modeled PDF of landslide size obtained for several landscapes match the ones from earthquakes-driven landslides catalogues for the same landscape. In turn, this allows us to invert landslide effective mechanical parameters, friction and cohesion, associated to those specific events, including Chi-Chi, Wenchuan, Niigata and Gorkha earthquakes. The cohesion and friction ranges (25-35 degrees and 5-20 kPa) are in good agreement with previously inverted values. Our results demonstrate that reduced complexity mechanics is efficient to model the distribution of unstable depths, and show the role of landscape variability in landslide size

  14. THE METHODOLOGY OF VALORISING AND ASSESSING LANDSCAPE

    Directory of Open Access Journals (Sweden)

    Stanisław Jacek Bacior

    2017-01-01

    Full Text Available Landscape evaluation process requires access to particular information resources making it possible to regionalize (divide into zones the area under investigation. Thus, the starting point is landscape assessment and evaluation followed by regionalization. As a result of this step, we determine certain areas that are homogenous with regards to their landscape assets Keywords: assessing landscape, structure of rural areas, spatial planning of rural areas.

  15. Europe: the paradox of landscape change

    OpenAIRE

    Sluis, van der, Theo

    2017-01-01

    This thesis explores the processes of change in European rural landscapes. Landscapes have evolved over millennia as a result of human influence on the physical environment. Europe has a wide variety of landscapes that can alter within a relatively short distance, and which often form part of the national cultural identity of a European country. Central to this thesis, however, are insights into the processes of landscape change. In this context, the overall objective of this thesis is: To as...

  16. Introducing native landscape ecology to Hanford cleanup

    International Nuclear Information System (INIS)

    Jim, R.; Nguyen, G.; Barry, B.

    1995-01-01

    Responsible management of environmental and public health risk requires a fundamental understanding of the intra-, inter-, and integral components of the hierarchical interaction dynamics within a pollution affected ecosystem. Because the ecosphere is a heterogeneous combination of many subecosystems of plant and animal species, its component interactions sustaining the complex whole are spatially mediated, and such an adaptive self-stabilizing ecomosaic often possesses long disintegration and regeneration times for the manifestation of observable consequences, quantitative assessment of its future structural and functional changes can be deceptive or plagued with irreducible uncertainty. This paper presents an holistic framework for the direct integration of native traditional environmental knowledge with the landscape ecology information system to refine and actualize the understanding of acceptable long-range risk and its collective estimation for an endangered population or community. An illustrative application of riparian zone restoration in the Hanford reach for wild salmon runs and habitat preservation is also discussed

  17. Evidence and opportunities for integrating landscape ecology into natural resource planning across multiple-use landscapes

    Science.gov (United States)

    Trammel, E. Jamie; Carter, Sarah; Haby, Travis S.; Taylor, Jason J.

    2018-01-01

    Enhancing natural resource management has been a focus of landscape ecology since its inception, but numerous authors argue that landscape ecology has not yet been effective in achieving the underlying goal of planning and designing sustainable landscapes. We developed nine questions reflecting the application of fundamental research topics in landscape ecology to the landscape planning process and reviewed two recent landscape-scale plans in western North America for evidence of these concepts in plan decisions. Both plans considered multiple resources, uses, and values, including energy development, recreation, conservation, and protection of cultural and historic resources. We found that land use change and multiscale perspectives of resource uses and values were very often apparent in planning decisions. Pattern-process relationships, connectivity and fragmentation, ecosystem services, landscape history, and climate change were reflected less frequently. Landscape sustainability was considered only once in the 295 decisions reviewed, and outputs of landscape models were not referenced. We suggest six actionable opportunities for further integrating landscape ecology concepts into landscape planning efforts: 1) use landscape sustainability as an overarching goal, 2) adopt a broad ecosystem services framework, 3) explore the role of landscape history more comprehensively, 4) regularly consider and accommodate potential effects of climate change, 5) use landscape models to support plan decisions, and 6) promote a greater presence of landscape ecologists within agencies that manage large land bases and encourage active involvement in agency planning efforts. Together these actions may improve the defensibility, durability, and sustainability of landscape plan decisions.

  18. Computational Investigations of Post-Transcriptional Regulation

    DEFF Research Database (Denmark)

    Rasmussen, Simon Horskjær

    and miRNA regulation was studied by cross-linking immunoprecipitation (CLIP) and RBP double knockdown experiments. A comprehensive analysis of 107 CLIP datasets of 49 RBPs demonstrated that RBPs modulate miRNA regulation. Results suggest it is mediated by RBP-binding hotspots that likely...... investigated using high-throughput data. Analysis of IMP RIP-seq, iCLIP and RNA-seq datasets identified transcripts associated with cytoplasmic IMP ribonucleoproteins. Many of these transcripts were functionally involved in actin cytoskeletal remodeling. Further analyses of this data permitted estimation...... of a bipartite motif, composed of an AU-rich and a CA-rich domain. In addition, a regulatory motif discovery method was developed and applied to identify motifs using differential expression data and CLIP-data in the above investigations. This thesis increased the understanding of the role of RBPs in mi...

  19. Flowers and Landscape by Serendipity.

    Science.gov (United States)

    Pippin, Sandi

    2003-01-01

    Describes an art lesson in which students sketch drawings of flowers and use watercolor paper and other materials to paint a landscape. Explains that the students also learn about impressionism in this lesson. Discusses how the students prepare the paper and create their artwork. (CMK)

  20. Landscape design methods in architecture

    NARCIS (Netherlands)

    Jauslin, D.T.

    2012-01-01

    Landscape has been used as a metaphor or conceptual reference for an increasing amount of excellent architectural projects in the last two decades. The phenomenon seems to be a substantial innovation of architecture with an interesting potential for artistic, social and ecological gains. To be able

  1. Biography of an Industrial Landscape

    DEFF Research Database (Denmark)

    Riesto, Svava

    Biography of an Industrial Landscape tells the story of one of the most significant urban redevelopment projects in northern Europe at the turn of the century. Examining the reinvention of the Carlsberg brewery site in Copenhagen as a city district, Svava Riesto unpacks the deeper assumptions abo...

  2. Eucalyptus as a landscape tree

    Science.gov (United States)

    W. Douglas Hamilton

    1983-01-01

    Ninety-two species of Eucalyptus were evaluated at the University of California re- search station in San Jose. The purpose: to find acceptable new street and park trees. Growth rates and horticultural characteristics were noted. Forty-three species were studied in locations statewide to evaluate site adaptation and landscape usefulness; flooded, cold, dry, saline....

  3. Dutch Architecture with Landscape Methods

    NARCIS (Netherlands)

    Abrami, F.; Bijster, J.; Bitarafan, N.; Cao, Z.; Cui, Y.; Liu, Y.; Ruan, L.; Maas, M.; Mayr, R.; Rozenmuller, M.; Toriano, L.; Yoshitake, M.; Jauslin, D.

    2009-01-01

    14 Project Documentations and Analysis of Dutch Architecture with Landscape Methods. MVRDV Villa VPRO, Powerhouse Company Villa 1, Herman Herzberger Coda Museum, NL Architects Basket Ba, SeARCH Posbank Pavillion, Wiel Arets Hedge House, OMA Kunsthal and Educatorium, Maaskant Johnson Wax, Diller &

  4. Language's Landscape of the Mind.

    Science.gov (United States)

    Tracy, Janet

    2000-01-01

    Describes how the author's 6 middle school students living in a village in the Yukon, 100 miles off the road system just below the arctic circle, enthusiastically wrote stories or poems about their lives. The students shared their works via an online electronic conferencing system with students from the unimaginably different landscape of the…

  5. Selected Landscape Plants. Slide Script.

    Science.gov (United States)

    McCann, Kevin

    This slide script, part of a series of slide scripts designed for use in vocational agriculture classes, deals with commercially important woody ornamental landscape plants. Included in the script are narrations for use with a total of 253 slides illustrating 92 different plants. Several slides are used to illustrate each plant: besides a view of…

  6. Ecological networks in urban landscapes

    NARCIS (Netherlands)

    Cook, E.A.

    2000-01-01

    This research focuses on the topic of ecological networks in urban landscapes. Analysis and planning of ecological networks is a relatively new phenomenon and is a response to fragmentation and deterioration of quality of natural systems. In agricultural areas and with existing nature

  7. Monarto’s Contested Landscape

    Directory of Open Access Journals (Sweden)

    Paul Walker

    2015-11-01

    Full Text Available The proposal to develop a new city at Monarto in South Australia during the 1970s was an important project of the reforming government of Don Dunstan. Dunstan’s view was that Monarto would be a city environmentally suited to the tough conditions of its site, and to an ‘Australian way of life’. As planning and preliminary design proceeded from 1972 to 1975, the landscape potential of the city’s selected site became central to its conception. This paper draws on new research comprising interviews with key participants and archival material to examine four issues: the adoption of an environmental orientation in Australian urban planning and discourse in the 1970s; strategies in the design proposals that seemingly gave Monarto validity even as the demographic and political drivers for it dissolved away; the investigations that supported Monarto’s landscape strategies; and attitudes to social and cultural history that the Monarto project adopted. While ultimately the plan for Monarto was abandoned, the projected city’s landscape can be seen as a theatre for competing values in relation to natural and cultural heritage and design ambitions. The paper situates Monarto within national and international urban discourse that is more complex than has been previously acknowledged, indicative of competing values and ideologies in the planning, landscape and design discourses of the period.

  8. Surface fluxes in heterogeneous landscape

    Energy Technology Data Exchange (ETDEWEB)

    Bay Hasager, C

    1997-01-01

    The surface fluxes in homogeneous landscapes are calculated by similarity scaling principles. The methodology is well establish. In heterogeneous landscapes with spatial changes in the micro scale range, i e from 100 m to 10 km, advective effects are significant. The present work focus on these effects in an agricultural countryside typical for the midlatitudes. Meteorological and satellite data from a highly heterogeneous landscape in the Rhine Valley, Germany was collected in the large-scale field experiment TRACT (Transport of pollutants over complex terrain) in 1992. Classified satellite images, Landsat TM and ERS SAR, are used as basis for roughness maps. The roughnesses were measured at meteorological masts in the various cover classes and assigned pixel by pixel to the images. The roughness maps are aggregated, i e spatially averaged, into so-called effective roughness lengths. This calculation is performed by a micro scale aggregation model. The model solves the linearized atmospheric flow equations by a numerical (Fast Fourier Transform) method. This model also calculate maps of friction velocity and momentum flux pixel wise in heterogeneous landscapes. It is indicated how the aggregation methodology can be used to calculate the heat fluxes based on the relevant satellite data i e temperature and soil moisture information. (au) 10 tabs., 49 ills., 223 refs.

  9. Space Strategies for the New Learning Landscape

    Science.gov (United States)

    Dugdale, Shirley

    2009-01-01

    The Learning Landscape is the total context for students' learning experiences and the diverse landscape of learning settings available today--from specialized to multipurpose, from formal to informal, and from physical to virtual. The goal of the Learning Landscape approach is to acknowledge this richness and maximize encounters among people,…

  10. Europe: the paradox of landscape change

    NARCIS (Netherlands)

    Sluis, van der Theo

    2017-01-01

    This thesis explores the processes of change in European rural landscapes. Landscapes have evolved over millennia as a result of human influence on the physical environment. Europe has a wide variety of landscapes that can alter within a relatively short distance, and which often form part of the

  11. Research needs for our national landscapes

    Science.gov (United States)

    Elwood L. Shafer

    1979-01-01

    The prevailing research problem for our national landscapes is: How shall we organize, control, and coordinate public and private development so as to protect, maintain, improve, and manage those landscape features that we value most? Research questions discussed include: environmental/political conflicts, taxation and zoning, landscape classification, public...

  12. Sustaining ecosystem services in cultural landscapes

    Directory of Open Access Journals (Sweden)

    Tobias Plieninger

    2014-06-01

    Full Text Available Classical conservation approaches focus on the man-made degradation of ecosystems and tend to neglect the social-ecological values that human land uses have imprinted on many environments. Throughout the world, ingenious land-use practices have generated unique cultural landscapes, but these are under pressure from agricultural intensification, land abandonment, and urbanization. In recent years, the cultural landscapes concept has been broadly adopted in science, policy, and management. The interest in both outstanding and vernacular landscapes finds expression in the UNESCO World Heritage Convention, the European Landscape Convention, and the IUCN Protected Landscape Approach. These policies promote the protection, management, planning, and governance of cultural landscapes. The ecosystem services approach is a powerful framework to guide such efforts, but has rarely been applied in landscape research and management. With this paper, we introduce a special feature that aims to enhance the theoretical, empirical and practical knowledge of how to safeguard the resilience of ecosystem services in cultural landscapes. It concludes (1 that the usefulness of the ecosystem services approach to the analysis and management of cultural landscapes should be reviewed more critically; (2 that conventional ecosystem services assessment needs to be complemented by socio-cultural valuation; (3 that cultural landscapes are inherently changing, so that a dynamic view on ecosystem services and a focus on drivers of landscape change are needed; and (4 that managing landscapes for ecosystem services provision may benefit from a social-ecological resilience perspective.

  13. Ecosystem services in changing landscapes: An introduction

    Science.gov (United States)

    Louis Iverson; Cristian Echeverria; Laura Nahuelhual; Sandra. Luque

    2014-01-01

    The concept of ecosystem services from landscapes is rapidly gaining momentum as a language to communicate values and benefits to scientists and lay alike. Landscape ecology has an enormous contribution to make to this field, and one could argue, uniquely so. Tools developed or adapted for landscape ecology are being increasingly used to assist with the quantification...

  14. Modelling non-Euclidean movement and landscape connectivity in highly structured ecological networks

    Science.gov (United States)

    Sutherland, Christopher; Fuller, Angela K.; Royle, J. Andrew

    2015-01-01

    Movement is influenced by landscape structure, configuration and geometry, but measuring distance as perceived by animals poses technical and logistical challenges. Instead, movement is typically measured using Euclidean distance, irrespective of location or landscape structure, or is based on arbitrary cost surfaces. A recently proposed extension of spatial capture-recapture (SCR) models resolves this issue using spatial encounter histories of individuals to calculate least-cost paths (ecological distance: Ecology, 94, 2013, 287) thereby relaxing the Euclidean assumption. We evaluate the consequences of not accounting for movement heterogeneity when estimating abundance in highly structured landscapes, and demonstrate the value of this approach for estimating biologically realistic space-use patterns and landscape connectivity.

  15. Predictors of breeding site occupancy by amphibians in montane landscapes

    Science.gov (United States)

    Groff, Luke A.; Loftin, Cynthia S.; Calhoun, Aram J.K.

    2017-01-01

    Ecological relationships and processes vary across species’ geographic distributions, life stages and spatial, and temporal scales. Montane landscapes are characterized by low wetland densities, rugged topographies, and cold climates. Consequently, aquatic-dependent and low-vagility ectothermic species (e.g., pool-breeding amphibians) may exhibit unique ecological associations in montane landscapes. We evaluated the relative importance of breeding- and landscape-scale features associated with spotted salamander (Ambystoma maculatum) and wood frog (Lithobates sylvaticus) wetland occupancy in Maine's Upper Montane-Alpine Zone ecoregion, and we determined whether models performed better when the inclusive landscape-scale covariates were estimated with topography-weighted or circular buffers. We surveyed 135 potential breeding sites during May 2013–June 2014 and evaluated environmental relationships with multi-season implicit dynamics occupancy models. Breeding site occupancy by both species was influenced solely by breeding-scale habitat features. Spotted salamander occupancy probabilities increased with previous or current beaver (Castor canadensis) presence, and models generally were better supported when the inclusive landscape-scale covariates were estimated with topography-weighted rather than circular buffers. Wood frog occupancy probabilities increased with site area and percent shallows, but neither buffer type was better supported than the other. Model rank order and support varied between buffer types, but model inferences did not. Our results suggest pool-breeding amphibian conservation in montane Maine include measures to maintain beaver populations and large wetlands with proportionally large areas of shallows ≤1-m deep. Inconsistencies between our study and previous studies substantiate the value of region-specific research for augmenting species’ conservation management plans and suggest the application of out-of-region inferences may promote

  16. Quantitative reconstruction of past Danish landscapes: The first results

    DEFF Research Database (Denmark)

    Odgaard, Bent Vad; Nielsen, Anne Birgitte

    We present a first attempt at pollen based quantitative reconstruction of land cover around 9 Danish lake sites for the past 2500 years, based on models of pollen dispersal and -deposition (Prentice, 1985; Sugita, 1993, 1994), and pollen productivity estimates produced from a historical calibrati...... are then used in the Landscape Reconstruction Algorithm, LRA, (Sugita & Walker, 2000; Sugita, in press) to separate background and local pollen signals at small sites, thus providing reconstructions of local vegetation around the sites....

  17. URBAN LANDSCAPE QUALITY AND FACTORS THAT HAVE INFLUENCE ON LANDSCAPE QUALITY IN LATGALE REGION

    OpenAIRE

    Matisovs, Ivars

    2005-01-01

    The paper deals with urban landscape individualities in the cities and towns of Latgale region. Also show facilities and methods of integrated assessment of urban landscape quality. Article provides information about specifics of urban landscape and factors, that have influence on landscape quality. The paper presents the results of Daugavpils and Rēzekne urban landscape quality complex assessment, that have been realised in 2003- 2005. This results don’t establish significant disparities bet...

  18. Climate change impact on landscape fire and forest biomass dynamics

    International Nuclear Information System (INIS)

    Li, C.

    2004-01-01

    The aim of this study was to improve current understandings of fire regimes. The estimation of biomass dynamics at the stand scale is essential for understanding landscape scale biomass dynamics, particularly in order to understand the potential effects of fire regimes. This study presented a synthesis of research results obtained from stand scale studies together with fire behaviour and weather variables. Landscape structure, topography and climate conditions were also considered. Integration of the data was conducted with the SEM-LAND model, a spatially explicit model for landscape dynamics. Equations for the model were presented, including fire initiation and spread, as well as a lightning fire process and simulated fire suppression. Results indicated that fire suppression could alter the distribution of fire sizes. The effect of tree and stand mortality on forest biomass estimates was also discussed along with the impact of climate change on fire regimes. Results indicate that fire activities are likely to increase. Results also demonstrate that fire frequency and size distribution are correlated without human intervention. Theoretical negative exponential forest age distribution is not always supported by empirical observations. Point-based fire frequency and fire cycle definitions are special cases from a computational perspective. Detection of quantitative interrelationships may simplify preconditions for estimating fire regimes, and serve as a means to address incomplete empirical observations. 12 refs., 3 figs

  19. Landscapes of the Kruger National Park

    Directory of Open Access Journals (Sweden)

    W. P. D Gertenbach

    1983-12-01

    Full Text Available Knowledge on the abiotic and biotic components of the Kruger National Park (KNP system has increased to such an extent, that it was possible to zonate the KNP into landscapes. A landscape was defined as an area with a specific geomorphology, climate, soil and vegetation pattern together with the associated fauna. On this basis 35 landscapes were identified and described in terms of the components mentioned in the definition. The objective of classification is that future management should be based on these landscapes. Relevant management considerations may change, but the landscape a@ a basic functional unit should not be negotiable.

  20. Purification effects of five landscape plants on river landscape water

    Science.gov (United States)

    Ling, Sun; Lei, Zheng; Mao, Qinqing; Ji, Qingxin

    2017-12-01

    Five species of landscape plants which are scindapsus aureus, water hyacinth, cockscomb, calendula officinalis and salvia splendens were used as experimental materials to study their removal effects on nitrogen, phosphorus, chemical oxygen demand (CODMn) and suspended solids (SS) in urban river water. The results show that the 5 landscape plants have good adaptability and vitality in water body, among them, water hyacinth had the best life signs than the other 4 plants, and its plant height and root length increased significantly. They have certain removal effects on the nitrogen, phosphorus, CODMn (Chemical Oxygen Demand) and SS (Suspended Substance) in the landscape water of Dalong Lake, Xuzhou. Scindapsus aureus, water hyacinth, cockscomb, calendula officinalis and salvia splendens on the removal rate of total nitrogen were 76.69%, 78.57%, 71.42%, 69.64%, 67.86%; the ammonia nitrogen removal rate were 71.06%, 74.28%, 67.85%, 63.02%, 59.81%;the total phosphorus removal rate were 78.70%, 81.48%, 73.15%, 72.22%, 68.52%;the orthophosphate removal rates were 78.37%, 80.77%, 75.96%, 75.96%, 71.15%;the removal rate of CODMn was 52.5%, 55.35%, 46.02%, 45.42%, 44.19%; the removal rate of SS was 81.4%, 86%, 79.1%, 76.7%, 74.42%.The purification effect of 5 kinds of landscape plants of Dalong Lake in Xuzhou City: water hyacinth> scindapsus aureus>cockscomb>calendula officinalis>salvia splendens.

  1. Social network models predict movement and connectivity in ecological landscapes

    Science.gov (United States)

    Fletcher, Robert J.; Acevedo, M.A.; Reichert, Brian E.; Pias, Kyle E.; Kitchens, Wiley M.

    2011-01-01

    Network analysis is on the rise across scientific disciplines because of its ability to reveal complex, and often emergent, patterns and dynamics. Nonetheless, a growing concern in network analysis is the use of limited data for constructing networks. This concern is strikingly relevant to ecology and conservation biology, where network analysis is used to infer connectivity across landscapes. In this context, movement among patches is the crucial parameter for interpreting connectivity but because of the difficulty of collecting reliable movement data, most network analysis proceeds with only indirect information on movement across landscapes rather than using observed movement to construct networks. Statistical models developed for social networks provide promising alternatives for landscape network construction because they can leverage limited movement information to predict linkages. Using two mark-recapture datasets on individual movement and connectivity across landscapes, we test whether commonly used network constructions for interpreting connectivity can predict actual linkages and network structure, and we contrast these approaches to social network models. We find that currently applied network constructions for assessing connectivity consistently, and substantially, overpredict actual connectivity, resulting in considerable overestimation of metapopulation lifetime. Furthermore, social network models provide accurate predictions of network structure, and can do so with remarkably limited data on movement. Social network models offer a flexible and powerful way for not only understanding the factors influencing connectivity but also for providing more reliable estimates of connectivity and metapopulation persistence in the face of limited data.

  2. Social network models predict movement and connectivity in ecological landscapes.

    Science.gov (United States)

    Fletcher, Robert J; Acevedo, Miguel A; Reichert, Brian E; Pias, Kyle E; Kitchens, Wiley M

    2011-11-29

    Network analysis is on the rise across scientific disciplines because of its ability to reveal complex, and often emergent, patterns and dynamics. Nonetheless, a growing concern in network analysis is the use of limited data for constructing networks. This concern is strikingly relevant to ecology and conservation biology, where network analysis is used to infer connectivity across landscapes. In this context, movement among patches is the crucial parameter for interpreting connectivity but because of the difficulty of collecting reliable movement data, most network analysis proceeds with only indirect information on movement across landscapes rather than using observed movement to construct networks. Statistical models developed for social networks provide promising alternatives for landscape network construction because they can leverage limited movement information to predict linkages. Using two mark-recapture datasets on individual movement and connectivity across landscapes, we test whether commonly used network constructions for interpreting connectivity can predict actual linkages and network structure, and we contrast these approaches to social network models. We find that currently applied network constructions for assessing connectivity consistently, and substantially, overpredict actual connectivity, resulting in considerable overestimation of metapopulation lifetime. Furthermore, social network models provide accurate predictions of network structure, and can do so with remarkably limited data on movement. Social network models offer a flexible and powerful way for not only understanding the factors influencing connectivity but also for providing more reliable estimates of connectivity and metapopulation persistence in the face of limited data.

  3. Landscape and variation of RNA secondary structure across the human transcriptome.

    OpenAIRE

    Wan, Y; Qu, K; Zhang, QC; Flynn, RA; Manor, O; Ouyang, Z; Zhang, J; Spitale, RC; Snyder, MP; Segal, E; Chang, HY

    2014-01-01

    In parallel to the genetic code for protein synthesis, a second layer of information is embedded in all RNA transcripts in the form of RNA structure. RNA structure influences practically every step in the gene expression program. However, the nature of most RNA structures or effects of sequence variation on structure are not known. Here we report the initial landscape and variation of RNA secondary structures (RSSs) in a human family trio (mother, father and their child). This provides a comp...

  4. Assessment of landscape diversity and determination of landscape hotspots - a case of Slovenia

    Science.gov (United States)

    Perko, Drago; Ciglič, Rok; Hrvatin, Mauro

    2017-04-01

    Areas with high landscape diversity can be regarded as landscape hotspots, and vice versa areas with low landscape diversity can be marked as landscape coldspots. The main purpose of this paper is to use quantitative geoinformatical approach and identify parts of our test area (the country of Slovenia) that can be described as very diverse according to natural landscapes and natural elements. We used different digital raster data of natural elements and landscape classifications and defined landscape diversity and landscape hotspots. We defined diversity for each raster pixel by counting the number of different unique types of landscape elements and types of landscapes in its neighborhood. Namely, the method was used separately to define diversity according to natural elements (types of relief forms, rocks, and vegetation) and diversity according to existing geographical landscape classifications of Slovenia (types of landscapes). In both cases one-tenth of Slovenia's surface with the highest landscape diversity was defined as landscape hotspots. The same applies to the coldspots. Additionally we tested the same method of counting different types of landscapes in certain radius also for the area of Europe in order to find areas that are more diverse at continental level. By doing so we were able to find areas that have similar level of diversity as Slovenia according to different European landscape classifications. Areas with landscape diversity may have an advantage in economic development, especially in tourism. Such areas are also important for biodiversity, habitat, and species diversity. On the other hand, localities where various natural influences mix can also be areas where it is hard to transfer best practices from one place to another because of the varying responses of the landscapes to human intervention. Thus it is important to know where areas with high landscape diversity are.

  5. Competing Wind Energy Discourses, Contested Landscapes

    Directory of Open Access Journals (Sweden)

    Antje Otto

    2014-10-01

    Full Text Available The impairment of landscapes is a concern constantly raised against wind energy developments in Germany as in other countries. Often, landscapes or landscape types are treated in the literature as essentialist or at least as uncontested categories. We analyse two examples of local controversies about wind energy, in which “landscape” is employed by supporters and opponents alike, from a poststructuralist and discourse theoretical angle. The aim is to identify and compare landscape constructs produced in the micro discourses of wind energy objectors and proponents at local level (a within each case, (b between the two cases and (c with landscape constructs that were previously found in macro discourses. One major finding is that several different landscapes can exist at one and the same place. Furthermore there seems to be a relatively stable set of competing landscape concepts which is reproduced in specific controversies. The paper concludes by highlighting practical consequences and by identifying promising avenues of further research.

  6. Regional and landscape-scale variability of Landsat-observed vegetation dynamics in northwest Siberian tundra

    International Nuclear Information System (INIS)

    Frost, Gerald V; Epstein, Howard E; Walker, Donald A

    2014-01-01

    Widespread increases in Arctic tundra productivity have been documented for decades using coarse-scale satellite observations, but finer-scale observations indicate that changes have been very uneven, with a high degree of landscape- and regional-scale heterogeneity. Here we analyze time-series of the Normalized Difference Vegetation Index (NDVI) observed by Landsat (1984–2012), to assess landscape- and regional-scale variability of tundra vegetation dynamics in the northwest Siberian Low Arctic, a little-studied region with varied soils, landscape histories, and permafrost attributes. We also estimate spatio-temporal rates of land-cover change associated with expansion of tall alder (Alnus) shrublands, by integrating Landsat time-series with very-high-resolution imagery dating to the mid-1960s. We compiled Landsat time-series for eleven widely-distributed landscapes, and performed linear regression of NDVI values on a per-pixel basis. We found positive net NDVI trends (‘greening’) in nine of eleven landscapes. Net greening occurred in alder shrublands in all landscapes, and strong greening tended to correspond to shrublands that developed since the 1960s. Much of the spatial variability of greening within landscapes was linked to landscape physiography and permafrost attributes, while between-landscape variability largely corresponded to differences in surficial geology. We conclude that continued increases in tundra productivity in the region are likely in upland tundra landscapes with fine-textured, cryoturbated soils; these areas currently tend to support discontinuous vegetation cover, but are highly susceptible to rapid increases in vegetation cover, as well as land-cover changes associated with the development of tall shrublands. (paper)

  7. Legislative Framework for Landscape Planning in Latvia

    Science.gov (United States)

    Nitavska, Natalija; Zigmunde, Daiga

    2017-10-01

    With the adoption and the ratification of the European Landscape Convention a legally justified need for a clear landscape policy was grounded in the European countries. It includes the elaboration of the new and the improvement of the existing legislative documents on landscape planning, protection and management. The aim of the particular study is to analyse the existing legislative documents in Latvia influencing landscape planning on different scales / and the implementation of the European Landscape Convention. The study emphasizes the complex structure of the Latvian legislative framework affected by the distribution of the normative documents under the various ministries. Therefore, the main problem is unclear responsibility levels and organizational system for solving the issues regarding landscape planning, protection and management. Thus the various discussions between the involved disciplines and responsible institutions are arising. Two groups of the legislative documents influencing the implementation of the landscape policy in Latvia are detected within the study. The first group is strategic documents determining main landscape planning principles and directions at European, national, regional and professional or sectoral level. The second group is operational documents providing a set of actions for the landscape planning, protection and management at the local or the municipality level. The study concludes that operational documents developed by the municipalities are in high importance because of their direct influence on the landscape planning in Latvia. This often leads to the different landscape planning requirements included in the normative documents of the neighbouring municipalities, although the spatial and ecological borders of the visual landscape do not fit with the formal borders of the municipalities. Thus, it is essential to develop the common principles and actions that would be incumbent on all municipalities to provide the

  8. Isolated guitar transcription using a deep belief network

    Directory of Open Access Journals (Sweden)

    Gregory Burlet

    2017-03-01

    Full Text Available Music transcription involves the transformation of an audio recording to common music notation, colloquially referred to as sheet music. Manually transcribing audio recordings is a difficult and time-consuming process, even for experienced musicians. In response, several algorithms have been proposed to automatically analyze and transcribe the notes sounding in an audio recording; however, these algorithms are often general-purpose, attempting to process any number of instruments producing any number of notes sounding simultaneously. This paper presents a polyphonic transcription algorithm that is constrained to processing the audio output of a single instrument, specifically an acoustic guitar. The transcription system consists of a novel note pitch estimation algorithm that uses a deep belief network and multi-label learning techniques to generate multiple pitch estimates for each analysis frame of the input audio signal. Using a compiled dataset of synthesized guitar recordings for evaluation, the algorithm described in this work results in an 11% increase in the f-measure of note transcriptions relative to Zhou et al.’s (2009 transcription algorithm in the literature. This paper demonstrates the effectiveness of deep, multi-label learning for the task of polyphonic transcription.

  9. Inflation in random Gaussian landscapes

    Energy Technology Data Exchange (ETDEWEB)

    Masoumi, Ali; Vilenkin, Alexander; Yamada, Masaki, E-mail: ali@cosmos.phy.tufts.edu, E-mail: vilenkin@cosmos.phy.tufts.edu, E-mail: Masaki.Yamada@tufts.edu [Institute of Cosmology, Department of Physics and Astronomy, Tufts University, Medford, MA 02155 (United States)

    2017-05-01

    We develop analytic and numerical techniques for studying the statistics of slow-roll inflation in random Gaussian landscapes. As an illustration of these techniques, we analyze small-field inflation in a one-dimensional landscape. We calculate the probability distributions for the maximal number of e-folds and for the spectral index of density fluctuations n {sub s} and its running α {sub s} . These distributions have a universal form, insensitive to the correlation function of the Gaussian ensemble. We outline possible extensions of our methods to a large number of fields and to models of large-field inflation. These methods do not suffer from potential inconsistencies inherent in the Brownian motion technique, which has been used in most of the earlier treatments.

  10. Magical Landscapes and Designed Cities

    DEFF Research Database (Denmark)

    Raahauge, Kirsten Marie

    2008-01-01

    with “something special,” a feel-good, (almost spiritual) healing power (just moments away from the bustling city). In Melanesia, such a spiritual force goes by the name of “mana”. Århus’ mana landscapes are only invested with this huge, floating quality because they are near the city. Furthermore, they are seen...... from the point of view of the city, where order, design, planning and commerce are important cityscape qualities. The article deals with the way in which these two parts of the city, landscape and brandscape are complementary parts of the city-web. Analytical points made by Mauss, Lévi......-Strauss and Greimas are discussed in connection with the empirical setting of the city of Århus...

  11. A landscape of field theories

    Energy Technology Data Exchange (ETDEWEB)

    Maxfield, Travis [Enrico Fermi Institute, University of Chicago,Chicago, IL 60637 (United States); Robbins, Daniel [George P. and Cynthia W. Mitchell Institute for Fundamental Physics and Astronomy,Texas A& M University,College Station, TX 77843-4242 (United States); Sethi, Savdeep [Enrico Fermi Institute, University of Chicago,Chicago, IL 60637 (United States)

    2016-11-28

    Studying a quantum field theory involves a choice of space-time manifold and a choice of background for any global symmetries of the theory. We argue that many more choices are possible when specifying the background. In the context of branes in string theory, the additional data corresponds to a choice of supergravity tensor fluxes. We propose the existence of a landscape of field theory backgrounds, characterized by the space-time metric, global symmetry background and a choice of tensor fluxes. As evidence for this landscape, we study the supersymmetric six-dimensional (2,0) theory compactified to two dimensions. Different choices of metric and flux give rise to distinct two-dimensional theories, which can preserve differing amounts of supersymmetry.

  12. DNA template dependent accuracy variation of nucleotide selection in transcription.

    Directory of Open Access Journals (Sweden)

    Harriet Mellenius

    Full Text Available It has been commonly assumed that the effect of erroneous transcription of DNA genes into messenger RNAs on peptide sequence errors are masked by much more frequent errors of mRNA translation to protein. We present a theoretical model of transcriptional accuracy. It uses experimentally estimated standard free energies of double-stranded DNA and RNA/DNA hybrids and predicts a DNA template dependent transcriptional accuracy variation spanning several orders of magnitude. The model also identifies high-error as well a high-accuracy transcription motifs. The source of the large accuracy span is the context dependent variation of the stacking free energy of pairs of correct and incorrect base pairs in the ever moving transcription bubble. Our model predictions have direct experimental support from recent single molecule based identifications of transcriptional errors in the C. elegans transcriptome. Our conclusions challenge the general view that amino acid substitution errors in proteins are mainly caused by translational errors. It suggests instead that transcriptional error hotspots are the dominating source of peptide sequence errors in some DNA template contexts, while mRNA translation is the major cause of protein errors in other contexts.

  13. How wind power landscapes change

    DEFF Research Database (Denmark)

    Möller, Bernd

    2006-01-01

    Following 25 years of continuous development, Danish wind energy landscapes are going to face changes. Ceased on-shore construction, unresolved re-powering and stalled regional planning characterize the situation overshadowed by off-shore development. One of the factors inhibiting development...... in general. However, the pattern of visibility will become askew, and the present homogenous distribution of visibility will disappear. This skewness, together with changing ownership and receding local involvement, could eventually lead to lower popular acceptance of wind power....

  14. Biodiversity conservation in agricultural landscapes

    OpenAIRE

    Josefsson, Jonas

    2015-01-01

    Agricultural industrialization alters rural landscapes in Europe, causing large-scale and rapid loss of important biodiversity. The principal instruments to protect farmland biodiversity are various agri-environmental measures (AEMs) in the EU Common Agricultural Policy (CAP). However, growing awareness of shortcomings to CAP biodiversity integration prompts examination of causes and potential solutions. This thesis assesses the importance of structural heterogeneity of crop and non-crop habi...

  15. Unveiling the Antarctic subglacial landscape.

    Science.gov (United States)

    Warner, Roland; Roberts, Jason

    2010-05-01

    Better knowledge of the subglacial landscape of Antarctica is vital to reducing uncertainties regarding prediction of the evolution of the ice sheet. These uncertainties are associated with bedrock geometry for ice sheet dynamics, including possible marine ice sheet instabilities and subglacial hydrological pathways (e.g. Wright et al., 2008). Major collaborative aerogeophysics surveys motivated by the International Polar Year (e.g. ICECAP and AGAP), and continuing large scale radar echo sounding campaigns (ICECAP and NASA Ice Bridge) are significantly improving the coverage. However, the vast size of Antarctica and logistic difficulties mean that data gaps persist, and ice thickness data remains spatially inhomogeneous. The physics governing large scale ice sheet flow enables ice thickness, and hence bedrock topography, to be inferred from knowledge of ice sheet surface topography and considerations of ice sheet mass balance, even in areas with sparse ice thickness measurements (Warner and Budd, 2000). We have developed a robust physically motivated interpolation scheme, based on these methods, and used it to generate a comprehensive map of Antarctic bedrock topography, using along-track ice thickness data assembled for the BEDMAP project (Lythe et al., 2001). This approach reduces ice thickness biases, compared to traditional inverse distance interpolation schemes which ignore the information available from considerations of ice sheet flow. In addition, the use of improved balance fluxes, calculated using a Lagrangian scheme, eliminates the grid orientation biases in ice fluxes associated with finite difference methods (Budd and Warner, 1996, Le Brocq et al., 2006). The present map was generated using a recent surface DEM (Bamber et al., 2009, Griggs and Bamber, 2009) and accumulation distribution (van de Berg et al., 2006). Comparing our results with recent high resolution regional surveys gives confidence that all major subglacial topographic features are

  16. Landscape modelling case studies for Olkiluoto site in 2005-2006

    International Nuclear Information System (INIS)

    Broed, R.

    2007-05-01

    This report documents the landscape modelling test cases implemented in the fall of 2005, complemented in 2006. The objective of the report is to illustrate the application of the landscape modelling methodology, to investigate the important factors of influence and to clarify methodological aspects. The results of this analysis are intended to serve as a basis for future assessments. Landscape modelling represents an approach for estimating doses to inhabitants of a landscape consisting of several interacting ecosystems which are affected by the contamination from potential radionuclide releases from a deep geological repository. From the model outputs, Landscape Dose Conversion Factors (LDFs) are calculated. These represent, for each radionuclide of concern, an estimate of the equilibrium dose arising from a constant unit release of activity into the landscape objects. Modelling is undertaken in the current report for static landscapes corresponding to future landscape configurations forecasted for four different points in time. The results of this modelling are not yet suitable for practical application to estimate doses which could result from the planned repository at the Olkiluoto site. To suit this eventual purpose, refinements of the modelling and reduced uncertainty of the important parameters used in the models will be necessary. The current report intends rather to investigate the important factors influencing modelled future doses arising from the planned repository and to clarify methodological aspects. Notwithstanding the restrictions of the current modelling, important conclusions already can be drawn from the results presented in this report. Several methodological aspects are addressed in this report. These are, in particular, the impact of the landscape configurations on the resulting dose estimates, the importance of model parameters and assumptions for the assessment results, the database for radionuclides requiring consideration, the importance

  17. State Transitions in Semiarid Landscapes

    Science.gov (United States)

    Phillips, J. D.

    2012-04-01

    The U.S. Department of Agriculture has developed a large number of state-and-transition models (STM) to predict and interpret changes in vegetation communities in drylands of the southwestern U.S. These are represented as box-and-arrow models indicating potential changes in response to various combinations of management practices and environmental forcings. Analysis of the 320 STMs developed for areas within the state of Texas reveals two important aspects of environmental change in semiarid environments. First, the STMs are highly local—they are specific to very particular combinations of landform, soil, and climate. This is consistent with the perfect landscape concept in geomorphology, which emphasizes the irreducible importance of geographically and historically contingent local factors in addition to universal laws or principles in determining the state or condition of landscapes. Second, analysis of the STMs using algebraic graph theory shows that a majority of them have structures that tend to amplify effects of change and disturbances. In many cases the STMs represent a form of self-organization characterized by the potential of divergent behavior rather than convergence toward a dominant pattern or outcome. These results indicate that geomorphic, hydrologic, and ecological responses to climate and land use change are likely to be highly variable and idiosyncratic, both within and between semiarid landscapes of Texas.

  18. Implementing Forest Landscape Restorationin Ethiopia

    Directory of Open Access Journals (Sweden)

    Till Pistorius

    2017-02-01

    Full Text Available Driven by various initiatives and international policy processes, the concept of Forest Landscape Restoration, is globally receiving renewed attention. It is seen internationally and in national contexts as a means for improving resilience of land and communities in the face of increasing environmental degradation through different forest activities. Ethiopia has made a strong voluntary commitment in the context of the Bonn Challenge—it seeks to implement Forest Landscape Restoration (FLR on 15 million ha. In the context of rural Ethiopia, forest establishment and restoration provide a promising approach to reverse the widespread land degradation, which is exacerbated by climate change and food insecurity. This paper presents an empirical case study of FLR opportunities in the Amhara National Regional State, Ethiopia’s largest spans of degraded and barren lands. Following the Restoration Opportunity Assessment Methodology, the study categorizes the main types of landscapes requiring restoration, identifies and prioritizes respective FLR options, and details the costs and benefits associated with each of the five most significant opportunities: medium to large‐scale afforestation and reforestation activities on deforested or degraded marginal land not suitable for agriculture, the introduction of participatory forest management, sustainable woodland management combined with value chain investments, restoration of afro‐alpine and sub‐afro‐alpine areas and the establishment of woodlots.

  19. Aridity and decomposition processes in complex landscapes

    Science.gov (United States)

    Ossola, Alessandro; Nyman, Petter

    2015-04-01

    Decomposition of organic matter is a key biogeochemical process contributing to nutrient cycles, carbon fluxes and soil development. The activity of decomposers depends on microclimate, with temperature and rainfall being major drivers. In complex terrain the fine-scale variation in microclimate (and hence water availability) as a result of slope orientation is caused by differences in incoming radiation and surface temperature. Aridity, measured as the long-term balance between net radiation and rainfall, is a metric that can be used to represent variations in water availability within the landscape. Since aridity metrics can be obtained at fine spatial scales, they could theoretically be used to investigate how decomposition processes vary across complex landscapes. In this study, four research sites were selected in tall open sclerophyll forest along a aridity gradient (Budyko dryness index ranging from 1.56 -2.22) where microclimate, litter moisture and soil moisture were monitored continuously for one year. Litter bags were packed to estimate decomposition rates (k) using leaves of a tree species not present in the study area (Eucalyptus globulus) in order to avoid home-field advantage effects. Litter mass loss was measured to assess the activity of macro-decomposers (6mm litter bag mesh size), meso-decomposers (1 mm mesh), microbes above-ground (0.2 mm mesh) and microbes below-ground (2 cm depth, 0.2 mm mesh). Four replicates for each set of bags were installed at each site and bags were collected at 1, 2, 4, 7 and 12 months since installation. We first tested whether differences in microclimate due to slope orientation have significant effects on decomposition processes. Then the dryness index was related to decomposition rates to evaluate if small-scale variation in decomposition can be predicted using readily available information on rainfall and radiation. Decomposition rates (k), calculated fitting single pool negative exponential models, generally

  20. Governing Forest Landscape Restoration: Cases from Indonesia

    Directory of Open Access Journals (Sweden)

    Cora van Oosten

    2014-05-01

    Full Text Available Forest landscape restoration includes both the planning and implementation of measures to restore degraded forests within the perspective of the wider landscape. Governing forest landscape restoration requires fundamental considerations about the conceptualisation of forested landscapes and the types of restoration measures to be taken, and about who should be engaged in the governance process. A variety of governance approaches to forest landscape restoration exist, differing in both the nature of the object to be governed and the mode of governance. This paper analyses the nature and governance of restoration in three cases of forest landscape restoration in Indonesia. In each of these cases, both the original aim for restoration and the initiators of the process differ. The cases also differ in how deeply embedded they are in formal spatial planning mechanisms at the various political scales. Nonetheless, the cases show similar trends. All cases show a dynamic process of mobilising the landscape’s stakeholders, plus a flexible process of crafting institutional space for conflict management, negotiation and decision making at the landscape level. As a result, the landscape focus changed over time from reserved forests to forested mosaic lands. The cases illustrate that the governance of forest landscape restoration should not be based on strict design criteria, but rather on a flexible governance approach that stimulates the creation of novel public-private institutional arrangements at the landscape level.

  1. Habitat and landscape characteristics underlying anuran community structure along an urban-rural gradient.

    Science.gov (United States)

    Pillsbury, Finn C; Miller, James R

    2008-07-01

    Urbanization has been cited as an important factor in worldwide amphibian declines, and although recent work has illustrated the important influence of broad-scale ecological patterns and processes on amphibian populations, little is known about the factors structuring amphibian communities in urban landscapes. We therefore examined amphibian community responses to wetland habitat availability and landscape characteristics along an urban-rural gradient in central Iowa, USA, a region experiencing rapid suburban growth. We conducted call surveys at 61 wetlands to estimate anuran calling activity, and quantified wetland habitat structure and landscape context. We used canonical correspondence analysis (CCA) to examine patterns in anuran community structure and identify the most important variables associated with those patterns. Urban density at the landscape scale had a significant negative influence on overall anuran abundance and diversity. While every species exhibited a decrease in abundance with increasing urban density, this pattern was especially pronounced for species requiring post-breeding upland habitats. Anurans most affected by urbanization were those associated with short hydroperiods, early breeding activity, and substantial upland habitat use. We suggest that broad-scale landscape fragmentation is an important factor underlying anuran community structure in this region, possibly due to limitations on the accessibility of otherwise suitable habitat in fragmented urban landscapes. This study underscores the importance of a regional approach to amphibian conservation in urban and urbanizing areas; in fragmented landscapes, a network of interconnected wetland and upland habitats may be more likely to support a successful, diverse anuran community than will isolated sites.

  2. Multi-scale Analysis of High Resolution Topography: Feature Extraction and Identification of Landscape Characteristic Scales

    Science.gov (United States)

    Passalacqua, P.; Sangireddy, H.; Stark, C. P.

    2015-12-01

    With the advent of digital terrain data, detailed information on terrain characteristics and on scale and location of geomorphic features is available over extended areas. Our ability to observe landscapes and quantify topographic patterns has greatly improved, including the estimation of fluxes of mass and energy across landscapes. Challenges still remain in the analysis of high resolution topography data; the presence of features such as roads, for example, challenges classic methods for feature extraction and large data volumes require computationally efficient extraction and analysis methods. Moreover, opportunities exist to define new robust metrics of landscape characterization for landscape comparison and model validation. In this presentation we cover recent research in multi-scale and objective analysis of high resolution topography data. We show how the analysis of the probability density function of topographic attributes such as slope, curvature, and topographic index contains useful information for feature localization and extraction. The analysis of how the distributions change across scales, quantified by the behavior of modal values and interquartile range, allows the identification of landscape characteristic scales, such as terrain roughness. The methods are introduced on synthetic signals in one and two dimensions and then applied to a variety of landscapes of different characteristics. Validation of the methods includes the analysis of modeled landscapes where the noise distribution is known and features of interest easily measured.

  3. Inverted edge effects on carbon stocks in human-dominated landscapes

    Science.gov (United States)

    Romitelli, I.; Keller, M.; Vieira, S. A.; Metzger, J. P.; Reverberi Tambosi, L.

    2017-12-01

    Although the importance of tropical forests to regulate greenhouse gases is well documented, little is known about what factors affect the ability of these forests to store carbon in human-dominated landscapes. Among those factors, the landscape structure, particularly the amount of forest cover, the type of matrix and edge effects, can have important roles. We tested how carbon stock is influenced by a combination of factors of landscape composition (pasture and forest cover), landscape configuration (edge effect) and relief factors (slope, elevation and aspect). To test those relationships, we performed a robust carbon stock estimation with inventory and LiDAR data in human-dominated landscapes from the Brazilian Atlantic forest region. The study area showed carbon stock mean 45.49 ± 9.34 Mg ha-1. The interaction between forest cover, edge effect and slope was the best combination explanatory of carbon stock. We observed an inverted edge effect pattern where carbon stock is higher close to the edges of the studied secondary forests. This inverted edge effect observed contradicts the usual pattern reported in the literature for mature forests. We suppose this pattern is related with a positive effect that edge conditions can have stimulating forest regeneration, but the underlying processes to explain the observed pattern should still be tested. Those results suggest that Carbon stocks in human-dominated and fragmented landscapes can be highly affected by the landscape structure, and particularly that edges conditions can favor carbon sequestration in regenerating tropical forests.

  4. Assessment of visual landscape quality using IKONOS imagery.

    Science.gov (United States)

    Ozkan, Ulas Yunus

    2014-07-01

    The assessment of visual landscape quality is of importance to the management of urban woodlands. Satellite remote sensing may be used for this purpose as a substitute for traditional survey techniques that are both labour-intensive and time-consuming. This study examines the association between the quality of the perceived visual landscape in urban woodlands and texture measures extracted from IKONOS satellite data, which features 4-m spatial resolution and four spectral bands. The study was conducted in the woodlands of Istanbul (the most important element of urban mosaic) lying along both shores of the Bosporus Strait. The visual quality assessment applied in this study is based on the perceptual approach and was performed via a survey of expressed preferences. For this purpose, representative photographs of real scenery were used to elicit observers' preferences. A slide show comprising 33 images was presented to a group of 153 volunteers (all undergraduate students), and they were asked to rate the visual quality of each on a 10-point scale (1 for very low visual quality, 10 for very high). Average visual quality scores were calculated for landscape. Texture measures were acquired using the two methods: pixel-based and object-based. Pixel-based texture measures were extracted from the first principle component (PC1) image. Object-based texture measures were extracted by using the original four bands. The association between image texture measures and perceived visual landscape quality was tested via Pearson's correlation coefficient. The analysis found a strong linear association between image texture measures and visual quality. The highest correlation coefficient was calculated between standard deviation of gray levels (SDGL) (one of the pixel-based texture measures) and visual quality (r = 0.82, P landscapes can be estimated by using texture measures extracted from satellite data in combination with appropriate modelling techniques.

  5. Immigration rates in fragmented landscapes--empirical evidence for the importance of habitat amount for species persistence.

    Directory of Open Access Journals (Sweden)

    Thomas Püttker

    Full Text Available BACKGROUND: The total amount of native vegetation is an important property of fragmented landscapes and is known to exert a strong influence on population and metapopulation dynamics. As the relationship between habitat loss and local patch and gap characteristics is strongly non-linear, theoretical models predict that immigration rates should decrease dramatically at low levels of remaining native vegetation cover, leading to patch-area effects and the existence of species extinction thresholds across fragmented landscapes with different proportions of remaining native vegetation. Although empirical patterns of species distribution and richness give support to these models, direct measurements of immigration rates across fragmented landscapes are still lacking. METHODOLOGY/PRINCIPAL FINDINGS: Using the Brazilian Atlantic forest marsupial Gray Slender Mouse Opossum (Marmosops incanus as a model species and estimating demographic parameters of populations in patches situated in three landscapes differing in the total amount of remaining forest, we tested the hypotheses that patch-area effects on population density are apparent only at intermediate levels of forest cover, and that immigration rates into forest patches are defined primarily by landscape context surrounding patches. As expected, we observed a positive patch-area effect on M. incanus density only within the landscape with intermediate forest cover. Density was independent of patch size in the most forested landscape and the species was absent from the most deforested landscape. Specifically, the mean estimated numbers of immigrants into small patches were lower in the landscape with intermediate forest cover compared to the most forested landscape. CONCLUSIONS/SIGNIFICANCE: Our results reveal the crucial importance of the total amount of remaining native vegetation for species persistence in fragmented landscapes, and specifically as to the role of variable immigration rates in

  6. Landscape and land use history of Eurajoki between 1840 and 2007: Analysis of geographical data and landscape transformation

    International Nuclear Information System (INIS)

    Koistinen, T.; Kaeyhkoe, N.

    2011-11-01

    , vectorizing of the selected elements, standardizing of the heterogeneous spatial data and analyzing and estimating of the quality of the produced data. In addition report includes description of used landscape change study methods and visualizations of the produced spatial data and change analysis results. The future possibilities and restrictions of the data are also discussed. Main challenges for the use are thematic differencies and inconsistencies between the original map products. Different scales and geometric errors cause also some concerns for the future use. The spatial data produced from the more general map products can however turn out to be useful for example as approaching maps. The time scale of the study starts from the 1840's and ends in 2007. The maps used in this project turned out to be very varying in their consistency and reliability. This alternation was evident also between the landscape elements. Fields, meadows and buildings were depicted in the most consistent manner between the maps, altough meadow as a concept has somewhat changed during the research period. Most of the meadows in Eurajoki disappeared by the 1903-1904 as most of them were ploughed into fields. Measuring the changes in small lakes between the historical spatial data and the modern land use information was more challenging as precision of depiction was so different between the products. Comparing wetlands was also very difficult task because the way of classifying and depicting of them varied from one historical map to another. The basic structure of settlements has maintained during the whole study period although the housing in different parts of the municipal has somewhat changed it's emphasis. The basic composition of roadnetwork has also remained throughout the study period. The only clear new feature in the landscape is the highway that was built in 1950's. (orig.)

  7. RNA-guided transcriptional regulation

    Science.gov (United States)

    Church, George M.; Mali, Prashant G.; Esvelt, Kevin M.

    2016-02-23

    Methods of modulating expression of a target nucleic acid in a cell are provided including introducing into the cell a first foreign nucleic acid encoding one or more RNAs complementary to DNA, wherein the DNA includes the target nucleic acid, introducing into the cell a second foreign nucleic acid encoding a nuclease-null Cas9 protein that binds to the DNA and is guided by the one or more RNAs, introducing into the cell a third foreign nucleic acid encoding a transcriptional regulator protein or domain, wherein the one or more RNAs, the nuclease-null Cas9 protein, and the transcriptional regulator protein or domain are expressed, wherein the one or more RNAs, the nuclease-null Cas9 protein and the transcriptional regulator protein or domain co-localize to the DNA and wherein the transcriptional regulator protein or domain regulates expression of the target nucleic acid.

  8. Transcriptional control of megakaryocyte development.

    Science.gov (United States)

    Goldfarb, A N

    2007-10-15

    Megakaryocytes are highly specialized cells that arise from a bipotent megakaryocytic-erythroid progenitor (MEP). This developmental leap requires coordinated activation of megakaryocyte-specific genes, radical changes in cell cycle properties, and active prevention of erythroid differentiation. These programs result from upregulation of megakaryocyte-selective transcription factors, downregulation of erythroid-selective transcription factors and ongoing mediation of common erythro-megakaryocytic transcription factors. Unlike most developmental programs, no single lineage-unique family of master regulators exerts executive control over the megakaryocytic plan. Rather, an assemblage of non-unique factors and signals converge to determine lineage and differentiation. In human megakaryopoiesis, hereditary disorders of platelet production have confirmed contributions from three distinct transcription factor families. Murine models have extended this repertoire to include multiple additional factors. At a mechanistic level, the means by which these non-unique factors collaborate in the establishment of a perfectly unique cell type remains a central question.

  9. Incorporating bioenergy into sustainable landscape designs

    DEFF Research Database (Denmark)

    Dale, Virginia H.; Kline, Keith L.; Buford, Marilyn A.

    2016-01-01

    The paper describes an approach to landscape design that focuses on integrating bioenergy production with other components of environmental, social and economic systems. Landscape design as used here refers to a spatially explicit, collaborative plan for management of landscapes and supply chains...... land-management objectives from a wide array of stakeholders, up-front planning requirements, and the complexity and level of effort needed for successful stakeholder involvement. A landscape design process may be stymied by insufficient data or participation. An impetus for coordination is critical....... Landscape design can involve multiple scales and build on existing practices to reduce costs or enhance services. Appropriately applied to a specific context, landscape design can help people assess trade-offs when making choices about locations, types of feedstock, transport, refining and distribution...

  10. Linking ecosystem services with cultural landscape research

    DEFF Research Database (Denmark)

    Schaich, Harald; Biding, Claudia; Plieninger, Tobias

    2010-01-01

    The concept of ecosystem services facilitates the valuation of the multiple services from ecosystems and landscapes, the identification of trade-offs between different land use scenarios, and also informs decision making in land use planning. Unfortunately, cultural services have been mostly...... neglected within the ecosystem services framework. This could result in trade-off assessments which are biased and mislead ecosystem management and landscape planning. However, cultural landscape research approaches have proven valuable in the assessment of different nonmaterial landscape values...... and cultural services. In this paper, we compare the objectives, approaches, and methodologies adopted by ecosystem services research and cultural landscape research through a bibliographic research. Both research communities investigate the human dimension of ecosystems and landscapes and, hence, study...

  11. Processes of aesthetic transformation in ordinary landscapes

    DEFF Research Database (Denmark)

    Krarup, Jonna Majgaard

    2004-01-01

    it was distributed systematically as an almost industrially produced landscape element. Windbreaks are now regarded as a traditional element in the Danish agricultural landscape. As a landscape element it is an international phenomenon known and used in Germany, France, England etc. Originally local farming...... practices, natural conditions, techniques and national legislation in the respective countries, formed the aesthetic expression. In this respect one could speak of the impact of northern nature on the aesthetic expression of the Danish windbreaks, as well as the impact from national phenomena....... These features determined the specific aesthetic and architectural identity of ordinary Danish, i.e. Nordic, landscapes. Contemporary cultural changes such as the aesthetification of everyday life and of ordinary landscape, i.e. farming landscape, are now manifest in the way the windbreaks are motivated...

  12. Roads Belong In the Urban Landscape

    DEFF Research Database (Denmark)

    Clemmensen, Thomas Juel

    2012-01-01

    In spite of being an essential part of the system of automobility and as such playing an important role in the development of urban landscapes, road networks seldom attracts much attention among architects involved in the planning and design of urban landscapes. One reason is probably found...... in the dominance of the zoning approach to planning, where road planning easily becomes isolated and reduced to a matter of traffic regulation and transport economy. Another possible reason could be, as suggested by the Australian landscape architect Christopher Sawyer, that road networks like other...... as landscape architects engage with road networks in profound ways, which moves beyond the purely visual and pictorial? Is it possible to conceptually (re)locate road networks in the landscape? The paper will address these questions by discussing different understandings of landscape and its relation...

  13. Genetic Variation in Past and Current Landscapes: Conservation Implications Based on Six Endemic Florida Scrub Plants

    International Nuclear Information System (INIS)

    Menges, E.S.; Pickert, R.; Dolan, R.W.; Yahr, R.; Gordon, D.R.

    2010-01-01

    If genetic variation is often positively correlated with population sizes and the presence of nearby populations and suitable habitats, landscape proxies could inform conservation decisions without genetic analyses. For six Florida scrub endemic plants (Dicerandra frutescens, Eryngium cuneifolium, Hypericum cumulicola, Liatris ohlingerae, Nolina brittoniana, and Warea carteri), we relate two measures of genetic variation, expected heterozygosity and alleles per polymorphic locus (APL), to population size and landscape variables. Presettlement areas were estimated based on soil preferences and GIS soils maps. Four species showed no genetic patterns related to population or landscape factors. The other two species showed significant but inconsistent patterns. For Liatris ohlingerae, APL was negatively related to population density and weakly, positively related to remaining presettlement habitat within 32 km. For Nolina brittoniana, APL increased with population size. The rather weak effects of population area/size and both past and current landscape structures suggest that genetic variation needs to be directly measured and not inferred for conservation planning.

  14. National Capital Planning Commission Meeting Transcripts

    Data.gov (United States)

    National Capital Planning Commission — Transcripts of the monthly (with the exception of August) National Capital Planning Commission meeting transcripts are provided for research to confirm actions taken...

  15. Landscape Architectural Design as Scientific Inquiry?

    OpenAIRE

    Lenzholzer, S.

    2011-01-01

    This presentation discusses ‘landscape architectural design as scientific inquiry’ and exemplifies this with the description of a design process within climate-responsive design leading to new design knowledge. ‘Research and design’ are issues that need increasing attention within landscape architecture academia. Substantial contributions on ‘research’ and ‘design’ exist within architectural theory [1,2,3,4]. However, within landscape architecture, there are only few publications on this topi...

  16. Architecture and Landscape. Approaches from archaeology

    Directory of Open Access Journals (Sweden)

    Rebeca Blanco-Rotea

    2017-11-01

    Full Text Available This work proposes a theoretical and conceptual basis for the study of the fortified landscapes of the Galician- Portuguese border in the Modern Age. From this theoretical framework there was designed a research program that studies these landscapes. It proposes an approach to the study of this type of archaeological record from the Landscape Archeology and the Archeology of Architecture, introducing the concepts of built space and Archeology of Built Space.

  17. Trends in landscape research and landscape planning : implications for PhD students

    NARCIS (Netherlands)

    Tress, G.; Tress, B.; Fry, G.; Antrop, M.

    2005-01-01

    This chapter introduces the contents of the book through an analysis of current trends in landscape research and landscape planning and a discussion of the consequences of these trends for PhD students.

  18. How Landscape Ecology Can Promote the Development of Sustainable Landscapes in Europe

    DEFF Research Database (Denmark)

    Brandt, Jesper; Antrop, Marc; Ramos, Isabel Loupa

    2013-01-01

    related concepts. International cooperation demands a certain harmonization of these concepts for better mutual understanding. The 2000 European Landscape Convention provided an important momentum to rethink research, policy and management of landscapes from the perspective of sustainable development...

  19. The semiotics of landscape design communication: towards a critical visual research approach in landscape architecture.

    NARCIS (Netherlands)

    Raaphorst, K.M.C.; Duchhart, I.; Knaap, van der W.G.M.; Roeleveld, Gerda; Brink, van den A.

    2017-01-01

    In landscape architecture, visual representations are the primary means of communication between stakeholders in design processes. Despite the reliance on visual representations, little critical research has been undertaken by landscape architects on how visual communication forms work or their

  20. Modeling the relationship between landscape characteristics and water quality in a typical highly intensive agricultural small watershed, Dongting lake basin, south central China.

    Science.gov (United States)

    Li, Hongqing; Liu, Liming; Ji, Xiang

    2015-03-01

    Understanding the relationship between landscape characteristics and water quality is critically important for estimating pollution potential and reducing pollution risk. Therefore, this study examines the relationship between landscape characteristics and water quality at both spatial and temporal scales. The study took place in the Jinjing River watershed in 2010; seven landscape types and four water quality pollutions were chosen as analysis parameters. Three different buffer areas along the river were drawn to analyze the relationship as a function of spatial scale. The results of a Pearson's correlation coefficient analysis suggest that "source" landscape, namely, tea gardens, residential areas, and paddy lands, have positive effects on water quality parameters, while forests exhibit a negative influence on water quality parameters because they represent a "sink" landscape and the sub-watershed level is identified as a suitable scale. Using the principal component analysis, tea gardens, residential areas, paddy lands, and forests were identified as the main landscape index. A stepwise multiple regression analysis was employed to model the relationship between landscape characteristics and water quality for each season. The results demonstrate that both landscape composition and configuration affect water quality. In summer and winter, the landscape metrics explained approximately 80.7 % of the variance in the water quality variables, which was higher than that for spring and fall (60.3 %). This study can help environmental managers to understand the relationships between landscapes and water quality and provide landscape ecological approaches for water quality control and land use management.

  1. Quantitative analyses of empirical fitness landscapes

    International Nuclear Information System (INIS)

    Szendro, Ivan G; Franke, Jasper; Krug, Joachim; Schenk, Martijn F; De Visser, J Arjan G M

    2013-01-01

    The concept of a fitness landscape is a powerful metaphor that offers insight into various aspects of evolutionary processes and guidance for the study of evolution. Until recently, empirical evidence on the ruggedness of these landscapes was lacking, but since it became feasible to construct all possible genotypes containing combinations of a limited set of mutations, the number of studies has grown to a point where a classification of landscapes becomes possible. The aim of this review is to identify measures of epistasis that allow a meaningful comparison of fitness landscapes and then apply them to the empirical landscapes in order to discern factors that affect ruggedness. The various measures of epistasis that have been proposed in the literature appear to be equivalent. Our comparison shows that the ruggedness of the empirical landscape is affected by whether the included mutations are beneficial or deleterious and by whether intragenic or intergenic epistasis is involved. Finally, the empirical landscapes are compared to landscapes generated with the rough Mt Fuji model. Despite the simplicity of this model, it captures the features of the experimental landscapes remarkably well. (paper)

  2. Landscape Character of Pongkor Mining Ecotourism Area

    Science.gov (United States)

    Kusumoarto, A.; Gunawan, A.; Machfud; Hikmat, A.

    2017-10-01

    Pongkor Mining Ecotourism Area has a diverse landscape character as a potential landscape resources for the development of ecotourism destination. This area is part of the Mount of Botol Resort, Halimun Salak National Park (HSNP). This area also has a fairly high biodiversity. This study aims to identify and analysis the category of landscape character in the Pongkor Mining Ecotourism Area for the development of ecotourism destination. This study used a descriptive approach through field surveys and interviews, was carried out through two steps : 1) identify the landscape character, and 2) analysis of the landscape character. The results showed that in areas set aside for ecotourism destination in Pongkor Mining, landscape character category scattered forests, tailing ponds, river, plain, and the built environment. The Category of landscape character most dominant scattered in the area is forest, here is the river, plain, tailing ponds, the built environment, and plain. The landscape character in a natural environment most preferred for ecotourism activities. The landscape character that spread in the natural environment and the built environment is a potential that must be protected and modified such as elimination of incongruous element, accentuation of natural form, alteration of the natural form, intensification and enhanced visual quality intensively to be developed as a ecotourism destination area.

  3. Urban landscape infrastructures: Designing operative landscape structures for the built environment

    OpenAIRE

    Nijhuis, S.; Jauslin, D.T.

    2015-01-01

    This paper explores infrastructure as a type of landscape and landscape as a type of infrastructure. The hybridisation of the two concepts, landscape and infrastructure, seeks to redefine infrastructure beyond its strictly utilitarian definition, while allowing design disciplines to gain operative force in territorial transformation processes. This paper aims to put forward urban landscape infrastructures as a design concept, considering them as armatures for urban development and for facilit...

  4. From landscape to inflationary perturbations

    International Nuclear Information System (INIS)

    Hector, Cecelie

    2012-07-01

    We discuss a quantum tunneling event in a piecewise potential where the false vacuum part is either linear or quartic and the true vacuum is described by a quartic potential. We find exact solutions for these tunneling processes and explain how exact tunneling solutions can give information about the local shape of the string theory landscape. We investigate the existence of bounce solutions for effective potentials with sharp minima and maxima. We also partly derive the two-point correlation function for a λφ 4 -theory on a de Sitter background for a massless minimally coupled scalar field φ. (orig.)

  5. From landscape to inflationary perturbations

    Energy Technology Data Exchange (ETDEWEB)

    Hector, Cecelie

    2012-07-15

    We discuss a quantum tunneling event in a piecewise potential where the false vacuum part is either linear or quartic and the true vacuum is described by a quartic potential. We find exact solutions for these tunneling processes and explain how exact tunneling solutions can give information about the local shape of the string theory landscape. We investigate the existence of bounce solutions for effective potentials with sharp minima and maxima. We also partly derive the two-point correlation function for a {lambda}{phi}{sup 4}-theory on a de Sitter background for a massless minimally coupled scalar field {phi}. (orig.)

  6. Quality criteria for landscape visualisation

    International Nuclear Information System (INIS)

    Waldi, H.-P.; Witt, U. de

    1996-01-01

    The rapid expansion of wind energy utilisation in Western Europe can strain the limits of social acceptance with citizens living in wind development areas. One of the problems wind farm engineers and local authorities face is the visual impact of wind turbines. To determine the influence on the landscape visualisations of wind farms photorealistic compositions are used. In many cases it is part of the planning procedure. The quality of this visualization can strongly influence the success of the permission procedure. We will give criteria which can give help to reduce the possibility of unwanted manipulations. (author)

  7. Urban landscape infrastructures : Designing operative landscape structures for the built environment

    NARCIS (Netherlands)

    Nijhuis, S.; Jauslin, D.T.

    2015-01-01

    This paper explores infrastructure as a type of landscape and landscape as a type of infrastructure. The hybridisation of the two concepts, landscape and infrastructure, seeks to redefine infrastructure beyond its strictly utilitarian definition, while allowing design disciplines to gain operative

  8. The Globalized Landscape: Rural Landscape Change and Policy in the United States and European Union

    NARCIS (Netherlands)

    Nassauer, J.I.; Wascher, D.M.

    2008-01-01

    While some rural areas draw increasing populations to their landscape amenities and some are changed by the long reach of metropolitan sprawl, agriculture defines, and dominates rural landscapes. Amenity characteristics and ecological services of many rural landscapes occur in the context of

  9. Relationships between avian richness and landscape structure at multiple scales using multiple landscapes

    Science.gov (United States)

    Michael S. Mitchell; Scott H. Rutzmoser; T. Bently Wigley; Craig Loehle; John A. Gerwin; Patrick D. Keyser; Richard A. Lancia; Roger W. Perry; Christopher L. Reynolds; Ronald E. Thill; Robert Weih; Don White; Petra Bohall Wood

    2006-01-01

    Little is known about factors that structure biodiversity on landscape scales, yet current land management protocols, such as forest certification programs, place an increasing emphasis on managing for sustainable biodiversity at landscape scales. We used a replicated landscape study to evaluate relationships between forest structure and avian diversity at both stand...

  10. Understanding the whole city as landscape. A multivariate approach to urban landscape morphology

    Directory of Open Access Journals (Sweden)

    Richard Stiles

    2014-05-01

    Full Text Available The European Landscape Convention implies a requirement for signatory states to identify their urban landscapes which goes beyond the traditional focus on individual parks and green spaces and the links between them. Landscape ecological approaches can provide a useful model for identifying urban landscape types across a whole territory, but the variables relevant for urban landscapes are very different to those usually addressing rural areas. This paper presents an approach to classifying the urban landscape of Vienna that was developed in a research project funded by the Austrian Ministry for Transport, Innovation and Technology: ‘Urban Fabric and Microclimate Response’. Nine landscape types and a number of sub-types were defined, using a multivariate statistical approach which takes account of both morphological and urban climate related variables. Although the variables were selected to objectively reflect the factors that could best represent the urban climatic characteristics of the urban landscape, the results also provided a widely plausible representation of the structure of the city’s landscapes. Selected examples of the landscape types that were defined in this way were used both to simulate current microclimatic conditions and also to model the effects of possible climatic amelioration measures. Finally the paper looks forward to developing a more general-purpose urban landscape typology that allows investigating a much broader complex of urban landscape functions.

  11. Characterizing structural transitions using localized free energy landscape analysis.

    Directory of Open Access Journals (Sweden)

    Nilesh K Banavali

    Full Text Available Structural changes in molecules are frequently observed during biological processes like replication, transcription and translation. These structural changes can usually be traced to specific distortions in the backbones of the macromolecules involved. Quantitative energetic characterization of such distortions can greatly advance the atomic-level understanding of the dynamic character of these biological processes.Molecular dynamics simulations combined with a variation of the Weighted Histogram Analysis Method for potential of mean force determination are applied to characterize localized structural changes for the test case of cytosine (underlined base flipping in a GTCAGCGCATGG DNA duplex. Free energy landscapes for backbone torsion and sugar pucker degrees of freedom in the DNA are used to understand their behavior in response to the base flipping perturbation. By simplifying the base flipping structural change into a two-state model, a free energy difference of upto 14 kcal/mol can be attributed to the flipped state relative to the stacked Watson-Crick base paired state. This two-state classification allows precise evaluation of the effect of base flipping on local backbone degrees of freedom.The calculated free energy landscapes of individual backbone and sugar degrees of freedom expectedly show the greatest change in the vicinity of the flipping base itself, but specific delocalized effects can be discerned upto four nucleotide positions away in both 5' and 3' directions. Free energy landscape analysis thus provides a quantitative method to pinpoint the determinants of structural change on the atomic scale and also delineate the extent of propagation of the perturbation along the molecule. In addition to nucleic acids, this methodology is anticipated to be useful for studying conformational changes in all macromolecules, including carbohydrates, lipids, and proteins.

  12. LANDSCAPE ARCHAEOLOGY ALONG LIMES TRANSALUTANUS

    Directory of Open Access Journals (Sweden)

    Eugen S. Teodor

    2014-09-01

    Full Text Available The project addresses the historical monuments comprised in the longest Roman ‘linear defence’ structure present on the Romanian territory.Despite it being the longest, this historic structure is the least protected and the least known in its technical details. Was indeed Limes Transalutanus an incomplete limes (lacking civilian settlements, for example, an odd construction (a vallum without fossa, an early-alarm line rather than a proper defensive line? Taking on these historical and archaeological challenges, the team attempts to develop an investigation technology applicable to large scale archaeological landscapes - a full evaluation chain, involving aerial survey, surface survey, geophysical investigation, multispectral images analysis, statistic evaluation and archaeological diggings. This technological chain will be systematically applied on the whole length of the objective, that is, on a 155 km distance. The attempt to find answers to issues related to the earth works’ functionality, layout, structure, chronology and relation with adjacent sites will be grounded on exploring the relations of the monument with the surrounding environment, by focussing on finding methods to reconstruct the features of the ancient landscapes, like systematic drilling, palynological tests and toponymical studies.

  13. Landscape evolution by subglacial quarrying

    DEFF Research Database (Denmark)

    Ugelvig, Sofie Vej; Egholm, D.L.; Iverson, Neal R.

    In glacial landscape evolution models, subglacial erosion rates are often related to basal sliding or ice discharge by a power-law. This relation can be justified for bedrock abrasion because rock debris transported in the basal ice drives the erosion. However, a simple relation between rates of ...... evolution models. Geology, v. 40, no. 8, 679-682 (2012). Schoof, C. The effect of cavitation on glacier sliding. Proc. R. Soc. A , 461, 609-627 (2005). Jaeger, J.C., and Cook, N.G.W. Fundamentals of rock mechanics: New York, Chapman and Hall, 593 p. (1979)......In glacial landscape evolution models, subglacial erosion rates are often related to basal sliding or ice discharge by a power-law. This relation can be justified for bedrock abrasion because rock debris transported in the basal ice drives the erosion. However, a simple relation between rates...... of sliding and erosion is not well supported when considering models for quarrying of rock blocks from the bed. Iverson (2012) introduced a new subglacial quarrying model that operates from the theory of adhesive wear. The model is based on the fact that cavities, with a high level of bedrock differential...

  14. The Landscape of the Gibbet

    Science.gov (United States)

    Tarlow, Sarah; Dyndor, Zoe

    2015-01-01

    ABSTRACT From the Murder Act of 1752 until the Anatomy Act of 1832 it was forbidden to bury the bodies of executed murderers unless they had first been anatomised or ‘hung in chains’ (gibbeted). This paper considers some of the observations of the Wellcome-funded project ‘Harnessing the Power of the Criminal Corpse’ as they relate to the practice of gibbeting. The nature of hanging in chains is briefly described before an extensive discussion of the criteria by which gibbets, which often remained standing for many decades, were selected. These are: proximity to the scene of crime, visibility, and practicality. Exceptions, in the forms of those sentenced by the Admiralty Courts, and those sentenced in and around London, are briefly considered. Hanging in chains was an infrequent punishment (anatomical dissection was far more frequently practised) but it was the subject of huge public interest and attracted thousands of people. There was no specified time for which a body should remain hanging, and the gibbet often became a known landmark and a significant place in the landscape. There is a remarkable contrast between anatomical dissection, which obliterates and anonymises the body of the individual malefactor, and hanging in chains, which leaves a highly personalised and enduring imprint on the actual and imaginative landscape. PMID:27335506

  15. Landscape for biological diversity in Europe

    NARCIS (Netherlands)

    Jongman, R.H.G.

    2002-01-01

    The European landscape reflects its agricultural legacy, but agriculture is losing its dominant position in the rural economy. The rural landscapes of Europe are in a process of polarization between intensive land use and naturalistic areas. In addition to this process, fragmentation of the

  16. Airborne laser altimeter measurements of landscape topography

    International Nuclear Information System (INIS)

    Ritchie, J.C.

    1995-01-01

    Measurements of topography can provide a wealth of information on landscape properties for managing hydrologic and geologic systems and conserving natural and agricultural resources. This article discusses the application of an airborne laser altimeter to measure topography and other landscape surface properties. The airborne laser altimeter makes 4000 measurements per second with a vertical recording resolution of 5 cm. Data are collected digitally with a personal computer. A video camera, borehole sighted with the laser, records an image for locating flight lines. GPS data are used to locate flight line positions on the landscape. Laser data were used to measure vegetation canopy topography, height, cover, and distribution and to measure microtopography of the land surface and gullies with depths of 15–20 cm. Macrotopography of landscape profiles for segments up to 4 km were in agreement with available topographic maps but provided more detail. Larger gullies with and without vegetation, and stream channel cross sections and their associated floodplains have also been measured and reported in other publications. Landscape segments for any length could be measured for either micro- or macrotopography. Airborne laser altimeter measurements of landscape profiles can provide detailed information on landscape properties or specific needs that will allow better decisions on the design and location of structures (i.e., roads, pipe, and power lines) and for improving the management and conservation of natural and agricultural landscapes. (author)

  17. Determinants of a traditional agricultural landscape

    Directory of Open Access Journals (Sweden)

    Janina Borysiak

    2018-03-01

    Full Text Available The study aim was to define the landscape determinants as certificates of natural and cultural heritage which identify the young glacial landscape under traditional agricultural management. These studies were conducted in the upper Parsęta basin (Pomerania, Poland covered by the many annual environmental monitoring programs since 1994. The aim of this monitoring is to observe changes in geoecosystems of the temperate climate zone. The parameters of the abiotic landscape subsystem have been monitored in a wide range of terms, whereas biotic elements and cultural resources only in a very limited way. This was the reason for undertaking complementary studies. The paper presents the so-called “zero-state” for 2014, which will be a reference point from which to track the direction of landscape changes in the future. The abiotic, geobotanical, and cultural determinants of this state chosen have been characterized on the basis of field mapping data and the available literature. They were chosen based on the methodology of landscape audit to define the specificity of the traditional agricultural landscape. They were selected on the basis of assessment criteria for landscape structure: complexity (diversification of land use and cover, naturalness (syngenesis of plant communities, hydrochemical properties of surface waters, coherence of composition with natural conditions, stewardship (intensity of use, crop weeds, ecological succession, fallows, anthropogenic denudation, aesthetic and visual perception, historicity (continuity of natural landscape elements, continuation of traditional agricultural use, architectural objects, and disharmonious elements.

  18. Simulating natural selection in landscape genetics

    Science.gov (United States)

    E. L. Landguth; S. A. Cushman; N. Johnson

    2012-01-01

    Linking landscape effects to key evolutionary processes through individual organism movement and natural selection is essential to provide a foundation for evolutionary landscape genetics. Of particular importance is determining how spatially- explicit, individual-based models differ from classic population genetics and evolutionary ecology models based on ideal...

  19. Editorial: What do we mean by "landscape"?

    Science.gov (United States)

    Paul H. Gobster; Wei-Ning. Xiang

    2012-01-01

    As a prelude to revising the Aims and Scope of Landscape and Urban Planning (LAND), our last editorial discussed the journal’s "intellectual landscape" as revealed by an analysis of conceptual and proximal relationships between articles published in LAND and 50 other research journals. The six conceptual themes we identified--ecology, planning and management...

  20. Using the Linguistic Landscape to Bridge Languages

    Science.gov (United States)

    Mari, Vanessa

    2018-01-01

    In this article Vanessa Mari describes how she uses the linguistic landscape to bridge two or more languages with students learning English. The linguistic landscape is defined by Landry and Bourhis (1997, 25) as "the language of public road signs, advertising billboards, street names, place names, commercial shop signs, and public signs on…

  1. Landscape Architectural Design as Scientific Inquiry?

    NARCIS (Netherlands)

    Lenzholzer, S.

    2011-01-01

    This presentation discusses ‘landscape architectural design as scientific inquiry’ and exemplifies this with the description of a design process within climate-responsive design leading to new design knowledge. ‘Research and design’ are issues that need increasing attention within landscape

  2. NATURE MANAGEMENT, LANDSCAPE AND THE CAP

    OpenAIRE

    Brouwer, Floor M.; Godeschalk, Frans E.

    2004-01-01

    The integration of nature management, landscape and environmental concerns into the Common Agricultural Policy (CAP) has gained momentum with the CAP reforms adopted in June 2003. The report explores instruments and approaches that contribute to the inte-gration of nature conservation and landscape concerns into the CAP. A broader use of the CAP instruments might help to achieve nature types in the Netherlands.

  3. Sustainable energy landscapes : designing, planning, and development

    NARCIS (Netherlands)

    Stremke, S.; Dobbelsteen, van den A.

    2013-01-01

    In the near future the appearance and spatial organization of urban and rural landscapes will be strongly influenced by the generation of renewable energy. One of the critical tasks will be the re-integration of these sustainable energy landscapes into the existing environment—which people value and

  4. 40 CFR 247.15 - Landscaping products.

    Science.gov (United States)

    2010-07-01

    ... hydroseeding and as an over-spray for straw mulch in landscaping, erosion control, and soil reclamation. (b) Compost made from recovered organic materials. (c) Garden and soaker hoses containing recovered plastic or rubber. (d) Lawn and garden edging containing recovered plastic or rubber. (e) Plastic lumber landscaping...

  5. Landscape Sustainability in a Sonoran Desert City

    Directory of Open Access Journals (Sweden)

    Chris A. Martin

    2008-01-01

    Full Text Available The objective of this paper is to discuss concepts of landscape sustainability in the Phoenix metropolitan area. Phoenix is situated in the greater Salt River Valley of the lower Sonoran Desert in the southwest United States. In this paper I use the ecological frameworks of ecosystem services and resiliency as a metric for understanding landscape sustainability. An assessment of landscape sustainability performance benchmarks were made by surveying research findings of scientists affiliated with the Central Arizona Phoenix Long Term Ecological Research Project (CAP LTER. In Phoenix, present day emphases on cultural, aesthetic, and habitat formation ecosystem services within an arid ecoregion of low natural resilience coupled to a complex matrix of socioeconomic stratification, excessive landscape water use and pruning practices has had the undesired effect of degrading landscape sustainability. This has been measured as mixed patterns of plant diversity and human-altered patterns of carbon regulation, microclimate control, and trophic dynamics. In the future, sustainable residential landscaping in desert cities such as Phoenix may be fostered through use of water-conserving irrigation technologies, oasis-style landscape design motifs, recycling of landscape green waste, and conservative plant pruning strategies.

  6. Community identities as visions for landscape change

    Science.gov (United States)

    William P. Stewart; Derek Liebert; Kevin W. Larkin

    2004-01-01

    Residents' felt senses of their community can play substantial roles in determining visions for landscape change. Community identities are often anchored in tangible environments and events of a community, and have the potential to serve as visions for landscape planning processes. Photo-elicitation is applied in this study to connect community-based meanings to...

  7. Thinking big: linking rivers to landscapes

    Science.gov (United States)

    Joan O’Callaghan; Ashley E. Steel; Kelly M. Burnett

    2012-01-01

    Exploring relationships between landscape characteristics and rivers is an emerging field, enabled by the proliferation of satellite date, advances in statistical analysis, and increased emphasis on large-scale monitoring. Landscapes features such as road networks, underlying geology, and human developments, determine the characteristics of the rivers flowing through...

  8. Designing agricultural landscapes for natural pest control

    NARCIS (Netherlands)

    Steingrover, E.G.; Geertsema, W.; Wingerden, van W.K.R.E.

    2010-01-01

    The green–blue network of semi-natural non-crop landscape elements in agricultural landscapes has the potential to enhance natural pest control by providing various resources for the survival of beneficial insects that suppress crop pests. A study was done in the Hoeksche Waard to explore how

  9. Energy forest cultivation and the landscape

    International Nuclear Information System (INIS)

    Bell, Simon

    1994-01-01

    The place of energy forestry in the landscape is discussed, principally with reference to Britain and Europe. The importance of design as a means of ensuring an attractive appearance, while meeting functional and economic requirements, is stressed. Simple design principles which help energy forests, mainly short rotation arable coppice, to fit into the landscape are suggested. (author)

  10. Spurious correlations and inference in landscape genetics

    Science.gov (United States)

    Samuel A. Cushman; Erin L. Landguth

    2010-01-01

    Reliable interpretation of landscape genetic analyses depends on statistical methods that have high power to identify the correct process driving gene flow while rejecting incorrect alternative hypotheses. Little is known about statistical power and inference in individual-based landscape genetics. Our objective was to evaluate the power of causalmodelling with partial...

  11. Providing Campus Environmental Coherence by Landscaping.

    Science.gov (United States)

    Pawsey, Maurice R.

    1982-01-01

    A landscaping approach aimed at integrating greatly contrasting building types and materials resulting from unplanned growth used these elements to create design continuity; paving, planting, landscape furniture, planting and lawn protection, signs, lights, placement of posters and notices, and bicycle racks. (MSE)

  12. 3D-models in landscape architecture

    NARCIS (Netherlands)

    Nijhuis, S.; Stellingwerff, M.C.

    2011-01-01

    Landscape architecture consists of a basic attitude that involves four principles of study and practice. These are: anamnesis (palimpsest), process, three-dimensional space and scale-continuum (relational context). The core of landscape architecture as a design discipline is the construction and

  13. Landscape and Heritage: trajectories and consequences

    DEFF Research Database (Denmark)

    Harvey, David

    2015-01-01

    supporting and often parallel endeavour of academic, policy and popular inquiry that explores the significance of landscape and heritage as meaningful categories of an emergent and processual nature. Despite such a parallel trajectory, however, the actual practices of landscape and heritage studies still...

  14. Longwave infrared observation of urban landscapes

    Science.gov (United States)

    Goward, S. N.

    1981-01-01

    An investigation is conducted regarding the feasibility to develop improved methods for the identification and analysis of urban landscapes on the basis of a utilization of longwave infrared observations. Attention is given to landscape thermal behavior, urban thermal properties, modeled thermal behavior of pavements and buildings, and observed urban landscape thermal emissions. The differential thermal behavior of buildings, pavements, and natural areas within urban landscapes is found to suggest that integrated multispectral solar radiant reflectance and terrestrial radiant emissions data will significantly increase potentials for analyzing urban landscapes. In particular, daytime satellite observations of the considered type should permit better identification of urban areas and an analysis of the density of buildings and pavements within urban areas. This capability should enhance the utility of satellite remote sensor data in urban applications.

  15. Populating the Landscape: a top down approach

    CERN Document Server

    Hawking, Stephen William; Hertog, Thomas

    2006-01-01

    We put forward a framework for cosmology that combines the string landscape with no boundary initial conditions. In this framework, amplitudes for alternative histories for the universe are calculated with final boundary conditions only. This leads to a top down approach to cosmology, in which the histories of the universe depend on the precise question asked. We study the observational consequences of no boundary initial conditions on the landscape, and outline a scheme to test the theory. This is illustrated in a simple model landscape that admits several alternative inflationary histories for the universe. Only a few of the possible vacua in the landscape will be populated. We also discuss in what respect the top down approach differs from other approaches to cosmology in the string landscape, like eternal inflation.

  16. INNOVATION LANDSCAPE AS PRIORITY CONDITION OF INDUSTRIAL AND TERRITORIAL DEVELOPMENT

    Directory of Open Access Journals (Sweden)

    Y. A. Salikov

    2015-01-01

    Full Text Available A rational development of industrial territories and regions implies the improvement of their cooperation in economic sector of the country, perfecting the territorial structure of husbandry, rational exploration of natural resources, usage of promising technologies, mobilization of investment etc. Along with this, the improvement of the existing and formation of a new industrial manufacture structure should be implemented with consideration of key market aspects, connected with competitiveness and innovations. Thus, an important condition of industrial structure development is the formation of innovative landscape representing the entirety of innovative territorial subjects that use innovative technologies, management tools for creation the product. In narrow sense, innovative landscape can be understood as an integrative entirety of parameters including socio-economic conditions, state administrative body, innovative economic subjects, existence of innovative infrastructure and cluster interactions etc. A methodic approach to comparative estimation of industrial regions innovative landscape parameters considered in the article lets identify its state and structural characteristics with the purpose of making more reasonable decisions on productive forces location and o n the increase of innovativeness level of industrial territories and regions.

  17. Responding to Landscape Change: Stakeholder Participation and Social Capital in Five European Landscapes

    Directory of Open Access Journals (Sweden)

    Thanasis Kizos

    2018-01-01

    Full Text Available The concept of landscape has been increasingly used, in the last decades, in policy and land use planning, both in regard to so-called “special” and to “ordinary” or “everyday” landscapes. This has raised the importance of local and public participation in all issues that refer to landscapes and the definition of the groups that “have a stake” in the landscape. In this paper, we provide insights into how stakeholders perceive the dynamics of local processes of landscape change (and continuity and which processes of landscape change they perceive as important, in positive and negative ways, from five communities within the European Union. These landscapes involve different landscape issues “at stake”, different national and local planning and decision-making traditions and practices, and varying degrees of engagement. The understanding of these complexities and the unraveling of the insights is done through the concept of social capital and its different forms. We report on three series of workshops that have been organized to discuss landscape issues and approaches or ideas for landscape management. We witnessed interactions between the different stakeholders and gained insights into how social capital affects landscape change. We found that despite differences, similarities emerged concerning the interplay between “expert” and “local” knowledge and between “insideness” and “outsideness”. Social capital plays an important part, as it provides the template for personal and collective evaluation of landscape changes, who should manage these changes and how they should be managed. These findings are important to develop in-depth insights on dynamics and values of cultural landscapes and visions for re-coupling social and ecological components in cultural landscapes and translate them into policy and management options.

  18. Learning topography with Tangible Landscape games

    Science.gov (United States)

    Petrasova, A.; Tabrizian, P.; Harmon, B. A.; Petras, V.; Millar, G.; Mitasova, H.; Meentemeyer, R. K.

    2017-12-01

    Understanding topography and its representations is crucial for correct interpretation and modeling of surface processes. However, novice earth science and landscape architecture students often find reading topographic maps challenging. As a result, many students struggle to comprehend more complex spatial concepts and processes such as flow accumulation or sediment transport.We developed and tested a new method for teaching hydrology, geomorphology, and grading using Tangible Landscape—a tangible interface for geospatial modeling. Tangible Landscape couples a physical and digital model of a landscape through a real-time cycle of hands-on modeling, 3D scanning, geospatial computation, and projection. With Tangible Landscape students can sculpt a projection-augmented topographic model of a landscape with their hands and use a variety of tangible objects to immediately see how they are changing geospatial analytics such as contours, profiles, water flow, or landform types. By feeling and manipulating the shape of the topography, while seeing projected geospatial analytics, students can intuitively learn about 3D topographic form, its representations, and how topography controls physical processes. Tangible Landscape is powered by GRASS GIS, an open source geospatial platform with extensive libraries for geospatial modeling and analysis. As such, Tangible Landscape can be used to design a wide range of learning experiences across a large number of geoscience disciplines.As part of a graduate level course that teaches grading, 16 students participated in a series of workshops, which were developed as serious games to encourage learning through structured play. These serious games included 1) diverting rain water to a specified location with minimal changes to landscape, 2) building different combinations of landforms, and 3) reconstructing landscapes based on projected contour information with feedback.In this poster, we will introduce Tangible Landscape, and

  19. Arthropod but not bird predation in ethiopian homegardens is higher in tree-poor than in tree-rich landscapes.

    Science.gov (United States)

    Lemessa, Debissa; Hambäck, Peter A; Hylander, Kristoffer

    2015-01-01

    Bird and arthropod predation is often associated with natural pest control in agricultural landscapes, but the rates of predation may vary with the amount of tree cover or other environmental factors. We examined bird and arthropod predation in three tree-rich and three tree-poor landscapes across southwestern Ethiopia. Within each landscape we selected three tree-rich and three tree-poor homegardens in which we recorded the number of tree species and tree stems within 100 × 100 m surrounding the central house. To estimate predation rates, we attached plasticine caterpillars on leaves of two coffee and two avocado shrubs in each homegarden, and recorded the number of attacked caterpillars for 7-9 consecutive weeks. The overall mean daily predation rate was 1.45% for birds and 1.60% for arthropods. The rates of arthropod predation varied among landscapes and were higher in tree-poor landscapes. There was no such difference for birds. Within landscapes, predation rates from birds and arthropods did not vary between tree-rich and tree-poor homegardens in either tree-rich or tree-poor landscapes. The most surprising result was the lack of response by birds to tree cover at either spatial scale. Our results suggest that in tree-poor landscapes there are still enough non-crop habitats to support predatory arthropods and birds to deliver strong top-down effect on crop pests.

  20. Arthropod but not bird predation in ethiopian homegardens is higher in tree-poor than in tree-rich landscapes.

    Directory of Open Access Journals (Sweden)

    Debissa Lemessa

    Full Text Available Bird and arthropod predation is often associated with natural pest control in agricultural landscapes, but the rates of predation may vary with the amount of tree cover or other environmental factors. We examined bird and arthropod predation in three tree-rich and three tree-poor landscapes across southwestern Ethiopia. Within each landscape we selected three tree-rich and three tree-poor homegardens in which we recorded the number of tree species and tree stems within 100 × 100 m surrounding the central house. To estimate predation rates, we attached plasticine caterpillars on leaves of two coffee and two avocado shrubs in each homegarden, and recorded the number of attacked caterpillars for 7-9 consecutive weeks. The overall mean daily predation rate was 1.45% for birds and 1.60% for arthropods. The rates of arthropod predation varied among landscapes and were higher in tree-poor landscapes. There was no such difference for birds. Within landscapes, predation rates from birds and arthropods did not vary between tree-rich and tree-poor homegardens in either tree-rich or tree-poor landscapes. The most surprising result was the lack of response by birds to tree cover at either spatial scale. Our results suggest that in tree-poor landscapes there are still enough non-crop habitats to support predatory arthropods and birds to deliver strong top-down effect on crop pests.

  1. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

    DEFF Research Database (Denmark)

    Kröger, Carsten; Dillon, Shane C.; Cameron, Andrew D. S.

    2012-01-01

    More than 50 y of research have provided great insight into the physiology, metabolism, and molecular biology of Salmonella enterica serovar Typhimurium (S. Typhimurium), but important gaps in our knowledge remain. It is clear that a precise choreography of gene expression is required......-thirds of these TSSs were associated with σ70 (including phoP, slyA, and invF) from which we identified the −10 and −35 motifs of σ70-dependent S. Typhimurium gene promoters. Overall, we corrected the location of important genes and discovered 18 times more promoters than identified previously. S. Typhimurium...

  2. Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003

    NARCIS (Netherlands)

    Bottacini, Francesca; Zomer, Aldert; Milani, Christian; Ferrario, Chiara; Lugli, Gabriele Andrea; Egan, Muireann; Ventura, Marco; van Sinderen, Douwe

    2017-01-01

    BACKGROUND: Bifidobacterium breve represents a common member of the infant gut microbiota and its presence in the gut has been associated with host well being. For this reason it is relevant to investigate and understand the molecular mechanisms underlying the establishment, persistence and

  3. Transcriptional landscape of ncRNA and Repeat elements in somatic cells

    KAUST Repository

    Ghosheh, Yanal

    2016-01-01

    The advancement of Nucleic acids (DNA and RNA) sequencing technology has enabled many projects targeted towards the identification of genome structure and transcriptome complexity of organisms. The first conclusions of the human and mouse projects

  4. Genotype to phenotype mapping and the fitness landscape of the E. coli lac promoter.

    Directory of Open Access Journals (Sweden)

    Jakub Otwinowski

    Full Text Available Genotype-to-phenotype maps and the related fitness landscapes that include epistatic interactions are difficult to measure because of their high dimensional structure. Here we construct such a map using the recently collected corpora of high-throughput sequence data from the 75 base pairs long mutagenized E. coli lac promoter region, where each sequence is associated with its phenotype, the induced transcriptional activity measured by a fluorescent reporter. We find that the additive (non-epistatic contributions of individual mutations account for about two-thirds of the explainable phenotype variance, while pairwise epistasis explains about 7% of the variance for the full mutagenized sequence and about 15% for the subsequence associated with protein binding sites. Surprisingly, there is no evidence for third order epistatic contributions, and our inferred fitness landscape is essentially single peaked, with a small amount of antagonistic epistasis. There is a significant selective pressure on the wild type, which we deduce to be multi-objective optimal for gene expression in environments with different nutrient sources. We identify transcription factor (CRP and RNA polymerase binding sites in the promotor region and their interactions without difficult optimization steps. In particular, we observe evidence for previously unexplored genetic regulatory mechanisms, possibly kinetic in nature. We conclude with a cautionary note that inferred properties of fitness landscapes may be severely influenced by biases in the sequence data.

  5. Dark matter in axion landscape

    Directory of Open Access Journals (Sweden)

    Ryuji Daido

    2017-02-01

    Full Text Available If there are a plethora of axions in nature, they may have a complicated potential and create an axion landscape. We study a possibility that one of the axions is so light that it is cosmologically stable, explaining the observed dark matter density. In particular we focus on a case in which two (or more shift-symmetry breaking terms conspire to make the axion sufficiently light at the potential minimum. In this case the axion has a flat-bottomed potential. In contrast to the case in which a single cosine term dominates the potential, the axion abundance as well as its isocurvature perturbations are significantly suppressed. This allows an axion with a rather large mass to serve as dark matter without fine-tuning of the initial misalignment, and further makes higher-scale inflation to be consistent with the scenario.

  6. Energy transition: towards landscape devastation?

    International Nuclear Information System (INIS)

    Posokhow, Andre

    2013-09-01

    The author criticizes some aspects of the content of the French policy for energy transition. He states that the objective of reduction of greenhouse emissions is unreachable and moreover useless when China keeps on opening new coal-fired power stations. He states that temperatures do not increase any longer and that it is not sure that CO 2 emissions are responsible for past increases. He outlines that the power of wind turbines is only a quarter of their theoretical one, that replacing nuclear energy by wind energy would require the installation of 33.000 wind turbines. He states that objectives of energy saving are not credible, and that the energy mix predictions are fuzzy. He outlines contradictions about the nuclear power station life duration, states that the installation of 210 wind turbines per district would devastate the French landscape

  7. Precision cosmology and the landscape

    International Nuclear Information System (INIS)

    Bousso, Raphael; Bousso, Raphael

    2006-01-01

    After reviewing the cosmological constant problem--why is Lambda not huge?--I outline the two basic approaches that had emerged by the late 1980s, and note that each made a clear prediction. Precision cosmological experiments now indicate that the cosmological constant is nonzero. This result strongly favors the environmental approach, in which vacuum energy can vary discretely among widely separated regions in the universe. The need to explain this variation from first principles constitutes an observational constraint on fundamental theory. I review arguments that string theory satisfies this constraint, as it contains a dense discretuum of metastable vacua. The enormous landscape of vacua calls for novel, statistical methods of deriving predictions, and it prompts us to reexamine our description of spacetime on the largest scales. I discuss the effects of cosmological dynamics, and I speculate that weighting vacua by their entropy production may allow for prior-free predictions that do not resort to explicitly anthropic arguments

  8. Monitoring the agricultural landscape for insect resistance

    Science.gov (United States)

    Casas, Joseph; Glaser, J. A.; Copenhaver, Ken

    Farmers in 25 countries on six continents are using plant biotechnology to solve difficult crop production challenges and conserve the environment. In fact, 13.3 million farmers, which include 90 percent of the farming in developing countries, choose to plant biotech crops. Over the past decade, farmers increased area planted in genetically modified (GM) crops by more than 10 percent each year, thus increasing their farm income by more than 44 billion US dollars (1996-2007), and achieved economic, environmental and social benefits in crops such as soybeans, canola, corn and cotton. To date, total acres of biotech crops harvested exceed more than 2 billion with a proven 13-year history of safe use. Over the next decade, expanded adoption combined with current research on 57 crops in 63 countries will broaden the advantages of genetically modified foods for growers, consumers and the environment. Genetically modified (GM) crops with the ability to produce toxins lethal to specific insect pests are covering a larger percentage of the agricultural landscape every year. The United States department of Agriculture (USDA) estimated that 63 percent of corn and 65 percent of cotton contained these specific genetic traits in 2009. The toxins could protect billions of dollars of loss from insect damage for crops valued at greater than 165 billion US dollars in 2008. The stable and efficient production of these crops has taken on even more importance in recent years with their use, not only as a food source, but now also a source of fuel. It is in the best interest of the United States Environmental Protection Agency (USEPA) to ensure the continued efficacy of toxin producing GM crops as their use reduces pesticides harmful to humans and animals. However, population genetics models have indicated the risk of insect pests developing resistance to these toxins if a high percentage of acreage is grown in these crops. The USEPA is developing methods to monitor the agricultural

  9. Transcriptional regulation of hepatic lipogenesis.

    Science.gov (United States)

    Wang, Yuhui; Viscarra, Jose; Kim, Sun-Joong; Sul, Hei Sook

    2015-11-01

    Fatty acid and fat synthesis in the liver is a highly regulated metabolic pathway that is important for very low-density lipoprotein (VLDL) production and thus energy distribution to other tissues. Having common features at their promoter regions, lipogenic genes are coordinately regulated at the transcriptional level. Transcription factors, such as upstream stimulatory factors (USFs), sterol regulatory element-binding protein 1C (SREBP1C), liver X receptors (LXRs) and carbohydrate-responsive element-binding protein (ChREBP) have crucial roles in this process. Recently, insights have been gained into the signalling pathways that regulate these transcription factors. After feeding, high blood glucose and insulin levels activate lipogenic genes through several pathways, including the DNA-dependent protein kinase (DNA-PK), atypical protein kinase C (aPKC) and AKT-mTOR pathways. These pathways control the post-translational modifications of transcription factors and co-regulators, such as phosphorylation, acetylation or ubiquitylation, that affect their function, stability and/or localization. Dysregulation of lipogenesis can contribute to hepatosteatosis, which is associated with obesity and insulin resistance.

  10. Structural insights into transcription complexes

    NARCIS (Netherlands)

    Berger, I.; Blanco, A.G.; Boelens, R.; Cavarelli, J.; Coll, M.; Folkers, G.E.; Nie, Y.; Pogenberg, V.; Schultz, P.; Wilmanns, M.; Moras, D.; Poterszman, A.

    2011-01-01

    Control of transcription allows the regulation of cell activity in response to external stimuli and research in the field has greatly benefited from efforts in structural biology. In this review, based on specific examples from the European SPINE2-COMPLEXES initiative, we illustrate the impact of

  11. Transcription factor-based biosensor

    Science.gov (United States)

    Dietrich, Jeffrey A; Keasling, Jay D

    2013-10-08

    The present invention provides for a system comprising a BmoR transcription factor, a .sigma..sup.54-RNA polymerase, and a pBMO promoter operatively linked to a reporter gene, wherein the pBMO promoter is capable of expression of the reporter gene with an activated form of the BmoR and the .sigma..sup.54-RNA polymerase.

  12. Neogeomorphology, prediction, and the anthropic landscape

    Science.gov (United States)

    Haff, P. K.

    The surface of the earth is undergoing profound change due to human impact. By some measures the level of human impact is comparable to the effects of major classical geomorphic processes such as fluvial sediment transport. This change is occurring rapidly, has no geologic precedent, and may represent an irreversible transition to a new and novel landscape with which we have no experience. For these reasons prediction of future landscape evolution will be of increasing importance. The combination of physical and social forces that drive modern landscape change represents the Anthropic Force. Neogeomorphology is the study of the Anthropic Force and its present and likely future effects on the landscape. Unique properties associated with the Anthropic Force include consciousness, intention and design. These properties support the occurrence of nonclassical geomorphic phenomena, such as landscape planning, engineering, and management. The occurrence of short time-scale phenomena induced by anthropic landscape change, the direct effects of this change on society, and the ability to anticipate and intentionally influence the future trajectory of the global landscape underscore the importance of prediction in a neogeomorphic world.

  13. Defining the landscape of adaptive genetic diversity.

    Science.gov (United States)

    Eckert, Andrew J; Dyer, Rodney J

    2012-06-01

    Whether they are used to describe fitness, genome architecture or the spatial distribution of environmental variables, the concept of a landscape has figured prominently in our collective reasoning. The tradition of landscapes in evolutionary biology is one of fitness mapped onto axes defined by phenotypes or molecular sequence states. The characteristics of these landscapes depend on natural selection, which is structured across both genomic and environmental landscapes, and thus, the bridge among differing uses of the landscape concept (i.e. metaphorically or literally) is that of an adaptive phenotype and its distribution across geographical landscapes in relation to selective pressures. One of the ultimate goals of evolutionary biology should thus be to construct fitness landscapes in geographical space. Natural plant populations are ideal systems with which to explore the feasibility of attaining this goal, because much is known about the quantitative genetic architecture of complex traits for many different plant species. What is less known are the molecular components of this architecture. In this issue of Molecular Ecology, Parchman et al. (2012) pioneer one of the first truly genome-wide association studies in a tree that moves us closer to this form of mechanistic understanding for an adaptive phenotype in natural populations of lodgepole pine (Pinus contorta Dougl. ex Loud.). © 2012 Blackwell Publishing Ltd.

  14. EVERYDAY LANDSCAPE AND MEANING IN URBAN LIVING

    Directory of Open Access Journals (Sweden)

    LAKSHMI PRIYA RAJENDRAN

    2013-11-01

    Full Text Available This paper conceptualizes landscape from a temporal and spatial perspective which emphasizes peoples’ interactions and activities as an inherent part of understanding the landscape itself. Today, peoples’ interaction with the landscape has become more complex, largely owing to the changing notions of place in contemporary urban living. In this context, the paper examines the role and significance of the landscapes of everyday life in urban environment and delineates how it (reconstructs ordinary human and social meanings that are necessary conditions for our existence. The paper is presented in three sections. In the first section, it discusses the concept of everyday life and its relevance in the contemporary urban living. In the following section, it examines the complexities encountered in urban landscapes today .The third section of the paper discusses how meaningful interaction experienced with everyday landscapes offer valuable insights for addressing the challenges posed by the complexities of urban city living. The paper concludes by highlighting the need for attention towards the largely neglected or overlooked domains of ‘ordinary’ everyday landscape by designer professionals, which plays a crucial role in creating meaningful relationship between people and place.

  15. Virtual Museums for Landscape Valorization and Communication

    Science.gov (United States)

    Pietroni, E.

    2017-08-01

    Research in the domain of landscape virtual reconstructions has been mainly focused on digitization and recording inside GIS systems, or real time visualization, paying a minor attention to the development of a methodological approach for the landscape narration, combing different registers, conceptual, emotional incitements and, thus, able to arouse in the public a feeling of emotional "sensing" and self- identification. The landscape reflects also the human activities in the territory and the communities' cultural patterns, their sense of "belonging". In a virtual museum of landscapes, the multidisciplinary approach, the multiplication of perspectives and voices, storytelling, acquire primary importance. A Virtual Museum of landscapes should integrate both holistic and delimited visions. The holistic vision requires a diachronic approach, including both present and past phases of life. On the other side, delimited, or "monographic", representations are useful to go deeper into specific and exemplar stories, regarding specific groups of people. Beside, the emergence of new social media enhancing cultural interactions among people induce the creation of specific social platforms for Cultural Heritage for the active participation of a large number of stakeholders. Co-creation scenarios and tools can be particularly promising. Aton is an example of front-end VR social platform in the web end, for the efficient streaming of medium/large landscape, their exploration and characterization. The Tiber Valley Virtual Museum is an example of sensorial cultural landscape. Starting from the acquisition of topographical data through integrated technologies, several multi-sensory scenarios have been created, inside which visitors can feel embodied and involved.

  16. Do geographically isolated wetlands influence landscape functions?

    Science.gov (United States)

    Cohen, Matthew J.; Creed, Irena F.; Alexander, Laurie C.; Basu, Nandita; Calhoun, Aram J.K.; Craft, Christopher; D’Amico, Ellen; DeKeyser, Edward S.; Fowler, Laurie; Golden, Heather E.; Jawitz, James W.; Kalla, Peter; Kirkman, L. Katherine; Lane, Charles R.; Lang, Megan; Leibowitz, Scott G.; Lewis, David Bruce; Marton, John; McLaughlin, Daniel L.; Mushet, David M.; Raanan-Kiperwas, Hadas; Rains, Mark C.; Smith, Lora; Walls, Susan C.

    2015-01-01

    Geographically isolated wetlands (GIWs), those surrounded by uplands, exchange materials, energy, and organisms with other elements in hydrological and habitat networks, contributing to landscape functions, such as flow generation, nutrient and sediment retention, and biodiversity support. GIWs constitute most of the wetlands in many North American landscapes, provide a disproportionately large fraction of wetland edges where many functions are enhanced, and form complexes with other water bodies to create spatial and temporal heterogeneity in the timing, flow paths, and magnitude of network connectivity. These attributes signal a critical role for GIWs in sustaining a portfolio of landscape functions, but legal protections remain weak despite preferential loss from many landscapes. GIWs lack persistent surface water connections, but this condition does not imply the absence of hydrological, biogeochemical, and biological exchanges with nearby and downstream waters. Although hydrological and biogeochemical connectivity is often episodic or slow (e.g., via groundwater), hydrologic continuity and limited evaporative solute enrichment suggest both flow generation and solute and sediment retention. Similarly, whereas biological connectivity usually requires overland dispersal, numerous organisms, including many rare or threatened species, use both GIWs and downstream waters at different times or life stages, suggesting that GIWs are critical elements of landscape habitat mosaics. Indeed, weaker hydrologic connectivity with downstream waters and constrained biological connectivity with other landscape elements are precisely what enhances some GIW functions and enables others. Based on analysis of wetland geography and synthesis of wetland functions, we argue that sustaining landscape functions requires conserving the entire continuum of wetland connectivity, including GIWs.

  17. Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels

    KAUST Repository

    Wang, Xiaolei; Kuwahara, Hiroyuki; Gao, Xin

    2014-01-01

    high-quality estimates of such complex affinity landscapes is, thus, essential to the control of gene expression and the advance of synthetic biology. Results: Here, we propose a two-round prediction method that is based on support vector regression

  18. Detrital carbon pools in temperate forests: magnitude and potential for landscape-scale assessment

    Science.gov (United States)

    John Bradford; Peter Weishampel; Marie-Louise Smith; Randall Kolka; Richard A. Birdsey; Scott V. Ollinger; Michael G. Ryan

    2009-01-01

    Reliably estimating carbon storage and cycling in detrital biomass is an obstacle to carbon accounting. We examined carbon pools and fluxes in three small temperate forest landscapes to assess the magnitude of carbon stored in detrital biomass and determine whether detrital carbon storage is related to stand structural properties (leaf area, aboveground biomass,...

  19. Novel Kalman filter algorithm for statistical monitoring of extensive landscapes with synoptic sensor data

    Science.gov (United States)

    Raymond L. Czaplewski

    2015-01-01

    Wall-to-wall remotely sensed data are increasingly available to monitor landscape dynamics over large geographic areas. However, statistical monitoring programs that use post-stratification cannot fully utilize those sensor data. The Kalman filter (KF) is an alternative statistical estimator. I develop a new KF algorithm that is numerically robust with large numbers of...

  20. Landscape effects on reproduction of Euschistus servus (Hemiptera: Pentatomidae), a mobile, polyphagous, multivoltine arthropod herbivore

    Science.gov (United States)

    The brown stink bug is an economic pest of many crops in the southeastern US. In this study we characterized the complexity, land-use intensity and distances between differently-cropped fields on landscapes in two regions of southern Georgia, USA. We estimated brown stink bug reproduction, predator ...

  1. Shared Solar. Current Landscape, Market Potential, and the Impact of Federal Securities Regulation

    Energy Technology Data Exchange (ETDEWEB)

    Feldman, David [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Brockway, Anna M. [U.S. Department of Energy, Washington, DC (United States); Ulrich, Elaine [U.S. Department of Energy, Washington, DC (United States); Margolis, Robert [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2015-04-07

    This report provides a high-level overview of the current U.S. shared solar landscape, the impact that a given shared solar program’s structure has on requiring federal securities oversight, as well as an estimate of market potential for U.S. shared solar deployment.

  2. Shared Solar. Current Landscape, Market Potential, and the Impact of Federal Securities Regulation

    Energy Technology Data Exchange (ETDEWEB)

    Feldman, David [National Renewable Energy Lab. (NREL), Golden, CO (United States); Brockway, Anna M. [Office of Energy Efficiency and Renewable Energy (EERE), Washington, DC (United States); Ulrich, Elaine [Office of Energy Efficiency and Renewable Energy (EERE), Washington, DC (United States); Margolis, Robert [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2015-04-01

    This report provides a high-level overview of the current U.S. shared solar landscape and the impact that a given shared solar program’s structure has on requiring federal securities oversight, as well as an estimate of market potential for U.S. shared solar deployment.

  3. Feedbacks in human-landscape systems

    Science.gov (United States)

    Chin, Anne

    2015-04-01

    As human interactions with Earth systems intensify in the "Anthropocene", understanding the complex relationships among human activity, landscape change, and societal responses to those changes is increasingly important. Interdisciplinary research centered on the theme of "feedbacks" in human-landscape systems serves as a promising focus for unraveling these interactions. Deciphering interacting human-landscape feedbacks extends our traditional approach of considering humans as unidirectional drivers of change. Enormous challenges exist, however, in quantifying impact-feedback loops in landscapes with significant human alterations. This paper illustrates an example of human-landscape interactions following a wildfire in Colorado (USA) that elicited feedback responses. After the 2012 Waldo Canyon Fire, concerns for heightened flood potential and debris flows associated with post-fire hydrologic changes prompted local landowners to construct tall fences at the base of a burned watershed. These actions changed the sediment transport regime and promoted further landscape change and human responses in a positive feedback cycle. The interactions ultimately increase flood and sediment hazards, rather than dampening the effects of fire. A simple agent-based model, capable of integrating social and hydro-geomorphological data, demonstrates how such interacting impacts and feedbacks could be simulated. Challenges for fully capturing human-landscape feedback interactions include the identification of diffuse and subtle feedbacks at a range of scales, the availability of data linking impact with response, the identification of multiple thresholds that trigger feedback mechanisms, and the varied metrics and data needed to represent both the physical and human systems. By collaborating with social scientists with expertise in the human causes of landscape change, as well as the human responses to those changes, geoscientists could more fully recognize and anticipate the coupled

  4. Landscape genetics of high mountain frog metapopulations

    Science.gov (United States)

    Murphy, M.A.; Dezzani, R.; Pilliod, D.S.; Storfer, A.

    2010-01-01

    Explaining functional connectivity among occupied habitats is crucial for understanding metapopulation dynamics and species ecology. Landscape genetics has primarily focused on elucidating how ecological features between observations influence gene flow. Functional connectivity, however, may be the result of both these between-site (landscape resistance) landscape characteristics and at-site (patch quality) landscape processes that can be captured using network based models. We test hypotheses of functional connectivity that include both between-site and at-site landscape processes in metapopulations of Columbia spotted frogs (Rana luteiventris) by employing a novel justification of gravity models for landscape genetics (eight microsatellite loci, 37 sites, n = 441). Primarily used in transportation and economic geography, gravity models are a unique approach as flow (e.g. gene flow) is explained as a function of three basic components: distance between sites, production/attraction (e.g. at-site landscape process) and resistance (e.g. between-site landscape process). The study system contains a network of nutrient poor high mountain lakes where we hypothesized a short growing season and complex topography between sites limit R. luteiventris gene flow. In addition, we hypothesized production of offspring is limited by breeding site characteristics such as the introduction of predatory fish and inherent site productivity. We found that R. luteiventris connectivity was negatively correlated with distance between sites, presence of predatory fish (at-site) and topographic complexity (between-site). Conversely, site productivity (as measured by heat load index, at-site) and growing season (as measured by frost-free period between-sites) were positively correlated with gene flow. The negative effect of predation and positive effect of site productivity, in concert with bottleneck tests, support the presence of source-sink dynamics. In conclusion, gravity models provide a

  5. Metrics to describe the effects of landscape pattern on hydrology in a lotic peatland

    Science.gov (United States)

    Yuan, J.; Cohen, M. J.; Kaplan, D. A.; Acharya, S.; Larsen, L.; Nungesser, M.

    2013-12-01

    Strong reciprocal interactions exist between landscape patterns and ecological processes. Hydrology is the dominant abiotic driver of ecological processes in wetlands, particularly flowing wetlands, but is both the control on and controlled by the geometry of vegetation patterning. Landscape metrics are widely used to quantitatively link pattern and process. Our goal here was to use several candidate spatial pattern metrics to predict the effects of wetland vegetation pattern on hydrologic regime, specifically hydroperiod, in the ridge-slough patterned landscape of the Everglades. The metrics focus on the capacity for longitudinally connected flow, and thus the ability of this low-gradient patterned landscape to route water from upstream. We first explored flow friction cost (FFC), a weighted spatial distance procedure wherein ridges have a high flow cost than sloughs by virtue of their elevation and vegetation structure, to evaluate water movement through different landscape configurations. We also investigated existing published flow metrics, specifically the Directional Connectivity Index (DCI) and Landscape Discharge Competence (LDC), that seek to quantify connectivity, one of the sentinel targets of ecological restoration. Hydroperiod was estimated using a numerical hydrologic model (SWIFT 2D) in real and synthetic landscapes with varying vegetation properties ( patch anisotropy, ridge density). Synthetic landscapes were constrained by the geostatistical properties of the best conserved patterned, and contained five anisotropy levels and seven ridge density levels. These were used to construct the relationship between landscape metrics and hydroperiod. Then, using historical images from 1940 to 2004, we applied the metrics toback-cast hydroperiod. Current vegetation maps were used to test scale dependency for each metric. Our results suggest that both FFC and DCI are good predictors of hydroperiod under free flowing conditions, and that they can be used

  6. Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis

    Directory of Open Access Journals (Sweden)

    Alexandre A.S.F. Raposo

    2015-03-01

    Full Text Available The proneural transcription factor Ascl1 coordinates gene expression in both proliferating and differentiating progenitors along the neuronal lineage. Here, we used a cellular model of neurogenesis to investigate how Ascl1 interacts with the chromatin landscape to regulate gene expression when promoting neuronal differentiation. We find that Ascl1 binding occurs mostly at distal enhancers and is associated with activation of gene transcription. Surprisingly, the accessibility of Ascl1 to its binding sites in neural stem/progenitor cells remains largely unchanged throughout their differentiation, as Ascl1 targets regions of both readily accessible and closed chromatin in proliferating cells. Moreover, binding of Ascl1 often precedes an increase in chromatin accessibility and the appearance of new regions of open chromatin, associated with de novo gene expression during differentiation. Our results reveal a function of Ascl1 in promoting chromatin accessibility during neurogenesis, linking the chromatin landscape at Ascl1 target regions with the temporal progression of its transcriptional program.

  7. Landscape predictions from cosmological vacuum selection

    Energy Technology Data Exchange (ETDEWEB)

    Bousso, Raphael; Bousso, Raphael; Yang, Sheng

    2007-04-23

    In Bousso-Polchinski models with hundreds of fluxes, we compute the effects of cosmological dynamics on the probability distribution of landscape vacua. Starting from generic initial conditions, we find that most fluxes are dynamically driven into a different and much narrower range of values than expected from landscape statistics alone. Hence, cosmological evolution will access only a tiny fraction of the vacua with small cosmological constant. This leads to a host of sharp predictions. Unlike other approaches to eternal inflation, the holographic measure employed here does not lead to staggering, an excessive spread of probabilities that would doom the string landscape as a solution to the cosmological constant problem.

  8. Landscape predictions from cosmological vacuum selection

    International Nuclear Information System (INIS)

    Bousso, Raphael; Yang, I-S.

    2007-01-01

    In Bousso-Polchinski models with hundreds of fluxes, we compute the effects of cosmological dynamics on the probability distribution of landscape vacua. Starting from generic initial conditions, we find that most fluxes are dynamically driven into a different and much narrower range of values than expected from landscape statistics alone. Hence, cosmological evolution will access only a tiny fraction of the vacua with small cosmological constant. This leads to a host of sharp predictions. Unlike other approaches to eternal inflation, the holographic measure employed here does not lead to staggering, an excessive spread of probabilities that would doom the string landscape as a solution to the cosmological constant problem

  9. Exploring geovisualization symbology for landscape genetics

    DEFF Research Database (Denmark)

    Aoidh, Eoin Mac; Martinsohn, Jann Th.; Maes, Gregory E.

    2013-01-01

    or genetic expertise. While specialist applications exist, alternative accessible solutions do not provide adequate support for the visualization of multi‐attribute spatially referenced genetic population structure information. As a solution, we document our exploration for an appropriate symbology...... to communicate landscape genetic information through an accessible, web‐based interface. A full problem description, review of available technologies, development rationale, and discussion of the symbology exploration are provided.......Landscape genetics, which considers genetic population structure in the context of spatially referenced parameters in the surrounding landscape, has been shown to be extremely useful for wildlife management. Unfortunately its widespread uptake beyond the research community is hampered due to a lack...

  10. Topology topical thoughts on the contemporary landscape

    CERN Document Server

    Bucher, Annemarie; Körner, Stefan; Krull, Wilhelm; Kühn, Norbert; Kuster, Hansjörg; Lampugnani, Vittorio Magnago; Schäfer, Lothar; Schwartz, Joseph; Seelis, Martin; Seiler, Michael; Stokman, Antje; Tessin, Wulf; Girot, Christophe; Kirchengast, Albert; Freytag, Anette; Richter, Dunja

    2014-01-01

    How can an abstract term like ""Topology"" become pertinent and effective to landscape thinking today? There is a schism between the way landscape is understood scientifically, either as a normative network or an environmental system, and the way the same place exists emotionally for people. This disparity which prevails in today''s landscape calls for a change of approach, both in terms of action and perception. Topology, in this instance, is not confined to the science of continuous surfaces in mathematics, it can pay greater attention to deeper spatial, physical, poetic and philosophical va

  11. Fairy circle landscapes under the sea

    KAUST Repository

    Ruiz-Reynés, Daniel

    2017-08-03

    Short-scale interactions yield large-scale vegetation patterns that, in turn, shape ecosystem function across landscapes. Fairy circles, which are circular patches bare of vegetation within otherwise continuous landscapes, are characteristic features of semiarid grasslands. We report the occurrence of submarine fairy circle seascapes in seagrass meadows and propose a simple model that reproduces the diversity of seascapes observed in these ecosystems as emerging from plant interactions within the meadow. These seascapes include two extreme cases, a continuous meadow and a bare landscape, along with intermediate states that range from the occurrence of persistent but isolated fairy circles, or solitons, to seascapes with multiple fairy circles, banded vegetation, and

  12. Denmark seen from above: communicating landscape change

    DEFF Research Database (Denmark)

    Svenningsen, Stig Roar; Hansen, Mette Dahl; Dupont, Henrik

    . This poster will explore the potential for a new way of communicating landscape change to a broader public audience by using a newly developed portal with digitized and geo-referenced historical oblique aerial photographs from 1939 to 1990s, provided by the Danish Royal Library. The basic idea is, popularly....... Especially the possibility to view the change of the local landscape in the neighbourhood presents a good starting point for discussions and critical reflection of the changes taking place in the landscape, which are the point of reference for people in their understanding of their environment. In order...

  13. Are there Traps in Quantum Control Landscapes?

    International Nuclear Information System (INIS)

    Pechen, Alexander N.; Tannor, David J.

    2011-01-01

    There has been great interest in recent years in quantum control landscapes. Given an objective J that depends on a control field ε the dynamical landscape is defined by the properties of the Hessian δ 2 J/δε 2 at the critical points δJ/δε=0. We show that contrary to recent claims in the literature the dynamical control landscape can exhibit trapping behavior due to the existence of special critical points and illustrate this finding with an example of a 3-level Λ system. This observation can have profound implications for both theoretical and experimental quantum control studies.

  14. Landscape-geochemical factors of deposit formation

    International Nuclear Information System (INIS)

    Batulin, S.G.

    1980-01-01

    Effect of landscape-geochemical factors on hydrogenic formation of uranium ores is considered. The primary attention is paid to finding reasons for hydrogeochemical background increase in the regions of arid climate. Problems of uranium distribution in alluvial landscapes, hydrogeochemical regime of ground waters, reflecting the effect of waters of the zone of aeration are revealed. Chemical composition of porous solutions in the zone of aeration, as well as historical geochemindstry of landscape a its role from the view point of uranium solution formation in the arid zone are considered [ru

  15. Fairy circle landscapes under the sea

    KAUST Repository

    Ruiz-Reyné s, Daniel; Gomila, Damià ; Sintes, Tomà s; Herná ndez-Garcí a, Emilio; Marbà , Nú ria; Duarte, Carlos M.

    2017-01-01

    Short-scale interactions yield large-scale vegetation patterns that, in turn, shape ecosystem function across landscapes. Fairy circles, which are circular patches bare of vegetation within otherwise continuous landscapes, are characteristic features of semiarid grasslands. We report the occurrence of submarine fairy circle seascapes in seagrass meadows and propose a simple model that reproduces the diversity of seascapes observed in these ecosystems as emerging from plant interactions within the meadow. These seascapes include two extreme cases, a continuous meadow and a bare landscape, along with intermediate states that range from the occurrence of persistent but isolated fairy circles, or solitons, to seascapes with multiple fairy circles, banded vegetation, and

  16. Roads Belong in the Urban Landscape

    DEFF Research Database (Denmark)

    Clemmensen, Thomas Juel

    2013-01-01

    Roads are often associated with a fragmentation or splintering of landscapes and their natural connectivity; particularly in relation to ‘green infrastructure’ they are often considered problematic elements that rupture and barricade. Conversely, as part of larger networks, roads can be considered...... important elements in the creation of new, ‘green infrastructures’ that can qualify urban landscapes in terms of improving their overall porosity and connectivity. This argument will be unfolded and substantiated in this article through theoretical reflections which conceptually re-locate road networks...... in the urban landscape, supported by relevant reference projects that illustrate the potential of road networks as a platform for ‘green infrastructure’....

  17. Coupling movement and landscape ecology for animal conservation in production landscapes.

    Science.gov (United States)

    Doherty, Tim S; Driscoll, Don A

    2018-01-10

    Habitat conversion in production landscapes is among the greatest threats to biodiversity, not least because it can disrupt animal movement. Using the movement ecology framework, we review animal movement in production landscapes, including areas managed for agriculture and forestry. We consider internal and external drivers of altered animal movement and how this affects navigation and motion capacities and population dynamics. Conventional management approaches in fragmented landscapes focus on promoting connectivity using structural changes in the landscape. However, a movement ecology perspective emphasizes that manipulating the internal motivations or navigation capacity of animals represents untapped opportunities to improve movement and the effectiveness of structural connectivity investments. Integrating movement and landscape ecology opens new opportunities for conservation management in production landscapes. © 2018 The Authors.

  18. Energy landscapes of resting-state brain networks

    Directory of Open Access Journals (Sweden)

    Takamitsu eWatanabe

    2014-02-01

    Full Text Available During rest, the human brain performs essential functions such as memory maintenance, which are associated with resting-state brain networks (RSNs including the default-mode network (DMN and frontoparietal network (FPN. Previous studies based on spiking-neuron network models and their reduced models, as well as those based on imaging data, suggest that resting-state network activity can be captured as attractor dynamics, i.e., dynamics of the brain state toward an attractive state and transitions between different attractors. Here, we analyze the energy landscapes of the RSNs by applying the maximum entropy model, or equivalently the Ising spin model, to human RSN data. We use the previously estimated parameter values to define the energy landscape, and the disconnectivity graph method to estimate the number of local energy minima (equivalent to attractors in attractor dynamics, the basin size, and hierarchical relationships among the different local minima. In both of the DMN and FPN, low-energy local minima tended to have large basins. A majority of the network states belonged to a basin of one of a few local minima. Therefore, a small number of local minima constituted the backbone of each RSN. In the DMN, the energy landscape consisted of two groups of low-energy local minima that are separated by a relatively high energy barrier. Within each group, the activity patterns of the local minima were similar, and different minima were connected by relatively low energy barriers. In the FPN, all dominant energy were separated by relatively low energy barriers such that they formed a single coarse-grained global minimum. Our results indicate that multistable attractor dynamics may underlie the DMN, but not the FPN, and assist memory maintenance with different memory states.

  19. Exploring the visual landscape : advances in physiognomic landscape research in the Netherlands

    OpenAIRE

    Nijhuis, S.; Lammeren, van, R.J.A.; Hoeven, van der, F.

    2011-01-01

    The book is the second volume in the Research in Urbanism Series of IOS Press and is about the combination of landscape research and planning, visual perception and Geographic Information Science. It offers clues for visual landscape assessment of spaces in cities, parks and rural areas. In that respect, it extends the long tradition in the Netherlands on physiognomic landscape research and shows the state of the art at this moment. ‘Exploring the Visual Landscape’ offers important clues for ...

  20. Determining landscape extent for succession and disturbance simulation modeling

    Science.gov (United States)

    Eva C. Karau; Robert E. Keane

    2007-01-01

    Dividing regions into manageable landscape units presents special problems in landscape ecology and land management. Ideally, a landscape should be large enough to capture a broad range of vegetation, environmental and disturbance dynamics, but small enough to be useful for focused management objectives. The purpose of this study was to determine the optimal landscape...

  1. Alternative staffing services. Contract transcription.

    Science.gov (United States)

    Tessier, C

    1992-03-01

    Contract medical transcription services can be of great assistance in meeting the demands for transcription, without jeopardizing patient, physician, or institutional confidentiality. You simply must require the contract service to provide at least the same degree of protection and preservation of confidentiality that you should require inhouse. To achieve this you must make these requirements explicit, comprehensive, comprehensible, believable, and enforceable. Discuss the requirements with prospective contractors. Review them at least annually with existing contractors and when contracts are due for renewal. Be sure to specify the consequence of breaching confidentiality, and if there are breaches, enforce the terms of the contract. Consult your institution's legal counsel both in developing the contract and in enforcing its provisions. Take into consideration your department's and institution's policies, AHIMA's statement on confidentiality, as well as local, state, and federal laws. Above all, never lose sight of the patient. Ultimately, it is not patient information that you are obligated to protect. It is the patient.

  2. Decoding transcriptional enhancers: Evolving from annotation to functional interpretation.

    Science.gov (United States)

    Engel, Krysta L; Mackiewicz, Mark; Hardigan, Andrew A; Myers, Richard M; Savic, Daniel

    2016-09-01

    Deciphering the intricate molecular processes that orchestrate the spatial and temporal regulation of genes has become an increasingly major focus of biological research. The differential expression of genes by diverse cell types with a common genome is a hallmark of complex cellular functions, as well as the basis for multicellular life. Importantly, a more coherent understanding of gene regulation is critical for defining developmental processes, evolutionary principles and disease etiologies. Here we present our current understanding of gene regulation by focusing on the role of enhancer elements in these complex processes. Although functional genomic methods have provided considerable advances to our understanding of gene regulation, these assays, which are usually performed on a genome-wide scale, typically provide correlative observations that lack functional interpretation. Recent innovations in genome editing technologies have placed gene regulatory studies at an exciting crossroads, as systematic, functional evaluation of enhancers and other transcriptional regulatory elements can now be performed in a coordinated, high-throughput manner across the entire genome. This review provides insights on transcriptional enhancer function, their role in development and disease, and catalogues experimental tools commonly used to study these elements. Additionally, we discuss the crucial role of novel techniques in deciphering the complex gene regulatory landscape and how these studies will shape future research. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. The Maritime Cultural Landscape of Northern Patagonia

    Science.gov (United States)

    Lira, Nicolás

    2017-12-01

    This article is a contribution to the study of the indigenous navigation and its boats in the region of northern Patagonia. This article also aims to contribute to the understanding of indigenous navigation practices and technologies and their origins from prehistoric times to the mid-twentieth century. It presents and discusses the concept of Westerdahl's Maritime Cultural Landscape in relation to other landscape concepts. This model is applied to northern Patagonia in order to discuss if it is possible to speak of a true maritime culture in the region. For this purpose, archaeological, historical and ethnographic data are presented in an integrative and innovative methodology for the discipline. Finally, the Maritime Cultural Landscape model will allow the integration of aquatic and terrestrial landscapes as routes traveled by native inhabitants of northern Patagonia and southern Chile, and propose an important and diversified maritime, river and lake tradition.

  4. Building the landscapes of Monte di Procida

    Directory of Open Access Journals (Sweden)

    Carmine Piscopo

    2014-02-01

    Full Text Available A coastal landscape, peppered with ancient formations and recent damage, characterized by labyrinthine paths leading towards sandy beaches, from which strips of land start. The aim of the article is to present the City Plan (PUC2 for this particular landscape, currently being prepared. Themes in the plan are the strengthening of links to the coast, exploitation of Mediterranean architecture, regeneration of the network of paths, and mitigation of the effects due to climatechange. This strategy comes from the survey and interpretation of the area and takes account of the changing character of the landscape, in which "landscape units" have been identified and articulated in order to build a new architecture of the places.

  5. Investigation of landscape and lake acidification relationships

    Energy Technology Data Exchange (ETDEWEB)

    Rush, R.M.; Honea, R.B.; Krug, E.C.; Peplies, R.W.; Dobson, J.E.; Baxter, F.P.

    1985-10-01

    This interim report presents the rationale and initial results for a program designed to gather and analyze information essential to a better understanding of lake acidification in the northeastern United States. The literature pertinent to a study of landscape and lake acidification relationships is reviewed and presented as the rationale for a landscape/lake acidification study. The results of a study of Emmons Pond in northwestern Connecticut are described and lead to the conclusion that a landscape change was a contributor to the acidification of this pond. A regional study of sixteen lakes in southern New England using Landsat imagery is described, and preliminary observations from a similar study in the Adirondack Mountains are given. These results indicate that satellite imagery can be useful in identifying types of ground cover important to landscape/lake acidification relationships.

  6. Landscape Conservative Cooperatives for New Mexico

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Landscape conservation cooperatives (LCCs) are conservation-science partnerships between the U.S. Fish and Wildlife Service, U.S. Geological Survey (USGS), and other...

  7. Sustainable landscaping practices for enhancing vegetation establishment.

    Science.gov (United States)

    2016-02-01

    Soil compaction can severely limit the success of vegetation establishment. Current grading and landscaping : practices commonly produce compacted soils of varied textures and profiles within SHA medians and roadsides, : resulting in limited capacity...

  8. Missing Linkages in California's Landscape [ds420

    Data.gov (United States)

    California Natural Resource Agency — The critical need for conserving landscape linkages first came to the forefront of conservation thinking in California in November 2000, when a statewide interagency...

  9. Vacuum selection on the string landscape

    International Nuclear Information System (INIS)

    Tetteh-Lartey, Edward

    2007-01-01

    I examine some nonanthropic approaches to the string landscape. These approaches are based on finding the initial conditions of the universe using the wave function of the multiverse to select the most probable vacuum out of this landscape. All approaches tackled so far seem to have their own problems and there is no clear-cut alternative to anthropic reasoning. I suggest that finding the initial conditions may be irrelevant since all possible vacua on the landscape are possible initial state conditions and eternal inflation could generate all the other vacua. We are now left to reason out why we are observing the small value of the cosmological constant. I address this issue in the context of noncritical string theory in which all values of the cosmological constant on the landscape are departures from the critical equilibrium state

  10. Our Common Landscapes For The Future

    DEFF Research Database (Denmark)

    Brandt, Jesper

    2017-01-01

    Foreword for Marc Antrop and Veerle van Eetvelde: Landscape Perspectives – The Holistic Nature of Landscapes Our common landscapes for the future by Jesper Brandt The solution of the ecological crisis through a transformation towards sustainable development is the most urgent challenge in our time....... It is not just a question of CO2 and conversion toward renewable energy. The reestablishment and conscious development of our common landscapes at all spatial scales for the combined benefits of biodiversity, our cultural heritage and the preservation and development of ecosystem services will probably...... be the most comprehensive and necessary social task in the future, if a conversion towards a sustainable development shall succeed in due time. This is so because it will be necessary to ensure that the potential material wealth of modern society will be transformed into a good, fruitful and healthy life...

  11. Sustaining ecosystem services in cultural landscapes

    DEFF Research Database (Denmark)

    Plieninger, Tobias; van der Horst, Dan; Schleyer, Christian

    2014-01-01

    Classical conservation approaches focus on the man-made degradation of ecosystems and tend to neglect the socialecological values that human land uses have imprinted on many environments. Throughout the world, ingenious land-use practices have generated unique cultural landscapes...... research and management. With this paper, we introduce a special feature that aims to enhance the theoretical, empirical and practical knowledge of how to safeguard the resilience of ecosystem services in cultural landscapes. It concludes (1) that the usefulness of the ecosystem services approach...... to the analysis and management of cultural landscapes should be reviewed more critically; (2) that conventional ecosystem services assessment needs to be complemented by socio-cultural valuation; (3) that cultural landscapes are inherently changing, so that a dynamic view on ecosystem services and a focus...

  12. Applying Landscape Science to Natural Resource Management

    Directory of Open Access Journals (Sweden)

    Guy M. Robinson

    2013-03-01

    Full Text Available This is the introduction to the Ecology and Society special feature on "Applying Landscape Science to Natural Resource Management". Primarily drawing upon examples from Australia, the nine papers in the feature illustrate how landscape science seeks to integrate information from diverse sources to generate management solutions for implementation by individual land managers, communities, and governments at different levels. This introduction refers to the genesis of the feature, briefly outlines the nature and content of landscape science, and then summarizes key features of the nine papers. These are organized into two sections: one deals with inputs from human agents in the landscape, and one with the development of models enabling different management scenarios and environmental changes to be envisaged, understood, and applied to policy development.

  13. Missing Linkages in California's Landscape [ds420

    Data.gov (United States)

    California Department of Resources — The critical need for conserving landscape linkages first came to the forefront of conservation thinking in California in November 2000, when a statewide interagency...

  14. Agrarian Landscape Management in a Modernized World

    DEFF Research Database (Denmark)

    Christensen, Andreas Aagaard

    ) A historical analysis of social drivers of land use change affecting agrarian landscapes in the Western world in the period 1700-2000 based on a litterature review of modernization theory applied to two local scale historical case studies of changes in landscape structure; (2) A national scale analysis based...... on archival and cartographic sources of the way selected modernization processes affected rural land use patterns in New Zealand in the period from its first Europeancolonial exploration in the 17th century until the present. (3) A global scale analysis of historical patterns of modernization affecting rural...... land use patterns within the Western world based on historical cartographic evidence, (4) A local scale analysis of the decision making practices of landscape managers in four modern case landscapes in Denmark and New Zealand, based on interview surveys conducted in 2011 and 2012. Findings indicate...

  15. The post-transcriptional operon

    DEFF Research Database (Denmark)

    Tenenbaum, Scott A.; Christiansen, Jan; Nielsen, Henrik

    2011-01-01

    model (PTO) is used to describe data from an assortment of methods (e.g. RIP-Chip, CLIP-Chip, miRNA profiling, ribosome profiling) that globally address the functionality of mRNA. Several examples of post-transcriptional operons have been documented in the literature and demonstrate the usefulness...... of the model in identifying new participants in cellular pathways as well as in deepening our understanding of cellular responses....

  16. Energy landscapes, landscapes in transition. How to prepare one's territory to the deployment of renewable energies

    International Nuclear Information System (INIS)

    2014-06-01

    This guide first defines the notion of landscape, outlines what is at stake with decentralised renewable energy production, and presents the various important aspects of a deployment of decentralised renewable energy production. It describes how to define a general strategy for the integration of this production: relationship between energy and landscape, project implementation, partnership, tools to anticipate changes, evolution of social demand through dialogue, conciliation of technical and financial constraints and landscape ambitions. An appendix proposes legal and bibliographical information: legal relationships between energy and landscape, possible arrangements for PLU (plan local d'urbanisme, local urban plan) and SCOT (schema de coherence territoriale, territorial planning document)

  17. Importance of pollinators in changing landscapes for world crops.

    Science.gov (United States)

    Klein, Alexandra-Maria; Vaissière, Bernard E; Cane, James H; Steffan-Dewenter, Ingolf; Cunningham, Saul A; Kremen, Claire; Tscharntke, Teja

    2007-02-07

    The extent of our reliance on animal pollination for world crop production for human food has not previously been evaluated and the previous estimates for countries or continents have seldom used primary data. In this review, we expand the previous estimates using novel primary data from 200 countries and found that fruit, vegetable or seed production from 87 of the leading global food crops is dependent upon animal pollination, while 28 crops do not rely upon animal pollination. However, global production volumes give a contrasting perspective, since 60% of global production comes from crops that do not depend on animal pollination, 35% from crops that depend on pollinators, and 5% are unevaluated. Using all crops traded on the world market and setting aside crops that are solely passively self-pollinated, wind-pollinated or parthenocarpic, we then evaluated the level of dependence on animal-mediated pollination for crops that are directly consumed by humans. We found that pollinators are essential for 13 crops, production is highly pollinator dependent for 30, moderately for 27, slightly for 21, unimportant for 7, and is of unknown significance for the remaining 9. We further evaluated whether local and landscape-wide management for natural pollination services could help to sustain crop diversity and production. Case studies for nine crops on four continents revealed that agricultural intensification jeopardizes wild bee communities and their stabilizing effect on pollination services at the landscape scale.

  18. Thermal Characteristics of Urban Landscapes

    Science.gov (United States)

    Luvall, Jeffrey C.; Quattrochi, Dale A.

    1998-01-01

    Although satellite data are very useful for analysis of the urban heat island effect at a coarse scale, they do not lend themselves to developing a better understanding of which surfaces across the city contribute or drive the development of the urban heat island effect. Analysis of thermal energy responses for specific or discrete surfaces typical of the urban landscape (e.g., asphalt, building rooftops, vegetation) requires measurements at a very fine spatial scale (i.e., less than 15 m) to adequately resolve these surfaces and their attendant thermal energy regimes. Additionally, very fine scale spatial resolution thermal infrared data, such as that obtained from aircraft, are very useful for demonstrating to planning officials, policy makers, and the general populace the benefits of the urban forest. These benefits include mitigating the urban heat island effect, making cities more aesthetically pleasing and more habitable environments, and aid in overall cooling of the community. High spatial resolution thermal data are required to quantify how artificial surfaces within the city contribute to an increase in urban heating and the benefit of cool surfaces (e.g., surface coatings that reflect much of the incoming solar radiation as opposed to absorbing it thereby lowering urban temperatures). The TRN (thermal response number) is a technique using aircraft remotely sensed surface temperatures to quantify the thermal response of urban surfaces. The TRN was used to quantify the thermal response of various urban surface types ranging from completely vegetated surfaces to asphalt and concrete parking lots for Huntsville, AL.

  19. Ecosystems science: Genes to landscapes

    Science.gov (United States)

    ,

    2018-05-09

    Bountiful fisheries, healthy and resilient wildlife, flourishing forests and vibrant grasslands are coveted resources that benefit all Americans. U.S. Geological Survey (USGS) science supports the conservation and management of the Nation’s fish and wildlife, and the landscapes they inhabit. Our biological resources—ecosystems and the wild things that live in them—are the foundation of our conservation heritage and an economic asset to current and future generations of Americans.The USGS Ecosystems Mission Area, the biological research arm of the Department of the Interior (DOI), provides science to help America achieve sustainable management and conservation of its biological resources. This work is done within the broader mission of the USGS—to serve the Nation with science that advances understanding of our natural resources, informs land and water stewardship, and helps safeguard communities from natural and environmental hazards. The Ecosystems Mission Area provides research, technical assistance, and education conducted by Cooperative Research Units and Science Centers located in nearly every State.The quality of life and economic strength in America hinges on healthy ecosystems that support living things and natural processes. Ecosystem science better enables society to understand how and why ecosystems change and to guide actions that can prevent damage to, and restore and sustain ecosystems. It is through this knowledge that informed decisions are made about natural resources that can enhance our Nation’s economic and environmental well-being.

  20. Do geographically isolated wetlands influence landscape functions?

    OpenAIRE

    Cohen, Matthew J.; Creed, Irena F.; Alexander, Laurie; Basu, Nandita B.; Calhoun, Aram J. K.; Craft, Christopher; D’Amico, Ellen; DeKeyser, Edward; Fowler, Laurie; Golden, Heather E.; Jawitz, James W.; Kalla, Peter; Kirkman, L. Katherine; Lane, Charles R.; Lang, Megan

    2016-01-01

    Geographically isolated wetlands (GIWs), those surrounded by uplands, exchange materials, energy, and organisms with other elements in hydrological and habitat networks, contributing to landscape functions, such as flow generation, nutrient and sediment retention, and biodiversity support. GIWs constitute most of the wetlands in many North American landscapes, provide a disproportionately large fraction of wetland edges where many functions are enhanced, and form complexes with other water bo...

  1. Landscape in Green Infrastructures & Interscalar Planning

    OpenAIRE

    Galan, Juanjo

    2015-01-01

    The transversal and interdisciplinary quality of landscape makes it an essential and useful element in regional and local planning. On the other hand, Green Infrastructures provide an exceptional tool to put in relation different planning scales and offer new possibilities and functions for the design and management of open spaces. The Strategic Plan for the Calderona Mountain Range (Valencia province, Spain) shows how these two concepts: Landscape and Green Infrastructure can work hand in...

  2. Landscaping Considerations for Urban Stream Restoration Projects

    National Research Council Canada - National Science Library

    Bailey, Pam

    2004-01-01

    ... after restoration and its functionality for public use. The landscaping component of such stream and riparian restoration projects must be emphasized given its importance of visual success and public perception. The purpose of this technical note is to address landscaping considerations associated with urban stream and riparian restoration projects, and provide ideas to managers for enhancing the visual appeal and aesthetic qualities of urban projects.

  3. Implementing forest landscape restoration, a practitioner's guide

    Science.gov (United States)

    John Stanturf; Stephanie Mansourian; Michael (eds.). Kleine

    2017-01-01

    Forest landscape restoration (FLR) in a nutshell FLR was defined in 2000 by a group of 30 specialists as “a planned process that aims to regain ecological integrity and enhance human wellbeing in deforested or degraded landscapes”. It does not seek to recreate past ecosystems given the uncertainty concerning the “past”, the significantly altered conditions of the...

  4. Characterising landscape variation through spatial folksonomies

    OpenAIRE

    Derungs, Curdin; Purves, Ross S

    2016-01-01

    Describing current, past and future landscapes for inventory and policy making purposes requires classifications capturing variation in, for example, land use and land cover. Typical land cover classifi- cations for such purposes result from a top-down process and rely on expert conceptualisations, and thus provide limited space for incorporating more widely held views of key landscape elements. In this paper we introduce the notion of spatial folksonomies, which we define as a tuple linking ...

  5. Sustaining ecosystem services in cultural landscapes

    OpenAIRE

    Plieninger, T.; van der Horst, D.; Schleyer, C.; Bieling, C.

    2014-01-01

    Classical conservation approaches focus on the man-made degradation of ecosystems and tend to neglect the social-ecological values that human land uses have imprinted on many environments. Throughout the world, ingenious land-use practices have generated unique cultural landscapes, but these are under pressure from agricultural intensification, land abandonment, and urbanization. In recent years, the cultural landscapes concept has been broadly adopted in science, policy, and management. The ...

  6. Historic Landscape Survey, Maxwell AFB, Alabama

    Science.gov (United States)

    2013-08-01

    signifies Maxwell AFB’s historic landscapes. 2.1 The pre-military landscape Prehistory in the southeastern United States is generally designated as...the period of Native American occupation before Spanish explorers made contact in the fifteenth and sixteenth centuries. In Alabama, the prehistory ... prehistory or history is made clear.56 A historic property is determined to be either significant or not significant by applying standardized National

  7. Production of the 2400 kb Duchenne muscular dystrophy (DMD) gene transcript; transcription time and cotranscriptional splicing

    Energy Technology Data Exchange (ETDEWEB)

    Tennyson, C.N.; Worton, R.G. [Univ. of Toronto and the Hospital for Sick Children, Ontario (Canada)

    1994-09-01

    The largest known gene in any organism is the human DMD gene which has 79 exons that span 2400 kb. The extreme nature of the DMD gene raises questions concerning the time required for transcription and whether splicing begins before transcription is complete. DMD gene transcription is induced as cultured human myoblasts differentiate to form multinucleated myotubes, providing a system for studying the kinetics of transcription and splicing. Using quantitative RT-PCR, transcript accumulation was monitored from four different regions within the gene following induction of expression. By comparing the accumulation of transcripts from the 5{prime} and 3{prime} ends of the gene we have shown that approximately 12 hours are required to transcribe 1770 kb of the gene, extrapolating to a time of 16 hours for the transcription unit expressed in muscle. Comparison of accumulation profiles for spliced and total transcript demonstrated that transcripts are spliced at the 5{prime} end before transcription is complete, providing strong evidence for cotranscriptional splicing of DMD gene transcripts. Finally, the rate of transcript accumulation was reduced at the 3{prime} end of the gene relative to the 5{prime} end, perhaps due to premature termination of transcription complexes as they traverse this enormous transcription unit. The lag between transcription initiation and the appearance of complete transcripts could be important in limiting transcript production in dividing cells and to the timing of mRNA appearance in differentiating muscle.

  8. Mutual interdependence of splicing and transcription elongation.

    Science.gov (United States)

    Brzyżek, Grzegorz; Świeżewski, Szymon

    2015-01-01

    Transcription and splicing are intrinsically linked, as splicing needs a pre-mRNA substrate to commence. The more nuanced view is that the rate of transcription contributes to splicing regulation. On the other hand there is accumulating evidence that splicing has an active role in controlling transcription elongation by DNA-dependent RNA polymerase II (RNAP II). We briefly review those mechanisms and propose a unifying model where splicing controls transcription elongation to provide an optimal timing for successive rounds of splicing.

  9. Landscape structure and the speed of adaptation

    International Nuclear Information System (INIS)

    Claudino, Elder S.; Campos, Paulo R.A.

    2014-01-01

    The role of fragmentation in the adaptive process is addressed. We investigate how landscape structure affects the speed of adaptation in a spatially structured population model. As models of fragmented landscapes, here we simulate the percolation maps and the fractal landscapes. In the latter the degree of spatial autocorrelation can be suited. We verified that fragmentation can effectively affect the adaptive process. The examination of the fixation rates and speed of adaptation discloses the dichotomy exhibited by percolation maps and fractal landscapes. In the latter, there is a smooth change in the pace of the adaptation process, as the landscapes become more aggregated higher fixation rates and speed of adaptation are obtained. On the other hand, in random percolation the geometry of the percolating cluster matters. Thus, the scenario depends on whether the system is below or above the percolation threshold. - Highlights: • The role of fragmentation on the adaptive process is addressed. • Our approach makes the linkage between population genetics and landscape ecology. • Fragmentation affects gene flow and thus influences the speed of adaptation. • The level of clumping determines how the speed of adaptation is influenced

  10. Nonequilibrium landscape theory of neural networks.

    Science.gov (United States)

    Yan, Han; Zhao, Lei; Hu, Liang; Wang, Xidi; Wang, Erkang; Wang, Jin

    2013-11-05

    The brain map project aims to map out the neuron connections of the human brain. Even with all of the wirings mapped out, the global and physical understandings of the function and behavior are still challenging. Hopfield quantified the learning and memory process of symmetrically connected neural networks globally through equilibrium energy. The energy basins of attractions represent memories, and the memory retrieval dynamics is determined by the energy gradient. However, the realistic neural networks are asymmetrically connected, and oscillations cannot emerge from symmetric neural networks. Here, we developed a nonequilibrium landscape-flux theory for realistic asymmetrically connected neural networks. We uncovered the underlying potential landscape and the associated Lyapunov function for quantifying the global stability and function. We found the dynamics and oscillations in human brains responsible for cognitive processes and physiological rhythm regulations are determined not only by the landscape gradient but also by the flux. We found that the flux is closely related to the degrees of the asymmetric connections in neural networks and is the origin of the neural oscillations. The neural oscillation landscape shows a closed-ring attractor topology. The landscape gradient attracts the network down to the ring. The flux is responsible for coherent oscillations on the ring. We suggest the flux may provide the driving force for associations among memories. We applied our theory to rapid-eye movement sleep cycle. We identified the key regulation factors for function through global sensitivity analysis of landscape topography against wirings, which are in good agreements with experiments.

  11. Landscape degradation at different spatial scales caused by aridification

    OpenAIRE

    Meyer Burghard Christian; Mezősi Gábor; Kovács Ferenc

    2017-01-01

    Landscape responses to degradation caused by aridification bring the landscape system into a new equilibrium state. The system transformation may entail irreversible changes to its constituting parameters. This paper analyses the impact of aridification on landscape degradation processes in the sand-covered landscapes of the Hungarian Danube-Tisza Interfluve region at the regional, landscape, and local site scales. Changes in groundwater level (well data), lake surface area (Modified Normaliz...

  12. Interplay between DNA supercoiling and transcription elongation.

    Science.gov (United States)

    Ma, Jie; Wang, Michelle

    2014-01-01

    Transcription-coupled DNA supercoiling has been shown to be an important regulator of transcription that is broadly present in the cell. Here we review experimental work which shows that RNA polymerase is a powerful torsional motor that can alter DNA topology and structure, and DNA supercoiling in turn directly affects transcription elongation.

  13. The Role of Epigenetic Regulation in Transcriptional Memory in the Immune System.

    Science.gov (United States)

    Woodworth, A M; Holloway, A F

    The immune system is exquisitely poised to identify, respond to, and eradicate pathogens from the body, as well as to produce a more rapid and augmented response to a subsequent encounter with the pathogen. These cellular responses rely on the highly coordinated and rapid activation of gene expression programs as well as the ability of the cell to retain a memory of the initial gene response. It is clear that chromatin structure and epigenetic mechanisms play a crucial role in determining these gene responses, and in fact the immune system has proved an instructive model for investigating the multifaceted mechanisms through which the chromatin landscape contributes to gene expression programs. These mechanisms include modifications to the DNA and histone proteins, the positioning, composition, and remodeling of nucleosomes, as well as the formation of higher-order chromatin structures. Moreover, it is now apparent that epigenetic mechanisms also provide an instrument by which cells can retain memory of the initial transcriptional response, "priming" the genome so that it can respond more quickly to subsequent exposure to the signal. Here, we use the immune system as a model to demonstrate the complex interplay between transcription factors and the chromatin landscape required to orchestrate precise gene responses to external stimuli and further to demonstrate how these interactions can establish memory of past transcriptional events. We focus on what we have learnt from the immune system and how this can inform our understanding of other cellular systems. © 2017 Elsevier Inc. All rights reserved.

  14. Selecting landscape metrics as indicators of spatial heterogeneity-A comparison among Greek landscapes

    Science.gov (United States)

    Plexida, Sofia G.; Sfougaris, Athanassios I.; Ispikoudis, Ioannis P.; Papanastasis, Vasilios P.

    2014-02-01

    This paper investigates the spatial heterogeneity of three landscapes along an altitudinal gradient and different human land use. The main aim was the identification of appropriate landscape indicators using different extents. ASTER image was used to create a land cover map consisting of three landscapes which differed in altitude and land use. A number of landscape metrics quantifying patch complexity, configuration, diversity and connectivity were derived from the thematic map at the landscape level. There were significant differences among the three landscapes regarding these four aspects of landscape heterogeneity. The analysis revealed a specific pattern of land use where lowlands are being increasingly utilized by humans (percentage of agricultural land = 65.84%) characterized by physical connectedness (high values of Patch Cohesion Index) and relatively simple geometries (low values of fractal dimension index). The landscape pattern of uplands was found to be highly diverse based upon the Shannon Diversity index. After selecting the scale (600 ha) where metrics values stabilized, it was shown that metrics were more correlated at the small scale of 60 ha. From the original 24 metrics, 14 individual metrics with high Spearman correlation coefficient and Variance Inflation Factor criterion were eliminated, leaving 10 representative metrics for subsequent analysis. Data reduction analysis showed that Patch Density, Area-Weighted Mean Fractal Dimension Index and Patch Cohesion Index are suitable to describe landscape patterns irrespective of the scale. A systematic screening of these metrics could enhance a deeper understanding of the results obtained by them and contribute to a sustainable landscape management of Mediterranean landscapes.

  15. Sustainable pest regulation in agricultural landscapes: a review on landscape composition, biodiversity and natural pest control.

    Science.gov (United States)

    Bianchi, F J J A; Booij, C J H; Tscharntke, T

    2006-07-22

    Agricultural intensification has resulted in a simplification of agricultural landscapes by the expansion of agricultural land, enlargement of field size and removal of non-crop habitat. These changes are considered to be an important cause of the rapid decline in farmland biodiversity, with the remaining biodiversity concentrated in field edges and non-crop habitats. The simplification of landscape composition and the decline of biodiversity may affect the functioning of natural pest control because non-crop habitats provide requisites for a broad spectrum of natural enemies, and the exchange of natural enemies between crop and non-crop habitats is likely to be diminished in landscapes dominated by arable cropland. In this review, we test the hypothesis that natural pest control is enhanced in complex patchy landscapes with a high proportion of non-crop habitats as compared to simple large-scale landscapes with little associated non-crop habitat. In 74% and 45% of the studies reviewed, respectively, natural enemy populations were higher and pest pressure lower in complex landscapes versus simple landscapes. Landscape-driven pest suppression may result in lower crop injury, although this has rarely been documented. Enhanced natural enemy activity was associated with herbaceous habitats in 80% of the cases (e.g. fallows, field margins), and somewhat less often with wooded habitats (71%) and landscape patchiness (70%). The similar contributions of these landscape factors suggest that all are equally important in enhancing natural enemy populations. We conclude that diversified landscapes hold most potential for the conservation of biodiversity and sustaining the pest control function.

  16. History of the incipient Icelandic plume: Observations from ancient buried landscapes

    Science.gov (United States)

    Stucky de Quay, Gaia; Roberts, Gareth G.; Watson, Jonathan S.; Jackson, Christopher A.-L.

    2017-04-01

    Ancient buried terrestrial landscapes contain records of vertical motions which can be used to probe histories of geodynamical processes. In the North Atlantic Ocean, sedimentary basins contain excellent evidence that the continental shelf experienced staged subaerial exposure. For example, now buried landscapes were uplifted, rapidly eroded, and drowned close to the Paleocene-Eocene boundary. We use commercial wells and three-dimensional seismic data to reconstruct a 57-55 Ma landscape now buried 1.5 km beneath the seabed in the Bressay area of the northern North Sea. Geochemical analyses of organic matter from core samples intersecting the erosional landscape indicate the presence of angiosperm (flowering plant) debris. Combined with the presence of coarse clastic material, mapped beach ridges, and dendritic drainage patterns, these observations indicate that this landscape was of terrestrial origin. Longitudinal profiles of ancient rivers were extracted and inverted for an uplift rate history. The best-fitting uplift rate history has three phases and total cumulative uplift of 350 m. Biostratigraphic data from surrounding marine stratigraphy indicate that this landscape formed within 1-1.5 Ma. This uplift history is similar to that of a slightly older buried landscape in the Faeroe-Shetland basin 400 km to the west. These records of vertical motion can explained by pulses of anomalously hot asthenosphere spreading out from the incipient Icelandic plume. Using simple isostatic calculations we estimate that the maximum thermal anomaly beneath Bressay was 50˚. Our observations suggest that a thermal anomaly departed the Icelandic plume as early as 58.5 Ma and had highest average temperatures at 55.6 Ma.

  17. High trees increase sunflower seed predation by birds in an agricultural landscape of Israel

    Directory of Open Access Journals (Sweden)

    Jessica eSchäckermann

    2014-07-01

    Full Text Available Natural habitats in agricultural landscapes promote agro-ecosystem services but little is known about negative effects (dis-services derived by natural habitats such as crop seed predation. Birds are important seed predators and use high landscape structures to perch and hide. High trees in agricultural landscapes may therefore drive seed predation. We examined if the presence, the distance and the percentages of high trees (tree height >5 m and the percentages of natural habitat surrounding sunflower fields, increased seed predation by birds in Israel. At the field scale, we assessed seed predation across a sample grid of an entire field. At the landscape scale, we assessed seed predation at the field margins and interiors of 20 sunflower fields. Seed predation was estimated as the percentage of removed seeds from sunflower heads. Distances of sample points to the closest high tree and percentage of natural habitat and of high trees in a 1km radius surrounding the fields were measured.We found that seed predation increased with decreasing distance to the closest high tree at the field and landscape scale. At the landscape scale, the percentage of high trees and natural habitat did not increase seed predation. Seed predation in the fields increased by 37 %, with a maximum seed predation of 92 %, when a high tree was available within zero to 50 m to the sunflower fields. If the closest high tree was further away, seed predation was less than 5 %. Sunflower seed predation by birds can be reduced, when avoiding sowing sunflowers within a radius of 50 m to high trees. Farmers should plan to grow crops, not sensitive to bird seed predation, closer to trees to eventually benefit from ecosystem services provided by birds, such as predation of pest insects, while avoiding these locations for growing crops sensitive to bird seed predation. Such management recommendations are directing towards sustainable agricultural landscapes.

  18. Parameter Estimation

    DEFF Research Database (Denmark)

    Sales-Cruz, Mauricio; Heitzig, Martina; Cameron, Ian

    2011-01-01

    of optimisation techniques coupled with dynamic solution of the underlying model. Linear and nonlinear approaches to parameter estimation are investigated. There is also the application of maximum likelihood principles in the estimation of parameters, as well as the use of orthogonal collocation to generate a set......In this chapter the importance of parameter estimation in model development is illustrated through various applications related to reaction systems. In particular, rate constants in a reaction system are obtained through parameter estimation methods. These approaches often require the application...... of algebraic equations as the basis for parameter estimation.These approaches are illustrated using estimations of kinetic constants from reaction system models....

  19. Directing traffic on DNA-How transcription factors relieve or induce transcriptional interference.

    Science.gov (United States)

    Hao, Nan; Palmer, Adam C; Dodd, Ian B; Shearwin, Keith E

    2017-03-15

    Transcriptional interference (TI) is increasingly recognized as a widespread mechanism of gene control, particularly given the pervasive nature of transcription, both sense and antisense, across all kingdoms of life. Here, we discuss how transcription factor binding kinetics strongly influence the ability of a transcription factor to relieve or induce TI.

  20. Landscape evolution by subglacial quarrying

    Science.gov (United States)

    Ugelvig, Sofie V.; Egholm, David L.; Iverson, Neal R.

    2014-05-01

    In glacial landscape evolution models, subglacial erosion rates are often related to basal sliding or ice discharge by a power-law. This relation can be justified for bedrock abrasion because rock debris transported in the basal ice drives the erosion. However, a simple relation between rates of sliding and erosion is not well supported when considering models for quarrying of rock blocks from the bed. Iverson (2012) introduced a new subglacial quarrying model that operates from the theory of adhesive wear. The model is based on the fact that cavities, with a high level of bedrock differential stress, form along the lee side of bed obstacles when the sliding velocity is to high to allow for the ice to creep around the obstacles. The erosion rate is quantified by considering the likelihood of rock fracturing on topographic bumps. The model includes a statistical treatment of the bedrock weakness: larger rock bodies have lower strengths since they have greater possibility of containing a large flaw [Jaeger and Cook, 1979]. Inclusion of this effect strongly influences the erosion rates and questions the dominant role of sliding rate in standard models for subglacial erosion. Effective pressure, average bedslope, and bedrock fracture density are primary factors that, in addition to sliding rate, influence the erosion rate of this new quarrying model [Iverson, 2012]. We have implemented the quarrying model in a depth-integrated higher-order ice-sheet model [Egholm et al. 2011], coupled to a model for glacial hydrology. In order to also include the effects of cavitation on the subglacial sliding rate, we use a sliding law proposed by Schoof (2005), which includes an upper limit for the stress that can be supported at the bed. Computational experiments show that the combined influence of pressure, sliding rate and bed slope leads to realistically looking landforms such as U-shaped valleys, cirques, hanging valleys and overdeepenings. Compared to model results using a