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Sample records for model suitably expressed

  1. Validation of suitable reference genes for expression studies in different pilocarpine-induced models of mesial temporal lobe epilepsy.

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    Thalita Ewellyn Batista Sales Marques

    Full Text Available It is well recognized that the reference gene in a RT-qPCR should be properly validated to ensure that gene expression is unaffected by the experimental condition. We investigated eight potential reference genes in two different pilocarpine PILO-models of mesial temporal lobe epilepsy (MTLE performing a stability expression analysis using geNorm, NormFinder and BestKepeer softwares. Then, as a validation strategy, we conducted a relative expression analysis of the Gfap gene. Our results indicate that in the systemic PILO-model Actb, Gapdh, Rplp1, Tubb2a and Polr1a mRNAs were highly stable in hippocampus of rats from all experimental and control groups, whereas Gusb revealed to be the most variable one. In fact, we observed that using Gusb for normalization, the relative mRNA levels of the Gfap gene differed from those obtained with stable genes. On the contrary, in the intrahippocampal PILO-model, all softwares included Gusb as a stable gene, whereas B2m was indicated as the worst candidate gene. The results obtained for the other reference genes were comparable to those observed for the systemic Pilo-model. The validation of these data by the analysis of the relative expression of Gfap showed that the upregulation of the Gfap gene in the hippocampus of rats sacrificed 24 hours after status epilepticus (SE was undetected only when B2m was used as the normalizer. These findings emphasize that a gene that is stable in one pathology model may not be stable in a different experimental condition related to the same pathology and therefore, the choice of reference genes depends on study design.

  2. Habitat Suitability Index Models: Eastern wild turkey

    Science.gov (United States)

    Schroeder, Richard L.

    1985-01-01

    A review and synthesis of existing information were used to develop a Habitat Suitability Index (HSI) model for the eastern wild turkey (Meleagris gallopavo sylvestris). The model consolidates habitat use information into a framework appropriate for field application, and is scaled to produce an index between 0.0 (unsuitable habitat) to 1.0 (optimum habitat). HSI models are designed to be used with Habitat Evaluation Procedures previously developed by the U.S. Fish and Wildlife Service.

  3. Habitat Suitability Index Models: Swamp rabbit

    Science.gov (United States)

    Allen, Arthur W.

    1985-01-01

    A review and synthesis of existing information were used to develop a Habitat Suitability Index (HSI) model for the swamp rabbit (Sylvilagus aquaticus). The model consolidates habitat use information into a framework appropriate for field application, and is scaled to produce an index between 0.0 (unsuitable habitat) to 1.0 (optimum habitat). HSI models are designed to be used with Habitat Evaluation Procedures previously developed by the U.S. Fish and Wildlife Service.

  4. Habitat Suitability Index Models: Red king crab

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    Jewett, Stephen C.; Onuf, Christopher P.

    1988-01-01

    A review and synthesis of existing information were used to develop a Habitat Suitability Index (HSI) model for evaluating habitat of different life stages of red king crab (Paralithodes camtschatica). A model consolidates habitat use information into a framework appropriate for field application, and is scaled to produce an index between 0.0 (unsuitable habitat) and 1.0 (optimum habitat) in Alaskan coastal waters, especially in the Gulf of Alaska and the southeastern Bering Sea. HSI models are designed to be used with Habitat Evaluation Procedures previously developed by the U.S. Fish and Wildlife Service.

  5. Global habitat suitability models of terrestrial mammals

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    Rondinini, Carlo; Di Marco, Moreno; Chiozza, Federica; Santulli, Giulia; Baisero, Daniele; Visconti, Piero; Hoffmann, Michael; Schipper, Jan; Stuart, Simon N.; Tognelli, Marcelo F.; Amori, Giovanni; Falcucci, Alessandra; Maiorano, Luigi; Boitani, Luigi

    2011-01-01

    Detailed large-scale information on mammal distribution has often been lacking, hindering conservation efforts. We used the information from the 2009 IUCN Red List of Threatened Species as a baseline for developing habitat suitability models for 5027 out of 5330 known terrestrial mammal species, based on their habitat relationships. We focused on the following environmental variables: land cover, elevation and hydrological features. Models were developed at 300 m resolution and limited to within species' known geographical ranges. A subset of the models was validated using points of known species occurrence. We conducted a global, fine-scale analysis of patterns of species richness. The richness of mammal species estimated by the overlap of their suitable habitat is on average one-third less than that estimated by the overlap of their geographical ranges. The highest absolute difference is found in tropical and subtropical regions in South America, Africa and Southeast Asia that are not covered by dense forest. The proportion of suitable habitat within mammal geographical ranges correlates with the IUCN Red List category to which they have been assigned, decreasing monotonically from Least Concern to Endangered. These results demonstrate the importance of fine-resolution distribution data for the development of global conservation strategies for mammals. PMID:21844042

  6. Uncertainty in Various Habitat Suitability Models and Its Impact on Habitat Suitability Estimates for Fish

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    Yu-Pin Lin

    2015-07-01

    Full Text Available Species distribution models (SDMs are extensively used to project habitat suitability of species in stream ecological studies. Owing to complex sources of uncertainty, such models may yield projections with varying degrees of uncertainty. To better understand projected spatial distributions and the variability between habitat suitability projections, this study uses five SDMs that are based on the outputs of a two-dimensional hydraulic model to project the suitability of habitats and to evaluate the degree of variability originating from both differing model types and the split-sample procedure. The habitat suitability index (HSI of each species is based on two stream flow variables, including current velocity (V, water depth (D, as well as the heterogeneity of these flow conditions as quantified by the information entropy of V and D. The six SDM approaches used to project fish abundance, as represented by HSI, included two stochastic models: the generalized linear model (GLM and the generalized additive model (GAM; as well as three machine learning models: the support vector machine (SVM, random forest (RF and the artificial neural network (ANN, and an ensemble model (where the latter is the average of the preceding five models. The target species Sicyopterus japonicas was found to prefer habitats with high current velocities. The relationship between mesohabitat diversity and fish abundance was indicated by the trends in information entropy and weighted usable area (WUA over the study area. This study proposes a method for quantifying habitat suitability, and for assessing the uncertainties in HSI and WUA that are introduced by the various SDMs and samples. This study also demonstrated both the merits of the ensemble modeling approach and the necessity of addressing model uncertainty.

  7. Modeling approach suitable for energy system

    Energy Technology Data Exchange (ETDEWEB)

    Goetschel, D. V.

    1979-01-01

    Recently increased attention has been placed on optimization problems related to the determination and analysis of operating strategies for energy systems. Presented in this paper is a nonlinear model that can be used in the formulation of certain energy-conversion systems-modeling problems. The model lends itself nicely to solution approaches based on nonlinear-programming algorithms and, in particular, to those methods falling into the class of variable metric algorithms for nonlinearly constrained optimization.

  8. Comprehensive Suitability Evaluation of Tea Crops Using GIS and a Modified Land Ecological Suitability Evaluation Model

    Institute of Scientific and Technical Information of China (English)

    LI Bo; ZHANG Feng; ZHANG Li-Wen; HUANG Jing-Feng; JIN Zhi-Feng; D. K. GUPTA

    2012-01-01

    Tea (Camellia sinensis) is one of the most valuable cash crops in southern China; however,the planting distribution of tea crops is not optimal and the production and cultivation regions of tea crops are restricted by law and custom.In order to evaluate the suitability of tea crops in Zhejiang Province,the annual mean temperature,the annual accumulated temperature above 10 ℃,the frequency of extremely low temperature below -13 ℃,the mean humidity from April to October,slope,aspect,altitude,soil type,and soil texture were selected from climate,topography,and soil factors as factors for land ecological evaluation by the Delphi method based on the ecological characteristics of tea crops.These nine factors were quantitatively analyzed using a geographic information system (GIS).The grey relational analysis (GRA) was combined with the analytic hierarchy process (AHP) to address the uncertainties during the process of evaluating the traditional land ecological suitability,and a modified land ecological suitability evaluation (LESE) model was built.Based on the land-use map of Zhejiang Province,the regions that were completely unsuitable for tea cultivation in the province were eliminated and then the spatial distribution of the ecological suitability of tea crops was generated using the modified LESE model and GIS.The results demonstrated that the highly,moderately,and non-suitable regions for the cultivation of tea crops in Zhejiang Province were 27552.66,42724.64,and 26507.97 km2,and accounted for 28.47%,44.14%,and 27.39% of the total evaluation area,respectively.Validation of the method showed a high degree of coincidence with the current planting distribution of tea crops in Zhejiang Province.The modified LESE model combined with GIS could be useful in quickly and accurately evaluating the land ecological suitability of tea crops,providing a scientific basis for the rational distribution of tea crops and acting as a reference to land policy makers and land

  9. Fuzzy modeling of farmers' knowledge for land suitability classification

    NARCIS (Netherlands)

    Sicat, R.S.; Carranza, E.J.M.; Nidumolu, U.B.

    2005-01-01

    In a case study, we demonstrate fuzzy modeling of farmers' knowledge (FK) for agricultural land suitability classification using GIS. Capture of FK was through rapid rural participatory approach. The farmer respondents consider, in order of decreasing importance, cropping season, soil color, soil te

  10. EXPERT MODEL OF LAND SUITABILITY ASSESSMENT FOR CROPS

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    Boris Đurđević

    2010-12-01

    Full Text Available A total of 17404 soil samples (2003rd-2009th year were analysed in the eastern Croatia. The largest number of soil samples belongs to the Osijek-Baranya county, which together with both Eastern sugar beet Factories (Osijek and Županja, conduct the soil fertility control (~4200 samples/yr.. Computer model suitability assessment for crops, supported by GIS, proved to be fast, efficient enough reliable in terms of the number of analyzed soil samples. It allows the visualization of the agricultural area and prediction of its production properties for the purposes of analysis, planning and rationalization of agricultural production. With more precise data about the soil (soil, climate and reliable Digital Soil Map of Croatia, the model could be an acceptable, not only to evaluate the suitability for growing different crops but also their need for fertilizer, necessary machinery, repairs (liming, and other measures of organic matter input. The abovementioned aims to eliminate or reduce effects of limiting factors in primary agricultural production. Assessment of the relative benefits of soil presented by computer model for the crops production and geostatistical method kriging in the Osijek-Baranya county showed: 1 Average soil suitability being 60.06 percent. 2 Kriging predicted that 51751 ha (17.16% are of limited resources (N1 for growing crops whereas a 86142 ha (28.57% of land is limited suitably (S3, b 132789 ha (44.04% are moderately suitable (S2 and c 30772 ha (10.28% are of excellent fertility (S1. A large number of eastern Croatian land data showed that the computer-geostatistical model for determination of soil benefits for growing crops was automated, fast and simple to use and suitable for the implementation of GIS and automatically downloading the necessary benefit indicators from the input base (land, analytical and climate as well as data from the digital soil maps able to: a visualize the suitability for soil tillage, b predict the

  11. A Suitable Artificial Intelligence Model for Inventory Level Optimization

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    Tereza Sustrova

    2016-05-01

    Full Text Available Purpose of the article: To examine suitable methods of artificial neural networks and their application in business operations, specifically to the supply chain management. The article discusses construction of an artificial neural networks model that can be used to facilitate optimization of inventory level and thus improve the ordering system and inventory management. For the data analysis from the area of wholesale trade with connecting material is used. Methodology/methods: Methods used in the paper consists especially of artificial neural networks and ANN-based modelling. For data analysis and preprocessing, MS Office Excel software is used. As an instrument for neural network forecasting MathWorks MATLAB Neural Network Tool was used. Deductive quantitative methods for research are also used. Scientific aim: The effort is directed at finding whether the method of prediction using artificial neural networks is suitable as a tool for enhancing the ordering system of an enterprise. The research also focuses on finding what architecture of the artificial neural networks model is the most suitable for subsequent prediction. Findings of the research show that artificial neural networks models can be used for inventory management and lot-sizing problem successfully. A network with the TRAINGDX training function and TANSIG transfer function and 6-8-1 architecture can be considered the most suitable for artificial neural network, as it shows the best results for subsequent prediction.. Conclusions resulting from the paper are beneficial for further research. It can be concluded that the created model of artificial neural network can be successfully used for predicting order size and therefore for improving the order cycle of an enterprise.

  12. Understanding Peripheral Bat Populations Using Maximum-Entropy Suitability Modeling

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    Barnhart, Paul R.; Gillam, Erin H.

    2016-01-01

    Individuals along the periphery of a species distribution regularly encounter more challenging environmental and climatic conditions than conspecifics near the center of the distribution. Due to these potential constraints, individuals in peripheral margins are expected to change their habitat and behavioral characteristics. Managers typically rely on species distribution maps when developing adequate management practices. However, these range maps are often too simplistic and do not provide adequate information as to what fine-scale biotic and abiotic factors are driving a species occurrence. In the last decade, habitat suitability modelling has become widely used as a substitute for simplistic distribution mapping which allows regional managers the ability to fine-tune management resources. The objectives of this study were to use maximum-entropy modeling to produce habitat suitability models for seven species that have a peripheral margin intersecting the state of North Dakota, according to current IUCN distributions, and determine the vegetative and climatic characteristics driving these models. Mistnetting resulted in the documentation of five species outside the IUCN distribution in North Dakota, indicating that current range maps for North Dakota, and potentially the northern Great Plains, are in need of update. Maximum-entropy modeling showed that temperature and not precipitation were the variables most important for model production. This fine-scale result highlights the importance of habitat suitability modelling as this information cannot be extracted from distribution maps. Our results provide baseline information needed for future research about how and why individuals residing in the peripheral margins of a species’ distribution may show marked differences in habitat use as a result of urban expansion, habitat loss, and climate change compared to more centralized populations. PMID:27935936

  13. Modelling white-water rafting suitability in a hydropower regulated Alpine River.

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    Carolli, Mauro; Zolezzi, Guido; Geneletti, Davide; Siviglia, Annunziato; Carolli, Fabiano; Cainelli, Oscar

    2017-02-01

    Cultural and recreational river ecosystem services and their relations with the flow regime are still poorly investigated. We develop a modelling-based approach to assess recreational flow requirements and the spatially distributed river suitability for white-water rafting, a typical service offered by mountain streams, with potential conflicts of interest with hydropower regulation. The approach is based on the principles of habitat suitability modelling using water depth as the main attribute, with preference curves defined through interviews with local rafting guides. The methodology allows to compute streamflow thresholds for conditions of suitability and optimality of a river reach in relation to rafting. Rafting suitability response to past, present and future flow management scenarios can be predicted on the basis of a hydrological model, which is incorporated in the methodology and is able to account for anthropic effects. Rafting suitability is expressed through a novel metric, the "Rafting hydro-suitability index" (RHSI) which quantifies the cumulative duration of suitable and optimal conditions for rafting. The approach is applied on the Noce River (NE Italy), an Alpine River regulated by hydropower production and affected by hydropeaking, which influences suitability at a sub-daily scale. A dedicated algorithm is developed within the hydrological model to resemble hydropeaking conditions with daily flow data. In the Noce River, peak flows associated with hydropeaking support rafting activities in late summer, highlighting the dual nature of hydropeaking in regulated rivers. Rafting suitability is slightly reduced under present, hydropower-regulated flow conditions compared to an idealized flow regime characterised by no water abstractions. Localized water abstractions for small, run-of-the-river hydropower plants are predicted to negatively affect rafting suitability. The proposed methodology can be extended to support decision making for flow

  14. Assessment of Suitable Reference Genes for Quantitative Gene Expression Studies in Melon Fruits.

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    Kong, Qiusheng; Gao, Lingyun; Cao, Lei; Liu, Yue; Saba, Hameed; Huang, Yuan; Bie, Zhilong

    2016-01-01

    Melon (Cucumis melo L.) is an attractive model plant for investigating fruit development because of its morphological, physiological, and biochemical diversity. Quantification of gene expression by quantitative reverse transcription polymerase chain reaction (qRT-PCR) with stably expressed reference genes for normalization can effectively elucidate the biological functions of genes that regulate fruit development. However, the reference genes for data normalization in melon fruits have not yet been systematically validated. This study aims to assess the suitability of 20 genes for their potential use as reference genes in melon fruits. Expression variations of these genes were measured in 24 samples that represented different developmental stages of fertilized and parthenocarpic melon fruits by qRT-PCR analysis. GeNorm identified ribosomal protein L (CmRPL) and cytosolic ribosomal protein S15 (CmRPS15) as the best pair of reference genes, and as many as five genes including CmRPL, CmRPS15, TIP41-like family protein (CmTIP41), cyclophilin ROC7 (CmCYP7), and ADP ribosylation factor 1 (CmADP) were required for more reliable normalization. NormFinder ranked CmRPS15 as the best single reference gene, and RAN GTPase gene family (CmRAN) and TATA-box binding protein (CmTBP2) as the best combination of reference genes in melon fruits. Their effectiveness was further validated by parallel analyses on the activities of soluble acid invertase and sucrose phosphate synthase, and expression profiles of their respective encoding genes CmAIN2 and CmSPS1, as well as sucrose contents during melon fruit ripening. The validated reference genes will help to improve the accuracy of gene expression studies in melon fruits.

  15. Assessment of Suitable Reference Genes for Quantitative Gene Expression Studies in Melon Fruits

    Science.gov (United States)

    Kong, Qiusheng; Gao, Lingyun; Cao, Lei; Liu, Yue; Saba, Hameed; Huang, Yuan; Bie, Zhilong

    2016-01-01

    Melon (Cucumis melo L.) is an attractive model plant for investigating fruit development because of its morphological, physiological, and biochemical diversity. Quantification of gene expression by quantitative reverse transcription polymerase chain reaction (qRT-PCR) with stably expressed reference genes for normalization can effectively elucidate the biological functions of genes that regulate fruit development. However, the reference genes for data normalization in melon fruits have not yet been systematically validated. This study aims to assess the suitability of 20 genes for their potential use as reference genes in melon fruits. Expression variations of these genes were measured in 24 samples that represented different developmental stages of fertilized and parthenocarpic melon fruits by qRT-PCR analysis. GeNorm identified ribosomal protein L (CmRPL) and cytosolic ribosomal protein S15 (CmRPS15) as the best pair of reference genes, and as many as five genes including CmRPL, CmRPS15, TIP41-like family protein (CmTIP41), cyclophilin ROC7 (CmCYP7), and ADP ribosylation factor 1 (CmADP) were required for more reliable normalization. NormFinder ranked CmRPS15 as the best single reference gene, and RAN GTPase gene family (CmRAN) and TATA-box binding protein (CmTBP2) as the best combination of reference genes in melon fruits. Their effectiveness was further validated by parallel analyses on the activities of soluble acid invertase and sucrose phosphate synthase, and expression profiles of their respective encoding genes CmAIN2 and CmSPS1, as well as sucrose contents during melon fruit ripening. The validated reference genes will help to improve the accuracy of gene expression studies in melon fruits. PMID:27536316

  16. Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis

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    Schlegel Brigitte

    2004-03-01

    Full Text Available Abstract Background High-throughput protein structure analysis of individual protein domains requires analysis of large numbers of expression clones to identify suitable constructs for structure determination. For this purpose, methods need to be implemented for fast and reliable screening of the expressed proteins as early as possible in the overall process from cloning to structure determination. Results 88 different E. coli expression constructs for 17 human protein domains were analysed using high-throughput cloning, purification and folding analysis to obtain candidates suitable for structural analysis. After 96 deep-well microplate expression and automated protein purification, protein domains were directly analysed using 1D 1H-NMR spectroscopy. In addition, analytical hydrophobic interaction chromatography (HIC was used to detect natively folded protein. With these two analytical methods, six constructs (representing two domains were quickly identified as being well folded and suitable for structural analysis. Conclusion The described approach facilitates high-throughput structural analysis. Clones expressing natively folded proteins suitable for NMR structure determination were quickly identified upon small scale expression screening using 1D 1H-NMR and/or analytical HIC. This procedure is especially effective as a fast and inexpensive screen for the 'low hanging fruits' in structural genomics.

  17. Cervine tibia morphology and mechanical strength: a suitable tibia model?

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    Throop, Alexander D W; Landauer, Alexander K; Clark, Alexander Martin; Kuxhaus, Laurel

    2015-03-01

    Animal models for orthopaedic implant testing are well-established but morphologically dissimilar to human tibiae; notably, most are shorter. The purpose of this study was to quantitatively evaluate the morphology and mechanical properties of the cervine tibia, particularly with regard to its suitability for testing orthopaedic implants. Two endosteal and eleven periosteal measurements were made on 15 cervine tibiae. The mechanical strength in axial compression and torsion was measured using 11 tibiae. The cervine tibia is morphologically similar to the human tibia and more closely matches the length of the human tibia than current tibia models (ovine, porcine, and caprine). The distal epiphysis dimensions are notably different, but no more so than the current tibia models. The torsional stiffness of the cervine tibia is within the range of previously reported values for human tibiae. Furthermore, in many regions, cervine tibiae are abundant and locally available at a low cost. Given these mechanical and morphological data, coupled with potential cost savings if regionally available, the cervine tibia may be an appropriate model for orthopaedic implant testing.

  18. Investigation of HER2 expression in canine mammary tumors by antibody-based, transcriptomic and mass spectrometry analysis: is the dog a suitable animal model for human breast cancer?

    Science.gov (United States)

    Burrai, G P; Tanca, A; De Miglio, M R; Abbondio, M; Pisanu, S; Polinas, M; Pirino, S; Mohammed, S I; Uzzau, S; Addis, M F; Antuofermo, E

    2015-11-01

    Canine mammary tumors (CMTs) share many features with human breast cancer (HBC), specifically concerning cancer-related pathways. Although the human epidermal growth factor receptor 2 (HER2) plays a significant role as a therapeutic and prognostic biomarker in HBC, its relevance in the pathogenesis and prognosis of CMT is still controversial. The aim of this study was to investigate HER2 expression in canine mammary hyperplasic and neoplastic tissues as well as to evaluate the specificity of the most commonly used polyclonal anti HER2 antibody by multiple molecular approaches. HER2 protein and RNA expression were determined by immunohistochemistry (IHC) and by quantitative real-time (qRT) PCR. A strong cell membrane associated with non-specific cytoplasmic staining was observed in 22% of carcinomas by IHC. Adenomas and carcinomas exhibited a significantly higher HER2 mRNA expression when compared to normal mammary glands, although no significant difference between benign and malignant tumors was noticed by qRT-PCR. The IHC results suggest a lack of specificity of the FDA-approved antibody in CMT samples as further demonstrated by Western immunoblotting (WB) and reverse phase protein arrays (RPPA). Furthemore, HER2 was not detected by mass spectrometry (MS) in a protein-expressing carcinoma at the IHC investigation. This study highlights that caution needs to be used when trying to translate from human to veterinary medicine information concerning cancer-related biomarkers and pathways. Further investigations are necessary to carefully assess the diagnostic and biological role specifically exerted by HER2 in CMTs and the use of canine mammary tumors as a model of HER2 over-expressing breast cancer.

  19. Screening for the Most Suitable Reference Genes for Gene Expression Studies in Equine Milk Somatic Cells.

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    Jakub Cieslak

    Full Text Available Apart from the well-known role of somatic cell count as a parameter reflecting the inflammatory status of the mammary gland, the composition of cells isolated from milk is considered as a valuable material for gene expression studies in mammals. Due to its unique composition, in recent years an increasing interest in mare's milk consumption has been observed. Thus, investigating the genetic background of horse's milk variability presents and interesting study model. Relying on 39 milk samples collected from mares representing three breeds (Polish Primitive Horse, Polish Cold-blooded Horse, Polish Warmblood Horse we aimed to investigate the utility of equine milk somatic cells as a source of mRNA and to screen the best reference genes for RT-qPCR using geNorm and NormFinder algorithms. The results showed that despite relatively low somatic cell counts in mare's milk, the amount and the quality of the extracted RNA are sufficient for gene expression studies. The analysis of the utility of 7 potential reference genes for RT-qPCR experiments for the normalization of equine milk somatic cells revealed some differences between the outcomes of the applied algorithms, although in both cases the KRT8 and TOP2B genes were pointed as the most stable. Analysis by geNorm showed that the combination of 4 reference genes (ACTB, GAPDH, TOP2B and KRT8 is required for apropriate RT-qPCR experiments normalization, whereas NormFinder algorithm pointed the combination of KRT8 and RPS9 genes as the most suitable. The trial study of the relative transcript abundance of the beta-casein gene with the use of various types and numbers of internal control genes confirmed once again that the selection of proper reference gene combinations is crucial for the final results of each real-time PCR experiment.

  20. Identification and validation of suitable endogenous reference genes for gene expression studies in human peripheral blood

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    Turner Renee J

    2009-08-01

    Full Text Available Abstract Background Gene expression studies require appropriate normalization methods. One such method uses stably expressed reference genes. Since suitable reference genes appear to be unique for each tissue, we have identified an optimal set of the most stably expressed genes in human blood that can be used for normalization. Methods Whole-genome Affymetrix Human 2.0 Plus arrays were examined from 526 samples of males and females ages 2 to 78, including control subjects and patients with Tourette syndrome, stroke, migraine, muscular dystrophy, and autism. The top 100 most stably expressed genes with a broad range of expression levels were identified. To validate the best candidate genes, we performed quantitative RT-PCR on a subset of 10 genes (TRAP1, DECR1, FPGS, FARP1, MAPRE2, PEX16, GINS2, CRY2, CSNK1G2 and A4GALT, 4 commonly employed reference genes (GAPDH, ACTB, B2M and HMBS and PPIB, previously reported to be stably expressed in blood. Expression stability and ranking analysis were performed using GeNorm and NormFinder algorithms. Results Reference genes were ranked based on their expression stability and the minimum number of genes needed for nomalization as calculated using GeNorm showed that the fewest, most stably expressed genes needed for acurate normalization in RNA expression studies of human whole blood is a combination of TRAP1, FPGS, DECR1 and PPIB. We confirmed the ranking of the best candidate control genes by using an alternative algorithm (NormFinder. Conclusion The reference genes identified in this study are stably expressed in whole blood of humans of both genders with multiple disease conditions and ages 2 to 78. Importantly, they also have different functions within cells and thus should be expressed independently of each other. These genes should be useful as normalization genes for microarray and RT-PCR whole blood studies of human physiology, metabolism and disease.

  1. Western Monarch and Milkweed Habitat Suitability Modeling Project- MaxEnt Model Outputs

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    US Fish and Wildlife Service, Department of the Interior — Products include relative habitat suitability models of five milkweed species thought to be important to western monarchs that enough data points to allow for...

  2. Identifying suitable reference genes for gene expression analysis in developing skeletal muscle in pigs

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    Guanglin Niu

    2016-12-01

    Full Text Available The selection of suitable reference genes is crucial to accurately evaluate and normalize the relative expression level of target genes for gene function analysis. However, commonly used reference genes have variable expression levels in developing skeletal muscle. There are few reports that systematically evaluate the expression stability of reference genes across prenatal and postnatal developing skeletal muscle in mammals. Here, we used quantitative PCR to examine the expression levels of 15 candidate reference genes (ACTB, GAPDH, RNF7, RHOA, RPS18, RPL32, PPIA, H3F3, API5, B2M, AP1S1, DRAP1, TBP, WSB, and VAPB in porcine skeletal muscle at 26 different developmental stages (15 prenatal and 11 postnatal periods. We evaluated gene expression stability using the computer algorithms geNorm, NormFinder, and BestKeeper. Our results indicated that GAPDH and ACTB had the greatest variability among the candidate genes across prenatal and postnatal stages of skeletal muscle development. RPS18, API5, and VAPB had stable expression levels in prenatal stages, whereas API5, RPS18, RPL32, and H3F3 had stable expression levels in postnatal stages. API5 and H3F3 expression levels had the greatest stability in all tested prenatal and postnatal stages, and were the most appropriate reference genes for gene expression normalization in developing skeletal muscle. Our data provide valuable information for gene expression analysis during different stages of skeletal muscle development in mammals. This information can provide a valuable guide for the analysis of human diseases.

  3. Identifying suitable reference genes for gene expression analysis in developing skeletal muscle in pigs.

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    Niu, Guanglin; Yang, Yalan; Zhang, YuanYuan; Hua, Chaoju; Wang, Zishuai; Tang, Zhonglin; Li, Kui

    2016-01-01

    The selection of suitable reference genes is crucial to accurately evaluate and normalize the relative expression level of target genes for gene function analysis. However, commonly used reference genes have variable expression levels in developing skeletal muscle. There are few reports that systematically evaluate the expression stability of reference genes across prenatal and postnatal developing skeletal muscle in mammals. Here, we used quantitative PCR to examine the expression levels of 15 candidate reference genes (ACTB, GAPDH, RNF7, RHOA, RPS18, RPL32, PPIA, H3F3, API5, B2M, AP1S1, DRAP1, TBP, WSB, and VAPB) in porcine skeletal muscle at 26 different developmental stages (15 prenatal and 11 postnatal periods). We evaluated gene expression stability using the computer algorithms geNorm, NormFinder, and BestKeeper. Our results indicated that GAPDH and ACTB had the greatest variability among the candidate genes across prenatal and postnatal stages of skeletal muscle development. RPS18, API5, and VAPB had stable expression levels in prenatal stages, whereas API5, RPS18, RPL32, and H3F3 had stable expression levels in postnatal stages. API5 and H3F3 expression levels had the greatest stability in all tested prenatal and postnatal stages, and were the most appropriate reference genes for gene expression normalization in developing skeletal muscle. Our data provide valuable information for gene expression analysis during different stages of skeletal muscle development in mammals. This information can provide a valuable guide for the analysis of human diseases.

  4. Identification of housekeeping genes suitable for gene expression analysis in Jian carp (Cyprinus carpio var. jian).

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    Tang, Yong-kai; Yu, Ju-hua; Xu, Pao; Li, Jian-lin; Li, Hong-xia; Ren, Hong-tao

    2012-10-01

    Jian carp (Cyprinus carpio var. jian) is an important economic fish species cultured in China. In this report, we performed a systematic analysis to identify an appropriate housekeeping (HK) gene for the study of gene expression in Jian carp. For this purpose, partial DNA sequences of four potential candidate genes (elongation factor 1 alpha (EF-1α), glyceraldehyde-3-phosphate (GAPDH), beta-actin (ACTB), and 18S ribosomal RNA (18S rRNA) were isolated, and their expression levels were studied using RNA extracted from nine tissues (forebrain, hypothalamus, liver, fore-intestine, hind-intestine, ovary, muscle, heart, kidney) in juvenile and adult Jian carp. Gene expression levels were quantified by quantitative real time RT-PCR (qRT-PCR), and expression stability was evaluated by comparing the coefficients of variation (CV) of the Ct values. The results showed that EF-1α was the most suitable HK gene in all tissues of juvenile and adult Jian carp. However, at distinct juvenile and adult developmental stages, there was not a single optimal gene for normalization of expression levels in all tissues. EF-1α was the most stable gene only in forebrain, hypothalamus, liver, heart, and kidney. These results provide data that can be expected to aid gene expression analysis in Jian carp research, but underline the importance of identifying the optimal HK gene for each new experimental paradigm.

  5. Validation of Suitable Reference Genes for Expression Normalization in Echinococcus spp. Larval Stages

    Science.gov (United States)

    Espínola, Sergio Martin; Ferreira, Henrique Bunselmeyer; Zaha, Arnaldo

    2014-01-01

    In recent years, a significant amount of sequence data (both genomic and transcriptomic) for Echinococcus spp. has been published, thereby facilitating the analysis of genes expressed during a specific stage or involved in parasite development. To perform a suitable gene expression quantification analysis, the use of validated reference genes is strongly recommended. Thus, the aim of this work was to identify suitable reference genes to allow reliable expression normalization for genes of interest in Echinococcus granulosus sensu stricto (s.s.) (G1) and Echinococcus ortleppi upon induction of the early pre-adult development. Untreated protoscoleces (PS) and pepsin-treated protoscoleces (PSP) from E. granulosus s.s. (G1) and E. ortleppi metacestode were used. The gene expression stability of eleven candidate reference genes (βTUB, NDUFV2, RPL13, TBP, CYP-1, RPII, EF-1α, βACT-1, GAPDH, ETIF4A-III and MAPK3) was assessed using geNorm, Normfinder, and RefFinder. Our qPCR data showed a good correlation with the recently published RNA-seq data. Regarding expression stability, EF-1α and TBP were the most stable genes for both species. Interestingly, βACT-1 (the most commonly used reference gene), and GAPDH and ETIF4A-III (previously identified as housekeeping genes) did not behave stably in our assay conditions. We propose the use of EF-1α as a reference gene for studies involving gene expression analysis in both PS and PSP experimental conditions for E. granulosus s.s. and E. ortleppi. To demonstrate its applicability, EF-1α was used as a normalizer gene in the relative quantification of transcripts from genes coding for antigen B subunits. The same EF-1α reference gene may be used in studies with other Echinococcus sensu lato species. This report validates suitable reference genes for species of class Cestoda, phylum Platyhelminthes, thus providing a foundation for further validation in other epidemiologically important cestode species, such as those from the

  6. LAND SUITABILITY SCENARIOS FOR ARID COASTAL PLAINS USING GIS MODELING: SOUTHWESTERN SINAI COASTAL PLAIN, EGYPT

    Directory of Open Access Journals (Sweden)

    Ahmed Mohamed Wahid

    2009-12-01

    Full Text Available Site selection analysis was carried out to find the best suitable lands for development activities in an example of promising coastal plains, southwestern Sinai, Egypt. Two GIS models were developed to represent two scenarios of land use suitability in the study area using GIS Multi Criteria Analysis Modeling. The factors contributed in the analysis are the Topography, Land cover, Existing Land use, Flash flood index, Drainage lines and Water points. The first scenario was to classify the area according to various gradual ranges of suitability. According to this scenario, the area is classified into five classes of suitability. The percentage of suitability values are 51.16, 6.13, 22.32, 18.49 and 1.89% for unsuitable, least suitable, low suitable, suitable and high suitable, respectively. The second scenario is developed for a particular kind of land use planning; tourism and recreation projects. The suitability map of this scenario was classified into five values. Unsuitable areas represent 51.18% of the study area, least suitable 16.67%, low suitable 22.85%, suitable 8.61%, and high suitable 0.68%. The best area for locating development projects is the area surrounding El-Tor City and close to the coast. This area could be an urban extension of El-Tor City with more economical and environmental management.

  7. LAND SUITABILITY SCENARIOS FOR ARID COASTAL PLAINS USING GIS MODELING: SOUTHWESTERN SINAI COASTAL PLAIN, EGYPT

    Directory of Open Access Journals (Sweden)

    Ahmed Wahid

    2009-01-01

    Full Text Available Site selection analysis was carried out to find the best suitable lands for development activities in an example of promising coastal plains, southwestern Sinai, Egypt. Two GIS models were developed to represent two scenarios of land use suitability in the study area using GIS Multi Criteria Analysis Modeling. The factors contributed in the analysis are the Topography, Land cover, Existing Land use, Flash flood index, Drainage lines and Water points. The first scenario was to classify the area according to various gradual ranges of suitability. According to this scenario, the area is classified into five classes of suitability. The percentage of suitability values are 51.16, 6.13, 22.32, 18.49 and 1.89% for unsuitable, least suitable, low suitable, suitable and high suitable, respectively. The second scenario is developed for a particular kind of land use planning; tourism and recreation projects. The suitability map of this scenario was classified into five values. Unsuitable areas represent 51.18% of the study area, least suitable 16.67%, low suitable 22.85%, suitable 8.61%, and high suitable 0.68%. The best area for locating development projects is the area surrounding El-Tor City and close to the coast. This area could be an urban extension of El-Tor City with more economical and environmental management.

  8. A habitat suitability model for Pacific oysters (Crassostrea gigas) in the Oosterschelde

    NARCIS (Netherlands)

    Schellekens, T.; Wijsman, J.W.M.; Brink, van den A.M.

    2012-01-01

    The modelled habitat suitability maps show a reasonable estimation of the suitability for oysters throughout the Delta and can be used to broadly indicate the consequences of the effect of climate change and infrastructural changes on the habitat suitability for oysters. The largest effect on the su

  9. Validation of suitable reference genes for quantitative gene expression analysis in Panax ginseng

    Directory of Open Access Journals (Sweden)

    Meizhen eWang

    2016-01-01

    Full Text Available Reverse transcription-qPCR (RT-qPCR has become a popular method for gene expression studies. Its results require data normalization by housekeeping genes. No single gene is proved to be stably expressed under all experimental conditions. Therefore, systematic evaluation of reference genes is necessary. With the aim to identify optimum reference genes for RT-qPCR analysis of gene expression in different tissues of Panax ginseng and the seedlings grown under heat stress, we investigated the expression stability of eight candidate reference genes, including elongation factor 1-beta (EF1-β, elongation factor 1-gamma (EF1-γ, eukaryotic translation initiation factor 3G (IF3G, eukaryotic translation initiation factor 3B (IF3B, actin (ACT, actin11 (ACT11, glyceraldehyde-3-phosphate dehydrogenase (GAPDH and cyclophilin ABH-like protein (CYC, using four widely used computational programs: geNorm, Normfinder, BestKeeper, and the comparative ΔCt method. The results were then integrated using the web-based tool RefFinder. As a result, EF1-γ, IF3G and EF1-β were the three most stable genes in different tissues of P. ginseng, while IF3G, ACT11 and GAPDH were the top three-ranked genes in seedlings treated with heat. Using three better reference genes alone or in combination as internal control, we examined the expression profiles of MAR, a multiple function-associated mRNA-like non-coding RNA (mlncRNA in P. ginseng. Taken together, we recommended EF1-γ/IF3G and IF3G/ACT11 as the suitable pair of reference genes for RT-qPCR analysis of gene expression in different tissues of P. ginseng and the seedlings grown under heat stress, respectively. The results serve as a foundation for future studies on P. ginseng functional genomics.

  10. Suitability of commonly used housekeeping genes in gene expression studies for space radiation research

    Science.gov (United States)

    Arenz, A.; Stojicic, N.; Lau, P.; Hellweg, C. E.; Baumstark-Khan, C.

    Research on the effects of ionizing radiation exposure involves the use of real-time reverse transcription polymerase chain reaction (qRT-PCR) for measuring changes in gene expression. Several variables need to be controlled for gene expression analysis, such as different amounts of starting material between the samples, variations in enzymatic efficiencies of the reverse transcription step, and differences in RNA integrity. Normalization of the obtained data to an invariant endogenous control gene (reference gene) is the elementary step in relative quantification strategy. There is a strong correlation between the quality of the normalized data and the stability of the reference gene itself. This is especially relevant when the samples have been obtained after exposure to radiation qualities inducing different amounts and kinds of damage, leading to effects on cell cycle delays or even on cell cycle blocks. In order to determine suitable reference genes as internal controls in qRT-PCR assays after exposure to ionizing radiation, we studied the gene expression levels of nine commonly used reference genes which are constitutively expressed in A549 lung cancer cells. Expression levels obtained for ACTB, B2M, GAPDH, PBGD, 18S rRNA, G6PDH, HPRT, UBC, TFRC and SDHA were determined after exposure to 2 and 6 Gy X-radiation. Gene expression data for Growth arrest and damage-inducible gene 45 (GADD45α) and Cyclin-dependent kinase inhibitor 1A (CDKN1A/p21CIP1) were selected to elucidate the influence of normalization by using appropriate and inappropriate internal control genes. According to these results, we strongly recommend the use of a panel of reference genes instead of only one.

  11. Habitat Suitability Index Models: Gulf of Mexico American Oyster

    Science.gov (United States)

    Cake, Edwin W.

    1983-01-01

    The American or eastern oyster (Crassostrea virrinica [Gmelin]), a bivalve in the family Ostreidae, is an important commercia and recreational species along the Atlantic and Gulf of Mexico coasts of North America and other areas (U.S. Pacific coast and Hawaii) where it has been introduced (Galtsoff 1964). It evolved over the last 25 million years (Miocene and Pliocene epochs) from an ancestral, Atlantic-Pacific species that also gave rise to the Central American oyster of the Pacific coast, Crassostrea corteziensis (Hertlein) (Stenzel 1971). It evolved to fill a eurytopic niche in coastal estuaries where it forms massive reefs in nearshore bays, sounds, lagoons, and river mouths. Its existence depends on suitable substratum (cultch and firm bottom sediments) and acceptable sal-inity conditions. The location and distribution of oyster reefs in a salt marsh-estuari ne ecosystem are not acci denta 1; rather, they result from the interacti on of many bi 01 ogi ca 1, chemica1, geo1ogi ca1, and phys i ca 1 processes (Butler 1954a; Marshall 1954; Bahr and Lanier 1981).

  12. Suitability Analysis of Continuous-Use Reliability Growth Projection Models

    Science.gov (United States)

    2015-03-26

    exists for all types, shapes, and sizes. The primary focus of this study is a comparison of reliability growth projection models designed for...requirements to use reliability growth models, recent studies have noted trends in reliability failures throughout the DoD. In [14] Dr. Michael Gilmore...so a strict exponential distribu- tion was used to stay within their assumptions. In reality, however, reliability growth models often must be used

  13. Physiology-based modelling approaches to characterize fish habitat suitability

    NARCIS (Netherlands)

    Teal, L.R.; Marras, Stefano; Peck, M.A.; Domenici, Paolo

    2015-01-01

    Models are useful tools for predicting the impact of global change on species distribution and abundance. As ectotherms, fish are being challenged to adapt or track changes in their environment, either in time through a phenological shift or in space by a biogeographic shift. Past modelling efforts

  14. Groundwater suitability recharge zones modelling - A GIS application

    Science.gov (United States)

    Dabral, S.; Bhatt, B.; Joshi, J. P.; Sharma, N.

    2014-11-01

    Groundwater quality in Gujarat state is highly variable and due to multiplicity of factors viz. influenced by direct sea water encroachment, inherent sediment salinity, water logging, overexploitation leading to overall deterioration in ground water quality, coupled with domestic and industrial pollution etc. The groundwater scenario in the state is not very encouraging due to imbalance between recharge and groundwater exploitation. Further, the demand for water has increased manifold owing to agricultural, industrial and domestic requirement and this has led to water scarcity in many parts of the state, which is likely to become more severe in coming future due to both natural and manmade factors. Therefore, sustainable development of groundwater resource requires precise quantitative assessment based on reasonably valid scientific principles. Hence, delineation of groundwater potential zones (GWPZ), has acquired great significance. The present study focuses on the integrated Geospatial and Multi-Criteria Decision Making (MCDM) techniques to determine the most important contributing factors that affect the groundwater resources and also to delineate the potential zones for groundwater recharge. The multiple thematic layers of influencing parameters viz. geology, geomorphology, soil, slope, drainage density and land use, weightages were assigned to the each factor according to their relative importance as per subject experts opinion owing to the natural setup of the region. The Analytical Hierarchy Process (AHP) was applied to these factors and potential recharge zones were identified. The study area for the assessment of groundwater recharge potential zones is Mahi-Narmada inter-stream region of Gujarat state. The study shows that around 28 % region has the excellent suitability of the ground water recharge.

  15. Identification of suitable reference genes for gene expression studies of shoulder instability.

    Directory of Open Access Journals (Sweden)

    Mariana Ferreira Leal

    Full Text Available Shoulder instability is a common shoulder injury, and patients present with plastic deformation of the glenohumeral capsule. Gene expression analysis may be a useful tool for increasing the general understanding of capsule deformation, and reverse-transcription quantitative polymerase chain reaction (RT-qPCR has become an effective method for such studies. Although RT-qPCR is highly sensitive and specific, it requires the use of suitable reference genes for data normalization to guarantee meaningful and reproducible results. In the present study, we evaluated the suitability of a set of reference genes using samples from the glenohumeral capsules of individuals with and without shoulder instability. We analyzed the expression of six commonly used reference genes (ACTB, B2M, GAPDH, HPRT1, TBP and TFRC in the antero-inferior, antero-superior and posterior portions of the glenohumeral capsules of cases and controls. The stability of the candidate reference gene expression was determined using four software packages: NormFinder, geNorm, BestKeeper and DataAssist. Overall, HPRT1 was the best single reference gene, and HPRT1 and B2M composed the best pair of reference genes from different analysis groups, including simultaneous analysis of all tissue samples. GenEx software was used to identify the optimal number of reference genes to be used for normalization and demonstrated that the accumulated standard deviation resulting from the use of 2 reference genes was similar to that resulting from the use of 3 or more reference genes. To identify the optimal combination of reference genes, we evaluated the expression of COL1A1. Although the use of different reference gene combinations yielded variable normalized quantities, the relative quantities within sample groups were similar and confirmed that no obvious differences were observed when using 2, 3 or 4 reference genes. Consequently, the use of 2 stable reference genes for normalization, especially

  16. Habitat suitability index model for black bear (Ursus americanus)

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This descriptive model applies only to black bear in the coastal forests and adjacent vegetative communities, which extend from Afognak Island and the shores of...

  17. Critical Appraisal of Translational Research Models for Suitability in Performance Assessment of Cancer Centers

    OpenAIRE

    Rajan, Abinaya; Sullivan, Richard; Bakker, Suzanne; van Harten, Wim H.

    2012-01-01

    This study aimed to critically appraise translational research models for suitability in performance assessment of cancer centers. Process models, such as the Process Marker Model and Lean and Six Sigma applications, seem to be suitable for performance assessment of cancer centers. However, they must be thoroughly tested in practice.

  18. Integration of QSAR models for bioconcentration suitable for REACH

    Energy Technology Data Exchange (ETDEWEB)

    Gissi, Andrea [Laboratory of Chemistry and Environmental Toxicology, IRCCS - Istituto di Ricerche Farmacologiche “Mario Negri”, via Giuseppe La Masa 19, 20156 Milan (Italy); Dipartimento di Farmacia — Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, via Orabona 4, I-70125 Bari (Italy); Nicolotti, Orazio; Carotti, Angelo; Gadaleta, Domenico [Dipartimento di Farmacia — Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, via Orabona 4, I-70125 Bari (Italy); Lombardo, Anna [Laboratory of Chemistry and Environmental Toxicology, IRCCS - Istituto di Ricerche Farmacologiche “Mario Negri”, via Giuseppe La Masa 19, 20156 Milan (Italy); Benfenati, Emilio, E-mail: benfenati@marionegri.it [Laboratory of Chemistry and Environmental Toxicology, IRCCS - Istituto di Ricerche Farmacologiche “Mario Negri”, via Giuseppe La Masa 19, 20156 Milan (Italy)

    2013-07-01

    QSAR (Quantitative Structure Activity Relationship) models can be a valuable alternative method to replace or reduce animal test required by REACH. In particular, some endpoints such as bioconcentration factor (BCF) are easier to predict and many useful models have been already developed. In this paper we describe how to integrate two popular BCF models to obtain more reliable predictions. In particular, the herein presented integrated model relies on the predictions of two among the most used BCF models (CAESAR and Meylan), together with the Applicability Domain Index (ADI) provided by the software VEGA. Using a set of simple rules, the integrated model selects the most reliable and conservative predictions and discards possible outliers. In this way, for the prediction of the 851 compounds included in the ANTARES BCF dataset, the integrated model discloses a R{sup 2} (coefficient of determination) of 0.80, a RMSE (Root Mean Square Error) of 0.61 log units and a sensitivity of 76%, with a considerable improvement in respect to the CAESAR (R{sup 2} = 0.63; RMSE = 0.84 log units; sensitivity 55%) and Meylan (R{sup 2} = 0.66; RMSE = 0.77 log units; sensitivity 65%) without discarding too many predictions (118 out of 851). Importantly, considering solely the compounds within the new integrated ADI, the R{sup 2} increased to 0.92, and the sensitivity to 85%, with a RMSE of 0.44 log units. Finally, the use of properly set safety thresholds applied for monitoring the so called “suspicious” compounds, which are those chemicals predicted in proximity of the border normally accepted to discern non-bioaccumulative from bioaccumulative substances, permitted to obtain an integrated model with sensitivity equal to 100%. - Highlights: • Applying two independent QSAR models for bioconcentration factor increases the prediction. • The concordance of the models is an important component of the integration. • The measurement of the applicability domain improves the

  19. Suitability of sheet bending modelling techniques in CAPP applications

    NARCIS (Netherlands)

    Streppel, A.H.; de Vin, L.J.; de Vin, L.J.; Brinkman, J.; Brinkman, J.; Kals, H.J.J.

    1993-01-01

    The use of CNC machine tools, together with decreasing lot sizes and stricter tolerance prescriptions, has led to changes in sheet-metal part manufacturing. In this paper, problems introduced by the difference between the actual material behaviour and the results obtained from analytical models and

  20. Large-Scale Recombinant Expression and Purification of Human Tyrosinase Suitable for Structural Studies

    Science.gov (United States)

    Lai, Xuelei; Soler-Lopez, Montserrat; Wichers, Harry J.

    2016-01-01

    Human tyrosinase (TYR) is a glycoprotein that initiates the first two reactions in the melanin biosynthesis pathway. Mutations in its encoding gene cause Oculocutaneous Albinism type I (OCA1), the most severe form of albinism, which is a group of autosomal recessive disorders characterized by reduced or absent production of melanin in skin, hair and eyes. Despite extensive structural and characterization studies of its homologues in lower eukaryotic organisms, the catalytic mechanism of human TYR and the molecular basis of OCA1 are largely unknown. In this work, we have carried out a large-scale recombinant expression of TYR that has enabled us to obtain high yields of pure and active protein, required for crystallization trials and screening of skin whitening agents, which is highly demanded in the cosmetic industry. Addition of an N-terminal honeybee melittin signal peptide for secretion of the produced protein into the (protein-free) medium, as well as a cleavable His-tag at the C-terminus, was crucial for increasing the yield of pure protein. We have successfully crystallized two TYR variants, in both glycosylated and deglycosylated forms, showing preliminary X-ray diffraction patterns at 3.5 Å resolution. Hence, we have established an expression and purification protocol suitable for the crystal structure determination of human TYR, which will give unique atomic insight into the nature and conformation of the residues that shape the substrate binding pocket that will ultimately lead to efficient compound design. PMID:27551823

  1. Gunnison sage-grouse lek site suitability modeling

    Science.gov (United States)

    Ouren, Douglas S.; Ignizio, Drew A.; Siders, Melissa; Childers, Theresa; Tucker, Karen; Seward, Nathan

    2014-01-01

    suite of spatial data, geographic information system tools, and maximum entropy species distribution tools. Based on expert knowledge and landscape variables, the modeling process evolved into a hybrid approach for delineating areas that would have a significant probability for supporting GUSG lekking activities. Based on model results, a sampling protocol was developed for model verification. The results of this project provide wildlife managers with a more sophisticated methodology to evaluate GUSG habitat for potential lekking sites.

  2. Suitability of Modern Software Development Methodologies for Model Driven Development

    Directory of Open Access Journals (Sweden)

    Ruben Picek

    2009-12-01

    Full Text Available As an answer to today’s growing challenges in software industry, wide spectrum of new approaches of software development has occurred. One prominent direction is currently most promising software development paradigm called Model Driven Development (MDD. Despite a lot of skepticism and problems, MDD paradigm is being used and improved to accomplish many inherent potential benefits. In the methodological approach of software development it is necessary to use some kind of development process. Modern methodologies can be classified into two main categories: formal or heavyweight and agile or lightweight. But when it is a question about MDD and development process for MDD, currently known methodologies are very poor or better said they don't have any explanation of MDD process. As the result of research, in this paper, author examines the possibilities of using existing modern software methodologies in context of MDD paradigm.

  3. Evaluating habitat suitability models for nesting white-headed woodpeckers in unburned forest

    Science.gov (United States)

    Quresh S. Latif; Victoria A. Saab; Kim Mellen-Mclean; Jonathan G. Dudley

    2015-01-01

    Habitat suitability models can provide guidelines for species conservation by predicting where species of interest are likely to occur. Presence-only models are widely used but typically provide only relative indices of habitat suitability (HSIs), necessitating rigorous evaluation often using independently collected presence-absence data. We refined and evaluated...

  4. A Robust Sound Perception Model Suitable for Neuromorphic Implementation

    Directory of Open Access Journals (Sweden)

    Martin eCoath

    2014-01-01

    Full Text Available We have recently demonstrated the emergence of dynamic feature sensitivity through exposure to formative stimuli in a real-time neuromorphic system implementing a hybrid analogue/digital network of spiking neurons. This network, inspired by models of auditory processing in mammals, includes several mutually connected layers with distance-dependent transmission delays and learning in the form of spike timing dependent plasticity, which effects stimulus-driven changes in the network connectivity.Here we present results that demonstrate that the network is robust to a range of variations in the stimulus pattern, such as are found in naturalistic stimuli and neural responses. This robustness is a property critical to the development of realistic, electronic neuromorphic systems.We analyse the variability of the response of the network to `noisy' stimuli which allows us to characterize the acuity in information-theoretic terms. This provides an objective basis for the quantitative comparison of networks, their connectivity patterns, and learning strategies, which can inform future design decisions. We also show, using stimuli derived from speech samples, that the principles are robust to other challenges, such as variable presentation rate, that would have to be met by systems deployed in the real world. Finally we demonstrate the potential applicability of the approach to real sounds.

  5. A geospatial suitability model for drought-tolerant switchgrass

    Science.gov (United States)

    Lewis, S. M.; Kelly, M.

    2011-12-01

    A perennial grass native to the North America, switchgrass (Panicum virgatum) has been targeted by the USDA as a model mass bioenergy crop to replace petroleum energy products and meet policy demands. Although highly water use efficient, as a warm-season crop, switchgrass requires a significant amount of water during the growing season (April -September). However, locations that have highly reliable water availability are also ideal for profitable food crops (e.g. corn and soy growing regions) and food competition is a significant concern in regards to biofuel crops being grown on productive agricultural lands. Drier, marginal lands (lands on which normal agricultural crops are difficult to cultivate) are therefore potentially ideal locations to grow biofuel crops to ensure that food competition is not an issue. Genetics scientists at UC Davis are in the process of developing a modified variety of switchgrass that can withstand extended periods of drought while not substantially affecting overall yield. As this product is being developed, it is important to identify the potential geographical niche for this new drought-tolerant variety of switchgrass. This project introduces a geospatial approach that utilizes both physical and economic variables to identify ideal geographic locations for this innovative crop.

  6. Evaluation of suitable reference genes for gene expression studies in porcine PBMCs in response to LPS and LTA

    Directory of Open Access Journals (Sweden)

    Cinar Mehmet Ulas

    2013-02-01

    Full Text Available Abstract Background As an in vitro model porcine peripheral blood mononuclear cells (PBMCs is frequently used as for immunogenetic research with the stimulation of bacterial antigens. To investigate the immunocompetence of PBMCs for recognition of Gram-positive and Gram-negative bacteria and in order to dissect the pathogenesis of diseases, gene expression assay is most commonly used. The gene expressions are required to normalize for reference genes which have tremendous effect on the results of expression study. The reference genes should be stably expressed between different cells under a variety of experimental conditions, but recent influx of data showed that expression stability of reference genes are varied under different experimental conditions. But data regarding the expression stability of reference genes in porcine PBMCs are limited. Therefore, this study was aimed to know whether the expression stability of commonly used reference genes in PBMCs is affected by various bacterial antigens under different experimental conditions in pigs. Results The mRNA expression stability of nine commonly used reference genes (B2M, BLM, GAPDH, HPRT1, PPIA, RPL4, SDHA, TBP and YWHAZ was determined by RT-qPCR in PBMCs that were stimulated by LPS and LTA in vitro as well as cells un-stimulated control and non-cultured were also consider for this experiment. mRNA expression levels of all genes were found to be affected by the type of stimulation and duration of the stimulation (P  Conclusion There was discrepancy in the ranking order of reference genes obtained by different analysing algorithms (geNorm and NormFinder. In conclusion, the geometric mean of the RPL4, B2M and PPIA seemed to be the most appropriate combination of reference genes for accurate normalization of gene expression data in porcine PBMCs without knowing the type of bacterial pathogenic status of the animals and in the case of mixed infection with Gram-negative and Gram

  7. Predicting habitat suitability for rare plants at local spatial scales using a species distribution model.

    Science.gov (United States)

    Gogol-Prokurat, Melanie

    2011-01-01

    If species distribution models (SDMs) can rank habitat suitability at a local scale, they may be a valuable conservation planning tool for rare, patchily distributed species. This study assessed the ability of Maxent, an SDM reported to be appropriate for modeling rare species, to rank habitat suitability at a local scale for four edaphic endemic rare plants of gabbroic soils in El Dorado County, California, and examined the effects of grain size, spatial extent, and fine-grain environmental predictors on local-scale model accuracy. Models were developed using species occurrence data mapped on public lands and were evaluated using an independent data set of presence and absence locations on surrounding lands, mimicking a typical conservation-planning scenario that prioritizes potential habitat on unsurveyed lands surrounding known occurrences. Maxent produced models that were successful at discriminating between suitable and unsuitable habitat at the local scale for all four species, and predicted habitat suitability values were proportional to likelihood of occurrence or population abundance for three of four species. Unfortunately, models with the best discrimination (i.e., AUC) were not always the most useful for ranking habitat suitability. The use of independent test data showed metrics that were valuable for evaluating which variables and model choices (e.g., grain, extent) to use in guiding habitat prioritization for conservation of these species. A goodness-of-fit test was used to determine whether habitat suitability values ranked habitat suitability on a continuous scale. If they did not, a minimum acceptable error predicted area criterion was used to determine the threshold for classifying habitat as suitable or unsuitable. I found a trade-off between model extent and the use of fine-grain environmental variables: goodness of fit was improved at larger extents, and fine-grain environmental variables improved local-scale accuracy, but fine-grain variables

  8. Suitable reference genes for accurate gene expression analysis in parsley (Petroselinum crispum for abiotic stresses and hormone stimuli

    Directory of Open Access Journals (Sweden)

    Meng-Yao Li

    2016-09-01

    Full Text Available Parsley is one of the most important vegetable in Apiaceae family and widely used in food industry, medicinal and cosmetic. The recent studies in parsley are mainly focus on chemical composition, further research involving the analysis of the gene functions and expressions will be required. qPCR is a powerful method for detecting very low quantities of target transcript levels and widely used for gene expression studies. To ensure the accuracy of results, a suitable reference gene is necessary for expression normalization. In this study, three software geNorm, NormFinder, and BestKeeper were used to evaluate the expression stabilities of eight candidate reference genes (GAPDH, ACTIN, eIF-4α, SAND, UBC, TIP41, EF-1α, and TUB under various conditions including abiotic stresses (heat, cold, salt, and drought and hormone stimuli treatments (GA, SA, MeJA, and ABA. The results showed that EF-1α and TUB were identified as the most stable genes for abiotic stresses, while EF-1α, GAPDH, and TUB were the top three choices for hormone stimuli treatments. Moreover, EF-1α and TUB were the most stable reference genes across all the tested samples, while UBC was the least stable one. The expression analysis of PcDREB1 and PcDREB2 further verified that the selected stable reference genes were suitable for gene expression normalization. This study provides a guideline for selection the suitable reference genes in gene expression in parsley.

  9. Identification of reference genes suitable for normalization of RT-qPCR expression data in Saccharomyces cerevisiae during alcoholic fermentation.

    Science.gov (United States)

    Vaudano, Enrico; Noti, Olta; Costantini, Antonella; Garcia-Moruno, Emilia

    2011-08-01

    Expression data from RT-qPCR (reverse transcription quantitative PCR) needs to be normalized to account for experimental variability among samples caused by differential yields of the transcripts in RNA extraction or in the reverse transcription. The most common method is to normalize against one or more reference genes (RG). We have selected RGs suitable for normalization of RT-qPCR raw data in Saccharomyces cerevisiae during alcoholic fermentation. The RGs were evaluated by three different statistical methods. The suitability of the selected RG sets was compared with ACT1, a commonly used non-validated single RG, by normalizing the expression of two target genes. Expression profiles of the target genes revealed the risk of misleading interpretation of expression data due to an unreliable RG.

  10. Assessment of brown trout habitat suitability in the Jucar River Basin (SPAIN): comparison of data-driven approaches with fuzzy-logic models and univariate suitability curves.

    Science.gov (United States)

    Muñoz-Mas, Rafael; Martínez-Capel, Francisco; Schneider, Matthias; Mouton, Ans M

    2012-12-01

    The implementation of the Water Framework Directive implies the determination of an environmental flow (E-flow) in each running water body. In Spain, many of the minimum flow assessments were determined with the physical habitat simulation system based on univariate habitat suitability curves. Multivariate habitat suitability models, widely applied in habitat assessment, are potentially more accurate than univariate suitability models. This article analyses the microhabitat selection by medium-sized (10-20 cm) brown trout (Salmo trutta fario) in three streams of the Jucar River Basin District (eastern Iberian Peninsula). The data were collected with an equal effort sampling approach. Univariate habitat suitability curves were built with a data-driven process for depth, mean velocity and substrate classes; three types of data-driven fuzzy models were generated with the FISH software: two models of presence-absence and a model of abundance. FISH applies a hill-climbing algorithm to optimize the fuzzy rules. A hydraulic model was calibrated with the tool River-2D in a segment of the Cabriel River (Jucar River Basin). The fuzzy-logic models and three methods to produce a suitability index from the three univariate curves were applied to evaluate the river habitat in the tool CASiMiR©. The comparison of results was based on the spatial arrangement of habitat suitability and the curves of weighted usable area versus discharge. The differences were relevant in different aspects, e.g. in the estimated minimum environmental flow according to the Spanish legal norm for hydrological planning. This work demonstrates the impact of the model's selection on the habitat suitability modelling and the assessment of environmental flows, based on an objective data-driven procedure; the conclusions are important for the water management in the Jucar River Basin and other river systems in Europe, where the environmental flows are a keystone for the achievement of the goals established

  11. Model suitability to assess regional potato yield patterns in northern Ecuador

    NARCIS (Netherlands)

    Soltani Largani, A.; Stoorvogel, J.J.; Veldkamp, A.

    2013-01-01

    A wide range of scenario studies aiming at rural development require regional patterns of crop yield. This study aims to evaluate three different modeling approaches for their suitability to assess regional potato yield patterns. The three model approaches include (1) an empirical model; (2) a proce

  12. Modeling the Agroecological Land Suitability for Coffea arabica L. in Central America

    Science.gov (United States)

    Lara, Leonel; Rasche, Livia; Schneider, Uwe

    2016-04-01

    Coffee production is an important income source for small farms in Central America, but climate change threatens the production. In order to develop efficient adaptation strategies, an assessment of local conditions and opportunities is essential. Lack or uncertainty of information are common challenges for such assessments. A tool to resolve these challenges is Bayesian network analysis. In this study, we developed ALECA, the first Bayesian network model to evaluate the agroecological land suitability for Coffea arabica L. A new set of suitability functions was created and subsequently used to populate the conditional probability tables of the variables. The variables include temperature, precipitation and dry season length for the climate, slope and aspect for the landform, and soil pH, cation exchange capacity and texture for the soil component. We validated ALECA by comparing a map of current coffee areas, and specific coffee areas with known suitability for coffee production in Central America to the suitability evaluations of the model; and proceeded to explore 1) the capabilities of the model to manage data uncertainty, and 2) the changes to suitability scores under climate change. The results showed that the area suitable for coffee production will decline in Central America under climate change, underlining the need for models like ALECA, which can be used to produce reliable land evaluations at local, national and regional scales under uncertainty.

  13. Comparing habitat suitability and connectivity modeling methods for conserving pronghorn migrations.

    Directory of Open Access Journals (Sweden)

    Erin E Poor

    Full Text Available Terrestrial long-distance migrations are declining globally: in North America, nearly 75% have been lost. Yet there has been limited research comparing habitat suitability and connectivity models to identify migration corridors across increasingly fragmented landscapes. Here we use pronghorn (Antilocapra americana migrations in prairie habitat to compare two types of models that identify habitat suitability: maximum entropy (Maxent and expert-based (Analytic Hierarchy Process. We used distance to wells, distance to water, NDVI, land cover, distance to roads, terrain shape and fence presence to parameterize the models. We then used the output of these models as cost surfaces to compare two common connectivity models, least-cost modeling (LCM and circuit theory. Using pronghorn movement data from spring and fall migrations, we identified potential migration corridors by combining each habitat suitability model with each connectivity model. The best performing model combination was Maxent with LCM corridors across both seasons. Maxent out-performed expert-based habitat suitability models for both spring and fall migrations. However, expert-based corridors can perform relatively well and are a cost-effective alternative if species location data are unavailable. Corridors created using LCM out-performed circuit theory, as measured by the number of pronghorn GPS locations present within the corridors. We suggest the use of a tiered approach using different corridor widths for prioritizing conservation and mitigation actions, such as fence removal or conservation easements.

  14. Comparing Habitat Suitability and Connectivity Modeling Methods for Conserving Pronghorn Migrations

    Science.gov (United States)

    Poor, Erin E.; Loucks, Colby; Jakes, Andrew; Urban, Dean L.

    2012-01-01

    Terrestrial long-distance migrations are declining globally: in North America, nearly 75% have been lost. Yet there has been limited research comparing habitat suitability and connectivity models to identify migration corridors across increasingly fragmented landscapes. Here we use pronghorn (Antilocapra americana) migrations in prairie habitat to compare two types of models that identify habitat suitability: maximum entropy (Maxent) and expert-based (Analytic Hierarchy Process). We used distance to wells, distance to water, NDVI, land cover, distance to roads, terrain shape and fence presence to parameterize the models. We then used the output of these models as cost surfaces to compare two common connectivity models, least-cost modeling (LCM) and circuit theory. Using pronghorn movement data from spring and fall migrations, we identified potential migration corridors by combining each habitat suitability model with each connectivity model. The best performing model combination was Maxent with LCM corridors across both seasons. Maxent out-performed expert-based habitat suitability models for both spring and fall migrations. However, expert-based corridors can perform relatively well and are a cost-effective alternative if species location data are unavailable. Corridors created using LCM out-performed circuit theory, as measured by the number of pronghorn GPS locations present within the corridors. We suggest the use of a tiered approach using different corridor widths for prioritizing conservation and mitigation actions, such as fence removal or conservation easements. PMID:23166656

  15. Simultaneous modeling of habitat suitability, occupancy, and relative abundance: African elephants in Zimbabwe.

    Science.gov (United States)

    Martin, Julien; Chamaillé-Jammes, Simon; Nichols, James D; Fritz, Hervé; Hines, James E; Fonnesbeck, Christopher J; MacKenzie, Darryl I; Bailey, Larissa L

    2010-06-01

    The recent development of statistical models such as dynamic site occupancy models provides the opportunity to address fairly complex management and conservation problems with relatively simple models. However, surprisingly few empirical studies have simultaneously modeled habitat suitability and occupancy status of organisms over large landscapes for management purposes. Joint modeling of these components is particularly important in the context of management of wild populations, as it provides a more coherent framework to investigate the population dynamics of organisms in space and time for the application of management decision tools. We applied such an approach to the study of water hole use by African elephants in Hwange National Park, Zimbabwe. Here we show how such methodology may be implemented and derive estimates of annual transition probabilities among three dry-season states for water holes: (1) unsuitable state (dry water holes with no elephants); (2) suitable state (water hole with water) with low abundance of elephants; and (3) suitable state with high abundance of elephants. We found that annual rainfall and the number of neighboring water holes influenced the transition probabilities among these three states. Because of an increase in elephant densities in the park during the study period, we also found that transition probabilities from low abundance to high abundance states increased over time. The application of the joint habitat-occupancy models provides a coherent framework to examine how habitat suitability and factors that affect habitat suitability influence the distribution and abundance of organisms. We discuss how these simple models can further be used to apply structured decision-making tools in order to derive decisions that are optimal relative to specified management objectives. The modeling framework presented in this paper should be applicable to a wide range of existing data sets and should help to address important ecological

  16. Simultaneous modeling of habitat suitability, occupancy, and relative abundance: African elephants in Zimbabwe

    Science.gov (United States)

    Martin, Julien; Chamaille-Jammes, Simon; Nichols, James D.; Fritz, Herve; Hines, James E.; Fonnesbeck, Christopher J.; MacKenzie, Darryl I.; Bailey, Larissa L.

    2010-01-01

    The recent development of statistical models such as dynamic site occupancy models provides the opportunity to address fairly complex management and conservation problems with relatively simple models. However, surprisingly few empirical studies have simultaneously modeled habitat suitability and occupancy status of organisms over large landscapes for management purposes. Joint modeling of these components is particularly important in the context of management of wild populations, as it provides a more coherent framework to investigate the population dynamics of organisms in space and time for the application of management decision tools. We applied such an approach to the study of water hole use by African elephants in Hwange National Park, Zimbabwe. Here we show how such methodology may be implemented and derive estimates of annual transition probabilities among three dry-season states for water holes: (1) unsuitable state (dry water holes with no elephants); (2) suitable state (water hole with water) with low abundance of elephants; and (3) suitable state with high abundance of elephants. We found that annual rainfall and the number of neighboring water holes influenced the transition probabilities among these three states. Because of an increase in elephant densities in the park during the study period, we also found that transition probabilities from low abundance to high abundance states increased over time. The application of the joint habitat–occupancy models provides a coherent framework to examine how habitat suitability and factors that affect habitat suitability influence the distribution and abundance of organisms. We discuss how these simple models can further be used to apply structured decision-making tools in order to derive decisions that are optimal relative to specified management objectives. The modeling framework presented in this paper should be applicable to a wide range of existing data sets and should help to address important ecological

  17. Fuzzy rule-based macroinvertebrate habitat suitability models for running waters

    NARCIS (Netherlands)

    Broekhoven, Van E.; Adriaenssens, V.; Baets, De B.; Verdonschot, P.F.M.

    2006-01-01

    A fuzzy rule-based approach was applied to a macroinvertebrate habitat suitability modelling problem. The model design was based on a knowledge base summarising the preferences and tolerances of 86 macroinvertebrate species for four variables describing river sites in springs up to small rivers in t

  18. Modelling and mapping the suitability of European forest formations at 1-km resolution

    DEFF Research Database (Denmark)

    Casalegno, Stefano; Amatulli, Giuseppe; Bastrup-Birk, Annemarie;

    2011-01-01

    Proactive forest conservation planning requires spatially accurate information about the potential distribution of tree species. The most cost-efficient way to obtain this information is habitat suitability modelling i.e. predicting the potential distribution of biota as a function of environmental...... factors. Here, we used the bootstrap-aggregating machine-learning ensemble classifier Random Forest (RF) to derive a 1-km resolution European forest formation suitability map. The statistical model use as inputs more than 6,000 field data forest inventory plots and a large set of environmental variables...... for map applicability. The European forest suitability map is now available for further applications in forest conservation and climate change issues....

  19. Modeling and Validation of Environmental Suitability for Schistosomiasis Transmission Using Remote Sensing.

    Science.gov (United States)

    Walz, Yvonne; Wegmann, Martin; Dech, Stefan; Vounatsou, Penelope; Poda, Jean-Noël; N'Goran, Eliézer K; Utzinger, Jürg; Raso, Giovanna

    2015-11-01

    Schistosomiasis is the most widespread water-based disease in sub-Saharan Africa. Transmission is governed by the spatial distribution of specific freshwater snails that act as intermediate hosts and human water contact patterns. Remote sensing data have been utilized for spatially explicit risk profiling of schistosomiasis. We investigated the potential of remote sensing to characterize habitat conditions of parasite and intermediate host snails and discuss the relevance for public health. We employed high-resolution remote sensing data, environmental field measurements, and ecological data to model environmental suitability for schistosomiasis-related parasite and snail species. The model was developed for Burkina Faso using a habitat suitability index (HSI). The plausibility of remote sensing habitat variables was validated using field measurements. The established model was transferred to different ecological settings in Côte d'Ivoire and validated against readily available survey data from school-aged children. Environmental suitability for schistosomiasis transmission was spatially delineated and quantified by seven habitat variables derived from remote sensing data. The strengths and weaknesses highlighted by the plausibility analysis showed that temporal dynamic water and vegetation measures were particularly useful to model parasite and snail habitat suitability, whereas the measurement of water surface temperature and topographic variables did not perform appropriately. The transferability of the model showed significant relations between the HSI and infection prevalence in study sites of Côte d'Ivoire. A predictive map of environmental suitability for schistosomiasis transmission can support measures to gain and sustain control. This is particularly relevant as emphasis is shifting from morbidity control to interrupting transmission. Further validation of our mechanistic model needs to be complemented by field data of parasite- and snail

  20. Modeling and Validation of Environmental Suitability for Schistosomiasis Transmission Using Remote Sensing.

    Directory of Open Access Journals (Sweden)

    Yvonne Walz

    2015-11-01

    Full Text Available Schistosomiasis is the most widespread water-based disease in sub-Saharan Africa. Transmission is governed by the spatial distribution of specific freshwater snails that act as intermediate hosts and human water contact patterns. Remote sensing data have been utilized for spatially explicit risk profiling of schistosomiasis. We investigated the potential of remote sensing to characterize habitat conditions of parasite and intermediate host snails and discuss the relevance for public health.We employed high-resolution remote sensing data, environmental field measurements, and ecological data to model environmental suitability for schistosomiasis-related parasite and snail species. The model was developed for Burkina Faso using a habitat suitability index (HSI. The plausibility of remote sensing habitat variables was validated using field measurements. The established model was transferred to different ecological settings in Côte d'Ivoire and validated against readily available survey data from school-aged children.Environmental suitability for schistosomiasis transmission was spatially delineated and quantified by seven habitat variables derived from remote sensing data. The strengths and weaknesses highlighted by the plausibility analysis showed that temporal dynamic water and vegetation measures were particularly useful to model parasite and snail habitat suitability, whereas the measurement of water surface temperature and topographic variables did not perform appropriately. The transferability of the model showed significant relations between the HSI and infection prevalence in study sites of Côte d'Ivoire.A predictive map of environmental suitability for schistosomiasis transmission can support measures to gain and sustain control. This is particularly relevant as emphasis is shifting from morbidity control to interrupting transmission. Further validation of our mechanistic model needs to be complemented by field data of parasite- and

  1. Modeling freshwater snail habitat suitability and areas of potential snail-borne disease transmission in Uganda

    Directory of Open Access Journals (Sweden)

    A.S. Stensgaard

    2006-11-01

    Full Text Available Geographic information system (GIS-based modeling of an intermediate host snail species’ environmental requirements using known occurrence records can provide estimates of its spatial distribution. When other data are lacking, this can be used as a rough spatial prediction of potential snail-borne disease transmission areas. Furthermore, knowledge of abiotic factors affecting intra-molluscan parasitic development can be used to make “masks” based on remotely sensed climatic data, and these can in turn be used to refine these predictions. We used data from a recent freshwater snail survey from Uganda, environmental data and the genetic algorithm for rule-set prediction (GARP to map the potential distribution of snail species known to act as intermediate hosts of several human and animal parasites. The results suggest that large areas of Uganda are suitable habitats for many of these snail species, indicating a large potential for disease transmission. The lack of parasitological data still makes it difficult to determine the magnitude of actual disease transmission, but the predicted snail distributions might be used as indicators of potential present and future risk areas. Some of the predicted snail distribution maps were furthermore combined with temperature masks delineating suitable temperature regimes of the parasites they host. This revealed the coinciding suitable areas for snail and parasite, but also areas suitable for host snails, but apparently not for the parasites. Assuming that the developed models correctly reflect areas suitable for transmission, the applied approach could prove useful for targeting control interventions.

  2. In search of suitable reference genes for gene expression studies of human renal cell carcinoma by real-time PCR

    Directory of Open Access Journals (Sweden)

    Kristiansen Glen

    2007-06-01

    Full Text Available Abstract Background Housekeeping genes are commonly used as endogenous reference genes for the relative quantification of target genes in gene expression studies. No conclusive systematic study comparing the suitability of different candidate reference genes in clear cell renal cell carcinoma has been published to date. To remedy this situation, 10 housekeeping genes for normalizing purposes of RT-PCR measurements already recommended in various studies were examined with regard to their usefulness as reference genes. Results The expression of the potential reference genes was examined in matched malignant and non-malignant tissue specimens from 25 patients with clear cell renal cell carcinoma. Quality assessment of isolated RNA performed with a 2100 Agilent Bioanalyzer showed a mean RNA integrity number of 8.7 for all samples. The between-run variations related to the crossing points of PCR reactions of a control material ranged from 0.17% to 0.38%. The expression of all genes did not depend on age, sex, and tumour stage. Except the genes TATA box binding protein (TBP and peptidylprolyl isomerase A (PPIA, all genes showed significant differences in expression between malignant and non-malignant pairs. The expression stability of the candidate reference genes was additionally controlled using the software programs geNorm and NormFinder. TBP and PPIA were validated as suitable reference genes by normalizing the target gene ADAM9 using these two most stably expressed genes in comparison with up- and down-regulated housekeeping genes of the panel. Conclusion Our study demonstrated the suitability of the two housekeeping genes PPIA and TBP as endogenous reference genes when comparing malignant tissue samples with adjacent normal tissue samples from clear cell renal cell carcinoma. Both genes are recommended as reference genes for relative gene quantification in gene profiling studies either as single gene or preferably in combination.

  3. Assessing the Application of a Geographic Presence-Only Model for Land Suitability Mapping.

    Science.gov (United States)

    Heumann, Benjamin W; Walsh, Stephen J; McDaniel, Phillip M

    2011-09-01

    Recent advances in ecological modeling have focused on novel methods for characterizing the environment that use presence-only data and machine-learning algorithms to predict the likelihood of species occurrence. These novel methods may have great potential for land suitability applications in the developing world where detailed land cover information is often unavailable or incomplete. This paper assesses the adaptation and application of the presence-only geographic species distribution model, MaxEnt, for agricultural crop suitability mapping in a rural Thailand where lowland paddy rice and upland field crops predominant. To assess this modeling approach, three independent crop presence datasets were used including a social-demographic survey of farm households, a remote sensing classification of land use/land cover, and ground control points, used for geodetic and thematic reference that vary in their geographic distribution and sample size. Disparate environmental data were integrated to characterize environmental settings across Nang Rong District, a region of approximately 1,300 sq. km in size. Results indicate that the MaxEnt model is capable of modeling crop suitability for upland and lowland crops, including rice varieties, although model results varied between datasets due to the high sensitivity of the model to the distribution of observed crop locations in geographic and environmental space. Accuracy assessments indicate that model outcomes were influenced by the sample size and the distribution of sample points in geographic and environmental space. The need for further research into accuracy assessments of presence-only models lacking true absence data is discussed. We conclude that the Maxent model can provide good estimates of crop suitability, but many areas need to be carefully scrutinized including geographic distribution of input data and assessment methods to ensure realistic modeling results.

  4. Modelling agricultural suitability along soil transects under current conditions and improved scenario of soil factors

    Science.gov (United States)

    Abd-Elmabod, Sameh K.; Jordán, Antonio; Fleskens, Luuk; van der Ploeg, Martine; Muñoz-Rojas, Miriam; Anaya-Romero, María; van der Salm, Renée J.; De la Rosa, Diego

    2015-04-01

    Agricultural land suitability analysis and improvement of soils by addressing major limitations may be a strategy for climate change adaptation. This study aims to investigate the influence of topography and variability of soil factors on the suitability of 12 annual, semiannual and perennial Mediterranean crops in the province of Seville (southern Spain). In order to represent the variability in elevation, lithology and soil, two latitudinal and longitudinal (S-N and W-E) soil transects (TA and TB) were considered including 63 representative points at regular 4 km intervals. These points were represented by 41 soil profiles from the SDBm soil database -Seville. Almagra model, a component of the agro-ecological decision support system MicroLEIS, was used to assess soil suitability. Results were grouped into five soil suitability classes: S1-optimum, S2-high, S3-moderate, S4-marginal and S5-not suitable. Each class was divided in subclasses according to the main soil limiting factors: depth (p), texture (t), drainage (d), carbonate content (c), salinity (s), sodium saturation (a), and the degree of development of the soil profile (g). This research also aimed to maximize soil potential by improving limiting factors d, c, s and a after soil restoration. Therefore, management techniques were also considered as possible scenarios in this study. The results of the evaluation showed that soil suitability ranged between S1 and S5p - S5s along of the transects. In the northern extreme of transect TA, high content of gravels and coarse texture are limiting factors (soils are classified as S4t) In contrast, the limiting factor in the eastern extreme of transect TB is the shallow useful depth (S5p subclass). The absence of calcium carbonate becomes a limiting factor in some parts of TA. In contrast, the excessive content of calcium carbonate appeared to be a limiting factor for crops in some intermediate points of TB transect. For both transects, soil salinity is the main

  5. Selection of suitable reference genes for quantitative gene expression studies in milk somatic cells of lactating cows (Bos indicus).

    Science.gov (United States)

    Varshney, N; Mohanty, A K; Kumar, S; Kaushik, J K; Dang, A K; Mukesh, M; Mishra, B P; Kataria, R; Kimothi, S P; Mukhopadhyay, T K; Malakar, D; Prakash, B S; Grover, S; Batish, V K

    2012-06-01

    We assessed the suitability of 9 internal control genes (ICG) in milk somatic cells of lactating cows to find suitable reference genes for use in quantitative PCR (qPCR). Eighteen multiparous lactating Sahiwal cows were used, 6 in each of 3 lactation stages: early (25 ± 5 d in milk), mid (160 ± 15 d in milk), and late (275 ± 25 d in milk) lactation. Nine candidate reference genes [glyceraldehyde 3-phosphate dehydrogenase (GAPDH), protein phosphatase 1 regulatory subunit 11 (PPP1R11), β-actin (ACTB), β-2 microglobulin (B2M), 40S ribosomal protein S15a (RPS15A), ubiquitously expressed transcript (UXT), mitochondrial GTPase 1 (MTG1), 18S rRNA (RN18S1), and ubiquitin (UBC)] were evaluated. Three genes, β-casein (CSN2), lactoferrin (LTF), and cathelicidin (CAMP) were chosen as target genes. Very high amplification was observed in 7 ICG and very low level amplification was observed in 2 ICG (UXT and MTG1). Thus, UXT and MTG1 were excluded from further analysis. The qPCR data were analyzed by 2 software packages, geNorm and NormFinder, to determine suitable reference genes, based on their stability and expression. Overall, PPP1R11, ACTB, UBC, and GAPDH were stably expressed among all candidate reference genes. Therefore, these genes could be used as ICG for normalization of qPCR data in milk somatic cells through lactation.

  6. IDENTIFYING OPERATIONAL REQUIREMENTS TO SELECT SUITABLE DECISION MODELS FOR A PUBLIC SECTOR EPROCUREMENT DECISION SUPPORT SYSTEM

    Directory of Open Access Journals (Sweden)

    Mohamed Adil

    2014-10-01

    Full Text Available Public sector procurement should be a transparent and fair process. Strict legal requirements are enforced on public sector procurement to make it a standardised process. To make fair decisions on selecting suppliers, a practical method which adheres to legal requirements is important. The research that is the base for this paper aimed at identifying a suitable Multi-Criteria Decision Analysis (MCDA method for the specific legal and functional needs of the Maldivian Public Sector. To identify such operational requirements, a set of focus group interviews were conducted in the Maldives with public officials responsible for procurement decision making. Based on the operational requirements identified through focus groups, criteria-based evaluation is done on published MCDA methods to identify the suitable methods for e-procurement decision making. This paper describes the identification of the operational requirements and the results of the evaluation to select suitable decision models for the Maldivian context.

  7. Modelling seasonal habitat suitability for wide-ranging species: Invasive wild pigs in northern Australia.

    Science.gov (United States)

    Froese, Jens G; Smith, Carl S; Durr, Peter A; McAlpine, Clive A; van Klinken, Rieks D

    2017-01-01

    Invasive wildlife often causes serious damage to the economy and agriculture as well as environmental, human and animal health. Habitat models can fill knowledge gaps about species distributions and assist planning to mitigate impacts. Yet, model accuracy and utility may be compromised by small study areas and limited integration of species ecology or temporal variability. Here we modelled seasonal habitat suitability for wild pigs, a widespread and harmful invader, in northern Australia. We developed a resource-based, spatially-explicit and regional-scale approach using Bayesian networks and spatial pattern suitability analysis. We integrated important ecological factors such as variability in environmental conditions, breeding requirements and home range movements. The habitat model was parameterized during a structured, iterative expert elicitation process and applied to a wet season and a dry season scenario. Model performance and uncertainty was evaluated against independent distributional data sets. Validation results showed that an expert-averaged model accurately predicted empirical wild pig presences in northern Australia for both seasonal scenarios. Model uncertainty was largely associated with different expert assumptions about wild pigs' resource-seeking home range movements. Habitat suitability varied considerably between seasons, retracting to resource-abundant rainforest, wetland and agricultural refuge areas during the dry season and expanding widely into surrounding grassland floodplains, savanna woodlands and coastal shrubs during the wet season. Overall, our model suggested that suitable wild pig habitat is less widely available in northern Australia than previously thought. Mapped results may be used to quantify impacts, assess risks, justify management investments and target control activities. Our methods are applicable to other wide-ranging species, especially in data-poor situations.

  8. Human Organotypic Lung Tumor Models: Suitable For Preclinical 18F-FDG PET-Imaging

    OpenAIRE

    Fecher, David; Hofmann, Elisabeth; Buck, Andreas; BUNDSCHUH, RALPH; Nietzer, Sarah; Dandekar, Gudrun; Walles, Thorsten; Walles, Heike; Lückerath, Katharina; Steinke, Maria

    2016-01-01

    Development of predictable in vitro tumor models is a challenging task due to the enormous complexity of tumors in vivo. The closer the resemblance of these models to human tumor characteristics, the more suitable they are for drug-development and –testing. In the present study, we generated a complex 3D lung tumor test system based on acellular rat lungs. A decellularization protocol was established preserving the architecture, important ECM components and the basement membrane of the lung. ...

  9. Renal tissue thawed for 30 minutes is still suitable for gene expression analysis.

    Directory of Open Access Journals (Sweden)

    Yi Ma

    Full Text Available Some biosamples obtained from biobanks may go through thawing before processing. We aim to evaluate the effects of thawing at room temperature for different time periods on gene expression analysis. A time course study with four time points was conducted to investigate the expression profiling on 10 thawed normal mice renal tissue samples through Affymetrix GeneChip mouse gene 2.0 st array. Microarray results were validated by quantitative real time polymerase chain reactions (qPCR on 6 candidate reference genes and 11 target genes. Additionally, we used geNorm plus and NormFinder to identify the most stably expressed reference genes over time. The results showed RNA degraded more after longer incubation at room temperature. However, microarray results showed only 240 genes (0.91% altered significantly in response to thawing at room temperature. The signal of majority altered probe sets decreased with thawing time, and the crossing point (Cp values of all candidate reference genes correlated positively with the thawing time (p<0.05. The combination of B2M, ACTB and PPIA was identified as the best choice for qPCR normalization. We found most target genes were stable by using this normalization method. However, serious gene quantification errors were resulted from improper reference genes. In conclusion, thirty minutes of thawing at room temperature has a limited impact on microarray and qPCR analysis, gene expression variations due to RNA degradation in early period after thawing can be largely reduced by proper normalization.

  10. Comparison of different synthetic 5-min rainfall time series regarding their suitability for urban drainage modelling

    Science.gov (United States)

    van der Heijden, Sven; Callau Poduje, Ana; Müller, Hannes; Shehu, Bora; Haberlandt, Uwe; Lorenz, Manuel; Wagner, Sven; Kunstmann, Harald; Müller, Thomas; Mosthaf, Tobias; Bárdossy, András

    2015-04-01

    For the design and operation of urban drainage systems with numerical simulation models, long, continuous precipitation time series with high temporal resolution are necessary. Suitable observed time series are rare. As a result, intelligent design concepts often use uncertain or unsuitable precipitation data, which renders them uneconomic or unsustainable. An expedient alternative to observed data is the use of long, synthetic rainfall time series as input for the simulation models. Within the project SYNOPSE, several different methods to generate synthetic precipitation data for urban drainage modelling are advanced, tested, and compared. The presented study compares four different approaches of precipitation models regarding their ability to reproduce rainfall and runoff characteristics. These include one parametric stochastic model (alternating renewal approach), one non-parametric stochastic model (resampling approach), one downscaling approach from a regional climate model, and one disaggregation approach based on daily precipitation measurements. All four models produce long precipitation time series with a temporal resolution of five minutes. The synthetic time series are first compared to observed rainfall reference time series. Comparison criteria include event based statistics like mean dry spell and wet spell duration, wet spell amount and intensity, long term means of precipitation sum and number of events, and extreme value distributions for different durations. Then they are compared regarding simulated discharge characteristics using an urban hydrological model on a fictitious sewage network. First results show a principal suitability of all rainfall models but with different strengths and weaknesses regarding the different rainfall and runoff characteristics considered.

  11. Modelling the habitat suitability of cetaceans: Example of the sperm whale in the northwestern Mediterranean Sea

    Science.gov (United States)

    Praca, Emilie; Gannier, Alexandre; Das, Krishna; Laran, Sophie

    2009-04-01

    Cetaceans are mobile and spend long periods underwater. Because of this, modelling their habitat could be subject to a serious problem of false absence. Furthermore, extensive surveys at sea are time and money consuming, and presence-absence data are difficult to apply. This study compares the ability of two presence-absence and two presence-only habitat modelling methods and uses the example of the sperm whale ( Physeter macrocephalus) in the northwestern Mediterranean Sea. The data consist of summer visual and acoustical detections of sperm whales, compiled between 1998 and 2005. Habitat maps were computed using topographical and hydrological eco-geographical variables. Four methods were compared: principal component analysis (PCA), ecological niche factor analysis (ENFA), generalized linear model (GLM) and multivariate adaptive regression splines (MARS). The evaluation of the models was achieved by calculating the receiver operating characteristic (ROC) of the models and their respective area under the curve (AUC). Presence-absence methods (GLM, AUC=0.70, and MARS, AUC=0.79) presented better AUC than presence-only methods (PCA, AUC=0.58, and ENFA, AUC=0.66), but this difference was not statistically significant, except between the MARS and the PCA models. The four models showed an influence of both topographical and hydrological factors, but the resulting habitat suitability maps differed. The core habitat on the continental slope was well highlighted by the four models, while GLM and MARS maps also showed a suitable habitat in the offshore waters. Presence-absence methods are therefore recommended for modelling the habitat suitability of cetaceans, as they seem more accurate to highlight complex habitat. However, the use of presence-only techniques, in particular ENFA, could be very useful for a first model of the habitat range or when important surveys at sea are not possible.

  12. Identification of housekeeping genes suitable for gene expression analysis in the pearl mussel, Hyriopsis cumingii, during biomineralization.

    Science.gov (United States)

    Bai, Zhiyi; Lin, Jingyun; Ma, Keyi; Wang, Guiling; Niu, Donghong; Li, Jiale

    2014-08-01

    Quantitative real-time polymerase chain reaction is a sensitive technique for quantifying gene expression levels. One or more appropriate reference genes must be selected to accurately compare mRNA transcript levels across different samples and tissues. The freshwater pearl, Hyriopsis cumingii (Lea), is an important economic species cultured in China. To date, no reference genes for gene expression analysis in this species have been validated. This study aimed to compare the relative expression of seven housekeeping genes across different tissue types and in the mantle or pearl sac during three biomineralization processes: seasonal shell growth, shell healing and pearl-sac formation in H. cumingii. Three programs evaluated the expression stabilities of the seven genes: BestKeeper, geNorm and NormFinder. The beta actin gene (ACTB), commonly used as a housekeeping gene in many studies, was the least stable. The expressions of Ubiquitin (Ubi) and Ribosomal protein L18 (Rpl18) and Elongation factor 1-alpha (EF1α) were more stable than the remaining four genes. Therefore, we suggest that Ubi, Rpl18 and EF1α are suitable reference genes. The three selected reference genes are expected to facilitate analysis of gene expressions during shell or pearl formation in H. cumingii.

  13. General basin modeling for site suitability. Draft report 1. Baseline data

    Energy Technology Data Exchange (ETDEWEB)

    1979-04-01

    This report summarizes work completed by Golder Associates under Task 2 - Site Suitability specifically for modeling of fluid flow and mass transport in sedimentary basins containing thick shale or salt. It also describes ongoing and future work on the above topic. The purpose of the study is to develop a general model for a nuclear waste repository situated in a deep sedimentary basin environment. The model will be used in conjunction with Golder's fluid flow and mass transport codes to study specific aspects of nuclide transport by groundwater flow.

  14. ANALYSIS OF ASSEMBLY SUITABILITY OF THE HYBRID NODE BASED ON WELD DISTORTION PREDICTION MODELS

    Directory of Open Access Journals (Sweden)

    Tomasz Urbański

    2015-08-01

    Full Text Available The article presents an analysis of assembly suitability of the innovative hybrid node. Weld distortions are a factor that affects significantly the quality of a structure during its pre-fabrication stage, thus increasing manufacturing costs . For the purposes of this analysis, such distortion forms were chosen that are the highest-ranking ones in the technological hierarchy. The analysis was performed taking advantage of significant parameters in order to demonstrate the possibilities of using mathematical models determined on the basis of a designed experiment to modify the construction technology as early as during the stage of the hybrid node’s manufacture. It was shown that using the above-mentioned theoretical models a technological assessment of the structural component can be performed by selecting such system of parameters that will produce distortions at a level acceptable from the point of view of further assembly suitability.

  15. High Resolution Habitat Suitability Modelling For Restricted-Range Hawaiian Alpine Arthropod Species

    Science.gov (United States)

    Stephenson, N. M.

    2016-12-01

    Mapping potentially suitable habitat is critical for effective species conservation and management but can be challenging in areas exhibiting complex heterogeneity. An approach that combines non-intrusive spatial data collection techniques and field data can lead to a better understanding of landscapes and species distributions. Nysius wekiuicola, commonly known as the wēkiu bug, is the most studied arthropod species endemic to the Maunakea summit in Hawai`i, yet details about its geographic distribution and habitat use remain poorly understood. To predict the geographic distribution of N. wekiuicola, MaxEnt habitat suitability models were generated from a diverse set of input variables, including fifteen years of species occurrence data, high resolution digital elevation models, surface mineralogy maps derived from hyperspectral remote sensing, and climate data. Model results indicate that elevation (78.2 percent), and the presence of nanocrystalline hematite surface minerals (13.7 percent) had the highest influence, with lesser contributions from aspect, slope, and other surface mineral classes. Climatic variables were not included in the final analysis due to auto-correlation and coarse spatial resolution. Biotic factors relating to predation and competition also likely dictate wēkiu bug capture patterns and influence our results. The wēkiu bug range and habitat suitability models generated as a result of this study will be directly incorporated into management and restoration goals for the summit region and can also be adapted for other arthropod species present, leading to a more holistic understanding of metacommunity dynamics. Key words: Microhabitat, Structure from Motion, Lidar, MaxEnt, Habitat Suitability

  16. Modelling Fish Habitat Suitability in the Eastern English Channel. Application to community habitat level

    OpenAIRE

    Vaz, Sandrine; Carpentier, Andre; Loots, Christophe; Koubbi, Philippe

    2004-01-01

    Valuable marine habitats and living resources can be found in the Eastern English Channel and in 2003, a Franco-British Interreg IIIA project, ‘Eastern Channel Habitat Atlas for Marine Resource Management’ (CHARM), was initiated to support decision-making for management of essential fish habitats. Fish habitat corresponds to geographic areas within which ranges of environmental factors define the presence of a particular species. Habitat Suitability index (HSI) modelling was used to relate fi...

  17. Selection of suitable reference genes for gene expression studies in Staphylococcus capitis during growth under erythromycin stress.

    Science.gov (United States)

    Cui, Bintao; Smooker, Peter M; Rouch, Duncan A; Deighton, Margaret A

    2016-08-01

    Accurate and reproducible measurement of gene transcription requires appropriate reference genes, which are stably expressed under different experimental conditions to provide normalization. Staphylococcus capitis is a human pathogen that produces biofilm under stress, such as imposed by antimicrobial agents. In this study, a set of five commonly used staphylococcal reference genes (gyrB, sodA, recA, tuf and rpoB) were systematically evaluated in two clinical isolates of Staphylococcus capitis (S. capitis subspecies urealyticus and capitis, respectively) under erythromycin stress in mid-log and stationary phases. Two public software programs (geNorm and NormFinder) and two manual calculation methods, reference residue normalization (RRN) and relative quantitative (RQ), were applied. The potential reference genes selected by the four algorithms were further validated by comparing the expression of a well-studied biofilm gene (icaA) with phenotypic biofilm formation in S. capitis under four different experimental conditions. The four methods differed considerably in their ability to predict the most suitable reference gene or gene combination for comparing icaA expression under different conditions. Under the conditions used here, the RQ method provided better selection of reference genes than the other three algorithms; however, this finding needs to be confirmed with a larger number of isolates. This study reinforces the need to assess the stability of reference genes for analysis of target gene expression under different conditions and the use of more than one algorithm in such studies. Although this work was conducted using a specific human pathogen, it emphasizes the importance of selecting suitable reference genes for accurate normalization of gene expression more generally.

  18. Suitability of endogenous reference genes for gene expression studies with human intraocular endothelial cells

    Directory of Open Access Journals (Sweden)

    Wei Ruoxin

    2013-02-01

    Full Text Available Abstract Background The use of quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR has become widely applied as a method to measure transcript abundance. In order to be reflective of biological processes during health and disease this method is dependent on normalisation of data against stable endogenous controls. However, these genes can vary in their stability in different cell types. The importance of reference gene validation for a particular cell type is now well recognised and is an important step in any gene expression study. Results Cultured primary human choroidal and retinal endothelial cells were treated with the immunostimulant polyinosinic: polycytidylic acid or untreated. qRT-PCR was used to quantify the expression levels of 10 commonly used endogenous control genes, TBP, HPRT1, GAPDH, GUSB, PPIA, RPLP0, B2M, 18S rRNA, PGK1 and ACTB. Three different mathematical algorithms, GeNorm, NormFinder, and BestKeeper were used to analyse gene stability to give the most representative validation. In choroidal endothelial cells the most stable genes were ranked as HPRT1 and GUSB by GeNorm and NormFinder and HPRT1 and PPIA by BestKeeper. In retinal endothelial cells the most stable genes ranked were TBP and PGK1 by GeNorm and NormFinder and HPRT1 by BestKeeper. The least stable gene for both cell types was 18S with all 3 algorithms. Conclusions We have identified the most stable endogenous control genes in intraocular endothelial cells. It is suggested future qRT-PCR studies using these cells would benefit from adopting the genes identified in this study as the most appropriate endogenous control genes.

  19. Assessment of Managed Aquifer Recharge Site Suitability Using a GIS and Modeling.

    Science.gov (United States)

    Russo, Tess A; Fisher, Andrew T; Lockwood, Brian S

    2015-01-01

    We completed a two-step regional analysis of a coastal groundwater basin to (1) assess regional suitability for managed aquifer recharge (MAR), and (2) quantify the relative impact of MAR activities on groundwater levels and sea water intrusion. The first step comprised an analysis of surface and subsurface hydrologic properties and conditions, using a geographic information system (GIS). Surface and subsurface data coverages were compiled, georeferenced, reclassified, and integrated (including novel approaches for combining related datasets) to derive a spatial distribution of MAR suitability values. In the second step, results from the GIS analysis were used with a regional groundwater model to assess the hydrologic impact of potential MAR placement and operating scenarios. For the region evaluated in this study, the Pajaro Valley Groundwater Basin, California, GIS results suggest that about 7% (15 km2) of the basin may be highly suitable for MAR. Modeling suggests that simulated MAR projects placed near the coast help to reduce sea water intrusion more rapidly, but these projects also result in increased groundwater flows to the ocean. In contrast, projects placed farther inland result in more long-term reduction in sea water intrusion and less groundwater flowing to the ocean. This work shows how combined GIS analysis and modeling can assist with regional water supply planning, including evaluation of options for enhancing groundwater resources.

  20. Separation of the bioclimatic spaces of Himalayan tree rhododendron species predicted by ensemble suitability models

    Directory of Open Access Journals (Sweden)

    Sailesh Ranjitkar

    2014-08-01

    Full Text Available The tree rhododendrons include the most widely distributed Himalayan Rhododendron species belonging to the subsection Arborea. Distributions of two members of this sub-species were modelled using bioclimatic data for current conditions (1950–2000. A subset of the least correlated bioclimatic variables was used for ecological niche modelling (ENM. We used an ENM ensemble method in the BiodiversityR R-package to map the suitable climatic space for tree rhododendrons based on 217 point location records. Ensemble bioclimatic models for tree rhododendrons had high predictive power with bioclimatic variables, which also separated the climatic spaces for the two species. Tree rhododendrons were found occurring in a wide range of climate and the distributional limits were associated with isothermality, temperature ranges, temperature of the wettest quarter, and precipitation of the warmest quarter of the year. The most suitable climatic space for tree rhododendrons was predicted to be in western Yunnan, China, with suitability declining towards the west and east. Its occurrence in a wide range of climatic settings with highly dissected habitats speaks to the adaptive capacity of the species, which might open up future options for their conservation planning in regions where they are listed as threatened.

  1. Review and Extension of Suitability Assessment Indicators of Weather Model Output for Analyzing Decentralized Energy Systems

    Directory of Open Access Journals (Sweden)

    Hans Schermeyer

    2015-12-01

    Full Text Available Electricity from renewable energy sources (RES-E is gaining more and more influence in traditional energy and electricity markets in Europe and around the world. When modeling RES-E feed-in on a high temporal and spatial resolution, energy systems analysts frequently use data generated by numerical weather models as input since there is no spatial inclusive and comprehensive measurement data available. However, the suitability of such model data depends on the research questions at hand and should be inspected individually. This paper focuses on new methodologies to carry out a performance evaluation of solar irradiation data provided by a numerical weather model when investigating photovoltaic feed-in and effects on the electricity grid. Suitable approaches of time series analysis are researched from literature and applied to both model and measurement data. The findings and limits of these approaches are illustrated and a new set of validation indicators is presented. These novel indicators complement the assessment by measuring relevant key figures in energy systems analysis: e.g., gradients in energy supply, maximum values and volatility. Thus, the results of this paper contribute to the scientific community of energy systems analysts and researchers who aim at modeling RES-E feed-in on a high temporal and spatial resolution using weather model data.

  2. [Assessment on the ecological suitability in Zhuhai City, Guangdong, China, based on minimum cumulative resistance model].

    Science.gov (United States)

    Li, Jian-fei; Li, Lin; Guo, Luo; Du, Shi-hong

    2016-01-01

    Urban landscape has the characteristics of spatial heterogeneity. Because the expansion process of urban constructive or ecological land has different resistance values, the land unit stimulates and promotes the expansion of ecological land with different intensity. To compare the effect of promoting and hindering functions in the same land unit, we firstly compared the minimum cumulative resistance value of promoting and hindering functions, and then looked for the balance of two landscape processes under the same standard. According to the ecology principle of minimum limit factor, taking the minimum cumulative resistance analysis method under two expansion processes as the evaluation method of urban land ecological suitability, this research took Zhuhai City as the study area to estimate urban ecological suitability by relative evaluation method with remote sensing image, field survey, and statistics data. With the support of ArcGIS, five types of indicators on landscape types, ecological value, soil erosion sensitivity, sensitivity of geological disasters, and ecological function were selected as input parameters in the minimum cumulative resistance model to compute urban ecological suitability. The results showed that the ecological suitability of the whole Zhuhai City was divided into five levels: constructive expansion prohibited zone (10.1%), constructive expansion restricted zone (32.9%), key construction zone (36.3%), priority development zone (2.3%), and basic cropland (18.4%). Ecological suitability of the central area of Zhuhai City was divided into four levels: constructive expansion prohibited zone (11.6%), constructive expansion restricted zone (25.6%), key construction zone (52.4%), priority development zone (10.4%). Finally, we put forward the sustainable development framework of Zhuhai City according to the research conclusion. On one hand, the government should strictly control the development of the urban center area. On the other hand, the

  3. Simple Attenauation Models of Metallic Cables Suitable for G.fast Frequencies

    Directory of Open Access Journals (Sweden)

    Pavel Lafata

    2015-01-01

    Full Text Available Recently, a new xDSL successor called G.fast, which can occupy frequencies up to 106 or 212~MHz, has been introduced in ITU-T G.9700 series of recommendations. Moreover, a new model of transmission characteristics suitable for various types of metallic cables has been designed and described as well. The model is based on 9 parameters specified for each type of metallic cable and can provide accurate estimations. However, its complexity together with the number of required parameters makes its practical application questionable, since the most important metallic cable characteristic, the attenuation, can be estimated using much simpler models. Therefore, two innovative attenuation models suitable for frequencies up to 250 MHz were designed and they will be introduced in this paper. The main motivation was to achieve an accurate approximation of attenuation character for various types of metallic cables, while maintaining low mathematical complexity and a number of necessary parameters. Both models were compared with attenuation characteristics measured for variety types of real metallic cables and also with other standard attenuation models. The results are included in this article as well.

  4. Use of a Three Dimensional Printed Cardiac Model to Assess Suitability for Biventricular Repair.

    Science.gov (United States)

    Farooqi, Kanwal M; Gonzalez-Lengua, Carlos; Shenoy, Rajesh; Sanz, Javier; Nguyen, Khanh

    2016-05-01

    Three dimensional (3D) printing is rapidly gaining interest in the medical field for use in presurgical planning. We present the case of a seven-year-old boy with double outlet right ventricle who underwent a bidirectional Glenn anastomosis. We used a 3D cardiac model to assess his suitability for a biventricular repair. He underwent a left ventricle-to-aorta baffle with a right ventricle-to-pulmonary artery conduit placement. He did well postoperatively and was discharged home with no evidence of baffle obstruction and good biventricular function. A 3D printed model can provide invaluable intracardiac spatial information in these complex patients.

  5. A Dynamic Knowledge Model for Design of Suitable Sowing Date and Sowing Rate in Winter Wheat

    Institute of Scientific and Technical Information of China (English)

    ZHU Yan; CAO Wei-xing; JIANG Dong; DAI Ting-bo

    2002-01-01

    Based on research concerning dynamic relationships of winter wheat growth to environments and production conditions, a winter wheat model for selecting suitable sowing date, population density and sowing rate under different varieties, spatial and temporal environments was developed. Case studies on sowing date with the data sets of five different eco-sites, three climatic years and soil fertility levels, and on population density and sowing rate with the data sets of two different variety types, three different soil types, soil fertility levels, sowing dates and grain yield levels indicate a good model performance for decision-making.

  6. Modelling of Moving Coil Actuators in Fast Switching Valves Suitable for Digital Hydraulic Machines

    DEFF Research Database (Denmark)

    Nørgård, Christian; Roemer, Daniel Beck; Bech, Michael Møller

    2015-01-01

    The efficiency of digital hydraulic machines is strongly dependent on the valve switching time. Recently, fast switching have been achieved by using a direct electromagnetic moving coil actuator as the force producing element in fast switching hydraulic valves suitable for digital hydraulic...... machines. Mathematical models of the valve switching, targeted for design optimisation of the moving coil actuator, are developed. A detailed analytical model is derived and presented and its accuracy is evaluated against transient electromagnetic finite element simulations. The model includes...... an estimation of the eddy currents generated in the actuator yoke upon current rise, as they may have significant influence on the coil current response. The analytical model facilitates fast simulation of the transient actuator response opposed to the transient electro-magnetic finite element model which...

  7. An Expert-Based Assessment Model for Evaluating Habitat Suitability of Pond-Breeding Amphibians

    Directory of Open Access Journals (Sweden)

    Shin-Ruoh Juang

    2017-02-01

    reliability of the habitat suitability assessment model. In brief, the proposed method can be applied, not only to assess the sustainability of frog habitats and degradation risks, but also to determine which locations may require future attention regarding conservation implementation. Furthermore, findings in this study provide useful background knowledge to all associated stakeholders when designing and implementing plans of wildlife habitat management and restoration at farm ponds.

  8. The model thin film alumina catalyst support suitable for catalysis-oriented surface science studies

    Energy Technology Data Exchange (ETDEWEB)

    Nartova, Anna V., E-mail: avnartova@gmail.com [Boreskov Institute of Catalysis SB RAS, Lavrentieva Ave., 5, Novosibirsk, 630090 (Russian Federation); Novosibirsk State University, Pirogova St., 2, Novosibirsk, 630090 (Russian Federation); Bukhtiyarov, Andrey V., E-mail: avb@catalysis.ru [Boreskov Institute of Catalysis SB RAS, Lavrentieva Ave., 5, Novosibirsk, 630090 (Russian Federation); Kvon, Ren I., E-mail: kvon@catalysis.ru [Boreskov Institute of Catalysis SB RAS, Lavrentieva Ave., 5, Novosibirsk, 630090 (Russian Federation); Bukhtiyarov, Valerii I., E-mail: vib@catalysis.ru [Boreskov Institute of Catalysis SB RAS, Lavrentieva Ave., 5, Novosibirsk, 630090 (Russian Federation); Novosibirsk State University, Pirogova St., 2, Novosibirsk, 630090 (Russian Federation)

    2015-09-15

    Graphical abstract: - Highlights: • New model catalyst on “AlOx-thin film/FeCrAl” support is presented. • Metal substrate minimizes sample charging, allows fast and uniform heating. • Surface is rough to model the catalyst support's morphology. • Planar alumina is stable in air/gases/solutions and similar to γ-Al{sub 2}O{sub 3}. • New model support is suitable for in situ XPS, STM, TPD, TPR, etc. - Abstract: The preparation of thin continuous alumina film at the surface of metal substrate in UHV (ultra high vacuum) conditions is described. The peculiarities of the obtained films studied by XPS (X-ray photoelectron spectroscopy) and STM (scanning tunneling microscopy) are discussed. The long-term durability of the oxide film was tested and proved both under ambient conditions and in acidic aqueous solutions. The stability of the planar alumina samples toward oxidation by oxygen was checked in the wide ranges of gas pressure and sample temperature. The suggested procedure ensures the controlled and reproducible preparation of thin alumina films – model support appropriate for wet chemistry catalyst preparation, suitable for STM and for other Surface Science techniques studies of alumina supported metal catalysts.

  9. Predictive habitat suitability models to aid conservation of elasmobranch diversity in the central Mediterranean Sea

    Science.gov (United States)

    Lauria, V.; Gristina, M.; Attrill, M. J.; Fiorentino, F.; Garofalo, G.

    2015-08-01

    Commercial fisheries have dramatically impacted elasmobranch populations worldwide. With high capture and bycatch rates, the abundance of many species is rapidly declining and around a quarter of the world’s sharks and rays are threatened with extinction. At a regional scale this negative trend has also been evidenced in the central Mediterranean Sea, where bottom-trawl fisheries have affected the biomass of certain rays (e.g. Raja clavata) and sharks (e.g. Mustelus spp.). Detailed knowledge of elasmobranch habitat requirements is essential for biodiversity conservation and fisheries management, but this is often hampered by a poor understanding of their spatial ecology. Habitat suitability models were used to investigate the habitat preference of nine elasmobranch species and their overall diversity (number of species) in relation to five environmental predictors (i.e. depth, sea surface temperature, surface salinity, slope and rugosity) in the central Mediterranean Sea. Results showed that depth, seafloor morphology and sea surface temperature were the main drivers for elasmobranch habitat suitability. Predictive distribution maps revealed different species-specific patterns of suitable habitat while high assemblage diversity was predicted in deeper offshore waters (400-800 m depth). This study helps to identify priority conservation areas and diversity hot-spots for rare and endangered elasmobranchs in the Mediterranean Sea.

  10. Aedes aegypti Global Suitability Maps Using a Water Container Energy Balance Model for Dengue Risk Applications

    Science.gov (United States)

    Steinhoff, D.

    2015-12-01

    Dengue infections are estimated to total nearly 400 million per year worldwide, with both the geographic range and the magnitude of infections having increased in the past 50 years. The primary dengue vector mosquito Aedes aegypti is closely associated with humans. It lives exclusively in urban and semi-urban areas, preferentially bites humans, and spends its developmental stages in artificial water containers. Climate regulates the development of Ae. aegypti immature mosquitoes in artificial containers. Potential containers for Ae. aegypti immature development include, but are not limited to, small sundry items (e.g., bottles, cans, plastic containers), buckets, tires, barrels, tanks, and cisterns. Successful development of immature mosquitoes from eggs to larvae, pupae, and eventually adults is largely dependent on the availability of water and the thermal properties of the water in the containers. Recent work has shown that physics-based approaches toward modeling container water properties are promising for resolving the complexities of container water dynamics and the effects on immature mosquito development. An energy balance container model developed by the author, termed the Water Height And Temperature in Container Habitats Energy Model (WHATCH'EM), solves for water temperature and height for user-specified containers with readily available weather data. Here we use WHATCH'EM with NASA Earth Science products used as input to construct global suitability maps based on established water temperature ranges for immature Ae. aegypti mosquitoes. A proxy for dengue risk is provided from habitat suitability, but also population estimates, as Ae. aegypti is closely associated with human activity. NASA gridded Global Population of the World data is used to mask out rural areas with low dengue risk. Suitability maps are illustrated for a variety of containers (size, material, color) and shading scenarios.

  11. Temporal habitat suitability modeling of Caspian shad (Alosa spp. in the southern Caspian Sea

    Directory of Open Access Journals (Sweden)

    Ali Haghi Vayghan

    2015-11-01

    Full Text Available To comprehensively manage an ecosystem such as that of the Caspian Sea, the world’s largest lake, detailed knowledge of the habitat traits of the living organisms in the ecosystem is essential. The present study examined environmental variables and used the Habitat Suitability Index (HSI model to determine the most preferred seasonal habitat and optimal environmental range of Caspian shad (Alosa spp. The fish preferred deep waters with low levels of total organic matter and sea level anomaly in winter and productive areas with a high concentration of chlorophyll-a (Chla and relatively high benthos biomass in spring. The number per unit area (NPUA-based HSI model determined that the geometric mean model (GMM was the optimal model for defining a suitable habitat in winter. For spring, the arithmetic mean model (or GMM in the NPUA-based HSI model most accurately predicted preferred habitat for Caspian shad. The average NPUA in both seasons increased with the HSI; areas with an HSI of between 0.4 and 0.6 in spring and between 0.6 and 0.8 in winter had a high percentage of total catch. Areas with an HSI of more than 0.5 had over 91% and 63% of the total catch in spring and winter, respectively, demonstrating the reliability of the NPUA-based HSI model in predicting Caspian shad habitat. The present study shows that remotely sensed data plus depth are the most critical environmental variables in Caspian shad habitats and that Chla and SLA are the most critical remotely sensed parameters for near real-time prediction of Caspian shad habitat.

  12. Development of a Habitat Suitability Index Model for the Sage Sparrow on the Hanford Site

    Energy Technology Data Exchange (ETDEWEB)

    Duberstein, Corey A.; Simmons, Mary Ann; Sackschewsky, Michael R.; Becker, James M.

    2008-01-01

    Mitigation threshold guidelines for the Hanford Site are based on habitat requirements of the sage sparrow (Amphispiza belli) and only apply to areas with a mature sagebrush (Artemisia tridentata) overstory and a native understory. The sage sparrow habitat requirements are based on literature values and are not specific to the Hanford Site. To refine these guidelines for the Site, a multi-year study was undertaken to quantify habitat characteristics of sage sparrow territories. These characteristics were then used to develop a habitat suitability index (HSI) model which can be used to estimate the habitat value of specific locations on the Site.

  13. Habitat suitability criteria via parametric distributions: estimation, model selection and uncertainty

    Science.gov (United States)

    Som, Nicholas A.; Goodman, Damon H.; Perry, Russell W.; Hardy, Thomas B.

    2016-01-01

    Previous methods for constructing univariate habitat suitability criteria (HSC) curves have ranged from professional judgement to kernel-smoothed density functions or combinations thereof. We present a new method of generating HSC curves that applies probability density functions as the mathematical representation of the curves. Compared with previous approaches, benefits of our method include (1) estimation of probability density function parameters directly from raw data, (2) quantitative methods for selecting among several candidate probability density functions, and (3) concise methods for expressing estimation uncertainty in the HSC curves. We demonstrate our method with a thorough example using data collected on the depth of water used by juvenile Chinook salmon (Oncorhynchus tschawytscha) in the Klamath River of northern California and southern Oregon. All R code needed to implement our example is provided in the appendix. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

  14. Creating a Ruggedness Layer for Use in Habitat Suitability Modeling for Ikh Nart Nature Reserve, Mongolia

    Directory of Open Access Journals (Sweden)

    Nanette Bragin

    2013-12-01

    Full Text Available Spatially-explicit wildlife habitat models are increasingly used to study optimal habitat for species of conservation focus. A ruggedness layer, that summarizes aspect and slope, provides a useful tool for analyses conducted in a Geographic Information System (GIS, such as developing a habitat suitability index model to measure species habitat use. Ruggedness layers prove especially useful in areas where topography represents a key habitat component. We created a ruggedness layer for the Ikh Nart Nature Reserve and surrounding areas in northern Dornogobi Aimag (province, Mongolia. Using a 90 m Shuttle Radar Topography Mission (SRTM digital elevation model (DEM and ArcGIS 10 spatial analyst, we created 9 categories for ruggedness. When combined with other thematic layers such as vegetation, the ruggedness layer becomes a powerful tool for analyzing habitat use by individual animals. The results of such analyses may inform decision makers in protected area planning and conservation of endangered species.

  15. Helicobacter pylori-infected animal models are extremely suitable for the investigation of gastric carcinogenesis

    Institute of Scientific and Technical Information of China (English)

    Masaaki Kodama; Kazunari Murakami; Ryugo Sato; Tadayoshi Okimoto; Akira Nishizono; Toshio Fujioka

    2005-01-01

    Although various animal models have been developed to clarify gastric carcinogenesis, apparent mechanism of gastric cancer was not clarified in recent years. Since the recognition of the pathogenicity of Helicobacter pylori (Hpylori), several animal models with Hpylori infection have been developed to confirm the association between Hpylori and gastric cancer. Nonhuman primate and rodent models were suitable for this study. Japanese monkey model revealed atrophic gastritis and p53mutation after long-term infection of Hpylori. Mongolian gerbil model showed the development of gastric carcinoma with H pylori infection alone, as well as with combination of chemical carcinogens, such as N-methylN-nitrosourea and N-methyl-N-nitro-N'-nitrosoguanidine.The histopathological changes of these animal models after Hpylori inoculation are closely similar to those in human beings with Hpylori infection. Eradication therapy attenuated the development of gastric cancer in Hpyloriinfected Mongolian gerbil. Although several features of animal models differ from those seen in human beings,these experimental models provide a starting point for further studies to clarify the mechanism of gastric carcinogenesis as a result of Hpylori infection and assist the planning of eradication therapy to prevent gastric carcinoma.

  16. Modeling "habitat suitability" for a herbicide resistant weed using a species distribution model and presence-only data

    Science.gov (United States)

    Herbicide resistant weeds are like invasive weeds: prompt management is needed to prevent their spread. For invasive weeds, first reports of a weed's occurrence are often analyzed with species distribution models (SDM) to prioritize detection and treatment. Suitability of other areas as habitat for ...

  17. Predictive modeling of suitable habitats for threatened marine invertebrates and implications for conservation assessment in Brazil

    Directory of Open Access Journals (Sweden)

    Rafael A. Magris

    2010-01-01

    Full Text Available Spatial analysis and modeling tools were employed to predict suitable habitat distribution for threatened marine invertebrates and estimate the overlap between highly suitable areas for these species and the Brazilian marine protected areas (MPAs. Records of the occurrence of species were obtained from the collections included in the Ocean Biogeographic Information System (OBIS-Brazil, with additional records culled from the literature. The distribution data of 16 out of 33 threatened species, with at least ten occurrences in the available records, were selected for modeling by Maxent algorithm (Maximum Entropy Modeling based on environmental variables (temperature, salinity, bathymetry and their derivatives. The resulting maps were filtered with a fixed threshold of 0.5 (to distinguish only the highly suitable areas and superimposed on MPA digital maps. The algorithm produced reasonable predictions of the species' potential distributions, showing that the patterns predicted by the model are largely consistent with current knowledge of the species. The distribution of the highly suitable areas showed little overlapping with Brazilian MPAs. This study showed how the habitat suitability for threatened species can be assessed using GIS applications and modeling tools.Neste estudo foram utilizadas análises espaciais e ferramentas de modelagem para predizer a distribuição dos hábitats adequados aos invertebrados marinhos ameaçados e estimar a sobreposição destas áreas em relação às áreas marinhas protegidas existentes. Registros de ocorrência das espécies foram obtidos das coleções incluídas no Ocean Biogeographic Information System (OBIS-Brasil e de dados provenientes da literatura. Dados de distribuição de 16 das 33 espécies ameaçadas, com pelo menos 10 registros de ocorrência, foram selecionados para modelagem utilizando o algoritmo Maxent (Maximum Entropy Modeling e variáveis ambientais (temperatura, salinidade, batimetria

  18. Hyperspectral Mapping of the Invasive Species Pepperweed and the Development of a Habitat Suitability Model

    Science.gov (United States)

    Nguyen, A.; Gole, A.; Randall, J.; Dlott, G. A.; Zhang, S.; Alfaro, B.; Schmidt, C.; Skiles, J. W.

    2011-12-01

    Mapping and predicting the spatial distribution of invasive plant species is central to habitat management, however difficult to implement at landscape and regional scales. Remote sensing techniques can reduce the cost of field campaigns and can provide a regional and multi-temporal view of invasive species spread. Invasive perennial pepperweed (Lepidium latifolium) is now widespread in fragmented estuaries of the South San Francisco Bay, and is shown to degrade native vegetation in estuaries and adjacent habitats, thereby reducing forage and shelter for wildlife. The purpose of this study is to map the current distribution of pepperweed in estuarine areas of the South San Francisco Bay Salt Pond Restoration Project, and create a habitat suitability model to predict future spread. Pepperweed reflectance data were collected in-situ with a GER 1500 spectroradiometer along with 88 corresponding pepperweed presence and absence points used for building the statistical models. The spectral angle mapper (SAM) classification algorithm was used to distinguish the reflectance spectrum of pepperweed and map its distribution using an EO-1 Hyperion satellite image. To map pepperweed, a supervised classification was performed on an ASTER image with a resulting classification accuracy of 71.8%. We generated a weighted overlay analysis model within a geographic information system (GIS) framework to predict areas in the study site most susceptible to pepperweed colonization. Variables for the model included propensity for disturbance, status of pond restoration, proximity to water channels, and terrain curvature. A Generalized Additive Model (GAM) was also used to generate a probability map and investigate the statistical probability that each variable contributed to predict pepperweed spread. Results from the GAM revealed distance to channels, distance to ponds and curvature were statistically significant (p < 0.01) in determining the locations of suitable pepperweed habitats.

  19. Development of a Layout Model Suitable for the Food Processing Industry

    Directory of Open Access Journals (Sweden)

    W. N. C. Wanniarachchi

    2016-01-01

    Full Text Available The food processing industry is a subset of the manufacturing sector with unique challenges. Among these, ensuring food hygiene and preventing contamination are two issues of prime importance. Hence, designers have to overcome such challenges when designing facilities suitable for food processing. The paper formulates a model that simplifies the layout planning process for the food processing facilities (FPF in order to help the designers. A generalised framework that helps to visualise the Facilities Layout Problem (FLP was initially developed. A layout model for FPF was then developed considering the unique features that need to be present in the layout. The model classifies the areas of FPF into five: primary, secondary, utilities, warehouse, and administration based on the activities and the level of risk present in food processing. It further proposes specific locations for the five sections in the factory layout. In order to test the performance of the framework and the model, a case study was conducted in a malted milk powder processing facility in Sri Lanka by changing its layout according to the proposed model. The framework and the model showed promise in its implementation. However, the approach and the layout model need to be evaluated in further cases in order to ascertain their usability and performance.

  20. Identification of suitable reference genes for gene expression studies using quantitative polymerase chain reaction in lung cancer in vitro.

    Science.gov (United States)

    Ali, Hassan; Du, Zhenwu; Li, Xiuying; Yang, Qiwei; Zhang, Yu Cheng; Wu, Mei; Li, Yi; Zhang, Guizhen

    2015-05-01

    The present study aimed to examine 10 housekeeping genes (HKGs), including 18s ribosomal RNA (18S), glyceraldehyde‑3‑phosphate dehydrogenase (GAPDH), ribosomal protein large P0 (RPLP0), β‑actin (ACTB), peptidylprolyl isomerase A (PPIA), phosphoglycerate kinase‑1 (PGK1), β‑2‑microglobulin (B2M), ribosomal protein LI3a (RPL13A), hypoxanthine phosphoribosyl transferase‑1 (HPRT1) and TATA box binding protein (TBP) in order to identify the most stable and suitable reference genes for use in expression studies in non‑small cell lung cancer. The mRNA expression encoding the panel of the 10 HKGs was determined using reverse transcription‑quantitative PCR (RT‑qPCR) in human lung cancer cell lines. Three software programs, BestKeeper, NormFinder and geNorm, were used to ascertain the most suitable reference genes to normalize the RNA input. The present study examined three lung cancer cell lines (A549, NCI‑H446 and NCI‑H460). The analysis of the experimental data using BestKeeper software revealed that all 10 HKGs were stable, with GADPH, followed by 18S being the most stable genes and PPIA and HPRT1 being the least stable genes. The NormFinder software results demonstrated that PPIA followed by ACTB were the most stable and B2M and RPLP0 were the least stable. The geNorm software results revealed that ACTB and PGK1, followed by PPIA were the most stable genes and B2M and RPLP0 were identified as the least stable genes. Due to discrepancies in the ranking orders of the reference genes obtained by different analyzing software programs, it was not possible to determine a single universal reference gene. The suitability of selected reference genes requires unconditional validation prior to each study. Based on the three analyzing programs, ACTB, PPIA and PGK1 were the most stable reference genes in lung cancer cell lines.

  1. Evaluation of suitable reference genes for gene expression studies in porcine alveolar macrophages in response to LPS and LTA

    Directory of Open Access Journals (Sweden)

    Cinar Mehmet

    2012-02-01

    Full Text Available Abstract Background To obtain reliable quantitative real-time PCR data, normalization relative to stable housekeeping genes (HKGs is required. However, in practice, expression levels of 'typical' housekeeping genes have been found to vary between tissues and under different experimental conditions. To date, validation studies of reference genes in pigs are relatively rare and have never been performed in porcine alveolar macrophages (AMs. In this study, expression stability of putative housekeeping genes were identified in the porcine AMs in response to the stimulation with two pathogen-associated molecular patterns (PAMPs lipopolysaccharide (LPS and lipoteichoic acid (LTA. Three different algorithms (geNorm, Normfinder and BestKeeper were applied to assess the stability of HKGs. Results The mRNA expression stability of nine commonly used reference genes (B2M, BLM, GAPDH, HPRT1, PPIA, RPL4, SDHA, TBP and YWHAZ was determined by qRT-PCR in AMs that were stimulated by LPS and LTA in vitro. mRNA expression levels of all genes were found to be affected by the type of stimulation and duration of the stimulation (P SDHA, B2M and RPL4 showed a high expression stability in the irrespective to the stimulation group, while SDHA, YWHAZ and RPL4 showed high stability in non-stimulated control group. In all cases, GAPDH showed the least stability in geNorm. NormFinder revealed that SDHA was the most stable gene in all the groups. Moreover, geNorm software suggested that the geometric mean of the three most stable genes would be the suitable combination for accurate normalization of gene expression study. Conclusions There was discrepancy in the ranking order of reference genes obtained by different analysing algorithms. In conclusion, the geometric mean of the SDHA, YWHAZ and RPL4 seemed to be the most appropriate combination of HKGs for accurate normalization of gene expression data in porcine AMs without knowing the type of bacterial pathogenic status of

  2. A 3-D model of superfluid helium suitable for numerical analysis

    CERN Document Server

    Darve, C; Van Sciver, S W

    2009-01-01

    The two-fluid description is a very successful phenomenological representation of the properties of Helium II. A 3-D model suitable for numerical analysis based on the Landau-Khalatnikov description of Helium II is proposed. In this paper we introduce a system of partial differential equations that is both complete and consistent as well as practical, to be used for a 3-D solution of the flow of Helium II. The development of a 3-D numerical model for Helium II is motivated by the need to validate experimental results obtained by observing the normal component velocity distribution in a Helium II thermal counter-flow using the Particle Image Velocimetry (PIV) technique.

  3. Climate suitability for European ticks: assessing species distribution models against null models and projection under AR5 climate.

    Science.gov (United States)

    Williams, Hefin Wyn; Cross, Dónall Eoin; Crump, Heather Louise; Drost, Cornelis Jan; Thomas, Christopher James

    2015-08-28

    There is increasing evidence that the geographic distribution of tick species is changing. Whilst correlative Species Distribution Models (SDMs) have been used to predict areas that are potentially suitable for ticks, models have often been assessed without due consideration for spatial patterns in the data that may inflate the influence of predictor variables on species distributions. This study used null models to rigorously evaluate the role of climate and the potential for climate change to affect future climate suitability for eight European tick species, including several important disease vectors. We undertook a comparative assessment of the performance of Maxent and Mahalanobis Distance SDMs based on observed data against those of null models based on null species distributions or null climate data. This enabled the identification of species whose distributions demonstrate a significant association with climate variables. Latest generation (AR5) climate projections were subsequently used to project future climate suitability under four Representative Concentration Pathways (RCPs). Seven out of eight tick species exhibited strong climatic signals within their observed distributions. Future projections intimate varying degrees of northward shift in climate suitability for these tick species, with the greatest shifts forecasted under the most extreme RCPs. Despite the high performance measure obtained for the observed model of Hyalomma lusitanicum, it did not perform significantly better than null models; this may result from the effects of non-climatic factors on its distribution. By comparing observed SDMs with null models, our results allow confidence that we have identified climate signals in tick distributions that are not simply a consequence of spatial patterns in the data. Observed climate-driven SDMs for seven out of eight species performed significantly better than null models, demonstrating the vulnerability of these tick species to the effects of

  4. The 9LLUC/Wistar rat glioma model is not suitable for immunotherapy

    Institute of Scientific and Technical Information of China (English)

    Liping Yang; Jingxiang Zhao; Guihong Zhou; Yunfang Wang; Lusi Li; Hongfeng Yuan; Xue Nan; Lidong Guan; Xuetao Pei

    2012-01-01

    The availability of a well-characterized animal brain tumor model will play an important role in identifying treatments for human brain tumors. Wistar rats bearing 9L glioma cells can develop solid, well-circumcised tumors, and may be a useful animal model for the evaluation of various therapeutic approaches for gliosarcomas. In this study, the 9L/Wistar rat glioma model was produced by intracerebral implantation of 9LLUC glioma cells syngenic to Fischer 344 (F344) rats. Bioluminescence imaging showed that tumors progressively grew from day 7 to day 21 in 9LLUC/F344 rats, and tumor regression was found in some 9LLUC/Wistar rats. Hematoxylin-eosin staining verified that intracranial tumors were gliomas. Immunohistochemistry results demonstrated that no CD4- and CD8-positive cells were found in the syngeneic 9LLUC/F344 model. However, many infiltrating CD4- and CD8-positive cells were observed within the tumors of the 9LLUC/Wistar model. Our data suggests that compared with 9L/F344 rats, 9L glioma Wistar rats may not be suitable for evaluating brain glioma immunotherapies, even though the model induced an immune response and exhibited tumor regression.

  5. A Hysteresis Model Suitable For Numerical Simulation Of Moisture Content in Wood

    DEFF Research Database (Denmark)

    Frandsen, Henrik Lund; Svensson, Staffan; Damkilde, Lars

    2007-01-01

    The equilibrium moisture content in wood depends not only on the current relative humidity in the ambient air but also on the history of the relative humidity variations. This hysteresis dependency of sorption in wood implies that in the worst case the moisture content for a given relative humidi...... temperatures. These features make the model relatively easy to implement into a numerical method, e.g. the Finite Element Method....... may deviate by 30-35%. While researchers seem to have reached a general agreement on the hypothesis for the sorption hysteresis phenomenon, only a few models describing the phenomenon are available. Current models as the independent domain model have numerical deficiencies and drawbacks. This paper...... presents a new hysteresis model, which mathematically resolves in closed form expressions, with the current relative humidity and moisture content as the only input parameters. Furthermore, the model has the advantage of being applicable to different sorption isotherms, i.e. different species and different...

  6. Modeling habitat suitability of the invasive clam Corbicula fluminea in a Neotropical shallow lagoon, southern Brazil

    Directory of Open Access Journals (Sweden)

    T. C. L. Silveira

    Full Text Available Abstract This study aimed to model the habitat suitability for an invasive clam Corbicula fluminea in a coastal shallow lagoon in the southern Neotropical region (–30.22, –50.55. The lagoon (19km2, maximum deep 2.5m was sampled with an Ekman dredge in an orthogonal matrix comprising 84 points. At each sampling point, were obtained environmental descriptors as depth, organic matter content (OMC, average granulometry (Avgran, and the percentage of sand (Pcsand. Prediction performance of Generalized Linear Models (GLM, Generalized Additive Models (GAM and Boosted Regression Tree (BRT were compared. Also, niche overlapping with other native clam species (Castalia martensi, Neocorbicula limosa and Anodontites trapesialis was examined. A BRT model with 1400 trees was selected as the best model, with cross-validated correlation of 0.82. The relative contributions of predictors were Pcsand-42.6%, OMC-35.8%, Avgran-10.9% and Depth-10.8%. Were identified that C. fluminea occur mainly in sandy sediments with few organic matter, in shallow areas nor by the shore. The PCA showed a wide niche overlap with the native clam species C. martensi, N. limosa and A. trapesialis.

  7. Optimization of Land Use Suitability for Agriculture Using Integrated Geospatial Model and Genetic Algorithms

    Science.gov (United States)

    Mansor, S. B.; Pormanafi, S.; Mahmud, A. R. B.; Pirasteh, S.

    2012-08-01

    In this study, a geospatial model for land use allocation was developed from the view of simulating the biological autonomous adaptability to environment and the infrastructural preference. The model was developed based on multi-agent genetic algorithm. The model was customized to accommodate the constraint set for the study area, namely the resource saving and environmental-friendly. The model was then applied to solve the practical multi-objective spatial optimization allocation problems of land use in the core region of Menderjan Basin in Iran. The first task was to study the dominant crops and economic suitability evaluation of land. Second task was to determine the fitness function for the genetic algorithms. The third objective was to optimize the land use map using economical benefits. The results has indicated that the proposed model has much better performance for solving complex multi-objective spatial optimization allocation problems and it is a promising method for generating land use alternatives for further consideration in spatial decision-making.

  8. Global alterations in areas of suitability for maize production from climate change and using a mechanistic species distribution model (CLIMEX).

    Science.gov (United States)

    Ramirez-Cabral, Nadiezhda Y Z; Kumar, Lalit; Shabani, Farzin

    2017-07-19

    At the global level, maize is the third most important crop on the basis of harvested area. Given its importance, an assessment of the variation in regional climatic suitability under climate change is critical. CliMond 10' data were used to model the potential current and future climate distribution of maize at the global level using the CLIMEX distribution model with climate data from two general circulation models, CSIRO-Mk3.0 and MIROC-H, assuming an A2 emissions scenario for 2050 and 2100. The change in area under future climate was analysed at continental level and for major maize-producing countries of the world. Regions between the tropics of Cancer and Capricorn indicate the highest loss of climatic suitability, contrary to poleward regions that exhibit an increase of suitability. South America shows the highest loss of climatic suitability, followed by Africa and Oceania. Asia, Europe and North America exhibit an increase in climatic suitability. This study indicates that globally, large areas that are currently suitable for maize cultivation will suffer from heat and dry stresses that may constrain production. For the first time, a model was applied worldwide, allowing for a better understanding of areas that are suitable and that may remain suitable for maize.

  9. Land Suitability Assessment in the Catchment Area of Four Southwestern Atlantic Coastal Lagoons: Multicriteria and Optimization Modeling

    Science.gov (United States)

    Rodriguez-Gallego, Lorena; Achkar, Marcel; Conde, Daniel

    2012-07-01

    In the present study, a land suitability assessment was conducted in the basin of four Uruguayan coastal lagoons (Southwestern Atlantic) to analyze the productive development while minimizing eutrophication, biodiversity loss and conflicts among different land uses. Suitable land for agriculture, forest, livestock ranching, tourism and conservation sectors were initially established based on a multi-attribute model developed using a geographic information system. Experts were consulted to determine the requirements for each land use sector and the incompatibilities among land use types. The current and potential conflicts among incompatible land use sectors were analyzed by overlapping land suitability maps. We subsequently applied a multi-objective model where land (pixels) with similar suitability was clustered into "land suitability groups", using a two-phase cluster analysis and the Akaike Information Criterion. Finally, a linear programming optimization procedure was applied to allocate land use sectors into land suitable groups, maximizing total suitability and minimizing interference among sectors. Results indicated that current land use overlapped by 4.7 % with suitable land of other incompatible sectors. However, the suitable land of incompatible sectors overlapped in 20.3 % of the study area, indicating a high potential for the occurrence of future conflict. The highest competition was between agriculture and conservation, followed by forest and agriculture. We explored scenarios where livestock ranching and tourism intensified, and found that interference with conservation and agriculture notably increased. This methodology allowed us to analyze current and potential land use conflicts and to contribute to the strategic planning of the study area.

  10. Modeling freshwater snail habitat suitability and areas of potential snail-borne disease transmission in Uganda

    DEFF Research Database (Denmark)

    Stensgaard, Anna-Sofie; Jørgensen, Aslak; Kabatereine, N B

    2006-01-01

    Geographic information system (GIS-based modeling of an intermediate host snail species environmental requirements using known occurrence records can provide estimates of its spatial distribution. When other data are lacking, this can be used as a rough spatial prediction of potential snail......-borne disease transmission areas. Furthermore, knowledge of abiotic factors affecting intra-molluscan parasitic development can be used to make "masks" based on remotely sensed climatic data, and these can in turn be used to refine these predictions. We used data from a recent freshwater snail survey from...... Uganda, environmental data and the genetic algorithm for rule-set prediction (GARP) to map the potential distribution of snail species known to act as intermediate hosts of several human and animal parasites. The results suggest that large areas of Uganda are suitable habitats for many of these snail...

  11. Predictive mechanistic bioenergetics to model habitat suitability of shellfish culture in coastal lakes

    Science.gov (United States)

    Rinaldi, A.; Montalto, V.; Manganaro, A.; Mazzola, A.; Mirto, S.; Sanfilippo, M.; Sarà, G.

    2014-05-01

    Quantitative tools based on mechanistic modelling of functional traits able to enhance the sustainability of aquaculture and most other human activities (i.e. reducing the likelihood of detrimental impacts optimising productions), are especially important factors in the decision to site aquaculture facilities in coastal lakes, ponds and lagoons and, in the case of detrimental impact, to adopt mitigation measures. We tested the ability of mechanistic functional trait based models to predict life history traits of cultivable shellfish in shallow coastal lakes. Dynamic Energy Budget (DEB) models were run to generate spatially explicit predictions of Mytilus galloprovincialis life history (LH) traits (e.g. body size and fecundity). Using fortnightly data of food supply and hourly data of body temperatures, and exploiting the power of mechanistic rules, we estimated the amount of faeces ejected by a fixed quantity of organisms cultivated in two shallow Southern Mediterranean (Sicily) lakes. These differed in terms of temperature and food density, implying large differences in life history traits of mussels in the two study areas. This information could help facilitate the selection of sites where environmental conditions are more suitable for aquaculture and contextually compatible with sustainability. The validation exercise obtained by comparing the predicted and observed data was nearly consistent. Therefore, a mechanistic functional traits-based model seems able to capture the link between habitat characteristics and functional traits of organisms, delineating the fundamental portion of an ecological niche, the possibility of predicting LH traits and potential ecological applications in the management of natural coastal resources.

  12. Position Sensorless Control of IPMSMs Based on a Novel Flux Model Suitable for Maximum Torque Control

    Science.gov (United States)

    Matsumoto, Atsushi; Hasegawa, Masaru; Matsui, Keiju

    In this paper, a novel position sensorless control method for interior permanent magnet synchronous motors (IPMSMs) that is based on a novel flux model suitable for maximum torque control has been proposed. Maximum torque per ampere (MTPA) control is often utilized for driving IPMSMs with the maximum efficiency. In order to implement this control, generally, the parameters are required to be accurate. However, the inductance varies dramatically because of magnetic saturation, which has been one of the most important problems in recent years. Therefore, the conventional MTPA control method fails to achieve maximum efficiency for IPMSMs because of parameter mismatches. In this paper, first, a novel flux model has been proposed for realizing the position sensorless control of IPMSMs, which is insensitive to Lq. In addition, in this paper, it has been shown that the proposed flux model can approximately estimate the maximum torque control (MTC) frame, which as a new coordinate aligned with the current vector for MTPA control. Next, in this paper, a precise estimation method for the MTC frame has been proposed. By this method, highly accurate maximum torque control can be achieved. A decoupling control algorithm based on the proposed model has also been addressed in this paper. Finally, some experimental results demonstrate the feasibility and effectiveness of the proposed method.

  13. Febrile seizures: an appropriate-aged model suitable for long-term studies

    Science.gov (United States)

    Baram, Tallie Z.; Gerth, Angelika; Schultz, Linda

    2012-01-01

    Seizures induced by fever are the most prevalent age-specific seizures in infants and young children. Whether they result in long-term sequelae such as neuronal loss and temporal lobe epilepsy is controversial. Prospective studies of human febrile seizures have found no adverse effects on the developing brain. However, adults with temporal lobe epilepsy and associated limbic cell loss frequently have a history of prolonged febrile seizures in early life. These critical issues may be resolved using appropriate animal models. Published models of hyperthermic seizures have used ‘adolescent’ and older rats, have yielded a low percentage of animals with actual seizures, or have suffered from a high mortality, rendering them unsuitable for long-term studies. This article describes the establishment of a model of febrile seizures using the infant rat. Hyperthermia was induced by a regulated stream of mildly heated air, and the seizures were determined by both behavioral and electroencephalographic (EEG) criteria. Stereotyped seizures were generated in 93.6% of 10–11-day-old rats. EEG correlates of these; seizures were not evident in cortical recordings, but were clearly present in depth recordings from the amygdala and hippocampus. Prolonged febrile seizures could be induced without bums, yielding a low mortality (11%) and long-term survival. In summary, an infant rat paradigm of EEG-confirmed, hyperthermia-induced seizures which is suitable for long-term studies is described. This model should be highly valuable for studying the mechanisms and sequelae of febrile seizures. PMID:9051269

  14. Habitat Suitability Model for the Distribution of Ixodes scapularis (Acari: Ixodidae) in Minnesota.

    Science.gov (United States)

    Johnson, T L; Bjork, J K H; Neitzel, D F; Dorr, F M; Schiffman, E K; Eisen, R J

    2016-05-01

    Ixodes scapularis Say, the black-legged tick, is the primary vector in the eastern United States of several pathogens causing human diseases including Lyme disease, anaplasmosis, and babesiosis. Over the past two decades, I. scapularis-borne diseases have increased in incidence as well as geographic distribution. Lyme disease exists in two major foci in the United States, one encompassing northeastern states and the other in the Upper Midwest. Minnesota represents a state with an appreciable increase in counties reporting I. scapularis-borne illnesses, suggesting geographic expansion of vector populations in recent years. Recent tick distribution records support this assumption. Here, we used those records to create a fine resolution, subcounty-level distribution model for I. scapularis using variable response curves in addition to tests of variable importance. The model identified 19% of Minnesota as potentially suitable for establishment of the tick and indicated with high accuracy (AUC = 0.863) that the distribution is driven by land cover type, summer precipitation, maximum summer temperatures, and annual temperature variation. We provide updated records of established populations near the northwestern species range limit and present a model that increases our understanding of the potential distribution of I. scapularis in Minnesota.

  15. Suitability of Water Harvesting in the Upper Blue Nile Basin, Ethiopia: A First Step towards a Mesoscale Hydrological Modeling Framework

    Directory of Open Access Journals (Sweden)

    Yihun T. Dile

    2016-01-01

    Full Text Available Extreme rainfall variability has been one of the major factors to famine and environmental degradation in Ethiopia. The potential for water harvesting in the Upper Blue Nile Basin was assessed using two GIS-based Multicriteria Evaluation methods: (1 a Boolean approach to locate suitable areas for in situ and ex situ systems and (2 a weighted overlay analysis to classify suitable areas into different water harvesting suitability levels. The sensitivity of the results was analyzed to the influence given to different constraining factors. A large part of the basin was suitable for water harvesting: the Boolean analysis showed that 36% of the basin was suitable for in situ and ex situ systems, while the weighted overlay analysis showed that 6–24% of the basin was highly suitable. Rainfall has the highest influence on suitability for water harvesting. Implementing water harvesting in nonagricultural land use types may further increase the benefit. Assessing water harvesting suitability at the larger catchment scale lays the foundation for modeling of water harvesting at mesoscale, which enables analysis of the potential and implications of upscaling of water harvesting practices for building resilience against climatic shocks. A complete water harvesting suitability study requires socioeconomic analysis and stakeholder consultation.

  16. Hyperspectral Mapping of the Invasive Species Pepperweed and the Development of a Habitat Suitability Model

    Science.gov (United States)

    Nguyen, Andrew; Gole, Alexander; Randall, Jarom; Dlott, Glade; Zhang, Sylvia; Alfaro, Brian; Schmidt, Cindy; Skiles, J. W.

    2011-01-01

    Mapping and predicting the spatial distribution of invasive plant species is central to habitat management, however difficult to implement at landscape and regional scales. Remote sensing techniques can reduce the impact field campaigns have on these ecologically sensitive areas and can provide a regional and multi-temporal view of invasive species spread. Invasive perennial pepperweed (Lepidium latifolium) is now widespread in fragmented estuaries of the South San Francisco Bay, and is shown to degrade native vegetation in estuaries and adjacent habitats, thereby reducing forage and shelter for wildlife. The purpose of this study is to map the present distribution of pepperweed in estuarine areas of the South San Francisco Bay Salt Pond Restoration Project (Alviso, CA), and create a habitat suitability model to predict future spread. Pepperweed reflectance data were collected in-situ with a GER 1500 spectroradiometer along with 88 corresponding pepperweed presence and absence points used for building the statistical models. The spectral angle mapper (SAM) classification algorithm was used to distinguish the reflectance spectrum of pepperweed and map its distribution using an image from EO-1 Hyperion. To map pepperweed, we performed a supervised classification on an ASTER image with a resulting classification accuracy of 71.8%. We generated a weighted overlay analysis model within a geographic information system (GIS) framework to predict areas in the study site most susceptible to pepperweed colonization. Variables for the model included propensity for disturbance, status of pond restoration, proximity to water channels, and terrain curvature. A Generalized Additive Model (GAM) was also used to generate a probability map and investigate the statistical probability that each variable contributed to predict pepperweed spread. Results from the GAM revealed distance to channels, distance to ponds and curvature were statistically significant (p habitats.

  17. Modelling a suitable location for Urban Solid Waste Management using AHP method and GIS -A geospatial approach and MCDM Model

    Science.gov (United States)

    Iqbal, M.; Islam, A.; Hossain, A.; Mustaque, S.

    2016-12-01

    Multi-Criteria Decision Making(MCDM) is advanced analytical method to evaluate appropriate result or decision from multiple criterion environment. Present time in advanced research, MCDM technique is progressive analytical process to evaluate a logical decision from various conflict. In addition, Present day Geospatial approach (e.g. Remote sensing and GIS) also another advanced technical approach in a research to collect, process and analyze various spatial data at a time. GIS and Remote sensing together with the MCDM technique could be the best platform to solve a complex decision making process. These two latest process combined very effectively used in site selection for solid waste management in urban policy. The most popular MCDM technique is Weighted Linear Method (WLC) where Analytical Hierarchy Process (AHP) is another popular and consistent techniques used in worldwide as dependable decision making. Consequently, the main objective of this study is improving a AHP model as MCDM technique with Geographic Information System (GIS) to select a suitable landfill site for urban solid waste management. Here AHP technique used as a MCDM tool to select the best suitable landfill location for urban solid waste management. To protect the urban environment in a sustainable way municipal waste needs an appropriate landfill site considering environmental, geological, social and technical aspect of the region. A MCDM model generate from five class related which related to environmental, geological, social and technical using AHP method and input the result set in GIS for final model location for urban solid waste management. The final suitable location comes out that 12.2% of the area corresponds to 22.89 km2 considering the total study area. In this study, Keraniganj sub-district of Dhaka district in Bangladesh is consider as study area which is densely populated city currently undergoes an unmanaged waste management system especially the suitable landfill sites for

  18. 基于计算智能的土地适宜性评价模型%Model of Land Suitability Evaluation Based on Computational Intelligence

    Institute of Scientific and Technical Information of China (English)

    焦利民; 刘耀林

    2007-01-01

    A novel model of land suitability evaluation is built based on computational intelligence (CI). A fuzzy neural network (FNN) is constructed by the integration of fuzzy logic and artificial neural network (ANN). The structure and process of this network is clear. Fuzzy rules (knowledge) are expressed in the model explicitly, and can be self-adjusted by learning from samples. Genetic algorithm (GA) is employed as the learning algorithm to train the network, and makes the training of the model efficient. This model is a self-learning and self-adaptive system with a rule set revised by training.

  19. A model of Suitability evaluation of tourism development for Suburban mining wasteland and its empirical research

    Institute of Scientific and Technical Information of China (English)

    Qiao Lifang; Zhang Yichuan; Feng Lei

    2008-01-01

    The model of suitability evaluation of tourism development for suburban mining wasteland was established in Fengquan District of Xinxiang City, with measurable methods to provide the basis for its tourism development and landscape planning. The construction and evaluation of the model was conducted with AHP method from the follow-ing four aspects: ecological importance, landscape importance, economic importance and social importance, vail-dated with the case. In the established evaluation system, weight values of six indexes are higher than 0.05, among which the weight of industrial characteristics is the highest, and the weight of area, pollution conditions, air quality conditions, landscape diversity and topography were also higher. There are still seven indicators with weight values of higher than 0.02, including land price, transportation accessibility, geological conditions, water conditions finan- cial security, distance to cities and similar competition. Weight values of five indexes are lower than 0.02, including government function, vegetation conditions, soil conditions, urban economic level and major tourism environment.We have tried to set a weighting set by AHP to avoid the shortcomings in ordinary weighting process, to perform the tourism evaluation with a maturely-developed method and solve the multi-indicator evaluation problems which in-volve the fuzziness and variability of scaling effectively. Our calculating method is a simple, reasonable, quantitative and feasible one. With general significance to non-structuralized project as development of wasteland.

  20. A Novel Protocol to Differentiate Induced Pluripotent Stem Cells by Neuronal microRNAs to Provide a Suitable Cellular Model.

    Science.gov (United States)

    Zare, Mehrak; Soleimani, Masoud; Akbarzadeh, Abolfazl; Bakhshandeh, Behnaz; Aghaee-Bakhtiari, Seyed Hamid; Zarghami, Nosratollah

    2015-08-01

    Neurodegenerative diseases are one of the most challenging subjects in medicine. Investigation of their underlying genetic or epigenetic factors is hampered by lack of suitable models. Patient-specific induced pluripotent stem cells (iPS cells) represent a valuable approach to provide a proper model for poorly understood mechanisms of neuronal diseases and the related drug screenings. miR-124 and miR-128 are the two brain-enriched miRNAs with different time-points of expression during neuronal development. Herein, we transduced human iPS cells with miR-124 and miR-128 harboring lentiviruses sequentially. The transduced plasmids contained GFP and puromycin antibiotic-resistant genes for easier selection and identification. Morphological assessment and immunocytochemistry (overexpressions of beta-tubulin and neuron-specific enolase) confirmed that induced hiPS cells by miR-124 and miR-128 represent similar characteristics to those of mature neurons. In addition, the upregulation of neuron-specific enolase, beta-tubulin, Map2, GFAP, and BDNF was detected by quantitative real-time PCR. In conclusion, it seems that our novel protocol remarks the combinatorial effect of miR-124 and miR-128 on neural differentiation in the absence of any extrinsic factor. Moreover, such cellular models could be used in personalized drug screening and applied for more effective therapies.

  1. Evaluation of excess carbon 14 and strontium 90 data for suitability to test two-dimensional stratospheric models

    Science.gov (United States)

    Johnston, Harold

    1989-12-01

    From reports by the Atomic Energy Commission concerning the atmospheric distribution of radionucleides following the nuclear bomb tests of 1958-1959 and 1961-1962, excess carbon 14 data from the period 1959-1970 and strontium 90 data from 1963-1967 are reviewed for possible use as inert tracers to test two-dimensional stratospheric-tropospheric models. Contrary to some views expressed in the literature, it is concluded that the carbon 14 data are suitable to test (1) the altitude (at 4 latitudes) of the transition region between troposphere and stratosphere with respect to transport of an inert tracer, (2) some aspects of transport between the northern and southern hemispheres, (3) horizontal and vertical transport as the vertical profile between 4.5 and 33 km and at 31°N evolves from a skewed Gaussian in 1963 to an almost stair-step profile in 1966, and (4) the long-term one-dimensional aspect of a two-dimensional model over the period 1966-1970. More tentatively, it is concluded that the strontium 90 data may be used as a model for the distribution and gross settling rate of the natural stratospheric aerosol layer between 15 and 25 km. Data from difficultly obtained laboratory reports and suggested initial conditions and boundary conditions are included as a microfiche supplement to this paper.

  2. Suitability of porcine chondrocyte micromass culture to model osteoarthritis in vitro.

    Science.gov (United States)

    Schlichting, Niels; Dehne, Tilo; Mans, Karsten; Endres, Michaela; Stuhlmüller, Bruno; Sittinger, Michael; Kaps, Christian; Ringe, Jochen

    2014-07-07

    In vitro tissue models are useful tools for the development of novel therapy strategies in cartilage repair and care. The limited availability of human primary tissue and high costs of animal models hamper preclinical tests of innovative substances and techniques. In this study we tested the potential of porcine chondrocyte micromass cultures to mimic human articular cartilage and essential aspects of osteoarthritis (OA) in vitro. Primary chondrocytes were enzymatically isolated from porcine femoral condyles and were maintained in 96-multiwell format to establish micromass cultures in a high-throughput scale. Recombinant porcine tumor necrosis factor alpha (TNF-α) was used to induce OA-like changes documented on histological (Safranin O, collagen type II staining), biochemical (hydroxyproline assay, dimethylmethylene blue method), and gene expression level (Affymetrix porcine microarray, real time PCR) and were compared with published data from human articular cartilage and human micromass cultures. After 14 days in micromass culture, porcine primary chondrocytes produced ECM rich in proteoglycans and collagens. On gene expression level, significant correlations of detected genes with porcine cartilage (r = 0.90), human cartilage (r = 0.71), and human micromass culture (r = 0.75) were observed including 34 cartilage markers such as COL2A1, COMP, and aggrecan. TNF-α stimulation led to significant proteoglycan (-75%) and collagen depletion (-50%). Comparative expression pattern analysis revealed the involvement of catabolic enzymes (MMP1, -2, -13, ADAM10), chemokines (IL8, CCL2, CXCL2, CXCL12, CCXL14), and genes associated with cell death (TNFSF10, PMAIPI, AHR) and skeletal development (GPNMB, FRZB) including transcription factors (WIF1, DLX5, TWIST1) and growth factors (IGFBP1, -3, TGFB1) consistent with published data from human OA cartilage. Expression of genes related to cartilage ECM formation (COL2A1, COL9A1, COMP, aggrecan) as well as hypertrophic bone

  3. The characterization of obese polycystic ovary syndrome rat model suitable for exercise intervention.

    Directory of Open Access Journals (Sweden)

    Chuyan Wu

    Full Text Available To develop a new polycystic ovary syndrome (PCOS rat model suitable for exercise intervention.Thirty six rats were randomly divided into three experimental groups: PCOS rats with high-fat diet (PF, n = 24, PCOS rats with ordinary diet (PO, n = 6, and control rats with ordinary diet (CO, n = 6. Two kinds of PCOS rat model were made by adjustment diet structure and testosterone injection for 28 days. After a successful animal model, PF model rats were randomly assigned to three groups: exercise with a continuation of high-fat diet (PF-EF, n = 6, sedentary with a continuation of high-fat diet (PF-SF, n = 6, exercise with an ordinary diet (PF-EO, n = 6. Fasting blood glucose (FBG and insulin (FINS, estrogen (E2, progesterone (P, and testosterone (T in serum were determined by RIA, and ovarian morphology was evaluated by Image-Pro plus 6.0.Body weight, Lee index, FINS increased significantly in PF rat model. Serum levels of E2 and T were significantly higher in PF and PO than in CO. Ovary organ index and ovarian areas were significant lower in PF than in CO. After intervention for 2 weeks, the levels of 1 h postprandial blood glucose (PBG1, 2 h postprandial blood glucose (PBG2, FINS and the serum levels of T decreased significantly in PF-EF rats and PF-EO rats. The ratio of FBG/FINS was significant higher in PF-EO rats than in PF-SF rats. Ovarian morphology showed that the numbers of preantral follicles and atretic follicles decreased significantly, and the numbers of antral follicles and corpora lutea increased significantly in the rats of PF-EF and PF-EO.By combination of high-fat diet and testosterone injection, the obese PCOS rat model is conformable with the lifestyle habits of fatty foods and insufficient exercise, and has metabolic and reproductive characteristics of human PCOS. This model can be applied to study exercise intervention.

  4. Application of NASA Observational Data and Habitat Suitability Modeling to Wavyleaf Basketgrass (Oplismenus hirtellus)

    Science.gov (United States)

    Hawkins, C.; Suss, C.

    2011-12-01

    In 1997, a rapidly spreading invasive grass known as Wavyleaf Basketgrass (Oplismenus hirtellus, WLBG), was found in Maryland's Patapsco Valley State Park. It is a low-lying, trailing perennial grass, branching and rooting at the lower stem nodes. The leaves are short and hairy, and produce a sticky substance that can adhere to passing animals and further its dispersion. WLBG is similar to Japanese stiltgrass, which has taken over Eastern forests in the last 25 years. WLBG, a stoloniferous grass, covers the forest floor, crowds out native herbaceous plants, and negatively alters the habitats of plants and animals in that ecosystem. It has spread beyond the park into the surrounding areas and other parts of Maryland and Virginia. How it arrived to Maryland is still unknown but mitigation efforts are clearly required and are being undertaken by the Maryland Department of Natural Resources (MD DNR) Wildlife and Heritage Service (WHS). The maximum entropy (MaxEnt) method was used to model the potential distribution of WLBG in the Maryland region. MaxEnt models species distributions from presence-only records, making it particularly well-suited for the types of data collected by resource managers such as the WHS. Input into the MaxEnt model were a combination of in situ presence points and covariates (environmental predictors) comprised of environmental data and NASA Earth observation data that are ecologically relevant to WLBG. These environmental predictors include temperature and precipitation data, soil classifications, landcover measures and classifications, and topology data including elevation, aspect, and slope. The remotely sensed data layers include products derived from Landsat 5 and 7, Moderate Resolution Imaging Spectroradiometer (MODIS), and the Shuttle Radar Topography Mission (SRTM). MaxEnt produced a list of top covariate contributors and created habitat suitability maps to predict potential areas where WLBG may spread.

  5. Modeling pyramidal sensors in ray-tracing software by a suitable user-defined surface

    Science.gov (United States)

    Antichi, Jacopo; Munari, Matteo; Magrin, Demetrio; Riccardi, Armando

    2016-04-01

    Following the unprecedented results in terms of performances delivered by the first light adaptive optics system at the Large Binocular Telescope, there has been a wide-spread and increasing interest on the pyramid wavefront sensor (PWFS), which is the key component, together with the adaptive secondary mirror, of the adaptive optics (AO) module. Currently, there is no straightforward way to model a PWFS in standard sequential ray-tracing software. Common modeling strategies tend to be user-specific and, in general, are unsatisfactory for general applications. To address this problem, we have developed an approach to PWFS modeling based on user-defined surface (UDS), whose properties reside in a specific code written in C language, for the ray-tracing software ZEMAX™. With our approach, the pyramid optical component is implemented as a standard surface in ZEMAX™, exploiting its dynamic link library (DLL) conversion then greatly simplifying ray tracing and analysis. We have utilized the pyramid UDS DLL surface-referred to as pyramidal acronyms may be too risky (PAM2R)-in order to design the current PWFS-based AO system for the Giant Magellan Telescope, evaluating tolerances, with particular attention to the angular sensitivities, by means of sequential ray-tracing tools only, thus verifying PAM2R reliability and robustness. This work indicates that PAM2R makes the design of PWFS as simple as that of other optical standard components. This is particularly suitable with the advent of the extremely large telescopes era for which complexity is definitely one of the main challenges.

  6. Predicting the potential environmental suitability for Theileria orientalis transmission in New Zealand cattle using maximum entropy niche modelling.

    Science.gov (United States)

    Lawrence, K E; Summers, S R; Heath, A C G; McFadden, A M J; Pulford, D J; Pomroy, W E

    2016-07-15

    The tick-borne haemoparasite Theileria orientalis is the most important infectious cause of anaemia in New Zealand cattle. Since 2012 a previously unrecorded type, T. orientalis type 2 (Ikeda), has been associated with disease outbreaks of anaemia, lethargy, jaundice and deaths on over 1000 New Zealand cattle farms, with most of the affected farms found in the upper North Island. The aim of this study was to model the relative environmental suitability for T. orientalis transmission throughout New Zealand, to predict the proportion of cattle farms potentially suitable for active T. orientalis infection by region, island and the whole of New Zealand and to estimate the average relative environmental suitability per farm by region, island and the whole of New Zealand. The relative environmental suitability for T. orientalis transmission was estimated using the Maxent (maximum entropy) modelling program. The Maxent model predicted that 99% of North Island cattle farms (n=36,257), 64% South Island cattle farms (n=15,542) and 89% of New Zealand cattle farms overall (n=51,799) could potentially be suitable for T. orientalis transmission. The average relative environmental suitability of T. orientalis transmission at the farm level was 0.34 in the North Island, 0.02 in the South Island and 0.24 overall. The study showed that the potential spatial distribution of T. orientalis environmental suitability was much greater than presumed in the early part of the Theileria associated bovine anaemia (TABA) epidemic. Maximum entropy offers a computer efficient method of modelling the probability of habitat suitability for an arthropod vectored disease. This model could help estimate the boundaries of the endemically stable and endemically unstable areas for T. orientalis transmission within New Zealand and be of considerable value in informing practitioner and farmer biosecurity decisions in these respective areas.

  7. Coralline hydroxyapatite is a suitable bone graft substitute in an intra-articular goat defect model.

    Science.gov (United States)

    Koëter, S; Tigchelaar, S J; Farla, P; Driessen, L; van Kampen, A; Buma, P

    2009-07-01

    Intra-articular defects can be filled with an autologous bone graft taken from the iliac crest. This can be indicated after trauma or following correcting osteotomy. Patients may encounter donor site morbidity after this procedure. In this in vivo study, we studied if coralline hydroxyapatite (CHA) is a suitable material to replace autologous bone graft to fill a defect in the femoral trochlea of goats. CHA did not evoke any negative reaction in the synovium, and the articular cartilage was comparable to controls. In the bone graft group, we found scattered areas of (enchondral formed) bone. Most bone graft had been resorbed or remodeled, and the scarce remnants were incorporated into new bone. Resorption of CHA was limited or absent and most CHA was surrounded by new bone. In areas with fragmented CHA, close to the joint surface, numerous giant cells were found. The study shows that in this animal model, CHA inserted in a defect that directly communicates with the joint space incorporates into bone. This study did not show any negative effects of CHA in a joint environment.

  8. Which model based on fluorescence quenching is suitable to study the interaction between trans-resveratrol and BSA?

    Science.gov (United States)

    Wei, Xin Lin; Xiao, Jian Bo; Wang, Yuanfeng; Bai, Yalong

    2010-01-01

    There are several models by means of quenching fluorescence of BSA to determine the binding parameters. The binding parameters obtained from different models are quite different from each other. Which model is suitable to study the interaction between trans-resveratrol and BSA? Herein, twelve models based fluorescence quenching of BSA were compared. The number of binding sites increasing with increased binding constant for similar compounds binding to BSA maybe one approach to resolve this question. For example, here eleven flavonoids were tested to illustrate that the double logarithm regression curve is suitable to study binding polyphenols to BSA.

  9. Is the climate right for pleistocene rewilding? Using species distribution models to extrapolate climatic suitability for mammals across continents.

    Directory of Open Access Journals (Sweden)

    Orien M W Richmond

    Full Text Available Species distribution models (SDMs are increasingly used for extrapolation, or predicting suitable regions for species under new geographic or temporal scenarios. However, SDM predictions may be prone to errors if species are not at equilibrium with climatic conditions in the current range and if training samples are not representative. Here the controversial "Pleistocene rewilding" proposal was used as a novel example to address some of the challenges of extrapolating modeled species-climate relationships outside of current ranges. Climatic suitability for three proposed proxy species (Asian elephant, African cheetah and African lion was extrapolated to the American southwest and Great Plains using Maxent, a machine-learning species distribution model. Similar models were fit for Oryx gazella, a species native to Africa that has naturalized in North America, to test model predictions. To overcome biases introduced by contracted modern ranges and limited occurrence data, random pseudo-presence points generated from modern and historical ranges were used for model training. For all species except the oryx, models of climatic suitability fit to training data from historical ranges produced larger areas of predicted suitability in North America than models fit to training data from modern ranges. Four naturalized oryx populations in the American southwest were correctly predicted with a generous model threshold, but none of these locations were predicted with a more stringent threshold. In general, the northern Great Plains had low climatic suitability for all focal species and scenarios considered, while portions of the southern Great Plains and American southwest had low to intermediate suitability for some species in some scenarios. The results suggest that the use of historical, in addition to modern, range information and randomly sampled pseudo-presence points may improve model accuracy. This has implications for modeling range shifts of

  10. Is the climate right for pleistocene rewilding? Using species distribution models to extrapolate climatic suitability for mammals across continents.

    Science.gov (United States)

    Richmond, Orien M W; McEntee, Jay P; Hijmans, Robert J; Brashares, Justin S

    2010-09-22

    Species distribution models (SDMs) are increasingly used for extrapolation, or predicting suitable regions for species under new geographic or temporal scenarios. However, SDM predictions may be prone to errors if species are not at equilibrium with climatic conditions in the current range and if training samples are not representative. Here the controversial "Pleistocene rewilding" proposal was used as a novel example to address some of the challenges of extrapolating modeled species-climate relationships outside of current ranges. Climatic suitability for three proposed proxy species (Asian elephant, African cheetah and African lion) was extrapolated to the American southwest and Great Plains using Maxent, a machine-learning species distribution model. Similar models were fit for Oryx gazella, a species native to Africa that has naturalized in North America, to test model predictions. To overcome biases introduced by contracted modern ranges and limited occurrence data, random pseudo-presence points generated from modern and historical ranges were used for model training. For all species except the oryx, models of climatic suitability fit to training data from historical ranges produced larger areas of predicted suitability in North America than models fit to training data from modern ranges. Four naturalized oryx populations in the American southwest were correctly predicted with a generous model threshold, but none of these locations were predicted with a more stringent threshold. In general, the northern Great Plains had low climatic suitability for all focal species and scenarios considered, while portions of the southern Great Plains and American southwest had low to intermediate suitability for some species in some scenarios. The results suggest that the use of historical, in addition to modern, range information and randomly sampled pseudo-presence points may improve model accuracy. This has implications for modeling range shifts of organisms in response

  11. Land suitability assessment in the catchment area of four Southwestern Atlantic coastal lagoons: multicriteria and optimization modeling.

    Science.gov (United States)

    Rodriguez-Gallego, Lorena; Achkar, Marcel; Conde, Daniel

    2012-07-01

    In the present study, a land suitability assessment was conducted in the basin of four Uruguayan coastal lagoons (Southwestern Atlantic) to analyze the productive development while minimizing eutrophication, biodiversity loss and conflicts among different land uses. Suitable land for agriculture, forest, livestock ranching, tourism and conservation sectors were initially established based on a multi-attribute model developed using a geographic information system. Experts were consulted to determine the requirements for each land use sector and the incompatibilities among land use types. The current and potential conflicts among incompatible land use sectors were analyzed by overlapping land suitability maps. We subsequently applied a multi-objective model where land (pixels) with similar suitability was clustered into "land suitability groups", using a two-phase cluster analysis and the Akaike Information Criterion. Finally, a linear programming optimization procedure was applied to allocate land use sectors into land suitable groups, maximizing total suitability and minimizing interference among sectors. Results indicated that current land use overlapped by 4.7 % with suitable land of other incompatible sectors. However, the suitable land of incompatible sectors overlapped in 20.3 % of the study area, indicating a high potential for the occurrence of future conflict. The highest competition was between agriculture and conservation, followed by forest and agriculture. We explored scenarios where livestock ranching and tourism intensified, and found that interference with conservation and agriculture notably increased. This methodology allowed us to analyze current and potential land use conflicts and to contribute to the strategic planning of the study area.

  12. Vacuum Drying of Barberry Fruit (Berberis vulgaris and Selection of a Suitable Thin Layer Drying Model

    Directory of Open Access Journals (Sweden)

    Akram Sharifi

    2013-02-01

    Full Text Available In an investigation on kinetics of seedless barberry drying at 35, 45 and 55°C in vacuum and with water vapor and citric acid pre-treatments, the value of effective moisture Diffusivity (Deff was calculated using the second Fick's diffusion equation, activation energy was determined and drying process was simulated by 10 common mathematical equations of thin layer-drying models. Results which were obtained from regression analysis of studied models showed that approximation of diffusion model had the best fitting for vacuum-drying of barberries through available data. Drying barberry took place in the falling rate drying period and pre-treated samples had higher drying rate. The effective diffusivity coefficient for vacuum-drying of barberry fruits was evaluated between 0.022810-10 and 0.253810-10m2/s, which increased along with temperature rise. An Arrhenius equation for drying of seedless barberry with activation energy values ranged from 27.618 to 92.493 kJ/mol expressed the effect of temperature on moisture diffusivity.

  13. Development and validation of a habitat suitability model for the non-indigenous seagrass Zostera japonica in North America

    Science.gov (United States)

    We developed a spatially-explicit, flexible 3-parameter habitat suitability model that can be used to identify and predict areas at higher risk for non-native dwarf eelgrass (Zostera japonica) invasion. The model uses simple environmental parameters (depth, nearshore slope, and s...

  14. Assessment of Chinese sturgeon habitat suitability in the Yangtze River (China): Comparison of generalized additive model, data-driven fuzzy logic model, and preference curve model

    Science.gov (United States)

    Yi, Yujun; Sun, Jie; Zhang, Shanghong; Yang, Zhifeng

    2016-05-01

    To date, a wide range of models have been applied to evaluate aquatic habitat suitability. In this study, three models, including the expert knowledge-based preference curve model (PCM), data-driven fuzzy logic model (DDFL), and generalized additive model (GAM), are used on a common data set to compare their effectiveness and accuracy. The true skill statistic (TSS) and the area under the receiver operating characteristics curve (AUC) are used to evaluate the accuracy of the three models. The results indicate that the two data-based methods (DDFL and GAM) yield better accuracy than the expert knowledge-based PCM, and the GAM yields the best accuracy. There are minor differences in the suitable ranges of the physical habitat variables obtained from the three models. The hydraulic habitat suitability index (HHSI) calculated by the PCM is the largest, followed by the DDFL and then the GAM. The results illustrate that data-based models can describe habitat suitability more objectively and accurately when there are sufficient data. When field data are lacking, combining expertise with data-based models is recommended. When field data are difficult to obtain, an expert knowledge-based model can be used as a replacement for the data-based methods.

  15. Modeling suitable habitat of invasive red lionfish Pterois volitans (Linnaeus, 1758) in North and South America’s coastal waters

    Science.gov (United States)

    Evangelista, Paul H.; Young, Nicholas E.; Schofield, Pamela J.; Jarnevich, Catherine S.

    2016-01-01

    We used two common correlative species-distribution models to predict suitable habitat of invasive red lionfish Pterois volitans (Linnaeus, 1758) in the western Atlantic and eastern Pacific Oceans. The Generalized Linear Model (GLM) and the Maximum Entropy (Maxent) model were applied using the Software for Assisted Habitat Modeling. We compared models developed using native occurrences, using non-native occurrences, and using both native and non-native occurrences. Models were trained using occurrence data collected before 2010 and evaluated with occurrence data collected from the invaded range during or after 2010. We considered a total of 22 marine environmental variables. Models built with non-native only or both native and non-native occurrence data outperformed those that used only native occurrences. Evaluation metrics based on the independent test data were highest for models that used both native and non-native occurrences. Bathymetry was the strongest environmental predictor for all models and showed increasing suitability as ocean floor depth decreased, with salinity ranking the second strongest predictor for models that used native and both native and non-native occurrences, indicating low habitat suitability for salinities species distribution models for invasive species.

  16. Predicting environmental suitability for a rare and threatened species (Lao newt, Laotriton laoensis using validated species distribution models.

    Directory of Open Access Journals (Sweden)

    Amanda J Chunco

    Full Text Available The Lao newt (Laotriton laoensis is a recently described species currently known only from northern Laos. Little is known about the species, but it is threatened as a result of overharvesting. We integrated field survey results with climate and altitude data to predict the geographic distribution of this species using the niche modeling program Maxent, and we validated these predictions by using interviews with local residents to confirm model predictions of presence and absence. The results of the validated Maxent models were then used to characterize the environmental conditions of areas predicted suitable for L. laoensis. Finally, we overlaid the resulting model with a map of current national protected areas in Laos to determine whether or not any land predicted to be suitable for this species is coincident with a national protected area. We found that both area under the curve (AUC values and interview data provided strong support for the predictive power of these models, and we suggest that interview data could be used more widely in species distribution niche modeling. Our results further indicated that this species is mostly likely geographically restricted to high altitude regions (i.e., over 1,000 m elevation in northern Laos and that only a minute fraction of suitable habitat is currently protected. This work thus emphasizes that increased protection efforts, including listing this species as endangered and the establishment of protected areas in the region predicted to be suitable for L. laoensis, are urgently needed.

  17. Deep-sea benthic megafaunal habitat suitability modelling: A global-scale maximum entropy model for xenophyophores

    Science.gov (United States)

    Ashford, Oliver S.; Davies, Andrew J.; Jones, Daniel O. B.

    2014-12-01

    Xenophyophores are a group of exclusively deep-sea agglutinating rhizarian protozoans, at least some of which are foraminifera. They are an important constituent of the deep-sea megafauna that are sometimes found in sufficient abundance to act as a significant source of habitat structure for meiofaunal and macrofaunal organisms. This study utilised maximum entropy modelling (Maxent) and a high-resolution environmental database to explore the environmental factors controlling the presence of Xenophyophorea and two frequently sampled xenophyophore species that are taxonomically stable: Syringammina fragilissima and Stannophyllum zonarium. These factors were also used to predict the global distribution of each taxon. Areas of high habitat suitability for xenophyophores were highlighted throughout the world's oceans, including in a large number of areas yet to be suitably sampled, but the Northeast and Southeast Atlantic Ocean, Gulf of Mexico and Caribbean Sea, the Red Sea and deep-water regions of the Malay Archipelago represented particular hotspots. The two species investigated showed more specific habitat requirements when compared to the model encompassing all xenophyophore records, perhaps in part due to the smaller number and relatively more clustered nature of the presence records available for modelling at present. The environmental variables depth, oxygen parameters, nitrate concentration, carbon-chemistry parameters and temperature were of greatest importance in determining xenophyophore distributions, but, somewhat surprisingly, hydrodynamic parameters were consistently shown to have low importance, possibly due to the paucity of well-resolved global hydrodynamic datasets. The results of this study (and others of a similar type) have the potential to guide further sample collection, environmental policy, and spatial planning of marine protected areas and industrial activities that impact the seafloor, particularly those that overlap with aggregations of

  18. [Study on ecological suitability of Gardenia jasminoides based on ArcGIS and Maxent model].

    Science.gov (United States)

    Miao, Qi; Yuan, Yuan-Jian; Luo, Guang-Ming; Wei, Chun-Hua; Rao, Ya-Qi; Gong, Yu-Hong; Zhang, Lan; Shao, Jian; Dong, Yan-Kai

    2016-09-01

    The application of ArcGIS and Maxent modelto analyze the ecological suitability of Gardenia jasminoides.Taking 85 batches of Gardenia as the basis of analysis, the selection of ecological factors for the growth of Gardenia. The results showed that the average precipitation in April, the average precipitation in November and the average precipitation in August were the most important factors affecting the growth of Gardenia. The relative concentration of Gardenia suitable growth region,north to the south of Shaanxi province, south of Henan, central Anhui, south to the north of Hainan province, west to central Sichuan province, east of Zhejiang coastal area, northeast of Taiwan. Copyright© by the Chinese Pharmaceutical Association.

  19. A predictive model of suitability for minimally invasive parathyroid surgery in the treatment of primary hyperparathyroidism [corrected].

    LENUS (Irish Health Repository)

    Kavanagh, Dara O

    2012-05-01

    Improved preoperative localizing studies have facilitated minimally invasive approaches in the treatment of primary hyperparathyroidism (PHPT). Success depends on the ability to reliably select patients who have PHPT due to single-gland disease. We propose a model encompassing preoperative clinical, biochemical, and imaging studies to predict a patient\\'s suitability for minimally invasive surgery.

  20. Habitat suitability models for predicting the occurrence of vulnerable marine ecosystems in the seas around New Zealand

    Science.gov (United States)

    Anderson, Owen F.; Guinotte, John M.; Rowden, Ashley A.; Tracey, Dianne M.; Mackay, Kevin A.; Clark, Malcolm R.

    2016-09-01

    Spatial management planning for vulnerable marine ecosystems (VME) across broad areas of un-sampled seafloor requires detailed predictions of species distribution. We utilised two habitat suitability modelling techniques, boosted regression trees (BRT) and maximum entropy (MaxEnt), to create potential distribution maps for 11 VME indicator taxa in the New Zealand area and adjacent seas. New bathymetry data were combined with existing environmental, chemical and physical data to produce a set of 45 predictor variables describing conditions at the seafloor. Nine of these variables were selected for use in the models based on low covariance and high explanatory power. Historical biological survey data were used to provide models with absence data (BRT) or target-group background data (MaxEnt). Model agreement was high, with each model predicting similar areas of suitable habitat both in the vicinity of known VME indicator taxa presence locations as well as across broad regions of un-sampled seafloor. Model performance measures, including cross-validation testing against sets of spatially independent data, did not clearly indicate a preferred modelling method across all taxa. Previous habitat suitability modelling efforts have rarely accounted for model precision, and in this study we used a bootstrap re-sampling technique to produce model uncertainty maps to accompany each habitat suitability map. Because of the similar performance of BRT and MaxEnt methods in this study, we conclude that the best approach to incorporating the results into decision-support tools for spatial conservation planning is to average predictions and uncertainty from both.

  1. An iterative and targeted sampling design informed by habitat suitability models for detecting focal plant species over extensive areas.

    Science.gov (United States)

    Wang, Ophelia; Zachmann, Luke J; Sesnie, Steven E; Olsson, Aaryn D; Dickson, Brett G

    2014-01-01

    Prioritizing areas for management of non-native invasive plants is critical, as invasive plants can negatively impact plant community structure. Extensive and multi-jurisdictional inventories are essential to prioritize actions aimed at mitigating the impact of invasions and changes in disturbance regimes. However, previous work devoted little effort to devising sampling methods sufficient to assess the scope of multi-jurisdictional invasion over extensive areas. Here we describe a large-scale sampling design that used species occurrence data, habitat suitability models, and iterative and targeted sampling efforts to sample five species and satisfy two key management objectives: 1) detecting non-native invasive plants across previously unsampled gradients, and 2) characterizing the distribution of non-native invasive plants at landscape to regional scales. Habitat suitability models of five species were based on occurrence records and predictor variables derived from topography, precipitation, and remotely sensed data. We stratified and established field sampling locations according to predicted habitat suitability and phenological, substrate, and logistical constraints. Across previously unvisited areas, we detected at least one of our focal species on 77% of plots. In turn, we used detections from 2011 to improve habitat suitability models and sampling efforts in 2012, as well as additional spatial constraints to increase detections. These modifications resulted in a 96% detection rate at plots. The range of habitat suitability values that identified highly and less suitable habitats and their environmental conditions corresponded to field detections with mixed levels of agreement. Our study demonstrated that an iterative and targeted sampling framework can address sampling bias, reduce time costs, and increase detections. Other studies can extend the sampling framework to develop methods in other ecosystems to provide detection data. The sampling methods

  2. Environmental variables and definitive host distribution: a habitat suitability modelling for endohelminth parasites in the marine realm

    Science.gov (United States)

    Kuhn, Thomas; Cunze, Sarah; Kochmann, Judith; Klimpel, Sven

    2016-08-01

    Marine nematodes of the genus Anisakis are common parasites of a wide range of aquatic organisms. Public interest is primarily based on their importance as zoonotic agents of the human Anisakiasis, a severe infection of the gastro-intestinal tract as result of consuming live larvae in insufficiently cooked fish dishes. The diverse nature of external impacts unequally influencing larval and adult stages of marine endohelminth parasites requires the consideration of both abiotic and biotic factors. Whereas abiotic factors are generally more relevant for early life stages and might also be linked to intermediate hosts, definitive hosts are indispensable for a parasite’s reproduction. In order to better understand the uneven occurrence of parasites in fish species, we here use the maximum entropy approach (Maxent) to model the habitat suitability for nine Anisakis species accounting for abiotic parameters as well as biotic data (definitive hosts). The modelled habitat suitability reflects the observed distribution quite well for all Anisakis species, however, in some cases, habitat suitability exceeded the known geographical distribution, suggesting a wider distribution than presently recorded. We suggest that integrative modelling combining abiotic and biotic parameters is a valid approach for habitat suitability assessments of Anisakis, and potentially other marine parasite species.

  3. The crab Carcinus maenas as a suitable experimental model in ecotoxicology.

    Science.gov (United States)

    Rodrigues, Elsa Teresa; Pardal, Miguel Ângelo

    2014-09-01

    Aquatic ecotoxicology broadly focuses on how aquatic organisms interact with pollutants in their environment in order to determine environmental hazard and potential risks to humans. Research has produced increasing evidence on the pivotal role of aquatic invertebrates in the assessment of the impact of pollutants on the environment. Its potential use to replace fish bioassays, which offers ethical advantages, has already been widely studied. Nevertheless, the selection of adequate invertebrate experimental models, appropriate experimental designs and bioassays, as well as the control of potential confounding factors in toxicity testing are of major importance to obtain scientifically valid results. Therefore, the present study reviews more than four decades of published research papers in which the Green crab Carcinus maenas was used as an experimental test organism. In general, the surveyed literature indicates that C. maenas is sensitive to a wide range of aquatic pollutants and that its biological responses are linked to exposure concentrations or doses. Current scientific knowledge regarding the biology and ecology of C. maenas and the extensive studies on toxicology found for the present review recognise the Green crab as a reliable estuarine/marine model for routine testing in ecotoxicology research and environmental quality assessment, especially in what concerns the application of the biomarker approach. Data gathered provide valuable information for the selection of adequate and trustworthy bioassays to be used in C. maenas toxicity testing. Since the final expression of high quality testing is a reliable outcome, the present review recommends gender, size and morphotype separation in C. maenas experimental designs and data evaluation. Moreover, the organisms' nutritional status should be taken into account, especially in long-term studies. Studies should also consider the crabs' resilience when facing historical and concurrent contamination. Finally

  4. A combined strategy of "in silico" transcriptome analysis and web search engine optimization allows an agile identification of reference genes suitable for normalization in gene expression studies.

    Science.gov (United States)

    Faccioli, Primetta; Ciceri, Gian Paolo; Provero, Paolo; Stanca, Antonio Michele; Morcia, Caterina; Terzi, Valeria

    2007-03-01

    Traditionally housekeeping genes have been employed as endogenous reference (internal control) genes for normalization in gene expression studies. Since the utilization of single housekeepers cannot assure an unbiased result, new normalization methods involving multiple housekeeping genes and normalizing using their mean expression have been recently proposed. Moreover, since a gold standard gene suitable for every experimental condition does not exist, it is also necessary to validate the expression stability of every putative control gene on the specific requirements of the planned experiment. As a consequence, finding a good set of reference genes is for sure a non-trivial problem requiring quite a lot of lab-based experimental testing. In this work we identified novel candidate barley reference genes suitable for normalization in gene expression studies. An advanced web search approach aimed to collect, from publicly available web resources, the most interesting information regarding the expression profiling of candidate housekeepers on a specific experimental basis has been set up and applied, as an example, on stress conditions. A complementary lab-based analysis has been carried out to verify the expression profile of the selected genes in different tissues and during heat shock response. This combined dry/wet approach can be applied to any species and physiological condition of interest and can be considered very helpful to identify putative reference genes to be shortlisted every time a new experimental design has to be set up.

  5. A restoration suitability index model for the eastern oyster (Crassostrea virginica in the Mission-Aransas Estuary, TX, USA.

    Directory of Open Access Journals (Sweden)

    Jennifer Beseres Pollack

    Full Text Available Oyster reefs are one of the most threatened marine habitats on earth, with habitat loss resulting from water quality degradation, coastal development, destructive fishing practices, overfishing, and storm impacts. For successful and sustainable oyster reef restoration efforts, it is necessary to choose sites that support long-term growth and survival of oysters. Selection of suitable sites is critically important as it can greatly influence mortality factors and may largely determine the ultimate success of the restoration project. The application of Geographic Information Systems (GIS provides an effective methodology for identifying suitable sites for oyster reef restoration and removes much of the uncertainty involved in the sometimes trial and error selection process. This approach also provides an objective and quantitative tool for planning future oyster reef restoration efforts. The aim of this study was to develop a restoration suitability index model and reef quality index model to characterize locations based on their potential for successful reef restoration within the Mission-Aransas Estuary, Texas, USA. The restoration suitability index model focuses on salinity, temperature, turbidity, dissolved oxygen, and depth, while the reef quality index model focuses on abundance of live oysters, dead shell, and spat. Size-specific Perkinsus marinus infection levels were mapped to illustrate general disease trends. This application was effective in identifying suitable sites for oyster reef restoration, is flexible in its use, and provides a mechanism for considering alternative approaches. The end product is a practical decision-support tool that can be used by coastal resource managers to improve oyster restoration efforts. As oyster reef restoration activities continue at small and large-scales, site selection criteria are critical for assisting stakeholders and managers and for maximizing long-term sustainability of oyster resources.

  6. Tumor cell culture on collagen–chitosan scaffolds as three-dimensional tumor model: A suitable model for tumor studies

    Directory of Open Access Journals (Sweden)

    Aziz Mahmoudzadeh

    2016-07-01

    Full Text Available Tumor cells naturally live in three-dimensional (3D microenvironments, while common laboratory tests and evaluations are done in two-dimensional (2D plates. This study examined the impact of cultured 4T1 cancer cells in a 3D collagen–chitosan scaffold compared with 2D plate cultures. Collagen–chitosan scaffolds were provided and passed confirmatory tests. 4T1 tumor cells were cultured on scaffolds and then tumor cells growth rate, resistance to X-ray radiation, and cyclophosphamide as a chemotherapy drug were analyzed. Furthermore, 4T1 cells were extracted from the scaffold model and were injected into the mice. Tumor growth rate, survival rate, and systemic immune responses were evaluated. Our results showed that 4T1 cells infiltrated the scaffolds pores and constructed a 3D microenvironment. Furthermore, 3D cultured tumor cells showed a slower proliferation rate, increased levels of survival to the X-ray irradiation, and enhanced resistance to chemotherapy drugs in comparison with 2D plate cultures. Transfer of extracted cells to the mice caused enhanced tumor volume and decreased life span. This study indicated that collagen–chitosan nanoscaffolds provide a suitable model of tumor that would be appropriate for tumor studies.

  7. Expression modeling for expression-invariant face recognition

    NARCIS (Netherlands)

    Haar, F.B. Ter; Veltkamp, R.C.

    2010-01-01

    Morphable face models have proven to be an effective tool for 3D face modeling and face recognition, but the extension to 3D face scans with expressions is still a challenge. The two main difficulties are (1) how to build a new morphable face model that deals with expressions, and (2) how to fit thi

  8. Modelling suitable estuarine habitats for Zostera noltii , using Ecological Niche Factor Analysis and Bathymetric LiDAR

    Science.gov (United States)

    Valle, Mireia; Borja, Ángel; Chust, Guillem; Galparsoro, Ibon; Garmendia, Joxe Mikel

    2011-08-01

    Predicting species distribution and habitat suitability is of considerable use in supporting the implementation of environmental legislation, protection and conservation of marine waters and ecosystem-based management. As other seagrasses, Zostera noltii has declined worldwide, mainly due to human pressures, such as eutrophication and habitat loss. In the case of the Basque Country (northern Spain), the species is present only in 3 out of 12 estuaries. From the literature, it is known that at least 6 of these estuaries were formerly vegetated by this seagrass. Consequently, efforts to monitor and restore (potential) habitats have been enhanced. Therefore, we aim: (i) to determine the main environmental variables explaining Zostera noltii distribution, within the Basque estuaries based upon the Oka estuary; (ii) to model habitat suitability for this species, as a wider applicable management-decision tool for seagrass restoration; and (iii) to assess the applicability and predicted accuracy of the model by using internal and external validation methods. For this purpose, Ecological Niche Factor Analysis (ENFA) has been used to model habitat suitability, based upon topographical variables, obtained from bathymetric Light Detection And Ranging (LiDAR); sediment characteristics variables; and hydrodynamic variables. The results obtained from the ecological factors of the ENFA (Marginality: 1.00; Specialization: 2.59) indicate that the species habitat differs considerably from the mean environmental conditions over the study area; likewise, that the species is restrictive in the selection of the range of conditions within which it dwells. The main environmental variables relating to the species distribution, in order of importance, are: mean grain size; redox potential; intertidal height; sediment sorting; slope of intertidal flat; percentage of gravels; and percentage of organic matter content. The model has a high predicted accuracy (Boyce index: 0.92). Model

  9. GPS-based regional ionospheric models and their suitability in Antarctica

    Institute of Scientific and Technical Information of China (English)

    AN Jiachun; WANG Zemin; NING Xinguo

    2014-01-01

    There are a number of ionospheric models available for research and application, such as the polynomial model, generalized trigonometric series function model, low degree spherical harmonic function model, adjusted spherical harmonic function model, and spherical cap harmonic function analysis. Using observations from more than 40 continuously operating stations across Antarctica in 2010, ifve models are compared with regard to their precision and applicability to polar regions. The results show that all the models perform well in Antarctica with 0.1 TECU of residual mean value and 2 TECU of root mean square error.

  10. An integrated geographic information system approach for modeling the suitability of conifer habitat in an alpine environment

    Science.gov (United States)

    McGregor, Stephen J.

    1998-01-01

    Alpine periglacial environments within the forest-alpine tundra ecotone (FATE) may be among the first to reflect changes in habitat characteristics as a consequence of climatic change. Previous FATE studies used Integrated Geographic Information System (IGIS) techniques to collect and model biophysical data but lacked the necessary detail to model the micro-scale patterns and compositions of habitat within alpine periglacial environments. This paper describes several promising data collection, integration, and cartographic modeling techniques used in an IGIS approach to model alpine periglacial environments in Glacier National Park (GNP), Montana, USA. High-resolution (I X I m) multi-spectral remote sensing data and differentially corrected Global Positioning System (DGPS) data were integrated with other biophysical data using a raster-based IGIS approach. Biophysical factors, hypothesized to influence the pattern and composition of the FATE and the alpine tundra ecosystem, were derived from the high-resolution remote sensing data, in-situ GPS data, high-resolution models of digital elevation, and other thematic data using image processing techniques and cartographic modeling. Suitability models of conifer habitat were created using indices generated from the IGIS database. This IGIS approach identified suitable conifer habitat within the FATE and permitted the modeling of micro-scale periglacial features and alpine tundra communities that are absent from traditional approaches of landscape-scale (30 X 30 m) modeling.

  11. Dynamic Model of Kaplan Turbine Regulating System Suitable for Power System Analysis

    Directory of Open Access Journals (Sweden)

    Jie Zhao

    2015-01-01

    Full Text Available Accurate modeling of Kaplan turbine regulating system is of great significance for grid security and stability analysis. In this paper, Kaplan turbine regulating system model is divided into the governor system model, the blade control system model, and the turbine and water diversion system model. The Kaplan turbine has its particularity, and the on-cam relationship between the wicket gate opening and the runner blade angle under a certain water head on the whole range was obtained by high-order curve fitting method. Progressively the linearized Kaplan turbine model, improved ideal Kaplan turbine model, and nonlinear Kaplan turbine model were developed. The nonlinear Kaplan turbine model considered the correction function of the blade angle on the turbine power, thereby improving the model simulation accuracy. The model parameters were calculated or obtained by the improved particle swarm optimization (IPSO algorithm. For the blade control system model, the default blade servomotor time constant given by value of one simplified the modeling and experimental work. Further studies combined with measured test data verified the established model accuracy and laid a foundation for further research into the influence of Kaplan turbine connecting to the grid.

  12. A resource-based modelling framework to assess habitat suitability for steppe birds in semiarid Mediterranean agricultural systems.

    Directory of Open Access Journals (Sweden)

    Laura Cardador

    Full Text Available European agriculture is undergoing widespread changes that are likely to have profound impacts on farmland biodiversity. The development of tools that allow an assessment of the potential biodiversity effects of different land-use alternatives before changes occur is fundamental to guiding management decisions. In this study, we develop a resource-based model framework to estimate habitat suitability for target species, according to simple information on species' key resource requirements (diet, foraging habitat and nesting site, and examine whether it can be used to link land-use and local species' distribution. We take as a study case four steppe bird species in a lowland area of the north-eastern Iberian Peninsula. We also compare the performance of our resource-based approach to that obtained through habitat-based models relating species' occurrence and land-cover variables. Further, we use our resource-based approach to predict the effects that change in farming systems can have on farmland bird habitat suitability and compare these predictions with those obtained using the habitat-based models. Habitat suitability estimates generated by our resource-based models performed similarly (and better for one study species than habitat based-models when predicting current species distribution. Moderate prediction success was achieved for three out of four species considered by resource-based models and for two of four by habitat-based models. Although, there is potential for improving the performance of resource-based models, they provide a structure for using available knowledge of the functional links between agricultural practices, provision of key resources and the response of organisms to predict potential effects of changing land-uses in a variety of context or the impacts of changes such as altered management practices that are not easily incorporated into habitat-based models.

  13. Predicting spatial and temporal distribution of Indo-Pacific lionfish (Pterois volitans) in Biscayne Bay through habitat suitability modeling

    Science.gov (United States)

    Bernal, Nicholas A.; DeAngelis, Donald L.; Schofield, Pamela J.; Sullivan Sealey, Kathleen

    2014-01-01

    Invasive species may exhibit higher levels of growth and reproduction when environmental conditions are most suitable, and thus their effects on native fauna may be intensified. Understanding potential impacts of these species, especially in the nascent stages of a biological invasion, requires critical information concerning spatial and temporal distributions of habitat suitability. Using empirically supported environmental variables (e.g., temperature, salinity, dissolved oxygen, rugosity, and benthic substrate), our models predicted habitat suitability for the invasive lionfish (Pterois volitans) in Biscayne Bay, Florida. The use of Geographic Information Systems (GIS) as a platform for the modeling process allowed us to quantify correlations between temporal (seasonal) fluctuations in the above variables and the spatial distribution of five discrete habitat quality classes, whose ranges are supported by statistical deviations from the apparent best conditions described in prior studies. Analysis of the resulting models revealed little fluctuation in spatial extent of the five habitat classes on a monthly basis. Class 5, which represented the area with environmental variables closest to the best conditions for lionfish, occupied approximately one-third of Biscayne Bay, with subsequent habitats declining in area. A key finding from this study was that habitat suitability increased eastward from the coastline, where higher quality habitats were adjacent to the Atlantic Ocean and displayed marine levels of ambient water quality. Corroboration of the models with sightings from the USGS-NAS database appeared to support our findings by nesting 79 % of values within habitat class 5; however, field testing (i.e., lionfish surveys) is necessary to confirm the relationship between habitat classes and lionfish distribution.

  14. A suitable model plant for control of the set fuel cell-DC/DC converter

    Energy Technology Data Exchange (ETDEWEB)

    Andujar, J.M.; Segura, F.; Vasallo, M.J. [Departamento de Ingenieria Electronica, Sistemas Informaticos y Automatica, E.P.S. La Rabida, Universidad de Huelva, Ctra. Huelva - Palos de la Frontera, S/N, 21819 La Rabida - Palos de la Frontera Huelva (Spain)

    2008-04-15

    In this work a state and transfer function model of the set made up of a proton exchange membrane (PEM) fuel cell and a DC/DC converter is developed. The set is modelled as a plant controlled by the converter duty cycle. In addition to allow setting the plant operating point at any point of its characteristic curve (two interesting points are maximum efficiency and maximum power points), this approach also allows the connection of the fuel cell to other energy generation and storage devices, given that, as they all usually share a single DC bus, a thorough control of the interconnected devices is required. First, the state and transfer function models of the fuel cell and the converter are obtained. Then, both models are related in order to achieve the fuel cell+DC/DC converter set (plant) model. The results of the theoretical developments are validated by simulation on a real fuel cell model. (author)

  15. A Presence-Only Model of Suitable Roosting Habitat for the Endangered Indiana Bat in the Southern Appalachians.

    Directory of Open Access Journals (Sweden)

    Kristina R Hammond

    Full Text Available We know little about how forest bats, which are cryptic and mobile, use roosts on a landscape scale. For widely distributed species like the endangered Indiana bat Myotis sodalis, identifying landscape-scale roost habitat associations will be important for managing the species in different regions where it occurs. For example, in the southern Appalachian Mountains, USA, M. sodalis roosts are scattered across a heavily forested landscape, which makes protecting individual roosts impractical during large-scale management activities. We created a predictive spatial model of summer roosting habitat to identify important predictors using the presence-only modeling program MaxEnt and an information theoretic approach for model comparison. Two of 26 candidate models together accounted for >0.93 of AICc weights. Elevation and forest type were top predictors of presence; aspect north/south and distance-to-ridge were also important. The final average best model indicated that 5% of the study area was suitable habitat and 0.5% was optimal. This model matched our field observations that, in the southern Appalachian Mountains, optimal roosting habitat for M. sodalis is near the ridge top in south-facing mixed pine-hardwood forests at elevations from 260-575 m. Our findings, coupled with data from other studies, suggest M. sodalis is flexible in roost habitat selection across different ecoregions with varying topography and land use patterns. We caution that, while mature pine-hardwood forests are important now, specific areas of suitable and optimal habitat will change over time. Combining the information theoretic approach with presence-only models makes it possible to develop landscape-scale habitat suitability maps for forest bats.

  16. Gluconate as suitable potential reduction supplier in Corynebacterium glutamicum: cloning and expression of gntP and gntK in Escherichia coli.

    Science.gov (United States)

    Porco, Antonietta; Gamero, Elida E; Mylonás, Elena; Istúriz, Tomás

    2008-01-01

    Corynebacterium glutamicum is widely used in the industrial production of amino acids. We have found that this bacterium grows exponentially on a mineral medium supplemented with gluconate. Gluconate permease and Gluconokinase are expressed in an inducible form and, 6-phosphogluconate dehydrogenase, although constitutively expressed, shows a 3-fold higher specific level in gluconate grown cells than those grown in fructose under similar conditions. Interestingly, these activities are lower than those detected in the strain Escherichia coli M1-8, cultivated under similar conditions. Additionally, here we also confirmed that this bacterium lacks 6-phosphogluconate dehydratase activity. Thus, gluconate must be metabolized through the pentose phosphate pathway. Genes encoding gluconate transport and its phosphorylation were cloned from C. glutamicum, and expressed in suitable E. coli mutants. Sequence analysis revealed that the amino acid sequences obtained from these genes, denoted as gntP and gntK, were similar to those found in other bacteria. Analysis of both genes by RT-PCR suggested constitutive expression, in disagreement with the inducible character of their corresponding activities. The results suggest that gluconate might be a suitable source of reduction potential for improving the efficiency in cultures engaged in amino acids production. This is the first time that gluconate specific enzymatic activities are reported in C. glutamicum.

  17. Is a Swine Model of Arteriovenous Malformation Suitable for Human Extracranial Arteriovenous Malformation? A Preliminary Study

    Energy Technology Data Exchange (ETDEWEB)

    Lv, Ming-ming, E-mail: lvmingming001@163.com [Ninth People' s Hospital, Shanghai Jiao Tong University School of Medicine, Department of Oral and Maxillofacial Surgery, Shanghai Key Laboratory of Stomatology (China); Fan, Xin-dong, E-mail: fanxindong@yahoo.com.cn [Ninth People' s Hospital, Shanghai Jiao Tong University School of Medicine, Department of Radiology (China); Su, Li-xin, E-mail: sulixin1975@126.com [Ninth People' s Hospital, Shanghai Jiao Tong University School of Medicine, Department of Oral and Maxillofacial Surgery, Shanghai Key Laboratory of Stomatology (China)

    2013-10-15

    Objective: A chronic arteriovenous malformation (AVM) model using the swine retia mirabilia (RMB) was developed and compared with the human extracranial AVM (EAVM) both in hemodynamics and pathology, to see if this brain AVM model can be used as an EAVM model. Methods: We created an arteriovenous fistula between the common carotid artery and the external jugular vein in eight animals by using end-to-end anastomosis. All animals were sacrificed 1 month after surgery, and the bilateral retia were obtained at autopsy and performed hematoxylin and eosin staining and immunohistochemistry. Pre- and postsurgical hemodynamic evaluations also were conducted. Then, the blood flow and histological changes of the animal model were compared with human EAVM. Results: The angiography after operation showed that the blood flow, like human EAVM, flowed from the feeding artery, via the nidus, drained to the draining vein. Microscopic examination showed dilated lumina and disrupted internal elastic lamina in both RMB of model and nidus of human EAVM, but the thickness of vessel wall had significant difference. Immunohistochemical reactivity for smooth muscle actin, angiopoietin 1, and angiopoietin 2 were similar in chronic model nidus microvessels and human EAVM, whereas vascular endothelial growth factor was significant difference between human EAVM and RMB of model. Conclusions: The AVM model described here is similar to human EAVM in hemodynamics and immunohistochemical features, but there are still some differences in anatomy and pathogenetic mechanism. Further study is needed to evaluate the applicability and efficacy of this model.

  18. Investigation of the Suitability of the Bazant Endochronic Material Model for Modelling the Concrete in a SAMSON Analysis of a Reinforced Concrete Beam.

    Science.gov (United States)

    1979-07-01

    with the complexities of a hypoelastic model , the endochronic model allows inelastic strains to accumulate gradually by characterizing the inelastic...I I ‘ S I I I ( ~~NVESTIGATION OF THE I SUITABILITY OF THE BAZANT ENDOCHRONIC I MATERIAL MODEL FOR MODELLING THE CONCRETE IN A SAMSON ~NALYSIS OF I A...MATERIAL MO-DEL FOR MODELLING THE JAN — May 1979 CONC RETE IN A SAMSON ANALYSIS OF A REINFORCED 6. PERFORMING ORG. REPORT NUMBER CONCRETE BEAM

  19. Comparison and clinical suitability of eight prediction models for cardiac surgery-related acute kidney injury

    NARCIS (Netherlands)

    Kiers, H.D.; Boogaard, M.H.W.A. van den; Schoenmakers, M.C.J.; Hoeven, J.G. van der; Swieten, H.A. van; Heemskerk, S.; Pickkers, P.

    2013-01-01

    BACKGROUND: Cardiac surgery-related acute kidney injury (CS-AKI) results in increased morbidity and mortality. Different models have been developed to identify patients at risk of CS-AKI. While models that predict dialysis and CS-AKI defined by the RIFLE criteria are available, their predictive powe

  20. Modelling of Moving Coil Actuators in Fast Switching Valves Suitable for Digital Hydraulic Machines

    DEFF Research Database (Denmark)

    Nørgård, Christian; Roemer, Daniel Beck; Bech, Michael Møller

    2015-01-01

    an estimation of the eddy currents generated in the actuator yoke upon current rise, as they may have significant influence on the coil current response. The analytical model facilitates fast simulation of the transient actuator response opposed to the transient electro-magnetic finite element model which...

  1. Determination of suitable drying curve model for bread moisture loss during baking

    Science.gov (United States)

    Soleimani Pour-Damanab, A. R.; Jafary, A.; Rafiee, S.

    2013-03-01

    This study presents mathematical modelling of bread moisture loss or drying during baking in a conventional bread baking process. In order to estimate and select the appropriate moisture loss curve equation, 11 different models, semi-theoretical and empirical, were applied to the experimental data and compared according to their correlation coefficients, chi-squared test and root mean square error which were predicted by nonlinear regression analysis. Consequently, of all the drying models, a Page model was selected as the best one, according to the correlation coefficients, chi-squared test, and root mean square error values and its simplicity. Mean absolute estimation error of the proposed model by linear regression analysis for natural and forced convection modes was 2.43, 4.74%, respectively.

  2. Developing a Suitable Model for Water Uptake for Biodegradable Polymers Using Small Training Sets

    Directory of Open Access Journals (Sweden)

    Loreto M. Valenzuela

    2016-01-01

    Full Text Available Prediction of the dynamic properties of water uptake across polymer libraries can accelerate polymer selection for a specific application. We first built semiempirical models using Artificial Neural Networks and all water uptake data, as individual input. These models give very good correlations (R2>0.78 for test set but very low accuracy on cross-validation sets (less than 19% of experimental points within experimental error. Instead, using consolidated parameters like equilibrium water uptake a good model is obtained (R2=0.78 for test set, with accurate predictions for 50% of tested polymers. The semiempirical model was applied to the 56-polymer library of L-tyrosine-derived polyarylates, identifying groups of polymers that are likely to satisfy design criteria for water uptake. This research demonstrates that a surrogate modeling effort can reduce the number of polymers that must be synthesized and characterized to identify an appropriate polymer that meets certain performance criteria.

  3. Habitat suitability index model for mountain goats (Oreamnos kennedyi Elliot) in coastal southcentral Alaska

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This preliminary descriptive model applies only to mountain goats that inhabit the coastal-facing slopes that support forests of Sitka spruce (Picea sitchensis)...

  4. Mathematical modelling of migration: A suitable tool for the enforcement authorities?

    DEFF Research Database (Denmark)

    Petersen, Jens Højslev; Trier, Xenia Thorsager; Fabech, B.

    2005-01-01

    A few years ago, it became accepted that the plastics industry could use migration modelling for compliance testing. When a calculation confirms that the migration of a compound from a plastic material or article is below the specific migration limit, this is considered sufficient documentation...... for compliance with legislation. In the case of non-compliance, the result needs to be verified experimentally. The European Commission recommends that the enforcement authorities use migration modelling as well to avoid long and expensive analysis. The aim of the present work was to investigate the practical...... possibilities of implementing migration-modelling software as a tool in official food control and possibly in improving the own-check programmes of Danish plastic-converting plants. Food inspectors from nine regional food control centres initially attended a training course in the use of a commercial modelling...

  5. Habitat suitability index model for moose (Alces alces) on the Kenai peninsula

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This descriptive model applies only to moose on the Kenai Peninsula and was specifically developed for use in the evaluation of potential impacts on moose resulting...

  6. A Temperature-Dependent Thermal Model of IGBT Modules Suitable for Circuit-Level Simulations

    OpenAIRE

    Wu,Rui; Wang, Huai; Ma, Ke; Ghimire, Pramod; Iannuzzo, Francesco; Blaabjerg, Frede

    2014-01-01

    Thermal impedance of IGBT modules may vary with operating conditions due to that the thermal conductivity and heat capacity of materials are temperature dependent. This paper proposes a Cauer thermal model for a 1700 V/1000 A IGBT module with temperature-dependent thermal resistances and thermal capacitances. The temperature effect is investigated by Finite Element Method (FEM) simulation based on the geometry and material information of the IGBT module. The developed model is ready for circu...

  7. A 3-D thermal regime model suitable for cold accumulation zones of polythermal mountain glaciers

    Science.gov (United States)

    Gilbert, A.; Gagliardini, O.; Vincent, C.; Wagnon, P.

    2014-09-01

    Analysis of the thermal and mechanical response of high altitude glaciers to climate change is crucial to assess future glacier hazards associated with thermal regime changes. This paper presents a new fully thermo-mechanically coupled transient thermal regime model including enthalpy transport, firn densification, full-Stokes porous flow, free surface evolution, strain heating, surface meltwater percolation, and refreezing. The model is forced by daily air temperature data and can therefore be used to perform prognostic simulations for different future climate scenarios. The set of equations is solved using the finite element ice sheet/ice flow model Elmer/Ice. This model is applied to the Col du Dôme glacier (Mont Blanc area, 4250 m a.s.l., France) where a comprehensive data set is available. The results show that the model is capable of reproducing observed density and velocity fields as well as borehole temperature evolution. The strong spatial variability of englacial temperature change observed at Col du Dôme is well reproduced. This spatial variability is mainly a result of the variability of the slope aspect of the glacier surface and snow accumulation. Results support the use of this model to study the influence of climate change on cold accumulation zones, in particular to estimate where and under what conditions glaciers will become temperate in the future.

  8. Selection of a suitable model for the prediction of soil water content in north of Iran

    Energy Technology Data Exchange (ETDEWEB)

    Esmaeelnejad, L.; Ramezanpour, H.; Seyedmohammadi, H.; Shabanpou, M.

    2015-07-01

    Multiple Linear Regression (MLR), Artificial Neural Network (ANN) and Rosetta model were employed to develop pedotransfers functions (PTFs) for soil moisture prediction using available soil properties for northern soils of Iran. The Rosetta model is based on ANN works in a hierarchical approach to predict water retention curves. For this purpose, 240 soil samples were selected from the south of Guilan province, Gilevan region, northern Iran. The data set was divided into two subsets for calibration and testing of the models. The general performance of PTFs was evaluated using coefficient of determination (R2), root mean square error (RMSE) and mean biased error between the observed and predicted values. Results showed that ANN with two hidden layers, Tan-sigmoid and linear functions for hidden and output layers respectively, performed better than the others in predicting soil moisture. In the other hand, ANN can model non-linear functions and showed to perform better than MLR. After ANN, MLR had better accuracy than Rosetta. The developed PTFs resulted in more accurate estimation at matric potentials of 100, 300, 500, 1000, 1500 kPa. Whereas, Rosetta model resulted in slightly better estimation than derived PTFs at matric potentials of 33 kPa. This research can provide the scientific basis for the study of soil hydraulic properties and be helpful for the estimation of soil water retention in other places with similar conditions, too.. (Author)

  9. Selection of a suitable model for the prediction of soil water content in north of Iran

    Directory of Open Access Journals (Sweden)

    Leila Esmaeelnejad

    2015-03-01

    Full Text Available Multiple Linear Regression (MLR, Artificial Neural Network (ANN and Rosetta model were employed to develop pedotransfers functions (PTFs for soil moisture prediction using available soil properties for northern soils of Iran. The Rosetta model is based on ANN works in a hierarchical approach to predict water retention curves. For this purpose, 240 soil samples were selected from the south of Guilan province, Gilevan region, northern Iran. The data set was divided into two subsets for calibration and testing of the models. The general performance of PTFs was evaluated using coefficient of determination (R2, root mean square error (RMSE and mean biased error between the observed and predicted values. Results showed that ANN with two hidden layers, Tan-sigmoid and linear functions for hidden and output layers respectively, performed better than the others in predicting soil moisture. In the other hand, ANN can model non-linear functions and showed to perform better than MLR. After ANN, MLR had better accuracy than Rosetta. The developed PTFs resulted in more accurate estimation at matric potentials of 100, 300, 500, 1000, 1500 kPa. Whereas, Rosetta model resulted in slightly better estimation than derived PTFs at matric potentials of 33 kPa. This research can provide the scientific basis for the study of soil hydraulic properties and be helpful for the estimation of soil water retention in other places with similar conditions, too.

  10. Species Distribution Models and Ecological Suitability Analysis for Potential Tick Vectors of Lyme Disease in Mexico

    Directory of Open Access Journals (Sweden)

    Patricia Illoldi-Rangel

    2012-01-01

    Full Text Available Species distribution models were constructed for ten Ixodes species and Amblyomma cajennense for a region including Mexico and Texas. The model was based on a maximum entropy algorithm that used environmental layers to predict the relative probability of presence for each taxon. For Mexico, species geographic ranges were predicted by restricting the models to cells which have a higher probability than the lowest probability of the cells in which a presence record was located. There was spatial nonconcordance between the distributions of Amblyomma cajennense and the Ixodes group with the former restricted to lowlands and mainly the eastern coast of Mexico and the latter to montane regions with lower temperature. The risk of Lyme disease is, therefore, mainly present in the highlands where some Ixodes species are known vectors; if Amblyomma cajennense turns out to be a competent vector, the area of risk also extends to the lowlands and the east coast.

  11. A Temperature-Dependent Thermal Model of IGBT Modules Suitable for Circuit-Level Simulations

    DEFF Research Database (Denmark)

    Wu, Rui; Wang, Huai; Ma, Ke

    2014-01-01

    Thermal impedance of IGBT modules may vary with operating conditions due to that the thermal conductivity and heat capacity of materials are temperature dependent. This paper proposes a Cauer thermal model for a 1700 V/1000 A IGBT module with temperature-dependent thermal resistances and thermal ...... relevant reliability aspect performance. A test bench is built up with an ultra-fast infrared (IR) camera to validate the proposed thermal impedance model.......Thermal impedance of IGBT modules may vary with operating conditions due to that the thermal conductivity and heat capacity of materials are temperature dependent. This paper proposes a Cauer thermal model for a 1700 V/1000 A IGBT module with temperature-dependent thermal resistances and thermal...

  12. Modelization of the Current and Future Habitat Suitability of Rhododendron ferrugineum Using Potential Snow Accumulation.

    Directory of Open Access Journals (Sweden)

    Benjamin Komac

    Full Text Available Mountain areas are particularly sensitive to climate change. Species distribution models predict important extinctions in these areas whose magnitude will depend on a number of different factors. Here we examine the possible impact of climate change on the Rhododendron ferrugineum (alpenrose niche in Andorra (Pyrenees. This species currently occupies 14.6 km2 of this country and relies on the protection afforded by snow cover in winter. We used high-resolution climatic data, potential snow accumulation and a combined forecasting method to obtain the realized niche model of this species. Subsequently, we used data from the high-resolution Scampei project climate change projection for the A2, A1B and B1 scenarios to model its future realized niche model. The modelization performed well when predicting the species's distribution, which improved when we considered the potential snow accumulation, the most important variable influencing its distribution. We thus obtained a potential extent of about 70.7 km(2 or 15.1% of the country. We observed an elevation lag distribution between the current and potential distribution of the species, probably due to its slow colonization rate and the small-scale survey of seedlings. Under the three climatic scenarios, the realized niche model of the species will be reduced by 37.9-70.1 km(2 by the end of the century and it will become confined to what are today screes and rocky hillside habitats. The particular effects of climate change on seedling establishment, as well as on the species' plasticity and sensitivity in the event of a reduction of the snow cover, could worsen these predictions.

  13. Modelization of the Current and Future Habitat Suitability of Rhododendron ferrugineum Using Potential Snow Accumulation

    Science.gov (United States)

    Komac, Benjamin; Esteban, Pere; Trapero, Laura; Caritg, Roger

    2016-01-01

    Mountain areas are particularly sensitive to climate change. Species distribution models predict important extinctions in these areas whose magnitude will depend on a number of different factors. Here we examine the possible impact of climate change on the Rhododendron ferrugineum (alpenrose) niche in Andorra (Pyrenees). This species currently occupies 14.6 km2 of this country and relies on the protection afforded by snow cover in winter. We used high-resolution climatic data, potential snow accumulation and a combined forecasting method to obtain the realized niche model of this species. Subsequently, we used data from the high-resolution Scampei project climate change projection for the A2, A1B and B1 scenarios to model its future realized niche model. The modelization performed well when predicting the species’s distribution, which improved when we considered the potential snow accumulation, the most important variable influencing its distribution. We thus obtained a potential extent of about 70.7 km2 or 15.1% of the country. We observed an elevation lag distribution between the current and potential distribution of the species, probably due to its slow colonization rate and the small-scale survey of seedlings. Under the three climatic scenarios, the realized niche model of the species will be reduced by 37.9–70.1 km2 by the end of the century and it will become confined to what are today screes and rocky hillside habitats. The particular effects of climate change on seedling establishment, as well as on the species’ plasticity and sensitivity in the event of a reduction of the snow cover, could worsen these predictions. PMID:26824847

  14. A Temperature-Dependent Thermal Model of IGBT Modules Suitable for Circuit-Level Simulations

    DEFF Research Database (Denmark)

    Wu, Rui; Wang, Huai; Pedersen, Kristian Bonderup;

    2016-01-01

    A basic challenge in the IGBT transient simulation study is to obtain the realistic junction temperature, which demands not only accurate electrical simulations but also precise thermal impedance. This paper proposed a transient thermal model for IGBT junction temperature simulations during short...... circuits or overloads. The updated Cauer thermal model with varying thermal parameters is obtained by means of FEM thermal simulations with temperature-dependent physical parameters. The proposed method is applied to a case study of a 1700 V/1000 A IGBT module. Furthermore, a testing setup is built up...

  15. Modelling of optically stimulated luminescence of zircon : assessment of the suitability for dating

    NARCIS (Netherlands)

    Turkin, A.A.; Vainshtein, D.I.; Hartog, H.W. den

    2006-01-01

    The mineral zircon, ZrSiO4, is a candidate material for optical dating because it exhibits luminescence after exposure to natural radioactivity. The kinetic model of zircon thermally stimulated luminescence proposed before has been modified and used to investigate optically Stimulated luminescence (

  16. Are individual based models a suitable approach to estimate population vulnerability? - a case study

    Directory of Open Access Journals (Sweden)

    Eva Maria Griebeler

    2011-04-01

    Full Text Available European populations of the Large Blue Butterfly Maculinea arion have experienced severe declines in the last decades, especially in the northern part of the species range. This endangered lycaenid butterfly needs two resources for development: flower buds of specific plants (Thymus spp., Origanum vulgare, on which young caterpillars briefly feed, and red ants of the genus Myrmica, whose nests support caterpillars during a prolonged final instar. I present an analytically solvable deterministic model to estimate the vulnerability of populations of M. arion. Results obtained from the sensitivity analysis of this mathematical model (MM are contrasted to the respective results that had been derived from a spatially explicit individual based model (IBM for this butterfly. I demonstrate that details in landscape configuration which are neglected by the MM but are easily taken into consideration by the IBM result in a different degree of intraspecific competition of caterpillars on flower buds and within host ant nests. The resulting differences in mortalities of caterpillars lead to erroneous estimates of the extinction risk of a butterfly population living in habitat with low food plant coverage and low abundance in host ant nests. This observation favors the use of an individual based modeling approach over the deterministic approach at least for the management of this threatened butterfly.

  17. lpxC and yafS are the most suitable internal controls to normalize real time RT-qPCR expression in the phytopathogenic bacteria Dickeya dadantii.

    Directory of Open Access Journals (Sweden)

    Florence Hommais

    Full Text Available BACKGROUND: Quantitative RT-PCR is the method of choice for studying, with both sensitivity and accuracy, the expression of genes. A reliable normalization of the data, using several reference genes, is critical for an accurate quantification of gene expression. Here, we propose a set of reference genes, of the phytopathogenic bacteria Dickeya dadantii and Pectobacterium atrosepticum, which are stable in a wide range of growth conditions. RESULTS: We extracted, from a D. dadantii micro-array transcript profile dataset comprising thirty-two different growth conditions, an initial set of 49 expressed genes with very low variation in gene expression. Out of these, we retained 10 genes representing different functional categories, different levels of expression (low, medium, and high and with no systematic variation in expression correlating with growth conditions. We measured the expression of these reference gene candidates using quantitative RT-PCR in 50 different experimental conditions, mimicking the environment encountered by the bacteria in their host and directly during the infection process in planta. The two most stable genes (ABF-0017965 (lpxC and ABF-0020529 (yafS were successfully used for normalization of RT-qPCR data. Finally, we demonstrated that the ortholog of lpxC and yafS in Pectobacterium atrosepticum also showed stable expression in diverse growth conditions. CONCLUSIONS: We have identified at least two genes, lpxC (ABF-0017965 and yafS (ABF-0020509, whose expressions are stable in a wide range of growth conditions and during infection. Thus, these genes are considered suitable for use as reference genes for the normalization of real-time RT-qPCR data of the two main pectinolytic phytopathogenic bacteria D. dadantii and P. atrosepticum and, probably, of other Enterobacteriaceae. Moreover, we defined general criteria to select good reference genes in bacteria.

  18. Modeling a habitat suitability index for the eastern fall cohort of Ommastrephes bartramii in the central North Pacific Ocean

    Institute of Scientific and Technical Information of China (English)

    CHEN Xinjun; TIAN Siquan; LIU Bilin; CHEN Yong

    2011-01-01

    The eastern fall cohort of the neon flying squid, Ommastrephes bartramii, has been commercially exploited by the Chinese squid jigging fleet in the central North Pacific Ocean since the late 1990s. To understand and identify their optimal habitat, we have developed a habitat suitability index (HSI) model using two potential important environmental variables - sea surface temperature (SST) and sea surface height anomaly (SSHA) - and fishery data from the main fishing ground (165°-180°E) during June and July of 1999-2003. A geometric mean model (GMM), minimum model (MM) and arithmetic weighted model (AWM) with different weights were compared and the best HSI model was selected using Akaike's information criterion (AIC). The performance of the developed HSI model was evaluated using fishery data for 2004. This study suggests that the highest catch per unit effort (CPUE) and fishing effort are closely related to SST and SSHA. The best SST- and SSHA-based suitability index (SI) regression models were SISST-bsed = 0.7SIeffort-SST + 0.3 SICPUE-SST, and SISSHA-based = 0.5SIeffon-SSHA + 0.5SICP,UE-SSHA,respectively, showing that fishing effort is more important than CPUE in the estimation of SI. The bestHSI model was the AWM, defined as HSI=0.3SISST-based+ 0.7SISSHA-based, indicating that SSHA is moreimportant than SST in estimating the HSI of squid. In 2004, monthly HSI values greater than 0.6 coincidedwith the distribution of productive fishing ground and high CPUE in June and July, suggesting that themodels perform well. The proposed model provides an important tool in our efforts to develop forecastingcapacity of squid spatial dynamics.

  19. Land Suitability Modeling using a Geographic Socio-Environmental Niche-Based Approach: A Case Study from Northeastern Thailand.

    Science.gov (United States)

    Heumann, Benjamin W; Walsh, Stephen J; Verdery, Ashton M; McDaniel, Phillip M; Rindfuss, Ronald R

    2013-01-01

    Understanding the pattern-process relations of land use/land cover change is an important area of research that provides key insights into human-environment interactions. The suitability or likelihood of occurrence of land use such as agricultural crop types across a human-managed landscape is a central consideration. Recent advances in niche-based, geographic species distribution modeling (SDM) offer a novel approach to understanding land suitability and land use decisions. SDM links species presence-location data with geospatial information and uses machine learning algorithms to develop non-linear and discontinuous species-environment relationships. Here, we apply the MaxEnt (Maximum Entropy) model for land suitability modeling by adapting niche theory to a human-managed landscape. In this article, we use data from an agricultural district in Northeastern Thailand as a case study for examining the relationships between the natural, built, and social environments and the likelihood of crop choice for the commonly grown crops that occur in the Nang Rong District - cassava, heavy rice, and jasmine rice, as well as an emerging crop, fruit trees. Our results indicate that while the natural environment (e.g., elevation and soils) is often the dominant factor in crop likelihood, the likelihood is also influenced by household characteristics, such as household assets and conditions of the neighborhood or built environment. Furthermore, the shape of the land use-environment curves illustrates the non-continuous and non-linear nature of these relationships. This approach demonstrates a novel method of understanding non-linear relationships between land and people. The article concludes with a proposed method for integrating the niche-based rules of land use allocation into a dynamic land use model that can address both allocation and quantity of agricultural crops.

  20. a Dynamically Interactive Column Physics Model Suitable for Diagnosing Regional Climate Variability and GCM Errors

    Science.gov (United States)

    Sardeshmukh, P.

    2002-12-01

    Climate diagnosis increasingly involves understanding the evolution of relatively weak signals in a high-order chaotic system of strongly interacting components. Assessing the sensitivity of the full system to perturbations (or errors) is problematic: forward "brute force" calculations are too expensive, and backward "adjoint" calculations assume linearity. Fortunately, for many specific problems it is not necessary to consider the full complexity of climate interactions; diagnosis with simpler models can be very useful. The simplification usually involves restricting the focus to component subsystems (atmosphere, ocean, land, cryosphere etc) or using models that emphasize "dynamics" over "physics" or vice versa. In growing recognition of climate sensitivity to the details of atmospheric physics, attention is increasingly turning toward diagnostic models with complex physics and simplified dynamics. Single column models (SCMs) that consider complex diabatic interactions within a single atmospheric column are the best and most extreme examples of these, and the focus of this study. For regional studies, the use of SCMs is problematic because, in part, advection by the large-scale circulation is typically decoupled from diabatic interactions. This decoupling, while apparently necessary to make an SCM workable at all, can nevertheless lead to rapid spurious error growth in SCM experiments, especially in the tropics. An SCM framework that couples the vertical advective tendencies to the column physics is developed here. Conceptually, the column is viewed as being embedded in a region of uniform background winds, temperature and humidity, which allows all fluctuating advection terms to be specified in terms of vertical velocity, temperature, and humidity. The vertical velocity at any instant is given by a formula that links the vertical temperature advection to the history of the SCM-generated diabatic heating rates up to that instant. The parameters in this coupling

  1. A Suitable Software Process Improvement Model for the UK Healthcare Industry

    Science.gov (United States)

    Nguyen, Tien D.; Guo, Hong; Naguib, Raouf N. G.

    Over the recent years, the UK Healthcare sector has been the prime focus of many reports and industrial surveys, particularly in the field of software development and management issues. This signals the importance of growing concerns regarding quality issues in the Healthcare domain. In response to this, a new tailored Healthcare Process Improvement (SPI) model is proposed, which takes into consideration both signals from the industry and insights from literature.

  2. Using environmental niche modeling to find suitable habitats for the Hard-ground Barasingha in Madhya Pradesh, India

    Directory of Open Access Journals (Sweden)

    C. P. Singh

    2015-09-01

    Full Text Available The subspecies of Swamp Deer, the Hard-ground Barasingha (Rucervus duvaucelii branderi Pocock, is presently found only in Kanha Tiger Reserve (KTR in Madhya Pradesh, India. This subspecies is highly vulnerable to extinction, and reintroduction in suitable sites is the need of the hour.  Environmental niche models (GARP, SVM, ED, CSM aimed at providing a detailed prediction of species distribution by relating presence of species to 19 bioclimatic indices were developed, using swamp deer occurrence records in KTR. The predictions were appropriately weighted with the prevailing LU/LC classes to identify suitable habitats in Madhya Pradesh, India. The result shows that the southern region of Madhya Pradesh is suitable for the sustenance of Barasingha with varying degrees of habitability. Vicarious validation shows that most of these forest areas were the same as that of historical records dating back to 50 years. However, land use maps can help identify areas where this subspecies can be reintroduced. 

  3. Is Afrikaans a suitable model in planning the development of African Languages?

    Directory of Open Access Journals (Sweden)

    Stanley G M Ridge

    2008-08-01

    Full Text Available The repeated claim that Afrikaans provides a useful model for planning the development of theAfrican languages is examined critically in this article with a view to elucidating importantissues in South African language planning. The first part acknowledges the fascination of alanguage which has developed sofast for all domains of use, before examining thefactors whichdrove that development, identifying particularly its affinity to Dutch and its tempestuous politicaland social history as making it a deceptive model for African languages. The second partexplores some aspects of its history which do suggest valuable perspectives for other languagesat this stage of our history. The examples discussed are language medium in schooling, thedangers of loss of confidence in a language considered with the possibilities of effective statusinterventions, and the complex issues surrounding language standards. The third part brieflyexamines the history of Afrikaans's ambiguous relation to English. It notes the persistence of theEnglish 'enemy' metaphor along with a practical demand for English, considers the racialpolitics of the statutory equality debate at the time of Union, and analyses three distortionsoccasioned by an ambiguous attitude to English in a contemporary discussion of the role of Afrikaans. Finally, the notion of a model or example is itself questioned. The article proposesdeveloping a deeper understanding of actual needs and attitudes in an ongoing process oflanguage planning as the most likely way of doingjustice to all South Africa's languages.Die herhaalde aanspraak dat Afrikaans 'n bruikbare model bied waarvolgens die ontwikkelingvan Afrika-tale beplan kan word, word in hierdie artikel krities ondersoek met die oog daaropom belangrike vraagstukke in die Suid-Afrikaanse taalbeplanning toe te lig. Die eerste deel geeerkenning aan die bekoring van 'n taal wat op aile gebruiksterreine baie vinnig ontwikkel het,voordat die faktore wat aan

  4. Suitability of Lake Erie for bigheaded carps based on bioenergetic models and remote sensing

    Science.gov (United States)

    Anderson, Karl R.; Chapman, Duane C.; Wynne, Timothy; Masagounder, Karthik; Paukert, Craig

    2015-01-01

    Algal blooms in the Great Lakes are a potential food source for silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis; together bigheaded carps). Understanding these blooms thus plays an important role in understanding the invasion potential of bigheaded carps. We used remote sensing imagery, temperatures, and improved species specific bioenergetics models to determine algal concentrations sufficient for adult bigheaded carps. Depending on water temperature we found that bigheaded carp require between 2 and 7 μg/L chlorophyll or between 0.3 and 1.26 × 105cells/mL Microcystis to maintain body weight. Algal concentrations in the western basin and shoreline were found to be commonly several times greater than the concentrations required for weight maintenance. The remote sensing images show that area of sufficient algal foods commonly encompassed several hundred square kilometers to several thousands of square kilometers when blooms form. From 2002 to 2011, mean algal concentrations increased 273%–411%. This indicates Lake Erie provides increasingly adequate planktonic algal food for bigheaded carps. The water temperatures and algal concentrations detected in Lake Erie from 2008 to 2012 support positive growth rates such that a 4 kg silver carp could gain between 19 and 57% of its body weight in a year. A 5 kg bighead carp modeled at the same water temperatures could gain 20–81% of their body weight in the same period. The remote sensing imagery and bioenergetic models suggest that bigheaded carps would not be food limited if they invaded Lake Erie.

  5. [Habitat suitability assessment of medicinal Polyporus umbellatusin China based on Maxent modeling].

    Science.gov (United States)

    Liu, Meng-meng; Xing, Yong-mei; Guo, Shun-xing

    2015-07-01

    Geographic distribution of Polyporus umbellatus was predicted by using distribution records. Based on 42 distribution records from 12 provinces and bioclimatic data (1950-2000), georaphic distribution of P. umbellatus was modeled using Maxent. The results showed thatthe Receiver Operating Characteristic (ROC) curve analysis method was used to assess the accuracy of MAXENT model and the area under ROC curve (AUC) value of MAXENT was 0. 960 which suggested that the result of assessment was dependable. The geographic distribution pattern of were divided into three distribution block based on distribution values of 0.5-0.8: small area of Heilongjiang, Jilin, Liaoning and Hebei province, the board area of Yunnan, Guizhou and Sichuan, the southeast area of Tibet and the most area of Shanxi and Shannxi, the southeast board area of Shannxi, Gansu and Ningxia. Jackknife Test showed that average precipitation in warm seasons had the greatest contribution to the distribution gain of P. umbellatus, followed by mean temperature of driest quarter and annual mean temperature. The object suggests the potential distribution areasof P. umbellatus which is useful for the habitat conservation and introduction of P. umbellatus.

  6. a Geometric Processing Workflow for Transforming Reality-Based 3d Models in Volumetric Meshes Suitable for Fea

    Science.gov (United States)

    Gonizzi Barsanti, S.; Guidi, G.

    2017-02-01

    Conservation of Cultural Heritage is a key issue and structural changes and damages can influence the mechanical behaviour of artefacts and buildings. The use of Finite Elements Methods (FEM) for mechanical analysis is largely used in modelling stress behaviour. The typical workflow involves the use of CAD 3D models made by Non-Uniform Rational B-splines (NURBS) surfaces, representing the ideal shape of the object to be simulated. Nowadays, 3D documentation of CH has been widely developed through reality-based approaches, but the models are not suitable for a direct use in FEA: the mesh has in fact to be converted to volumetric, and the density has to be reduced since the computational complexity of a FEA grows exponentially with the number of nodes. The focus of this paper is to present a new method aiming at generate the most accurate 3D representation of a real artefact from highly accurate 3D digital models derived from reality-based techniques, maintaining the accuracy of the high-resolution polygonal models in the solid ones. The approach proposed is based on a wise use of retopology procedures and a transformation of this model to a mathematical one made by NURBS surfaces suitable for being processed by volumetric meshers typically embedded in standard FEM packages. The strong simplification with little loss of consistency possible with the retopology step is used for maintaining as much coherence as possible between the original acquired mesh and the simplified model, creating in the meantime a topology that is more favourable for the automatic NURBS conversion.

  7. Model based optimization of wind erosion control by tree shelterbelt for suitable land management

    Science.gov (United States)

    Bartus, M.; Farsang, A.; Szatmári, J.; Barta, K.

    2012-04-01

    The degradation of soil by wind erosion causes huge problem in many parts of the world. The wind erodes the upper, nutrition rich part of the soil, therefore erosion causes soil productivity loss. The length of tree shelterbelts was significantly reduced by the collectivisation (1960-1989) and the wind erosion affected areas expanded in Hungary. The tree shelterbelt is more than just a tool of wind erosion control; by good planning it can increase the yield. The tree shelterbelt reduces the wind speed and changes the microclimate providing better condition to plant growth. The aim of our work is to estimate wind erosion risk and to find the way to reduce it by tree shelterbelts. A GIS based model was created to calculate the risk and the optimal windbreak position was defined to reduce the wind erosion risk to the minimum. The model is based on the DIN 19706 (Ermitlung der Erosiongefährdung von Böden durch Wind, Estimation of Wind Erosion Risk) German standard. The model uses five input data: structure and carbon content of soil, average yearly wind speed at 10 meters height, the cultivated plants and the height and position of windbreak. The study field (16km2) was chosen near Szeged (SE Hungary). In our investigation, the cultivated plant species and the position and height of windbreaks were modified. Different scenarios were made using the data of the land management in the last few years. The best case scenario (zero wind erosion) and the worst case scenario (with no tree shelter belt and the worst land use) were made to find the optimal windbreak position. Finally, the research proved that the tree shelterbelts can provide proper protection against wind erosion, but for optimal land management the cultivated plant types should also controlled. As a result of the research, a land management plan was defined to reduce the wind erosion risk on the study field, which contains the positions of new tree shelterbelts planting and the optimal cultivation.

  8. Excretory-secretory antigens: a suitable candidate for immunization against ocular toxoplasmosis in a murine model.

    Science.gov (United States)

    Norouzpour Deilami, Kiumars; Daryani, Ahmad; Ahmadpour, Ehsan; Sharif, Mehdi; Dadimoghaddam, Yousef; Sarvi, Shahabeddin; Alizadeh, Ahad

    2014-12-01

    Toxoplasmosis, responsible for ocular impairment, is caused by Toxoplasma gondii. We investigated the effect of Toxoplasma excretory-secretory antigens (ESA) on parasite load and distribution in the eye tissue of a murine model. Case and control groups were immunized with ESA and PBS, respectively. Two weeks after the second immunization, the mice were challenged intraperitoneally with virulent RH strain of Toxoplasma; eye tissue samples of both groups were collected daily (days 1, 2, 3, and the last day before death). Parasite load was determined using real-time quantitative PCR targeted at the B1 gene. Compared to the control group, infected mice that received ESA vaccine presented a considerable decrease in parasite load in the eye tissue, demonstrating the effect of ESA on parasite load and distribution. Diminution of parasite load in mouse eye tissue indicated that ESA might help control disease-related complications and could be a valuable immunization candidate against ocular toxoplasmosis.

  9. A novel scintillation imager with charge-spread discrimination. Analytical models suitable for crystal-arrays

    Science.gov (United States)

    Scafè, Raffaele; Pellegrini, Rosanna; Cinti, Maria N.; Puccini, Marco; Pani, Roberto

    2016-10-01

    Present paper describes a method for obtaining the physical quantities characterizing single-events based on fitting experimental 2-D charge-profiles to two analytical models. First results are presented regarding a 10×10 LuYAP:Ce array of 2×2×10 mm3 crystal pixels coupled to a H10966 Hamamatsu 8×8 multi-anode assembly under radio-isotopic irradiations and from self-activity. Results show that a photo multiplier tube with cross plate anode configuration would be preferable than a multi anode one due to uniformity, cost, and connections constraints. Among the results a plot of charge spread Vs. charge is to be cited because it was not yet published in scientific literature.

  10. The use of urinary proteomics in the assessment of suitability of mouse models for ageing.

    Science.gov (United States)

    Nkuipou-Kenfack, Esther; Schanstra, Joost P; Bajwa, Seerat; Pejchinovski, Martin; Vinel, Claire; Dray, Cédric; Valet, Philippe; Bascands, Jean-Loup; Vlahou, Antonia; Koeck, Thomas; Borries, Melanie; Busch, Hauke; Bechtel-Walz, Wibke; Huber, Tobias B; Rudolph, Karl L; Pich, Andreas; Mischak, Harald; Zürbig, Petra

    2017-01-01

    Ageing is a complex process characterised by a systemic and progressive deterioration of biological functions. As ageing is associated with an increased prevalence of age-related chronic disorders, understanding its underlying molecular mechanisms can pave the way for therapeutic interventions and managing complications. Animal models such as mice are commonly used in ageing research as they have a shorter lifespan in comparison to humans and are also genetically close to humans. To assess the translatability of mouse ageing to human ageing, the urinary proteome in 89 wild-type (C57BL/6) mice aged between 8-96 weeks was investigated using capillary electrophoresis coupled to mass spectrometry (CE-MS). Using age as a continuous variable, 295 peptides significantly correlated with age in mice were identified. To investigate the relevance of using mouse models in human ageing studies, a comparison was performed with a previous correlation analysis using 1227 healthy subjects. In mice and humans, a decrease in urinary excretion of fibrillar collagens and an increase of uromodulin fragments was observed with advanced age. Of the 295 peptides correlating with age, 49 had a strong homology to the respective human age-related peptides. These ortholog peptides including several collagen (N = 44) and uromodulin (N = 5) fragments were used to generate an ageing classifier that was able to discriminate the age among both wild-type mice and healthy subjects. Additionally, the ageing classifier depicted that telomerase knock-out mice were older than their chronological age. Hence, with a focus on ortholog urinary peptides mouse ageing can be translated to human ageing.

  11. Suitability of a Coupled Hydrodynamic Water Quality Model to Predict Changes in Water Quality from Altered Meteorological Boundary Conditions

    Directory of Open Access Journals (Sweden)

    Leon van der Linden

    2015-01-01

    Full Text Available Downscaled climate scenarios can be used to inform management decisions on investment in infrastructure or alternative water sources within water supply systems. Appropriate models of the system components, such as catchments, rivers, lakes and reservoirs, are required. The climatic sensitivity of the coupled hydrodynamic water quality model ELCOM-CAEDYM was investigated, by incrementally altering boundary conditions, to determine its suitability for evaluating climate change impacts. A series of simulations were run with altered boundary condition inputs for the reservoir. Air and inflowing water temperature (TEMP, wind speed (WIND and reservoir inflow and outflow volumes (FLOW were altered to investigate the sensitivity of these key drivers over relevant domains. The simulated water quality variables responded in broadly plausible ways to the altered boundary conditions; sensitivity of the simulated cyanobacteria population to increases in temperature was similar to published values. However the negative response of total chlorophyll-a suggested by the model was not supported by an empirical analysis of climatic sensitivity. This study demonstrated that ELCOM-CAEDYM is sensitive to climate drivers and may be suitable for use in climate impact studies. It is recommended that the influence of structural and parameter derived uncertainty on the results be evaluated. Important factors in determining phytoplankton growth were identified and the importance of inflowing water quality was emphasized.

  12. Assessing the Habitat Suitability of Dam Reservoirs: A Quantitative Model and Case Study of the Hantan River Dam, South Korea

    Directory of Open Access Journals (Sweden)

    Hyeongsik Kang

    2016-11-01

    Full Text Available The main objective of this study was to investigate ecologically healthy regions near a dam reservoir. This study developed a model for assessing habitat suitability as a proxy for the ecological value of reservoirs. Three main factors comprising nine assessment variables were selected and classified as having a habitat suitability (HS between 0 and 1: (1 geomorphic factors of altitude, slope steepness, and slope aspect; (2 vegetation factors of forest physiognomy, vegetation type, and tree age; and (3 ecological factors of land cover, ecological quality index, and environmental conservation value assessment. The spatial distribution of the nine HS indices was determined using geographic information systems and combined into one HS index value to determine ecologically healthy regions. The assessment model was applied to areas surrounding the Hantan River Dam, South Korea. To verify the model, wildlife location data from the national ecosystem survey of the Ministry of Environment were used. Areas with an HS index between 0.73 and 1 were found to contain 72% of observed wildlife locations. Ecologically healthy areas were identified by adding the indices of each variable. The methods shown here will be useful for establishing ecological restoration plans for dam reservoirs in South Korea.

  13. How to Choose the Suitable Template for Homology Modelling of GPCRs: 5-HT7 Receptor as a Test Case.

    Science.gov (United States)

    Shahaf, Nir; Pappalardo, Matteo; Basile, Livia; Guccione, Salvatore; Rayan, Anwar

    2016-09-01

    G protein-coupled receptors (GPCRs) are a super-family of membrane proteins that attract great pharmaceutical interest due to their involvement in almost every physiological activity, including extracellular stimuli, neurotransmission, and hormone regulation. Currently, structural information on many GPCRs is mainly obtained by the techniques of computer modelling in general and by homology modelling in particular. Based on a quantitative analysis of eighteen antagonist-bound, resolved structures of rhodopsin family "A" receptors - also used as templates to build 153 homology models - it was concluded that a higher sequence identity between two receptors does not guarantee a lower RMSD between their structures, especially when their pair-wise sequence identity (within trans-membrane domain and/or in binding pocket) lies between 25 % and 40 %. This study suggests that we should consider all template receptors having a sequence identity ≤50 % with the query receptor. In fact, most of the GPCRs, compared to the currently available resolved structures of GPCRs, fall within this range and lack a correlation between structure and sequence. When testing suitability for structure-based drug design, it was found that choosing as a template the most similar resolved protein, based on sequence resemblance only, led to unsound results in many cases. Molecular docking analyses were carried out, and enrichment factors as well as attrition rates were utilized as criteria for assessing suitability for structure-based drug design.

  14. Chronic kidney disease induced by adenine: a suitable model of growth retardation in uremia.

    Science.gov (United States)

    Claramunt, Débora; Gil-Peña, Helena; Fuente, Rocío; García-López, Enrique; Loredo, Vanessa; Hernández-Frías, Olaya; Ordoñez, Flor A; Rodríguez-Suárez, Julián; Santos, Fernando

    2015-07-01

    Growth retardation is a major manifestation of chronic kidney disease (CKD) in pediatric patients. The involvement of the various pathogenic factors is difficult to evaluate in clinical studies. Here, we present an experimental model of adenine-induced CKD for the study of growth failure. Three groups (n = 10) of weaning female rats were studied: normal diet (control), 0.5% adenine diet (AD), and normal diet pair fed with AD (PF). After 21 days, serum urea nitrogen, creatinine, parathyroid hormone (PTH), weight and length gains, femur osseous front advance as an index of longitudinal growth rate, growth plate histomorphometry, chondrocyte proliferative activity, bone structure, aorta calcifications, and kidney histology were analyzed. Results are means ± SE. AD rats developed renal failure (serum urea nitrogen: 70 ± 6 mg/dl and creatinine: 0.6 ± 0.1 mg/dl) and secondary hyperparathyroidism (PTH: 480 ± 31 pg/ml). Growth retardation of AD rats was demonstrated by lower weight (AD rats: 63.3 ± 4.8 g, control rats: 112.6 ± 4.7 g, and PF rats: 60.0 ± 3.8 g) and length (AD rats: 7.2 ± 0.2 cm, control rats: 11.1 ± 0.3 cm, and PF rats: 8.1 ± 0.3 cm) gains as well as lower osseous front advances (AD rats: 141 ± 13 μm/day, control rats: 293 ± 16 μm/day, and PF rats: 251 ± 10 μm/day). The processes of chondrocyte maturation and proliferation were impaired in AD rats, as shown by lower growth plate terminal chondrocyte height (21.7 ± 2.3 vs. 26.2 ± 1.9 and 23.9 ± 1.3 μm in control and PF rats) and proliferative activity index (AD rats: 30 ± 2%, control rats: 38 ± 2%, and PF rats: 42 ± 3%). The bone primary spongiosa structure of AD rats was markedly disorganized. In conclusion, adenine-induced CKD in young rats is associated with growth retardation and disturbed endochondral ossification. This animal protocol may be a useful new experimental model to study growth in CKD.

  15. Novel electrospun gelatin/oxycellulose nanofibers as a suitable platform for lung disease modeling

    Energy Technology Data Exchange (ETDEWEB)

    Švachová, Veronika, E-mail: xcsvachova@fch.vutbr.cz [Institute of Materials Chemistry, Brno University of Technology (Czech Republic); Vojtová, Lucy [CEITEC – Central European Institute of Technology, Brno University of Technology (Czech Republic); SCITEG, a.s., Brno (Czech Republic); Pavliňák, David [Department of Physical Electronics, Masaryk University (Czech Republic); Vojtek, Libor [Institute of Experimental Biology, Masaryk University (Czech Republic); Sedláková, Veronika [Department of Histology and Embryology, Masaryk University (Czech Republic); International Clinical Research, St. Anne' s University Hospital, Brno (Czech Republic); Hyršl, Pavel [Institute of Experimental Biology, Masaryk University (Czech Republic); Alberti, Milan [Department of Physical Electronics, Masaryk University (Czech Republic); Jaroš, Josef; Hampl, Aleš [Department of Histology and Embryology, Masaryk University (Czech Republic); International Clinical Research, St. Anne' s University Hospital, Brno (Czech Republic); Jančář, Josef [Institute of Materials Chemistry, Brno University of Technology (Czech Republic); CEITEC – Central European Institute of Technology, Brno University of Technology (Czech Republic); SCITEG, a.s., Brno (Czech Republic)

    2016-10-01

    Novel hydrolytically stable gelatin nanofibers modified with sodium or calcium salt of oxycellulose were prepared by electrospinning method. The unique inhibitory effect of these nanofibers against Escherichia coli bacteria was examined by luminometric method. Biocompatibility of these gelatin/oxycellulose nanofibers with eukaryotic cells was tested using human lung adenocarcinoma cell line NCI-H441. Cells firmly adhered to nanofiber surface, as determined by scanning electron microscopy, and no signs of cell dying were detected by fluorescent live/dead assay. We propose that the newly developed gelatin/oxycellulose nanofibers could be used as promising scaffold for lung disease modeling and anti-cancer drug testing. - Highlights: • Novel hydrolytically stable gelatin nanofibers modified with oxycellulose were prepared by electrospinning. • ATR–FTIR spectroscopy and EDX confirmed the presence of oxycellulose in the nanofibers. • Nanofibers modified with calcium salt of oxycellulose exhibited significant antibacterial properties. • Nanofibers modified with sodium salt of oxycellulose revealed excellent biocompatibility with cell line NCI-H441.

  16. Evaluation of habitat suitability index models by global sensitivity and uncertainty analyses: a case study for submerged aquatic vegetation.

    Science.gov (United States)

    Zajac, Zuzanna; Stith, Bradley; Bowling, Andrea C; Langtimm, Catherine A; Swain, Eric D

    2015-07-01

    Habitat suitability index (HSI) models are commonly used to predict habitat quality and species distributions and are used to develop biological surveys, assess reserve and management priorities, and anticipate possible change under different management or climate change scenarios. Important management decisions may be based on model results, often without a clear understanding of the level of uncertainty associated with model outputs. We present an integrated methodology to assess the propagation of uncertainty from both inputs and structure of the HSI models on model outputs (uncertainty analysis: UA) and relative importance of uncertain model inputs and their interactions on the model output uncertainty (global sensitivity analysis: GSA). We illustrate the GSA/UA framework using simulated hydrology input data from a hydrodynamic model representing sea level changes and HSI models for two species of submerged aquatic vegetation (SAV) in southwest Everglades National Park: Vallisneria americana (tape grass) and Halodule wrightii (shoal grass). We found considerable spatial variation in uncertainty for both species, but distributions of HSI scores still allowed discrimination of sites with good versus poor conditions. Ranking of input parameter sensitivities also varied spatially for both species, with high habitat quality sites showing higher sensitivity to different parameters than low-quality sites. HSI models may be especially useful when species distribution data are unavailable, providing means of exploiting widely available environmental datasets to model past, current, and future habitat conditions. The GSA/UA approach provides a general method for better understanding HSI model dynamics, the spatial and temporal variation in uncertainties, and the parameters that contribute most to model uncertainty. Including an uncertainty and sensitivity analysis in modeling efforts as part of the decision-making framework will result in better-informed, more robust

  17. Evaluation of habitat suitability index models by global sensitivity and uncertainty analyses: a case study for submerged aquatic vegetation

    Science.gov (United States)

    Zajac, Zuzanna; Stith, Bradley M.; Bowling, Andrea C.; Langtimm, Catherine A.; Swain, Eric D.

    2015-01-01

    Habitat suitability index (HSI) models are commonly used to predict habitat quality and species distributions and are used to develop biological surveys, assess reserve and management priorities, and anticipate possible change under different management or climate change scenarios. Important management decisions may be based on model results, often without a clear understanding of the level of uncertainty associated with model outputs. We present an integrated methodology to assess the propagation of uncertainty from both inputs and structure of the HSI models on model outputs (uncertainty analysis: UA) and relative importance of uncertain model inputs and their interactions on the model output uncertainty (global sensitivity analysis: GSA). We illustrate the GSA/UA framework using simulated hydrology input data from a hydrodynamic model representing sea level changes and HSI models for two species of submerged aquatic vegetation (SAV) in southwest Everglades National Park: Vallisneria americana (tape grass) and Halodule wrightii (shoal grass). We found considerable spatial variation in uncertainty for both species, but distributions of HSI scores still allowed discrimination of sites with good versus poor conditions. Ranking of input parameter sensitivities also varied spatially for both species, with high habitat quality sites showing higher sensitivity to different parameters than low-quality sites. HSI models may be especially useful when species distribution data are unavailable, providing means of exploiting widely available environmental datasets to model past, current, and future habitat conditions. The GSA/UA approach provides a general method for better understanding HSI model dynamics, the spatial and temporal variation in uncertainties, and the parameters that contribute most to model uncertainty. Including an uncertainty and sensitivity analysis in modeling efforts as part of the decision-making framework will result in better-informed, more robust

  18. Analysis and Characterization of Damage Utilizing an Orthotropic Generalized Composite Material Model Suitable for Use in Impact Problems

    Science.gov (United States)

    Goldberg, Robert K.; Carney, Kelly S.; DuBois, Paul; Hoffarth, Canio; Rajan, Subramaniam; Blankenhorn, Gunther

    2016-01-01

    The need for accurate material models to simulate the deformation, damage and failure of polymer matrix composites under impact conditions is becoming critical as these materials are gaining increased usage in the aerospace and automotive communities. In order to address a series of issues identified by the aerospace community as being desirable to include in a next generation composite impact model, an orthotropic, macroscopic constitutive model incorporating both plasticity and damage suitable for implementation within the commercial LS-DYNA computer code is being developed. The plasticity model is based on extending the Tsai-Wu composite failure model into a strain hardening-based orthotropic plasticity model with a non-associative flow rule. The evolution of the yield surface is determined based on tabulated stress-strain curves in the various normal and shear directions and is tracked using the effective plastic strain. To compute the evolution of damage, a strain equivalent semi-coupled formulation is used in which a load in one direction results in a stiffness reduction in multiple material coordinate directions. A detailed analysis is carried out to ensure that the strain equivalence assumption is appropriate for the derived plasticity and damage formulations that are employed in the current model. Procedures to develop the appropriate input curves for the damage model are presented and the process required to develop an appropriate characterization test matrix is discussed

  19. The Øie-Tozer model of drug distribution and its suitability for drugs with different pharmacokinetic behavior.

    Science.gov (United States)

    Stepensky, David

    2011-10-01

    Drug distribution is a major pharmacokinetic process that affects the time course of drug concentrations in tissues, biological fluids and the resulting pharmacological activities. Drug distribution may follow different pathways and patterns, and is governed by the drug's physicochemical properties and the body's physiology. The classical Øie-Tozer model is frequently used for predicting volume of drug distribution and for pharmacokinetic calculations. In this review, the suitability of the Øie-Tozer model for drugs that exhibit different distribution patterns is critically analyzed and illustrated. The method used is a pharmacokinetic modeling and simulation approach. It is demonstrated that the major limitation of the Øie-Tozer model stems from its focus on the total drug concentrations and not on the active (unbound) concentrations. Moreover, the Øie-Tozer model may be inappropriate for drugs with nonlinear or complex pharmacokinetic behavior, such as biopharmaceuticals, drug conjugates or for drugs incorporated into drug delivery systems. Distribution mechanisms and alternative distribution models for these drugs are discussed. The Øie-Tozer model can serve for predicting unbound volume of drug distribution for 'classical' small molecular mass drugs with linear pharmacokinetics. However, more detailed mechanism-based distribution models should be used in preclinical and clinical settings for drugs that exhibit more complex pharmacokinetic behavior.

  20. Standardization of Data Elements of Audiology Records: A Suitable Model for Iran

    Directory of Open Access Journals (Sweden)

    Seyed Mahmoud Latifi

    2012-03-01

    Full Text Available Background and Aim: Providing high quality health care is not possible without information related to the past and current condition of the patient. Records show which services, where, when and by whom was delivered. Documentation is referred to the process of precisely recording the information regarding patient care and treatment. The purpose of this study is to determine the essential data set required in audiology record keeping and designing a model for Iran.Methods: In an applied research of a descriptive-comparative type which was carried out in 2010, data elements of audiology records of domestic and foreign patient notes were used to compile a check list which was subjected to debate by Iranian audiologists in Delphi method. 110 audiologists and 17 faculty members responded to the opinion poll.Results: From 51 elements which were subjected to discussion, 37 elements by more than 75 percent of the participants, nine elements by 50 to 75 percent of the participants and five elements by less than 50 percent of the participants, were agreed upon. The only element to be considered more important by faculty members than audiologists was "Gender" (p=0.018. Seventy percent of the participants valued the effectiveness of information in patient records very high.Conclusion: The minimum data set for audiology records must include demographic information, past medical history, patient assessment and treatment plan. With reference to record design principles this information was used to develop amodel for patient audiology record which also included the necessary instructions for completing it.

  1. Predicting the effects of proposed Mississippi River diversions on oyster habitat quality; application of an oyster habitat suitability index model

    Science.gov (United States)

    Soniat, Thomas M.; Conzelmann, Craig P.; Byrd, Jason D.; Roszell, Dustin P.; Bridevaux, Joshua L.; Suir, Kevin J.; Colley, Susan B.

    2013-01-01

    In an attempt to decelerate the rate of coastal erosion and wetland loss, and protect human communities, the state of Louisiana developed its Comprehensive Master Plan for a Sustainable Coast. The master plan proposes a combination of restoration efforts including shoreline protection, marsh creation, sediment diversions, and ridge, barrier island, and hydrological restoration. Coastal restoration projects, particularly the large-scale diversions of fresh water from the Mississippi River, needed to supply sediment to an eroding coast potentially impact oyster populations and oyster habitat. An oyster habitat suitability index model is presented that evaluates the effects of a proposed sediment and freshwater diversion into Lower Breton Sound. Voluminous freshwater, needed to suspend and broadly distribute river sediment, will push optimal salinities for oysters seaward and beyond many of the existing reefs. Implementation and operation of the Lower Breton Sound diversion structure as proposed would render about 6,173 ha of hard bottom immediately east of the Mississippi River unsuitable for the sustained cultivation of oysters. If historical harvests are to be maintained in this region, a massive and unprecedented effort to relocate private leases and restore oyster bottoms would be required. Habitat suitability index model results indicate that the appropriate location for such efforts are to the east and north of the Mississippi River Gulf Outlet.

  2. Climatic suitability of Aedes albopictus in Europe referring to climate change projections: comparison of mechanistic and correlative niche modelling approaches.

    Science.gov (United States)

    Fischer, D; Thomas, S M; Neteler, M; Tjaden, N B; Beierkuhnlein, C

    2014-02-13

    The Asian tiger mosquito, Aedes albopictus, is capable of transmitting a broad range of viruses to humans. Since its introduction at the end of the 20th century, it has become well established in large parts of southern Europe. As future expansion as a result of climate change can be expected, determining the current and projected future climatic suitability of this invasive mosquito in Europe is of interest. Several studies have tried to detect the potential habitats for this species, but differing data sources and modelling approaches must be considered when interpreting the findings. Here, various modelling methodologies are compared with special emphasis on model set-up and study design. Basic approaches and model algorithms for the projection of spatio-temporal trends within the 21st century differ substantially. Applied methods range from mechanistic models (e.g. overlay of climatic constraints based on geographic information systems or rather process-based approaches) to correlative niche models. We conclude that spatial characteristics such as introduction gateways and dispersal pathways need to be considered. Laboratory experiments addressing the climatic constraints of the mosquito are required for improved modelling results. However, the main source of uncertainty remains the insufficient knowledge about the species' ability to adapt to novel environments.

  3. Identification of Suitable Reference Genes for Investigating Gene Expression in Anterior Cruciate Ligament Injury by Using Reverse Transcription-Quantitative PCR.

    Directory of Open Access Journals (Sweden)

    Mariana Ferreira Leal

    Full Text Available The anterior cruciate ligament (ACL is one of the most frequently injured structures during high-impact sporting activities. Gene expression analysis may be a useful tool for understanding ACL tears and healing failure. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR has emerged as an effective method for such studies. However, this technique requires the use of suitable reference genes for data normalization. Here, we evaluated the suitability of six reference genes (18S, ACTB, B2M, GAPDH, HPRT1, and TBP by using ACL samples of 39 individuals with ACL tears (20 with isolated ACL tears and 19 with ACL tear and combined meniscal injury and of 13 controls. The stability of the candidate reference genes was determined by using the NormFinder, geNorm, BestKeeper DataAssist, and RefFinder software packages and the comparative ΔCt method. ACTB was the best single reference gene and ACTB+TBP was the best gene pair. The GenEx software showed that the accumulated standard deviation is reduced when a larger number of reference genes is used for gene expression normalization. However, the use of a single reference gene may not be suitable. To identify the optimal combination of reference genes, we evaluated the expression of FN1 and PLOD1. We observed that at least 3 reference genes should be used. ACTB+HPRT1+18S is the best trio for the analyses involving isolated ACL tears and controls. Conversely, ACTB+TBP+18S is the best trio for the analyses involving (1 injured ACL tears and controls, and (2 ACL tears of patients with meniscal tears and controls. Therefore, if the gene expression study aims to compare non-injured ACL, isolated ACL tears and ACL tears from patients with meniscal tear as three independent groups ACTB+TBP+18S+HPRT1 should be used. In conclusion, 3 or more genes should be used as reference genes for analysis of ACL samples of individuals with and without ACL tears.

  4. Identification of Suitable Reference Genes for Investigating Gene Expression in Anterior Cruciate Ligament Injury by Using Reverse Transcription-Quantitative PCR.

    Science.gov (United States)

    Leal, Mariana Ferreira; Astur, Diego Costa; Debieux, Pedro; Arliani, Gustavo Gonçalves; Silveira Franciozi, Carlos Eduardo; Loyola, Leonor Casilla; Andreoli, Carlos Vicente; Smith, Marília Cardoso; Pochini, Alberto de Castro; Ejnisman, Benno; Cohen, Moises

    2015-01-01

    The anterior cruciate ligament (ACL) is one of the most frequently injured structures during high-impact sporting activities. Gene expression analysis may be a useful tool for understanding ACL tears and healing failure. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) has emerged as an effective method for such studies. However, this technique requires the use of suitable reference genes for data normalization. Here, we evaluated the suitability of six reference genes (18S, ACTB, B2M, GAPDH, HPRT1, and TBP) by using ACL samples of 39 individuals with ACL tears (20 with isolated ACL tears and 19 with ACL tear and combined meniscal injury) and of 13 controls. The stability of the candidate reference genes was determined by using the NormFinder, geNorm, BestKeeper DataAssist, and RefFinder software packages and the comparative ΔCt method. ACTB was the best single reference gene and ACTB+TBP was the best gene pair. The GenEx software showed that the accumulated standard deviation is reduced when a larger number of reference genes is used for gene expression normalization. However, the use of a single reference gene may not be suitable. To identify the optimal combination of reference genes, we evaluated the expression of FN1 and PLOD1. We observed that at least 3 reference genes should be used. ACTB+HPRT1+18S is the best trio for the analyses involving isolated ACL tears and controls. Conversely, ACTB+TBP+18S is the best trio for the analyses involving (1) injured ACL tears and controls, and (2) ACL tears of patients with meniscal tears and controls. Therefore, if the gene expression study aims to compare non-injured ACL, isolated ACL tears and ACL tears from patients with meniscal tear as three independent groups ACTB+TBP+18S+HPRT1 should be used. In conclusion, 3 or more genes should be used as reference genes for analysis of ACL samples of individuals with and without ACL tears.

  5. Distribution of the Habitat Suitability of the Main Malaria Vector in French Guiana Using Maximum Entropy Modeling.

    Science.gov (United States)

    Moua, Yi; Roux, Emmanuel; Girod, Romain; Dusfour, Isabelle; de Thoisy, Benoit; Seyler, Frédérique; Briolant, Sébastien

    2016-12-22

    Malaria is an important health issue in French Guiana. Its principal mosquito vector in this region is Anopheles darlingi Root. Knowledge of the spatial distribution of this species is still very incomplete due to the extent of French Guiana and the difficulty to access most of the territory. Species distribution modeling based on the maximal entropy procedure was used to predict the spatial distribution of An. darlingi using 39 presence sites. The resulting model provided significantly high prediction performances (mean 10-fold cross-validated partial area under the curve and continuous Boyce index equal to, respectively, 1.11-with a level of omission error of 20%-and 0.42). The model also provided a habitat suitability map and environmental response curves in accordance with the known entomological situation. Several environmental characteristics that had a positive correlation with the presence of An. darlingi were highlighted: nonpermanent anthropogenic changes of the natural environment, the presence of roads and tracks, and opening of the forest. Some geomorphological landforms and high altitude landscapes appear to be unsuitable for An. darlingi The species distribution modeling was able to reliably predict the distribution of suitable habitats for An. darlingi in French Guiana. Results allowed completion of the knowledge of the spatial distribution of the principal malaria vector in this Amazonian region, and identification of the main factors that favor its presence. They should contribute to the definition of a necessary targeted vector control strategy in a malaria pre-elimination stage, and allow extrapolation of the acquired knowledge to other Amazonian or malaria-endemic contexts.

  6. Suitable Concentrations of Uric Acid Can Reduce Cell Death in Models of OGD and Cerebral Ischemia-Reperfusion Injury.

    Science.gov (United States)

    Zhang, Bin; Yang, Ning; Lin, Shao-Peng; Zhang, Feng

    2017-07-01

    Cerebral infarction (CI) is a common clinical cerebrovascular disease, and to explore the pathophysiological mechanisms and seek effective treatment means are the hotspot and difficult point in medical research nowadays. Numerous studies have confirmed that uric acid plays an important role in CI, but the mechanism has not yet been clarified. When treating HT22 and BV-2 cells with different concentrations of uric acid, uric acid below 450 μM does not have significant effect on cell viability, but uric acid more than 500 μM can significantly inhibit cell viability. After establishing models of OGD (oxygen-glucose deprivation) with HT22 and BV-2 cells, uric acid at a low concentration (50 μM) cannot improve cell viability and apoptosis, and Reactive oxygen species (ROS) levels during OGD/reoxygenation; a suitable concentration (300 μM) of uric acid can significantly improve cell viability and apoptosis, and reduce ROS production during OGD/reoxygenation; but a high concentration (1000 μM) of uric acid can further reduce cell viability and enhance ROS production. After establishing middle cerebral artery occlusion of male rats with suture method, damage and increase of ROS production in brain tissue could be seen, and after adding suitable concentration of uric acid, the degree of brain damage and ROS production was reduced. Therefore, different concentrations of uric acid should have different effect, and suitable concentrations of uric acid have neuroprotective effect, and this finding may provide guidance for study on the clinical curative effect of uric acid.

  7. The suitability of an in situ perfusion model for permeability determinations: utility for BCS class I biowaiver requests.

    Science.gov (United States)

    Kim, Jae-Seung; Mitchell, Stefanie; Kijek, Paul; Tsume, Yasuhiro; Hilfinger, John; Amidon, Gordon L

    2006-01-01

    The FDA has published recommendations for sponsors who wish to request a waiver of in vivo bioavailability (BA) or bioequivalence (BE) studies for immediate release (IR) solid oral dosage forms based on the Biopharmaceutics Classification System (BCS). Biowaivers can be requested for IR formulations in which the active ingredient is shown to be a BCS class I drug: that is, a drug showing high permeability and high solubility over a pH range of 1-7.5. For permeability determinations, a variety of experimental methods can be used, such as the rat in situ single pass perfusion or Caco-2 cell culture models, once the suitability of the particular method is established. Following the recommended procedure for assessing the suitability of permeability determinations, we determined the permeability of 20 test drugs using the in situ single pass perfusion model in rats. The test compounds were coperfused through jejunal intestinal segments with an internal permeability reference standard (metoprolol) over a 90 min time period. Sample analysis was performed by HPLC, and the ratio of the effective permeability, Peff (cm/s), of test compound to that of metoprolol was determined. To address the question of test drug permeabilities that approach that of the internal standard, we propose that a statistical analysis such as the "0.8-1.25 rule" used for in vivo or in vitro bioequivalence studies provide guidance for permeability classification using the in situ single pass perfusion model. We developed a method using the 90% confidence interval of the permeability ratio of the test to internal reference standard in order to differentiate between high and low permeability compounds. This analysis allowed for the proper permeability classification of all of the test compounds and suggests a robust means for assessing drug permeability classification.

  8. Quantification of climate change implications for water-based management: A case study of oyster suitability sites occurrence model along the Kenya coast

    Science.gov (United States)

    Aura, Christopher Mulanda; Musa, Safina; Osore, Melckzedeck K.; Kimani, Edward; Alati, Victor Mwakha; Wambiji, Nina; Maina, George W.; Charo-Karisa, Harrison

    2017-01-01

    To ensure long-term sustainability of the littoral marine ecosystem for water-based management and aquaculture potential, it is necessary to quantify and project the effect of sea warming on the resident biota. This study evaluated the potential of an oyster Suitability Sites Occurrence Model (SSOM) to predict the status of littoral areas in the future due to sea warming. Data sources comprised Moderate Resolution Imaging Spectroradiometer (MODIS) and Landsat 7 ETM +. The suitable sites were ranked on a scale of 1 (least suitable) to 5 (most suitable). In the suitability model, score 5 had the highest proportion (35.8%) of oyster suitability which shrank to 16.2% with a 4 °C increase in sea temperature. Future increases in sea temperature are likely to cause shrinkage in the spatial extent of most suitable and suitable oyster sites. Thus changes in marine oyster suitability in littoral zones are predicted to worsen gradually as sea temperatures increase in the future. Differences in the recorded sea temperature of ≤ 6 °C within and between sites may influence spatial variations in oyster habitat due to future sea warming. Such concepts could form an alternative scientific basis for quantification of potential global climate change effects on biodiversity for marine systems policy adaptation analysis, aquaculture potential, and management.

  9. Identification and evaluation of suitable reference genes for gene expression studies in the whitefly Bemisia tabaci (Asia I) by reverse transcription quantitative realtime PCR.

    Science.gov (United States)

    Collins, Carl; Patel, Mitulkumar V; Colvin, John; Bailey, David; Seal, Susan

    2014-05-02

    This study presents a reliable method for performing reverse transcription quantitative realtime PCR (RT-qPCR) to measure gene expression in the whitefly Bemisia tabaci (Asia I) (Gennadius) (Hemiptera: Aleyrodidae), utilising suitable reference genes for data normalisation. We identified orthologs of commonly used reference genes (actin (ACT), cyclophilin 1 (CYP1), elongation factor 1α (EF1A), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), ribosomal protein L13a (RPL13A), and α-tubulin (TUB1A)), measured the levels of their transcripts by RT-qPCR during development and in response to thermal stress, and evaluated their suitability as endogenous controls using geNorm, BestKeeper, and NormFinder programs. Overall, TUB1A, RPL13A, and CYP1 were the most stable reference genes during B. tabaci development, and TUB1A, GAPDH, and RPL13A were the most stable reference genes in the context of thermal stress. An analysis of the effects of reference gene choice on the transcript profile of a developmentally-regulated gene encoding vitellogenin demonstrated the importance of selecting the correct endogenous controls for RT-qPCR studies. We propose the use of TUB1A, RPL13A, and CYP1 as endogenous controls for transcript profiling studies of B. tabaci development, whereas the combination of TUB1A, GAPDH, and RPL13A should be employed for studies into thermal stress. The data pre- sented here will assist future transcript profiling studies in whiteflies.

  10. Identification and Evaluation of Suitable Reference Genes for Gene Expression Studies in the Whitefly Bemisia tabaci (Asia I) by Reverse Transcription Quantitative Real-Time PCR

    Science.gov (United States)

    Collins, Carl; Patel, Mitulkumar V.; Colvin, John; Bailey, David; Seal, Susan

    2014-01-01

    This study presents a reliable method for performing reverse transcription quantitative real-time PCR (RT-qPCR) to measure gene expression in the whitefly Bemisia tabaci (Asia I) (Gennadius) (Hemiptera: Aleyrodidae), utilising suitable reference genes for data normalisation. We identified orthologs of commonly used reference genes (actin (ACT), cyclophilin 1 (CYP1), elongation factor 1α (EF1A), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), ribosomal protein L13a (RPL13A), and α-tubulin (TUB1A)), measured the levels of their transcripts by RT-qPCR during development and in response to thermal stress, and evaluated their suitability as endogenous controls using geNorm, BestKeeper, and NormFinder programs. Overall, TUB1A, RPL13A, and CYP1 were the most stable reference genes during B. tabaci development, and TUB1A, GAPDH, and RPL13A were the most stable reference genes in the context of thermal stress. An analysis of the effects of reference gene choice on the transcript profile of a developmentally-regulated gene encoding vitellogenin demonstrated the importance of selecting the correct endogenous controls for RT-qPCR studies. We propose the use of TUB1A, RPL13A, and CYP1 as endogenous controls for transcript profiling studies of B. tabaci development, whereas the combination of TUB1A, GAPDH, and RPL13A should be employed for studies into thermal stress. The data presented here will assist future transcript profiling studies in whiteflies. PMID:25373210

  11. Predicting Suitable Habitats for the Vulnerable Eastern Hoolock Gibbon, Hoolock leuconedys, in India Using the MaxEnt Model.

    Science.gov (United States)

    Sarma, Kuladip; Kumar, Awadhesh; Krishna, Murali; Medhi, Mintu; Tripathi, Om Prakash

    2015-01-01

    The eastern hoolock gibbon, Hoolock leuconedys, is categorized as Vulnerable on the IUCN Red List and assessed as a Schedule I species of the Wildlife (Protection) Act of 1972 in India. We predict the potential habitat of H. leuconedys in the state of Arunachal Pradesh, India, using the Maximum Entropy (MaxEnt) distribution modelling algorithm. The model was developed using 90 known localities of H. leuconedys in the state. Nineteen environmental parameters along with 12 normalized difference vegetation index (NDVI) layers, elevation and land use and land cover (LULC) were used in the modelling. Amongst the environmental input variables, the precipitation of the coldest quarter (BIO 19) had the highest contribution to the model (26.03%) and the twelve NDVI layers collectively contributed 60.91%. Two districts, Lower Dibang Valley and Lohit, which are known to contain H. leuconedys, occupied 64.75% of the predicted distribution area of the species. Thus, we aid in the identification of suitable areas for the reintroduction program of H. leuconedys that is planned by the Gibbon Conservation Breeding Centre, Biological Park, Itanagar, Arunachal Pradesh, India. © 2015 S. Karger AG, Basel.

  12. A Novel Closed-Chest Porcine Model of Chronic Ischemic Heart Failure Suitable for Experimental Research in Cardiovascular Disease

    Directory of Open Access Journals (Sweden)

    Giuseppe Biondi-Zoccai

    2013-01-01

    Full Text Available Cardiac pathologies are among the leading causes of mortality and morbidity in industrialized countries, with myocardial infarction (MI representing one of the major conditions leading to heart failure (HF. Hitherto, the development of consistent, stable, and reproducible models of closed-chest MI in large animals, meeting the clinical realism of a patient with HF subsequent to chronic ischemic necrosis, has not been successful. We hereby report the design and ensuing application of a novel porcine experimental model of closed-chest chronic ischemia suitable for biomedical research, mimicking post-MI HF. We also emphasize the key procedural steps involved in replicating this unprecedented model, from femoral artery and vein catheterization to MI induction by permanent occlusion of the left anterior descending coronary artery through superselective deployment of platinum-nylon coils, as well as endomyocardial biopsy sampling for histologic analysis and cell harvesting. Our model could indeed represent a valuable contribution and tool for translational research, providing precious insights to understand and overcome the many hurdles concerning, and currently quenching, the preclinical steps mandatory for the clinical translation of new cardiovascular technologies for personalized HF treatments.

  13. Protein Alpha Shape (PAS) Dock: A new gaussian-based score function suitable for docking in homology modelled protein structures

    Science.gov (United States)

    Tøndel, Kristin; Anderssen, Endre; Drabløs, Finn

    2006-03-01

    Protein Alpha Shape (PAS) Dock is a new empirical score function suitable for virtual library screening using homology modelled protein structures. Here, the score function is used in combination with the geometry search method Tabu search. A description of the protein binding site is generated using gaussian property fields like in Protein Alpha Shape Similarity Analysis (PASSA). Gaussian property fields are also used to describe the ligand properties. The overlap between the receptor and ligand hydrophilicity and lipophilicity fields is maximised, while minimising steric clashes. Gaussian functions introduce a smoothing of the property fields. This makes the score function robust against small structural variations, and therefore suitable for use with homology models. This also makes it less critical to include protein flexibility in the docking calculations. We use a fast and simplified version of the score function in the geometry search, while a more detailed version is used for the final prediction of the binding free energies. This use of a two-level scoring makes PAS-Dock computationally efficient, and well suited for virtual screening. The PAS-Dock score function is trained on 218 X-ray structures of protein- ligand complexes with experimental binding affinities. The performance of PAS-Dock is compared to two other docking methods, AutoDock and MOE-Dock, with respect to both accuracy and computational efficiency. According to this study, PAS-Dock is more computationally efficient than both AutoDock and MOE-Dock, and gives a better prediction of the free energies of binding. PAS-Dock is also more robust against structural variations than AutoDock.

  14. DIGE proteome analysis reveals suitability of ischemic cardiac in vitro model for studying cellular response to acute ischemia and regeneration.

    Directory of Open Access Journals (Sweden)

    Sina Haas

    Full Text Available Proteomic analysis of myocardial tissue from patient population is suited to yield insights into cellular and molecular mechanisms taking place in cardiovascular diseases. However, it has been limited by small sized biopsies and complicated by high variances between patients. Therefore, there is a high demand for suitable model systems with the capability to simulate ischemic and cardiotoxic effects in vitro, under defined conditions. In this context, we established an in vitro ischemia/reperfusion cardiac disease model based on the contractile HL-1 cell line. To identify pathways involved in the cellular alterations induced by ischemia and thereby defining disease-specific biomarkers and potential target structures for new drug candidates we used fluorescence 2D-difference gel electrophoresis. By comparing spot density changes in ischemic and reperfusion samples we detected several protein spots that were differentially abundant. Using MALDI-TOF/TOF-MS and ESI-MS the proteins were identified and subsequently grouped by functionality. Most prominent were changes in apoptosis signalling, cell structure and energy-metabolism. Alterations were confirmed by analysis of human biopsies from patients with ischemic cardiomyopathy.With the establishment of our in vitro disease model for ischemia injury target identification via proteomic research becomes independent from rare human material and will create new possibilities in cardiac research.

  15. Expressing Model Constraints Visually with VMQL

    DEFF Research Database (Denmark)

    Störrle, Harald

    2011-01-01

    OCL is the de facto standard language for expressing constraints and queries on UML models. However, OCL expressions are very difficult to create, understand, and maintain, even with the sophisticated tool support now available. In this paper, we propose to use the Visual Model Query Language (VMQL......) for specifying constraints on UML models. We examine VMQL's usability by controlled experiments and its expressiveness by a representative sample. We conclude that VMQL is less expressive than OCL, although expressive enough for most of the constraints in the sample. In terms of usability, however, VMQL...... is superior to OCL, although the experimental evidence we present here is not as compelling as the one we presented when comparing VMQL and OCL on model querying....

  16. HABITAT SUITABILITY MODELING FOR EXPLORATION OF THE SPATIAL DISTRIBUTION OF KASHMIR MUSK DEER IN DACHIGAM NATIONAL PARK, KASHMIR

    Directory of Open Access Journals (Sweden)

    Mudasir Ali

    2014-01-01

    Full Text Available Musk deer are highly important as a medicinal species that are severely exploited throughout their range of occurrence due to the medicinal value of the musk produced only by the male individuals. Methods used for studying the populations and distributions of other ungulates do not work well with musk deer and the presence of a unified methodology for studying musk deer appear to be lacking worldwide. Therefore, the development of a simple predictive model for studying the distribution of the musk deer habitats stands as an important task to be accomplished. Two kinds of research questions were pursued during the present study-examining through field research what kind of habitat musk deer used and mapping the habitat in the park using a GIS and remote sensing environment. The parameters which were found to have a profound influence in predicting the species’s spatial distribution have been used in the modeling of the current habitat suitability for the Kashmir musk deer (Moschus cupreus. The study was conducted at the upper reaches (elevations 2200 m and above of the Dachigam National Park, Kashmir (34°05΄18.40΄΄N-34°06΄04.69΄΄N and 75°03΄32.05΄΄E-75°04΄27.26΄΄E during January 2005-January 2008 to evaluate the characteristics of the musk deer habitats. The environmental attributes which were found to have a profound influence in predicting the species’s spatial distribution included the slope exposures in the range of 293°Northwest -68° Northeast, slope gradients of 25-40° and elevations of 2100 m and above, with the preference ratings of aspect > slope > elevation and, therefore, were considered for the development of the habitat suitability model for prediction of the spatial distribution of the Kashmir musk deer. The current suitable musk deer habitat in Dachigam National Park is estimated in the extent of about 40 sq. km. (~28% area of the national

  17. Model output for deep-sea coral habitat suitability in the U.S. North and Mid-Atlantic from 2013 (NCEI Accession 0145923)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset was created for potential use as an environmental predictor in spatial predictive models of deep-sea coral habitat suitability. Deep-sea corals are of...

  18. A high resolution hydrodynamic model system suitable for novel harmful algal bloom modelling in areas of complex coastline and topography.

    Science.gov (United States)

    Aleynik, Dmitry; Dale, Andrew C; Porter, Marie; Davidson, Keith

    2016-03-01

    Fjordic coastlines provide sheltered locations for finfish and shellfish aquaculture, and are often subject to harmful algal blooms (HABs) some of which develop offshore and are then advected to impact nearshore aquaculture. Numerical models are a potentially important tool for providing early warning of such HAB events. However, the complex topography of fjordic shelf regions is a significant challenge to modelling. This is frequently compounded by complex bathymetry and local weather patterns. Existing structured grid models do not provide the resolution needed to represent these coastlines in their wider shelf context. In a number of locations advectively transported blooms of the ichthyotoxic dinoflagellate Karenia mikimotoi are of particular concern for the finfish industry. Here were present a novel hydrodynamic model of the coastal waters to the west of Scotland that is based on unstructured finite volume methodology, providing a sufficiently high resolution hydrodynamical structure to realistically simulate the transport of particles (such as K. mikimotoi cells) within nearshore waters where aquaculture sites are sited. Model-observation comparisons reveal close correspondence of tidal elevations for major semidiurnal and diurnal tidal constituents. The thermohaline structure of the model and its current fields are also in good agreement with a number of existing observational datasets. Simulations of the transport of Lagrangian drifting buoys, along with the incorporation of an individual-based biological model, based on a bloom of K. mikimotoi, demonstrate that unstructured grid models have considerable potential for HAB prediction in Scotland and in complex topographical regions elsewhere.

  19. Analysis of the suitability of the German soil texture classification for the regional scale application of physical based hydrological model

    Directory of Open Access Journals (Sweden)

    H. Bormann

    2007-01-01

    Full Text Available Regional scale hydrological simulations are mostly based on the use of standard data sets such as soil maps which are based on soil texture classification schemes. This paper analyses the suitability of the German soil texture classification for the application of a physically based soil-vegetation-atmosphere-transfer scheme. Theoretical soil columns are defined to be able to represent the entire soil texture triangle by a 1% grid of the three particle size classes: sand, clay and silt. These theoretical soil columns are characterized by a homogenous soil texture and consist of two layers of increasing bulk density and decreasing content of organic matter with depth. Soil hydraulic parameterisation is derived by applying a pedotransfer function. Continuous water balance calculations are carried out for a ten year period for all grid cells of the 1% grid. The results of the water balance calculations are compared to the simulation results of the centre of gravity of the respective soil texture class. Texture class specific mean deviations and root mean squared deviations are calculated from the differences between the 1% pixels and texture class representatives. The results reveal that the loam and silt texture classes show only small deviations from the centres of gravity. For a few sand texture classes and most of the clay texture classes deviations are considerably large. Assuming an equal distributed probability of occurrence of all realisations within a soil texture class, an uncertainty of more than 100 mm/a with respect to runoff and actual evapotranspiration is detected for four clay texture classes, two sand texture classes and one silt texture class. These results are confirmed by a sensitivity analysis investigating the model response for a grid cell compared to the neighboured grid cells. High sensitivities mainly appear for sandy and clayey soils while the sensitivity of the model for loam and silt soils is smaller. Resuming it can

  20. Selection of a Suitable Wall Pressure Spectrum Model for Estimating Flow-Induced Noise in Sonar Applications

    Directory of Open Access Journals (Sweden)

    V. Bhujanga Rao

    1995-01-01

    Full Text Available Flow-induced structural noise of a sonar dome in which the sonar transducer is housed, constitutes a major source of self-noise above a certain speed of the vessel. Excitation of the sonar dome structure by random pressure fluctuations in turbulent boundary layer flow leads to acoustic radiation into the interior of the dome. This acoustic radiation is termed flow-induced structural noise. Such noise contributes significantly to sonar self-noise of submerged vessels cruising at high speed and plays an important role in surface ships, torpedos, and towed sonars as well. Various turbulent boundary layer wall pressure models published were analyzed and the most suitable analytical model for the sonar dome application selected while taking into account high frequency, fluid loading, low wave number contribution, and pressure gradient effects. These investigations included type of coupling that exists between turbulent boundary layer pressure fluctuations and dome wall structure of a typical sonar dome. Comparison of theoretical data with measured data onboard a ship are also reported.

  1. Status study of knowledge management in universities and to provide a suitable model (Case Study: Ferdowsi University of Mashhad)

    Science.gov (United States)

    Jahangir, Mustafa; Asadi, M. Mahdi

    2010-05-01

    issues can be considered as indicated. So pay attention to the importance of knowledge management in universities as a knowledge based organizations, the necessity of research in this field is felt more than before. In addition to the field of knowledge management models is presented in the assessment challenges, needs and characteristics of a local model for knowledge management establishment in its reach. Research objectives were:1. overall ssessment of the case, Ferdowsi University of Mashhad in terms of being a knowledge based and nowledge management assets 2. Study of knowledge management in universities and the case Ferdowsi University 3. To specify the main challenges of knowledge management in universities and the case Ferdowsi University 4. Identify factors influencing the proposed model of knowledge management in universities 5. Suggest a suitable model of knowledge management in universities 6. Requirements determination, elements and components required for deployment of knowledge management system based on the model presented. Research findings were In this section, using descriptive statistics and inferential questions back and study research examined the assumptions feeds. Keyword: knowledge management, suitable model, Mashhad

  2. LANL* V1.0: a radiation belt drift shell model suitable for real-time and reanalysis applications

    Directory of Open Access Journals (Sweden)

    G. D. Reeves

    2009-02-01

    Full Text Available We describe here a new method for calculating the magnetic drift invariant, L*, that is used for modeling radiation belt dynamics and for other space weather applications. L* (pronounced L-star is directly proportional to the integral of the magnetic flux contained within the surface defined by a charged particle moving in the Earth's geomagnetic field. Under adiabatic changes to the geomagnetic field L* is a conserved quantity, while under quasi-adiabatic fluctuations diffusion (with respect to a particle's L* is the primary term in equations of particle dynamics. In particular the equations of motion for the very energetic particles that populate the Earth's radiation belts are most commonly expressed by diffusion in three dimensions: L*, energy (or momentum, and pitch angle (the dot product of velocity and the magnetic field vector. Expressing dynamics in these coordinates reduces the dimensionality of the problem by referencing the particle distribution functions to values at the magnetic equatorial point of a magnetic "drift shell" (or L-shell irrespective of local time (or longitude. While the use of L* aids in simplifying the equations of motion, practical applications such as space weather forecasting using realistic geomagnetic fields require sophisticated magnetic field models that, in turn, require computationally intensive numerical integration. Typically a single L* calculation can require on the order of 105 calls to a magnetic field model and each point in the simulation domain and each calculated pitch angle has a different value of L*. We describe here the development and validation of a neural network surrogate model for calculating L* in sophisticated geomagnetic field models with a high degree of fidelity at computational speeds that are millions of times faster than direct numerical field line mapping and integration. This new surrogate model has applications to real-time radiation belt forecasting, analysis of data sets

  3. Predicting future thermal habitat suitability of competing native and invasive fish species: from metabolic scope to oceanographic modelling.

    Science.gov (United States)

    Marras, Stefano; Cucco, Andrea; Antognarelli, Fabio; Azzurro, Ernesto; Milazzo, Marco; Bariche, Michel; Butenschön, Momme; Kay, Susan; Di Bitetto, Massimiliano; Quattrocchi, Giovanni; Sinerchia, Matteo; Domenici, Paolo

    2015-01-01

    Global increase in sea temperatures has been suggested to facilitate the incoming and spread of tropical invaders. The increasing success of these species may be related to their higher physiological performance compared with indigenous ones. Here, we determined the effect of temperature on the aerobic metabolic scope (MS) of two herbivorous fish species that occupy a similar ecological niche in the Mediterranean Sea: the native salema (Sarpa salpa) and the invasive marbled spinefoot (Siganus rivulatus). Our results demonstrate a large difference in the optimal temperature for aerobic scope between the salema (21.8°C) and the marbled spinefoot (29.1°C), highlighting the importance of temperature in determining the energy availability and, potentially, the distribution patterns of the two species. A modelling approach based on a present-day projection and a future scenario for oceanographic conditions was used to make predictions about the thermal habitat suitability (THS, an index based on the relationship between MS and temperature) of the two species, both at the basin level (the whole Mediterranean Sea) and at the regional level (the Sicilian Channel, a key area for the inflow of invasive species from the Eastern to the Western Mediterranean Sea). For the present-day projection, our basin-scale model shows higher THS of the marbled spinefoot than the salema in the Eastern compared with the Western Mediterranean Sea. However, by 2050, the THS of the marbled spinefoot is predicted to increase throughout the whole Mediterranean Sea, causing its westward expansion. Nevertheless, the regional-scale model suggests that the future thermal conditions of Western Sicily will remain relatively unsuitable for the invasive species and could act as a barrier for its spread westward. We suggest that metabolic scope can be used as a tool to evaluate the potential invasiveness of alien species and the resilience to global warming of native species.

  4. Determination of the Most Suitable Technology Transfer Strategy for Wind Turbines Using an Integrated AHP-TOPSIS Decision Model

    Directory of Open Access Journals (Sweden)

    A. Dinmohammadi

    2017-05-01

    Full Text Available The high-speed development of industrial products and goods in the world has caused “technology” to be considered as a crucial competitive advantage for most large organizations. In recent years, developing countries have considerably tended to promote their technological and innovative capabilities through importing high-tech equipment owned and operated by developed countries. There are currently a variety of solutions to transfer a particular technology from a developed country. The selection of the most profitable technology transfer strategy is a very complex decision-making problem for technology importers as it involves different technical, environmental, social, and economic aspects. In this study, a hybrid multiple-criteria decision making (MCDM model based on the analytic hierarchy process (AHP and the technique for order of preference by similarity to ideal solution (TOPSIS is proposed to evaluate and prioritise various technology transfer strategies for wind turbine systems. For this purpose, a number of criteria and sub-criteria are defined from the viewpoint of wind energy investors, wind turbine manufacturers, and wind farm operators. The relative importance of criteria and sub-criteria with respect to the ultimate goal are computed using the eigenvalue method and then, the technology transfer alternatives are ranked based on their relative closeness to the ideal solution. The model is finally applied to determine the most suitable wind turbine technology transfer strategy among four options of reverse engineering, technology skills training, turn-key contracts, and technology licensing for the renewable energy sector of Iran, and the results are compared with those obtained by classical decision-making models.

  5. Making fate and exposure models for freshwater ecotoxicity in life cycle assessment suitable for organic acids and bases.

    Science.gov (United States)

    van Zelm, Rosalie; Stam, Gea; Huijbregts, Mark A J; van de Meent, Dik

    2013-01-01

    Freshwater fate and exposure factors were determined for organic acids and bases, making use of the knowledge on electrical interaction of ionizing chemicals and their sorption to particles. The fate factor represents the residence time in the environment whereas exposure factors equal the dissolved fraction of a chemical. Multimedia fate, exposure, and effect model USES-LCA was updated to take into account the influence of ionization, based upon the acid dissociation constant (pK(a)) of a chemical, and the environmental pH. Freshwater fate (FF) and exposure (XF) factors were determined for 415 acids and 496 bases emitted to freshwater, air, and soil. The relevance of taking account of the degree of ionization of chemicals was tested by determining the ratio (R) of the new vs. fate and exposure factors determined with USES-LCA suitable for neutral chemicals only. Our results show that the majority of freshwater fate and exposure factors of chemicals that are largely ionized in the environment are larger with the ionics model compared to the factors determined with the neutrals model version. R(FF) ranged from 2.4×10(-1) to 1.6×10(1) for freshwater emissions, from 1.2×10(-2) to 2.0×10(4) for soil emissions and from 5.8×10(-2) to 6.0×10(3) for air emissions, and R(XF) from 5.3×10(-1) to 2.2×10(1). Prediction of changed solid-water partitioning, implying a change in runoff and in removal via sedimentation, and prediction of negligible air-water partition coefficient, leading to negligible volatilization were the main contributors to the changes in freshwater fate factors. Copyright © 2012 Elsevier Ltd. All rights reserved.

  6. Silvicolous on a small scale: possibilities and limitations of habitat suitability models for small, elusive mammals in conservation management and landscape planning.

    Directory of Open Access Journals (Sweden)

    Nina I Becker

    Full Text Available Species distribution and endangerment can be assessed by habitat-suitability modelling. This study addresses methodical aspects of habitat suitability modelling and includes an application example in actual species conservation and landscape planning. Models using species presence-absence data are preferable to presence-only models. In contrast to species presence data, absences are rarely recorded. Therefore, many studies generate pseudo-absence data for modelling. However, in this study model quality was higher with null samples collected in the field. Next to species data the choice of landscape data is crucial for suitability modelling. Landscape data with high resolution and ecological relevance for the study species improve model reliability and quality for small elusive mammals like Muscardinus avellanarius. For large scale assessment of species distribution, models with low-detailed data are sufficient. For regional site-specific conservation issues like a conflict-free site for new wind turbines, high-detailed regional models are needed. Even though the overlap with optimally suitable habitat for M. avellanarius was low, the installation of wind plants can pose a threat due to habitat loss and fragmentation. To conclude, modellers should clearly state the purpose of their models and choose the according level of detail for species and environmental data.

  7. Silvicolous on a small scale: possibilities and limitations of habitat suitability models for small, elusive mammals in conservation management and landscape planning.

    Science.gov (United States)

    Becker, Nina I; Encarnação, Jorge A

    2015-01-01

    Species distribution and endangerment can be assessed by habitat-suitability modelling. This study addresses methodical aspects of habitat suitability modelling and includes an application example in actual species conservation and landscape planning. Models using species presence-absence data are preferable to presence-only models. In contrast to species presence data, absences are rarely recorded. Therefore, many studies generate pseudo-absence data for modelling. However, in this study model quality was higher with null samples collected in the field. Next to species data the choice of landscape data is crucial for suitability modelling. Landscape data with high resolution and ecological relevance for the study species improve model reliability and quality for small elusive mammals like Muscardinus avellanarius. For large scale assessment of species distribution, models with low-detailed data are sufficient. For regional site-specific conservation issues like a conflict-free site for new wind turbines, high-detailed regional models are needed. Even though the overlap with optimally suitable habitat for M. avellanarius was low, the installation of wind plants can pose a threat due to habitat loss and fragmentation. To conclude, modellers should clearly state the purpose of their models and choose the according level of detail for species and environmental data.

  8. Deep-sea benthic megafaunal habitat suitability modelling: A global-scale maximum entropy model for xenophyophores

    OpenAIRE

    Ashford, Oliver S; Davies, Andrew J.; Jones, Daniel O. B.

    2014-01-01

    Xenophyophores are a group of exclusively deep-sea agglutinating rhizarian protozoans, at least some of which are foraminifera. They are an important constituent of the deep-sea megafauna that are sometimes found in sufficient abundance to act as a significant source of habitat structure for meiofaunal and macrofaunal organisms. This study utilised maximum entropy modelling (Maxent) and a high-resolution environmental database to explore the environmental factors controlling the presence of X...

  9. A nesting site suitability model for rock partridge (Alectoris graeca in the Apennine Mountains using logistic regression

    Directory of Open Access Journals (Sweden)

    Lorenzo Boccia

    2010-01-01

    Full Text Available The rock partridge has undergone a decline throughout its entire distribution area, including the population of the central Italian Apennine Mountains. Areas of suitable habitat for this species have been reduced due to landscape fragmentation and the dynamics of domestic animal and wildlife management. The present study was conducted in the Province of Rieti, Lazio Region. Geograph- ical and land use predictors were evaluated in a GIS environment to identify the most relevant factors influencing the presence of rock partridge during the nesting period. Logistic regression was then imple- mented to create a model, characterised by a good level of adequacy, for predicting rock partridge nesting site habitat characteristics. Correct predictions of presence and absence were made in 65.2% and 98.6% of cases, respectively. The ROC value was 0.771, which is statistically significant (P<0.001. The results show that, on a local scale, slope (log, distance from forests, and the presence of bare rocks were statisti- cally significant factors. On a landscape scale, the percentage of forests, the presence of sparse vegetation (over 60%, and a negative Mean Shape Index (MSI were found to be statistically significant.

  10. Evaluating the Suitability of Using Rat Models for Preclinical Efficacy and Side Effects with Inhaled Corticosteroids Nanosuspension Formulations

    Directory of Open Access Journals (Sweden)

    Chiang Po-Chang

    2010-01-01

    rat LPS model using IT administration of nanosuspensions of ICS is a useful tool to demonstrate pulmonary-targeted efficacy and to differentiate the side effects. However, it is only suitable at sub-maximum efficacious levels.

  11. Evaluating the Suitability of Using Rat Models for Preclinical Efficacy and Side Effects with Inhaled Corticosteroids Nanosuspension Formulations

    Science.gov (United States)

    Chiang, Po-Chang; Hu, Yiding; Blom, Jason D.; Thompson, David C.

    2010-06-01

    Inhaled corticosteroids (ICS) are often prescribed as first-line therapy for patients with asthma Despite their efficacy and improved safety profile compared with oral corticosteroids, the potential for systemic side effects continues to cause concern. In order to reduce the potential for systemic side effects, the pharmaceutical industry has begun efforts to generate new drugs with pulmonary-targeted topical efficacy. One of the major challenges of this approach is to differentiate both efficacy and side effects (pulmonary vs. systemic) in a preclinical animal model. In this study, fluticasone and ciclesonide were used as tool compounds to explore the possibility of demonstrating both efficacy and side effects in a rat model using pulmonary delivery via intratracheal (IT) instillation with nanosuspension formulations. The inhibition of neutrophil infiltration into bronchoalveolar lavage fluid (BALF) and cytokine (TNFα) production were utilized to assess pulmonary efficacy, while adrenal and thymus involution as well as plasma corticosterone suppression was measured to assess systemic side effects. Based on neutrophil infiltration and cytokine production data, the ED50s for ciclesonide and fluticasone were calculated to be 0.1 and 0.03 mg, respectively. At the ED50, the average adrenal involution was 7.6 ± 5.3% for ciclesonide versus 16.6 ± 5.1% for fluticasone, while the average thymus involution was 41.0 ± 4.3% for ciclesonide versus 59.5 ± 5.8% for fluticasone. However, the differentiation became less significant when the dose was pushed to the EDmax (0.3 mg for ciclesonide, 0.1 mg for fluticasone). Overall, the efficacy and side effect profiles of the two compounds exhibited differentiation at low to mid doses (0.03-0.1 mg ciclesonide, 0.01-0.03 mg fluticasone), while this differentiation diminished at the maximum efficacious dose (0.3 mg ciclesonide, 0.1 mg fluticasone), likely due to overdosing in this model. We conclude that the rat LPS model using IT

  12. LANL* V1.0: a radiation belt drift shell model suitable for real-time and reanalysis applications

    Directory of Open Access Journals (Sweden)

    J. Koller

    2009-07-01

    Full Text Available We describe here a new method for calculating the magnetic drift invariant, L*, that is used for modeling radiation belt dynamics and for other space weather applications. L* (pronounced L-star is directly proportional to the integral of the magnetic flux contained within the surface defined by a charged particle moving in the Earth's geomagnetic field. Under adiabatic changes to the geomagnetic field L* is a conserved quantity, while under quasi-adiabatic fluctuations diffusion (with respect to a particle's L* is the primary term in equations of particle dynamics. In particular the equations of motion for the very energetic particles that populate the Earth's radiation belts are most commonly expressed by diffusion in three dimensions: L*, energy (or momentum, and pitch angle (the dot product of velocity and the magnetic field vector. Expressing dynamics in these coordinates reduces the dimensionality of the problem by referencing the particle distribution functions to values at the magnetic equatorial point of a magnetic "drift shell" (or L-shell irrespective of local time (or longitude. While the use of L* aids in simplifying the equations of motion, practical applications such as space weather forecasting using realistic geomagnetic fields require sophisticated magnetic field models that, in turn, require computationally intensive numerical integration. Typically a single L* calculation can require on the order of 105 calls to a magnetic field model and each point in the simulation domain and each calculated pitch angle has a different value of L*. We describe here the development and validation of a neural network surrogate model for calculating L* in sophisticated geomagnetic field models with a high degree of fidelity at computational speeds that are millions of times faster than direct numerical field line mapping and integration. This new surrogate model has

  13. Topological Expression Model of Satellite Gear Mechanism

    Institute of Scientific and Technical Information of China (English)

    Yang Ping

    2005-01-01

    By investigation of the topological characteristics of the kinematic structure of Satellite Gear Mechanism (SGM) with graph theory, the graph model of SGM is analyzed, and a topological expression model between input and output of SGM is established based on systematic design point. Meanwhile, the mathematical expression for SGM is deduced by integrating matrix theory and graph theory; thus, the topological characteristics of the kinematic structure of SGM can be converted into a matrix model, and the topological design problem of SGM into a matrix operation problem. In addition, a brief discussion about the measures for identification of isomorphism of the graph mode is made.

  14. Pollen-based quantitative reconstructions of Holocene regional vegetation cover (plant-functional types and land-cover types) in Europe suitable for climate modelling.

    Science.gov (United States)

    Trondman, A-K; Gaillard, M-J; Mazier, F; Sugita, S; Fyfe, R; Nielsen, A B; Twiddle, C; Barratt, P; Birks, H J B; Bjune, A E; Björkman, L; Broström, A; Caseldine, C; David, R; Dodson, J; Dörfler, W; Fischer, E; van Geel, B; Giesecke, T; Hultberg, T; Kalnina, L; Kangur, M; van der Knaap, P; Koff, T; Kuneš, P; Lagerås, P; Latałowa, M; Lechterbeck, J; Leroyer, C; Leydet, M; Lindbladh, M; Marquer, L; Mitchell, F J G; Odgaard, B V; Peglar, S M; Persson, T; Poska, A; Rösch, M; Seppä, H; Veski, S; Wick, L

    2015-02-01

    We present quantitative reconstructions of regional vegetation cover in north-western Europe, western Europe north of the Alps, and eastern Europe for five time windows in the Holocene [around 6k, 3k, 0.5k, 0.2k, and 0.05k calendar years before present (bp)] at a 1° × 1° spatial scale with the objective of producing vegetation descriptions suitable for climate modelling. The REVEALS model was applied on 636 pollen records from lakes and bogs to reconstruct the past cover of 25 plant taxa grouped into 10 plant-functional types and three land-cover types [evergreen trees, summer-green (deciduous) trees, and open land]. The model corrects for some of the biases in pollen percentages by using pollen productivity estimates and fall speeds of pollen, and by applying simple but robust models of pollen dispersal and deposition. The emerging patterns of tree migration and deforestation between 6k bp and modern time in the REVEALS estimates agree with our general understanding of the vegetation history of Europe based on pollen percentages. However, the degree of anthropogenic deforestation (i.e. cover of cultivated and grazing land) at 3k, 0.5k, and 0.2k bp is significantly higher than deduced from pollen percentages. This is also the case at 6k in some parts of Europe, in particular Britain and Ireland. Furthermore, the relationship between summer-green and evergreen trees, and between individual tree taxa, differs significantly when expressed as pollen percentages or as REVEALS estimates of tree cover. For instance, when Pinus is dominant over Picea as pollen percentages, Picea is dominant over Pinus as REVEALS estimates. These differences play a major role in the reconstruction of European landscapes and for the study of land cover-climate interactions, biodiversity and human resources. © 2014 The Authors Global Change Biology Published by John Wiley & Sons Ltd.

  15. Regionalization of Habitat Suitability of Masson’s Pine based on geographic information system and Fuzzy Matter-Element Model

    Science.gov (United States)

    Zhou, Xiuteng; Zhao, Manxi; Zhou, Liangyun; Yang, Guang; Huang, Luqi; Yan, Cuiqi; Huang, Quanshu; Ye, Liang; Zhang, Xiaobo; Guo, Lanpin; Ke, Xiao; Guo, Jiao

    2016-01-01

    Pine needles have been widely used in the development of anti-hypertensive and anti-hyperlipidemic agents and health food. However, the widespread distribution of this tree poses great obstacles to the quality control and efficacy evaluation. To facilitate the effective and rational exploitation of Masson’s pine (Pinus massoniana Lamb), as well as ensure effective development of Masson’s pine needles as a medicinal agent, we investigated the spatial distribution of habitat suitability and evaluated the optimal ranges of ecological factors of P. massoniana with 280 samples collected from 12 provinces in China through the evaluation of four constituents known to be effective medicinally. The results of habitat suitability evaluation were also verified by Root Mean Square Error (RMSE). Finally, five ecological factors were chosen in the establishment of a habitat suitability evaluation system. The most suitable areas for P. massoniana growth were mainly concentrated in the middle and lower reaches of the Yangtze River basin, such as Sichuan, Guizhou, and Jiangxi provinces, while the best quality needles were from Guizhou, Sichuan, and the junction area of Chongqing, Hunan, and Hubei provinces. This information revealed that suitable areas for effective constituent accumulation of Masson’s pine needles accounted for only 7.41% of its distribution area. PMID:27694967

  16. Regionalization of Habitat Suitability of Masson’s Pine based on geographic information system and Fuzzy Matter-Element Model

    Science.gov (United States)

    Zhou, Xiuteng; Zhao, Manxi; Zhou, Liangyun; Yang, Guang; Huang, Luqi; Yan, Cuiqi; Huang, Quanshu; Ye, Liang; Zhang, Xiaobo; Guo, Lanpin; Ke, Xiao; Guo, Jiao

    2016-10-01

    Pine needles have been widely used in the development of anti-hypertensive and anti-hyperlipidemic agents and health food. However, the widespread distribution of this tree poses great obstacles to the quality control and efficacy evaluation. To facilitate the effective and rational exploitation of Masson’s pine (Pinus massoniana Lamb), as well as ensure effective development of Masson’s pine needles as a medicinal agent, we investigated the spatial distribution of habitat suitability and evaluated the optimal ranges of ecological factors of P. massoniana with 280 samples collected from 12 provinces in China through the evaluation of four constituents known to be effective medicinally. The results of habitat suitability evaluation were also verified by Root Mean Square Error (RMSE). Finally, five ecological factors were chosen in the establishment of a habitat suitability evaluation system. The most suitable areas for P. massoniana growth were mainly concentrated in the middle and lower reaches of the Yangtze River basin, such as Sichuan, Guizhou, and Jiangxi provinces, while the best quality needles were from Guizhou, Sichuan, and the junction area of Chongqing, Hunan, and Hubei provinces. This information revealed that suitable areas for effective constituent accumulation of Masson’s pine needles accounted for only 7.41% of its distribution area.

  17. Spatial transferability of habitat suitability models of Nephrops norvegicus among fished areas in the Northeast Atlantic: sufficiently stable for marine resource conservation?

    Directory of Open Access Journals (Sweden)

    Valentina Lauria

    Full Text Available Knowledge of the spatial distribution and habitat associations of species in relation to the environment is essential for their management and conservation. Habitat suitability models are useful in quantifying species-environment relationships and predicting species distribution patterns. Little is known, however, about the stability and performance of habitat suitability models when projected into new areas (spatial transferability and how this can inform resource management. The aims of this study were to model habitat suitability of Norway lobster (Nephrops norvegicus in five fished areas of the Northeast Atlantic (Aran ground, Irish Sea, Celtic Sea, Scotland Inshore and Fladen ground, and to test for spatial transferability of habitat models among multiple regions. Nephrops burrow density was modelled using generalised additive models (GAMs with predictors selected from four environmental variables (depth, slope, sediment and rugosity. Models were evaluated and tested for spatial transferability among areas. The optimum models (lowest AICc for different areas always included depth and sediment as predictors. Burrow densities were generally greater at depth and in finer sediments, but relationships for individual areas were sometimes more complex. Aside from an inclusion of depth and sediment, the optimum models differed between fished areas. When it came to tests of spatial transferability, however, most of the models were able to predict Nephrops density in other areas. Furthermore, transferability was not dependent on use of the optimum models since competing models were also able to achieve a similar level of transferability to new areas. A degree of decoupling between model 'fitting' performance and spatial transferability supports the use of simpler models when extrapolating habitat suitability maps to different areas. Differences in the form and performance of models from different areas may supply further information on the processes

  18. Identification of Suitable Reference Genes for mRNA Studies in Bone Marrow in a Mouse Model of Hematopoietic Stem Cell Transplantation.

    Science.gov (United States)

    Li, H; Chen, C; Yao, H; Li, X; Yang, N; Qiao, J; Xu, K; Zeng, L

    2016-10-01

    Bone marrow micro-environment changes during hematopoietic stem cell transplantation (HSCT) with subsequent alteration of genes expression. Quantitative polymerase chain reaction (q-PCR) is a reliable and reproducible technique for the analysis of gene expression. To obtain more accurate results, it is essential to find a reference during HSCT. However, which gene is suitable during HSCT remains unclear. This study aimed to identify suitable reference genes for mRNA studies in bone marrow after HSCT. C57BL/6 mice were treated with either total body irradiation (group T) or busulfan/cyclophosphamide (BU/CY) (group B) followed by infusion of bone marrow cells. Normal mice without treatments were served as a control. All samples (group T + group B + control) were defined as group G. On days 7, 14, and 21 after transplantation, transcription levels of 7 candidate genes, ACTB, B2M, GAPDH, HMBS, HPRT, SDHA, and YWHAZ, in bone marrow cells were measured by use of real-time quantitative PCR. The expression stability of these 7 candidate reference genes were analyzed by 2 statistical software programs, GeNorm and NormFinder. Our results showed that ACTB displayed the highest expression in group G, with lowest expression of PSDHA in group T and HPRT in groups B and G. Analysis of expression stability by use of GeNorm or NormFinder demonstrated that expression of B2M in bone marrow were much more stable during HSCT, compared with other candidate genes including commonly used reference genes GAPDH and ACTB. ACTB could be used as a suitable reference gene for mRNA studies in bone marrow after HSCT. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Linking habitat suitability and seed dispersal models in order to analyse the effectiveness of hydrological fen restoration strategies

    NARCIS (Netherlands)

    Loon, A.H. van; Soomers, H.; Schot, P.P.; Bierkens, M.F.P.; Griffioen, J.; Wassen, M.J.

    2011-01-01

    The effectiveness of measures targeted at the restoration of populations of endangered species in anthropogenically dominated regions is often limited by a combination of insufficient restoration of habitat quality and dispersal failure. Therefore, the joint prediction of suitable habitat and seed d

  20. Formulating a poorly water soluble drug into an oral solution suitable for paediatric patients; lorazepam as a model drug

    NARCIS (Netherlands)

    A.C. Van Der Vossen (Anna C.); I. Van Der Velde (Iris); O. Smeets (Oscar); Postma, D.J.; Eckhardt, M.; A. Vermes (Andras); B.C.P. Koch (Birgit C. P.); A.G. Vulto (Arnold); L.M. Hanff (Lidwien)

    2017-01-01

    textabstractIntroduction Many drugs are unavailable in suitable oral paediatric dosage forms, and pharmacists often have to compound drugs to provide paediatric patients with an acceptable formulation in the right dose. Liquid formulations offer the advantage of dosing flexibility and ease of admini

  1. Habitat Suitability Modeling of Bornean Orangutan (Pongo pygmaeus pygmaeus in Betung Kerihun National Park, Danau Sentarum and Corridor, West Kalimantan

    Directory of Open Access Journals (Sweden)

    Hari Prayogo

    2014-09-01

    Full Text Available Conservation areas such as national parks became the last safe area for biodiversity in Indonesia, especially for orangutan, because they have permanent status, and other forest areas may change at any time. Currently, there have been tremendous numbers of land use changes in orangutan habitats such as the development of roads, large scale plantations, settlements, farming as well as logging.  However, the available national parks still offer secure places for orangutans. This research was conducted to study the impact of spatial land use policy on the habitat distribution of orangutans. A remote sensing technology was used to study the habitat distribution and suitability of orangutan in Betung Kerihun National Park (BKNP, Danau Sentarum National Park (DSNP and a corridor which connects these 2 parks. Seven parameters have been observed to characterize the habitat of orangutans. Habitat suitability levels of three research sites i.e. BKNP, corridor, and DSNP were 53.72%, 42.94%, and 3.34% which is considered as high, moderate, and low level of habitat suitability, respectively. These results were obtained with 93.63% of validation.Keywords: orangutan, habitat suitability, remote sensing technology, validation

  2. Bayesian modeling of differential gene expression.

    Science.gov (United States)

    Lewin, Alex; Richardson, Sylvia; Marshall, Clare; Glazier, Anne; Aitman, Tim

    2006-03-01

    We present a Bayesian hierarchical model for detecting differentially expressing genes that includes simultaneous estimation of array effects, and show how to use the output for choosing lists of genes for further investigation. We give empirical evidence that expression-level dependent array effects are needed, and explore different nonlinear functions as part of our model-based approach to normalization. The model includes gene-specific variances but imposes some necessary shrinkage through a hierarchical structure. Model criticism via posterior predictive checks is discussed. Modeling the array effects (normalization) simultaneously with differential expression gives fewer false positive results. To choose a list of genes, we propose to combine various criteria (for instance, fold change and overall expression) into a single indicator variable for each gene. The posterior distribution of these variables is used to pick the list of genes, thereby taking into account uncertainty in parameter estimates. In an application to mouse knockout data, Gene Ontology annotations over- and underrepresented among the genes on the chosen list are consistent with biological expectations.

  3. Chemically synthesized glycosides of hydroxylated flavylium ions as suitable models of anthocyanins: binding to iron ions and human serum albumin, antioxidant activity in model gastric conditions.

    Science.gov (United States)

    Al Bittar, Sheiraz; Mora, Nathalie; Loonis, Michèle; Dangles, Olivier

    2014-12-11

    Polyhydroxylated flavylium ions, such as 3',4',7-trihydroxyflavylium chloride (P1) and its more water-soluble 7-O-β-d-glucopyranoside (P2), are readily accessible by chemical synthesis and suitable models of natural anthocyanins in terms of color and species distribution in aqueous solution. Owing to their catechol B-ring, they rapidly bind FeIII, weakly interact with FeII and promote its autoxidation to FeIII. Both pigments inhibit heme-induced lipid peroxidation in mildly acidic conditions (a model of postprandial oxidative stress in the stomach), the colorless (chalcone) forms being more potent than the colored forms. Finally, P1 and P2 are moderate ligands of human serum albumin (HSA), their likely carrier in the blood circulation, with chalcones having a higher affinity for HSA than the corresponding colored forms.

  4. Chemically Synthesized Glycosides of Hydroxylated Flavylium Ions as Suitable Models of Anthocyanins: Binding to Iron Ions and Human Serum Albumin, Antioxidant Activity in Model Gastric Conditions

    Directory of Open Access Journals (Sweden)

    Sheiraz Al Bittar

    2014-12-01

    Full Text Available Polyhydroxylated flavylium ions, such as 3',4',7-trihydroxyflavylium chloride (P1 and its more water-soluble 7-O-β-d-glucopyranoside (P2, are readily accessible by chemical synthesis and suitable models of natural anthocyanins in terms of color and species distribution in aqueous solution. Owing to their catechol B-ring, they rapidly bind FeIII, weakly interact with FeII and promote its autoxidation to FeIII. Both pigments inhibit heme-induced lipid peroxidation in mildly acidic conditions (a model of postprandial oxidative stress in the stomach, the colorless (chalcone forms being more potent than the colored forms. Finally, P1 and P2 are moderate ligands of human serum albumin (HSA, their likely carrier in the blood circulation, with chalcones having a higher affinity for HSA than the corresponding colored forms.

  5. Intrathecal long-term gene expression by self-complementary adeno-associated virus type 1 suitable for chronic pain studies in rats

    Directory of Open Access Journals (Sweden)

    Janssen William GM

    2006-01-01

    Full Text Available Abstract Background Intrathecal (IT gene transfer is an attractive approach for targeting spinal mechanisms of nociception but the duration of gene expression achieved by reported methods is short (up to two weeks impairing their utility in the chronic pain setting. The overall goal of this study was to develop IT gene transfer yielding true long-term transgene expression defined as ≥ 3 mo following a single vector administration. We defined "IT" administration as atraumatic injection into the lumbar cerebrospinal fluid (CSF modeling a lumbar puncture. Our studies focused on recombinant adeno-associated virus (rAAV, one of the most promising vector types for clinical use. Results Conventional single stranded rAAV2 vectors performed poorly after IT delivery in rats. Pseudotyping of rAAV with capsids of serotypes 1, 3, and 5 was tested alone or in combination with a modification of the inverted terminal repeat. The former alters vector tropism and the latter allows packaging of self-complementary rAAV (sc-rAAV vectors. Combining both types of modification led to the identification of sc-rAAV2/l as a vector that performed superiorly in the IT space. IT delivery of 3 × 10e9 sc-rAAV2/l particles per animal led to stable expression of enhanced green fluorescent protein (EGFP for ≥ 3 mo detectable by Western blotting, quantitative PCR, and in a blinded study by confocal microscopy. Expression was strongest in the cauda equina and the lower sections of the spinal cord and only minimal in the forebrain. Microscopic examination of the SC fixed in situ with intact nerve roots and meninges revealed strong EGFP fluorescence in the nerve roots. Conclusion sc-rAAVl mediates stable IT transgene expression for ≥ 3 mo. Our findings support the underlying hypothesis that IT target cells for gene transfer lack the machinery for efficient conversion of the single-stranded rAAV genome into double-stranded DNA and favor uptake of serotype 1 vectors over 2

  6. State density formalism of the Iwamoto-Harada model: A suitable tool to treat cluster emission from heavy-ion collisions with account for spin variables

    Directory of Open Access Journals (Sweden)

    Běták Emil

    2017-01-01

    Full Text Available We study the possibility to include the cluster emission into the statistical pre-equilibrium (exciton model suitable also for heavy ion collisions. The direct motivation of this paper is a possibility of producing superdeformed nuclei, which are easier to be detected in heavy-ion reactions than in those induced by light projectiles (nucleons, deuterons, α-particles.

  7. Modelling the spatial and seasonal distribution of suitable habitats of schistosomiasis intermediate host snails using Maxent in Ndumo area, KwaZulu-Natal Province, South Africa.

    Science.gov (United States)

    Manyangadze, Tawanda; Chimbari, Moses John; Gebreslasie, Michael; Ceccato, Pietro; Mukaratirwa, Samson

    2016-11-04

    Schistosomiasis is a snail-borne disease endemic in sub-Saharan Africa transmitted by freshwater snails. The distribution of schistosomiasis coincides with that of the intermediate hosts as determined by climatic and environmental factors. The aim of this paper was to model the spatial and seasonal distribution of suitable habitats for Bulinus globosus and Biomphalaria pfeifferi snail species (intermediate hosts for Schistosoma haematobium and Schistosoma mansoni, respectively) in the Ndumo area of uMkhanyakude district, South Africa. Maximum Entropy (Maxent) modelling technique was used to predict the distribution of suitable habitats for B. globosus and B. pfeifferi using presence-only datasets with ≥ 5 and ≤ 12 sampling points in different seasons. Precipitation, maximum and minimum temperatures, Normalised Difference Vegetation Index (NDVI), Normalised Difference Water Index (NDWI), pH, slope and Enhanced Vegetation Index (EVI) were the background variables in the Maxent models. The models were validated using the area under the curve (AUC) and omission rate. The predicted suitable habitats for intermediate snail hosts varied with seasons. The AUC for models in all seasons ranged from 0.71 to 1 and the prediction rates were between 0.8 and 0.9. Although B. globosus was found at more localities in the Ndumo area, there was also evidence of cohabiting with B. pfiefferi at some of the locations. NDWI had significant contribution to the models in all seasons. The Maxent model is robust in snail habitat suitability modelling even with small dataset of presence-only sampling sites. Application of the methods and design used in this study may be useful in developing a control and management programme for schistosomiasis in the Ndumo area.

  8. Identifying optimal sites for natural recovery and restoration of impacted biogenic habitats in a special area of conservation using hydrodynamic and habitat suitability modelling

    Science.gov (United States)

    Elsäßer, Björn; Fariñas-Franco, Jose M.; Wilson, Conor David; Kregting, Louise; Roberts, Dai

    2013-03-01

    Selection of sites for successful restoration of impacted shellfish populations depends on understanding the dispersion capability and habitat requirements of the species involved. In Strangford Lough, Northern Ireland, the horse mussel (Modiolus modiolus) biogenic reefs cover only a fraction of their historical range with the remaining reefs badly damaged and requiring restoration. Previous experimental trials suggest that translocation of horse mussels accelerates reef recovery and has therefore been proposed as a suitable restoration technique. We used a series of coupled hydrodynamic and particle dispersal models to assess larval dispersion from remnant and translocated populations to identify suitable areas for adult live M. modiolus translocation in Strangford Lough, Northern Ireland. A maximum entropy model (MAXENT) was used to identify if dispersing larvae could reach habitat suitable for adult M. modiolus. From these we predicted if translocated mussels will reseed themselves or be able to act as larval sources for nearby reefs. The dispersal models showed that the remnant M. modiolus populations are largely self-recruiting with little connectivity between them. The majority of larvae settled near the sources and movement was largely dependent on the tides and not influenced by wind or waves. Higher reef elevation resulted in larvae being able to disperse further away from the release point. However, larval numbers away from the source population are likely to be too low for successful recruitment. There was also little connectivity between the Irish Sea and Strangford Lough as any larvae entering the Lough remained predominantly in the Strangford Narrows. The areas covered by these self-seeding populations are suitable for M. modiolus translocation according to the MAXENT model. As a result of this work and in conjunction with other field work we propose a combination of total protection of all remaining larval sources and small scale translocations onto

  9. Modeling and design considerations of a photovoltaic energy source feeding a synchronous reluctance motor suitable for pumping systems

    Directory of Open Access Journals (Sweden)

    M. Nabil

    2012-12-01

    Full Text Available This paper presents the performance analysis of a photovoltaic (PV energy source driving a synchronous reluctance (SyncRel motor. The design considerations of the PV array, suitable for driving a centrifugal pump, are studied. Three design approaches are proposed at an average insolation of 0.5 kW/m2. These approaches depend upon determining the system operating point firstly and then maintaining this point on the PV generator characteristics. The first approach takes motor starting current into account as an additional design criterion. The second one is based on achieving the maximum power at the system operating point. The third approach considers maintaining voltage regulation of the PV generator at a pre-specified suitable value. A sample of the simulation results is introduced using the SyncRel motor measured parameters and the estimated parameters of the PV array. It has been found that the minimum number of cells can be achieved using the second approach.

  10. 75 FR 68222 - Suitability

    Science.gov (United States)

    2010-11-05

    ...; ] OFFICE OF PERSONNEL MANAGEMENT 5 CFR PART 731 RIN 3206-AL90 Suitability AGENCY: U.S. Office of Personnel... possible, of security and suitability standards. Public Trust Positions Public trust positions are those...) for a new public trust reinvestigation. Likewise, a suitability investigation based on a change...

  11. The Expressive Gaze Model: Using Gaze to Express Emotion

    Science.gov (United States)

    2010-07-01

    Thomas and O. Johnston, Disney Animation : The Illusion of Life, Abbeville Press, 1981. 2. B. Lance and S.C. Marsella, “Emotionally Expressive Head and...Thomas and Ollie Johnston Early animators realized that the eyes are an important aspect of the human face regarding the communication and expression...of emotion. They also found that properly animating believ- able, emotionally expressive gaze is extremely dif- ficult. If it’s done improperly

  12. State density formalism of the Iwamoto-Harada model: A suitable tool to treat cluster emission from heavy-ion collisions with account for spin variables

    Science.gov (United States)

    Běták, Emil; Cseh, József

    2017-09-01

    We study the possibility to include the cluster emission into the statistical pre-equilibrium (exciton) model suitable also for heavy ion collisions. The direct motivation of this paper is a possibility of producing superdeformed nuclei, which are easier to be detected in heavy-ion reactions than in those induced by light projectiles (nucleons, deuterons, α-particles). Note to the reader: the pdf file has been changed on September 22, 2017.

  13. A Spatially Explicit, Multi-Criteria Decision Support Model for Loggerhead Sea Turtle Nesting Habitat Suitability: A Remote Sensing-Based Approach

    Directory of Open Access Journals (Sweden)

    Lauren Dunkin

    2016-07-01

    Full Text Available Nesting habitat for the federally endangered loggerhead sea turtle (Caretta caretta were designated as critical in 2014 for beaches along the Atlantic Coast and Gulf of Mexico. Nesting suitability is routinely determined based on site specific information. Given the expansive geographic location of the designated critical C. caretta nesting habitat and the highly dynamic coastal environment, understanding nesting suitability on a regional scale is essential for monitoring the changing status of the coast as a result of hydrodynamic forces and maintenance efforts. The increasing spatial resolution and temporal frequency of remote sensing data offers the opportunity to study this dynamic environment on a regional scale. Remote sensing data were used as input into the spatially-explicit, multi-criteria decision support model to determine nesting habitat suitability. Results from the study indicate that the morphological parameters used as input into the model are well suited to provide a regional level approach with the results from the optimized model having sensitivity and detection prevalence values greater than 80% and the detection rate being greater than 70%. The approach can be implemented in various geographic locations to better communicate priorities and evaluate management strategies as a result of changes to the dynamic coastal environment.

  14. Suitability of Volatility Models for Forecasting Stock Market Returns: A Study on the Indian National Stock Exchange

    Directory of Open Access Journals (Sweden)

    Trilochan Tripathy

    2010-01-01

    Full Text Available Problem statement: Measuring volatility is an important issue for stock market traders. Also, volatility has been used as a proxy for riskiness associated with the asset. This study aims to compare the different volatility models based on how well they model the volatility of the India NSE. Approach: The study has made use of five models which are Historical/Rolling Window Moving Average Estimator, (ii Exponentially Weighted Moving Average (EWMA, (iii GARCH models, (iv Extreme Value Indicators (EVI and (v Volatility Index (VIX.The data includes the daily closing, high, low and open values of the NSE returns from 2005-2008. The model comparison was done on how well the models explained the ex-post volatility. Walds constants test was used to test which method best suited the requirements. Results: It was concluded that the AGARCH and VIX models proved to be the best methods. At the same time Extreme Value models fail to perform because of the low frequency data being used. Conclusions: As other research suggests these models perform best when they are applied to high frequency data such as the daily or intraday data. EVIs give the best forecasting performance followed by the GARCH and VIX models."

  15. LANL* V1.0: a radiation belt drift shell model suitable for real-time and reanalysis applications

    Energy Technology Data Exchange (ETDEWEB)

    Koller, Josep [Los Alamos National Laboratory; Reeves, Geoffrey D [Los Alamos National Laboratory; Friedel, Reiner H W [Los Alamos National Laboratory

    2008-01-01

    Space weather modeling, forecasts, and predictions, especially for the radiation belts in the inner magnetosphere, require detailed information about the Earth's magnetic field. Results depend on the magnetic field model and the L* (pron. L-star) values which are used to describe particle drift shells. Space wather models require integrating particle motions along trajectories that encircle the Earth. Numerical integration typically takes on the order of 10{sup 5} calls to a magnetic field model which makes the L* calculations very slow, in particular when using a dynamic and more accurate magnetic field model. Researchers currently tend to pick simplistic models over more accurate ones but also risking large inaccuracies and even wrong conclusions. For example, magnetic field models affect the calculation of electron phase space density by applying adiabatic invariants including the drift shell value L*. We present here a new method using a surrogate model based on a neural network technique to replace the time consuming L* calculations made with modern magnetic field models. The advantage of surrogate models (or meta-models) is that they can compute the same output in a fraction of the time while adding only a marginal error. Our drift shell model LANL* (Los Alamos National Lab L-star) is based on L* calculation using the TSK03 model. The surrogate model has currently been tested and validated only for geosynchronous regions but the method is generally applicable to any satellite orbit. Computations with the new model are several million times faster compared to the standard integration method while adding less than 1% error. Currently, real-time applications for forecasting and even nowcasting inner magnetospheric space weather is limited partly due to the long computing time of accurate L* values. Without them, real-time applications are limited in accuracy. Reanalysis application of past conditions in the inner magnetosphere are used to understand

  16. Assessment of the suitability of GOCE-based geoid models for the unification of the North American vertical datums

    Science.gov (United States)

    Amjadiparvar, Babak; Sideris, Michael

    2015-04-01

    Precise gravimetric geoid heights are required when the unification of vertical datums is performed using the Geodetic Boundary Value Problem (GBVP) approach. Five generations of Global Geopotential Models (GGMs) derived from Gravity field and steady-state Ocean Circulation Explorer (GOCE) observations have been computed and released so far (available via IAG's International Centre for Global Earth Models, ICGEM, http://icgem.gfz-potsdam.de/ICGEM/). The performance of many of these models with respect to geoid determination has been studied in order to select the best performing model to be used in height datum unification in North America. More specifically, Release-3, 4 and 5 of the GOCE-based global geopotential models have been evaluated using GNSS-levelling data as independent control values. Comparisons against EGM2008 show that each successive release improves upon the previous one, with Release-5 models showing an improvement over EGM2008 in Canada and CONUS between spherical harmonic degrees 100 and 210. In Alaska and Mexico, a considerable improvement over EGM2008 was brought by the Release-5 models when used up to spherical harmonic degrees of 250 and 280, respectively. The positive impact of the Release-5 models was also felt when a gravimetric geoid was computed using the GOCE-based GGMs together with gravity and topography data in Canada. This geoid model, with appropriately modified Stokes kernel between spherical harmonic degrees 190 and 260, performed better than the official Canadian gravimetric geoid model CGG2013, thus illustrating the advantages of using the latest release GOCE-based models for vertical datum unification in North America.

  17. Incorporation of Failure Into an Orthotropic Three-Dimensional Model with Tabulated Input Suitable for Use in Composite Impact Problems

    Science.gov (United States)

    Goldberg, Robert K.; Carney, Kelly S.; Dubois, Paul; Hoffarth, Canio; Khaled, Bilal; Shyamsunder, Loukham; Rajan, Subramaniam; Blankenhorn, Gunther

    2017-01-01

    The need for accurate material models to simulate the deformation, damage and failure of polymer matrix composites under impact conditions is becoming critical as these materials are gaining increased use in the aerospace and automotive communities. The aerospace community has identified several key capabilities which are currently lacking in the available material models in commercial transient dynamic finite element codes. To attempt to improve the predictive capability of composite impact simulations, a next generation material model is being developed for incorporation within the commercial transient dynamic finite element code LS-DYNA. The material model, which incorporates plasticity, damage and failure, utilizes experimentally based tabulated input to define the evolution of plasticity and damage and the initiation of failure as opposed to specifying discrete input parameters such as modulus and strength. The plasticity portion of the orthotropic, three-dimensional, macroscopic composite constitutive model is based on an extension of the Tsai-Wu composite failure model into a generalized yield function with a non-associative flow rule. For the damage model, a strain equivalent formulation is used to allow for the uncoupling of the deformation and damage analyses. In the damage model, a semi-coupled approach is employed where the overall damage in a particular coordinate direction is assumed to be a multiplicative combination of the damage in that direction resulting from the applied loads in various coordinate directions. For the failure model, a tabulated approach is utilized in which a stress or strain based invariant is defined as a function of the location of the current stress state in stress space to define the initiation of failure. Failure surfaces can be defined with any arbitrary shape, unlike traditional failure models where the mathematical functions used to define the failure surface impose a specific shape on the failure surface. In the current

  18. airGR: an R-package suitable for large sample hydrology presenting a suite of lumped hydrological models

    Science.gov (United States)

    Thirel, G.; Delaigue, O.; Coron, L.; Perrin, C.; Andreassian, V.

    2016-12-01

    Lumped hydrological models are useful and convenient tools for research, engineering and educational purposes. They propose catchment-scale representations of the precipitation-discharge relationship. Thanks to their limited data requirements, they can be easily implemented and run. With such models, it is possible to simulate a number of hydrological key processes over the catchment with limited structural and parametric complexity, typically evapotranspiration, runoff, underground losses, etc. The Hydrology Group at Irstea (Antony) has been developing a suite of rainfall-runoff models over the past 30 years with the main objectives of designing models as efficient as possible in terms of streamflow simulation, applicable to a wide range of catchments and having low data requirements. This resulted in a suite of models running at different time steps (from hourly to annual) applicable for various issues including water balance estimation, forecasting, simulation of impacts and scenario testing. Recently, Irstea has developed an easy-to-use R-package (R Core Team, 2015; Coron et al., 2016), called airGR, to make these models widely available. It includes: - the water balance annual GR1A (Mouehli et al., 2006), - the monthly GR2M (Mouehli, 2003) models, - three versions of the daily model, namely GR4J (Perrin et al., 2003), GR5J (Le Moine, 2008) and GR6J (Pushpalatha et al., 2011), - the hourly GR4H model (Mathevet, 2005), - a degree-day snow module CemaNeige (Valéry et al., 2014). The airGR package has been designed to facilitate the use by non-expert users and allow the addition of evaluation criteria, models or calibration algorithm selected by the end-user. Each model core is coded in FORTRAN to ensure low computational time. The other package functions (i.e. mainly the calibration algorithm and the efficiency criteria) are coded in R. The package is already used for educational purposes. It allows for convenient implementation of model inter-comparisons and

  19. Assessing suitable area for Acacia dealbata Mill. in the Ceira River Basin (Central Portugal based on maximum entropy modelling approach

    Directory of Open Access Journals (Sweden)

    Jorge Pereira

    2015-12-01

    Full Text Available Biological invasion by exotic organisms became a key issue, a concern associated to the deep impacts on several domains described as resultant from such processes. A better understanding of the processes, the identification of more susceptible areas, and the definition of preventive or mitigation measures are identified as critical for the purpose of reducing associated impacts. The use of species distribution modeling might help on the purpose of identifying areas that are more susceptible to invasion. This paper aims to present preliminary results on assessing the susceptibility to invasion by the exotic species Acacia dealbata Mill. in the Ceira river basin. The results are based on the maximum entropy modeling approach, considered one of the correlative modelling techniques with better predictive performance. Models which validation is based on independent data sets present better performance, an evaluation based on the AUC of ROC accuracy measure.

  20. Modelling and Design of a 3 kW Permanent Magnet Synchronous Generator suitable for Variable Speed Small Wind Turbines

    OpenAIRE

    Acharya Parash; Papadakis Antonis; Shaikh Muhammad Naveed

    2016-01-01

    This paper presents the modeling and design of a 3 kW Permanent Magnet Synchronous Generator (PMSG) used for a variable speed wind turbine. Initially, the PMSG is modeled in the d-q reference frame. Different optimized parameters of the generator are extracted from the design and used in simulation of the PMSG. The generator output power is matched with the power of the turbine such that the generator is not either over-sized or under-sized.

  1. Shorebird Habitat Suitability Indicies

    Data.gov (United States)

    Arctic Landscape Conservation Cooperative — This dataset consists of predicted habitat suitability indices and species richness for eight shorebird species (Black-bellied Plover [Pluvialis squatarola],...

  2. Model of turn-on characteristics of InP-based Geiger-mode avalanche photodiodes suitable for circuit simulations

    Science.gov (United States)

    Jordy, George; Donnelly, Joseph

    2015-05-01

    A model for the turn-on characteristics of separate-absorber-multiplier InP-based Geiger-mode Avalanche Photodiodes (APDs) has been developed. Verilog-A was used to implement the model in a manner that can be incorporated into circuit simulations. Rather than using SPICE elements to mimic the voltage and current characteristics of the APD, Verilog-A can represent the first order nonlinear differential equations that govern the avalanche current of the APD. This continuous time representation is fundamentally different than the piecewise linear characteristics of other models. The model is based on a driving term for the differential current, which is given by the voltage overbias minus the voltage drop across the device's space-charge resistance RSC. This drop is primarily due to electrons transiting the separate absorber. RSC starts off high and decreases with time as the initial breakdown filament spreads laterally to fill the APD. With constant bias voltage, the initial current grows exponentially until space charge effects reduce the driving function. With increasing current the driving term eventually goes to zero and the APD current saturates. On the other hand, if the APD is biased with a capacitor, the driving term becomes negative as the capacitor discharges, reducing the current and driving the voltage below breakdown. The model parameters depend on device design and are obtained from fitting the model to Monte-Carlo turn-on simulations that include lateral spreading of the carriers of the relevant structure. The Monte-Carlo simulations also provide information on the probability of avalanche, and jitter due to where the photon is absorbed in the APD.

  3. Skeletal muscle fibrosis in the mdx/utrn+/- mouse validates its suitability as a murine model of Duchenne muscular dystrophy.

    Science.gov (United States)

    Gutpell, Kelly M; Hrinivich, William T; Hoffman, Lisa M

    2015-01-01

    Various therapeutic approaches have been studied for the treatment of Duchenne muscular dystrophy (DMD), but none of these approaches have led to significant long-term effects in patients. One reason for this observed inefficacy may be the use of inappropriate animal models for the testing of therapeutic agents. The mdx mouse is the most widely used murine model of DMD, yet it does not model the fibrotic progression observed in patients. Other murine models of DMD are available that lack one or both alleles of utrophin, a functional analog of dystrophin. The aim of this study was to compare fibrosis and myofiber damage in the mdx, mdx/utrn+/- and double knockout (dko) mouse models. We used Masson's trichrome stain and percentage of centrally-nucleated myofibers as indicators of fibrosis and myofiber regeneration, respectively, to assess disease progression in diaphragm and gastrocnemius muscles harvested from young and aged wild-type, mdx, mdx/utrn+/- and dko mice. Our results indicated that eight week-old gastrocnemius muscles of both mdx/utrn+/- and dko hind limb developed fibrosis whereas age-matched mdx gastrocnemius muscle did not (p = 0.002). The amount of collagen found in the mdx/utrn+/- diaphragm was significantly higher than that found in the corresponding diaphragm muscles of wild-type animals, but not of mdx animals (p = 0.0003). Aged mdx/utrn+/- mice developed fibrosis in both diaphragm and gastrocnemius muscles compared to wild-type controls (p = 0.003). Mdx diaphragm was fibrotic in aged mice as well (p = 0.0235), whereas the gastrocnemius muscle in these animals was not fibrotic. We did not measure a significant difference in collagen staining between wild-type and mdx gastrocnemius muscles. The results of this study support previous reports that the moderately-affected mdx/utrn+/- mouse is a better model of DMD, and we show here that this difference is apparent by 2 months of age.

  4. Modelling and Design of a 3 kW Permanent Magnet Synchronous Generator suitable for Variable Speed Small Wind Turbines

    Directory of Open Access Journals (Sweden)

    Acharya Parash

    2016-01-01

    Full Text Available This paper presents the modeling and design of a 3 kW Permanent Magnet Synchronous Generator (PMSG used for a variable speed wind turbine. Initially, the PMSG is modeled in the d-q reference frame. Different optimized parameters of the generator are extracted from the design and used in simulation of the PMSG. The generator output power is matched with the power of the turbine such that the generator is not either over-sized or under-sized.

  5. Prospects for population expansion of the exotic aoudad (Ammotragus lervia; Bovidae) in the Iberian Peninsula: clues from habitat suitability modelling

    DEFF Research Database (Denmark)

    Cassinello, Jorge; Acevedo, Pelayo; Hortal, Joaquín

    2006-01-01

    ) environmental variables (climate and habitat type), and (2) potential aoudad landscape avoidance and human disturbance variables. We compared both niche descriptions to study the impact of human interference on niche selection of the species. ENFA models were calibrated using data on the population expanded...

  6. Chapter 13 Application of landscape and habitat suitability models to conservation: the Hoosier National Forest land-management plan

    Science.gov (United States)

    Chadwick D. Rittenhouse; Stephen R. Shifley; William D. Dijak; Zhaofei Fan; Frank R., III Thompson; Joshua J. Millspaugh; Judith A. Perez; Cynthia M. Sandeno

    2011-01-01

    We demonstrate an approach to integrated land-management planning and quantify differences in vegetation and avian habitat conditions among 5 management alternatives as part of the Hoosier National Forest planning process. The alternatives differed in terms of the type, extent, magnitude, frequency, and location of management activities. We modeled ecological processes...

  7. 76 FR 69601 - Suitability

    Science.gov (United States)

    2011-11-09

    ... RIN 3206-AL90 Suitability AGENCY: U.S. Office of Personnel Management. ACTION: Final rule. SUMMARY... reinvestigation) as determined by the Director of the Office of Personnel Management, to ensure their suitability... public trust positions with a frequency as determined by the Director of the Office of...

  8. Determining the Suitability of Different Digital Elevation Models and Satellite Images for Fancy Maps. An Example of Cyprus

    Science.gov (United States)

    Drachal, J.; Kawel, A. K.

    2016-06-01

    The article describes the possibility of developing an overall map of the selected area on the basis of publicly available data. Such a map would take the form designed by the author with the colors that meets his expectations and a content, which he considers to be appropriate. Among the data available it was considered the use of satellite images of the terrain in real colors and, in the form of shaded relief, digital terrain models with different resolutions of the terrain mesh. Specifically the considered data were: MODIS, Landsat 8, GTOPO-30, SRTM-30, SRTM-1, SRTM-3, ASTER. For the test area the island of Cyprus was chosen because of the importance in tourism, a relatively small area and a clearly defined boundary. In the paper there are shown and discussed various options of the Cyprus terrain image obtained synthetically from variants of Modis, Landsat and digital elevation models of different resolutions.

  9. Integrated engineering - A SME-suitable model for Business and Information Systems Engineering (BISE) towards the smart factory

    OpenAIRE

    Wurtz G.; Kolmel B.

    2012-01-01

    Part 17: Designing Collaborative Networks; International audience; Integrated Engineering is a BISE-model and combines the following dimensions within an network-oriented SME: Cooperation engineering: networking of product features, process features and project parameters (internal Relationship Management);Collaborative networking: initiation, management, controlling of business relationships along the value chain (external RM);Corporate range: adaptation of the xRM-principles to the product ...

  10. Replacement Value - Representation of Fair Value in Accounting. Techniques and Modeling Suitable for the Income Based Approach

    OpenAIRE

    MANEA MARINELA – DANIELA

    2011-01-01

    The term fair value is spread within the sphere of international standards without reference to any detailed guidance on how to apply. However, specialized tangible assets, which are rarely sold, the rule IAS 16 "Intangible assets " makes it possible to estimate fair value using an income approach or a replacement cost or depreciation. The following material is intended to identify potential modeling of fair value as an income-based approach, appealing to techniques used by professional evalu...

  11. Regional parent flood frequency distributions in Europe - Part 1: Is the GEV model suitable as a pan-European parent?

    Science.gov (United States)

    Salinas, J. L.; Castellarin, A.; Viglione, A.; Kohnová, S.; Kjeldsen, T. R.

    2014-11-01

    This study addresses the question of the existence of a parent flood frequency distribution on a European scale. A new database of L-moment ratios of flood annual maximum series (AMS) from 4105 catchments was compiled by joining 13 national data sets. Simple exploration of the database presents the generalized extreme value (GEV) distribution as a potential pan-European flood frequency distribution, being the three-parameter statistical model that with the closest resemblance to the estimated average of the sample L-moment ratios. Additional Monte Carlo simulations show that the variability in terms of sample skewness and kurtosis present in the data is larger than in a hypothetical scenario where all the samples were drawn from a GEV model. Overall, the generalized extreme value distribution fails to represent the kurtosis dispersion, especially for the longer sample lengths and medium to high skewness values, and therefore may be rejected in a statistical hypothesis testing framework as a single pan-European parent distribution for annual flood maxima. The results presented in this paper suggest that one single statistical model may not be able to fit the entire variety of flood processes present at a European scale, and presents an opportunity to further investigate the catchment and climatic factors controlling European flood regimes and their effects on the underlying flood frequency distributions.

  12. Developing a suitable model for supplier selection based on supply chain risks: an empirical study from Iranian pharmaceutical companies.

    Science.gov (United States)

    Mehralian, Gholamhossein; Rajabzadeh Gatari, Ali; Morakabati, Mohadese; Vatanpour, Hossein

    2012-01-01

    The supply chain represents the critical link between the development of new product and the market in pharmaceutical industry. Over the years, improvements made in supply chain operations have focused largely on ways to reduce cost and gain efficiencies in scale. In addition, powerful regulatory and market forces have provided new incentives for pharmaceutical firms to basically rethink the way they produce and distribute products, and also to re-imagine the role of the supply chain in driving strategic growth, brand differentiation and economic value in the health continuum. The purpose of this paper is to formulate basic factors involved in risk analysis of pharmaceutical industry, and also determine the effective factors involved in suppliers selection and their priorities. This paper is based on the results of literature review, experts' opinion acquisition, statistical analysis and also using MADM models on data gathered from distributed questionnaires. The model consists of the following steps and components: first factors involved in to supply chain risks are determined. Based on them a framework is considered. According the result of statistical analysis and MADM models the risk factors are formulated. The paper determines the main components and influenceial factors involving in the supply chain risks. Results showed that delivery risk can make an important contribution to mitigate the risk of pharmaceutical industry.

  13. Construction and analysis of a human hepatotoxicity database suitable for QSAR modeling using post-market safety data.

    Science.gov (United States)

    Zhu, Xiao; Kruhlak, Naomi L

    2014-07-01

    Drug-induced liver injury (DILI) is one of the most common drug-induced adverse events (AEs) leading to life-threatening conditions such as acute liver failure. It has also been recognized as the single most common cause of safety-related post-market withdrawals or warnings. Efforts to develop new predictive methods to assess the likelihood of a drug being a hepatotoxicant have been challenging due to the complexity and idiosyncrasy of clinical manifestations of DILI. The FDA adverse event reporting system (AERS) contains post-market data that depict the morbidity of AEs. Here, we developed a scalable approach to construct a hepatotoxicity database using post-market data for the purpose of quantitative structure-activity relationship (QSAR) modeling. A set of 2029 unique and modelable drug entities with 13,555 drug-AE combinations was extracted from the AERS database using 37 hepatotoxicity-related query preferred terms (PTs). In order to determine the optimal classification scheme to partition positive from negative drugs, a manually-curated DILI calibration set composed of 105 negatives and 177 positives was developed based on the published literature. The final classification scheme combines hepatotoxicity-related PT data with supporting information that optimize the predictive performance across the calibration set. Data for other toxicological endpoints related to liver injury such as liver enzyme abnormalities, cholestasis, and bile duct disorders, were also extracted and classified. Collectively, these datasets can be used to generate a battery of QSAR models that assess a drug's potential to cause DILI.

  14. Is murine gammaherpesvirus-68 (MHV-68) a suitable immunotoxicological model for examining immunomodulatory drug-associated viral recrudescence?

    Science.gov (United States)

    Aligo, Jason; Walker, Mindi; Bugelski, Peter; Weinstock, Daniel

    2015-01-01

    Immunosuppressive agents are used for treatment of a variety of autoimmune diseases including rheumatoid arthritis (RA), systemic lupus erythematosis (SLE), and psoriasis, as well as for prevention of tissue rejection after organ transplantation. Recrudescence of herpesvirus infections, and increased risk of carcinogenesis from herpesvirus-associated tumors are related with immunosuppressive therapy in humans. Post-transplant lymphoproliferative disorder (PTLD), a condition characterized by development of Epstein Barr Virus (EBV)-associated B-lymphocyte lymphoma, and Kaposi's Sarcoma (KS), a dermal tumor associated with Kaposi Sarcoma-associated virus (KSHV), may develop in solid organ transplant patients. KS also occurs in immunosuppressed Acquired Immunodeficiency (AIDS) patients. Kaposi Sarcoma-associated virus (KSHV) is a herpes virus genetically related to EBV. Murine gammaherpes-virus-68 (MHV-68) is proposed as a mouse model of gammaherpesvirus infection and recrudescence and may potentially have relevance for herpesvirus-associated neoplasia. The pathogenesis of MHV-68 infection in mice mimics EBV/KSHV infection in humans with acute lytic viral replication followed by dissemination and establishment of persistent latency. MHV-68-infected mice may develop lymphoproliferative disease that is accelerated by disruption of the immune system. This manuscript first presents an overview of gammaherpesvirus pathogenesis and immunology as well as factors involved in viral recrudescence. A description of different types of immunodeficiency then follows, with particular focus on viral association with lymphomagenesis after immunosuppression. Finally, this review discusses different gammaherpesvirus animal models and describes a proposed MHV-68 model to further examine the interplay of immunomodulatory agents and gammaherpesvirus-associated neoplasia.

  15. A Method for Teaching the Modeling of Manikins Suitable for Third-Person 3-D Virtual Worlds and Games

    Directory of Open Access Journals (Sweden)

    Nick V. Flor

    2012-08-01

    Full Text Available Virtual Worlds have the potential to transform the way people learn, work, and play. With the emerging fields of service science and design science, professors and students at universities are in a unique position to lead the research and development of innovative and value-adding virtual worlds. However, a key barrier in the development of virtual worlds—especially for business, technical, and non-artistic students—is the ability to model human figures in 3-D for use as avatars and automated characters in virtual worlds. There are no articles in either research or teaching journals which describe methods that non-artists can use to create 3-D human figures. This paper presents a repeatable and flexible method I have taught successfully to both artists and business students, which allows them to quickly model human-like figures (manikins that are sufficient for prototype purposes and that allows students and researchers alike to explore the development of new kinds of virtual worlds.

  16. Assessing suitability of multispectral satellites for mapping benthic macroalgal cover in turbid coastal waters by means of model simulations

    Science.gov (United States)

    Kutser, Tiit; Vahtmäe, Ele; Martin, Georg

    2006-04-01

    One of the objectives of monitoring benthic algal cover is to observe short- and long-term changes in species distribution and structure of coastal benthic habitats as indicators of ecological state. Mapping benthic algal cover with conventional methods (diving) provides great accuracy and high resolution, yet is very expensive and is limited by the time and manpower necessary. We measured reflectance spectra of three indicator species for the Baltic Sea: Cladophora glomerata (green macroalgae), Furcellaria lumbricalis (red macroalgae), and Fucus vesiculosus (brown macroalgae) and used a bio-optical model in an attempt to estimate whether these algae are separable from each other and sandy bottom or deep water by means of satellite remote sensing. Our modelling results indicate that to some extent it is possible to map the studied species with multispectral satellite sensors in turbid waters. However, the depths where the macroalgae can be detected are often shallower than the maximum depths where the studied species usually grow. In waters deeper than just a few meters, the differences between the studied bottom types are seen only in band 2 (green) of the multispectral sensors under investigation. It means that multispectral sensors are capable of detecting difference in brightness only in one band which is insufficient for recognition of different bottom types in waters where no or few in situ data are available. Configuration of MERIS spectral bands allows the recognition of red, green and brown macroalgae based on their spectral signatures provided the algal belts are wider than MERIS spatial resolution. Commercial stock of F. lumbricalis in West-Estonian Archipelago covers area where MERIS 300 m spatial resolution is adequate. However, strong attenuation of light in the water column and signal to noise ratio of the sensor do not allow mapping of Furcellaria down to maximum depths where it occurs.

  17. Identifying patients suitable for palliative care - a descriptive analysis of enquiries using a Case Management Process Model approach

    Directory of Open Access Journals (Sweden)

    Kuhn Ulrike

    2012-11-01

    Full Text Available Abstract Background In Germany, case management in a palliative care unit was first implemented in 2005 at the Department of Palliative Medicine at the University Hospital Cologne. One of the purposes of this case management is to deal with enquiries from patients and their relatives as well as medical professionals. Using the Case Management Process Model of the Case Management Society of America as a reference, this study analysed (a how this case management was used by different enquiring groups and (b how patients were identified for case management and for palliative care services. The first thousand enquiries were analysed considering patient variables, properties of the enquiring persons and the content of the consultations. Results Most enquiries to the case management were made by telephone. The majority of requests regarded patients with oncological disease (84.3 %. The largest enquiring group was composed of patients and relatives (40.8 %, followed by internal professionals of the hospital (36.1 %. Most of the enquiring persons asked for a patient’s admission to the palliative care ward (46.4 %. The second most frequent request was for consultation and advice (30.9 %, followed by requests for the palliative home care service (13.3 %. Frequent reasons for actual admissions were the need for the treatment of pain, the presence of symptoms and the need for nursing care. More than half of the enquiries concerning admission to the palliative care ward were followed by an admission. Conclusions Case management has been made public among the relevant target groups. Case management as described by the Case Management Process Model helps to identify patients likely to benefit from case management and palliative care services. In addition, with the help of case management palliative patients may be allocated to particular health care services.

  18. The suitability of the IEC 61400-2 wind model for small wind turbines operating in the built environment★

    Directory of Open Access Journals (Sweden)

    Evans Samuel P.

    2017-01-01

    Full Text Available This paper investigates the applicability of the assumed wind fields in International Electrotechnical Commission (IEC standard 61400 Part 2, the design standard for small wind turbines, for a turbine operating in the built environment, and the effects these wind fields have on the predicted performance of a 5 kW Aerogenesis turbine using detailed aeroelastic models developed in Fatigue Aerodynamics Structures and Turbulence (FAST. Detailed wind measurements were acquired at two built environment sites: from the rooftop of a Bunnings Ltd. warehouse at Port Kennedy (PK (Perth, Australia and from the small wind turbine site at the University of Newcastle at Callaghan (Newcastle, Australia. For both sites, IEC 61400-2 underestimates the turbulence intensity for the majority of the measured wind speeds. A detailed aeroelastic model was built in FAST using the assumed wind field from IEC 61400-2 and the measured wind fields from PK and Callaghan as an input to predict key turbine performance parameters. The results of this analysis show a modest increase in the predicted mean power for the higher turbulence regimes of PK and Callaghan as well as higher variation in output power. Predicted mean rotor thrust and blade flapwise loading showed a minor increase due to higher turbulence, with mean predicted torque almost identical but with increased variations due to higher turbulence. Damage equivalent loading for the blade flapwise moment was predicted to be 58% and 11% higher for a turbine operating at Callaghan and PK respectively, when compared with IEC 61400-2 wind field. Time series plots for blade flapwise moments and power spectral density plots in the frequency domain show consistently higher blade flapwise bending moments for the Callaghan site with both the sites showing a once-per-revolution response.

  19. Functional heterologous expression and purification of a mammalian methyl-CpG binding domain in suitable yield for DNA methylation profiling assays.

    Science.gov (United States)

    Boyd, Mary E; Heimer, Brandon W; Sikes, Hadley D

    2012-04-01

    DNA methylation is a major epigenetic modification in mammalian cells, and patterns involving methylation of cytosine bases, known as CpG methylation, have been implicated in the development of many types of cancer. Methyl binding domains (MBDs) excised from larger mammalian methyl-CpG-binding proteins specifically recognize methyl-cytosine bases of CpG dinucleotides in duplex DNA. Previous molecular diagnostic studies involving MBDs have employed Escherichia coli for protein expression with either low soluble yields or the use of time-consuming denaturation-renaturation purification procedures to improve yields. Efficient MBD-based diagnostics require expression and purification methods that maximize protein yield and minimize time and resource expenditure. This study is a systematic optimization analysis of MBD expression using both SDS-PAGE and microscopy and it provides a comparison of protein yield from published procedures to that from the conditions found to be optimal in these experiments. Protein binding activity and specificity were verified using a DNA electrophoretic mobility shift assay, and final protein yield was improved from the starting conditions by a factor of 65 with a simple, single-step purification.

  20. Expression of a highly antigenic and native-like folded extracellular domain of the human α1 subunit of muscle nicotinic acetylcholine receptor, suitable for use in antigen specific therapies for Myasthenia Gravis.

    Directory of Open Access Journals (Sweden)

    Athanasios Niarchos

    Full Text Available We describe the expression of the extracellular domain of the human α1 nicotinic acetylcholine receptor (nAChR in lepidopteran insect cells (i-α1-ECD and its suitability for use in antigen-specific therapies for Myasthenia Gravis (MG. Compared to the previously expressed protein in P. pastoris (y-α1-ECD, i-α1-ECD had a 2-fold increased expression yield, bound anti-nAChR monoclonal antibodies and autoantibodies from MG patients two to several-fold more efficiently and resulted in a secondary structure closer to that of the crystal structure of mouse α1-ECD. Our results indicate that i-α1-ECD is an improved protein for use in antigen-specific MG therapeutic strategies.

  1. Suitability of digital elevation models generated by uav photogrammetry for slope stability assessment (case study of landslide in Svätý Anton, Slovakia

    Directory of Open Access Journals (Sweden)

    Rusnák Miloš

    2016-12-01

    Full Text Available Assessing the accuracy of photogrammetrically-derived digital elevation models (DEMs from UAV is essential in many geoscience disciplines. The suitability of different DEM devised for slope stability assessment was evaluated in the example of the landslide in Svätý Anton village in Slovakia. Aerial data was acquired during a one-day field campaign in autumn 2014. The point cloud from 218 images (54,607,748 points was manually classified into 7 different classes for filtering vegetation cover and buildings. Assessment of vertical differences between the UAV derived elevation model and real terrain surface was based on comparison of control points targeted by GPS (337 points and unclassified and ground classified point cloud for raster elevation models with 1, 5, 10, 20 and 50 cm pixel resolution.

  2. Development of computational fluid dynamics--habitat suitability (CFD-HSI) models to identify potential passage--Challenge zones for migratory fishes in the Penobscot River

    Science.gov (United States)

    Haro, Alexander J.; Dudley, Robert W.; Chelminski, Michael

    2012-01-01

    A two-dimensional computational fluid dynamics-habitat suitability (CFD–HSI) model was developed to identify potential zones of shallow depth and high water velocity that may present passage challenges for five anadromous fish species in the Penobscot River, Maine, upstream from two existing dams and as a result of the proposed future removal of the dams. Potential depth-challenge zones were predicted for larger species at the lowest flow modeled in the dam-removal scenario. Increasing flows under both scenarios increased the number and size of potential velocity-challenge zones, especially for smaller species. This application of the two-dimensional CFD–HSI model demonstrated its capabilities to estimate the potential effects of flow and hydraulic alteration on the passage of migratory fish.

  3. Abundance and Distribution Patterns of Thunnus albacares in Isla del Coco National Park through Predictive Habitat Suitability Models

    Science.gov (United States)

    Gonzáles-Andrés, Cristina; F. M. Lopes, Priscila; Cortés, Jorge; Sánchez-Lizaso, José Luis; Pennino, Maria Grazia

    2016-01-01

    Information on the distribution and habitat preferences of ecologically and commercially important species is essential for their management and protection. This is especially important as climate change, pollution, and overfishing change the structure and functioning of pelagic ecosystems. In this study, we used Bayesian hierarchical spatial-temporal models to map the Essential Fish Habitats of the Yellowfin tuna (Thunnus albacares) in the waters around Isla del Coco National Park, Pacific Costa Rica, based on independent underwater observations from 1993 to 2013. We assessed if observed changes in the distribution and abundance of this species are related with habitat characteristics, fishing intensity or more extreme climatic events, including the El Niño Southern Oscillation, and changes on the average sea surface temperature. Yellowfin tuna showed a decreasing abundance trend in the sampled period, whereas higher abundances were found in shallow and warmer waters, with high concentration of chlorophyll-a, and in surrounding seamounts. In addition, El Niño Southern Oscillation events did not seem to affect Yellowfin tuna distribution and abundance. Understanding the habitat preferences of this species, using approaches as the one developed here, may help design integrated programs for more efficient management of vulnerable species. PMID:27973538

  4. Abundance and Distribution Patterns of Thunnus albacares in Isla del Coco National Park through Predictive Habitat Suitability Models.

    Science.gov (United States)

    Gonzáles-Andrés, Cristina; F M Lopes, Priscila; Cortés, Jorge; Sánchez-Lizaso, José Luis; Pennino, Maria Grazia

    2016-01-01

    Information on the distribution and habitat preferences of ecologically and commercially important species is essential for their management and protection. This is especially important as climate change, pollution, and overfishing change the structure and functioning of pelagic ecosystems. In this study, we used Bayesian hierarchical spatial-temporal models to map the Essential Fish Habitats of the Yellowfin tuna (Thunnus albacares) in the waters around Isla del Coco National Park, Pacific Costa Rica, based on independent underwater observations from 1993 to 2013. We assessed if observed changes in the distribution and abundance of this species are related with habitat characteristics, fishing intensity or more extreme climatic events, including the El Niño Southern Oscillation, and changes on the average sea surface temperature. Yellowfin tuna showed a decreasing abundance trend in the sampled period, whereas higher abundances were found in shallow and warmer waters, with high concentration of chlorophyll-a, and in surrounding seamounts. In addition, El Niño Southern Oscillation events did not seem to affect Yellowfin tuna distribution and abundance. Understanding the habitat preferences of this species, using approaches as the one developed here, may help design integrated programs for more efficient management of vulnerable species.

  5. Computational fluid dynamics-habitat suitability index (CFD-HSI) modelling as an exploratory tool for assessing passability of riverine migratory challenge zones for fish

    Science.gov (United States)

    Haro, Alexander J.; Chelminski, Michael; Dudley, Robert W.

    2015-01-01

    We developed two-dimensional computational fluid hydraulics-habitat suitability index (CFD-HSI) models to identify and qualitatively assess potential zones of shallow water depth and high water velocity that may present passage challenges for five major anadromous fish species in a 2.63-km reach of the main stem Penobscot River, Maine, as a result of a dam removal downstream of the reach. Suitability parameters were based on distribution of fish lengths and body depths and transformed to cruising, maximum sustained and sprint swimming speeds. Zones of potential depth and velocity challenges were calculated based on the hydraulic models; ability of fish to pass a challenge zone was based on the percent of river channel that the contiguous zone spanned and its maximum along-current length. Three river flows (low: 99.1 m3 sec-1; normal: 344.9 m3 sec-1; and high: 792.9 m3 sec-1) were modelled to simulate existing hydraulic conditions and hydraulic conditions simulating removal of a dam at the downstream boundary of the reach. Potential depth challenge zones were nonexistent for all low-flow simulations of existing conditions for deeper-bodied fishes. Increasing flows for existing conditions and removal of the dam under all flow conditions increased the number and size of potential velocity challenge zones, with the effects of zones being more pronounced for smaller species. The two-dimensional CFD-HSI model has utility in demonstrating gross effects of flow and hydraulic alteration, but may not be as precise a predictive tool as a three-dimensional model. Passability of the potential challenge zones cannot be precisely quantified for two-dimensional or three-dimensional models due to untested assumptions and incomplete data on fish swimming performance and behaviours.

  6. Analysis of Tubespins as a suitable scale-down model of bioreactors for high cell density CHO cell culture.

    Science.gov (United States)

    Gomez, Natalia; Ambhaikar, Malhar; Zhang, Li; Huang, Chung-Jr; Barkhordarian, Hedieh; Lull, Jonathan; Gutierrez, Chris

    2017-03-01

    High cell density (HCD) culture increases recombinant protein productivity via higher biomass. Compared to traditional fed-batch cultures, HCD is achieved by increased nutrient availability and removal of undesired metabolic components via regular medium replenishment. HCD process development is usually performed in instrumented lab-scale bioreactors (BR) that require time and labor for setup and operation. To potentially minimize resources and cost during HCD experiments, we evaluated a 2-week 50-mL Tubespin (TS) simulated HCD process where daily medium exchanges mimic the medium replacement rate in BR. To best assess performance differences, we cultured 13 different CHO cell lines in simulated HCD as satellites from simultaneous BR, and compared growth, metabolism, productivity and product quality. Overall, viability, cell-specific productivity and metabolism in TS were comparable to BR, but TS cell growth and final titer were lower by 25 and 15% in average, respectively. Peak viable cell densities were lower in TS than BR as a potential consequence of lower pH, different medium exchange strategy and dissolved oxygen limitations. Product quality attributes highly dependent on intrinsic molecule or cell line characteristics (e.g., galactosylation, afucosylation, aggregation) were comparable in both scales. However, product quality attributes that can change extracellularly as a function of incubation time (e.g., deamidation, C-terminal lysine, fragmentation) were in general lower in TS because of shorter residence time than HCD BR. Our characterization results and two case studies show that TS-simulated HCD cultures can be effectively used as a simple scale-down model for relative comparisons among cell lines for growth or productivity (e.g., clone screening), and for investigating effects on protein galactosylation. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:490-499, 2017. © 2017 American Institute of Chemical Engineers.

  7. Pleurodeles waltl, amphibian, Urodele, is a suitable biological model for embryological and physiological space experiments on a vertebrate

    Science.gov (United States)

    Gualandris-Parisot, L.; Husson, D.; Foulquier, F.; Kan, P.; Davet, J.; Aimar, C.; Dournon, C.; Duprat, A. M.

    2001-01-01

    Pleurodeles waltl (amphibian, Urodele) is an appropriate biological model for space experiments on a vertebrate. One reason for interest in this animal concerns the study of the effects of absence of gravity on embryonic development. First, after mating (on Earth) the females retain live, functional sperm in their cloacum for up to 5 months, allowing normal in vivo fertilisation after hormonal stimulation. Second, their development is slow, which allows analyses of all the key stages of ontogenesis from the oocyte to swimming tailbud embryos or larvae. We have performed detailed studies and analyses of the effects of weightlessness on amphibian Pleurodeles embryos, fertilised and allowed to develop until the swimming larvae stage. These experiments were performed in space during three missions on the MIR-station: FERTILE I, FERTILE II and NEUROGENESIS respectively in 1996, 1998 and 1999. We show that in microgravity abnormalities appeared at specific stages of development compared to 1g-centrifuge control embryos and 1g-ground control embryos. In this report we describe abnormalities occurring in the central nervous system. These modifications occur during the neurulation process (delay in the closure of the neural tube and failure of closure of this tube in the cephalic area) and at the early tailbud stage (microcephaly observed in 40% of the microgravity-embryos). However, if acephalic and microcephalic embryos are not taken into account, these abnormalities did not disturb further morphological, biochemical and functional development and the embryos were able to regulate and a majority of normal hatching and swimming larvae were obtained in weightlessness with a developmental time-course equivalent to that of 1g-centrifuge control embryos (on the MIR station) and 1g-ground control embryos.

  8. Use of CFD modeling for estimating spatial representativeness of urban air pollution monitoring sites and suitability of their locations

    Energy Technology Data Exchange (ETDEWEB)

    Santiago, J. L.; Martin, F.

    2015-07-01

    A methodology to estimate the spatial representativeness of air pollution monitoring sites is applied to two urban districts. This methodology is based on high resolution maps of air pollution computed by using Computational Fluid Dynamics (CFD) modelling tools. Traffic-emitted NO{sub 2} dispersion is simulated for several meteorological conditions taking into account the effect of the buildings on air flow and pollutant dispersion and using a steady state CFD-RANS approach. From these results, maps of average pollutant concentrations for January -May 2011 are computed as a combination of the simulated scenarios. Two urban districts of Madrid City were simulated. Spatial representativeness areas for 32 different sites within the same district (including the site of the operative air quality stations) have been estimated by computing the portion of the domains with average NO{sub 2} concentration differing less than a 20% of the concentration at each candidate monitoring site. New parameters such as the ratio AR between the representativeness area and the whole domain area or the representativeness index (IR) has been proposed to discuss and compare the representativeness areas. Significant differences between the spatial representativeness of the candidate sites of both studied districts have been found. The sites of the Escuelas Aguirre district have generally smaller representativeness areas than those of the Plaza de Castilla. More stations are needed to cover the Escuelas Aguirre district than for the Plaza de Castilla one. The operative air quality station of the Escuelas Aguirre district is less representative than the station of the Plaza de Castilla district. The cause of these differences seems to be the differences in urban structure of both districts prompting different ventilation. (Author)

  9. Use of CFD modeling for estimating spatial representativeness of urban air pollution monitoring sites and suitability of their locations

    Energy Technology Data Exchange (ETDEWEB)

    Santiago, J.L.; Martin, F.

    2015-07-01

    A methodology to estimate the spatial representativeness of air pollution monitoring sites is applied to two urban districts. This methodology is based on high resolution maps of air pollution computed by using Computational Fluid Dynamics (CFD) modelling tools. Traffic-emitted NO2 dispersion is simulated for several meteorological conditions taking into account the effect of the buildings on air flow and pollutant dispersion and using a steady state CFD-RANS approach. From these results, maps of average pollutant concentrations for January–May 2011 are computed as a combination of the simulated scenarios. Two urban districts of Madrid City were simulated. Spatial representativeness areas for 32 different sites within the same district (including the site of the operative air quality stations) have been estimated by computing the portion of the domains with average NO2 concentration differing less than a 20% of the concentration at each candidate monitoring site. New parameters such as the ratio AR between the representativeness area and the whole domain area or the representativeness index (IR) has been proposed to discuss and compare the representativeness areas. Significant differences between the spatial representativeness of the candidate sites of both studied districts have been found. The sites of the Escuelas Aguirre district have generally smaller representativeness areas than those of the Plaza de Castilla. More stations are needed to cover the Escuelas Aguirre district than for the Plaza de Castilla one. The operative air quality station of the Escuelas Aguirre district is less representative than the station of the Plaza de Castilla district. The cause of these differences seems to be the differences in urban structure of both districts prompting different ventilation. (Author)

  10. Isolation and selection of suitable reference genes for real-time PCR analyses in the skeletal muscle of the fine flounder in response to nutritional status: assessment and normalization of gene expression of growth-related genes.

    Science.gov (United States)

    Fuentes, Eduardo N; Safian, Diego; Valdés, Juan Antonio; Molina, Alfredo

    2013-08-01

    In the present study, different reference genes were isolated, and their stability in the skeletal muscle of fine flounder subjected to different nutritional states was assessed using geNorm and NormFinder. The combinations between 18S and ActB; Fau and 18S; and Fau and Tubb were chosen as the most stable gene combinations in feeding, long-term fasting and refeeding, and short-term refeeding conditions, respectively. In all periods, ActB was identified as the single least stable gene. Subsequently, the expression of the myosin heavy chain (MYH) and the insulin-like growth factor-I receptor (IGF-IR) was assessed. A large variation in MYH and IGF-IR expression was found depending on the reference gene that was chosen for normalizing the expression of both genes. Using the most stable reference genes, mRNA levels of MYH decreased and IGF-IR increased during fasting, with both returning to basal levels during refeeding. However, the drop in mRNA levels for IGF-IR occurred during short-term refeeding, in contrast with the observed events in the expression of MYH, which occurred during long-term refeeding. The present study highlights the vast differences incurred when using unsuitable versus suitable reference genes for normalizing gene expression, pointing out that normalization without proper validation could result in a bias of gene expression.

  11. The development and validation of a multivariable model to predict whether patients referred for total knee replacement are suitable surgical candidates at the time of initial consultation.

    Science.gov (United States)

    Churchill, Laura; Malian, Samuel J; Chesworth, Bert M; Bryant, Dianne; MacDonald, Steven J; Marsh, Jacquelyn D; Giffin, J Robert

    2016-12-01

    In previous studies, 50%-70% of patients referred to orthopedic surgeons for total knee replacement (TKR) were not surgical candidates at the time of initial assessment. The purpose of our study was to identify and cross-validate patient self-reported predictors of suitability for TKR and to determine the clinical utility of a predictive model to guide the timing and appropriateness of referral to a surgeon. We assessed pre-consultation patient data as well as the surgeon's findings and post-consultation recommendations. We used multivariate logistic regression to detect self-reported items that could identify suitable surgical candidates. Patients' willingness to undergo surgery, higher rating of pain, greater physical function, previous intra-articular injections and patient age were the factors predictive of patients being offered and electing to undergo TKR. The application of the model developed in our study would effectively reduce the proportion of nonsurgical referrals by 25%, while identifying the vast majority of surgical candidates (> 90%). Using patient-reported information, we can correctly predict the outcome of specialist consultation for TKR in 70% of cases. To reduce long waits for first consultation with a surgeon, it may be possible to use these items to educate and guide referring clinicians and patients to understand when specialist consultation is the next step in managing the patient with severe osteoarthritis of the knee.

  12. The Invasive Species Forecasting System (ISFS): An iRODS-Based, Cloud-Enabled Decision Support System for Invasive Species Habitat Suitability Modeling

    Science.gov (United States)

    Gill, Roger; Schnase, John L.

    2012-01-01

    The Invasive Species Forecasting System (ISFS) is an online decision support system that allows users to load point occurrence field sample data for a plant species of interest and quickly generate habitat suitability maps for geographic regions of interest, such as a national park, monument, forest, or refuge. Target customers for ISFS are natural resource managers and decision makers who have a need for scientifically valid, model- based predictions of the habitat suitability of plant species of management concern. In a joint project involving NASA and the Maryland Department of Natural Resources, ISFS has been used to model the potential distribution of Wavyleaf Basketgrass in Maryland's Chesapeake Bay Watershed. Maximum entropy techniques are used to generate predictive maps using predictor datasets derived from remotely sensed data and climate simulation outputs. The workflow to run a model is implemented in an iRODS microservice using a custom ISFS file driver that clips and re-projects data to geographic regions of interest, then shells out to perform MaxEnt processing on the input data. When the model completes, all output files and maps from the model run are registered in iRODS and made accessible to the user. The ISFS user interface is a web browser that uses the iRODS PHP client to interact with the ISFS/iRODS- server. ISFS is designed to reside in a VMware virtual machine running SLES 11 and iRODS 3.0. The ISFS virtual machine is hosted in a VMware vSphere private cloud infrastructure to deliver the online service.

  13. Genome-wide expression profiling of five mouse models identifies similarities and differences with human psoriasis.

    Directory of Open Access Journals (Sweden)

    William R Swindell

    Full Text Available Development of a suitable mouse model would facilitate the investigation of pathomechanisms underlying human psoriasis and would also assist in development of therapeutic treatments. However, while many psoriasis mouse models have been proposed, no single model recapitulates all features of the human disease, and standardized validation criteria for psoriasis mouse models have not been widely applied. In this study, whole-genome transcriptional profiling is used to compare gene expression patterns manifested by human psoriatic skin lesions with those that occur in five psoriasis mouse models (K5-Tie2, imiquimod, K14-AREG, K5-Stat3C and K5-TGFbeta1. While the cutaneous gene expression profiles associated with each mouse phenotype exhibited statistically significant similarity to the expression profile of psoriasis in humans, each model displayed distinctive sets of similarities and differences in comparison to human psoriasis. For all five models, correspondence to the human disease was strong with respect to genes involved in epidermal development and keratinization. Immune and inflammation-associated gene expression, in contrast, was more variable between models as compared to the human disease. These findings support the value of all five models as research tools, each with identifiable areas of convergence to and divergence from the human disease. Additionally, the approach used in this paper provides an objective and quantitative method for evaluation of proposed mouse models of psoriasis, which can be strategically applied in future studies to score strengths of mouse phenotypes relative to specific aspects of human psoriasis.

  14. Predicting Effects of Climate Change on Habitat Suitability of Red Spruce (Picea rubens Sarg. in the Southern Appalachian Mountains of the USA: Understanding Complex Systems Mechanisms through Modeling

    Directory of Open Access Journals (Sweden)

    Kyung Ah Koo

    2015-04-01

    Full Text Available Alpine, subalpine and boreal tree species, of low genetic diversity and adapted to low optimal temperatures, are vulnerable to the warming effects of global climate change. The accurate prediction of these species’ distributions in response to climate change is critical for effective planning and management. The goal of this research is to predict climate change effects on the distribution of red spruce (Picea rubens Sarg. in the Great Smoky Mountains National Park (GSMNP, eastern USA. Climate change is, however, conflated with other environmental factors, making its assessment a complex systems problem in which indirect effects are significant in causality. Predictions were made by linking a tree growth simulation model, red spruce growth model (ARIM.SIM, to a GIS spatial model, red spruce habitat model (ARIM.HAB. ARIM.SIM quantifies direct and indirect interactions between red spruce and its growth factors, revealing the latter to be dominant. ARIM.HAB spatially distributes the ARIM.SIM simulations under the assumption that greater growth reflects higher probabilities of presence. ARIM.HAB predicts the future habitat suitability of red spruce based on growth predictions of ARIM.SIM under climate change and three air pollution scenarios: 10% increase, no change and 10% decrease. Results show that suitable habitats shrink most when air pollution increases. Higher temperatures cause losses of most low-elevation habitats. Increased precipitation and air pollution produce acid rain, which causes loss of both low- and high-elevation habitats. The general prediction is that climate change will cause contraction of red spruce habitats at both lower and higher elevations in GSMNP, and the effects will be exacerbated by increased air pollution. These predictions provide valuable information for understanding potential impacts of global climate change on the spatiotemporal distribution of red spruce habitats in GSMNP.

  15. GIS-based suitability modeling and multi-criteria decision analysis for utility scale solar plants in four states in the Southeast U.S

    Science.gov (United States)

    Tisza, Kata

    Photovoltaic (PV) development shows significantly smaller growth in the Southeast U.S., than in the Southwest; which is mainly due to the low cost of fossil-fuel based energy production in the region and the lack of solar incentives. However, the Southeast has appropriate insolation conditions (4.0-6.0 KWh/m2/day) for photovoltaic deployment and in the past decade the region has experienced the highest population growth for the entire country. These factors, combined with new renewable energy portfolio policies, could create an opportunity for PV to provide some of the energy that will be required to sustain this growth. The goal of the study was to investigate the potential for PV generation in the Southeast region by identifying suitable areas for a utility-scale solar power plant deployment. Four states with currently low solar penetration were studied: Georgia, North Carolina, South Carolina and Tennessee. Feasible areas were assessed with Geographic Information Systems (GIS) software using solar, land use and population growth criteria combined with proximity to transmission lines and roads. After the GIS-based assessment of the areas, technological potential was calculated for each state. Multi-decision analysis model (MCDA) was used to simulate the decision making method for a strategic PV installation. The model accounted for all criteria necessary to consider in case of a PV development and also included economic and policy criteria, which is thought to be a strong influence on the PV market. Three different scenarios were established, representing decision makers' theoretical preferences. Map layers created in the first part were used as basis for the MCDA and additional technical, economic and political/market criteria were added. A sensitivity analysis was conducted to test the model's robustness. Finally, weighted criteria were assigned to the GIS map layers, so that the different preference systems could be visualized. As a result, lands suitable for

  16. Habitat Suitability Index Models: Mink

    Science.gov (United States)

    Allen, Arthur W.

    1983-01-01

    The mink (Mustela vison) is a predatory, semiaquatic mammal that is generally associated with stream and river banks, lake shores, fresh and saltwater marshes, and marine shore habitats (Gerell 1970).  Mink are chiefly nocturnal and remain active throughout the year (Marshall 1936); Gerell 1969; Burgess 1978).  The species is adaptable in its use of habitat, modifying daily habits according to environmental conditions, particularly prey availability (Wise et al. 1981; Linn and Birds 1981; Birks and Linn 1982).  The species is tolerant of human activity and will inhabit suboptimum habitats as long as an adequate food source is available; however, mink will be more mobile and change home ranges more frequently under such conditions (Linn pers. comm.).

  17. Phylogenetic modeling of heterogeneous gene-expression microarray data from cancerous specimens.

    Science.gov (United States)

    Abu-Asab, Mones S; Chaouchi, Mohamed; Amri, Hakima

    2008-09-01

    The qualitative dimension of gene expression data and its heterogeneous nature in cancerous specimens can be accounted for by phylogenetic modeling that incorporates the directionality of altered gene expressions, complex patterns of expressions among a group of specimens, and data-based rather than specimen-based gene linkage. Our phylogenetic modeling approach is a double algorithmic technique that includes polarity assessment that brings out the qualitative value of the data, followed by maximum parsimony analysis that is most suitable for the data heterogeneity of cancer gene expression. We demonstrate that polarity assessment of expression values into derived and ancestral states, via outgroup comparison, reduces experimental noise; reveals dichotomously expressed asynchronous genes; and allows data pooling as well as comparability of intra- and interplatforms. Parsimony phylogenetic analysis of the polarized values produces a multidimensional classification of specimens into clades that reveal shared derived gene expressions (the synapomorphies); provides better assessment of ontogenic pathways and phyletic relatedness of specimens; efficiently utilizes dichotomously expressed genes; produces highly predictive class recognition; illustrates gene linkage and multiple developmental pathways; provides higher concordance between gene lists; and projects the direction of change among specimens. Further implication of this phylogenetic approach is that it may transform microarray into diagnostic, prognostic, and predictive tool.

  18. Water-quality models to assess algal community dynamics, water quality, and fish habitat suitability for two agricultural land-use dominated lakes in Minnesota, 2014

    Science.gov (United States)

    Smith, Erik A.; Kiesling, Richard L.; Ziegeweid, Jeffrey R.

    2017-07-20

    Fish habitat can degrade in many lakes due to summer blue-green algal blooms. Predictive models are needed to better manage and mitigate loss of fish habitat due to these changes. The U.S. Geological Survey (USGS), in cooperation with the Minnesota Department of Natural Resources, developed predictive water-quality models for two agricultural land-use dominated lakes in Minnesota—Madison Lake and Pearl Lake, which are part of Minnesota’s sentinel lakes monitoring program—to assess algal community dynamics, water quality, and fish habitat suitability of these two lakes under recent (2014) meteorological conditions. The interaction of basin processes to these two lakes, through the delivery of nutrient loads, were simulated using CE-QUAL-W2, a carbon-based, laterally averaged, two-dimensional water-quality model that predicts distribution of temperature and oxygen from interactions between nutrient cycling, primary production, and trophic dynamics.The CE-QUAL-W2 models successfully predicted water temperature and dissolved oxygen on the basis of the two metrics of mean absolute error and root mean square error. For Madison Lake, the mean absolute error and root mean square error were 0.53 and 0.68 degree Celsius, respectively, for the vertical temperature profile comparisons; for Pearl Lake, the mean absolute error and root mean square error were 0.71 and 0.95 degree Celsius, respectively, for the vertical temperature profile comparisons. Temperature and dissolved oxygen were key metrics for calibration targets. These calibrated lake models also simulated algal community dynamics and water quality. The model simulations presented potential explanations for persistently large total phosphorus concentrations in Madison Lake, key differences in nutrient concentrations between these lakes, and summer blue-green algal bloom persistence.Fish habitat suitability simulations for cool-water and warm-water fish indicated that, in general, both lakes contained a large

  19. Assessment of the Suitability of a Global Hydrodynamic Model in Simulating a Regional-scale Extreme Flood at Finer Spatial Resolutions

    Science.gov (United States)

    Mateo, C. M. R.; Yamazaki, D.; Kim, H.; Champathong, A.; Oki, T.

    2015-12-01

    Global river models (GRMs) are elemental for large-scale predictions and impact analyses. However, they have limited capability in providing accurate flood information at fine resolution for practical purposes. Hyperresolution (~1km resolution) modelling is believed to improve the representation of topographical constraints, which consequently result to better predictions of surface water flows and flood inundation at regional to global scales. While numerous studies have shown that finer resolutions improve the predictions of catchment-scale floods using local-scale hydrodynamic models, the impact of finer spatial resolution on predictions of large-scale floods using GRMs is rarely examined. In this study, we assessed the suitability of a state-of-the-art hydrodynamic GRM, CaMa-Flood, in the hyperresolution simulation of a regional-scale flood. The impacts of finer spatial resolution and representation of sub-grid processes on simulating the 2011 immense flooding in Chao Phraya River Basin, Thailand was investigated. River maps ranging from 30-arcsecond (~1km) to 5-arcminute (~10km) spatial resolutions were generated from 90m resolution HydroSHEDS maps and SRTM3 DEM. Simulations were executed in each spatial resolution with the new multi-directional downstream connectivity (MDC) scheme in CaMa-Flood turned on and off. While the predictive capability of the model slightly improved with finer spatial resolution when MDC scheme is turned on, it significantly declined when MDC scheme is turned off; bias increased by 35% and NSE-coefficient decreased by 60%. These findings indicate that GRMs which assume single-downstream-grid flows are not suitable for hyperresolution modelling because of their limited capability to realistically represent floodplain connectivity. When simulating large-scale floods, MDC scheme is necessary for the following functions: provide additional storage for ovehrbank flows, enhance connectivity between floodplains which allow more realistic

  20. Evaluating the suitability of the SWAN/COSMO-2 model system to simulate short-crested surface waves for a narrow lake with complex bathymetry

    Directory of Open Access Journals (Sweden)

    Michael Graf

    2013-07-01

    Full Text Available The spectral wave model SWAN (Simulating Waves Nearshore was applied to Lake Zurich, a narrow pre-Alpine lake in Switzerland. The aim of the study is to investigate whether the model system consisting of SWAN and the numerical weather prediction model COSMO-2 is a suitable tool for wave forecasts for the pre-Alpine Lake Zurich. SWAN is able to simulate short-crested wind-generated surface waves. The model was forced with a time varying wind field taken from COSMO-2 with hourly outputs. Model simulations were compared with measured wave data at one near-shore site during a frontal passage associated with strong on-shore winds. The overall course of the measured wave height is well captured in the SWAN simulation: the wave amplitude significantly increases during the frontal passage followed by a transient drop in amplitude. The wave pattern on Lake Zurich is quite complex. It strongly depends on the inherent variability of the wind field and on the external forcing due to the surrounding complex topography. The influence of the temporal wind resolution is further studied with two sensitivity experiments. The first one considers a low-pass filtered wind field, based on a 2-h running mean of COSMO-2 output, and the second experiment uses simple synthetic gusts, which are implemented into the SWAN model and take into account short-term fluctuations of wind speed at 1-sec resolution. The wave field significantly differs for the 1-h and 2-h simulations, but is only negligibly affected by the gusts.

  1. Terrain correlation suitability

    Science.gov (United States)

    Tang, Wang; McClintock, Robert L.

    1994-07-01

    Terrain-aided navigation (TAN), also referred to as terrain correlation, is a technique that has proven to be highly successful as a navigational aid for autonomous, unmanned guided missiles. Qualitatively speaking, the effectiveness of terrain correlation is a function of signal- to-noise (S/N) ratio. The signal is equivalent to terrain roughness, while the noise is the combination of reference map errors, radar altimeter errors, and INS altitude errors. However, it is not practical to use only a single parameter, such as S/N, to define the suitability of terrain correlation. This paper discusses the shortcomings of the conventional single-parameter approach to the terrain contour matching algorithm (TERCOM) used in cruise missile guidance systems scene selection. A more comprehensive technique is then presented that analyzes the terrain correlation suitability based on a Monte Carlo simulation technique. A figure-of-merit (FOM) for terrain correlation suitability, computed from sample statistics, is introduced and simulation results are provided to illustrate the feasibility of using a multi-parameter FOM technique. The preliminary results indicate that the proposed approach could provide a cost effective enhancement to the TAN-based mission planning process.

  2. Quantitative modeling of a gene's expression from its intergenic sequence.

    Directory of Open Access Journals (Sweden)

    Md Abul Hassan Samee

    2014-03-01

    Full Text Available Modeling a gene's expression from its intergenic locus and trans-regulatory context is a fundamental goal in computational biology. Owing to the distributed nature of cis-regulatory information and the poorly understood mechanisms that integrate such information, gene locus modeling is a more challenging task than modeling individual enhancers. Here we report the first quantitative model of a gene's expression pattern as a function of its locus. We model the expression readout of a locus in two tiers: 1 combinatorial regulation by transcription factors bound to each enhancer is predicted by a thermodynamics-based model and 2 independent contributions from multiple enhancers are linearly combined to fit the gene expression pattern. The model does not require any prior knowledge about enhancers contributing toward a gene's expression. We demonstrate that the model captures the complex multi-domain expression patterns of anterior-posterior patterning genes in the early Drosophila embryo. Altogether, we model the expression patterns of 27 genes; these include several gap genes, pair-rule genes, and anterior, posterior, trunk, and terminal genes. We find that the model-selected enhancers for each gene overlap strongly with its experimentally characterized enhancers. Our findings also suggest the presence of sequence-segments in the locus that would contribute ectopic expression patterns and hence were "shut down" by the model. We applied our model to identify the transcription factors responsible for forming the stripe boundaries of the studied genes. The resulting network of regulatory interactions exhibits a high level of agreement with known regulatory influences on the target genes. Finally, we analyzed whether and why our assumption of enhancer independence was necessary for the genes we studied. We found a deterioration of expression when binding sites in one enhancer were allowed to influence the readout of another enhancer. Thus, interference

  3. Applications of Little's Law to stochastic models of gene expression

    CERN Document Server

    Elgart, Vlad; Kulkarni, Rahul V

    2010-01-01

    The intrinsic stochasticity of gene expression can lead to large variations in protein levels across a population of cells. To explain this variability, different sources of mRNA fluctuations ('Poisson' and 'Telegraph' processes) have been proposed in stochastic models of gene expression. Both Poisson and Telegraph scenario models explain experimental observations of noise in protein levels in terms of 'bursts' of protein expression. Correspondingly, there is considerable interest in establishing relations between burst and steady-state protein distributions for general stochastic models of gene expression. In this work, we address this issue by considering a mapping between stochastic models of gene expression and problems of interest in queueing theory. By applying a general theorem from queueing theory, Little's Law, we derive exact relations which connect burst and steady-state distribution means for models with arbitrary waiting-time distributions for arrival and degradation of mRNAs and proteins. The de...

  4. Suitability Assessment of an ICE-Based Micro-CCHP Unit in Different Spanish Climatic Zones: Application of an Experimental Model in Transient Simulation

    Directory of Open Access Journals (Sweden)

    Guillermo Rey

    2016-11-01

    Full Text Available Tri-generation plants will have an important role in the near future in the residential sector where heating and cooling demands come into play throughout the year. Depending on the building’s location, the characteristics of its enclosure and its use, the thermal loads and demands will be different. This article analyses and compares a combined cooling, heating and power (CCHP system tested in the laboratory and a single household located in Spain. The cooling capacity is obtained using a reversible heat pump where the compressor is driven directly by a gas engine with internal combustion engine (ICE technology. The tests were carried out in a work bench at three different operating speeds. A variable-speed model is developed in the TRNSYS simulation environment with an operating strategy following the thermal load (FTL. Once the micro-CCHP system was modeled with experimental data and validated, it was dynamically simulated to analyze its performance in different climatic zones defined in the Spanish “Código Técnico de la Edificación” (CTE. This study reveals that the micro-CCHP system is suitable in mild weathers during the summer season.

  5. Suitability evaluation of precipitation data using SWAT model%基于SWAT模型的降雨数据适用性评价

    Institute of Scientific and Technical Information of China (English)

    张小丽; 彭勇; 王本德; 王海霞

    2014-01-01

    为评价降雨产品在流域尺度水文模拟中的适用性,该文首先依据实际降雨数据评价 GLDAS、TMPA 和ERA-Interim 3种降雨产品在研究流域的可替代性。多指标模糊优选评价表明,基于双线性插值法的 TMPA 和ERA-Interim降雨产品数据在日、月尺度上的模拟效果均较好,相对误差(Bias)分别为5.48%和7.46%,均小于10%,相关系数(CC)在0.82~0.98之间,具有站点降雨的可替代性,可作为水文模型的输入。然后用此2种降雨产品分别驱动SWAT模型,进行研究流域的水文模拟精度分析。TMPA产品的日、月尺度水文模拟结果的Bias分别为10.88%和11.03%,纳什系数(NSE)分别为0.46和0.78,而ERA-Interim的日、月尺度水文模拟结果的Bias分别为9.11%和9.27%,NSE分别为0.44和0.70。以Bias、CC和NSE为特征指标的多指标模糊优选模型的评价结果为:TMPA产品日、月尺度水文模拟结果的相对隶属度值分别为0.51和0.53,大于ERA-Interim的相对隶属度值0.49和0.47,表明TMPA产品更适用于流域尺度的水文模拟。该文评价方法及结论可为类似流域尺度的水文模拟提供参考。%Precipitation is the important forcing data for hydrological models. However, the precision of hydrological modeling in many regions of the world is limited by the lack of precipitation data. To overcome such limitation, some available globally gridded high resolution precipitation datasets have been used to simulate runoff. Although these precipitation products have been proved to have certain accuracy and good potential for hydrologic simulation, selecting the most optimal precipitation product for certain regions is still important because the accuracy and hydrological utility of precipitation dataset vary in different regions. In this study, the suitability of three precipitation products: GLDAS, TMPA and ERA-Interim for hydrological modeling are evaluated using the multi

  6. General expression for linear and nonlinear time series models

    Institute of Scientific and Technical Information of China (English)

    Ren HUANG; Feiyun XU; Ruwen CHEN

    2009-01-01

    The typical time series models such as ARMA, AR, and MA are founded on the normality and stationarity of a system and expressed by a linear difference equation; therefore, they are strictly limited to the linear system. However, some nonlinear factors are within the practical system; thus, it is difficult to fit the model for real systems with the above models. This paper proposes a general expression for linear and nonlinear auto-regressive time series models (GNAR). With the gradient optimization method and modified AIC information criteria integrated with the prediction error, the parameter estimation and order determination are achieved. The model simulation and experiments show that the GNAR model can accurately approximate to the dynamic characteristics of the most nonlinear models applied in academics and engineering. The modeling and prediction accuracy of the GNAR model is superior to the classical time series models. The proposed GNAR model is flexible and effective.

  7. Experimental infection with the Toxoplasma gondii ME-49 strain in the Brazilian BR-1 mini pig is a suitable animal model for human toxoplasmosis.

    Science.gov (United States)

    Miranda, Farlen José Bebber; Souza, Diogo Benchimol de; Frazão-Teixeira, Edwards; Oliveira, Fábio Conceição de; Melo, João Cardoso de; Mariano, Carlos Magno Anselmo; Albernaz, Antonio Peixoto; Carvalho, Eulógio Carlos Queiróz de; Oliveira, Francisco Carlos Rodrigues de; Souza, Wanderley de; DaMatta, Renato Augusto

    2015-02-01

    Toxoplasma gondii causes toxoplasmosis, a worldwide disease. Experimentation with pigs is necessary for the development of new therapeutic approaches to human diseases. BR-1 mini pigs were intramuscularly infected with T. gondii with tachyzoites (RH strain) or orally infected with cysts (ME-49 strain). Haematology and serum biochemistry were analysed and buffy coat cells were inoculated in mice to determine tachyzoite circulation. No alterations were observed in erythrocyte and platelet values; however, band neutrophils increased seven days after infection with ME-49. Serology of the mice inoculated with pig blood leucocytes revealed circulating ME-49 or RH strain tachyzoites in the pigs' peripheral blood at two and seven or nine days post-infection. The tachyzoites were also directly observed in blood smears from the infected pigs outside and inside leucocytes for longer periods. Alanine-aminotransferase was high at days 21 and 32 in the RH infected pigs. After 90 days, the pigs were euthanised and their tissue samples were processed and inoculated into mice. The mice serology revealed the presence of parasites in the hearts, ileums and mesenteric lymph nodes of the pigs. Additionally, cysts in the mice were only observed after pig heart tissue inoculation. The infected pigs presented similar human outcomes with relatively low pathogenicity and the BR-1 mini pig model infected with ME-49 is suitable to monitor experimental toxoplasmosis.

  8. Experimental infection with the Toxoplasma gondii ME-49 strain in the Brazilian BR-1 mini pig is a suitable animal model for human toxoplasmosis

    Directory of Open Access Journals (Sweden)

    Farlen José Bebber Miranda

    2015-02-01

    Full Text Available Toxoplasma gondii causes toxoplasmosis, a worldwide disease. Experimentation with pigs is necessary for the development of new therapeutic approaches to human diseases. BR-1 mini pigs were intramuscularly infected with T. gondii with tachyzoites (RH strain or orally infected with cysts (ME-49 strain. Haematology and serum biochemistry were analysed and buffy coat cells were inoculated in mice to determine tachyzoite circulation. No alterations were observed in erythrocyte and platelet values; however, band neutrophils increased seven days after infection with ME-49. Serology of the mice inoculated with pig blood leucocytes revealed circulating ME-49 or RH strain tachyzoites in the pigs' peripheral blood at two and seven or nine days post-infection. The tachyzoites were also directly observed in blood smears from the infected pigs outside and inside leucocytes for longer periods. Alanine-aminotransferase was high at days 21 and 32 in the RH infected pigs. After 90 days, the pigs were euthanised and their tissue samples were processed and inoculated into mice. The mice serology revealed the presence of parasites in the hearts, ileums and mesenteric lymph nodes of the pigs. Additionally, cysts in the mice were only observed after pig heart tissue inoculation. The infected pigs presented similar human outcomes with relatively low pathogenicity and the BR-1 mini pig model infected with ME-49 is suitable to monitor experimental toxoplasmosis.

  9. Experimental infection with the Toxoplasma gondii ME-49 strain in the Brazilian BR-1 mini pig is a suitable animal model for human toxoplasmosis

    Science.gov (United States)

    Miranda, Farlen José Bebber; de Souza, Diogo Benchimol; Frazão-Teixeira, Edwards; de Oliveira, Fábio Conceição; de Melo, João Cardoso; Mariano, Carlos Magno Anselmo; Albernaz, Antonio Peixoto; de Carvalho, Eulógio Carlos Queiróz; de Oliveira, Francisco Carlos Rodrigues; de Souza, Wanderley; DaMatta, Renato Augusto

    2015-01-01

    Toxoplasma gondii causes toxoplasmosis, a worldwide disease. Experimentation with pigs is necessary for the development of new therapeutic approaches to human diseases. BR-1 mini pigs were intramuscularly infected with T. gondii with tachyzoites (RH strain) or orally infected with cysts (ME-49 strain). Haematology and serum biochemistry were analysed and buffy coat cells were inoculated in mice to determine tachyzoite circulation. No alterations were observed in erythrocyte and platelet values; however, band neutrophils increased seven days after infection with ME-49. Serology of the mice inoculated with pig blood leucocytes revealed circulating ME-49 or RH strain tachyzoites in the pigs' peripheral blood at two and seven or nine days post-infection. The tachyzoites were also directly observed in blood smears from the infected pigs outside and inside leucocytes for longer periods. Alanine-aminotransferase was high at days 21 and 32 in the RH infected pigs. After 90 days, the pigs were euthanised and their tissue samples were processed and inoculated into mice. The mice serology revealed the presence of parasites in the hearts, ileums and mesenteric lymph nodes of the pigs. Additionally, cysts in the mice were only observed after pig heart tissue inoculation. The infected pigs presented similar human outcomes with relatively low pathogenicity and the BR-1 mini pig model infected with ME-49 is suitable to monitor experimental toxoplasmosis. PMID:25742268

  10. Spawning areas of eastern Baltic cod revisited: Using hydrodynamic modelling to reveal spawning habitat suitability, egg survival probability, and connectivity patterns

    Science.gov (United States)

    Hinrichsen, H.-H.; Lehmann, A.; Petereit, C.; Nissling, A.; Ustups, D.; Bergström, U.; Hüssy, K.

    2016-04-01

    In the highly variable environment of the Baltic Sea two genetically distinct cod stocks exist, one west of the island of Bornholm, which is referred to as the western stock, and one to the east of Bornholm, the eastern stock. A hydrodynamic model combined with a Lagrangian particle tracking technique was utilised to provide spatially and temporally resolved long-term information on environmentally-related (i) spawning habitat size, (ii) egg/yolk-sac larval survival, (iii) separation of causes of mortality, and (iv) connectivity between spawning areas of eastern Baltic cod. Simulations were performed to quantify processes generating heterogeneity in spatial distribution of cod eggs and yolk sac larvae up to the first-feeding stage. The spatial extent of cod eggs represented as virtual drifters is primarily determined by oxygen and salinity conditions at spawning, which define the habitat requirement to which cod's physiology is suited for egg development. The highest habitat suitability occurred in the Bornholm Basin, followed by the Gdansk Deep, while relatively low habitat suitability was obtained for the Arkona and the Gotland Basin. During drift egg and yolk sac larval survival is to a large extent affected by sedimentation. Eggs initially released in the western spawning grounds (Arkona and Bornholm Basin) were more affected by sedimentation than those released in the eastern spawning grounds (Gdansk Deep and Gotland Basin). Highest relative survival of eastern Baltic cod eggs occurred in the Bornholm Basin, with a pronounced decrease towards the Gdansk Deep and the Gotland Basin. Relatively low survival rates in the Gdansk Deep and in the Gotland Basin were attributable to oxygen-dependent mortality. Low oxygen content had almost no impact on survival in the Arkona Basin. For all spawning areas temperature dependent mortality was only evident after severe winters. Egg buoyancy in relation to topographic features like bottom sills and strong bottom slopes

  11. Development of a ground hydrology model suitable for global climate modeling using soil morphology and vegetation cover, and an evaluation of remotely sensed information

    Science.gov (United States)

    Zobler, L.; Lewis, R.

    1988-01-01

    The long-term purpose was to contribute to scientific understanding of the role of the planet's land surfaces in modulating the flows of energy and matter which influence the climate, and to quantify and monitor human-induced changes to the land environment that may affect global climate. Highlights of the effort include the following: production of geo-coded, digitized World Soil Data file for use with the Goddard Institute for Space Studies (GISS) climate model; contribution to the development of a numerical physically-based model of ground hydrology; and assessment of the utility of remote sensing for providing data on hydrologically significant land surface variables.

  12. Gene expression and behaviour in mouse models of HD.

    Science.gov (United States)

    Bowles, K R; Brooks, S P; Dunnett, S B; Jones, L

    2012-06-01

    Huntington's disease (HD) is an autosomal dominant neurodegenerative disease, resulting in expansion of the CAG repeat in exon 1 of the HTT gene. The resulting mutant huntingtin protein has been implicated in the disruption of a variety of cellular functions, including transcription. Mouse models of HD have been central to the development of our understanding of gene expression changes in this disease, and are now beginning to elucidate the relationship between gene expression and behaviour. Here, we review current mouse models of HD and their characterisation in terms of gene expression. In addition, we look at how this can inform behaviours observed in mouse models of disease. The relationship between gene expression and behaviour in mouse models of HD is important, as this will further our knowledge of disease progression and its underlying molecular events, highlight new treatment targets, and potentially provide new biomarkers for therapeutic trials. Copyright © 2011 Elsevier Inc. All rights reserved.

  13. CONCEPTUAL MODELING BASED ON LOGICAL EXPRESSION AND EVOLVEMENT

    Institute of Scientific and Technical Information of China (English)

    Yl Guodong; ZHANG Shuyou; TAN Jianrong; JI Yangjian

    2007-01-01

    Aiming at the problem of abstract and polytype information modeling in product conceptual design, a method of conceptual modeling based on logical expression and evolvement is presented. Based on the logic expressions of the product conceptual design information, a function/logic/structure mapping model is set up. First, the function semantics is transformed into logical expressions through function/logic mapping. Second, the methods of logical evolvement are utilized to describe the function analysis, function/structure mapping and structure combination. Last, the logical structure scheme is transformed into geometrical sketch through logic/structure mapping. The conceptual design information and modeling process are described uniformly with logical methods in the model, and an effective method for computer aided conceptual design based on the model is implemented.

  14. Distributed modelling of water resources in the Lower Jordan River Basin - from present day variability to suitability for new water sources

    Science.gov (United States)

    Gunkel, Anne; Lange, Jens

    2010-05-01

    The Middle East is characterized by a high temporal and spatial variability of rainfall. As a result, water resources are not reliable and severe drought events are frequent, worsening the natural water scarcity. Single high magnitude events may dominate the water balance of entire seasons - a fact that is poorly represented in the assessments of available water resources that are normally based on long term averages. Therefore, a distributed hydrological model with a high temporal and spatial resolution is applied to the Lower Jordan River basin (LJRB). The focus is hereby to capture the variability of rainfall and to investigate how this signal is amplified in the hydrological cycle in this arid and semi arid environment. Rainfall variability is addressed through a volume scanning rainfall radar providing precipitation data with a resolution of 5 minutes for entire seasons that serves as input to a conceptual hydrological model. The raw radar data recorded by a C-Band system was pre-corrected by a multiple regression approach prior to regionalization to the LJRB, ground truthing with rainfall station data and conditional merging. Despite certain uncertainties, the data documents the accentuated rainfall variability in the entire LJRB. In order to include the full range of present rainfall variability, one average and two extreme seasons (wet and dry) are studied. Hydrological modelling is undertaken with a new modelling tool created by coupling two hydrological models, TRAIN and ZIN, complementing each other in respect to the addressed processes and water fluxes. The resulting modelling tool enables conceptual modelling of the processes relevant for semi-arid / arid environments with a high temporal and spatial resolution. The model is applied to the large scale LJRB (16,000 km²) in order to simulate all components of the water balance for three rainy seasons representing the present climate variability. Under given conditions of low data availability, the

  15. [Cultural regionalization for Notopterygium incisum based on 3S technology platform. I. Evaluation for growth suitability for N. incisum based on ecological factors analysis by Maxent and ArcGIS model].

    Science.gov (United States)

    Sun, Hong-bing; Sun, Hui; Jiang, Shun-yuan; Zhou, Yi; Cao, Wen-long; Ji, Ming-chang; Zhy, Wen-tao; Yan, Han-jing

    2015-03-01

    Growth suitability as assessment indicators for medicinal plants cultivation was proposed based on chemical quality determination and ecological factors analysis by Maxent and ArcGIS model. Notopterygium incisum, an endangered Chinese medicinal plant, was analyzed as a case, its potential distribution areas at different suitability grade and regionalization map were formulated based on growth suitability theory. The results showed that the most suitable habitats is Sichuan province, and more than 60% of the most suitable areawas located in the western Sichuan such as Aba and Ganzi prefectures for N. incisum. The results indicated that habitat altitude, average air temperature in September, and vegetation types were the dominant factors contributing to the grade of plant growth, precipitation and slope were the major factors contributing to notopterol accumulation in its underground parts, while isoimperatorin in its underground parts was negatively corelated with precipitation and slope of its habitat. However, slope as a factor influencing chemical components seemed to be a pseudo corelationship. Therefore, there were distinguishing differences between growth suitability and quality suitability for medicinal plants, which was helpful to further research and practice of cultivation regionalization, wild resource monitoring and large-scale cultivation of traditional Chinese medicine plants.

  16. Integrated multi-criteria decision making techniques AHP with Geographic Information System for Modelling of suitable Landfill location: a case study in Keraniganj of Dhaka city, Bangladesh.

    Science.gov (United States)

    Iqbal, M.

    2015-12-01

    This study is approaches a GIS based multi-criteria decision making technique to select potential land fill in Keraniganj of Dhaka city in Bangladesh. Site selection of landfill for Municipal solid waste is an important concern for the urban government in whole world. Dhaka city is highly dense populated city in Bangladesh and municipal solid waste generation rate is increase rapidly day by day. These large amount of generated municipal waste needs appropriate landfill considering environmental, geological, social and technical aspect of the region. The traditional process of site selection process is much difficult, time consuming and costly and needs to replace by a new approaches. An integration of Geographical Information System (GIS) and Multi-criteria Evaluation (MCE) method is best combination to solve complex decision and used to select suitable site. Analytical Hierarchy process (AHP) is world widely most popular decision making MCE technique. In this study AHP used as a multi-criteria decision making to compare five suitability attributes with each other and evaluate weight according to attributes potentiality. Various type raster map layer created using GIS tool for this study. Five suitability raster was assigned with the AHP calculated weight value. A combined weighted spatial layer obtained name as suitability map which is overlapped with a restriction raster map, as result a final suitable map was obtained. The result shows that 12.2% of the area is suitable for constructing landfill site where 4.9% is very high suitable, 2.6% is moderate suitable and 4.7% is low suitable. The final site is constructed after detail field investigation, other technical investigation, land ownership status and public acceptancy. Suitable site selection for non-hazardous landfill is not easy and its needs to consider many environmental factor at time. GIS tool combining with many decision making tool such as multi-criteria evaluation can solve this problem. A combining

  17. DFT modeling on the suitable crown ether architecture for complexation with Cs⁺ and Sr²⁺ metal ions.

    Science.gov (United States)

    Boda, Anil; Ali, Sk Musharaf; Shenoi, Madhav R K; Rao, Hanmanth; Ghosh, Sandip K

    2011-05-01

    Crown ether architectures were explored for the inclusion of Cs(+) and Sr(2+) ions within nano-cavity of macrocyclic crown ethers using density functional theory (DFT) modeling. The modeling was undertaken to gain insight into the mechanism of the complexation of Cs(+) and Sr(2+) ion with this ligand experimentally. The selectivity of Cs(+) and Sr(2+) ions for a particular size of crown ether has been explained based on the fitting and binding interaction of the guest ions in the narrow cavity of crown ethers. Although, Di-Benzo-18-Crown-6 (DB18C6) and Di-Benzo-21-Crown-7 (DB21C7) provide suitable host architecture for Sr(2+) and Cs(+) ions respectively as the ion size match with the cavity of the host, but consideration of binding interaction along with the cavity matching both DB18C6 and DB21C7 prefers Sr(2+) ion. The calculated values of binding enthalpy of Cs metal ion with the crown ethers were found to be in good agreement with the experimental results. The gas phase binding enthalpy for Sr(2+) ion with crown ether was higher than Cs metal ion. The ion exchange reaction between Sr and Cs always favors the selection of Sr metal ion both in the gas and in micro-solvated systems. The gas phase selectivity remains unchanged in micro-solvated phase. We have demonstrated the effect of micro-solvation on the binding interaction between the metal ions (Cs(+) and Sr(2+)) and the macrocyclic crown ethers by considering micro-solvated metal ions up to eight water molecules directly attached to the metal ion and also by considering two water molecules attached to metal-ion-crown ether complexes. A metal ion exchange reaction involving the replacement of strontium ion in metal ion-crown ether complexes with cesium ion contained within a metal ion-water cluster serves as the basis for modeling binding preferences in solution. The calculated O-H stretching frequency of H(2)O molecule in micro-solvated metal ion-crown complexes is more red-shifted in comparison to hydrated

  18. Improper hydrogen bonded cyclohexane C-Hax···Yax contacts: theoretical predictions and experimental evidence from 1H NMR spectroscopy of suitable axial cyclohexane models.

    Science.gov (United States)

    Kolocouris, Antonios; Zervos, Nikolaos; De Proft, Frank; Koch, Andreas

    2011-06-03

    C-H(ax)···Y(ax) contacts are a textbook prototype of steric hindrance in organic chemistry. The nature of these contacts is investigated in this work. MP2/6-31+G(d,p) calculations predicted the presence of improper hydrogen bonded C-H(ax)···Y(ax) contacts of different strength in substituted cyclohexane rings. To support the theoretical predictions with experimental evidence, several synthetic 2-substituted adamantane analogues (1-24) with suitable improper H-bonded C-H(ax)···Y(ax) contacts of different strength were used as models of a substituted cyclohexane ring. The (1)H NMR signal separation, Δδ(γ-CH(2)), within the cyclohexane ring γ-CH(2)s is raised when the MP2/6-31+G(d,p) calculated parameters, reflecting the strength of the H-bonded C-H(ax)···Y(ax) contact, are increased. In molecules with enhanced improper H-bonded contacts C-H(ax)···Y(ax), like those having sterically crowded contacts (Y(ax) = t-Bu) or contacts including considerable electrostatic attractions (Y(ax) = O-C or O═C) the calculated DFT steric energies of the γ-axial hydrogens are considerably reduced reflecting their electron cloud compression. The results suggest that the proton H(ax) electron cloud compression, caused by the C-H(ax)···Y(ax) contacts, and the resulting increase in Δδ(γ-CH(2)) value can be effected not just from van der Waals spheres compression, but more generally from electrostatic attraction forces and van der Waals repulsion, both of which are improper H-bonding components.

  19. How to Evaluate the Rice Cultivation Suitability?

    Institute of Scientific and Technical Information of China (English)

    Wenxi; LI; Yueping; ZHANG; Changsong; WANG; Wei; MAO; Tianwen; HANG; Ming; CHEN; Bingning; ZHANG

    2013-01-01

    To rationally allocate farmland resources,and scientifically make farming industrial planning,we take Yizheng City in Jiangsu Province as the research object,and select 13 indicators.Based on Farmland Resources Management Information System in Yizheng City,we establish AHP model,and membership function model,for the evaluation of farmland suitability of rice.The results show that the farmland area in the highly suitable areas accounts for 10.2%of the total farmland area;the farmland area in the suitable areas accounts for 56.08%of the total farmland area;the farmland area in the marginally suitable areas accounts for 25.50%of the total farmland area;the farmland area in the unsuitable areas accounts for 8.22%of the total farmland area.There is significant positive correlation between the actual yield of rice surveyed and suitability index obtained through evaluation(R2=0.1964,319 samples);the actual yield of rice in the highly suitable areas is higher than in the marginally suitable areas and suitable areas,and the rice yield is the lowest in the unsuitable areas.

  20. Mapping past, present, and future climatic suitability for invasive Aedes aegypti and Aedes albopictus in the United States: a process-based modeling approach using CMIP5 downscaled climate scenarios

    Science.gov (United States)

    Donnelly, M. A. P.; Marcantonio, M.; Melton, F. S.; Barker, C. M.

    2016-12-01

    The ongoing spread of the mosquitoes, Aedes aegypti and Aedes albopictus, in the continental United States leaves new areas at risk for local transmission of dengue, chikungunya, and Zika viruses. All three viruses have caused major disease outbreaks in the Americas with infected travelers returning regularly to the U.S. The expanding range of these mosquitoes raises questions about whether recent spread has been enabled by climate change or other anthropogenic influences. In this analysis, we used downscaled climate scenarios from the NASA Earth Exchange Global Daily Downscaled Projections (NEX GDDP) dataset to model Ae. aegypti and Ae. albopictus population growth rates across the United States. We used a stage-structured matrix population model to understand past and present climatic suitability for these vectors, and to project future suitability under CMIP5 climate change scenarios. Our results indicate that much of the southern U.S. is suitable for both Ae. aegypti and Ae. albopictus year-round. In addition, a large proportion of the U.S. is seasonally suitable for mosquito population growth, creating the potential for periodic incursions into new areas. Changes in climatic suitability in recent decades for Ae. aegypti and Ae. albopictus have occurred already in many regions of the U.S., and model projections of future climate suggest that climate change will continue to reshape the range of Ae. aegypti and Ae. albopictus in the U.S., and potentially the risk of the viruses they transmit.

  1. Mapping Past, Present, and Future Climatic Suitability for Invasive Aedes Aegypti and Aedes Albopictus in the United States: A Process-Based Modeling Approach Using CMIP5 Downscaled Climate Scenarios

    Science.gov (United States)

    Donnelly, Marisa Anne Pella; Marcantonio, Matteo; Melton, Forrest S.; Barker, Christopher M.

    2016-01-01

    The ongoing spread of the mosquitoes, Aedes aegypti and Aedes albopictus, in the continental United States leaves new areas at risk for local transmission of dengue, chikungunya, and Zika viruses. All three viruses have caused major disease outbreaks in the Americas with infected travelers returning regularly to the U.S. The expanding range of these mosquitoes raises questions about whether recent spread has been enabled by climate change or other anthropogenic influences. In this analysis, we used downscaled climate scenarios from the NASA Earth Exchange Global Daily Downscaled Projections (NEX GDDP) dataset to model Ae. aegypti and Ae. albopictus population growth rates across the United States. We used a stage-structured matrix population model to understand past and present climatic suitability for these vectors, and to project future suitability under CMIP5 climate change scenarios. Our results indicate that much of the southern U.S. is suitable for both Ae. aegypti and Ae. albopictus year-round. In addition, a large proportion of the U.S. is seasonally suitable for mosquito population growth, creating the potential for periodic incursions into new areas. Changes in climatic suitability in recent decades for Ae. aegypti and Ae. albopictus have occurred already in many regions of the U.S., and model projections of future climate suggest that climate change will continue to reshape the range of Ae. aegypti and Ae. albopictus in the U.S., and potentially the risk of the viruses they transmit.

  2. Screening for suitable areas for Aquifer Thermal Energy Storage within the Brussels Capital Region, Belgium using coupled groundwater flow and heat transport modelling tools

    Science.gov (United States)

    Anibas, Christian; Kukral, Janik; Touhidul Mustafa, Syed Md; Huysmans, Marijke

    2017-04-01

    Urban areas have a great potential for shallow geothermal systems. Their energy demand is high, but currently they have only a limited potential to cover their own energy demand. The transition towards a low-carbon energy regime offers alternative sources of energy an increasing potential. Urban areas however pose special challenges for the successful exploitation of shallow geothermal energy. High building densities limit the available space for drillings and underground investigations. Urban heat island effects and underground structures influence the thermal field, groundwater pollution and competing water uses limit the available subsurface. To tackle these challenges in the Brussels Capital Region, Belgium two projects 'BruGeo' and the recently finished 'Prospective Research of Brussels project 2015-PRFB-228' address the investigation in urban geothermal systems. They aim to identify the key factors of the underground with respect to Aquifer Thermal Energy Storage (ATES) installations like thermal properties, aquifer thicknesses, groundwater flow velocities and their heterogeneity. Combined numerical groundwater and heat transport models are applied for the assessment of both open and closed loop shallow geothermal systems. The Brussels Capital Region comprises of the Belgian Capital, the City of Brussels and 18 other municipalities covering 161 km2 with almost 1.2 million inhabitants. Beside the high population density the Brussels Capital Region has a pronounced topography and a relative complex geology. This is both a challenge and an opportunity for the exploitation of shallow geothermal energy. The most important shallow hydrogeological formation in the Brussels-Capital Region are the Brussels Sands with the Brussels Sands Aquifer. Scenarios where developed using criteria for the hydrogeological feasibility of ATES installations such as saturated aquifer thickness, groundwater flow velocity and the groundwater head below surface. The Brussels Sands

  3. Modeling of gap gene expression in Drosophila Kruppel mutants.

    Directory of Open Access Journals (Sweden)

    Konstantin Kozlov

    Full Text Available The segmentation gene network in Drosophila embryo solves the fundamental problem of embryonic patterning: how to establish a periodic pattern of gene expression, which determines both the positions and the identities of body segments. The gap gene network constitutes the first zygotic regulatory tier in this process. Here we have applied the systems-level approach to investigate the regulatory effect of gap gene Kruppel (Kr on segmentation gene expression. We acquired a large dataset on the expression of gap genes in Kr null mutants and demonstrated that the expression levels of these genes are significantly reduced in the second half of cycle 14A. To explain this novel biological result we applied the gene circuit method which extracts regulatory information from spatial gene expression data. Previous attempts to use this formalism to correctly and quantitatively reproduce gap gene expression in mutants for a trunk gap gene failed, therefore here we constructed a revised model and showed that it correctly reproduces the expression patterns of gap genes in Kr null mutants. We found that the remarkable alteration of gap gene expression patterns in Kr mutants can be explained by the dynamic decrease of activating effect of Cad on a target gene and exclusion of Kr gene from the complex network of gap gene interactions, that makes it possible for other interactions, in particular, between hb and gt, to come into effect. The successful modeling of the quantitative aspects of gap gene expression in mutant for the trunk gap gene Kr is a significant achievement of this work. This result also clearly indicates that the oversimplified representation of transcriptional regulation in the previous models is one of the reasons for unsuccessful attempts of mutant simulations.

  4. On the Computational Expressiveness of Model Transformation Languages

    DEFF Research Database (Denmark)

    Al-Sibahi, Ahmad Salim

    2015-01-01

    Common folklore in the model transformation community dictates that most transformation languages are Turing-complete. It is however seldom that a proof or an explanation is provided on why such property holds; due to the widely different features and execution models in these language, it is not......Common folklore in the model transformation community dictates that most transformation languages are Turing-complete. It is however seldom that a proof or an explanation is provided on why such property holds; due to the widely different features and execution models in these language......, it is not immediately obvious what their computational expressiveness is. In this paper we present an analysis that clarifies the computational expressiveness of a large number of model transformation languages. The analysis confirms the folklore for all model transformation languages, except the bidirectional ones...

  5. Reconstructing dynamic mental models of facial expressions in prosopagnosia reveals distinct representations for identity and expression.

    Science.gov (United States)

    Richoz, Anne-Raphaëlle; Jack, Rachael E; Garrod, Oliver G B; Schyns, Philippe G; Caldara, Roberto

    2015-04-01

    The human face transmits a wealth of signals that readily provide crucial information for social interactions, such as facial identity and emotional expression. Yet, a fundamental question remains unresolved: does the face information for identity and emotional expression categorization tap into common or distinct representational systems? To address this question we tested PS, a pure case of acquired prosopagnosia with bilateral occipitotemporal lesions anatomically sparing the regions that are assumed to contribute to facial expression (de)coding (i.e., the amygdala, the insula and the posterior superior temporal sulcus--pSTS). We previously demonstrated that PS does not use information from the eye region to identify faces, but relies on the suboptimal mouth region. PS's abnormal information use for identity, coupled with her neural dissociation, provides a unique opportunity to probe the existence of a dichotomy in the face representational system. To reconstruct the mental models of the six basic facial expressions of emotion in PS and age-matched healthy observers, we used a novel reverse correlation technique tracking information use on dynamic faces. PS was comparable to controls, using all facial features to (de)code facial expressions with the exception of fear. PS's normal (de)coding of dynamic facial expressions suggests that the face system relies either on distinct representational systems for identity and expression, or dissociable cortical pathways to access them. Interestingly, PS showed a selective impairment for categorizing many static facial expressions, which could be accounted for by her lesion in the right inferior occipital gyrus. PS's advantage for dynamic facial expressions might instead relate to a functionally distinct and sufficient cortical pathway directly connecting the early visual cortex to the spared pSTS. Altogether, our data provide critical insights on the healthy and impaired face systems, question evidence of deficits

  6. [Ecology suitability study of Ephedra intermedia].

    Science.gov (United States)

    Ma, Xiao-Hui; Lu, You-Yuan; Huang, De-Dong; Zhu, Tian-Tian; Lv, Pei-Lin; Jin, Ling

    2017-06-01

    The study aims at predicting ecological suitability of Ephedra intermedia in China by using maximum entropy Maxent model combined with GIS, and finding the main ecological factors affecting the distribution of E. intermedia suitability in appropriate growth area. Thirty-eight collected samples of E. intermedia and E. intermedia and 116 distribution information from CVH information using ArcGIS technology were analyzed. MaxEnt model was applied to forecast the E. intermedia in our country's ecology. E. intermedia MaxEnt ROC curve model training data and testing data sets the AUC value was 0.986 and 0.958, respectively, which were greater than 0.9, tending to be 1.The calculated E. intermedia habitat suitability by the model showed a high accuracy and credibility, which indicated that MaxEnt model could well predict the potential distribution area of E. intermedia in China. Copyright© by the Chinese Pharmaceutical Association.

  7. Embryo quality predictive models based on cumulus cells gene expression

    Directory of Open Access Journals (Sweden)

    Devjak R

    2016-06-01

    Full Text Available Since the introduction of in vitro fertilization (IVF in clinical practice of infertility treatment, the indicators for high quality embryos were investigated. Cumulus cells (CC have a specific gene expression profile according to the developmental potential of the oocyte they are surrounding, and therefore, specific gene expression could be used as a biomarker. The aim of our study was to combine more than one biomarker to observe improvement in prediction value of embryo development. In this study, 58 CC samples from 17 IVF patients were analyzed. This study was approved by the Republic of Slovenia National Medical Ethics Committee. Gene expression analysis [quantitative real time polymerase chain reaction (qPCR] for five genes, analyzed according to embryo quality level, was performed. Two prediction models were tested for embryo quality prediction: a binary logistic and a decision tree model. As the main outcome, gene expression levels for five genes were taken and the area under the curve (AUC for two prediction models were calculated. Among tested genes, AMHR2 and LIF showed significant expression difference between high quality and low quality embryos. These two genes were used for the construction of two prediction models: the binary logistic model yielded an AUC of 0.72 ± 0.08 and the decision tree model yielded an AUC of 0.73 ± 0.03. Two different prediction models yielded similar predictive power to differentiate high and low quality embryos. In terms of eventual clinical decision making, the decision tree model resulted in easy-to-interpret rules that are highly applicable in clinical practice.

  8. Modeling considerations for using expression data from multiple species.

    Science.gov (United States)

    Siewert, Elizabeth; Kechris, Katerina J

    2013-10-15

    Although genome-wide expression data sets from multiple species are now more commonly generated, there have been few studies on how to best integrate this type of correlated data into models. Starting with a single-species, linear regression model that predicts transcription factor binding sites as a case study, we investigated how best to take into account the correlated expression data when extending this model to multiple species. Using a multivariate regression model, we accounted for the phylogenetic relationships among the species in two ways: (i) a repeated-measures model, where the error term is constrained; and (ii) a Bayesian hierarchical model, where the prior distributions of the regression coefficients are constrained. We show that both multiple-species models improve predictive performance over the single-species model. When compared with each other, the repeated-measures model outperformed the Bayesian model. We suggest a possible explanation for the better performance of the model with the constrained error term. Copyright © 2013 John Wiley & Sons, Ltd.

  9. Sequential logic model deciphers dynamic transcriptional control of gene expressions.

    Directory of Open Access Journals (Sweden)

    Zhen Xuan Yeo

    Full Text Available BACKGROUND: Cellular signaling involves a sequence of events from ligand binding to membrane receptors through transcription factors activation and the induction of mRNA expression. The transcriptional-regulatory system plays a pivotal role in the control of gene expression. A novel computational approach to the study of gene regulation circuits is presented here. METHODOLOGY: Based on the concept of finite state machine, which provides a discrete view of gene regulation, a novel sequential logic model (SLM is developed to decipher control mechanisms of dynamic transcriptional regulation of gene expressions. The SLM technique is also used to systematically analyze the dynamic function of transcriptional inputs, the dependency and cooperativity, such as synergy effect, among the binding sites with respect to when, how much and how fast the gene of interest is expressed. PRINCIPAL FINDINGS: SLM is verified by a set of well studied expression data on endo16 of Strongylocentrotus purpuratus (sea urchin during the embryonic midgut development. A dynamic regulatory mechanism for endo16 expression controlled by three binding sites, UI, R and Otx is identified and demonstrated to be consistent with experimental findings. Furthermore, we show that during transition from specification to differentiation in wild type endo16 expression profile, SLM reveals three binary activities are not sufficient to explain the transcriptional regulation of endo16 expression and additional activities of binding sites are required. Further analyses suggest detailed mechanism of R switch activity where indirect dependency occurs in between UI activity and R switch during specification to differentiation stage. CONCLUSIONS/SIGNIFICANCE: The sequential logic formalism allows for a simplification of regulation network dynamics going from a continuous to a discrete representation of gene activation in time. In effect our SLM is non-parametric and model-independent, yet

  10. [Cultural regionalization for Coptis chinensis based on 3S technology platform Ⅰ. Study on growth suitability for Coptis chinensis based on ecological factors analysis by Maxent and ArcGIS model].

    Science.gov (United States)

    Liu, Xin; Yang, Yan-Fang; Song, Hong-Ping; Zhang, Xiao-Bo; Huang, Lu-Qi; Wu, He-Zhen

    2016-09-01

    At the urgent request of Coptis chinensis planting,growth suitability as assessment indicators for C. chinensis cultivation was proposed and analyzed in this paper , based on chemical quality determination and ecological fators analysis by Maxent and ArcGIS model. Its potential distribution areas at differernt suitability grade and regionalization map were formulated based on statistical theory and growth suitability theory. The results showed that the most suitable habitats is some parts of Chongqing and Hubei province, such as Shizhu, Lichuan, Wulong, Wuxi, Enshi. There are seven ecological factor is the main ecological factors affect the growth of Coptidis Rhizoma, including altitude, precipitation in February and September and the rise of precipitation and altitude is conducive to the accumulation of total alkaloid content in C. chinensis. Therefore, The results of the study not only illustrates the most suitable for the surroundings of Coptidis Rhizoma, also helpful to further research and practice of cultivation regionalization, wild resource monitoring and large-scale cultivation of traditional Chinese medicine plants. Copyright© by the Chinese Pharmaceutical Association.

  11. Selection and Performance-Degradation Modeling of LiMO2/Li4Ti5O12 and LiFePO4/C Battery Cells as Suitable Energy Storage Systems for Grid Integration With Wind Power Plants

    DEFF Research Database (Denmark)

    Swierczynski, Maciej Jozef; Stroe, Daniel Ioan; Stan, Ana-Irina

    2014-01-01

    as the requirement criterion while Li–ion batteries where found as the devices which could best fulfil this requirement. Since accurate and fast battery performance models are indispensable for studying the virtual power plant behavior under different operating conditions, impedance-based performance......-degradation models were developed for the two most suitable Li–ion chemistries for the primary frequency regulation service: LiMO2 /Li4Ti5O12 and LiFePO4/C....

  12. Predicting Suitable field workdays for soil tillage in North Central ...

    African Journals Online (AJOL)

    Oladimeji S. Ife

    A simulation model was developed to predict suitable field workdays for tillage operations in North Central ... KEYWORDS: Suitable field workdays, tillage, agro –meteorology, tractability. 1. ... approach, the calculation of the components.

  13. Modelling of Arabidopsis LAX3 expression suggests auxin homeostasis.

    Science.gov (United States)

    Mellor, Nathan; Péret, Benjamin; Porco, Silvana; Sairanen, Ilkka; Ljung, Karin; Bennett, Malcolm; King, John

    2015-02-07

    Emergence of new lateral roots from within the primary root in Arabidopsis has been shown to be regulated by the phytohormone auxin, via the expression of the auxin influx carrier LAX3, mediated by the ARF7/19 IAA14 signalling module (Swarup et al., 2008). A single cell model of the LAX3 and IAA14 auxin response was formulated and used to demonstrate that hysteresis and bistability may explain the experimentally observed 'all-or-nothing' LAX3 spatial expression pattern in cortical cells containing a gradient of auxin concentrations. The model was tested further by using a parameter fitting algorithm to match model output with qRT-PCR mRNA expression data following exogenous auxin treatment. It was found that the model is able to show good agreement with the data, but only when the exogenous auxin signal is degraded over time, at a rate higher than that measured in the experimental medium, suggesting the triggering of an endogenous auxin homeostasis mechanism. Testing the model over a more physiologically relevant range of extracellular auxin shows bistability and hysteresis still occur when using the optimised parameters, providing the rate of LAX3 active auxin transport is sufficiently high relative to passive diffusion.

  14. Rock suitability classification RSC 2012

    Energy Technology Data Exchange (ETDEWEB)

    McEwen, T. (ed.) [McEwen Consulting, Leicester (United Kingdom); Kapyaho, A. [Geological Survey of Finland, Espoo (Finland); Hella, P. [Saanio and Riekkola, Helsinki (Finland); Aro, S.; Kosunen, P.; Mattila, J.; Pere, T.

    2012-12-15

    This report presents Posiva's Rock Suitability Classification (RSC) system, developed for locating suitable rock volumes for repository design and construction. The RSC system comprises both the revised rock suitability criteria and the procedure for the suitability classification during the construction of the repository. The aim of the classification is to avoid such features of the host rock that may be detrimental to the favourable conditions within the repository, either initially or in the long term. This report also discusses the implications of applying the RSC system for the fulfilment of the regulatory requirements concerning the host rock as a natural barrier and the site's overall suitability for hosting a final repository of spent nuclear fuel.

  15. Reverse engineering model structures for soil and ecosystem respiration: the potential of gene expression programming

    Science.gov (United States)

    Ilie, Iulia; Dittrich, Peter; Carvalhais, Nuno; Jung, Martin; Heinemeyer, Andreas; Migliavacca, Mirco; Morison, James I. L.; Sippel, Sebastian; Subke, Jens-Arne; Wilkinson, Matthew; Mahecha, Miguel D.

    2017-09-01

    Accurate model representation of land-atmosphere carbon fluxes is essential for climate projections. However, the exact responses of carbon cycle processes to climatic drivers often remain uncertain. Presently, knowledge derived from experiments, complemented by a steadily evolving body of mechanistic theory, provides the main basis for developing such models. The strongly increasing availability of measurements may facilitate new ways of identifying suitable model structures using machine learning. Here, we explore the potential of gene expression programming (GEP) to derive relevant model formulations based solely on the signals present in data by automatically applying various mathematical transformations to potential predictors and repeatedly evolving the resulting model structures. In contrast to most other machine learning regression techniques, the GEP approach generates readable models that allow for prediction and possibly for interpretation. Our study is based on two cases: artificially generated data and real observations. Simulations based on artificial data show that GEP is successful in identifying prescribed functions, with the prediction capacity of the models comparable to four state-of-the-art machine learning methods (random forests, support vector machines, artificial neural networks, and kernel ridge regressions). Based on real observations we explore the responses of the different components of terrestrial respiration at an oak forest in south-eastern England. We find that the GEP-retrieved models are often better in prediction than some established respiration models. Based on their structures, we find previously unconsidered exponential dependencies of respiration on seasonal ecosystem carbon assimilation and water dynamics. We noticed that the GEP models are only partly portable across respiration components, the identification of a general terrestrial respiration model possibly prevented by equifinality issues. Overall, GEP is a promising

  16. Evaluation of Plaid Models in Biclustering of Gene Expression Data

    Directory of Open Access Journals (Sweden)

    Hamid Alavi Majd

    2016-01-01

    Full Text Available Background. Biclustering algorithms for the analysis of high-dimensional gene expression data were proposed. Among them, the plaid model is arguably one of the most flexible biclustering models up to now. Objective. The main goal of this study is to provide an evaluation of plaid models. To that end, we will investigate this model on both simulation data and real gene expression datasets. Methods. Two simulated matrices with different degrees of overlap and noise are generated and then the intrinsic structure of these data is compared with biclusters result. Also, we have searched biologically significant discovered biclusters by GO analysis. Results. When there is no noise the algorithm almost discovered all of the biclusters but when there is moderate noise in the dataset, this algorithm cannot perform very well in finding overlapping biclusters and if noise is big, the result of biclustering is not reliable. Conclusion. The plaid model needs to be modified because when there is a moderate or big noise in the data, it cannot find good biclusters. This is a statistical model and is a quite flexible one. In summary, in order to reduce the errors, model can be manipulated and distribution of error can be changed.

  17. A Highly Efficient Gene Expression Programming (GEP Model for Auxiliary Diagnosis of Small Cell Lung Cancer.

    Directory of Open Access Journals (Sweden)

    Zhuang Yu

    Full Text Available Lung cancer is an important and common cancer that constitutes a major public health problem, but early detection of small cell lung cancer can significantly improve the survival rate of cancer patients. A number of serum biomarkers have been used in the diagnosis of lung cancers; however, they exhibit low sensitivity and specificity.We used biochemical methods to measure blood levels of lactate dehydrogenase (LDH, C-reactive protein (CRP, Na+, Cl-, carcino-embryonic antigen (CEA, and neuron specific enolase (NSE in 145 small cell lung cancer (SCLC patients and 155 non-small cell lung cancer and 155 normal controls. A gene expression programming (GEP model and Receiver Operating Characteristic (ROC curves incorporating these biomarkers was developed for the auxiliary diagnosis of SCLC.After appropriate modification of the parameters, the GEP model was initially set up based on a training set of 115 SCLC patients and 125 normal controls for GEP model generation. Then the GEP was applied to the remaining 60 subjects (the test set for model validation. GEP successfully discriminated 281 out of 300 cases, showing a correct classification rate for lung cancer patients of 93.75% (225/240 and 93.33% (56/60 for the training and test sets, respectively. Another GEP model incorporating four biomarkers, including CEA, NSE, LDH, and CRP, exhibited slightly lower detection sensitivity than the GEP model, including six biomarkers. We repeat the models on artificial neural network (ANN, and our results showed that the accuracy of GEP models were higher than that in ANN. GEP model incorporating six serum biomarkers performed by NSCLC patients and normal controls showed low accuracy than SCLC patients and was enough to prove that the GEP model is suitable for the SCLC patients.We have developed a GEP model with high sensitivity and specificity for the auxiliary diagnosis of SCLC. This GEP model has the potential for the wide use for detection of SCLC in less

  18. Solanum venturii, a suitable model system for virus-induced gene silencing studies in potato reveals StMKK6 as an important player in plant immunity

    NARCIS (Netherlands)

    Dobnik, David; Lazar, Ana; Stare, Tjaša; Gruden, Kristina; Vleeshouwers, Vivianne G.A.A.; Žel, Jana

    2016-01-01

    Background: Virus-induced gene silencing (VIGS) is an optimal tool for functional analysis of genes in plants, as the viral vector spreads throughout the plant and causes reduced expression of selected gene over the whole plant. Potato (Solanum tuberosum) is one of the most important food crops,

  19. Modeling Three-Dimensional Chromosome Structures Using Gene Expression Data.

    Science.gov (United States)

    Xiao, Guanghua; Wang, Xinlei; Khodursky, Arkady B

    2011-03-01

    Recent genomic studies have shown that significant chromosomal spatial correlation exists in gene expression of many organisms. Interestingly, coexpression has been observed among genes separated by a fixed interval in specific regions of a chromosome chain, which is likely caused by three-dimensional (3D) chromosome folding structures. Modeling such spatial correlation explicitly may lead to essential understandings of 3D chromosome structures and their roles in transcriptional regulation. In this paper, we explore chromosomal spatial correlation induced by 3D chromosome structures, and propose a hierarchical Bayesian method based on helical structures to formally model and incorporate the correlation into the analysis of gene expression microarray data. It is the first study to quantify and infer 3D chromosome structures in vivo using expression microarrays. Simulation studies show computing feasibility of the proposed method and that, under the assumption of helical chromosome structures, it can lead to precise estimation of structural parameters and gene expression levels. Real data applications demonstrate an intriguing biological phenomenon that functionally associated genes, which are far apart along the chromosome chain, are brought into physical proximity by chromosomal folding in 3D space to facilitate their coexpression. It leads to important biological insight into relationship between chromosome structure and function.

  20. Modeling and Annotating the Expressive Semantics of Dance Videos

    CERN Document Server

    Kannan, Rajkumar

    2010-01-01

    Dance videos are interesting and semantics-intensive. At the same time, they are the complex type of videos compared to all other types such as sports, news and movie videos. In fact, dance video is the one which is less explored by the researchers across the globe. Dance videos exhibit rich semantics such as macro features and micro features and can be classified into several types. Hence, the conceptual modeling of the expressive semantics of the dance videos is very crucial and complex. This paper presents a generic Dance Video Semantics Model (DVSM) in order to represent the semantics of the dance videos at different granularity levels, identified by the components of the accompanying song. This model incorporates both syntactic and semantic features of the videos and introduces a new entity type called, Agent, to specify the micro features of the dance videos. The instantiations of the model are expressed as graphs. The model is implemented as a tool using J2SE and JMF to annotate the macro and micro fea...

  1. Test of the suitability of ECOPATH/ECOSIM modelling software as a compliment to estimate flows of carbon, C-14 and radionuclides in the Oeregrundsgrepen area

    Energy Technology Data Exchange (ETDEWEB)

    Sandberg, Johannes [Stockholm Univ. (Sweden). Dept. of Systems Ecology

    2004-04-01

    In this study it was evaluated whether the ECOPATH with ECOSIM software could be used as a standard platform to facilitate for radioecologists to construct and study transport and accumulation of radionuclides in aquatic food webs. The evaluation was based upon: 1) a previously published food web model of carbon/carbon-14 flow for the Oeregrundsgrepen area, Baltic Sea, 2) a generic model, 3) an ECOSIM model and 4) an ECOTRACE model. The results presented clearly shows that there is great potential for a successful development of this scientific approach in the future. The original carbon flows and assumptions was easily incorporated into the ECOPATH with ECOSIM modelling environment. The carbon flows differed only negligible between the two models, except for the benthic flows, which was more accurately described in this study. Further, by using ECOPATH it was easily discovered that the growth efficiencies used in the original model was quite high, being 47% for most of the heterotrophs, which are high from an ecological point of view. However, that is probably due to differences in how the carbon flows have been estimated in the original versus the present study. It is likely, however that the carbon demand has been underestimated in the original model. The generic model was parameterised from data available through the software as well from the diets and assumptions used in the original carbon model. The use of these parameters resulted in carbon flows, which was between 0.7 to 11 times the flows estimated by the ECOPATH model. The difference was greatest for primary producers being 3.7 to 11 times the original flows. Thus, depending on the question one is addressing it was suggested that the use of generic parameters is best for making test models of carbon and radionuclide flows in ecosystems, where the data set for validation is limited. Finally, the ECOPATH and ECOSIM model was well suited to drive a C-14 flow model, such as ECOTRACER for each of the

  2. 生境适宜度指数模型研究进展%Research advances in habitat suitability index model

    Institute of Scientific and Technical Information of China (English)

    金龙如; 孙克萍; 贺红士; 周宇飞

    2008-01-01

    生境适宜度指数(habitat suitability index,HSI)模型作为一种生境评价方法,在土地管理规划和评估中得到大量应用.本文总结了HSI模型在野生动物生境评价中的开发及应用,重点介绍了利用3S技术进行HSI建模及与其他模型耦合进行生境评价的现状;阐述了利用多种统计方法对HSI模型的评估和验证;探讨了HSI模型在主观性和非通用性等方面存在的问题和局限性,最后,就HSI模型在野生动物生境评价中的发展前景进行了展望.

  3. The suitability of BV2 cells as alternative model system for primary microglia cultures or for animal experiments examining brain inflammation.

    Science.gov (United States)

    Henn, Anja; Lund, Søren; Hedtjärn, Maj; Schrattenholz, Andreé; Pörzgen, Peter; Leist, Marcel

    2009-01-01

    The role of microglia in neurodegeneration, toxicology and immunity is an expanding area of biomedical research requiring large numbers of animals. Use of a microglia-like cell line would accelerate many research programmes and reduce the necessity of continuous cell preparations and animal experimentation, provided that the cell line reproduces the in vivo situation or primary microglia (PM) with high fidelity. The immortalised murine microglial cell line BV-2 has been used frequently as a substitute for PM, but recently doubts were raised as to their suitability. Here, we re-evaluated strengths and potential short-comings of BV-2 cells. Their response to lipopolysaccharide was compared with the response of microglia in vitro and in vivo. Transcriptome (480 genes) and proteome analyses after stimulation with lipopolysaccharide indicated a reaction pattern of BV-2 with many similarities to that of PM, although the average upregulation of genes was less pronounced. The cells showed a normal regulation of NO production and a functional response to IFN-gamma, important parameters for appropriate interaction with T cells and neurons. BV-2 were also able to stimulate other glial cells. They triggered the translocation of NF-kappaB, and a subsequent production of IL-6 in astrocytes. Thus, BV-2 cells appear to be a valid substitute for PM in many experimental settings, incuding complex cell-cell interaction studies.

  4. What Kind of Capsule Endoscope Is Suitable for a Controllable Self-Propelling Capsule Endoscope? Experimental Study Using a Porcine Stomach Model for Clinical Application (with Videos)

    Science.gov (United States)

    Ota, Kazuhiro; Nouda, Sadaharu; Takeuchi, Toshihisa; Iguchi, Munetaka; Kojima, Yuichi; Kuramoto, Takanori; Inoue, Takuya; Shindo, Yasunori; Uesugi, Kenshiro; Fujito, Yoshiaki; Nishihara, Hironori; Ohtsuka, Naotake; Higuchi, Kazuhide

    2015-01-01

    Background We have been developing the Self-Propelling Capsule Endoscope (SPCE) that allows for controllability from outside of the body and real-time observation. What kind of capsule endoscope (CE) is suitable for a controllable SPCE is unclear and a very critical point for clinical application. We compared observing ability of three kinds of SPCEs with different viewing angles and frame rates. Methods Eleven buttons were sewed in an excised porcine stomach. Four examiners controlled the SPCE using PillCamSB2, -ESO2, and -COLON2 (Given Imaging Ltd., Israel), for 10 minutes each with the aim of detecting as many buttons and examining them as closely as possible. The ability to find lesions was assessed based on the number of detected buttons. The SPCE-performance score (SPS) was used to evaluate the ability to examine the lesions in detail. Results The SPCE-ESO2, -COLON2, and -SB2 detected 11 [interquartile range (IQR): 0], 10.5 (IQR, 0.5), and 8 (IQR, 1.0) buttons, respectively. The SPCE-ESO2 and -COLON2 had a significantly better ability to detect lesions than the -SB2 (p stomach. PMID:26447694

  5. Validation of a simple turbulence model suitable for closure of temporally-filtered Navier-Stokes equations using a helium plume.

    Energy Technology Data Exchange (ETDEWEB)

    Tieszen, Sheldon Robert; Domino, Stefan Paul; Black, Amalia Rebecca

    2005-06-01

    A validation study has been conducted for a turbulence model used to close the temporally filtered Navier Stokes (TFNS) equations. A turbulence model was purposely built to support fire simulations under the Accelerated Strategic Computing (ASC) program. The model was developed so that fire transients could be simulated and it has been implemented in SIERRA/Fuego. The model is validated using helium plume data acquired for the Weapon System Certification Campaign (C6) program in the Fire Laboratory for Model Accreditation and Experiments (FLAME). The helium plume experiments were chosen as the first validation problem for SIERRA/Fuego because they embody the first pair-wise coupling of scalar and momentum fields found in fire plumes. The validation study includes solution verification through grid and time step refinement studies. A formal statistical comparison is used to assess the model uncertainty. The metric uses the centerline vertical velocity of the plume. The results indicate that the simple model is within the 95% confidence interval of the data for elevations greater than 0.4 meters and is never more than twice the confidence interval from the data. The model clearly captures the dominant puffing mode in the fire but under resolves the vorticity field. Grid dependency of the model is noted.

  6. Kinetic models of gene expression including non-coding RNAs

    Science.gov (United States)

    Zhdanov, Vladimir P.

    2011-03-01

    In cells, genes are transcribed into mRNAs, and the latter are translated into proteins. Due to the feedbacks between these processes, the kinetics of gene expression may be complex even in the simplest genetic networks. The corresponding models have already been reviewed in the literature. A new avenue in this field is related to the recognition that the conventional scenario of gene expression is fully applicable only to prokaryotes whose genomes consist of tightly packed protein-coding sequences. In eukaryotic cells, in contrast, such sequences are relatively rare, and the rest of the genome includes numerous transcript units representing non-coding RNAs (ncRNAs). During the past decade, it has become clear that such RNAs play a crucial role in gene expression and accordingly influence a multitude of cellular processes both in the normal state and during diseases. The numerous biological functions of ncRNAs are based primarily on their abilities to silence genes via pairing with a target mRNA and subsequently preventing its translation or facilitating degradation of the mRNA-ncRNA complex. Many other abilities of ncRNAs have been discovered as well. Our review is focused on the available kinetic models describing the mRNA, ncRNA and protein interplay. In particular, we systematically present the simplest models without kinetic feedbacks, models containing feedbacks and predicting bistability and oscillations in simple genetic networks, and models describing the effect of ncRNAs on complex genetic networks. Mathematically, the presentation is based primarily on temporal mean-field kinetic equations. The stochastic and spatio-temporal effects are also briefly discussed.

  7. Niche suitability affects development: skull asymmetry increases in less suitable areas.

    Directory of Open Access Journals (Sweden)

    Renan Maestri

    Full Text Available For conservation purposes, it is important to take into account the suitability of a species to particular habitats; this information may predict the long-term survival of a species. In this sense, morphological measures of developmental stress, such as fluctuating asymmetry, can be proxies for an individual's performance in different regions. In this study, we conducted tests to determine whether areas with different levels of suitability for a species (generated by ecological niche models were congruent with morphological markers that reflect environmental stress and morphological variance. We generated a Maxent niche model and compared the suitability assessments of several areas with the skull morphology data (fluctuating asymmetry and morphological disparity of populations of the Atlantic forest endemic to Brazil rodent Akodon cursor. Our analyses showed a significant negative relationship between suitability levels and fluctuating asymmetry levels, which indicates that in less suitable areas, the individuals experience numerous disturbances during skull ontogeny. We have not found an association between morphological variance and environmental suitability. As expected, these results suggest that in environments with a lower suitability, developmental stress is increased. Such information is helpful in the understanding of the species evolution and in the selection of priority areas for the conservation of species.

  8. Towards the development of a fully coupled arterial-venous 1D model: suitability of using a 1D finite volume method with staggered spatial discretization

    CSIR Research Space (South Africa)

    Bogaers, Alfred EJ

    2012-07-01

    Full Text Available In this paper we outline the development of a 1D finite volume model to solve for blood flow through the arterial system. The model is based on a staggered spatial discretization which leads to a stable solution scheme. This scheme can accurately...

  9. Murine 3T3-L1 adipocyte cell differentiation model: validated reference genes for qPCR gene expression analysis.

    Directory of Open Access Journals (Sweden)

    Tatjana Arsenijevic

    Full Text Available BACKGROUND: Analysis of gene expression at the mRNA level, using real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR, mandatorily requires reference genes (RGs as internal controls. However, increasing evidences have shown that RG expression may vary considerably under experimental conditions. We sought for an appropriate panel of RGs to be used in the 3T3-L1 cell line model during their terminal differentiation into adipocytes. To this end, the expression levels of a panel of seven widely used RG mRNAs were measured by qRT-PCR. The 7 RGs evaluated were ß-actin (ACTB, glyceraldehyde-3-phosphate dehydrogenase (GAPDH, hypoxanthine phosphoribosyl-transferase I (HPRT, ATP synthase H+ transporting mitochondrial F1 complex beta subunit (ATP-5b, tyrosine 3-monooxygenase/tryptophan 5- monooxygenase activation protein, zeta polypeptide (Ywhaz, Non-POU-domain containing octamer binding protein (NoNo, and large ribosomal protein L13a (RPL. METHODOLOGY/PRINCIPAL FINDINGS: Using three Excel applications, GeNorm, NormFinder and BestKeeper, we observed that the number and the stability of potential RGs vary significantly during differentiation of 3T3-L1 cells into adipocytes. mRNA expression analyses using qRT-PCR revealed that during the entire differentiation program, only NoNo expression is relatively stable. Moreover, the RG sets that were acceptably stable were different depending on the phase of the overall differentiation process (i.e. mitotic clonal expansion versus the terminal differentiation phase. RPL, ACTB, and Ywhaz, are suitable for terminal differentiation, whereas ATP-5b and HPRT, are suitable during mitotic clonal expansion. CONCLUSION: Our results demonstrate that special attention must be given to the choice of suitable RGs during the various well defined phases of adipogenesis to ensure accurate data analysis and that the use of several RGs is absolutely required. Consequently, our data show for the first time

  10. Statement on the suitability of the BEEHAVE model for its potential use in a regulatory context and for the risk assessment of multiple stressors in honeybees at the landscape level

    DEFF Research Database (Denmark)

    EFSA PPR Panel (EFSA Panel on Plant Protection Products and their Residues); Topping, Christopher John

    2015-01-01

    The Panel has interpreted the Terms of Reference by carrying out a stepwise evaluation of the BEEHAVE simulation model with a view to assessing its suitability for use in a regulatory context and for risk assessment of multiple stressors at the landscape level. The EFSA opinion on good modelling...... usable in a regulatory context primarily because it needs a pesticide module. BEEHAVE has a Varroa/virus module, although this seems to underestimate the impact of Varroa/virus on colony survival, and additional stressors (chemical and biological) would need to be added to allow investigation...

  11. Modeling and Experimental Validation of a Volumetric Expander Suitable for Waste Heat Recovery from an Automotive Internal Combustion Engine Using an Organic Rankine Cycle with Ethanol

    Directory of Open Access Journals (Sweden)

    José Galindo

    2016-04-01

    Full Text Available Waste heat recovery (WHR in exhaust gas flow of automotive engines has proved to be a useful path to increase the overall efficiency of internal combustion engines (ICE. Recovery potentials of up to 7% are shown in several works in the literature. However, most of them are theoretical estimations. Some present results from prototypes fed by steady flows generated in an auxiliary gas tank and not with actual engine exhaust gases. This paper deals with the modeling and experimental validation of an organic Rankine cycle (ORC with a swash-plate expander integrated in a 2 L turbocharged petrol engine using ethanol as working fluid. A global simulation model of the ORC was developed with a maximum difference of 5%, validated with experimental results. Considering the swash-plate as the main limiting factor, an additional specific submodel was implemented to model the physical phenomena in this element. This model allows simulating the fluid dynamic behavior of the swash-plate expander using a 0D model (Amesim. Differences up to 10.5% between tests and model results were found.

  12. The ecological module of BOATS-1.0: a bioenergetically-constrained model of marine upper trophic levels suitable for studies of fisheries and ocean biogeochemistry

    Science.gov (United States)

    Carozza, D. A.; Bianchi, D.; Galbraith, E. D.

    2015-12-01

    Environmental change and the exploitation of marine resources have had profound impacts on marine communities, with potential implications for ocean biogeochemistry and food security. In order to study such global-scale problems, it is helpful to have computationally efficient numerical models that predict the first-order features of fish biomass production as a function of the environment, based on empirical and mechanistic understandings of marine ecosystems. Here we describe the ecological module of the BiOeconomic mArine Trophic Size-spectrum (BOATS) model, which takes an Earth-system approach to modeling fish biomass at the global scale. The ecological model is designed to be used on an Earth System model grid, and determines size spectra of fish biomass by explicitly resolving life history as a function of local temperature and net primary production. Biomass production is limited by the availability of photosynthetic energy to upper trophic levels, following empirical trophic efficiency scalings, and by well-established empirical temperature-dependent growth rates. Natural mortality is calculated using an empirical size-based relationship, while reproduction and recruitment depend on both the food availability to larvae from net primary production and the production of eggs by mature adult fish. We describe predicted biomass spectra and compare them to observations, and conduct a sensitivity study to determine how the change as a function of net primary production and temperature. The model relies on a limited number of parameters compared to similar modeling efforts, while retaining realistic representations of biological and ecological processes, and is computationally efficient, allowing extensive parameter-space analyses even when implemented globally. As such, it enables the exploration of the linkages between ocean biogeochemistry, climate, and upper trophic levels at the global scale, as well as a representation of fish biomass for idealized studies

  13. The ecological module of BOATS-1.0: a bioenergetically constrained model of marine upper trophic levels suitable for studies of fisheries and ocean biogeochemistry

    Science.gov (United States)

    Carozza, David Anthony; Bianchi, Daniele; Galbraith, Eric Douglas

    2016-04-01

    Environmental change and the exploitation of marine resources have had profound impacts on marine communities, with potential implications for ocean biogeochemistry and food security. In order to study such global-scale problems, it is helpful to have computationally efficient numerical models that predict the first-order features of fish biomass production as a function of the environment, based on empirical and mechanistic understandings of marine ecosystems. Here we describe the ecological module of the BiOeconomic mArine Trophic Size-spectrum (BOATS) model, which takes an Earth-system approach to modelling fish biomass at the global scale. The ecological model is designed to be used on an Earth-system model grid, and determines size spectra of fish biomass by explicitly resolving life history as a function of local temperature and net primary production. Biomass production is limited by the availability of photosynthetic energy to upper trophic levels, following empirical trophic efficiency scalings, and by well-established empirical temperature-dependent growth rates. Natural mortality is calculated using an empirical size-based relationship, while reproduction and recruitment depend on both the food availability to larvae from net primary production and the production of eggs by mature adult fish. We describe predicted biomass spectra and compare them to observations, and conduct a sensitivity study to determine how they change as a function of net primary production and temperature. The model relies on a limited number of parameters compared to similar modelling efforts, while retaining reasonably realistic representations of biological and ecological processes, and is computationally efficient, allowing extensive parameter-space analyses even when implemented globally. As such, it enables the exploration of the linkages between ocean biogeochemistry, climate, and upper trophic levels at the global scale, as well as a representation of fish biomass for

  14. The ecological module of BOATS-1.0: a bioenergetically-constrained model of marine upper trophic levels suitable for studies of fisheries and ocean biogeochemistry

    Directory of Open Access Journals (Sweden)

    D. A. Carozza

    2015-12-01

    Full Text Available Environmental change and the exploitation of marine resources have had profound impacts on marine communities, with potential implications for ocean biogeochemistry and food security. In order to study such global-scale problems, it is helpful to have computationally efficient numerical models that predict the first-order features of fish biomass production as a function of the environment, based on empirical and mechanistic understandings of marine ecosystems. Here we describe the ecological module of the BiOeconomic mArine Trophic Size-spectrum (BOATS model, which takes an Earth-system approach to modeling fish biomass at the global scale. The ecological model is designed to be used on an Earth System model grid, and determines size spectra of fish biomass by explicitly resolving life history as a function of local temperature and net primary production. Biomass production is limited by the availability of photosynthetic energy to upper trophic levels, following empirical trophic efficiency scalings, and by well-established empirical temperature-dependent growth rates. Natural mortality is calculated using an empirical size-based relationship, while reproduction and recruitment depend on both the food availability to larvae from net primary production and the production of eggs by mature adult fish. We describe predicted biomass spectra and compare them to observations, and conduct a sensitivity study to determine how the change as a function of net primary production and temperature. The model relies on a limited number of parameters compared to similar modeling efforts, while retaining realistic representations of biological and ecological processes, and is computationally efficient, allowing extensive parameter-space analyses even when implemented globally. As such, it enables the exploration of the linkages between ocean biogeochemistry, climate, and upper trophic levels at the global scale, as well as a representation of fish biomass for

  15. A generic 3D kinetic model of gene expression

    Science.gov (United States)

    Zhdanov, Vladimir

    2012-04-01

    Recent experiments show that mRNAs and proteins can be localized both in prokaryotic and eukaryotic cells. To describe such situations, I present a 3D mean-field kinetic model aimed primarily at gene expression in prokaryotic cells, including the formation of mRNA, its translation into protein, and slow diffusion of these species. Under steady-state conditions, the mRNA and protein spatial distribution is described by simple exponential functions. The protein concentration near the gene transcribed into mRNA is shown to depend on the protein and mRNA diffusion coefficients and degradation rate constants.

  16. Modeling classic attenuation regulation of gene expression in bacteria.

    Science.gov (United States)

    Lyubetsky, Vassily A; Pirogov, Sergey A; Rubanov, Lev I; Seliverstov, Alexander V

    2007-02-01

    A model is proposed primarily for the classical RNA attenuation regulation of gene expression through premature transcription termination. The model is based on the concept of the RNA secondary structure macrostate within the regulatory region between the ribosome and RNA-polymerase, on hypothetical equation describing deceleration of RNA-polymerase by a macrostate and on views of transcription and translation initiation and elongation, under different values of the four basic model parameters which were varied. A special effort was made to select adequate model parameters. We first discuss kinetics of RNA folding and define the concept of the macrostate as a specific parentheses structure used to construct a conventional set of hairpins. The originally developed software that realizes the proposed model offers functionality to fully model RNA secondary folding kinetics. Its performance is compared to that of a public server described in Ref. 1. We then describe the delay in RNA-polymerase shifting to the next base or its premature termination caused by an RNA secondary structure or, herefrom, a macrostate. In this description, essential concepts are the basic and excited states of the polymerase first introduced in Ref. 2: the polymerase shifting to the next base can occur only in the basic state, and its detachment from DNA strand - only in excited state. As to the authors' knowledge, such a model incorporating the above-mentioned attenuation characteristics is not published elsewhere. The model was implemented in an application with command line interface for running in batch mode in Windows and Linux environments, as well as a public web server.(3) The model was tested with a conventional Monte Carlo procedure. In these simulations, the estimate of correlation between the premature transcription termination probability p and concentration c of charged amino acyl-tRNA was obtained as function p(c) for many regulatory regions in many bacterial genomes, as well as

  17. Improvement of different source function expressions in SWAN model for the Bohai Sea

    Institute of Scientific and Technical Information of China (English)

    YIN Baoshu; YANG Dezhou; SHA Rina; CHENG Minghua

    2005-01-01

    The simulating wave nearshore (SWAN) wave model has been widely used in coastal areas, lakes and estuaries. However, we found a poor agreement between modeling results and measurements in analyzing the chosen four typical cases when we used the default parameters of the source function formulas of the SWAN to make wave simulation for the Bohai Sea. Also, it was found that at the same wind process the simulated results of two wind generation expressions (Komen, Janssen) demonstrated a large difference. Further study showed that the proportionality coefficient α in linear growth term of wave growth source function plays an unperceived role in the process of wave development. Based on experiments and analysis, we thought that the coefficient α should change rather than be a constant. Therefore, the coefficient α changing with the variation of friction velocity U* was introduced into the linear growth term of wave growth source function. Four weather processes were adopted to validate the improvement in the linear growth term. The results from the improved coefficient α agree much better with the measurements than those from the default constant coefficient α. Furthermore, the large differences of results between Komen wind generation expression and Janssen wind generation expression were eliminated. We also experimented with the four weather processes to test the new white-capping mechanisms based on the cumulative steepness method. It was found that the parameters of the new white-capping mechanisms are not suitable for the Bohai Sea, but Alkyon' s white-capping mechanisms can be applicable to the Bohai Sea after amendments, demonstrating that this improvement of parameter α can improve the simulated results of the Bohai Sea.

  18. Assessing the Suitability of the ClOud Reflection Algorithm (CORA) in Modelling the Evolution of an Artificial Plasma Cloud in the Ionosphere

    Science.gov (United States)

    Jackson-Booth, N.

    2016-12-01

    Artificial Ionospheric Modification (AIM) attempts to modify the ionosphere in order to alter the propagation environment. It can be achieved through injecting the ionosphere with aerosols, chemicals or radio signals. The effects of any such release can be detected through the deployment of sensors, including ground based high frequency (HF) sounders. During the Metal Oxide Space Clouds (MOSC) experiment (undertaken in April/May 2013 in the Kwajalein Atoll, part of the Marshall Islands) several oblique ionograms were recorded from a ground based HF system. These ionograms were collected over multiple geometries and allowed the effects on the HF propagation environment to be understood. These ionograms have subsequently been used in the ClOud Reflection Algorithm (CORA) to attempt to model the evolution of the cloud following release. This paper describes the latest validation results from CORA, both from testing against ionograms, but also other independent models of cloud evolution from MOSC. For all testing the various cloud models (including that generated by CORA) were incorporated into a background ionosphere through which a 3D numerical ray trace was run to produce synthetic ionograms that could be compared with the ionograms recorded during MOSC.

  19. Model transcriptional networks with continuously varying expression levels

    Directory of Open Access Journals (Sweden)

    Carneiro Mauricio O

    2011-12-01

    Full Text Available Abstract Background At a time when genomes are being sequenced by the hundreds, much attention has shifted from identifying genes and phenotypes to understanding the networks of interactions among genes. We developed a gene network developmental model expanding on previous models of transcription regulatory networks. In our model, each network is described by a matrix representing the interactions between transcription factors, and a vector of continuous values representing the transcription factor expression in an individual. Results In this work we used the gene network model to look at the impact of mating as well as insertions and deletions of genes in the evolution of complexity of these networks. We found that the natural process of diploid mating increases the likelihood of maintaining complexity, especially in higher order networks (more than 10 genes. We also show that gene insertion is a very efficient way to add more genes to a network as it provides a much higher chance of developmental stability. Conclusions The continuous model affords a more complete view of the evolution of interacting genes. The notion of a continuous output vector also incorporates the reality of gene networks and graded concentrations of gene products.

  20. Environmental Suitability for Leasing Property

    Science.gov (United States)

    This is a Memorandum of Understanding between the U.S. Environmental Protection Agency and the U.S. Department of Defense, regarding the procedures to determine environmental suitability for leasing property available as a result of a base closure or realignment.

  1. Rheology and density of glucose syrup and honey: Determining their suitability for usage in analogue and fluid dynamic models of geological processes

    Science.gov (United States)

    Schellart, W. P.

    2011-06-01

    Analogue models of lithospheric deformation and fluid dynamic models of mantle flow mostly use some kind of syrup such as honey or glucose syrup to simulate the low-viscosity sub-lithospheric mantle. This paper describes detailed rheological tests and density measurements of three brands of glucose syrup and three brands of honey. Additional tests have been done for one brand of glucose syrup that was diluted with water to various degrees (2%, 5% and 10% by weight). The rheological tests have been done to test the effect of shear strain, shear rate and temperature on the dynamic viscosity of the syrup. The results show that the viscosity of all glucose syrups and honeys is independent of shear strain (i.e. no strain hardening or softening). The viscosity of the glucose syrups is independent of shear rate (γ˙), i.e. linear-viscous or Newtonian, in the range γ˙=10-4-10 s with stress exponents that are almost identical to one ( n = 0.995-1.004). All the honeys show a very weak, but consistent, decrease in viscosity with increasing shear rate of 7-14% from 10 -3 to 10 0 s -1 and have stress exponents more distinct from one ( n = 1.007-1.026). All syrups have a viscosity that is strongly dependent on temperature in the range 0-50 °C, where viscosity decreases with increasing temperature. Such decrease can be fitted with exponential and Arrhenius functions, with the latter giving the best results. Furthermore, the viscosity of glucose syrup decreases approximately exponentially with increasing water content. Oscillation tests indicate that the rheology of all the syrups is entirely dominated by viscous behaviour and not by elastic behaviour at frequencies of 10 -3-10 2 Hz. Finally, the density investigations show that the density of glucose syrup and honey decreases approximately linearly with increasing temperature in the range 10-70 °C, with coefficients of thermal volumetric expansion at 20 °C of 3.89-3.95 × 10 -4 °C -1 and 4.57-4.81 × 10 -4 °C -1 for

  2. Is the fluid mosaic (and the accompanying raft hypothesis a suitable model to describe fundamental features of biological membranes? What may be missing?

    Directory of Open Access Journals (Sweden)

    Luis Alberto Bagatolli

    2013-11-01

    Full Text Available The structure, dynamics, and stability of lipid bilayers are controlled by thermodynamic forces, leading to overall tensionless membranes with a distinct lateral organization and a conspicuous lateral pressure profile. Bilayers are also subject to built-in curvature-stress instabilities that may be released locally or globally in terms of morphological changes leading to the formation of non-lamellar and curved structures. A key controller of the bilayer’s propensity to form curved structures is the average molecular shape of the different lipid molecules. Via the curvature stress, molecular shape mediates a coupling to membrane-protein function and provides a set of physical mechanisms for formation of lipid domains and laterally differentiated regions in the plane of the membrane. Unfortunately, these relevant physical features of membranes are often ignored in the most popular models for biological membranes. Results from a number of experimental and theoretical studies emphasize the significance of these fundamental physical properties and call for a refinement of the fluid mosaic model (and the accompanying raft hypothesis.

  3. Standardizing data exchange for clinical research protocols and case report forms: An assessment of the suitability of the Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model (ODM).

    Science.gov (United States)

    Huser, Vojtech; Sastry, Chandan; Breymaier, Matthew; Idriss, Asma; Cimino, James J

    2015-10-01

    Efficient communication of a clinical study protocol and case report forms during all stages of a human clinical study is important for many stakeholders. An electronic and structured study representation format that can be used throughout the whole study life-span can improve such communication and potentially lower total study costs. The most relevant standard for representing clinical study data, applicable to unregulated as well as regulated studies, is the Operational Data Model (ODM) in development since 1999 by the Clinical Data Interchange Standards Consortium (CDISC). ODM's initial objective was exchange of case report forms data but it is increasingly utilized in other contexts. An ODM extension called Study Design Model, introduced in 2011, provides additional protocol representation elements. Using a case study approach, we evaluated ODM's ability to capture all necessary protocol elements during a complete clinical study lifecycle in the Intramural Research Program of the National Institutes of Health. ODM offers the advantage of a single format for institutions that deal with hundreds or thousands of concurrent clinical studies and maintain a data warehouse for these studies. For each study stage, we present a list of gaps in the ODM standard and identify necessary vendor or institutional extensions that can compensate for such gaps. The current version of ODM (1.3.2) has only partial support for study protocol and study registration data mainly because it is outside the original development goal. ODM provides comprehensive support for representation of case report forms (in both the design stage and with patient level data). Inclusion of requirements of observational, non-regulated or investigator-initiated studies (outside Food and Drug Administration (FDA) regulation) can further improve future revisions of the standard.

  4. Fully Bayesian mixture model for differential gene expression: simulations and model checks.

    Science.gov (United States)

    Lewin, Alex; Bochkina, Natalia; Richardson, Sylvia

    2007-01-01

    We present a Bayesian hierarchical model for detecting differentially expressed genes using a mixture prior on the parameters representing differential effects. We formulate an easily interpretable 3-component mixture to classify genes as over-expressed, under-expressed and non-differentially expressed, and model gene variances as exchangeable to allow for variability between genes. We show how the proportion of differentially expressed genes, and the mixture parameters, can be estimated in a fully Bayesian way, extending previous approaches where this proportion was fixed and empirically estimated. Good estimates of the false discovery rates are also obtained. Different parametric families for the mixture components can lead to quite different classifications of genes for a given data set. Using Affymetrix data from a knock out and wildtype mice experiment, we show how predictive model checks can be used to guide the choice between possible mixture priors. These checks show that extending the mixture model to allow extra variability around zero instead of the usual point mass null fits the data better. A software package for R is available.

  5. 应用AMMI模型评价烤烟品种产量适宜性%Using AMMI model to evaluate tobacco variety' s yield suitability

    Institute of Scientific and Technical Information of China (English)

    查宏波; 郑丽华; 黄韡; 胡启贤; 黄跃辉; 王崇玉; 方再龙; 周芸; 石建兴; 赵声春

    2012-01-01

    利用AMMI模型对2010年昭通烟区8个烤烟品种区域试验的产量性状进行统计分析,结果表明:在8个参试品种中,各品种产量的基因型(品种)效应、环境效应和基因型(品种)×环境互作效应均达极显著水平.云烟97平均产量最高,PVH19平均产量最低,丰产性表现顺序为:云烟97>云烟99>云烟203>云烟87> KRK26> K326>红花大金元>PVH19;稳定性表现顺序为:云烟99> K326>云烟97>云烟203>云烟87> KRK26> PVH19>红花大金元;在参试地点环境范围内,品种云烟97和云烟99表现较佳,模型分析结果与各品种实际表现情况一致.%Yields of 8 flue-cured tobacco varieties were analyzed using AMMI model with data from trials in Zhaotong tobacco growing areas in 2010. Results showed that effects of genotype, environment, and genotype X environment on yield were significant at 1% level for all 8 varieties. The average yield of Yunyan97 was the highest and that of PVH19 was the lowest. The order of yield is as follows: Yunyan97 > Yunyan99 > Yunyan203 > Yunyan87 > KRK26 > K326 > Honghua Dajinyuan > PVH19. While stability is in the order of Yunyan99 > K326 > Yunyan97 > Yunyan203 > Yunyan87 > KRK26 > PVH19 > Honghua Dajinyuan. Yunyan97 and Yunyan99 showed better characters. For all varieties in the trial, AMMI model prediction is the same as actual performance.

  6. A hidden Markov model approach for determining expression from genomic tiling micro arrays

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Gardner, P. P.; Arctander, Peter;

    2006-01-01

    HMM, that adaptively models tiling data prior to predicting expression on genomic sequence. A hidden Markov model (HMM) is used to model the distributions of tiling array probe scores in expressed and non-expressed regions. The HMM is trained on sets of probes mapped to regions of annotated expression and non......]. Results can be downloaded and viewed from our web site [2]. Conclusion The value of adaptive modelling of fluorescence scores prior to categorisation into expressed and non-expressed probes is demonstrated. Our results indicate that our adaptive approach is superior to the previous analysis in terms...

  7. Applying the basin model: Assessing habitat suitability of young-of-the-year demersal fishes on the New York Bight continental shelf

    Science.gov (United States)

    Sullivan, Mark C.; Cowen, Robert K.; Able, Kenneth W.; Fahay, Michael P.

    2006-09-01

    The extent to which young-of-the-year (YOY) fish habitats become saturated with new recruits has remained relatively unevaluated for temperate, demersal, continental shelf fishes. MacCall's [1990. Dynamic Geography of Marine Fish Populations. Washington Sea Grant Program, University of Washington Press, Seattle, Washington] basin model was used as a framework for examining the dynamics of an assemblage of recently settled fishes in relation to available microhabitat on the New York Bight continental shelf (USA). For four abundant species (three flatfish, one merlucciid hake), density-specific patterns of microhabitat selection, spatial dispersion and overall cross-shelf habitat use were investigated using a research submersible over three cross-shelf transects during the late summer settlement season. Typically, recruits that saturated YOY habitats (>1 ind/m 2) were randomly distributed within underwater transects and formed weak associations with specific microhabitats. At lower densities (ecologically important substrates (i.e. Limanda ferruginea, sand wave crests/low shell hash). For Citharichthys arctifrons, clumping appeared to increase with complexity of the habitat. Several less-abundant species (i.e. Urophycis chuss, Tautogolabrus adspersus) formed tight associations with rare habitat features and may consequently encounter the greatest bottleneck for space during the benthic/pelagic transition. Although restricted by the scale of observation, these results begin to elucidate the mechanisms by which habitat quality and quantity moderate recruitment on the continental shelf.

  8. Research on Items Suitable for Online Auction

    Institute of Scientific and Technical Information of China (English)

    LUO Zhanghua; LIU Lu; WU Lihua

    2004-01-01

    Based on the classification to the attribute information of auctioned commodity, the valuation signal of auctioned commodity is categorized into two groups: codable valuation signal and un-codable valuation signal. A valuation signal model is developed and used to reason under the environment of common valuation auction. The results show that the value of commodity auctioned online tends to be lower and the commodity with bigger factor that can be described online is more suitable for online auction.

  9. Genome-Wide Expression Profiling of Five Mouse Models Identifies Similarities and Differences with Human Psoriasis

    NARCIS (Netherlands)

    Swindell, William R.; Johnston, Andrew; Carbajal, Steve; Han, Gangwen; Wohn, Christian; Lu, Jun; Xing, Xianying; Nair, Rajan P.; Voorhees, John J.; Elder, James T.; Wang, Xiao-Jing; Sano, Shigetoshi; Prens, Errol P.; DiGiovanni, John; Pittelkow, Mark R.; Ward, Nicole L.; Gudjonsson, Johann E.

    2011-01-01

    Development of a suitable mouse model would facilitate the investigation of pathomechanisms underlying human psoriasis and would also assist in development of therapeutic treatments. However, while many psoriasis mouse models have been proposed, no single model recapitulates all features of the huma

  10. Genome-wide expression profiling of five mouse models identifies similarities and differences with human psoriasis

    NARCIS (Netherlands)

    W.R. Swindell (William R.); A. Johnston (Andrew); S. Carbajal (Steve); G. Han (Gangwen); C.T. Wohn (Christopher); J. Lu (Jun); X. Xing (Xianying); R.P. Nair (Rajan P.); J.J. Voorhees (John); J.T. Elder (James); X.J. Wang (Xian Jiang); S. Sano (Shigetoshi); E.P. Prens (Errol); J. DiGiovanni (John); M.R. Pittelkow (Mark R.); N.L. Ward (Nicole); J.E. Gudjonsson (Johann Eli)

    2011-01-01

    textabstractDevelopment of a suitable mouse model would facilitate the investigation of pathomechanisms underlying human psoriasis and would also assist in development of therapeutic treatments. However, while many psoriasis mouse models have been proposed, no single model recapitulates all features

  11. Genome-wide expression profiling of five mouse models identifies similarities and differences with human psoriasis

    NARCIS (Netherlands)

    W.R. Swindell (William R.); A. Johnston (Andrew); S. Carbajal (Steve); G. Han (Gangwen); C.T. Wohn (Christopher); J. Lu (Jun); X. Xing (Xianying); R.P. Nair (Rajan P.); J.J. Voorhees (John); J.T. Elder (James); X.J. Wang (Xian Jiang); S. Sano (Shigetoshi); E.P. Prens (Errol); J. DiGiovanni (John); M.R. Pittelkow (Mark R.); N.L. Ward (Nicole); J.E. Gudjonsson (Johann Eli)

    2011-01-01

    textabstractDevelopment of a suitable mouse model would facilitate the investigation of pathomechanisms underlying human psoriasis and would also assist in development of therapeutic treatments. However, while many psoriasis mouse models have been proposed, no single model recapitulates all features

  12. Design, modeling, expression, and chemoselective PEGylation of a new nanosize cysteine analog of erythropoietin.

    Science.gov (United States)

    Cohan, Reza Ahangari; Madadkar-Sobhani, Armin; Khanahmad, Hossein; Roohvand, Farzin; Aghasadeghi, Mohammad Reza; Hedayati, Mohammad Hossein; Barghi, Zahra; Ardestani, Mehdi Shafiee; Inanlou, Davoud Nouri; Norouzian, Dariush

    2011-01-01

    Recombinant human erythropoietin (rhEPO) is considered to be one of the most pivotal pharmaceutical drugs in the market because of its clinical application in the treatment of anemia-associated disorders worldwide. However, like other therapeutic proteins, it does not have suitable pharmacokinetic properties for it to be administrated at least two to three times per week. Chemoselective cysteine PEGylation, employing molecular dynamics and graphics in in silico studies, can be considered to overcome such a problem. A special kind of EPO analog was elicited based on a literature review, homology modeling, molecular dynamic simulation, and factors affecting the PEGylation reaction. Then, cDNA of the selected analog was generated by site-directed mutagenesis and subsequently cloned into the expression vector. The construct was transfected to Chinese hamster ovary/dhfr(-) cells, and highly expressed clones were selected via methotrexate amplification. Ion-immobilized affinity and size exclusion (SE) chromatography techniques were used to purify the expressed analog. Thereafter, chemoselective PEGylation was performed and a nanosize PEGylated EPO was obtained through dialysis. The in vitro biologic assay and in vivo pharmacokinetic parameters were studied. Finally, E31C analog Fourier transform infrared, analytical SE-high-performance liquid chromatography, zeta potential, and size before and after PEGylation were characterized. The findings indicate that a novel nanosize EPO31-PEG has a five-fold longer terminal half-life in rats with similar biologic activity compared with unmodified rhEPO in proliferation cell assay. The results also show that EPO31-PEG size and charge versus unmodified protein was increased in a nanospectrum, and this may be one criterion of EPO biologic potency enhancement. This kind of novel engineered nanosize PEGylated EPO has remarkable advantages over rhEPO.

  13. Differential expression analysis for RNAseq using Poisson mixed models.

    Science.gov (United States)

    Sun, Shiquan; Hood, Michelle; Scott, Laura; Peng, Qinke; Mukherjee, Sayan; Tung, Jenny; Zhou, Xiang

    2017-06-20

    Identifying differentially expressed (DE) genes from RNA sequencing (RNAseq) studies is among the most common analyses in genomics. However, RNAseq DE analysis presents several statistical and computational challenges, including over-dispersed read counts and, in some settings, sample non-independence. Previous count-based methods rely on simple hierarchical Poisson models (e.g. negative binomial) to model independent over-dispersion, but do not account for sample non-independence due to relatedness, population structure and/or hidden confounders. Here, we present a Poisson mixed model with two random effects terms that account for both independent over-dispersion and sample non-independence. We also develop a scalable sampling-based inference algorithm using a latent variable representation of the Poisson distribution. With simulations, we show that our method properly controls for type I error and is generally more powerful than other widely used approaches, except in small samples (n <15) with other unfavorable properties (e.g. small effect sizes). We also apply our method to three real datasets that contain related individuals, population stratification or hidden confounders. Our results show that our method increases power in all three data compared to other approaches, though the power gain is smallest in the smallest sample (n = 6). Our method is implemented in MACAU, freely available at www.xzlab.org/software.html. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Suitable scale of Weigan River plain oasis

    Institute of Scientific and Technical Information of China (English)

    HU ShunJun; SONG YuDong; TIAN ChangYan; LI YueTan; LI XiuCang; CHEN XiaoBing

    2007-01-01

    Desert coexists with oasis in long time, and the existence and development of oasis system demand better oasis vegetation ecological system. Oasis scale of arid zone plain encircling water should be determined in case of desertification caused by land over-reclamation under the circumstance of water resources shortage. Steady oasis with virtuous circle must have appropriate land use structure for agriculture, forestry and graziery. The study on the suitable scale and developmental space of oasis will provide theoretical and applicable foundation for effective construction of oases. By analyzing the hydrothermal, water and soil balance, an optimal mathematical model has been established. Based on hydrometeorology data collected for years in Weigan River plain, and by the principle of water balance,a calculation has been made of the water resources for evapotranspiration and the optimal acreage of oasis and cultivated land, which shows that the water resources for evapotranspiration in the Weigan River plain oasis is 22.32×108 m3 and the optimal oasis acreage under the condition of conventional irrigation mode is 3716.06 km2, in which the suitable cultivated land acreage is 1564.79 km2. Under the condition of water-saving irrigation, the suitable oasis acreage is 5515.49 km2, in which the suitable cultivated land acreage is 2322.31 km2. The oasis area had reached 4123 km2, and the cultivated land acreage had reached 1507 km2 after the Agriculture Irrigation Drainage Water Project of World Bank Loan in Weigan River basin was finished in 1997. The oasis and cultivated land acreage will be more suitable, and the oasis scale can be enlarged moderately by means of water saving irrigation.

  15. A PURE NODAL-ANALYSIS METHOD SUITABLE FOR ANALOG CIRCUITS USING NULLORS

    Directory of Open Access Journals (Sweden)

    E. Tlelo-Cuautle

    2003-09-01

    Full Text Available A novel technique suitable for computer-aided analysis of analog integrated circuits (ICs is introduced. This technique uses the features of both nodal-analysis (NA and symbolic analysis, at nullor level. First, the nullor is used to model the ideal behavior of several analog devices, namely: transistors, opamps, OTAs, and current conveyors. From this modeling approach, it is shown how to transform circuits working in voltage-mode to current-mode and vice-versa. Second, it is demonstrated that using nullors, all non-NA-compatible elements can be transformed into NA-compatible ones, this results in a computationally-improved pure-NA method. Third, the computation of fully-symbolic expressions using , is described. It is demonstrated that a symbolic expression gives more insight in the behavior and performance of the circuit. Finally, several examples demonstrate the suitability and appropriateness of the proposed method to be used in education.

  16. Small suitability of the DLEC1, MLH1 and TUSC4 mRNA expression analysis as potential prognostic or differentiating markers for NSCLC patients in the Polish population

    Indian Academy of Sciences (India)

    JACEK KORDIAK; KAROLINA H. CZARNECKA; DOROTA PASTUSZAK-LEWANDOSKA; ADAM ANTCZAK; MONIKA MIGDALSKA-SE¸K; EWA NAWROT; DARIA DOMAN´ SKA- SENDEROWSKA; JUSTYNA KISZAŁKIEWICZ; EWA BRZEZIAN´ SKA- LASOTA

    2017-06-01

    According to the latest data, lung cancer is one of the most common cancer worldwide, men contributing nearly 21.2% and women 8.6% of all diagnosed cancers. Late detection of tumour drastically reduces the chance for a cure.Thus, it is important to search for candidate biomarkers for screening of early stage nonsmall cell lung carcinoma (NSCLC). Tumour suppressor genes, DLEC1, TUSC4 and MLH1, localized on 3p21 are recognized to play a rolein NSCLC carcinogenesis. The aim of this study was to assess the relationship between the DLEC1, TUSC4 and MLH1 mRNA expression, and clinical features of NSCLC patients, tobacco addiction, and tumour histopathologicalcharacteristics. The DLEC1, TUSC4 and MLH1 expression was analysed in lung tumour tissue samples obtained from 69 patients diagnosed with NSCLC: squamous cell carcinoma (n = 34), adenocarcinoma (n = 24), large cell carcinoma (n = 5), carcinoma adenosquamosum (n = 5). A decreased gene expression (RQ < 0.7) was observed for DLEC1 in 60.9% of tumour samples, for MLH1 in 50.7% and for TUSC4 in 26% of NSCLC samples. DLEC1 was decreased in more aggressive subtypes: large cell carcinoma and adenocarcinoma-squamous cell carcinoma. The simultaneousdownregulation of two of the studied genes, DLEC1 andMLH1,was observed in 30.4% of NSCLCsamples, highlighting the importance of these two genes in lung carcinogenesis. We found no correlation between the DLEC1, TUSC4 andMLH1 gene expression and NSCLC patient characteristics (gender, age and smoking) or cancer histopathology. No significant differences in the gene expression among NSCLC subtypes indicate the weakness of DLEC1, TUSC4 and MLH1 expression analysis as potential differentiating markers of NSCLC subtypes in the Polish population.

  17. Construction of habitat suitability models(HSMs)for benthic macroinvertebrate and their applications to instream environmental flows:A case study in Xiangxi River of Three Gorges Reservior region,China

    Institute of Scientific and Technical Information of China (English)

    Fengqing Li; Qinghua Cai; Xiaocheng Fu; Jiankang Liu

    2009-01-01

    Based on a long-term ecological monitoring,the present study chose the most dominant benthic macroinvertebrate(Baetis spp.)as tar-get organisms in Xiangxi River,built the habitat suitability models(HSMs)for water depth,current velocity and substrate,respectively,which is the first aquatic organisms model for habitat suitability in the Chinese Mainland with a long-term consecutive in situ measurement.In order to protect the biointegrity and function of the river ecosystem,the theory system of instream environmental flow should be categorized into three hierarchies, namely minimum required instream flow(hydrological level),minimum instream environmental flow(bio-species level),and optimum instream environmental flow(ecosystem level).These three hierarchies of instream environmental flow models were then constructed with the hydropogical and seighted usable area(WUA)method.The results show that the minimum required instream flow of Yiangxi River calculated by the Tennant method(10% of the mean annual flow)was 0.615m3s-1;the minimum instream environmental flow accounted for 19.22% of the mean annual flow(namely 1.182m3s-1),which was the damaged river channel flow in the dry season;and 42.91% of the mean annual flow(namely 2.639m3s-1)should be viewed as the optimum instream environmental flow in order to protect the health of the river ecosystem,maintain the instream biodiversity,and reduce the impact of small hydropower stations nearby the Xiangxi River.We recommend that the hydrological and biological methods can help establish better instream environmental flow models and design best management practices for use in the small hydropower station project.

  18. Mapping global environmental suitability for Zika virus.

    Science.gov (United States)

    Messina, Jane P; Kraemer, Moritz Ug; Brady, Oliver J; Pigott, David M; Shearer, Freya M; Weiss, Daniel J; Golding, Nick; Ruktanonchai, Corrine W; Gething, Peter W; Cohn, Emily; Brownstein, John S; Khan, Kamran; Tatem, Andrew J; Jaenisch, Thomas; Murray, Christopher Jl; Marinho, Fatima; Scott, Thomas W; Hay, Simon I

    2016-04-19

    Zika virus was discovered in Uganda in 1947 and is transmitted by Aedes mosquitoes, which also act as vectors for dengue and chikungunya viruses throughout much of the tropical world. In 2007, an outbreak in the Federated States of Micronesia sparked public health concern. In 2013, the virus began to spread across other parts of Oceania and in 2015, a large outbreak in Latin America began in Brazil. Possible associations with microcephaly and Guillain-Barré syndrome observed in this outbreak have raised concerns about continued global spread of Zika virus, prompting its declaration as a Public Health Emergency of International Concern by the World Health Organization. We conducted species distribution modelling to map environmental suitability for Zika. We show a large portion of tropical and sub-tropical regions globally have suitable environmental conditions with over 2.17 billion people inhabiting these areas.

  19. Cytochrome P450 1A1 and 1B1 in human blood lymphocytes are not suitable as biomarkers of exposure to dioxin-like compounds: polymorphisms and interindividual variation in expression and inducibility.

    Science.gov (United States)

    van Duursen, Majorie B M; Sanderson, J Thomas; van den Berg, Martin

    2005-05-01

    Cytochrome P450 1A1 (CYP1A1) and 1B1 (CYP1B1) are phase I enzymes, the expression of which can be affected by many environmental compounds, including dioxins and dioxin-like compounds. Because CYP1A1 and CYP1B1 expression can easily be determined in peripheral blood lymphocytes, it is often suggested as biomarker of exposure to these compounds. In this study we investigated the interindividual differences in constitutive and induced CYP1A1-catalyzed ethoxyresorufin-O-deethylase (EROD) activity and CYP1A1 and CYP1B1 gene expression in human blood lymphocytes in a group of ten non-smoking females. Freshly isolated lymphocytes were cultured in medium containing the mitogen PHA and were exposed to the most potent dioxin, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) or the less potent dioxin-like polychlorinated biphenyl 126 (PCB126). In addition, we determined the occurrence of the CYP1A1 MspI and CYP1B1 Leu432Val polymorphisms. All individuals showed a concentration-dependent increase of EROD activity by TCDD, which was significantly correlated with an increase in CYP1A1, but not CYP1B1 expression. The maximum induced EROD activity by TCDD was very different among the individuals, but the EC50 values were about the same. PCB126 also caused a concentration-dependent increase of EROD activity, but was a factor 100-1000 less potent than TCDD among the individuals. The allele frequencies for CYP1A1 MspI and CYP1B1 Leu432Val reflected a normal Caucasian population and in this study the polymorphisms had no apparent effect on the expression and activity of these enzymes. Our study shows a large interindividual variability in constitutive and induced EROD activity, and CYP1A1 and CYP1B1 expression in human lymphocytes. In addition, dioxin concentrations at which effects were observed in our in vitro study are about 10-fold higher than the human blood levels found in vivo, indicating that EROD activity and CYP1A1 and CYP1B1 expression in human lymphocytes might not be

  20. Habitat suitability index models: Cutthroat trout

    Science.gov (United States)

    Hickman, Terry J.; Raleigh, Robert F.

    1982-01-01

    Cutthroat trout, Salmo clarki, are a polytypic species consisting of several geographically distinct forms with a broad distribution and a great amount of genetic diversity (Hickman 1978; Behnke 1979). Behnke (1979) recognized 13 extant subspecies: Coastal cutthroat (S. c. clarki) in coastal streams from Prince William Sound, Alaska to the Eel Rlver in California; mountain cutthroat (~. ~. alpestris) in upper Columbia and F~Dser River drainages of British Columbia; west slope cutthroat (S. c. lewisi) in the upper Columbia, Salmon, Clearwater, South Saskatchewan and upper Missouri drainages of Montana and Idaho; an undescribed subspecies in the Alvord basin, Oregon; Lahonton cutthroat (S. c ..henshawi), Pauite cutthroat (S. c. seleniris), and an undescribed- subspecies in the Humboldt River drafnage of the Lahontan basin of Nevada and California; Yellowstone cutthroat (S. c. bouvieri) in the Yellowstone drainage of Wyoming and Montana and the Snake River drainage of Wyoming, Idaho, and Nevada; an undescribed subspecies (fine spotted) in the upper Snake River, Wyoming; Bonneville cutthroat (S. c. utah) in the Bonneville basin in Utah, Nevada, Idaho, and Wyoming; Colorado River cutthroat (~. ~. pleuriticus) in the Colorado River drainage in Wyoming, Utah, New Mexico, and Colorado; greenback cutthroat (S. c. stomias) in the South Platte and Arkansas River systems; and Rio Grande cutthroat (~. ~. virginalis) in the Rio Grande River drainage of Colorado and New Mexico. Many of these 13 subspecies are included on Federal or State endangered or threatened species lists.Temperature and chemical preferences, migration, and other ecological and life history attributes vary among cutthroat subspecies (Behnke 1979). Differences in growth rate (Carlander 1969; Scott and Crossman 1973; Behnke 1979) and food preferences have also been reported (Trojnar and Behnke 1974) between some subspecies.

  1. Habitat Suitability Index Models: Mottled duck

    Science.gov (United States)

    Rorabaugh, James C.; Zwank, Phillip J.

    1983-01-01

    The mottled duck is a mallard-like resident species of the Gulf of Mexico coast, from the marshes of Pearl River on the Lou i si ana-Ht ss t ss ipp i border to the Al varado Lagoon near Veracruz, Mexico (Bell rose 1976). The highest densities of nesting mottl ed ducks are found in brackish to fresh coastal marshes (H. Bateman, Louisiana Department of Wildl ife and Fisheries, Baton Rouge; pers , comm.). Mottled ducks also inhabit prairie land near prairie potholes in Texas and flooded rice fields in Texas (Engel ing 1950) and Louisiana (Linscombe 1972).

  2. View-constrained latent variable model for multi-view facial expression classification

    NARCIS (Netherlands)

    Eleftheriadis, Stefanos; Rudovic, Ognjen; Pantic, Maja

    2014-01-01

    We propose a view-constrained latent variable model for multi-view facial expression classification. In this model, we first learn a discriminative manifold shared by multiple views of facial expressions, followed by the expression classification in the shared manifold. For learning, we use the expr

  3. Nonparametric Bayesian Sparse Factor Models with application to Gene Expression modelling

    CERN Document Server

    Knowles, David

    2010-01-01

    A nonparametric Bayesian extension of Factor Analysis (FA) is proposed where observed data Y is modeled as a linear superposition, G, of a potentially infinite number of hidden factors, X. The Indian Buffet Process (IBP) is used as a prior on G to incorporate sparsity and to allow the number of latent features to be inferred. The model's utility for modeling gene expression data is investigated using randomly generated datasets based on a known sparse connectivity matrix for E. Coli, and on three biological datasets of increasing complexity.

  4. 40 CFR 203.5 - Suitable substitute decision.

    Science.gov (United States)

    2010-07-01

    ... PROGRAMS LOW-NOISE-EMISSION PRODUCTS § 203.5 Suitable substitute decision. (a) If the Administrator... decide whether such product is a suitable substitute for any class or model or product being purchased by... substitute for any product or class of products being purchased by the Federal Government for its use, the...

  5. Evaluation of Agricultural Land Suitability: Application of Fuzzy Indicators

    Science.gov (United States)

    The problem of evaluation of agricultural land suitability is considered as a fuzzy modeling task. The application of individual fuzzy indicators provides an opportunity for assessment of lsand suitability of lands as degree or grade of performance when the lands are used for agricultural purposes....

  6. Technical suitability mapping of feedstocks for biological hydrogen production

    NARCIS (Netherlands)

    Panagiotopoulos, I.A.; Karaoglanoglou, L.S.; Koullas, D.P.; Bakker, R.R.; Claassen, P.A.M.; Koukios, E.G.

    2015-01-01

    The objective of this work was to map and compare the technical suitability of different raw materials for biological hydrogen production. Our model was based on hydrogen yield potential, sugar mobilization efficiency, fermentability and coproduct yield and value. The suitability of the studied r

  7. Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution.

    Science.gov (United States)

    Rohlfs, Rori V; Nielsen, Rasmus

    2015-09-01

    A number of methods have been developed for modeling the evolution of a quantitative trait on a phylogeny. These methods have received renewed interest in the context of genome-wide studies of gene expression, in which the expression levels of many genes can be modeled as quantitative traits. We here develop a new method for joint analyses of quantitative traits within- and between species, the Expression Variance and Evolution (EVE) model. The model parameterizes the ratio of population to evolutionary expression variance, facilitating a wide variety of analyses, including a test for lineage-specific shifts in expression level, and a phylogenetic ANOVA that can detect genes with increased or decreased ratios of expression divergence to diversity, analogous to the famous Hudson Kreitman Aguadé (HKA) test used to detect selection at the DNA level. We use simulations to explore the properties of these tests under a variety of circumstances and show that the phylogenetic ANOVA is more accurate than the standard ANOVA (no accounting for phylogeny) sometimes used in transcriptomics. We then apply the EVE model to a mammalian phylogeny of 15 species typed for expression levels in liver tissue. We identify genes with high expression divergence between species as candidates for expression level adaptation, and genes with high expression diversity within species as candidates for expression level conservation and/or plasticity. Using the test for lineage-specific expression shifts, we identify several candidate genes for expression level adaptation on the catarrhine and human lineages, including genes putatively related to dietary changes in humans. We compare these results to those reported previously using a model which ignores expression variance within species, uncovering important differences in performance. We demonstrate the necessity for a phylogenetic model in comparative expression studies and show the utility of the EVE model to detect expression divergence

  8. Identification of process suitable diluent

    Energy Technology Data Exchange (ETDEWEB)

    Dean R. Peterman

    2014-01-01

    The Sigma Team for Minor Actinide Separation (STMAS) was formed within the USDOE Fuel Cycle Research and Development (FCRD) program in order to develop more efficient methods for the separation of americium and other minor actinides (MA) from used nuclear fuel. The development of processes for MA separations is driven by the potential benefits; reduced long-term radiotoxicty of waste placed in a geologic repository, reduced timeframe of waste storage, reduced repository heat load, the possibility of increased repository capacity, and increased utilization of energy potential of used nuclear fuel. The research conducted within the STMAS framework is focused upon the realization of significant simplifications to aqueous recycle processes proposed for MA separations. This report describes the research efforts focused upon the identification of a process suitable diluent for a flowsheet concept for the separation of MA which is based upon the dithiophosphinic acid (DPAH) extractants previously developed at the Idaho National Laboratory (INL).

  9. Suitable footwear for enhanced safety

    CERN Multimedia

    2004-01-01

    Safety shoes are the theme of a new safety campaign. Always remember that accidents can happen - even to your feet! When entering hazardous areas such as underground halls, work sites, experiment assembly sites, workshops etc., sandals, ordinary shoes or similar light footwear should not be worn. Whatever the risks to which you may be exposed, always think safety and wear suitable footwear, i.e. safety shoes, which have non-slip soles and steel reinforcements to protect your feet from being crushed, fractured or pierced. Is it serious, Doctor? "Some traumas resulting from foot-related accidents - open fractures for instance - can be quite serious," explains CERN Works Doctor Véronique Fassnacht. "But the most common injuries are sprained ankles sustained during simple falls caused by differences in floor-levels (e.g. false floors). Fractures, bruising, surface wounds or deep wounds caused by objects falling onto the top of the foot are also quite common." ...

  10. Suitability study of sampled-data model of TCSC for SSO analysis%TCSC采样-数据模型在次同步振荡分析中的适用性研究

    Institute of Scientific and Technical Information of China (English)

    向昌明; 吴熙; 蒋平

    2013-01-01

    Since frequency of the analysis component of Subsynchronous Oscillation (SSO) problem is neither at the power frequency nor within the range of low frequency, Quasi-Steady-State (QSS) model cannot be used to analyze SSO. For the same reason, we also cannot consider the analysis component of SSO as electricity signals at power frequency with low frequency modulation to analyze SSO problem. The dynamic model TCSC must be effective throughout the whole frequency range of SSO. Hence, verification of the suitability of TCSC dynamic model is of great significance. This paper proposes a method to verify the suitability of TCSC dynamic model through comparing damping characteristics throughout the whole frequency range of SSO. On one hand, sample-data model of TCSC is adopted, and small signal analysis method is utilized to establish state space matrices of system. Then a series of matric transformation is applied so as to obtain electrical damping characteristics of system. On the other hand, time simulation model is constructed in PSCAD, where the model of TCSC is precise to the device-level. Then, test signal method is adopted to obtain electrical damping characteristics of system. Finally, electrical damping characteristics obtained by the two methods are compared. The simulation result shows that the sample-data-based model of TCSC is accurate and suitable for the analysis of SSO problem.%由于电力系统次同步振荡(SSO)问题要分析的是既非工频又非低频的成分,故不能采用工频准稳态模型或认为工频电量上有低频调制来进行分析,使用的TCSC动态数学模型必须在整个次同步振荡范围内都有效,因此TCSC动态模型适用性验证的工作非常重要。提出通过对比含TCSC系统在整个次同步频域内的阻尼特性来验证TCSC动态模型的适用性。一方面,TCSC采用采样-数据模型,运用小扰动分析法建立系统的状态空间矩阵,并通过矩阵变换直接求取系统

  11. Complement factor B expression profile in a spontaneous uveitis model.

    Science.gov (United States)

    Zipplies, Johanna K; Kirschfink, Michael; Amann, Barbara; Hauck, Stefanie M; Stangassinger, Manfred; Deeg, Cornelia A

    2010-12-01

    Equine recurrent uveitis serves as a spontaneous model for human autoimmune uveitis. Unpredictable relapses and ongoing inflammation in the eyes of diseased horses as well as in humans lead to destruction of the retina and finally result in blindness. However, the molecular mechanisms leading to inflammation and retinal degeneration are not well understood. An initial screening for differentially regulated proteins in sera of uveitic cases compared to healthy controls revealed an increase of the alternative pathway complement component factor B in ERU cases. To determine the activation status of the complement system, sera were subsequently examined for complement split products. We could demonstrate a significant higher concentration of the activation products B/Ba, B/Bb, Bb neoantigen, iC3b and C3d in uveitic condition compared to healthy controls, whereas for C5b-9 no differences were detected. Additionally, we investigated complement activation directly in the retina by immunohistochemistry, since it is the main target organ of this autoimmune disease. Interestingly, infiltrating cells co-expressed activated factor Bb neoantigen, complement split product C3d as well as CD68, a macrophage marker. In this study, we could demonstrate activation of the complement system both systemically as well as in the eye, the target organ of spontaneous recurrent uveitis. Based on these novel findings, we postulate a novel role for macrophages in connection with complement synthesis at the site of inflammation.

  12. Some combinatorial models for reduced expressions in Coxeter groups

    CERN Document Server

    Denoncourt, Hugh

    2011-01-01

    Stanley's formula for the number of reduced expressions of a permutation regarded as a Coxeter group element raises the question of how to enumerate the reduced expressions of an arbitrary Coxeter group element. We provide a framework for answering this question by constructing combinatorial objects that represent the inversion set and the reduced expressions for an arbitrary Coxeter group element. The framework also provides a formula for the length of an element formed by deleting a generator from a Coxeter group element. Fan and Hagiwara, et al$.$ showed that for certain Coxeter groups, the short-braid avoiding elements characterize those elements that give reduced expressions when any generator is deleted from a reduced expression. We provide a characterization that holds in all Coxeter groups. Lastly, we give applications to the freely braided elements introduced by Green and Losonczy, generalizing some of their results that hold in simply-laced Coxeter groups to the arbitrary Coxeter group setting.

  13. A structured population modeling framework for quantifying and predicting gene expression noise in flow cytometry data.

    Science.gov (United States)

    Flores, Kevin B

    2013-07-01

    We formulated a structured population model with distributed parameters to identify mechanisms that contribute to gene expression noise in time-dependent flow cytometry data. The model was validated using cell population-level gene expression data from two experiments with synthetically engineered eukaryotic cells. Our model captures the qualitative noise features of both experiments and accurately fit the data from the first experiment. Our results suggest that cellular switching between high and low expression states and transcriptional re-initiation are important factors needed to accurately describe gene expression noise with a structured population model.

  14. Evaluation of Suitability of Bankruptcy

    OpenAIRE

    Mackevičius, Jonas; Silvanavičiūtė, Simona

    2006-01-01

    Financial data is the main source of enterprise bankruptcy prediction. Applying bankruptcy prediction models, which consist of significant financial ratios, is one of the most simple as well as accurate ways for predicting bankruptcy of enterprises. With the help of these models, the threat of bankruptcy could be noticed several years before the process of bankruptcy actually starts. The research has proved the linear discriminant models (Altman, Springate, Taffler & Tisshaw) to be the mo...

  15. 基于模糊证据权模型的青藏高原区土地适宜性评价%Land suitability evaluation in Qinghai-Tibet Plateau based on fuzzy weight of evidence model

    Institute of Scientific and Technical Information of China (English)

    金贵; 王占岐; 胡学东; 胡守庚; 张道军

    2013-01-01

    the exploitation and utilization of reserved arable land. This paper took the reserved arable land of 18 counties in the“Three Rivers”Area region of Tibet as an example. Eight factors of landform, climate, soil and water, that is, slope, elevation, slope direction, temperature, rainfall, soil depth, organic matter content, and distance to water area, were adopted as evaluation factors. The fuzzy weight of evidence model, which is both knowledge and data driven, was employed to get the grade of natural suitability evaluation of reserve resources of arable land, which was then compared with the result evaluated by a comprehensive index model. Evaluation results showed as follows:first, 99.38%of“reference objects”of the arable land are above the third grade on the basis of five suitability grades in total, which means that the fuzzy weight of evidence model could evaluate the natural suitability of reserved arable land effectively. Second, compared with the evaluation results of a comprehensive index model, 90.83%of the arable land resources are above the third grade, which shows the fuzzy weight of evidence model is more objective and reasonable than the comprehensive index model in this case. And it also overcomes the subjective arbitrariness in weight determination and the computation complexity by various natural conditions. Third, 11 434.1 km2 of reserved arable land had suitable natural quality, among which grade 1, 2, 3, 4, and 5 accounted for 9.6%, 5.5%, 38.6%, 22.8%, and 23.4%respectively. And we suggest that Shigatse, Konggar, Chanang, Lhazê, Nêdong, Lhasa, and Bainang counties should be the main areas for exploitation of reserved arable land in the future.

  16. Ecological variables governing habitat suitability and the distribution ...

    African Journals Online (AJOL)

    Ecological variables governing habitat suitability and the distribution of the endangered ... This cryptic species is not evenly distributed throughout its restricted range and ... A multiple logistic regression model highlighted the importance of soil ...

  17. Coupling of pollination services and coffee suitability under climate change.

    Science.gov (United States)

    Imbach, Pablo; Fung, Emily; Hannah, Lee; Navarro-Racines, Carlos E; Roubik, David W; Ricketts, Taylor H; Harvey, Celia A; Donatti, Camila I; Läderach, Peter; Locatelli, Bruno; Roehrdanz, Patrick R

    2017-09-26

    Climate change will cause geographic range shifts for pollinators and major crops, with global implications for food security and rural livelihoods. However, little is known about the potential for coupled impacts of climate change on pollinators and crops. Coffee production exemplifies this issue, because large losses in areas suitable for coffee production have been projected due to climate change and because coffee production is dependent on bee pollination. We modeled the potential distributions of coffee and coffee pollinators under current and future climates in Latin America to understand whether future coffee-suitable areas will also be suitable for pollinators. Our results suggest that coffee-suitable areas will be reduced 73-88% by 2050 across warming scenarios, a decline 46-76% greater than estimated by global assessments. Mean bee richness will decline 8-18% within future coffee-suitable areas, but all are predicted to contain at least 5 bee species, and 46-59% of future coffee-suitable areas will contain 10 or more species. In our models, coffee suitability and bee richness each increase (i.e., positive coupling) in 10-22% of future coffee-suitable areas. Diminished coffee suitability and bee richness (i.e., negative coupling), however, occur in 34-51% of other areas. Finally, in 31-33% of the future coffee distribution areas, bee richness decreases and coffee suitability increases. Assessing coupled effects of climate change on crop suitability and pollination can help target appropriate management practices, including forest conservation, shade adjustment, crop rotation, or status quo, in different regions.

  18. Site suitability criteria for solidified high level waste repositories

    Energy Technology Data Exchange (ETDEWEB)

    Heckman, R.A.; Holdsworth, T.; Towse, D.F.

    1979-03-07

    Activities devoted to development of regulations, criteria, and standards for storage of solidified high-level radioactive wastes are reported. The work is summarized in sections on site suitability regulations, risk calculations, geological models, aquifer models, human usage model, climatology model, and repository characteristics. Proposed additional analytical work is also summarized. (JRD)

  19. Using Video Modeling to Teach Children with PDD-NOS to Respond to Facial Expressions

    Science.gov (United States)

    Axe, Judah B.; Evans, Christine J.

    2012-01-01

    Children with autism spectrum disorders often exhibit delays in responding to facial expressions, and few studies have examined teaching responding to subtle facial expressions to this population. We used video modeling to train 3 participants with PDD-NOS (age 5) to respond to eight facial expressions: approval, bored, calming, disapproval,…

  20. Expression

    Directory of Open Access Journals (Sweden)

    Wang-Xia Wang

    2014-02-01

    Full Text Available The miR-15/107 family comprises a group of 10 paralogous microRNAs (miRNAs, sharing a 5′ AGCAGC sequence. These miRNAs have overlapping targets. In order to characterize the expression of miR-15/107 family miRNAs, we employed customized TaqMan Low-Density micro-fluid PCR-array to investigate the expression of miR-15/107 family members, and other selected miRNAs, in 11 human tissues obtained at autopsy including the cerebral cortex, frontal cortex, primary visual cortex, thalamus, heart, lung, liver, kidney, spleen, stomach and skeletal muscle. miR-103, miR-195 and miR-497 were expressed at similar levels across various tissues, whereas miR-107 is enriched in brain samples. We also examined the expression patterns of evolutionarily conserved miR-15/107 miRNAs in three distinct primary rat brain cell preparations (enriched for cortical neurons, astrocytes and microglia, respectively. In primary cultures of rat brain cells, several members of the miR-15/107 family are enriched in neurons compared to other cell types in the central nervous system (CNS. In addition to mature miRNAs, we also examined the expression of precursors (pri-miRNAs. Our data suggested a generally poor correlation between the expression of mature miRNAs and their precursors. In summary, we provide a detailed study of the tissue and cell type-specific expression profile of this highly expressed and phylogenetically conserved family of miRNA genes.

  1. In vitro and in vivo investigation of matrix metalloproteinase expression in metastatic tumor models

    Energy Technology Data Exchange (ETDEWEB)

    Sprague, Jennifer E. [Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110 (United States); Li Wenping [Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110 (United States); Liang Kexian [Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110 (United States); Achilefu, Samuel [Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110 (United States); Anderson, Carolyn J. [Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110 (United States)]. E-mail: andersoncj@wustl.edu

    2006-02-15

    Introduction: Overexpression of matrix metalloproteinases (MMPs), particularly MMP-2 and MMP-9, has been correlated with poor prognosis in several cancer types including lung, colon and breast. Noninvasive detection of MMP expression might allow physicians to better determine when more aggressive cancer therapy is appropriate. The peptide CTT (CTTHWGFTLC) was identified as a selective inhibitor of MMP-2/9 that inhibits the growth of MDA-MB-435 human breast cancer xenografts. Methods: CTT was conjugated with the bifunctional chelator DOTA (1,4,7,10-tetraazacyclotetradecane-N,N',N'',N'''-tetraacetic acid) for radiolabeling with {sup 64}Cu (t {sub 1/2}=12.7 h, 17.4% {beta}{sup +}, 39% {beta}{sup -}), a radionuclide suitable for positron emission tomography (PET). In vitro affinity was determined in a fluorogenic substrate assay. Tumor gelatinase targeting was evaluated in both biodistribution and microPET imaging studies. Results: Cu(II)-DOTA-CTT inhibited hMMP-2 (EC{sub 5}=8.7 {mu}M) and mMMP-9 (EC{sub 5}=18.2 {mu}M) with similar affinity to CTT (hMMP-2 EC{sub 5}=13.2 {mu}M; mMMP-9 EC{sub 5}=11.0 {mu}M). In biodistribution and microPET imaging studies, {sup 64}Cu-DOTA-CTT was taken up by MMP-2/9-positive B16F10 murine melanoma tumors. Subsequently, imaging studies using {sup 64}Cu-DOTA-CTT were performed on MDA-MB-435 tumor-bearing mice. With zymography, tumor MMP-2/9 expression in this model was shown to be inconsistent, resulting in microPET detection of the MDA-MB-435 tumor in only 1 of 24 imaged mice. Following limited imaging success, {sup 64}Cu-DOTA-CTT was shown to have poor in vivo stability. Conclusions: Despite some evidence for selective uptake of {sup 64}Cu-DOTA-CTT by gelatinase-expressing tumors, the low affinity for MMP-2 and MMP-9 and in vivo instability make this an inadequate radioligand for in vivo tumor evaluation.

  2. Design, modeling, expression, and chemoselective PEGylation of a new nanosize cysteine analog of erythropoietin

    Directory of Open Access Journals (Sweden)

    Ahangari Cohan R

    2011-06-01

    Full Text Available Reza Ahangari Cohan1, Armin Madadkar-Sobhani2,3, Hossein Khanahmad1, Farzin Roohvand4, Mohammad Reza Aghasadeghi4, Mohammad Hossein Hedayati5, Zahra Barghi5, Mehdi Shafiee Ardestani4, Davoud Nouri Inanlou1, Dariush Norouzian11Research and Development Department, Production and Research Complex, Pasteur Institute of Iran, Tehran, Iran; 2Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran; 3Department of Life Sciences, Barcelona Supercomputing Center, Barcelona, Spain; 4Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran; 5Quality Control Department, Production and Research Complex, Pasteur Institute of Iran, Tehran, IranBackground: Recombinant human erythropoietin (rhEPO is considered to be one of the most pivotal pharmaceutical drugs in the market because of its clinical application in the treatment of anemia-associated disorders worldwide. However, like other therapeutic proteins, it does not have suitable pharmacokinetic properties for it to be administrated at least two to three times per week. Chemoselective cysteine PEGylation, employing molecular dynamics and graphics in in silico studies, can be considered to overcome such a problem.Methods: A special kind of EPO analog was elicited based on a literature review, homology modeling, molecular dynamic simulation, and factors affecting the PEGylation reaction. Then, cDNA of the selected analog was generated by site-directed mutagenesis and subsequently cloned into the expression vector. The construct was transfected to Chinese hamster ovary/dhfr- cells, and highly expressed clones were selected via methotrexate amplification. Ion-immobilized affinity and size exclusion (SE chromatography techniques were used to purify the expressed analog. Thereafter, chemoselective PEGylation was performed and a nanosize PEGylated EPO was obtained through dialysis. The in vitro biologic assay and in vivo pharmacokinetic parameters were

  3. Validating Internal Control Genes for the Accurate Normalization of qPCR Expression Analysis of the Novel Model Plant Setaria viridis.

    Directory of Open Access Journals (Sweden)

    Julia Lambret-Frotté

    Full Text Available Employing reference genes to normalize the data generated with quantitative PCR (qPCR can increase the accuracy and reliability of this method. Previous results have shown that no single housekeeping gene can be universally applied to all experiments. Thus, the identification of a suitable reference gene represents a critical step of any qPCR analysis. Setaria viridis has recently been proposed as a model system for the study of Panicoid grasses, a crop family of major agronomic importance. Therefore, this paper aims to identify suitable S. viridis reference genes that can enhance the analysis of gene expression in this novel model plant. The first aim of this study was the identification of a suitable RNA extraction method that could retrieve a high quality and yield of RNA. After this, two distinct algorithms were used to assess the gene expression of fifteen different candidate genes in eighteen different samples, which were divided into two major datasets, the developmental and the leaf gradient. The best-ranked pair of reference genes from the developmental dataset included genes that encoded a phosphoglucomutase and a folylpolyglutamate synthase; genes that encoded a cullin and the same phosphoglucomutase as above were the most stable genes in the leaf gradient dataset. Additionally, the expression pattern of two target genes, a SvAP3/PI MADS-box transcription factor and the carbon-fixation enzyme PEPC, were assessed to illustrate the reliability of the chosen reference genes. This study has shown that novel reference genes may perform better than traditional housekeeping genes, a phenomenon which has been previously reported. These results illustrate the importance of carefully validating reference gene candidates for each experimental set before employing them as universal standards. Additionally, the robustness of the expression of the target genes may increase the utility of S. viridis as a model for Panicoid grasses.

  4. Radio-deoxynucleoside Analogs used for Imaging tk Expression in a Transgenic Mouse Model of Induced Hepatocellular Carcinoma

    Directory of Open Access Journals (Sweden)

    Haibin Tian, Xincheng Lu, Hong Guo, David Corn, Joseph Molter, Bingcheng Wang, Guangbin Luo, Zhenghong Lee

    2012-01-01

    -to-background ratio as well as tracer clearance.Conclusion: The newly created knock-in mouse model was used to demonstrate the use of the dual-reporter genes driven by well-characterized cancer-specific transcriptional units in conjunction with in vivo imaging as a paradigm in studying naturally occurring cancer in live animals. While BLI is suitable for small animal imaging with luc expression, PET with L-FMAU seemed be the choice for liver injury or liver cancer imaging with this animal model for future investigations.

  5. Undertaking industrial land spatial suitability evaluation based on hierarchical fuzzy matter element model%基于层次模糊物元模型的承接产业用地空间适宜评价

    Institute of Scientific and Technical Information of China (English)

    范树平; 刘友兆; 张红梅; 侯长莉; 常冬寅

    2015-01-01

    It is of vital importance for the central and western regions to distinguish the undertaken industrial types as well as land space layout on the basis of transferring industry, ecological environment and land development strategy. In this paper, Chizhou City, the typical representative of undertaking industrial types, from the perspectives of location quotient and comparative labor productivity, constructs industrial transfer identification model and identifies regional undertaken industrial type. From four criterion layers of natural environment, infrastructure, development degree and development benefit, construct the identification model and the evaluation index system and its city domain and the classical domain;using analytic hierarchy process (AHP) and fuzzy matter element analysis method and mathematical software such as Matlab7.0, Arcgis and Excel, identify the regional industrial types undertaken and evaluate the industrial land development suitability. Research shows that Chizhou City industry location quotient varies from the maximum value of 10.5421 to the minimum value of 0.0315, which demonstrates that the degree of industrial agglomeration is relatively high while the comparative labor productivity is low overall, only 5 types of industry more than 1. Industry location quotient and comparative labor productivity are low, which shows that industrial development difference is small and without obvious hierarchical gradient. According to industry transfer identification model, the Chizhou industry is classified into 4 types, of which the numbers of competitive advantage industry and weak industry respectively reach 12 and 15, and stay out industry and undertaken industry account for only 5 and 2. Based on the advantages of the three core resources, i.e. mineral resource, ecological resource and tourism resource, five categories of industry including mineral mining industry, textile and garment industry, equipment manufacturing industry, wood furniture

  6. Construction and Pre-Test of a Semantic Expressiveness Measure for Conceptual Models

    OpenAIRE

    Poels, G; Maes, A.; Gailly, F; R. PAEMELEIRE

    2004-01-01

    One quality attributed to McCarthy’s Resources-Events-Agents (REA) accounting model is semantic expressiveness. Compared to accounting models without a semantic orientation like the Debit-Credit-Account (DCA) model, the REA model is claimed to better represent the economic phenomena underlying an accounting system. The alleged benefits of this increased semantic expressiveness include easier integration with representations of non-accounting information and better user understanding of accoun...

  7. Predictive Modeling of Expressed Emotions in Music Using Pairwise Comparisons

    DEFF Research Database (Denmark)

    Madsen, Jens; Jensen, Bjørn Sand; Larsen, Jan

    2013-01-01

    We introduce a two-alternative forced-choice (2AFC) experimental paradigm to quantify expressed emotions in music using the arousal and valence (AV) dimensions. A wide range of well-known audio features are investigated for predicting the expressed emotions in music using learning curves...... and essential baselines. We furthermore investigate the scalability issues of using 2AFC in quantifying emotions expressed in music on large-scale music databases. The possibility of dividing the annotation task between multiple individuals, while pooling individuals’ comparisons is investigated by looking...... at the subjective differences of ranking emotion in the AV space. We find this to be problematic due to the large variation in subjects’ rankings of excerpts. Finally, solving scalability issues by reducing the number of pairwise comparisons is analyzed. We compare two active learning schemes to selecting...

  8. Selection of Reference Genes for Gene Expression Studies related to lung injury in a preterm lamb model.

    Science.gov (United States)

    Pereira-Fantini, Prue M; Rajapaksa, Anushi E; Oakley, Regina; Tingay, David G

    2016-05-23

    Preterm newborns often require invasive support, however even brief periods of supported ventilation applied inappropriately to the lung can cause injury. Real-time quantitative reverse transcriptase-PCR (qPCR) has been extensively employed in studies of ventilation-induced lung injury with the reference gene 18S ribosomal RNA (18S RNA) most commonly employed as the internal control reference gene. Whilst the results of these studies depend on the stability of the reference gene employed, the use of 18S RNA has not been validated. In this study the expression profile of five candidate reference genes (18S RNA, ACTB, GAPDH, TOP1 and RPS29) in two geographical locations, was evaluated by dedicated algorithms, including geNorm, Normfinder, Bestkeeper and ΔCt method and the overall stability of these candidate genes determined (RefFinder). Secondary studies examined the influence of reference gene choice on the relative expression of two well-validated lung injury markers; EGR1 and IL1B. In the setting of the preterm lamb model of lung injury, RPS29 reference gene expression was influenced by tissue location; however we determined that individual ventilation strategies influence reference gene stability. Whilst 18S RNA is the most commonly employed reference gene in preterm lamb lung studies, our results suggest that GAPDH is a more suitable candidate.

  9. 45 CFR 12a.4 - Suitability determination.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Suitability determination. 12a.4 Section 12a.4... PROPERTY TO ASSIST THE HOMELESS § 12a.4 Suitability determination. (a) Suitability determination. Within 30... determination to the landholding agency. Properties that are under lease, contract, license, or agreement by...

  10. 24 CFR 581.4 - Suitability determination.

    Science.gov (United States)

    2010-04-01

    ... reviewed for suitability. HUD will maintain a written public record of the following: (1) The suitability... 24 Housing and Urban Development 3 2010-04-01 2010-04-01 false Suitability determination. 581.4... (Continued) OFFICE OF ASSISTANT SECRETARY FOR COMMUNITY PLANNING AND DEVELOPMENT, DEPARTMENT OF HOUSING...

  11. Modeling Expressed Emotions in Music using Pairwise Comparisons

    DEFF Research Database (Denmark)

    Madsen, Jens; Nielsen, Jens Brehm; Jensen, Bjørn Sand

    2012-01-01

    We introduce a two-alternative forced-choice experimental paradigm to quantify expressed emotions in music using the two wellknown arousal and valence (AV) dimensions. In order to produce AV scores from the pairwise comparisons and to visualize the locations of excerpts in the AV space, we...

  12. Modeling Expressed Emotions in Music using Pairwise Comparisons

    DEFF Research Database (Denmark)

    Madsen, Jens; Nielsen, Jens Brehm; Jensen, Bjørn Sand

    2012-01-01

    We introduce a two-alternative forced-choice experimental paradigm to quantify expressed emotions in music using the two wellknown arousal and valence (AV) dimensions. In order to produce AV scores from the pairwise comparisons and to visualize the locations of excerpts in the AV space, we...

  13. A hidden Markov model approach for determining expression from genomic tiling micro arrays

    Directory of Open Access Journals (Sweden)

    Krogh Anders

    2006-05-01

    Full Text Available Abstract Background Genomic tiling micro arrays have great potential for identifying previously undiscovered coding as well as non-coding transcription. To-date, however, analyses of these data have been performed in an ad hoc fashion. Results We present a probabilistic procedure, ExpressHMM, that adaptively models tiling data prior to predicting expression on genomic sequence. A hidden Markov model (HMM is used to model the distributions of tiling array probe scores in expressed and non-expressed regions. The HMM is trained on sets of probes mapped to regions of annotated expression and non-expression. Subsequently, prediction of transcribed fragments is made on tiled genomic sequence. The prediction is accompanied by an expression probability curve for visual inspection of the supporting evidence. We test ExpressHMM on data from the Cheng et al. (2005 tiling array experiments on ten Human chromosomes 1. Results can be downloaded and viewed from our web site 2. Conclusion The value of adaptive modelling of fluorescence scores prior to categorisation into expressed and non-expressed probes is demonstrated. Our results indicate that our adaptive approach is superior to the previous analysis in terms of nucleotide sensitivity and transfrag specificity.

  14. The suitability of internal versus external successors

    DEFF Research Database (Denmark)

    Boyd, Britta; Royer, Susanne

    2012-01-01

    of family business succession in order to understand when family successors are preferred because of their family-specific experiential knowledge. A case study analysis from the German-Danish border region explores how a family firm has used internal successors for the last 12 successions. We argue...... that in industries where tacit knowledge forms the basis for competitive advantage, the use of internal successors can help family firms excel after a transition of power has occurred. Theoretical and practical implications are discussed to enhance the long-term perspective for family businesses.......Understanding knowledge transfer in family firm succession is important for the survival of family firms. Previous research has begun to explore the suitability of internal versus external successor in family firms with regard to relevant knowledge types. This paper builds on the contingency model...

  15. 空间质量作用模型预测小分子离子交换平衡%Suitability of Steric Mass-action Model for Ion-exchange Equilibrium of Micromolecule

    Institute of Scientific and Technical Information of China (English)

    陈卫东; 王艳东; 苏志国

    2005-01-01

    The steric mass-action (SMA) model has been widely reported in the literature for ion-exchange and metal-affinity interaction adsorption equilibrium of biomacromolecules. In this paper, the usefulness of SMA model is analyzed for describing micromolecule ion-exchange equilibrium onto cation exchangers, CM Sephadex C-25 and treamline SP. Batch adsorption experiments with ephedrine hydrochloride as a model adsorbate are carried out to determine the model parameters, that is, steric factor, characteristic charge and equilibrium constant. The result shows that the SMA model parameters of micromolecule cannot be obtained using the nonlinear least-square fitting method as protein's due to the remarkable difference between the molecular mass and dimension of micromolecule and protein. It is considered that the small size of the adsorbates dealt with in this study justifies the neglect of steric hindrances arising from adsorbate bulkiness. Thus, the three-parameter SMA model is reduced to two-parameter one (i.e., steric factor is equal to zero) for describing micromolecule ion-exchange equilibrium. It is found that the equilibrium constant for CM Sephadex C-25 increases with increasing ionic strength, while the equilibrium constant for Streamline SP shows an opposite trend. This is probably due to the remarkable difference between the physical properties of the two adsorbents. Then, the relationship between the equilibrium constant and ionic strength is described by an expression. The computer simulations show that, the theoretical model with the correlation is promising in the prediction of micromolecule adsorption decrease with increasing ionic strength in a wide range of salt concentration.

  16. Gene Expression Profiling in an in Vitro Model of Angiogenesis

    OpenAIRE

    Kahn, Jeanne; Mehraban, Fuad; Ingle, Gladys; Xin, Xiaohua; Bryant, Juliet E.; Vehar, Gordon; Schoenfeld, Jill; Grimaldi, Chrisopher J.; Peale, Franklin; Draksharapu, Aparna; Lewin, David A.; Gerritsen, Mary E.

    2000-01-01

    In the present study we have used a novel, comprehensive mRNA profiling technique (GeneCalling) for determining differential gene expression profiles of human endothelial cells undergoing differentiation into tubelike structures. One hundred fifteen cDNA fragments were identified and shown to represent 90 distinct genes. Although some of the genes identified have previously been implicated in angiogenesis, potential roles for many new genes, including OX-40, white protein homolog, KIAA0188, a...

  17. Global gene expression profile progression in Gaucher disease mouse models

    Directory of Open Access Journals (Sweden)

    Zhang Wujuan

    2011-01-01

    Full Text Available Abstract Background Gaucher disease is caused by defective glucocerebrosidase activity and the consequent accumulation of glucosylceramide. The pathogenic pathways resulting from lipid laden macrophages (Gaucher cells in visceral organs and their abnormal functions are obscure. Results To elucidate this pathogenic pathway, developmental global gene expression analyses were conducted in distinct Gba1 point-mutated mice (V394L/V394L and D409 V/null. About 0.9 to 3% of genes had altered expression patterns (≥ ± 1.8 fold change, representing several categories, but particularly macrophage activation and immune response genes. Time course analyses (12 to 28 wk of INFγ-regulated pro-inflammatory (13 and IL-4-regulated anti-inflammatory (11 cytokine/mediator networks showed tissue differential profiles in the lung and liver of the Gba1 mutant mice, implying that the lipid-storage macrophages were not functionally inert. The time course alterations of the INFγ and IL-4 pathways were similar, but varied in degree in these tissues and with the Gba1 mutation. Conclusions Biochemical and pathological analyses demonstrated direct relationships between the degree of tissue glucosylceramides and the gene expression profile alterations. These analyses implicate IFNγ-regulated pro-inflammatory and IL-4-regulated anti-inflammatory networks in differential disease progression with implications for understanding the Gaucher disease course and pathophysiology.

  18. A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels

    Directory of Open Access Journals (Sweden)

    Wu Steven H

    2012-06-01

    Full Text Available Abstract Background Two-dimensional polyacrylamide gel electrophoresis (2D PAGE is commonly used to identify differentially expressed proteins under two or more experimental or observational conditions. Wu et al (2009 developed a univariate probabilistic model which was used to identify differential expression between Case and Control groups, by applying a Likelihood Ratio Test (LRT to each protein on a 2D PAGE. In contrast to commonly used statistical approaches, this model takes into account the two possible causes of missing values in 2D PAGE: either (1 the non-expression of a protein; or (2 a level of expression that falls below the limit of detection. Results We develop a global Bayesian model which extends the previously described model. Unlike the univariate approach, the model reported here is able treat all differentially expressed proteins simultaneously. Whereas each protein is modelled by the univariate likelihood function previously described, several global distributions are used to model the underlying relationship between the parameters associated with individual proteins. These global distributions are able to combine information from each protein to give more accurate estimates of the true parameters. In our implementation of the procedure, all parameters are recovered by Markov chain Monte Carlo (MCMC integration. The 95% highest posterior density (HPD intervals for the marginal posterior distributions are used to determine whether differences in protein expression are due to differences in mean expression intensities, and/or differences in the probabilities of expression. Conclusions Simulation analyses showed that the global model is able to accurately recover the underlying global distributions, and identify more differentially expressed proteins than the simple application of a LRT. Additionally, simulations also indicate that the probability of incorrectly identifying a protein as differentially expressed (i.e., the False

  19. Identification of endogenous reference genes for the analysis of microRNA expression in the hippocampus of the pilocarpine-induced model of mesial temporal lobe epilepsy.

    Directory of Open Access Journals (Sweden)

    Mykaella Andrade de Araújo

    Full Text Available Real-time quantitative RT-PCR (qPCR is one of the most powerful techniques for analyzing miRNA expression because of its sensitivity and specificity. However, in this type of analysis, a suitable normalizer is required to ensure that gene expression is unaffected by the experimental condition. To the best of our knowledge, there are no reported studies that performed a detailed identification and validation of suitable reference genes for miRNA qPCR during the epileptogenic process. Here, using a pilocarpine (PILO model of mesial temporal lobe epilepsy (MTLE, we investigated five potential reference genes, performing a stability expression analysis using geNorm and NormFinder softwares. As a validation strategy, we used each one of the candidate reference genes to measure PILO-induced changes in microRNA-146a levels, a gene whose expression pattern variation in the PILO injected model is known. Our results indicated U6SnRNA and SnoRNA as the most stable candidate reference genes. By geNorm analysis, the normalization factor should preferably contain at least two of the best candidate reference genes (snoRNA and U6SnRNA. In fact, when normalized using the best combination of reference genes, microRNA-146a transcripts were found to be significantly increased in chronic stage, which is consistent with the pattern reported in different models. Conversely, when reference genes were individually employed for normalization, we failed to detect up-regulation of the microRNA-146a gene in the hippocampus of epileptic rats. The data presented here support that the combination of snoRNA and U6SnRNA was the minimum necessary for an accurate normalization of gene expression at the different stages of epileptogenesis that we tested.

  20. Robust modeling of differential gene expression data using normal/independent distributions: a Bayesian approach.

    Directory of Open Access Journals (Sweden)

    Mojtaba Ganjali

    Full Text Available In this paper, the problem of identifying differentially expressed genes under different conditions using gene expression microarray data, in the presence of outliers, is discussed. For this purpose, the robust modeling of gene expression data using some powerful distributions known as normal/independent distributions is considered. These distributions include the Student's t and normal distributions which have been used previously, but also include extensions such as the slash, the contaminated normal and the Laplace distributions. The purpose of this paper is to identify differentially expressed genes by considering these distributional assumptions instead of the normal distribution. A Bayesian approach using the Markov Chain Monte Carlo method is adopted for parameter estimation. Two publicly available gene expression data sets are analyzed using the proposed approach. The use of the robust models for detecting differentially expressed genes is investigated. This investigation shows that the choice of model for differentiating gene expression data is very important. This is due to the small number of replicates for each gene and the existence of outlying data. Comparison of the performance of these models is made using different statistical criteria and the ROC curve. The method is illustrated using some simulation studies. We demonstrate the flexibility of these robust models in identifying differentially expressed genes.

  1. Connecting protein and mRNA burst distributions for stochastic models of gene expression

    CERN Document Server

    Elgart, Vlad; Fenley, Andrew T; Kulkarni, Rahul V

    2011-01-01

    The intrinsic stochasticity of gene expression can lead to large variability in protein levels for genetically identical cells. Such variability in protein levels can arise from infrequent synthesis of mRNAs which in turn give rise to bursts of protein expression. Protein expression occurring in bursts has indeed been observed experimentally and recent studies have also found evidence for transcriptional bursting, i.e. production of mRNAs in bursts. Given that there are distinct experimental techniques for quantifying the noise at different stages of gene expression, it is of interest to derive analytical results connecting experimental observations at different levels. In this work, we consider stochastic models of gene expression for which mRNA and protein production occurs in independent bursts. For such models, we derive analytical expressions connecting protein and mRNA burst distributions which show how the functional form of the mRNA burst distribution can be inferred from the protein burst distributio...

  2. Mapping marine habitat suitability and uncertainty of Bayesian networks: a case study using Pacific benthic macrofauna

    Science.gov (United States)

    Andrea Havron; Chris Goldfinger; Sarah Henkel; Bruce G. Marcot; Chris Romsos; Lisa Gilbane

    2017-01-01

    Resource managers increasingly use habitat suitability map products to inform risk management and policy decisions. Modeling habitat suitability of data-poor species over large areas requires careful attention to assumptions and limitations. Resulting habitat suitability maps can harbor uncertainties from data collection and modeling processes; yet these limitations...

  3. A Model of the Perception of Facial Expressions of Emotion by Humans: Research Overview and Perspectives.

    Science.gov (United States)

    Martinez, Aleix; Du, Shichuan

    2012-05-01

    In cognitive science and neuroscience, there have been two leading models describing how humans perceive and classify facial expressions of emotion-the continuous and the categorical model. The continuous model defines each facial expression of emotion as a feature vector in a face space. This model explains, for example, how expressions of emotion can be seen at different intensities. In contrast, the categorical model consists of C classifiers, each tuned to a specific emotion category. This model explains, among other findings, why the images in a morphing sequence between a happy and a surprise face are perceived as either happy or surprise but not something in between. While the continuous model has a more difficult time justifying this latter finding, the categorical model is not as good when it comes to explaining how expressions are recognized at different intensities or modes. Most importantly, both models have problems explaining how one can recognize combinations of emotion categories such as happily surprised versus angrily surprised versus surprise. To resolve these issues, in the past several years, we have worked on a revised model that justifies the results reported in the cognitive science and neuroscience literature. This model consists of C distinct continuous spaces. Multiple (compound) emotion categories can be recognized by linearly combining these C face spaces. The dimensions of these spaces are shown to be mostly configural. According to this model, the major task for the classification of facial expressions of emotion is precise, detailed detection of facial landmarks rather than recognition. We provide an overview of the literature justifying the model, show how the resulting model can be employed to build algorithms for the recognition of facial expression of emotion, and propose research directions in machine learning and computer vision researchers to keep pushing the state of the art in these areas. We also discuss how the model can

  4. Teaching Socially Expressive Behaviors to Children with Autism through Video Modeling

    Science.gov (United States)

    Charlop, Marjorie H.; Dennis, Brian; Carpenter, Michael H.; Greenberg, Alissa L.

    2010-01-01

    Children with autism often lack complex socially expressive skills that would allow them to engage others more successfully. In the present study, video modeling was used to promote appropriate verbal comments, intonation, gestures, and facial expressions during social interactions of three children with autism. In baseline, the children rarely…

  5. Effectiveness of Teaching Naming Facial Expression to Children with Autism via Video Modeling

    Science.gov (United States)

    Akmanoglu, Nurgul

    2015-01-01

    This study aims to examine the effectiveness of teaching naming emotional facial expression via video modeling to children with autism. Teaching the naming of emotions (happy, sad, scared, disgusted, surprised, feeling physical pain, and bored) was made by creating situations that lead to the emergence of facial expressions to children…

  6. Can expressions of anger enhance creativity? A test of the emotions as social information (EASI) model

    NARCIS (Netherlands)

    van Kleef, G.A.; Anastasopoulou, C.; Nijstad, B.A.

    2010-01-01

    We investigated whether expressions of anger can enhance creative performance. Building on the emotions as social information (EASI) model (Van Kleef, 2009), we predicted that the interpersonal effects of anger expressions on creativity depend on the target's epistemic motivation (EM)—the desire to

  7. Can expressions of anger enhance creativity? A test of the emotions as social information (EASI) model

    NARCIS (Netherlands)

    van Kleef, Gerben A.; Anastasopoulou, Christina; Nijstad, Bernard A.

    2010-01-01

    We investigated whether expressions of anger can enhance creative performance. Building on the emotions as social information (EASI) model (Van Kleef, 2009), we predicted that the interpersonal effects of anger expressions on creativity depend on the target's epistemic motivation (EM) the desire to

  8. Defining suitable reference genes for RT-qPCR analysis on intestinal epithelial cells.

    Science.gov (United States)

    Sirakov, Maria; Borra, Marco; Cambuli, Francesca Maria; Plateroti, Michelina

    2013-07-01

    The study of the mammalian intestinal epithelium concerns several aspects of cellular and molecular biology. In fact, most of these studies aim to define molecular components or mechanisms related with the control of stemness and the balance between cell proliferation and differentiation in physiopathological conditions. It is worth mentioning that real-time quantitative reverse transcription-polymerase chain reaction (RT-qPCR) approaches are commonly used, but only a few studies are available regarding suitable reference genes to normalize gene expression data. The present study was designed to validate potential reference genes in freshly isolated proliferating or differentiated epithelial cells from the mouse intestine. We also extended our analysis to the IEC6 intestinal epithelial cells, as a promising model to study intestinal physiopathology in vitro. The stability of six potential reference genes (Hprt1, Ppia, Gapdh, Rplp0, Ppib, and Vil1) has been tested both in epithelial cells isolated from the mouse intestine and in the IEC6 cell line. The software programs-geNorm and Normfinder-were used to obtain an estimation of the expression stability of each gene and, by comparing the results, to identify the most suitable genes for RT-qPCR data normalization. These multiple approaches allowed us to select different suitable reference genes for the correct quantification of mRNAs depending on the differentiated or proliferative nature of the cells.

  9. Integrated Analysis of Expression Profile Based on Differentially Expressed Genes in Middle Cerebral Artery Occlusion Animal Models

    Directory of Open Access Journals (Sweden)

    Huaqiang Zhou

    2016-05-01

    Full Text Available Stroke is one of the most common causes of death, only second to heart disease. Molecular investigations about stroke are in acute shortage nowadays. This study is intended to explore a gene expression profile after brain ischemia reperfusion. Meta-analysis, differential expression analysis, and integrated analysis were employed on an eight microarray series. We explored the functions and pathways of target genes in gene ontology (GO enrichment analysis and constructed a protein-protein interaction network. Meta-analysis identified 360 differentially expressed genes (DEGs for Mus musculus and 255 for Rattus norvegicus. Differential expression analysis identified 44 DEGs for Mus musculus and 21 for Rattus norvegicus. Timp1 and Lcn2 were overexpressed in both species. The cytokine-cytokine receptor interaction and chemokine signaling pathway were highly enriched for the Kyoto Encyclopedia of Genes and Genomes (KEGG pathway. We have exhibited a global view of the potential molecular differences between middle cerebral artery occlusion (MCAO animal model and sham for Mus musculus or Rattus norvegicus, including the biological process and enriched pathways in DEGs. This research helps contribute to a clearer understanding of the inflammation process and accurate identification of ischemic infarction stages, which might be transformed into a therapeutic approach.

  10. Differential expression of interferon responsive genes in rodent models of transmissible spongiform encephalopathy disease

    Directory of Open Access Journals (Sweden)

    Lazar Jozef

    2007-03-01

    Full Text Available Abstract Background The pathological hallmarks of transmissible spongiform encephalopathy (TSE diseases are the deposition of a misfolded form of a host-encoded protein (PrPres, marked astrocytosis, microglial activation and spongiosis. The development of powerful gene based technologies has permitted increased levels of pro-inflammatory cytokines to be demonstrated. However, due to the use of assays of differing sensitivities and typically the analysis of a single model system it remained unclear whether this was a general feature of these diseases or to what extent different model systems and routes of infection influenced the relative levels of expression. Similarly, it was not clear whether the elevated levels of cytokines observed in the brain were accompanied by similar increases in other tissues that accumulate PrPres, such as the spleen. Results The level of expression of the three interferon responsive genes, Eif2ak2, 2'5'-OAS, and Mx2, was measured in the brains of Syrian hamsters infected with scrapie 263K, VM mice infected with bovine spongiform encephalopathy and C57BL/6 mice infected with the scrapie strain ME7. Glial fibrillary acidic expression confirmed the occurrence of astrocytosis in all models. When infected intracranially all three models showed a similar pattern of increased expression of the interferon responsive genes at the onset of clinical symptoms. At the terminal stage of the disease the level and pattern of expression of the three genes was mostly unchanged in the mouse models. In contrast, in hamsters infected by either the intracranial or intraperitoneal routes, both the level of expression and the expression of the three genes relative to one another was altered. Increased interferon responsive gene expression was not observed in a transgenic mouse model of Alzheimer's disease or the spleens of C57BL/6 mice infected with ME7. Concurrent increases in TNFα, TNFR1, Fas/ApoI receptor, and caspase 8 expression in ME

  11. Increased Cerebral Tff1 Expression in Two Murine Models of Neuroinflammation

    Directory of Open Access Journals (Sweden)

    Eva B Znalesniak

    2016-11-01

    Full Text Available Background/Aims: The trefoil factor family (TFF peptide TFF1 is a typical secretory product of the gastric mucosa and a very low level of expression occurs in nearly all regions of the murine brain. TFF1 possesses a lectin activity and binding to a plethora of transmembrane glycoproteins could explain the diverse biological effects of TFF1 (e.g., anti-apoptotic effect. It was the aim to test whether TFF expression is changed during neuroinflammation. Methods: Expression profiling was performed using semi-quantitative RT-PCR analyses in two murine models of neuroinflammation, i.e. Toxoplasma gondii-induced encephalitis and experimental autoimmune encephalomyelitis (EAE, the latter being the most common animal model of multiple sclerosis. Tff1 expression was also localized using RNA in situ hybridization histochemistry. Results: We report for the first time on a significant transcriptional induction in cerebral Tff1 expression in both T. gondii-induced encephalitis and EAE. In contrast, Tff2 and Tff3 expression were not altered. Tff1 transcripts were predominantly localized in the internal granular layer of the cerebellum indicating neuronal expression. Furthermore, also glial cells are expected to express Tff1. Characterization of both experimental models by expression profiling (e.g., inflammasome sensors, inflammatory cytokines, microglial marker Iba1, ependymin related protein 1 revealed differences concerning the expression of the inflammasome sensor Nlrp1 and interleukin 17a. Conclusion: The up-regulated expression of Tff1 is probably the result of a complex inflammatory process as its expression is induced by tumor necrosis factor α as well as interleukins 1β and 17. However on the transcript level, Tff1KO mice did not show any significant signs of an altered immune response after infection with T. gondii in comparison with the wild type animals.

  12. A Unified Channel Charges Expression for Analytic MOSFET Modeling

    Directory of Open Access Journals (Sweden)

    Hugues Murray

    2012-01-01

    Full Text Available Based on a 1D Poissons equation resolution, we present an analytic model of inversion charges allowing calculation of the drain current and transconductance in the Metal Oxide Semiconductor Field Effect Transistor. The drain current and transconductance are described by analytical functions including mobility corrections and short channel effects (CLM, DIBL. The comparison with the Pao-Sah integral shows excellent accuracy of the model in all inversion modes from strong to weak inversion in submicronics MOSFET. All calculations are encoded with a simple C program and give instantaneous results that provide an efficient tool for microelectronics users.

  13. Simulation model of spring maize developmental stages in Northeast China based on climatic suitability%基于气候适宜度的东北地区春玉米发育期模拟模型

    Institute of Scientific and Technical Information of China (English)

    侯英雨; 王良宇; 毛留喜; 吕厚荃; 王建林

    2012-01-01

    Based on the eco-physiological development processes of spring maize and the principle of the physiological development time for specific type of crops at a given development stage being a constant, a simulation model for spring maize developmental stages was established by the scale of physiological development time. In the published methods for determining crop physiological development time, only the daily thermal and photo-periodical effectiveness is considered, and some specific genetic parameters are introduced to adjust the genotypic differences. However, it is difficult to gain these parameters in real time in large regional scale when simulation model comes into use operationally. In this paper, the physiological development time during the development stages of spring maize was determined based on the climatic suitability, with the joint effects of sunlight, air temperature, and precipitation on the crop development processes considered. The validation of the model with the data from the agro-meteorological observation stations in Northeast China in 2009 and 2010 indicated that there was a high goodness of fit between the simulated results and the observed values. The correlation coefficient between the simulated results and observed values was over 0. 84 in vegetative growth stage and over 0. 77 in reproductive growth stage. Moreover, the root mean square error (RMSE) between the simulated results and the observed values during the whole crop growth period was 3. 8 days. Therefore, this model was relatively robust on mechanistic explanation, had high operability, and could be applied to simulate and predict the date and duration of different growth stages of maize in agro-meteorological information service.%以春玉米的生理生态发育过程为基础,基于作物生理发育时间恒定原理,建立了可推广应用的作物发育期模拟模型.本文充分考虑光、温、水对作物生育进程的综合影响,设计了基于气候适宜度来

  14. Ras signalling regulates differentiation and UCP1 expression in models of brown adipogenesis

    DEFF Research Database (Denmark)

    Murholm, Maria; Dixen, Karen; Hansen, Jacob B

    2010-01-01

    on two unrelated models of mouse brown adipocyte differentiation. RESULTS: A constitutively active H-Ras mutant (Ras V12) caused a complete block of adipose conversion, as manifested by a lack of both lipid accumulation and induction of adipocyte gene expression. The Ras V12-mediated impediment......-Ras mutant (Ras N17) did not inhibit differentiation, but led to increased expression of genes important for energy dissipation in brown fat cells, including UCP1. GENERAL SIGNIFICANCE: These data suggest that the intensity of Ras signalling is important for differentiation and UCP1 expression in models...

  15. The Nonlinear Magnetosphere: Expressions in MHD and in Kinetic Models

    Science.gov (United States)

    Hesse, Michael; Birn, Joachim

    2011-01-01

    Like most plasma systems, the magnetosphere of the Earth is governed by nonlinear dynamic evolution equations. The impact of nonlinearities ranges from large scales, where overall dynamics features are exhibiting nonlinear behavior, to small scale, kinetic, processes, where nonlinear behavior governs, among others, energy conversion and dissipation. In this talk we present a select set of examples of such behavior, with a specific emphasis on how nonlinear effects manifest themselves in MHD and in kinetic models of magnetospheric plasma dynamics.

  16. Selection of the suitable reference genes for gene expression analysis of human peripheral blood from patients with colorectal cancer%结直肠癌患者外周血基因表达分析中参照基因的选择

    Institute of Scientific and Technical Information of China (English)

    杜玉珍; 彭伟; 高锋

    2011-01-01

    Objective To select the suitable endogenous reference genes in peripheral blood from patients with colorectal cancer for gene expression analysis.Methods The expressions of candidate reference genes ( ACTB,GAPDH, GUSB, UBC, B2M, PBGD and 18S rRNA) were determined in peripheral blood of 8 healthy subjects and 8 patients with colorectal cancer by real-time relative quantitative reverse transcription polymerase chain reaction ( RTPCR) dilution method.The stability of candidate reference genes was analyzed by geNorm and NormFinder software programs and t test.The suitable reference genes were analyzed.Results By geNorm software, ACTB, GAPDH and GUSB were identified as the stable and reliable reference genes.By NormFinder algorithms, GAPDH was the stable reference gene, which was followed by B2M, ACTB and GUSB.The candidate reference genes were GAPDH and B2M.All candidate reference genes showed statistical significance in the expression between the patients and the healthy subjects except ACTB, GUSB and UBC.Conclusions The housekeeping genes of ACTB and GUSB are the suitable reference genes in peripheral blood from patients with colorectal cancer for expression analysis, while PBGD and 18S rRNA are not reliable.%目的 筛选结直肠癌患者全血样本的合适内参照基因.方法 以ACTB、GAPDH、GUSB、UBC、B2M、PBGD和18S rRNA为候选基因,用实时相对定量逆转录聚合酶链反应(RT-PCR)稀释法检测其在8例结直肠癌患者和8名健康人全血中的表达水平,再用geNorm和NormFinder程序及两样本均数t检验评价候选参照基因的稳定性,探寻应用于结直肠癌患者全血基因表达检测的合适参照基因.结果 geNorm评估发现,最适合的参照基因是ACTB、GAPDH和GUSB;NormFinder计算结果 认为GAPDH稳定性最好,B2M、ACTB和GUSB次之,推荐的参照基因组合是GAPDH和B2M;候选基因表达水平的组间比较(结直肠癌组和健康组)发现,除ACTB、GUSB和UBC之外,其他候选参照基因

  17. 华北地区杨树烂皮病发生发展气象适宜度预报模型%Forecasting Model of Meteorological Suitability for Occurrence and Development of Valsa sordida Nits in North China

    Institute of Scientific and Technical Information of China (English)

    王纯枝; 郭安红; 王玉玲; 周玉江; 毛留喜

    2011-01-01

    Based on the data of meteorology and monitoring on Valsa sordida Nits during 2002 - 2008 in 18 observation stations of Hebei province, the relationship between the occurrence and development of Valsa sordida Nits and meteorological conditions was analyzed applying correlation and regression analysis method. The results showed that the precipitation, rain day, relative humidity and temperature-humidity coefficient were positively related to the incidence of Valsa sordida Nits. It was favorable to the development of Valsa sordida Nits as the precipitation, rain day, relative humidity and temperature-humidity coefficient increased, while it was not favorable to the development of Valsa sordida Nits as the sunshine duration, extreme air temperature increased. The key meteorological factors which affected the occurrence and development of Valsa sordida Nits in Hebei province were temperature-humidity coefficients in March and April,the sunshine hours in the third ten days of March and April, air temperature in the first and third ten days of April, the extremely minimum air temperature in the first ten days of March and April and also last December respectively. The meteorological suitability forecasting model was established based on the normalized key meteorological factors. The validation results by the historical return test showed that forecasting accuracy for meteorological suitability models was 91% by comparing meteorological grade with actual grade. The meteorological grade of the occurrence fastigium during May to June in 2009 was forecasted with forecasting accuracy by 78% by trial forecast. The meteorological conditions in March and April were the key environmental factors affecting the occurrence and development of this disease in North China. The model could be put into the operational application in North China.%利用河北省18个代表站点2002-2008年杨树烂皮病病情资料和相应气象资料,通过相关、回归分析等方法,分析河

  18. Selection of reference genes in different myocardial regions of an in vivo ischemia/reperfusion rat model for normalization of antioxidant gene expression.

    Science.gov (United States)

    Vesentini, Nicoletta; Barsanti, Cristina; Martino, Alessandro; Kusmic, Claudia; Ripoli, Andrea; Rossi, AnnaMaria; L'Abbate, Antonio

    2012-02-29

    Changes in cardiac gene expression due to myocardial injury are usually assessed in whole heart tissue. However, as the heart is a heterogeneous system, spatial and temporal heterogeneity is expected in gene expression. In an ischemia/reperfusion (I/R) rat model we evaluated gene expression of mitochondrial and cytoplasmatic superoxide dismutase (MnSod, Cu-ZnSod) and thioredoxin reductase (trxr1) upon short (4 h) and long (72 h) reperfusion times in the right ventricle (RV), and in the ischemic/reperfused (IRR) and the remote region (RR) of the left ventricle. Gene expression was assessed by Real-time reverse-transcription quantitative PCR (RT-qPCR). In order to select most stable reference genes suitable for normalization purposes, in each myocardial region we tested nine putative reference genes by geNorm analysis. The genes investigated were: Actin beta (actb), Glyceraldehyde-3-P-dehydrogenase (gapdh), Ribosomal protein L13A (rpl13a), Tyrosine 3-monooxygenase (ywhaz), Beta-glucuronidase (gusb), Hypoxanthine guanine Phosphoribosyltransferase 1 (hprt), TATA binding box protein (tbp), Hydroxymethylbilane synthase (hmbs), Polyadenylate-binding protein 1 (papbn1). According to our findings, most stable reference genes in the RV and RR were hmbs/hprt and hmbs/tbp/hprt respectively. In the IRR, six reference genes were recommended for normalization purposes; however, in view of experimental feasibility limitations, target gene expression could be normalized against the three most stable reference genes (ywhaz/pabp/hmbs) without loss of sensitivity. In all cases MnSod and Cu-ZnSod expression decreased upon long reperfusion, the former in all myocardial regions and the latter in IRR alone. trxr1 expression did not vary. This study provides a validation of reference genes in the RV and in the anterior and posterior wall of the LV of cardiac ischemia/reperfusion model and shows that gene expression should be assessed separately in each region.

  19. Selection of reference genes in different myocardial regions of an in vivo ischemia/reperfusion rat model for normalization of antioxidant gene expression

    Directory of Open Access Journals (Sweden)

    Vesentini Nicoletta

    2012-02-01

    Full Text Available Abstract Background Changes in cardiac gene expression due to myocardial injury are usually assessed in whole heart tissue. However, as the heart is a heterogeneous system, spatial and temporal heterogeneity is expected in gene expression. Results In an ischemia/reperfusion (I/R rat model we evaluated gene expression of mitochondrial and cytoplasmatic superoxide dismutase (MnSod, Cu-ZnSod and thioredoxin reductase (trxr1 upon short (4 h and long (72 h reperfusion times in the right ventricle (RV, and in the ischemic/reperfused (IRR and the remote region (RR of the left ventricle. Gene expression was assessed by Real-time reverse-transcription quantitative PCR (RT-qPCR. In order to select most stable reference genes suitable for normalization purposes, in each myocardial region we tested nine putative reference genes by geNorm analysis. The genes investigated were: Actin beta (actb, Glyceraldehyde-3-P-dehydrogenase (gapdh, Ribosomal protein L13A (rpl13a, Tyrosine 3-monooxygenase (ywhaz, Beta-glucuronidase (gusb, Hypoxanthine guanine Phosphoribosyltransferase 1 (hprt, TATA binding box protein (tbp, Hydroxymethylbilane synthase (hmbs, Polyadenylate-binding protein 1 (papbn1. According to our findings, most stable reference genes in the RV and RR were hmbs/hprt and hmbs/tbp/hprt respectively. In the IRR, six reference genes were recommended for normalization purposes; however, in view of experimental feasibility limitations, target gene expression could be normalized against the three most stable reference genes (ywhaz/pabp/hmbs without loss of sensitivity. In all cases MnSod and Cu-ZnSod expression decreased upon long reperfusion, the former in all myocardial regions and the latter in IRR alone. trxr1 expression did not vary. Conclusions This study provides a validation of reference genes in the RV and in the anterior and posterior wall of the LV of cardiac ischemia/reperfusion model and shows that gene expression should be assessed separately in

  20. Integration of gene expression data into genome-scale metabolic models

    DEFF Research Database (Denmark)

    Åkesson, M.; Förster, Jochen; Nielsen, Jens

    2004-01-01

    of gene expression from chemostat and batch cultures of Saccharomyces cerevisiae were combined with a recently developed genome-scale model, and the computed metabolic flux distributions were compared to experimental values from carbon labeling experiments and metabolic network analysis. The integration......A framework for integration of transcriptome data into stoichiometric metabolic models to obtain improved flux predictions is presented. The key idea is to exploit the regulatory information in the expression data to give additional constraints on the metabolic fluxes in the model. Measurements...... of expression data resulted in improved predictions of metabolic behavior in batch cultures, enabling quantitative predictions of exchange fluxes as well as qualitative estimations of changes in intracellular fluxes. A critical discussion of correlation between gene expression and metabolic fluxes is given....

  1. [Research on distribution and quality suitability division of Desmodium styracifolium].

    Science.gov (United States)

    Li, Dan; Tang, Xiao-Min; Zhu, Shou-Dong; Yang, Quan; Cheng, Xuan-Xuan; Zhang, Chun-Rong; Pan, Li-Ming; Chen, Duan-Ni

    2017-02-01

    The research on distribution and quality suitability division of Desmodium styracifolium were formulated by Maxent and ArcGIS model based on the content of schaftoside and polysaccharide of D. styracifolium and its field research in the south and southwest areas of China (Guangdong, Guangxi, Hainan and Yunnan), and the most suitable habitats of distribution suitability and quality suitability were screened. The distribution suitability results indicated that average air temperature in April,mean temperature of coldest quarter, soil type, coldness index were found as the four dominant factors contributing to the plant distribution. The quality suitability results indicated that: ①Polysaccharide content and precipitation in April show significant positive correlation;Schaftoside content and mean temperature of April, mean temperature of coldest quarter show significant negative correlation. Schaftoside content shows significant negative correlation with the precipitation in October and November and the sunshine duration in April and May, while there is a significant positive correlation between schaftoside content and precipitation in April and temperature seasonality standard deviation, and a highly significant positive correlation was found between schaftoside content and precipitation in February and March. ②The quality zoning map was drawn depend on general content of polysaccharide and schaftoside as the index of quality. And this research provides scientific location basis for the production regionalization, cultivation bases selection and directive breeding of D. styracifolium. Copyright© by the Chinese Pharmaceutical Association.

  2. Lightweight Expression of Granular Objects (LEGO) Content Modeling Using the SNOMED CT Observables Model to Represent Nursing Assessment Data.

    Science.gov (United States)

    Johnson, Christie

    2016-01-01

    This poster presentation presents a content modeling strategy using the SNOMED CT Observable Model to represent large amounts of detailed clinical data in a consistent and computable manner that can support multiple use cases. Lightweight Expression of Granular Objects (LEGOs) represent question/answer pairs on clinical data collection forms, where a question is modeled by a (usually) post-coordinated SNOMED CT expression. LEGOs transform electronic patient data into a normalized consumable, which means that the expressions can be treated as extensions of the SNOMED CT hierarchies for the purpose of performing subsumption queries and other analytics. Utilizing the LEGO approach for modeling clinical data obtained from a nursing admission assessment provides a foundation for data exchange across disparate information systems and software applications. Clinical data exchange of computable LEGO patient information enables the development of more refined data analytics, data storage and clinical decision support.

  3. A penalized likelihood approach for bivariate conditional normal models for dynamic co-expression analysis.

    Science.gov (United States)

    Chen, Jun; Xie, Jichun; Li, Hongzhe

    2011-03-01

    Gene co-expressions have been widely used in the analysis of microarray gene expression data. However, the co-expression patterns between two genes can be mediated by cellular states, as reflected by expression of other genes, single nucleotide polymorphisms, and activity of protein kinases. In this article, we introduce a bivariate conditional normal model for identifying the variables that can mediate the co-expression patterns between two genes. Based on this model, we introduce a likelihood ratio (LR) test and a penalized likelihood procedure for identifying the mediators that affect gene co-expression patterns. We propose an efficient computational algorithm based on iterative reweighted least squares and cyclic coordinate descent and have shown that when the tuning parameter in the penalized likelihood is appropriately selected, such a procedure has the oracle property in selecting the variables. We present simulation results to compare with existing methods and show that the LR-based approach can perform similarly or better than the existing method of liquid association and the penalized likelihood procedure can be quite effective in selecting the mediators. We apply the proposed method to yeast gene expression data in order to identify the kinases or single nucleotide polymorphisms that mediate the co-expression patterns between genes.

  4. Bayesian models and meta analysis for multiple tissue gene expression data following corticosteroid administration

    Directory of Open Access Journals (Sweden)

    Kelemen Arpad

    2008-08-01

    Full Text Available Abstract Background This paper addresses key biological problems and statistical issues in the analysis of large gene expression data sets that describe systemic temporal response cascades to therapeutic doses in multiple tissues such as liver, skeletal muscle, and kidney from the same animals. Affymetrix time course gene expression data U34A are obtained from three different tissues including kidney, liver and muscle. Our goal is not only to find the concordance of gene in different tissues, identify the common differentially expressed genes over time and also examine the reproducibility of the findings by integrating the results through meta analysis from multiple tissues in order to gain a significant increase in the power of detecting differentially expressed genes over time and to find the differential differences of three tissues responding to the drug. Results and conclusion Bayesian categorical model for estimating the proportion of the 'call' are used for pre-screening genes. Hierarchical Bayesian Mixture Model is further developed for the identifications of differentially expressed genes across time and dynamic clusters. Deviance information criterion is applied to determine the number of components for model comparisons and selections. Bayesian mixture model produces the gene-specific posterior probability of differential/non-differential expression and the 95% credible interval, which is the basis for our further Bayesian meta-inference. Meta-analysis is performed in order to identify commonly expressed genes from multiple tissues that may serve as ideal targets for novel treatment strategies and to integrate the results across separate studies. We have found the common expressed genes in the three tissues. However, the up/down/no regulations of these common genes are different at different time points. Moreover, the most differentially expressed genes were found in the liver, then in kidney, and then in muscle.

  5. Exact protein distributions for stochastic models of gene expression using partitioning of Poisson processes

    Science.gov (United States)

    Pendar, Hodjat; Platini, Thierry; Kulkarni, Rahul V.

    2013-04-01

    Stochasticity in gene expression gives rise to fluctuations in protein levels across a population of genetically identical cells. Such fluctuations can lead to phenotypic variation in clonal populations; hence, there is considerable interest in quantifying noise in gene expression using stochastic models. However, obtaining exact analytical results for protein distributions has been an intractable task for all but the simplest models. Here, we invoke the partitioning property of Poisson processes to develop a mapping that significantly simplifies the analysis of stochastic models of gene expression. The mapping leads to exact protein distributions using results for mRNA distributions in models with promoter-based regulation. Using this approach, we derive exact analytical results for steady-state and time-dependent distributions for the basic two-stage model of gene expression. Furthermore, we show how the mapping leads to exact protein distributions for extensions of the basic model that include the effects of posttranscriptional and posttranslational regulation. The approach developed in this work is widely applicable and can contribute to a quantitative understanding of stochasticity in gene expression and its regulation.

  6. Facial expression judgments support a socio-relational model, rather than a negativity bias model of political psychology.

    Science.gov (United States)

    Vigil, Jacob M; Strenth, Chance

    2014-06-01

    Self-reported opinions and judgments may be more rooted in expressive biases than in cognitive processing biases, and ultimately operate within a broader behavioral style for advertising the capacity - versus the trustworthiness - dimension of human reciprocity potential. Our analyses of facial expression judgments of likely voters are consistent with this thesis, and directly contradict one major prediction from the authors' "negativity-bias" model.

  7. Parental Expression of Disappointment: Should It Be a Factor in Hoffman's Model of Parental Discipline?

    Science.gov (United States)

    Patrick, Renee B.; Gibbs, John C.

    2007-01-01

    The authors addressed whether parental expression of disappointment should be included as a distinct factor in M. L. Hoffman's (2000) well-established typology of parenting styles (induction, love withdrawal, power assertion). Hoffman's 3-factor model, along with a more inclusive 4-factor model (induction, love withdrawal, power assertion, and…

  8. Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

    DEFF Research Database (Denmark)

    Ma, Ding; Yang, Laurence; Fleming, Ronan M. T.

    2017-01-01

    Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many...

  9. Angiogenesis inhibition using an oncolytic herpes simplex virus expressing endostatin in a murine lung cancer model.

    Science.gov (United States)

    Goodwin, Jonathan M; Schmitt, Anthony D; McGinn, Christopher M; Fuchs, Bryan C; Kuruppu, Darshini; Tanabe, Kenneth K; Lanuti, Michael

    2012-03-01

    Herpes-mediated viral oncolysis alone is not sufficient to completely eradicate tumors. In this study we used a replication conditional, endostatin-expressing herpes simplex virus-1 mutant (HSV-Endo) in a murine lung cancer model. We hypothesized that the anti-angiogenic action of endostatin would improve upon the oncolytic effect of HSV-1. HSV-Endo was evaluated in a pulmonary metastases and orthotopic flank model, where there was significantly less tumor burden and reduced microvessel density compared to a control virus. Endostatin expression appears to improve the anti-tumor effect of HSV-1 in a lung cancer model.

  10. Projected shifts in Coffea arabica suitability among major global producing regions due to climate change.

    Directory of Open Access Journals (Sweden)

    Oriana Ovalle-Rivera

    Full Text Available Regional studies have shown that climate change will affect climatic suitability for Arabica coffee (Coffea arabica within current regions of production. Increases in temperature and changes in precipitation patterns will decrease yield, reduce quality and increase pest and disease pressure. This is the first global study on the impact of climate change on suitability to grow Arabica coffee. We modeled the global distribution of Arabica coffee under changes in climatic suitability by 2050s as projected by 21 global circulation models. The results suggest decreased areas suitable for Arabica coffee in Mesoamerica at lower altitudes. In South America close to the equator higher elevations could benefit, but higher latitudes lose suitability. Coffee regions in Ethiopia and Kenya are projected to become more suitable but those in India and Vietnam to become less suitable. Globally, we predict decreases in climatic suitability at lower altitudes and high latitudes, which may shift production among the major regions that produce Arabica coffee.

  11. Projected Shifts in Coffea arabica Suitability among Major Global Producing Regions Due to Climate Change

    Science.gov (United States)

    Ovalle-Rivera, Oriana; Läderach, Peter; Bunn, Christian; Obersteiner, Michael; Schroth, Götz

    2015-01-01

    Regional studies have shown that climate change will affect climatic suitability for Arabica coffee (Coffea arabica) within current regions of production. Increases in temperature and changes in precipitation patterns will decrease yield, reduce quality and increase pest and disease pressure. This is the first global study on the impact of climate change on suitability to grow Arabica coffee. We modeled the global distribution of Arabica coffee under changes in climatic suitability by 2050s as projected by 21 global circulation models. The results suggest decreased areas suitable for Arabica coffee in Mesoamerica at lower altitudes. In South America close to the equator higher elevations could benefit, but higher latitudes lose suitability. Coffee regions in Ethiopia and Kenya are projected to become more suitable but those in India and Vietnam to become less suitable. Globally, we predict decreases in climatic suitability at lower altitudes and high latitudes, which may shift production among the major regions that produce Arabica coffee. PMID:25875230

  12. Differential cytokine gene expression according to outcome in a hamster model of leptospirosis.

    Directory of Open Access Journals (Sweden)

    Frédérique Vernel-Pauillac

    Full Text Available BACKGROUND: Parameters predicting the evolution of leptospirosis would be useful for clinicians, as well as to better understand severe leptospirosis, but are scarce and rarely validated. Because severe leptospirosis includes septic shock, similarities with predictors evidenced for sepsis and septic shock were studied in a hamster model. METHODOLOGY/PRINCIPAL FINDINGS: Using an LD50 model of leptospirosis in hamsters, we first determined that 3 days post-infection was a time-point that allowed studying the regulation of immune gene expression and represented the onset of the clinical signs of the disease. In the absence of tools to assess serum concentrations of immune effectors in hamsters, we determined mRNA levels of various immune genes, especially cytokines, together with leptospiraemia at this particular time-point. We found differential expression of both pro- and anti-inflammatory mediators, with significantly higher expression levels of tumor necrosis factor alpha, interleukin 1alpha, cyclo-oxygenase 2 and interleukin 10 genes in nonsurvivors compared to survivors. Higher leptospiraemia was also observed in nonsurvivors. Lastly, we demonstrated the relevance of these results by comparing their respective expression levels using a LD100 model or an isogenic high-passage nonvirulent variant. CONCLUSIONS/SIGNIFICANCE: Up-regulated gene expression of both pro- and anti-inflammatory immune effectors in hamsters with fatal outcome in an LD50 model of leptospirosis, together with a higher Leptospira burden, suggest that these gene expression levels could be predictors of adverse outcome in leptospirosis.

  13. Land Suitability Assessmemtin Continental Grits of

    African Journals Online (AJOL)

    use types (LUTs). using a qualitative physical land evaluation methodology. The results indicated that the ..... Suggested land characteristics and scores for suitability evaluation for cereals ..... the FAO framework: an example from Zambia.

  14. Suitable long tendon technologies and practices

    CSIR Research Space (South Africa)

    Altounyan, P

    2001-10-01

    Full Text Available effective long tendon support systems suitable in South African coalmines. Appropriate test procedures for the evaluation of the performance of long tendon systems were also determined and are detailed in this report....

  15. Impact of animal strain on gene expression in a rat model of acute cardiac rejection

    Directory of Open Access Journals (Sweden)

    Norsworthy Kelly J

    2009-06-01

    Full Text Available Abstract Background The expression levels of many genes show wide natural variation among strains or populations. This study investigated the potential for animal strain-related genotypic differences to confound gene expression profiles in acute cellular rejection (ACR. Using a rat heart transplant model and 2 different rat strains (Dark Agouti, and Brown Norway, microarrays were performed on native hearts, transplanted hearts, and peripheral blood mononuclear cells (PBMC. Results In heart tissue, strain alone affected the expression of only 33 probesets while rejection affected the expression of 1368 probesets (FDR 10% and FC ≥ 3. Only 13 genes were affected by both strain and rejection, which was Conclusion In ACR, genetic background has a large impact on the transcriptome of immune cells, but not heart tissue. Gene expression studies of ACR should avoid study designs that require cross strain comparisons between leukocytes.

  16. Selecting Suitable Sites for Wind Energy Development in Ghana*

    African Journals Online (AJOL)

    Michae O. Mensah

    2016-06-01

    Jun 1, 2016 ... Selecting Suitable Sites for Wind Energy Development in Ghana*. D. Sarpong, P. E. .... from observations and computer model-derived were also used for the .... such as forest and game reserves, tourist sites, etc. (iv) Siting in ...

  17. Cyclooxygenases (COX-1 and COX-2) for tissue engineering of articular cartilage--from a developmental model to first results of tissue and scaffold expression.

    Science.gov (United States)

    Brochhausen, Christoph; Zehbe, Rolf; Gross, Ulrich; Libera, Jeanette; Schubert, Helmut; Nüsing, Rolf M; Klaus, Günter; Kirkpatrick, C James

    2008-01-01

    Tissue engineering of articular cartilage remains an ongoing challenge. Since tissue regeneration recapitulates ontogenetic processes the growth plate can be regarded as an innovative model to target suitable signalling molecules and growth factors for the tissue engineering of cartilage. In the present study we analysed the expression of cyclooxygenases (COX) in a short-term chondrocyte culture in gelatin-based scaffolds and in articular cartilage of rats and compared it with that in the growth plate. Our results demonstrate the strong cellular expression of COX-1 but only a focal weak expression of COX-2 in the seeded scaffolds. Articular cartilage of rats expresses homogeneously COX-1 and COX-2 with the exception of the apical cell layer. Our findings indicate a functional role of COX in the metabolism of articular chondrocytes. The expression of COX in articular cartilage and in the seeded scaffolds opens interesting perspectives to improve the proliferation and differentiation of chondrocytes in scaffold materials by addition of specific receptor ligands of the COX system.

  18. 应用AMMI模型分析烤烟品种的产量适宜性%Analyzing Yield Suitability of Flue-cured Tobacco Varieties with AMMI Model

    Institute of Scientific and Technical Information of China (English)

    黄平俊; 易建华; 蒲文宣; 孙在军; 杨小年; 张新要; 刘万峰; 宋卫武

    2013-01-01

    利用AMMI模型对2011年烤烟品种区域试验5个试点10个参试品种的产量性状进行统计分析.结果表明:(1)参试品种产量的环境效应和基因×环境互作效应均达到极显著水平.在品种试验中对产量影响作用大小顺序依次为环境、基因与环境互作、基因.(2)参试品种丰产性顺序为:AH1002>AH 1001 >03-8-4>03-6-1>‘K326’>6507>03-4-3>2010A7>2010A 10>2010A6;稳定性顺序为:03-6-1>2010A 10>AH 1001 >AH 1002>2010A6>03-4-3>‘K326’>2010A7>6507>03-8-4.(3)参试地点环境范围内,AH1002、AH1001丰产性好,稳产性较好,适宜在各试点种植;2010A10丰产差,但适应性较好,在品种推广时需要慎重;03-8-4丰产性较好,但稳产性较差,在推广时应选择适宜的地区种植.%The yield character of five pilots and ten varieties were analyzed for tobacco regional trial in 2011 with AMMI model. The result showed that: (1) the effects of environment and genotype x environment on yield were significant at 1%, the order o